Chemistry transport models (CTMs) play an important role in understanding fluxes and atmospheric distribution of carbon dioxide (CO_{2}). They have been widely used for modeling CO_{2} transport through forward simulations and inferring fluxes through inversion systems. With the increasing availability of high-resolution observations, it has been become possible to estimate CO_{2} fluxes at higher spatial resolution. In this work, we implemented CO_{2} transport in the Model for Prediction Across Scales – Atmosphere (MPAS-A). The objective is to use the variable-resolution capability of MPAS-A to enable a high-resolution CO_{2} simulation in a limited region with a global model. Treating CO_{2} as an inert tracer, we implemented in MPAS-A (v6.3) the CO_{2} transport processes, including advection, vertical mixing by boundary layer scheme, and convective transport. We first evaluated the newly implemented model's tracer mass conservation and then its CO_{2} simulation accuracy. A 1-year (2014) MPAS-A simulation is evaluated at the global scale using CO_{2} measurements from 50 near-surface stations and 18 Total Carbon Column Observing Network (TCCON) stations. The simulation is also compared with two global models: National Oceanic and Atmospheric Administration (NOAA) CarbonTracker v2019 (CT2019) and European Centre for Medium-Range Weather Forecasts (ECMWF) Integrated Forecasting System (IFS). A second set of simulation (2016–2018) is used to evaluate MPAS-A at regional scale using Atmospheric Carbon and Transport – America (ACT-America) aircraft CO_{2} measurements over the eastern United States. This simulation is also compared with CT2019 and a 27 km WRF-Chem simulation. The global-scale evaluations show that MPAS-A is capable of representing the spatial and temporal CO_{2} variation with a comparable level of accuracy as IFS of similar horizontal resolution. The regional-scale evaluations show that MPAS-A is capable of representing the observed atmospheric CO_{2} spatial structures related to the midlatitude synoptic weather system, including the warm versus cold sector distinction, boundary layer to free troposphere difference, and frontal boundary CO_{2} enhancement. MPAS-A's performance in representing these CO_{2} spatial structures is comparable to the global model CT2019 and regional model WRF-Chem.

How information is encoded in bio-molecular sequences is difficult to quantify since such an analysis usually requires sampling an exponentially large genetic space. Here we show how information theory reveals both robust and compressed encodings in the largest complete genotype-phenotype map (over 5 trillion sequences) obtained to date.

1 aG, Nitash, C1 aAdami, Christoph uhttps://www.sciencedirect.com/science/article/pii/S157106452100040301657nas a2200241 4500008004100000022001400041245010800055210006900163300001000232490000800242520091000250653001601160653002801176653001701204100001501221700001501236700001301251700001701264700001601281700002601297700002001323856007201343 2021 eng d a0168-583X00aParticle-in-cell techniques for the study of space charge effects in the Advanced Cryogenic Gas Stopper0 aParticleincell techniques for the study of space charge effects a61-700 v4963 aLinear gas stoppers are widely used to convert high-energy, rare-isotope beams and reaction products into low-energy beams with small transverse emittance and energy spread. Stopping of the high-energy ions is achieved through interaction with a buffer gas, typically helium, generating large quantities of He+/e− pairs. The Advanced Cryogenic Gas Stopper (ACGS) was designed for fast, efficient stopping and extraction of high-intensity, rare-isotope beams. As part of the design process, a comprehensive particle-in-cell code was developed to optimize the transport and extraction of rare isotopes from the ACGS in the presence of space charge, including He+/e− dynamics, buffer gas interactions including gas flow, radio-frequency carpets, and ion extraction through a nozzle or orifice. Details of the simulations are presented together with comparison to experiment when available.

10aGas stopper10aParticle-in-cell method10aSpace charge1 aRingle, R.1 aBollen, G.1 aLund, K.1 aNicoloff, C.1 aSchwarz, S.1 aSumithrarachchi, C.S.1 aVillari, A.C.C. uhttps://www.sciencedirect.com/science/article/pii/S0168583X2100111702141nas a2200157 4500008004100000245007600041210007100117260001200188300000600200520164900206100002401855700002501879700002001904700001801924856004101942 2021 eng d00aA rare earth metallocene containing a 2{,}2′-azopyridyl radical anion0 arare earth metallocene containing a 2 2′azopyridyl radical anion c10/2021 a-3 aIntroducing spin onto organic ligands that are coordinated to rare earth metal ions allows direct exchange with metal spin centres. This is particularly relevant for the deeply buried 4f-orbitals of the lanthanide ions that can give rise to unparalleled magnetic properties. For efficacy of exchange coupling{,} the donor atoms of the radical ligand require high-spin density. Such molecules are extremely rare owing to their reactive nature that renders isolation and purification difficult. Here{,} we demonstrate that a 2{,}2′-azopyridyl (abpy) radical (S = 1/2) bound to the rare earth metal yttrium can be realized. This molecule represents the first rare earth metal complex containing an abpy radical and is unambigously characterized by X-ray crystallography{,} NMR{,} UV-Vis-NIR{,} and IR spectroscopy. In addition{,} the most stable isotope 89Y with a natural abundance of 100% and a nuclear spin of ½ allows an in-depth analysis of the yttrium–radical complex via EPR and HYSCORE spectroscopy. Further insight into the electronic ground state of the radical azobispyridine-coordinated metal complex was realized through unrestricted DFT calculations{,} which suggests that the unpaired spin density of the SOMO is heavily localized on the azo and pyridyl nitrogen atoms. The experimental results are supported by NBO calculations and give a comprehensive picture of the spin density of the azopyridyl ancillary ligand. This unexplored azopyridyl radical anion in heavy element chemistry bears crucial implications for the design of molecule-based magnets particularly comprising anisotropic lanthanide ions.

1 aIV, Francis, Delano1 aCastellanos, Ernesto1 aMcCracken, John1 aDemir, Selvan uhttp://dx.doi.org/10.1039/D1SC04285H03088nas a2200253 4500008004100000022001400041245011400055210006900169300001200238490000800250520227400258653002902532653002402561653003102585653001902616653001902635100001602654700001802670700002502688700001802713700001402731700001702745856007202762 2021 eng d a1462-901100aSynthesizing social and environmental sensing to monitor the impact of large-scale infrastructure development0 aSynthesizing social and environmental sensing to monitor the imp a527-5400 v1243 aThe booming development of large-scale infrastructure projects (LSIPs) facilitated by China’s Belt and Road Initiative (BRI) has drawn global concern regarding the scale, pace, and potential impact. Studies have largely focused on the geopolitical impact (i.e., politics and international relations) but less is known about social and environmental impact. This is in large part because consistent, high-resolution, cross-boundary social and environmental data at large scales are rather limited. To address the knowledge gap, this research developed a novel Socio-Environmental Sensing (SES) approach by synthesizing remote sensing imagery and geotagged Twitter data to map the socio-environmental impact of LSIPs. We demonstrated the applicability of this approach using two BRI flagship projects, namely, the Mombasa-Nairobi Standard Gauge Railway (SGR) in Kenya and the China-Pakistan Economic Corridor (CPEC) in Pakistan. Our analysis shows that both projects have led to a substantial loss of natural land (e.g., 3.7 % loss of vegetation in Kenya, and 23.3 % reduction of the glacier in Pakistan) but gains in artificial land (e.g., 4.2 % increase in cropland in Kenya, and 34.6 % expansion of built-up land in Pakistan). In addition, the BRI-LSIPs have largely improved local economic development, because nighttime light imagery revealed that regions near the BRI-LSIP sites became much brighter than other regions. Regarding the social aspect, we found that public sentiment toward the projects was largely positive and improved over time, which contradicts the prevalent pessimism to BRI-LSIPs by critics. Nevertheless, sentiment also presented strong spatial heterogeneity – regions around the BRI transportation hubs (usually large cities) most showed more positive sentiment than other regions. By spatially joining the georeferenced sentiment scores with environmental indicators from remote sensing, we further found that positive sentiment improved more in more developed regions, but only changed slightly in other regions. This study provides a novel approach to assess the socio-environmental impact of large-scale projects, and the findings would be useful for informing the implementation of future BRI projects across the globe.

10aBelt and road initiative10aIntegrated analysis10aLarge-scale infrastructure10aRemote sensing10aSocial sensing1 aLi, Yingjie1 aZhang, Yuqian1 aTiffany, Leigh, Anne1 aChen, Ruishan1 aCai, Meng1 aLiu, Jianguo uhttps://www.sciencedirect.com/science/article/pii/S146290112100205702313nas a2200253 4500008004100000022001400041245006500055210006200120300001100182490000800193520153300201653002501734653002501759653003301784653002701817653002801844653001801872100001901890700001501909700001501924700002601939700002301965856007101988 2020 eng d a0012-821X00aGlobal variations of Earth's 520- and 560-km discontinuities0 aGlobal variations of Earths 520 and 560km discontinuities a1166000 v5523 aWe investigate seismic discontinuities in the mantle transition zone (MTZ) by analyzing SS precursors recorded at global seismic stations. Our observations confirm the global existence of the 520-km discontinuity. Although substantial regional depth variations in the 520-km discontinuity are generally correlated with temperature in the mid-MTZ, they cannot be fully explained by the Clapeyron slope of the wadsleyite-ringwoodite phase transition, suggesting both thermal and compositional heterogeneities in the MTZ. A second discontinuity at âŒ560-km depth, previously interpreted as splitting of the 520-km discontinuity, is most commonly detected in cold subduction zones and hot mantle regions. The depth separation between the 520- and 560-km discontinuities varies from âŒ80 km in cold regions to âŒ40 km in hot areas. The exsolution of calcium-perovskite (Ca-pv) from majorite garnet has been proposed to explain the velocity and density changes across the 560-km discontinuity. However, the gradual exsolution of perovskite and partitioning of Ca and Al between perovskite and garnet appear inconsistent with the relatively âsharpâ discontinuity in seismic observations and thus need to be revisited in the future. Nevertheless, because the only known transition in major minerals at this depth in the MTZ is the formation of Ca-pv, the existence of the 560-km discontinuity may imply localized high calcium concentrations in the mid-MTZ possibly related to the recycling of oceanic crust.

10a520-km discontinuity10a560-km discontinuity10amantle phase transformations10amantle transition zone10aoceanic crust recycling10aSS precursors1 aTian, Dongdong1 aLv, Mingda1 aWei, Shawn1 aDorfman, Susannah, M.1 aShearer, Peter, M. uhttp://www.sciencedirect.com/science/article/pii/S0012821X2030544601046nas a2200169 4500008004100000020001400041245011600055210006900171260001500240300001500255490000700270520047600277100002600753700002800779700002200807856004700829 2020 eng d a1572-976100aA hierarchical analysis of habitat area, connectivity, and quality on amphibian diversity across spatial scales0 ahierarchical analysis of habitat area connectivity and quality o c2020/02/01 a529 - -5440 v353 aHabitat fragmentation can alter species distributions and lead to reduced diversity at multiple scales. Yet, the literature describing fragmentation effects on biodiversity patterns is contradictory, possibly because most studies fail to integrate spatial scale into experimental designs and statistical analyses. Thus, it is difficult to extrapolate the effects of fragmentation to large-scaled systems in which conservation management is of immediate importance.

1 aWright, Alexander, D.1 aGrant, Evan, H. Campbel1 aZipkin, Elise, F. uhttps://doi.org/10.1007/s10980-019-00963-z01979nas a2200181 4500008004100000022001400041245009400055210006900149300001400218490000800232520138200240100002501622700002301647700003301670700001901703700001901722856005601741 2020 eng d a0036-807500aOceanic plateau of the Hawaiian mantle plume head subducted to the uppermost lower mantle0 aOceanic plateau of the Hawaiian mantle plume head subducted to t a983–9870 v3703 aVolcanic island and seamount chains form from deep-seated plumes of hot material upwelling through the mantle. The most famous of these is the Hawaiian-Emperor seamount chain. However, a large volcanic structure associated with a plume head that should precede the chain has long been missing. Wei et al. finally identified the likely location of this structure in the mantle under eastern Russia. The structure was likely subducted 20 million to 30 million years ago, and the location helps constrain several geodynamic processes.Science, this issue p. 983The Hawaiian-Emperor seamount chain that includes the Hawaiian volcanoes was created by the Hawaiian mantle plume. Although the mantle plume hypothesis predicts an oceanic plateau produced by massive decompression melting during the initiation stage of the Hawaiian hot spot, the fate of this plateau is unclear. We discovered a megameter-scale portion of thickened oceanic crust in the uppermost lower mantle west of the Sea of Okhotsk by stacking seismic waveforms of SS precursors. We propose that this thick crust represents a major part of the oceanic plateau that was created by the Hawaiian plume head 100 million years ago and subducted 20 million to 30 million years ago. Our discovery provides temporal and spatial clues of the early history of the Hawaiian plume for future plate reconstructions.

1 aWei, Songqiao, Shawn1 aShearer, Peter, M.1 aLithgow-Bertelloni, Carolina1 aStixrude, Lars1 aTian, Dongdong uhttps://science.sciencemag.org/content/370/6519/98302011nas a2200133 4500008004100000245007800041210006900119490000700188520156800195100002101763700001901784700002701803856004701830 2017 eng d00aIce cover, winter circulation, and exchange in Saginaw Bay and Lake Huron0 aIce cover winter circulation and exchange in Saginaw Bay and Lak0 v623 aWinter circulation exerts a strong control on the release and timing of nutrients and contaminants from bays into the adjoining lakes. To estimate winter residence times of solutes in the presence of ice cover, we used an ice model coupled to hydrodynamic, thermal and solute transport models of Saginaw Bay and Lake Huron for two low (2010 and 2013) and two high (2009 and 2014) ice years. The models were tested using temperature data from thermistor chains and current data from ADCP moorings deployed during the winter- time. Simulated water temperatures compared favorably to lake-wide average surface temperatures derived from NOAA’s AVHRR satellite imagery. Simulated results of ice cover are in agreement with observed data from the Great Lakes Ice Atlas. Our results indicate that ice cover significantly dampens water movement producing almost stagnant conditions around February. Estimates of residence times for Saginaw Bay (defined as the e-folding flushing time based on vertically integrated dye concentrations) show that the mean resi- dence times in a low ice year (2013) are 2.2 months for the inner bay, and 3.5 months for the entire bay. The corresponding numbers for a high ice year (2014) are 4.9 and 5.3 months, respectively. Considering the entire bay, solutes stored in the bay can be expected to be released into the lake between March (low ice year) and April (high ice year). These results are expected to aid in understanding the behavior of contami- nants in the Great Lakes during the winter months and in early spring.

1 aNguyen, Tuan, D.1 aHawley, Nathan1 aPhanikumar, Mantha, S. uhttp://www.egr.msu.edu/~phani/lno10431.pdf02090nas a2200169 4500008004100000245011800041210006900159260001200228490000800240520151400248100001801762700001601780700001301796700001801809700002101827856007201848 2017 eng d00aManifold methods for assimilating geophysical and meteorological data in Earth system models and their components0 aManifold methods for assimilating geophysical and meteorological c11/20160 v5443 aA novel manifold method of reconstructing dynamically evolving spatial fields is presented for assimilating data from sensor networks in integrated land surface – subsurface, oceanic/lake models. The method was developed based on the assumption that data can be mapped onto an underlying differential manifold. In this study, the proposed method was used to reconstruct meteorological forcing over Lake Michigan, the bathymetry of an inland lake (Gull Lake), and precipitation over the Grand River watershed in Michigan. In the first case study, hourly meteorological forcing data were reconstructed and used to run a three-dimensional hydrodynamic model of Lake Michigan and to quantify the improvement that results from the use of the new method. In the second example, the bathymetry of Gull Lake was reconstructed from measured scatter point data using the manifold technique. A hydrodynamic model of Gull Lake was developed and refined using the improved bathymetry. In the last case study, improved daily participation data for a six-year period over the Grand River watershed were used as input to an integrated, distributed hydrologic model. All three examples illustrate the superior performance of the manifold method over standard methods in terms of accuracy and computational efficiency. Our results also indicate that using the cross-validation technique to evaluate the performance of data reconstruction methods can lead to misleading conclusions about their relative performance.

1 aSafaie, Ammar1 aDang, Chinh1 aQiu, Han1 aRadha, Hayder1 aPhanikumar, M.S. uhttp://hydrology1.weebly.com/uploads/6/6/2/1/66216077/jh_safaie.pdf00381nas a2200109 4500008004100000245005300041210005300094490000700147100002200154700002400176856007100200 2015 eng d00aNumerical Study of High Speed Evaporating Sprays0 aNumerical Study of High Speed Evaporating Sprays0 v701 aJaberi, Farhad, A1 aIrannejad, Abolfazl uhttp://www.sciencedirect.com/science/article/pii/S030193221400234100535nas a2200133 4500008004100000245008300041210006900124260001600193300002400209490000700233100002000240700001900260856012200279 2015 eng d00aTwist-averaged boundary conditions for nuclear pasta Hartree-Fock calculations0 aTwistaveraged boundary conditions for nuclear pasta HartreeFock c2015/10/21/ a045806-1 - 045806-60 v921 aSchuetrumpf, B.1 aNazarewicz, W. uhttps://icer.msu.edu/research/publications/twist-averaged-boundary-conditions-nuclear-pasta-hartree-fock-calculations00467nas a2200121 4500008004100000245010600041210006900147260001500216490000700231100001600238700002000254856007100274 2014 eng d00aBonds, bands, and band gaps in tetrahedrally bonded ternary compounds: The role of group V lone pairs0 aBonds bands and band gaps in tetrahedrally bonded ternary compou cApril 20140 v751 aDo, Dat, T.1 aMahanti, S., D. uhttp://www.sciencedirect.com/science/article/pii/S002236971300389201517nas a2200577 4500008004100000245010300041210006900144260001200213490000800225100001500233700001500248700001900263700001900282700001400301700001800315700001500333700001700348700001500365700002200380700001300402700001500415700001500430700001300445700001500458700001400473700001700487700001900504700001400523700001400537700001500551700001300566700001600579700001600595700001900611700001600630700001600646700001600662700001500678700001400693700001400707700001400721700001400735700001500749700001600764700001900780700001800799700001600817700001500833700001900848856007200867 2014 eng d00aDetermining the rp-Process Flow through 56Ni: Resonances in 57Cu(p,g)58Zn Indentified with GRETINA0 aDetermining the rpProcess Flow through 56Ni Resonances in 57Cupg c07/20140 v1131 aLanger, C.1 aMontes, F.1 aAprahamian, A.1 aBardayan, D.W.1 aBazin, D.1 aBrown, B., A.1 aBrowne, J.1 aCrawford, H.1 aCyburt, R.1 aDomingo-Pardo, C.1 aGade, A.1 aGeorge, S.1 aHosmer, P.1 aKeek, L.1 aKontos, A.1 aLee, I.Y.1 aLemasson, A.1 aLunderberg, E.1 aMaeda, Y.1 aMatos, M.1 aMeisel, Z.1 aNoji, S.1 aNunes, F.M.1 aNystrom, A.1 aPerdikakis, G.1 aPereira, J.1 aQuinn, S.J.1 aRecchia, F.1 aSchatz, H.1 aScott, M.1 aSiegl, K.1 aSimon, A.1 aSmith, M.1 aSpyrou, A.1 aStevens, J.1 aStroberg, S.R.1 aWeisshaar, D.1 aWheeler, J.1 aWimmer, K.1 aZegers, R.G.T. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.03250201103nas a2200361 4500008004100000245007800041210006900119260001200188490000800200100002500208700002200233700001900255700002000274700002100294700002100315700002500336700002400361700002300385700002000408700002300428700001800451700002400469700002400493700001700517700002200534700002400556700002300580700002000603700002400623700002200647700002200669856005000691 2014 eng d00aGill bacteria enable a novel digestive strategy in a wood-feeding mollusk0 aGill bacteria enable a novel digestive strategy in a woodfeeding c11/20140 v1111 aO'Connor, Roberta, M1 aFung, Jennifer, M1 aSharp, Koty, H1 aBenner, Jack, S1 aMcClung, Colleen1 aCushing, Shelley1 aLamkin, Elizabeth, R1 aFomenkov, Alexey, I1 aHenrissat, Bernard1 aLonder, Yuri, Y1 aScholz, Matthew, B1 aPosfai, Janos1 aMalfatti, Stephanie1 aTringe, Susannah, G1 aWoyke, Tanja1 aMalmstrom, Rex, R1 aColeman-Derr, Devin1 aAltamia, Marvin, A1 aDedrick, Sandra1 aKaluziak, Stefan, T1 aHaywood, Margo, G1 aDistel, Daniel, L uhttp://www.pnas.org/content/111/47/E5096.full00456nas a2200121 4500008004100000245006000041210006000101260001900161100001700180700002000197700001700217856010000234 2014 eng d00aHigh Fidelity Simulations of Turbulent Spray Combustion0 aHigh Fidelity Simulations of Turbulent Spray Combustion cJune 1-4, 20141 aIrannejad, A1 aBanaeizadeh, A.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/high-fidelity-simulations-turbulent-spray-combustion00748nas a2200241 4500008004100000245008800041210006900129260001200198490000700210100001800217700001800235700002000253700002500273700002200298700001800320700002100338700001700359700001600376700001600392700001700408700001300425856006800438 2014 eng d00aHigh-precision B(E2) Measurements of Semi-Magic 58,60,62,64Ni by Coulomb Excitation0 aHighprecision BE2 Measurements of SemiMagic 58606264Ni by Coulom c09/20140 v901 aAllmond, J.M.1 aBrown, B., A.1 aStuchbery, A.E.1 aGalindo-Uribarri, A.1 aPadilla-Rodal, E.1 aRadford, D.C.1 aBatchelder, J.C.1 aHoward, M.E.1 aLiang, J.F.1 aManning, B.1 aVarner, R.L.1 aYu, C.H. uhttp://journals.aps.org/prc/abstract/10.1103/PhysRevC.90.03430900830nas a2200265 4500008004100000245009900041210007100140260001200211490000700223100001400230700002600244700001800270700001700288700002100305700001700326700001700343700001500360700001900375700001800394700001700412700002200429700001500451700001800466856008000484 2014 eng d00aHigh-resolution two-proton stripping to 2p-1h 7/2− states via the 59Co(3He,nγ)61Cu reaction0 aHighresolution twoproton stripping to 2p1h 72− states via the 59 c10/20140 v501 aPapka, P.1 aSharpey-Schafer, J.F.1 aBrown, B., A.1 aDinoko, T.S.1 aKhaleel, E.A.M.A1 aLawrie, E.A.1 aLawrie, J.J.1 aLi, K.C.W.1 aMajola, S.N.T.1 aRichter, W.A.1 aShirinda, O.1 aStankiewicz, M.A.1 aVymers, P.1 aWiedeking, M. uhttps://people.nscl.msu.edu/~brown/brown-all-papers/541-2014-epja50.158.pdf02323nas a2200133 4500008004100000245010700041210006900148260000900217520176600226653011701992100001302109700001302122856005402135 2014 eng d00aHost plant-specific remodeling of midgut physiology in the generalist insect herbivore Trichoplusia ni0 aHost plantspecific remodeling of midgut physiology in the genera c20143 aSpecies diversity in terrestrial ecosystems is influenced by plant defense compounds that alter the behavior, physiology, and host preference of insect herbivores. Although it is established that insects evolved the ability to detoxify specific allelochemicals, the mechanisms by which polyphagous insects cope with toxic compounds in diverse host plants are not well understood. Here, we used defended and non-defended plant genotypes to study how variation in chemical defense affects midgut responses of the lepidopteran herbivore Trichoplusia ni, which is a pest of a wide variety of native and cultivated plants. The genome-wide midgut transcriptional response of T. ni larvae to glucosinolate-based defenses in the crucifer Arabidopsis thaliana was characterized by strong induction of genes encoding Phase I and II detoxification enzymes. In contrast, the response of T. ni to proteinase inhibitors and other jasmonate-regulated defenses in tomato (Solanum lycopersicum) was dominated by changes in the expression of digestive enzymes and, strikingly, concomitant repression of transcripts encoding detoxification enzymes. Unbiased proteomic analyses of T. ni feces demonstrated that tomato defenses remodel the complement of T.ni digestive enzymes, which was associated with increased amounts of serine proteases and decreased lipase protein abundance upon encountering tomato defense chemistry. These collective results indicate that T. ni adjusts its gut physiology to the presence of host plant-specific chemical defenses, and further suggest that plants may exploit this digestive flexibility as a defensive strategy to suppress the production of enzymes that detoxify allelochemicals. Copyright © 2014 Elsevier Ltd. All rights reserved.

10aArabidopsis thaliana; Gut physiology; Herbivore; Jasmonate; Solanum lycopersicum; Transcriptome; Trichoplusia ni1 aM, Herde1 aGA, Howe uhttp://www.ncbi.nlm.nih.gov/pubmed/?term=2472701900462nas a2200121 4500008004100000245010700041210006900148260001200217490000700229100001700236700001600253856007100269 2014 eng d00aHost plant-specific remodeling of midgut physiology in the generalist insect herbivore Trichoplusia ni0 aHost plantspecific remodeling of midgut physiology in the genera c07/20140 v501 aHerde, Marco1 aHowe, Gregg uhttp://www.sciencedirect.com/science/article/pii/S096517481400063000401nas a2200109 4500008004100000245006900041210006900110490000700179100001700186700001700203856007100220 2014 eng d00aLarge Eddy Simulation of Turbulent Spray Breakup and Evaporation0 aLarge Eddy Simulation of Turbulent Spray Breakup and Evaporation0 v611 aIrannejad, A1 aJaberi, F.A. uhttp://www.sciencedirect.com/science/article/pii/S030193221400010X00411nas a2200109 4500008004100000245007600041210006900117490000800186100001800194700001700212856007200229 2014 eng d00aLarge Low-Energy M1 Strength for 56,57Fe Within the Nuclear Shell Model0 aLarge LowEnergy M1 Strength for 5657Fe Within the Nuclear Shell 0 v1131 aBrown, B., A.1 aLarsen, R.C. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.25250200501nas a2200133 4500008004100000245009400041210007000135260001200205490000700217100001800224700001400242700001800256856009300274 2014 eng d00aNeutrinoless double-β decay of 82Se in the shell model: Beyond the closure approximation0 aNeutrinoless doubleβ decay of 82Se in the shell model Beyond the c05/20140 v891 aSen'kov, R.A.1 aHoroi, M.1 aBrown, B., A. uhttps://people.nscl.msu.edu/~brown/brown-all-papers/529-2014-PhysRevC.89.054304-se82.pdf00465nas a2200121 4500008004100000245009900041210006900140490000700209100002200216700001100238700001700249856007700266 2014 eng d00aNumerical Investigations of Shock Wave Interactions with a Supersonic Turbulent Boundary Layer0 aNumerical Investigations of Shock Wave Interactions with a Super0 v261 aJammalamadaka, A.1 aLi, Z.1 aJaberi, F.A. uhttp://scitation.aip.org/content/aip/journal/pof2/26/5/10.1063/1.487349501353nas a2200529 4500008004100000245006100041210005900102260001200161490000700173100001900180700001500199700002300214700001600237700001800253700001900271700001400290700001200304700001900316700001900335700001500354700002000369700001700389700001300406700001900419700001500438700001700453700001800470700001400488700001200502700001400514700001200528700001100540700001800551700002000569700001700589700001200606700001800618700001400636700001300650700001600663700001700679700001600696700001500712700001300727700001500740856006800755 2014 eng d00aShell and Shape Evolution at N=28: The 40Mg Ground State0 aShell and Shape Evolution at N28 The 40Mg Ground State c04/20140 v801 aCrawford, H.L.1 aFallon, P.1 aMacchiavelli, A.O.1 aClark, R.M.1 aBrown, B., A.1 aTostevin, J.A.1 aBazin, D.1 aAoi, N.1 aDoornenbal, P.1 aMatsushita, M.1 aScheit, H.1 aSteppenbeck, D.1 aTakeuchi, S.1 aBaba, H.1 aCampbell, C.M.1 aCromaz, M.1 aIdeguchi, E.1 aKobayashi, N.1 aKondo, Y.1 aLee, G.1 aLee, I.Y.1 aLee, J.1 aLi, K.1 aMichimasa, S.1 aMotobayashi, T.1 aNakamura, T.1 aOta, S.1 aPaschalis, S.1 aPetri, M.1 aSako, T.1 aSakurai, H.1 aShimoura, S.1 aTakechi, M.1 aTogano, Y.1 aWang, H.1 aYoneda, K. uhttp://journals.aps.org/prc/abstract/10.1103/PhysRevC.89.04130300357nas a2200121 4500008004100000245003800041210003200079260001200111490000800123100001800131700001500149856007100164 2014 eng d00aThe Shell-Model Code NuShellX@MSU0 aShellModel Code NuShellXMSU c06/20140 v1201 aBrown, B., A.1 aRae, W.D.M uhttp://www.sciencedirect.com/science/article/pii/S009037521400474800473nas a2200109 4500008004100000245013600041210006900177490000700246100003000253700002200283856005800305 2014 eng d00aSpatially-Explicit Integrated Uncertainty and Sensitivity Analysis of Criteria Weights in Multicriteria Land Suitability Evaluation0 aSpatiallyExplicit Integrated Uncertainty and Sensitivity Analysi0 v571 aLigmann-Zielinskaa, Arika1 aJankowskib, Piotr uhttp://www.geo.msu.edu/~stsa/pubs/EMS2014_reprint.pdf00479nas a2200121 4500008004100000245008100041210006900122490000800191100002000199700001700219700001100236856011000247 2014 eng d00aTwo-Phase Filtered Mass Density Function for LES of Turbulent Reacting Flows0 aTwoPhase Filtered Mass Density Function for LES of Turbulent Rea0 v7601 aBanaeizadeh, A.1 aJaberi, F.A.1 aLi, Z. uhttp://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9402098&fileId=S002211201400573400595nas a2200169 4500008004100000245012700041210006900168260000900237490000800246100001600254700001400270700001500284700001500299700001300314700002000327856007800347 2014 eng d00aUntangling the contributions of image charge and laser profile for optimal photoemission of high-brightness electron beams0 aUntangling the contributions of image charge and laser profile f c20140 v1161 aPortman, J.1 aZhang, H.1 aMakino, K.1 aRuan, C.Y.1 aBerz, M.1 aDuxbury, P., M. uhttp://scitation.aip.org/content/aip/journal/jap/116/17/10.1063/1.490058200727nas a2200181 4500008004100000245016300041210006900204260001200273490000700285100001400292700001800306700001900324700001600343700002200359700002300381700001600404856012500420 2014 eng d00aWRF Model Sensitivity to Land Surface Model and Cumulus Parameterization under Short-Term Climate Extremes over the Southern Great Plains of the United States0 aWRF Model Sensitivity to Land Surface Model and Cumulus Paramete c10/20140 v271 aPei, Lisi1 aMoore, Nathan1 aZhong, Shiyuan1 aLuo, Lifeng1 aHyndman, David, W1 aHeilman, Warren, E1 aGao, Zhiqiu uhttps://icer.msu.edu/research/publications/wrf-model-sensitivity-land-surface-model-cumulus-parameterization-under-short00370nas a2200109 4500008004100000245005900041210005900100260001200159490000700171100001400178856006800192 2013 eng d00aAccuracy of the new pairing theory and its improvement0 aAccuracy of the new pairing theory and its improvement c12/20130 v881 aJia, L.Y. uhttp://journals.aps.org/prc/abstract/10.1103/PhysRevC.88.06432101343nas a2200445 4500008004100000245010100041210006900142260001200211490000800223653001600231653003200247653005600279653002800335653003400363100001500397700001800412700001400430700001900444700001800463700001600481700001500497700001700512700001200529700001200541700001500553700002100568700001800589700001800607700002200625700001500647700001600662700001500678700001400693700001400707700001400721700001100735700001200746700001300758856012600771 2013 eng d00aCLASH: The Enhanced Lensing Efficiency of the Highly Elongated Merging Cluster MACS J0416.1-24030 aCLASH The Enhanced Lensing Efficiency of the Highly Elongated Me c01/20130 v76210adark matter10agalaxies: clusters: general10agalaxies: clusters: individual: MACS J0416.1–240310aGalaxies: High-Redshift10agravitational lensing: strong1 aZitrin, A.1 aMeneghetti, M1 aUmetsu, K1 aBroadhurst, T.1 aBartelmann, M1 aBouwens, R.1 aBradley, L1 aCarrasco, M.1 aCoe, D.1 aFord, H1 aKelson, D.1 aKoekemoer, A., M1 aMedezinski, E1 aMoustakas, J.1 aMoustakas, L., A.1 aNonino, M.1 aPostman, M.1 aRosati, P.1 aSeidel, G1 aSeitz, S.1 aSendra, I1 aShu, X1 aVega, J1 aZheng, W uhttps://icer.msu.edu/research/publications/clash-enhanced-lensing-efficiency-highly-elongated-merging-cluster-macs-j0416101343nas a2200445 4500008004100000245010100041210006900142260001200211490000800223653001600231653003200247653005600279653002800335653003400363100001500397700001800412700001400430700001900444700001800463700001600481700001500497700001700512700001200529700001200541700001500553700002100568700001800589700001800607700002200625700001500647700001600662700001500678700001400693700001400707700001400721700001100735700001200746700001300758856012600771 2013 eng d00aCLASH: The Enhanced Lensing Efficiency of the Highly Elongated Merging Cluster MACS J0416.1-24030 aCLASH The Enhanced Lensing Efficiency of the Highly Elongated Me c01/20130 v76210adark matter10agalaxies: clusters: general10agalaxies: clusters: individual: MACS J0416.1–240310aGalaxies: High-Redshift10agravitational lensing: strong1 aZitrin, A.1 aMeneghetti, M1 aUmetsu, K1 aBroadhurst, T.1 aBartelmann, M1 aBouwens, R.1 aBradley, L1 aCarrasco, M.1 aCoe, D.1 aFord, H1 aKelson, D.1 aKoekemoer, A., M1 aMedezinski, E1 aMoustakas, J.1 aMoustakas, L., A.1 aNonino, M.1 aPostman, M.1 aRosati, P.1 aSeidel, G1 aSeitz, S.1 aSendra, I1 aShu, X1 aVega, J1 aZheng, W uhttps://icer.msu.edu/research/publications/clash-enhanced-lensing-efficiency-highly-elongated-merging-cluster-macs-j041-001273nas a2200433 4500008004100000245006800041210006600109260001200175490000800187653001300195653002800208653001900236653001300255653001500268100001300283700001600296700002300312700001600335700001500351700001800366700001900384700002100403700002100424700002000445700001600465700001400481700002700495700001800522700002000540700002300560700001900583700002200602700002500624700002200649700001800671700002300689700001800712856010900730 2013 eng d00aCLASH: Three Strongly Lensed Images of a Candidate z 11 Galaxy0 aCLASH Three Strongly Lensed Images of a Candidate z 11 Galaxy c01/20130 v76210aclusters10adistances and redshifts10aearly universe10agalaxies10aindividual1 aCoe, Dan1 aZitrin, Adi1 aCarrasco, Mauricio1 aShu, Xinwen1 aZheng, Wei1 aPostman, Marc1 aBradley, Larry1 aKoekemoer, Anton1 aBouwens, Rychard1 aBroadhurst, Tom1 aMonna, Anna1 aHost, Ole1 aMoustakas, Leonidas, A1 aFord, Holland1 aMoustakas, John1 avan der Wel, Arjen1 aDonahue, Megan1 aRodney, Steven, A1 aBen{\'ıtez, Narciso1 aJouvel, Stephanie1 aSeitz, Stella1 aKelson, Daniel, D.1 aRosati, Piero uhttps://icer.msu.edu/research/publications/clash-three-strongly-lensed-images-candidate-z%C2%A011-galaxy01262nas a2200433 4500008004100000245006700041210006500108260001200173490000800185653001300193653002800206653001900234653001300253653001500266100001300281700001600294700002300310700001600333700001500349700001800364700001900382700002100401700002100422700002000443700001600463700001400479700002700493700001800520700002000538700002300558700001900581700002200600700002200622700002200644700001800666700002300684700001800707856010300725 2013 eng d00aCLASH: Three Strongly Lensed Images of a Candidate z~11 Galaxy0 aCLASH Three Strongly Lensed Images of a Candidate z11 Galaxy c01/20130 v76210aclusters10adistances and redshifts10aearly universe10agalaxies10aindividual1 aCoe, Dan1 aZitrin, Adi1 aCarrasco, Mauricio1 aShu, Xinwen1 aZheng, Wei1 aPostman, Marc1 aBradley, Larry1 aKoekemoer, Anton1 aBouwens, Rychard1 aBroadhurst, Tom1 aMonna, Anna1 aHost, Ole1 aMoustakas, Leonidas, A1 aFord, Holland1 aMoustakas, John1 avan der Wel, Arjen1 aDonahue, Megan1 aRodney, Steven, A1 aBenítez, Narciso1 aJouvel, Stephanie1 aSeitz, Stella1 aKelson, Daniel, D.1 aRosati, Piero uhttps://icer.msu.edu/research/publications/clash-three-strongly-lensed-images-candidate-z11-galaxy00555nas a2200121 4500008004100000245012400041210006900165300000600234653002100240100002500261700002100286856012600307 2013 eng d00aEstimating wounding of lake trout by sea lamprey in the upper Great Lakes: Allowing for changing size-specific patterns0 aEstimating wounding of lake trout by sea lamprey in the upper Gr a-10aAD Model Builder1 aPrichard, Carson, G.1 aBence, James, R. uhttps://icer.msu.edu/research/publications/estimating-wounding-lake-trout-sea-lamprey-upper-great-lakes-allowing-changing00445nas a2200109 4500008004100000245006900041210006800110260001600178100002900194700001700223856009500240 2013 eng d00aGadget Avalanche: A Technology Literacy Course for Novice Adults0 aGadget Avalanche A Technology Literacy Course for Novice Adults aAtlanta, GA1 aLuchini-Colbry, Kathleen1 aColbry, Dirk uhttp://www.asee.org/file_server/papers/attachment/file/0003/4344/ASEE2013-Gadget-FINAL.pdf00482nas a2200109 4500008004100000245008200041210006900123260002500192490000700217100002600224856012200250 2013 eng d00aHeterogeneous relaxation dynamics in amorphous materials under cyclic loading0 aHeterogeneous relaxation dynamics in amorphous materials under c aTampa, FloridabIEEE0 v871 aPriezjev, Nikolai, V. uhttps://icer.msu.edu/research/publications/heterogeneous-relaxation-dynamics-amorphous-materials-under-cyclic-loading01392nas a2200133 4500008004100000245010200041210006900143260002600212520084200238100001701080700001901097700002001116856012201136 2013 eng d00aThe Institute for Cyber-Enabled Research: Regional Organization to Promote Computation in Science0 aInstitute for CyberEnabled Research Regional Organization to Pro aSan Diego, California3 aThe Institute for Cyber-Enabled Research (iCER) at Michigan State University (MSU) was established in 2009 to coordinate and support multidisciplinary resources for computation and computational sciences. iCER is the home of MSU's centralized High Performance Computing resources, which include a heterogeneous compute cluster with various hardware designed to meet the needs of different scientists. The goal of iCER is not to maximize Flops, but instead to maximize the amount of quality science being accomplished. This paper outlines many of the initiatives that iCER has taken to support researchers at MSU and throughout Michigan; describes the structure and evolution of iCER and its relationship with XSEDE and offers insights for other institutions interested in putting together a similar computational organization.

1 aColbry, Dirk1 aPunch, William1 aBauer, Wolfgang uhttps://icer.msu.edu/research/publications/institute-cyber-enabled-research-regional-organization-promote-computation00600nas a2200157 4500008004100000245010100041210006900142300001200211490000700223100001700230700001300247700002000260700001700280700002100297856012400318 2013 eng d00aIntra-aggregate pore structures are related to total C distribution within soil macro-aggregates0 aIntraaggregate pore structures are related to total C distributi a686-8750 v571 aAnanyeva, K.1 aWang, W.1 aSmucker, A.J.M.1 aRivers, M.L.1 aKravchenko, A.N. uhttps://icer.msu.edu/research/publications/intra-aggregate-pore-structures-are-related-total-c-distribution-within-soil02605nas a2200157 4500008004100000245012800041210006900169300001600238490000700254520198900261100001902250700002002269700001802289700002702307856011302334 2013 eng d00aThe joint effects of efficacy and compliance: a study of household water treatment effectiveness against childhood diarrhea0 ajoint effects of efficacy and compliance a study of household wa a1181–11900 v473 aThe effectiveness of household water treatment ({HWT)} at reducing diarrheal disease is related to the efficacy of the {HWT} method at removing pathogens, how people comply with {HWT}, and the relative contributions of other pathogen exposure routes. We define compliance with {HWT} as the proportion of drinking water treated by a community. Although many {HWT} methods are efficacious at removing or inactivating pathogens, their effectiveness within actual communities is decreased by imperfect compliance. However, the quantitative relationship between compliance and effectiveness is poorly understood. To assess the effectiveness of {HWT} on childhood diarrhea incidence via drinking water for three pathogen types (bacterial, viral, and protozoan), we developed a quantitative microbial risk assessment ({QMRA)} model. We examined the relationship between log(10) removal values ({LRVs)} and compliance with {HWT} for scenarios varying by: baseline incidence of diarrhea; etiologic fraction of diarrhea by pathogen type; pattern of compliance within a community; and size of contamination spikes in source water. Benefits from increasing {LRVs} strongly depend on compliance. For perfect compliance, diarrheal incidence decreases as {LRVs} increase. However, if compliance is incomplete, there are diminishing returns from increasing {LRVs} in most of the scenarios we considered. Higher {LRVs} are more beneficial if: contamination spikes are large; contamination levels are generally high; or some people comply perfectly. The effectiveness of {HWT} interventions at the community level may be limited by imperfect compliance, such that the benefits of high {LRVs} are not realized. Compliance with {HWT} should be carefully measured during {HWT} field studies and {HWT} dissemination programs. Studies of pathogen concentrations in a variety of developing-country source waters are also needed. Guidelines are needed for measuring and promoting compliance with {HWT.}

1 aEnger, Kyle, S1 aNelson, Kara, L1 aRose, Joan, B1 aEisenberg, Joseph, N S uhttps://icer.msu.edu/research/publications/joint-effects-efficacy-compliance-study-household-water-treatment01528nas a2200121 4500008004100000245007900041210006900120260004200189520109200231100002401323700001901347856004001366 2013 eng d00aLarge Eddy Simulation of Evaporating Spray with a Stochastic Breakup Model0 aLarge Eddy Simulation of Evaporating Spray with a Stochastic Bre aWarrendale, {PA}b{SAE} International3 aLarge Eddy Simulations of atomization and evaporation of liquid fuel sprays in diesel engine conditions are performed with stochastic breakup and non-equilibrium droplet heat and mass transfer models. The size and number density of the droplets generated by the breakup model are assumed to be governed by a Fokker-Planck equation, describing the evolution of the {PDF} of droplet radii. The fragmentation intensity spectrum is considered to be Gaussian and the scale of Lagrangian relative velocity fluctuations is included in the breakup frequency calculations. The aerodynamic interactions of droplets in the dense part of the spray are modeled by correcting the relative velocity of droplets in the wake of other droplets. The stochastic breakup model is employed together with the wake interaction model for simulations of non-evaporating and evaporating sprays in various gas temperature and pressure conditions. The predicted results for physical spray parameters, such as the spray penetration length are found to be in good agreement with the available experimental data.

1 aIrannejad, Abolfazl1 aJaberi, Farhad uhttp://papers.sae.org/2013-01-1101/00506nas a2200109 4500008004100000245010300041210006900144260002600213100001700239700001500256856012500271 2013 eng d00aLarge Eddy Simulation of Spray Mixing and Combustion with Two-Phase Filtered Mass Density Function0 aLarge Eddy Simulation of Spray Mixing and Combustion with TwoPha aSan Diego, California1 aIrannejad, A1 aJaberi, F. uhttps://icer.msu.edu/research/publications/large-eddy-simulation-spray-mixing-combustion-two-phase-filtered-mass-density00562nas a2200133 4500008004100000245012600041210006900167490001200236100002000248700001600268700001500284700001500299856011400314 2013 eng d00aLarge-Eddy Simulations of Turbulent Flows in Internal Combustion Engines, International Journal of Heat and Mass Transfer0 aLargeEddy Simulations of Turbulent Flows in Internal Combustion 0 vVol. 601 aBanaeizadeh, A.1 aAfshari, A.1 aSchock, H.1 aJaberi, F. uhttps://icer.msu.edu/research/publications/large-eddy-simulations-turbulent-flows-internal-combustion-engines00447nas a2200097 4500008004100000245009400041210006900135490000700204100002000211856011800231 2013 eng d00aMolecular dynamics simulations of oscillatory Couette flows with slip boundary conditions0 aMolecular dynamics simulations of oscillatory Couette flows with0 v141 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/molecular-dynamics-simulations-oscillatory-couette-flows-slip-boundary00703nas a2200217 4500008004100000245005900041210005400100300001400154490000800168653001900176653002800195653004000223100002300263700002000286700002000306700001600326700001800342700001900360700001600379856009000395 2013 eng d00aThe nature of the H₂-emitting gas in the Crab nebula0 anature of the H₂emitting gas in the Crab nebula a1257-12790 v43010aISM: molecules10aISM: supernova remnants10asupernovae: individual: Crab nebula1 aRichardson, C., T.1 aBaldwin, J., A.1 aFerland, G., J.1 aLoh, E., D.1 aKuehn, C., A.1 aFabian, A., C.1 aSalomé, P. uhttps://icer.msu.edu/research/publications/nature-h%E2%82%82-emitting-gas-crab-nebula00475nas a2200133 4500008004100000245006700041210006600108260001200174490000700186100001900193700001800212700002300230856008800253 2013 eng d00aNeutrino-pair emission from hot nuclei during stellar collapse0 aNeutrinopair emission from hot nuclei during stellar collapse c07/20140 v881 aMisch, Wendell1 aBrown, B., A.1 aFuller, George, M. uhttps://people.nscl.msu.edu/~brown/brown-all-papers/512-2013-PhysRevC.88.015807.pdf01427nas a2200133 4500008004100000245008600041210006900127260004200196520096600238100001901204700001501223700001501238856004001253 2013 eng d00aNumerical Simulations of Turbulent Sprays with a Multicomponent Evaporation Model0 aNumerical Simulations of Turbulent Sprays with a Multicomponent aWarrendale, {PA}b{SAE} International3 aA multicomponent droplet evaporation model which discretizes the one-dimensional mass and temperature profiles inside a droplet with a finite volume method has been developed and implemented into a large-eddy simulation ({LES)} model for spray simulations. The {LES} and multicomponent models were used along with the {KH-RT} secondary droplet breakup model to simulate realistic fuel sprays in a closed vessel. The effect of various spray and ambient gas parameters on the liquid penetration length of different single component and multicomponent fuels was investigated. The numerical results indicate that the spray penetration length decreases non-linearly with increasing gas temperature or pressure and is less sensitive to changes in ambient gas conditions at higher temperatures or pressures. The spray models and {LES} were found to predict the experimental results for n-hexadecane and two multicomponent surrogate diesel fuels reasonably well.

1 aSrivastava, S.1 aSchock, H.1 aJaberi, F. uhttp://papers.sae.org/2013-01-1603/00719nam a2200169 4500008004100000020002200041245012800063210006900191260005100260300001200311100001800323700002000341700001800361700001900379700002700398856012400425 2013 eng d a978-3-642-33573-000aProceedings of the 21st International Meshing Roundtable: An h-r Moving Mesh Method for One-Dimensional Time-Dependent PDEs0 aProceedings of the 21st International Meshing Roundtable An hr M aBerlin, HeidelbergbSpringer Berlin Heidelberg a39 - 541 aOng, Benjamin1 aRussell, Robert1 aRuuth, Steven1 aJiao, Xiangmin1 aWeill, Jean-Christophe uhttps://icer.msu.edu/research/publications/proceedings-21st-international-meshing-roundtable-h-r-moving-mesh-method-one00659nas a2200181 4500008004100000245012500041210006900166300001200235490000700247100001900254700001600273700001400289700001300303700001500316700001600331700001500347856011500362 2013 eng d00aRelationships between intra-aggregate pore structures and distributions of Escherichia coli within soil macro-aggregates0 aRelationships between intraaggregate pore structures and distrib a134-1420 v631 aA., Kravchenko1 aChun, H.-C.1 aMazer, M.1 aWang, W.1 aRose, J.B.1 aSmucker, A.1 aRivers, M. uhttps://icer.msu.edu/research/publications/relationships-between-intra-aggregate-pore-structures-distributions00583nas a2200145 4500008004100000245008800041210006900129260003400198100001700232700001500249700001700264700001500281700001700296856012400313 2013 eng d00aSpeeding up Scientific Imaging Workflows: Design of Automated Image Annotation Tool0 aSpeeding up Scientific Imaging Workflows Design of Automated Ima aTampa, FloridabIEEEc01/20131 aColbry, Dirk1 aDyer, Fred1 aDworkin, Ian1 aWang, Yang1 aWang, Lifeng uhttps://icer.msu.edu/research/publications/speeding-scientific-imaging-workflows-design-automated-image-annotation-tool00459nas a2200109 4500008004100000245009000041210006900131260002500200100001700225700002900242856007800271 2013 eng d00aSTEM inSight: Developing a Research Skills Course for First- and Second-Year Students0 aSTEM inSight Developing a Research Skills Course for First and S aAtlanta, GAc06/20131 aColbry, Dirk1 aLuchini-Colbry, Kathleen uhttp://www.asee.org/file_server/papers/attachment/file/0003/3803/6188.pdf00509nas a2200121 4500008004100000245009000041210006900131490001200200100002200212700001100234700001700245856012500262 2013 eng d00aSubgrid-Scale Models for Large-Eddy Simulations of Shock-Boundary Layer Interactions,0 aSubgridScale Models for LargeEddy Simulations of ShockBoundary L0 v Vol. 51 aJammalamadaka, A.1 aLi, Z.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/subgrid-scale-models-large-eddy-simulations-shock-boundary-layer-interactions00520nas a2200133 4500008004100000245008600041210007000127300001400197490000600211100001400217700001800231700001300249856012400262 2012 eng d00aAggregation of α-synuclein is kinetically controlled by intramolecular diffusion0 aAggregation of αsynuclein is kinetically controlled by intramole a2336-23410 v71 aAhmad, B.1 aLapidus, L.J.1 aChen, Y. uhttps://icer.msu.edu/research/publications/aggregation-%CE%B1-synuclein-kinetically-controlled-intramolecular-diffusion00651nas a2200157 4500008004100000245015400041210006900195100001500264700001200279700001700291700002100308700001800329700001600347700001200363856011800375 2012 eng d00aAlternative splicing of a multi-drug transporter from Pseudoperonospora cubensis generates an RXLR effector protein that elicits a rapid cell death.0 aAlternative splicing of a multidrug transporter from Pseudoperon1 aSavory, E.1 aZou, C.1 aAdhikari, B.1 aHamilton, J., P.1 aBuell, C., R.1 aShiu, S.-H.1 aDay, B. uhttps://icer.msu.edu/research/publications/alternative-splicing-multi-drug-transporter-pseudoperonospora-cubensis00557nas a2200133 4500008004100000245011100041210006900152300001400221490000700235100002200242700001800264700001700282856012400299 2012 eng d00aALTITUDINAL CLINAL VARIATION IN WING SIZE AND SHAPE IN AFRICAN DROSOPHILA MELANOGASTER: ONE CLINE OR MANY?0 aALTITUDINAL CLINAL VARIATION IN WING SIZE AND SHAPE IN AFRICAN D a438–4520 v671 aPitchers, William1 aPool, John, E1 aDworkin, Ian uhttps://icer.msu.edu/research/publications/altitudinal-clinal-variation-wing-size-shape-african-drosophila-melanogaster01651nas a2200553 4500008004100000245022000041210006900261260001200330653006000342100001500402700001500417700001500432700001200447700001400459700001300473700001200486700001300498700001600511700001700527700001300544700001700557700001500574700001500589700001800604700001800622700001200640700001500652700001300667700001400680700001900694700001800713700001500731700001800746700001200764700001500776700001500791700001500806700002000821700001400841700001400855700001200869700001800881700001600899700001400915700001500929700001300944700001400957856012600971 2012 eng d00aA Census of Star-Forming Galaxies in the z~9-10 Universe based on HST+Spitzer Observations Over 19 CLASH clusters: Three Candidate z~9-10 Galaxies and Improved Constraints on the Star Formation Rate Density at z~9.20 aCensus of StarForming Galaxies in the z910 Universe based on HST c11/201210aAstrophysics - Cosmology and Extragalactic Astrophysics1 aBouwens, R1 aBradley, L1 aZitrin, A.1 aCoe, D.1 aFranx, M.1 aZheng, W1 aSmit, R1 aHost, O.1 aPostman, M.1 aMoustakas, L1 aLabbe, I1 aCarrasco, M.1 aMolino, A.1 aDonahue, M1 aKelson, D., D1 aMeneghetti, M1 aJha, S.1 aBenitez, N1 aLemze, D1 aUmetsu, K1 aBroadhurst, T.1 aMoustakas, J.1 aRosati, P.1 aBartelmann, M1 aFord, H1 aGraves, G.1 aGrillo, C.1 aInfante, L1 aJiminez-Teja, Y1 aJouvel, S1 aLahav, O.1 aMaoz, D1 aMedezinski, E1 aMelchior, P1 aMerten, J1 aNonino, M.1 aOgaz, S.1 aSeitz, S. uhttps://icer.msu.edu/research/publications/census-star-forming-galaxies-z9-10-universe-based-hstspitzer-observations-over01350nas a2200457 4500008004100000245009300041210006900134260001200203490000800215653001600223653003200239653005400271653002800325653003400353100001500387700001800402700001500420700001200435700002200447700001600469700001100485700001300496700001700509700001600526700001900542700001200561700001300573700001400586700001800600700001800618700001500636700001500651700001500666700001500681700001300696700001800709700001500727700001500742700001300757856012200770 2012 eng d00aCLASH: Discovery of a Bright z ~= 6.2 Dwarf Galaxy Quadruply Lensed by MACS J0329.6-02110 aCLASH Discovery of a Bright z 62 Dwarf Galaxy Quadruply Lensed b c03/20120 v74710adark matter10agalaxies: clusters: general10agalaxies: clusters: individual: MACS J0329.6-021110aGalaxies: High-Redshift10agravitational lensing: strong1 aZitrin, A.1 aMoustakas, J.1 aBradley, L1 aCoe, D.1 aMoustakas, L., A.1 aPostman, M.1 aShu, X1 aZheng, W1 aBenítez, N.1 aBouwens, R.1 aBroadhurst, T.1 aFord, H1 aHost, O.1 aJouvel, S1 aKoekemoer, A.1 aMeneghetti, M1 aRosati, P.1 aDonahue, M1 aGrillo, C.1 aKelson, D.1 aLemze, D1 aMedezinski, E1 aMolino, A.1 aNonino, M.1 aOgaz, S. uhttps://icer.msu.edu/research/publications/clash-discovery-bright-z-62-dwarf-galaxy-quadruply-lensed-macs-j03296-021102193nas a2200733 4500008004100000245009800041210006900139260001200208490000800220653002800228653001600256653005400272653003400326653003200360100002000392700002300412700001800435700001900453700001600472700002000488700002000508700002300528700001900551700002200570700001300592700001800605700002100623700001900644700001700663700002200680700001900702700002100721700001800742700002200760700001800782700002000800700002000820700002100840700002000861700001800881700002200899700001900921700001800940700002200958700001400980700001700994700002001011700002401031700002401055700002501079700002201104700002101126700001901147700001801166700002701184700001901211700001601230700002001246700002001266700001501286700001801301700001501319856012501334 2012 eng d00aCLASH: Mass Distribution in and around MACS J1206.2-0847 from a Full Cluster Lensing Analysis0 aCLASH Mass Distribution in and around MACS J120620847 from a Ful c08/20120 v75510acosmology: observations10adark matter10agalaxies: clusters: individual: MACS J1206.2-084710agravitational lensing: strong10agravitational lensing: weak1 aUmetsu, Keiichi1 aMedezinski, Elinor1 aNonino, Mario1 aMerten, Julian1 aZitrin, Adi1 aMolino, Alberto1 aGrillo, Claudio1 aCarrasco, Mauricio1 aDonahue, Megan1 aMahdavi, Andisheh1 aCoe, Dan1 aPostman, Marc1 aKoekemoer, Anton1 aCzakon, Nicole1 aSayers, Jack1 aMroczkowski, Tony1 aGolwala, Sunil1 aKoch, Patrick, M1 aLin, Kai-Yang1 aMolnar, Sandor, M1 aRosati, Piero1 aBalestra, Italo1 aMercurio, Amata1 aScodeggio, Marco1 aBiviano, Andrea1 aAnguita, Timo1 aInfante, Leopoldo1 aSeidel, Gregor1 aSendra, Irene1 aJouvel, Stephanie1 aHost, Ole1 aLemze, Doron1 aBroadhurst, Tom1 aMeneghetti, Massimo1 aMoustakas, Leonidas1 aBartelmann, Matthias1 aBenítez, Narciso1 aBouwens, Rychard1 aBradley, Larry1 aFord, Holland1 aJiménez-Teja, Yolanda1 aKelson, Daniel1 aLahav, Ofer1 aMelchior, Peter1 aMoustakas, John1 aOgaz, Sara1 aSeitz, Stella1 aZheng, Wei uhttps://icer.msu.edu/research/publications/clash-mass-distribution-around-macs-j12062-0847-full-cluster-lensing-analysis01974nas a2200733 4500008004100000245008800041210006900129260001200198490000800210653001600218653003200234653005600266653002800322653003400350100001500384700001500399700001500414700001500429700001600444700001200460700001400472700001500486700001900501700001400520700001700534700001600551700001700567700001700584700001500601700001200616700001300628700002000641700001800661700001300679700001800692700001600710700001400726700001500740700001300755700001500768700001500783700001200798700001500810700001400825700001400839700001300853700001700866700001200883700001600895700001800911700001600929700001800945700001400963700001500977700002200992700001301014700001401027700001501041700001401056700001401070700001401084700002001098856012201118 2012 eng d00aCLASH: New Multiple Images Constraining the Inner Mass Profile of MACS J1206.2-08470 aCLASH New Multiple Images Constraining the Inner Mass Profile of c04/20120 v74910adark matter10agalaxies: clusters: general10agalaxies: clusters: individual: MACS J1206.2–084710aGalaxies: High-Redshift10agravitational lensing: strong1 aZitrin, A.1 aRosati, P.1 aNonino, M.1 aGrillo, C.1 aPostman, M.1 aCoe, D.1 aSeitz, S.1 aEichner, T1 aBroadhurst, T.1 aJouvel, S1 aBalestra, I.1 aMercurio, A1 aScodeggio, M1 aBenítez, N.1 aBradley, L1 aFord, H1 aHost, O.1 aJimenez-Teja, Y1 aKoekemoer, A.1 aZheng, W1 aBartelmann, M1 aBouwens, R.1 aCzoske, O1 aDonahue, M1 aGraur, O1 aGraves, G.1 aInfante, L1 aJha, S.1 aKelson, D.1 aLahav, O.1 aLazkoz, R1 aLemze, D1 aLombardi, M.1 aMaoz, D1 aMcCully, C.1 aMedezinski, E1 aMelchior, P1 aMeneghetti, M1 aMerten, J1 aMolino, A.1 aMoustakas, L., A.1 aOgaz, S.1 aPatel, B.1 aRegoes, E.1 aRiess, A.1 aRodney, S1 aUmetsu, K1 aVan der Wel, A. uhttps://icer.msu.edu/research/publications/clash-new-multiple-images-constraining-inner-mass-profile-macs-j12062-084701835nas a2200637 4500008004100000245007600041210006900117260001200186490000800198100001300206700002000219700001600239700001900255700002300274700001800297700002300315700001800338700002400356700002300380700002400403700002200427700001900449700002100468700001500489700001800504700002000522700002200542700001700564700002200581700001500603700002000618700001400638700001800652700002000670700001800690700002700708700002000735700002000755700001700775700002500792700002200817700002100839700001400860700002200874700001600896700002200912700001900934700002400953700001400977700002400991700001901015700001601034700001801050700001801068856011101086 2012 eng d00aCLASH: Precise New Constraints on the Mass Profile Galaxy Cluster A22610 aCLASH Precise New Constraints on the Mass Profile Galaxy Cluster c09/20120 v7571 aCoe, Dan1 aUmetsu, Keiichi1 aZitrin, Adi1 aDonahue, Megan1 aMedezinski, Elinor1 aPostman, Marc1 aCarrasco, Mauricio1 aAnguita, Timo1 aGeller, Margaret, J1 aRines, Kenneth, J.1 aDiaferio, Antonaldo1 aKurtz, Michael, J1 aBradley, Larry1 aKoekemoer, Anton1 aZheng, Wei1 aNonino, Mario1 aMolino, Alberto1 aMahdavi, Andisheh1 aLemze, Doron1 aInfante, Leopoldo1 aOgaz, Sara1 aMelchior, Peter1 aHost, Ole1 aFord, Holland1 aGrillo, Claudio1 aRosati, Piero1 aJiménez-Teja, Yolanda1 aMoustakas, John1 aAscaso, Begoña1 aLahav, Ofer;1 aBartelmann, Matthias1 aBenítez, Narciso1 aBouwens, Rychard1 aGraur, Or1 aGraves, Genevieve1 aJha, Saurab1 aJouvel, Stephanie1 aKelson, Daniel1 aMoustakas, Leonidas1 aMaoz, Dan1 aMeneghetti, Massimo1 aMerten, Julian1 aRiess, Adam1 aRodney, Steve1 aSeitz, Stella uhttps://icer.msu.edu/research/publications/clash-precise-new-constraints-mass-profile-galaxy-cluster-a226100583nas a2200145 4500008004100000245010200041210006900143490000800212100002000220700001800240700001900258700001700277700001900294856012400313 2012 eng d00aClimate Change and Risk Projection: Dynamic Models of Tsetse and African Trypanosomiasis in Kenya0 aClimate Change and Risk Projection Dynamic Models of Tsetse and 0 v1021 aMessina, Joseph1 aMoore, Nathan1 aDeVisser, Mark1 aMcCord, Paul1 aWalker, Edward uhttps://icer.msu.edu/research/publications/climate-change-risk-projection-dynamic-models-tsetse-african-trypanosomiasis00553nas a2200133 4500008004100000245008700041210006900128260003500197300001100232490000700243100002900250700002000279856012000299 2012 eng d00aComputational study of the thermal conductivity in defective carbon nanostructures0 aComputational study of the thermal conductivity in defective car bAmerican Physical SocietycSep a1254180 v861 aFthenakis, Zacharias, G.1 aTománek, David uhttps://icer.msu.edu/research/publications/computational-study-thermal-conductivity-defective-carbon-nanostructures00461nas a2200133 4500008004100000245005200041210005200093260003100145100002000176700001400196700001700210700001500227856008500242 2012 eng d00aCoordination of Vision and Action in Chameleons0 aCoordination of Vision and Action in Chameleons aAlbuquerque, {NM}c06/20121 aIngle, Nicholis1 aDoor, Tim1 aColbry, Dirk1 aDyer, Fred uhttps://icer.msu.edu/research/publications/coordination-vision-action-chameleons00497nas a2200121 4500008004100000245008500041210007000126300001400196490000700210100001400217700001800231856012600249 2012 eng d00aCurcumin Prevents Aggregation in α-Synuclein by Increasing Reconfiguration Rate0 aCurcumin Prevents Aggregation in αSynuclein by Increasing Reconf a9193-91990 v121 aAhmad, B.1 aLapidus, L.J. uhttps://icer.msu.edu/research/publications/curcumin-prevents-aggregation-%CE%B1-synuclein-increasing-reconfiguration-rate00495nas a2200109 4500008004100000245008600041210006900127260002300196100001700219700002500236856012400261 2012 eng d00aCyberGreen: Hands-On Engineering Research in Sustainability and Supercomputing”0 aCyberGreen HandsOn Engineering Research in Sustainability and Su aAda, Ohioc03/20121 aColbry, Dirk1 aLuchini-Colbry, Katy uhttps://icer.msu.edu/research/publications/cybergreen-hands-engineering-research-sustainability-supercomputing%E2%80%9D00580nas a2200145 4500008004100000245009200041210006900133260003500202300001100237490000800248100001600256700002200272700002000294856012000314 2012 eng d00aDesigning Electrical Contacts to ${\mathrm{MoS}}_{2}$ Monolayers: A Computational Study0 aDesigning Electrical Contacts to mathrm MoS 2 Monolayers A Compu bAmerican Physical SocietycApr a1568020 v1081 aPopov, Igor1 aSeifert, Gotthard1 aTománek, David uhttps://icer.msu.edu/research/publications/designing-electrical-contacts-mathrmmos-2-monolayers-computational-study00486nas a2200133 4500008004100000245006700041210006700108300001400175490000700189100001900196700002100215700001300236856010300249 2012 eng d00aDynamics of Performing and Remembering Organizational Routines0 aDynamics of Performing and Remembering Organizational Routines a1536-15580 v491 aMiller, K., D.1 aPentland, B., T.1 aChoi, S. uhttps://icer.msu.edu/research/publications/dynamics-performing-remembering-organizational-routines00531nas a2200121 4500008004100000245010600041210006900147260001200216490000800228100002400236700002600260856012300286 2012 eng d00aEffects of crossflow velocity and transmembrane pressure on microfiltration of oil-in-water emulsions0 aEffects of crossflow velocity and transmembrane pressure on micr c10/20120 v4231 aDarvishzadeh, Tohid1 aPriezjev, Nikolai, V. uhttps://icer.msu.edu/research/publications/effects-crossflow-velocity-transmembrane-pressure-microfiltration-oil-water00586nas a2200157 4500008004100000245009300041210006900134490000700203100001800210700001300228700001600241700001600257700001800273700001600291856012100307 2012 eng d00aEvaluating DEM source and resolution uncertainties in the Soil and Water Assessment Tool0 aEvaluating DEM source and resolution uncertainties in the Soil a0 v271 aLin, Shengpan1 aJing, C.1 aColes, N.A.1 aChaplot, V.1 aMoore, Nathan1 aWu, Jiaping uhttps://icer.msu.edu/research/publications/evaluating-dem-source-resolution-uncertainties-soil-water-assessment-tool00579nas a2200145 4500008004100000245010200041210006900143490000700212100001800219700001600237700001800253700001900271700002000290856012300310 2012 eng d00aEvaluation of estimating daily maximum and minimum air temperature with MODIS data in east Africa0 aEvaluation of estimating daily maximum and minimum air temperatu0 v141 aLin, Shengpan1 aWu, Jiaping1 aMoore, Nathan1 aDeVisser, Mark1 aMessina, Joseph uhttps://icer.msu.edu/research/publications/evaluation-estimating-daily-maximum-minimum-air-temperature-modis-data-east01463nas a2200145 4500008004100000245007000041210006900111300001100180490000700191520100600198100002101204700001901225700001801244856005501262 2012 eng d00aEvolution and stability of altruist strategies in microbial games0 aEvolution and stability of altruist strategies in microbial game a0119140 v853 aWhen microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory ({EGT).} We study the predictions of {EGT} for the bacterial “suicide bomber” game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters.

1 aAdami, Christoph1 aSchossau, Jory1 aHintze, Arend uhttp://link.aps.org/doi/10.1103/PhysRevE.85.01191400612nas a2200157 4500008004100000245010000041210006900141100001800210700001700228700001500245700002100260700001900281700002100300700001200321856012100333 2012 eng d00aExpression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis0 aExpression profiling of Cucumis sativus in response to infection1 aBuell, C., R.1 aAdhikari, B.1 aSavory, E.1 aVaillancourt, B.1 aChilds, K., L.1 aHamilton, J., P.1 aDay, B. uhttps://icer.msu.edu/research/publications/expression-profiling-cucumis-sativus-response-infection-pseudoperonospora00551nas a2200133 4500008004100000245009300041210006900134260003500203300001100238490000800249100001400257700002000271856012600291 2012 eng d00aFormation and Stability of Cellular Carbon Foam Structures: An \textit{Ab Initio} Study0 aFormation and Stability of Cellular Carbon Foam Structures An te bAmerican Physical SocietycSep a1355010 v1091 aZhu, Zhen1 aTománek, David uhttps://icer.msu.edu/research/publications/formation-stability-cellular-carbon-foam-structures-textitab%C2%A0initio-study00575nas a2200157 4500008004100000245007200041210006900113260003500182300001100217490000800228100001700236700002200253700001800275700002000293856010400313 2012 eng d00aHelicity in Ropes of Chiral Nanotubes: Calculations and Observation0 aHelicity in Ropes of Chiral Nanotubes Calculations and Observati bAmerican Physical SocietycJun a2355010 v1081 aTeich, David1 aSeifert, Gotthard1 aIijima, Sumio1 aTománek, David uhttps://icer.msu.edu/research/publications/helicity-ropes-chiral-nanotubes-calculations-observation00441nas a2200097 4500008004100000245008000041210006900121490000800190100002600198856011900224 2012 eng d00aInterfacial friction between semiflexible polymers and crystalline surfaces0 aInterfacial friction between semiflexible polymers and crystalli0 v1361 aPriezjev, Nikolai, V. uhttps://icer.msu.edu/research/publications/interfacial-friction-between-semiflexible-polymers-crystalline-surfaces00554nas a2200145 4500008004100000245008200041210006900123300001400192490000700206100001300213700002100226700002000247700001700267856012400284 2012 eng d00aIntra-aggregate pore characteristics: X-ray computed microtomography analysis0 aIntraaggregate pore characteristics Xray computed microtomograph a1159-11710 v761 aWang, W.1 aKravchenko, A.N.1 aSmucker, A.J.M.1 aRivers, M.L. uhttps://icer.msu.edu/research/publications/intra-aggregate-pore-characteristics-x-ray-computed-microtomography-analysis00465nas a2200097 4500008004100000245008400041210006900125260003100194100001700225856012500242 2012 eng d00aLessons Learned When Building a Greenfield High Performance Computing Ecosystem0 aLessons Learned When Building a Greenfield High Performance Comp aSan Diego, California, USA1 aKeen, Andrew uhttps://icer.msu.edu/research/publications/lessons-learned-when-building-greenfield-high-performance-computing-ecosystem01554nas a2200529 4500008004100000245007700041210006900118260001200187490000800199100001500207700001800222700001600240700002000256700001600276700002200292700001500314700002000329700001900349700001300368700002700381700002300408700001800431700002200449700001800471700002200489700002100511700002100532700002300553700002500576700002000601700001900621700002000640700002200660700002000682700002300702700001600725700001700741700002000758700002400778700001900802700001800821700001500839700001800854700002000872700002300892856010900915 2012 eng d00aA magnified young galaxy from about 500 million years after the Big Bang0 amagnified young galaxy from about 500 million years after the Bi c09/20120 v4891 aZheng, Wei1 aPostman, Marc1 aZitrin, Adi1 aMoustakas, John1 aShu, Xinwen1 aJouvel, Stephanie1 aHøst, Ole1 aMolino, Alberto1 aBradley, Larry1 aCoe, Dan1 aMoustakas, Leonidas, A1 aCarrasco, Mauricio1 aFord, Holland1 aBenítez, Narciso1 aLauer, Tod, R1 aSeitz, Stella;, B1 aBouwens, Rychard1 aKoekemoer, Anton1 aMedezinski, Elinor1 aBartelmann, Matthias1 aBroadhurst, Tom1 aDonahue, Megan1 aGrillo, Claudio1 aInfante, Leopoldo1 aJha, Saurabh, W1 aKelson, Daniel, D.1 aLahav, Ofer1 aLemze, Doron1 aMelchior, Peter1 aMeneghetti, Massimo1 aMerten, Julian1 aNonino, Mario1 aOgaz, Sara1 aRosati, Piero1 aUmetsu, Keiichi1 avan der Wel, Arjen uhttps://icer.msu.edu/research/publications/magnified-young-galaxy-about-500-million-years-after-big-bang01334nas a2200493 4500008004100000245015700041210006900198260001200267490000800279100001600287700001300303700002200316700001300338700001400351700001400365700001400379700001300393700001500406700001200421700001800433700001500451700001400466700001500480700001300495700001500508700001400523700001300537700001300550700001400563700001200577700001400589700001400603700001500617700001500632700001100647700001800658700001800676700001500694700001500709700001500724700001400739700001500753856007200768 2012 eng d00aMass Measurements of the Neutron-Deficient 41Ti, 45Cr, 49Fe, and 53Ni Nuclides: ￼First Test of the Isobaric Multiplet Mass Equation in fp-Shell Nuclei0 aMass Measurements of the NeutronDeficient 41Ti 45Cr 49Fe and 53N c09/20120 v1091 aZhang, Y.H.1 aXu, H.S.1 aLitvinov, Yu., A.1 aTu, X.L.1 aYan, X.L.1 aTypel, S.1 aBlaum, K.1 aWang, M.1 aZhou, X.H.1 aSun, Y.1 aBrown, B., A.1 aYuan, Y.J.1 aXia, J.W.1 aYang, J.C.1 aAudi, G.1 aChen, X.C.1 aJia, G.B.1 aHu, Z.G.1 aMa, X.W.1 aMao, R.S.1 aMei, B.1 aShuai, P.1 aSun, Z.Y.1 aWang, S.T.1 aXiao, G.Q.1 aXu, X.1 aYamaguchi, T.1 aYamaguchi, Y.1 aZang, Y.D.1 aZhao, H.W.1 aZhao, T.C.1 aZhang, W.1 aZhan, W.L. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.10250102241nas a2200193 4500008004100000245007100041210006900112300001400181490000700195520159700202653002101799653002801820653002501848653003001873653003501903100002501938700001301963856007101976 2012 eng d00aMedical image-based simulation of abdominal aortic aneurysm growth0 aMedical imagebased simulation of abdominal aortic aneurysm growt a107–1170 v423 aAdvances in theoretical modeling of biological tissue growth and remodeling ({G&R)} and computational biomechanics have been helpful to capture salient features of vascular remodeling during the progression of vascular diseases. Nevertheless, application of such advances to individualized diagnosis and clinical treatment of diseases such as abdominal aortic aneurysm ({AAA)} remains challenging. As a step toward that goal, in this paper, we present a computational framework necessary towards patient-specific modeling of {AAA} growth. Prior to {AAA} simulations, using an inverse optimization method, initial material parameters are identified for a healthy aorta such that a homeostatic condition is satisfied for the given medical image-based geometrical model under physiological conditions. Various shapes of {AAAs} are then computationally created by inducing elastin degradation with different spatio-temporal distributions. The simulation results emphasize the role of extent of elastin damage, geometric complexity of an enlarged {AAA}, and sensitivity of stress-mediated collagen turnover on the wall stress distribution and the rate of expansion. The results also show that the distributions of stress and local expansion initially correspond to the extent of elastin damage, but change via stress-mediated tissue {G&R} depending on the aneurysm shape. Finally, we suggest that the current framework can be utilized along with medical images from an individual patient to predict the {AAA} shape and mechanical properties in the near future via an inverse scheme.

10aAneurysm rupture10aFinite element analysis10aInverse optimization10aPatient-specific modeling10aVascular growth and remodeling1 aZeinali-Davarani, S.1 aBaek, S. uhttp://www.sciencedirect.com/science/article/pii/S009364131200010900547nas a2200109 4500008004100000245011200041210006900153260005900222100001900281700001900300856011800319 2012 eng d00aMethylmercury (MeHg) disrupts fluo4 fluorescence in cerebellar slices from GABAA receptor alpha6 (-/-) mice0 aMethylmercury MeHg disrupts fluo4 fluorescence in cerebellar sli aSan Francisco, CAbSociety of Toxicology 2012c03/20121 aBradford, A, B1 aAtchison, W, D uhttps://icer.msu.edu/research/publications/methylmercury-mehg-disrupts-fluo4-fluorescence-cerebellar-slices-gabaa00600nas a2200145 4500008004100000245011800041210006900159100001500228700001700243700002100260700002100281700001800302700001200320856012200332 2012 eng d00amRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection0 amRNASeq analysis of the Pseudoperonospora cubensis transcriptome1 aSavory, E.1 aAdhikari, B.1 aHamilton, J., P.1 aVaillancourt, B.1 aBuell, C., R.1 aDay, B. uhttps://icer.msu.edu/research/publications/mrna-seq-analysis-pseudoperonospora-cubensis-transcriptome-during-cucumber00561nas a2200157 4500008004100000245006000041210006000101260003500161300001100196490000800207100001700215700002900232700002200261700002000283856010000303 2012 eng d00aNanomechanical energy storage in twisted nanotube ropes0 aNanomechanical energy storage in twisted nanotube ropes bAmerican Physical SocietycDec a2555010 v1091 aTeich, David1 aFthenakis, Zacharias, G.1 aSeifert, Gotthard1 aTománek, David uhttps://icer.msu.edu/research/publications/nanomechanical-energy-storage-twisted-nanotube-ropes00440nas a2200145 4500008004100000245003600041210003300077260001200110300001600122490000700138100002700145700002300172700002200195856007700217 2012 eng d00aA Parallel Space-Time Algorithm0 aParallel SpaceTime Algorithm c01/2012 aC233 - C2480 v341 aChristlieb, Andrew, J.1 aHaynes, Ronald, D.1 aOng, Benjamin, W. uhttps://icer.msu.edu/research/publications/parallel-space-time-algorithm00607nas a2200169 4500008004100000245011700041210007300158260001900231490000700250100001200257700002100269700002000290700001800310700002100328700001700349856007100366 2012 eng d00aPhysics of bandgap formation in Cu–Sb–Se based novel thermoelectrics: the role of Sb valency and Cu d levels0 aPhysics of bandgap formation in Cu–Sb–Se based novel thermoelect cSeptember 20120 v241 aDo, Dat1 aOzolins, Vidvuds1 aMahanti, S., D.1 aLee, Mal-Soon1 aZhang, Yongsheng1 aWolverton, C uhttp://iopscience.iop.org.proxy1.cl.msu.edu/0953-8984/24/41/41550204058nas a2200097 4500008004100000245009900041210006900140520362900209100002303838856009903861 2012 eng d00aPreventing diarrheal infections with household water treatment: lessons from simulation models0 aPreventing diarrheal infections with household water treatment l3 aDiarrheal disease kills two million children per year in developing countries. Diarrhea is controlled in industrialized countries by systems to remove sewage and distribute clean water. These systems are difficult to fund, build, and maintain in developing countries, so simpler technologies are promoted: e.g., household water treatment ({HWT)}, handwashing, and latrines. These technologies, however, require consistent effort by individuals for proper use and maintenance, defined here as 'compliance'. Measuring compliance is difficult, and often neglected. It is important to understand how the extent and pattern of compliance within communities affects the prevention of diarrhea by {HWT}, while accounting for biases in field trials and characteristics of natural transmission systems, such as the presence of multiple pathogens, transient spikes of contamination, and multiple transmission routes. This question was answered by: reanalyzing and generalizing results from a {HWT} field trial, using a quantitative microbial risk assessment ({QMRA)} model to adjust for bias (chapter 3); examining the joint effects of {HWT} antimicrobial efficacy and compliance on prevention of diarrhea (chapter 4); and using a model of diarrheal infection transmission incorporating multiple routes of infection to further examine efficacy and compliance issues with {HWT} (chapter 5). The {QMRA} model of the field trial found that compliance greatly affected {HWT} effectiveness: with low compliance, 10% of diarrhea was prevented; with high compliance, 90% was prevented. It also estimated source water pathogen concentrations source water that were consistent with measurements from other developing countries. The model found that the effect of an imperfect placebo device used during the field trial depended on the assumed level of compliance during the field trial. The {QMRA} model was modified to examine how {HWT} compliance and antimicrobial effectiveness jointly altered diarrheal disease risk. Given perfect compliance, increasing antimicrobial effectiveness always lowered risk. If compliance was incomplete, increasing antimicrobial effectiveness eventually ceased to lower risk, except in a few scenarios with high incidence, high compliance, or large water contamination spikes. The pattern of compliance by communities also influenced risk; e.g., risk was lower if 90% of people used {HWT} perfectly and 10% never used {HWT}, than if 100% of people used {HWT} 90% of the time. A preliminary transmission model simulated a community in which infected people shed pathogens, which were ingested by other people via exposure to land, drinking water, their household environment, or visits from other households. It found similar results to the {QMRA} models regarding compliance. Transmission of diarrheal pathogens by household visits appeared unimportant compared to other routes; however, visits consisted of exchanges of pathogens between household environments. Other types of visits (e.g., shared child care) might lead to greater transfer of pathogens and a greater influence of visits on illness. The model also inferred that viruses and protozoa were attenuated (removed from the system, e.g., by decay or sequestration) {\textasciitilde}10 times faster than bacteria. Future sensitivity and uncertainty analyses will highlight important aspects of the model and its parameters that contribute to its results. The amount and pattern of compliance strongly affects diarrhea prevention by {HWT.} Further research should be conducted on improving compliance with {HWT} in developing countries.

1 aEnger, Kyle, Scott uhttp://www.openthesis.org/documents/Preventing-diarrheal-infections-with-household-601272.html00460nas a2200097 4500008004100000245009900041210006900140490001300209100001600222856012400238 2012 eng d00aThe role of standing genetic variation in adaptation of digital organisms to a new environment0 arole of standing genetic variation in adaptation of digital orga0 v13: 3-101 aAnderson, C uhttps://icer.msu.edu/research/publications/role-standing-genetic-variation-adaptation-digital-organisms-new-environment00666nas a2200193 4500008004100000245008400041210006900125260000800194300001100202490000800213100002400221700001600245700001900261700001900280700002100299700001900320700002000339856011300359 2012 eng d00aSelective probe of the morphology and local vibrations at carbon nanoasperities0 aSelective probe of the morphology and local vibrations at carbon bAIP a0645050 v1361 aFujimori, Toshihiko1 aUrita, Koki1 aTomanek, David1 aOhba, Tomonori1 aMoriguchi, Isamu1 aEndo, Morinobu1 aKaneko, Katsumi uhttps://icer.msu.edu/research/publications/selective-probe-morphology-local-vibrations-carbon-nanoasperities00574nas a2200145 4500008004100000245008800041210006900129260002100198100001600219700001800235700001700253700001700270700001700287856012400304 2012 eng d00aSimultaneous Iterative Reconstruction Techniques for Computerized Tomography on GPU0 aSimultaneous Iterative Reconstruction Techniques for Computerize aEast Lansing, MI1 aXin, Junjun1 aBardel, Chuck1 aColbry, Dirk1 aUdpa, Lalita1 aUdpa, Satish uhttps://icer.msu.edu/research/publications/simultaneous-iterative-reconstruction-techniques-computerized-tomography-gpu00745nas a2200205 4500008004100000245008900041210006900130300001600199490000600215100001900221700001800240700002200258700002200280700001700302700002400319700002700343700002400370700002000394856012500414 2012 eng d00aSynthesis and Transformation of Linear Adamantane Assemblies inside Carbon Nanotubes0 aSynthesis and Transformation of Linear Adamantane Assemblies ins a8674–86830 v61 aZhang, Jinying1 aFeng, Yanquan1 aIshiwata, Hitoshi1 aMiyata, Yasumitsu1 aKitaura, Ryo1 aDahl, Jeremy, E. P.1 aCarlson, Robert, M. K.1 aShinohara, Hisanori1 aTománek, David uhttps://icer.msu.edu/research/publications/synthesis-transformation-linear-adamantane-assemblies-inside-carbon-nanotubes00700nas a2200193 4500008004100000020002200041245007400063210006900137260003700206300001400243653001200257653002200269653002700291100001800318700001400336700002400350700001900374856011300393 2011 eng d a978-1-4503-0813-700aApproximate kernel k-means: solution to large scale kernel clustering0 aApproximate kernel kmeans solution to large scale kernel cluster aSan Diego, CA, USAbACMc08/2011 a895–90310ak-means10akernel clustering10alarge-scale clustering1 aChitta, Radha1 aJin, Rong1 aHavens, Timothy, C.1 aJain, Anil, K. uhttps://icer.msu.edu/research/publications/approximate-kernel-k-means-solution-large-scale-kernel-clustering00383nas a2200109 4500008004100000245005300041210005200094300001200146490000600158100002000164856008900184 2011 eng d00aCalling to Be Your Best: Your Calling to Science0 aCalling to Be Your Best Your Calling to Science a86–870 v11 aTománek, David uhttps://icer.msu.edu/research/publications/calling-be-your-best-your-calling-science00583nas a2200145 4500008004100000245011100041210006900152300001200221490000800233100001300241700002100254700002000275700001700295856012500312 2011 eng d00aComparison of image segmentation methods in simulated 2D and 3D microtomographic images of soil aggregates0 aComparison of image segmentation methods in simulated 2D and 3D a231-2410 v1621 aWang, W.1 aKravchenko, A.N.1 aSmucker, A.J.M.1 aRivers, M.L. uhttps://icer.msu.edu/research/publications/comparison-image-segmentation-methods-simulated-2d-3d-microtomographic-images00670nas a2200169 4500008004100000245011800041210006900159100002100228700002200249700001700271700001400288700001700302700001600319700002200335700001800357856012500375 2011 eng d00aThe Comprehensive Phytopathogen Genomics Resource: An electronic resource for data-mining plant pathogen genomes0 aComprehensive Phytopathogen Genomics Resource An electronic reso1 aHamilton, J., P.1 aNeeno-Eckwall, E.1 aAdhikari, B.1 aPerna, N.1 aTisserat, N.1 aLeach, J.E.1 aLévesque, C., A.1 aBuell, C., R. uhttps://icer.msu.edu/research/publications/comprehensive-phytopathogen-genomics-resource-electronic-resource-data-mining00693nas a2200181 4500008004100000245011800041210006900159490000800228100001800236700002300254700002200277700001900299700001900318700002000337700001600357700001500373856012300388 2011 eng d00aEast African Food Security as Influenced by Future Climate Change and Land Use Change at Local to Regional Scales0 aEast African Food Security as Influenced by Future Climate Chang0 v1071 aMoore, Nathan1 aAlagarswamy, Gopal1 aPijanowski, Bryan1 aThornton, Phil1 aLofgren, Brent1 aOlson, Jennifer1 aYanda, Pius1 aQi, Jiaguo uhttps://icer.msu.edu/research/publications/east-african-food-security-influenced-future-climate-change-land-use-change00500nas a2200133 4500008004100000245006700041210006600108490000700174100002200181700001800203700002200221700001600243856010700259 2011 eng d00aEvaluating error propagation in coupled land-atmosphere models0 aEvaluating error propagation in coupled landatmosphere models0 v151 aPijanowski, Bryan1 aMoore, Nathan1 aMauree, Desaraden1 aNiyogi, Dev uhttps://icer.msu.edu/research/publications/evaluating-error-propagation-coupled-land-atmosphere-models00362nas a2200109 4500008004100000245004700041210004600088300001400134490000600148100001900154856007900173 2011 eng d00aFame on Sale: Pitfalls of the Ranking Game0 aFame on Sale Pitfalls of the Ranking Game a355–3560 v11 aTomanek, David uhttps://icer.msu.edu/research/publications/fame-sale-pitfalls-ranking-game00411nas a2200133 4500008004100000245003900041210003900080260001200119300001400131490000700145100002300152700001800175856008400193 2011 eng d00aImplicit Parallel Time Integrators0 aImplicit Parallel Time Integrators c11/2011 a167 - 1790 v491 aChristlieb, Andrew1 aOng, Benjamin uhttps://icer.msu.edu/research/publications/implicit-parallel-time-integrators-002110nas a2200157 4500008004100000245006200041210006200103300001400165490000700179520164900186100002101835700001701856700001801873700001801891856004301909 2011 eng d00aInformation Content of Colored Motifs in Complex Networks0 aInformation Content of Colored Motifs in Complex Networks a375–3900 v173 aWe study complex networks in which the nodes are tagged with different colors depending on their function (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (much more than the uncolored structural motifs can be) and that the relative frequency with which these motifs appear in the network can be used to define its information content. This information is defined in such a way that a network with random coloration (but keeping the relative number of nodes with different colors the same) has zero color information content. Thus, colored motif information captures the exceptionality of coloring in the motifs that is maintained via selection. We study the motif information content of the C. elegans brain as well as the evolution of colored motif information in networks that reflect the interaction between instructions in genomes of digital life organisms. While we find that colored motif information appears to capture essential functionality in the C. elegans brain (where the color assignment of nodes is straightforward), it is not obvious whether the colored motif information content always increases during evolution, as would be expected from a measure that captures network complexity. For a single choice of color assignment of instructions in the digital life form Avida, we find rather that colored motif information content increases or decreases during evolution, depending on how the genomes are organized, and therefore could be an interesting tool to dissect genomic rearrangements.

1 aAdami, Christoph1 aQian, Jifeng1 aRupp, Matthew1 aHintze, Arend uhttp://dx.doi.org/10.1162/artl_a_0004500554nas a2200145 4500008004100000245009200041210006900133300001400202490000700216100002100223700001300244700002000257700001700277856011400294 2011 eng d00aLong-term differences in tillage and land use affect intra-aggregate pore heterogeneity0 aLongterm differences in tillage and land use affect intraaggrega a1658-16660 v751 aKravchenko, A.N.1 aWang, W.1 aSmucker, A.J.M.1 aRivers, M.L. uhttps://icer.msu.edu/research/publications/long-term-differences-tillage-land-use-affect-intra-aggregate-pore00478nas a2200097 4500008004100000245009900041210006900140260003000209100001700239856012400256 2011 eng d00aMODELS TO AID IN THE SELECTION OF PROCEDURES USED TO MANAGE LAKE ERIE WALLEYE (SANDER VITREUS)0 aMODELS TO AID IN THE SELECTION OF PROCEDURES USED TO MANAGE LAKE bMichigan State University1 aBerger, A.M. uhttps://icer.msu.edu/research/publications/models-aid-selection-procedures-used-manage-lake-erie-walleye-sander-vitreus00476nas a2200097 4500008004100000245011600041210006900157490000800226100002000234856012400254 2011 eng d00aMolecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures0 aMolecular diffusion and slip boundary conditions at smooth surfa0 v1351 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/molecular-diffusion-slip-boundary-conditions-smooth-surfaces-periodic-random00518nas a2200109 4500008004100000245012900041210006900170490000800239100001700247700002000264856012400284 2011 eng d00aMolecular Dynamics Study of Thermal Transport in GaAs-SAM-GaAs Junctions with Ab-initio Characterization of Thiol-GaAs Bonds0 aMolecular Dynamics Study of Thermal Transport in GaAsSAMGaAs Jun0 v1091 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/molecular-dynamics-study-thermal-transport-gaas-sam-gaas-junctions-ab-initio00538nas a2200109 4500008004100000245014900041210006900190490000800259100001700267700002000284856012400304 2011 eng d00aMolecular dynamics study of thermal transport in GaAs-self-assembly monolayer-GaAs junctions with ab initio characterization of thiol-GaAs bonds0 aMolecular dynamics study of thermal transport in GaAsselfassembl0 v1091 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/molecular-dynamics-study-thermal-transport-gaas-self-assembly-monolayer-gaas00414nas a2200109 4500008004100000245005900041210005800100100001600158700001400174700001900188856009700207 2011 eng d00aMulti-label Learning with Incomplete Class Assignments0 aMultilabel Learning with Incomplete Class Assignments1 aBucak, S.S.1 aJin, Rong1 aJain, Anil, K. uhttps://icer.msu.edu/research/publications/multi-label-learning-incomplete-class-assignments00587nas a2200145 4500008004100000245011300041210006900154300001100223490000800234100001800242700001500260700002300275700002000298856012300318 2011 eng d00aNanoconfinement effects on the reversibility of hydrogen storage in ammonia borane: A first-principles study0 aNanoconfinement effects on the reversibility of hydrogen storage a2145010 v1341 aChang, Kiseok1 aKim, Eunja1 aWeck, Philippe, F.1 aTománek, David uhttps://icer.msu.edu/research/publications/nanoconfinement-effects-reversibility-hydrogen-storage-ammonia-borane-first00695nas a2200181 4500008004100000245010800041210006900149300000800218490000800226653002800234653002500262653003000287100001800317700002000335700001800355700001900373856012100392 2011 eng d00aThe Nature of the Warm/Hot Intergalactic Medium. I. Numerical Methods, Convergence, and O VI Absorption0 aNature of the WarmHot Intergalactic Medium I Numerical Methods C a6-+0 v73110acosmology: observations10aintergalactic medium10aquasars: absorption lines1 aSmith, B., D.1 aHallman, E., J.1 aShull, J., M.1 aO'Shea, B., W. uhttps://icer.msu.edu/research/publications/nature-warm-hot-intergalactic-medium-i-numerical-methods-convergence-o-vi00480nas a2200121 4500008004100000245007900041210006900120100001400189700001800203700001800221700001400239856010500253 2011 eng d00aOn the Performance of Indirect Encoding Across the Continuum of Regularity0 aPerformance of Indirect Encoding Across the Continuum of Regular1 aClune, J.1 aStanley, K.O.1 aPennock, R.T.1 aOfria, C. uhttps://icer.msu.edu/research/publications/performance-indirect-encoding-across-continuum-regularity03167nas a2200157 4500008004100000020002200041245005400063210005400117260002700171300000700198520266300205653001302868653002102881100001702902856009002919 2011 eng d a978-1-4503-0888-500aReducing the barrier to entry using portable apps0 aReducing the barrier to entry using portable apps aNew York, NY, USAbACM a473 aAn increasing number of turnkey, domain specific software packages are available to help users take advantage of advanced cyber-infrastructure and resources such as {TeraGrid.} However, novice users of cyber-infrastructure are often overwhelmed by the complexities of using cyber-infrastructure. For instance, the user may need to install multiple software tools just to connect with advanced hardware, and successfully installing and navigating this software frequently requires the use of Command Line Interfaces {(CLI)} that are unfamiliar to novice users. Even when applications provide a Graphical User Interface {(GUI)}, special software (such as an X11 server) may be required to use the interface. Installing, configuring and running this software is generally a multi-step process that can be overly confusing to novice users and presents a barrier to entry, particularly in research domains not traditionally associated with advanced computation. Scientific gateways (such as the {TeraGrid} Portal [1]) are one possible solution to this problem. However, not all research projects or High Performance Computing {(HPC)} centers have the resources necessary to provide scientific gateways. We have developed an alternative solution: a "plug and play" {HPC} system portal stored on a {USB} thumb drive. The thumb drive contains all the software necessary to connect to traditional cyber-infrastructure and all programs run directly from the thumb drive – no installation or setup is required. To access the software from a Windows-based machine, the user simply connects the thumb drive and runs the desired programs. The current thumb drive includes all the typical software necessary to connect to an {HPC} resource, such as X11 [2], ssh [3], and scp [4]. Since the software is pre-installed on the drive, it can also be preconfigured with the necessary preferences required to immediately connect to the resource. This presentation will describe the development process for the {"Portable} Apps" [5] {HPC} thumb drive, including lessons learned and suggestions for adapting the paradigm for other systems. The Portable Apps drive has been successfully distributed to both expert and novice {HPC} users at Michigan State University {(MSU)} and has proved to be a popular and easy-to-use tool for accessing local and national cyber-infrastructure resources, including {TeraGrid} [6]. This presentation will offer specific suggestions for adapting the Portable Apps idea (such as procedures for site specific applications [7]) and developing similar outreach and educational tools for other institutions and resources.

10aoutreach10aresearch portals1 aColbry, Dirk uhttps://icer.msu.edu/research/publications/reducing-barrier-entry-using-portable-apps00557nas a2200145 4500008004100000245008300041210006900124260003500193300001100228490000700239100002000246700001400266700002000280856011100300 2011 eng d00aSearch for the largest two-dimensional aggregates of boron: An ab initio study0 aSearch for the largest twodimensional aggregates of boron An ab bAmerican Physical SocietycMay a1934050 v831 aBoustani, Ihsan1 aZhu, Zhen1 aTománek, David uhttps://icer.msu.edu/research/publications/search-largest-two-dimensional-aggregates-boron-ab-initio-study00613nas a2200169 4500008004100000245008300041210006900124300001400193490000800207100001800215700002000233700001900253700001700272700001800289700001700307856011900324 2011 eng d00aSecond-order selection for evolvability in a large Escherichia coli population0 aSecondorder selection for evolvability in a large Escherichia co a1433-14360 v3311 aWoods, R., J.1 aBarrick, J., E.1 aCooper, T., F.1 aShrestha, U.1 aKauth, M., R.1 aLenski, R.E. uhttps://icer.msu.edu/research/publications/second-order-selection-evolvability-large-escherichia-coli-population-000580nas a2200157 4500008004100000245008300041210006900124490000800193100001800201700001500219700001900234700001700253700001800270700001700288856011700305 2011 eng d00aSecond-order selection for evolvability in a large Escherichia coli population0 aSecondorder selection for evolvability in a large Escherichia co0 v3311 aWoods, R., J.1 aBarrick, E1 aCooper, T., F.1 aShrestha, U.1 aKauth, M., R.1 aLenski, R.E. uhttps://icer.msu.edu/research/publications/second-order-selection-evolvability-large-escherichia-coli-population00643nas a2200157 4500008004100000245014700041210006900188260002200257300001200279490000800291100001400299700001800313700001400331700001800345856012200363 2011 eng d00aSelective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory0 aSelective pressures for accurate altruism targeting evidence fro bThe Royal Society a666-6740 v2781 aClune, J.1 aGoldsby, H.J.1 aOfria, C.1 aPennock, R.T. uhttps://icer.msu.edu/research/publications/selective-pressures-accurate-altruism-targeting-evidence-digital-evolution00594nas a2200145 4500008004100000245008500041210006900126653003900195100001900234700001600253700002000269700001900289700002400308856011600332 2011 eng d00aSignatures of minor mergers in Milky Way-like disc kinematics: Ringing revisited0 aSignatures of minor mergers in Milky Waylike disc kinematics Rin10aAstrophysics - Galaxy Astrophysics1 aGómez, F., A.1 aMinchev, I.1 aVillalobos, Á.1 aO'Shea, B., W.1 aWilliams, M., E. K. uhttps://icer.msu.edu/research/publications/signatures-minor-mergers-milky-way-disc-kinematics-ringing-revisited00518nas a2200133 4500008004100000245007400041210006900115260001900184100002400203700001800227700001900245700001400264856010600278 2011 eng d00aSpeedup of fuzzy and possibilistic c-means for large-scale clustering0 aSpeedup of fuzzy and possibilistic cmeans for largescale cluster aTaipei, Taiwan1 aHavens, Timothy, C.1 aChitta, Radha1 aJain, Anil, K.1 aJin, Rong uhttps://icer.msu.edu/research/publications/speedup-fuzzy-possibilistic-c-means-large-scale-clustering00656nas a2200181 4500008004100000245008800041210006900129490000700198100001800205700002000223700002200243700002000265700001500285700001800300700002200318700002000340856011400360 2010 eng d00aAdapting MODIS-derived LAI and fractional cover into the RAMS model for East Africa0 aAdapting MODISderived LAI and fractional cover into the RAMS mod0 v301 aMoore, Nathan1 aTorbick, Nathan1 aPijanowski, Bryan1 aLofrgren, Brent1 aWang, Jing1 aKim, Dong-Yun1 aAndresen, Jeffrey1 aOlson, Jennifer uhttps://icer.msu.edu/research/publications/adapting-modis-derived-lai-fractional-cover-rams-model-east-africa01232nas a2200121 4500008004100000245007800041210006900119260007200188520070000260100002000960700002000980856011001000 2010 eng d00aBeyond NomBank: A Study of Implicit Argumentation for Nominal Predicates0 aBeyond NomBank A Study of Implicit Argumentation for Nominal Pre aUppsala, SwedenbAssociation for Computational Linguisticsc07/20103 aDespite its substantial coverage, Nom- Bank does not account for all within- sentence arguments and ignores extra- sentential arguments altogether. These ar- guments, which we call implicit, are im- portant to semantic processing, and their recovery could potentially benefit many NLP applications. We present a study of implicit arguments for a select group of frequent nominal predicates. We show that implicit arguments are pervasive for these predicates, adding 65% to the coverage of NomBank. We demonstrate the feasibil- ity of recovering implicit arguments with a supervised classification model. Our re- sults and analyses provide a baseline for future work on this emerging task.

1 aGerber, Matthew1 aChai, Joyce, Y. uhttps://icer.msu.edu/research/publications/beyond-nombank-study-implicit-argumentation-nominal-predicates01865nas a2200145 4500008004100000245012500041210006900166260001200235300001400247490000800261520129200269100001701561700001801578856012301596 2010 eng d00aConformational Sampling of Influenza Fusion Peptide in Membrane Bilayers as a Function of Termini and Protonation States0 aConformational Sampling of Influenza Fusion Peptide in Membrane c12/2009 a1407-14160 v1143 aInfluenza fusion peptide is critical for mediating the fusion of viral and host cell membranes during viral entry. The interaction of monomeric influenza fusion peptide with membranes is studied with replica exchange molecular dynamics simulations using a new implicit membrane model to effectively reach microsecond to millisecond time scales. The conformational sampling of the fusion peptide was studied as a function of different N- and C-termini, including an experimental construct with an additional C-terminal tag, as well as a function of protonation of acidic residues. It is found that the influenza fusion peptide mostly adopts helical structures with a pronounced kink at residues 11−13 with both N-terminal and C-terminal helices oriented mostly parallel to the membrane surface. A charged C-terminus and the presence of a charge C-terminal tag significantly alters the conformational sampling of the fusion peptide and results in more diverse conformational ensembles that include obliquely inserted N-terminal peptide structures. Protonation of acidic residues also affects the conformational sampling, however, based on pKa shift estimates the overall effect of pH = 5 on the conformational sampling of the influenza fusion peptide appears to be only minor.

1 aPanahi, Afra1 aFeig, Michael uhttps://icer.msu.edu/research/publications/conformational-sampling-influenza-fusion-peptide-membrane-bilayers-function01129nas a2200157 4500008004100000245011900041210006900160260001200229300001000241490000800251520054300259100001800802700002200820700001700842856011200859 2010 eng d00aConformational Sampling of S- and R-Warfarin in Polar Solvents: Implications for Stereoselective Complex Formation0 aConformational Sampling of S and RWarfarin in Polar Solvents Imp c06/2010 a41-510 v9493 aMolecular dynamics simulations of the open side chain conformation of ionic and neutral S- and R-warfarin in aqueous solvent and acetonitrile are described. In all cases, warfarin is found to sample a broad conformational ensemble with major and minor states due to torsional degrees of freedom associated with its side chain. Thermodynamics and kinetics of transitions between these states are analyzed from the simulations and interpreted in the context of stereoselective interactions in biological and non-biological complexes.

1 aFeig, Michael1 aGebreyohannes, K.1 aMcGuffin, V. uhttps://icer.msu.edu/research/publications/conformational-sampling-s-r-warfarin-polar-solvents-implications00548nas a2200157 4500008004100000245006600041210006500107260001200172300001600184490000800200100001300208700002000221700002300241700002000264856010600284 2010 eng d00aDefect-induced rigidity enhancement in layered semiconductors0 aDefectinduced rigidity enhancement in layered semiconductors c07/2010 a1200 - 12030 v1501 aRak, Zs.1 aMahanti, S., D.1 aMandal, Krishna, C1 aFernelius, N.C. uhttps://icer.msu.edu/research/publications/defect-induced-rigidity-enhancement-layered-semiconductors00375nas a2200121 4500008004100000245004100041210004100082300001100123490000700134100001900141700001200160856008100172 2010 eng d00aDifferent Truths in Different Worlds0 aDifferent Truths in Different Worlds a97-1140 v211 aMiller, K., D.1 aLin, S. uhttps://icer.msu.edu/research/publications/different-truths-different-worlds00620nas a2200145 4500008004100000245012900041210006900170260001200239490000700251100001300258700002000271700002300291700002000314856014000334 2010 eng d00aDoping dependence of electronic and mechanical properties of GaSe_{1−x}Te_{x} and Ga_{1−x}In_{x}Se from first principles0 aDoping dependence of electronic and mechanical properties of GaS c10/20100 v821 aRak, Zs.1 aMahanti, S., D.1 aMandal, Krishna, C1 aFernelius, N.C. uhttps://icer.msu.edu/research/publications/doping-dependence-electronic-mechanical-properties-gase-1%E2%88%92xte-x-ga-1%E2%88%92xin-xse01655nas a2200157 4500008004100000245010300041210006900144260001200213300001200225490000700237520107200244100001901316700002401335700001801359856012001377 2010 eng d00aEffect of membrane thickness on conformational sampling of phospholamban from computer simulations0 aEffect of membrane thickness on conformational sampling of phosp c03/2010 a805-8140 v983 aThe conformational sampling of monomeric, membrane-bound phospholamban is described from computer simulations. Phospholamban (PLB) plays a key role as a regulator of sarcoplasmic reticulum calcium ATPase. An implicit membrane model is used in conjunction with replica exchange molecular dynamics simulations to reach μs-ms timescales. The implicit membrane model was also used to study the effect of different membrane thicknesses by scaling the low-dielectric region. The conformational sampling with the membrane model mimicking dipalmitoylphosphatidylcholine bilayers is in good agreement overall with experimental measurements, but consists of a wide variety of different conformations including structures not described previously. The conformational ensemble shifts significantly in the presence of thinner or thicker membranes. This has implications for the structure and dynamics of PLB in physiological membranes and offers what we believe to be a new interpretation of previous experimental measurements of PLB in detergents and microsomal membrane.

1 aSayadi, Maryam1 aTanizaki, Seiichiro1 aFeig, Michael uhttps://icer.msu.edu/research/publications/effect-membrane-thickness-conformational-sampling-phospholamban-computer00498nas a2200109 4500008004100000245010800041210006900149490000800218100001700226700002000243856012500263 2010 eng d00aEquilibrium Molecular Dynamics Study of Lattice Thermal Conductivity/Conductance of Au-SAM-Au Junctions0 aEquilibrium Molecular Dynamics Study of Lattice Thermal Conducti0 v1321 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/equilibrium-molecular-dynamics-study-lattice-thermal-conductivity-conductance00577nas a2200145 4500008004100000245010100041210006900142300001400211490000700225100002000232700001800252700002200270700001700292856012200309 2010 eng d00aEscherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects0 aEscherichia coli rpoB mutants have increased evolvability in pro a1338-13470 v271 aBarrick, J., E.1 aKauth, M., R.1 aStrelioff, C., C.1 aLenski, R.E. uhttps://icer.msu.edu/research/publications/escherichia-coli-rpob-mutants-have-increased-evolvability-proportion-their00680nas a2200157 4500008004100000245012900041210006900170653006000239100002100299700000500320700001900325700001800344700001800362700001700380856012500397 2010 eng d00aGalaxy Cluster Radio Relics in Adaptive Mesh Refinement Cosmological Simulations: Relic Properties and Scaling Relationships0 aGalaxy Cluster Radio Relics in Adaptive Mesh Refinement Cosmolog10aAstrophysics - Cosmology and Extragalactic Astrophysics1 aSkillman, S., W.1 a1 aO'Shea, B., W.1 aBurns, J., O.1 aSmith, B., D.1 aTurk, M., J. uhttps://icer.msu.edu/research/publications/galaxy-cluster-radio-relics-adaptive-mesh-refinement-cosmological-simulations00758nas a2200205 4500008004100000245009500041210006900136300001400205490000800219653002800227653002200255653001800277653002500295653002300320653003100343100001800374700002100392700001900413856012000432 2010 eng d00aGalaxy Clusters at the Edge: Temperature, Entropy, and Gas Dynamics Near the Virial Radius0 aGalaxy Clusters at the Edge Temperature Entropy and Gas Dynamics a1105-11120 v72110acosmology: observations10acosmology: theory10ahydrodynamics10aintergalactic medium10amethods: numerical10aX-rays: galaxies: clusters1 aBurns, J., O.1 aSkillman, S., W.1 aO'Shea, B., W. uhttps://icer.msu.edu/research/publications/galaxy-clusters-edge-temperature-entropy-gas-dynamics-near-virial-radius00492nas a2200109 4500008004100000245009800041210006900139490002000208100001100228700001700239856012600256 2010 eng d00aA High-Order Finite-Difference Method for Numerical Simulations of Supersonic Turbulent Flows0 aHighOrder FiniteDifference Method for Numerical Simulations of S0 vTo be published1 aLi, Z.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/high-order-finite-difference-method-numerical-simulations-supersonic-turbulent01333nas a2200133 4500008004100000245003900041210003900080260001200119490000700131520093800138100002301076700001801099856008201117 2010 eng d00aImplicit Parallel Time Integrators0 aImplicit Parallel Time Integrators c12/20100 v463 aIn this work, we discuss a family of parallel implicit time integrators for multicore and potentially multi-node or multi-gpgpu systems. The method is an extension of Revisionist Integral Deferred Correction (RIDC) by Christlieb, Macdonald and Ong (SISC- 2010) which constructed parallel explicit time integrators. The key idea is to re-write the defect correction framework so that, after initial startup costs, each correction loop can be lagged behind the previous correction loop in a manner that facilitates running the predictor and correctors in parallel. In this paper, we show that RIDC provides a framework to use p cores to generate a pth-order implicit solution to an initial value problem (IVP) in approximately the same wall clock time as a single core, backward Euler implementation (p ≤ 12). The construction, convergence and stability of the schemes are presented, along with supporting numerical evidence.

1 aChristlieb, Andrew1 aOng, Benjamin uhttps://icer.msu.edu/research/publications/implicit-parallel-time-integrators00525nas a2200145 4500008004100000245006900041210006900110260000800179300001400187100001400201700001900215700001900234700001400253856011200267 2010 eng d00aInvestigating whether HyperNEAT produces modular neural networks0 aInvestigating whether HyperNEAT produces modular neural networks bACM a635–6421 aClune, J.1 aBeckmann, B.E.1 aMcKinley, P.K.1 aOfria, C. uhttps://icer.msu.edu/research/publications/investigating-whether-hyperneat-produces-modular-neural-networks00481nas a2200121 4500008004100000245008100041210006900122260001200191490000600203100001800209700002000227856011200247 2010 eng d00aA landscape and climate data logistic model of tsetse distributions in Kenya0 alandscape and climate data logistic model of tsetse distribution c07/20100 v51 aMoore, Nathan1 aMessina, Joseph uhttps://icer.msu.edu/research/publications/landscape-climate-data-logistic-model-tsetse-distributions-kenya00493nas a2200109 4500008004100000245008500041210006900126260002500195100002200220700001700242856012400259 2010 eng d00aLarge -Scale Simulations of Incident Shock-Turbulent Boundary Layer Interactions0 aLarge Scale Simulations of Incident ShockTurbulent Boundary Laye aOrlando, FLc01/20101 aJammalamadaka, A.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/large-scale-simulations-incident-shock-turbulent-boundary-layer-interactions01408nas a2200181 4500008004100000245009500041210006900136260001200205300001400217490000700231520071100238653009300949653000801042100001701050700001901067700001701086856012301103 2010 eng d00aLarge-Eddy Simulations of Turbulent Methane Jet Flames with Filtered Mass Density Function0 aLargeEddy Simulations of Turbulent Methane Jet Flames with Filte c05/2010 a2551-25620 v533 aThe filtered mass density function (FMDF) model (Jaberi et al. 1999 [1]) is employed for large eddy simulations (LES) of “high speed” partially-premixed methane jet flames with the “flamelet” and “finite-rate” kinetics models. The FMDF is the joint probability density function (PDF) of the scalars and is determined via the solution of a set of stochastic differential equations. The LES/FMDF is implemented using a highly scalable, parallel hybrid Eulerian–Lagrangian numerical scheme. The LES/FMDF results are shown to compare well with the experimental data for all flow conditions when “appropriate” reaction and mixing models are employed.

10aFiltered mass density function; PDF methods; Monte-Carlo simulations; Methane jet flames10aLES1 aYaldizli, M.1 aMehravaran, K.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/large-eddy-simulations-turbulent-methane-jet-flames-filtered-mass-density-001381nas a2200133 4500008004100000245006700041210006600108260003100174520088700205100001101092700001701103700002001120856010701140 2010 eng d00aLarge-Scale Simulations of Supersonic Turbulent Reacting Flows0 aLargeScale Simulations of Supersonic Turbulent Reacting Flows aOrlando, FLbAIAAc01/20103 aThe scalar filtered mass density function (FMDF) is further developed and employed for large-eddy simulations (LES) of high speed turbulent flows in complex geometries. LES/FMDF is implemented via an efficient, hybrid numerical method. In this method, the filtered compressible Navier-Stokes equations in curvilinear coordinate systems are solved with a generalized, high-order, multi-block, compact differencing scheme. Turbulent mixing and combustion are modeled with the FMDF. The LES/FMDF method is used for simulations of isotropic turbulent flow in a piston-cylinder assembly, the flow in a shock tube and a supersonic co-axial helium-air jet. The critical role of pressure in the FMDF equation when applied to compressible flows is studied. It is shown that LES/FMDF is reliable and is able to simulate compressible turbulent mixing and combustion in supersonic flows.

1 aLi, Z.1 aJaberi, F.A.1 aBanaeizadeh, A. uhttps://icer.msu.edu/research/publications/large-scale-simulations-supersonic-turbulent-reacting-flows00963nas a2200289 4500008004100000245007500041210006900116300001200185490000900197653001400206653002500220653003000245653002400275653002200299653002300321653001300344653001400357653001500371653003700386653001900423653004100442100001900483700001900502700002600521700001700547856010900564 2010 eng d00aLocal and Global Radiative Feedback from Population III Star Formation0 aLocal and Global Radiative Feedback from Population III Star For a128-1330 v129410aDistances10aPopulation III stars10aPre-main sequence objects10aprotostellar clouds10aradial velocities10aradiative transfer10aredshift10aredshifts10ascattering10aspatial distribution of galaxies10astar formation10ayoung stellar objects and protostars1 aO'Shea, B., W.1 aWhalen, D., J.1 aWhalen, Bromm, {D. J.1 aYoshida}, N. uhttps://icer.msu.edu/research/publications/local-global-radiative-feedback-population-iii-star-formation01985nas a2200133 4500008004100000245009900041210006900140260001200209490000700221520146000228100001801688700002001706856012501726 2010 eng d00aModeling the combined effect of surface roughness and shear rate on slip flow of simple fluids0 aModeling the combined effect of surface roughness and shear rate c01/20100 v813 aMolecular dynamics (MD) and continuum simulations are carried out to investigate the influence of shear rate and surface roughness on slip flow of a Newtonian fluid. For weak wall-fluid interaction energy, the nonlinear shear-rate dependence of the intrinsic slip length in the flow over an atomically flat surface is computed by MD simulations. We describe laminar flow away from a curved boundary by means of the effective slip length defined with respect to the mean height of the surface roughness. Both the magnitude of the effective slip length and the slope of its rate dependence are significantly reduced in the presence of periodic surface roughness. We then numerically solve the Navier-Stokes equation for the flow over the rough surface using the rate-dependent intrinsic slip length as a local boundary condition. Continuum simulations reproduce the behavior of the effective slip length obtained from MD simulations at low shear rates. The slight discrepancy between MD and continuum results at high shear rates is explained by examination of the local velocity profiles and the pressure distribution along the wavy surface. We found that in the region where the curved boundary faces the mainstream flow, the local slip is suppressed due to the increase in pressure. The results of the comparative analysis can potentially lead to the development of an efficient algorithm for modeling rate-dependent slip flows over rough surfaces.

1 aNiavarani, A.1 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/modeling-combined-effect-surface-roughness-shear-rate-slip-flow-simple-fluids00501nas a2200109 4500008004100000245011100041210006900152100001600221700001400237700001900251856012100270 2010 eng d00aMulti-label Multiple Kernel Learning by Stochastic Approximation: Application to Visual Object Recognition0 aMultilabel Multiple Kernel Learning by Stochastic Approximation 1 a.S.Bucak, S1 aJin, Rong1 aJain, Anil, K. uhttps://icer.msu.edu/research/publications/multi-label-multiple-kernel-learning-stochastic-approximation-application01728nas a2200145 4500008004100000245014900041210006900190260001200259300001400271490000800285520113400293100001201427700001901439856012401458 2010 eng d00aMulti-level Extension of the Cluster-In-Molecule Local Correlation Methodology: Merging Coupled-Cluster and Moller-Plesset Perturbation Theories0 aMultilevel Extension of the ClusterInMolecule Local Correlation c05/2010 a6721-67270 v1143 aA multilevel extension of the local correlation “cluster-in-molecule” (CIM) framework, which enables one to combine different quantum chemistry methods to treat different regions in a large molecular system without splitting it into ad hoc fragments and saturating dangling bonds, is proposed. The resulting schemes combine higher-level methods, such as the completely renormalized coupled-cluster (CC) approach with singles, doubles, and noniterative triples, termed CR-CC(2,3), to treat the reactive part of a large molecular system, and lower-order methods, such as the second-order Møller−Plesset perturbation theory (MP2), to handle the chemically inactive regions. The multilevel CIM-CC/MP2 approaches preserve the key features of all CIM methods, such as the use of orthonormal localized orbitals and coarse-grain parallelism, while substantially reducing the already relatively low costs of the single-level CIM-CC calculations. Illustrative calculations include bond breaking in dodecane and the reactions of the bis(2,4,4-trimethylpentyl)dithiophosphinic acid with one and two water molecules.

1 aLi, Wei1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/multi-level-extension-cluster-molecule-local-correlation-methodology-merging00483nas a2200109 4500008004100000245009600041210006900137490000700206100001700213700002000230856012300250 2010 eng d00aNon-Equilibrium Molecular Dynamics Study of Thermal Energy Transport in Au-SAM-Au Junctions0 aNonEquilibrium Molecular Dynamics Study of Thermal Energy Transp0 v531 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/non-equilibrium-molecular-dynamics-study-thermal-energy-transport-au-sam-au01480nas a2200121 4500008004100000245008700041210006900128260003100197520098000228100001101208700001701219856012201236 2010 eng d00aNumerical Investigations of Shock-Turbulence Interactions in a Planar Mixing Layer0 aNumerical Investigations of ShockTurbulence Interactions in a Pl aOrlando, FLbAIAAc01/20103 aDirect numerical simulation (DNS) and large-eddy simulation (LES) of spatially developing supersonic mixing layer, interacting with an oblique shock wave are conducted with a new high-order Monotonicity-Preserving scheme. Without the incident shock, the mixing layer grows linearly and exhibits self-similar behavior after the transition. With the shock, significant small-scale turbulence is generated just behind the shock. With an increase in shock angle, the intensity of the shock-generated turbulence is increased and its peak position shifts away from the mixing layer centerline. The effects of turbulence on the shock are also shown to be very significant, such that normal shocklets and large adverse pressure gradients are created in some conditions. Comparison with the DNS data indicates that the LES with the modified kinetic energy viscosity (MKEV) subgrid stress model is able to predict the main features of the flow and shock-turbulence interactions.

1 aLi, Z.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/numerical-investigations-shock-turbulence-interactions-planar-mixing-layer00457nas a2200121 4500008004100000245006400041210006400105100001800169700001600187700001100203700001900214856010200233 2010 eng d00aOne Class Matrix Completion with Low Density Factorizations0 aOne Class Matrix Completion with Low Density Factorizations1 aSindhwani, V.1 aBucak, S.S.1 aHu, J.1 aMojsilovic, A. uhttps://icer.msu.edu/research/publications/one-class-matrix-completion-low-density-factorizations00640nas a2200205 4500008004100000245005900041210005100100300001200151490000800163653002200171653002300193653002100216100001900237700001700256700001800273700001500291700002100306700001900327856008800346 2010 eng d00aOn the Origin of the Highest Redshift Gamma-Ray Bursts0 aOrigin of the Highest Redshift GammaRay Bursts a117-1260 v70810abinaries: general10agamma rays: bursts10astars: formation1 aBelczynski, K.1 aHolz, D., E.1 aFryer, C., L.1 aBerger, E.1 aHartmann, D., H.1 aO'Shea, B., W. uhttps://icer.msu.edu/research/publications/origin-highest-redshift-gamma-ray-bursts00444nas a2200145 4500008004100000245003600041210003500077260001200112300001400124490000700138100002700145700002500172700002200197856007900219 2010 eng d00aParallel High-Order Integrators0 aParallel HighOrder Integrators c01/2010 a818 - 8350 v321 aChristlieb, Andrew, J.1 aMacdonald, Colin, B.1 aOng, Benjamin, W. uhttps://icer.msu.edu/research/publications/parallel-high-order-integrators01190nas a2200169 4500008004100000245011200041210006900153260001200222300001400234490000700248520055700255100002500812700002600837700001900863700001800882856012000900 2010 eng d00aPRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy0 aPRIMOPRIMONA A coarsegrained model for proteins and nucleic acid c04/2010 a1266-12810 v783 aThe new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed. This model combines one to several heavy atoms into coarse-grained sites that are chosen to allow an analytical, high-resolution reconstruction of all-atom models based on molecular bonding geometry constraints. The accuracy of proposed reconstruction method in terms of structure and energetics is tested and compared with other popular reconstruction methods for a variety of protein and nucleic acid test sets. Proteins 2010. © 2009 Wiley-Liss, Inc.

1 aGopal, Srinivasa, M.1 aMukherjee, Shayantani1 aCheng, Yi-Ming1 aFeig, Michael uhttps://icer.msu.edu/research/publications/primo-primona-coarse-grained-model-proteins-nucleic-acids-preserves-near02260nas a2200133 4500008004100000245014300041210006900184260001200253490000700265520169300272100001901965700001901984856012302003 2010 eng d00aA Process-Based, Distributed Hydrologic Model Based on a Large-Scale Method for Surface - Subsurface Coupling, Advances in Water Resources0 aProcessBased Distributed Hydrologic Model Based on a LargeScale c09/20100 v333 aProcess-based watershed models are useful tools for understanding the impacts of natural and anthropogenic influences on water resources and for predicting water and solute fluxes exported from watersheds to receiving water bodies. The applicability of process-based hydrologic models has been previously limited to small catchments and short time frames. Computational demands, especially the solution to the three-dimensional subsurface flow domain, continue to pose significant constraints. This paper documents the mathematical development, numerical testing and the initial application of a new distributed hydrologic model PAWS (Process-based Adaptive Watershed Simulator). The model solves the governing equations for the major hydrologic processes efficiently so that large scale applications become relevant. PAWS evaluates the integrated hydrologic response of the surface–subsurface system using a novel non-iterative method that couples runoff and groundwater flow to vadose zone processes approximating the 3D Richards equation. The method is computationally efficient and produces physically consistent solutions. All flow components have been independently verified using analytical solutions and experimental data where applicable. The model is applied to a medium-sized watershed in Michigan (1169 km2) achieving high performance metrics in terms of streamflow prediction at two gages during the calibration and verification periods. PAWS uses public databases as input and possesses full capability to interact with GIS datasets. Future papers will describe applications to other watersheds and the development and application of fate and transport modules.

1 aShen, Chaopeng1 aPhanikumar, M. uhttps://icer.msu.edu/research/publications/process-based-distributed-hydrologic-model-based-large-scale-method-surface00852nas a2200241 4500008004100000245009300041210006900134260000800203300001400211490000800225653004400233653003800277653002300315653003100338100002000369700002100389700000500410700001800415700001900433700001800452700001900470856012100489 2010 eng d00aThe Properties of X-ray Cold Fronts in a Statistical Sample of Simulated Galaxy Clusters0 aProperties of Xray Cold Fronts in a Statistical Sample of Simula cdec a1053-10680 v72510agalaxies: clusters: intracluster medium10alarge-scale structure of universe10amethods: numerical10aX-rays: galaxies: clusters1 aHallman, E., J.1 aSkillman, S., W.1 a1 aSmith, B., D.1 aO'Shea, B., W.1 aBurns, J., O.1 aNorman, M., L. uhttps://icer.msu.edu/research/publications/properties-x-ray-cold-fronts-statistical-sample-simulated-galaxy-clusters00453nas a2200097 4500008004100000245009400041210006900135490000700204100002000211856012400231 2010 eng d00aRelationship between induced fluid structure and boundary slip in nanoscale polymer films0 aRelationship between induced fluid structure and boundary slip i0 v821 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/relationship-between-induced-fluid-structure-boundary-slip-nanoscale-polymer00625nas a2200157 4500008004100000245014200041210006900183260002300252300000800275490000600283100001700289700001200306700001800318700001100336856012000347 2010 eng d00aThermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects0 aThermodynamic modeling of transcription sensitivity analysis dif bBioMed Central Ltd a1420 v41 aDresch, J.M.1 aLiu, X.1 aArnosti, D.N.1 aAy, A. uhttps://icer.msu.edu/research/publications/thermodynamic-modeling-transcription-sensitivity-analysis-differentiates01438nas a2200133 4500008004100000245010400041210006900145260001700214300001600231520090000247100001701147700001801164856012201182 2010 eng d00aOn the Use of Genetic Programming for Automated Refactoring and the Introduction of Design Patterns0 aUse of Genetic Programming for Automated Refactoring and the Int bACMc07/2010 a1341–13483 aMaintaining an object-oriented design for a piece of software is a difficult, time-consuming task. Prior approaches to au- tomated design refactoring have focused on making small, iterative changes to a given software design. However, such approaches do not take advantage of composition of design changes, thus limiting the richness of the refactoring strate- gies that they can generate. In order to address this prob- lem, this paper introduces an approach that supports com- position of design changes and makes the introduction of design patterns a primary goal of the refactoring process. The proposed approach uses genetic programming and soft- ware engineering metrics to identify the most suitable set of refactorings to apply to a software design. We illustrate the efficacy of this approach by applying it to a large set of published models, as well as a real-world case study.

1 aJensen, A.C.1 aCheng, B.H.C. uhttps://icer.msu.edu/research/publications/use-genetic-programming-automated-refactoring-introduction-design-patterns00512nas a2200133 4500008004100000245008700041210006900128260001200197490000700209100000500216700001600221700001900237856012200256 2009 eng d00aAb Initio Coupled-Cluster and Configuration Interaction Calculations for O Using V0 aAb Initio CoupledCluster and Configuration Interaction Calculati c05/20090 v791 a1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/ab-initio-coupled-cluster-configuration-interaction-calculations-o-using-v00470nas a2200145 4500008004100000245005100041210005000092260001100142300001600153490000700169100001300176700002000189700002300209856009200232 2009 eng d00aAb Initio Studies of Hydrogen Defects in CdTe0 aAb Initio Studies of Hydrogen Defects in CdTe c8/2009 a1539 - 15470 v381 aRak, Zs.1 aMahanti, S., D.1 aMandal, Krishna, C uhttps://icer.msu.edu/research/publications/ab%C2%A0initio-studies-hydrogen-defects-cdte01184nas a2200157 4500008004100000245009900041210006900140260001200209300001200221490000800233520062000241100000500861700002200866700001900888856011900907 2009 eng d00aCenter-of-Mass Problem in Truncated Configuration Interaction and Coupled-Cluster Calculations0 aCenterofMass Problem in Truncated Configuration Interaction and c08/2009 a334-3390 v6793 aThe problem of center-of-mass (CM) contaminations in ab initio nuclear structure calculations using configuration interaction (CI) and coupled-cluster (CC) approaches is analyzed. A rigorous and quantitative scheme for diagnosing the CM contamination of intrinsic observables is proposed and applied to ground-state calculations for 4He and 16O. The CI and CC calculations for 16O based on model spaces defined via a truncation of the single-particle basis lead to sizable CM contaminations, while the importance-truncated no-core shell model based on the NmaxΩ space is virtually free of CM contaminations.

1 a1 aGour, Jeffrey, R.1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/center-mass-problem-truncated-configuration-interaction-coupled-cluster01289nas a2200205 4500008004100000245006500041210006500106260001200171300001100183490000800194520066500202100001800867700001900885700002000904700001600924700001100940700001800951700002000969856009400989 2009 eng d00aConstraints on the Density Dependence of the Symmetry Energy0 aConstraints on the Density Dependence of the Symmetry Energy c03/2009 a1227010 v1023 aCollisions involving {112Sn} and {124Sn} nuclei have been simulated with the improved quantum molecular dynamics transport model. The results of the calculations reproduce isospin diffusion data from two different observables and the ratios of neutron and proton spectra. By comparing these data to calculations performed over a range of symmetry energies at saturation density and different representations of the density dependence of the symmetry energy, constraints on the density dependence of the symmetry energy at subnormal density are obtained. The results from the present work are compared to constraints put forward in other recent analyses.

1 aTsang, M., B.1 aZhang, Yingxun1 aDanielewicz, P.1 aFamiano, M.1 aLi, Z.1 aLynch, W., G.1 aSteiner, A., W. uhttps://icer.msu.edu/research/publications/constraints-density-dependence-symmetry-energy00626nas a2200193 4500008004100000245005900041210005900100300001200159490000800171653002200179653001600201653001900217653002400236653002100260100001800281700001600299700001900315856009800334 2009 eng d00aDark Matter Annihilation and Primordial Star Formation0 aDark Matter Annihilation and Primordial Star Formation a574-5830 v69210acosmology: theory10adark matter10aearly universe10agalaxies: formation10astars: formation1 aNatarajan, A.1 aTan, J., C.1 aO'Shea, B., W. uhttps://icer.msu.edu/research/publications/dark-matter-annihilation-primordial-star-formation01895nas a2200217 4500008004100000245008800041210006900129260001200198490000700210520117900217653001901396653001701415653002801432653001901460653001501479653001401494653001301508100001801521700002001539856011801559 2009 eng d00aThe effective slip length and vortex formation in laminar flow over a rough surface0 aeffective slip length and vortex formation in laminar flow over c05/20090 v213 aThe flow of viscous incompressible fluid over a periodically corrugated surface is investigated numerically by solving the Navier–Stokes equation with the local slip and no-slip boundary conditions. We consider the effective slip length which is defined with respect to the level of the mean height of the surface roughness. With increasing corrugation amplitude the effective no-slip boundary plane is shifted toward the bulk of the fluid, which implies a negative effective slip length. The analysis of the wall shear stress indicates that a flow circulation is developed in the grooves of the rough surface provided that the local boundary condition is no-slip. By applying a local slip boundary condition, the center of the vortex is displaced toward the bottom of the grooves and the effective slip length increases. When the intrinsic slip length is larger than the corrugation amplitude, the flow streamlines near the surface are deformed to follow the boundary curvature, the vortex vanishes, and the effective slip length saturates to a constant value. Inertial effects promote vortex flow formation in the grooves and reduce the effective slip length.

10aexternal flows10alaminar flow10aNavier-Stokes equations10arough surfaces10ashear flow10aslip flow10avortices1 aNiavarani, A.1 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/effective-slip-length-vortex-formation-laminar-flow-over-rough-surface00515nas a2200121 4500008004100000245009400041210006900135100001600204700002300220700001400243700001900257856011700276 2009 eng d00aEfficient Multi-label Ranking for Multi-class Learning: Application to Object Recognition0 aEfficient Multilabel Ranking for Multiclass Learning Application1 a.S.Bucak, S1 aMallapragada, P.K.1 aJin, Rong1 aJain, Anil, K. uhttps://icer.msu.edu/research/publications/efficient-multi-label-ranking-multi-class-learning-application-object00556nas a2200157 4500008004100000245007300041210006900114260001200183300001400195490000700209100001300216700002000229700002300249700002000272856010600292 2009 eng d00aElectronic structure of substitutional defects and vacancies in GaSe0 aElectronic structure of substitutional defects and vacancies in c02/2009 a344 - 3550 v701 aRak, Zs.1 aMahanti, S., D.1 aMandal, Krishna, C1 aFernelius, N.C. uhttps://icer.msu.edu/research/publications/electronic-structure-substitutional-defects-vacancies-gase00517nas a2200133 4500008004100000245008000041210006900121300001400190100001400204700001900218700001400237700001800251856011400269 2009 eng d00aEvolving coordinated quadruped gaits with the HyperNEAT generative encoding0 aEvolving coordinated quadruped gaits with the HyperNEAT generati a2764-27711 aClune, J.1 aBeckmann, B.E.1 aOfria, C.1 aPennock, R.T. uhttps://icer.msu.edu/research/publications/evolving-coordinated-quadruped-gaits-hyperneat-generative-encoding01687nas a2200145 4500008004100000245011000041210006900151260002800220520109700248100001901345700001701364700001901381700001601400856012501416 2009 eng d00aExperimental and Computational Analysis of Fuel Mixing in a Low Pressure Direct Injection Gasoline Engine0 aExperimental and Computational Analysis of Fuel Mixing in a Low aVail, Coloradoc07/20093 aAn experimental and computational investigation of the fuel spray mixing in an optically accessible single-cylinder direct-injection engine under realistic operating conditions was performed. High speed flow visualization in the op- tical engine was performed with images taken at a rate of 10,000 frames per second. The numerical simulations were carried out using the KIVA-3V software, which uses the discrete particle method for modeling the spray, with the secondary droplet breakup modeled by the Taylor Analogy Breakup (TAB) model. The nozzle configuration, jet orientation, injection flow rate and other injection parameters were matched with the experimental conditions. The simulated spray patterns in the cylinder were shown to compare well with the fuel distribution images obtained from the high speed flow visualization. The computational and experimental results for the fuel impingement on the cyl- inder walls, piston and valves, and those for the spark plug wetting and evaporated fuel mixing indicate the strong dependency of the fuel-air mixing to the spray pattern.

1 aSrivastava, S.1 aJaberi, F.A.1 aSchock, Harold1 aHung, David uhttps://icer.msu.edu/research/publications/experimental-computational-analysis-fuel-mixing-low-pressure-direct-injection00505nas a2200133 4500008004100000245008200041210006900123300000900192490000800201100001700209700001300226700001900239856011300258 2009 eng d00aThe Formation of Population III Binaries from Cosmological Initial Conditions0 aFormation of Population III Binaries from Cosmological Initial C a601-0 v3251 aTurk, M., J.1 aAbel, T.1 aO'Shea, B., W. uhttps://icer.msu.edu/research/publications/formation-population-iii-binaries-cosmological-initial-conditions00506nas a2200121 4500008004100000245009000041210006900131100001400200700001900214700001800233700001400251856011900265 2009 eng d00aHybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation0 aHybrID A Hybridization of Indirect and Direct Encodings for Evol1 aClune, J.1 aBeckmann, B.E.1 aPennock, R.T.1 aOfria, C. uhttps://icer.msu.edu/research/publications/hybrid-hybridization-indirect-direct-encodings-evolutionary-computation01283nas a2200133 4500008004100000245009500041210006900136260005900205520071100264100001700975700001900992700001701011856012101028 2009 eng d00aLarge-Eddy Simulations of Turbulent Methane Jet Flames with Filtered Mass Density Function0 aLargeEddy Simulations of Turbulent Methane Jet Flames with Filte aAnn Arbor, MichiganbThe Combustion Institutec05/20093 aThe filtered mass density function (FMDF) model (Jaberi et al. 1999 [1]) is employed for large eddy simulations (LES) of “high speed” partially-premixed methane jet flames with the “flamelet” and “finite-rate” kinetics models. The FMDF is the joint probability density function (PDF) of the scalars and is determined via the solution of a set of stochastic differential equations. The LES/FMDF is implemented using a highly scalable, parallel hybrid Eulerian–Lagrangian numerical scheme. The LES/FMDF results are shown to compare well with the experimental data for all flow conditions when “appropriate” reaction and mixing models are employed.

1 aYaldizli, M.1 aMehravaran, K.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/large-eddy-simulations-turbulent-methane-jet-flames-filtered-mass-density01565nas a2200121 4500008004100000245005800041210005700099260007700156520108400233100001101317700001701328856009801345 2009 eng d00aLarge-Scale Simulations of High Speed Turbulent Flows0 aLargeScale Simulations of High Speed Turbulent Flows aOrlando, FLbAmerican Institute of Aeronautics and Astronauticsc01/20093 aThis paper briefly describes a new class of high-order Monotonicity-Preserving (MP) finite difference methods recently developed for direct numerical simulation (DNS) and large-eddy simulation (LES) of high-speed turbulent flows. The MP method has been implemented together with high-order compact (COMP) and weighted essentially non- oscillatory (WENO) methods in a generalized three-dimensional (3D) code and has been applied to various 1D, 2D and 3D problems. For the LES, compressible versions of the gradient-based subgrid-scale closures are employed. Detailed and extensive analysis of various flows indicates that MP schemes have less numerical dissipation and faster grid convergence than WENO schemes. Simulations conducted with high-order MP schemes preserve sharp changes in flow variables without spurious oscillations and capture the turbulence at the smallest simulated scales. The non-conservative form of the scalar equation solved with MP schemes are shown to generate the same results as COMP schemes for supersonic mixing problems involving shock waves.

1 aLi, Z.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/large-scale-simulations-high-speed-turbulent-flows02843nas a2200157 4500008004100000245022400041210006900265260001200334300001400346490000800360520214900368100001902517700001602536700001402552856011902566 2009 eng d00aLeft-Eigenstate Completely Renormalized Equation-of-motion Coupled-Cluster Methods: Review of Key Concepts, Extension to Excited States of Open-Shell Systems, and Comparison with Electron-Attached and ionized Approaches0 aLeftEigenstate Completely Renormalized Equationofmotion CoupledC c11/2009 a3268-33040 v1093 aThe recently proposed left-eigenstate completely renormalized (CR) coupled-cluster (CC) method with singles, doubles, and noniterative triples, termed CR-CC(2,3) Piecuch and Włoch, J Chem Phys, 2005, 123, 224105; Piecuch et al. Chem Phys Lett, 2006, 418, 467 and the companion CR-EOMCC(2,3) methodology, which has been previously applied to singlet excited states of closed-shell molecular systems Włoch et al. Mol Phys, 2006, 104, 2149 and in which relatively inexpensive noniterative corrections due to triple excitations derived from the biorthogonal method of moments of CC equations (MMCC) are added to the CC singles and doubles (CCSD) or equation-of-motion (EOM) CCSD energies, have been extended to excited states of open-shell species. The resulting highly efficient computer codes for the open-shell CR-EOMCC(2,3) approach exploiting the recursively generated intermediates and fast matrix multiplication routines have been developed and interfaced with the GAMESS package, enabling CR-EOMCC(2,3) calculations for singlet as well as nonsinglet ground and excited states of closed- and open-shell systems using the restricted Hartree–Fock or restricted open-shell Hartree–Fock references. A number of important mathematical and algorithmic details related to formal aspects and computer implementation of the CR-EOMCC(2,3) method have been discussed, in addition to overviewing the key concepts behind the CR-EOMCC(2,3) and biorthogonal MMCC methodologies for ground and excited states, and the numerical results involving low-lying states of the CH, CNC, C2N, N3, and NCO species, including states dominated by two-electron transitions, have been presented. The results of the CR-EOMCC(2,3) calculations have been compared with other CC/EOMCC approaches, including the EOMCCSD and EOMCC singles, doubles, and triples methods, and their full and active-space valence counterparts based on the electron-attached and ionized EOMCC methodologies, and the predecessor of CR-EOMCC(2,3) termed CR-EOMCCSD(T) Kowalski and Piecuch, J Chem Phys, 2004, 120, 1715. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

1 aPiecuch, Piotr1 aGour, J., R1 aWloch, M. uhttps://icer.msu.edu/research/publications/left-eigenstate-completely-renormalized-equation-motion-coupled-cluster01658nas a2200133 4500008004100000245006400041210006300105260005900168520114000227100002001367700001901387700001701406856010101423 2009 eng d00aLES/FMDF of Spray Combustion in Internal Combustion Engines0 aLESFMDF of Spray Combustion in Internal Combustion Engines aAnn Arbor, MichiganbThe Combustion Institutec05/20063 aThe two-phase filtered mass density function (FMDF) model is employed for large-eddy simulation (LES) of turbulent spray combustion in internal combustion (IC) engines. The LES/FMDF is implemented with an efficient, hybrid numerical method. In this method, the filtered compressible Navier-Stokes equations in curvilinear coordinate systems are solved with a generalized, high-order, multi-block, compact differencing scheme. The spray and the FMDF are implemented with Lagrangian methods. The LES/FMDF methodology has been used for simulations of turbulent combustion in a rapid compression machine (RCM) and in a direct-injection spark-ignition (DISI) engine. For both RCM and DISI engine, the complex interactions among turbulent velocity, fuel droplets and combustion are shown to be well captured with the LES/FMDF. The results for the DISI engine indicate that the size, velocity, evaporation and combustion of the sprayed fuel droplets are strongly affected by the unsteady, vortical motions generated by the incoming air during the intake stroke. In turn, the droplets are found to change the in-cylinder flow structure.

1 aBanaeizadeh, A.1 aSchock, Harold1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/les-fmdf-spray-combustion-internal-combustion-engines01687nas a2200157 4500008004100000245009400041210006900135260001200204490000800216520112100224100001201345700001901357700001601376700001501392856012201407 2009 eng d00aLocal Correlation Calculations Using Standard and Renormalized Coupled-Cluster Approaches0 aLocal Correlation Calculations Using Standard and Renormalized C c09/20090 v1313 ahe linear scaling local correlation approach, termed “cluster-in-molecule” (CIM), is extended to the coupled-cluster (CC) theory with singles and doubles (CCSD) and CC methods with singles, doubles, and noniterative triples, including CCSD(T) and the completely renormalized CR-CC(2,3) approach. The resulting CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) methods are characterized by (i) the linear scaling of the CPU time with the system size, (ii) the use of orthonormal orbitals in the CC subsystem calculations, (iii) the natural parallelism, (iv) the high computational efficiency, enabling calculations for much larger systems and at higher levels of CC theory than previously possible, and (v) the purely noniterative character of local triples corrections. By comparing the results of the canonical and CIM-CC calculations for normal alkanes and water clusters, it is shown that the CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) approaches accurately reproduce the corresponding canonical CC correlation and relative energies, while offering savings in the computer effort by orders of magnitude.

1 aLi, Wei1 aPiecuch, Piotr1 aGour, J., R1 aLi, Shuhua uhttps://icer.msu.edu/research/publications/local-correlation-calculations-using-standard-renormalized-coupled-cluster02324nas a2200157 4500008004100000245021700041210007300258260001200331300001200343490000800355520162000363100001401983700001601997700001902013856013402032 2009 eng d00aLow-Lying Valence Excited States of CNC, C₂N, N₃ and NCO Studied Using the Electron-Attached and Ionized Symmetry-Adapted Cluster Configuration-Interaction and Equation-of-Motion Coupled-Cluster Methodologies0 aLowLying Valence Excited States of CNC C₂N N₃ and NCO Studied Us c04/2009 a871-8800 v1073 aLow-lying valence excited states of four open-shell triatomic molecules, CNC, C2N, N3, and NCO, are investigated using the electron-attached (EA) and ionized (IP) symmetry-adapted-cluster configuration-interaction (SAC-CI) general-R as well as the full and active-space EA and IP equation-of-motion coupled-cluster (EOMCC) methods. A comparison is made with experiment and with the results of the completely renormalized (CR) CC calculations with singles, doubles, and non-iterative triples defining the CR-CC(2,3) approach. Adiabatic excitation energies of the calculated states are in reasonable agreement with the experimental values, provided that the 3-particle-2-hole (3p-2h) components in the electron attaching operator, as in the EA SAC-CI SDT-R and EA EOMCCSD(3p-2h) approaches, are included in the calculations for the excited states of C2N and CNC which have a predominantly two-electron character. The results also reveal that the active-space EA/IP EOMCC schemes with up to 3p-2h/3h-2p excitations are able to accurately reproduce the results of their much more expensive parent methods while requiring significantly less computational effort. Furthermore, the more 'black-box' CR-CC(2,3) approach calculates the lowest state of each symmetry with the same accuracy as that obtained with the EA/IP SAC-CI SDT-R and EA/IP EOMCCSD(3p-2h/3h-2p) methods, confirming the significance of higher-order correlation effects in obtaining an accurate description of excited states of radicals, particularly the valence excited states of the CNC and C2N species dominated by two-electron processes.

1 aEhara, M.1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/low-lying-valence-excited-states-cnc-c%E2%82%82n-n%E2%82%83-nco-studied-using-electron01793nas a2200145 4500008004100000245015600041210006900197260001200266300001400278490000800292520118900300100001601489700001901505856012301524 2009 eng d00aMethod of Moments for the Continuous Transition Between the Brillouin-Wigner-Type and Rayleigh-Schrodinger-Type Multireference Coupled Cluster Theories0 aMethod of Moments for the Continuous Transition Between the Bril c01/2009 a1209-12210 v1073 aWe apply the method of moments to the multireference (MR) coupled cluster (CC) formalism representing the continuous transition between the Brillouin-Wigner-type and Rayleigh-Schr\"{o}dinger-type theories based on the Jeziorski-Monkhorst wave function ansatz and derive the formula for the noniterative energy corrections to the corresponding MRCC energies that recover the exact, full configuration interaction energies in the general model space case, including complete and incomplete model spaces. We also extend the relationship between the generalized moments of the state-universal (SU) MRCC equations within the Jeziorski-Monkhorst and Kucharski-Bartlett formulations of the SUMRCC theory to the general model space case. Finally, we argue that in the complete model space case, the relationship between moments of the SUMRCC equations corresponding to the Jeziorski-Monkhorst and Kucharski-Bartlett formulations of the SUMRCC theory, derived in this work, implies an equivalence of these two formulations of the SUMRCC approach, provided that the disconnected linked terms are included in the Kucharski-Bartlett formulation, and verify this statement numerically.

1 aPittner, J.1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/method-moments-continuous-transition-between-brillouin-wigner-type-rayleigh00490nas a2200109 4500008004100000245007600041210006900117260005600186100001100242700001700253856011000270 2009 eng d00aA New Model for Numerical Simulations of Two-Phase Turbulent Combustion0 aNew Model for Numerical Simulations of TwoPhase Turbulent Combus aAnn Arbor, MIbNational Combustion Meetingc05/20091 aLi, Z.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/new-model-numerical-simulations-two-phase-turbulent-combustion01341nas a2200145 4500008004100000245009000041210006900131260005000200520075100250100001901001700001901020700001701039700001601056856012301072 2009 eng d00aNumerical Simulation of a Direct-Injection Spark-Ignition Engine with Different Fuels0 aNumerical Simulation of a DirectInjection SparkIgnition Engine w aDetroit, MichiganbSAE Internationalc04/20093 aThis paper focuses on the numerical investigation of the mixing and combustion of ethanol and gasoline in a single-cylinder 3-valve direct-injection spark-ignition engine. The numerical simulations are conducted with the KIVA code with global reaction models. However, an ignition delay model mitigates some of the deficiencies of the global one-step reaction model and is implemented via a two-dimensional look-up table, which was created using available detailed kinetics models. Simulations demonstrate the problems faced by ethanol operated engines and indicate that some of the strategies used for emission control and downsizing of gasoline engines can be employed for enhancing the combustion efficiency of ethanol operated engines.

1 aSrivastava, S.1 aSchock, Harold1 aJaberi, F.A.1 aHung, David uhttps://icer.msu.edu/research/publications/numerical-simulation-direct-injection-spark-ignition-engine-different-fuels03043nas a2200133 4500008004100000245009200041210006900133260005000202300000800252490001000260520249600270100001902766856012402785 2009 eng d00aA process-based distributed hydrologic model and its application to a Michigan watersed0 aprocessbased distributed hydrologic model and its application to aEast LansingbMichigan State Universityc2009 a2880 vPh.D.3 aThe PAWS (Process-based Adaptive Watershed Simulator) model is a novel distributed hydrologic model that is based on solving partial differential equations (PDE) for physical conservation laws of the hydrologic cycle. The objective is to create an efficient physically-based modeling framework to describe the linkages between processes at different scales and to improve the applicability of physically-based models. The model simulates evapotranspiration, overland flow, channel flow, unsaturated soil moisture, groundwater flow, depression storage, vegetation growth and snowpack. PAWS focuses on the dynamic surface- subsurface interactions and integrated responses by efficiently coupling runoff and groundwater flow to the vadose zone processes governed by the Richards equation. This novel approach solves a long-standing bottleneck in PDE-based subsurface flow modeling by removing the computational limitations while maintaining physically consistent solutions. Surface flow is solved by ail efficient Runge-Kutta Finite Volume (RKFV) scheme. We follow the Freeze and Harlan (1969) blueprint in that we believe each component of the model should be verifiable by itself. All flow components have been independently verified using analytical solutions and experimental data where applicable. PAWS utilizes readily available data from national databases. The model is applied to a medium-sized watershed in Michigan achieving high performance metrics in terms of streamflow prediction at two gages during the calibration period and the verification period. The baseflow flow periods are described particularly well. Starting from a rough initial estimate of the groundwater heads, the model describes the observed groundwater heads well (R 2 =0.98). The annual hydrologic fluxes are close to those estimated by a calibrated SWAT model. The model is considerably less expensive than previous physically-based models of similar complexity. The model is able to elucidate the complex interactions of processes in space and time. Such detailed, quantitative and mechanistic descriptions cannot be produced by conceptual models. The watershed is found to be a subsurface-dominated system with saturation excess being the main runoff generation mechanism. Infiltration, recharge and ET are also found to be strongly related to topography and groundwater flow. The large seasonal variation of energy input drives the strong annual cycle and markedly different responses in streamflow.

1 aShen, Chaopeng uhttps://icer.msu.edu/research/publications/process-based-distributed-hydrologic-model-its-application-michigan-watersed03073nas a2200133 4500008004100000020001800041245009300059210006900152260005300221490002500274520249600299100001902795856012502814 2009 eng d a978110964010600aA process-based distributed hydrologic model and its application to a Michigan watershed0 aprocessbased distributed hydrologic model and its application to aEast LansingbMichigan State Universityc08/20100 vDoctor of Philosophy3 aThe PAWS (Process-based Adaptive Watershed Simulator) model is a novel distributed hydrologic model that is based on solving partial differential equations (PDE) for physical conservation laws of the hydrologic cycle. The objective is to create an efficient physically-based modeling framework to describe the linkages between processes at different scales and to improve the applicability of physically-based models. The model simulates evapotranspiration, overland flow, channel flow, unsaturated soil moisture, groundwater flow, depression storage, vegetation growth and snowpack. PAWS focuses on the dynamic surface- subsurface interactions and integrated responses by efficiently coupling runoff and groundwater flow to the vadose zone processes governed by the Richards equation. This novel approach solves a long-standing bottleneck in PDE-based subsurface flow modeling by removing the computational limitations while maintaining physically consistent solutions. Surface flow is solved by ail efficient Runge-Kutta Finite Volume (RKFV) scheme. We follow the Freeze and Harlan (1969) blueprint in that we believe each component of the model should be verifiable by itself. All flow components have been independently verified using analytical solutions and experimental data where applicable. PAWS utilizes readily available data from national databases. The model is applied to a medium-sized watershed in Michigan achieving high performance metrics in terms of streamflow prediction at two gages during the calibration period and the verification period. The baseflow flow periods are described particularly well. Starting from a rough initial estimate of the groundwater heads, the model describes the observed groundwater heads well (R 2 =0.98). The annual hydrologic fluxes are close to those estimated by a calibrated SWAT model. The model is considerably less expensive than previous physically-based models of similar complexity. The model is able to elucidate the complex interactions of processes in space and time. Such detailed, quantitative and mechanistic descriptions cannot be produced by conceptual models. The watershed is found to be a subsurface-dominated system with saturation excess being the main runoff generation mechanism. Infiltration, recharge and ET are also found to be strongly related to topography and groundwater flow. The large seasonal variation of energy input drives the strong annual cycle and markedly different responses in streamflow.

1 aShen, Chaopeng uhttps://icer.msu.edu/research/publications/process-based-distributed-hydrologic-model-its-application-michigan-watershed00586nas a2200193 4500008004100000245004700041210004700088260001200135490000800147100001900155700001800174700001900192700001800211700002100229700002200250700001900272700002000291856008100311 2009 eng d00aProtecting the Amazon with Protected Areas0 aProtecting the Amazon with Protected Areas c08/20090 v1061 aWalker, Robert1 aMoore, Nathan1 aArima, Eugenio1 aPerz, Stephen1 aSimmons, Cynthia1 aCaldas, Marcellus1 aVergara, Dante1 aBohrer, Claudio uhttps://icer.msu.edu/research/publications/protecting-amazon-protected-areas01222nas a2200133 4500008004100000245005400041210005000095260007900145520072000224100002000944700002000964700001700984856008701001 2009 eng d00aThe Role of Implicit Argumentation in Nominal SRL0 aRole of Implicit Argumentation in Nominal SRL aBoulder, Colorado, USAbAssociation for Computational Linguisticsc06/20093 aNominals frequently surface without overtly expressed arguments. In order to measure the potential benefit of nominal SRL for down- stream processes, such nominals must be ac- counted for. In this paper, we show that a state-of-the-art nominal SRL system with an overall argument F1 of 0.76 suffers a perfor- mance loss of more than 9% when nominals with implicit arguments are included in the evaluation. We then develop a system that takes implicit argumentation into account, im- proving overall performance by nearly 5%. Our results indicate that the degree of implicit argumentation varies widely across nominals, making automated detection of implicit argu- mentation an important step for nominal SRL.

1 aGerber, Matthew1 aChai, Joyce, Y.1 aMeyers, Adam uhttps://icer.msu.edu/research/publications/role-implicit-argumentation-nominal-srl00872nas a2200241 4500008004100000245011600041210006900157260000800226300001400234490000800248653003200256653002800288653002200316653003200338653001800370653002300388100002000411700001900431700001800450700001800468700001900486856012500505 2009 eng d00aThe Santa Fe Light Cone Simulation Project. II. The Prospects for Direct Detection of the Whim with SZE Surveys0 aSanta Fe Light Cone Simulation Project II The Prospects for Dire cjun a1795-18020 v69810acosmic microwave background10acosmology: observations10acosmology: theory10agalaxies: clusters: general10ahydrodynamics10amethods: numerical1 aHallman, E., J.1 aO'Shea, B., W.1 aSmith, B., D.1 aBurns, J., O.1 aNorman, M., L. uhttps://icer.msu.edu/research/publications/santa-fe-light-cone-simulation-project-ii-prospects-direct-detection-whim-sze00607nas a2200181 4500008004100000245007300041210006900114260001100183490000700194100001400201700001300215700001500228700001800243700002000261700001900281700001600300856010900316 2009 eng d00aScanning tunneling microscopy study of the CeTe3 charge density wave0 aScanning tunneling microscopy study of the CeTe3 charge density c2/20090 v791 aTomic, A.1 aRak, Zs.1 aVeazey, J.1 aMalliakas, C.1 aMahanti, S., D.1 aKanatzidis, M.1 aTessmer, S. uhttps://icer.msu.edu/research/publications/scanning-tunneling-microscopy-study-cete3-charge-density-wave00490nas a2200121 4500008004100000245008500041210006900126300001400195100001400209700001400223700001800237856011300255 2009 eng d00aThe sensitivity of HyperNEAT to different geometric representations of a problem0 asensitivity of HyperNEAT to different geometric representations a675–6821 aClune, J.1 aOfria, C.1 aPennock, R.T. uhttps://icer.msu.edu/research/publications/sensitivity-hyperneat-different-geometric-representations-problem01699nas a2200133 4500008004100000245007000041210006900111260001200180300001300192490000700205520123100212100002001443856010201463 2009 eng d00aShear rate threshold for the boundary slip in dense polymer films0 aShear rate threshold for the boundary slip in dense polymer film c09/2009 a11 Pages0 v803 aThe shear rate dependence of the slip length in thin polymer films confined between atomically flat surfaces is investigated by molecular dynamics simulations. The polymer melt is described by the bead-spring model of linear flexible chains. We found that at low shear rates the velocity profiles acquire a pronounced curvature near the wall and the absolute value of the negative slip length is approximately equal to the thickness of the viscous interfacial layer. At higher shear rates, the velocity profiles become linear and the slip length increases rapidly as a function of shear rate. The gradual transition from no-slip to steady-state slip flow is associated with faster relaxation of the polymer chains near the wall evaluated from decay of the time autocorrelation function of the first normal mode. We also show that at high melt densities the friction coefficient at the interface between the polymer melt and the solid wall follows a power-law decay as a function of the slip velocity. At large slip velocities the friction coefficient is determined by the product of the surface-induced peak in the structure factor, the temperature, and the contact density of the first fluid layer near the solid wall.

1 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/shear-rate-threshold-boundary-slip-dense-polymer-films00397nas a2200133 4500008004100000245003800041210003800079300001200117490000700129100001900136700001900155700001200174856007700186 2009 eng d00aStrategies for Online Communities0 aStrategies for Online Communities a808-8220 v511 aMiller, K., D.1 aFabian, F., H.1 aLin, S. uhttps://icer.msu.edu/research/publications/strategies-online-communities01591nas a2200217 4500008004100000245007600041210006900117260001200186300001100198490000800209520092200217100001801139700001501157700001501172700001601187700001401203700001201217700001801229700001501247856011101262 2009 eng d00aSurvey of Excited State Neutron Spectroscopic Factors for Z=8-28 Nuclei0 aSurvey of Excited State Neutron Spectroscopic Factors for Z828 N c01/2009 a0625010 v1023 aWe have extracted 565 neutron spectroscopic factors of sd and fp shell nuclei by systematically analyzing more than 2000 measured (d, p) angular distributions. We are able to compare 125 of the extracted spectroscopic factors to values predicted by large-basis shell-model calculations and evaluate the accuracies of spectroscopic factors predicted by different shell-model interactions in these regions. We find that the spectroscopic factors predicted for most excited states of sd-shell nuclei using the latest {USDA} or {USDB} interactions agree with the experimental values. For fp shell nuclei, the inability of the current models to account for the core excitation and fragmentation of the states leads to considerable discrepancies. In particular, the agreement between data and shell-model predictions for Ni isotopes is not better than a factor of 2 using either the {GXPF1A} or the {XT} interaction.

1 aTsang, M., B.1 aLee, Jenny1 aSu, S., C.1 aDai, J., Y.1 aHoroi, M.1 aLiu, H.1 aLynch, W., G.1 aWarren, S. uhttps://icer.msu.edu/research/publications/survey-excited-state-neutron-spectroscopic-factors-z8-28-nuclei01629nas a2200157 4500008004100000245004900041210004900090300001100139490000700150520115100157100001201308700002001320700002301340700002001363856008801383 2009 eng d00aTheoretical studies of defect states in GaTe0 aTheoretical studies of defect states in GaTe a0155040 v213 aUsing first principle electronic structure calculations within density functional theory and the supercell model, we have investigated the nature and formation energies of defect states associated with Ga and Te vacancies and Ge and Sn substitutional impurities in GaTe. We have also calculated the band structure of pure GaTe for comparison with systems with defects and also to find out the importance of spin–orbit interaction (SOI) on its band structure. We find that the top valence band at the Γ-point shifts up in energy by 0.1 eV due to the mixing of Te p x –p y and p z bands, this splitting being considerably smaller than in atoms where it is 0.8 eV. From an analysis of charge densities and band structures associated with the defect states, we find that most of them are strongly localized and lie deep in the band gap region. The calculated binding energy of the deep defect state and the ε(−1 / −2) transition level associated with the Ga vacancy appears to be in good agreement with experiment. Formation energy calculations suggest that V Ga is the preferred intrinsic defect in GaTe.

1 aRak, Zs1 aMahanti, S., D.1 aMandal, Krishna, C1 aFernelius, N.C. uhttps://icer.msu.edu/research/publications/theoretical-studies-defect-states-gate-002667nas a2200157 4500008004100000245008500041210006900126260001200195300001400207490000800221520211000229100001902339700001302358700001802371856012002389 2009 eng d00aThermochemical Kinetics for Multi-reference Systems: Addition Reactions of Ozone0 aThermochemical Kinetics for Multireference Systems Addition Reac c04/2009 a5786-57990 v1133 aThe 1,3-dipolar cycloadditions of ozone to ethyne and ethene provide extreme examples of multireference singlet-state chemistry, and they are examined here to test the applicability of several approaches to thermochemical kinetics of systems with large static correlation. Four different multireference diagnostics are applied to measure the multireference characters of the reactants, products, and transition states; all diagnostics indicate significant multireference character in the reactant portion of the potential energy surfaces. We make a more complete estimation of the effect of quadruple excitations than was previously available, and we use this with CCSDT/CBS estimation of Wheeler et al. (Wheeler, S. E.; Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2008, 112, 1798.) to make new best estimates of the van der Waals association energy, the barrier height, and the reaction energy to form the cycloadduct for both reactions. Comparing with these best estimates, we present comprehensive mean unsigned errors for a variety of coupled cluster, multilevel, and density functional methods. Several computational aspects of multireference reactions are considered: (i) the applicability of multilevel theory, (ii) the convergence of coupled cluster theory for reaction barrier heights, (iii) the applicability of completely renormalized coupled cluster methods to multireference systems, (iv) the treatment by density functional theory, (v) the multireference perturbation theory for multireference reactions, and (vi) the relative accuracy of scaling-type multilevel methods as compared with additive ones. It is found that scaling-type multilevel methods do not perform better than the additive-type multilevel methods. Among the 48 tested density functionals, only M05 reproduces the best estimates within their uncertainty. Multireference perturbation theory based on the complete-active-space reference wave functions constructed using a small number of reaction-specific active orbitals gives accurate forward barrier heights; however, it significantly underestimates reaction energies.

1 aPiecuch, Piotr1 aZhao, Y.1 aTruhlar, D.G. uhttps://icer.msu.edu/research/publications/thermochemical-kinetics-multi-reference-systems-addition-reactions-ozone00639nas a2200193 4500008004100000245007100041210006900112260000800181300001200189490000800201653001900209653002100228100001800249700001700267700001900284700001900303700001900322856010400341 2009 eng d00aThree Modes of Metal-Enriched Star Formation in the Early Universe0 aThree Modes of MetalEnriched Star Formation in the Early Univers cjan a441-4510 v69110aearly universe10astars: formation1 aSmith, B., D.1 aTurk, M., J.1 aSigurdsson, S.1 aO'Shea, B., W.1 aNorman, M., L. uhttps://icer.msu.edu/research/publications/three-modes-metal-enriched-star-formation-early-universe01702nas a2200133 4500008004100000245007000041210006800111260001200179490000700191520123400198100001101432700001701443856010801460 2009 eng d00aTurbulence-Interface Interactions in a Two-Fluid Homogeneous Flow0 aTurbulenceInterface Interactions in a TwoFluid Homogeneous Flow c09/20090 v213 aThe two-way interactions between the turbulent velocity field and the interface in an incompressible two-fluid homogeneous turbulent flow are studied with a recently developed Lagrangian–Eulerian interfacial particle level-set method. The numerical results confirm that the rate of change of the interface area is directly related to the work done by the surface tension force. While the surface tension damps the surrounding turbulence in the “interface stretching period” to oppose the increase in interface area, it is shown to actually increase the turbulent kinetic energy when the interface experiences compression. Additionally, the surface tension force is found to generate strong vortical motions close to the interface through the baroclinic torque effects. There is also an increase in strain rate and the viscous dissipation rate of turbulent kinetic energy in the interface region. The effect of interface on the surrounding turbulence appears primarily in the direction perpendicular to the interface. Analysis of the vorticity and kinetic energy equations indicates that the turbulence-interface interactions are strongly dependent on the fluids’ density ratio and the Weber number.

1 aLi, Z.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/turbulence-interface-interactions-two-fluid-homogeneous-flow00459nas a2200109 4500008004100000245007700041210006900118490000800187100001700195700002000212856011700232 2008 eng d00aAb-initio Molecular Dynamics Study of Nanoscale Thermal Energy Transport0 aAbinitio Molecular Dynamics Study of Nanoscale Thermal Energy Tr0 v1301 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/ab-initio-molecular-dynamics-study-nanoscale-thermal-energy-transport02100nas a2200181 4500008004100000245008800041210006900129300001000198490000800208520148500216100001401701700001601715700001501731700001401746700001901760700001801779856012101797 2008 eng d00aApplication of Renormalized Coupled- Cluster Methods to Potential Function of Water0 aApplication of Renormalized Coupled Cluster Methods to Potential a59-780 v1203 aThe goal of this paper is to examine the performance of the conventional and renormalized single-reference coupled-cluster (CC) methods in calculations of the potential energy surface of the water molecule. A comparison with the results of the internally contracted multi-reference configuration interaction calculations including the quasi-degenerate Davidson correction (MRCI(Q)) and the spectroscopically accurate potential energy surface of water resulting from the use of the energy switching (ES) approach indicates that the relatively inexpensive completely renormalized (CR) CC methods with singles (S), doubles (D), and a non-iterative treatment of triples (T) or triples and quadruples (TQ), such as CR-CCSD(T), CR-CCSD(TQ), and the recently developed rigorously size extensive extension of CR-CCSD(T), termed CR-CC(2,3), provide substantial improvements in the results of conventional CCSD(T) and CCSD(TQ) calculations at larger internuclear separations. It is shown that the CR-CC(2,3) results corrected for the effect of quadruply excited clusters through the CR-CC(2,3)+Q approach can compete with the highly accurate MRCI(Q) data. The excellent agreement between the CR-CC(2,3)+Q and MRCI(Q) results suggests ways of improving the global potential energy surface of water resulting from the use of the ES approach in the regions of intermediate bond stretches and intermediate energies connecting the region of the global minimum with the asymptotic regions.

1 aZheng, J.1 aGour, J., R1 aLutz, J.J.1 aWloch, M.1 aPiecuch, Piotr1 aTruhlar, D.G. uhttps://icer.msu.edu/research/publications/application-renormalized-coupled-cluster-methods-potential-function-water00777nas a2200229 4500008004100000245009000041210006900131260000800200300001200208490000800220653002200228653002800250653003000278653002100308100001100329700001900340700002000359700001900379700001100398700001500409856012300424 2008 eng d00aThe Biermann Battery in Cosmological MHD Simulations of Population III Star Formation0 aBiermann Battery in Cosmological MHD Simulations of Population I cdec aL57-L600 v68810acosmology: theory10aGalaxies: High-Redshift10aMagnetohydrodynamics: MHD10astars: formation1 aXu, H.1 aO'Shea, B., W.1 aCollins, D., C.1 aNorman, M., L.1 aLi, H.1 aLi, Shuhua uhttps://icer.msu.edu/research/publications/biermann-battery-cosmological-mhd-simulations-population-iii-star-formation02156nas a2200181 4500008004100000245022700041210006900268260001200337490000800349520139600357100001401753700001601767700001501783700001401798700001901812700001801831856012501849 2008 eng d00aA Comparative Assessment of the Perturbative and Renormalized Coupled Cluster Theories with a Non-iterative Treatment of Triple Excitations for Thermochemical Kinetics, Including a Study of Basis Set and Core Correlation E0 aComparative Assessment of the Perturbative and Renormalized Coup c01/20080 v1283 aThe CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis sets, namely, MG3S, aug-cc-pVTZ, aug-cc-pV(T+d)Z, aug-cc-pCVTZ, and aug-cc-pCV(T+d)Z, are tested against the DBH24 database of diverse reaction barrier heights. The calculations confirm that the inclusion of connected triple excitations is essential to achieving high accuracy for thermochemical kinetics. They show that various noniterative ways of incorporating connected triple excitations in coupled cluster theory, including the CCSD(T) approach, the full CR-CC(2,3) method, and approximate variants of CR-CC(2,3) similar to the triples corrections of the CCSD(2) approaches, are all about equally accurate for describing the effects of connected triply excited clusters in studies of activation barriers. The effect of freezing core electrons on the results of the CCSD, CCSD(T), and CR-CC(2,3) calculations for barrier heights is also examined. It is demonstrated that to include core correlation most reliably, a basis set including functions that correlate the core and that can treat core-valence correlation is required. On the other hand, the frozen-core approximation using valence-optimized basis sets that lead to relatively small computational costs of CCSD(T) and CR-CC(2,3) calculations can achieve almost as high accuracy as the analogous fully correlated calculations.

1 aZheng, J.1 aGour, J., R1 aLutz, J.J.1 aWloch, M.1 aPiecuch, Piotr1 aTruhlar, D.G. uhttps://icer.msu.edu/research/publications/comparative-assessment-perturbative-renormalized-coupled-cluster-theories-non00743nas a2200205 4500008004100000245010000041210006900141300001400210490000800224653002200232653001800254653002100272653002300293100002100316700001900337700002000356700001800376700001900394856012400413 2008 eng d00aCosmological Shocks in Adaptive Mesh Refinement Simulations and the Acceleration of Cosmic Rays0 aCosmological Shocks in Adaptive Mesh Refinement Simulations and a1063-10770 v68910acosmology: theory10ahydrodynamics10aISM: Cosmic Rays10amethods: numerical1 aSkillman, S., W.1 aO'Shea, B., W.1 aHallman, E., J.1 aBurns, J., O.1 aNorman, M., L. uhttps://icer.msu.edu/research/publications/cosmological-shocks-adaptive-mesh-refinement-simulations-acceleration-cosmic00729nas a2200217 4500008004100000245007100041210006700112260000800179300001000187490000800197653003000205653002200235653001800257653002200275653003400297100001900331700001900350700001900369700001900388856010400407 2008 eng d00aThe Destruction of Cosmological Minihalos by Primordial Supernovae0 aDestruction of Cosmological Minihalos by Primordial Supernovae cjul a49-670 v68210aCosmology: Early Universe10acosmology: theory10ahydrodynamics10aStars: Early-Type10aStars: Supernovae: Individual1 aWhalen, D., J.1 avan Veelen, B.1 aO'Shea, B., W.1 aNorman, M., L. uhttps://icer.msu.edu/research/publications/destruction-cosmological-minihalos-primordial-supernovae01908nas a2200133 4500008004100000245008100041210006900122260003200191520138900223100001101612700001701623700001701640856011701657 2008 eng d00aFiltered Mass Density Function for Numerical Simulations of Spray Combustion0 aFiltered Mass Density Function for Numerical Simulations of Spra aReno, NevadabAIAAc01/20083 aThis paper briefly describes our recent efforts on the modeling and numerical simulations of two-phase turbulent reacting flows in realistic combustion systems with a new large-eddy simulation (LES) model. The model is constructed based on the two-phase extension of scalar filtered mass density function (FMDF) and a Lagrangian-Eulerian- Lagrangian mathematical/numerical methodology. In this methodology, the “resolved” fluid velocity field is obtained by solving the filtered form of the compressible Navier-Stokes equations with a high-order finite difference scheme. The liquid (droplet) phase and scalar (temperature and species mass fractions) fields are both obtained by stochastic Lagrangian models. There are two-way interactions between the phases and all the Eulerian and Lagrangian fields. The LES/FMDF is used for systematic analysis of turbulent combustion in the spray-controlled dump combustor and double-swirl spray burner for various flow and spray parameters. The effects of fuel type, spray angle, mass loading ratio, droplet size distribution, fuel/air composition, wall, and inflow/outflow conditions on the combustion are investigated. It has been found that the main features of the turbulence and combustion are modified by changing the inflow/outflow conditions. The LES/FMDF results also confirm the significance of the spray parameters.

1 aLi, Z.1 aJaberi, F.A.1 aYaldizli, M. uhttps://icer.msu.edu/research/publications/filtered-mass-density-function-numerical-simulations-spray-combustion00489nas a2200133 4500008004100000245006800041210006700109260001300176300001400189100001400203700001400217700001800231856010600249 2008 eng d00aHow a generative encoding fares as problem-regularity decreases0 aHow a generative encoding fares as problemregularity decreases bSpringer a358–3671 aClune, J.1 aOfria, C.1 aPennock, R.T. uhttps://icer.msu.edu/research/publications/how-generative-encoding-fares-problem-regularity-decreases00670nas a2200193 4500008004100000245007800041210006900119260000800188300001200196490000800208653003000216653002200246653002200268100001900290700001900309700001400328700001900342856011500361 2008 eng d00aHow the First Stars Regulated Local Star Formation. I. Radiative Feedback0 aHow the First Stars Regulated Local Star Formation I Radiative F cjun a925-9410 v67910aCosmology: Early Universe10acosmology: theory10aISM: H II Regions1 aWhalen, D., J.1 aO'Shea, B., W.1 aSmidt, J.1 aNorman, M., L. uhttps://icer.msu.edu/research/publications/how-first-stars-regulated-local-star-formation-i-radiative-feedback02418nas a2200169 4500008004100000245011500041210006900156260001100225300001400236490000700250520174400257653007702001100001102078700001702089700001902106856012302125 2008 eng d00aA Hybrid Langrangian-Eulerian Particle-Level Set Method for numerical Simulations of Two-Fluid Turbulent Flows0 aHybrid LangrangianEulerian ParticleLevel Set Method for numerica c4/2008 a2271-23000 v563 aA coupled Lagrangian interface-tracking and Eulerian level set (LS) method is developed and implemented for numerical simulations of two-fluid flows. In this method, the interface is identified based on the locations of notional particles and the geometrical information concerning the interface and fluid properties, such as density and viscosity, are obtained from the LS function. The LS function maintains a signed distance function without an auxiliary equation via the particle-based Lagrangian re-initialization technique. To assess the new hybrid method, numerical simulations of several ‘standard interface-moving’ problems and two-fluid laminar and turbulent flows are conducted. The numerical results are evaluated by monitoring the mass conservation, the turbulence energy spectral density function and the consistency between Eulerian and Lagrangian components. The results of our analysis indicate that the hybrid particle-level set method can handle interfaces with complex shape change, and can accurately predict the interface values without any significant (unphysical) mass loss or gain, even in a turbulent flow. The results obtained for isotropic turbulence by the new particle-level set method are validated by comparison with those obtained by the ‘zero Mach number’, variable-density method. For the cases with small thermal/mass diffusivity, both methods are found to generate similar results. Analysis of the vorticity and energy equations indicates that the destabilization effect of turbulence and the stability effect of surface tension on the interface motion are strongly dependent on the density and viscosity ratios of the fluids. Copyright q 2007 John Wiley & Sons, Ltd.

10atwo-fluid turbulent flows; particle-level set method; interface tracking1 aLi, Z.1 aJaberi, F.A.1 aShih, T., I-P. uhttps://icer.msu.edu/research/publications/hybrid-langrangian-eulerian-particle-level-set-method-numerical-simulations01478nas a2200193 4500008004100000245010300041210006900144260001200213300001400225490000800239520081400247100001901061700002001080700001601100700001101116700001801127700001801145856012101163 2008 eng d00aThe influence of cluster emission and the symmetry energy on neutron-proton spectral double ratios0 ainfluence of cluster emission and the symmetry energy on neutron c02/2008 a145–1480 v6643 aThe emissions of neutrons, protons and bound clusters from central {124Sn} + {124Sn} and {112Sn} + {112Sn} collisions are simulated using the Improved Quantum Molecular Dynamics model for two different density-dependent symmetry-energy functions. The calculated neutron-proton spectral double ratios for these two systems are sensitive to the density dependence of the symmetry energy, consistent with previous work. Cluster emission increases the double ratios in the low energy region relative to values calculated in a coalescence-invariant approach. To circumvent uncertainties in cluster production and secondary decays, it is important to have more accurate measurements of the neutron-proton ratios at higher energies in the center of mass system, where the influence of such effects is reduced.

1 aZhang, Yingxun1 aDanielewicz, P.1 aFamiano, M.1 aLi, Z.1 aLynch, W., G.1 aTsang, M., B. uhttps://icer.msu.edu/research/publications/influence-cluster-emission-symmetry-energy-neutron-proton-spectral-double00471nas a2200121 4500008004100000245006500041210006500106260002000171100001600191700002000207700001700227856010500244 2008 eng d00aLarge Eddy Simulation of High Speed Turbulent Reacting Flows0 aLarge Eddy Simulation of High Speed Turbulent Reacting Flows aHawaiic12/20081 aZhaorui, Li1 aBanaeizadeh, A.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/large-eddy-simulation-high-speed-turbulent-reacting-flows01959nas a2200157 4500008004100000020002200041245006000063210006000123260003800183520141500221100002001636700001601656700001701672700001501689856009701704 2008 eng d a978-0-7918-4327-700aLarge Eddy Simulations of Turbulent Flows in IC Engines0 aLarge Eddy Simulations of Turbulent Flows in IC Engines aBrooklyn, New YorkbASMEc08/20083 aA new computational methodology is developed and tested for large eddy simulation (LES) of turbulent flows in internal combustion (IC) engines. In this methodology, the filtered compressible Navier-Stokes equations in curvilinear coordinate systems are solved via a generalized, high-order, multi-block, compact differencing scheme and various subgrid-scale (SGS) stress closures. Both reacting and nonreacting flows with and without spray are considered. The LES models have been applied to a piston-cylinder assembly with a stationary open valve and harmonically moving flat piston. The flow in a direct-injection spark-ignition (DISI) engine is also considered. It is observed that during the intake stroke of the engine operation, large-scale unsteady turbulent flow motions are developed behind the intake valves. The physical features of these turbulent motions and the ability of LES to capture them are studied and tested by simulating the flow in a simple configuration involving a stationary valve. The flow statistics predicted by LES are shown to compare well with the available experimental data. The DISI configuration includes all the complexities involved in a realistic single-cylinder IC engine, such as the complex geometry, moving valves, moving piston, spray and combustion. The spray combustion is simulated with the recently developed two-phase filtered mass density (FMDF) model.

1 aBanaeizadeh, A.1 aAfshari, A.1 aJaberi, F.A.1 aSchock, H. uhttps://icer.msu.edu/research/publications/large-eddy-simulations-turbulent-flows-ic-engines00522nas a2200121 4500008004100000050001900041245006500060210006400125260007800189100001700267700001100284856010500295 2008 eng d aAIAA 2008-115400aLarge Eddy Simulations of Two-Phase Turbulent Reacting Flows0 aLarge Eddy Simulations of TwoPhase Turbulent Reacting Flows aReno, NevadabAMERICAN INSTITUTE OF AERONAUTICS AND ASTRONAUTICSc01/20081 aJaberi, F.A.1 aLi, Z. uhttps://icer.msu.edu/research/publications/large-eddy-simulations-two-phase-turbulent-reacting-flows01219nas a2200169 4500008004100000245007600041210006900117260001100186300001200197490000700209520061500216653003100831653004000862100001600902700001700918856011400935 2008 eng d00aLarge-Eddy Simulation of a Dispersed Particle-Laden Turbulent Round Jet0 aLargeEddy Simulation of a Dispersed ParticleLaden Turbulent Roun c2/2008 a683-6950 v513 aThe numerical results obtained by large-eddy simulation (LES) of a particle-laden axisymmetric turbulent jet are compared with the available experimental data. The results indicate that with a new stochastic subgrid-scale (SGS) closure, the effects of the particles on the carrier gas and those of the carrier gas on the particles are correctly captured by the LES. Additional numerical experiments are conducted and used to investigate the effects of particle size, mass-loading ratio, and other flow/particle parameters on the statistics of both the carrier gas phase and the particle dispersed phase.

10aParticle-laden jet; dilute10atwo-phase flows; turbulent jet; LES1 aAlmeida, T.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/large-eddy-simulation-dispersed-particle-laden-turbulent-round-jet02380nas a2200169 4500008004100000245007800041210006900119260001200188300001400200490000700214520170600221653001501927653012301942100001602065700001702081856011202098 2008 eng d00aLarge-Eddy Simulation of Turbulent Flow in an Axisymmetric Dump Combustor0 aLargeEddy Simulation of Turbulent Flow in an Axisymmetric Dump C c07/2008 a1576-15920 v463 aA hybrid Eulerian–Lagrangian, mathematical/computational methodology is developed and evaluated for large- eddy simulations of turbulent combustion in complex geometries. The formulation for turbulence is based on the standard subgrid-scale stress models. The formulation for subgrid-scale combustion is based on the filtered mass density function and its equivalent stochastic Lagrangian equations. An algorithm based on high-order compact differencing on generalized multiblock grids is developed for numerical solution of the coupled Eulerian–Lagrangian equations. The results obtained by large-eddy simulations/filtered mass density function show the computational method to be more efficient than existing methods for similar hybrid systems. The consistency, convergence, and accuracy of the filtered mass density function and its Lagrangian–Monte Carlo solver is established for both reacting and nonreacting flows in a dump combustor. The results show that the finite difference and the Monte Carlo numerical methods employed are both accurate and consistent. The results for a reacting premixed dump combustor also agree well with available experimental data. Additionally, the results obtained for other nonreacting turbulent flows are found to be in good agreement with the experimental and high-order numerical data. Filtered mass density function simulations are performed to examine the effects of boundary conditions, subgrid-scale models, as well as physical and geometrical parameters on dump-combustor flows. The results generated for combustors with and without an inlet nozzle are found to be similar as long as appropriate boundary conditions are employed.

10acombustion10aGas turbine; modeling; combustion chamber; Monte Carlo method; Lagragian Method; turbulent flow; large eddy simulation1 aAfshari, A.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/large-eddy-simulation-turbulent-flow-axisymmetric-dump-combustor00667nas a2200181 4500008004100000245010900041210006900150260003000219300001300249490000600262100001400268700001600282700001400298700001700312700001600329700001700345856012300362 2008 eng d00aNatural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes0 aNatural selection fails to optimize mutation rates for longterm bPublic Library of Science ae10001870 v41 aClune, J.1 aMisevic, D.1 aOfria, C.1 aLenski, R.E.1 aElena, S.F.1 aSanjuán, R. uhttps://icer.msu.edu/research/publications/natural-selection-fails-optimize-mutation-rates-long-term-adaptation-rugged01785nas a2200217 4500008004100000245008800041210006900129260001200198490000800210520105900218653001701277653003001294653001801324653001301342653001501355653001401370653002201384100001801406700002001424856012301444 2008 eng d00aRheological study of polymer flow past rough surfaces with slip boundary conditions0 aRheological study of polymer flow past rough surfaces with slip c10/20080 v1293 aThe slip phenomena in thin polymer films confined by either flat or periodically corrugated surfaces are investigated by molecular dynamics and continuum simulations. For atomically flat surfaces and weak wall-fluid interactions, the shear rate dependence of the slip length has a distinct local minimum which is followed by a rapid increase at higher shear rates. For corrugated surfaces with wavelength larger than the radius of gyration of polymer chains, the effective slip length decays monotonically with increasing corrugation amplitude. At small amplitudes, this decay is reproduced accurately by the numerical solution of the Stokes equation with constant and rate-dependent local slip length. When the corrugation wavelength is comparable to the radius of gyration, the continuum predictions overestimate the effective slip length obtained from molecular dynamics simulations. The analysis of the conformational properties indicates that polymer chains tend to stretch in the direction of shear flow above the crests of the wavy surface.

10aliquid films10amolecular dynamics method10apolymer melts10arheology10ashear flow10aslip flow10asurface roughness1 aNiavarani, A.1 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/rheological-study-polymer-flow-past-rough-surfaces-slip-boundary-conditions01604nas a2200193 4500008004100000245009100041210006900132260001200201490000700213520093400220653002301154653001501177653001601192653001801208653002801226100001801254700002001272856011801292 2008 eng d00aSlip boundary conditions for shear flow of polymer melts past atomically flat surfaces0 aSlip boundary conditions for shear flow of polymer melts past at c04/20080 v773 aMolecular dynamics simulations are carried out to investigate the dynamic behavior of the slip length in thin polymer films confined between atomically smooth thermal surfaces. For weak wall-fluid interactions, the shear rate dependence of the slip length acquires a distinct local minimum followed by a rapid growth at higher shear rates. With increasing fluid density, the position of the local minimum is shifted to lower shear rates. We found that the ratio of the shear viscosity to the slip length, which defines the friction coefficient at the liquid/solid interface, undergoes a transition from a nearly constant value to power law decay as a function of the slip velocity. In a wide range of shear rates and fluid densities, the friction coefficient is determined by the product of the value of the surface-induced peak in the structure factor and the contact density of the first fluid layer near the solid wall.

10amolecular dynamics10ashear rate10aslip length10aslip velocity10asmooth thermal surfaces1 aNiavarani, A.1 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/slip-boundary-conditions-shear-flow-polymer-melts-past-atomically-flat02436nas a2200205 4500008004100000245012200041210006900163260001200232300001400244490000800258520172300266100001701989700001602006700001402022700001402036700001902050700001802069700001802087856012502105 2008 eng d00aStereoelectronic Effects on Molecular Geometries and State-Energy Splittings of Ligated Monocopper Diozygen Complexes0 aStereoelectronic Effects on Molecular Geometries and StateEnergy c03/2008 a3754-37670 v1123 aThe relative energies of side-on versus end-on binding of molecular oxygen to a supported Cu(I) species, and the singlet versus triplet nature of the ground electronic state, are sensitive to the nature of the supporting ligands and, in particular, depend upon their geometric arrangement relative to the O2 binding site. Highly correlated ab initio and density functional theory electronic structure calculations demonstrate that optimal overlap (and oxidative charge transfer) occurs for the side-on geometry, and this is promoted by ligands that raise the energy, thereby enhancing resonance, of the filled Cu dxz orbital that hybridizes with the in-plane π* orbital of O2. Conversely, ligands that raise the energy of the filled Cu dz2 orbital foster a preference for end-on binding as this is the only mode that permits good overlap with the in-plane O2 π*. Because the overlap of Cu dz2 with O2 π* is reduced as compared to the overlap of Cu dxz with the same O2 orbital, the resonance is also reduced, leading to generally more stable triplet states relative to singlets in the end-on geometry as compared to the side-on geometry, where singlet ground states become more easily accessible once ligands are stronger donors. Biradical Cu(II)-O2 superoxide character in the electronic structure of the supported complexes leads to significant challenges for accurate quantum chemical calculations that are best addressed by exploiting the spin-purified M06L local density functional, single-reference completely renormalized coupled-cluster theory, or multireference second-order perturbation theory, all of which provide predictions that are qualitatively and quantitatively consistent with one another.

1 aCramer, C.J.1 aGour, J., R1 aKinal, A.1 aWloch, M.1 aPiecuch, Piotr1 aShahi, A.R.M.1 aGagliardi, L. uhttps://icer.msu.edu/research/publications/stereoelectronic-effects-molecular-geometries-state-energy-splittings-ligated02163nas a2200193 4500008004100000245008900041210006900130260001200199300001200211490000800223520143600231653002801667653008201695100001701777700001701794700001901811700001701830856012201847 2008 eng d00aThe Structure of Partially-Premixed Methane Flames in High Intensity Turbulent Flows0 aStructure of PartiallyPremixed Methane Flames in High Intensity c09/2008 a692-7140 v1543 aDirect numerical simulations (DNS) are conducted to study the structure of partially premixed and non-premixed methane flames in high-intensity two-dimensional isotropic turbulent flows. The results obtained via “flame normal analysis” show local extinction and reignition for both non-premixed and partially premixed flames. Dynamical analysis of the flame with a Lagrangian method indicates that the time integrated strain rate characterizes the finite-rate chemistry effects and the flame extinction better than the strain rate. It is observed that the flame behavior is affected by the “pressure-dilatation” and “viscous-dissipation” in addition to strain rate. Consistent with previous studies, high vorticity values are detected close to the reaction zone, where the vorticity generation by the “baroclinic torque” was found to be significant. The influences of (initial) Reynolds and Damköhler numbers, and various air–fuel premixing levels on flame and turbulence variables are also studied. It is observed that the flame extinction occurs similarly in flames with different fuel–air premixing. Our simulations also indicate that the CO emission increases as the partial premixing of the fuel with air increases. Higher values of the temperature, the OH mass fraction and the CO mass fraction are observed within the flame zone at higher Reynolds numbers.

10aDNS; Methane combustion10aturbulent reacting flows; partially premixed flames; reduced chemistry models1 aYaldizli, M.1 aMohammad, H.1 aMehravaran, K.1 aJaberi, F.A. uhttps://icer.msu.edu/research/publications/structure-partially-premixed-methane-flames-high-intensity-turbulent-flows00488nas a2200157 4500008004100000245004900041210004900090260001200139300001100151490000700162100001200169700002000181700002300201700002000224856008600244 2008 eng d00aTheoretical studies of defect states in GaTe0 aTheoretical studies of defect states in GaTe c01/2009 a0155040 v211 aRak, Zs1 aMahanti, S., D.1 aMandal, Krishna, C1 aFernelius, N.C. uhttps://icer.msu.edu/research/publications/theoretical-studies-defect-states-gate01816nas a2200217 4500008004100000245009100041210006900132260001200201490000700213520109300220653002301313653001901336100001401355700001801369700001601387700001201403700002001415700001801435700001901453856012601472 2008 eng d00aTransport Model Simulations of Projectile Fragmentation Reactions at 140 {MeV/nucleon}0 aTransport Model Simulations of Projectile Fragmentation Reaction c08/20080 v783 aThe collisions in four different reaction systems using {\$ˆ{40,48}\$Ca} and {\$ˆ{58,64}\$Ni} isotope beams and a Be target have been simulated using the Heavy Ion Phase Space Exploration and the Antisymmetrized Molecular Dynamics models. The present study mainly focuses on the model predictions for the excitation energies of the hot fragments and the cross sections of the final fragments produced in these reactions. The effects of various factors influencing the final fragment cross sections, such as the choice of the statistical decay code and its parameters have been explored. The predicted fragment cross sections are compared to the projectile fragmentation cross sections measured with the A1900 mass separator. At {\$E/A=140\$} {MeV,} reaction dynamics can significantly modify the detection efficiencies for the fragments and make them different from the efficiencies applied to the measured data reported in the previous work. The effects of efficiency corrections on the validation of event generator codes are discussed in the context of the two models.

10aNuclear Experiment10aNuclear Theory1 aMocko, M.1 aTsang, M., B.1 aLacroix, D.1 aOno, A.1 aDanielewicz, P.1 aLynch, W., G.1 aCharity, R., J uhttps://icer.msu.edu/research/publications/transport-model-simulations-projectile-fragmentation-reactions-140-mev-nucleon02707nas a2200301 4500008004100000245017900041210006900220260001200289300001300301490000800314520164400322653003101966653003301997653002402030653001902054653001802073653001802091653001502109653002202124653002102146653003002167100001602197700001902213700001602232700001402248700001802262856012502280 2007 eng d00aActive-Space Symmetry-Adapted-Cluster Configuration-Interaction and Equation-of-Motion Cluster Methods for High Accuracy Calculations of Potential Energy Surfaces of Radicals0 aActiveSpace SymmetryAdaptedCluster ConfigurationInteraction and c04/2007 a28 pages0 v1263 aThe electron-attached (EA) and ionized (IP) symmetry-adapted-cluster configuration-interaction (SAC-CI) methods and their equation-of-motion coupled-cluster (EOMCC) analogs provide an elegant framework for studying open-shell systems. As shown in this study, these schemes require the presence of higher-order excitations, such as the four-particle-three-hole (4p-3h) or four-hole–three-particle (4h-3p) terms, in the electron attaching or ionizing operator R in order to produce accurate ground- and excited-state potential energy surfaces of radicals along bond breaking coordinates. The full inclusion of the 4p-3h/4h-3p excitations in the EA/IP SAC-CI and EOMCC methods leads to schemes which are far too expensive for calculations involving larger radicals and realistic basis sets. In order to reduce the large costs of such schemes without sacrificing accuracy, the active-space EA/IP EOMCC methodology [ J. R. Gour et al., J. Chem. Phys. 123, 134113 (2005) ] is extended to the EA/IP SAC-CI approaches with 4p-3h/4h-3p excitations. The resulting methods, which use a physically motivated set of active orbitals to pick out the most important 3p-2h/3h-2p and 4p-3h/4h-3p excitations, represent practical computational approaches for high-accuracy calculations of potential energy surfaces of radicals. To illustrate the potential offered by the active-space EA/IP SAC-CI approaches with up to 4p-3h/4h-3p excitations, the results of benchmark calculations for the potential energy surfaces of the low-lying doublet states of CH and OH are presented and compared with other SAC-CI and EOMCC methods, and full CI results.

10aconfiguration interactions10acoupled cluster calculations10aelectron attachment10aexcited states10afree radicals10aground states10aionisation10aorganic compounds10aoxygen compounds10apotential energy surfaces1 aOhtsuka, Y.1 aPiecuch, Piotr1 aGour, J., R1 aEhara, M.1 aNakatsuji, H. uhttps://icer.msu.edu/active-space-symmetry-adapted-cluster-configuration-interaction-and-equation-motion-cluster-methods01936nas a2200157 4500008004100000245009100041210006900132260001200201300001200213490000800225520137300233100001101606700001701617700001901634856012501653 2007 eng d00aBreaking Bonds with the Left Eigenstate Completely Renormalized Coupled-Cluster Method0 aBreaking Bonds with the Left Eigenstate Completely Renormalized c11/2007 a6 pages0 v1273 aThe recently developed [ P. Piecuch and M. Wloch, J. Chem. Phys. 123, 224105 (2005) ] size-extensive left eigenstate completely renormalized (CR) coupled-cluster (CC) singles (S), doubles (D), and noniterative triples (T) approach, termed CR-CC(2,3) and abbreviated in this paper as CCL, is compared with the full configuration interaction (FCI) method for all possible types of single bond-breaking reactions between C, H, Si, and Cl (except H2) and the H2SiSiH2 double bond-breaking reaction. The CCL method is in excellent agreement with FCI in the entire region R = 1–3Re for all of the studied single bond-breaking reactions, where R and Re are the bond distance and the equilibrium bond length, respectively. The CCL method recovers the FCI results to within approximately 1 mhartree in the region R = 1–3Re of the H–SiH3, H–Cl, H3Si–SiH3, Cl–CH3, H–CH3, and H3C–SiH3 bonds. The maximum errors are −2.1, 1.6, and 1.6 mhartree in the R = 1–3Re region of the H3C–CH3, Cl–Cl, and H3Si–Cl bonds, respectively, while the discrepancy for the H2SiSiH2 double bond-breaking reaction is 6.6 (8.5) mhartree at R = 2(3)Re. CCL also predicts more accurate relative energies than the conventional CCSD and CCSD(T) approaches, and the predecessor of CR-CC(2,3) termed CR-CCSD(T).

1 aGe, Y.1 aGordon, M.S.1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/breaking-bonds-left-eigenstate-completely-renormalized-coupled-cluster-method03686nas a2200145 4500008004100000245018100041210006900222260001200291300001200303490000800315520305800323100001403381700001903395856012603414 2007 eng d00aComputational Investigation of the Conrotatory and Disrotatory Isomerization Channels of Bicyclo[1.1.0]butane to Buta-1,3-diene: A Completely Renormalized Coupled-Cluster Study0 aComputational Investigation of the Conrotatory and Disrotatory I c01/2007 a734-7420 v1113 aThe conrotatory and disrotatory mechanisms of the isomerization of bicyclo[1.1.0]butane to trans-buta-1,3-diene have been computationally investigated with the CASSCF, MCQDPT2, (U)B3LYP, CCSD(T), CR-CCSD(T), and CR-CC(2,3) approaches. The coupled-cluster (CC) methods, including the CC approach with singles, doubles, and noniterative triples (CCSD(T)), and its completely renormalized (CR) extensions called CR-CCSD(T) and CR-CC(2,3), and the density functional theory B3LYP approach do an excellent job of correctly predicting the activation barrier for the conrotatory pathway, which corresponds to a weakly biradical transition state (TS), producing values within experimental error bars. In particular, the recently developed CR-CC(2,3) method gives 40.8 or 41.1 kcal/mol, in perfect agreement with the experimental value of 40.6 ± 2.5 kcal/mol. The complete-active-space self-consistent-field (CASSCF) approach and the second-order multireference perturbation theory (MCQDPT2) are less accurate in describing the conrotatory barrier than CR-CC(2,3). The higher energy disrotatory pathway, which has not been characterized experimentally and which involves a strongly biradical TS, poses a great challenge for many methods. CCSD(T) fails, predicting the activation barrier for the disrotatory pathway significantly below the conrotatory barrier, contradicting the experimental result that the conrotatory pathway describes the mechanism. The strongly biradical character of the disrotatory TS, spin contamination, and the proximity of singlet and triplet potential energy surfaces cause difficulties for B3LYP, which does not link this TS with gauche-buta-1,3-diene. No such difficulties occur in the CASSCF calculations, which offer a proper description of the structure of the disrotatory TS that links it with the reactant and product molecules. The CR-CC(2,3) approach, which accurately balances dynamical and nondynamical correlations in systems containing closed-shell and biradical structures, predicts the activation enthalpy for the disrotatory mechanism of 66 kcal/mol. CR-CCSD(T) gives 69 kcal/mol. In agreement with experiment and earlier multireference configuration interaction calculations of Nguyen and Gordon, CR-CCSD(T) and CR-CC(2,3) favor the conrotatory mechanism. The CASSCF, MCQDPT2, and B3LYP methods correctly place the disrotatory barrier above the conrotatory one, but, on the basis of a comparison with the accurate CR-CC(2,3) results, they underestimate the activation energy for the disrotatory pathway. All CC approaches employed in this study produce very good estimates of the enthalpy of isomerization of bicyclo[1.1.0]butane into buta-1,3-diene, the experimental value of which is −25.9 ± 0.4 kcal/mol, giving about −28 kcal/mol, when trans-buta-1,3-diene is used as a product, and −25 kcal/mol, when the nearly isoenergetic gauche-buta-1,3-diene rotamer is used as a product. The CC reaction enthalpies are more accurate than those obtained with CASSCF, MCQDPT2, and B3LYP.

1 aKinal, A.1 aPiecuch, Piotr uhttps://icer.msu.edu/computational-investigation-conrotatory-and-disrotatory-isomerization-channels-bicyclo110butane-buta01210nas a2200193 4500008004100000245008000041210006900121260001200190300001200202490000700214520059600221100001400817700001600831700001400847700002100861700001800882700001900900856009700919 2007 eng d00aCoupled-Cluster and Configuration-Interaction Calculations for Heavy Nuclei0 aCoupledCluster and ConfigurationInteraction Calculations for Hea c03/2007 a4 pages0 v983 aWe compare coupled-cluster (CC) and configuration-interaction (CI) results for 56Ni obtained in the pf-shell basis, focusing on practical CC approximations that can be applied to systems with dozens or hundreds of correlated fermions. The weight of the reference state and the strength of correlation effects are controlled by the gap between the f7/2 orbit and the f5/2, p3/2, p1/2 orbits. Independent of the gap, the CC method with 1p-1h and 2p-2h clusters and a noniterative treatment of 3p-3h clusters is as accurate as the more demanding CI approach truncated at the 4p-4h level.

1 aHoroi, M.1 aGour, J., R1 aWloch, M.1 aLodriguito, M.D.1 aBrown, B., A.1 aPiecuch, Piotr uhttps://icer.msu.edu/coupled-cluster-and-configuration-interaction-calculations-heavy-nuclei01203nas a2200205 4500008004100000245005500041210005300096260001200149300001300161490000700174520063000181100001400811700001900825700001700844700001600861700001500877700001400892700001900906856007200925 2007 eng d00aCoupled-Cluster Theory for Three-Body Hamiltonians0 aCoupledCluster Theory for ThreeBody Hamiltonians c09/2007 a11 pages0 v763 aWe derive coupled-cluster equations for three-body Hamiltonians. The equations for the one- and two-body cluster amplitudes are presented in a factorized form that leads to an efficient numerical implementation. We employ low-momentum two- and three-nucleon interactions and calculate the binding energy of 4He. The results show that the main contribution of the three-nucleon interaction stems from its density-dependent zero-, one-, and two-body terms that result from the normal ordering of the Hamiltonian in coupled-cluster theory. The residual three-body terms that remain after normal ordering can be neglected.

1 aHagen, G.1 aPapenbrock, T.1 aDean, D., J.1 aSchwenk, A.1 aNHogga, A.1 aWloch, M.1 aPiecuch, Piotr uhttps://icer.msu.edu/coupled-cluster-theory-three-body-hamiltonians01385nas a2200217 4500008004100000245007200041210006900113260001200182300001100194490000800205520071100213653002200924653002400946653001700970653003000987653000901017653002201026653001501048100002001063856008401083 2007 eng d00aEffect of surface roughness on rate-dependent slip in simple fluids0 aEffect of surface roughness on ratedependent slip in simple flui c10/2007 a1447080 v1273 aMolecular dynamics simulations are used to investigate the influence of molecular-scale surface roughness on the slip behavior in thin liquid films. The slip length increases almost linearly with the shear rate for atomically smooth rigid walls and incommensurate structures of the liquid/solid interface. The thermal fluctuations of the wall atoms lead to an effective surface roughness, which makes the slip length weakly dependent on the shear rate. With increasing the elastic stiffness of the wall, the surface roughness smoothes out and the strong rate dependence is restored again. Both periodically and randomly corrugated rigid surfaces reduce the slip length and its shear rate dependence.

10aelastic constants10ainterface roughness10aliquid films10amolecular dynamics method10aslip10asurface roughness10athin films1 aPriezjev, N., V uhttps://icer.msu.edu/effect-surface-roughness-rate-dependent-slip-simple-fluids01855nas a2200157 4500008004100000245017000041210006900211260001200280300001600292490000800308520120900316100001401525700001601539700001901555856012301574 2007 eng d00aExtension of the Renormalized Coupled-Cluster Methods Exploiting Left Eigenstates of the Similarity-Transformed Hamiltonian to Open- Shell Systems: A Benchmark Study0 aExtension of the Renormalized CoupledCluster Methods Exploiting c11/2007 a11359-113820 v1113 aThe recently formulated completely renormalized coupled-cluster method with singles, doubles, and noniterative triples, exploiting the biorthogonal form of the method of moments of coupled-cluster equations (Piecuch, P.; Włoch, M. J. Chem. Phys. 2005, 123, 224105; Piecuch, P.; Włoch, M.; Gour, J. R.; Kinal, A. Chem. Phys. Lett. 2006, 418, 467), termed CR-CC(2,3), is extended to open-shell systems. Test calculations for bond breaking in the OH radical and the ion and singlet−triplet gaps in the CH2, HHeH, and (HFH)- biradical systems indicate that the CR-CC(2,3) approach employing the restricted open-shell Hartree−Fock (ROHF) reference is significantly more accurate than the widely used CCSD(T) method and other noniterative triples coupled-cluster approximations without making the calculations substantially more expensive. A few molecular examples, including the activation energies of the C2H4 + H → C2H5 forward and reverse reactions and the triplet states of the CH2 and H2Si2O2 biradicals, are used to show that the dependence of the ROHF-based CR-CC(2,3) energies on the method of canonicalization of the ROHF orbitals is, for all practical purposes, negligible.

1 aWloch, M.1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/extension-renormalized-coupled-cluster-methods-exploiting-left-eigenstates-similarity-transformed01888nas a2200133 4500008004100000245008100041210006900122260003200191520138900223100001701612700001101629700001701640856009701657 2007 eng d00aFiltered Mass Density Function for Numerical Simulations of Spray Combustion0 aFiltered Mass Density Function for Numerical Simulations of Spra aReno, NevadabAIAAc01/20083 aThis paper briefly describes our recent efforts on the modeling and numerical simulations of two-phase turbulent reacting flows in realistic combustion systems with a new large-eddy simulation (LES) model. The model is constructed based on the two-phase extension of scalar filtered mass density function (FMDF) and a Lagrangian-Eulerian- Lagrangian mathematical/numerical methodology. In this methodology, the “resolved” fluid velocity field is obtained by solving the filtered form of the compressible Navier-Stokes equations with a high-order finite difference scheme. The liquid (droplet) phase and scalar (temperature and species mass fractions) fields are both obtained by stochastic Lagrangian models. There are two-way interactions between the phases and all the Eulerian and Lagrangian fields. The LES/FMDF is used for systematic analysis of turbulent combustion in the spray-controlled dump combustor and double-swirl spray burner for various flow and spray parameters. The effects of fuel type, spray angle, mass loading ratio, droplet size distribution, fuel/air composition, wall, and inflow/outflow conditions on the combustion are investigated. It has been found that the main features of the turbulence and combustion are modified by changing the inflow/outflow conditions. The LES/FMDF results also confirm the significance of the spray parameters.

1 aYaldizli, M.1 aLi, Z.1 aJaberi, F.A. uhttps://icer.msu.edu/filtered-mass-density-function-numerical-simulations-spray-combustion-001318nas a2200133 4500008004100000245006100041210006000102260003200162520086300194100001601057700001701073700001901090856007501109 2007 eng d00aLES/FMDF of Turbulent Combustion in Complex Flow Systems0 aLESFMDF of Turbulent Combustion in Complex Flow Systems aReno, NevadabAIAAc01/20073 aA high-order Lagrangian/Eulerian method based on the the filtered mass density func- tion (FMDF) for subgrid-scale (SGS) combustion closure was developed to perform large eddy simulation (LES) of turbulent reacting flows in complex geometrical configurations in multi-block structured grids. In particular, an efficient algorithm has been developed to search and locate particles in multi-block, hexahedral-structured grid system. Also, the consistency, convergence, and accuracy of the FMDF and the Monte Carlo solution of its equivalent stochastic differential equations were assessed. The consistency between Eulerian and Lagrangian fields were established for a reacting flow in a dump combustor. The results obtained for a reacting flow in an axisymmetric, premixed dump-combustor, were found to compare favorably with measured experimental data.

1 aAfshari, A.1 aJaberi, F.A.1 aShih, T., I-P. uhttps://icer.msu.edu/lesfmdf-turbulent-combustion-complex-flow-systems01291nas a2200169 4500008004100000020002600041245012100067210006900188260004600257490000800303520060900311100001900920700002400939700001500963700001700978856012600995 2007 eng d aISBN13: 978084123843500aNew Alternatives for Accurate Electronic Structure Calculations of Potential Energy Surfaces Involving Bond Breaking0 aNew Alternatives for Accurate Electronic Structure Calculations aWashington, DCbAmerican Chemical Sociegy0 v9583 aThe method of moments of coupled-cluster equations (MMCC) is extended to potential energy surfaces involving multiple bond breaking by developing the quasi-variational (QV) and quadratic (Q) variants of the MMCC theory. The QVMMCC and QMMCC methods are related to the extended CC (ECC) theory, in which products involving cluster operators and their deexcitation counterparts mimic the effects of higher-order clusters. The test calculations for N2 show that the QMMCC and ECC methods can provide spectacular improvements in the description of multiple bond breaking by the standard CC approaches.

1 aPiecuch, Piotr1 aPimienta, I., S. O.1 aFan, P.-D.1 aKowalski, K. uhttps://icer.msu.edu/new-alternatives-accurate-electronic-structure-calculations-potential-energy-surfaces-involving-bond01300nas a2200133 4500008004100000245007900041210006900120260005000189520079100239100001701030700001101047700001701058856009101075 2007 eng d00aA New Model for Large Eddy Simulations of Multi-Phase Turbulent Combustion0 aNew Model for Large Eddy Simulations of MultiPhase Turbulent Com aCincinnati, OhiobAIAA/ASME/SAI/ASEEc07/20073 aNumerical simulations of a spray-controlled lean premixed dump combustor are con- ducted via a two-phase large eddy simulation (LES) methodology. In this methodology, the velocity field is obtained by a high-order finite difference method. The subgrid gas- liquid combustion closure is based on the two-phase filtered mass density function (FMDF) method and the spray is modeled with a Lagrangian scheme. The effects of spray, fuel/air composition, and inflow/outflow conditions on the combustion are investigated. It has been found that the main features of the turbulence and combustion inside the dump combustor are very differently modified by the spray for different spray parameters. The LES/FMDF results also indicate the significance of the inflow and outflow conditions.

1 aYaldizli, M.1 aLi, Z.1 aJaberi, J.A. uhttps://icer.msu.edu/new-model-large-eddy-simulations-multi-phase-turbulent-combustion01659nas a2200145 4500008004100000020001800041245007700059210006900136260003700205520113400242100001101376700001701387700001701404856009201421 2007 eng d a0-7918-4803-500aNumerical Simulations of Two-Phase Turbulent Combustion in Spray Burners0 aNumerical Simulations of TwoPhase Turbulent Combustion in Spray aLas Vegas, NevadabASMEc09/20073 aThe complex interactions among turbulence, combustion and spray in liquid-fuel burners are modeled and simulated via a new two-phase Lagrangian-Eulerian-Lagrangian large eddy simulation (LES) methodology. In this methodology, the spray is modeled with a Lagrangian mathematical/computational method which allows two-way mass, momentum and energy coupling between phases. The subgrid gas-liquid combustion is based on the two-phase filtered mass density function (FMDF) that has several advantages over “conventional” two-phase combustion models. The LES/FMDF is employed in conjunction with non-equilibrium reaction and droplet models. Simulations of turbulent combustion in a spray-controlled double-swirl burner are conducted via LES/FMDF. The generated results are used for better understanding of spray combustion in realistic turbulent flow configurations. The effects of spray angle, mass loading ratio, fuel type, droplet size distribution, wall and inflow/outflow conditions on the flow and combustion are investigated. The LES/FMDF predictions are shown to be consistent with the experimental results.

1 aLi, Z.1 aYaldizli, M.1 aJaberi, F.A. uhttps://icer.msu.edu/numerical-simulations-two-phase-turbulent-combustion-spray-burners01199nas a2200133 4500008004100000245006200041210006100103260001200164300001000176490000700186520077300193100002000966856007900986 2007 eng d00aRate-dependent slip boundary conditions for simple fluids0 aRatedependent slip boundary conditions for simple fluids c05/2007 a516050 v753 aThe dynamic behavior of the slip length in a fluid flow confined between atomically smooth surfaces is investigated using molecular dynamics simulations. At weak wall-fluid interactions, the slip length increases nonlinearly with the shear rate provided that the liquid/solid interface forms incommensurable structures. A gradual transition to the linear rate dependence is observed upon increasing the wall-fluid interaction. We found that the slip length can be well described by a function of a single variable that in turn depends on the in-plane structure factor, contact density, and temperature of the first fluid layer near the solid wall. Extensive simulations show that this formula is valid in a wide range of shear rates and wall-fluid interactions.

1 aPriezjev, N., V uhttps://icer.msu.edu/rate-dependent-slip-boundary-conditions-simple-fluids03587nas a2200145 4500008004100000245011300041210006900154300001100223490000700234520302500241100001903266700001403285700002103299856012103320 2007 eng d00aRenormalized Coupled-Cluster Methods: Theoretical Foundations and Application to Potential Function of Water0 aRenormalized CoupledCluster Methods Theoretical Foundations and a63-1210 v163 aConventional single-reference methods fail when bond breaking and other situations characterized by larger non-dynamical correlation effects are examined. In consequence, the adequate treatment of molecular potential energy surfaces involving signiﬁcant bond rearrangements has been the domain of expert multi-reference methods. The question arises if one can develop practical single-reference procedures that could be applied to at least some of the most frequent multi-reference situations, such as single and double bond dissociations. This question is addressed in the present paper by examining the performance of the conventional and renormalized coupled-cluster (CC) methods in calculations of the potential enery surface of the water molecule. A comparison with the results of the highly accurate internally contracted multi-reference conﬁguration interaction calculations including the quasi-degenerate Davidson correction (MRCI(Q)) and the spectroscopically accurate potential energy surface of water resulting from the use of the energy switching (ES) approach indicates that the relatively inexpensive completely renormalized (CR) CC methods with singles (S), doubles (D), and a non-iterative treatment of triples (T) or triples and quadruples (TQ), such as CR-CCSD(T), CR-CCSD(TQ), and the recently developed rigorously size extensive extension of the CR-CCSD(T), termed CR-CC(2,3), provide considerable improvements in the results of conventional CCSD(T) and CCSD(TQ) calculations at larger internuclear separations. It is shown that the CR-CC(2,3) results a posteriori corrected for the effect of quadruply excited clusters (the CR-CC(2,3)+Q approach) can compete with the highly accurate MRCI(Q) data. The excellent agreement between the CR-CC(2,3)+Q and MRCI(Q) results suggests ways of improving the global potential energy surface of water resulting from the use of the ES approach in the regions of intermediate bond stretches and intermediate and higher energies connecting the region of the global minimum with the asymptotic regions. In addition to the examination of the performance of the CR-CCSD(T), CR-CCSD(TQ), CR-CC(2,3), and CR-CC(2,3)+Q approaches, we provide a thorough review of the method of moments of CC equations (MMCC), as applied to ground electronic states, including the most recent biorthogonal formulation of MMCC theory employing the left eigenstates of the similarity-transformed Hamiltonian, and other mathematical and physical concepts that lie behind all renormalized CC approximations. In particular, we discuss the similarities and differences between the older CR-CCSD(T) and CR-CCSD(TQ) approximations and the recently formulated size extensive renormalized CC methods, such as CR-CC(2,3), and open questions that emerge in the process of designing higher-order schemes based on the biorthogonalMMCC formalism, such as CR-CC(2,4), which describe the combined effect of triples (already present in CR-CC(2,3) calculations) and quadruples in a proper manner.

1 aPiecuch, Piotr1 aWloch, M.1 aVerandas, A.J.C. uhttps://icer.msu.edu/renormalized-coupled-cluster-methods-theoretical-foundations-and-application-potential-function01279nas a2200457 4500008004100000245014900041210006900190260001200259490000700271100001700278700001500295700001600310700001500326700001700341700001600358700001400374700001400388700001800402700001600420700001300436700001600449700001900465700001500484700001700499700001400516700001400530700001400544700001500558700001600573700001700589700001700606700001700623700001500640700001700655700001400672700001400686700001300700700001800713700001900731856007100750 2007 eng d00aShape and Structure of N = Z 64Ge: Electromagnetic Transition Rates from the Application ￼of the Recoil Distance Method to a Knockout Reaction0 aShape and Structure of N Z 64Ge Electromagnetic Transition Rates c07/20070 v991 aStarosta, K.1 aDewald, A.1 aDunomes, A.1 aAdrich, P.1 aAmthor, A.M.1 aBaumann, T.1 aBazin, D.1 aBowen, M.1 aBrown, B., A.1 aChester, A.1 aGade, A.1 aGalaviz, D.1 aGlasmacher, T.1 aGinter, T.1 aHausmann, M.1 aHoroi, M.1 aJolie, J.1 aMelon, B.1 aMiller, D.1 aMoeller, V.1 aNorris, R.P.1 aPissulla, T.1 aPortillo, M.1 aRother, W.1 aShimbara, Y.1 aStolz, A.1 aVaman, C.1 aVoss, P.1 aWeisshaar, D.1 aZelevinsky, V. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.04250300468nas a2200133 4500008004100000245006400041210006400105490000700169100001800176700001900194700001900213700002800232856007400260 2007 eng d00aUncertainty and the changing hydroclimatology of the Amazon0 aUncertainty and the changing hydroclimatology of the Amazon0 v341 aMoore, Nathan1 aWalker, Robert1 aArima, Eugenio1 ada Silva, Renato, Ramos uhttps://icer.msu.edu/uncertainty-and-changing-hydroclimatology-amazon01096nas a2200385 4500008004100000245011100041210006900152260001200221490000700233100001400240700001700254700001400271700001800285700001800303700001900321700001600340700001500356700001600371700001300387700001600400700001900416700002600435700001400461700001500475700001600490700002000506700001700526700001700543700001400560700001600574700001400590700001900604700001600623856007100639 2007 eng d00aZ = 0 Shell Gap near 100Sn from Intermediate-Energy Coulomb Excitations ￼in Even-Mass 106-112Sn Isotopes0 aZ 0 Shell Gap near 100Sn from IntermediateEnergy Coulomb Excitat c10/20070 v991 aVaman, C.1 aAndreoiu, C.1 aBazin, D.1 aBeccerril, A.1 aBrown, B., A.1 aCampbell, C.M.1 aChester, A.1 aCook, J.M.1 aDinca, D.C.1 aGade, A.1 aGalaviz, D.1 aGlasmacher, T.1 aHjorth-Jensen}, M., {1 aHoroi, M.1 aMiller, D.1 aMoeller, V.1 aMueller, W., F.1 aSchiller, A.1 aStarosta, K.1 aStolz, A.1 aTerry, J.R.1 aVolya, A.1 aZelevinsky, V.1 aZwahlen, H. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.16250101273nas a2200205 4500008004100000245008900041210006900130260001200199300001200211490000700223520060600230100001900836700001400855700001700869700001600886700002600902700001900928700001700947856010300964 2006 eng d00aAb Initio Coupled-Cluster Calculations for Nuclei Using Methods of Quantum Chemistry0 aAb Initio CoupledCluster Calculations for Nuclei Using Methods o c09/2005 a485-4880 v253 aWe report preliminary large scale ab initio calculations of ground and excited states of 16O using quantum chemistry inspired coupled cluster methods and realistic two-body interactions. By using the renormalized Hamiltonians obtained with a no-core G-matrix approach, we obtain the virtually converged results at the level of two-body interactions. Due to the polynomial scaling with the system size that characterizes coupled cluster methods, we can probe large model spaces with up to seven major oscillator shells, for which standard non-truncated shell-model calculations are not possible.

1 aPiecuch, Piotr1 aWloch, M.1 aDean, D., J.1 aGour, J., R1 aHjorth-Jensen}, M., {1 aPapenbrock, T.1 aKowalski, K. uhttps://icer.msu.edu/ab-initio-coupled-cluster-calculations-nuclei-using-methods-quantum-chemistry01862nas a2200181 4500008004100000245005700041210005600098260001200154300001400166490000800180520132100188100001501509700001901524700002001543700001801563700002401581856007501605 2006 eng d00aAb initio determination of solid-state nanostructure0 aAb initio determination of solidstate nanostructure c07/2005 a655–6580 v4403 aAdvances in materials science and molecular biology followed rapidly from the ability to characterize atomic structure using single crystals1, 2, 3, 4. Structure determination is more difficult if single crystals are not available5. Many complex inorganic materials that are of interest in nanotechnology have no periodic long-range order and so their structures cannot be solved using crystallographic methods6. Here we demonstrate that ab initio structure solution of these nanostructured materials is feasible using diffraction data in combination with distance geometry methods. Precise, sub-ångström resolution distance data are experimentally available from the atomic pair distribution function (PDF)6, 7. Current PDF analysis consists of structure refinement from reasonable initial structure guesses6, 7 and it is not clear, a priori, that sufficient information exists in the PDF to obtain a unique structural solution. Here we present and validate two algorithms for structure reconstruction from precise unassigned interatomic distances for a range of clusters. We then apply the algorithms to find a unique, ab initio, structural solution for C60 from PDF data alone. This opens the door to sub-ångström resolution structure solution of nanomaterials, even when crystallographic methods fail.

1 aJuhás, P.1 aCherba, D., M.1 aDuxbury, P., M.1 aPunch, W., F.1 aBillinge, S., J. L. uhttps://icer.msu.edu/ab-initio-determination-solid-state-nanostructure01812nas a2200169 4500008004100000245007100041210006900112260001200181300001100193490000700204520127500211100001901486700002001505700001701525700002301542856007701565 2006 eng d00aAb initio studies of the electronic structure of defects in {PbTe}0 aAb initio studies of the electronic structure of defects in PbTe c10/2006 a1552050 v743 aUnderstanding the detailed electronic structure of deep defect states in narrow band-gap semiconductors has been a challenging problem. Recently, self-consistent ab initio calculations within density functional theory using supercell models have been successful in tackling this problem. In this paper, we carry out such calculations in {PbTe,} a well-known narrow band-gap semiconductor, for a large class of defects: cationic and anionic substitutional impurities of different valence, and cationic and anionic vacancies. For the cationic defects, we study the chemical trends in the position of defect levels by looking at series of compounds {RPb2n−1Te2n,} where R is vacancy or monovalent, divalent, or trivalent atom. Similarly, for anionic defects, we study compounds {MPb2nTe2n−1,} where M is vacancy, S, Se or I. We find that the density of states near the top of the valence band and the bottom of the conduction band get significantly modified for most of these defects. This suggests that the transport properties of {PbTe} in the presence of impurities may not always be interpreted by simple carrier doping (from bound impurity states in the gap) concepts, confirming such ideas developed from qualitative and semiquantitative arguments.

1 aAhmad, Salameh1 aMahanti, S., D.1 aHoang, Khang1 aKanatzidis, M., G. uhttps://icer.msu.edu/ab-initio-studies-electronic-structure-defects-pbte01498nas a2200181 4500008004100000245011900041210006900160260001200229300001200241490000800253520084400261100001901105700001501124700001701139700001501156700002401171856012101195 2006 eng d00aAutomated derivation and parallel computer implementation of renormalized and active-space coupled-cluster methods0 aAutomated derivation and parallel computer implementation of ren c08/2005 a79–970 v1063 aOur recent efforts that have led to an automated derivation and computer implementation of the renormalized and active-space coupled-cluster {(CC)} methods with Tensor Contraction Engine {(TCE)} are summarized. The {TCE-generated} renormalized and active-space {CC} computer codes are parallel and applicable to closed- and open-shell references, enabling accurate calculations of potential energy surfaces along bond-breaking coordinates and excited states displaying a significant multi-reference character. The effectiveness of the new codes in describing electronic quasi-degeneracies is illustrated by the renormalized {CC} calculations of the potential energy curve of {HCl} and the active-space {CC} calculations for the low-lying excited states of the Be3 system. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

1 aPiecuch, Piotr1 aHirata, So1 aKowalski, K.1 aFan, P.-D.1 aWindus, Theresa, L. uhttps://icer.msu.edu/automated-derivation-and-parallel-computer-implementation-renormalized-and-active-space-coupled01532nas a2200145 4500008004100000245015700041210006900198260001200267300001400279490000700293520091200300100003001212700001801242856012601260 2006 eng d00aBalancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations0 aBalancing an accurate representation of the molecular surface in c04/2006 a719–7290 v273 aDifferent integrator time steps in {NVT} and {NVE} simulations of protein and nucleic acid systems are tested with the {GBMV} {(Generalized} Born using Molecular Volume) and {GBSW} {(Generalized} Born with simple {SWitching)} methods. The simulation stability and energy conservation is investigated in relation to the agreement with the Poisson theory. It is found that very close agreement between generalized Born methods and the Poisson theory based on the commonly used sharp molecular surface definition results in energy drift and simulation artifacts in molecular dynamics simulation protocols with standard 2-fs time steps. New parameters are proposed for the {GBMV} method, which maintains very good agreement with the Poisson theory while providing energy conservation and stable simulations at time steps of 1 to 1.5 fs. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 719-729, 2006

1 aChocholouscaronová, Jana1 aFeig, Michael uhttps://icer.msu.edu/balancing-accurate-representation-molecular-surface-generalized-born-formalisms-integrator-stability00864nas a2200193 4500008004100000245003800041210003800079300001400117490000700131520031100138653006000449100001900509700001700528700001600545700001400561700002600575700001400601856005500615 2006 eng d00aCoupled Cluster Theory for Nuclei0 aCoupled Cluster Theory for Nuclei a5338-53450 v203 aThis presentation focuses on some of the recent developments in low-energy nuclear structure theory, with emphasis on applications of coupled-cluster theory. We report on results for ground and excited states in 4He and 16O, and about extensions of coupled-cluster theory to treat three-body forces.

10aNuclear structure; light nuclei; coupled-cluster theory1 aPapenbrock, T.1 aDean, D., J.1 aGour, J., R1 aHagen, G.1 aHjorth-Jensen}, M., {1 aWloch, M. uhttps://icer.msu.edu/coupled-cluster-theory-nuclei01833nas a2200181 4500008004100000245006500041210006400106260001100170300001300181490000700194520127600201100001901477700001601496700002601512700001401538700001701552856008201569 2006 eng d00aCoupled-Cluster Calculations for Valence Systems around 16 O0 aCoupledCluster Calculations for Valence Systems around 16 O c8/2006 a18 pages0 v743 aWe study the ground and low-lying excited states of 15O, 17O, 15N, and 17F using modern two-body nucleon-nucleon interactions and the suitably designed variants of the ab initio equation-of-motion coupled-cluster theory aimed at an accurate description of systems with valence particles and holes. A number of properties of 15O, 17O, 15N, and 17F, including ways the energies of ground and excited states of valence systems around 16O change as functions of the number of nucleons, are correctly reproduced by the equation-of-motion coupled-cluster calculations performed in up to eight major-oscillator shells. Certain disagreements with experiment are in part because of the degrees of freedom such as three-body interactions not accounted for in our effective two-body Hamiltonians. In particular, the calculated binding energies of 15O/15N and 17O/17F enable us to rationalize the discrepancy between the experimental and recently published [Phys. Rev. Lett. 94, 212501 (2005)] equation-of-motion coupled-cluster excitation energies for the Jπ=3- state of 16O. Our calculations demonstrate the feasibility of the equation-of-motion coupled-cluster methods to deal with valence systems around closed-shell nuclei and to provide results for systems beyond A=16.

1 aPiecuch, Piotr1 aGour, J., R1 aHjorth-Jensen}, M., {1 aWloch, M.1 aDean, D., J. uhttps://icer.msu.edu/coupled-cluster-calculations-valence-systems-around-16-o01855nas a2200181 4500008004100000245006400041210006300105260001200168300001100180490000700191520130200198100001601500700001901516700002601535700001401561700001701575856008101592 2006 eng d00aCoupled-cluster calculations for valence systems around O160 aCoupledcluster calculations for valence systems around O16 c08/2006 a0243100 v743 aWe study the ground and low-lying excited states of {15O,} {17O,} {15N,} and {17F} using modern two-body nucleon-nucleon interactions and the suitably designed variants of the ab initio equation-of-motion coupled-cluster theory aimed at an accurate description of systems with valence particles and holes. A number of properties of {15O,} {17O,} {15N,} and {17F,} including ways the energies of ground and excited states of valence systems around {16O} change as functions of the number of nucleons, are correctly reproduced by the equation-of-motion coupled-cluster calculations performed in up to eight major-oscillator shells. Certain disagreements with experiment are in part because of the degrees of freedom such as three-body interactions not accounted for in our effective two-body Hamiltonians. In particular, the calculated binding energies of {15O/15N} and {17O/17F} enable us to rationalize the discrepancy between the experimental and recently published {[Phys.} Rev. Lett. 94, 212501 (2005)] equation-of-motion coupled-cluster excitation energies for the Jπ=3- state of {16O.} Our calculations demonstrate the feasibility of the equation-of-motion coupled-cluster methods to deal with valence systems around closed-shell nuclei and to provide results for systems beyond A=16.

1 aGour, J., R1 aPiecuch, Piotr1 aHjorth-Jensen}, M., {1 aWloch, M.1 aDean, D., J. uhttps://icer.msu.edu/coupled-cluster-calculations-valence-systems-around-o1600328nam a2200109 4500008004100000020001800041245003800059210003700097260002000134490000700154856005700161 2006 eng d a1-59454-989-300aCoupled-Cluster Theory for Nuclei0 aCoupledCluster Theory for Nuclei bNova Publishers0 v20 uhttps://icer.msu.edu/coupled-cluster-theory-nuclei-001464nas a2200157 4500008004100000245008100041210006900122260001200191300001400203490000700217520087700224653008001101100001601181700001701197856009201214 2006 eng d00aDirect Numerical Simulations of a Planar Jet Laden with Evaporating Droplets0 aDirect Numerical Simulations of a Planar Jet Laden with Evaporat c07/2006 a2113-21230 v493 aA direct numerical simulation (DNS) study is conducted on the various aspects of phase interactions in a planar turbulent gas-jet laden with non-evaporative and evaporative liquid droplets. A compressible computational model utilizing a finite difference scheme for the carrier gas and a Lagrangian solver for the droplet phase is used to conduct the numerical experiments. The effects of droplet time constant, mass-loading and mass/momentum/energy coupling between phases on droplet and gas-jet fields are investigated. Significant changes in velocity, temperature, density and turbulence production on account of the coupling between the liquid and gas phases are observed in non-isothermal jets with evaporating droplets. Most of these changes are attributed to the density stratification in the carrier gas that is caused by droplet momentum and heat transfer.

10adroplet-laden turbulent jet; two-phase planar jet; droplet evaporation; DNS1 aAlmeida, T.1 aJaberi, F.A. uhttps://icer.msu.edu/direct-numerical-simulations-planar-jet-laden-evaporating-droplets01911nas a2200193 4500008004100000245014700041210006900188260001200257300001300269490000800282520117900290653003301469653001801502653002201520653002201542100001601564700001901580856011801599 2006 eng d00aEfficient Formulation and Computer Implementation of the Active-Space Electron-Attached and Ionized Equation-of-Motion Coupled-Cluster Methods0 aEfficient Formulation and Computer Implementation of the ActiveS c12/2006 a17 pages0 v1253 aThe efficient, general-purpose implementations of the active-space electron-attached (EA) and ionized (IP) equation-of-motion coupled-cluster (EOMCC) methods including up to 3p-2h and 3h-2p excitations, called EA-EOMCCSDt and IP-EOMCCSDt, respectively, are discussed. The details of the algorithm that enables one to achieve a high degree of code vectorization for the active-space methods and the factorized forms of the EA- and IP-EOMCCSDt equations that maximize the benefits of using active orbitals in the process of selecting the dominant 3p-2h and 3h-2p excitations are presented. The results of benchmark calculations for the low-lying doublet and quartet states of the CH and SH radicals reveal that the active-space EA-EOMCCSDt and IP-EOMCCSDt methods are capable of producing results for the electronic excitations in open-shell systems that match the high accuracy of EA- and IP-EOMCC calculations with a full treatment of 3p-2h and 3h-2p excitations, even when the excited states of interest display a manifestly multideterminantal nature, with the costs that can be on the same order of those characterizing the basic EOMCC singles and doubles approach.

10acoupled cluster calculations10afree radicals10aorganic compounds10asulphur compounds1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/efficient-formulation-and-computer-implementation-active-space-electron-attached-and-ionized02232nas a2200253 4500008004100000245008800041210006900129260001100198300001400209490000800223520146400231100001901695700001601714700001401730700001701744700001501761700001801776700001401794700001701808700001401825700001801839700001501857856010601872 2006 eng d00aExperimental and Theoretical UV Characterizations of Acetyloacetone and its Isomers0 aExperimental and Theoretical UV Characterizations of Acetyloacet c2/2006 a3920-39260 v1103 aCryogenic matrix isolation experiments have allowed the measurement of the UV absorption spectra of the high-energy non-chelated isomers of acetylacetone, these isomers being produced by UV irradiation of the stable chelated form. Their identification has been done by coupling selective UV-induced isomerization, infrared spectroscopy, and harmonic vibrational frequency calculations using density functional theory. The relative energies of the chelated and non-chelated forms of acetylacetone in the S0 state have been obtained using density functional theory and coupled-cluster methods. For each isomer of acetylacetone, we have calculated the UV transition energies and dipole oscillator strengths using the excited-state coupled-cluster methods, including EOMCCSD (equation-of-motion coupled-cluster method with singles and doubles) and CR-EOMCCSD(T) (the completely renormalized EOMCC approach with singles, doubles, and non-iterative triples). For dipole-allowed transition energies, there is a very good agreement between experiment and theory. In particular, the CR-EOMCCSD(T) approach explains the blue shift in the electronic spectrum due to the formation of the non-chelated species after the UV irradiation of the chelated form of acetylacetone. Both experiment and CR-EOMCCSD(T) theory identify two among the seven non-chelated forms to be characterized by red-shifted UV transitions relative to the remaining five non-chelated isomers.

1 aPiecuch, Piotr1 aCoussan, S.1 aFerro, Y.1 aTrivella, A.1 aRoubin, P.1 aWieczorek, R.1 aManca, C.1 aKowalski, K.1 aWloch, M.1 aKucharski, S.1 aMusial, M. uhttps://icer.msu.edu/experimental-and-theoretical-uv-characterizations-acetyloacetone-and-its-isomers01765nas a2200169 4500008004100000245014000041210006900181260001100250300001400261490000800275520098500283653015801268100001901426700001601445700001401461856012001475 2006 eng d00aExtension of the Active-Space Equation-of- Motion Coupled-Cluster Methods to Radical Systems: The EA-EOMCCSDt and IPEOMCCSDt Approaches0 aExtension of the ActiveSpace Equationof Motion CoupledCluster Me c7/2006 a2854-28740 v1063 aThe development of the active-space variants of the electron-attached (EA) and ionized (IP) equation-of-motion coupled-cluster (EOMCC) methods, in which higher-than-doubly excited components of the cluster operator T and higher than 2p-1h or 2h-1p components of the electron attaching and ionizing operators R are defined through the use of active orbitals, is discussed. As shown by preliminary test calculations of adiabatic excitation energies and potential energy curves for the low-lying states of the CH and OH radicals, the basic active-space EA-EOMCC and IP-EOMCC methods, referred to as the EA-EOMCCSDt and IP-EOMCCSDt approaches, are capable of accuratelydescribing the ground and excited states of open-shell systems, even at the moderately stretched nuclear geometries and even for states with a strong multi-determinantal or doubly excited character, at the low costs that are on the order of those characterizing the standard EOMCC singles and doubles method.

10aoupled-cluster theory;equation-of-a motion coupled-cluster method;active-space coupled-cluster approaches;electronic-attached and ionized states;radicals1 aPiecuch, Piotr1 aGour, J., R1 aWloch, M. uhttps://icer.msu.edu/extension-active-space-equation-motion-coupled-cluster-methods-radical-systems-ea-eomccsdt-and00839nas a2200145 4500008004100000245009700041210006900138260001500207300001200222490000800234520030100242100002100543700001900564856011000583 2006 eng d00aExtrapolating Potential Energy Surfaces by Scaling Electron Correlation at a Single Geometry0 aExtrapolating Potential Energy Surfaces by Scaling Electron Corr c10/30/2006 a448-4530 v4303 aIt is shown that the molecular potential energy surface corresponding to a high level of ab initio theory can be accurately predicted by performing calculations with smaller basis sets and then scaling the electron correlation at a single point calculated with the larger target basis set.

1 aVarandas, A.J.C.1 aPiecuch, Piotr uhttps://icer.msu.edu/extrapolating-potential-energy-surfaces-scaling-electron-correlation-single-geometry01233nas a2200145 4500008004100000245007200041210006800113260001200181300001600193490000700209520074700216100002000963700002300983856008101006 2006 eng d00aThe ground state of chargeless fermions with finite magnetic moment0 aground state of chargeless fermions with finite magnetic moment c02/2006 a1239–12490 v393 aWe consider the ground state of a system of chargeless fermions, such as neutrinos, of mass m and magnetic moment m interacting through long-range magnetic dipole interaction, within the framework of a {Hartree-Fock} variational approach. At high densities the uniform paramagnetic state becomes unstable towards a ferromagnetic state with quadrupolar deformation of the Fermi surface. The exchange energy which is attractive dominates the repulsive kinetic energy. If we let the density be a variable, then above a certain density the system will collapse to an infinite density state unless another short-range interaction stops the collapse. In the case of large deformations, the possibility of a purely dipolar deformation exists.

1 aMahanti, S., D.1 aJha, Sudhanshu, S. uhttps://icer.msu.edu/ground-state-chargeless-fermions-finite-magnetic-moment01358nas a2200301 4500008004100000245003200041210003100073260001200104300001100116490000700127520059800134100002000732700002000752700001800772700002200790700001900812700001400831700002400845700001900869700002000888700001400908700001500922700001400937700001800951700001900969700001800988856005001006 2006 eng d00aHalf-life and spin of 60Mng0 aHalflife and spin of 60Mng c04/2006 a0443220 v733 aA value of 0.28±0.02 s has been deduced for the half-life of the ground state of {60Mn,} in sharp contrast to the previously adopted value of 51±6 s. Access to the low-spin {60Mn} ground state was accomplished via β decay of the 0+ {60Cr} parent nuclide. New low-energy states in {60Mn} have been identified from β-delayed γ-ray spectroscopy. The new, shorter half-life of {60Mng} is not suggestive of isospin-forbidden β decay, and new spin and parity assignments of 1+ and 4+ have been adopted for the ground and isomeric β-decaying states, respectively, of {60Mn.}

1 aLiddick, S., N.1 aMantica, P., F.1 aBrown, B., A.1 aCarpenter, M., P.1 aDavies, A., D.1 aHoroi, M.1 aJanssens, R., V. F.1 aMorton, A., C.1 aMueller, W., F.1 aPavan, J.1 aSchatz, H.1 aStolz, A.1 aTabor, S., L.1 aTomlin, B., E.1 aWiedeking, M. uhttps://icer.msu.edu/half-life-and-spin-60mng00743nas a2200277 4500008004100000245003200041210003100073260001200104490000700116100002000123700002000143700001800163700002200181700001900203700001400222700002400236700001900260700002000279700001400299700001500313700001400328700001800342700001900360700001800379856006800397 2006 eng d00aHalf-life and spin of 60Mng0 aHalflife and spin of 60Mng c04/20060 v731 aLiddick, S., N.1 aMantica, P., F.1 aBrown, B., A.1 aCarpenter, M., P.1 aDavies, A., D.1 aHoroi, M.1 aJanssens, R., V. F.1 aMorton, A., C.1 aMueller, W., F.1 aPavan, J.1 aSchatz, H.1 aStolz, A.1 aTabor, S., L.1 aTomlin, B., E.1 aWiedeking, M. uhttp://journals.aps.org/prc/abstract/10.1103/PhysRevC.73.04432202648nas a2200157 4500008004100000245016100041210006900202260001500271300000900286490000800295520182400303653020902127100001502336700001602351856012302367 2006 eng d00aIntriguing Accuracies of the Exponential Wave Function Expansions Exploiting Finite Two-Body Correlation Operators in Calculations for Many-Electron Systems0 aIntriguing Accuracies of the Exponential Wave Function Expansion c08/31/2006 a3-160 v7683 aFollowing the ideas laid down by Nooijen and Nakatsuji, several authors have considered an intriguing possibility of representing the exact many-electron wave functions by the exponential cluster expansions involving two-body correlation operators. In particular, inspired by the symmetric form of the Horn–Weinstein exact energy formula, and exploiting the variational principle and numerical analysis, we have demonstrated that one can obtain nearly exact ground-state wave functions for a few many-electron systems using the exponential cluster expansion involving a finite two-body operator acting on the Hartree–Fock determinant [P. Piecuch et al., Phys. Rev. Lett. 90 (2003) 113001]. After summarizing these earlier findings and making some additional comments on the nature of the exponential cluster expansions involving two-body correlation operators, we examine the following issues: (i) the improvements in the accuracy and convergence toward the full configuration interaction (CI) limit offered by cluster operators containing two-body as well as one-body components, (ii) the improvements in the accuracy resulting from the use of multi-determinantal reference states, and (iii) the potential accuracy of the exponential wave function expansions involving finite one- and two-body cluster operators in excited-state calculations. All calculations are performed for an eight electron model system, which is simple enough to allow for the exact, full CI, and other electronic structure calculations, which has fewer independent parameters in the Hamiltonian than the dimension of the corresponding full CI problem, and which enables one to examine ground and excited states with a varying degree of configurational quasi-degeneracy by simple changes in the corresponding nuclear geometry.

10axact many-electron wave functions; Generalized coupled-cluster methods; Two-body correlation operators; Nooijen's conjecture; Variational calculations; Multi-determinantal reference states; Excited states1 aFan, P.-D.1 aPiecuch, P. uhttps://icer.msu.edu/intriguing-accuracies-exponential-wave-function-expansions-exploiting-finite-two-body-correlation01624nas a2200145 4500008004100000245014800041210006900189260001100258300001200269490000800281520103500289100001901324700001401343856012101357 2006 eng d00aIs the Mechanism of the [2+2] Cycloaddition of Cyclopentyne to Ethylene Concerted or Biradical? A Completely Renormalized Coupled Cluster Study0 aMechanism of the 22 Cycloaddition of Cyclopentyne to Ethylene Co c6/2005 a367-3780 v1103 aThe mechanism of the [2+2] cycloaddition reaction of cyclopentyne to ethylene has been studied using the completely renormalized coupled cluster method with singles, doubles, and noniterative triples (CR−CCSD(T)). In agreement with the experimentally observed stereochemistry, the CR−CCSD(T) method favors the concerted pathway involving a [2+1] transition state, whereas the popular CCSD(T) method, which is often regarded as the “gold standard” of electronic structure theory, and low-order multireference methods support the less probable biradical mechanism. In addition, the CCSD(T) approach produces an erroneous description of some transition states and intermediates, particularly those which have a significant biradical character. The CR−CCSD(T) calculations indicate that the reaction is a highly exothermic (Δ = −68 kcal/mol), predominantly concerted process with a relatively low activation barrier on the order of 13−16 kcal/mol which permits its thermal occurrence.

1 aPiecuch, Piotr1 aKinal, A. uhttps://icer.msu.edu/mechanism-22-cycloaddition-cyclopentyne-ethylene-concerted-or-biradical-completely-renormalized01686nas a2200133 4500008004100000245010300041210006900144300001400213490000800227520116200235100002401397700001801421856011301439 2006 eng d00aMolecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model0 aMolecular Dynamics Simulations of Large Integral Membrane Protei a548–5560 v1103 aThe heterogeneous dielectric generalized Born {(HDGB)} methodology is an the extension of the {GBMV} model for the simulation of integral membrane proteins with an implicit membrane environment. Three large integral membrane proteins, the bacteriorhodopsin monomer and trimer and the {BtuCD} protein, were simulated with the {HDGB} model in order to evaluate how well thermodynamic and dynamic properties are reproduced. Effects of the truncation of electrostatic interactions were examined. For all proteins, the {HDGB} model was able to generate stable trajectories that remained close to the starting experimental structures, in excellent agreement with explicit membrane simulations. Dynamic properties evaluated through a comparison of B-factors are also in good agreement with experiment and explicit membrane simulations. However, overall flexibility was slightly underestimated with the {HDGB} model unless a very large electrostatic cutoff is employed. Results with the {HDGB} model are further compared with equivalent simulations in implicit aqueous solvent, demonstrating that the membrane environment leads to more realistic simulations.

1 aTanizaki, Seiichiro1 aFeig, Michael uhttps://icer.msu.edu/molecular-dynamics-simulations-large-integral-membrane-proteins-implicit-membrane-model01919nas a2200181 4500008004100000245010400041210006900145260001200214300001100226490000800237520110200245653019501347100001901542700002101561700001701582700001401599856012401613 2006 eng d00aNon-Iterative Coupled- Cluster Methods Employing Multi-Reference Perturbation Theory Wave Functions0 aNonIterative Coupled Cluster Methods Employing MultiReference Pe c10/2006 a89-1040 v7713 aA new class of non-iterative coupled-cluster (CC) methods, which improve the results of standard CC and equation-of-motion (EOM) CC calculations for ground and excited-state potential energy surfaces along bond breaking coordinates and for excited states dominated by two-electron transitions, is explored. The proposed approaches combine the method of moments of coupled-cluster equations (MMCC), in which the a posteriori corrections due to higher-order correlations are added to standard CC/EOMCC energies, with the multi-reference many-body perturbation theory (MRMBPT), which provides information about the most essential non-dynamic and dynamic correlation effects that are relevant to electronic quasi-degeneracies. The performance of the basic MRMBPT-corrected MMCC approximation, in which inexpensive non-iterative corrections due to triple excitations are added to ground- and excited-state energies obtained with the CC/EOMCC singles and doubles approach, is illustrated by the results of a few test calculations, including bond breaking in HF and H2O, and excited states of CH+.

10aCoupled-cluster theory; Equation-of-motion coupled-cluster methods; Method of moments of coupled-cluster equations; Multi-reference perturbation theory; Non-iterative coupled-cluster methods1 aPiecuch, Piotr1 aLodriguito, M.D.1 aKowalski, K.1 aWloch, M. uhttps://icer.msu.edu/non-iterative-coupled-cluster-methods-employing-multi-reference-perturbation-theory-wave-functions00503nas a2200145 4500008004100000245007200041210006900113300001100182490000700193100001900200700001400219700001900233700001600252856008900268 2006 eng d00aNon-iterative Coupled-Cluster Methods for Excited Electronic States0 aNoniterative CoupledCluster Methods for Excited Electronic State a45-1060 v151 aPiecuch, Piotr1 aWloch, M.1 aLodriguito, M.1 aGour, J., R uhttps://icer.msu.edu/non-iterative-coupled-cluster-methods-excited-electronic-states00506nas a2200157 4500008004100000245007300041210006900114260001200183490000700195100001400202700001800216700001500234700001400249700001700263856006800280 2006 eng d00aShell model analysis of the 56Ni spectrum in the full pf model space0 aShell model analysis of the 56Ni spectrum in the full pf model s c06/20060 v731 aHoroi, M.1 aBrown, B., A.1 aOtsuka, T.1 aHonma, M.1 aMizusaki, T. uhttp://journals.aps.org/prc/abstract/10.1103/PhysRevC.73.06130501338nas a2200169 4500008004100000245011100041210006900152260001200221300001400233490000800247520073400255100001900989700001401008700001601022700001401038856011601052 2006 eng d00aSingle-reference, size-extensive, non-iterative coupled-cluster approaches to bond breaking and biradicals0 aSinglereference sizeextensive noniterative coupledcluster approa c02/2006 a467–4740 v4183 aWe propose the non-iterative, completely renormalized (CR) coupled-cluster (CC) approaches, including the CR-CC(2, 3) method which offers considerable improvements over the CCSD(T) approach without a significant increase in the computer effort. The CR-CC(2, 3) method, in which the CCSD (CC singles and doubles) energy is corrected for the effect of triples, is size extensive, competitive with CCSD(T) in calculations for non-degenerate states, and as accurate as the expensive CC approach with singles, doubles, and triples in the bond-breaking region. Calculations of the activation enthalpy for the thermal isomerizations of cyclopropane involving trimethylene suggest that CR-CC(2, 3) may be applicable to biradicals.

1 aPiecuch, Piotr1 aWloch, M.1 aGour, J., R1 aKinal, A. uhttps://icer.msu.edu/single-reference-size-extensive-non-iterative-coupled-cluster-approaches-bond-breaking-and01465nas a2200181 4500008004100000245010100041210006900142260001500211300001600226490000800242520084100250100001701091700001401108700001401122700001901136700001801155856011001173 2006 eng d00aTheoretical Characterization of End-on and Side-on Peroxide Coordination in Ligated Cu2O2 Models0 aTheoretical Characterization of Endon and Sideon Peroxide Coordi c09/15/2006 a11557-115680 v1103 aThe relative energetics of μ-η1:η1 (trans end-on) and μ-η2:η2 (side-on) peroxo isomers of Cu2O2 fragments supported by 0, 2, 4, and 6 ammonia ligands have been computed with various density functional, coupled-cluster, and multiconfigurational protocols. There is substantial disagreement between the different levels for most cases, although completely renormalized coupled-cluster methods appear to offer the most reliable predictions. The significant biradical character of the end-on peroxo isomer proves problematic for the density functionals, while the demands on active space size and the need to account for interactions between different states in second-order perturbation theory prove challenging for the multireference treatments. In the latter case, it proved impossible to achieve any convincing convergence.

1 aCramer, C.J.1 aKinal, A.1 aWloch, M.1 aPiecuch, Piotr1 aGagliardi, L. uhttps://icer.msu.edu/theoretical-characterization-end-and-side-peroxide-coordination-ligated-cu2o2-models02131nas a2200181 4500008004100000245012100041210006900162260001200231300001600243490000800259520146800267100001701735700001401752700001901766700002401785700001801809856012201827 2006 eng d00aTheoretical Models on the Cu2O2 Torture Track. Mechanistic Implications for Oxytyrosinase and Small-molecule Analogs0 aTheoretical Models on the Cu2O2 Torture Track Mechanistic Implic c06/2007 a1991–20040 v1103 aAccurately describing the relative energetics of alternative bis(mu-oxo) and mu-eta2:eta2 peroxo isomers of Cu2O2 cores supported by 0, 2, 4, and 6 ammonia ligands is remarkably challenging for a wide variety of theoretical models, primarily owing to the difficulty of maintaining a balanced description of rapidly changing dynamical and nondynamical electron correlation effects and a varying degree of biradical character along the isomerization coordinate. The completely renormalized coupled-cluster level of theory including triple excitations and extremely efficient pure density functional levels of theory quantitatively agree with one another and also agree qualitatively with experimental results for Cu2O2 cores supported by analogous but larger ligands. Standard coupled-cluster methods, such as CCSD(T), are in most cases considerably less accurate and exhibit poor convergence in predicted relative energies. Hybrid density functionals significantly underestimate the stability of the bis(mu-oxo) form, with the magnitude of the error being directly proportional to the percentage Hartree-Fock exchange in the functional. Single-root CASPT2 multireference second-order perturbation theory, by contrast, significantly overestimates the stability of bis(mu-oxo) isomers. Implications of these results for modeling the mechanism of C-H bond activation by supported Cu2O2 cores, like that found in the active site of oxytyrosinase, are discussed.

1 aCramer, C.J.1 aWloch, M.1 aPiecuch, Piotr1 aPuzzarini, Cristina1 aGagliardi, L. uhttps://icer.msu.edu/theoretical-models-cu2o2-torture-track-mechanistic-implications-oxytyrosinase-and-small-molecule00614nas a2200157 4500008004100000245012500041210006900166260001100235300001400246490000800260100001900268700001400287700002100301700001600322856011800338 2006 eng d00aTwo New Classes of Non-Iterative Coupled-Cluster Methods Derived from the Method of Moments of Coupled-Cluster Equations0 aTwo New Classes of NonIterative CoupledCluster Methods Derived f c7/2006 a2149-21720 v1041 aPiecuch, Piotr1 aWloch, M.1 aLogriguito, M.D.1 aGour, J., R uhttps://icer.msu.edu/two-new-classes-non-iterative-coupled-cluster-methods-derived-method-moments-coupled-cluster02773nas a2200145 4500008004100000245019000041210006900231260001200300300000900312490000700321520214700328100001502475700001902490856011802509 2006 eng d00aThe Usefulness of Exponential Wave Function Expansions Employing One- and Two-Body Cluster Operators in Electronic Structure Theory: The Extended and Generalized Coupled-Cluster Methods0 aUsefulness of Exponential Wave Function Expansions Employing One c12/2006 a1-570 v513 aIn this paper, the applicability of exponential cluster expansions involving one- and two-body operators in high accuracy ab initio electronic structure calculations is examined. First, the extended coupled-cluster method with singles and doubles (ECCSD) is tested in the demanding studies of systems with strong quasi-degeneracies, including potential energy surfaces involving multiple bond breaking. The numerical results show that the single-reference ECCSD method is capable of providing a qualitatively correct description of quasi-degenerate electronic states and potential energy surfaces involving bond breaking, eliminating, in particular, the failures and the unphysical behavior of standard coupled-cluster methods in similar cases. It is also demonstrated that one can obtain entire potential energy surfaces with millihartree accuracies by combining the ECCSD theory with the non-iterative a posteriori corrections obtained by using the generalized variant of the method of moments of coupled-cluster equations. This is one of the first instances where the relatively simple single-reference formalism, employing only one- and two-body clusters in the design of the relevant energy expressions, provides a highly accurate description of the dynamic and significant non-dynamic correlation effects characterizing quasi-degenerate and multiply bonded systems. Second, an evidence is presented that one may be able to represent the virtually exact ground- and excited-state wave functions of many-electron systems by exponential cluster expansions employing general two-body or one- and two-body operators. Calculations for small many-electron model systems indicate the existence of finite two-body parameters that produce the numerically exact wave functions for ground and excited states. This finding may have a significant impact on future quantum calculations for many-electron systems, since normally one needs triply excited, quadruply excited, and other higher-than-doubly excited Slater determinants, in addition to all singly and doubly excited determinants, to obtain the exact or virtually exact wave functions.

1 aFan, P.-D.1 aPiecuch, Piotr uhttps://icer.msu.edu/usefulness-exponential-wave-function-expansions-employing-one-and-two-body-cluster-operators01260nas a2200205 4500008004100000245004300041210004200084260001200126300001100138490000700149520068900156100001500845700001700860700001600877700002600893700001700919700001900936700001600955856008300971 2005 eng d00aAb Initio Coupled-Cluster Study of 16O0 aAb Initio CoupledCluster Study of 16O c06/2005 a2125010 v943 aWe report converged results for the ground and excited states and matter density of 16O using realistic two-body nucleon-nucleon interactions and coupled-cluster methods and algorithms developed in quantum chemistry. Most of the binding is obtained with the coupled-cluster singles and doubles approach. Additional binding due to three-body clusters (triples) is minimal. The coupled-cluster method with singles and doubles provides a good description of the matter density, charge radius, charge form factor, and excited states of a one-particle, one-hole nature, but it cannot describe the first-excited 0+ state. Incorporation of triples has no effect on the latter finding.

1 aWłoch, M.1 aDean, D., J.1 aGour, J., R1 aHjorth-Jensen}, M., {1 aKowalski, K.1 aPapenbrock, T.1 aPiecuch, P. uhttps://icer.msu.edu/research/publications/ab-initio-coupled-cluster-study-16o01233nas a2200193 4500008004100000245004100041210004000082260001200122490000700134520068900141100001900830700001400849700001700863700001600880700002600896700001700922700001900939856008100958 2005 eng d00aAb Initio Coupled-Cluster Study of O0 aAb Initio CoupledCluster Study of O c06/20050 v943 aWe report converged results for the ground and excited states and matter density of 16O using realistic two-body nucleon-nucleon interactions and coupled-cluster methods and algorithms developed in quantum chemistry. Most of the binding is obtained with the coupled-cluster singles and doubles approach. Additional binding due to three-body clusters (triples) is minimal. The coupled-cluster method with singles and doubles provides a good description of the matter density, charge radius, charge form factor, and excited states of a one-particle, one-hole nature, but it cannot describe the first-excited 0+ state. Incorporation of triples has no effect on the latter finding.

1 aPiecuch, Piotr1 aWloch, M.1 aDean, D., J.1 aGour, J., R1 aHjorth-Jensen}, M., {1 aKowalski, K.1 aPapenbrock, T. uhttps://icer.msu.edu/research/publications/ab-initio-coupled-cluster-study-o01316nas a2200181 4500008004100000245006800041210006600109260001200175300001200187490000800199520074000207100001900947700001700966700001500983700001400998700001701012856010501029 2005 eng d00aActive-Space Coupled-Cluster Study of Electronic States of Be 30 aActiveSpace CoupledCluster Study of Electronic States of Be 3 c08/2005 a6 pages0 v1233 aThe active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods with all single and double excitations with triple excitations defined via active orbitals (CCSDt, EOMCCSDt), as implemented with TENSOR CONTRACTION ENGINE, are applied to the challenging Be3 system, which is characterized by a large number of low-lying excited states dominated by two-electron transitions and significant high-order correlation effects in the ground electronic state. It is demonstrated that the CCSDt and EOMCCSDt methods provide an excellent description of complicated electronic quasidegeneracies present in the Be3 cluster. Different strategies for defining triple excitations within the CCSDt∕EOMCCSDt approach are discussed.

1 aPiecuch, Piotr1 aKowalski, K.1 aHirata, S.1 aWloch, M.1 aWindus, T.L. uhttps://icer.msu.edu/research/publications/active-space-coupled-cluster-study-electronic-states-be-301392nas a2200181 4500008004100000245015300041210006900194300001600263490000800279520065800287653003300945653001800978653003200996100002201028700001901050700001701069856012401086 2005 eng d00aActive-space equation-of-motion coupled-cluster methods for excited states of radicals and other open-shell systems: {EA-EOMCCSDt} and {IP-EOMCCSDt}0 aActivespace equationofmotion coupledcluster methods for excited a134113–140 v1233 aThe previously developed active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods are extended to radicals and other open-shell systems by combining them with the electron attached (EA) and ionized (IP) EOMCC approaches. As illustrated by the calculations for the CH and OH radicals, the resulting EA-EOMCCSDt and IP-EOMCCSDt theories are capable of providing a highly accurate description of the electronic spectra of radical systems, including excited states displaying a manifestly multideterminantal nature, with the low costs that are not much greater that those characterizing the standard EOMCC singles and doubles method.

10acoupled cluster calculations10afree radicals10amolecular electronic states1 aGour, Jeffrey, R.1 aPiecuch, Piotr1 aWloch, Marta uhttps://icer.msu.edu/research/publications/active-space-equation-motion-coupled-cluster-methods-excited-states-radicals00613nas a2200145 4500008004100000245014900041210006900190260001200259300001300271490000800284100001900292700001600311700001400327856012600341 2005 eng d00aActive-Space Equation-of=Motion Coupled-Cluster Methods for Excited States of Radicals and Other Open-Shell Systems: EA-EOMCCSDt and IP-EOMCCSDt0 aActiveSpace EquationofMotion CoupledCluster Methods for Excited c10/2005 a14 pages0 v1231 aPiecuch, Piotr1 aGour, J., R1 aWloch, M. uhttps://icer.msu.edu/research/publications/active-space-equation-ofmotion-coupled-cluster-methods-excited-states-radicals01208nas a2200145 4500008004100000245017600041210006900217260001500286300001400301490000800315520057100323100001900894700002300913856012600936 2005 eng d00aBalancing Dynamic and Non-Dynamic Correlation for Diradical and Aromatic Transition States: A Renormalized Coupled-Cluster Study of the Cope Rearrangement of 1,5-Hexadiene0 aBalancing Dynamic and NonDynamic Correlation for Diradical and A c02/05/2005 a2608-26140 v1273 aSingle-reference coupled-cluster calculations employing the completely renormalized CCSD(T) (CR-CCSD(T)) approach have been used to examine the mechanism of the Cope rearrangement of 1,5-hexadiene. In agreement with multireference perturbation theory, the CR-CCSD(T) method favors the concerted mechanism of the Cope rearrangement involving an aromatic transition state. The CCSD(T) approach, which is often regarded as the “gold standard” of electronic structure theory, seems to fail in this case, favoring pathways through diradical structures.

1 aPiecuch, Piotr1 aMcGuire}, M., J. { uhttps://icer.msu.edu/research/publications/balancing-dynamic-non-dynamic-correlation-diradical-aromatic-transition-states02028nas a2200193 4500008004100000245012400041210006900165260005600234300001000290490000800300520128900308100001901597700001401616700001601630700001701646700002601663700001901689856012601708 2005 eng d00aBridging Quantum Chemistry and Nuclear Structure Theory: Coupled-Cluster Calculations for Closed- and Open-Shell Nuclei0 aBridging Quantum Chemistry and Nuclear Structure Theory CoupledC aMelville, NYbAmerican Institute of Physicsc7/2005 a28-450 v7773 aWe review basic elements of the single-reference coupled-cluster theory and discuss large scale ab initio calculations of ground and excited states of 15O, 16O, and 17O using coupled-cluster methods and algorithms developed in quantum chemistry. By using realistic two-body interactions and the renormalized form of the Hamiltonian obtained with a no-core G-matrix approach, we obtain the converged results for 16O and promising preliminary results for 15O and 17O at the level of two-body interactions. The calculated properties other than energies include matter density, charge radius, and charge form factor. The relatively low costs of coupled-cluster calculations, which are characterized by the low-order polynomial scaling with the system size, enable us to probe large model spaces with up to 7 or 8 major oscillator shells, for which non-truncated shell-model calculations for nuclei with A = 15 17 active particles are presently not possible. We argue that the use of coupled-cluster methods and computer algorithms developed by quantum chemists to calculate properties of nuclei is an important step toward the development of accurate and affordable many-body theories that cross the boundaries of various physical sciences. ©2005 American Institute of Physics

1 aPiecuch, Piotr1 aWloch, M.1 aGour, J., R1 aDean, D., J.1 aHjorth-Jensen}, M., {1 aPapenbrock, T. uhttps://icer.msu.edu/bridging-quantum-chemistry-and-nuclear-structure-theory-coupled-cluster-calculations-closed-and-open01552nas a2200169 4500008004100000245026000041210006900301260001200370300001600382490000800398520078000406100001901186700001501205700001801220700002301238856012101261 2005 eng d00aCan a Single-Reference Approach Provide a Balanced Description of Ground and Excited States? A Comparison of the Completely Renormalized Equation-of-the-Motion Coupled-Cluster Method with Multi-Reference Quasi-Degenerate Perturbation Theory Near a Conical0 aCan a SingleReference Approach Provide a Balanced Description of c11/2005 a11643-116460 v1093 aWe calculated the two lowest electronically adiabatic potential energy surfaces of ammonia in the region of the conical intersection and at a sequence of geometries along which one of the N-H bonds is broken. We employed both a multireference (MR) method and a single-reference (SR) method. The MR calculations are based on multiconfiguration quasidegenerate perturbation theory (MC-QDPT) with a 6-311+G(3df,3pd) basis set. The SR calculations, carried out with the same basis, employ the completely renormalized equation-ofmotion coupled-cluster method with singles and doubles, and a noniterative treatment of triples, denoted CR-EOMCCSD(T). At 91 geometries used for comparison, including geometries near a conical intersection, the surfaces agree to 7% on average.

1 aPiecuch, Piotr1 aNangia, S.1 aTruhlar, D.G.1 aMcGuire}, M., J. { uhttps://icer.msu.edu/research/publications/can-single-reference-approach-provide-balanced-description-ground-excited01534nas a2200265 4500008004100000245007500041210006900116260001500185300001200200490000800212520073300220100001900953700002000972700001600992700001301008700001701021700001401038700002201052700001801074700001401092700001701106700001301123700001701136856011501153 2005 eng d00aComparison of Low-Order Multireference Many-Body Perturbation Theories0 aComparison of LowOrder Multireference ManyBody Perturbation Theo c04/01/2005 a9 pages0 v1223 aTests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.

1 aPiecuch, Piotr1 aChaudhuri, R.K.1 aFreed, K.F.1 aHose, G.1 aKowalski, K.1 aWloch, M.1 aChattopadhyay, S.1 aMukherjee, D.1 aRolik, R.1 aSzabados, A.1 aToth, G.1 aSurjan, P.R. uhttps://icer.msu.edu/research/publications/comparison-low-order-multireference-many-body-perturbation-theories01895nas a2200133 4500008004100000245012300041210006900164260001400233490000800247520134500255100001901600700001901619856012301638 2005 eng d00aA Comparison of Renormalized Coupled-Cluster and Multireference Methods with Full Configuration Interaction Benchmarks0 aComparison of Renormalized CoupledCluster and Multireference Met c3/22/20050 v1223 aUnusual bonding and electronic near degeneracies make the lowest-lying singlet states of the C2 molecule particularly challenging for electronic structure theory. Here we compare two alternative approaches to modeling bond-breaking reactions and excited states: sophisticated multireference configuration interaction and multireference perturbation theory methods, and a more "black box," single-reference approach, the completely renormalized coupled-cluster method. These approximate methods are assessed in light of their ability to reproduce the full configuration interaction potential energy curves for the X1Sigmag+, B1Deltag, and B' 1Sigmag+ states of C2, which are numerically exact solutions of the electronic Schrodinger equation within the space spanned by a 6-31G* basis set. Both the multireference methods and the completely renormalized coupled-cluster approach provide dramatic improvements over the standard single-reference methods. The multireference methods are nearly as reliable for this challenging test case as for simpler reactions which break only single bonds. The completely renormalized coupled-cluster approach has difficulty for large internuclear separations R in this case, but over the wide range of R=1.0-2.0 A, it compares favorably with the more complicated multireference methods.

1 aPiecuch, Piotr1 aSherrill, C.D. uhttps://icer.msu.edu/comparison-renormalized-coupled-cluster-and-multireference-methods-full-configuration-interaction00768nas a2200169 4500008004100000245007500041210006900116260002500185520018800210100001900398700001700417700002200434700001700456700001900473700001400492856009200506 2005 eng d00aCoupled Cluster Approaches to Nuclei, Ground States and Excited States0 aCoupled Cluster Approaches to Nuclei Ground States and Excited S aPaestum, Italyc20053 aWe present recent coupled-cluster studies of nuclei, with an emphasis on ground state and excited states of closed shell nuclei. Perspectives for future studies are delineated.

1 aPiecuch, Piotr1 aDean, D., J.1 aJhorth-Jensen, M.1 aKowalski, K.1 aPapenbrock, T.1 aWloch, M. uhttps://icer.msu.edu/coupled-cluster-approaches-nuclei-ground-states-and-excited-states01444nas a2200109 4500008004100000245013100041210006900172260001100241490000700252520095200259856012301211 2005 eng d00aCoupled-Cluster Calculations for Ground and Excited States of Closed- and Open-Shell Nuclei Using Methods of Quantum Chemistry0 aCoupledCluster Calculations for Ground and Excited States of Clo c7/20050 v313 aWe discuss large-scale ab initio calculations of ground and excited states of 16O and preliminary calculations for 15O and 17O using coupled-cluster methods and algorithms developed in quantum chemistry. By using realistic two-body interactions and the renormalized form of the Hamiltonian obtained with a no-core G-matrix approach, we are able to obtain the virtually converged results for 16O and promising results for 15O and 17O at the level of two-body interactions. The calculated properties other than binding and excitation energies include charge radius and charge form factor. The relatively low costs of coupled-cluster calculations, which are characterized by the low-order polynomial scaling with the system size, enable us to probe large model spaces with up to seven or eight major oscillator shells, for which nontruncated shell-model calculations for nuclei with A = 15–17 active particles are presently not possible.

uhttps://icer.msu.edu/coupled-cluster-calculations-ground-and-excited-states-closed-and-open-shell-nuclei-using-methods01156nas a2200157 4500008004100000245012800041210006900169260001200238490000800250520055100258100001900809700001400828700001600842700001700858856012300875 2005 eng d00aExtension of Renormalized Coupled-Cluster Methods Including Triple Excitations to Electronic States of Open-Shell Molecules0 aExtension of Renormalized CoupledCluster Methods Including Tripl c06/20050 v1223 aThe general-purpose open-shell implementation of the completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] is reported. Benchmark calculations for the low-lying doublet and quartet states of the CH radical show that the CR-EOMCCSD(T) method is capable of providing a highly accurate description of ground and excited states of open-shell molecules. This includes states with strong double excitation character, for which the conventional EOMCCSD approach fails.

1 aPiecuch, Piotr1 aWloch, M.1 aGour, J., R1 aKowalski, K. uhttps://icer.msu.edu/research/publications/extension-renormalized-coupled-cluster-methods-including-triple-excitations02334nas a2200133 4500008004100000245006900041210006800110260001500178490000800193520185400201100001902055700001702074856010902091 2005 eng d00aExtensive Generalization of Renormalized Coupled-Cluster Methods0 aExtensive Generalization of Renormalized CoupledCluster Methods c02/09/20050 v1223 aThe recently developed completely renormalized (CR) coupled-cluster (CC) methods with singles, doubles, and noniterative triples or triples and quadruples [CR-CCSD(T) or CR-CCSD(TQ), respectively], which are based on the method of moments of CC equations (MMCC) [K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000)], eliminate the failures of the standard CCSD(T) and CCSD(TQ) methods at larger internuclear separations, but they are not rigorously size extensive. Although the departure from strict size extensivity of the CR-CCSD(T) and CR-CCSD(TQ) methods is small, it is important to examine the possibility of formulating the improved CR-CC methods, which are as effective in breaking chemical bonds as the existing CR-CCSD(T) and CR-CCSD(TQ) approaches, which are as easy to use as the CR-CCSD(T) and CR-CCSD(TQ) methods, and which can be made rigorously size extensive. This may be particularly useful for the applications of CR-CC methods and other MMCC approaches in calculations of potential energy surfaces of large many-electron systems and van der Waals molecules, where the additive separability of energies in the noninteracting limit is very important. In this paper, we propose different types of CR-CC approximations, termed the locally renormalized (LR) CCSD(T) and CCSD(TQ) methods, which become rigorously size extensive if the orbitals are localized on nointeracting fragments. The LR-CCSD(T) and LR-CCSD(TQ) methods rely on the form of the energy expression in terms of the generalized moments of CC equations, derived in this work, termed the numerator-denominator-connected MMCC expansion. The size extensivity and excellent performance of the LR-CCSD(T) and LR-CCSD(TQ) methods are illustrated numerically by showing the results for the dimers of stretched HF and LiH molecules and bond breaking in HF and H2O.

1 aPiecuch, Piotr1 aKowalski, K. uhttps://icer.msu.edu/research/publications/extensive-generalization-renormalized-coupled-cluster-methods01726nas a2200157 4500008004100000245013900041210006900180260001200249300001400261490000800275520111600283100001901399700001701418700001701435856011601452 2005 eng d00aNoniterative Corrections to Extended Coupled-Cluster Energies Employing the Generalized Method of Moments of Coupled-Cluster Equations0 aNoniterative Corrections to Extended CoupledCluster Energies Emp c08/2005 a2191-22130 v1033 aIt is shown that the extended coupled-cluster method with singles and doubles (ECCSD) does not suffer from the non-variational collapse observed in the standard CCSD calculations when multiple bond breaking is examined. This interesting feature of the single-reference ECCSD theory is used to design the non-iterative CC methods with singles, doubles and non-iterative triples and quadruples, which provide a highly accurate and variational description of potential energy surfaces involving multiple bond breaking with computational steps that scale as with the system size. This is accomplished with the help of the generalized version of the method of moments of coupled-cluster equations (GMMCC), which can be used to correct the results of non-standard CC calculations, such as ECCSD. The theoretical considerations are illustrated by the preliminary results of the ECCSD-based GMMCC calculations for triple bond breaking in N2. Keywords: Coupled-cluster theory; Extended coupled-cluster method; Method of moments of coupled-cluster equations; Non-iterative coupled-cluster approaches; Bond breaking

1 aPiecuch, Piotr1 aFan, {P.-D.}1 aKowalski, K. uhttps://icer.msu.edu/research/publications/noniterative-corrections-extended-coupled-cluster-energies-employing01746nas a2200217 4500008004100000245008700041210006900128260001200197300001200209490000800221520103700229100001901266700001701285700001601302700001401318700002601332700001701358700001901375700001401394856012001408 2005 eng d00aNuclear Structure Calculations with Coupled-Cluster Methods from Quantum Chemistry0 aNuclear Structure Calculations with CoupledCluster Methods from c04/2005 a299-3080 v7523 aWe present several coupled-cluster calculations of ground and excited states of 4He and 16O employing methods from quantum chemistry. A comparison of coupled cluster results with the results of exact diagonalization of the hamiltonian in the same model space and other truncated shell-model calculations shows that the quantum chemistry inspired coupled cluster approximations provide an excellent description of ground and excited states of nuclei, with much less computational effort than traditional large-scale shell-model approaches. Unless truncations are made, for nuclei like 16O, full-fledged shell-model calculations with four or more major shells are not possible. However, these and even larger systems can be studied with the coupled cluster methods due to the polynomial rather than factorial scaling inherent in standard shell-model studies. This makes the coupled cluster approaches, developed in quantum chemistry, viable methods for describing weakly bound systems of interest for future nuclear facilities.

1 aPiecuch, Piotr1 aDean, D., J.1 aGour, J., R1 aHagen, G.1 aHjorth-Jensen}, M., {1 aKowalski, K.1 aPapenbrock, T.1 aWloch, M. uhttps://icer.msu.edu/research/publications/nuclear-structure-calculations-coupled-cluster-methods-quantum-chemistry02915nas a2200313 4500008004100000245011100041210006900152260001200221300001600233490000800249520189000257653002102147653003102168653003302199653001302232653001902245653001302264653001802277653002102295653002302316653001802339653002202357653002202379653002902401653001002430100001902440700001702459856012502476 2005 eng d00aRenormalized coupled-cluster methods exploiting left eigenstates of the similarity-transformed Hamiltonian0 aRenormalized coupledcluster methods exploiting left eigenstates c12/2005 a224105–100 v1233 aCompletely renormalized (CR) coupled-cluster (CC) approaches, such as CR-CCSD(T), in which one corrects the standard CC singles and doubles (CCSD) energy for the effects of triply (T) and other higher-than-doubly excited clusters [ K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000) ], are reformulated in terms of the left eigenstates 〈Φ∣L of the similarity-transformed Hamiltonian of CC theory. The resulting CR-CCSD(T)L or CR-CC(2,3) and other CR-CCL methods are derived from the new biorthogonal form of the method of moments of CC equations (MMCC) in which, in analogy to the original MMCC theory, one focuses on the noniterative corrections to standard CC energies that recover the exact, full configuration-interaction energies. One of the advantages of the biorthogonal MMCC theory, which will be further analyzed and extended to excited states in a separate paper, is a rigorous size extensivity of the basic ground-state CR-CCL approximations that result from it, which was slightly violated by the original CR-CCSD(T) and CR-CCSD(TQ) approaches. This includes the CR-CCSD(T)L or CR-CC(2,3) method discussed in this paper, in which one corrects the CCSD energy by the relatively inexpensive noniterative correction due to triples. Test calculations for bond breaking in HF, F2, and H2O indicate that the noniterative CR-CCSD(T)L or CR-CC(2,3) approximation is very competitive with the standard CCSD(T) theory for nondegenerate closed-shell states, while being practically as accurate as the full CC approach with singles, doubles, and triples in the bond-breaking region. Calculations of the activation enthalpy for the thermal isomerizations of cyclopropane involving the trimethylene biradical as a transition state show that the noniterative CR-CCSD(T)L approximation is capable of providing activation enthalpies which perfectly agree with experiment.

10abonds (chemical)10aconfiguration interactions10acoupled cluster calculations10aenthalpy10aexcited states10afluorine10aground states10aheat of reaction10ahydrogen compounds10aisomerisation10amethod of moments10aorganic compounds10areaction kinetics theory10awater1 aPiecuch, Piotr1 aWloch, Marta uhttps://icer.msu.edu/renormalized-coupled-cluster-methods-exploiting-left-eigenstates-similarity-transformed-hamiltonian01158nas a2200229 4500008004100000245007700041210006900118260001500187300001400202490000800216520046200224100001900686700001600705700001700721700001700738700001700755700001400772700001700786700002200803700001500825856008800840 2005 eng d00aWhere Does the Planar-to-Nonplanar Turnover Occur in Small Gold Clusters0 aWhere Does the PlanartoNonplanar Turnover Occur in Small Gold Cl c12/30/2004 a1049-10520 v1273 aSeveral levels of theory, including both Gaussian-based and plane wave density functional theory (DFT), second-order perturbation theory (MP2), and coupled cluster methods (CCSD(T)), are employed to study Au6 and Au8 clusters. All methods predict that the lowest energy isomer of Au6 is planar. For Au8, both DFT methods predict that the two lowest isomers are planar. In contrast, both MP2 and CCSD(T) predict the lowest Au8 isomers to be nonplanar.

1 aPiecuch, Piotr1 aOlson, R.M.1 aVarganov, S.1 aGordon, M.S.1 aChretien, S.1 aMetiu, H.1 aKowalski, K.1 aKucharski, S., A.1 aMusial, M. uhttps://icer.msu.edu/where-does-planar-nonplanar-turnover-occur-small-gold-clusters02386nas a2200241 4500008004100000245015000041210006900191260001200260300001400272490000800286520138300294653017701677100001901854700001701873700002401890700001501914700002101929700002301950700002201973700001301995700001502008856012102023 2004 eng d00aMethod of moments of coupled-cluster equations: a new formalism for designing accurate electronic structure methods for ground and excited states0 aMethod of moments of coupledcluster equations a new formalism fo c07/2004 a349–3930 v1123 aThe method of moments of coupled-cluster equations {(MMCC),} which provides a systematic way of improving the results of the standard coupled-cluster {(CC)} and equation-of-motion {CC} {(EOMCC)} calculations for the ground- and excited-state energies of atomic and molecular systems, is described. The {MMCC} theory and its generalized {MMCC} {(GMMCC)} extension that enables one to use the cluster operators resulting from the standard as well as nonstandard {CC} calculations, including those obtained with the extended {CC} {(ECC)} approaches, are based on rigorous mathematical relationships that define the many-body structure of the differences between the full configuration interaction {(CI)} and {CC} or {EOMCC} energies. These relationships can be used to design the noniterative corrections to the {CC/EOMCC} energies that work for chemical bond breaking and potential energy surfaces of excited electronic states, including excited states dominated by double excitations, where the standard single-reference {CC/EOMCC} methods fail. Several {MMCC} and {GMMCC} approximations are discussed, including the renormalized and completely renormalized {CC/EOMCC} methods for closed- and open-shell states, the quadratic {MMCC} approaches, the {CI-corrected} {MMCC} methods, and the {GMMCC} approaches for multiple bond breaking based on the {ECC} cluster amplitudes.

10aCoupled-cluster theory - Method of moments of coupled-cluster equations - Renormalized coupled-cluster methods - extended coupled cluster theory - Potential energy surfaces1 aPiecuch, Piotr1 aKowalski, K.1 aPimienta, I., S. O.1 aFan, P.-D.1 aLodriguito, M.D.1 aMcGuire}, M., J. {1 aKucharski, S., A.1 aKuś, T.1 aMusial, M. uhttps://icer.msu.edu/research/publications/method-moments-coupled-cluster-equations-new-formalism-designing-accurate