Isolable heteroleptic tris(metallocenes) containing five-membered and larger rings remain extremely scarce. The utilization of tripositive rare-earth-metal ions with ionic radii >1 Å allowed access to unprecedented and sterically congested dibenzocyclooctatetraenyl (dbCOT) metallocenes, [K(crypt-222)][Cptet2RE(η2-dbCOT)] (RE = Y (1), Dy (2); Cptet = tetramethylcyclopentadienyl), through a salt metathesis reaction involving Cptet2RE(BPh4) and the potassium salt of the dbCOT dianion. The solid-state structures were investigated by single-crystal X-ray diffraction, magnetometry, and IR spectroscopy and provided evidence for the first crystallographically characterized (dbCOT)2– anion in a complex containing d- or f-block metals. Remarkably, the (Cptet)− ligands force a distortion from planarity within the (dbCOT)2– moiety, engendering a rare η2-bonding motif, as opposed to the classical η8 conformation observed in complexes bearing a (COT)2– ion. The η2 coordination mode was proven crystallographically between 100 and 298 K and computationally (DFT and NBO). Furthermore, nucleus independent chemical shift (NICS) calculations uncovered significant ring current within the dbCOT ligand. The solution-state properties of 1 and 2 were analyzed via cyclic voltammetry, NMR, and UV–vis spectroscopy. Cyclic voltammograms of 1 and 2 exhibit a quasi-reversible feature indicating the accessibility of complexes with dbCOT in two oxidation states (dbCOT2–/3–•). Importantly, the dysprosium congener, 2, is a zero-field single-molecule magnet (SMM).Isolable heteroleptic tris(metallocenes) containing five-membered and larger rings remain extremely scarce. The utilization of tripositive rare-earth-metal ions with ionic radii >1 Å allowed access to unprecedented and sterically congested dibenzocyclooctatetraenyl (dbCOT) metallocenes, [K(crypt-222)][Cptet2RE(η2-dbCOT)] (RE = Y (1), Dy (2); Cptet = tetramethylcyclopentadienyl), through a salt metathesis reaction involving Cptet2RE(BPh4) and the potassium salt of the dbCOT dianion. The solid-state structures were investigated by single-crystal X-ray diffraction, magnetometry, and IR spectroscopy and provided evidence for the first crystallographically characterized (dbCOT)2– anion in a complex containing d- or f-block metals. Remarkably, the (Cptet)− ligands force a distortion from planarity within the (dbCOT)2– moiety, engendering a rare η2-bonding motif, as opposed to the classical η8 conformation observed in complexes bearing a (COT)2– ion. The η2 coordination mode was proven crystallographically between 100 and 298 K and computationally (DFT and NBO). Furthermore, nucleus independent chemical shift (NICS) calculations uncovered significant ring current within the dbCOT ligand. The solution-state properties of 1 and 2 were analyzed via cyclic voltammetry, NMR, and UV–vis spectroscopy. Cyclic voltammograms of 1 and 2 exhibit a quasi-reversible feature indicating the accessibility of complexes with dbCOT in two oxidation states (dbCOT2–/3–•). Importantly, the dysprosium congener, 2, is a zero-field single-molecule magnet (SMM).

VL - 61 SN - 0020-1669 UR - https://doi.org/10.1021/acs.inorgchem.1c03230 IS - 5 ER - TY - JOUR T1 - Isolation of the elusive bisbenzimidazole Bbim3−˙ radical anion and its employment in a metal complex JF - Chemical Science Y1 - 2022 A1 - Benner, Florian A1 - Demir, Selvan AB -The discovery of singular organic radical ligands is a formidable challenge due to high reactivity arising from the unpaired electron. Matching radical ligands with metal ions to engender magnetic coupling is crucial for eliciting preeminent physical properties such as conductivity and magnetism that are crucial for future technologies. The metal-radical approach is especially important for the lanthanide ions exhibiting deeply buried 4f-orbitals. The radicals must possess a high spin density on the donor atoms to promote strong coupling. Combining diamagnetic 89Y (I = 1/2) with organic radicals allows for invaluable insight into the electronic structure and spin-density distribution. This approach is hitherto underutilized, possibly owing to the challenging synthesis and purification of such molecules. Herein, evidence of an unprecedented bisbenzimidazole radical anion (Bbim3−˙) along with its metalation in the form of an yttrium complex, [K(crypt-222)][(Cp*2Y)2(μ-Bbim˙)] is provided. Access of Bbim3−˙ was feasible through double-coordination to the Lewis acidic metal ion and subsequent one-electron reduction, which is remarkable as Bbim2− was explicitly stated to be redox-inactive in closed-shell complexes. Two molecules containing Bbim2− (1) and Bbim3−˙ (2), respectively, were thoroughly investigated by X-ray crystallography, NMR and UV/Vis spectroscopy. Electrochemical studies unfolded a quasi-reversible feature and emphasize the role of the metal centre for the Bbim redox-activity as neither the free ligand nor the Bbim2− complex led to analogous CV results. Excitingly, a strong delocalization of the electron density through the Bbim3−˙ ligand was revealed via temperature-dependent EPR spectroscopy and confirmed through DFT calculations and magnetometry, rendering Bbim3−˙ an ideal candidate for single-molecule magnet design.

SN - 2041-6520 UR - http://dx.doi.org/10.1039/D1SC07245E JO - Chem. Sci. ER - TY - JOUR T1 - Phytochemical drug discovery for COVID-19 using high-resolution computational docking and machine learning assisted binder prediction JF - Journal of Biomolecular Structure and Dynamics Y1 - 2022 A1 - Wang, Zirui A1 - Belecciu, Theodore A1 - Eaves, Joelle A1 - Reimers, Mark A1 - Bachmann, Michael A1 - Woldring, Daniel AB -The COVID-19 pandemic has resulted in millions of deaths around the world. Multiple vaccines are in use, but there are many underserved locations that do not have adequate access to them. Variants may emerge that are highly resistant to existing vaccines, and therefore cheap and readily obtainable therapeutics are needed. Phytochemicals, or plant chemicals, can possibly be such therapeutics. Phytochemicals can be used in a polypharmacological approach, where multiple viral proteins are inhibited and escape mutations are made less likely. Finding the right phytochemicals for viral protein inhibition is challenging, but *in-silico* screening methods can make this a more tractable problem. In this study, we screen a wide range of natural drug products against a comprehensive set of SARS-CoV-2 proteins using a high-resolution computational workflow. This workflow consists of a structure-based virtual screening (SBVS), where an initial phytochemical library was docked against all selected protein structures. Subsequently, ligand-based virtual screening (LBVS) was employed, where chemical features of 34 lead compounds obtained from the SBVS were used to predict 53 lead compounds from a larger phytochemical library via supervised learning. A computational docking validation of the 53 predicted leads obtained from LBVS revealed that 28 of them elicit strong binding interactions with SARS-CoV-2 proteins. Thus, the inclusion of LBVS resulted in a 4-fold increase in the lead discovery rate. Of the total 62 leads, 18 showed promising pharmacokinetic properties in a computational ADME screening. Collectively, this study demonstrates the advantage of incorporating machine learning elements into a virtual screening workflow.

A series of multinuclear metallocenes composed of a tBusalophen dianion bound to two rare earth metal ions{,} where each is encased in a bis-pentamethylcyclopentadienyl scaffold{,} was realized. The isolated molecules (Cp*2RE)2(μ-tBusalophen){,} where RE = Gd (1){,} Dy (2){,} and Y (3){,} constitute the first salophen-bridged metallocene complexes for any metal ion. 1–3 were characterised by X-ray crystallography{,} cyclic voltammetry{,} IR{,} NMR{,} and UV-Vis-NIR spectroscopy. Cyclic voltammograms of 1–3 excitingly exhibit quasi-reversable features attributed to the (tBusalophen2−/tBusalophen3−˙) redox couple. DFT calculations on 3 uncovered the highest occupied molecular orbital to be primarily localized on the metallocene and phenolate moieties of the tBusalophen ligand. Furthermore{,} the nuclear spin I = ½ for yttrium allowed the collection of 89Y NMR spectra for 3. Magnetic studies revealed slow magnetic relaxation{,} placing 2 among dysprosocenium-based single-molecule magnets containing a doubly anionic ligand in the equatorial plane.

UR - http://dx.doi.org/10.1039/D1QI01331A ER - TY - JOUR T1 - Development and evaluation of CO2 transport in MPAS-A v6.3 JF - Geoscientific Model Development Y1 - 2021 A1 - Zheng, T. A1 - Feng, S. A1 - Davis, K. J. A1 - Pal, S. A1 - Morguí, J.-A. AB -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.

VL - 38 UR - https://www.sciencedirect.com/science/article/pii/S1571064521000403 ER - TY - JOUR T1 - Particle-in-cell techniques for the study of space charge effects in the Advanced Cryogenic Gas Stopper JF - Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms Y1 - 2021 A1 - R. Ringle A1 - G. Bollen A1 - K. Lund A1 - C. Nicoloff A1 - S. Schwarz A1 - C.S. Sumithrarachchi A1 - A.C.C. Villari KW - Gas stopper KW - Particle-in-cell method KW - Space charge AB -Linear 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.

VL - 496 UR - https://www.sciencedirect.com/science/article/pii/S0168583X21001117 ER - TY - JOUR T1 - A rare earth metallocene containing a 2{,}2′-azopyridyl radical anion JF - Chem. Sci. Y1 - 2021 A1 - Delano IV, Francis A1 - Castellanos, Ernesto A1 - McCracken, John A1 - Demir, Selvan AB -Introducing 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.

UR - http://dx.doi.org/10.1039/D1SC04285H ER - TY - JOUR T1 - Synthesizing social and environmental sensing to monitor the impact of large-scale infrastructure development JF - Environmental Science & Policy Y1 - 2021 A1 - Yingjie Li A1 - Yuqian Zhang A1 - Leigh Anne Tiffany A1 - Ruishan Chen A1 - Meng Cai A1 - Jianguo Liu KW - Belt and road initiative KW - Integrated analysis KW - Large-scale infrastructure KW - Remote sensing KW - Social sensing AB -The 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.

VL - 124 UR - https://www.sciencedirect.com/science/article/pii/S1462901121002057 ER - TY - JOUR T1 - Global variations of Earth's 520- and 560-km discontinuities JF - Earth and Planetary Science Letters Y1 - 2020 A1 - Dongdong Tian A1 - Mingda Lv A1 - S. Shawn Wei A1 - Susannah M. Dorfman A1 - Peter M. Shearer KW - 520-km discontinuity KW - 560-km discontinuity KW - mantle phase transformations KW - mantle transition zone KW - oceanic crust recycling KW - SS precursors AB -We 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.

VL - 552 UR - http://www.sciencedirect.com/science/article/pii/S0012821X20305446 ER - TY - JOUR T1 - A hierarchical analysis of habitat area, connectivity, and quality on amphibian diversity across spatial scales Y1 - 2020 A1 - Wright, Alexander D. A1 - Grant, Evan H. Campbell A1 - Zipkin, Elise F. AB -Habitat 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.

VL - 35 SN - 1572-9761 UR - https://doi.org/10.1007/s10980-019-00963-z IS - 2 JO - Landscape Ecology ER - TY - JOUR T1 - Oceanic plateau of the Hawaiian mantle plume head subducted to the uppermost lower mantle JF - Science Y1 - 2020 A1 - Wei, Songqiao Shawn A1 - Shearer, Peter M. A1 - Lithgow-Bertelloni, Carolina A1 - Stixrude, Lars A1 - Tian, Dongdong AB -Volcanic 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.

VL - 370 UR - https://science.sciencemag.org/content/370/6519/983 ER - TY - JOUR T1 - Ice cover, winter circulation, and exchange in Saginaw Bay and Lake Huron JF - Limnology and Oceanography Y1 - 2017 A1 - Tuan D. Nguyen A1 - Nathan Hawley A1 - Mantha S. Phanikumar AB -Winter 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.

VL - 62 UR - http://www.egr.msu.edu/~phani/lno10431.pdf IS - 1 ER - TY - JOUR T1 - Manifold methods for assimilating geophysical and meteorological data in Earth system models and their components JF - Journal of Hydrology Y1 - 2017 A1 - Ammar Safaie A1 - Chinh Dang A1 - Han Qiu A1 - Hayder Radha A1 - Phanikumar, M.S. AB -A 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.

VL - 544 UR - http://hydrology1.weebly.com/uploads/6/6/2/1/66216077/jh_safaie.pdf ER - TY - JOUR T1 - Numerical Study of High Speed Evaporating Sprays JF - International Journal of Multiphase Flow Y1 - 2015 A1 - Farhad A Jaberi A1 - Irannejad, Abolfazl VL - 70 UR - http://www.sciencedirect.com/science/article/pii/S0301932214002341 ER - TY - JOUR T1 - Twist-averaged boundary conditions for nuclear pasta Hartree-Fock calculations Y1 - 2015 A1 - B. Schuetrumpf A1 - W. Nazarewicz VL - 92 JO - Physical Review C ER - TY - JOUR T1 - Bonds, bands, and band gaps in tetrahedrally bonded ternary compounds: The role of group V lone pairs JF - Journal of Physics and Chemistry of Solids Y1 - 2014 A1 - Do, Dat T. A1 - S. D. Mahanti VL - 75 UR - http://www.sciencedirect.com/science/article/pii/S0022369713003892 IS - 4 ER - TY - JOUR T1 - Determining the rp-Process Flow through 56Ni: Resonances in 57Cu(p,g)58Zn Indentified with GRETINA JF - PHYSICAL REVIEW LETTERS Y1 - 2014 A1 - C. Langer A1 - F. Montes A1 - A. Aprahamian A1 - D.W. Bardayan A1 - D. Bazin A1 - B. A. Brown A1 - J. Browne A1 - H. Crawford A1 - R. Cyburt A1 - C. Domingo-Pardo A1 - A. Gade A1 - S. George A1 - P. Hosmer A1 - L. Keek A1 - A. Kontos A1 - I.Y. Lee A1 - A. Lemasson A1 - E. Lunderberg A1 - Y. Maeda A1 - M. Matos A1 - Z. Meisel A1 - S. Noji A1 - F.M. Nunes A1 - A. Nystrom A1 - G. Perdikakis A1 - J. Pereira A1 - S.J. Quinn A1 - F. Recchia A1 - H. Schatz A1 - M. Scott A1 - K. Siegl A1 - A. Simon A1 - M. Smith A1 - A. Spyrou A1 - J. Stevens A1 - S.R. Stroberg A1 - D. Weisshaar A1 - J. Wheeler A1 - K. Wimmer A1 - R.G.T. Zegers VL - 113 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.032502 ER - TY - JOUR T1 - Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk JF - PNAS Y1 - 2014 A1 - Roberta M O'Connor A1 - Jennifer M Fung A1 - Koty H Sharp A1 - Jack S Benner A1 - Colleen McClung A1 - Shelley Cushing A1 - Elizabeth R Lamkin A1 - Alexey I Fomenkov A1 - Bernard Henrissat A1 - Yuri Y Londer A1 - Matthew B Scholz A1 - Janos Posfai A1 - Stephanie Malfatti A1 - Susannah G Tringe A1 - Tanja Woyke A1 - Rex R Malmstrom A1 - Devin Coleman-Derr A1 - Marvin A Altamia A1 - Sandra Dedrick A1 - Stefan T Kaluziak A1 - Margo G Haywood A1 - Daniel L Distel VL - 111 UR - http://www.pnas.org/content/111/47/E5096.full IS - 47 ER - TY - Generic T1 - High Fidelity Simulations of Turbulent Spray Combustion T2 - Canadian Society for Mechanical Engineering International Congress Y1 - 2014 A1 - Irannejad, A A1 - Banaeizadeh, A. A1 - Jaberi, F.A. JF - Canadian Society for Mechanical Engineering International Congress ER - TY - JOUR T1 - High-precision B(E2) Measurements of Semi-Magic 58,60,62,64Ni by Coulomb Excitation JF - PHYSICAL REVIEW C Y1 - 2014 A1 - J.M. Allmond A1 - B. A. Brown A1 - A.E. Stuchbery A1 - A. Galindo-Uribarri A1 - E. Padilla-Rodal A1 - D.C. Radford A1 - J.C. Batchelder A1 - M.E. Howard A1 - J.F. Liang A1 - B. Manning A1 - R.L. Varner A1 - C.H. Yu VL - 90 UR - http://journals.aps.org/prc/abstract/10.1103/PhysRevC.90.034309 ER - TY - JOUR T1 - High-resolution two-proton stripping to 2p-1h 7/2− states via the 59Co(3He,nγ)61Cu reaction JF - THE EUROPEAN PHYSICAL JOURNAL A Y1 - 2014 A1 - P. Papka A1 - J.F. Sharpey-Schafer A1 - B. A. Brown A1 - T.S. Dinoko A1 - E.A.M.A Khaleel A1 - E.A. Lawrie A1 - J.J. Lawrie A1 - K.C.W. Li A1 - S.N.T. Majola A1 - W.A. Richter A1 - O. Shirinda A1 - M.A. Stankiewicz A1 - P. Vymers A1 - M. Wiedeking VL - 50 UR - https://people.nscl.msu.edu/~brown/brown-all-papers/541-2014-epja50.158.pdf ER - TY - JOUR T1 - Host plant-specific remodeling of midgut physiology in the generalist insect herbivore Trichoplusia ni JF - Insect Biochemistry and Molecular Biology Y1 - 2014 A1 - Herde, Marco A1 - Howe, Gregg VL - 50 UR - http://www.sciencedirect.com/science/article/pii/S0965174814000630 ER - TY - JOUR T1 - Host plant-specific remodeling of midgut physiology in the generalist insect herbivore Trichoplusia ni Y1 - 2014 A1 - Herde M A1 - Howe GA KW - Arabidopsis thaliana; Gut physiology; Herbivore; Jasmonate; Solanum lycopersicum; Transcriptome; Trichoplusia ni AB -Species 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.

UR - http://www.ncbi.nlm.nih.gov/pubmed/?term=24727019 ER - TY - JOUR T1 - Large Eddy Simulation of Turbulent Spray Breakup and Evaporation JF - International Journal of Multiphase Flow Y1 - 2014 A1 - Irannejad, A A1 - Jaberi, F.A. VL - 61 UR - http://www.sciencedirect.com/science/article/pii/S030193221400010X ER - TY - JOUR T1 - Large Low-Energy M1 Strength for 56,57Fe Within the Nuclear Shell Model JF - PHYSICAL REVIEW LETTERS Y1 - 2014 A1 - B. A. Brown A1 - R.C. Larsen VL - 113 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.252502 ER - TY - JOUR T1 - Neutrinoless double-β decay of 82Se in the shell model: Beyond the closure approximation JF - PHYSICAL REVIEW C Y1 - 2014 A1 - R.A. Sen'kov A1 - M. Horoi A1 - B. A. Brown VL - 89 UR - https://people.nscl.msu.edu/~brown/brown-all-papers/529-2014-PhysRevC.89.054304-se82.pdf ER - TY - JOUR T1 - Numerical Investigations of Shock Wave Interactions with a Supersonic Turbulent Boundary Layer JF - Physics of Fluids Y1 - 2014 A1 - A. Jammalamadaka A1 - Li, Z. A1 - Jaberi, F.A. VL - 26 UR - http://scitation.aip.org/content/aip/journal/pof2/26/5/10.1063/1.4873495 IS - 5 ER - TY - JOUR T1 - Shell and Shape Evolution at N=28: The 40Mg Ground State JF - PHYSICAL REVIEW C Y1 - 2014 A1 - H.L. Crawford A1 - P. Fallon A1 - A.O. Macchiavelli A1 - R.M. Clark A1 - B. A. Brown A1 - J.A. Tostevin A1 - D. Bazin A1 - N. Aoi A1 - P. Doornenbal A1 - M. Matsushita A1 - H. Scheit A1 - D. Steppenbeck A1 - S. Takeuchi A1 - H. Baba A1 - C.M. Campbell A1 - M. Cromaz A1 - E. Ideguchi A1 - N. Kobayashi A1 - Y. Kondo A1 - G. Lee A1 - I.Y. Lee A1 - J. Lee A1 - K. Li A1 - S. Michimasa A1 - T. Motobayashi A1 - T. Nakamura A1 - S. Ota A1 - S. Paschalis A1 - M. Petri A1 - T. Sako A1 - H. Sakurai A1 - S. Shimoura A1 - M. Takechi A1 - Y. Togano A1 - H. Wang A1 - K. Yoneda VL - 80 UR - http://journals.aps.org/prc/abstract/10.1103/PhysRevC.89.041303 ER - TY - JOUR T1 - The Shell-Model Code NuShellX@MSU JF - Nuclear Data Sheets Y1 - 2014 A1 - B. A. Brown A1 - W.D.M Rae VL - 120 UR - http://www.sciencedirect.com/science/article/pii/S0090375214004748 ER - TY - JOUR T1 - Spatially-Explicit Integrated Uncertainty and Sensitivity Analysis of Criteria Weights in Multicriteria Land Suitability Evaluation JF - Environmental Modelling & Software Y1 - 2014 A1 - Ligmann-Zielinskaa, Arika A1 - Jankowskib, Piotr VL - 57 UR - http://www.geo.msu.edu/~stsa/pubs/EMS2014_reprint.pdf ER - TY - JOUR T1 - Two-Phase Filtered Mass Density Function for LES of Turbulent Reacting Flows JF - Journal of Fluid Mechanics Y1 - 2014 A1 - Banaeizadeh, A. A1 - Jaberi, F.A. A1 - Li, Z. VL - 760 UR - http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9402098&fileId=S0022112014005734 ER - TY - JOUR T1 - Untangling the contributions of image charge and laser profile for optimal photoemission of high-brightness electron beams JF - Journal of Applied Physics Y1 - 2014 A1 - J. Portman A1 - H. Zhang A1 - K. Makino A1 - C.Y. Ruan A1 - M. Berz A1 - P. M. Duxbury VL - 116 UR - http://scitation.aip.org/content/aip/journal/jap/116/17/10.1063/1.4900582 ER - TY - JOUR T1 - WRF Model Sensitivity to Land Surface Model and Cumulus Parameterization under Short-Term Climate Extremes over the Southern Great Plains of the United States JF - Journal of Climate Y1 - 2014 A1 - Pei, Lisi A1 - Moore, Nathan A1 - Zhong, Shiyuan A1 - Luo, Lifeng A1 - Hyndman, David W A1 - Heilman, Warren E A1 - Gao, Zhiqiu VL - 27 IS - 20 ER - TY - JOUR T1 - Accuracy of the new pairing theory and its improvement JF - PHYSICAL REVIEW C Y1 - 2013 A1 - L.Y. Jia VL - 88 UR - http://journals.aps.org/prc/abstract/10.1103/PhysRevC.88.064321 ER - TY - JOUR T1 - CLASH: The Enhanced Lensing Efficiency of the Highly Elongated Merging Cluster MACS J0416.1-2403 JF - The Astrophysical Journal Letters Y1 - 2013 A1 - Zitrin, A. A1 - Meneghetti, M A1 - Umetsu, K A1 - Broadhurst, T. A1 - Bartelmann, M A1 - Bouwens, R. A1 - Bradley, L A1 - Carrasco, M. A1 - Coe, D. A1 - Ford, H A1 - Kelson, D. A1 - Koekemoer, A. M A1 - Medezinski, E A1 - Moustakas, J. A1 - Moustakas, L. A. A1 - Nonino, M. A1 - Postman, M. A1 - Rosati, P. A1 - Seidel, G A1 - Seitz, S. A1 - Sendra, I A1 - Shu, X A1 - Vega, J A1 - Zheng, W KW - dark matter KW - galaxies: clusters: general KW - galaxies: clusters: individual: MACS J0416.1–2403 KW - Galaxies: High-Redshift KW - gravitational lensing: strong VL - 762 IS - 2 ER - TY - JOUR T1 - CLASH: The Enhanced Lensing Efficiency of the Highly Elongated Merging Cluster MACS J0416.1-2403 JF - The Astrophysical Journal Letters Y1 - 2013 A1 - Zitrin, A. A1 - Meneghetti, M A1 - Umetsu, K A1 - Broadhurst, T. A1 - Bartelmann, M A1 - Bouwens, R. A1 - Bradley, L A1 - Carrasco, M. A1 - Coe, D. A1 - Ford, H A1 - Kelson, D. A1 - Koekemoer, A. M A1 - Medezinski, E A1 - Moustakas, J. A1 - Moustakas, L. A. A1 - Nonino, M. A1 - Postman, M. A1 - Rosati, P. A1 - Seidel, G A1 - Seitz, S. A1 - Sendra, I A1 - Shu, X A1 - Vega, J A1 - Zheng, W KW - dark matter KW - galaxies: clusters: general KW - galaxies: clusters: individual: MACS J0416.1–2403 KW - Galaxies: High-Redshift KW - gravitational lensing: strong VL - 762 ER - TY - JOUR T1 - CLASH: Three Strongly Lensed Images of a Candidate z 11 Galaxy JF - The Astrophysical Journal Y1 - 2013 A1 - Coe, Dan A1 - Zitrin, Adi A1 - Carrasco, Mauricio A1 - Shu, Xinwen A1 - Zheng, Wei A1 - Postman, Marc A1 - Bradley, Larry A1 - Koekemoer, Anton A1 - Bouwens, Rychard A1 - Broadhurst, Tom A1 - Monna, Anna A1 - Host, Ole A1 - Moustakas, Leonidas A A1 - Ford, Holland A1 - Moustakas, John A1 - van der Wel, Arjen A1 - Donahue, Megan A1 - Rodney, Steven A A1 - Ben{\'ıtez, Narciso A1 - Jouvel, Stephanie A1 - Seitz, Stella A1 - Kelson, Daniel D. A1 - Rosati, Piero KW - clusters KW - distances and redshifts KW - early universe KW - galaxies KW - individual VL - 762 ER - TY - JOUR T1 - CLASH: Three Strongly Lensed Images of a Candidate z~11 Galaxy JF - The Astrophysical Journal Y1 - 2013 A1 - Coe, Dan A1 - Zitrin, Adi A1 - Carrasco, Mauricio A1 - Shu, Xinwen A1 - Zheng, Wei A1 - Postman, Marc A1 - Bradley, Larry A1 - Koekemoer, Anton A1 - Bouwens, Rychard A1 - Broadhurst, Tom A1 - Monna, Anna A1 - Host, Ole A1 - Moustakas, Leonidas A A1 - Ford, Holland A1 - Moustakas, John A1 - van der Wel, Arjen A1 - Donahue, Megan A1 - Rodney, Steven A A1 - Benítez, Narciso A1 - Jouvel, Stephanie A1 - Seitz, Stella A1 - Kelson, Daniel D. A1 - Rosati, Piero KW - clusters KW - distances and redshifts KW - early universe KW - galaxies KW - individual VL - 762 IS - 1 ER - TY - JOUR T1 - Estimating wounding of lake trout by sea lamprey in the upper Great Lakes: Allowing for changing size-specific patterns JF - Journal of Great Lakes Research Y1 - 2013 A1 - Carson G. Prichard A1 - James R. Bence KW - AD Model Builder ER - TY - CONF T1 - Gadget Avalanche: A Technology Literacy Course for Novice Adults T2 - Proceedings of the 2013 Conference of the American Society for Engineering Education Y1 - 2013 A1 - Luchini-Colbry, Kathleen A1 - Dirk Colbry JF - Proceedings of the 2013 Conference of the American Society for Engineering Education CY - Atlanta, GA UR - http://www.asee.org/file_server/papers/attachment/file/0003/4344/ASEE2013-Gadget-FINAL.pdf ER - TY - JOUR T1 - Heterogeneous relaxation dynamics in amorphous materials under cyclic loading JF - Physical Review E Y1 - 2013 A1 - Nikolai V. Priezjev PB - IEEE CY - Tampa, Florida VL - 87 IS - 5 ER - TY - CONF T1 - The Institute for Cyber-Enabled Research: Regional Organization to Promote Computation in Science T2 - In proceedings of 2013 XSEDE Conference Y1 - 2013 A1 - Dirk Colbry A1 - Punch, William A1 - Bauer, Wolfgang AB -The 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.

JF - In proceedings of 2013 XSEDE Conference CY - San Diego, California ER - TY - JOUR T1 - Intra-aggregate pore structures are related to total C distribution within soil macro-aggregates JF - Soil Biology and Biochemistry Y1 - 2013 A1 - K. Ananyeva A1 - W. Wang A1 - A.J.M. Smucker A1 - M.L. Rivers A1 - A.N. Kravchenko VL - 57 ER - TY - JOUR T1 - The joint effects of efficacy and compliance: a study of household water treatment effectiveness against childhood diarrhea JF - Water research Y1 - 2013 A1 - Enger, Kyle S A1 - Nelson, Kara L A1 - Rose, Joan B A1 - Eisenberg, Joseph N S AB -The 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.}

VL - 47 N1 - {PMID:} 23290123 ER - TY - ABST T1 - Large Eddy Simulation of Evaporating Spray with a Stochastic Breakup Model Y1 - 2013 A1 - Irannejad, Abolfazl A1 - Jaberi, Farhad AB -Large 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.

PB - {SAE} International CY - Warrendale, {PA} UR - http://papers.sae.org/2013-01-1101/ ER - TY - Generic T1 - Large Eddy Simulation of Spray Mixing and Combustion with Two-Phase Filtered Mass Density Function T2 - 43rd AIAA Fluid Dynamics Conference Y1 - 2013 A1 - Irannejad, A A1 - Jaberi, F. JF - 43rd AIAA Fluid Dynamics Conference CY - San Diego, California ER - TY - JOUR T1 - Large-Eddy Simulations of Turbulent Flows in Internal Combustion Engines, International Journal of Heat and Mass Transfer Y1 - 2013 A1 - Banaeizadeh, A. A1 - Afshari, A. A1 - H. Schock A1 - Jaberi, F. VL - Vol. 60 IS - No. 10 ER - TY - JOUR T1 - Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions JF - Microfluidics and Nanofluidics Y1 - 2013 A1 - N. V Priezjev VL - 14 IS - 1-2 ER - TY - JOUR T1 - The nature of the H₂-emitting gas in the Crab nebula JF - \mnras Y1 - 2013 A1 - Richardson, C. T. A1 - Baldwin, J. A. A1 - Ferland, G. J. A1 - Loh, E. D. A1 - Kuehn, C. A. A1 - Fabian, A. C. A1 - Salomé, P. KW - ISM: molecules KW - ISM: supernova remnants KW - supernovae: individual: Crab nebula VL - 430 ER - TY - JOUR T1 - Neutrino-pair emission from hot nuclei during stellar collapse JF - PHYSICAL REVIEW C Y1 - 2013 A1 - G. Wendell Misch A1 - B. A. Brown A1 - George M. Fuller VL - 88 UR - https://people.nscl.msu.edu/~brown/brown-all-papers/512-2013-PhysRevC.88.015807.pdf ER - TY - ABST T1 - Numerical Simulations of Turbulent Sprays with a Multicomponent Evaporation Model Y1 - 2013 A1 - S. Srivastava A1 - H. Schock A1 - Jaberi, F. AB -A 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.

PB - {SAE} International CY - Warrendale, {PA} UR - http://papers.sae.org/2013-01-1603/ ER - TY - BOOK T1 - Proceedings of the 21st International Meshing Roundtable: An h-r Moving Mesh Method for One-Dimensional Time-Dependent PDEs Y1 - 2013 A1 - Benjamin Ong A1 - Russell, Robert A1 - Ruuth, Steven ED - Jiao, Xiangmin ED - Weill, Jean-Christophe PB - Springer Berlin Heidelberg CY - Berlin, Heidelberg SN - 978-3-642-33573-0 ER - TY - JOUR T1 - Relationships between intra-aggregate pore structures and distributions of Escherichia coli within soil macro-aggregates JF - Applied Soil Ecology Y1 - 2013 A1 - Kravchenko A. A1 - H.-C. Chun A1 - M. Mazer A1 - W. Wang A1 - J.B. Rose A1 - A. Smucker A1 - M. Rivers VL - 63 ER - TY - CONF T1 - Speeding up Scientific Imaging Workflows: Design of Automated Image Annotation Tool T2 - Workshop on Computer Centered Human Vision Y1 - 2013 A1 - Dirk Colbry A1 - Dyer, Fred A1 - Dworkin, Ian A1 - Wang, Yang A1 - Wang, Lifeng JF - Workshop on Computer Centered Human Vision PB - IEEE CY - Tampa, Florida ER - TY - CONF T1 - STEM inSight: Developing a Research Skills Course for First- and Second-Year Students T2 - Proceedings of the 2013 Conference of the American Society for Engineering Education Y1 - 2013 A1 - Dirk Colbry A1 - Luchini-Colbry, Kathleen JF - Proceedings of the 2013 Conference of the American Society for Engineering Education CY - Atlanta, GA UR - http://www.asee.org/file_server/papers/attachment/file/0003/3803/6188.pdf ER - TY - JOUR T1 - Subgrid-Scale Models for Large-Eddy Simulations of Shock-Boundary Layer Interactions, JF - AIAA Journal Y1 - 2013 A1 - A. Jammalamadaka A1 - Li, Z. A1 - Jaberi, F.A. VL - Vol. 5 IS - No. 5 ER - TY - JOUR T1 - Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion JF - Proceedings of the National Academy of Sciences Y1 - 2012 A1 - B. Ahmad A1 - L.J. Lapidus A1 - Y. Chen VL - 7 IS - 109 ER - TY - JOUR T1 - Alternative splicing of a multi-drug transporter from Pseudoperonospora cubensis generates an RXLR effector protein that elicits a rapid cell death. JF - PLoS ONE, in press Y1 - 2012 A1 - Savory, E. A1 - Zou, C. A1 - Adhikari, B. A1 - Hamilton, J. P. A1 - C. R. Buell A1 - Shiu, S.-H. A1 - B. Day ER - TY - JOUR T1 - ALTITUDINAL CLINAL VARIATION IN WING SIZE AND SHAPE IN AFRICAN DROSOPHILA MELANOGASTER: ONE CLINE OR MANY? JF - Evolution Y1 - 2012 A1 - Pitchers, William A1 - Pool, John E A1 - Dworkin, Ian VL - 67 ER - TY - JOUR T1 - A 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~9.2 JF - Astrophysical Journal Y1 - 2012 A1 - Bouwens, R, A1 - Bradley, L A1 - Zitrin, A. A1 - Coe, D. A1 - Franx, M. A1 - Zheng, W A1 - Smit, R A1 - Host, O. A1 - Postman, M. A1 - Moustakas, L A1 - Labbe, I A1 - Carrasco, M. A1 - Molino, A. A1 - Donahue, M A1 - Kelson, D. D A1 - Meneghetti, M A1 - Jha, S. A1 - Benitez, N A1 - Lemze, D A1 - Umetsu, K A1 - Broadhurst, T. A1 - Moustakas, J. A1 - Rosati, P. A1 - Bartelmann, M A1 - Ford, H A1 - Graves, G. A1 - Grillo, C. A1 - Infante, L A1 - Jiminez-Teja, Y A1 - Jouvel, S A1 - Lahav, O. A1 - Maoz, D A1 - Medezinski, E A1 - Melchior, P A1 - Merten, J A1 - Nonino, M. A1 - Ogaz, S. A1 - Seitz, S. KW - Astrophysics - Cosmology and Extragalactic Astrophysics ER - TY - JOUR T1 - CLASH: Discovery of a Bright z ~= 6.2 Dwarf Galaxy Quadruply Lensed by MACS J0329.6-0211 JF - The Astrophysical Journal Letters Y1 - 2012 A1 - Zitrin, A. A1 - Moustakas, J. A1 - Bradley, L A1 - Coe, D. A1 - Moustakas, L. A. A1 - Postman, M. A1 - Shu, X A1 - Zheng, W A1 - Benítez, N. A1 - Bouwens, R. A1 - Broadhurst, T. A1 - Ford, H A1 - Host, O. A1 - Jouvel, S A1 - Koekemoer, A. A1 - Meneghetti, M A1 - Rosati, P. A1 - Donahue, M A1 - Grillo, C. A1 - Kelson, D. A1 - Lemze, D A1 - Medezinski, E A1 - Molino, A. A1 - Nonino, M. A1 - Ogaz, S. KW - dark matter KW - galaxies: clusters: general KW - galaxies: clusters: individual: MACS J0329.6-0211 KW - Galaxies: High-Redshift KW - gravitational lensing: strong VL - 747 IS - 1 ER - TY - JOUR T1 - CLASH: Mass Distribution in and around MACS J1206.2-0847 from a Full Cluster Lensing Analysis JF - The Astrophysical Journal Y1 - 2012 A1 - Umetsu, Keiichi A1 - Medezinski, Elinor A1 - Nonino, Mario A1 - Merten, Julian A1 - Zitrin, Adi A1 - Molino, Alberto A1 - Grillo, Claudio A1 - Carrasco, Mauricio A1 - Donahue, Megan A1 - Mahdavi, Andisheh A1 - Coe, Dan A1 - Postman, Marc A1 - Koekemoer, Anton A1 - Czakon, Nicole A1 - Sayers, Jack A1 - Mroczkowski, Tony A1 - Golwala, Sunil A1 - Koch, Patrick M A1 - Lin, Kai-Yang A1 - Molnar, Sandor M A1 - Rosati, Piero A1 - Balestra, Italo A1 - Mercurio, Amata A1 - Scodeggio, Marco A1 - Biviano, Andrea A1 - Anguita, Timo A1 - Infante, Leopoldo A1 - Seidel, Gregor A1 - Sendra, Irene A1 - Jouvel, Stephanie A1 - Host, Ole A1 - Lemze, Doron A1 - Broadhurst, Tom A1 - Meneghetti, Massimo A1 - Moustakas, Leonidas A1 - Bartelmann, Matthias A1 - Benítez, Narciso A1 - Bouwens, Rychard A1 - Bradley, Larry A1 - Ford, Holland A1 - Jiménez-Teja, Yolanda A1 - Kelson, Daniel A1 - Lahav, Ofer A1 - Melchior, Peter A1 - Moustakas, John A1 - Ogaz, Sara A1 - Seitz, Stella A1 - Zheng, Wei KW - cosmology: observations KW - dark matter KW - galaxies: clusters: individual: MACS J1206.2-0847 KW - gravitational lensing: strong KW - gravitational lensing: weak VL - 755 IS - 1 ER - TY - JOUR T1 - CLASH: New Multiple Images Constraining the Inner Mass Profile of MACS J1206.2-0847 JF - The Astrophysical Journal Y1 - 2012 A1 - Zitrin, A. A1 - Rosati, P. A1 - Nonino, M. A1 - Grillo, C. A1 - Postman, M. A1 - Coe, D. A1 - Seitz, S. A1 - Eichner, T A1 - Broadhurst, T. A1 - Jouvel, S A1 - Balestra, I. A1 - Mercurio, A A1 - Scodeggio, M A1 - Benítez, N. A1 - Bradley, L A1 - Ford, H A1 - Host, O. A1 - Jimenez-Teja, Y A1 - Koekemoer, A. A1 - Zheng, W A1 - Bartelmann, M A1 - Bouwens, R. A1 - Czoske, O A1 - Donahue, M A1 - Graur, O A1 - Graves, G. A1 - Infante, L A1 - Jha, S. A1 - Kelson, D. A1 - Lahav, O. A1 - Lazkoz, R A1 - Lemze, D A1 - Lombardi, M. A1 - Maoz, D A1 - McCully, C. A1 - Medezinski, E A1 - Melchior, P A1 - Meneghetti, M A1 - Merten, J A1 - Molino, A. A1 - Moustakas, L. A. A1 - Ogaz, S. A1 - Patel, B. A1 - Regoes, E. A1 - Riess, A. A1 - Rodney, S A1 - Umetsu, K A1 - Van der Wel, A. KW - dark matter KW - galaxies: clusters: general KW - galaxies: clusters: individual: MACS J1206.2–0847 KW - Galaxies: High-Redshift KW - gravitational lensing: strong VL - 749 IS - 2 ER - TY - JOUR T1 - CLASH: Precise New Constraints on the Mass Profile Galaxy Cluster A2261 JF - The Astrophysical Journal Y1 - 2012 A1 - Coe, Dan A1 - Umetsu, Keiichi A1 - Zitrin, Adi A1 - Donahue, Megan A1 - Medezinski, Elinor A1 - Postman, Marc A1 - Carrasco, Mauricio A1 - Anguita, Timo A1 - Geller, Margaret J A1 - Rines, Kenneth J. A1 - Diaferio, Antonaldo A1 - Kurtz, Michael J A1 - Bradley, Larry A1 - Koekemoer, Anton A1 - Zheng, Wei A1 - Nonino, Mario A1 - Molino, Alberto A1 - Mahdavi, Andisheh A1 - Lemze, Doron A1 - Infante, Leopoldo A1 - Ogaz, Sara A1 - Melchior, Peter A1 - Host, Ole A1 - Ford, Holland A1 - Grillo, Claudio A1 - Rosati, Piero A1 - Jiménez-Teja, Yolanda A1 - Moustakas, John A1 - Ascaso, Begoña A1 - Lahav, Ofer; A1 - Bartelmann, Matthias A1 - Benítez, Narciso A1 - Bouwens, Rychard A1 - Graur, Or A1 - Graves, Genevieve A1 - Jha, Saurab A1 - Jouvel, Stephanie A1 - Kelson, Daniel A1 - Moustakas, Leonidas A1 - Maoz, Dan A1 - Meneghetti, Massimo A1 - Merten, Julian A1 - Riess, Adam A1 - Rodney, Steve A1 - Seitz, Stella VL - 757 IS - 1 ER - TY - JOUR T1 - Climate Change and Risk Projection: Dynamic Models of Tsetse and African Trypanosomiasis in Kenya JF - Annals of the Association of American Geographers Y1 - 2012 A1 - Messina, Joseph A1 - Moore, Nathan A1 - DeVisser, Mark A1 - McCord, Paul A1 - Walker, Edward VL - 102 IS - 5 ER - TY - JOUR T1 - Computational study of the thermal conductivity in defective carbon nanostructures JF - Phys. Rev. B Y1 - 2012 A1 - Fthenakis, Zacharias G. A1 - David Tománek PB - American Physical Society VL - 86 ER - TY - CONF T1 - Coordination of Vision and Action in Chameleons T2 - 49th Animal Behavior Society Annual Meeting Y1 - 2012 A1 - Ingle, Nicholis A1 - Door, Tim A1 - Dirk Colbry A1 - Dyer, Fred JF - 49th Animal Behavior Society Annual Meeting CY - Albuquerque, {NM} ER - TY - JOUR T1 - Curcumin Prevents Aggregation in α-Synuclein by Increasing Reconfiguration Rate JF - Journal of Biological Chemistry Y1 - 2012 A1 - B. Ahmad A1 - L.J. Lapidus VL - 12 IS - 287 ER - TY - CONF T1 - CyberGreen: Hands-On Engineering Research in Sustainability and Supercomputing” T2 - ASEE North Central Section 2012 Conference Y1 - 2012 A1 - Dirk Colbry A1 - Luchini-Colbry, Katy JF - ASEE North Central Section 2012 Conference CY - Ada, Ohio ER - TY - JOUR T1 - Designing Electrical Contacts to ${\mathrm{MoS}}_{2}$ Monolayers: A Computational Study JF - Phys. Rev. Lett. Y1 - 2012 A1 - Popov, Igor A1 - Seifert, Gotthard A1 - David Tománek PB - American Physical Society VL - 108 ER - TY - JOUR T1 - Dynamics of Performing and Remembering Organizational Routines JF - Journal of Management Studies Y1 - 2012 A1 - Miller, K. D. A1 - Pentland, B. T. A1 - Choi, S. VL - 49 IS - 8 ER - TY - JOUR T1 - Effects of crossflow velocity and transmembrane pressure on microfiltration of oil-in-water emulsions JF - Journal of Membrane Science Y1 - 2012 A1 - Tohid Darvishzadeh A1 - Nikolai V. Priezjev VL - 423 ER - TY - JOUR T1 - Evaluating DEM source and resolution uncertainties in the Soil and Water Assessment Tool JF - Stochastic Environmental Research & Risk Assessment Y1 - 2012 A1 - Lin, Shengpan A1 - C. Jing A1 - N.A. Coles A1 - V. Chaplot A1 - Moore, Nathan A1 - Wu, Jiaping VL - 27 IS - 1 ER - TY - JOUR T1 - Evaluation of estimating daily maximum and minimum air temperature with MODIS data in east Africa JF - Journal of Applied Earth Observations and Geoinformation Y1 - 2012 A1 - Lin, Shengpan A1 - Wu, Jiaping A1 - Moore, Nathan A1 - DeVisser, Mark A1 - Messina, Joseph VL - 14 IS - 1 ER - TY - JOUR T1 - Evolution and stability of altruist strategies in microbial games JF - Physical Review E Y1 - 2012 A1 - Adami, Christoph A1 - Schossau, Jory A1 - Hintze, Arend AB -When 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.

VL - 85 UR - http://link.aps.org/doi/10.1103/PhysRevE.85.011914 ER - TY - JOUR T1 - Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis JF - PLoS ONE, in press Y1 - 2012 A1 - C. R. Buell A1 - Adhikari, B. A1 - Savory, E. A1 - Vaillancourt, B. A1 - Childs, K. L. A1 - Hamilton, J. P. A1 - B. Day ER - TY - JOUR T1 - Formation and Stability of Cellular Carbon Foam Structures: An \textit{Ab Initio} Study JF - Phys. Rev. Lett. Y1 - 2012 A1 - Zhen Zhu A1 - David Tománek PB - American Physical Society VL - 109 ER - TY - JOUR T1 - Helicity in Ropes of Chiral Nanotubes: Calculations and Observation JF - Phys. Rev. Lett. Y1 - 2012 A1 - Teich, David A1 - Seifert, Gotthard A1 - Iijima, Sumio A1 - David Tománek PB - American Physical Society VL - 108 ER - TY - JOUR T1 - Interfacial friction between semiflexible polymers and crystalline surfaces JF - J. Chem. Phys. Y1 - 2012 A1 - Nikolai V. Priezjev VL - 136 ER - TY - JOUR T1 - Intra-aggregate pore characteristics: X-ray computed microtomography analysis JF - Soil Sci. Soc Am J. Y1 - 2012 A1 - W. Wang A1 - A.N. Kravchenko A1 - A.J.M. Smucker A1 - M.L. Rivers VL - 76 ER - TY - CONF T1 - Lessons Learned When Building a Greenfield High Performance Computing Ecosystem T2 - 26th Large Installation System Administration conference {LISA) Y1 - 2012 A1 - Keen, Andrew JF - 26th Large Installation System Administration conference {LISA) CY - San Diego, California, USA ER - TY - JOUR T1 - A magnified young galaxy from about 500 million years after the Big Bang JF - Nature Y1 - 2012 A1 - Zheng, Wei A1 - Postman, Marc A1 - Zitrin, Adi A1 - Moustakas, John A1 - Shu, Xinwen A1 - Jouvel, Stephanie A1 - Høst, Ole A1 - Molino, Alberto A1 - Bradley, Larry A1 - Coe, Dan A1 - Moustakas, Leonidas A A1 - Carrasco, Mauricio A1 - Ford, Holland A1 - Benítez, Narciso A1 - Lauer, Tod R A1 - Seitz, Stella; B A1 - Bouwens, Rychard A1 - Koekemoer, Anton A1 - Medezinski, Elinor A1 - Bartelmann, Matthias A1 - Broadhurst, Tom A1 - Donahue, Megan A1 - Grillo, Claudio A1 - Infante, Leopoldo A1 - Jha, Saurabh W A1 - Kelson, Daniel D. A1 - Lahav, Ofer A1 - Lemze, Doron A1 - Melchior, Peter A1 - Meneghetti, Massimo A1 - Merten, Julian A1 - Nonino, Mario A1 - Ogaz, Sara A1 - Rosati, Piero A1 - Umetsu, Keiichi A1 - van der Wel, Arjen VL - 489 IS - 7416 ER - TY - JOUR T1 - Mass Measurements of the Neutron-Deficient 41Ti, 45Cr, 49Fe, and 53Ni Nuclides: ￼First Test of the Isobaric Multiplet Mass Equation in fp-Shell Nuclei JF - PHYSICAL REVIEW LETTERS Y1 - 2012 A1 - Y.H. Zhang A1 - H.S. Xu A1 - Yu. A. Litvinov A1 - X.L. Tu A1 - X.L. Yan A1 - S. Typel A1 - K. Blaum A1 - M. Wang A1 - X.H. Zhou A1 - Y. Sun A1 - B. A. Brown A1 - Y.J. Yuan A1 - J.W. Xia A1 - J.C. Yang A1 - G. Audi A1 - X.C. Chen A1 - G.B. Jia A1 - Z.G. Hu A1 - X.W. Ma A1 - R.S. Mao A1 - B. Mei A1 - P. Shuai A1 - Z.Y. Sun A1 - S.T. Wang A1 - G.Q. Xiao A1 - X. Xu A1 - T. Yamaguchi A1 - Y. Yamaguchi A1 - Y.D. Zang A1 - H.W. Zhao A1 - T.C. Zhao A1 - W. Zhang A1 - W.L. Zhan VL - 109 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.102501 ER - TY - JOUR T1 - Medical image-based simulation of abdominal aortic aneurysm growth JF - Mechanics Research Communications Y1 - 2012 A1 - Zeinali-Davarani, S. A1 - Baek, S. KW - Aneurysm rupture KW - Finite element analysis KW - Inverse optimization KW - Patient-specific modeling KW - Vascular growth and remodeling AB -Advances 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.

VL - 42 UR - http://www.sciencedirect.com/science/article/pii/S0093641312000109 ER - TY - Generic T1 - Methylmercury (MeHg) disrupts fluo4 fluorescence in cerebellar slices from GABAA receptor alpha6 (-/-) mice Y1 - 2012 A1 - A B Bradford A1 - W D Atchison PB - Society of Toxicology 2012 CY - San Francisco, CA ER - TY - JOUR T1 - mRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection JF - PLoS ONE, in press Y1 - 2012 A1 - Savory, E. A1 - Adhikari, B. A1 - Hamilton, J. P. A1 - Vaillancourt, B. A1 - C. R. Buell A1 - B. Day ER - TY - JOUR T1 - Nanomechanical energy storage in twisted nanotube ropes JF - Phys. Rev. Lett. Y1 - 2012 A1 - Teich, David A1 - Fthenakis, Zacharias G. A1 - Seifert, Gotthard A1 - David Tománek PB - American Physical Society VL - 109 ER - TY - JOUR T1 - A Parallel Space-Time Algorithm JF - SIAM Journal on Scientific Computing Y1 - 2012 A1 - Christlieb, Andrew J. A1 - Haynes, Ronald D. A1 - Ong, Benjamin W. VL - 34 IS - 5 ER - TY - JOUR T1 - Physics of bandgap formation in Cu–Sb–Se based novel thermoelectrics: the role of Sb valency and Cu d levels JF - IOP Science Y1 - 2012 A1 - Do, Dat A1 - Ozolins,Vidvuds A1 - S. D. Mahanti A1 - Lee,Mal-Soon A1 - Zhang,Yongsheng A1 - C Wolverton VL - 24 UR - http://iopscience.iop.org.proxy1.cl.msu.edu/0953-8984/24/41/415502 IS - 41 ER - TY - THES T1 - Preventing diarrheal infections with household water treatment: lessons from simulation models Y1 - 2012 A1 - Enger, Kyle Scott AB -Diarrheal 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.

UR - http://www.openthesis.org/documents/Preventing-diarrheal-infections-with-household-601272.html ER - TY - Generic T1 - The role of standing genetic variation in adaptation of digital organisms to a new environment T2 - Proceedings of the 13th International Conference on Artificial Life Y1 - 2012 A1 - Anderson, CJR JF - Proceedings of the 13th International Conference on Artificial Life VL - 13: 3-10 ER - TY - JOUR T1 - Selective probe of the morphology and local vibrations at carbon nanoasperities JF - J. Chem. Phys. Y1 - 2012 A1 - Toshihiko Fujimori A1 - Koki Urita A1 - Tomanek, David A1 - Tomonori Ohba A1 - Isamu Moriguchi A1 - Morinobu Endo A1 - Katsumi Kaneko PB - AIP VL - 136 ER - TY - CONF T1 - Simultaneous Iterative Reconstruction Techniques for Computerized Tomography on GPU T2 - Inverse Problems Symposium Y1 - 2012 A1 - Xin, Junjun A1 - Bardel, Chuck A1 - Dirk Colbry A1 - Udpa, Lalita A1 - Udpa, Satish JF - Inverse Problems Symposium CY - East Lansing, MI ER - TY - JOUR T1 - Synthesis and Transformation of Linear Adamantane Assemblies inside Carbon Nanotubes JF - ACS Nano Y1 - 2012 A1 - Zhang, Jinying A1 - Feng, Yanquan A1 - Ishiwata, Hitoshi A1 - Miyata, Yasumitsu A1 - Kitaura,Ryo A1 - Dahl, Jeremy E. P. A1 - Carlson, Robert M. K. A1 - Shinohara, Hisanori A1 - David Tománek VL - 6 ER - TY - CONF T1 - Approximate kernel k-means: solution to large scale kernel clustering T2 - Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining Y1 - 2011 A1 - Chitta, Radha A1 - Jin, Rong A1 - Havens, Timothy C. A1 - Jain, Anil K. KW - k-means KW - kernel clustering KW - large-scale clustering JF - Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining T3 - KDD '11 PB - ACM CY - San Diego, CA, USA SN - 978-1-4503-0813-7 ER - TY - JOUR T1 - Calling to Be Your Best: Your Calling to Science JF - Mater. Express Y1 - 2011 A1 - David Tománek VL - 1 ER - TY - JOUR T1 - Comparison of image segmentation methods in simulated 2D and 3D microtomographic images of soil aggregates JF - Geoderma Y1 - 2011 A1 - W. Wang A1 - A.N. Kravchenko A1 - A.J.M. Smucker A1 - M.L. Rivers VL - 162 ER - TY - JOUR T1 - The Comprehensive Phytopathogen Genomics Resource: An electronic resource for data-mining plant pathogen genomes JF - Database, doi: 10.1093/database/bar053. Y1 - 2011 A1 - Hamilton, J. P. A1 - Neeno-Eckwall, E. A1 - Adhikari, B. A1 - Perna, N. A1 - Tisserat, N. A1 - Leach, J.E. A1 - Lévesque, C. A. A1 - C. R. Buell ER - TY - JOUR T1 - East African Food Security as Influenced by Future Climate Change and Land Use Change at Local to Regional Scales JF - Climatic Change Y1 - 2011 A1 - Moore, Nathan A1 - Alagarswamy, Gopal A1 - Pijanowski, Bryan A1 - Thornton, Phil A1 - Lofgren, Brent A1 - Olson, Jennifer A1 - Yanda, Pius A1 - Qi, Jiaguo VL - 107 ER - TY - JOUR T1 - Evaluating error propagation in coupled land-atmosphere models JF - Earth Interactions Y1 - 2011 A1 - Pijanowski, Bryan A1 - Moore, Nathan A1 - Mauree, Desaraden A1 - Niyogi, Dev VL - 15 ER - TY - JOUR T1 - Fame on Sale: Pitfalls of the Ranking Game JF - Mater. Express Y1 - 2011 A1 - Tomanek, David VL - 1 ER - TY - JOUR T1 - Implicit Parallel Time Integrators JF - Journal of Scientific Computing Y1 - 2011 A1 - Andrew Christlieb A1 - Benjamin Ong VL - 49 IS - 2 ER - TY - JOUR T1 - Information Content of Colored Motifs in Complex Networks JF - Artificial Life Y1 - 2011 A1 - Adami, Christoph A1 - Qian, Jifeng A1 - Rupp, Matthew A1 - Hintze, Arend AB -We 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.

VL - 17 UR - http://dx.doi.org/10.1162/artl_a_00045 ER - TY - JOUR T1 - Long-term differences in tillage and land use affect intra-aggregate pore heterogeneity JF - Soil Sci. Soc Am J Y1 - 2011 A1 - A.N. Kravchenko A1 - W. Wang A1 - A.J.M. Smucker A1 - M.L. Rivers VL - 75 ER - TY - THES T1 - MODELS TO AID IN THE SELECTION OF PROCEDURES USED TO MANAGE LAKE ERIE WALLEYE (SANDER VITREUS) Y1 - 2011 A1 - Berger, A.M. PB - Michigan State University ER - TY - JOUR T1 - Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures JF - J. Chem. Phys. Y1 - 2011 A1 - N. V Priezjev VL - 135 ER - TY - JOUR T1 - Molecular Dynamics Study of Thermal Transport in GaAs-SAM-GaAs Junctions with Ab-initio Characterization of Thiol-GaAs Bonds JF - J. of App. Phys. Y1 - 2011 A1 - Tengfei Luo A1 - John R. Lloyd VL - 109 ER - TY - JOUR T1 - Molecular dynamics study of thermal transport in GaAs-self-assembly monolayer-GaAs junctions with ab initio characterization of thiol-GaAs bonds JF - J. of App. Phys. Y1 - 2011 A1 - Tengfei Luo A1 - John R. Lloyd VL - 109 ER - TY - CONF T1 - Multi-label Learning with Incomplete Class Assignments T2 - Proceedings of IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2011) Y1 - 2011 A1 - S.S. Bucak A1 - Jin, Rong A1 - Jain, Anil K. JF - Proceedings of IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2011) ER - TY - JOUR T1 - Nanoconfinement effects on the reversibility of hydrogen storage in ammonia borane: A first-principles study JF - J. Chem. Phys. Y1 - 2011 A1 - Chang, Kiseok A1 - Kim, Eunja A1 - Weck, Philippe F. A1 - David Tománek VL - 134 ER - TY - JOUR T1 - The Nature of the Warm/Hot Intergalactic Medium. I. Numerical Methods, Convergence, and O VI Absorption JF - \apj Y1 - 2011 A1 - Smith, B. D. A1 - Hallman, E. J. A1 - Shull, J. M. A1 - O'Shea, B. W. KW - cosmology: observations KW - intergalactic medium KW - quasars: absorption lines VL - 731 ER - TY - JOUR T1 - On the Performance of Indirect Encoding Across the Continuum of Regularity JF - IEEE Transactions on Evolutionary Computation Y1 - 2011 A1 - Clune, J. A1 - Stanley, K.O. A1 - Pennock, R.T. A1 - Ofria, C. ER - TY - CONF T1 - Reducing the barrier to entry using portable apps T2 - Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery Y1 - 2011 A1 - Dirk Colbry KW - outreach KW - research portals AB -An 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.

JF - Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery T3 - {TG} '11 PB - ACM CY - New York, NY, USA SN - 978-1-4503-0888-5 ER - TY - JOUR T1 - Search for the largest two-dimensional aggregates of boron: An ab initio study JF - Phys. Rev. B Y1 - 2011 A1 - Ihsan Boustani A1 - Zhen Zhu A1 - David Tománek PB - American Physical Society VL - 83 ER - TY - JOUR T1 - Second-order selection for evolvability in a large Escherichia coli population JF - Science Y1 - 2011 A1 - Woods, R. J. A1 - Barrick, J. E. A1 - T. F. Cooper A1 - U. Shrestha A1 - M. R. Kauth A1 - Lenski, R.E. VL - 331 ER - TY - JOUR T1 - Second-order selection for evolvability in a large Escherichia coli population JF - Science Y1 - 2011 A1 - Woods, R. J. A1 - Barrick, E A1 - T. F. Cooper A1 - U. Shrestha A1 - M. R. Kauth A1 - Lenski, R.E. VL - 331 ER - TY - JOUR T1 - Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory JF - Proceedings of the Royal Society B: Biological Sciences Y1 - 2011 A1 - Clune, J. A1 - Goldsby, H.J. A1 - Ofria, C. A1 - Pennock, R.T. PB - The Royal Society VL - 278 ER - TY - JOUR T1 - Signatures of minor mergers in Milky Way-like disc kinematics: Ringing revisited JF - ArXiv e-prints Y1 - 2011 A1 - Gómez, F. A. A1 - Minchev, I. A1 - Villalobos, Á. A1 - O'Shea, B. W. A1 - Williams, M. E. K. KW - Astrophysics - Galaxy Astrophysics ER - TY - CONF T1 - Speedup of fuzzy and possibilistic c-means for large-scale clustering T2 - IEEE Int. Conf. Fuzzy Systems Y1 - 2011 A1 - Havens, Timothy C. A1 - Chitta, Radha A1 - Jain, Anil K. A1 - Jin, Rong JF - IEEE Int. Conf. Fuzzy Systems CY - Taipei, Taiwan ER - TY - JOUR T1 - Adapting MODIS-derived LAI and fractional cover into the RAMS model for East Africa JF - International Journal of Climatology Y1 - 2010 A1 - Moore, Nathan A1 - Torbick, Nathan A1 - Pijanowski, Bryan A1 - Lofrgren, Brent A1 - Wang, Jing A1 - Kim, Dong-Yun A1 - Andresen, Jeffrey A1 - Olson, Jennifer VL - 30 IS - 13 ER - TY - CONF T1 - Beyond NomBank: A Study of Implicit Argumentation for Nominal Predicates T2 - Association for Computational Linguistics Y1 - 2010 A1 - Matthew Gerber A1 - Joyce Y. Chai AB -Despite 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.

JF - Association for Computational Linguistics PB - Association for Computational Linguistics CY - Uppsala, Sweden ER - TY - JOUR T1 - Conformational Sampling of Influenza Fusion Peptide in Membrane Bilayers as a Function of Termini and Protonation States JF - Journal of Physical Chemistry B Y1 - 2010 A1 - Panahi, Afra A1 - Michael Feig AB -Influenza 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.

VL - 114 ER - TY - JOUR T1 - Conformational Sampling of S- and R-Warfarin in Polar Solvents: Implications for Stereoselective Complex Formation JF - Journal of Molecular Structure (Theochem) Y1 - 2010 A1 - Michael Feig A1 - K. Gebreyohannes A1 - V. McGuffin AB -Molecular 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.

VL - 949 IS - 1-3 ER - TY - JOUR T1 - Defect-induced rigidity enhancement in layered semiconductors JF - Solid State Communications Y1 - 2010 A1 - Rak, Zs. A1 - S. D. Mahanti A1 - Mandal, Krishna C A1 - Fernelius, N.C. VL - 150 IS - 27-28 ER - TY - JOUR T1 - Different Truths in Different Worlds JF - Organization Science Y1 - 2010 A1 - Miller, K. D. A1 - Lin, S. VL - 21 ER - TY - JOUR T1 - Doping dependence of electronic and mechanical properties of GaSe_{1−x}Te_{x} and Ga_{1−x}In_{x}Se from first principles JF - Physical Review B Y1 - 2010 A1 - Rak, Zs. A1 - S. D. Mahanti A1 - Mandal, Krishna C A1 - Fernelius, N.C. VL - 82 IS - 15 ER - TY - JOUR T1 - Effect of membrane thickness on conformational sampling of phospholamban from computer simulations JF - Biophysical Journal Y1 - 2010 A1 - Sayadi, Maryam A1 - Seiichiro Tanizaki A1 - Michael Feig AB -The 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.

VL - 98 IS - 5 ER - TY - JOUR T1 - Equilibrium Molecular Dynamics Study of Lattice Thermal Conductivity/Conductance of Au-SAM-Au Junctions JF - J. Heat Transfer Y1 - 2010 A1 - Tengfei Luo A1 - John R. Lloyd VL - 132 ER - TY - JOUR T1 - Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects JF - Molecular Biology and Evolution Y1 - 2010 A1 - Barrick, J. E. A1 - M. R. Kauth A1 - C. C. Strelioff A1 - Lenski, R.E. VL - 27 ER - TY - JOUR T1 - Galaxy Cluster Radio Relics in Adaptive Mesh Refinement Cosmological Simulations: Relic Properties and Scaling Relationships JF - ArXiv e-prints Y1 - 2010 A1 - Skillman, S. W. A1 - undefined A1 - O'Shea, B. W. A1 - Burns, J. O. A1 - Smith, B. D. A1 - Turk, M. J. KW - Astrophysics - Cosmology and Extragalactic Astrophysics ER - TY - JOUR T1 - Galaxy Clusters at the Edge: Temperature, Entropy, and Gas Dynamics Near the Virial Radius JF - \apj Y1 - 2010 A1 - Burns, J. O. A1 - Skillman, S. W. A1 - O'Shea, B. W. KW - cosmology: observations KW - cosmology: theory KW - hydrodynamics KW - intergalactic medium KW - methods: numerical KW - X-rays: galaxies: clusters VL - 721 ER - TY - JOUR T1 - A High-Order Finite-Difference Method for Numerical Simulations of Supersonic Turbulent Flows JF - International Journal of Numerical Methods in Fluids Y1 - 2010 A1 - Li, Z. A1 - Jaberi, F.A. VL - To be published ER - TY - JOUR T1 - Implicit Parallel Time Integrators JF - Journal of Scientific Computing Y1 - 2010 A1 - Andrew Christlieb A1 - Benjamin Ong AB -In 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.

VL - 46 IS - 1 ER - TY - CONF T1 - Investigating whether HyperNEAT produces modular neural networks T2 - Proceedings of the Genetic and Evolutionary Computation Conference Y1 - 2010 A1 - Clune, J. A1 - Beckmann, B.E. A1 - McKinley, P.K. A1 - Ofria, C. JF - Proceedings of the Genetic and Evolutionary Computation Conference PB - ACM ER - TY - JOUR T1 - A landscape and climate data logistic model of tsetse distributions in Kenya JF - PLoS One Y1 - 2010 A1 - Moore, Nathan A1 - Messina, Joseph VL - 5 IS - 7 ER - TY - CONF T1 - Large -Scale Simulations of Incident Shock-Turbulent Boundary Layer Interactions T2 - 48th AIAA Aerospace Sciences Meeting Y1 - 2010 A1 - A. Jammalamadaka A1 - Jaberi, F.A. JF - 48th AIAA Aerospace Sciences Meeting CY - Orlando, FL ER - TY - JOUR T1 - Large-Eddy Simulations of Turbulent Methane Jet Flames with Filtered Mass Density Function JF - International Journal of Heat and Mass Transfer Y1 - 2010 A1 - Yaldizli, M. A1 - Mehravaran, K. A1 - Jaberi, F.A. KW - Filtered mass density function; PDF methods; Monte-Carlo simulations; Methane jet flames KW - LES AB -The 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.

VL - 53 IS - 11-12 ER - TY - CONF T1 - Large-Scale Simulations of Supersonic Turbulent Reacting Flows T2 - 48th AIAA Aerospace Sciences Meeting Y1 - 2010 A1 - Li, Z. A1 - Jaberi, F.A. A1 - Banaeizadeh, A. AB -The 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.

JF - 48th AIAA Aerospace Sciences Meeting PB - AIAA CY - Orlando, FL ER - TY - CONF T1 - Local and Global Radiative Feedback from Population III Star Formation T2 - American Institute of Physics Conference Series Y1 - 2010 A1 - O'Shea, B. W. A1 - Whalen, D. J. ED - {D. J. Whalen, V. Bromm, ED - N. Yoshida} KW - Distances KW - Population III stars KW - Pre-main sequence objects KW - protostellar clouds KW - radial velocities KW - radiative transfer KW - redshift KW - redshifts KW - scattering KW - spatial distribution of galaxies KW - star formation KW - young stellar objects and protostars JF - American Institute of Physics Conference Series T3 - American Institute of Physics Conference Series VL - 1294 ER - TY - JOUR T1 - Modeling the combined effect of surface roughness and shear rate on slip flow of simple fluids JF - Physical Review E Y1 - 2010 A1 - A. Niavarani A1 - N. V Priezjev AB -Molecular 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.

VL - 81 IS - 1 ER - TY - CONF T1 - Multi-label Multiple Kernel Learning by Stochastic Approximation: Application to Visual Object Recognition T2 - Proceedings of Neural Information Processign Systems (NIPS 2010) Y1 - 2010 A1 - S.S.Bucak A1 - Jin, Rong A1 - Jain, Anil K. JF - Proceedings of Neural Information Processign Systems (NIPS 2010) ER - TY - JOUR T1 - Multi-level Extension of the Cluster-In-Molecule Local Correlation Methodology: Merging Coupled-Cluster and Moller-Plesset Perturbation Theories JF - Journal of Physical Chemistry A Y1 - 2010 A1 - Wei Li A1 - Piotr Piecuch AB -A 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.

VL - 114 IS - 24 ER - TY - JOUR T1 - Non-Equilibrium Molecular Dynamics Study of Thermal Energy Transport in Au-SAM-Au Junctions JF - Int. J. of Heat and Mass Transfer Y1 - 2010 A1 - Tengfei Luo A1 - John R. Lloyd VL - 53 ER - TY - CONF T1 - Numerical Investigations of Shock-Turbulence Interactions in a Planar Mixing Layer T2 - 48th AIAA Aerospace Sciences Meeting Y1 - 2010 A1 - Li, Z. A1 - Jaberi, F.A. AB -Direct 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.

JF - 48th AIAA Aerospace Sciences Meeting PB - AIAA CY - Orlando, FL ER - TY - CONF T1 - One Class Matrix Completion with Low Density Factorizations T2 - Proceedings of IEEE International Conference on Data Mining (ICDM 2010) Y1 - 2010 A1 - V. Sindhwani A1 - S.S. Bucak A1 - J. Hu A1 - A. Mojsilovic JF - Proceedings of IEEE International Conference on Data Mining (ICDM 2010) ER - TY - JOUR T1 - On the Origin of the Highest Redshift Gamma-Ray Bursts JF - \apj Y1 - 2010 A1 - Belczynski, K. A1 - Holz, D. E. A1 - Fryer, C. L. A1 - Berger, E. A1 - Hartmann, D. H. A1 - O'Shea, B. W. KW - binaries: general KW - gamma rays: bursts KW - stars: formation VL - 708 ER - TY - JOUR T1 - Parallel High-Order Integrators JF - SIAM Journal on Scientific Computing Y1 - 2010 A1 - Christlieb, Andrew J. A1 - Macdonald, Colin B. A1 - Ong, Benjamin W. VL - 32 IS - 2 ER - TY - JOUR T1 - PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy JF - Proteins: Structure, Function, and Bioinformatics Y1 - 2010 A1 - Gopal, Srinivasa M. A1 - Mukherjee, Shayantani A1 - Cheng, Yi-Ming A1 - Michael Feig AB -The 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.

VL - 78 IS - 5 ER - TY - JOUR T1 - A Process-Based, Distributed Hydrologic Model Based on a Large-Scale Method for Surface - Subsurface Coupling, Advances in Water Resources JF - Advances in Water Resources Y1 - 2010 A1 - Shen, Chaopeng A1 - M. Phanikumar AB -Process-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.

VL - 33 ER - TY - JOUR T1 - The Properties of X-ray Cold Fronts in a Statistical Sample of Simulated Galaxy Clusters JF - \apj Y1 - 2010 A1 - Hallman, E. J. A1 - Skillman, S. W. A1 - undefined A1 - Smith, B. D. A1 - O'Shea, B. W. A1 - Burns, J. O. A1 - Norman, M. L. KW - galaxies: clusters: intracluster medium KW - large-scale structure of universe KW - methods: numerical KW - X-rays: galaxies: clusters VL - 725 ER - TY - JOUR T1 - Relationship between induced fluid structure and boundary slip in nanoscale polymer films JF - Physical Review E Y1 - 2010 A1 - N. V Priezjev VL - 82 ER - TY - JOUR T1 - Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects JF - BMC Systems Biology Y1 - 2010 A1 - Dresch, J.M. A1 - Liu, X. A1 - Arnosti, D.N. A1 - Ay, A. PB - BioMed Central Ltd VL - 4 ER - TY - CONF T1 - On the Use of Genetic Programming for Automated Refactoring and the Introduction of Design Patterns T2 - Proceedings of the 12th annual conference on Genetic and Evolutionary Computation Y1 - 2010 A1 - Jensen, A.C. A1 - Cheng, B.H.C. AB -Maintaining 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.

JF - Proceedings of the 12th annual conference on Genetic and Evolutionary Computation PB - ACM ER - TY - JOUR T1 - Ab Initio Coupled-Cluster and Configuration Interaction Calculations for O Using V JF - Physical Review C Y1 - 2009 A1 - R. Roth, A1 - J. R Gour A1 - Piotr Piecuch VL - 79 IS - 5 ER - TY - JOUR T1 - Ab Initio Studies of Hydrogen Defects in CdTe JF - Journal of Electronic Materials Y1 - 2009 A1 - Rak, Zs. A1 - S. D. Mahanti A1 - Mandal, Krishna C VL - 38 IS - 8 ER - TY - JOUR T1 - Center-of-Mass Problem in Truncated Configuration Interaction and Coupled-Cluster Calculations JF - Physical Letters B Y1 - 2009 A1 - R. Roth, A1 - Jeffrey R. Gour A1 - Piotr Piecuch AB -The 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.

VL - 679 IS - 4 ER - TY - JOUR T1 - Constraints on the Density Dependence of the Symmetry Energy JF - Physical Review Letters Y1 - 2009 A1 - M. B. Tsang A1 - Yingxun Zhang A1 - P. Danielewicz A1 - M. Famiano A1 - Li, Z. A1 - W. G. Lynch A1 - A. W. Steiner AB -Collisions 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.

VL - 102 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Dark Matter Annihilation and Primordial Star Formation JF - \apj Y1 - 2009 A1 - Natarajan, A. A1 - Tan, J. C. A1 - O'Shea, B. W. KW - cosmology: theory KW - dark matter KW - early universe KW - galaxies: formation KW - stars: formation VL - 692 ER - TY - JOUR T1 - The effective slip length and vortex formation in laminar flow over a rough surface JF - Physics of Fluids Y1 - 2009 A1 - A. Niavarani A1 - N. V Priezjev KW - external flows KW - laminar flow KW - Navier-Stokes equations KW - rough surfaces KW - shear flow KW - slip flow KW - vortices AB -The 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.

VL - 21 IS - 5 ER - TY - CONF T1 - Efficient Multi-label Ranking for Multi-class Learning: Application to Object Recognition T2 - Proceedings of International conference on Computer Vision (ICCV 2009) Y1 - 2009 A1 - S.S.Bucak A1 - P.K. Mallapragada A1 - Jin, Rong A1 - Jain, Anil K. JF - Proceedings of International conference on Computer Vision (ICCV 2009) ER - TY - JOUR T1 - Electronic structure of substitutional defects and vacancies in GaSe JF - Journal of Physics and Chemistry of Solids Y1 - 2009 A1 - Rak, Zs. A1 - S. D. Mahanti A1 - Mandal, Krishna C A1 - Fernelius, N.C. VL - 70 IS - 2 ER - TY - CONF T1 - Evolving coordinated quadruped gaits with the HyperNEAT generative encoding T2 - Proceedings of the IEEE Congress on Evolutionary Computation Y1 - 2009 A1 - Clune, J. A1 - Beckmann, B.E. A1 - Ofria, C. A1 - Pennock, R.T. JF - Proceedings of the IEEE Congress on Evolutionary Computation ER - TY - CONF T1 - Experimental and Computational Analysis of Fuel Mixing in a Low Pressure Direct Injection Gasoline Engine T2 - International Conference on Liquid Atomization and Spray Systems Y1 - 2009 A1 - S. Srivastava A1 - Jaberi, F.A. A1 - Harold Schock A1 - David Hung AB -An 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.

JF - International Conference on Liquid Atomization and Spray Systems CY - Vail, Colorado ER - TY - JOUR T1 - The Formation of Population III Binaries from Cosmological Initial Conditions JF - Science Y1 - 2009 A1 - Turk, M. J. A1 - Abel, T. A1 - O'Shea, B. W. VL - 325 ER - TY - CONF T1 - HybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation T2 - Proceedings of the European Conference on Artificial Life Y1 - 2009 A1 - Clune, J. A1 - Beckmann, B.E. A1 - Pennock, R.T. A1 - Ofria, C. JF - Proceedings of the European Conference on Artificial Life ER - TY - CONF T1 - Large-Eddy Simulations of Turbulent Methane Jet Flames with Filtered Mass Density Function T2 - National Combustion Meeting Y1 - 2009 A1 - Yaldizli, M. A1 - Mehravaran, K. A1 - Jaberi, F.A. AB -The 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.

JF - National Combustion Meeting PB - The Combustion Institute CY - Ann Arbor, Michigan ER - TY - CONF T1 - Large-Scale Simulations of High Speed Turbulent Flows T2 - 47th AIAA Aerospace Sciences Meeting Y1 - 2009 A1 - Li, Z. A1 - Jaberi, F.A. AB -This 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.

JF - 47th AIAA Aerospace Sciences Meeting PB - American Institute of Aeronautics and Astronautics CY - Orlando, FL ER - TY - JOUR T1 - Left-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 Approaches JF - International Journal of Quantum Chemistry Y1 - 2009 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Wloch AB -The 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

VL - 109 IS - 14 ER - TY - CONF T1 - LES/FMDF of Spray Combustion in Internal Combustion Engines T2 - National Combustion Meeting Y1 - 2009 A1 - Banaeizadeh, A. A1 - Harold Schock A1 - Jaberi, F.A. AB -The 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.

JF - National Combustion Meeting PB - The Combustion Institute CY - Ann Arbor, Michigan ER - TY - JOUR T1 - Local Correlation Calculations Using Standard and Renormalized Coupled-Cluster Approaches JF - The Journal of Chemical Physics Y1 - 2009 A1 - Wei Li A1 - Piotr Piecuch A1 - J. R Gour A1 - Shuhua Li AB -he 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.

VL - 131 IS - 11 ER - TY - JOUR T1 - Low-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 Methodologies JF - Molecular Physics Y1 - 2009 A1 - M. Ehara A1 - J. R Gour A1 - Piotr Piecuch AB -Low-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.

VL - 107 IS - 8-12 ER - TY - JOUR T1 - Method of Moments for the Continuous Transition Between the Brillouin-Wigner-Type and Rayleigh-Schrodinger-Type Multireference Coupled Cluster Theories JF - Molecular Physics Y1 - 2009 A1 - J. Pittner A1 - Piotr Piecuch AB -We 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.

VL - 107 IS - 08-12 ER - TY - CONF T1 - A New Model for Numerical Simulations of Two-Phase Turbulent Combustion T2 - National Combustion Meeting Y1 - 2009 A1 - Li, Z. A1 - Jaberi, F.A. JF - National Combustion Meeting PB - National Combustion Meeting CY - Ann Arbor, MI ER - TY - CONF T1 - Numerical Simulation of a Direct-Injection Spark-Ignition Engine with Different Fuels T2 - SAE World Congress and Exhibit Y1 - 2009 A1 - S. Srivastava A1 - Harold Schock A1 - Jaberi, F.A. A1 - David Hung AB -This 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.

JF - SAE World Congress and Exhibit PB - SAE International CY - Detroit, Michigan ER - TY - THES T1 - A process-based distributed hydrologic model and its application to a Michigan watershed T2 - Environmental Engineering Y1 - 2009 A1 - Shen, Chaopeng AB -The 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.

JF - Environmental Engineering PB - Michigan State University CY - East Lansing VL - Doctor of Philosophy SN - 9781109640106 ER - TY - THES T1 - A process-based distributed hydrologic model and its application to a Michigan watersed Y1 - 2009 A1 - Shen, Chaopeng AB -The 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.

PB - Michigan State University CY - East Lansing VL - Ph.D. ER - TY - JOUR T1 - Protecting the Amazon with Protected Areas JF - PNAS Y1 - 2009 A1 - Robert Walker A1 - Moore, Nathan A1 - Arima, Eugenio A1 - Perz, Stephen A1 - Simmons, Cynthia A1 - Caldas, Marcellus A1 - Vergara, Dante A1 - Bohrer, Claudio VL - 106 ER - TY - CONF T1 - The Role of Implicit Argumentation in Nominal SRL T2 - North American Chapter of the Association for Computational Linguistics Y1 - 2009 A1 - Matthew Gerber A1 - Joyce Y. Chai A1 - Adam Meyers AB -Nominals 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.

JF - North American Chapter of the Association for Computational Linguistics PB - Association for Computational Linguistics CY - Boulder, Colorado, USA ER - TY - JOUR T1 - The Santa Fe Light Cone Simulation Project. II. The Prospects for Direct Detection of the Whim with SZE Surveys JF - \apj Y1 - 2009 A1 - Hallman, E. J. A1 - O'Shea, B. W. A1 - Smith, B. D. A1 - Burns, J. O. A1 - Norman, M. L. KW - cosmic microwave background KW - cosmology: observations KW - cosmology: theory KW - galaxies: clusters: general KW - hydrodynamics KW - methods: numerical VL - 698 ER - TY - JOUR T1 - Scanning tunneling microscopy study of the CeTe3 charge density wave JF - Physical Review B Y1 - 2009 A1 - Tomic, A. A1 - Rak, Zs. A1 - Veazey, J. A1 - Malliakas, C. A1 - S. D. Mahanti A1 - Kanatzidis, M. A1 - Tessmer, S. VL - 79 IS - 8 ER - TY - CONF T1 - The sensitivity of HyperNEAT to different geometric representations of a problem T2 - Proceedings of the Genetic and Evolutionary Computation Conference Y1 - 2009 A1 - Clune, J. A1 - Ofria, C. A1 - Pennock, R.T. JF - Proceedings of the Genetic and Evolutionary Computation Conference ER - TY - JOUR T1 - Shear rate threshold for the boundary slip in dense polymer films JF - Phys. Rev. E Y1 - 2009 A1 - N. V Priezjev AB -The 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.

VL - 80 IS - 3 ER - TY - JOUR T1 - Strategies for Online Communities JF - Strategic Management Journal Y1 - 2009 A1 - Miller, K. D. A1 - Fabian, F. H. A1 - Lin, S. VL - 51 ER - TY - JOUR T1 - Survey of Excited State Neutron Spectroscopic Factors for Z=8-28 Nuclei JF - Physical Review Letters Y1 - 2009 A1 - M. B. Tsang A1 - Jenny Lee A1 - S. C. Su A1 - J. Y. Dai A1 - M. Horoi A1 - H. Liu A1 - W. G. Lynch A1 - S. Warren AB -We 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.

VL - 102 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Theoretical studies of defect states in GaTe JF - Journal of Physics: Condensed Matter Y1 - 2009 A1 - Rak, Zs A1 - S. D. Mahanti A1 - Mandal, Krishna C A1 - Fernelius, N.C. AB -Using 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.

VL - 21 ER - TY - JOUR T1 - Thermochemical Kinetics for Multi-reference Systems: Addition Reactions of Ozone JF - Journal of Physical Chemistry A Y1 - 2009 A1 - Piotr Piecuch A1 - Zhao, Y. A1 - Truhlar, D.G. AB -The 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.

VL - 113 IS - 19 ER - TY - JOUR T1 - Three Modes of Metal-Enriched Star Formation in the Early Universe JF - \apj Y1 - 2009 A1 - Smith, B. D. A1 - Turk, M. J. A1 - Sigurdsson, S. A1 - O'Shea, B. W. A1 - Norman, M. L. KW - early universe KW - stars: formation VL - 691 ER - TY - JOUR T1 - Turbulence-Interface Interactions in a Two-Fluid Homogeneous Flow JF - Physics of Fluids Y1 - 2009 A1 - Li, Z. A1 - Jaberi, F.A. AB -The 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.

VL - 21 IS - 9 ER - TY - JOUR T1 - Ab-initio Molecular Dynamics Study of Nanoscale Thermal Energy Transport JF - J. Heat Transfer Y1 - 2008 A1 - Tengfei Luo A1 - John R. Lloyd VL - 130 ER - TY - JOUR T1 - Application of Renormalized Coupled- Cluster Methods to Potential Function of Water JF - Theoretical Chemistry Accounts: Theory, Computation, and Modeling (THEORETICA CHIMICA ACTA) Y1 - 2008 A1 - J. Zheng A1 - J. R Gour A1 - J.J. Lutz A1 - M. Wloch A1 - Piotr Piecuch A1 - Truhlar, D.G. AB -The 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.

VL - 120 IS - 1-3 ER - TY - JOUR T1 - The Biermann Battery in Cosmological MHD Simulations of Population III Star Formation JF - \apjl Y1 - 2008 A1 - Xu, H. A1 - O'Shea, B. W. A1 - Collins, D. C. A1 - Norman, M. L. A1 - Li, H. A1 - Shuhua Li KW - cosmology: theory KW - Galaxies: High-Redshift KW - Magnetohydrodynamics: MHD KW - stars: formation VL - 688 ER - TY - JOUR T1 - A 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 E JF - The Journal of Chemical Physics Y1 - 2008 A1 - J. Zheng A1 - J. R Gour A1 - J.J. Lutz A1 - M. Wloch A1 - Piotr Piecuch A1 - Truhlar, D.G. AB -The 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.

VL - 128 IS - 4 ER - TY - JOUR T1 - Cosmological Shocks in Adaptive Mesh Refinement Simulations and the Acceleration of Cosmic Rays JF - \apj Y1 - 2008 A1 - Skillman, S. W. A1 - O'Shea, B. W. A1 - Hallman, E. J. A1 - Burns, J. O. A1 - Norman, M. L. KW - cosmology: theory KW - hydrodynamics KW - ISM: Cosmic Rays KW - methods: numerical VL - 689 ER - TY - JOUR T1 - The Destruction of Cosmological Minihalos by Primordial Supernovae JF - \apj Y1 - 2008 A1 - Whalen, D. J. A1 - van Veelen, B. A1 - O'Shea, B. W. A1 - Norman, M. L. KW - Cosmology: Early Universe KW - cosmology: theory KW - hydrodynamics KW - Stars: Early-Type KW - Stars: Supernovae: Individual VL - 682 ER - TY - CONF T1 - Filtered Mass Density Function for Numerical Simulations of Spray Combustion T2 - 46th AIAA Aerospace Sciences Meeting and Exhibit Y1 - 2008 A1 - Li, Z. A1 - Jaberi, F.A. A1 - Yaldizli, M. AB -This 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.

JF - 46th AIAA Aerospace Sciences Meeting and Exhibit PB - AIAA CY - Reno, Nevada ER - TY - CONF T1 - How a generative encoding fares as problem-regularity decreases T2 - Parallel Problem Solving from Nature Y1 - 2008 A1 - Clune, J. A1 - Ofria, C. A1 - Pennock, R.T. JF - Parallel Problem Solving from Nature PB - Springer ER - TY - JOUR T1 - How the First Stars Regulated Local Star Formation. I. Radiative Feedback JF - \apj Y1 - 2008 A1 - Whalen, D. J. A1 - O'Shea, B. W. A1 - Smidt, J. A1 - Norman, M. L. KW - Cosmology: Early Universe KW - cosmology: theory KW - ISM: H II Regions VL - 679 ER - TY - JOUR T1 - A Hybrid Langrangian-Eulerian Particle-Level Set Method for numerical Simulations of Two-Fluid Turbulent Flows JF - International Journal for Numerical Methods in Fluids Y1 - 2008 A1 - Li, Z. A1 - Jaberi, F.A. A1 - Shih, T. I-P. KW - two-fluid turbulent flows; particle-level set method; interface tracking AB -A 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.

VL - 56 IS - 12 ER - TY - JOUR T1 - The influence of cluster emission and the symmetry energy on neutron-proton spectral double ratios JF - Physics Letters B Y1 - 2008 A1 - Yingxun Zhang A1 - P. Danielewicz A1 - M. Famiano A1 - Li, Z. A1 - W. G. Lynch A1 - M. B. Tsang AB -The 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.

VL - 664 ER - TY - CONF T1 - Large Eddy Simulation of High Speed Turbulent Reacting Flows Y1 - 2008 A1 - Zhaorui, Li A1 - Banaeizadeh, A. A1 - Jaberi, F.A. CY - Hawaii ER - TY - CONF T1 - Large Eddy Simulations of Turbulent Flows in IC Engines T2 - ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference (IDETC/CIE2008) Y1 - 2008 A1 - Banaeizadeh, A. A1 - Afshari, A. A1 - Jaberi, F.A. A1 - H. Schock AB -A 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.

JF - ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference (IDETC/CIE2008) PB - ASME CY - Brooklyn, New York SN - 978-0-7918-4327-7 ER - TY - CONF T1 - Large Eddy Simulations of Two-Phase Turbulent Reacting Flows T2 - 46TH AIAA Aerospace Sciences Meeting and Exhibit Y1 - 2008 A1 - Jaberi, F.A. A1 - Li, Z. JF - 46TH AIAA Aerospace Sciences Meeting and Exhibit PB - AMERICAN INSTITUTE OF AERONAUTICS AND ASTRONAUTICS CY - Reno, Nevada ER - TY - JOUR T1 - Large-Eddy Simulation of a Dispersed Particle-Laden Turbulent Round Jet JF - International Journal of Heat and Mass Transfer Y1 - 2008 A1 - Almeida, T. A1 - Jaberi, F.A. KW - Particle-laden jet; dilute KW - two-phase flows; turbulent jet; LES AB -The 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.

VL - 51 IS - 3-4 ER - TY - JOUR T1 - Large-Eddy Simulation of Turbulent Flow in an Axisymmetric Dump Combustor JF - AIAA Journal Y1 - 2008 A1 - Afshari, A. A1 - Jaberi, F.A. KW - combustion KW - Gas turbine; modeling; combustion chamber; Monte Carlo method; Lagragian Method; turbulent flow; large eddy simulation AB -A 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.

VL - 46 IS - 7 ER - TY - JOUR T1 - Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes JF - PLoS Computational Biology Y1 - 2008 A1 - Clune, J. A1 - Misevic, D. A1 - Ofria, C. A1 - Lenski, R.E. A1 - Elena, S.F. A1 - Sanjuán, R. PB - Public Library of Science VL - 4 ER - TY - JOUR T1 - Rheological study of polymer flow past rough surfaces with slip boundary conditions JF - Journal of Chemical Physics Y1 - 2008 A1 - A. Niavarani A1 - N. V Priezjev KW - liquid films KW - molecular dynamics method KW - polymer melts KW - rheology KW - shear flow KW - slip flow KW - surface roughness AB -The 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.

VL - 129 IS - 14 ER - TY - JOUR T1 - Slip boundary conditions for shear flow of polymer melts past atomically flat surfaces JF - Physical Review E Y1 - 2008 A1 - A. Niavarani A1 - N. V Priezjev KW - molecular dynamics KW - shear rate KW - slip length KW - slip velocity KW - smooth thermal surfaces AB -Molecular 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.

VL - 77 IS - 4 ER - TY - JOUR T1 - Stereoelectronic Effects on Molecular Geometries and State-Energy Splittings of Ligated Monocopper Diozygen Complexes JF - The Journal of Physical Chemistry Y1 - 2008 A1 - C.J. Cramer A1 - J. R Gour A1 - A. Kinal A1 - M. Wloch A1 - Piotr Piecuch A1 - A.R.M. Shahi A1 - L. Gagliardi AB -The 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.

VL - 112 IS - 16 ER - TY - JOUR T1 - The Structure of Partially-Premixed Methane Flames in High Intensity Turbulent Flows JF - Combustion and Flame Y1 - 2008 A1 - Yaldizli, M. A1 - Mohammad, H. A1 - Mehravaran, K. A1 - Jaberi, F.A. KW - DNS; Methane combustion KW - turbulent reacting flows; partially premixed flames; reduced chemistry models AB -Direct 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.

VL - 154 IS - 4 ER - TY - JOUR T1 - Theoretical studies of defect states in GaTe JF - Journal of Physics: Condensed Matter Y1 - 2008 A1 - Rak, Zs A1 - S. D. Mahanti A1 - Mandal, Krishna C A1 - Fernelius, N.C. VL - 21 IS - 1 ER - TY - JOUR T1 - Transport Model Simulations of Projectile Fragmentation Reactions at 140 {MeV/nucleon} JF - Physical Review C Y1 - 2008 A1 - M. Mocko A1 - M. B. Tsang A1 - D. Lacroix A1 - A. Ono A1 - P. Danielewicz A1 - W. G. Lynch A1 - R. J Charity KW - Nuclear Experiment KW - Nuclear Theory AB -The 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.

VL - 78 IS - 2 N1 - {Phys.Rev.C78:024612,2008} ER - TY - JOUR T1 - Active-Space Symmetry-Adapted-Cluster Configuration-Interaction and Equation-of-Motion Cluster Methods for High Accuracy Calculations of Potential Energy Surfaces of Radicals JF - The Journal of Chemical Physics Y1 - 2007 A1 - Y. Ohtsuka A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Ehara A1 - H. Nakatsuji KW - configuration interactions KW - coupled cluster calculations KW - electron attachment KW - excited states KW - free radicals KW - ground states KW - ionisation KW - organic compounds KW - oxygen compounds KW - potential energy surfaces AB -The 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.

VL - 126 IS - 16 ER - TY - JOUR T1 - Breaking Bonds with the Left Eigenstate Completely Renormalized Coupled-Cluster Method JF - The Journal of Chemical Physics Y1 - 2007 A1 - Y. Ge A1 - M.S. Gordon A1 - Piotr Piecuch AB -The 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).

VL - 127 IS - 17 ER - TY - JOUR T1 - Computational Investigation of the Conrotatory and Disrotatory Isomerization Channels of Bicyclo[1.1.0]butane to Buta-1,3-diene: A Completely Renormalized Coupled-Cluster Study JF - Journal of Physical Chemistry A Y1 - 2007 A1 - A. Kinal A1 - Piotr Piecuch AB -The 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.

VL - 111 IS - 4 ER - TY - JOUR T1 - Coupled-Cluster and Configuration-Interaction Calculations for Heavy Nuclei JF - Physical Review Lettters Y1 - 2007 A1 - M. Horoi A1 - J. R Gour A1 - M. Wloch A1 - M.D. Lodriguito A1 - B. A. Brown A1 - Piotr Piecuch AB -We 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.

VL - 98 IS - 11 ER - TY - JOUR T1 - Coupled-Cluster Theory for Three-Body Hamiltonians JF - Physical Review C Y1 - 2007 A1 - G. Hagen A1 - T. Papenbrock A1 - D. J. Dean A1 - A. Schwenk A1 - A. NHogga A1 - M. Wloch A1 - Piotr Piecuch AB -We 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.

VL - 76 IS - 3 ER - TY - JOUR T1 - Effect of surface roughness on rate-dependent slip in simple fluids JF - The Journal of Chemical Physics Y1 - 2007 A1 - N. V Priezjev KW - elastic constants KW - interface roughness KW - liquid films KW - molecular dynamics method KW - slip KW - surface roughness KW - thin films AB -Molecular 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.

VL - 127 IS - 14 ER - TY - JOUR T1 - Extension of the Renormalized Coupled-Cluster Methods Exploiting Left Eigenstates of the Similarity-Transformed Hamiltonian to Open- Shell Systems: A Benchmark Study JF - The Journal of Physical Chemistry A Y1 - 2007 A1 - M. Wloch A1 - J. R Gour A1 - Piotr Piecuch AB -The 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.

VL - 111 IS - 44 ER - TY - CONF T1 - Filtered Mass Density Function for Numerical Simulations of Spray Combustion T2 - 46th AIAA Aerospace Sciences Meeting and Exhibit Y1 - 2007 A1 - Yaldizli, M. A1 - Li, Z. A1 - Jaberi, F.A. AB -This 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.

JF - 46th AIAA Aerospace Sciences Meeting and Exhibit PB - AIAA CY - Reno, Nevada ER - TY - CONF T1 - LES/FMDF of Turbulent Combustion in Complex Flow Systems T2 - 45th AIAA Aerospace Sciences Meeting and Exhibit Y1 - 2007 A1 - Afshari, A. A1 - Jaberi, F.A. A1 - Shih, T. I-P. AB -A 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.

JF - 45th AIAA Aerospace Sciences Meeting and Exhibit PB - AIAA CY - Reno, Nevada ER - TY - CHAP T1 - New Alternatives for Accurate Electronic Structure Calculations of Potential Energy Surfaces Involving Bond Breaking T2 - Electron Correlation Methodology Y1 - 2007 A1 - Piotr Piecuch A1 - I. S. O. Pimienta A1 - P.-D. Fan A1 - K. Kowalski AB -The 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.

JF - Electron Correlation Methodology T3 - ACS Symposium Series PB - American Chemical Sociegy CY - Washington, DC VL - 958 SN - ISBN13: 9780841238435 ER - TY - CONF T1 - A New Model for Large Eddy Simulations of Multi-Phase Turbulent Combustion T2 - Proceedings of the 43rd AIAA/ASME/SAI/ASEE Joint Propulsion Conference Y1 - 2007 A1 - Yaldizli, M. A1 - Li, Z. A1 - J.A. Jaberi AB -Numerical 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.

JF - Proceedings of the 43rd AIAA/ASME/SAI/ASEE Joint Propulsion Conference PB - AIAA/ASME/SAI/ASEE CY - Cincinnati, Ohio ER - TY - Generic T1 - Numerical Simulations of Two-Phase Turbulent Combustion in Spray Burners T2 - ASME Conference Proceedings, Computers and Information in Engineering Conference Y1 - 2007 A1 - Li, Z. A1 - Yaldizli, M. A1 - Jaberi, F.A. AB -The 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.

JF - ASME Conference Proceedings, Computers and Information in Engineering Conference PB - ASME CY - Las Vegas, Nevada SN - 0-7918-4803-5 ER - TY - JOUR T1 - Rate-dependent slip boundary conditions for simple fluids JF - Physical Review E Y1 - 2007 A1 - N. V Priezjev AB -The 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.

VL - 75 IS - 5 ER - TY - CHAP T1 - Renormalized Coupled-Cluster Methods: Theoretical Foundations and Application to Potential Function of Water T2 - Progress in Theoretical Chemistry and Physics Y1 - 2007 A1 - Piotr Piecuch A1 - M. Wloch A1 - A.J.C. Verandas AB -Conventional 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.

JF - Progress in Theoretical Chemistry and Physics VL - 16 IS - Part 1 ER - TY - JOUR T1 - Shape and Structure of N = Z 64Ge: Electromagnetic Transition Rates from the Application ￼of the Recoil Distance Method to a Knockout Reaction JF - PHYSICAL REVIEW LETTERS Y1 - 2007 A1 - K. Starosta A1 - A. Dewald A1 - A. Dunomes A1 - P. Adrich A1 - A.M. Amthor A1 - T. Baumann A1 - D. Bazin A1 - M. Bowen A1 - B. A. Brown A1 - A. Chester A1 - A. Gade A1 - D. Galaviz A1 - T. Glasmacher A1 - T. Ginter A1 - M. Hausmann A1 - M. Horoi A1 - J. Jolie A1 - B. Melon A1 - D. Miller A1 - V. Moeller A1 - R.P. Norris A1 - T. Pissulla A1 - M. Portillo A1 - W. Rother A1 - Y. Shimbara A1 - A. Stolz A1 - C. Vaman A1 - P. Voss A1 - D. Weisshaar A1 - V. Zelevinsky VL - 99 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.042503 ER - TY - JOUR T1 - Uncertainty and the changing hydroclimatology of the Amazon JF - Geophysical Research Letters Y1 - 2007 A1 - Moore, Nathan A1 - Robert Walker A1 - Arima, Eugenio A1 - Ramos da Silva, Renato VL - 34 ER - TY - JOUR T1 - Z = 0 Shell Gap near 100Sn from Intermediate-Energy Coulomb Excitations ￼in Even-Mass 106-112Sn Isotopes JF - PHYSICAL REVIEW LETTERS Y1 - 2007 A1 - C. Vaman A1 - C. Andreoiu A1 - D. Bazin A1 - A. Beccerril A1 - B. A. Brown A1 - C.M. Campbell A1 - A. Chester A1 - J.M. Cook A1 - D.C. Dinca A1 - A. Gade A1 - D. Galaviz A1 - T. Glasmacher A1 - M. {Hjorth-Jensen} A1 - M. Horoi A1 - D. Miller A1 - V. Moeller A1 - W. F. Mueller A1 - A. Schiller A1 - K. Starosta A1 - A. Stolz A1 - J.R. Terry A1 - A. Volya A1 - V. Zelevinsky A1 - H. Zwahlen VL - 99 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.162501 ER - TY - JOUR T1 - Ab Initio Coupled-Cluster Calculations for Nuclei Using Methods of Quantum Chemistry JF - European Physics Journal A Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - D. J. Dean A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - T. Papenbrock A1 - K. Kowalski AB -We 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.

VL - 25 IS - 1 ER - TY - JOUR T1 - Ab initio determination of solid-state nanostructure JF - Nature Y1 - 2006 A1 - P. Juhás A1 - D. M. Cherba A1 - P. M. Duxbury A1 - W. F. Punch A1 - S. J. L. Billinge AB -Advances 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.

VL - 440 ER - TY - JOUR T1 - Ab initio studies of the electronic structure of defects in {PbTe} JF - Physical Review B Y1 - 2006 A1 - Salameh Ahmad A1 - S. D. Mahanti A1 - Khang Hoang A1 - M. G. Kanatzidis AB -Understanding 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.

VL - 74 IS - 15 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Automated derivation and parallel computer implementation of renormalized and active-space coupled-cluster methods JF - International Journal of Quantum Chemistry Y1 - 2006 A1 - Piotr Piecuch A1 - So Hirata A1 - K. Kowalski A1 - P.-D. Fan A1 - Theresa L. Windus AB -Our 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

VL - 106 IS - 1 ER - TY - JOUR T1 - Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations JF - Journal of Computational Chemistry Y1 - 2006 A1 - Jana Chocholouscaronová A1 - Michael Feig AB -Different 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

VL - 27 IS - 6 ER - TY - JOUR T1 - Coupled Cluster Theory for Nuclei JF - International Journal of Modern Physics B Y1 - 2006 A1 - T. Papenbrock A1 - D. J. Dean A1 - J. R Gour A1 - G. Hagen A1 - M. {Hjorth-Jensen} A1 - M. Wloch KW - Nuclear structure; light nuclei; coupled-cluster theory AB -This 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.

VL - 20 IS - 30-31 ER - TY - JOUR T1 - Coupled-Cluster Calculations for Valence Systems around 16 O JF - Physical Review C Y1 - 2006 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - M. Wloch A1 - D. J. Dean AB -We 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.

VL - 74 IS - 2 ER - TY - JOUR T1 - Coupled-cluster calculations for valence systems around O16 JF - Physical Review C Y1 - 2006 A1 - J. R Gour A1 - Piotr Piecuch A1 - M. {Hjorth-Jensen} A1 - M. Wloch A1 - D. J. Dean AB -We 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.

VL - 74 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - BOOK T1 - Coupled-Cluster Theory for Nuclei T2 - Condensed Matter Theories Y1 - 2006 JF - Condensed Matter Theories PB - Nova Publishers VL - 20 SN - 1-59454-989-3 ER - TY - JOUR T1 - Direct Numerical Simulations of a Planar Jet Laden with Evaporating Droplets JF - International Journal of Heat and Mass Transfer Y1 - 2006 A1 - Almeida, T. A1 - Jaberi, F.A. KW - droplet-laden turbulent jet; two-phase planar jet; droplet evaporation; DNS AB -A 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.

VL - 49 IS - 13-14 ER - TY - JOUR T1 - Efficient Formulation and Computer Implementation of the Active-Space Electron-Attached and Ionized Equation-of-Motion Coupled-Cluster Methods JF - Journal of Chemical Physics Y1 - 2006 A1 - J. R Gour A1 - Piotr Piecuch KW - coupled cluster calculations KW - free radicals KW - organic compounds KW - sulphur compounds AB -The 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.

VL - 125 IS - 23 ER - TY - JOUR T1 - Experimental and Theoretical UV Characterizations of Acetyloacetone and its Isomers JF - The Journal of Physical Chemistry A Y1 - 2006 A1 - Piotr Piecuch A1 - S. Coussan A1 - Y. Ferro A1 - A. Trivella A1 - P. Roubin A1 - R. Wieczorek A1 - C. Manca A1 - K. Kowalski A1 - M. Wloch A1 - S. Kucharski A1 - M. Musial AB -Cryogenic 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.

VL - 110 IS - 11 ER - TY - JOUR T1 - Extension of the Active-Space Equation-of- Motion Coupled-Cluster Methods to Radical Systems: The EA-EOMCCSDt and IPEOMCCSDt Approaches JF - International Journal of Quantum Chemistry Y1 - 2006 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Wloch KW - oupled-cluster theory;equation-of-a motion coupled-cluster method;active-space coupled-cluster approaches;electronic-attached and ionized states;radicals AB -The 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.

VL - 106 IS - 14 ER - TY - JOUR T1 - Extrapolating Potential Energy Surfaces by Scaling Electron Correlation at a Single Geometry JF - Chemical Physics Letters Y1 - 2006 A1 - A.J.C. Varandas A1 - Piotr Piecuch AB -It 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.

VL - 430 IS - 4-6 ER - TY - JOUR T1 - The ground state of chargeless fermions with finite magnetic moment JF - Journal of Physics A: Mathematical and General Y1 - 2006 A1 - S. D. Mahanti A1 - Sudhanshu S. Jha AB -We 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.

VL - 39 IS - 6 ER - TY - JOUR T1 - Half-life and spin of 60Mng JF - Physical Review C Y1 - 2006 A1 - S. N. Liddick A1 - P. F. Mantica A1 - B. A. Brown A1 - M. P. Carpenter A1 - A. D. Davies A1 - M. Horoi A1 - R. V. F. Janssens A1 - A. C. Morton A1 - W. F. Mueller A1 - J. Pavan A1 - H. Schatz A1 - A. Stolz A1 - S. L. Tabor A1 - B. E. Tomlin A1 - M. Wiedeking AB -A 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.}

VL - 73 IS - 4 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Half-life and spin of 60Mng JF - PHYSICAL REVIEW C Y1 - 2006 A1 - S. N. Liddick A1 - P. F. Mantica A1 - B. A. Brown A1 - M. P. Carpenter A1 - A. D. Davies A1 - M. Horoi A1 - R. V. F. Janssens A1 - A. C. Morton A1 - W. F. Mueller A1 - J. Pavan A1 - H. Schatz A1 - A. Stolz A1 - S. L. Tabor A1 - B. E. Tomlin A1 - M. Wiedeking VL - 73 UR - http://journals.aps.org/prc/abstract/10.1103/PhysRevC.73.044322 IS - 4 ER - TY - JOUR T1 - Intriguing Accuracies of the Exponential Wave Function Expansions Exploiting Finite Two-Body Correlation Operators in Calculations for Many-Electron Systems JF - Journal of Molecular Structure: THEOCHEM Y1 - 2006 A1 - P.-D. Fan A1 - P. Piecuch KW - xact many-electron wave functions; Generalized coupled-cluster methods; Two-body correlation operators; Nooijen's conjecture; Variational calculations; Multi-determinantal reference states; Excited states AB -Following 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.

VL - 768 IS - 1-3 ER - TY - JOUR T1 - Is the Mechanism of the [2+2] Cycloaddition of Cyclopentyne to Ethylene Concerted or Biradical? A Completely Renormalized Coupled Cluster Study JF - The Journal of Physical Chemistry Y1 - 2006 A1 - Piotr Piecuch A1 - A. Kinal AB -The 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.

VL - 110 IS - 2 ER - TY - JOUR T1 - Molecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model JF - The Journal of Physical Chemistry B Y1 - 2006 A1 - Seiichiro Tanizaki A1 - Michael Feig AB -The 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.

VL - 110 ER - TY - JOUR T1 - Non-Iterative Coupled- Cluster Methods Employing Multi-Reference Perturbation Theory Wave Functions JF - Journal of Molecular Structure: THEOCHEM Y1 - 2006 A1 - Piotr Piecuch A1 - M.D. Lodriguito A1 - K. Kowalski A1 - M. Wloch KW - Coupled-cluster theory; Equation-of-motion coupled-cluster methods; Method of moments of coupled-cluster equations; Multi-reference perturbation theory; Non-iterative coupled-cluster methods AB -A 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+.

VL - 771 IS - 1-3 ER - TY - CHAP T1 - Non-iterative Coupled-Cluster Methods for Excited Electronic States T2 - Progress in Theoretical Chemistry and Physics Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - M. Lodriguito A1 - J. R Gour JF - Progress in Theoretical Chemistry and Physics VL - 15 ER - TY - JOUR T1 - Shell model analysis of the 56Ni spectrum in the full pf model space JF - PHYSICAL REVIEW C Y1 - 2006 A1 - M. Horoi A1 - B. A. Brown A1 - T. Otsuka A1 - M. Honma A1 - T. Mizusaki VL - 73 UR - http://journals.aps.org/prc/abstract/10.1103/PhysRevC.73.061305 IS - 6 ER - TY - JOUR T1 - Single-reference, size-extensive, non-iterative coupled-cluster approaches to bond breaking and biradicals JF - Chemical Physics Letters Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - J. R Gour A1 - A. Kinal AB -We 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.

VL - 418 ER - TY - JOUR T1 - Theoretical Characterization of End-on and Side-on Peroxide Coordination in Ligated Cu2O2 Models JF - The Journal of Physical Chemistry A Y1 - 2006 A1 - C.J. Cramer A1 - A. Kinal A1 - M. Wloch A1 - Piotr Piecuch A1 - L. Gagliardi AB -The 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.

VL - 110 IS - 40 ER - TY - JOUR T1 - Theoretical Models on the Cu2O2 Torture Track. Mechanistic Implications for Oxytyrosinase and Small-molecule Analogs JF - The Journal of Physical Chemistry A Y1 - 2006 A1 - C.J. Cramer A1 - M. Wloch A1 - Piotr Piecuch A1 - Cristina Puzzarini A1 - L. Gagliardi AB -Accurately 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.

VL - 110 ER - TY - JOUR T1 - Two New Classes of Non-Iterative Coupled-Cluster Methods Derived from the Method of Moments of Coupled-Cluster Equations JF - Molecular Physics Y1 - 2006 A1 - Piotr Piecuch A1 - M. Wloch A1 - M.D. Logriguito A1 - J. R Gour VL - 104 IS - 13 & 14 ER - TY - JOUR T1 - The Usefulness of Exponential Wave Function Expansions Employing One- and Two-Body Cluster Operators in Electronic Structure Theory: The Extended and Generalized Coupled-Cluster Methods JF - Advances in Quantum Chemistry Y1 - 2006 A1 - P.-D. Fan A1 - Piotr Piecuch AB -In 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.

VL - 51 ER - TY - JOUR T1 - Ab Initio Coupled-Cluster Study of 16O JF - Physical Review Letters Y1 - 2005 A1 - M. Włoch A1 - D. J. Dean A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - K. Kowalski A1 - T. Papenbrock A1 - P. Piecuch AB -We 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.

VL - 94 IS - 21 ER - TY - JOUR T1 - Ab Initio Coupled-Cluster Study of O JF - Physical Review Letters Y1 - 2005 A1 - Piotr Piecuch A1 - M. Wloch A1 - D. J. Dean A1 - J. R Gour A1 - M. {Hjorth-Jensen} A1 - K. Kowalski A1 - T. Papenbrock AB -We 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.

VL - 94 ER - TY - JOUR T1 - Active-Space Coupled-Cluster Study of Electronic States of Be 3 JF - The Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - K. Kowalski A1 - S. Hirata A1 - M. Wloch A1 - T.L. Windus AB -The 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.

VL - 123 IS - 7 ER - TY - JOUR T1 - Active-space equation-of-motion coupled-cluster methods for excited states of radicals and other open-shell systems: {EA-EOMCCSDt} and {IP-EOMCCSDt} JF - The Journal of Chemical Physics Y1 - 2005 A1 - Jeffrey R. Gour A1 - Piotr Piecuch A1 - Marta Wloch KW - coupled cluster calculations KW - free radicals KW - molecular electronic states AB -The 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.

VL - 123 IS - 13 ER - TY - JOUR T1 - Active-Space Equation-of=Motion Coupled-Cluster Methods for Excited States of Radicals and Other Open-Shell Systems: EA-EOMCCSDt and IP-EOMCCSDt JF - Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - J. R Gour A1 - M. Wloch VL - 123 IS - 13 ER - TY - JOUR T1 - Balancing Dynamic and Non-Dynamic Correlation for Diradical and Aromatic Transition States: A Renormalized Coupled-Cluster Study of the Cope Rearrangement of 1,5-Hexadiene JF - Journal of the American Chemical Society Y1 - 2005 A1 - Piotr Piecuch A1 - M. J. {McGuire} AB -Single-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.

VL - 127 IS - 8 ER - TY - Generic T1 - Bridging Quantum Chemistry and Nuclear Structure Theory: Coupled-Cluster Calculations for Closed- and Open-Shell Nuclei T2 - American Institute of Physics Y1 - 2005 A1 - Piotr Piecuch A1 - M. Wloch A1 - J. R Gour A1 - D. J. Dean A1 - M. {Hjorth-Jensen} A1 - T. Papenbrock AB -We 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

JF - American Institute of Physics T3 - NUCLEI AND MESOSCOPIC PHYSICS: Workshop on Nuclei and Mesoscopic Physics: WNMP 2004 PB - American Institute of Physics CY - Melville, NY VL - 777 ER - TY - JOUR T1 - Can 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 Conical JF - Journal of Chemical Physics A Y1 - 2005 A1 - Piotr Piecuch A1 - S. Nangia A1 - Truhlar, D.G. A1 - M. J. {McGuire} AB -We 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.

VL - 109 IS - 51 ER - TY - JOUR T1 - Comparison of Low-Order Multireference Many-Body Perturbation Theories JF - Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - R.K. Chaudhuri A1 - K.F. Freed A1 - G. Hose A1 - K. Kowalski A1 - M. Wloch A1 - S. Chattopadhyay A1 - D. Mukherjee A1 - R. Rolik A1 - A. Szabados A1 - G. Toth A1 - P.R. Surjan AB -Tests 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.

VL - 122 IS - 13 ER - TY - JOUR T1 - A Comparison of Renormalized Coupled-Cluster and Multireference Methods with Full Configuration Interaction Benchmarks JF - Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - C.D. Sherrill AB -Unusual 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.

VL - 122 IS - 12 ER - TY - Generic T1 - Coupled Cluster Approaches to Nuclei, Ground States and Excited States T2 - Key Topics in Nuclear Structure, Proceedings of the 8th International Spring Seminar on Nuclear Physics Y1 - 2005 A1 - Piotr Piecuch A1 - D. J. Dean A1 - M. Jhorth-Jensen A1 - K. Kowalski A1 - T. Papenbrock A1 - M. Wloch AB -We 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.

JF - Key Topics in Nuclear Structure, Proceedings of the 8th International Spring Seminar on Nuclear Physics CY - Paestum, Italy ER - TY - JOUR T1 - Coupled-Cluster Calculations for Ground and Excited States of Closed- and Open-Shell Nuclei Using Methods of Quantum Chemistry JF - Journal of Physics G: Nuclear and Particle Physics Y1 - 2005 AB -We 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.

VL - 31 IS - 8 ER - TY - JOUR T1 - Extension of Renormalized Coupled-Cluster Methods Including Triple Excitations to Electronic States of Open-Shell Molecules JF - The Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - M. Wloch A1 - J. R Gour A1 - K. Kowalski AB -The 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.

VL - 122 IS - 21 ER - TY - JOUR T1 - Extensive Generalization of Renormalized Coupled-Cluster Methods JF - The Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - K. Kowalski AB -The 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.

VL - 122 IS - 7 ER - TY - JOUR T1 - Noniterative Corrections to Extended Coupled-Cluster Energies Employing the Generalized Method of Moments of Coupled-Cluster Equations JF - Molecular Physics Y1 - 2005 A1 - Piotr Piecuch A1 - {P.-D.} Fan A1 - K. Kowalski AB -It 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

VL - 103 IS - 15 & 16 ER - TY - JOUR T1 - Nuclear Structure Calculations with Coupled-Cluster Methods from Quantum Chemistry JF - Nuclear Physics A Y1 - 2005 A1 - Piotr Piecuch A1 - D. J. Dean A1 - J. R Gour A1 - G. Hagen A1 - M. {Hjorth-Jensen} A1 - K. Kowalski A1 - T. Papenbrock A1 - M. Wloch AB -We 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.

VL - 752 ER - TY - JOUR T1 - Renormalized coupled-cluster methods exploiting left eigenstates of the similarity-transformed Hamiltonian JF - The Journal of Chemical Physics Y1 - 2005 A1 - Piotr Piecuch A1 - Marta Wloch KW - bonds (chemical) KW - configuration interactions KW - coupled cluster calculations KW - enthalpy KW - excited states KW - fluorine KW - ground states KW - heat of reaction KW - hydrogen compounds KW - isomerisation KW - method of moments KW - organic compounds KW - reaction kinetics theory KW - water AB -Completely 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.

VL - 123 IS - 22 ER - TY - JOUR T1 - Where Does the Planar-to-Nonplanar Turnover Occur in Small Gold Clusters JF - Journal of the American Chemical Society Y1 - 2005 A1 - Piotr Piecuch A1 - R.M. Olson A1 - S. Varganov A1 - M.S. Gordon A1 - S. Chretien A1 - H. Metiu A1 - K. Kowalski A1 - S. A. Kucharski A1 - M. Musial AB -Several 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.

VL - 127 IS - 3 ER - TY - JOUR T1 - Method of moments of coupled-cluster equations: a new formalism for designing accurate electronic structure methods for ground and excited states JF - Theoretical Chemistry Accounts: Theory, Computation, and Modeling Y1 - 2004 A1 - Piotr Piecuch A1 - K. Kowalski A1 - I. S. O. Pimienta A1 - P.-D. Fan A1 - M.D. Lodriguito A1 - M. J. {McGuire} A1 - S. A. Kucharski A1 - T. Kuś A1 - M. Musial KW - Coupled-cluster theory - Method of moments of coupled-cluster equations - Renormalized coupled-cluster methods - extended coupled cluster theory - Potential energy surfaces AB -The 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.

VL - 112 ER -