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.

1 aSafaie, Ammar1 aDang, Chinh1 aQiu, Han1 aRadha, Hayder1 aPhanikumar, M.S. uhttp://hydrology1.weebly.com/uploads/6/6/2/1/66216077/jh_safaie.pdf00447nas a2200097 4500008004100000245009400041210006900135490000700204100002000211856011800231 2013 eng d00aMolecular dynamics simulations of oscillatory Couette flows with slip boundary conditions0 aMolecular dynamics simulations of oscillatory Couette flows with0 v141 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/molecular-dynamics-simulations-oscillatory-couette-flows-slip-boundary01554nas a2200529 4500008004100000245007700041210006900118260001200187490000800199100001500207700001800222700001600240700002000256700001600276700002200292700001500314700002000329700001900349700001300368700002700381700002300408700001800431700002200449700001800471700002200489700002100511700002100532700002300553700002500576700002000601700001900621700002000640700002200660700002000682700002300702700001600725700001700741700002000758700002400778700001900802700001800821700001500839700001800854700002000872700002300892856010900915 2012 eng d00aA magnified young galaxy from about 500 million years after the Big Bang0 amagnified young galaxy from about 500 million years after the Bi c09/20120 v4891 aZheng, Wei1 aPostman, Marc1 aZitrin, Adi1 aMoustakas, John1 aShu, Xinwen1 aJouvel, Stephanie1 aHøst, Ole1 aMolino, Alberto1 aBradley, Larry1 aCoe, Dan1 aMoustakas, Leonidas, A1 aCarrasco, Mauricio1 aFord, Holland1 aBenítez, Narciso1 aLauer, Tod, R1 aSeitz, Stella;, B1 aBouwens, Rychard1 aKoekemoer, Anton1 aMedezinski, Elinor1 aBartelmann, Matthias1 aBroadhurst, Tom1 aDonahue, Megan1 aGrillo, Claudio1 aInfante, Leopoldo1 aJha, Saurabh, W1 aKelson, Daniel, D.1 aLahav, Ofer1 aLemze, Doron1 aMelchior, Peter1 aMeneghetti, Massimo1 aMerten, Julian1 aNonino, Mario1 aOgaz, Sara1 aRosati, Piero1 aUmetsu, Keiichi1 avan der Wel, Arjen uhttps://icer.msu.edu/research/publications/magnified-young-galaxy-about-500-million-years-after-big-bang01334nas a2200493 4500008004100000245015700041210006900198260001200267490000800279100001600287700001300303700002200316700001300338700001400351700001400365700001400379700001300393700001500406700001200421700001800433700001500451700001400466700001500480700001300495700001500508700001400523700001300537700001300550700001400563700001200577700001400589700001400603700001500617700001500632700001100647700001800658700001800676700001500694700001500709700001500724700001400739700001500753856007200768 2012 eng d00aMass Measurements of the Neutron-Deficient 41Ti, 45Cr, 49Fe, and 53Ni Nuclides: ￼First Test of the Isobaric Multiplet Mass Equation in fp-Shell Nuclei0 aMass Measurements of the NeutronDeficient 41Ti 45Cr 49Fe and 53N c09/20120 v1091 aZhang, Y.H.1 aXu, H.S.1 aLitvinov, Yu., A.1 aTu, X.L.1 aYan, X.L.1 aTypel, S.1 aBlaum, K.1 aWang, M.1 aZhou, X.H.1 aSun, Y.1 aBrown, B., A.1 aYuan, Y.J.1 aXia, J.W.1 aYang, J.C.1 aAudi, G.1 aChen, X.C.1 aJia, G.B.1 aHu, Z.G.1 aMa, X.W.1 aMao, R.S.1 aMei, B.1 aShuai, P.1 aSun, Z.Y.1 aWang, S.T.1 aXiao, G.Q.1 aXu, X.1 aYamaguchi, T.1 aYamaguchi, Y.1 aZang, Y.D.1 aZhao, H.W.1 aZhao, T.C.1 aZhang, W.1 aZhan, W.L. uhttp://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.10250102241nas a2200193 4500008004100000245007100041210006900112300001400181490000700195520159700202653002101799653002801820653002501848653003001873653003501903100002501938700001301963856007101976 2012 eng d00aMedical image-based simulation of abdominal aortic aneurysm growth0 aMedical imagebased simulation of abdominal aortic aneurysm growt a107–1170 v423 aAdvances in theoretical modeling of biological tissue growth and remodeling ({G&R)} and computational biomechanics have been helpful to capture salient features of vascular remodeling during the progression of vascular diseases. Nevertheless, application of such advances to individualized diagnosis and clinical treatment of diseases such as abdominal aortic aneurysm ({AAA)} remains challenging. As a step toward that goal, in this paper, we present a computational framework necessary towards patient-specific modeling of {AAA} growth. Prior to {AAA} simulations, using an inverse optimization method, initial material parameters are identified for a healthy aorta such that a homeostatic condition is satisfied for the given medical image-based geometrical model under physiological conditions. Various shapes of {AAAs} are then computationally created by inducing elastin degradation with different spatio-temporal distributions. The simulation results emphasize the role of extent of elastin damage, geometric complexity of an enlarged {AAA}, and sensitivity of stress-mediated collagen turnover on the wall stress distribution and the rate of expansion. The results also show that the distributions of stress and local expansion initially correspond to the extent of elastin damage, but change via stress-mediated tissue {G&R} depending on the aneurysm shape. Finally, we suggest that the current framework can be utilized along with medical images from an individual patient to predict the {AAA} shape and mechanical properties in the near future via an inverse scheme.

10aAneurysm rupture10aFinite element analysis10aInverse optimization10aPatient-specific modeling10aVascular growth and remodeling1 aZeinali-Davarani, S.1 aBaek, S. uhttp://www.sciencedirect.com/science/article/pii/S009364131200010900547nas a2200109 4500008004100000245011200041210006900153260005900222100001900281700001900300856011800319 2012 eng d00aMethylmercury (MeHg) disrupts fluo4 fluorescence in cerebellar slices from GABAA receptor alpha6 (-/-) mice0 aMethylmercury MeHg disrupts fluo4 fluorescence in cerebellar sli aSan Francisco, CAbSociety of Toxicology 2012c03/20121 aBradford, A, B1 aAtchison, W, D uhttps://icer.msu.edu/research/publications/methylmercury-mehg-disrupts-fluo4-fluorescence-cerebellar-slices-gabaa00600nas a2200145 4500008004100000245011800041210006900159100001500228700001700243700002100260700002100281700001800302700001200320856012200332 2012 eng d00amRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection0 amRNASeq analysis of the Pseudoperonospora cubensis transcriptome1 aSavory, E.1 aAdhikari, B.1 aHamilton, J., P.1 aVaillancourt, B.1 aBuell, C., R.1 aDay, B. uhttps://icer.msu.edu/research/publications/mrna-seq-analysis-pseudoperonospora-cubensis-transcriptome-during-cucumber00478nas a2200097 4500008004100000245009900041210006900140260003000209100001700239856012400256 2011 eng d00aMODELS TO AID IN THE SELECTION OF PROCEDURES USED TO MANAGE LAKE ERIE WALLEYE (SANDER VITREUS)0 aMODELS TO AID IN THE SELECTION OF PROCEDURES USED TO MANAGE LAKE bMichigan State University1 aBerger, A.M. uhttps://icer.msu.edu/research/publications/models-aid-selection-procedures-used-manage-lake-erie-walleye-sander-vitreus00476nas a2200097 4500008004100000245011600041210006900157490000800226100002000234856012400254 2011 eng d00aMolecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures0 aMolecular diffusion and slip boundary conditions at smooth surfa0 v1351 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/molecular-diffusion-slip-boundary-conditions-smooth-surfaces-periodic-random00518nas a2200109 4500008004100000245012900041210006900170490000800239100001700247700002000264856012400284 2011 eng d00aMolecular Dynamics Study of Thermal Transport in GaAs-SAM-GaAs Junctions with Ab-initio Characterization of Thiol-GaAs Bonds0 aMolecular Dynamics Study of Thermal Transport in GaAsSAMGaAs Jun0 v1091 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/molecular-dynamics-study-thermal-transport-gaas-sam-gaas-junctions-ab-initio00538nas a2200109 4500008004100000245014900041210006900190490000800259100001700267700002000284856012400304 2011 eng d00aMolecular dynamics study of thermal transport in GaAs-self-assembly monolayer-GaAs junctions with ab initio characterization of thiol-GaAs bonds0 aMolecular dynamics study of thermal transport in GaAsselfassembl0 v1091 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/molecular-dynamics-study-thermal-transport-gaas-self-assembly-monolayer-gaas00414nas a2200109 4500008004100000245005900041210005800100100001600158700001400174700001900188856009700207 2011 eng d00aMulti-label Learning with Incomplete Class Assignments0 aMultilabel Learning with Incomplete Class Assignments1 aBucak, S.S.1 aJin, Rong1 aJain, Anil, K. uhttps://icer.msu.edu/research/publications/multi-label-learning-incomplete-class-assignments01985nas a2200133 4500008004100000245009900041210006900140260001200209490000700221520146000228100001801688700002001706856012501726 2010 eng d00aModeling the combined effect of surface roughness and shear rate on slip flow of simple fluids0 aModeling the combined effect of surface roughness and shear rate c01/20100 v813 aMolecular dynamics (MD) and continuum simulations are carried out to investigate the influence of shear rate and surface roughness on slip flow of a Newtonian fluid. For weak wall-fluid interaction energy, the nonlinear shear-rate dependence of the intrinsic slip length in the flow over an atomically flat surface is computed by MD simulations. We describe laminar flow away from a curved boundary by means of the effective slip length defined with respect to the mean height of the surface roughness. Both the magnitude of the effective slip length and the slope of its rate dependence are significantly reduced in the presence of periodic surface roughness. We then numerically solve the Navier-Stokes equation for the flow over the rough surface using the rate-dependent intrinsic slip length as a local boundary condition. Continuum simulations reproduce the behavior of the effective slip length obtained from MD simulations at low shear rates. The slight discrepancy between MD and continuum results at high shear rates is explained by examination of the local velocity profiles and the pressure distribution along the wavy surface. We found that in the region where the curved boundary faces the mainstream flow, the local slip is suppressed due to the increase in pressure. The results of the comparative analysis can potentially lead to the development of an efficient algorithm for modeling rate-dependent slip flows over rough surfaces.

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

1 aLi, Wei1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/multi-level-extension-cluster-molecule-local-correlation-methodology-merging01793nas a2200145 4500008004100000245015600041210006900197260001200266300001400278490000800292520118900300100001601489700001901505856012301524 2009 eng d00aMethod of Moments for the Continuous Transition Between the Brillouin-Wigner-Type and Rayleigh-Schrodinger-Type Multireference Coupled Cluster Theories0 aMethod of Moments for the Continuous Transition Between the Bril c01/2009 a1209-12210 v1073 aWe apply the method of moments to the multireference (MR) coupled cluster (CC) formalism representing the continuous transition between the Brillouin-Wigner-type and Rayleigh-Schr\"{o}dinger-type theories based on the Jeziorski-Monkhorst wave function ansatz and derive the formula for the noniterative energy corrections to the corresponding MRCC energies that recover the exact, full configuration interaction energies in the general model space case, including complete and incomplete model spaces. We also extend the relationship between the generalized moments of the state-universal (SU) MRCC equations within the Jeziorski-Monkhorst and Kucharski-Bartlett formulations of the SUMRCC theory to the general model space case. Finally, we argue that in the complete model space case, the relationship between moments of the SUMRCC equations corresponding to the Jeziorski-Monkhorst and Kucharski-Bartlett formulations of the SUMRCC theory, derived in this work, implies an equivalence of these two formulations of the SUMRCC approach, provided that the disconnected linked terms are included in the Kucharski-Bartlett formulation, and verify this statement numerically.

1 aPittner, J.1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/method-moments-continuous-transition-between-brillouin-wigner-type-rayleigh01624nas a2200145 4500008004100000245014800041210006900189260001100258300001200269490000800281520103500289100001901324700001401343856012101357 2006 eng d00aIs the Mechanism of the [2+2] Cycloaddition of Cyclopentyne to Ethylene Concerted or Biradical? A Completely Renormalized Coupled Cluster Study0 aMechanism of the 22 Cycloaddition of Cyclopentyne to Ethylene Co c6/2005 a367-3780 v1103 aThe mechanism of the [2+2] cycloaddition reaction of cyclopentyne to ethylene has been studied using the completely renormalized coupled cluster method with singles, doubles, and noniterative triples (CR−CCSD(T)). In agreement with the experimentally observed stereochemistry, the CR−CCSD(T) method favors the concerted pathway involving a [2+1] transition state, whereas the popular CCSD(T) method, which is often regarded as the “gold standard” of electronic structure theory, and low-order multireference methods support the less probable biradical mechanism. In addition, the CCSD(T) approach produces an erroneous description of some transition states and intermediates, particularly those which have a significant biradical character. The CR−CCSD(T) calculations indicate that the reaction is a highly exothermic (Δ = −68 kcal/mol), predominantly concerted process with a relatively low activation barrier on the order of 13−16 kcal/mol which permits its thermal occurrence.

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

1 aTanizaki, Seiichiro1 aFeig, Michael uhttps://icer.msu.edu/molecular-dynamics-simulations-large-integral-membrane-proteins-implicit-membrane-model02386nas a2200241 4500008004100000245015000041210006900191260001200260300001400272490000800286520138300294653017701677100001901854700001701873700002401890700001501914700002101929700002301950700002201973700001301995700001502008856012102023 2004 eng d00aMethod of moments of coupled-cluster equations: a new formalism for designing accurate electronic structure methods for ground and excited states0 aMethod of moments of coupledcluster equations a new formalism fo c07/2004 a349–3930 v1123 aThe method of moments of coupled-cluster equations {(MMCC),} which provides a systematic way of improving the results of the standard coupled-cluster {(CC)} and equation-of-motion {CC} {(EOMCC)} calculations for the ground- and excited-state energies of atomic and molecular systems, is described. The {MMCC} theory and its generalized {MMCC} {(GMMCC)} extension that enables one to use the cluster operators resulting from the standard as well as nonstandard {CC} calculations, including those obtained with the extended {CC} {(ECC)} approaches, are based on rigorous mathematical relationships that define the many-body structure of the differences between the full configuration interaction {(CI)} and {CC} or {EOMCC} energies. These relationships can be used to design the noniterative corrections to the {CC/EOMCC} energies that work for chemical bond breaking and potential energy surfaces of excited electronic states, including excited states dominated by double excitations, where the standard single-reference {CC/EOMCC} methods fail. Several {MMCC} and {GMMCC} approximations are discussed, including the renormalized and completely renormalized {CC/EOMCC} methods for closed- and open-shell states, the quadratic {MMCC} approaches, the {CI-corrected} {MMCC} methods, and the {GMMCC} approaches for multiple bond breaking based on the {ECC} cluster amplitudes.

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