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.

%B Journal of Hydrology %V 544 %8 11/2016 %G eng %U http://hydrology1.weebly.com/uploads/6/6/2/1/66216077/jh_safaie.pdf %& 383 %0 Journal Article %J Microfluidics and Nanofluidics %D 2013 %T Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions %A N. V Priezjev %B Microfluidics and Nanofluidics %V 14 %G eng %N 1-2 %0 Journal Article %J Nature %D 2012 %T A magnified young galaxy from about 500 million years after the Big Bang %A Zheng, Wei %A Postman, Marc %A Zitrin, Adi %A Moustakas, John %A Shu, Xinwen %A Jouvel, Stephanie %A Høst, Ole %A Molino, Alberto %A Bradley, Larry %A Coe, Dan %A Moustakas, Leonidas A %A Carrasco, Mauricio %A Ford, Holland %A Benítez, Narciso %A Lauer, Tod R %A Seitz, Stella; B %A Bouwens, Rychard %A Koekemoer, Anton %A Medezinski, Elinor %A Bartelmann, Matthias %A Broadhurst, Tom %A Donahue, Megan %A Grillo, Claudio %A Infante, Leopoldo %A Jha, Saurabh W %A Kelson, Daniel D. %A Lahav, Ofer %A Lemze, Doron %A Melchior, Peter %A Meneghetti, Massimo %A Merten, Julian %A Nonino, Mario %A Ogaz, Sara %A Rosati, Piero %A Umetsu, Keiichi %A van der Wel, Arjen %B Nature %V 489 %8 09/2012 %G eng %N 7416 %0 Journal Article %J PHYSICAL REVIEW LETTERS %D 2012 %T Mass Measurements of the Neutron-Deficient 41Ti, 45Cr, 49Fe, and 53Ni Nuclides: ￼First Test of the Isobaric Multiplet Mass Equation in fp-Shell Nuclei %A Y.H. Zhang %A H.S. Xu %A Yu. A. Litvinov %A X.L. Tu %A X.L. Yan %A S. Typel %A K. Blaum %A M. Wang %A X.H. Zhou %A Y. Sun %A B. A. Brown %A Y.J. Yuan %A J.W. Xia %A J.C. Yang %A G. Audi %A X.C. Chen %A G.B. Jia %A Z.G. Hu %A X.W. Ma %A R.S. Mao %A B. Mei %A P. Shuai %A Z.Y. Sun %A S.T. Wang %A G.Q. Xiao %A X. Xu %A T. Yamaguchi %A Y. Yamaguchi %A Y.D. Zang %A H.W. Zhao %A T.C. Zhao %A W. Zhang %A W.L. Zhan %B PHYSICAL REVIEW LETTERS %V 109 %8 09/2012 %G eng %U http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.102501 %0 Journal Article %J Mechanics Research Communications %D 2012 %T Medical image-based simulation of abdominal aortic aneurysm growth %A Zeinali-Davarani, S. %A Baek, S. %K Aneurysm rupture %K Finite element analysis %K Inverse optimization %K Patient-specific modeling %K Vascular growth and remodeling %XAdvances 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.

%B Mechanics Research Communications %V 42 %P 107–117 %G eng %U http://www.sciencedirect.com/science/article/pii/S0093641312000109 %0 Chart or Table %D 2012 %T Methylmercury (MeHg) disrupts fluo4 fluorescence in cerebellar slices from GABAA receptor alpha6 (-/-) mice %A A B Bradford %A W D Atchison %I Society of Toxicology 2012 %C San Francisco, CA %8 03/2012 %G eng %0 Journal Article %J PLoS ONE, in press %D 2012 %T mRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection %A Savory, E. %A Adhikari, B. %A Hamilton, J. P. %A Vaillancourt, B. %A C. R. Buell %A B. Day %B PLoS ONE, in press %G eng %0 Thesis %D 2011 %T MODELS TO AID IN THE SELECTION OF PROCEDURES USED TO MANAGE LAKE ERIE WALLEYE (SANDER VITREUS) %A Berger, A.M. %I Michigan State University %G eng %9 phd %0 Journal Article %J J. Chem. Phys. %D 2011 %T Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures %A N. V Priezjev %B J. Chem. Phys. %V 135 %G eng %0 Journal Article %J J. of App. Phys. %D 2011 %T Molecular Dynamics Study of Thermal Transport in GaAs-SAM-GaAs Junctions with Ab-initio Characterization of Thiol-GaAs Bonds %A Tengfei Luo %A John R. Lloyd %B J. of App. Phys. %V 109 %G eng %0 Journal Article %J J. of App. Phys. %D 2011 %T Molecular dynamics study of thermal transport in GaAs-self-assembly monolayer-GaAs junctions with ab initio characterization of thiol-GaAs bonds %A Tengfei Luo %A John R. Lloyd %B J. of App. Phys. %V 109 %G eng %0 Conference Paper %B Proceedings of IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2011) %D 2011 %T Multi-label Learning with Incomplete Class Assignments %A S.S. Bucak %A Jin, Rong %A Jain, Anil K. %B Proceedings of IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2011) %G eng %0 Journal Article %J Physical Review E %D 2010 %T Modeling the combined effect of surface roughness and shear rate on slip flow of simple fluids %A A. Niavarani %A N. V Priezjev %XMolecular 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.

%B Physical Review E %V 81 %8 01/2010 %G eng %N 1 %9 Physics %0 Conference Paper %B Proceedings of Neural Information Processign Systems (NIPS 2010) %D 2010 %T Multi-label Multiple Kernel Learning by Stochastic Approximation: Application to Visual Object Recognition %A S.S.Bucak %A Jin, Rong %A Jain, Anil K. %B Proceedings of Neural Information Processign Systems (NIPS 2010) %G eng %0 Journal Article %J Journal of Physical Chemistry A %D 2010 %T Multi-level Extension of the Cluster-In-Molecule Local Correlation Methodology: Merging Coupled-Cluster and Moller-Plesset Perturbation Theories %A Wei Li %A Piotr Piecuch %XA 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.

%B Journal of Physical Chemistry A %V 114 %P 6721-6727 %8 05/2010 %G eng %N 24 %0 Journal Article %J Molecular Physics %D 2009 %T Method of Moments for the Continuous Transition Between the Brillouin-Wigner-Type and Rayleigh-Schrodinger-Type Multireference Coupled Cluster Theories %A J. Pittner %A Piotr Piecuch %XWe 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.

%B Molecular Physics %V 107 %P 1209-1221 %8 01/2009 %G eng %N 08-12 %0 Journal Article %J The Journal of Physical Chemistry %D 2006 %T Is the Mechanism of the [2+2] Cycloaddition of Cyclopentyne to Ethylene Concerted or Biradical? A Completely Renormalized Coupled Cluster Study %A Piotr Piecuch %A A. Kinal %XThe 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.

%B The Journal of Physical Chemistry %V 110 %P 367-378 %8 6/2005 %G eng %N 2 %0 Journal Article %J The Journal of Physical Chemistry B %D 2006 %T Molecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model %A Seiichiro Tanizaki %A Michael Feig %XThe 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.

%B The Journal of Physical Chemistry B %V 110 %P 548–556 %G eng %0 Journal Article %J Theoretical Chemistry Accounts: Theory, Computation, and Modeling %D 2004 %T Method of moments of coupled-cluster equations: a new formalism for designing accurate electronic structure methods for ground and excited states %A Piotr Piecuch %A K. Kowalski %A I. S. O. Pimienta %A P.-D. Fan %A M.D. Lodriguito %A M. J. {McGuire} %A S. A. Kucharski %A T. Kuś %A M. Musial %K Coupled-cluster theory - Method of moments of coupled-cluster equations - Renormalized coupled-cluster methods - extended coupled cluster theory - Potential energy surfaces %XThe 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.

%B Theoretical Chemistry Accounts: Theory, Computation, and Modeling %V 112 %P 349–393 %8 07/2004 %G eng