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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 -