| Year |
Citation |
Score |
| 2020 |
Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. Plos Computational Biology. 16: e1007756. PMID 32251448 DOI: 10.1371/Journal.Pcbi.1007756 |
0.351 |
|
| 2020 |
Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophysical Journal. PMID 32032503 DOI: 10.1016/J.Bpj.2019.11.3400 |
0.413 |
|
| 2019 |
Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. Acm Transactions On Mathematical Software. Association For Computing Machinery. 45. PMID 31474782 DOI: 10.1145/3321515 |
0.307 |
|
| 2019 |
Zhou YC, Holst M, McCammon JA. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces. Journal of Mathematical Analysis and Applications. 340: 135-164. PMID 19461946 DOI: 10.1016/J.Jmaa.2007.07.084 |
0.345 |
|
| 2018 |
Grogan F, Holst M, Lindblom L, Amaro R. Reliability assessment for large-scale molecular dynamics approximations. The Journal of Chemical Physics. 147: 234106. PMID 29272950 DOI: 10.1063/1.5009431 |
0.313 |
|
| 2018 |
Holst M, Tiee C. Finite Element Exterior Calculus for Parabolic Evolution Problems On Riemannian Hypersurfaces Journal of Computational Mathematics. 36: 792-832. DOI: 10.4208/Jcm.1705-M2016-0545 |
0.518 |
|
| 2018 |
Holst M, Meier C, Tsogtgerel G. Non-CMC Solutions of the Einstein Constraint Equations on Compact Manifolds with Apparent Horizon Boundaries Communications in Mathematical Physics. 357: 467-517. DOI: 10.1007/S00220-017-3004-9 |
0.609 |
|
| 2017 |
Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, ... ... Holst MJ, et al. Improvements to the APBS biomolecular solvation software suite. Protein Science : a Publication of the Protein Society. PMID 28836357 DOI: 10.1002/Pro.3280 |
0.37 |
|
| 2017 |
Lee C, Moody J, Andrew McCammon J, Holst M, Amaro RE. Investigating Transport Properties with Multi-Scale Computable Mesh Models from Heterogeneous Structural Datasets Biophysical Journal. 112: 293a. DOI: 10.1016/J.Bpj.2016.11.1586 |
0.338 |
|
| 2016 |
Holst M, Sarbach O, Tiglio M, Vallisneri M. The emergence of gravitational wave science: 100 years of development of mathematical theory, detectors, numerical algorithms, and data analysis tools Bulletin of the American Mathematical Society. 53: 513-554. DOI: 10.1090/Bull/1544 |
0.312 |
|
| 2016 |
Holst M, Pollock S. Convergence of goal-oriented adaptive finite element methods for nonsymmetric problems Numerical Methods For Partial Differential Equations. 32: 479-509. DOI: 10.1002/Num.22002 |
0.711 |
|
| 2015 |
Vincent KP, Gonzales MJ, Gillette AK, Villongco CT, Pezzuto S, Omens JH, Holst MJ, McCulloch AD. High-order finite element methods for cardiac monodomain simulations. Frontiers in Physiology. 6: 217. PMID 26300783 DOI: 10.3389/Fphys.2015.00217 |
0.455 |
|
| 2015 |
Zhang Y, Key K, Holst M, Ovall J. Parallel Goal-Oriented Adaptive Finite Element Modeling for 3D Electromagnetic Exploration Seg Technical Program Expanded Abstracts. DOI: 10.1190/Segam2015-5877991.1 |
0.389 |
|
| 2015 |
Holst M, Meier C. Non-CMC solutions to the Einstein constraint equations on asymptotically Euclidean manifolds with apparent horizon boundaries Classical and Quantum Gravity. 32. DOI: 10.1088/0264-9381/32/2/025006 |
0.631 |
|
| 2015 |
Holst M, Pollock S, Zhu Y. Convergence of goal-oriented adaptive finite element methods for semilinear problems Computing and Visualization in Science. 17: 43-63. DOI: 10.1007/S00791-015-0243-1 |
0.714 |
|
| 2014 |
De Dios BA, Holst M, Zhu Y, Zikatanov L. Multilevel preconditioners for discontinuous Galerkin approximations of elliptic problems with jump coefficients Mathematics of Computation. 83: 1083-1120. DOI: 10.1090/S0025-5718-2013-02760-3 |
0.402 |
|
| 2014 |
Holst M, Meier C. Generalized Solutions to Semilinear Elliptic PDE with Applications to the Lichnerowicz Equation Acta Applicandae Mathematicae. 130: 163-203. DOI: 10.1007/S10440-013-9842-3 |
0.646 |
|
| 2013 |
Liao T, Zhang Y, Kekenes-Huskey PM, Cheng Y, Michailova A, McCulloch AD, Holst M, McCammon JA. Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes. Molecular Based Mathematical Biology (Online). 1. PMID 24352481 DOI: 10.2478/Mlbmb-2013-0009 |
0.337 |
|
| 2013 |
Gao Z, Yu Z, Holst M. Feature-preserving surface mesh smoothing via suboptimal Delaunay triangulation Graphical Models \/Graphical Models and Image Processing \/Computer Vision, Graphics, and Image Processing. 75: 23-38. PMID 23580890 DOI: 10.1016/J.Gmod.2012.10.007 |
0.43 |
|
| 2013 |
Holst M, Tsogtgerel G. The Lichnerowicz equation on compact manifolds with boundary Classical and Quantum Gravity. 30: 205011. DOI: 10.1088/0264-9381/30/20/205011 |
0.45 |
|
| 2013 |
De Dios BA, Holst M, Zhu Y, Zikatanov L. Multigrid Preconditioner for Nonconforming Discretization of Elliptic Problems with Jump Coefficients Lecture Notes in Computational Science and Engineering. 91: 183-190. DOI: 10.1007/978-3-642-35275-1_20 |
0.309 |
|
| 2013 |
Holst M, Szypowski R, Zhu Y. Adaptive Finite Element Methods with Inexact Solvers for the Nonlinear Poisson-Boltzmann Equation Lecture Notes in Computational Science and Engineering. 91: 167-174. DOI: 10.1007/978-3-642-35275-1_18 |
0.753 |
|
| 2013 |
Holst M, Szypowski R, Zhu Y. Two-grid methods for semilinear interface problems Numerical Methods For Partial Differential Equations. 29: 1729-1748. DOI: 10.1002/Num.21774 |
0.758 |
|
| 2012 |
Gao Z, Yu Z, Holst M. Quality tetrahedral mesh smoothing via boundary-optimized Delaunay triangulation Computer Aided Geometric Design. 29: 707-721. PMID 23144522 DOI: 10.1016/J.Cagd.2012.07.001 |
0.427 |
|
| 2012 |
Holst M, McCammon JA, Yu Z, Zhou Y, Zhu Y. ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Communications in Computational Physics. 11: 179-214. PMID 21949541 DOI: 10.4208/Cicp.081009.130611A |
0.555 |
|
| 2012 |
Cheng Y, Kekenes-Huskey P, Hake E, Holst J, McCammon A, Michailova P, Hake JE, Holst MJ, McCammon JA, Michailova AP. Multi-scale continuum modeling of biological processes: From molecular electro-diffusion to sub-cellular signaling transduction Computational Science and Discovery. 5. DOI: 10.1088/1749-4699/5/1/015002 |
0.308 |
|
| 2012 |
Estep D, Holst MJ, Målqvist A. Nonparametric density estimation for randomly perturbed elliptic problems III: Convergence, computational cost, and generalizations Journal of Applied Mathematics and Computing. 38: 367-387. DOI: 10.1007/S12190-011-0484-1 |
0.354 |
|
| 2012 |
Aksoylu B, Bond SD, Cyr EC, Holst M. Goal-oriented adaptivity and multilevel preconditioning for the poisson-boltzmann equation Journal of Scientific Computing. 52: 202-225. DOI: 10.1007/S10915-011-9539-6 |
0.747 |
|
| 2012 |
Holst M, Stern A. Geometric Variational Crimes: Hilbert Complexes, Finite Element Exterior Calculus, and Problems on Hypersurfaces Foundations of Computational Mathematics. 12: 263-293. DOI: 10.1007/S10208-012-9119-7 |
0.481 |
|
| 2012 |
Holst M, Stern A. Semilinear Mixed Problems on Hilbert Complexes and Their Numerical Approximation Foundations of Computational Mathematics. 12: 363-387. DOI: 10.1007/S10208-011-9110-8 |
0.507 |
|
| 2012 |
Chen L, Holst M, Xu J, Zhu Y. Local multilevel preconditioners for elliptic equations with jump coefficients on bisection grids Computing and Visualization in Science. 15: 271-289. DOI: 10.1007/S00791-013-0213-4 |
0.48 |
|
| 2011 |
Yu Z, Yao G, Hoshijima M, Michailova A, Holst M. Multiscale modeling of calcium dynamics in ventricular myocytes with realistic transverse tubules. Ieee Transactions On Bio-Medical Engineering. 58: 2947-51. PMID 21632291 DOI: 10.1109/Tbme.2011.2158316 |
0.342 |
|
| 2011 |
Holst M, Kungurtsev V. Numerical bifurcation analysis of conformal formulations of the Einstein constraints Physical Review D. 84: 124038. DOI: 10.1103/Physrevd.84.124038 |
0.435 |
|
| 2011 |
Chen L, Holst M. Efficient mesh optimization schemes based on Optimal Delaunay Triangulations Computer Methods in Applied Mechanics and Engineering. 200: 967-984. DOI: 10.1016/J.Cma.2010.11.007 |
0.334 |
|
| 2011 |
Holst M, Ovall JS, Szypowski R. An efficient, reliable and robust error estimator for elliptic problems in ℝ3 Applied Numerical Mathematics. 61: 675-695. DOI: 10.1016/J.Apnum.2011.01.002 |
0.735 |
|
| 2010 |
Lu B, Holst MJ, McCammon JA, Zhou YC. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. Journal of Computational Physics. 229: 6979-6994. PMID 21709855 DOI: 10.1016/J.Jcp.2010.05.035 |
0.496 |
|
| 2010 |
Holst MJ, Larson MG, Målqvist A, Söderlund R. Convergence analysis of finite element approximations of the Joule heating problem in three spatial dimensions Bit Numerical Mathematics. 50: 781-795. DOI: 10.1007/S10543-010-0287-Z |
0.463 |
|
| 2010 |
Holst M, Lunasin E, Tsogtgerel G. Analysis of a General Family of Regularized Navier-Stokes and MHD Models Journal of Nonlinear Science. 20: 523-567. DOI: 10.1007/S00332-010-9066-X |
0.306 |
|
| 2009 |
Bylaska EJ, Holst M, Weare JH. Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory. Journal of Chemical Theory and Computation. 5: 937-48. PMID 26609603 DOI: 10.1021/Ct800350J |
0.425 |
|
| 2009 |
Chen L, Holst MJ, Xu J. Convergence and Optimality of Adaptive Mixed Finite Element Methods Mathematics of Computation. 78: 35-53. DOI: 10.1090/S0025-5718-08-02155-8 |
0.497 |
|
| 2009 |
Korobkin O, Aksoylu B, Holst M, Pazos E, Tiglio M. Solving the Einstein constraint equations on multi-block triangulations using finite element methods Classical and Quantum Gravity. 26. DOI: 10.1088/0264-9381/26/14/145007 |
0.77 |
|
| 2009 |
Bylaska EJ, Holst M, Weare JH. Adaptive finite element method for solving the exact kohn-sham equation of density functional theory Journal of Chemical Theory and Computation. 5: 937-948. DOI: 10.1021/ct800350j |
0.342 |
|
| 2009 |
Holst M, Nagy G, Tsogtgerel G. Rough solutions of the Einstein constraints on closed manifolds without near-CMC conditions Communications in Mathematical Physics. 288: 547-613. DOI: 10.1007/S00220-009-0743-2 |
0.344 |
|
| 2008 |
Holst M, Nagy G, Tsogtgerel G. Far-from-constant mean curvature solutions of Einstein's constraint equations with positive Yamabe metrics. Physical Review Letters. 100: 161101-161101. PMID 18518180 DOI: 10.1103/Physrevlett.100.161101 |
0.387 |
|
| 2008 |
Yu Z, Holst MJ, Cheng Y, McCammon JA. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. Journal of Molecular Graphics & Modelling. 26: 1370-80. PMID 18337134 DOI: 10.1016/J.Jmgm.2008.01.007 |
0.391 |
|
| 2008 |
Yu Z, Holst MJ, Andrew McCammon J. High-fidelity geometric modeling for biomedical applications Finite Elements in Analysis and Design. 44: 715-723. DOI: 10.1016/J.Finel.2008.03.004 |
0.388 |
|
| 2008 |
Lu BZ, Zhou YC, Holst MJ, McCammon JA. Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications Communications in Computational Physics. 3: 973-1009. |
0.39 |
|
| 2007 |
Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA. Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. The Journal of Chemical Physics. 127: 135102. PMID 17919055 DOI: 10.1063/1.2775933 |
0.489 |
|
| 2007 |
Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophysical Journal. 92: 3397-406. PMID 17307827 DOI: 10.1529/Biophysj.106.102533 |
0.412 |
|
| 2007 |
Cheng Y, Suen JK, Radić Z, Bond SD, Holst MJ, McCammon JA. Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophysical Chemistry. 127: 129-39. PMID 17307283 DOI: 10.1016/J.Bpc.2007.01.003 |
0.342 |
|
| 2007 |
Chen L, Holst MJ, Xu J. The finite element approximation of the nonlinear Poisson-Boltzmann equation Siam Journal On Numerical Analysis. 45: 2298-2320. DOI: 10.1137/060675514 |
0.522 |
|
| 2006 |
Aksoylu B, Holst M. Optimality of multilevel preconditioners for local mesh refinement in three dimensions Siam Journal On Numerical Analysis. 44: 1005-1025. DOI: 10.1137/S0036142902406119 |
0.731 |
|
| 2005 |
Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophysical Journal. 88: 1659-65. PMID 15626705 DOI: 10.1529/Biophysj.104.053850 |
0.346 |
|
| 2005 |
Estep D, Holst M, Larson M. Generalized Green's functions and the effective domain of influence Siam Journal On Scientific Computing. 26: 1314-1339. DOI: 10.1137/S1064827502416319 |
0.45 |
|
| 2004 |
Holst M, Lindblom L, Owen R, Pfeiffer HP, Scheel MA, Kidder LE. Optimal constraint projection for hyperbolic evolution systems Physical Review D - Particles, Fields, Gravitation and Cosmology. 70: 084017-1-084017-17. DOI: 10.1103/Physrevd.70.084017 |
0.338 |
|
| 2003 |
Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophysical Journal. 84: 2234-41. PMID 12668432 DOI: 10.1016/S0006-3495(03)75029-2 |
0.344 |
|
| 2003 |
Aksoylu B, Bond S, Holst M. An odyssey into local refinement and multilevel preconditioning III: Implementation and numerical experiments Siam Journal On Scientific Computing. 25: 478-498. DOI: 10.1137/S1064827502407676 |
0.751 |
|
| 2003 |
Bank RE, Holst M. A New Paradigm for Parallel Adaptive Meshing Algorithms Siam Review. 45: 291-323. DOI: 10.1137/S003614450342061 |
0.458 |
|
| 2002 |
Estep D, Holst M, Mikulencak D. Accounting for stability: A posteriori error estimates based on residuals and variational analysis Communications in Numerical Methods in Engineering. 18: 15-30. DOI: 10.1002/Cnm.461 |
0.372 |
|
| 2001 |
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: Application to microtubules and the ribosome Proceedings of the National Academy of Sciences of the United States of America. 98: 10037-10041. PMID 11517324 DOI: 10.1073/Pnas.181342398 |
0.391 |
|
| 2001 |
Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers Ibm Journal of Research and Development. 45: 427-438. DOI: 10.1147/Rd.453.0427 |
0.435 |
|
| 2001 |
Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers Ibm Journal of Research and Development. 45: 427-438. DOI: 10.1147/rd.453.0427 |
0.364 |
|
| 2001 |
Bank RE, Holst M. A new paradigm for parallel adaptive meshing algorithms Siam Journal On Scientific Computing. 22: 1411-1443. DOI: 10.1137/S1064827599353701 |
0.45 |
|
| 2001 |
Ashby SF, Holst MJ, Manteuffel TA, Saylor PE. The role of the inner product in stopping criteria for conjugate gradient iterations Bit Numerical Mathematics. 41: 26-52. DOI: 10.1023/A:1021961616621 |
0.334 |
|
| 2001 |
Holst MJ. Adaptive Numerical Treatment of Elliptic Systems on Manifolds Advances in Computational Mathematics. 15: 139-191. DOI: 10.1023/A:1014246117321 |
0.557 |
|
| 2000 |
Baker N, Holst M, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems Journal of Computational Chemistry. 21: 1343-1352. DOI: 10.1002/1096-987X(20001130)21:15<1343::Aid-Jcc2>3.0.Co;2-K |
0.523 |
|
| 2000 |
Holst M, Baker N, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples Journal of Computational Chemistry. 21: 1319-1342. DOI: 10.1002/1096-987X(20001130)21:15<1319::Aid-Jcc1>3.0.Co;2-8 |
0.567 |
|
| 1997 |
Holst M, Vandewalle S. Schwarz Methods: To Symmetrize or Not to Symmetrize Siam Journal On Numerical Analysis. 34: 699-722. DOI: 10.1137/S0036142994275743 |
0.407 |
|
| 1997 |
Stetter HJ, Van Loan C, Holst M, Stenger F, Shu C, Mattheij R, Wright SJ, Coleman TF, Wahlbin LB. Book Review: Lectures on finite precision computations Mathematics of Computation. 66: 1751-1764. DOI: 10.1090/S0025-5718-97-00910-1 |
0.346 |
|
| 1995 |
Holst MJ, Saied F. Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods Journal of Computational Chemistry. 16: 337-364. DOI: 10.1002/Jcc.540160308 |
0.453 |
|
| 1994 |
Holst M, Kozack RE, Saied F, Subramaniam S. Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation. Proteins. 18: 231-245. PMID 8202464 DOI: 10.1002/Prot.340180304 |
0.426 |
|
| 1994 |
Holst M, Kozack RE, Saied F, Subramaniam S. Protein Electrostatics: Rapid Multigrid-Based Newton Algorithm for Solution of the Full Nonlinear Poisson-Boltzmann Equation Journal of Biomolecular Structure & Dynamics. 11: 1437-1445. PMID 7946084 DOI: 10.1080/07391102.1994.10508078 |
0.46 |
|
| 1993 |
Holst M, Saied F. Multigrid solution of the Poisson-Boltzmann equation Journal of Computational Chemistry. 14: 105-113. DOI: 10.1002/Jcc.540140114 |
0.481 |
|
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