Michael Holst

Title(s)	Professor, Mathematics
School	Vc-academic Affairs
Address	9500 Gilman Drive # La Jolla CA 92093
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Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput Biol. 2020 04; 16(4):e1007756. Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. PMID: 32251448; PMCID: PMC7162555.

View in: PubMed Mentions: 17 Fields:
Com Computational Biology
Translation:Humans Cells
Stability Analysis of a Bulk-Surface Reaction Model for Membrane Protein Clustering. Bull Math Biol. 2020 02 06; 82(2):30. Stolerman LM, Getz M, Smith SGL, Holst M, Rangamani P. PMID: 32025918.

View in: PubMed Mentions: 1 Fields:
Bio Biology Sta Statistics as Topic
Translation:Humans Cells
An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophys J. 2020 03 10; 118(5):1003-1008. Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. PMID: 32032503; PMCID: PMC7063475.

View in: PubMed Mentions: 10 Fields:
Bio Biophysics
Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations. Front Phys. 2020 Jan; 7. Vasan R, Rowan MP, Lee CT, Johnson GR, Rangamani P, Holst M. PMID: 36188416; PMCID: PMC9521042.

View in: PubMed Mentions: 3
The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. ACM Trans Math Softw. 2019 Aug; 45(3). Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. PMID: 31474782; PMCID: PMC6716611.

View in: PubMed Mentions: 3
Reliability assessment for large-scale molecular dynamics approximations. J Chem Phys. 2017 Dec 21; 147(23):234106. Grogan F, Holst M, Lindblom L, Amaro R. PMID: 29272950; PMCID: PMC5739912.

View in: PubMed Mentions: 3 Fields:
Bio Biophysics Che Chemistry Phy Physics
Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018 01; 27(1):112-128. 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, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. PMID: 28836357; PMCID: PMC5734301.

View in: PubMed Mentions: 697 Fields:
Bio Biochemistry
High-order finite element methods for cardiac monodomain simulations. Front Physiol. 2015; 6:217. Vincent KP, Gonzales MJ, Gillette AK, Villongco CT, Pezzuto S, Omens JH, Holst MJ, McCulloch AD. PMID: 26300783; PMCID: PMC4525671.

View in: PubMed Mentions: 8
Detecting glaucoma progression from localized rates of retinal changes in parametric and nonparametric statistical framework with type I error control. Invest Ophthalmol Vis Sci. 2014 Mar 19; 55(3):1684-95. Balasubramanian M, Arias-Castro E, Medeiros FA, Kriegman DJ, Bowd C, Weinreb RN, Holst M, Sample PA, Zangwill LM. PMID: 24519427; PMCID: PMC4586965.

View in: PubMed Mentions: 2 Fields:
Oph Ophthalmology
Translation:Humans
Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes. Mol Based Math Biol. 2013 Jul; 1. Liao T, Zhang Y, Kekenes-Huskey PM, Cheng Y, Michailova A, McCulloch AD, Holst M, McCammon JA. PMID: 24352481; PMCID: PMC3858848.

View in: PubMed Mentions: 6
Feature-preserving surface mesh smoothing via suboptimal Delaunay triangulation. Graph Models. 2013 Jan 01; 75(1):23-38. Gao Z, Yu Z, Holst M. PMID: 23580890; PMCID: PMC3619448.

View in: PubMed Mentions: 8
Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries. Front Physiol. 2012; 3:351. Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. PMID: 23060801; PMCID: PMC3463892.

View in: PubMed Mentions: 18
Quality Tetrahedral Mesh Smoothing via Boundary-Optimized Delaunay Triangulation. Comput Aided Geom Des. 2012 Dec 01; 29(9):707-721. Gao Z, Yu Z, Holst M. PMID: 23144522; PMCID: PMC3489504.

View in: PubMed Mentions: 4
Localized glaucomatous change detection within the proper orthogonal decomposition framework. Invest Ophthalmol Vis Sci. 2012 Jun 14; 53(7):3615-28. Balasubramanian M, Kriegman DJ, Bowd C, Holst M, Weinreb RN, Sample PA, Zangwill LM. PMID: 22491406; PMCID: PMC3406887.

View in: PubMed Mentions: 8 Fields:
Oph Ophthalmology
Translation:Humans
Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol. 2012 Sep 15; 590(18):4403-22. Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD. PMID: 22495592; PMCID: PMC3477749.

View in: PubMed Mentions: 51 Fields:
Phy Physiology
Translation:Animals Cells
ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Commun Comput Phys. 2012; 11(1):179-214. Holst M, McCammon JA, Yu Z, Zhou Y, Zhu Y. PMID: 21949541; PMCID: PMC3178275.

View in: PubMed Mentions: 14
Multiscale modeling of calcium dynamics in ventricular myocytes with realistic transverse tubules. IEEE Trans Biomed Eng. 2011 Oct; 58(10):2947-51. Yu Z, Yao G, Hoshijima M, Michailova A, Holst M. PMID: 21632291; PMCID: PMC3179564.

View in: PubMed Mentions: 3 Fields:
Bio Biomedical Engineering
Translation:Animals Cells
Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput Biol. 2010 Oct 28; 6(10):e1000972. Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP. PMID: 21060856; PMCID: PMC2965743.

View in: PubMed Mentions: 25 Fields:
Com Computational Biology
Translation:Animals Cells
Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. J Comput Phys. 2010 Sep 20; 229(19):6979-6994. Lu B, Holst MJ, McCammon JA, Zhou YC. PMID: 21709855; PMCID: PMC2922884.

View in: PubMed Mentions: 21
Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory. J Chem Theory Comput. 2009 Apr 14; 5(4):937-48. Bylaska EJ, Holst M, Weare JH. PMID: 26609603.

View in: PubMed Mentions: 1 Fields:
Bio Biochemistry Che Chemistry
Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart. J Cell Sci. 2009 Apr 01; 122(Pt 7):1005-13. Hayashi T, Martone ME, Yu Z, Thor A, Doi M, Holst MJ, Ellisman MH, Hoshijima M. PMID: 19295127; PMCID: PMC2720931.

View in: PubMed Mentions: 141 Fields:
Cel Cell Biology
Translation:Animals Cells
Multiscale modeling in rodent ventricular myocytes. IEEE Eng Med Biol Mag. 2009 Mar-Apr; 28(2):46-57. Lu S, Michailova A, Saucerman J, Cheng Y, Yu Z, Kaiser T, Li W, Bank R, Holst M, McCammon J, Hayashi T, Hoshijima M, Arzberger P, McCulloch A. PMID: 19349251; PMCID: PMC3197248.

View in: PubMed Mentions: 12 Fields:
Bio Biomedical Engineering
Translation:Animals Cells
Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase. Pac Symp Biocomput. 2009; 281-92. Cheng Y, Holst MJ, McCammon JA. PMID: 19209708; PMCID: PMC3107071.

View in: PubMed Mentions: 3 Fields:
Com Computational Biology
Translation:Cells
Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation. J Struct Biol. 2008 Dec; 164(3):304-13. Yu Z, Holst MJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA, Hoshijima M. PMID: 18835449; PMCID: PMC2790379.

View in: PubMed Mentions: 17 Fields:
Cel Cell Biology Mol Molecular Biology
Translation:Animals Cells
Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies. Biophys J. 2008 Nov 15; 95(10):4659-67. Cheng Y, Chang CE, Yu Z, Zhang Y, Sun M, Leyh TS, Holst MJ, McCammon JA. PMID: 18689458; PMCID: PMC2576392.

View in: PubMed Mentions: 14 Fields:
Bio Biophysics
Translation:Cells
Far-from-constant mean curvature solutions of Einstein's constraint equations with positive Yamabe metrics. Phys Rev Lett. 2008 Apr 25; 100(16):161101. Holst M, Nagy G, Tsogtgerel G. PMID: 18518180.

View in: PubMed Mentions: Fields:
Med Medicine (General)
A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces. J Math Anal Appl. 2008 Apr 01; 340(1):135-164. Zhou YC, Holst M, McCammon JA. PMID: 19461946; PMCID: PMC2423821.

View in: PubMed Mentions: 6
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model. 2008 Jun; 26(8):1370-80. Yu Z, Holst MJ, Cheng Y, McCammon JA. PMID: 18337134.

View in: PubMed Mentions: 35 Fields:
Mol Molecular Biology
Translation:Animals
Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B. 2008 Jan 17; 112(2):270-5. Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA. PMID: 18052268.

View in: PubMed Mentions: 10 Fields:
Che Chemistry
Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys. 2007 Oct 07; 127(13):135102. Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA. PMID: 17919055.

View in: PubMed Mentions: 22 Fields:
Bio Biophysics Che Chemistry Phy Physics
Translation:Cells
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J. 2007 May 15; 92(10):3397-406. Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. PMID: 17307827; PMCID: PMC1853150.

View in: PubMed Mentions: 20 Fields:
Bio Biophysics
Translation:Cells
Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophys Chem. 2007 May; 127(3):129-39. Cheng Y, Suen JK, Radic Z, Bond SD, Holst MJ, McCammon JA. PMID: 17307283; PMCID: PMC2040065.

View in: PubMed Mentions: 16 Fields:
Bio Biochemistry Bio Biophysics
Translation:Cells
Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J. 2005 Mar; 88(3):1659-65. Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. PMID: 15626705; PMCID: PMC1305222.

View in: PubMed Mentions: 14 Fields:
Bio Biophysics
Translation:Animals Cells
Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J. 2003 Apr; 84(4):2234-41. Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. PMID: 12668432; PMCID: PMC1302790.

View in: PubMed Mentions: 13 Fields:
Bio Biophysics
Translation:Cells
Protein electrostatics: rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation. J Biomol Struct Dyn. 1994 Jun; 11(6):1437-45. Holst M, Kozack RE, Saied F, Subramaniam S. PMID: 7946084.

View in: PubMed Mentions: 11 Fields:
Bio Biochemistry Mol Molecular Biology
Translation:Cells
Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation. Proteins. 1994 Mar; 18(3):231-45. Holst M, Kozack RE, Saied F, Subramaniam S. PMID: 8202464.

View in: PubMed Mentions: 14 Fields:
Bio Biochemistry