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Michael Holst

Title(s)Professor, Physics
SchoolAcademic Aff
Phone858-534-4899
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    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.
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    1. Stolerman LM, Getz M, Smith SGL, Holst M, Rangamani P. Stability Analysis of a Bulk-Surface Reaction Model for Membrane Protein Clustering. Bull Math Biol. 2020 Feb 06; 82(2):30. PMID: 32025918.
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    2. 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. Biophys J. 2020 Jan 22. PMID: 32032503.
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    3. 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 Trans Math Softw. 2019 Aug; 45(3). PMID: 31474782.
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    4. Grogan F, Holst M, Lindblom L, Amaro R. Reliability assessment for large-scale molecular dynamics approximations. J Chem Phys. 2017 Dec 21; 147(23):234106. PMID: 29272950.
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    5. 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. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018 01; 27(1):112-128. PMID: 28836357.
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    6. 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. Front Physiol. 2015; 6:217. PMID: 26300783.
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    7. Balasubramanian M, Arias-Castro E, Medeiros FA, Kriegman DJ, Bowd C, Weinreb RN, Holst M, Sample PA, Zangwill LM. 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. PMID: 24519427.
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    8. 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. Mol Based Math Biol. 2013 Jul; 1. PMID: 24352481.
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    9. Gao Z, Yu Z, Holst M. Feature-preserving surface mesh smoothing via suboptimal Delaunay triangulation. Graph Models. 2013 Jan 01; 75(1):23-38. PMID: 23580890.
      View in: PubMed
    10. Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. 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. PMID: 23060801.
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    11. Gao Z, Yu Z, Holst M. Quality Tetrahedral Mesh Smoothing via Boundary-Optimized Delaunay Triangulation. Comput Aided Geom Des. 2012 Dec 01; 29(9):707-721. PMID: 23144522.
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    12. Balasubramanian M, Kriegman DJ, Bowd C, Holst M, Weinreb RN, Sample PA, Zangwill LM. Localized glaucomatous change detection within the proper orthogonal decomposition framework. Invest Ophthalmol Vis Sci. 2012 Jun 14; 53(7):3615-28. PMID: 22491406.
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    13. Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD. Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol. 2012 Sep 15; 590(18):4403-22. PMID: 22495592.
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    14. Holst M, McCammon JA, Yu Z, Zhou Y, Zhu Y. ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Commun Comput Phys. 2012; 11(1):179-214. PMID: 21949541.
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    15. Yu Z, Yao G, Hoshijima M, Michailova A, Holst M. Multiscale modeling of calcium dynamics in ventricular myocytes with realistic transverse tubules. IEEE Trans Biomed Eng. 2011 Oct; 58(10):2947-51. PMID: 21632291.
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    16. Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP. 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. PMID: 21060856.
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    17. Lu B, Holst MJ, McCammon JA, Zhou YC. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. J Comput Phys. 2010 Sep 20; 229(19):6979-6994. PMID: 21709855.
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    18. Bylaska EJ, Holst M, Weare JH. 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. PMID: 26609603.
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    19. Hayashi T, Martone ME, Yu Z, Thor A, Doi M, Holst MJ, Ellisman MH, Hoshijima M. 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. PMID: 19295127.
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    20. 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. Multiscale modeling in rodent ventricular myocytes. IEEE Eng Med Biol Mag. 2009 Mar-Apr; 28(2):46-57. PMID: 19349251.
      View in: PubMed
    21. Cheng Y, Holst MJ, McCammon JA. Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase. Pac Symp Biocomput. 2009; 281-92. PMID: 19209708.
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    22. Yu Z, Holst MJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA, Hoshijima M. 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. PMID: 18835449.
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    23. Cheng Y, Chang CE, Yu Z, Zhang Y, Sun M, Leyh TS, Holst MJ, McCammon JA. 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. PMID: 18689458.
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    24. Holst M, Nagy G, Tsogtgerel G. Far-from-constant mean curvature solutions of Einstein's constraint equations with positive Yamabe metrics. Phys Rev Lett. 2008 Apr 25; 100(16):161101. PMID: 18518180.
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    25. Zhou YC, Holst M, McCammon JA. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces. J Math Anal Appl. 2008 Apr 01; 340(1):135-164. PMID: 19461946.
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    26. Yu Z, Holst MJ, Cheng Y, McCammon JA. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model. 2008 Jun; 26(8):1370-80. PMID: 18337134.
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    27. Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA. Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B. 2008 Jan 17; 112(2):270-5. PMID: 18052268.
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    28. Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA. Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys. 2007 Oct 07; 127(13):135102. PMID: 17919055.
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    29. 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. Biophys J. 2007 May 15; 92(10):3397-406. PMID: 17307827.
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    30. Cheng Y, Suen JK, Radic Z, Bond SD, Holst MJ, McCammon JA. Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophys Chem. 2007 May; 127(3):129-39. PMID: 17307283.
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    31. 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. Biophys J. 2005 Mar; 88(3):1659-65. PMID: 15626705.
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    32. Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J. 2003 Apr; 84(4):2234-41. PMID: 12668432.
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    33. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A. 2001 Aug 28; 98(18):10037-41. PMID: 11517324.
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    34. Holst M, Kozack RE, Saied F, Subramaniam S. 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. PMID: 7946084.
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    35. 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. 1994 Mar; 18(3):231-45. PMID: 8202464.
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