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Michael Holst

Title(s)Professor, Mathematics
SchoolVc-academic Affairs
Address9500 Gilman Drive #0112
La Jolla CA 92093
Phone8/5-34--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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. 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:    Fields:    
    3. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophys J. 2020 Mar 10; 118(5):1003-1008. Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. PMID: 32032503.
      View in: PubMed   Mentions:    Fields:    
    4. 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.
      View in: PubMed   Mentions:
    5. 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.
      View in: PubMed   Mentions: 1     Fields:    
    6. 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.
      View in: PubMed   Mentions: 78     Fields:    
    7. 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.
      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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    9. 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.
      View in: PubMed   Mentions:
    10. 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.
      View in: PubMed   Mentions:
    11. 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.
      View in: PubMed   Mentions:
    12. 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.
      View in: PubMed   Mentions:
    13. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    14. 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.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    15. 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.
      View in: PubMed   Mentions:
    16. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    17. 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.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    18. 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.
      View in: PubMed   Mentions:
    19. 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:    
    20. 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.
      View in: PubMed   Mentions: 112     Fields:    Translation:AnimalsCells
    21. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    22. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    23. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    24. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    25. 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:    
    26. 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.
      View in: PubMed   Mentions:
    27. 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: 30     Fields:    Translation:Animals
    28. 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:    
    29. 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: 18     Fields:    Translation:Cells
    30. 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.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    31. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    32. 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.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    33. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    34. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A. 2001 Aug 28; 98(18):10037-41. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. PMID: 11517324.
      View in: PubMed   Mentions: 2516     Fields:    Translation:Cells
    35. 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: 10     Fields:    Translation:Cells
    36. 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: 13     Fields:    
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