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Items: 20

1.

The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation.

Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ.

ACM Trans Math Softw. 2019 Aug;45(3). pii: 28. doi: 10.1145/3321515.

PMID:
31474782
2.

Improvements to the APBS biomolecular solvation software suite.

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.

Protein Sci. 2018 Jan;27(1):112-128. doi: 10.1002/pro.3280. Epub 2017 Oct 24.

3.

High-order finite element methods for cardiac monodomain simulations.

Vincent KP, Gonzales MJ, Gillette AK, Villongco CT, Pezzuto S, Omens JH, Holst MJ, McCulloch AD.

Front Physiol. 2015 Aug 5;6:217. doi: 10.3389/fphys.2015.00217. eCollection 2015.

4.

Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction.

Cheng Y, Kekenes-Huskey P, Hake J, Holst M, McCammon J, Michailova A.

Comput Sci Discov. 2012 Mar 20;5(1). pii: 015002.

5.

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.

Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP.

Front Physiol. 2012 Sep 10;3:351. doi: 10.3389/fphys.2012.00351. eCollection 2012.

6.

Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit.

Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD.

J Physiol. 2012 Sep 15;590(18):4403-22. doi: 10.1113/jphysiol.2012.227926. Epub 2012 Apr 10.

7.
8.

Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum.

Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP.

PLoS Comput Biol. 2010 Oct 28;6(10):e1000972. doi: 10.1371/journal.pcbi.1000972.

9.

Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart.

Hayashi T, Martone ME, Yu Z, Thor A, Doi M, Holst MJ, Ellisman MH, Hoshijima M.

J Cell Sci. 2009 Apr 1;122(Pt 7):1005-13. doi: 10.1242/jcs.028175.

10.
11.

Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation.

Yu Z, Holst MJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA, Hoshijima M.

J Struct Biol. 2008 Dec;164(3):304-13. doi: 10.1016/j.jsb.2008.09.004. Epub 2008 Sep 19.

12.

Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies.

Cheng Y, Chang CE, Yu Z, Zhang Y, Sun M, Leyh TS, Holst MJ, McCammon JA.

Biophys J. 2008 Nov 15;95(10):4659-67. doi: 10.1529/biophysj.108.140038. Epub 2008 Aug 8.

13.

Feature-preserving adaptive mesh generation for molecular shape modeling and simulation.

Yu Z, Holst MJ, Cheng Y, McCammon JA.

J Mol Graph Model. 2008 Jun;26(8):1370-80. doi: 10.1016/j.jmgm.2008.01.007. Epub 2008 Feb 7.

PMID:
18337134
14.

Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach.

Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA.

J Phys Chem B. 2008 Jan 17;112(2):270-5. Epub 2007 Dec 5.

PMID:
18052268
15.

Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution.

Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA.

J Chem Phys. 2007 Oct 7;127(13):135102.

PMID:
17919055
16.

Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations.

Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA.

Biophys J. 2007 May 15;92(10):3397-406. Epub 2007 Feb 16.

17.

Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models.

Cheng Y, Suen JK, Radić Z, Bond SD, Holst MJ, McCammon JA.

Biophys Chem. 2007 May;127(3):129-39. Epub 2007 Jan 19.

18.

Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods.

Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA.

Biophys J. 2005 Mar;88(3):1659-65. Epub 2004 Dec 30.

19.

Finite element simulations of acetylcholine diffusion in neuromuscular junctions.

Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA.

Biophys J. 2003 Apr;84(4):2234-41.

20.

Electrostatics of nanosystems: application to microtubules and the ribosome.

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA.

Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41. Epub 2001 Aug 21.

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