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Cheng Y, Kekenes-Huskey P, Hake J, et al. Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction. Comput Sci Discov. 2012;5(1)doi: 10.1088/1749-4699/5/1/015002.
Cheng, Y., Kekenes-Huskey, P., Hake, J., Holst, M., McCammon, J., & Michailova, A. (2012). Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction. Computational science & discovery, 5(1), . https://doi.org/10.1088/1749-4699/5/1/015002
Cheng, Y, et al. "Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction." Computational science & discovery vol. 5,1 (2012). doi: https://doi.org/10.1088/1749-4699/5/1/015002
Cheng Y, Kekenes-Huskey P, Hake J, Holst M, McCammon J, Michailova A. Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction. Comput Sci Discov. 2012 Mar 20;5(1). doi: 10.1088/1749-4699/5/1/015002. PMID: 23505398; PMCID: PMC3596845.
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Comput Sci Discov. 2012 Mar 20;5(1). doi: 10.1088/1749-4699/5/1/015002.

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

Computational science & discovery

Y Cheng, P Kekenes-Huskey, Je Hake, Mj Holst, Ja McCammon, Ap Michailova

Affiliations

  1. Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.

PMID: 23505398 PMCID: PMC3596845 DOI: 10.1088/1749-4699/5/1/015002

Abstract

This article provides a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally-validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times with increasing ionic strength and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a non-linear, reaction-diffusion system describing Ca

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