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Title: Hybrid finite element and Brownian dynamics method for charged particles

Abstract

Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented using a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species.

Authors:
;  [1];  [2];  [3];  [4];  [5];  [5]
  1. Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365 (United States)
  2. Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Suzhou, 215006 Jiangsu (China)
  3. Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0112 (United States)
  4. Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093 (United States)
  5. (United States)
Publication Date:
OSTI Identifier:
22660869
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 144; Journal Issue: 16; Other Information: (c) 2016 Author(s); Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; CHARGED PARTICLES; DIFFUSION; FINITE ELEMENT METHOD; ONE-DIMENSIONAL CALCULATIONS; STOCHASTIC PROCESSES

Citation Formats

Huber, Gary A., E-mail: ghuber@ucsd.edu, Miao, Yinglong, Zhou, Shenggao, Li, Bo, McCammon, J. Andrew, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, and Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636. Hybrid finite element and Brownian dynamics method for charged particles. United States: N. p., 2016. Web. doi:10.1063/1.4947086.
Huber, Gary A., E-mail: ghuber@ucsd.edu, Miao, Yinglong, Zhou, Shenggao, Li, Bo, McCammon, J. Andrew, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, & Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636. Hybrid finite element and Brownian dynamics method for charged particles. United States. doi:10.1063/1.4947086.
Huber, Gary A., E-mail: ghuber@ucsd.edu, Miao, Yinglong, Zhou, Shenggao, Li, Bo, McCammon, J. Andrew, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, and Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636. Thu . "Hybrid finite element and Brownian dynamics method for charged particles". United States. doi:10.1063/1.4947086.
@article{osti_22660869,
title = {Hybrid finite element and Brownian dynamics method for charged particles},
author = {Huber, Gary A., E-mail: ghuber@ucsd.edu and Miao, Yinglong and Zhou, Shenggao and Li, Bo and McCammon, J. Andrew and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365 and Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636},
abstractNote = {Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented using a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species.},
doi = {10.1063/1.4947086},
journal = {Journal of Chemical Physics},
number = 16,
volume = 144,
place = {United States},
year = {Thu Apr 28 00:00:00 EDT 2016},
month = {Thu Apr 28 00:00:00 EDT 2016}
}