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HandWiki. Biology Monte Carlo Method. Encyclopedia. Available online: https://encyclopedia.pub/entry/32794 (accessed on 23 September 2026).
HandWiki. Biology Monte Carlo Method. Encyclopedia. Available at: https://encyclopedia.pub/entry/32794. Accessed September 23, 2026.
HandWiki. "Biology Monte Carlo Method" Encyclopedia, https://encyclopedia.pub/entry/32794 (accessed September 23, 2026).
HandWiki. (2022, November 04). Biology Monte Carlo Method. In Encyclopedia. https://encyclopedia.pub/entry/32794
HandWiki. "Biology Monte Carlo Method." Encyclopedia. Web. 04 November, 2022.
Biology Monte Carlo Method
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The content is sourced from: https://handwiki.org/wiki/Biology:Biology_Monte_Carlo_method

Biology Monte Carlo methods (BioMOCA) have been developed at the University of Illinois at Urbana-Champaign to simulate ion transport in an electrolyte environment through ion channels or nano-pores embedded in membranes. It is a 3-D particle-based Monte Carlo simulator for analyzing and studying the ion transport problem in ion channel systems or similar nanopores in wet/biological environments. The system simulated consists of a protein forming an ion channel (or an artificial nanopores like a Carbon Nano Tube, CNT), with a membrane (i.e. lipid bilayer) that separates two ion baths on either side. BioMOCA is based on two methodologies, namely the Boltzmann transport Monte Carlo (BTMC) and particle-particle-particle-mesh (P3M). The first one uses Monte Carlo method to solve the Boltzmann equation, while the later splits the electrostatic forces into short-range and long-range components.

electrolyte ion channel electrostatic forces

References

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  3. Toghraee, Reza; Mashl, R. Jay; Lee, Kyu Il; Jakobsson, Eric; Ravaioli, Umberto (2009). "Simulation of charge transport in ion channels and nanopores with anisotropic permittivity". Journal of Computational Electronics (Springer Science and Business Media LLC) 8 (2): 98–109. doi:10.1007/s10825-009-0272-4. ISSN 1569-8025. PMID 20445807.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2863032
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  5. Schutz, Claudia N.; Warshel, Arieh (2001). "What are the dielectric "constants" of proteins and how to validate electrostatic models?". Proteins: Structure, Function, and Genetics (Wiley) 44 (4): 400–417. doi:10.1002/prot.1106. ISSN 0887-3585. PMID 11484218.  https://dx.doi.org/10.1002%2Fprot.1106
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  8. S. Selberherr, Analysis and Simulation of Semiconductor Devices, New York, Springer-Verlag Wien, (1984). ISBN:3-211-81800-6
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  13. Wang, Hai-Long; Toghraee, Reza; Papke, David; Cheng, Xiao-Lin; McCammon, J. Andrew; Ravaioli, Umberto; Sine, Steven M. (2009). "Single-Channel Current Through Nicotinic Receptor Produced by Closure of Binding Site C-Loop". Biophysical Journal (Elsevier BV) 96 (9): 3582–3590. doi:10.1016/j.bpj.2009.02.020. ISSN 0006-3495. PMID 19413963. Bibcode: 2009BpJ....96.3582W.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2711404
  14. "VMD - Visual Molecular Dynamics". http://www.ks.uiuc.edu/Research/vmd/. 
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