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.[1] 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)[2] and particle-particle-particle-mesh (P3M).[3] 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.
^van der Straaten, T.A.; Kathawala, G.; Trellakis, A.; Eisenberg §, R.S.; Ravaioli, U. (2005-02-15). "BioMOCA—a Boltzmann transport Monte Carlo model for ion channel simulation". Molecular Simulation. 31 (2–3). Informa UK Limited: 151–171. doi:10.1080/08927020412331308700. ISSN 0892-7022. S2CID 96166501.
^C. Jacoboni, P. Lugli, The Monte Carlo Method for Semiconductor Device Simulation, Springer Verlag, New York (1989)
^R. Hockney, J. Eastwood, Computer Simulation Using Particles, McGraw-Hill, New York (1981)
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BiologyMonteCarlomethods (BioMOCA) have been developed at the University of Illinois at Urbana-Champaign to simulate ion transport in an electrolyte...
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computational physics, computational biology and computational linguistics. In Bayesian statistics, Markov chain MonteCarlomethods are typically used to calculate...
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