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Monte Carlo simulations of various classes of asymmetric exclusion processes (ASEP) with open and periodic boundaries. ASEP is a paradigmatic model of non equilibrium statistical mechanics. It can be utilized to model various non-equilibrium phenomena in Biology such molecular motor transport and protein sysnthesis.

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dcelisgarza/ASEP

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ASEP Package for the Dynamics of Molecular Motors

Thank you for using our package, we hope you find it interesting and useful!

--Daniel Celis Garza, Hamid Teimouri, and Anatoly Kolomeisky.

You can read the paper published as a corollary of these codes here. However, the specific codes used in the paper---as well as those pertaining to more complex, unstudied systems---have not been released because they serve the basis for the study of increasingly complex systems at the Kolomeisky group.

This readme file contains instructions and explanations of the parameters used in the codes.

alpha = ENTRANCE rate at the LEFT boundary

eta = EXIT rate at the LEFT boundary (PASEP)

beta = EXIT rate at the RIGHT boundary

chi = ENTRANCE rate at the RIGHT boundary (PASEP)

gamma = FORWARD hopping rate (PASEP)

delta = BACKWARD hopping rate (PASEP)

epsilon = interaction ENERGY, scaled to kbT units

theta = energy SPLITTING between attraction and repulsion

q = BINDING rate

r = UNBINDING rate

J = particle FLUX

rho = DENSITY

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Monte Carlo simulations of various classes of asymmetric exclusion processes (ASEP) with open and periodic boundaries. ASEP is a paradigmatic model of non equilibrium statistical mechanics. It can be utilized to model various non-equilibrium phenomena in Biology such molecular motor transport and protein sysnthesis.

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