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Various Extensions of Original Born-Kramers-Slater Model for Reactions Kinetics Based on Brownian Motion and fokker-plank equation Including 1D, 2D, 3D, and Multi-dimensional Approaches

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Journal of Chemistry and Chemical Engineering 2017年第3期11卷 90-94页

作者： Michael Fundator DBASSE (Division of Behavioral and Social Sciences and Education) of the National Academy of Sciences Engineering and Medicine USA

Different extensions, such as Transition State theory of Eyring-Polanyi-Evans model of the original Born-Kramers-Slater Model for the Velocity of Chemical Reactions are discussed based on Smoluchowski and fokker-plank equations with various properties of Brownian motion and including 1-, 2-, 3-, and multi- dimensional models with applications in Neuroscience.

关键词： fokker-plank equation transition state theory tunneling.

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Molecular Chaperone-Dependent Polymer Translocation through Nanopores: The Effects of Chaperone Concentration and Chaperone-Polymer Interaction

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Chinese Journal of Polymer Science 2024年第1期42卷 125-132,I0011页

作者： Chang-Sheng Zuo Kang Wang Li-Zhen Sun Ting-Ting Sun Department of Physics Zhejiang University of Science and TechnologyHangzhou 310023China Department of Applied Physics Zhejiang University of TechnologyHangzhou 310014China

The polymer translocation through a nanopore from a donor space(or named cis side) to a receiver space(trans side) in the chaperone-induced crowded environment has attracted increasing attention in recent years due to its significance in biological systems and technological applications. In this work, we mainly focus on the effects of chaperone concentration and chaperone-polymer interaction on the polymer translocation. By assuming the polymer translocation to be a quasi-equilibrium process, the free energy F of the polymer can be estimated by Rosenbluth-Rosenbluth method and then the translocation time τ can be calculated by fokker-plank equation based on the obtained free energy landscape. Our calculation results show that the translocation time can be controlled by independently tuning the chaperone concentration and chaperone-polymer interaction at the cis side or the trans side. There exists a critical chaperone-polymer attraction ε~*=-0.2 at which the volume exclusion and interaction effects of the chaperone can balance each other. Additionally, we also find that at large chaperone-polymer attraction, the translocation time is mainly governed by the diffusion coefficient of the polymer.

关键词： Polymer translocation Rosenbluth-Rosenbluth method fokker-plank equation Free energy landscapes

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Approximation of the Mean Escape Time for a Tilted Periodic Potential

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Communications in Computational Physics 2019年第1期25卷 1-40页

作者： Tamra Heberling Lisa Davis Tomas Gedeon Los Alamos National Laboratory XTD-SSLos AlamosNM87545USA Department of Mathematical Sciences Montana State UniversityBozemanMT59717-2400USA

We present a formula approximating the mean escape time(MST)of a particle from a tilted multi-periodic potential *** potential function consists of a weighted sum of a finite number of component functions,each of which is *** this particular case,the least period of the potential function is a common period amongst all of its component *** approximation of the MST for the potential function is derived,and this approximation takes the form of a product of the MSTs for each of the individual periodic component *** first example illustrates the computational advantages of using the approximation for model validation and parameter tuning in the context of the biological application of DNA *** also use this formula to approximate the MST for an arbitrary tilted periodic potential by the product of MSTs of a finite number of its Fourier *** examples using truncated Fourier series are presented and analyzed.

关键词： Brownian Ratchet multi-periodic potential tilted periodic potential fokker-plank equation

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