A robust numerical algorithm for studying biomolecular transport processes

DOI10.1006/JTBI.2003.3200MaRDI QIDQ2177140zbMATH OpenOpenAlexWikidataFDO

Authors Hongyun Wang, Charles S. Peskin, T. C. Elston

Publication date 6 May 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1006/jtbi.2003.3200

Mathematics Subject Classification ID

Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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Cites work

• A macroscopic description of biomolecular transport
• Approximate Riemann solvers, parameter vectors, and difference schemes
• Brownian motors: noisy transport far from equilibrium
• Numerical analysis of the flux and force generated by a correlation ratchet mechanism

Cited in

(22)

• Asymptotic analysis of microtubule-based transport by multiple identical molecular motors
• Binding protein-dependent transporters: An answer of mathematics to biology
• A numerical algorithm for investigating the role of the motor-cargo linkage in molecular motor-driven transport
• Motor potential profile and a robust method for extracting it from time series of motor positions
• The stochastic chemomechanics of the F₁-ATPase molecular motor
• A matrix computational approach to kinesin neck linker extension
• An unstructured mesh convergent reaction-diffusion master equation for reversible reactions
• Mathematical and computational methods for studying energy transduction in protein motors
• Numerical methods for computing effective transport properties of flashing Brownian motors
• A first-passage kinetic Monte Carlo method for reaction-drift-diffusion processes
• SPECTRWM: Spectral Random Walk Method for the Numerical Solution of Stochastic Partial Differential Equations
• Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion PDEs
• Convergence Analysis of the Variational Operator Splitting Scheme for a Reaction-Diffusion System with Detailed Balance
• A Second-Order Accurate, Operator Splitting Scheme for Reaction-Diffusion Systems in an Energetic Variational Formulation
• Sticky Brownian Motion and Its Numerical Solution
• Continuous-time random walks for the numerical solution of stochastic differential equations
• A macroscopic description of biomolecular transport
• Large-deviation principles of switching Markov processes via Hamilton-Jacobi equations
• Predicting and explaining with models: a few remarks on mathematical immunology
• An unstructured mesh reaction-drift-diffusion master equation with reversible reactions
• A model for the oscillatory motion of single dynein molecules
• Renewal reward perspective on linear switching diffusion systems in models of intracellular transport

Describes a project that uses

Uses Software

• Matlab

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