Efficient Monte Carlo methods for simulating diffusion-reaction processes in complex systems

We briefly review the principles, mathematical bases, numerical shortcuts and applications of fast random walk (FRW) algorithms. This Monte Carlo technique allows one to simulate individual trajectories of diffusing particles in order to study various probabilistic characteristics (harmonic measure, first passage/exit time distribution, reaction rates, search times and strategies, etc.) and to solve the related partial differential equations. The adaptive character and flexibility of FRWs make them particularly efficient for simulating diffusive processes in porous, multiscale, heterogeneous, disordered or irregularly-shaped media.

[1]  D. Grebenkov,et al.  Optical trapping microrheology in cultured human cells , 2012, The European Physical Journal E.

[2]  Joseph A. Helpern,et al.  Random walk with barriers , 2010, Nature physics.

[3]  Sapoval General formulation of Laplacian transfer across irregular surfaces. , 1994, Physical review letters.

[4]  S. Taylor DIFFUSION PROCESSES AND THEIR SAMPLE PATHS , 1967 .

[5]  Paul T. Callaghan,et al.  Pulsed gradient spin echo nuclear magnetic resonance for molecules diffusing between partially reflecting rectangular barriers , 1994 .

[6]  K. Jacobson,et al.  Single-particle tracking: applications to membrane dynamics. , 1997, Annual review of biophysics and biomolecular structure.

[7]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[8]  Multiscaling analysis of large-scale off-lattice DLA , 1991 .

[9]  Salvatore Torquato,et al.  Efficient simulation technique to compute effective properties of heterogeneous media , 1989 .

[10]  Denis S. Grebenkov,et al.  Geometrical Structure of Laplacian Eigenfunctions , 2012, SIAM Rev..

[11]  A. Caspi,et al.  Enhanced diffusion in active intracellular transport. , 2000, Physical review letters.

[12]  K. M. Kolwankar,et al.  Brownian flights over a fractal nest and first-passage statistics on irregular surfaces. , 2006, Physical review letters.

[13]  G. Bond,et al.  Heterogeneous Catalysis: Principles and Applications , 1974 .

[14]  Pabitra N. Sen,et al.  Time dependent diffusion coefficient in a disordered medium , 1996 .

[15]  G. Milstein Numerical Integration of Stochastic Differential Equations , 1994 .

[16]  G. Weiss Overview of theoretical models for reaction rates , 1986 .

[17]  H P Huinink,et al.  Random-walk simulations of NMR dephasing effects due to uniform magnetic-field gradients in a pore. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[18]  The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application Multiple correlation function approach: rigorous , 2007 .

[19]  J. C. Jaeger,et al.  Conduction of Heat in Solids , 1952 .

[20]  B. Sapoval,et al.  Passivation of irregular surfaces accessed by diffusion , 2008, Proceedings of the National Academy of Sciences.

[21]  William S. Price,et al.  NMR Studies of Translational Motion: Principles and Applications , 2009 .

[22]  John Crank,et al.  The Mathematics Of Diffusion , 1956 .

[23]  J. Klafter,et al.  The dynamical foundation of fractal stream chemistry: The origin of extremely long retention times , 2001, cond-mat/0202326.

[24]  M. E. Muller Some Continuous Monte Carlo Methods for the Dirichlet Problem , 1956 .

[25]  G. Weiss Aspects and Applications of the Random Walk , 1994 .

[26]  D. Grebenkov,et al.  Kinetics of Active Surface-Mediated Diffusion in Spherically Symmetric Domains , 2012, 1206.2756.

[27]  T. Waigh,et al.  First-passage-probability analysis of active transport in live cells. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[28]  S. Havlin,et al.  Diffusion in disordered media , 2002 .

[29]  Partha P. Mitra,et al.  Time-Dependent Diffusion Coefficient of Fluids in Porous Media as a Probe of Surface-to-Volume Ratio , 1993 .

[30]  Per Linse,et al.  The NMR Self-Diffusion Method Applied to Restricted Diffusion. Simulation of Echo Attenuation from Molecules in Spheres and between Planes , 1993 .

[31]  Donald E. Marshall,et al.  Harmonic Measure: Jordan Domains , 2005 .

[32]  E. R. Rang Narrow Escape. , 1965, Science.

[33]  Feller William,et al.  An Introduction To Probability Theory And Its Applications , 1950 .

[34]  Z. Schuss,et al.  The narrow escape problem for diffusion in cellular microdomains , 2007, Proceedings of the National Academy of Sciences.

[35]  Y. Chiew,et al.  Computer simulation of diffusion‐controlled reactions in dispersions of spherical sinks , 1989 .

[36]  L. Sander,et al.  Diffusion-limited aggregation, a kinetic critical phenomenon , 1981 .

[37]  Lee,et al.  Random-walk simulation of diffusion-controlled processes among static traps. , 1989, Physical review. B, Condensed matter.

[38]  Denis S Grebenkov,et al.  A fast random walk algorithm for computing the pulsed-gradient spin-echo signal in multiscale porous media. , 2011, Journal of magnetic resonance.

[39]  H. Pfeifer Principles of Nuclear Magnetic Resonance Microscopy , 1992 .

[40]  D. Grebenkov Searching for partially reactive sites: Analytical results for spherical targets. , 2010, The Journal of chemical physics.

[41]  R. Bryant,et al.  Extreme-values statistics and dynamics of water at protein interfaces. , 2011, The journal of physical chemistry. B.

[42]  C. Sparrow The Fractal Geometry of Nature , 1984 .

[43]  K. Brownstein,et al.  Importance of classical diffusion in NMR studies of water in biological cells , 1979 .

[44]  M. Tachiya,et al.  Theory of diffusion‐controlled reactions on spherical surfaces and its application to reactions on micellar surfaces , 1981 .

[45]  Noam Agmon,et al.  Residence times in diffusion processes , 1984 .

[46]  L. Sander,et al.  Diffusion-limited aggregation , 1983 .

[47]  A Mohoric,et al.  Computer simulation of the spin-echo spatial distribution in the case of restricted self-diffusion. , 2001, Journal of magnetic resonance.

[48]  O. Bénichou,et al.  Optimizing intermittent reaction paths. , 2008, Physical chemistry chemical physics : PCCP.

[49]  P. V. von Hippel,et al.  Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. , 1981, Biochemistry.

[50]  K. Svoboda,et al.  Time-dependent diffusion of water in a biological model system. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[51]  D. Grebenkov SCALING PROPERTIES OF THE SPREAD HARMONIC MEASURES , 2006 .

[52]  M. Freidlin Functional Integration And Partial Differential Equations , 1985 .

[53]  Katja Lindenberg,et al.  Subdiffusive target problem: survival probability. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[54]  Pabitra N. Sen,et al.  Time-dependent diffusion coefficient as a probe of geometry , 2004 .

[55]  Joachim O Rädler,et al.  Temporal analysis of active and passive transport in living cells. , 2008, Physical review letters.

[56]  D. Grebenkov,et al.  Optimal reaction time for surface-mediated diffusion. , 2010, Physical review letters.

[57]  David A Weitz,et al.  Intracellular transport by active diffusion. , 2009, Trends in cell biology.

[58]  E. Cox,et al.  Physical nature of bacterial cytoplasm. , 2006, Physical review letters.

[59]  P. A. Prince,et al.  Lévy flight search patterns of wandering albatrosses , 1996, Nature.

[60]  D. Grebenkov,et al.  Interfacial territory covered by surface-mediated diffusion. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[61]  James W. Kirchner,et al.  implications for contaminant transport in catchments , 2000 .

[62]  D. Grebenkov Residence times and other functionals of reflected Brownian motion. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[63]  Arak M. Mathai,et al.  Mittag-Leffler Functions and Their Applications , 2009, J. Appl. Math..

[64]  D. Grebenkov,et al.  Mean First-Passage Time of Surface-Mediated Diffusion in Spherical Domains , 2011, 1101.5043.

[65]  D. Grebenkov What makes a boundary less accessible. , 2005, Physical review letters.

[66]  Denis S. Grebenkov,et al.  Partially Reflected Brownian Motion: A Stochastic Approach to Transport Phenomena , 2006, math/0610080.

[67]  David Holcman,et al.  Survival probability of diffusion with trapping in cellular neurobiology. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[68]  Denis S. Grebenkov,et al.  A fast random walk algorithm for computing diffusion-weighted NMR signals in multi-scale porous media: A feasibility study for a Menger sponge , 2013 .

[69]  Weihua Deng,et al.  ANALYSIS OF SINGLE PARTICLE TRAJECTORIES: FROM NORMAL TO ANOMALOUS DIFFUSION ∗ , 2009 .

[70]  Tom Chou,et al.  Multistage adsorption of diffusing macromolecules and viruses. , 2007, The Journal of chemical physics.

[71]  Karl K. Sabelfeld Monte Carlo Methods in Boundary Value Problems. , 1991 .

[72]  M. Moreau,et al.  Intermittent search strategies , 2011, 1104.0639.

[73]  Antoine Lejay,et al.  A Random Walk on Rectangles Algorithm , 2006 .

[74]  Denis S Grebenkov,et al.  Subdiffusion in a bounded domain with a partially absorbing-reflecting boundary. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[75]  R. Bass Diffusions and Elliptic Operators , 1997 .

[76]  P. V. von Hippel,et al.  Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor--operator interaction: equilibrium measurements. , 1981, Biochemistry.

[77]  Denis S. Grebenkov,et al.  NMR survey of reflected brownian motion , 2007 .

[78]  R. Metzler,et al.  In vivo anomalous diffusion and weak ergodicity breaking of lipid granules. , 2010, Physical review letters.

[79]  J. Bouchaud,et al.  Anomalous diffusion in disordered media: Statistical mechanisms, models and physical applications , 1990 .

[80]  S. Redner A guide to first-passage processes , 2001 .

[81]  Thomas C. Halsey,et al.  Diffusion‐Limited Aggregation: A Model for Pattern Formation , 2000 .

[82]  J. Klafter,et al.  The random walk's guide to anomalous diffusion: a fractional dynamics approach , 2000 .

[83]  K. Sabelfeld,et al.  Random Walks on Boundary for Solving PDEs , 1994 .

[84]  R. Eisenberg,et al.  Narrow Escape, Part I , 2004, math-ph/0412048.

[85]  A. Lejay,et al.  An Efficient Algorithm to Simulate a Brownian Motion Over Irregular Domains , 2010 .

[86]  Multifractal properties of the harmonic measure on Koch boundaries in two and three dimensions. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[87]  M. Weiss,et al.  Elucidating the origin of anomalous diffusion in crowded fluids. , 2009, Physical review letters.