Volume 13, Issue 4
Efficient Sampling in Event-Driven Algorithms for Reaction-Diffusion Processes

Mohammad Hossein Bani-Hashemian, Stefan Hellander & Per Lötstedt

Commun. Comput. Phys., 13 (2013), pp. 958-984.

Published online: 2013-08

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  • Abstract

In event-driven algorithms for simulation of diffusing, colliding, and reacting particles, new positions and events are sampled from the cumulative distribution function (CDF) of a probability distribution. The distribution is sampled frequently and it is important for the efficiency of the algorithm that the sampling is fast. The CDF is known analytically or computed numerically. Analytical formulas are sometimes rather complicated making them difficult to evaluate. The CDF may be stored in a table for interpolation or computed directly when it is needed. Different alternatives are compared for chemically reacting molecules moving by Brownian diffusion in two and three dimensions. The best strategy depends on the dimension of the problem, the length of the time interval, the density of the particles, and the number of different reactions.

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@Article{CiCP-13-958, author = {}, title = {Efficient Sampling in Event-Driven Algorithms for Reaction-Diffusion Processes}, journal = {Communications in Computational Physics}, year = {2013}, volume = {13}, number = {4}, pages = {958--984}, abstract = {

In event-driven algorithms for simulation of diffusing, colliding, and reacting particles, new positions and events are sampled from the cumulative distribution function (CDF) of a probability distribution. The distribution is sampled frequently and it is important for the efficiency of the algorithm that the sampling is fast. The CDF is known analytically or computed numerically. Analytical formulas are sometimes rather complicated making them difficult to evaluate. The CDF may be stored in a table for interpolation or computed directly when it is needed. Different alternatives are compared for chemically reacting molecules moving by Brownian diffusion in two and three dimensions. The best strategy depends on the dimension of the problem, the length of the time interval, the density of the particles, and the number of different reactions.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.271011.230312a}, url = {http://global-sci.org/intro/article_detail/cicp/7260.html} }
TY - JOUR T1 - Efficient Sampling in Event-Driven Algorithms for Reaction-Diffusion Processes JO - Communications in Computational Physics VL - 4 SP - 958 EP - 984 PY - 2013 DA - 2013/08 SN - 13 DO - http://dor.org/10.4208/cicp.271011.230312a UR - https://global-sci.org/intro/article_detail/cicp/7260.html KW - AB -

In event-driven algorithms for simulation of diffusing, colliding, and reacting particles, new positions and events are sampled from the cumulative distribution function (CDF) of a probability distribution. The distribution is sampled frequently and it is important for the efficiency of the algorithm that the sampling is fast. The CDF is known analytically or computed numerically. Analytical formulas are sometimes rather complicated making them difficult to evaluate. The CDF may be stored in a table for interpolation or computed directly when it is needed. Different alternatives are compared for chemically reacting molecules moving by Brownian diffusion in two and three dimensions. The best strategy depends on the dimension of the problem, the length of the time interval, the density of the particles, and the number of different reactions.

Mohammad Hossein Bani-Hashemian, Stefan Hellander & Per Lötstedt. (2020). Efficient Sampling in Event-Driven Algorithms for Reaction-Diffusion Processes. Communications in Computational Physics. 13 (4). 958-984. doi:10.4208/cicp.271011.230312a
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