ArticleBulletin of mathematical biology2014
Stochastic reaction-diffusion processes with embedded lower-dimensional structures.
Article in Bulletin of mathematical biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- Editorial: special issue on stochastic modelling of reaction-diffusion processes in biology.Bulletin of mathematical biology · 2014Article
- Physical constraints determine the logic of bacterial promoter architectures.Nucleic acids research · 2014Article
- Article
- Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures.The Journal of chemical physics · 2013Article
- The effects of transcription factor competition on gene regulation.Frontiers in genetics · 2013Article
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Authors and funding
4 authors.
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Abstract
Small copy numbers of many molecular species in biological cells require stochastic models of the chemical reactions between the molecules and their motion. Important reactions often take place on one-dimensional structures embedded in three dimensions with molecules migrating between the dimensions. Examples of polymer structures in cells are DNA, microtubules, and actin filaments. An algorithm for simulation of such systems is developed at a mesoscopic level of approximation. An arbitrarily shaped polymer is coupled to a background Cartesian mesh in three dimensions. The realization of the system is made with a stochastic simulation algorithm in the spirit of Gillespie. The method is applied to model problems for verification and two more detailed models of transcription factor interaction with the DNA.
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