Abstract:
:Particle-based simulators represent molecules of interest with point-like particles that diffuse and react in continuous space. These simulators are often used to investigate spatial or stochastic aspects of biochemical systems. This paper presents new particle-based simulation algorithms for modeling interactions between molecules and surfaces; they address irreversible and reversible molecular adsorption to, desorption from and transmission through membranes. Their central elements are: (i) relationships between adsorption, desorption and transmission coefficients on the one hand, and simulator interaction probabilities on the other, and (ii) probability densities for initial placements of desorbed molecules. These algorithms, which were implemented and tested in the Smoldyn simulator, are accurate, easy to implement and computationally efficient. They allow longer time steps and better address reversible processes than an algorithm that Erban and Chapman recently presented (Physical Biology 4:16-28, 2007). This paper also presents a method for simulating unbounded diffusion in a limited spatial domain using a partially absorbing boundary, as well as new solutions to the diffusion differential equation with reversible Robin boundary conditions.
journal_name
Phys Bioljournal_title
Physical biologyauthors
Andrews SSdoi
10.1088/1478-3975/6/4/046015subject
Has Abstractpub_date
2009-11-12 00:00:00pages
046015issue
4eissn
1478-3967issn
1478-3975pii
S1478-3975(09)23496-0journal_volume
6pub_type
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