ArticlePhysical biology2009
Accurate particle-based simulation of adsorption, desorption and partial transmission.
Article in Physical biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Modeling Diffusion Between Regions with Different Diffusion Coefficients.IEEE transactions on molecular, biological, and multi-scale communications · 2024Article
- Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity.Scientific reports · 2022Article
- Simulation of receptor triggering by kinetic segregation shows role of oligomers and close contacts.Biophysical journal · 2022Article
- From diffusion in compartmentalized media to non-Gaussian random walks.Scientific reports · 2021Article
- An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology.The Journal of chemical physics · 2019Article
- Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach.PLoS computational biology · 2018Article
- Article
- A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- The two-regime method for optimizing stochastic reaction-diffusion simulations.Journal of the Royal Society, Interface · 2012Article
- Sequestration of CaMKII in dendritic spines in silico.Journal of computational neuroscience · 2011Article
- Computational investigation of the changing patterns of subtype specific NMDA receptor activation during physiological glutamatergic neurotransmission.PLoS computational biology · 2011Article
- Detailed simulations of cell biology with Smoldyn 2.1.PLoS computational biology · 2010Article
Corrections and comments
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Authors and funding
1 author.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.