ArticleNeuroinformatics2010
Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.
Article in Neuroinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Close agreement between deterministic versus stochastic modeling of first-passage time to vesicle fusion.Biophysical journal · 2022Article
- Cell studio: A platform for interactive, 3D graphical simulation of immunological processes.APL bioengineering · 2018Article
- Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons.ACM transactions on modeling and computer simulation : a publication of the Association for Computing Machinery · 2017Article
- Explicit spatiotemporal simulation of receptor-G protein coupling in rod cell disk membranes.Biophysical journal · 2014Article
- Simulation tools for particle-based reaction-diffusion dynamics in continuous space.BMC biophysics · 2014Review
- Approaches and tools for modeling signaling pathways and calcium dynamics in neurons.Journal of neuroscience methods · 2013Review
- Modeling spatial aspects of intracellular dopamine signaling.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations.The Journal of chemical physics · 2012Article
- Hybrid spatial Gillespie and particle tracking simulation.Bioinformatics (Oxford, England) · 2012Article
- 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
- Spatial simulations in systems biology: from molecules to cells.International journal of molecular sciences · 2012Review
- The impacts of geometry and binding on CaMKII diffusion and retention in dendritic spines.Journal of computational neuroscience · 2011Article
- Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants.BMC systems biology · 2011Article
- An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping.The Journal of chemical physics · 2011Article
- Lobe specific Ca2+-calmodulin nano-domain in neuronal spines: a single molecule level analysis.PLoS computational biology · 2010Article
- Postsynaptic signal transduction models for long-term potentiation and depression.Frontiers in computational neuroscience · 2010Article
- Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron.IEEE/ACM transactions on computational biology and bioinformaticsArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.
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Registered trials
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.