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Literature DB >> 23044538

MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.

David Fange¹, Anel Mahmutovic, Johan Elf.

Abstract

SUMMARY: MesoRD is a tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries. MesoRD 1.0 supports scale-dependent reaction rate constants and reactions between reactants in neighbouring subvolumes. These new features make it possible to construct physically consistent models of diffusion-controlled reactions also at fine spatial discretization. AVAILABILITY: MesoRD is written in C++ and licensed under the GNU general public license (GPL). MesoRD can be downloaded at http://mesord.sourceforge.net. The MesoRD homepage, http://mesord.sourceforge.net, contains detailed documentation and news about recently implemented features. CONTACT: johan.elf@icm.uu.se.

Entities: Chemical

Mesh：

Year: 2012 PMID： 23044538 DOI： 10.1093/bioinformatics/bts584

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

10 in total

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2. Lost in presumption: stochastic reactions in spatial models.

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3. Modeling heterogeneous tumor growth dynamics and cell-cell interactions at single-cell and cell-population resolution.

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Review 4. Molecular simulations of cellular processes.

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5. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems.

Authors: Margaret E Johnson; Gerhard Hummer
Journal: Phys Rev X Date: 2014 Jul-Sep Impact factor: 15.762

MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.

1. Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates.

2. Lost in presumption: stochastic reactions in spatial models.

3. Modeling heterogeneous tumor growth dynamics and cell-cell interactions at single-cell and cell-population resolution.

Review 4. Molecular simulations of cellular processes.

5. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems.

6. Parallel solutions for voxel-based simulations of reaction-diffusion systems.

7. Simulated single molecule microscopy with SMeagol.

Review 8. Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.

9. Computationally Efficient Modelling of Stochastic Spatio-Temporal Dynamics in Biomolecular Networks.

10. tRNA tracking for direct measurements of protein synthesis kinetics in live cells.