Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems
We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine th...
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| Format: | Article |
| Language: | English |
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American Physical Society
2014-09-01
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| Series: | Physical Review X |
| Online Access: | http://doi.org/10.1103/PhysRevX.4.031037 |
| _version_ | 1818723469205962752 |
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| author | Margaret E. Johnson Gerhard Hummer |
| author_facet | Margaret E. Johnson Gerhard Hummer |
| author_sort | Margaret E. Johnson |
| collection | DOAJ |
| description | We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green’s function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions. |
| first_indexed | 2024-12-17T21:11:01Z |
| format | Article |
| id | doaj.art-85bfd097e6ed4d7b971077ac1702af5a |
| institution | Directory Open Access Journal |
| issn | 2160-3308 |
| language | English |
| last_indexed | 2024-12-17T21:11:01Z |
| publishDate | 2014-09-01 |
| publisher | American Physical Society |
| record_format | Article |
| series | Physical Review X |
| spelling | doaj.art-85bfd097e6ed4d7b971077ac1702af5a2022-12-21T21:32:28ZengAmerican Physical SocietyPhysical Review X2160-33082014-09-014303103710.1103/PhysRevX.4.031037Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction SystemsMargaret E. JohnsonGerhard HummerWe present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green’s function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions.http://doi.org/10.1103/PhysRevX.4.031037 |
| spellingShingle | Margaret E. Johnson Gerhard Hummer Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems Physical Review X |
| title | Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems |
| title_full | Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems |
| title_fullStr | Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems |
| title_full_unstemmed | Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems |
| title_short | Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems |
| title_sort | free propagator reweighting integrator for single particle dynamics in reaction diffusion models of heterogeneous protein protein interaction systems |
| url | http://doi.org/10.1103/PhysRevX.4.031037 |
| work_keys_str_mv | AT margaretejohnson freepropagatorreweightingintegratorforsingleparticledynamicsinreactiondiffusionmodelsofheterogeneousproteinproteininteractionsystems AT gerhardhummer freepropagatorreweightingintegratorforsingleparticledynamicsinreactiondiffusionmodelsofheterogeneousproteinproteininteractionsystems |