--- res: bibo_abstract: - Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions.@eng bibo_authorlist: - foaf_Person: foaf_givenName: Thomas R foaf_name: Sokolowski, Thomas R foaf_surname: Sokolowski foaf_workInfoHomepage: http://www.librecat.org/personId=3E999752-F248-11E8-B48F-1D18A9856A87 orcid: 0000-0002-1287-3779 - foaf_Person: foaf_givenName: Joris foaf_name: Paijmans, Joris foaf_surname: Paijmans - foaf_Person: foaf_givenName: Laurens foaf_name: Bossen, Laurens foaf_surname: Bossen - foaf_Person: foaf_givenName: Thomas foaf_name: Miedema, Thomas foaf_surname: Miedema - foaf_Person: foaf_givenName: Martijn foaf_name: Wehrens, Martijn foaf_surname: Wehrens - foaf_Person: foaf_givenName: Nils B. foaf_name: Becker, Nils B. foaf_surname: Becker - foaf_Person: foaf_givenName: Kazunari foaf_name: Kaizu, Kazunari foaf_surname: Kaizu - foaf_Person: foaf_givenName: Koichi foaf_name: Takahashi, Koichi foaf_surname: Takahashi - foaf_Person: foaf_givenName: Marileen foaf_name: Dogterom, Marileen foaf_surname: Dogterom - foaf_Person: foaf_givenName: Pieter Rein foaf_name: ten Wolde, Pieter Rein foaf_surname: ten Wolde bibo_doi: 10.1063/1.5064867 bibo_issue: '5' bibo_volume: 150 dct_date: 2019^xs_gYear dct_identifier: - UT:000458109300009 dct_isPartOf: - http://id.crossref.org/issn/0021-9606 - http://id.crossref.org/issn/1089-7690 dct_language: eng dct_publisher: AIP Publishing@ dct_title: eGFRD in all dimensions@ ...