ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units

Biedermann, Johann; Ullrich, Alexander; Schöneberg, Johannes; Noé, Frank

doi:10.1016/j.bpj.2014.12.025

Cited by 31 publications

(28 citation statements)

References 9 publications

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“…Thus, a complementary iPRD model was simulated with the ReaDDy software5153. An unconstricted ‘dome model’ and a ‘constricted model’ are set up with 180 Clathrin molecules/540 N-terminal domains as shown in Fig.…”

Section: Methodsmentioning

confidence: 99%

Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission

et al. 2017

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Clathrin-mediated endocytosis (CME) involves membrane-associated scaffolds of the bin-amphiphysin-rvs (BAR) domain protein family as well as the GTPase dynamin, and is accompanied and perhaps triggered by changes in local lipid composition. How protein recruitment, scaffold assembly and membrane deformation is spatiotemporally controlled and coupled to fission is poorly understood. We show by computational modelling and super-resolution imaging that phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] synthesis within the clathrin-coated area of endocytic intermediates triggers selective recruitment of the PX-BAR domain protein SNX9, as a result of complex interactions of endocytic proteins competing for phospholipids. The specific architecture induces positioning of SNX9 at the invagination neck where its self-assembly regulates membrane constriction, thereby providing a template for dynamin fission. These data explain how lipid conversion at endocytic pits couples local membrane constriction to fission. Our work demonstrates how computational modelling and super-resolution imaging can be combined to unravel function and mechanisms of complex cellular processes.

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Section: Methodsmentioning

confidence: 99%

Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission

et al. 2017

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“…Recently, several GPU-based high-performance simulators of reaction-diffusion systems have been reported [46,48,[50][51][52]74]. The ability to run fast simulations on common workstations equipped with GPUs supports wider application of the simulators.…”

Section: Resultsmentioning

confidence: 99%

pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems

Arjunan

Miyauchi

Iwamoto

et al. 2019

Preprint

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Background: Studies using quantitative experimental methods have shown that intracellular spatial distribution of molecules plays a central role in many cellular systems. Spatially resolved computer simulations can integrate quantitative data from these experiments to construct physically accurate models of the systems. Although computationally expensive, microscopic resolution reaction-diffusion simulators, such as Spatiocyte can directly capture intracellular effects comprising diffusion-limited reactions and volume exclusion from crowded molecules by explicitly representing individual diffusing molecules in space. To alleviate the steep computational cost typically associated with the simulation of large or crowded intracellular compartments, we present a parallelized Spatiocyte method called pSpatiocyte. Results: The new high-performance method employs unique parallelization schemes on hexagonal close-packed (HCP) lattice to efficiently exploit the resources of common workstations and large distributed memory parallel computers. We introduce a coordinate system for fast accesses to HCP lattice voxels, a parallelized event scheduler, a parallelized Gillespie's direct-method for unimolecular reactions, and a parallelized event for diffusion and bimolecular reaction processes. We verified the correctness of pSpatiocyte reaction and diffusion processes by comparison to theory. To evaluate the performance of pSpatiocyte, we performed a series of parallelized diffusion runs on the RIKEN K computer. In the case of fine lattice discretization with low voxel occupancy, pSpatiocyte exhibited 74% parallel efficiency and achieved a speedup of 7686 times with 663552 cores compared to the runtime with 64 cores. In the weak scaling performance, pSpatiocyte obtained efficiencies of at least 60% with up to 663552 cores. When executing the Michaelis-Menten benchmark model on an eight-core workstation, pSpatiocyte required 45-and 55-fold shorter runtimes than Smoldyn and the parallel version of ReaDDy, respectively. As a high-performance application example, we study the dual phosphorylation-dephosphorylation cycle of the MAPK system, a typical reaction network motif in cell signaling pathways. Conclusions: pSpatiocyte demonstrates good accuracies, fast runtimes and a significant performance advantage over well-known microscopic particle simulators for large-scale simulations of intracellular reaction-diffusion systems. The source code of pSpatiocyte is available at https://spatiocyte.org.

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“…PBRD acknowledges that chemical reactions are in-herently discrete and stochastic in nature [25], and that diffusion in cells is often not fast enough to justify well-stirred reaction kinetics [26][27][28]. A large number of recent software packages and codes implement some form of PBRD [29][30][31][32][33][34][35][36], see also the reviews [37,38]. Hydrodynamic interactions at this scale could be incorporated by particle-based coupling terms [39,40].…”

Section: Introductionmentioning

confidence: 99%

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

Dibak

Razo

Sancho

et al. 2018

The Journal of Chemical Physics

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Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.

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ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units

Cited by 31 publications

References 9 publications

Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission

Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission

pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

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