Name
Title | ||
|---|---|---|
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. |
Abstract | ||
|---|---|---|
The long-term goal of connecting scales in biological simulation can be facilitated by scale-agnostic methods. We demonstrate that the weighted ensemble (WE) strategy, initially developed for molecular simulations, applies effectively to spatially resolved cell-scale simulations. The WE approach runs an ensemble of parallel trajectories with assigned weights and uses a statistical resampling strategy of replicating and pruning trajectories to focus computational effort on difficult-to-sample regions. The method can also generate unbiased estimates of non-equilibrium and equilibrium observables, sometimes with significantly less aggregate computing time than would be possible using standard parallelization. Here, we use WE to orchestrate particle-based kinetic Monte Carlo simulations, which include spatial geometry (e.g., of organelles, plasma membrane) and biochemical interactions among mobile molecular species. We study a series of models exhibiting spatial, temporal and biochemical complexity and show that although WE has important limitations, it can achieve performance significantly exceeding standard parallel simulation-by orders of magnitude for some observables. |
Year | DOI | Venue |
|---|---|---|
2016 | 10.1371/journal.pcbi.1004611 | PLOS COMPUTATIONAL BIOLOGY |
Field | DocType | Volume |
Rare Event Sampling,Monte Carlo method,Observable,Computer science,Simulation,Systems biology,Algorithm,Stochastic process,Kinetic Monte Carlo,Probability distribution,Genetics,Resampling | Journal | 12 |
Issue | ISSN | Citations |
2 | 1553-7358 | 1 |
PageRank | References | Authors |
0.35 | 11 | 7 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Rory M. Donovan | 1 | 5 | 0.83 |
| José Juan Tapia | 2 | 22 | 2.12 |
| Devin P. Sullivan | 3 | 4 | 0.83 |
| James R Faeder | 4 | 409 | 31.02 |
| Robert F Murphy | 5 | 851 | 78.19 |
| Markus Dittrich | 6 | 4 | 1.17 |
| Daniel M Zuckerman | 7 | 4 | 1.87 |