An efficient and exact stochastic simulation method to analyze rare events in biochemical systems

An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.

In robust biological systems, wide deviations from highly controlled normal behavior may be rare, yet they may result in catastrophic complications. While in silico analysis has gained an appreciation as a tool to offer insights into system-level properties of biological systems, analysis of such rare events provides a particularly challenging computational problem. This paper proposes an effic...

Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems

The weighted stochastic simulation algorithm (wSSA) recently developed by Kuwahara and Mura and the refined wSSA proposed by Gillespie et al. based on the importance sampling technique open the door for efficient estimation of the probability of rare events in biochemical reaction systems. In this paper, we first apply the importance sampling technique to the next reaction method (NRM) of the s...

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events.

In recent years there has been substantial growth in the development of algorithms for characterizing rare events in stochastic biochemical systems. Two such algorithms, the state-dependent weighted stochastic simulation algorithm (swSSA) and the doubly weighted SSA (dwSSA) are extensions of the weighted SSA (wSSA) by H. Kuwahara and I. Mura [J. Chem. Phys. 129, 165101 (2008)]. The swSSA substa...

Efficient Rare Events Simulation of Gaussian Processes

A key feature of modern broadband networks is their ability to provide stringent Quality of Service (QoS) guarantees to different classes of users. A primary QoS parameter is the Cell Loss Probability (CLP), whose typical values can be very small and therefore difficult to estimate through standard Monte Carlo (MC) simulation, since long run times are required to achieve accurate results. In th...

An Efficient Algorithm to Inter and Intra-Cell Layout Problems in Cellular Manufacturing Systems with Stochastic Demands