Stochastic simulation has been a powerful tool for studying the dynamics of gene regulatory networks, particularly in terms of understanding how cell-phenotype stability and fate-transitions are impacted by noisy gene expression. However, gene networks often have dynamics characterized by multiple attractors. Stochastic simulation is often inefficient for such systems, because most of the simul...

A distributed replica dynamics (DRD) method is proposed to calculate rare-event molecular dynamics using distributed computational resources. Similar to Voter's parallel replica dynamics (PRD) method, the dynamics of independent replicas of the system are calculated on different computational clients. In DRD, each replica runs molecular dynamics from an initial state for a fixed simulation time...

in this paper, the important formation control problem of nonholonomic wheeled mobile robots is investigated via a leader-follower strategy. to this end, the dynamics model of the considered wheeled mobile robot is derived using lagrange equations of motion. then, using adams multi-body simulation software, the obtained dynamics of the wheeled system in matlab software is verified. after that, ...

A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(logN) per 1 event, and the constant coefficient of the complexity is smaller than conventional efficient algorithm based on the concept of Cell-Crossing Event. The maximum performance of more than 460 mil...

A mobile agent is an autonomous software agent capable of moving from one computer to another while performing its tasks. We view the agent as a discrete event system in the view of its computation and communication. This paper presents a methodology for modeling and simulation of such a mobile agent system as a discrete event system. The methodology is based on the Mobile Discrete Event System...

Molecular-dynamics algorithms for systems interacting through discrete or “hard” potentials are fundamentally different to the methods for continuous or “soft” potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and fairly specialized. We present DY...

Discrete molecular dynamics simulation (DMD) uses simplified and discretized models enabling simulations to advance by event rather than by timestep. DMD is an instance of discrete event simulation and so is difficult to scale: even in this multi-core era, all reported DMD codes are serial. In this paper we discuss the inherent difficulties of scaling DMD and present our method of parallelizing...