Biomedical subjects

Rosalind J Allen

Publications and source records attributed to Rosalind J Allen.

4 recordsLinked to original sources

PubMed2006

Forward flux sampling-type schemes for simulating rare events: efficiency analysis.

We analyze the efficiency of several simulation methods which we have recently proposed for calculating rate constants for rare events in stochastic dynamical systems in or out of equilibrium. We derive analytical expressions for the computational cost of using these methods and for the statistical error in the final estimate of the rate constant for a given computational cost. These expressions can be used to determine which method to use for a given problem, to optimize the choice of parameters, and to evaluate the significance of the results obtained. We apply the expressions to the two-dimensional nonequilibrium rare event problem proposed by Maier and Stein [Phys. Rev. E 48, 931 (1993)]. For this problem, our analysis gives accurate quantitative predictions for the computational efficiency of the three methods.

Journal Article↗

PubMed2006

Simulating rare events in equilibrium or nonequilibrium stochastic systems.

We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase-space density and are suitable for equilibrium or nonequilibrium systems in stationary state. All the methods use a series of interfaces in phase space, between the initial and final states, to generate transition paths as chains of connected partial paths, in a ratchetlike manner. No assumptions are made about the distribution of paths at the interfaces. The three methods differ in the way that the transition path ensemble is generated. We apply the algorithms to kinetic Monte Carlo simulations of a genetic switch and to Langevin dynamics simulations of intermittently driven polymer translocation through a pore. We find that the three methods are all of comparable efficiency, and that all the methods are much more efficient than brute-force simulation.

Journal Article↗

PubMed2005

Sampling rare switching events in biochemical networks.

Bistable biochemical switches are widely found in gene regulatory networks and signal transduction pathways. Their switching dynamics are difficult to study, however, because switching events are rare, and the systems are out of equilibrium. We present a simulation method for predicting the rate and mechanism of the flipping of these switches. We apply it to a genetic switch and find that it is highly efficient. The path ensembles for the forward and reverse processes do not coincide. The method is widely applicable to rare events and nonequilibrium processes.

Bacteriophage lambda↗

PubMed2004

Kinetic models of ion transport through a nanopore.

Kinetic equations for the stationary state distribution function of ions moving through narrow pores are solved for a number of 1D models of single ion transport. Ions move through pores of length L, under the action of a constant external field and of a concentration gradient. The interaction of single ions with the confining pore surface and with water molecules inside the pore are modeled by a Fokker-Planck term in the kinetic equation, or by uncorrelated collisions with thermalizing centers distributed along the pore. The temporary binding of ions to polar residues lining the pore is modeled by stopping traps or energy barriers. Analytic expressions for the stationary ion current through the pore are derived for several versions of the model, as functions of key physical parameters. In all cases, saturation of the current at high fields is predicted. Such simple models, for which results are analytic, may prove useful in the study of the current/voltage relations of ion channels through membranes.

Journal Article↗