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- Stephan Menz, Juan C. Latorre, Christof SchÃ¼tte, Wilhelm Huisinga
- Multiscale Modeling & Simulation
- 2012

The chemical master equation (CME) is the fundamental evolution equation of the stochastic description of biochemical reaction kinetics. In most applications it is impossible to solve the CME directly due to its high dimensionality. Instead indirect approaches based on realizations of the underlying Markov jump process are used such as the stochasticâ€¦ (More)

We examine stochastic coarse-graining strategies for two biomolecular systems. First, we compute the large-scale transport properties of the basic flashing ratchet mathematical model for (Brownian) molecular motors and consider in this light whether the underlying continuous-space, continuous-time Markovian model can be coarse-grained as a discrete-state,â€¦ (More)

We propose a numerical discretization scheme for the infinitesimal generator of a diffusion process based on a finite volume approximation. The resulting discrete-space operator can be interpreted as a jump process on the mesh whose invariant distribution is precisely the cell approximation of the Boltzmann invariant measure and preserves the detailedâ€¦ (More)

- Juan C. Latorre, Carsten Hartmann, Christof SchÃ¼tte
- ICCS
- 2010

We propose a nonequilibrium sampling method for computing free energy profiles along a given reaction coordinate. The method consists of two parts: a controlled Langevin sampler that generates nonequilibrium bridge paths conditioned by the reaction coordinate, and Jarzynskiâ€™s formula for reweighting the paths. Our derivation of the equations of motion ofâ€¦ (More)

The aim of this mini-review article is to clarify the relation between two distinct formulations of the thermodynamic free energy for collective variables which can be found in the molecular dynamics literature. In doing so, we discuss the different ensemble concepts underlying the two definitions and reveal their relation to strong confinement (restraints)â€¦ (More)

- Juan C. Latorre, A. A. Minzoni, C. A. Vargas, Noel F Smyth
- Chaos
- 2006

The effect of weak lateral dispersion of Zakharov-Kutznetsov-type on a Benjamin-Ono solitary wave is studied both asymptotically and numerically. The asymptotic solution is based on an approximate variational solution for the solitary wave, which is then modulated in time through the use of conservation equations. The effect of the dispersive radiation shedâ€¦ (More)

- Juan C. Latorre, Peter R. Kramer, Grigorios A. Pavliotis
- J. Comput. Physics
- 2014

Article history: Received 18 January 2013 Received in revised form 3 September 2013 Accepted 5 September 2013 Available online 13 September 2013

- Juan C. Latorre
- 2012

In this paper we revisit the problem of Brownian motion in a tilted periodic potential. We use homogenization theory to derive general formulas for the effective velocity and the effective diffusion tensor that are valid for arbitrary tilts. Furthermore, we obtain power series expansions for the velocity and the diffusion coefficient as functions of theâ€¦ (More)

- Eike Meerbach, Juan C. Latorre, Christof SchÃ¼tte
- Multiscale Modeling & Simulation
- 2012

Motivated from a molecular dynamics context we propose a sequential change point detection algorithm for vector-valued autoregressive models based on Bayesian model selection. The algorithm does not rely on any sampling procedure or assumptions underlying the dynamics of the transitions, and is designed to cope with high dimensional data. We show theâ€¦ (More)

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