Biomedical subjects

Weiqing Ren

Publications and source records attributed to Weiqing Ren.

3 recordsLinked to original sources

PubMed2005

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.

The finite-temperature string method proposed by E, et al. [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002)] is a very effective way of identifying transition mechanisms and transition rates between metastable states in systems with complex energy landscapes. In this paper, we discuss the theoretical background and algorithmic details of the finite-temperature string method, as well as the application to the study of isomerization reaction of the alanine dipeptide, both in vacuum and in explicit solvent. We demonstrate that the method allows us to identify directly the isocommittor surfaces, which are approximated by hyperplanes, in the region of configuration space where the most probable transition trajectories are concentrated. These results are verified subsequently by computing directly the committor distribution on the hyperplanes that define the transition state region.

Alanine↗

PubMed2005

Finite temperature string method for the study of rare events.

A method is presented for the study of rare events such as conformational changes arising in activated processes whose reaction coordinate is not known beforehand and for which the assumptions of transition state theory are invalid. The method samples the energy landscape adaptively and determines the isoprobability surfaces for the transition: by definition the trajectories initiated anywhere on one of these surfaces has equal probability to reach first one metastable set rather than the other. Upon weighting these surfaces by the equilibrium probability distribution, one obtains an effective transition pathway, i.e., a tube in configuration space inside which conformational changes occur with high probability, and the associated rate. The method is first validated on a simple two-dimensional example; then it is applied to a model of solid-solid transformation of a condensed system.

Journal Article↗

PubMed2003

Numerical simulations of self-focusing of ultrafast laser pulses.

Simulation of nonlinear propagation of intense ultrafast laser pulses is a hard problem, because of the steep spatial gradients and the temporal shocks that form during the propagation. In this study we adapt the iterative grid distribution method of Ren and Wang [J. Comput. Phys. 159, 246 (2000)] to solve the two-dimensional nonlinear Schrödinger equation with normal time dispersion, space-time focusing, and self-steepening. Our simulations show that, after the asymmetric temporal pulse splitting, the rear peak self-focuses faster than the front one. As a result, the collapse of the rear peak is arrested before that of the front peak. Unlike what has sometimes been conjectured, however, collapse of the two peaks is not arrested through multiple splittings, but rather through temporal dispersion.

Journal Article↗