Ensemble Metropolis Light Transport

This article proposes a Markov Chain Monte Carlo ( MCMC ) rendering algorithm based on a family of guided transition kernels. The kernels exploit properties of ensembles of light transport paths, which are distributed according to the lighting in the scene, and utilize this information to make informed decisions for guiding local path sampling. Critically, our approach does not require caching distributions in world space, saving time and memory, yet it is able to make guided sampling decisions based on whole paths. We show how this can be implemented efficiently by organizing the paths in each ensemble and designing transition kernels for MCMC rendering based on a carefully chosen subset of paths from the ensemble. This algorithm is easy to parallelize and leads to improvements in variance when rendering a variety of scenes.

Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method

Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of the most powerful and flexible path sampling techniques, can be helpful to reveal translocation paths and free energy barriers along those paths. Within the WE approach we show how Arg9 (nona-arginine) and Tat interact with a DOPC/DOPG(4:1) model membrane, and we present free energy (or potential mean of forces, PMFs) profiles of penetration, although a translocation across the membrane has not been observed in the current simulations. Two different compositions of lipid molecules were also tried and compared. Our approach can be applied to any CPPs interacting with various model membranes, and it will provide useful information regarding the transport mechanisms of CPPs.

Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path

Fleeting intermediates constitute dynamically-stepwise mechanisms. They have been characterized in molecular dynamics trajectories, but whether these intermediates form a free energy minimum to become entropic intermediate remains elusively defined. We developed a computational protocol known as entropic path sampling to evaluate the entropic variation of reacting species along a reaction path based on an ensemble of trajectories. Using cyclopentadiene dimerization as a model reaction, we observed a shallow entropic trap (–T∆S = –0.8 kcal/mol) along the reaction path which originates from an enhanced conformational flexibility as the reacting species enter into a flat energy region. As the reacting species further approach product formation, unfavorable entropic restriction fails to offset the potential energy drop, resulting in no free energy minimum along the post-TS pathway. Our results show that cyclopentadiene dimerization involves an entropic trap that leads to dynamic intermediates with elongated lifetime, but the reaction does not involve entropic intermediates.