Related papers: Approximating Free Energy and Committor Landscapes…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
We introduce an extension to the Weighted Ensemble (WE) path sampling method to restrict sampling to a one dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits…
Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals, requires…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods…
Transition path theory (TPT) offers a powerful formalism for extracting the rate and mechanism of rare dynamical transitions between metastable states. Most applications of TPT either focus on systems with modestly sized state spaces or use…
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To address this, we have developed a novel method termed…
Transition path theory computes statistics from ensembles of reactive trajectories. A common strategy for sampling reactive trajectories is to control the branching and pruning of trajectories so as to enhance the sampling of low…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
The presence of erratic or unstable paths in standard kinetic Monte Carlo simulations significantly undermines the accurate simulation and sampling of transition pathways. While typically reliable methods, such as the Gillespie algorithm,…
Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free energy calculations. Such methods can efficiently sample…
Weighted ensemble (WE) is an enhanced path-sampling method that is conceptually simple, widely applicable, and statistically exact. In a WE simulation, an ensemble of trajectories is periodically pruned or replicated to enhance sampling of…
I give an overview of rare event simulation techniques to generate dynamical pathways across high free energy barriers. The methods on which I will concentrate are the reactive flux approach, transition path sampling, (replica-exchange)…
We develop a methodology for the calculation of surface free energies based on the probability distribution of a wandering interface. Using a simple extension of the NpT sampling, we allow the interface area to randomly probe the available…
Transition-edge sensors (TESs) are capable of highly accurate single particle energy measurement. TESs have been used for a wide range of photon detection applications, particularly in astronomy, but very little consideration has been given…
We use transition path sampling to study evaporation in the SPC/E model of liquid water. Based on thousands of evaporation trajectories, we characterize the members of the transition state ensemble (TSE), which exhibit a liquid-vapor…