Diffusion of isobutane in silicalite studied by transition path sampling

Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations

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 limitation by collecting unbiased trajectories and capturing the relevant events. Moreover, the integration of machine learning can boost the sampling while simultaneously learning a quantitative representation of the mechanism. Still, the resulting trajectories are by construction non-Boltzmann-distributed, preventing the calculation of free energies and rates. We developed an algorithm to approximate the equilibrium path ensemble from machine-learning-guided path sampling data. At the same time, our algorithm provides efficient sampling, mechanism, free energy, and rates of rare molecular events at a very moderate computational cost. We tested the method on the folding of the mini-protein chignolin. Our algorithm is straightforward and data-efficient, opening the door to applications in many challenging molecular systems.

Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers

With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.

Diffusion in nanoporous materials: fundamental principles, insights and challenges

The increasing complexity of nanoporous catalysts and adsorbents presents a challenge to both the experimental measurement and theoretical modeling of transport behavior.

Transferable pair potentials for CdS and ZnS crystals

A set of interatomic pair potentials is developed for CdS and ZnS crystals. We show that a simple energy function, which has been used to describe the properties of CdSe [E. Rabani, J. Chem. Phys. 116, 258 (2002)], can be parametrized to accurately describe the lattice and elastic constants, and phonon dispersion relations of bulk CdS and ZnS in the wurtzite and rocksalt crystal structures. The predicted coexistence pressure of the wurtzite and rocksalt structures as well as the equation of state are in good agreement with experimental observations. These new pair potentials enable the study of a wide range of processes in bulk and nanocrystalline II-VI semiconductor materials.

Transition path sampling: throwing ropes over rough mountain passes, in the dark

This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.