▪ Abstract This article reviews the concepts and methods of transition path sampling. These
methods allow computational studies of rare events without requiring prior knowledge of …

The field of data-driven chemistry is undergoing an evolution, driven by innovations in
machine learning models for predicting molecular properties and behavior. Recent strides in …

SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding
domain (RBD), which transitions from a glycan-shielded 'down'to an exposed 'up'state to …

The following sections are included: Introduction Chain-of-states methods The NEB method
Implementation of the NEB method Application to an adatom hop on a surface What …

A comparison of chain-of-states based methods for finding minimum energy pathways
(MEPs) is presented. In each method, a set of images along an initial pathway between two …

A method is presented for determining activation free energies in complex molecular
systems. The method relies on knowledge of the minimum energy path and bases the …

" Physical phenomena can be modeled at varying degrees of complexity and at different
scales. Multiscale modeling provides a framework, based on fundamental principles, for …

We have developed a method to study transition pathways for rare events in complex
systems. The method can be used to determine rate constants for transitions between stable …

In this chapter we present the foundations and methodology of transition path sampling
comprehensively, including details important for its implementation. We first discuss the …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …