OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It
allows users to easily add new features, including forces with novel functional forms, new …

As molecular dynamics (MD) simulations continue to evolve into powerful computational
tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use …

Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions
involving multi-dimensional arrays efficiently. Since its introduction, it has been one of …

… In keeping with inspiration from the broader machine learning community, MSMBuilder
extends this formalism in the context of cross-validation through the work of McGibbon and …

The reactivity of reduced pyridinium with CO 2 was investigated as a function of catalyst
concentration, temperature, and pressure at platinum electrodes. Concentration experiments …

… However, treating dimensionality reduction as a preprocessing and applying probabilistic
models afterwards, as done by McGibbon, Schwantes, and Pande, 25 does not enable …

Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions
involving multi-dimensional arrays efficiently. Since its introduction, it has been one of …

We describe a flexible and broadly applicable energy refinement method, “nebterpolation,”
for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation…

Noncovalent interactions are of fundamental importance across the disciplines of chemistry,
materials science, and biology. Quantum chemical calculations on noncovalently bound …

Reaction coordinates are widely used throughout chemical physics to model and understand
complex chemical transformations. We introduce a definition of the natural reaction …