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DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation.…

As quantum computing advances towards practical applications, quantum operating systems become inevitable, where multi-programming -- the core functionality of operating systems -- enables concurrent execution of multiple quantum programs…

We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…

The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…

The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…

Accurate structural analysis is essential to gain physical knowledge and understanding of atomic-scale processes in materials from atomistic simulations. However, traditional analysis methods often reach their limits when applied to…

Dynamical systems, that are used to model power grids, the brain, and other physical systems, can exhibit coexisting stable states known as attractors. A powerful tool to understand such systems, as well as to better predict when they may…

Discovering the governing laws underpinning physical and chemical phenomena is a key step towards understanding and ultimately controlling systems in science and engineering. We introduce Discovery of Dynamical Systems via Moving Horizon…

Dynamical systems describe the changes in processes that arise naturally from their underlying physical principles, such as the laws of motion or the conservation of mass, energy or momentum. These models facilitate a causal explanation for…

While the structural dynamics of chromophores are of interest for a range of applications, it is experimentally very challenging to resolve the underlying microscopic mechanisms. Glassy dynamics are also challenging for atomistic…

We consider the segmentation of set of correlated time-series, the correlation being allowed to take an arbitrary form but being the same at each time-position. We show that encoding the dependency in a factor model enables us to use the…

In this short note, we discuss the basic approach to computational modeling of dynamical systems. If a dynamical system contains multiple time scales, ranging from very fast to slow, computational solution of the dynamical system can be…

Dynamic mode decomposition (DMD) is a leading tool for equation-free analysis of high-dimensional dynamical systems from observations. In this work, we focus on a combination of delay-coordinates embedding and DMD, i.e., delay-coordinates…

Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…

Multiscale modeling, which integrates material properties from ab initio calculations into continuum-scale simulations, is a promising strategy for optimizing semiconductor devices. However, a key challenge remains: while ab initio methods…

Mechanical and elastic properties of materials are among the most fundamental quantities for many engineering and industrial applications. Here, we present a formulation that is efficient and accurate for calculating the elastic and bending…

This paper introduces a novel framework for optimizing observer-based soft sensors through dynamic causality analysis. Traditional approaches to sensor selection often rely on linearized observability indices or statistical correlations…

Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in condensed phase. To facilitate effective development,…

We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…

Simulation of fluid flows is crucial for modeling physical phenomena like meteorology, aerodynamics, and biomedicine. Classical numerical solvers often require fine spatiotemporal grids to satisfy stability, consistency, and convergence…