Related papers: DYNASOR -- A tool for extracting dynamical structu…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…
A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered…
Diffusion probabilistic models (DPMs) have shown remarkable performance in visual synthesis but are computationally expensive due to the need for multiple evaluations during the sampling. Recent predictor-corrector diffusion samplers have…
Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only…
Dynamic Mode Decomposition (DMD) is a data-driven modal decomposition technique that extracts coherent spatio-temporal structures from high-dimensional time-series data. By decomposing the dynamics into a set of modes, each associated with…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
Causal loop diagrams (CLDs) are widely used in health and environmental research to represent hypothesized causal structures underlying complex problems. However, as qualitative and static representations, CLDs are limited in their ability…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
Dynamical systems are widely used in science and engineering to model systems consisting of several interacting components. Often, they can be given a causal interpretation in the sense that they not only model the evolution of the states…
Monte Carlo techniques play a central role in statistical mechanics approaches for connecting macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
We introduce PULSEDYN, a particle dynamics program in $C++$, to solve many-body nonlinear systems in one dimension. PULSEDYN is designed to make computing accessible to non-specialists in the field of nonlinear dynamics of many-body systems…
Molecular dynamics simulations (MDS) face challenges, including resource-heavy computations and the need to manually scan outputs to detect "interesting events," such as the formation and persistence of hydrogen bonds between atoms of…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
In materials science, the selection of structural descriptors for machine learning protocols strongly influences predictive performance and the degree of physical interpretability that can be achieved from the derived models. Although more…
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and…
This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the…
We present two methods for computing the dynamic structure factor for warm dense hydrogen without invoking either the Born-Oppenheimer approximation or the Chihara decomposition, by employing a wave-packet description that resolves the…
A molecular level analysis of segmental trajectories obtained from molecular dynamics simulations is used to obtain the full relaxation time spectrum in aging polymer glasses subject to three different deformation protocols. As in…