Related papers: VacHopPy: A Python package for vacancy hopping ana…
The Hofstadter model successfully describes the behavior of non-interacting quantum particles hopping on a lattice coupled to a gauge field, and hence is ubiquitous in many fields of research, including condensed matter, optical, and atomic…
We propose a framework for describing the dynamics associated with the adsorption of small molecules to liquid-vapor interfaces, using an intermediate resolution between traditional continuum theories that are bereft of molecular detail and…
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…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
Many of the purported virtues of Multi-Principal Element Alloys (MPEAs), such as corrosion, high-temperature oxidation and irradiation resistance, are highly sensitive to vacancy diffusivity. Similarly, solute interdiffusion is governed by…
diffpy$.$morph addresses a need to gain scientific insights from 1D scientific spectra in model independent ways. A powerful approach for this is to take differences between pairs of spectra and look for meaningful changes that might…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
In resent years, the software ecosystem for numerical simulation still remains fragmented, with different algorithms and discretization methods often implemented in isolation, each with distinct data structures and programming conventions.…
Magpy is a C++ accelerated Python package for modelling and simulating the magnetic dynamics of nano-sized particles. Nanoparticles are modelled as a system of three-dimensional macrospins and simulated with a set of coupled stochastic…
This article proposes a new way to construct computationally efficient `wrappers' around fine scale, microscopic, detailed descriptions of dynamical systems, such as molecular dynamics, to make predictions at the macroscale `continuum'…
Existing Python libraries and tools lack the ability to efficiently compute statistical test results for large datasets in the presence of missing values. This presents an issue as soon as constraints on runtime and memory availability…
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…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
Entropy scaling is a powerful technique that has been used for predicting transport properties of pure components over a wide range of states. However, modeling mixture diffusion coefficients by entropy scaling is an unresolved task. We…
Studies of the transport of wet water vapour are relevant for various areas of human activity, including the construction and production of building materials, mining, agriculture, environmental safety of technological processes, scientific…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
Nonlinear Optical Spectroscopy is a well-developed field with theoretical and experimental advances that have aided multiple fields including chemistry, biology and physics. However, accurate quantum dynamical simulations based on model…