Related papers: DYNASOR -- A tool for extracting dynamical structu…
Modern X-ray spectroscopy has proven itself as a robust tool for probing the electronic structure of atoms in complex environments. Despite working on energy scales that are much larger than those corresponding to nuclear motions, taking…
Phonons are fundamentally important for many materials properties, including thermal and electronic transport, superconductivity, and structural stability. Here, we describe a method to compute phonons in correlated materials using…
For almost a century, since Bernal\'s attempts at a molecular theory of liquid structure(Bernal [1]), correlation functions have been the bridge to compare theoretical calculations with experimental measurements in the study of disordered…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary…
Conventional kinesin is a dimeric motor protein that transports membranous organelles toward the plus-end of microtubules (MTs). Individual kinesin dimers show steadfast directionality and hundreds of consecutive steps, yetthe detailed…
We propose a new variable cell-shape molecular dynamics algorithm where the dynamical variables associated with the cell are the six independent dot products between the vectors defining the cell instead of the nine cartesian components of…
We propose an approach that links density functional theory (DFT) and molecular dynamics (MD) simulation to study fluid behavior in nanopores in contact with bulk (macropores). It consists of two principal steps. First, the theoretical…
Stochastic differential equations describe well many physical, biological and sociological systems, despite the simplification often made in their derivation. Here the usage of simple stochastic differential equations to characterize and…
We present a differentiable dynamics solver that is able to handle frictional contact for rigid and deformable objects within a unified framework. Through a principled mollification of normal and tangential contact forces, our method…
The udkm1Dsim toolbox is a collection of Python classes and routines to simulate the thermal, structural, and magnetic dynamics after laser excitation as well as the according X-ray scattering response in one-dimensional sample structures.…
Computational atomic-scale methods continue to provide new information about geometry, energetics, and transition states for interstitial elements in crystalline lattices. This data can be used to determine the diffusivity of interstitials…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
The software package DIALECT is introduced, which provides the capability of calculating excited-state properties and nonadiabatic dynamics of large molecular systems and can be applied to simulate energy and charge-transfer processes in…
Molecular adsorption is the first important step of many surface-mediated chemical processes, from catalysis to tribology. This phenomenon is controlled by physical/chemical interactions, which can be accurately described by first…
We have developed several distinct model systems of microtubule-based 3D active isotropic fluids and have compared their dynamical and structural properties. The non-equilibrium dynamics of these fluids is powered by three different types…
The discovery of new functional and stable materials is a big challenge due to its complexity. This work aims at the generation of new crystal structures with desired properties, such as chemical stability and specified chemical…
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…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…