Related papers: Irradiation driven molecular dynamics: A review
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
Diffusion Probabilistic Models (DPMs) have been recently utilized to deal with various blind image restoration (IR) tasks, where they have demonstrated outstanding performance in terms of perceptual quality. However, the task-specific…
We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
The amplification and maintenance of the observed magnetic fields in the ICM are usually attributed to the turbulent dynamo action. This is generally derived employing a collisional MHD model. However, in the ICM the ion mean free path…
To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…
Discrete diffusion models form a powerful class of generative models across diverse domains, including text and graphs. However, existing approaches face fundamental limitations. Masked diffusion models suffer from irreversible errors due…
Dynamic Mode Decomposition (DMD) is a popular data-driven analysis technique used to decompose complex, nonlinear systems into a set of modes, revealing underlying patterns and dynamics through spectral analysis. This review presents a…
Time-dependent density functional theory (TDDFT) is a widely used method to investigate electron dynamics under various external perturbations such as laser fields. In this work, we present a novel approach to accelerate real time TDDFT…
Methods for experimental reconstruction of molecular frame (MF) photoionization dynamics, and related properties - specifically MF photoelectron angular distributions (PADs) and continuum density matrices - are outlined and discussed.…
The dynamics of dissipative soft-sphere gases obeys Newton's equation of motion which are commonly solved numerically by (force-based) Molecular Dynamics schemes. With the assumption of instantaneous, pairwise collisions, the simulation can…
We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…
Turbulent diffuse molecular clouds can exhibit complicated morphologies caused by the interactions among radiation, chemistry, fluids, and fields. We performed full 3D simulations for turbulent diffuse molecular interstellar media,…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
We introduce sbml4md, a newly developed algorithm implemented as a software package to extract parameters of multimode anharmonic Brownian (MAB) models from molecular dynamics (MD) trajectories for simulating nonlinear vibrational spectra…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
Turbulent space and astrophysical plasmas exhibit a complex dynamics, which involves nonlinear coupling across different temporal and spatial scales. There is growing evidence that impulsive events, such as magnetic reconnection…
This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…