Related papers: Tripeptide-Dynamics from Empirical and Machine-Lea…
Nanoparticle sintering remains a critical challenge in heterogeneous catalysis. In this work, we present a unified deep potential (DP) model for Cu nanoparticles on three Al$_2$O$_3$ surfaces ($\gamma$-Al$_2$O$_3$(100),…
Experimental observations of multi-quantum relaxation of highly vibrationally excited NO scattering from Au(111) are a benchmark for the breakdown of Born-Oppenheimer approximation in molecule-surface systems. This remarkable vibrational…
Two-dimensional electronic spectroscopy (2DES) has enabled significant discoveries in both biological and synthetic energy-transducing systems. Although deriving chemical information from 2DES is a complex task, machine learning (ML) offers…
The mobility edges (MEs) in energy which separate extended and localized states are a central concept in understanding the localization physics. In one-dimensional (1D) quasiperiodic systems, while MEs may exist for certain cases, the…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
Electronic stopping (ES) of energetic atoms is not taken care of by the interatomic potentials used in molecular dynamics (MD) simulations when simulating collision cascades. The Lindhard-Scharff (LS) formula for electronic stopping is…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
We extend the DeePMD neural network architecture to predict electronic structure properties necessary to perform non-adiabatic dynamics simulations. While learning the excited state energies and forces follows a straightforward extension of…
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas…
The role of numerical accuracy in training and evaluating neural network-based potential energy surfaces is examined for different experimental observables. For observables that require third- and fourth-order derivatives of the total…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…
Using molecular dynamics simulations and integral equations (Rogers-Young, Percus-Yevick and hypernetted chain closures) we investigate the thermodynamic of particles interacting with continuous core-softened intermolecular potential.…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
The structural and dynamic properties of silica melts under high pressure are studied using molecular dynamics (MD) computer simulation. The interactions between the ions are modeled by a pairwise-additive potential, the so-called CHIK…
Aqueous hydrolysis is used to chemically recycle polyethylene terephthalate (PET) due to the production of high-quality terephthalic acid (TPA), the PET monomer. PET hydrolysis depends on various reaction conditions including PET size,…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
In this work, we study the damage in crystalline molybdenum material samples due to neutron bombardment in a primary knock-on atom range of 0.5-10 keV at room temperature. We perform machine learned molecular dynamics (MD) simulations with…