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All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis, with a focus on the coupling between chemical reactions and mechanical dynamics. Extending the classical Toner-Tu framework,…
Lipid membranes in a physiological context cannot be understood without taking into account their mobile environment. Here, we report on a high energy-resolution neutron backscattering study to investigate slow motions on nanosecond time…
Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
We propose a new model suitable for a nonequilibrium molecular dynamics (MD) simulation of electrical conductors. The model consists of classical electrons and atoms. The atoms compose a lattice vibration system. The electrons are scattered…
Neutrino-atom scattering provides a sensitive tool for probing nonstandard interactions of massive neutrinos in laboratory measurements. The ionization channel of this collision process plays an important role in experiments searching for…
Neutrons and x-rays are coherent probes, and their coherent properties are used in scattering experiments. Only coherent scattering probes can elucidate collective molecular motions. While phonons in crystals were studied for half a century…
The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SCN$^-$ anions as the reporter) and THz spectroscopy.…
The dynamics of a physical gel, namely the Low Molecular Mass Organic Gelator {\textit Methyl-4,6-O-benzylidene-$\alpha$ -D-mannopyranoside ($\alpha$-manno)} in water and toluene are probed by neutron scattering. Using high gelator…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
We present a molecular dynamics study of the collective dynamics of a flexible model for the fragile glass-former orthoterphenyl [ S. Mossa, R. Di leonardo, G. Ruocco, and M. Sampoli, Phys. Rev. E 62, 612 (2000)]. We study the behavior of…
Molecular dynamics simulations are often used to study sputtering and thin film growth. Compressive stresses in these thin films are generally assumed to be caused by a combination of forward sputtered (peened) built-in particles and…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Environmentally-benign, non-toxic electrolytes with combinatorial design spaces are excellent candidates for green solvents, green leaching agents, and carbon capture sources. Here, we examine one particular green solvent, ethaline, a 2:1…
An efficient approach for the simulation of ion scattering from solids is proposed. For every encountered atom, we take multiple samples of its thermal displacements among those which result in scattering with high probability to finally…
In the dynamics of atoms and molecules at metal surfaces, electron-hole pair excitations can play a crucial role. In the case of hyperthermal hydrogen atom scattering, they lead to nonadiabatic energy loss and highly inelastic scattering.…
The design of moderators and cold sources of neutrons is a key point in research-reactor physics, requiring extensive knowledge of the scattering properties of very important light molecular liquids such as methane, hydrogen and their…