Related papers: Relaxation of a steep density gradient in a simple…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
We use molecular dynamics simulations in two dimensions to investigate the possibility that a core-softened potential can reproduce static and dynamic anomalies found experimentally in liquid water: (i) the increase in specific volume upon…
Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…
Molecular dynamics simulations are used to examine the relationship between water-like anomalies and the liquid-liquid critical point in a family of model fluids with multi-Gaussian, core-softened pair interactions. The core-softened pair…
A continuum density-field formulation with particle-scale resolution is constructed to simultaneously incorporate the orientation dependence of interparticle interactions and the rotational invariance of the system, a fundamental but…
In this contribution we review a series of simple one dimensional lattice models that with an appropriate choice of parameters can account for various anomalous features of the behaviour of complex systems such as water. In particular, we…
Non-equilibrium phase coexistence is commonly observed in both biological and artificial systems, yet understanding it remains a significant challenge. Unlike equilibrium systems, where free energy provides a unifying framework, the absence…
Noneqiuilibrium dynamics of rotating droplets are studied by molecular dynamics simulations. Small deviations from the theoretical prediction are observed when the size of a droplet is small, and the deviations become smaller as the size of…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
Active glasses refer to a class of driven non-equilibrium systems that share remarkably similar dynamical behavior as conventional glass-formers in equilibrium. Glass-like dynamical characteristics have been observed in various biological…
Large-scale cosmological simulations of galaxy formation currently do not resolve the densities at which molecular hydrogen forms, implying that the atomic-to-molecular transition must be modeled either on the fly or in postprocessing. We…
The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is…
We study a microscopically realistic model of a physical gel and use computer simulations to investigate its static and dynamic properties at thermal equilibrium. The phase diagram comprises a sol phase, a coexistence region ending at a…
We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In…
We have carried out nonequilibrium molecular dynamics simulations of a system of crosslinked particles under shear flow conditions. As the fraction of crosslinks $p$ is increased the system approaches a gel point at which the shear…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
We uncover an unforeseen asymmetry in relaxation -- for a pair of thermodynamically equidistant temperature quenches, one from a lower and the other from a higher temperature, the relaxation at the ambient temperature is faster in case of…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations to study the transition between the dilute gas and the…
The main subject of this thesis rests on the study ---at different levels of description--- of instabilities in systems which are driven, i.e., maintained far from equilibrium by an external forcing. We focus here on two main classes,…