Related papers: Collective Variables for Conformational Polymorphi…
Understanding protein conformational dynamics is essential for elucidating biological function but remains challenging due to the wide range of timescales and the complexity of collective motions. Enhanced sampling methods overcome…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Investigating processes in complex molecular systems, which are characterized by many variables, is a crucial problem in computational physics. These systems can be reduced to a few meaningful degrees of freedom known as collective…
We describe here in detail the recently introduced methodology for simulation of structural transitions in crystals. The applications of the new scheme are illustrated on various kinds of crystals and the advantages with respect to previous…
Continuum models of plasticity fail to capture the richness of microstructural evolution because the continuum is a homogeneous construction. The present study shows that an alternative way is available at the mesoscale in the form of truly…
Engineering the free-energy surfaces (FES) of proteins and peptides is central to controlling conformational ensembles and their responses to perturbations. However, predicting how chemical modifications such as point mutations reshape the…
We present molecular dynamics (MD) simulations results for dense fluids of ultrasoft, fully-penetrable particles. These are a binary mixture and a polydisperse system of particles interacting via the generalized exponential model, which is…
Available simulation methods, suitable to describe solid-solid phase transitions occurring upon increasing of presssure and/or temperature, are based on empirical interatomic potentials: this restriction reduces the predictive power, and…
Changes in the dynamics of supported polymer films in comparison to bulk materials involve a complex convolution of effects, such as substrate interactions, roughness and compliance, in addition to film thickness. We consider molecular…
High-dimensional metastable molecular system can often be characterised by a few features of the system, i.e. collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep…
Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
This paper describes and validates for the first time the dynamic modelling of Liquid Crystal (LC)-based planar multi-resonant cells, as well as its use as bias signals synthesis tool to improve their reconfigurability time. The dynamic LC…
Molecular dynamics simulations at a constant electric potential are an essential tool to study electrochemical processes, providing microscopic information on the structural, thermodynamic, and dynamical properties. Despite the numerous…
To extend rational materials design and discovery into the space of metastable polymorphs, rapid and reliable assessment of their lifetimes is essential. Motivated by the early work of Buerger (1951), here we investigate the routes to…
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on…
The work discusses specifics of phase transitions for metastable states of substances. The objects of condensed media physics are primarily equilibrium states of substances with metastable phases viewed as an exception, while the…
We develop a unified continuum modeling framework for viscous fluids and hyperelastic solids using the Gibbs free energy as the thermodynamic potential. This framework naturally leads to a pressure primitive variable formulation for the…
Predicting phase stabilities of crystal polymorphs is central to computational materials science and chemistry. Such predictions are challenging because they first require searching for potential energy minima and then performing arduous…
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…