Related papers: Collective Variables for Conformational Polymorphi…
The dynamics of physical systems that require high-dimensional representation can often be captured in a few meaningful degrees of freedom called collective variables (CVs). However, identifying CVs is challenging and constitutes a…
The study of the rare transitions that take place between long lived metastable states is a major challenge in molecular dynamics simulations. Many of the methods suggested to address this problem rely on the identification of the slow…
Understanding the long-time dynamics of complex physical processes depends on our ability to recognize patterns. To simplify the description of these processes, we often introduce a set of reaction coordinates, customarily referred to as…
Enhanced sampling techniques such as umbrella sampling and metadynamics are now routinely used to provide information on how the thermodynamic potential, or free energy, depends on a small number of collective variables. The free energy…
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
In this work we describe the thermodynamics and mechanism of CO$_2$ polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics and committor analysis. We find that the…
Understanding polymorph selection in atomic and molecular systems and its control through thermodynamic conditions and external factors (such as seed characteristics) is fundamental to the design of targeted materials and holds great…
Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in…
Mutual information between local stress and local non-affine deformation is proposed as a collective field variable quantifying the {\em local softness} of soft materials. The liquid-solid transition in a simple liquid is considered as a…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
An accurate description of nonadiabatic dynamics of molecular species on metallic surfaces poses a serious computational challenge associated with a multitude of closely-spaced electronic states. We propose a mixed quantum-classical scheme…
Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…
Syndiotactic polystyrene (sPS) exhibits complex polymorphic behavior upon crystallization. Computational modeling of polymer crystallization has remained a challenging task because the relevant processes are slow on the molecular time…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
This paper reviews the current state-of-the-art in the simulation of the mechanical behavior of polycrystalline materials by means of computational homogenization. The key ingredients of this modelling strategy are presented in detail…
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic…
Enhanced sampling methods typically require predefined collective variables (CVs) that presuppose knowledge of reaction coordinates, restricting the discovery of unanticipated transition mechanisms or intermediates. Here, we show that a…
A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is…