Related papers: Electronic Collective Variables for Chemical React…
The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented…
Developing an efficient method to accelerate the speed of molecular dynamics is a central theme in the field of molecular simulation. One category among the methods are collective-variable-based methods, which rely on predefined collective…
This Brief Communication introduces a graph-neural-network architecture built on geometric vector perceptrons to predict the committor function directly from atomic coordinates, bypassing the need for hand-crafted collective variables…
Free energy biasing methods have proven to be powerful tools to accelerate the simulation of important conformational changes of molecules by modifying the sampling measure. However, most of these methods rely on the prior knowledge of…
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…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
Quantum chemical calculations have attracted much attention as a practical application of quantum computing. Quantum computers can prepare superpositions of electronic states with various numbers of electrons on qubits. This special feature…
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…
The phenomenon of solidification of a substance from its liquid phase is of the greatest practical and theoretical importance, and atomistic simulations can provide precious information towards its understanding and control. Unfortunately,…
Partial atomic charges are a useful and intuitive concept for understanding molecular properties and chemical reaction mechanisms, showing how changes in molecular geometry can affect the flow of electronic charge within a molecule.…
In molecular dynamics simulations, rare events, such as protein folding, are typically studied using enhanced sampling techniques, most of which are based on the definition of a collective variable (CV) along which acceleration occurs.…
Using the collective variables (CV) method the basic relations of statistical field theory of a multicomponent non-homogeneous fluids are reconsidered. The corresponding CV action depends on two sets of scalar fields - fields…
We examine theoretically a new idea for spatial and temporal control of chemical reactions. When chemical reactions take place in a mixture of solvents, an external electric field can alter the local mixture composition thereby accelerating…
We present a new interatomic potential for water captured in a charge-transfer embedded atom method (EAM) framework. The potential accounts for explicit, dynamical charge transfer in atoms as a function of the local chemical environment. As…
Many biological processes occur on time scales longer than those accessible to molecular dynamics simulations. Identifying collective variables (CVs) and introducing an external potential to accelerate them is a popular approach to address…
Modeling microstructure evolution in electrochemical systems is vital for understanding the mechanism of various electrochemical processes. In this work, we propose a general phase field framework that is fully variational and thus…
We present a unified formalism for describing chemical reaction rates of trapped, ultracold molecules. This formalism reduces the scattering to its essential features, namely, a propagation of the reactant molecules through a gauntlet of…
In molecular dynamics (MD) simulations, transitions between states are often rare events due to energy barriers that exceed the thermal temperature. Because of their infrequent occurrence and the huge number of degrees of freedom in…
We introduce a method for elucidating and modifying the functionality of systems dominated by rare events that relies on the automated tuning of their underlying free energy surface. The proposed approach seeks to construct collective…
The electronic charge density plays a central role in determining the behavior of matter at the atomic scale, but its computational evaluation requires demanding electronic-structure calculations. We introduce an atom-centered,…