Related papers: Electronic Collective Variables for Chemical React…
Chemical reactions can be understood as transformations of multigraphs (molecules) that preserve vertex labels (atoms) and degrees (sums of bonding and non-bonding electrons), thereby implying the atom-atom map of a reaction. The…
We present a novel learning framework that consistently embeds underlying physics while bypassing a significant drawback of most modern, data-driven coarse-grained approaches in the context of molecular dynamics (MD), i.e., the availability…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the…
The development of enhanced sampling methods has greatly extended the scope of atomistic simulations, allowing long-time phenomena to be studied with accessible computational resources. Many such methods rely on the identification of an…
Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…
Charge transport processes in disordered complex media are accompanied by anomalously slow relaxation for which usually a broad distribution of relaxation times is adopted. To account for those properties of the environment, a standard…
Photonic quantum computation refers to quantum computation that uses photons as the physical system for doing the quantum computation. The field is largely divided between discrete-variable (DV) and continuous-variable (CV) photonic quantum…
The demonstration of strong and ultrastrong coupling regimes of cavity QED with polyatomic molecules has opened new routes to control chemical dynamics at the nanoscale. We show that strong resonant coupling of a cavity field with an…
Electric vehicles (EVs) are critical to the transition to a low-carbon transportation system. The successful adoption of EVs heavily depends on energy consumption models that can accurately and reliably estimate electricity consumption.…
Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
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…
Quantum computers have the potential to simulate chemical systems beyond the capability of classical computers. Recent developments in hybrid quantum-classical approaches enable the determinations of the ground or low energy states 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…
Strong light-matter coupling within an optical cavity leverages the collective interactions of molecules and confined electromagnetic fields, giving rise to the possibilities of modifying chemical reactivity and molecular properties. While…
We consider a simple linear reversible isomerization reaction A <--> B under subdiffusion described by continuous time random walks (CTRW). The reactants' transformations take place independently on the motion and are described by constant…
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic…
Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…