Related papers: Multi-site Reaction Dynamics Through Multi-fragmen…
Molecular fragment or embedding methods are powerful techniques for overcoming scalability limitations in electronic structure theory by dividing large molecular systems into individual units that are small enough to be treated using…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
In this work, we derive a multi-fragment real-time extension of projected density matrix embedding theory (pDMET) designed to treat non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static…
In this article we present a new formulation and an associated algorithm for the simultaneous numerical simulation of multiple condensed phase explosives in direct contact with each other, which may also be confined by (or interacting with…
Atomic nuclei are complex, quantum many-body systems whose structure manifests itself through intrinsic quantum states associated with different excitation modes or degrees of freedom. Collective modes (vibration and/or rotation) dominate…
The reaction of volatile matter plays an important role in the process of bringing matter from the surface of the planet to the atmosphere. Therefore, by simulating the mixing and chemical reaction process of volatile matter in the…
The use of machine learning algorithms is an attractive way to produce very fast detector simulations for scattering reactions that can otherwise be computationally expensive. Here we develop a factorised approach where we deal with each…
Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…
Real-world networks are composed of diverse interacting and evolving entities, while most of existing researches simply characterize them as particular static networks, without consideration of the evolution trend in dynamic networks.…
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Reactive chemistry of molecular hydrogen at surfaces, notably dissociative sticking and hydrogen evolution, plays a crucial role in energy storage and fuel cells. Theoretical studies can help to decipher underlying mechanisms and reaction…
Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
We examine the performance of the density matrix embedding theory (DMET) recently proposed in [G. Knizia and G. K.-L. Chan, Phys. Rev. Lett. 109, 186404 (2012)]. The core of this method is to find a proper one-body potential that generates…
Embedded density functional theory (e-DFT) is used to describe the electronic structure of strongly interacting molecular subsystems. We present a general implementation of the Exact Embedding (EE) method [J. Chem. Phys. 133, 084103 (2010)]…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
The study of chemical reactions in environments under nonequilibrium conditions has been of interest recently in a variety of contexts, including current-induced reactions in molecular junctions and scanning tunneling microscopy…
Strongly correlated electron systems are challenging to calculate, and entanglement in such systems is not widely analyzed. We present an approach that can be used as a post-processing step for calculating the two-site reduced density…