Related papers: Binary contraction method for the construction of …
A model Hamiltonian for the reaction CH$_4^+ \rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose…
Reformulating hyperdynamics without using a transition state theory (TST) dividing surface makes it possible to accelerate conventional molecular dynamics (MD) simulation using a broader range of bias potentials. A new scheme to calculate…
We present a family of algorithms for the fast determination of reaction paths and barriers in phase space and the computation of the corresponding rates. The method requires the reaction times be large compared to the microscopic time,…
Heterogenous reactions typically consist of multiple elementary steps and their rate coefficients are of fundamental importance in elucidating the mechanisms and micro-kinetics of these processes. Transition-state theory (TST) for…
In this article, we review the analytical and numerical approaches for computing the phase space structures in two degrees-of-freedom Hamiltonian systems that arise in chemical reactions. In particular, these phase space structures are the…
We introduce the concept of a "transitory" dynamical system---one whose time-dependence is confined to a compact interval---and show how to quantify transport between two-dimensional Lagrangian coherent structures for the Hamiltonian case.…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
The framework of transition state theory relies on the determination of a geometric structure identifying reactivity. It replaces the laborious exercise of following many trajectories for a long time to provide chemical reaction rates and…
The decay of quantum complex systems through a potential barrier is often described with transition-state theory, also known as RRKM theory in chemistry. Here we derive the basic formula for transition-state theory based on a generic…
Transition state theory is a standard framework for predicting the rate of a chemical reaction. Although the transition state theory has been successfully applied to numerous chemical reaction analyses, many experimental and theoretical…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
We consider the existence of invariant manifolds in phase space governing reaction dynamics in situations where there are no saddle points on the potential energy surface in the relevant regions of configuration space. We point out that…
The time-dependent barrier passage of an anomalous damping system is studied via the generalized Langevin equation (GLE) with non-Ohmic memory damping friction tensor and corresponding thermal colored noise tensor describing a particle…
Phase segregation, the process by which the components of a binary mixture spontaneously separate, is a key process in the evolution and design of many chemical, mechanical, and biological systems. In this work, we present a data-driven…
Chemical selectivity is a phenomenon displayed by potential energy surfaces (PES) that is relevant for many organic chemical reactions whose PES feature a valley-ridge inflection point (VRI) in the region between two sequential index-1…
A simple variational Lagrangian is proposed for the time development of an arbitrary density matrix, employing the "factorization" of the density. Only the "kinetic energy" appears in the Lagrangian. The formalism applies to pure and mixed…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
This article introduces a new efficient particle method for the numerical simulation of crystallization and precipitation at the pore scale of real rock geometries extracted by X-Ray tomography. It is based on the coupling between…
A practical method for finding free energy barriers for transitions in high-dimensional classical and quantum systems is presented and used to calculate the dissociative sticking probability of H2 on a metal surface within transition state…