Related papers: Identifying Reaction Pathways in Phase Space via A…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
A time-dependent no-recrossing dividing surface is shown to lead to a new criterion for identifying reactive trajectories well before they are evolved to infinite time. Numerical dynamics simulations of a dissipative anharmonic…
Compaction in reactive porous media is modelled as a reaction-diffusion process with a moving boundary. Asymptotic analysis is used to find solutions for the coupled nonlinear compaction equations, and a traveling wave solution is obtained…
We show that neural networks can be optimized to represent minimum energy paths as continuous functions, offering a flexible alternative to discrete path-search methods such as Nudged Elastic Band (NEB). Our approach parameterizes reaction…
When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…
The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable…
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…
We experimentally demonstrate a method for reconstructing the transverse 4D phase space of an electron beam at the time of emission from downstream diagnostics of the 4D phase space. This method does not rely on detailed knowledge of the…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
Area-selective atomic layer deposition (AS-ALD) is an emerging technology in semiconductor manufacturing. However, accurately understanding inhibitor reactivity on surfaces remains challenging, particularly when the substrate is amorphous.…
In this paper, we provide a graphic formulation of non-isothermal reaction systems and show that a non-isothermal detailed balanced network system converges (locally) asymptotically to the unique equilibrium within the invariant manifold…
Reactivity boundaries that divide the origin and destination of trajectories are crucial of importance to reveal the mechanism of reactions, which was recently found to exist robustly even at high energies for index-one saddles [Phys. Rev.…
A method to approximate transmission probabilities for a nonseparable multidimensional barrier is applied to a waveguide model. The method uses complex barrier-crossing orbits to represent reaction probabilities in phase space and is…
The coherent state path integral formulation of certain many particle systems allows for their non perturbative study by the techniques of lattice field theory. In this paper we exploit this strategy by simulating the explicit example of…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
This paper studies the boundary behaviour at mechanical equilibrium at the ends of a finite interval of a class of systems of interacting particles with monotone decreasing repulsive force. Our setting covers pile-ups of dislocations,…
We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear…
The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have focused on analyzing the transition path ensemble using the…
We study general linear transport-reaction systems on an arbitrary dimensional hypercube with periodic boundary conditions. Transport-reaction systems are often used to model the finite speed movement and interaction of particles, bacteria…