Related papers: Minima Hopping Guided Path Search: An Efficient Me…
We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation…
Shortest path algorithms have played a key role in the past century, paving the way for modern day GPS systems to find optimal routes along static systems in fractions of a second. One application of these algorithms includes optimizing the…
Incorporating the concept of order parameter of the mean-field theory into the simulated annealing method, we presented a new optimization algorithm, the guided simulated annealing method. In this method mean-field order parameters are…
A strategy for finding transition paths connecting two stable basins is presented. The starting point is the Hamilton principle of stationary action; we show how it can be transformed into a minimum principle through the addition of…
Using a fast and accurate neural network potential we are able to systematically explore the energy landscape of large unit cells of bulk magnesium oxide with the minima hopping method. The potential is trained with a focus on the…
We first derive the Hamilton-Jacobi theory underlying continuous-time Markov processes, and then use the construction to develop a variational algorithm for estimating escape (least improbable or first passage) paths for a generic…
The minimum energy path (MEP) is the most probable transition path that connects two equilibrium states of a potential energy landscape. It has been widely used to study transition mechanisms as well as transition rates in the fields of…
Pathways-reduced analysis is one of the techniques used by the Fispact-II nuclear activation and transmutation software to study the sensitivity of the computed inventories to uncertainties in reaction cross-sections. Although deciding…
Predicting atomic-scale interfacial structures remains a central challenge in materials science due to their structural complexity and the difficulty of direct comparison between computational and experimental results. In this study, we…
Describing chemical reactions in solution on a molecular level is a challenging task due to the high mobility of weakly interacting solvent molecules which requires configurational sampling. For instance, polar and protic solvents can…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
Finding optimal pathways in chemical reaction networks is essential for elucidating and designing chemical processes, with significant applications such as synthesis planning and metabolic pathway analysis. Such a chemical pathway-finding…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
Path sampling allows the study of rare events like chemical reactions, nucleation and protein folding via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD)…
We study the relation of the potential energy landscape (PEL) topography to relaxation dynamics of a small model glass former of Lennard-Jones type. The mechanism under investigation is the hopping betweem superstructures of PEL mimima,…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods…
Power system restoration after a major blackout is a complex process, in which selection of energising paths is a key issue to realize unit and load restoration safely and efficiently. In general, the energising path scheme made beforehand…
Using random walk sampling methods for feature learning on networks, we develop a method for generating low-dimensional node embeddings for directed graphs and identifying transition states of stochastic chemical reacting systems. We…