Related papers: A preconditioning scheme for Minimum Energy Path f…
We present an efficient algorithm for calculating the minimum energy path (MEP) and energy barriers between local minima on a multidimensional potential energy surface (PES). Such paths play a central role in the understanding of transition…
Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where…
We study numerically the minimum energy path and energy barriers for dislocation nucleation in a two-dimensional atomistic model of strained epitaxial layers on a substrate with lattice misfit. Stress relaxation processes from coherent to…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of…
Efficient algorithms for the calculation of minimum energy paths of magnetic transitions are implemented within the geodesic nudged elastic band (GNEB) approach. While an objective function is not available for GNEB and a traditional line…
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…
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…
The nudged elastic band (NEB) method is a commonly used approach for the calculation of minimum energy pathways of kinetic processes. However, the final paths obtained rely heavily on the nature of the initially chosen path. This often…
We present a modified version of the nudged elastic band (NEB) algorithm to find minimum energy paths con-necting two known configurations. We show that replacing the harmonic band-energy term with a discretized version of the…
The minimum action method (MAM) is to calculate the most probable transition path in randomly perturbed stochastic dynamics, based on the idea of action minimization in the path space. The accuracy of the numerical path between different…
The nudged elastic band (NEB) method is the standard approach for finding minimum energy paths and transition states on potential energy surfaces. Practical NEB calculations require several pre-processing steps: endpoint minimization,…
Transition states and minimum energy paths are essential to understand and predict chemical reactivity. Double-ended methods represent a standard approach for their determination. We introduce a new double-ended method that optimizes…
A method combining denoising diffusion probabilistic models (DDPMs) with the string method is presented to generate minimum free energy paths between metastable states in molecular systems. It has been demonstrated in recent work that DDPMs…
Rare transition events in meta-stable systems under noisy fluctuations are crucial for many non-equilibrium physical and chemical processes. In these processes, the primary contributions to reactive flux are predominantly near the…
We study numerically the energetics and atomic mechanisms of misfit dislocation nucleation and stress relaxation in a two-dimensional atomistic model of strained epitaxial layers on a substrate with lattice misfit. Relaxation processes from…
The Minima Hopping global optimization method uses physically realizable molecular dynamics moves in combination with an energy feedback that guarantees the escape from any potential energy funnel. For the purpose of finding reactions…
Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner.…
The computational efficiency of stochastic simulation algorithms is notoriously limited by the kinetic trapping of the simulated trajectories within low energy basins. Here we present a new method that overcomes kinetic trapping while still…
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…