相关论文: PASTA: Python Algorithms for Searching Transition …
Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…
The increasing complexity and diversity of hardware accelerators in modern computing systems demand flexible, low-overhead program analysis tools. We present PASTA, a low-overhead and modular Program AnalysiS Tool Framework for…
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…
Transition state (TS) searches are a critical bottleneck in computational studies of chemical reactivity, as accurately capturing complex phenomena like bond breaking and formation events requires repeated evaluations of expensive ab-initio…
A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and…
Transition states, the first-order saddle points on the potential energy surfaces, govern the kinetics and mechanisms of chemical reactions and conformational changes. Locating them is challenging because transition pathways are…
Finding complex reaction and transformation pathways, involving many intermediate states, is in general not possible on the DFT level with existing simulation methods due to the very large number of required energy and force evaluations.…
Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and…
We present FIESTA, a model selection approach that significantly reduces the computational resources required to reliably identify state-of-the-art performance from large collections of candidate models. Despite being known to produce…
The state transition algorithm (STA), as an intelligent optimization method grounded in constructivist learning, has been demonstrated to be highly effective in solving complex optimization problems. However, the standard STA suffers from…
Tensor methods have gained increasingly attention from various applications, including machine learning, quantum chemistry, healthcare analytics, social network analysis, data mining, and signal processing, to name a few. Sparse tensors and…
Minimum energy path (MEP) search is a vital but often very time-consuming method to predict the transition states of versatile dynamic processes in chemistry, physics, and materials science. In this study, we reveal that the chemical bond…
PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for…
We present an extensive set of surface and chemisorption energies calculated using state of the art many-body perturbation theory. In the first part of the paper we consider ten surface reactions in the low coverage regime where…
State transition algorithm (STA) is a metaheuristic method for global optimization. Recently, a modified STA named parameter optimal state transition algorithm (POSTA) is proposed. In POSTA, the performance of expansion operator, rotation…
Many chemical reactions can be formulated in terms of particle diffusion in a complex energy landscape. Transition path theory (TPT) is a theoretical framework for describing the direct (reaction) pathways from reactant to product states…
Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
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…