Sep 2026· Journal of Chemical Theory and Computation· Vol 22, pp. 9847-9856· 0 citations· 75 references
Abstract
Efficiently exploring the global potential energy surface (PES) of different materials has been a challenging yet very important task for theoretical simulation. By accurately characterizing the global PES and strategically combining the genetic algorithm (GA) with the stochastic surface walking (SSW) method, here we propose a novel method for global PES exploration, achieving efficient localization of the global minimum. Notably, by leveraging the extensive configuration network sampled during the search, this framework further enables the automated identification of long-range, low-energy transition pathways between distant superbasins, providing deep insights into the structural evolution mechanisms. Through tests on different systems, such as atomic clusters, ligand-protected clusters, molecular clusters, surface-supported clusters, atomic crystals, and molecular crystals, it has been proven that the new algorithm is highly effective in describing the overall characteristics of the PES. It has shown significant improvements in exploring the global PES compared with standalone GA and SSW methods, especially for complex and large-scale chemical systems.
Reliable global optimization of atomic clusters is limited not only by the ruggedness of the potential energy surface but also by the quality of the starting population supplied to the search algorithm. We examine this issue for the Bonobo Optimizer (BO) using a workflow that combines external PyAR‐style population ini...
Bhrigu Chakraborty, A. Anoop· Journal of Computational Che...· 0 citations
A hybrid GA that integrates an information-theoretic local search strategy for unsupervised FS and effectively mitigates the premature convergence problem of conventional GAs and improves search efficiency and solution quality compared to traditional heuristic and evolutionary approaches is proposed.
Seyeon Son, Hyunki Lim· Computers, Materials & C...· 0 citations
This study reviews and analyzes the different AI-based strategies used to model protein structure and dynamics and simulate macromolecular assemblies, comparing them with traditional methods, and shows that hybrid solutions and combinations of methods can be devised to maximize their strengths.
Margherita Bini, Valentina Tozzini· Frontiers in Molecular Biosc...· 0 citations
This work proposes SLIDE, Sequence-free Landscape Inference for Directed Evolution, which provides an estimation for landscape ruggedness from a mutating population using only population-level phenotypic data and an estimation of mutation rate.
S. Towers, Jessica James, Harrsion Steel et al.· bioRxiv· 0 citations
This study developed and evaluated three different UQ frameworks based on advanced UQ methods and integrated with graph neural networks: Bayesian Neural Networks, Evidence Neural Networks, and Monte Carlo Dropout, and shows that ENN effectively reflects data adequacy, while MCD exhibits excellent robustness.
Zi-Xin Wen, Kai-Le Jiang, Hui-Fang Li et al.· Journal of Chemical Physics· 0 citations
Molecular dynamics (MD) simulations are invaluable tools for studying molecular behavior, offering insights into the time-dependent evolution of molecular systems. However, these simulations often face significant limitations in exploring the full conformational space of the complex systems. The high dimensionality and...
Akash Nagare, S. Wagh, Aneesh Kotipalli et al.· ACS Omega· 0 citations
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