Related papers: Protein Structure Prediction Using Basin-Hopping
In the dynamic field of materials science, the quest to find optimal structures with low potential energy is of great significance. Over the past two decades, the minima hopping algorithm has emerged as a successful tool in this pursuit. We…
We describe a global optimization technique using `basin-hopping' in which the potential energy surface is transformed into a collection of interpenetrating staircases. This method has been designed to exploit the features which recent work…
Global optimization is a challenging problem, with plenty of algorithms displaying empirical success, but scarce theoretical backing. In this work, we propose a new theoretical framework called Proximal Basin Hopping (PBH), carefully…
Anticipating the low energy arrangements of atoms in space is an indispensable scientific task. Modern stochastic approaches to searching for these configurations depend on the optimisation of structures to nearby local minima in the energy…
A method is presented that can find the global minimum of very complex condensed matter systems. It is based on the simple principle of exploring the configurational space as fast as possible and of avoiding revisiting known parts of this…
Optimization of non-convex loss surfaces containing many local minima remains a critical problem in a variety of domains, including operations research, informatics, and material design. Yet, current techniques either require extremely high…
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,…
During the last decades many metaheuristics for global numerical optimization have been proposed. Among them, Basin Hopping is very simple and straightforward to implement, although rarely used outside its original Physical Chemistry…
We present the Basin Hopping with Skipping (BH-S) algorithm for stochastic optimisation, which replaces the perturbation step of basin hopping (BH) with a so-called skipping proposal from the rare-event sampling literature. Empirical…
Theoretical design of global optimization algorithms can profitably utilize recent statistical mechanical treatments of potential energy surfaces (PES's). Here we analyze the basin-hopping algorithm to explain its success in locating the…
The ability to engineer optimized protein variants has transformative potential for biotechnology and medicine. Prior sequence-based optimization methods struggle with the high-dimensional complexities due to the epistasis effect and the…
A structure prediction method is presented based on the Minima Hopping method. Optimized moves on the configurational enthalpy surface are performed to escape local minima using variable cell shape molecular dynamics by aligning the initial…
Protein structure prediction is a critical problem linked to drug design, mutation detection, and protein synthesis, among other applications. To this end, evolutionary data has been used to build contact maps which are traditionally…
We created a computational workflow to analyze the potential energy surface (PES) of materials using machine-learned interatomic potentials in conjunction with the minima hopping algorithm. We demonstrate this method by producing a…
Basin-Hopping (BH) or Monte-Carlo Minimization (MCM) is so far the most reliable algorithms in chemical physics to search for the lowest-energy structure of atomic clusters and macromolecular systems. BH transforms the complex energy…
We present an adaptive and parallel implementation of the Basin Hopping (BH) algorithm for the global optimization of atomic clusters interacting via the Lennard-Jones (LJ) potential. The method integrates local energy minimization with…
In this report, we explore the use of a quantum optimization algorithm for obtaining low energy conformations of protein models. We discuss mappings between protein models and optimization variables, which are in turn mapped to a system of…
We compare Evolutionary Algorithms with Minima Hopping for global optimization in the field of cluster structure prediction. We introduce a new {\em average offspring} recombination operator and compare it with previously used operators.…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
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…