Related papers: Computationally Efficient Characterization of Pote…
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…
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…
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.…
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…
Associative memory Hamiltonian structure prediction potentials are not overly rugged, thereby suggesting their landscapes are like those of actual proteins. In the present contribution we show how basin-hopping global optimization can…
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…
Global dynamics in nonlinear stochastic systems is often difficult to analyze rigorously. Yet, many excellent numerical methods exist to approximate these systems. In this work, we propose a method to bridge the gap between computation and…
We report a new algorithm for constructing pathways between local minima that involve a large number of intervening transition states on the potential energy surface. A significant improvement in efficiency has been achieved by changing the…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
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.…
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…
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…
There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
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…
Many algorithms for finding reaction pathways require an initial estimate of the minimum energy path (MEP). Most estimation methods use a variational approach and thus must be seeded from an even simpler path, such as one generated by…
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…
We present a simple mathematical framework for the description of the dynamics of glassy systems in terms of a random walk in a complex energy landscape pictured as a network of minima. We show how to use the tools developed for the study…
An improved real-time quantum Monte Carlo procedure is presented and applied to describe the electronic transfer dynamics along molecular chains. The model consists of discrete electronic sites coupled to a thermal environment which is…
We describe a robust and efficient chain-of-states method for computing Minimum Energy Paths~(MEPs) associated to barrier-crossing events in poly-atomic systems. The path is parametrized in terms of a continuous variable $t \in [0,1]$ that…