Related papers: Finding reaction pathways with optimal atomic inde…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
Density functional theory (DFT) has become a standard tool for the study of point defects in materials. However, finding the most stable defective structures remains a very challenging task as it involves the solution of a multimodal…
We propose a cross-entropy minimization method for finding the reaction coordinate from a large number of collective variables in complex molecular systems. This method is an extension of the likelihood maximization approach describing the…
Autonomous agents face the challenge of coordinating multiple tasks (perception, motion planning, controller) which are computationally expensive on a single onboard computer. To utilize the onboard processing capacity optimally, it is…
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…
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…
Recently a non-empirical stochastic walker algorithm has been developed to search for the minimum-energy escape paths (MEP) from the minima of the potential surface [J. Phys. Soc. Jpn. 87, 063801 (2018); Physica A, 528, 121481 (2019)]. This…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
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…
Efficient and reliable identification and optimization of transition state structures is a longstanding challenge in computational chemistry. Popular chain-of-states methods require hundreds if not thousands of ab initio calculations to…
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…
The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same…
Machine learning interatomic potentials (MLIPs) have achieved remarkable accuracy on standard benchmarks, yet their ability to reproduce molecular kinetics -- critical for reaction rate calculations -- remains largely unexplored. We…
Molecular-level understanding of the interactions between the constituents of an atomic structure is essential for designing novel materials in various applications. This need goes beyond the basic knowledge of the number and types of…
We present a one-way shooting algorithm for transition path sampling that accepts every proposed trajectory, yet samples the correct transition path ensemble for systems with overdamped stochastic dynamics. The method is based on two key…
In this work, we present a transition-state optimization protocol based on the Mode-Tracking algorithm [J. Chem. Phys. 118 (2003) 1634]. By calculating only the eigenvector of interest instead of diagonalizing the full Hessian matrix and…
We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation…
It is possible in principle to probe the many--atom potential surface using density functional theory (DFT). This will allow us to apply DFT to the Hamiltonian formulation of atomic motion in monatomic liquids [\textit{Phys. Rev. E} {\bf…
In this study, we introduce a training protocol for developing machine learning force fields (MLFFs), capable of accurately determining energy barriers in catalytic reaction pathways. The protocol is validated on the extensively explored…
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…