Related papers: Finding reaction pathways with optimal atomic inde…

The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have focused on analyzing the transition path ensemble using the…

We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by…

For the theoretical understanding of the reactivity of complex chemical systems accurate relative energies between intermediates and transition states are required. Despite its popularity, density functional theory (DFT) often fails to…

Transition state or minimum energy path finding methods constitute a routine component of the computational chemistry toolkit. Standard analysis involves trajectories conventionally plotted in terms of the relative energy to the initial…

We propose a reinforcement learning based method to identify important configurations that connect reactant and product states along chemical reaction paths. By shooting multiple trajectories from these configurations, we can generate an…

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation single- and double-ended transition-state optimization algorithms - the freezing string and Berny optimization…

Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods…

This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…

Reaction paths and probabilities are inferred, in a usual Monte Carlo or Molecular Dynamic simulation, directly from the evolution of the positions of the particles. The process becomes time-consuming in many interesting cases in which the…

Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…

Predicting atomic-scale interfacial structures remains a central challenge in materials science due to their structural complexity and the difficulty of direct comparison between computational and experimental results. In this study, we…

Machine-learned interatomic potentials (MLPs) provide near density functional theory (DFT) accuracy at reduced computational cost, but their reliability depends on representative training data and often deteriorates in transition-state…

Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…

Understanding the transition events between metastable states in complex systems is an important subject in the fields of computational physics, chemistry and biology. The transition pathway plays an important role in characterizing the…

We propose an efficient method to compute reaction rate constants of thermally activated processes occurring in many-body systems at finite temperature. The method consists in two steps: first, paths are sampled using a transition path…

Locating the global minimum of a complex potential energy surface is facilitated by considering a homotopy, namely a family of surfaces that interpolate continuously from an arbitrary initial potential to the system under consideration.…

We present a method for solving the reaction-diffusion equation with general potential in free space. It is based on the approximation of the Feynman-Kac formula by a sequence of convolutions on sequentially diminishing grids. For…

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These…

The probability of trajectories of weakly diffusive processes to remain in the tubular neighbourhood of a smooth path is given by the Freidlin-Wentzell-Graham theory of large deviations. The most probable path between two states (the…

Computational high-throughput virtual screening is essential for identifying redox-active molecules for sustainable applications such as electrochemical carbon capture. A primary challenge in this approach is the high computational cost…