Related papers: Finding reaction pathways with optimal atomic inde…
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…
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,…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
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…
The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well represented as…
Transition-state searches are central to understanding reaction mechanisms, but the high computational cost of density-functional theory (DFT) limits their application in high-throughput catalyst and materials discovery. Machine-learned…
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…
Global optimization of transition paths in complex atomic scale systems is addressed in the context of misfit dislocation formation in a strained Ge film on Si(001). Such paths contain multiple intermediate minima connected by minimum…
Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…
In reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
Finding optimal pathways in chemical reaction networks is essential for elucidating and designing chemical processes, with significant applications such as synthesis planning and metabolic pathway analysis. Such a chemical pathway-finding…
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…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
We show that molecular dynamics based moves in the Minima Hopping (MH) method are more efficient than saddle point crossing moves which select the lowest possible saddle point. For binary systems we incorporate identity exchange moves in a…
We perform quantum Monte Carlo (QMC) calculations to determine minimum energy pathways of simple chemical reactions, and compare the computed geometries and reaction barriers with those obtained with density functional theory (DFT) and…
Chemical reactions are often associated with an energy barrier along the reaction pathway which hinders the spontaneity of the reaction. Changing the energy barrier along the reaction pathway allows one to modulate the performance of a…
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.…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
We construct path integrals for stochastic hybrid reaction-diffusion (RD) processes, in which the reaction terms depend on the discrete state of a randomly switching environment. We proceed by spatially discretizing a given RD system and…