Related papers: PASTA: Python Algorithms for Searching Transition …
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used…
Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability…
Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used…
Determining molecular abundances in astrophysical environments is crucial for interpreting observational data and constraining physical conditions in these regions. Chemical modelling tools are essential for simulating the complex processes…
$0^+$, $1^-$, $2^+$, and $3^-$ excitations of $^{28}\textrm{Si}$ are investigated via proton and $\alpha$ inelastic scattering off $^{28}\textrm{Si}$. The structure calculation of $^{28}\textrm{Si}$ is performed with the energy variation…
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…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
Estimating reaction rates and chemical stability is fundamental, yet efficient methods for large-scale simulations remain out of reach despite advances in modeling and exascale computing. Direct simulation is limited by short timescales;…
The calculation of minimum energy paths for transitions such as atomic and/or spin re-arrangements is an important task in many contexts and can often be used to determine the mechanism and rate of transitions. An important challenge is to…
The development of computational models for the numerical simulation of chemically reacting flows operating in the turbulent regime requires the solution of partial differential equations that represent the balance of mass, linear momentum,…
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…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
Tailored Pt nanoparticle catalysts are promising candidates to accelerate the oxygen reduction reaction (ORR) in fuel cells. However, the search for active nanoparticle catalysts is hindered by laborious effort of experimental synthesis and…
Parameter-efficient tuning aims at updating only a small subset of parameters when adapting a pretrained model to downstream tasks. In this work, we introduce PASTA, in which we only modify the special token representations (e.g., [SEP] and…
Transition state theory is a standard framework for predicting the rate of a chemical reaction. Although the transition state theory has been successfully applied to numerous chemical reaction analyses, many experimental and theoretical…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
Path optimization methods have been widely used and highly successful for the analysis of chemical reactions. Yet, they can fail to capture intrinsically multidimensional features of potential energy surfaces (PES). We introduce the nudged…