Related papers: Blind search for complex chemical pathways using H…

Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…

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…

Chemical kinetic mechanisms can be represented by sets of elementary reactions that are easily translated into mathematical terms using physicochemical relationships. The schematic representation of reactions captures the interactions…

Retrosynthesis is essential for designing synthetic pathways for complex molecules and can be revolutionized by AI to automate and accelerate chemical synthesis planning for drug discovery and materials science. Here, we propose a…

We developed an automated approach to construct the complex reaction network and explore the reaction mechanism for several reactant molecules. The nanoreactor type molecular dynamics was employed to generate possible chemical reactions, in…

Atomic-scale modeling has advanced rapidly through integration of machine learning, yet a key bottleneck remains. Even with an accurate potential energy surface and a clear target material, we still lack a practical atomistic dynamics…

Stochastic models are often used to help understand the behavior of intracellular biochemical processes. The most common such models are continuous time Markov chains (CTMCs). Parametric sensitivities, which are derivatives of expectations…

A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…

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…

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…

Efficient synthesis recipes are needed both to streamline the manufacturing of complex materials and to accelerate the realization of theoretically predicted materials. Oftentimes the solid-state synthesis of multicomponent oxides is…

A central challenge in materials science is characterizing chemical processes that are elusive to direct measurement, particularly in functional materials operating under realistic conditions. Here, we demonstrate that mechanical strain…

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…

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…

Reaction mechanism search tools have demonstrated the ability to provide insights into likely products and rate-limiting steps of reacting systems. However, reactions involving several concerted bond changes - as can be found in many key…

A lot of progress has been made in recent times for simulating accurately the ground state energy of small molecules and their potential energy surface, using quantum-classical hybrid computing architecture. While these single point energy…

We present a multimodal search tool that facilitates retrieval of chemical reactions, molecular structures, and associated text from scientific literature. Queries may combine molecular diagrams, textual descriptions, and reaction data,…

The primary emphasis of this work on kinetics is to illustrate the a posteriori approach to applications, where focus on data leads to novel outcomes, rather than the a priori tendencies of applied analysis which imposes constructs on the…

The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…

In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…