相关论文: Low-Dimensional Projection of Reactive Islands in …

Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when…

We consider a class of models describing an ensemble of identical interacting agents subject to multiplicative noise. In the thermodynamic limit, these systems exhibit continuous and discontinuous phase transitions in a, generally,…

In chemical or physical reaction dynamics, it is essential to distinguish precisely between reactants and products for all time. This task is especially demanding in time-dependent or driven systems because therein the dividing surface (DS)…

Transition State Theory overestimates reaction rates in solution because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing a…

We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective…

Transition path theory (TPT) offers a powerful formalism for extracting the rate and mechanism of rare dynamical transitions between metastable states. Most applications of TPT either focus on systems with modestly sized state spaces or use…

Biochemical reaction systems may be viewed as discrete event processes characterized by a number of states and state transitions. These systems may be modeled as state transition systems with transitions representing individual reaction…

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 focus on an efficient approach for quantification of uncertainty in complex chemical reaction networks with a large number of uncertain parameters. Parameter dimension reduction is accomplished by computing an active subspace that…

Transition states (TSs) govern the rates and outcomes of chemical reactions, making their accurate prediction a central challenge in computational chemistry. Although recent machine-learning models achieve near chemical accuracy in the…

A model is proposed for studying the reaction dynamics in complex quantum systems in which the complete mixing of states is hindered by an internal barrier. Such systems are often treated by the transition-state theory, also known in…

We consider stochastic descriptions of chemical reaction networks in which there are both fast and slow reactions, and for which the time scales are widely separated. We develop a computational algorithm that produces the generator of the…

Simulating chemical reactions is a central challenge in computational chemistry, characterized by an uneven difficulty profile: while equilibrium reactant and product geometries are often classically tractable, intermediate transition…

Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…

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…

Transition states (TSs) are crucial for understanding reaction mechanisms, yet their exploration is limited by the complexity of experimental and computational approaches. Here we propose TS-DFM, a flow matching framework that predicts TSs…

A method to generate reactive trajectories, namely equilibrium trajectories leaving a metastable state and ending in another one is proposed. The algorithm is based on simulating in parallel many copies of the system, and selecting the…

Transition state theory formally provides a simplifying approach for determining chemical reaction rates and pathways. Given an underlying potential energy surface for a reactive system, one can determine the dividing surface in phase space…

Identifying transition states (TSs), the high-energy configurations that molecules pass through during chemical reactions, is essential for understanding and designing chemical processes. However, accurately and efficiently identifying…

Complex systems are ubiquitous in nature and engineering, but their analysis and control are hampered by their high dimensionality and the influence of various factors on their dynamics. Dimensionality reduction aims to find a…