相关论文: Identifying Reaction Pathways in Phase Space via A…
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…
The free energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path…
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…
We propose an 'automatic' approach to analyze the results of the on-the-fly trajectory surface hopping simulation on the multi-channel nonadiabatic photoisomerization dynamics by considering the trajectory similarity and the configuration…
Recurrence quantification analysis is a method for measuring the complexity of dynamical systems. Recurrence determinism is a fundamental characteristic of it, closely related to correlation sum. In this paper, we study asymptotic behavior…
We present a means of studying rare reactive pathways in open quantum systems using Transition Path Theory and ensembles of quantum jump trajectories. This approach allows for elucidation of reactive paths for dissipative, nonadiabatic…
The accuracy of reaction energy profiles calculated with multi-configurational electronic structure methods and corrected by multi-reference perturbation theory depends crucially on consistent active orbital spaces selected along the…
Information geometry is based on classical Legendre duality but allows to incorporate additional structure such as algebraic constraints and Bregman divergence functions. It is naturally suited, and has been successfully used, to describe…
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…
We construct a quantum theory of light in nonlinear dielectric media with dispersion and absorption. We employ a mesoscopic model for the light-matter interaction that include a fourth-order nonlinearity in the material response.…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
We investigate the subtle effects of diffuse charge on interfacial kinetics by solving the governing equations for ion transport (Nernst-Planck) with realistic boundary conditions representing reaction kinetics (Butler-Volmer) and…
Inferring chemical reaction networks (CRN) from concentration time series is a challenge encouragedby the growing availability of quantitative temporal data at the cellular level. This motivates thedesign of algorithms to infer the…
A new asymptotic method is presented for the analysis of the traveling waves in the one-dimensional reaction-diffusion system with the diffusion with a finite velocity and Kolmogorov-Petrovskii-Piskunov kinetics. The analysis makes use of…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
A biological pathway represents a set of genes that serves a particular cellular or a physiological function. The genes within the same pathway are expected to function together and hence may interact with each other. It is also known that…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
This is a pedagogical account on reaction-diffusion systems and their relationship with integrable quantum spin chains. Reaction-diffusion systems are paradigmatic examples of non-equilibrium systems. Their long-time behaviour is strongly…
3D Scene Graphs integrate both metric and semantic information, yet their structure remains underutilized for improving path planning efficiency and interpretability. In this work, we present S-Path, a situationally-aware path planner that…
Several strategies in phase retrieval are unified by an iterative "difference map" constructed from a pair of elementary projections and a single real parameter $\beta$. For the standard application in optics, where the two projections…