相关论文: Data-driven Computation of Molecular Reaction Coor…
We developed a general theoretical approach and a user-ready computer code that permit to study the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule-molecule collisions. The method is a mixture…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of the…
Accurately predicting response properties of molecules such as the dynamic polarizability and hyperpolarizability using quantum mechanics has been a long-standing challenge with widespread applications in material and drug design. Classical…
Multi-adaptive Galerkin methods are extensions of the standard continuous and discontinuous Galerkin methods for the numerical solution of initial value problems for ordinary or partial differential equations. In particular, the…
Coarse-grained modeling in molecular simulations serves not only to extend accessible time and length scales beyond atomistic limits, but also to reduce high-dimensional chemical data to low-dimensional representations that expose the…
We present an efficient method for rigorous quantum calculations of cross sections for atom-molecule reactive scattering in the presence of a dc electric field. The wavefunction of the reaction complex is expanded in an overcomplete set of…
Simulation of surface processes is a key part of computational chemistry that offers atomic-scale insights into mechanisms of heterogeneous catalysis, diffusion dynamics, as well as quantum tunneling phenomena. The most common theoretical…
We introduce a simple method for characterizing reactive pathways in quantum systems. Flux auto- correlation and cross-correlation functions are employed to develop a quantitative measure of dynamical coupling in quantum transition events,…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
A method to calculate reactions in quantum mechanics is outlined. It is advantageous, in particular, in problems with many open channels of various nature i.e. when energy is not low. In the method there is no need to specify reaction…
The radiative transfer equation models the interaction of radiation with scattering and absorbing media and has important applications in various fields in science and engineering. It is an integro-differential equation involving time,…
We present a novel kernel-based machine learning algorithm for identifying the low-dimensional geometry of the effective dynamics of high-dimensional multiscale stochastic systems. Recently, the authors developed a mathematical framework…
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological,…
The prediction of stellar ($\gamma$,$\alpha$) reaction rates for heavy nuclei is based on the calculation of ($\alpha$,$\gamma$) cross sections at sub-Coulomb energies. These rates are essential for modeling the nucleosynthesis of so-called…
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…
For two molecules to react they first have to meet. Yet, reaction times are rarely on par with the first-passage times that govern such molecular encounters. A prime reason for this discrepancy is stochastic transitions between reactive and…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…