相关论文: Minimum Energy Paths and Transition States by Curv…

Similarly to gear systems in vehicles, most chemical reaction networks (CRNs) involved in energy transduction have at their disposal multiple transduction pathways, each characterized by distinct efficiencies. We conceptualize these…

Power system restoration after a major blackout is a complex process, in which selection of energising paths is a key issue to realize unit and load restoration safely and efficiently. In general, the energising path scheme made beforehand…

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Tran- sitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible…

Mapping reaction pathways and transition states (TS) is fundamental to chemistry but computationally expensive at scale. The minimum energy pathway (MEP) dictates reaction rates and mechanisms, yet recovering it via electronic-structure…

Using random walk sampling methods for feature learning on networks, we develop a method for generating low-dimensional node embeddings for directed graphs and identifying transition states of stochastic chemical reacting systems. We…

Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…

We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize…

The search for new computational tasks of quantum chemistry that can be performed on current quantum computers is important for the development of quantum computing and quantum chemistry. Although calculations of chemical reactions have a…

We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…

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…

Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…

A simple model of the two-state ratchet type is proposed for molecular chemical engines that convert chemical free energy into mechanical work and vice versa. The engine works by catalyzing a chemical reaction and turning a rotor.…

Finding optimal pathways in chemical reaction networks is essential for elucidating and designing chemical processes, with significant applications such as synthesis planning and metabolic pathway analysis. Such a chemical pathway-finding…

Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods…

Efficient algorithms for the calculation of minimum energy paths of magnetic transitions are implemented within the geodesic nudged elastic band (GNEB) approach. While an objective function is not available for GNEB and a traditional line…

Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…

Given a multidimensional free-energy or potential-energy landscape, finding reaction paths that connect an initial (or reactant) state and a final (or product) state is important for biophysics and materials science. The likelihood of a…

Shortcut to isothermality is a driving strategy to steer the system to its equilibrium states within finite time, and enables evaluating the impact of a control promptly. Finding optimal scheme to minimize the energy cost is of critical…

We present an integrated approach for the use of simulated data from full order discretization as well as projection-based Reduced Basis reduced order models for the training of machine learning approaches, in particular Kernel Methods, in…

It is demonstrated that the reaction path for a polyatomic molecule (applied to the HCO molecule) is easily calculated via ab-initio configuration interaction (CI) total energies. This Hamiltonian not only reproduces the CI calculations…