相关论文: Minimum Energy Paths and Transition States by Curv…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
In this paper we present a method for locating transition states and higher-order saddles on potential energy surfaces using double-ended classical trajectories. We then apply this method to 7- and 8-atom Lennard-Jones clusters, finding one…
Transition Path Theory (TPT) provides a rigorous framework to investigate the dynamics of rare thermally activated transitions. In this theory, a central role is played by the forward committor function q^+(x), which provides the ideal…
The signal from many single molecule experiments monitoring molecular processes, such as enzyme turnover via fluorescence and opening and closing of ion channel via the flux of ions, consists of a time series of stochastic on and off (or…
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 amplitude and probability of quantum transitions are represented as a path integrals in energy state space of the investigated multi-level quantum system. Using this approach we consider rotational dynamics of nitrogen molecules…
We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state…
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…
Modeling chemical reactions and complicated molecular systems has been proposed as the `killer application' of a future quantum computer. Accurate calculations of derivatives of molecular eigenenergies are essential towards this end,…
The nudged elastic band (NEB) method is the standard approach for finding minimum energy paths and transition states on potential energy surfaces. Practical NEB calculations require several pre-processing steps: endpoint minimization,…
Topological band theory has transformed our understanding of crystalline materials by classifying the connectivity and crossings of electronic energy levels. Extending these concepts to molecular systems has therefore attracted significant…
We consider constrained bilinear optimal control of second-order linear evolution partial differential equations (PDEs) with a reaction term on the half line, where control arises as a time-dependent reaction coefficient and constraints are…
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 reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided…
We consider a Markov process in continuous time with a finite number of discrete states. The time-dependent probabilities of being in any state of the Markov chain are governed by a set of ordinary differential equations, whose dimension…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
A central feature of quantum mechanics is that a measurement is intrinsically probabilistic. As a result, continuously monitoring a quantum system will randomly perturb its natural unitary evolution. The ability to control a quantum system…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
A central concern across the natural sciences is a quantitative understanding of the mechanism governing rare transitions between two metastable states. Recent research has uncovered a fundamental equality between the time-reversal…
Instanton theory is an established method to calculate rate constants of chemical reactions including atom tunneling. Technical and methodological improvements increased its applicability. Still, a large number of energy and gradient…