Related papers: Transition Path Theory from Biased Simulations
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…
Rare events such as conformational changes in biomolecules, phase transitions, and chemical reactions are central to the behavior of many physical systems, yet they are extremely difficult to study computationally because unbiased…
A central object in the computational studies of rare events is the committor function. Though costly to compute, the committor function encodes complete mechanistic information of the processes involving rare events, including reaction…
Transition path theory (TPT) is a mathematical framework for quantifying rare transition events between a pair of selected metastable states $A$ and $B$. Central to TPT is the committor function, which describes the probability to hit the…
Transition path theory provides a statistical description of the dynamics of a reaction in terms of local spatial quantities. In its original formulation, it is limited to reactions that consist of trajectories flowing from a reactant set A…
Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not…
Many chemical reactions can be formulated in terms of particle diffusion in a complex energy landscape. Transition path theory (TPT) is a theoretical framework for describing the direct (reaction) pathways from reactant to product states…
Rare event sampling algorithms are essential for understanding processes that occur infrequently on the molecular scale, yet they are important for the long-time dynamics of complex molecular systems. One of these algorithms, transition…
The reaction coordinate describing a transition between reactant and product is a fundamental concept in the theory of chemical reactions. Within transition-path theory, a quantitative definition of the reaction coordinate is found in the…
Transition path theory computes statistics from ensembles of reactive trajectories. A common strategy for sampling reactive trajectories is to control the branching and pruning of trajectories so as to enhance the sampling of low…
Many processes in nature such as conformal changes in biomolecules and clusters of interacting particles, genetic switches, mechanical or electromechanical oscillators with added noise, and many others are modeled using stochastic…
The conception of the conformal phase transiton (CPT), which is relevant for the description of non-perturbative dynamics in gauge theories, is introduced and elaborated. The main features of such a phase transition are established. In…
The Transition Path Theory (TPT) of complex systems has proven a robust means for statistically characterizing the ensemble of trajectories that connect any two preset flow regions, say $\mathcal A$ and $\mathcal B$, directly. More…
A set of analytical and computational tools based on transition path theory (TPT) is proposed to analyze flows in complex networks. Specifically, TPT is used to study the statistical properties of the reactive trajectories by which…
This dissertation unifies one of the central methods of classical rate calculation, `Transition-State Theory' (TST), with quantum mechanics, thereby deriving a rigorous `Quantum Transition-State Theory' (QTST). The resulting QTST is…
Given two distinct subsets $A,B$ in the state space of some dynamical system, Transition Path Theory (TPT) was successfully used to describe the statistical behavior of transitions from $A$ to $B$ in the ergodic limit of the stationary…
Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems. Current machine learning approaches use…
Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution 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…
In quantum multiparameter estimation, multiple to-be-estimated parameters are encoded in a quantum dynamics system by a unitary evolution. As the parameters vary, the system may undergo a topological phase transition (TPT). In this paper,…