Related papers: On Committor Functions in Milestoning

Computing long-timescale kinetics of biomolecular processes remains a major challenge for atomistic simulations. A way out is to exploit local kinetic information to construct the global stationary flux across the reaction space. The…

The probability that a configuration of a physical system reacts, or transitions from one metastable state to another, is quantified by the committor function. This function contains richly detailed mechanistic information about transition…

Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…

In the study of stochastic systems, the committor function describes the probability that a system starting from an initial configuration $x$ will reach a set $B$ before a set $A$. This paper introduces an efficient and interpretable…

The committor function is a central object of study in understanding transitions between metastable states in complex systems. However, computing the committor function for realistic systems at low temperatures is a challenging task, due to…

The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have focused on analyzing the transition path ensemble using the…

We propose a novel approach for computing committor functions, which describe transitions of a stochastic process between metastable states. The committor function satisfies a backward Kolmogorov equation, and in typical high-dimensional…

The committor functions are central to investigating rare but important events in molecular simulations. It is known that computing the committor function suffers from the curse of dimensionality. Recently, using neural networks to estimate…

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…

For a transition between two stable states, the committor is the probability that the dynamics leads to one stable state before the other. It can be estimated from trajectory data by minimizing an expression for the transition rate that…

Milestoning is a computational procedure that reduces the dynamics of complex systems to memoryless jumps between intermediates, or milestones, and only retains some information about the probability of these jumps and the time lags between…

Atomistic simulations are widely used to investigate reactive processes but are often limited by the rare event problem due to kinetic bottlenecks. We recently introduced an enhanced sampling approach based on the committor function,…

The committor function is a central object for quantifying the transitions between metastable states of dynamical systems. Recently, a number of computational methods based on deep neural networks have been developed for computing the…

Milestoning is an efficient method for rare event kinetics calculation using short trajectory parallelization. Mean first passage time (MFPT) is the key kinetic output of Milestoning, whose accuracy crucially depends the initial…

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…

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…

We introduce a general definition of a quantum committor in order to clarify reaction mechanisms and facilitate control in processes where coherent effects are important. With a quantum committor, we generalize the notion of a transition…

Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective…

In recent years, several climate subsystems have been identified that may undergo a relatively rapid transition compared to the changes in their forcing. Such transitions are rare events in general, and simulating long-enough trajectories…

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…