Related papers: Topological methods for searching barriers and rea…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
We analyze the efficiency of different methods for the calculation of reaction rates in the case of two simple analytical benchmark systems. Two classes of methods are considered: the first are based on the free energy calculation along a…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
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…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
Thermally activated escape over a potential barrier in the presence of periodic driving is considered. By means of novel time-dependent path-integral methods we derive asymptotically exact weak-noise expressions for both the instantaneous…
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…
Turbulent reacting flows occur in a variety of engineering applications such as chemical reactors and power generating equipment (gas turbines and internal combustion engines). Turbulent reacting flows are characterized by two main…
The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
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…
A topological computation method, called the MGSTD method, is applied to time-series data obtained from meteorological measurement. The method gives decomposition of the dynamics into invariant sets and gradient-like transitions between…
We construct algorithms and topological invariants that allow us to distinguish the topological type of a surface, as well as functions and vector fields for their topological equivalence. In the first part we discus the main structures…
Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…
We derive a novel efficient scheme to measure the rate constant of transitions between stable states separated by high free energy barriers in a complex environment within the framework of transition path sampling. The method is based on…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…