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A massively parallel method to build large transition rate matrices from temperature accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state…
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.…
We present a numerical study of mixing and reaction efficiency in closed domains. In particular we focus our attention on laminar flows. In the case of inert transport the mixing properties of the flows strongly depend on the details of the…
Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in molecule number have attracted much attention. Here, a method based on a Markov process with a tridiagonal transition matrix is applied to the analysis…
This work aims to study the energy transfer and recombination processes in N$_{2}$$\left(^{1}\sum^{+}_{g}\right)$+N$\left(^{4}S_{u}\right)$ and O$_{2}$$\left(^{3}\sum^{+}_{g}\right)$+O$\left(^{3}P_{2}\right)$ chemical systems when the…
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single…
Nuclear coherent population transfer (NCPT) plays an important role in the exploration and application of atomic nuclei. How to achieve high-fidelity NCPT remains so far challenging. Here, we investigate the complete population transfer of…
Two roads are presently being followed in order to establish the existence of a liquid-gas phase transition in finite nuclear systems from nuclear reactions at high energy. The clean experiment of observing the thermodynamic properties of a…
We develop a tracking model predictive control (MPC) scheme for nonlinear systems using the linearized dynamics at the current state as a prediction model. Under reasonable assumptions on the linearized dynamics, we prove that the proposed…
Transfer entropy (TE) is a popular measure of information flow found to perform consistently well in different settings. Symbolic transfer entropy (STE) is defined similarly to TE but on the ranks of the components of the reconstructed…
Whereas the importance of transient dynamics to the functionality and management of complex systems has been increasingly recognized, most of the studies are based on models. Yet in realistic situations the models are often unknown and what…
We define the concept of an "open" Markov process, or more precisely, continuous-time Markov chain, which is one where probability can flow in or out of certain states called "inputs" and "outputs". One can build up a Markov process from…
To transport high-quality quantum state between two distant qubits through one-dimensional spin chains, the perfect state transfer (PST) method serves as the first choice, due to its natively perfect transfer fidelity that is independent of…
Power systems, including synchronous generator systems, are typical systems that strive for stable operation. In this article, we numerically study the fault transient process of a synchronous generator system based on the first benchmark…
To determine the effect of nonradiative excitation energy transfer on the fluorescence of a rigid multicomponent solution, a new analytical method was developed by treating this transfer as a time-resolved Markov chain (TRMC). In the TRMC…
The discrete wavelet packet transform (DWPT) and discrete wavelet transform (DWT) are used to extract and study the dynamics of coherent structures in a turbulent rotating fluid. Three-dimensional (3D) turbulence is generated by strong…
In literature on stochastic thermodynamics it is stated that for a system connected to multiple thermal reservoirs, the transition rates between two energy levels equals the sum of transition rates corresponding to each thermal bath the…
In turbulent flows, energy production is associated with highly organized structures, known as coherent structures. Since these structures are three-dimensional, their detection remains challenging in the most common situation, when…
We consider the rate of transition for a particle between two metastable states coupled to a thermal environment for various magnitudes of the coupling strength, using the recently proposed infrequent metadynamics approach (Tiwary and…
Mesoscopic models in the reaction-diffusion framework have gained recognition as a viable approach to describing chemical processes in cell biology. The resulting computational problem is a continuous-time Markov chain on a discrete and…