Related papers: Modeling work-speed-accuracy trade-offs in a stoch…
Physical systems driven away from equilibrium by an external controller dissipate heat to the environment; the excess entropy production in the thermal reservoir can be interpreted as a "cost" to transform the system in a finite time. The…
Speed limit for classical stochastic Markov processes with discrete states is studied. We find that a trade-off inequality exists between the speed of the state transformation and the entropy production. The dynamical activity determines…
Traffic models based on cellular automata have high computational efficiency because of their simplicity in describing unrealistic vehicular behavior and the versatility of cellular automata to be implemented on parallel processing. On the…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
The study of motility control by smart agents offers a promising platform for systematically exploring the fundamental physical constraints underlying the functioning of bio-inspired micro-machines operating far from equilibrium. Here, we…
We investigate the efficiency of an isothermal Brownian work-to-work converter engine, composed of a Brownian particle coupled to a heat bath at a constant temperature. The system is maintained out of equilibrium by using two external…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner.…
Accurate simulations of molecules require high-level electronic-structure theory in combination with rigorous methods for approximating the quantum dynamics. Machine-learning approaches can significantly reduce the computational expense of…
We propose and analyse an autonomous engine, which combines ideas from electronic transport and self-oscillating heat engines. It is based on the electron-shuttling mechanism in conjunction with a rotational degree of freedom. We focus in…
High-fidelity physics simulations are powerful tools in the design and optimization of charged particle accelerators. However, the computational burden of these simulations often limits their use in practice for design optimization and…
Torque is ubiquitous in many molecular systems, including collisions, chemical reactions, vibrations, electronic excitations and especially rotor molecules. We present a straightforward theoretical method based on forces acting on atoms and…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
Rotation of a single bacterial flagellar motor is powered by multiple stators tethered to the cell wall. In a "power-stroke" model the observed independence of the speed at low load on the number of stators is explained by a…
The energetic optimization problem, e.g., searching for the optimal switch- ing protocol of certain system parameters to minimize the input work, has been extensively studied by stochastic thermodynamics. In current work, we study this…
Properties of transport of molecular motors are investigated. A simplified model based on the concept of Brownian ratchets is applied. We analyze a stochastic equation of motion by means of numerical methods. The transport is systematically…
Recent experiments on the bacterial flagellar motor have shown that the structure of this nanomachine, which drives locomotion in a wide range of bacterial species, is more dynamic than previously believed. Specifically, the number of…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
FoF1-ATP synthase is the ubiquitous membrane-bound enzyme in mitochondria, chloroplasts and bacteria which provides the 'chemical energy currency' adenosine triphosphate (ATP) for cellular processes. In Escherichia coli ATP synthesis is…
The study of stochastic thermodynamic machines is one of the main topics in nonequilibrium thermodynamics. In this study, within the framework of Fokker-Planck equation, and using the method of characteristics of partial differential…