Related papers: Molecular Motor or Molecular Clock: A Question of …
We consider nano-sized artificial or biological machines working in steady state enforced by imposing non-equilibrium concentrations of solutes or by applying external forces, torques or electric fields. For unicyclic and strongly coupled…
We investigate a model of a stochastic engine operating cyclically at constant bath temperature, which consists of an overdamped Brownian harmonic oscillator that plays the role of working substance and is elastically coupled to an active…
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…
Molecular motors are specialized proteins which perform active, directed transport of cellular cargoes on cytoskeletal filaments. In many cases, cargo motion powered by motor proteins is found to be bidirectional, and may be viewed as a…
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…
Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between 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…
A cyclic nature of quantum mechanical clock is discussed as ``quantization of time." Quantum mechanical clock is seen to be equivalent to the relativistic classical clock.
Energy transfer plays a vital role in many natural and technological processes. In this work, we study the effects of mechanical motion on the excitation transfer through a chain of interacting molecules with application to biological…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
Movements of molecular motors on cytoskeletal filaments are described by directed walks on a line. Detachment from this line is allowed to occur with a small probability. Motion in the surrounding fluid is described by symmetric random…
Molecular motors power directed transport of cargoes within cells. Even if a single motor is sufficient to transport a cargo, motors often cooperate in small teams. We discuss the cooperative cargo transport by several motors theoretically…
We model the dynamics of a processive or rotary molecular motor using a renewal processes, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation…
In the literature of Electromagnetism, the electromotive force of a "circuit" is often defined as work done on a unit charge during a complete tour of the latter around the circuit. We explain why this statement cannot be generally regarded…
The hopping model for cargo transport by molecular motors introduced in Refs. goldman1, goldman2, is extended here in order to incorporate the movement of cargo-motor complexes. In this context, hopping process expresses the possibility for…
We study dynamics of a classical particle in a one-dimensional potential, which is composed of two periodic components, that are time-independent, have equal amplitudes and periodicities. One of them is externally driven by a random force…
Molecular communication (MC) is a model of information transmission where the signal is transmitted by information-carrying molecules through their physical transport from a transmitter to a receiver through a communication channel. Prior…
We investigate the model of "reversible ratchet" with interacting particles, introduced by us earlier [Europhys. Lett. 84, 50009 (2008)]. We further clarify the effect of efficiency enhancement due to interaction and show that it is of…
The dynamics of active matter driven by interacting molecular motors has a non-potential structure at the local scale. However, we show that there exists a quasi-potential effectively describing the collective self-organization of the…
We investigate an optomechanical system as a model of an autonomous mechanical pendulum clock in the quantum regime, whose operation relies only on incoherent (thermal) resources. The escapement of the clock, the mechanism that translates…