相关论文: Toy model for molecular motors
A discrete-state model of the F1-ATPase molecular motor is developed which describes not only the dependences of the rotation and ATP consumption rates on the chemical concentrations of ATP, ADP, and inorganic phosphate, but also on…
We present a generalized energy-depot model in which the conversion rate of the internal energy into motion can be dependent on the position and the velocity of a particle. When the conversion rate is a general function of the velocity, the…
Catalysis-driven synthetic molecular motors operate in a loose mechanochemical coupling regime, one in which a decomposition of a fuel molecule does not reliably produce a forward step. In that regime, stochastic backward steps can…
Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1…
Theoretical physics is used for a toy model of molecular biology to assess conditions that lead to the edge of chaos (EOC) in a network of biomolecules. Results can enhance our ability to understand complex diseases and their treatment or…
The thermodynamic uncertainty relation provides an inequality relating any mean current, the associated dispersion and the entropy production rate for arbitrary non-equilibrium steady states. Applying it here to a general model of a…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
We study the flashing ratchet model of a Brownian motor, which consists in cyclical switching between the Fokker-Planck equation with an asymmetric ratchet-like potential and the pure diffusion equation. We show that the motor really…
The collective dynamics of $N$ weakly coupled processive molecular motors are considered theoretically. We show, using a discrete lattice model, that the velocity-force curves strongly depend on the effective dynamic interactions between…
Mean field approximation treats only coherent aspects of the evolution of a Bose Einstein condensate. However, in many experiments some atoms scatter out of the condensate. We study an analytic model of two counter-propagating atomic…
The traffic of molecular motors which interact through mutual exclusion is studied theoretically for half-open tube-like compartments. These half-open tubes mimic the shapes of axons. The mutual exclusion leads to traffic jams or density…
A transition rate model of cargo transport by $N$ molecular motors is proposed. Under the assumption of steady state, the force-velocity curve of multi-motor system can be derived from the force-velocity curve of single motor. Our work…
We study heat conduction in a one-dimensional chain of particles with longitudinal as well as transverse motions. The particles are connected by two-dimensional harmonic springs together with bending angle interactions. The problem is…
We introduce a discrete time microscopic single particle model for kinetic transport. The kinetics is modeled by a two-state Markov chain, the transport by deterministic advection plus a random space step. The position of the particle after…
Processive molecular motors which drive the traffic of organelles in cells move in a directed way along cytoskeletal filaments. On large time scales, they perform motor walks, i.e., peculiar random walks which arise from the repeated…
It is argued that the world is a dissipative dynamic system, a phase flow of which is formed by conformally-symplectic mapping. The key assumption is that the concept of energy in microcosm makes sense only for the steady motions…
A quantum mechanical model for the systems consisting of interacting bodies is considered. The model takes into account the noncommutativity of the space and impulse operators and the correlation equations for the indeterminacy of these…
We present a model of electron transport through a random distribution of interacting quantum dots embedded in a dielectric matrix to simulate realistic devices. The method underlying the model depends only on fundamental parameters of the…
Using molecular dynamics simulations, we study particle-transport in a system of interacting colloidal particles on a ring, where the system is driven by a time-dependent external potential, moving along the ring. We consider two driving…
We examine, using mixed classical-quantum electron-ion dynamics, electron transfer in a donor-acceptor-like molecular junction system based on polyacetylene. We identify two qualitatively-different transfer regimes: hopping and tunnelling.…