Related papers: Optimal rectification without forward-current supp…
Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying…
Living systems at the molecular scale are composed of many constituents with strong and heterogeneous interactions, operating far from equilibrium, and subject to strong fluctuations. These conditions pose significant challenges to…
Chemical gradients provide the primordial energy for biological functions by driving the mechanical movement of microscopic engines. Their thermodynamic properties remain elusive, especially concerning the dynamic change in energy demand in…
We demonstrate that confinement geometry can act as a rectifier in passive diffusion, optimally accelerating first-passage rates beyond free diffusion. Using analytic theory based on the Fick-Jacobs approach and Brownian dynamics…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
The efficiency at maximum power (EMP) for tight-coupling molecular motors is investigated within the framework of irreversible thermodynamics. It is found that the EMP depends merely on the constitutive relation between the thermodynamic…
Quadratic trapping potentials are widely used to experimentally probe biopolymers and molecular machines and drive transitions in steered molecular-dynamics simulations. Approximating energy landscapes as locally quadratic, we design…
In this study, through phenomenological comparison of the velocity-force data of processive motor proteins, including conventional kinesin, cytoplasmic dynein and myosin V, we found that, the ratio between motor velocities of two different…
A simple experimentally accessible realization of current rectification by molecules (molecular films) bridging metal electrodes is described. It is based on the spatial asymmetry of the molecule and requires only one resonant conducting…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Kinesin and related motor proteins utilize ATP fuel to propel themselves along the external surface of microtubules in a processive and directional fashion. We show that the observed step-like motion is possible through time varying charge…
The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular…
The intrinsic dynamics of most proteins are central to their function. Protein tyrosine kinases such as Abl1 undergo significant conformational changes that modulate their activity in response to different stimuli. These conformational…
Rectifying thermal white noise into directed motion is generally believed to require the consumption of energy or information, as exemplified by Maxwell's demon-type feedback controllers. Here we demonstrate a molecular rectification…
Here we generalize our previous model of molecular motors trafficking subdiffusing cargos in viscoelastic cytosol by (i) including mechanochemical coupling between cyclic conformational fluctuations of the motor protein driven by the…
In this paper we investigate the use of path-integral formalism and the concepts of entropy and traffic in the context of molecular motors. We show that together with time-reversal symmetry breaking arguments one can find bounds on…
We analyze experimental observations of microtubules undergoing small fluctuations about a "balance point" when mixed in solution of two different kinesin motor proteins, KLP61F and Ncd. It has been proposed that the microtubule movement is…
Two headed motor proteins, such as kinesin and dynein, hidrolyze environmental ATP in order to propel unidirectionally along cytoskeletal filaments such as microtubules. In the case of kinesin, protein heads bind primarily on the alpha…
We study fluctuating tilt Brownian ratchets based on fractional subdiffusion in sticky viscoelastic media characterized by a power law memory kernel. Unlike the normal diffusion case the rectification effect vanishes in the adiabatically…
In this paper, we propose a novel trajectory optimization algorithm for mobile manipulators under end-effector path, collision avoidance and various kinematic constraints. Our key contribution lies in showing how this highly non-linear and…