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Micro- and nano-scale systems driven by rapid changes in control parameters (control protocols) dissipate significant energy. In the fast-protocol limit, we find that protocols that minimize dissipation at fixed duration are universally…
During the past century, biologists and mathematicians investigated two mechanisms underlying bacteria motion: the run phase during which bacteria move in straight lines and the tumble phase in which they change their orientation. When…
We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
Fish typically swim by periodic bending of their bodies. Bending seems to follow a universal rule; it occurs at about one-third from the posterior end of the fish body with a maximum bending angle of about $30^o$. However, the hydrodynamic…
We present a model study of gliding assays in which actin filaments are moved by non-processive myosin motors. We show that even if the power stroke of the motor protein has no lateral component, the filaments will rotate around their axis…
Molecular machines composed of coupled subsystems transduce free energy between different external reservoirs, in the process internally transducing energy and information. While subsystem efficiencies of these molecular machines have been…
Membrane tubes are important elements for living cells to organize many functions. Experiments have found that membrane tube can be extracted from giant lipid vesicles by a group of kinesin. How these motors cooperate in extracting the…
Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the…
A novel mechanism for the appearance of oriented processes is investigated with a flexible dynamical system overcoming barriers. Under non-equilibrium condition with external driving, reaction paths deviate from that at equilibrium with an…
In legged locomotion, the relationship between different gait behaviors and energy consumption must consider the full-body dynamics and the robot control as a whole, which cannot be captured by simple models. This work studies the robot…
Actin is one of the most studied cytoskeleton proteins showing a very rich span of structures. It can self-assemble actively into dynamical structures that govern the mechanical properties of the cell, its motility and its division.…
In recent literature there has been a lot of interest in the phenomena of noise induced transport in the absence of an average bias occurring in spatially periodic systems far from equilibrium. One of the main motivations in this area is to…
The precise details of how myosin-V coordinates the biochemical reactions and mechanical motions of its two head elements to engineer effective processive molecular motion along actin filaments remain unresolved. We compare a quantitative…
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…
The motility of a fish keratocyte on a flat substrate exhibits two distinct regimes: the non-migrating and the migrating one. In both configurations the shape is fixed in time and, when the cell is moving, the velocity is constant in…
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 show that active transport processes in biological systems can be understood through a local equilibrium description formulated at the mesoscale, the scale to describe stochastic processes. This new approach uses the method established…
The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and…
A novel assay based on micropatterning and time-lapse microscopy has been developed for the study of nuclear migration dynamics in cultured mammalian cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6 glioma and…