Proton transport and torque generation in rotary biomotors

We analyze the dynamics of rotary biomotors within a simple nano-electromechanical model, consisting of a stator part and a ring-shaped rotor having twelve proton-binding sites. This model is closely related to the membrane-embedded F$_0$ motor of adenosine triphosphate (ATP) synthase, which converts the energy of the transmembrane electrochemical gradient of protons into mechanical motion of the rotor. It is shown that the Coulomb coupling between the negative charge of the empty rotor site and the positive stator charge, located near the periplasmic proton-conducting channel (proton source), plays a dominant role in the torque-generating process. When approaching the source outlet, the rotor site has a proton energy level higher than the energy level of the site, located near the cytoplasmic channel (proton drain). In the first stage of this torque-generating process, the energy of the electrochemical potential is converted into potential energy of the proton-binding sites on the rotor. Afterwards, the tangential component of the Coulomb force produces a mechanical torque. We demonstrate that, at low temperatures, the loaded motor works in the shuttling regime where the energy of the electrochemical potential is consumed without producing any unidirectional rotation. The motor switches to the torque-generating regime at high temperatures, when the Brownian ratchet mechanism turns on. In the presence of a significant external torque, created by ATP hydrolysis, the system operates as a proton pump, which translocates protons against the transmembrane potential gradient. Here we focus on the F$_0$ motor, even though our analysis is applicable to the bacterial flagellar motor.Comment: 24 pages, 5 figure

Stretching short biopolymers by fields and forces

We study the mechanical properties of semiflexible polymers when the contour length of the polymer is comparable to its persistence length. We compute the exact average end-to-end distance and shape of the polymer for different boundary conditions, and show that boundary effects can lead to significant deviations from the well-known long-polymer results. We also consider the case of stretching a uniformly charged biopolymer by an electric field, for which we compute the average extension and the average shape, which is shown to be trumpetlike. Our results also apply to long biopolymers when thermal fluctuations have been smoothed out by a large applied field or force.Comment: 10 pages, 7 figure

A model for the orientational ordering of the plant microtubule cortical array

The plant microtubule cortical array is a striking feature of all growing plant cells. It consists of a more or less homogeneously distributed array of highly aligned microtubules connected to the inner side of the plasma membrane and oriented transversely to the cell growth axis. Here we formulate a continuum model to describe the origin of orientational order in such confined arrays of dynamical microtubules. The model is based on recent experimental observations that show that a growing cortical microtubule can interact through angle dependent collisions with pre-existing microtubules that can lead either to co-alignment of the growth, retraction through catastrophe induction or crossing over the encountered microtubule. We identify a single control parameter, which is fully determined by the nucleation rate and intrinsic dynamics of individual microtubules. We solve the model analytically in the stationary isotropic phase, discuss the limits of stability of this isotropic phase, and explicitly solve for the ordered stationary states in a simplified version of the model.Comment: 15 pages, 5 figure

The Continuum Directed Random Polymer

Motivated by discrete directed polymers in one space and one time dimension, we construct a continuum directed random polymer that is modeled by a continuous path interacting with a space-time white noise. The strength of the interaction is determined by an inverse temperature parameter beta, and for a given beta and realization of the noise the path evolves in a Markovian way. The transition probabilities are determined by solutions to the one-dimensional stochastic heat equation. We show that for all beta > 0 and for almost all realizations of the white noise the path measure has the same Holder continuity and quadratic variation properties as Brownian motion, but that it is actually singular with respect to the standard Wiener measure on C([0,1]).Comment: 21 page

Quenched central limit theorem for the stochastic heat equation in weak disorder

We continue with the study of the mollified stochastic heat equation in $d\geq 3$ given by $d u_{\epsilon,t}=\frac 12\Delta u_{\epsilon,t}+ \beta \epsilon^{(d-2)/2} \,u_{\epsilon,t} \,d B_{\epsilon,t}$ with spatially smoothened cylindrical Wiener process $B$, whose (renormalized) Feynman-Kac solution describes the partition function of the continuous directed polymer. In an earlier work (\cite{MSZ16}), a phase transition was obtained, depending on the value of $\beta>0$ in the limiting object of the smoothened solution $u_\epsilon$ as the smoothing parameter $\epsilon\to 0$ This partition function naturally defines a quenched polymer path measure and we prove that as long as $\beta>0$ stays small enough while $u_\epsilon$ converges to a strictly positive non-degenerate random variable, the distribution of the diffusively rescaled Brownian path converges under the aforementioned polymer path measure to standard Gaussian distribution.Comment: Minor revisio

Power spectra of TASEPs with a localized slow site

The totally asymmetric simple exclusion process (TASEP) with a localized defect is revisited in this article with attention paid to the power spectra of the particle occupancy N(t). Intrigued by the oscillatory behaviors in the power spectra of an ordinary TASEP in high/low density phase(HD/LD) observed by Adams et al. (2007 Phys. Rev. Lett. 99 020601), we introduce a single slow site with hopping rate q<1 to the system. As the power spectrum contains time-correlation information of the particle occupancy of the system, we are particularly interested in how the defect affects fluctuation in particle number of the left and right subsystems as well as that of the entire system. Exploiting Monte Carlo simulations, we observe the disappearance of oscillations when the defect is located at the center of the system. When the defect is off center, oscillations are restored. To explore the origin of such phenomenon, we use a linearized Langevin equation to calculate the power spectrum for the sublattices and the whole lattice. We provide insights into the interactions between the sublattices coupled through the defect site for both simulation and analytical results.Comment: 16 pages, 6 figures; v2: Minor revision

Entropic phase separation of linked beads

We study theoretically a model system of a transient network of microemulsion droplets connected by telechelic polymers and explain recent experimental findings. Despite the absence of any specific interactions between either the droplets or polymer chains, we predict that as the number of polymers per drop is increased, the system undergoes a first order phase separation into a dense, highly connected phase, in equilibrium with dilute droplets, decorated by polymer loops. The phase transition is purely entropic and is driven by the interplay between the translational entropy of the drops and the configurational entropy of the polymer connections between them. Because it is dominated by entropic effects, the phase separation mechanism of the system is extremely robust and does not depend on the particlular physical realization of the network. The discussed model applies as well to other polymer linked particle aggregates, such as nano-particles connected with short DNA linkers

Phase diagram of self-assembled rigid rods on two-dimensional lattices: Theory and Monte Carlo simulations

Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a two-dimensional system of particles with two bonding sites that, by decreasing temperature or increasing density, polymerize reversibly into chains with discrete orientational degrees of freedom and, at the same time, undergo a continuous isotropic-nematic (IN) transition. A complete phase diagram was obtained as a function of temperature and density. The numerical results were compared with mean field (MF) and real space renormalization group (RSRG) analytical predictions about the IN transformation. While the RSRG approach supports the continuous nature of the transition, the MF solution predicts a first-order transition line and a tricritical point, at variance with the simulation results.Comment: 12 pages, 10 figures, supplementary informatio

Compression modulus of macroscopic fiber bundles

We study dense, disordered stacks of elastic macroscopic fibers. These stacks often exhibit non-linear elasticity, due to the coupling between the applied stress and the internal distribution of fiber contacts. We propose a theoretical model for the compression modulus of such systems, and illustrate our method by studying the conical shapes frequently observed at the extremities of ropes and other fiber structures. studying the conical shapes frequently observed at theextremities of ropes and other fiber structures