Stability and Dynamics of Crystals and Glasses of Motorized Particles

Many of the large structures of the cell, such as the cytoskeleton, are assembled and maintained far from equilibrium. We study the stabilities of various structures for a simple model of such a far-from-equilibrium organized assembly in which spherical particles move under the influence of attached motors. From the variational solutions of the manybody master equation for Brownian motion with motorized kicking we obtain a closed equation for the order parameter of localization. Thus we obtain the transition criterion for localization and stability limits for the crystalline phase and frozen amorphous structures of motorized particles. The theory also allows an estimate of nonequilibrium effective temperatures characterizing the response and fluctuations of motorized crystals and glasses.Comment: 5 pages, 3 figure

Dynamics of folding in Semiflexible filaments

We investigate the dynamics of a single semiflexible filament, under the action of a compressing force, using numerical simulations and scaling arguments. The force is applied along the end to end vector at one extremity of the filament, while the other end is held fixed. We find that, unlike in elastic rods the filament folds asymmetrically with a folding length which depends only on the bending stiffness and the applied force. It is shown that this behavior can be attributed to the exponentially falling tension profile in the filament. While the folding time depends on the initial configuration, at late time, the distance moved by the terminal point of the filament and the length of the fold shows a power law dependence on time with an exponent 1/2.Comment: 13 pages, Late

Kinetic regulation of coated vesicle secretion

The secretion of vesicles for intracellular transport often rely on the aggregation of specialized membrane-bound proteins into a coat able to curve cell membranes. The nucleation and growth of a protein coat is a kinetic process that competes with the energy-consuming turnover of coat components between the membrane and the cytosol. We propose a generic kinetic description of coat assembly and the formation of coated vesicles, and discuss its implication to the dynamics of COP vesicles that traffic within the Golgi and with the Endoplasmic Reticulum. We show that stationary coats of fixed area emerge from the competition between coat growth and the recycling of coat components, in a fashion resembling the treadmilling of cytoskeletal filaments. We further show that the turnover of coat components allows for a highly sensitive switching mechanism between a quiescent and a vesicle producing membrane, upon a slowing down of the exchange kinetics. We claim that the existence of this switching behaviour, also triggered by factors such as the presence of cargo and variation of the membrane mechanical tension, allows for efficient regulation of vesicle secretion. We propose a model, supported by different experimental observations, in which vesiculation of secretory membranes is impaired by the energy consuming desorption of coat proteins, until the presence of cargo or other factors triggers a dynamical switch into a vesicle producing state.Comment: 6 pages 4 figures accepted at PNA

The Force-Velocity Relation for Growing Biopolymers

The process of force generation by the growth of biopolymers is simulated via a Langevin-dynamics approach. The interaction forces are taken to have simple forms that favor the growth of straight fibers from solution. The force-velocity relation is obtained from the simulations for two versions of the monomer-monomer force field. It is found that the growth rate drops off more rapidly with applied force than expected from the simplest theories based on thermal motion of the obstacle. The discrepancies amount to a factor of three or more when the applied force exceeds 2.5kT/a, where a is the step size for the polymer growth. These results are explained on the basis of restricted diffusion of monomers near the fiber tip. It is also found that the mobility of the obstacle has little effect on the growth rate, over a broad range.Comment: Latex source, 9 postscript figures, uses psfig.st

Theory on quench-induced pattern formation: Application to the isotropic to smectic-A phase transitions

During catastrophic processes of environmental variations of a thermodynamic system, such as rapid temperature decreasing, many novel and complex patterns often form. To understand such phenomena, a general mechanism is proposed based on the competition between heat transfer and conversion of heat to other energy forms. We apply it to the smectic-A filament growth process during quench-induced isotropic to smectic-A phase transition. Analytical forms for the buckling patterns are derived and we find good agreement with experimental observation [Phys. Rev. {\bf E55} (1997) 1655]. The present work strongly indicates that rapid cooling will lead to structural transitions in the smectic-A filament at the molecular level to optimize heat conversion. The force associated with this pattern formation process is estimated to be in the order of $10^{-1}$ piconewton.Comment: 9 pages in RevTex form, with 3 postscript figures. Accepted by PR

Statistical mechanics of semiflexible ribbon polymers

The statistical mechanics of a ribbon polymer made up of two semiflexible chains is studied using both analytical techniques and simulation. The system is found to have a crossover transition at some finite temperature, from a type of short range order to a fundamentally different sort of short range order. In the high temperature regime, the 2-point correlation functions of the object are identical to worm-like chains, while in the low temperature regime they are different due to a twist structure. The crossover happens when the persistence length of individual strands becomes comparable to the thickness of the ribbon. In the low temperature regime, the ribbon is observed to have a novel ``kink-rod'' structure with a mutual exclusion of twist and bend in contrast to smooth worm-like chain behaviour. This is due to its anisotropic rigidity and corresponds to an {\it infinitely} strong twist-bend coupling. The double-stranded polymer is also studied in a confined geometry. It is shown that when the polymer is restricted in a particular direction to a size less than the bare persistence length of the individual strands, it develops zigzag conformations which are indicated by an oscillatory tangent-tangent correlation function in the direction of confinement. Increasing the separation of the confining plates leads to a crossover to the free behaviour, which takes place at separations close to the bare persistence length. These results are expected to be relevant for experiments which involve complexation of two or more stiff or semiflexible polymers.Comment: 20 pages, 11 figures. PRE (in press

Energy Transduction of Isothermal Ratchets: Generic Aspects and Specific Examples Close to and Far from Equilibrium

We study the energetics of isothermal ratchets which are driven by a chemical reaction between two states and operate in contact with a single heat bath of constant temperature. We discuss generic aspects of energy transduction such as Onsager relations in the linear response regime as well as the efficiency and dissipation close to and far from equilibrium. In the linear response regime where the system operates reversibly the efficiency is in general nonzero. Studying the properties for specific examples of energy landscapes and transitions, we observe in the linear response regime that the efficiency can have a maximum as a function of temperature. Far from equilibrium in the fully irreversible regime, we find a maximum of the efficiency with values larger than in the linear regime for an optimal choice of the chemical driving force. We show that corresponding efficiencies can be of the order of 50%. A simple analytic argument allows us to estimate the efficiency in this irreversible regime for small external forces.Comment: 16 pages, 10 figure

Building a community to engineer synthetic cells and organelles from the bottom-up

Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences, especially with researchers who are attempting to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from different disciplines to highlight progress in this field, including areas where synthetic cells are having socioeconomic and technological impact. Conference participants also identified the challenges involved in designing, manipulating and creating synthetic cells with hierarchical organization and function. A key conclusion is the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives

Finding the Cell Center by a Balance of Dynein and Myosin Pulling and Microtubule Pushing: A Computational Study

By comparing computer modeling predictions with observations, we conclude that strong dynein and weaker myosin-generated forces pull the microtubules inward competing with microtubule plus-ends pushing the microtubule aster outward and that the balance of these forces positions the centrosome at the cell center