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Rony Granek

Publications and source records attributed to Rony Granek.

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Equilibrium fluctuations of a quasi-spherical vesicle: role of the membrane dissipation

We theoretically investigate the thermally-driven curvature and lipid density fluctuations of a quasi-spherical vesicle, accounting for the dissipation due to monolayer viscosity and intermonolayer friction. The theory predicts that membrane curvature makes long-wavelength undulations sensitive to membrane viscosity and speeds up the relaxation of the lipid density fluctuations. Implications for the dynamic roughness and Dynamic Structure Factor measurements of submicron liposomes on nano-second time scales are discussed. Specifically, a clear stretched-exponential relaxation regime may not exist, in contrast to the behavior of planar membranes for which an anomalous diffusion exponent of 2/3 has been predicted [Zilman and Granek, Phys. Rev. Lett. (1996)].

cond-mat.soft

Non-equilibrium dynamics of disordered fractal spring network with active forces

We investigate the non-equilibrium dynamics of active bead-spring critical percolation clusters under the action of monopolar and dipolar forces. Previously, Langevin dynamics simulations of Rouse-type dynamics were performed on a deterministic fractal -- the Sierpinski gasket -- and combined with analytical theory [Chaos {\bf 34}, 113107 (2024)]. To study disordered fractals, we use here the critical (bond) percolation infinite cluster of square and triangular lattices, where beads (occupying nodes) are connected by harmonic springs. Two types of active stochastic forces, modeled as random telegraph processes, are considered: force monopoles, acting on individual nodes in random directions, and force dipoles, where extensile or contractile forces act between pairs of nodes, forming dipole links. A dynamical steady state is reached where the network is dynamically swelled for force monopoles. The time-averaged mean square displacement (MSD) shows sub-diffusive behavior at intermediate times longer than the force correlation time, whose anomalous exponent is solely controlled by the spectral dimension $(d_s)$ of the fractal network yielding MSD $\sim t^{\nu}$, with $\nu=1-\frac{d_s}{2}$, similar to the thermal system and in accord with the general analytic theory. In contrast, dipolar forces require a diverging time to reach a steady state, depending on the fraction of dipoles, and lead to network shrinkage. Within a quasi-steady-state assumption, we find a saturation behavior at the same temporal regime. Thereafter, a second ballistic-like rise is observed for networks with a low fraction of dipole forces, followed by a linear, diffusive increase. The second ballistic rise is, however, absent in networks fully occupied with force dipoles. These two behaviors are argued to result from local rotations of nodes, which are either persistent or fluctuating.

cond-mat.soft

Active fractal networks with stochastic force monopoles and force dipoles: Application to subdiffusion of chromosomal loci

Motivated by the well-known fractal packing of chromatin, we study the Rouse-type dynamics of elastic fractal networks with embedded, stochastically driven, active force monopoles and force dipoles that are temporally correlated. We compute, analytically -- using a general theoretical framework -- and {\it via} Langevin dynamics simulations, the mean square displacement (MSD) of a network bead. Following a short-time superdiffusive behavior, force monopoles yield anomalous subdiffusion with an exponent identical to that of the thermal system. In contrast, force dipoles do not induce subdiffusion, and the early superdiffusive MSD crosses over to a relatively small, system-size-independent saturation value. In addition, we find that force dipoles may lead to "crawling" rotational motion of the whole network, reminiscent of that found for triangular micro-swimmers and consistent with general theories of the rotation of deformable bodies. Moreover, force dipoles lead to network collapse beyond a critical force strength, which persists with increasing system size, signifying a true first-order dynamical phase transition. We apply our results to the motion of chromosomal loci in bacteria and yeast cells' chromatin, where anomalous sub-diffusion, MSD$\sim t^ν$ with $ν\simeq 0.4$, was found in both normal and ATP-depleted cells, albeit with different apparent diffusion coefficients. We show that the combination of thermal, monopolar, and dipolar forces in chromatin is typically dominated by the active monopolar and thermal forces, explaining the observed normal cells vs the ATP-depleted cells behavior.

cond-mat.soft

Curvature fluctuations of fluid vesicles reveal hydrodynamic dissipation within the bilayer

The biological function of membranes is closely related to their softness, which is often studied through the membranes' thermally-driven fluctuations. The analysis commonly assumes that the relaxation rate of a pure bending deformation is determined by the competition between membrane bending rigidity and viscous dissipation in the surrounding medium. Here, we reexamine this assumption and demonstrate that viscous flows within the membrane dominate the dynamics of bending fluctuations of non-planar membranes with a radius of curvature smaller than the Saffman-Delbrück length. Using flickering spectroscopy of giant vesicles made of DPPC:Cholesterol mixtures and pure diblock-copolymer membranes, we experimentally detect the signature of membrane dissipation in curvature fluctuations, and show that membrane viscosity can be reliably obtained from the short time behavior of the shape time correlations. The results indicate that the DPPC:Cholesterol membranes behave as a Newtonian fluid, while polymer membranes exhibit more complex rheology. Our study provides physical insights into the time scales of curvature remodeling of biological and synthetic membranes.

cond-mat.soft

Kinetics of actin networks formation measured by time resolved particle-tracking microrheology

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. However, only very few studies characterize the kinetics of the active actin self-assembly process beyond the formation of an entangled network. Here, we follow actin polymerization kinetics and organization into entangled networks using time resolved passive microrheology. We establish a relationship between the initial concentration of monomers, the active polymerization and network formation kinetics, and the viscoelastic properties from the onset of actin polymerization upto the formation of a steady state entangled network. Surprisingly, we find that at high enough initial monomer concentrations the elastic modulus of the forming actin networks overshoots and then relaxes with a -2/5 power law, that we attribute to rearrangements of the network into a steady state structure.

cond-mat.soft

Comment on: "Dynamics of Phospholipid Membranes beyond Thermal Undulations"

I introduce an alternative interpretation for the short-time anomalous diffusion observed by Gupta et al. using neutron spin echo. The interpretation involves the Brochard-Lennon "red blood cell" mode to describe membrane thickness fluctuations, and yields an anomalous diffusion exponent 1/3 that is consistent with the experimental results.

cond-mat.soft

Membrane undulations in a structured fluid: Universal dynamics at intermediate length and time scales

The dynamics of membrane undulations inside a viscous solvent is governed by distinctive, anomalous, power laws. Inside a viscoelastic continuous medium these universal behaviors are modified by the specific bulk viscoelastic spectrum. Yet, in structured fluids the continuum limit is reached only beyond a characteristic correlation length. We study the crossover to this asymptotic bulk dynamics. The analysis relies on a recent generalization of the hydrodynamic interaction in structured fluids, which shows a slow spatial decay of the interaction toward the bulk limit. For membranes which are weakly coupled to the structured medium we find a wide crossover regime characterized by different, universal, dynamic power laws. We discuss various systems for which this behavior is relevant, and delineate the time regime over which it may be observed.

cond-mat.soft

Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies

We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed bubbles ("loops") is accounted for. Considering base-pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base-pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of "bubbles", as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.

cond-mat.soft