arXiv subjects

D. Marenduzzo

Publications and source records attributed to D. Marenduzzo.

At least 91 records · Page 5Linked to original sources

arXiv2006

Depletion effects and loop formation in self-avoiding polymers

Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the enhanced viscous friction. For short chains, the enhanced friction slows down looping, while, for longer chains, the depletion attraction renders it more frequent and persistent. We discuss the possible relevance of the findings for chromatin looping in living cells.

cond-mat.soft↗

arXiv2006

Stall, spiculate or runaway - the fate of fibers growing towards fluctuating membranes

We solve the dynamic equations of motion for a growing semi-flexible polymer, or fiber, approaching a fluctuating membrane at an angle. At late times we find three different regimes: fiber {\em stalling}, when fiber growth stops due to membrane resistence, {\em run-away}, in which the polymer bends away from the membrane, and another regime in which the membrane response is nonlinear and tubular membrane {\em spicules} are formed. We discuss which regions of the resulting `phase diagram' are explored by (i) single and bundled actin fibers in living cells, (ii) sickle hemoglobin fibers in red blood cells, and (iii) microtubules growing within artificial vesicles. We complement our analysis with full 3-dimensional stochastic simulations.

cond-mat.soft↗

arXiv2006

Polymer packaging and ejection in viral capsids: shape matters

We use a mesoscale simulation approach to explore the impact of different capsid geometries on the packaging and ejection dynamics of polymers of different flexibility. We find that both packing and ejection times are faster for flexible polymers. For such polymers a sphere packs more quickly and ejects more slowly than an ellipsoid. For semiflexible polymers, however, the case relevant to DNA, a sphere both packs and ejects more easily. We interpret our results by considering both the thermodynamics and the relaxational dynamics of the polymers. The predictions could be tested with bio-mimetic experiments with synthetic polymers inside artificial vesicles. Our results suggest that phages may have evolved to be roughly spherical in shape to optimise the speed of genome ejection, which is the first stage in infection.

cond-mat.soft↗

arXiv2006

Rheology of cholesteric blue phases

Blue phases of cholesteric liquid crystals offer a spectacular example of naturally occurring disclination line networks. Here we numerically solve the hydrodynamic equations of motion to investigate the response of three types of blue phases to an imposed Poiseuille flow. We show that shear forces bend and twist and can unzip the disclination lines. Under gentle forcing the network opposes the flow and the apparent viscosity is significantly higher than that of an isotropic liquid. With increased forcing we find strong shear thinning corresponding to the disruption of the defect network. As the viscosity starts to drop, the imposed flow sets the network into motion. Disclinations break-up and re-form with their neighbours in the flow direction. This gives rise to oscillations in the time-dependent measurement of the average stress.

cond-mat.soft↗

arXiv2005

Knotting of random ring polymers in confined spaces

Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with effective strategies for simplifying the geometrical complexity of ring conformations without altering their knot type. By these means we extend previous studies and characterize in detail how the probability to form a given prime or composite knot behaves in terms of the number of ring segments, $N$, and confining radius, $R$. For $ 50 \le N \le 450 $ we show that the probability of forming a composite knot rises significantly with the confinement, while the occurrence probability of prime knots are, in general, non-monotonic functions of 1/R. The dependence of other geometrical indicators, such as writhe and chirality, in terms of $R$ and $N$ is also characterized. It is found that the writhe distribution broadens as the confining sphere narrows.

cond-mat.soft↗

arXiv2005

On the form of growing strings

Patterns and forms adopted by Nature, such as the shape of living cells, the geometry of shells and the branched structure of plants, are often the result of simple dynamical paradigms. Here we show that a growing self-interacting string attached to a tracking origin, modeled to resemble nascent polypeptides in vivo, develops helical structures which are more pronounced at the growing end. We also show that the dynamic growth ensemble shares several features of an equilibrium ensemble in which the growing end of the polymer is under an effective stretching force. A statistical analysis of native states of proteins shows that the signature of this non-equilibrium phenomenon has been fixed by evolution at the C-terminus, the growing end of a nascent protein. These findings suggest that a generic non-equilibrium growth process might have provided an additional evolutionary advantage for nascent proteins by favoring the preferential selection of helical structures.

cond-mat.soft↗

arXiv2005

Physics of thick polymers

We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by a special three body interaction and impacts on the behaviour both locally and non-locally. When thick polymers undergo compaction due to an attractive self-interaction, we find a new type of phase transition between a compact phase and a swollen phase at zero temperature on increasing the thickness. In the vicinity of this transition, short tubes form space filling helices and sheets as observed in protein native state structures. Upon increasing the chain length, or the number of chains, we numerically find a crossover from secondary structure motifs to a quite distinct class of structures akin to the semi-crystalline phase of polymers or amyloid fibers in polypeptides.

cond-mat.soft↗

arXiv2005

Switching hydrodynamics in multi-domain, twisted nematic, liquid crystal devices

We study the switching dynamics in two-domain and four-domain twisted nematic liquid crystal devices. The equilibrium configuration of these devices involves the coexistence of regions characterised by different handedness of the inherent director twist. At the boundaries between these regions there are typically disclinations lines. The dynamics of the disclination lines controls the properties, and in particular the switching speed, of the devices. We describe their motion using a numerical solution of the Beris-Edwards equations of liquid crystal hydrodynamics. Hence we are able to explain why a conventional two-domain device switches off slowly and to propose a device design which circumvents this problem. We also explain the patterns of disclination creation and annihilation that lead to switching in the four-domain twisted nematic device.

cond-mat.soft↗

arXiv2005

Numerical calculations of the phase diagram of cubic blue phases in cholesteric liquid crystals

We study the static properties of cubic blue phases by numerically minimising the three-dimensional, Landau-de Gennes free energy for a cholesteric liquid crystal close to the isotropic-cholesteric phase transition. Thus we are able to refine the powerful but approximate, semi-analytic frameworks that have been used previously. We obtain the equilibrium phase diagram and discuss it in relation to previous results. We find that the value of the chirality above which blue phases appear is shifted by 20% (towards experimentally more accessible regions) with respect to previous estimates. We also find that the region of stability of the O5 structure -- which has not been observed experimentally -- shrinks, while that of BP I (O8-) increases thus giving the correct order of appearance of blue phases at small chirality. We also study the approach to equilibrium starting from the infinite chirality solutions and we find that in some cases the disclination network has to assemble during the equilibration. In these situations disclinations are formed via the merging of isolated aligned defects.

cond-mat.soft↗

arXiv2005

Continuum model for polymers with finite thickness

We consider the continuum limit of a recently-introduced model for discretized thick polymers, or tubes. We address both analytically and numerically how the polymer thickness influences the decay of tangent-tangent correlations and find how the persistence length scales with the thickness and the torsional rigidity of the tube centerline. At variance with the worm-like chain model, the phase diagram that we obtain for a continuous tube is richer; in particular, for a given polymer thickness there exists a threshold value for the centerline torsional rigidity separating a simple exponential decay of the tangent-tangent correlation from an oscillatory one.

cond-mat.stat-mech↗

arXiv2004

Permeative flows in cholesteric liquid crystals

We use lattice Boltzmann simulations to solve the Beris-Edwards equations of motion for a cholesteric liquid crystal subjected to Poiseuille flow along the direction of the helical axis (permeative flow). The results allow us to clarify and extend the approximate analytic treatments currently available. We find that if the cholesteric helix is pinned at the boundaries there is an enormous viscosity increase. If, instead, the helix is free the velocity profile is flattened but the viscosity is essentially unchanged. We highlight the importance of secondary flows and, for higher flow velocities, we identify a flow-induced double twist structure in the director field -- reminiscent of the texture characteristic of blue phases.

cond-mat.soft↗

arXiv2003

Lattice Boltzmann Algorithm for three-dimensional liquid crystal hydrodynamics

We describe a lattice Boltzmann algorithm to simulate liquid crystal hydrodynamics in three dimensions. The equations of motion are written in terms of a tensor order parameter. This allows both the isotropic and the nematic phases to be considered. Backflow effects and the hydrodynamics of topological defects are naturally included in the simulations, as are viscoelastic effects such as shear-thinning and shear-banding. We describe the implementation of velocity boundary conditions and show that the algorithm can be used to describe optical bounce in twisted nematic devices and secondary flow in sheared nematics with an imposed twist.

cond-mat.stat-mech↗

arXiv2003

Rheology of distorted nematic liquid crystals

We use lattice Boltzmann simulations of the Beris--Edwards formulation of nematodynamics to probe the response of a nematic liquid crystal with conflicting anchoring at the boundaries under shear and Poiseuille flow. The geometry we focus on is that of the hybrid aligned nematic (HAN) cell, common in devices. In the nematic phase, backflow effects resulting from the elastic distortion in the director field render the velocity profile strongly non-Newtonian and asymmetric. As the transition to the isotropic phase is approached, these effects become progressively weaker. If the fluid is heated just above the transition point, however, another asymmetry appears, in the dynamics of shear band formation.

cond-mat.soft↗

arXiv2003

Elasticity of semiflexible polymers with and without self-interactions

A {\it new} formula for the force vs extension relation is derived from the discrete version of the so called {\it worm like chain} model. This formula correctly fits some recent experimental data on polymer stretching and some numerical simulations with pairwise repulsive potentials. For a more realistic Lennard-Jones potential the agreement with simulations is found to be good when the temperature is above the $θ$ temperature. For lower temperatures a plateau emerges, as predicted by some recent experimental and theoretical results, and our formula gives good results only in the high force regime. We briefly discuss how other kinds of self-interactions are expected to affect the elasticity of the polymer.

cond-mat.stat-mech↗

arXiv2003

Mechanical unfolding of directed polymers in a poor solvent: novel critical exponents

We study the thermodynamics of an exactly solvable model of a self-interacting partially directed self-avoiding walk (DSAW) in two dimensions, when a force is applied on one end of the chain. The critical force for the unfolding is determined exactly, as a function of the temperature, below the $Θ$-transition. The transition is second order and characterized by new critical exponents which are determined by a careful numerical analysis. The usual polymer critical index $ν$ on the critical line, and another one, which we call $ζ$, take a non-trivial value which is numerically close to 2/3.

cond-mat.stat-mech↗

arXiv2002

DNA sequence from the unzipping force? : one mutation problem

The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the zipped from the unzipped regions. We propose a comparison method (``differential force microscope'') to detect mutations. Two lattice models are treated as specific examples.

cond-mat.stat-mech↗

arXiv2002

Stretching of a polymer below the Theta point

The unfolding of a polymer below the $θ$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple steps, corresponding to transitions between different minima, in both cases. In the infinite length limit, these intermediate minima have a qualitative effect only in $d=2$. The phase diagram in d=2 is determined using transfer matrix techniques. Energy-entropy and renormalization group arguments are given which predict a qualitatively correct phase diagram and a change of the order of the transition from d=2 to d=3.

cond-mat.stat-mech↗

arXiv2002

Geometry of compact tubes and protein structures

Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures the well-known characteristics of polymers and their phases but also provides a natural explanation for many of the key features of protein behavior. There are two natural length scales associated with a tube subject to compaction -- the thickness of the tube and the range of the attractive interactions. For short tubes, when these length scales become comparable, one obtains marginally compact structures, which are relatively few in number compared to those in the generic compact phase of polymers. The motifs associated with the structures in this new phase include helices, hairpins and sheets. We suggest that Nature has selected this phase for the structures of proteins because of its many advantages including the few candidate strucures, the ability to squeeze the water out from the hydrophobic core and the flexibility and versatility associated with being marginally compact. Our results provide a framework for understanding the common features of all proteins.

physics.bio-ph↗