Biomedical subjects

D Marenduzzo

Publications and source records attributed to D Marenduzzo.

At least 19 recordsLinked to original sources

PubMed2006

Lattice Boltzmann algorithm to simulate isotropic-nematic emulsions.

We present lattice Boltzmann simulations of the dynamical equations of motion of a drop of isotropic fluid in a nematic liquid crystal solvent, both in the absence and in the presence of an electric field. The coupled equations we solve are the Beris-Edward equations for the dynamics of the tensor order parameter describing the nematic solvent, the Cahn-Hilliard equation for the concentration evolution, and the Navier-Stokes equations for the determination of the instantaneous velocity field. We implement the lattice Boltzmann algorithm to ensure that spurious velocities are close to zero in equilibrium. We first study the effects of the liquid crystal elastic constant, K, anchoring strength, W, and surface tension, sigma, on the shape of the droplet and on the director field texture in equilibrium. We then consider how the drop behaves as the director field is switched by an applied electric field. We also show that the algorithm allows us to follow the motion of a drop of isotropic fluid placed in a liquid crystal cell with a tilted director field at the boundaries.

Journal Article↗

PubMed2006

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.

Chromatin↗

PubMed2006

Stall, spiculate, or run away: The fate of fibers growing towards fluctuating membranes.

We study the dynamics of a growing semiflexible fiber approaching a membrane at an angle. At late times we find three regimes: fiber stalling, when growth stops, runaway, in which the fiber bends away from the membrane, and another regime in which spicules form. 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, and (iii) microtubules inside vesicles. We complement our analysis with 3D stochastic simulations.

Actin Cytoskeleton↗

PubMed2006

Permeative flows in cholesterics: shear and Poiseuille flows.

By using a lattice Boltzmann scheme that solves the Beris-Edwards equations of motion describing liquid-crystal hydrodynamics, we study the response of cholesterics to shear and Poiseuille flows. The geometry we focus on is a flow along the direction of the helical axis, which is known to give rise to permeation. For both shear and Poiseuille flow we find that the boundary conditions on the director field are crucial in determining the rheological properties of the liquid crystal. For helices pinned at the boundaries, a small forcing leads to a large viscosity increase whereas a stronger forcing induces a sharp decrease towards the Newtonian value. This shear thinning behavior is in agreement with experiments and previous analytic results. If, on the other hand, the director is free to rotate at the walls, different behaviors are found depending on the symmetry of the steady-state primary flow. Some of the cases considered are compared to a similar imposed flow but with the helix lying perpendicular to the plates, for which no viscosity increase is observed.

Journal Article↗

PubMed2006

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 biomimetic experiments with synthetic polymers inside artificial vesicles. Our results suggest that phages may have evolved to be roughly spherical in shape to optimize the speed of genome ejection, which is the first stage in infection.

Capsid↗

PubMed2006

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 < or =N < or =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, nonmonotonic functions of 1R. 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.

Computer Simulation↗

PubMed2005

Three-dimensional dynamic Monte Carlo simulations of elastic actin-like ratchets.

We present three-dimensional dynamic Monte Carlo simulations of the growth of a semiflexible fiber against a fluctuating obstacle. The natural reference for our numerical study are the elastic and Brownian ratchet models previously analyzed semianalytically. We find that the decay of the velocity versus applied load is exponential to a good degree of accuracy, provided we include in the load the drag force felt by the moving obstacle. If the fiber and obstacle only interact via excluded volume, there are small corrections to the Brownian ratchet predictions which suggest that tip fluctuations play a minor role. If on the other hand fiber and obstacle interact via a soft potential, the corrections are much larger when the obstacle diffuses slowly. This means that microscopic assumptions can profoundly affect the dynamics. We also identify and characterize a novel "pushing catastrophe"--which is distinct from the usual fiber buckling--in which the growth of the fiber decouples from the obstacle movement. The time distribution of catastrophes can be explained via an approximate analytical treatment, and our numerics suggest that the time taken to lose propulsive force is largely dependent on the fiber incidence angle. Our results are a first step in realizing numerical polymer models for the motion of sets or networks of semiflexible fibers close to a fluctuating membrane or obstacle.

Actins↗

PubMed2005

Form of growing strings.

Patterns and forms adopted by nature are often the results 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 nonequilibrium phenomenon has been fixed by evolution at the C terminus, the growing end of a nascent protein. These findings suggest how evolution may have built on the properties of a generic nonequilibrium growth process in favoring helical structures in nascent chains.

Biomimetic Materials↗

PubMed2005

Rheology of cholesteric blue phases.

Cholesteric blue phases are a spectacular example of disclination line networks. Here we numerically investigate their response 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 large. With increased forcing we find strong shear thinning corresponding to the disruption of the network. As the viscosity starts to drop, the imposed flow sets the network into motion. Disclinations break up and re-form with their neighbors along the flow.

Journal Article↗

PubMed2005

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 minimizing 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, semianalytic 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% (toward 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 blue phase I ( O-8 ) 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.

Journal Article↗

PubMed2005

A new interpolation formula for semiflexible polymers.

A new formula for the force vs. extension relation is derived from the discrete version of the so-called Worm-like chain model. This formula correctly fits some recent experimental data on polymer stretching. Moreover, we have compared our formula with a Monte Carlo simulation of a semiflexible polymer.

Algorithms↗

PubMed2004

Dynamics of polymer packaging.

We use the stochastic rotation dynamics algorithm to investigate the packaging of flexible and semiflexible polymers into a capsid that is permeable to solvent molecules. The model takes into account hydrodynamic interactions arising due to local flow. The flexible chain maintains a random configuration as it is being fed into the capsid, in contrast to the semiflexible chain, whose configuration is initially spool-like, becoming more random at high packing. We measure the packing rate, which is found to decrease with the percentage of the chain packed and highlight the difference between the flexible and semiflexible chains. Reflecting experiments, we find pauses in the packing process for individual chains as the motor loses grip of the fluctuating beads. We also find that hydrodynamics is important, in that the packaging rate is faster when flow is included.

Journal Article↗

PubMed2004

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.

Journal Article↗

PubMed2004

Interplay between shear flow and elastic deformations in liquid crystals.

We study shear flow in liquid crystal cells with elastic deformations using a lattice Boltzmann scheme that solves the full, three-dimensional Beris-Edwards equations of hydrodynamics. We consider first twisted and hybrid aligned nematic cells, in which the deformation is imposed by conflicting anchoring at the boundaries. We find that backflow renders the velocity profile non Newtonian, and that the director profile divides into two regions characterized by different director orientations. We next consider a cholesteric liquid crystal, in which a twist deformation is naturally present. We confirm the presence of secondary flow for small shear rates, and are able to follow the dynamical pathway of shear-induced unwinding, for higher shear rates. Finally, we analyze how the coupling between shear and elastic deformation can affect shear banding in an initially isotropic phase. We find that for a nematic liquid crystal, elastic distortions may cause an asymmetry in the dynamics of band formation, whereas for a cholesteric, shear can induce twist in an initially isotropic sample.

Journal Article↗

PubMed2004

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.

Colloids↗

PubMed2004

Stepwise unfolding of collapsed polymers.

Motivated by recent experimental data on DNA stretching in presence of polyvalent counterions, we study the force-induced unfolding of a homopolymer on and off lattice. In the fixed force ensemble the globule unravels via a series of steps due to surface effects which play an important role for finite-size chains. This holds both for flexible and stiff polymers. We discuss in a qualitative way how this result may impact on the interpretation of DNA stretching experiments showing peaks in the characteristic curves, by extracting from the raw data the corresponding elongation- versus-force characteristic curves. Furthermore, approximate analytical and numerical calculations, valid in a quasi-equilibrium fixed stretch ensemble, and if the initial low-temperature state is ordered in a spool, show that the average force versus elongation displays peaks related to the geometry of the initial configuration. We finally argue how the proposed mechanisms identified for the arising of peaks may couple in the experiments, and comment on the role of dynamic effects.

DNA↗

PubMed2003

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

We study the thermodynamics of an exactly solvable model of a self-interacting, partially directed self-avoiding walk 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 Theta transition. The transition is of second order and is characterized by new critical exponents that are determined by a careful numerical analysis. The usual polymer critical index nu on the critical line, and another one which we call zeta, takes a nontrivial value that is numerically close to 2/3.

Journal Article↗

PubMed2003

Stretching of a polymer below the theta point.

The unfolding of a polymer below the theta point when pulled by an external force is studied both in d=2 on the lattice and in d=3 off the lattice. At T=0 and for finite length chains, it is found that the globule unfolds via multiple steps, corresponding to transitions between different minima, in both cases. In d=3 one of these intermediates is a regular helix. In the infinite length limit, these steps have a qualitative effect only in d=2. The phase diagram in d=2 is determined via the transfer matrix. To rationalize these results, energy-entropy and renormalization group arguments are given.

Biopolymers↗