arXiv subjects

Ignacio Pagonabarraga

Publications and source records attributed to Ignacio Pagonabarraga.

119 records · Page 7Linked to original sources

arXiv2010

Dynamics of gravity driven three-dimensional thin films on hydrophilic-hydrophobic patterned substrates

We investigate numerically the dynamics of unstable gravity driven three-dimensional thin liquid films on hydrophilic-hydrophobic patterned substrates of longitudinal stripes and checkerboard arrangements. The thin film can be guided preferentially on hydrophilic longitudinal stripes, while fingers develop on adjacent hydrophobic stripes if their width is large enough. On checkerboard patterns, the film fingering occurs on hydrophobic domains, while lateral spreading is favoured on hydrophilic domains, providing a mechanism to tune the growth rate of the film. By means of kinematical arguments, we quantitatively predict the growth rate of the contact line on checkerboard arrangements, providing a first step towards potential techniques that control thin film growth in experimental setups.

cond-mat.soft↗

arXiv2007

Sedimentation of pairs of hydrodynamically interacting semiflexible filaments

We describe the effect of hydrodynamic interactions in the sedimentation of a pair of inextensible semiflexible filaments under a uniform constant force at low Reynolds numbers. We have analyzed the different regimes and the morphology of such polymers in simple geometries, which allow us to highlight the peculiarities of the interplay between elastic and hydrodynamic stresses. Cooperative and symmetry breaking effects associated to the geometry of the fibers gives rise to characteristic motion which give them distinct properties from rigid and elastic filaments.

cond-mat.soft↗

arXiv2006

Dynamic regimes of hydrodynamically coupled self-propelling particles

We analyze the collective dynamics of self-propelling particles (spps) which move at small Reynolds numbers including the hydrodynamic coupling to the suspending solvent through numerical simulations. The velocity distribution functions show marked deviations from Gaussian behavior at short times, and the mean-square displacement at long times shows a transition from diffusive to ballistic motion for appropriate driving mechanism at low concentrations. We discuss the structures the spps form at long times and how they correlate to their dynamic behavior.

cond-mat.soft↗

arXiv2006

Dynamic stability of spindles controlled by molecular motor kinetics

We analyze the role of the force-dependent kinetics of motor proteins in the stability of antiparallel arrays of polar filaments, such as those in the mitotic spindle. We determine the possible stable structures and show that there exists an instability associated to the collective behavior of motors that leads to the collapse of the spindle. Our analysis provides a general framework to understand several experimental observations in eukaryotic cell division.

q-bio.SC↗

arXiv2005

Lattice-Boltzmmann simulations of the sedimentation of charged disks

We report a series of Lattice-Boltzmann simulations of the sedimentation velocity of charged disks. In these simulations, we explicitly account for the hydrodynamic and electrostatic forces on disks and on their electrical double layer. By comparing our results with those for spheres with equal surface and charge, we can clarify the effect of the particle shape on the sedimentation process. We find that disks and spheres exhibit a different dependence of the sedimentation velocity on the Debye screening length. An analysis of the behavior of highly charged disks (beyond the scope of the linearized Poisson-Boltzmann equation) shows that, in that regime, the charge dependence of the sedimentation velocity of disks and spheres is similar. This suggests that, at high charge, the effective hydrodynamic shape of the disks becomes more spherical.

cond-mat.soft↗

arXiv2004

Polydisperse hard spheres at a hard wall

The structural properties of polydisperse hard spheres in the presence of a hard wall are investigated via Monte Carlo simulation and density functional theory (DFT). Attention is focussed on the local density distribution $ρ(σ,z)$, measuring the number density of particles of diameter $σ$ at a distance $z$ from the wall. The form of $ρ(σ,z)$ is obtained for bulk volume fractions $η_b=0.2$ and $η_b=0.4$ for two choices of the bulk parent distribution: a top-hat form, which we study for degrees of polydispersity $δ=11.5%$ and $δ=40.4%$, and a truncated Schulz form having $δ=40.7%$. Excellent overall agreement is found between the DFT and simulation results, particularly at $η_b=0.2$. A detailed analysis of $ρ(σ,z)$ confirms the presence of oscillatory size segregation effects observed in a previous DFT study (Pagonabarraga {\em et al.}, Phys. Rev. Lett. {\bf 84}, 911 (2000)). For large $δ$, the character of these oscillation is observed to depend strongly on the shape of the parent distribution. In the vicinity of the wall, attractive $σ$-dependent depletion interactions are found to greatly enhance the density of the largest particles. The local degree of polydispersity $δ(z)$ is suppressed in this region, while further from the wall it exhibits oscillations.

cond-mat.soft↗

arXiv2004

Discrete solution of the electrokinetic equations

We present a robust scheme for solving the electrokinetic equations. This goal is achieved by combining the lattice-Boltzmann method (LB) with a discrete solution of the convection-diffusion equation for the different charged and neutral species that compose the fluid. The method is based on identifying the elementary fluxes between nodes, which ensures the absence of spurious fluxes in equilibrium. We show how the model is suitable to study electro-osmotic flows. As an illustration, we show that, by introducing appropriate dynamic rules in the presence of solid interfaces, we can compute the sedimentation velocity (and hence the sedimentation potential) of a charged sphere. Our approach does not assume linearization of the Poisson-Boltzmann equation and allows us for a wide variation of the Peclet number.

cond-mat.stat-mech↗

arXiv2003

Kinetics of Fragmenting Freely Evolving Granular Gases

We investigate the effect of fragmentation on the homogeneous free cooling of inelastic hard spheres, using Boltzmann kinetic theory and Direct Monte Carlo simulations. We analyze in detail a model where dissipative collisions may subsequently lead to a break-up of the grains. With a given probability, two off-springs are then created from one of the two colliding partners, with conservation of mass, momentum and kinetic energy. We observe a scaling regime characterized by a single collisional average, that quantifies the deviations from Gaussian behaviour for the joint size and velocity distribution function. We also discuss the possibility of a catastrophe whereby the number of particles diverges in a finite time. This phenomenon appears correlated to a ``shattering'' transition marked by a delta singularity at vanishingly small grains for the rescaled size distribution.

cond-mat.stat-mech↗

arXiv2001

Lees-Edwards boundary conditions for lattice Boltzmann

Lees Edwards boundary conditions (LEbc) for Molecular Dynamics simulations are an extension of the well known periodic boundary conditions and allow the simulation of bulk systems in a simple shear flow. We show how the idea of LEbc can be implemented in lattice Boltzmann simulations and how LEbc can be used to overcome the problem of a maxinum shear rate that is limited to less than 1/Ly (with Ly the transverse system size) in traditional lattice Boltzmann implementations of shear flow.

cond-mat.soft↗

arXiv2001

Binary fluid demixing: The crossover region

By performing lattice Boltzmann simulations of a binary mixture, we scrutinize the dynamical scaling hypothesis for the spinodal decomposition of binary mixtures for the crossover region, i.e. the region of parameters in the growth curve where neither inertia nor viscous forces dominate the coarsening process. Our results give no evidence for a breakdown of scaling in this region, as might arise if the process were limited by molecular scale physics at the point of fluid pinch-off between domains. A careful data analysis allows us to refine previous estimates on the width of the crossover region which is somewhat narrower than previously reported.

cond-mat.soft↗

arXiv2000

Ludwig: A parallel Lattice-Boltzmann code for complex fluids

This paper describes `Ludwig', a versatile code for the simulation of Lattice-Boltzmann (LB) models in 3-D on cubic lattices. In fact `Ludwig' is not a single code, but a set of codes that share certain common routines, such as I/O and communications. If `Ludwig' is used as intended, a variety of complex fluid models with different equilibrium free energies are simple to code, so that the user may concentrate on the physics of the problem, rather than on parallel computing issues. Thus far, `Ludwig''s main application has been to symmetric binary fluid mixtures. We first explain the philosophy and structure of `Ludwig' which is argued to be a very effective way of developing large codes for academic consortia. Next we elaborate on some parallel implementation issues such as parallel I/O, and the use of MPI to achieve full portability and good efficiency on both MPP and SMP systems. Finally, we describe how to implement generic solid boundaries, and look in detail at the particular case of a symmetric binary fluid mixture near a solid wall. We present a novel scheme for the thermodynamically consistent simulation of wetting phenomena, in the presence of static and moving solid boundaries, and check its performance.

cond-mat.soft↗