Physics - Soft Condensed Matter Publications (50)

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Physics - Soft Condensed Matter Publications

Growth of hard--rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with kinetic Monte Carlo simulations and dynamic density functional theory while the continuum model is studied by dynamic Monte Carlo simulations equivalent to diffusive dynamics. The evolution of nematic order (excess of upright particles, "standing--up" transition) is an entropic effect and is mainly governed by the equilibrium solution, {rendering a continuous transition} (paper I, J. Read More


We show that a few cross-links (CLs) at specific points in a ring polymer can lead to a spatial organization of the chain. The specific pairs of cross-linked monomers were obtained from contact maps of bacterial DNA. So in effect, we establish how the DNA organizes itself hierarchically above the $100$ nm scale. Read More


Molecular Dynamics (MD) simulations are presented for a coarse-grained bead-spring model of ring polymer brushes under compression. Flexible polymer brushes are always disordered during compression, whereas semiflexible brushes tend to be ordered under sufficiently strong compression. Besides, the polymer monomer density of semiflexible polymer brush is very high near the polymer brush surface, inducing a peak value of free energy near the polymer brush surface. Read More


We consider the effect of introducing a small number of non-aligning agents in a well-formed flock. To this end, we modify a minimal model of active Brownian particles with purely repulsive (excluded volume) forces to introduce an alignment interaction that will be experienced by all the particles except for a small minority of "dissenters". We find that even a very small fraction of dissenters disrupts the flocking state. Read More


This paper investigates the relation between the density-scaling exponent $\gamma$ and the virial potential-energy correlation coefficient $R$ at several thermodynamic state points in three dimensions for the generalized $(2n,n)$ Lennard-Jones (LJ) system for $n=4, 9, 12, 18$, as well as for the standard $n=6$ LJ system in two, three, and four dimensions. The state points studied include many low-density states at which the virial potential-energy correlations are not strong. For these state points we find the roughly linear relation $\gamma\cong 3nR/d$ in $d$ dimensions. Read More


2017Jan
Affiliations: 1IEMN, 2IEMN, 3IEMN, 4IEMN, 5IEMN

In this paper, we study the dynamics of cylindrical armoured bubbles excited by mechanical vibrations. A step by step transition from cylindrical to spherical shape is reported as the intensity of the vibration is increased, leading to a reduction of the bubble surface and a dissemination of the excess particles. We demonstrate through energy balance that nonspherical armoured bubbles constitute a metastable state. Read More


Using Brownian dynamics (BD) simulations we investigate a dense system of charged colloids exposed to shear flow in a confined (slit-pore) geometry. The equilibrium system at zero flow consists of three, well-pronounced layers with square-like crystalline in-plane structure. We demonstrate that, for sufficiently large shear rates, the middle layer separates into two sublayers where the particles organize into moving lanes with opposite velocities. Read More


We investigate the ordering properties of vertically-vibrated monolayers of granular cylinders in a circular container at high packing fraction. In line with previous works by other groups, we identify liquid-crystalline ordering behaviour similar to that of two-dimensional hard rectangular particles subject to thermal equilibrium fluctuations. However, due to dissipation, there is a much stronger tendency for particles to cluster into parallel arrangements in the granular system. Read More


One of the hallmarks of active matter is its rich nonlinear dynamics and instabilities. Recent numerical simulations of phototactic algae showed that a thin jet of swimmers, obtained from hydrodynamic focusing inside a Poiseuille flow, was unstable to longitudinal perturbations with swimmers dynamically clustering (Jibuti et al., Phys. Read More


This paper presents data and a model for supercooled squalane's frequency-dependent shear modulus covering frequencies from 10 mHz to 30 kHz and temperatures from 168 K to 190 K; measurements are also reported for the glass phase down to 146 K. The data reveal a strong mechanical beta process. The data are fitted by an electrical equivalent-circuit model characterized by additivity of the dynamic shear compliances of the alpha and beta processes. Read More


The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation corrections. The direct integration simulation has several characteristics beneficial to free-energy calculations. Read More


Using data from contact maps of the DNA-polymer of {\em E. Coli} (at kilo base pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. By suitable Monte Carlo Simulations we show that the presence of these cross-links lead to a specific architecture and organization of the chain at large (micron) length scales of the DNA. Read More


2017Jan
Affiliations: 1CNISM and Dipartimento di Fisica e Astronomia 'G. Galilei'- Università di Padova, 2CNISM and Dipartimento di Fisica e Astronomia 'G. Galilei'- Università di Padova, 3CNISM and Dipartimento di Fisica e Astronomia 'G. Galilei'- Università di Padova, 4CNISM and Dipartimento di Fisica e Astronomia 'G. Galilei'- Università di Padova, 5NEST, Istituto Nanoscienze-CNR Pisa, 6NEST, Istituto Nanoscienze-CNR Pisa, 7NEST, Istituto Nanoscienze-CNR Pisa

We report on a comprehensive study of the unique adhesive properties of mats of polymethylmethacrylate (PMMA) nanofibers produced by electrospinning. Fibers are deposited on glass, varying the diameter and the relative orientation of the polymer filaments (random vs aligned configuration). While no significant variation is observed in the static contact angle (about 130{\deg}) of deposited water drops upon changing the average fiber diameter up to the micrometer scale, fibers are found to exhibit unequalled water adhesion. Read More


We compute the dielectric response of glasses starting from a microscopic system-bath Hamiltonian of the Zwanzig-Caldeira-Leggett type and using an ansatz from kinetic theory for the memory function in the resulting Generalized Langevin Equation. The resulting framework requires the knowledge of the vibrational density of states (DOS) as input, that we take from numerical evaluation of a marginally-stable harmonic disordered lattice, featuring a strong boson peak (excess of soft modes over Debye $\sim\omega_{p}^{2}$ law). The dielectric function calculated based on this ansatz is compared with experimental data for the paradigmatic case of glycerol at $T\lesssim T_{g}$. Read More


Amorphous solids or glasses are known to exhibit stretched-exponential decay over broad time intervals in several of their macroscopic observables: intermediate scattering function, dielectric relaxation modulus, time-elastic modulus etc. This behaviour is prominent especially near the glass transition. In this Letter we show, on the example of dielectric relaxation, that stretched-exponential relaxation is intimately related to the peculiar lattice dynamics of glasses. Read More


Reverse Monte Carlo modeling of liquid water, based on one neutron and one X-ray diffraction data set, applying also the most popular interatomic potential for water, SPC/E, has been performed. The strictly rigid geometry of SPC/E water molecules had to be loosened somewhat, in order to be able to produce a good fit to both sets of experimental data. In the final particle configurations, regularly shaped water molecules and straight hydrogen bonding angles were found to be consistent with diffraction results. Read More


We describe the basic properties and consequences of introducing active stresses, with principal direction along the local director, in cholesteric liquid crystals. The helical ground state is found to be linearly unstable to extensile stresses, without threshold in the limit of infinite system size, whereas contractile stresses are hydrodynamically screened by the cholesteric elasticity to give a finite threshold. This is confirmed numerically and the non-linear consequences of instability, in both extensile and contractile cases, are studied. Read More


Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as nanomotors. Experimental demonstration of chemotaxis for chemically-powered colloidal nanomotor was reported in the literature in the context of chemo-attraction in a still fluid or in a microfluidic channel where the gradient is sustained by a specific inlet geometry. Read More


We examine theoretically a new idea for spatial and temporal control of chemical reactions. When chemical reactions take place in a mixture of solvents, an external electric field can alter the local mixture composition thereby accelerating or decelerating the rate of reaction. The spatial distribution of electric field strength can be non-trivial and depends on the arrangement of the electrodes producing it. Read More


Assume a lower-dimensional solitonic structure embedded in a higher dimensional space, e.g., a 1D dark soliton embedded in 2D space, a ring dark soliton in 2D space, a spherical shell soliton in 3D space etc. Read More


We demonstrate an approach for background-free three-dimensional imaging of director fields in liquid crystals using stimulated Raman scattering microscopy. This imaging technique is implemented using a single femtosecond pulsed laser and a photonic crystal fiber, providing Stokes and pump frequencies needed to access Raman shifts of different chemical bonds of molecules and allowing for chemically selective and broadband imaging of both pristine liquid crystals and composite materials. Using examples of model three-dimensional structures of director fields, we show that the described technique is a powerful tool for mapping of long-range molecular orientation patterns in soft matter via polarized chemical-selective imaging. Read More


Living things avoid equilibrium using molecular machines. Such microscopic soft-matter objects encounter relatively large friction and fluctuations. We discuss design principles for effective molecular machine operation in this unfamiliar context. Read More


Electron paramagnetic resonance (EPR) spectra of 14N- and 15N-labelled perdeuterated TEMPONE radicals in water were measured at various radical concentrations and temperatures in the normal and supercooled states. EPR parameters of both nitroxide radicals were obtained by fitting the EPR spectra to spectral shape functions based on modified Bloch equations. From concentration dependences of EPR parameters describing spin dephasing, coherence transfer and hyperfine splitting, we determined linear concentration coefficients whose values depend on relative motion of radicals due to modulation of the Heisenberg spin exchange (HSE) and dipole-dipole (DD) interactions between them. Read More


We demonstrate facile optical manipulation of shape of birefringent colloidal microparticles made from liquid crystal elastomers. Using soft lithography and polymerization, we fabricate elastomeric microcylinders with weakly undulating director oriented on average along their long axes. These particles are infiltrated with gold nanospheres acting as heat transducers that allow for an efficient localized transfer of heat from a focused infrared laser beam to a submicrometer region within a microparticle. Read More


A promising approach in designing composite materials with unusual physical behavior combines solid nanostructures and orientationally ordered soft matter at the mesoscale. Such composites not only inherit properties of their constituents but also can exhibit emergent behavior, such as ferromagnetic ordering of colloidal metal nanoparticles forming mesoscopic magnetization domains when dispersed in a nematic liquid crystal. Here we demonstrate the optical patterning of domain structures and topological defects in such ferromagnetic liquid crystal colloids, which allows for altering their response to magnetic fields. Read More


A promising approach of designing mesostructured materials with novel physical behavior is to combine unique optical and electronic properties of solid nanoparticles with long-range ordering and facile response of soft matter to weak external stimuli. Here we design, practically realize, and characterize orientationally ordered nematic liquid crystalline dispersions of rod-like upconversion nanoparticles. Boundary conditions on particle surfaces, defined through surface functionalization, promote spontaneous unidirectional self-alignment of the dispersed rod-like nanoparticles, mechanically coupled to the molecular ordering direction of the thermotropic nematic liquid crystal host. Read More


We present an investigation of the effect of the interaction between a thin polystyrene film and its supporting substrate on its glass transition temperature (Tg). We modulate this interaction by depositing the film on end-tethered polystyrene grafted layers of controlled molecular parameters. By comparing Tg measurements versus film thickness for films deposited on different grafted layers and films deposited directly on a silicon substrate, we can conclude that there is no important effect of the film-subtrate interaction. Read More


Dynamics of active or self-propulsive Brownian particles in nonequilibrium status, has recently attracted great interest in many fields including biological entities and artificial micro/nanoscopic motors6. Understanding of their dynamics can provide insight into the statistical properties of biological and physical systems far from equilibrium. Generally, active Brownian particles can involve either translational or rotational motion. Read More


We present a generalized Landau-Brazovskii free energy for the solidification of chiral molecules on a spherical surface in the context of the assembly of viral shells. We encounter two types of icosahedral solidification transitions. The first type is a conventional first-order phase transition from the uniform to the icosahedral state. Read More


The ability of a feed-forward neural network to learn and classify different states of polymer configurations is systematically explored. Performing numerical experiments, we find that a simple network model can, after adequate training, recognize multiple structures, including gas-like coil, liquid-like globular, and crystalline anti-Mackay and Mackay structures. The network can be trained to identify the transition points between various states, which compare well with those identified by independent specific-heat calculations. Read More


Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and predicting protein structure and stability. Read More


Entropy generates stripe patterns in buckled colloidal monolayers. The Ising antiferromagnet on a deformable triangular lattice displays the same ground state as this colloidal system, but it remains unclear if ordering in the two systems is driven by the same geometric mechanism. By a real-space expansion we find that for buckled colloids bent stripes constitute the stable phase, whereas in the Ising antiferromagnet straight stripes are favored. Read More


We present a versatile setup for investigating the nanofluidic behavior of nanoparticles as a function of the gap distance between two confining surfaces. The setup is designed as an open system which operates with small amounts of dispersion of $\approx 20\,\mu$l, permits the use of coated and patterned samples, and allows high-numerical-aperture microscopy access. Piezo elements enable 5D relative positioning of the surfaces. Read More


We study numerically two-dimensional creeping viscoelastic flow past a biperiodic square array of cylinders within the Oldroyd B, fene-CR and fene-P constitutive models of dilute polymer solutions. Our results capture the initial mild decrease then dramatic upturn ('thickening') seen experimentally in the drag coefficient as a function of increasing Weissenberg number. By systematically varying the porosity of the flow geometry, we demonstrate two qualitatively different mechanisms underpinning this thickening effect: one that operates in the highly porous case of widely spaced obstacles, and another for more densely packed obstacles, with a crossover between these two mechanisms at intermediate porosities. Read More


Dense suspensions can exhibit an abrupt change in their viscosity in response to increasing shear rate. The origin of this discontinuous shear thickening (DST) has been ascribed to the transformation of lubricated contacts to frictional, particle-on-particle contacts. Recent research on the flowing and jamming behavior of dense suspensions has explored the intersection of ideas from granular physics and Stokesian fluid dynamics to better understand this transition from lubricated to frictional rheology. Read More


Systematic molecular dynamics studies, using three different water models and the OPLS-AA ethanol force field, of ethanol-water mixtures over the entire concentration range were reported in an earlier work, and the combinations that provided the best agreement with experimental X-ray diffraction data were selected for each mixture. These simulated systems are further analyzed in this work to examine cluster formation and percolation, using four different hydrogen bond definitions. Percolation analysis revealed that each mixture (even the one containing 80 mol % ethanol) is above the 3D percolation threshold, with fractal dimensions, df, between 2. Read More


It has recently been shown that yield in amorphous solids under oscillatory shear is a dynamical transition from asymptotically periodic to asymptotically chaotic, diffusive dynamics. However, the type and universality class of this transition are still undecided. Here we show that the diffusive behavior of the vector of coordinates of the particles comprising an amorphous solid when subject to oscillatory shear, is analogous to that of a particle diffusing in a percolating lattice, the so-called "ant in the labyrinth" problem, and that yield corresponds to a percolation transition in the lattice. Read More


The rapid expansion in the spectrum of two-dimensional (2D) materials has driven the efforts of research on the fabrication of 2D composites and heterostructures. Highly ordered structure of 2D materials provides an excellent platform for controlling the ultimate structure and properties of the composite material with precision. However, limited control over the structure of the adherent material and its interactions with highly ordered 2D materials results in defective composites with inferior performance. Read More


Water electrolysis performed in microsystems with a fast change of voltage polarity produces optically invisible nanobubbles containing H2 and O2 gases. In this form the gases are able to the reverse reaction of water formation. Here we report extreme phenomena observed in a millimeter-sized open system. Read More


Understanding the retention of hydrogen isotopes in liquid metals, such as lithium and tin, is of great importance in designing a liquid plasma-facing component in fusion reactors. However, experimental diffusivity data of hydrogen isotopes in liquid metals are still limited or controversial. We employ first-principles molecular dynamics simulations to predict diffusion coefficients of deuterium in liquid tin at temperatures ranging from 573 to 1673 K. Read More


A long elastic cylinder, radius $a$ and shear-modulus $\mu$, becomes unstable given sufficient surface tension $\gamma$. We show this instability can be simply understood by considering the energy, $E(\lambda)$, of such a cylinder subject to a homogenous longitudinal stretch $\lambda$. Although $E(\lambda)$ has a unique minimum, if surface tension is sufficient ($\Gamma\equiv\gamma/(a\mu)>\sqrt{32}$) it looses convexity in a finite region. Read More


Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Read More


Despite about forty years of investigations, the nature of the melting transition in two dimensions is not completely clear. In the framework of the most popular Berezinskii-Kosterlitz-Thouless-Halperin-Nelson-Young (BKTHNY) theory, 2D systems melt through two continuous Berezinskii-Kosterlitz-Thouless (BKT) transitions with intermediate hexatic phase. The conventional first-order transition is also possible. Read More


In this paper, we investigate how the drainage and rupture of surfactant-stabilised bubbles floating at the surface of a liquid pool depend on the concentration of surface-active molecules in water. Drainage measurements at the apex of bubbles indicate that the flow profile is increasingly plug-like as the surfactant concentration is decreased from several times the critical micellar concentration (cmc) to just below the cmc. High-speed observations of bubble bursting reveal that the position at which a hole nucleates in the bubble cap also depends on the surfactant concentration. Read More


Starting from a microscopic model of self-propelled hard spheres we use tools of non-equilibrium statistical mechanics and the kinetic theory of hard spheres to derive a Smoluchowski equation for interacting Active Brownian particles. We illustrate the utility of the statistical mechanics framework developed with two applications. First, we derive the steady state pressure of the hard sphere active fluid in terms of the microscopic parameters and second, we identify the critical density for the onset of motility-induced phase separation in this system. Read More


The separation of different kind of plastic particles is required in the process of waste recycling. For the separation drum processes passed through by a liquid are applicable. Thereby the separation is based on the principle that particles either sink or float in a liquid depending on their densities. Read More


We report on the nature of flow events for the gravity-driven discharge of glass beads through a hole that is small enough that the hopper is susceptible to clogging. In particular, we measure the average and standard deviation of the distribution of discharged masses as a function of both hole and grain sizes. We do so in air, which is usual, but also with the system entirely submerged under water. Read More


We show how active transport of ions can be interpreted as an entropy facilitated process. In this interpretation, the pore geometry through which substrates are transported can give rise to a driving force. This gives a direct link between the geometry and the changes in Gibbs energy required. Read More


We present an analysis for the ring closure probability of semiflexible polymers within the pure bend Worm Like Chain (WLC) model. The ring closure probability predicted from our analysis can be tested against fluorescent actin cyclization experiments.We also discuss the effect of ring closure on bend angle fluctuations in actin polymers. Read More