[ { "text": "Nonlinear mechanics of thermoreversibly associating dendrimer glasses: We model the mechanics of associating trivalent dendrimer network glasses\nwith a focus on their energy dissipation properties. Various combinations of\nsticky bond (SB) strength and kinetics are employed. The toughness\n(work-to-fracture) of these systems displays a surprising deformation-protocol\ndependence; different association parameters optimize different properties. In\nparticular, \"strong, slow\" SBs optimize strength, while \"weak, fast\" SBs\noptimize ductility via self-healing during deformation. We relate these\nobservations to breaking, reformation, and partner-switching of SBs during\ndeformation. These studies point the way to creating associating-polymer\nnetwork glasses with tailorable mechanical properties.", "category": "cond-mat_soft" }, { "text": "Quenches and crunchs: Does the system explore in aging the same part of\n the configuration space explored in equilibrium ?: Numerical studies are providing novel information on the physical processes\nassociated to physical aging. The process of aging has been shown to consist in\na slow process of explorations of deeper and deeper minima of the system\npotential energy surface. In this article we compare the properties of the\nbasins explored in equilibrium with those explored during the aging process\nboth for sudden temperature changes and for sudden density changes. We find\nthat the hypothesis that during the aging process the system explores the part\nof the configuration space explored in equilibrium holds only for shallow\nquenches or for the early aging dynamics. At longer times, systematic\ndeviations are observed. In the case of crunches, such deviations are much more\napparent.", "category": "cond-mat_soft" }, { "text": "Mechanisms and Rates of Nucleation of Amyloid Fibrils: The classical nucleation theory finds the rate of nucleation proportional to\nthe monomer concentration raised to the power, which is the `critical nucleaus\nsize', ${n_c}$. The implicit assumption, that amyloids nucleate in the same\nway, has been recently challenged by an alternative two-step mechanism, when\nthe soluble monomers first form a metastable aggregate (micelle), and then\nundergo conversion into the conformation rich in ${\\beta}$-strands that are\nable to form a stable growing nucleus for the protofilament. Here we put\ntogether the elements of extensive knowledge about aggregation and nucleation\nkinetics, using a specific case of A${\\beta_{1\\mathrm{-}42}}$ amyloidogenic\npeptide for illustration, to find theoretical expressions for the effective\nrate of amyloid nucleation. We find that at low monomer concentration in\nsolution, and also at low interaction energy between two peptide conformations\nin the micelle, the nucleation occurs via the classical route. At higher\nmonomer concentration, and a range of other interaction parameters between\npeptides, the two-step `aggregation-conversion' mechanism of nucleation takes\nover. In this regime, the effective rate of the process can be interpreted as a\npower of monomer concentration in a certain range of parameters, however, the\nexponent is determined by a complicated interplay of interaction parameters and\nis not related to the minimum size of the growing nucleus (which we find to be\n${\\sim}$ 7-8 for A${\\beta_{1-42}}$).", "category": "cond-mat_soft" }, { "text": "Rotational motion of a droplet induced by interfacial tension: Spontaneous rotation of a droplet induced by the Marangoni flow is analyzed\nin a two-dimensional system. The droplet with the small particle which supplies\na surfactant at the interface is considered. We calculated flow field around\nthe droplet using Stokes equation and found that advective nonlinearity breaks\nsymmetry for rotation. Theoretical calculation indicates that the droplet\nspontaneously rotates when the radius of the droplet is an appropriate size.\nThe theoretical results were validated through comparison with the experiments.", "category": "cond-mat_soft" }, { "text": "Vortex formation in a slowly rotating Bose-Einstein condensate confined\n in a harmonic-plus-gaussian laser trap: Motivated by the recent experiment at ENS [ V. Bretin, S. Stock, Y. Seurin\nand, J. Dalibard, Phys. Rev. Lett. {\\bf 92}, 050403 (2004)], we study a\nrotating (non-)interacting atomic Bose-Einstein condensate confined in a\nharmonic-plus-gaussian laser trap potential. By adjusting the amplitude of the\nlaser potential, one can make quadratic-plus-quartic potential,purely quartic\npotential, and quartic-minus-quadratic potential. We show that an interacting\nBose-Einstein condensate confined in a harmonic-plus-gaussian laser trap breaks\nthe rotational symmetry of the Hamiltonian when rotational frequency is greater\nthan one-half of the lowest energy surface mode frequency. We also show that by\nincreasing the amplitude of the gaussian laser trap, a vortex appears in a\nslowly rotating Bose-Einstein condensate. Moreover, one can also create a\nvortex in non-interacting Bose-Einstein condensate confined in\nharmonic-plus-gaussian laser potential.", "category": "cond-mat_soft" }, { "text": "Modeling liquid migration in active swollen gel spheres: Liquid migration in active soft solids is a very common phenomenon in Nature\nat different scales: from cells to leaves. It can be caused by mechanical as\nwell as chemical actions. The work focuses on the migration of liquid provoked\nby remodeling processes in an active impermeable gel sphere. Within this\ncontext, we present a consistent mathematical theory capable to gain a deep\nunderstanding of the phenomenon in both steady and transient conditions.", "category": "cond-mat_soft" }, { "text": "The elasto-/hydro-dynamics of quasicrystals with 12- and 18-fold\n symmetries in some soft matters and mathematical solutions: The observation recently of 12-fold quasicrystals in polymers, nanoparticle\nmixture and 12-fold and 18-fold quasicrystals in colloidal solutions are\nimportant events for the study of quasicrystals. To describe the mechanical\nbehaviour we propose a new solid-liquid phase quasicrystal model for some soft\nmatters including polymers and colloids. The so-called new solid-liquid phase,\nis a new phase model of anisotropic fluid, but different from liquid crystal\nphase, here the structure presents quasiperiodic symmetry. Based on the model,\nthe elasticity, fluidity and viscosity of the material have been studied, the\nrelevant mathematical theory has also been proposed. Some mathematical\nsolutions of the theory are discussed.", "category": "cond-mat_soft" }, { "text": "Heirarchical and synergistic self-assembly in composites of model\n Wormlike micellar-polymers and nanoparticles results in nanostructures with\n diverse morphologies: Using Monte Carlo simulations, we investigate the self-assembly of model\nnanoparticles inside a matrix of model equilibrium polymers (or matrix of\nWormlike micelles) as a function of the polymeric matrix density and the\nexcluded volume parameter between polymers and nanoparticles. In this paper, we\nshow morphological transitions in the system architecture via synergistic\nself-assembly of nanoparticles and the equilibrium polymers. In a synergistic\nself-assembly, the resulting morphology of the system is a result of the\ninteraction between both nanoparticles and the polymers, unlike the polymer\ntemplating method. We report the morphological transition of nanoparticle\naggregates from percolating network-like structures to non-percolating clusters\nas a result of the change in the excluded volume parameter between\nnanoparticles and polymeric chains. In parallel with the change in the\nself-assembled structures of nanoparticles, the matrix of equilibrium polymers\nalso shows a transition from a dispersed state to a percolating network-like\nstructure formed by the clusters of polymeric chains. We show that the shape\nanisotropy of the nanoparticle clusters formed is governed by the polymeric\ndensity resulting in rod-like, sheet-like or other anisotropic nanoclusters. It\nis also shown that the pore shape and the pore size of the porous network of\nnanoparticles can be changed by changing the minimum approaching distance\nbetween nanoparticles and polymers. We provide a theoretical understanding of\nwhy various nanostructures with very different morphologies are obtained.", "category": "cond-mat_soft" }, { "text": "Single-Trajectory Characterization of Active Swimmers in a Flow: We develop a maximum likelihood method to infer relevant physical properties\nof elongated active particles. Using individual trajectories of advected\nswimmers as input, we are able to accurately determine their rotational\ndiffusion coefficients and an effective measure of their aspect ratio, also\nproviding reliable estimators for the uncertainties of such quantities. We\nvalidate our theoretical construction using numerically generated active\ntrajectories upon no-flow, simple shear, and Poiseuille flow, with excellent\nresults. Being designed to rely on single-particle data, our method eases\napplications in experimental conditions where swimmers exhibit a strong\nmorphological diversity. We briefly discuss some of such ongoing experimental\napplications, specifically, in the characterization of swimming E.coli in a\nflow.", "category": "cond-mat_soft" }, { "text": "Efficient equilibration of confined and free-standing films of highly\n entangled polymer melts: Equilibration of polymer melts containing highly entangled long polymer\nchains in confinement or with free surfaces is a challenge for computer\nsimulations. We approach this problem by first studying polymer melts based on\nthe soft-sphere coarse-grained model confined between two walls with periodic\nboundary conditions in two directions parallel to the walls. Then we apply\nbackmapping to reinsert the microscopic details of the underlying bead-spring\nmodel. Tuning the strength of the wall potential, the monomer density of\nconfined polymer melts in equilibrium is kept at the bulk density even near the\nwalls. In a weak confining regime, we observe the same conformational\nproperties of chains as in the bulk melt showing that our confined polymer\nmelts have reached their equilibrated state. Our methodology provides an\nefficient way of equilibrating large polymer films with different thicknesses\nand is not confined to a specific underlying microscopic model. Switching off\nthe wall potential in the direction perpendicular to the walls, enables to\nstudy free-standing highly entangled polymer films or polymer films with one\nsupporting substrate.", "category": "cond-mat_soft" }, { "text": "Comment on \"Layering transition in confined molecular thin films:\n Nucleation and growth\": When fluid is confined between two molecularly smooth surfaces to a few\nmolecular diameters, it shows a large enhancement of its viscosity. From\nexperiments it seems clear that the fluid is squeezed out layer by layer. A\nsimple solution of the Stokes equation for quasi-two-dimensional confined flow,\nwith the assmption of layer-by-layer flow is found. The results presented here\ncorrect those in Phys. Rev. B, 50, 5590 (1994), and show that both the\nkinematic viscosity of the confined fluid and the coefficient of surface drag\ncan be obtained from the time dependence of the area squeezed out. Fitting our\nsolution to the available experimental data gives the value of viscosity which\nis ~7 orders of magnitude higher than that in the bulk.", "category": "cond-mat_soft" }, { "text": "Potential of Mean Force between a Spherical Particle Suspended in a\n Nematic Liquid Crystal and a Substrate: We consider a system where a spherical particle is suspended in a nematic\nliquid crystal confined between two walls. We calculate the liquid-crystal\nmediated potential of mean force between the sphere and a substrate by means of\nMonte Carlo simulations. Three methods are used: a traditional Monte Carlo\napproach, umbrella sampling, and a novel technique that combines canonical\nexpanded ensemble simulations with a recently proposed density of states\nformalism. The latter method offers clear advantages in that it ensures good\nsampling of phase space without prior knowledge of the energy landscape of the\nsystem. The resulting potential of mean force, computed as a function of the\nnormal distance between the sphere and a surface, suggests that the sphere is\nattracted to the surface, even in the absence of attractive molecular\ninteractions.", "category": "cond-mat_soft" }, { "text": "Conformational Properties of an Adsorbed Charged Polymer: The behavior of a strongly charged polymer adsorbed on an oppositely charged\nsurface of low-dielectric constant is formulated by the functional integral\nmethod. By separating the translational, conformational, and fluctuational\ndegrees of freedom, the scaling behaviors for both the height of the polymer\nand the thickness of the diffusion layer are determined. Unlike the results\npredicted by scaling theory, we identified the continuous crossover from the\nweak compression to the compression regime. All teh analytical results are\nfound to be consistent with Monte-Carlo simulations. Finally, an alternative\n(operational) definition of a charged polymer adsorption is proposed.", "category": "cond-mat_soft" }, { "text": "Reversibility and hysteresis of the sharp yielding transition of a\n colloidal glass under oscillatory shear: The mechanical response of glasses remains challenging to understand. Recent\nresults indicate that the oscillatory rheology of soft glasses is accompanied\nby a sharp non-equilibrium transition in the microscopic dynamics. Here, we use\nsimultaneous x-ray scattering and rheology to investigate the reversibility and\nhysteresis of the sharp sharp symmetry change from anisotropic solid to\nisotropic liquid dynamics observed in the oscillatory shear of colloidal\nglasses [D. V. Denisov, M. T. Dang, B. Struth, A. Zaccone, and P. Schall, Sci.\nRep. 5, 14359 (2015)]. We use strain sweeps with increasing and decreasing\nstrain amplitude to show that, in analogy to equilibrium transitions, this\nsharp symmetry change is reversible and exhibits systematic frequency-dependent\nhysteresis. Using the non-affine response formalism of amorphous solids, we\nshow that these hysteresis effects arise from frequency-dependent non-affine\nstructural cage rearrangements at large strain. These results consolidate the\nfirst-order like nature of the oscillatory shear transition and quantify\nrelated hysteresis effects both via measurements and theoretical modelling.", "category": "cond-mat_soft" }, { "text": "Colloids in Two-Dimensional Active Nematics: Conformal Cogs and\n Controllable Spontaneous Rotation: A major challenge in the study of active systems is to harness their\nnon-equilibrium dynamics into useful work. We address this by showing how to\ndesign colloids with controllable spontaneous propulsion or rotation when\nimmersed in active nematics. This is illustrated for discs with tilted\nanchoring and chiral cogs, for which we determine the nematic director through\nconformal mappings. Our analysis identifies two regimes of behaviour for chiral\ncogs: orientation-dependent handedness and persistent active rotation. Finally,\nwe provide design principles for active nematic colloids to achieve desired\nrotational dynamics.", "category": "cond-mat_soft" }, { "text": "Dispersing Nanoparticles in a Polymer Film via Solvent Evaporation: Large scale molecular dynamics simulations are used to study the dispersion\nof nanoparticles (NPs) in a polymer film during solvent evaporation. As the\nsolvent evaporates, a dense polymer-rich skin layer forms at the liquid/vapor\ninterface, which is either NP rich or poor depending on the strength of the\nNP/polymer interaction. When the NPs are strongly wet by the polymer, the NPs\naccumulate at the interface and form layers. However when the NPs are only\npartially wet by the polymer, most NPs are uniformly distributed in the bulk of\nthe polymer film with the dense skin layer serving as a barrier to prevent the\nNPs from moving to the interface. Our results point to a possible route to\nemploy less favorable NP/polymer interactions and fast solvent evaporation to\nuniformly disperse NPs in a polymer film, contrary to the common belief that\nstrong NP/polymer attractions are needed to make NPs well dispersed in polymer\nnanocomposites.", "category": "cond-mat_soft" }, { "text": "Mesoscopic theory for inhomogeneous mixtures: Mesoscopic density functional theory for inhomogeneous mixtures of sperical\nparticles is developed in terms of mesoscopic volume fractions by a systematic\ncoarse-graining procedure starting form microscopic theory. Approximate\nexpressions for the correlation functions and for the grand potential are\nobtained for weak ordering on mesoscopic length scales. Stability analysis of\nthe disordered phase is performed in mean-field approximation (MF) and beyond.\nMF shows existence of either a spinodal or a $\\lambda$-surface on the\nvolume-fractions - temperature phase diagram. Separation into homogeneous\nphases or formation of inhomogeneous distribution of particles occurs on the\nlow-temperature side of the former or the latter surface respectively,\ndepending on both the interaction potentials and the size ratios between\nparticles of different species. Beyond MF the spinodal surface is shifted, and\nthe instability at the $\\lambda$-surface is suppressed by fluctuations. We\ninterpret the $\\lambda$-surface as a borderline between homogeneous and\ninhomogeneous (containing clusters or other aggregates) structure of the\ndisordered phase. For two-component systems explicit expressions for the MF\nspinodal and $\\lambda$-surfaces are derived. Examples of interaction potentials\nof simple form are analyzed in some detail, in order to identify conditions\nleading to inhomogeneous structures.", "category": "cond-mat_soft" }, { "text": "Laminar Flow and Backrind Formation in Molding of Viscoelastic Silicone\n Rubber: When a thermoset polymer is cured at elevated temperature in a closed mold,\nthermal expansion can produce flaws in the finished product. Those flaws occur\nwhen rising internal pressure pushes the mold open and cured polymer flows out\nthrough gaps at the parting lines. Known as backrind, such defects are\nparticularly common in compression molding, where the increasing pressure of a\ntrapped, incompressible polymer can overwhelm the clamping pressure on the mold\nand expel polymer from the mold pocket. If that ejected material has already\ncured, it leaves behind structural damage and consequently a flaw in the\nfinished product.\n Backrind usually appears as a ragged seam line near the gap where cured\npolymer exited the mold. Its appearance is typically irregular and fragmented,\nsuggesting no particular pattern or uniformity to the process that produced it.\nIn such cases, the cured polymer acts predominantly as a viscoelastic solid as\nit is driven toward and through the parting line. The backrind's ragged\ncharacter results from tearing and fragmentation of that solid.\n It is possible, however, for the cured polymer to act predominantly as a\nviscoelastic liquid as it flows toward and through the parting line. Since the\nReynolds number is low, the flow is laminar and the backrind bears witness to\nthat laminar flow. More specifically, the backrind's observed shaped\ncorresponds to isochronous contours in the laminar flow toward the parting\nline, contours that can be predicted using computational fluid dynamics.", "category": "cond-mat_soft" }, { "text": "Phase transitions of a tethered membrane model on a torus with intrinsic\n curvature: A tethered surface model is investigated by using the canonical Monte Carlo\nsimulation technique on a torus with an intrinsic curvature. We find that the\nmodel undergoes a first-order phase transition between the smooth phase and the\ncrumpled one.", "category": "cond-mat_soft" }, { "text": "DNA versus RNA -- which shows higher electronic conduction?: In this study, we compare the charge transport properties of multiple (double\nstranded) dsRNA sequences with corresponding dsDNA sequences. Recent studies\nhave presented a contradictory picture of relative charge transport\nefficiencies in A-form DNA:RNA hybrids and dsDNA. Using a multiscale modelling\nframework, we compute conductance of dsDNA and dsRNA using Landauer formalism\nin coherent limit and Marcus-Hush theory in the incoherent limit. We find that\ndsDNA conducts better than dsRNA in both the charge transport regimes. Our\nanalysis shows that the structural differences in the twist angle and slide of\ndsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in\nthe incoherent hopping regime. In the coherent limit however, for the same base\npair length, the conductance of dsRNA is higher than that of dsDNA for the\nmorphologies where dsRNA has smaller end-to-end length relative to that of\ndsDNA.", "category": "cond-mat_soft" }, { "text": "Simple production of cellulose nanofibril microcapsules and the rheology\n of their suspensions: Microcapsules are commonly used in applications ranging from therapeutics to\npersonal care products due to their ability to deliver encapsulated species\nthrough their porous shells. Here, we demonstrate a simple and scalable\napproach to fabricate microcapsules with porous shells by interfacial\ncomplexation of cellulose nanofibrils and oleylamine, and investigate the\nrheological properties of suspensions of the resulting microcapsules. The\nsuspensions of neat capsules are viscous liquids whose viscosity increases with\nvolume fraction according to a modified Kreiger-Dougherty relation with a\nmaximum packing fraction of 0.73 and an intrinsic viscosity of 4. When\npolyacrylic acid (PAA) is added to the internal phase of the microcapsule,\nhowever, the suspensions become elastic and display yield stresses with\npower-law dependencies on capsule volume fraction and PAA concentration. The\nelasticity appears to originate from associative interactions between\nmicrocapsules induced by PAA that resides within the microcapsule shells. These\nresults demonstrate that it is possible to tune the rheological properties of\nmicrocapsule suspensions by changing only the composition of the internal\nphase, thereby providing a novel method to tailor complex fluid rheology.", "category": "cond-mat_soft" }, { "text": "1-D Cluster Array at the Three Phase Contact Line in Diluted Colloids\n Subjected to A.C. Electric Fields: Colloidal particles provide an efficient mean of building multiple scale\nstructured materials from colloidal dispersions. In this Brief Report, we\naccount for experimental evidence on the formation of a colloidal cluster array\nat a three-phase contact line. We study the influence of low frequency external\nalternating electric fields on a diluted colloidal dispersion opened to the\nair. We focus on the cluster formation and their evolution in the meniscus by\nmeasuring characteristic times and lengths. We observe that the clusters are\nseparated by a well-defined length and that, in our experimental conditions,\nthey survive between five a fifteen minutes. These new results could be of\ntechnological relevance in building tailored colloidal structures in\nnon-patterned substrates.", "category": "cond-mat_soft" }, { "text": "To grow or to shrink: A tale of two rubber balloons: Two identical rubber balloons are partially inflated with air (to different\nextent) and connected by a hose with a valve. It is found that depending on\nballoon volumes, when the valve is opened the air will flow either from the\nlarger (fuller) balloon to the smaller (emptier) balloon, or from the smaller\nballoon to the larger one. The phenomenon is explained in terms of the\nnon-ideal rubber elasticity of balloons. The full phase diagram for the air\nflow dynamics is constructed.", "category": "cond-mat_soft" }, { "text": "On the modulational stability of Gross-Pittaevskii type equations in 1+1\n dimensions: The modulational stability of the nonlinear Schr{\\\"o}dinger (NLS) equation is\nexamined in the cases with linear and quadratic external potential. This study\nis motivated by recent experimental studies in the context of matter waves in\nBose-Einstein condensates. The linear case can be examined by means of the\nTappert transformation and can be mapped to the NLS in the appropriate\n(constant acceleration) frame. The quadratic case can be examined by using a\nlens-type transformation that converts it into a regular NLS with an additional\nlinear growth term.", "category": "cond-mat_soft" }, { "text": "First-order phase transitions in lattice bilayers of Janus-like\n particles: Monte Carlo simulations: The first-order phase transitions in the lattice model of Janus-like\nparticles confined in slit-like pores are studied. We assume a cubic lattice\nwith molecules that can freely change their orientation on a lattice site.\nMoreover, the molecules can interact with the pore walls with\norientation-dependent forces. The performed calculations are limited to the\ncases of bilayers. Our emphasis is on the competition between the fluid-wall\nand fluid-fluid interactions. The oriented structures formed in the systems in\nwhich the fluid-wall interactions acting contrary to the fluid-fluid\ninteractions differ from those appearing in the systems with neutral walls or\nwith walls attracting the repulsive parts of fluid molecules.", "category": "cond-mat_soft" }, { "text": "Out-of-equilibrium interactions and collective locomotion of colloidal\n spheres with squirming of nematoelastic multipoles: Many living and artificial systems show a similar emergent behavior and\ncollective motions on different scales, starting from swarms of bacteria to\nsynthetic active particles, herds of mammals and crowds of people. What all\nthese systems often have in common is that new collective properties like\nflocking emerge from interactions between individual self-propelled or\nexternally driven units. Such systems are naturally out-of-equilibrium and\npropel at the expense of consumed energy. Mimicking nature by making\nself-propelled or externally driven particles and studying their individual and\ncollective motility may allow for deeper understanding of physical\nunderpinnings behind the collective motion of large groups of interacting\nobjects or beings. Here, using a soft matter system of colloids immersed into a\nliquid crystal, we show that resulting so-called nematoelastic multipoles can\nbe set into a bidirectional locomotion by external periodically oscillating\nelectric fields. Out-of-equilibrium elastic interactions between such colloids\nlead to collective flock-like behaviors, which emerge from time-varying\nelasticity-mediated interactions between externally driven propelling\nparticles. The repulsive elastic interactions in the equilibrium state can be\nturned into attractive interactions in the out-of-equilibrium state under\napplied electric fields. We probe this behavior at different number densities\nof colloidal particles and show that particles in a dense dispersion\ncollectively select the same direction of a coherent motion due to elastic\ninteractions between near neighbors. In our experimentally implemented design,\ntheir motion is highly ordered and without clustering or jamming often present\nin other colloidal transport systems, which is promising for technological and\nfundamental-science applications, like nano-cargo transport, out-of-equilibrium\nassembly and microrobotics.", "category": "cond-mat_soft" }, { "text": "Channel Flow of Smectic Films: The hydrodynamics of smectic films at an air-water interface is discussed,\nwith particular focus on the viscous response of the film under flow normal to\nthe layers. The corrections to the response functions of the smectic phase,\narising from the coupling between the flow and the smectic order parameter, are\ncalculated. The results for the effective viscosity are illustrated by\nanalysing smectic film flow in a channel geometry. Two limiting cases of the\nflow, namely, motion dominated by dislocation-induced shear-softening and\ndislocation-free motion dominated by the permeation mode of mass transfer, are\nstudied. The effect of drag from a finite depth liquid subphase is considered.\nThe results are compared to those for hexatic and liquid films.", "category": "cond-mat_soft" }, { "text": "Chiral oily streaks in a smectic-A liquid crystal: The liquid crystal octylcyanobiphenyl (8CB) was doped with the chiral agent\nCB15 and spin-coated onto a substrate treated for planar alignment of the\ndirector, resulting in a film of thickness several hundred nm in the smectic-A\nphase. In both doped and undoped samples, the competing boundary conditions -\nplanar alignment at the substrate and vertical alignment at the free surface -\ncause the liquid crystal to break into a series of flattened hemicylinders to\nsatisfy the boundary conditions. When viewed under an optical microscope with\ncrossed polarizers, this structure results in a series of dark and light\nstripes (\"oily streaks\") of period ~ 1 $\\mu$m. In the absence of chiral dopant\nthe stripes run perpendicular to the substrate's easy axis. However, when doped\nwith chiral CB15 at concentrations up to c = 4 wt-%, the stripe orientation\nrotates by a temperature-dependent angle $\\phi$ with respect to the c = 0\nstripe orientation, where $\\phi$ increases monotonically with c. $\\phi$ is\nlargest just below the nematic -- smectic-A transition temperature TNA and\ndecreases with decreasing temperature. As the temperature is lowered, $\\phi$\nrelaxes to a steady-state orientation close to zero within ~1$^\\circ$ C of TNA.\nWe suggest that the rotation phenomenon is a manifestation of the surface\nelectroclinic effect: The rotation is due to the weak smectic order parameter\nand resulting large director tilt susceptibility with respect to the smectic\nlayer normal near TNA, in conjunction with an effective surface electric field\ndue to polar interactions between the liquid crystal and substrate.", "category": "cond-mat_soft" }, { "text": "Can pulling cause right- to left-handed structural transitions in\n negatively supercoiled DNA double-helix?: The folding angle distribution of stretched and negatively supercoiled DNA\ndouble-helix is investigated based on a theoretical model we proposed earlier\n[H. Zhou et al., Phys. Rev. Lett. 82, 4560 (1999)]. It is shown that pulling\ncan transit a negatively supercoiled DNA double-helix from the right-handed\nB-form to a left-handed configuration which resembles DNA Z-form in some\nimportant respects. The energetics of this possible transition is calculated\nand the comparison with recent experimental observations are qualitatively\ndiscussed.", "category": "cond-mat_soft" }, { "text": "Anisotropic imbibition on surfaces patterned with polygonal posts: We present and interpret lattice Boltzmann simulations of thick films\nspreading on surfaces patterned with polygonal posts. We show that the\nmechanism of pinning and depinning differs with the direction of advance, and\ndemonstrate that this leads to anisotropic spreading within a certain range of\nmaterial contact angles.", "category": "cond-mat_soft" }, { "text": "Numerical study of the spherically-symmetric Gross-Pitaevskii equation\n in two space dimensions: We present a numerical study of the time-dependent and time-independent\nGross-Pitaevskii (GP) equation in two space dimensions, which describes the\nBose-Einstein condensate of trapped bosons at ultralow temperature with both\nattractive and repulsive interatomic interactions. Both time-dependent and\ntime-independent GP equations are used to study the stationary problems. In\naddition the time-dependent approach is used to study some evolution problems\nof the condensate. Specifically, we study the evolution problem where the trap\nenergy is suddenly changed in a stable preformed condensate. In this case the\nsystem oscillates with increasing amplitude and does not remain limited between\ntwo stable configurations. Good convergence is obtained in all cases studied.", "category": "cond-mat_soft" }, { "text": "Skinny emulsions take on granular matter: Our understanding of the structural features of foams and emulsions has\nadvanced significantly over the last 20 years. However, with a search for\n\"super-stable\" liquid dispersions, foam and emulsion science employs\nincreasingly complex formulations which create solid-like visco-elastic layers\nat the bubble/drop surfaces. These lead to elastic, adhesive and frictional\nforces between bubbles/drops, impacting strongly how they pack and deform\nagainst each other, asking for an adaptation of the currently available\nstructural description. The possibility to modify systematically the\ninterfacial properties makes these dispersions ideal systems for the\nexploration of soft granular materials with complex interactions.\n We present here a first systematic analysis of the structural features of\nsuch a system using a model silicone emulsion containing millimetre-sized\npolyethylene glycol drops (PEG). Solid-like drop surfaces are obtained by\npolymeric cross-linking reactions at the PEG-silicone interface. Using a novel\ndroplet-micromanipulator, we highlight the presence of elastic, adhesive and\nfrictional interactions between two drops. We then provide for the first time a\nfull tomographic analysis of the structural features of these emulsions. An\nin-depth analysis of the angle of repose, local volume fraction distributions,\npair correlation functions and the drop deformations for different skin\nformulations allow us to put in evidence the striking difference with\n\"ordinary\" emulsions having fluid-like drop surfaces. While strong analogies\nwith frictional hard-sphere systems can be drawn, these systems display a set\nof unique features due to the high deformability of the drops which await\nsystematic exploration.", "category": "cond-mat_soft" }, { "text": "Temperature distribution in a gas-solid fixed bed probed by rapid\n magnetic resonance imaging: Controlling the temperature distribution inside catalytic fixed bed reactors\nis crucial for yield optimization and process stability. Yet, in situ\ntemperature measurements with spatial and temporal resolution are still\nchallenging. In this work, we perform temperature measurements in a cylindrical\nfixed bed reactor by combining the capabilities of real-time magnetic resonance\nimaging (MRI) with the temperature-dependent proton resonance frequency (PRF)\nshift of water. Three-dimensional (3D) temperature maps are acquired while\nheating the bed from room temperature to 60~$^{\\circ}$C using hot air. The\nobtained results show a clear temperature gradient along the axial and radial\ndimensions and agree with optical temperature probe measurements with an\naverage error of $\\pm$ 1.5~$^{\\circ}$C. We believe that the MR thermometry\nmethodology presented here opens new perspectives for the fundamental study of\nmass and heat transfer in gas-solid fixed beds and in the future might be\nextended to the study of reactive gas-solid systems.", "category": "cond-mat_soft" }, { "text": "Statistical properties of a granular gas fluidized by turbulent air\n wakes: We perform experiments with a granular system that consists of a collection\nof identical hollow spheres (ping-pong balls). Particles rest on a horizontal\nmetallic grid and are confined within a circular region. Fluidization is\nachieved by means of a turbulent air current coming from below. Air flow is\nadjusted so that the balls do not elevate over the grid, as an approach to 2D\ndynamics. With a high-speed camera, we take images of the system. From these\nimages we can infer horizontal particle positions and velocities by means of\nparticle-tracking algorithms. With the obtained data we analyze: a) the\nsystematic measurement error in the determination of positions and velocities\nfrom our digital images; b) the degree of homogeneity achieved in our\nexperiments (which depends on possible deviations of the grid from the\nhorizontal and on the homogeneity of turbulent air wakes). Interestingly, we\nhave observed evidences of crystallization at high enough densities.", "category": "cond-mat_soft" }, { "text": "Transport of Particles in Liquid Crystals: Colloidal particles in a liquid crystal (LC) behave very differently from\ntheir counterparts in isotropic fluids. Elastic nature of the orientational\norder and surface anchoring of the director cause long-range anisotropic\ninteractions and lead to the phenomenon of levitation. The LC environment\nenables new mechanisms of particle transport that are reviewed in this work.\nAmong them the motion of particles caused by gradients of the director, and\neffects in the electric field: backflow powered by director reorientations,\ndielectrophoresis in LC with varying dielectric permittivity and LC-enabled\nnonlinear electrophoresis with velocity that depends on the square of the\napplied electric field and can be directed differently from the field\ndirection.", "category": "cond-mat_soft" }, { "text": "Packing of elastic wires in spherical cavities: We investigate the morphologies and maximum packing density of thin wires\npacked into spherical cavities. Using simulations and experiments, we find that\nordered as well as disordered structures emerge, depending on the amount of\ninternal torsion. We find that the highest packing densities are achieved in\nlow torsion packings for large systems, but in high torsion packings for small\nsystems. An analysis of both situations is given in terms of energetics and\ncomparison is made to analytical models of DNA packing in viral capsids.", "category": "cond-mat_soft" }, { "text": "Surface creasing of soft elastic continua as a Kosterlitz-Thouless\n transition: Harnessing a model from composite materials science, we show how point-like\ncusped surface features arise as quasi-particle excitations, termed \"ghost\nfibers\", on the surface of a homogeneous soft elastic material. These\ndeformations appear above a critical compressive strain at which ghost fiber\ndipoles unbind, analogous to vortices in the Kosterlitz-Thouless transition.\nFinite-length creases can be described in the same framework. Our predictions\nfor crease surface profiles and onset strain agree with previous experiments\nand simulations, and further experimental tests are proposed.", "category": "cond-mat_soft" }, { "text": "Realization of Bose-Einstein condensates in lower dimensions: Bose-Einstein condensates of sodium atoms have been prepared in optical and\nmagnetic traps in which the energy-level spacing in one or two dimensions\nexceeds the interaction energy between atoms, realizing condensates of lower\ndimensionality. The cross-over into two-dimensional and one-dimensional\ncondensates was observed by a change in aspect ratio and saturation of the\nrelease energy when the number of trapped atoms was reduced.", "category": "cond-mat_soft" }, { "text": "Pattern formation in two-dimensional hard-core/soft-shell systems with\n variable soft shell profiles: Hard-core/soft shell (HCSS) particles have been shown to self-assemble into a\nremarkably rich variety of structures under compression due to the simple\ninterplay between the hard-core and soft-shoulder length scales in their\ninteractions. Most studies in this area model the soft shell interaction as a\nsquare shoulder potential. Although appealing from a theoretical point of view,\nthe potential is physically unrealistic because there is no repulsive force in\nthe soft shell regime, unlike in experimental HCSS systems. To make the model\nmore realistic, here we consider HCSS particles with a range soft shell\npotential profiles beyond the standard square shoulder form and study the model\nusing both minimum energy calculations and Monte Carlo simulations. We find\nthat by tuning density and the soft shell profile, HCSS particles in the thin\nshell regime (i.e., shell to core ratio $r_1/r_0 \\leq \\sqrt{3}$) can form a\nlarge range of structures, including hexagons, chains, squares, rhomboids and\ntwo distinct zig-zag structures. Furthermore, by tuning the density and\n$r_1/r_0$, we find that HCSS particles with experimentally realistic linear\nramp soft shoulder repulsions can form honeycombs and quasicrystals with\n10-fold and 12-fold symmetry. Our study therefore suggests the exciting\npossibility of fabricating these exotic 2D structures experimentally through\ncolloidal self-assembly.", "category": "cond-mat_soft" }, { "text": "Template Dissolution Interfacial Patterning of Single Colloids for\n Nanoelectrochemistry and Nanosensing: Deterministic positioning and assembly of colloidal nanoparticles (NPs) onto\nsubstrates is a core requirement and a promising alternative to top down\nlithography to create functional nanostructures and nanodevices with intriguing\noptical, electrical, and catalytic features. Capillary-assisted particle\nassembly (CAPA) has emerged as an attractive technique to this end, as it\nallows controlled and selective assembly of a wide variety of NPs onto\npredefined topographical templates using capillary forces. One critical issue\nwith CAPA, however, lies in its final printing step, where high printing yields\nare possible only with the use of an adhesive polymer film. To address this\nproblem, we have developed a template dissolution interfacial patterning (TDIP)\ntechnique to assemble and print single colloidal AuNP arrays onto various\ndielectric and conductive substrates in the absence of any adhesion layer, with\nprinting yields higher than 98%. The TDIP approach grants direct access to the\ninterface between the AuNP and the target surface, enabling the use of\ncolloidal AuNPs as building blocks for practical applications. The versatile\napplicability of TDIP is demonstrated by the creation of direct electrical\njunctions for electro- and photoelectrochemistry and nanoparticle-on-mirror\ngeometries for single particle molecular sensing.", "category": "cond-mat_soft" }, { "text": "Dynamic Elastic Moduli in Magnetic Gels: Normal Modes and Linear\n Response: In the perspective of developing smart hybrid materials with customized\nfeatures, ferrogels and magnetorheological elastomers allow a synergy of\nelasticity and magnetism. The interplay between elastic and magnetic properties\ngives rise to a unique reversible control of the material behavior by applying\nan external magnetic field. Albeit few works have been performed on the\ntime-dependent properties so far, understanding the dynamic behavior is the key\nto model many practical situations, e.g. applications as vibration absorbers.\nHere we present a way to calculate the frequency-dependent elastic moduli based\non the decomposition of the linear response to an external stress in normal\nmodes. We use a minimal three-dimensional dipole-spring model to theoretically\ndescribe the magnetic and elastic interactions on the mesoscopic level.\nSpecifically, the magnetic particles carry permanent magnetic dipole moments\nand are spatially arranged in a prescribed way, before they are linked by\nelastic springs. An external magnetic field aligns the magnetic moments. On the\none hand, we study regular lattice-like particle arrangements to compare with\nprevious results in the literature. On the other hand, we calculate the dynamic\nelastic moduli for irregular, more realistic particle distributions. Our\napproach measures the tunability of the linear dynamic response as a function\nof the particle arrangement, the system orientation with respect to the\nexternal magnetic field, as well as the magnitude of the magnetic interaction\nbetween the particles. The strength of the present approach is that it\nexplicitly connects the relaxational modes of the system with the rheological\nproperties as well as with the internal rearrangement of the particles in the\nsample, providing new insight into the dynamics of these remarkable materials.", "category": "cond-mat_soft" }, { "text": "Dilute polymer solutions under shear flow: comprehensive qualitative\n analysis using a bead-spring chain model with a FENE-Fraenkel spring: Although the non-equilibrium behaviour of polymer solutions is generally well\nunderstood, particularly in extensional flow, there remain several unanswered\nquestions for dilute solutions in simple shear flow, and full quantitative\nagreement with experiments has not been achieved. For example, experimental\nviscosity data exhibit qualitative differences in shear-thinning exponents,\nshear rate for onset of shear-thinning and high-shear Newtonian plateaus\ndepending on polymer semiflexibility, contour length and solvent quality. While\npolymer models are able to incorporate all of these effects through various\nspring force laws, bending potentials, excluded volume (EV) potentials, and\nhydrodynamic interaction (HI), the inclusion of each piece of physics has not\nbeen systematically matched to experimentally observed behaviour. Furthermore,\nattempts to develop multiscale models (in the sense of representing an\narbitrarily small or large polymer chain) which can make quantitative\npredictions are hindered by the lack of ability to fully match the results of\nbead-rod models, often used to represent a polymer chain at the Kuhn step\nlevel, with bead-spring models, which take into account the entropic\nelasticity.In light of these difficulties, this work aims to develop a general\nmodel based on the so-called FENE-Fraenkel spring, originally formulated by\nLarson and coworkers [J. Chem. Phys. 124 (2006), 10.1063/1.2161210], which can\nspan the range from rigid rod to traditional entropic spring, as well as\ninclude a bending potential, EV and HI. As we show, this model can reproduce,\nand smoothly move between, a wide range of previously observed polymer solution\nrheology in shear flow.", "category": "cond-mat_soft" }, { "text": "The effect of an exterior electric field on the instability of\n dielectric plates: We investigate the theoretical nonlinear response, Hessian stability, and\npossible wrinkling behaviour of a voltage-activated dielectric plate immersed\nin a tank filled with silicone oil. Fixed rigid electrodes are placed on the\ntop and bottom of the tank, and an electric field is generated by a potential\ndifference between the electrodes. We solve the associated incremental boundary\nvalue problem of superimposed, inhomogeneous small-amplitude wrinkles,\nsignalling the onset of instability. We decouple the resulting bifurcation\nequation into symmetric and antisymmetric modes. For a neo-Hookean dielectric\nplate, we show that a potential difference between the electrodes can induce a\nthinning of the plate and thus an increase of its planar area, similar to the\nscenarios encountered when there is no silicone oil. However, we also find\nthat, depending on the material and geometric parameters, an increasing applied\nvoltage can also lead to a thickening of the plate, and thus a shrinking of its\narea. In that scenario, Hessian instability and wrinkling bifurcation may then\noccur spontaneously once some critical voltages are reached.", "category": "cond-mat_soft" }, { "text": "A sheet on deformable sphere: \"wrinklogami\" patterns suppress\n curvature-induced delamination: The adhesion of a stiff film onto a curved substrate often generates elastic\nstresses in the film that eventually give rise to its delamination. Here we\npredict that delamination of very thin films can be dramatically suppressed\nthrough tiny, smooth deformations of the substrate, dubbed here \"wrinklogami\",\nthat barely affect the macroscale topography. This \"pro-lamination\" effect\nreflects a surprising capability of smooth wrinkles to suppress compression in\nelastic films even when spherical or other doubly-curved topography is imposed,\nin a similar fashion to origami folds that enable construction of curved\nstructures from an unstretchable paper. We show that the emergence of a\nwrinklogami pattern signals a nontrivial isometry of the sheet to its planar,\nundeformed state, in the doubly asymptotic limit of small thickness and weak\ntensile load exerted by the adhesive substrate. We explain how such an\n\"asymptotic isometry\" concept broadens the standard usage of isometries for\ndescribing the response of elastic sheets to geomertric constraints and\nmechanical loads.", "category": "cond-mat_soft" }, { "text": "Temperature of maximum density and excess properties of short-chain\n alcohol aqueous solutions: A simplified model simulation study: We perform an extensive computational study of binary mixtures of water and\nshort-chain alcohols resorting to two-scale potential models to account for the\nsingularities of hydrogen bonded liquids. Water molecules are represented by a\nwell studied core softened potential which is known to qualitatively account\nfor a large number of water's characteristic anomalies. Along the same lines,\nalcohol molecules are idealized by dimers in which the hydroxyl groups interact\nwith each other and with water with a core softened potential as well.\nInteractions involving non-polar groups are all deemed purely repulsive. We\nfind that the qualitative behavior of excess properties (excess volume,\nenthalpy and constant pressure heat capacity) agrees with that found\nexperimentally for alcohols such as t-butanol in water. Moreover, we observe\nthat our simple solute under certain conditions acts as an \"structure-maker\",\nin the sense that the temperature of maximum density of the bulk water model\nincreases as the solute is added, i.e. the anomalous behavior of the solvent is\nenhanced by the solute.", "category": "cond-mat_soft" }, { "text": "Local structural features elucidate crystallization of complex\n structures: Complex crystal structures are composed of multiple local environments, and\nhow this type of order emerges spontaneously during crystal growth has yet to\nbe fully understood. We study crystal growth across various structures and\nalong different crystallization pathways, using self-assembly simulations of\nidentical particles that interact via multi-well isotropic pair potentials. We\napply an unsupervised machine learning method to features from\nbond-orientational order metrics to identify different local motifs present\nduring a given structure's crystallization process. In this manner, we\ndistinguish different crystallographic sites in highly complex structures.\nTailoring this newly developed order parameter to structures of varying\ncomplexity and coordination number, we study the emergence of local order along\na multi-step crystal growth pathway -- from a low-density fluid to a\nhigh-density, supercooled amorphous liquid droplet and to a bulk crystal. We\nfind a consistent under-coordination of the liquid relative to the average\ncoordination number in the bulk crystal. We use our order parameter to analyze\nthe geometrically frustrated growth of a Frank--Kasper phase and discover how\nstructural defects compete with the formation of crystallographic sites that\nare higher-coordinated than the liquid environments. The here-presented method\nfor classifying order on a particle-by-particle level have broad applicability\nto future studies of structural self-assembly and crystal growth, and they can\naid in the design of building blocks and for targeting pathways of formation of\nnovel soft-matter structures.", "category": "cond-mat_soft" }, { "text": "Bubble Statistics and Dynamics in Double-Stranded DNA: The dynamical properties of double-stranded DNA are studied in the framework\nof the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations\nare analyzed in terms of two probability functions describing coherently\nlocalized separations (\"bubbles\") of the double strand. We find that the\nresulting bubble distributions are more sharply peaked at the active sites than\nfound in thermodynamically obtained distributions. Our analysis ascribes this\nto the fact that the bubble life-times significantly afects the distribution\nfunction. We find that certain base-pair sequences promote long-lived bubbles\nand we argue that this is due to a length scale competition between the\nnonlinearity and disorder present in the system.", "category": "cond-mat_soft" }, { "text": "Thermalization of plastic flow versus stationarity of thermomechanical\n equilibrium in SGR theory: We discuss issues related to thermalization of plastic flow in the context of\nsoft glassy rheology (SGR) theory. An apparent problem with the theory in its\ncurrent form is that the stationarity of thermomechanical equilibrium obtained\nby requiring that its flow rule satisfy detailed balance in the absence of\napplied deformation requires plastic flow to be athermal. This prevents proper\napplication of SGR to small-molecule and polymer glasses where plastic flow is\noften well-thermalized. Clearly, one would like to have a SGR-like theory of\nthermalized plastic flow that satisfies stationarity. We discuss reasons why\nsuch a theory could prove very useful and clarify obstacles that must be\novercome in order to develop it.", "category": "cond-mat_soft" }, { "text": "Nucleation of stable cylinders from a metastable lamellar phase in a\n diblock copolymer melt: The nucleation of a droplet of stable cylinder phase from a metastable\nlamellar phase is examined within the single-mode approximation to the\nBrazovskii model for diblock copolymer melts. By employing a variational ansatz\nfor the droplet interfacial profile, an analytic expression for the interfacial\nfree-energy of an interface of arbitrary orientation between cylinders and\nlamellae is found. The interfacial free-energy is anisotropic, and is lower\nwhen the cylinder axis is perpendicular to the interface than when the\ncylinders lie along the interface. Consequently, the droplet shape computed via\nthe Wulff construction is lens-like, being flattened along the axis of the\ncylinders. The size of the critical droplet and the nucleation barrier are\ndetermined within classical nucleation theory. Near the lamellar/cylinder phase\nboundary, where classical nucleation theory is applicable, critical droplets of\nsize 30--400 cylinders across with aspect ratios of 4--10 and nucleation\nbarriers of 30--40 k_B T are typically found. The general trend is to larger\ncritical droplets, higher aspect ratios and smaller nucleation barriers as the\nmean-field critical point is approached.", "category": "cond-mat_soft" }, { "text": "The Origin of Persistent Shear Stress in Supercooled Liquids: We show that the long time tail of the shear stress autocorrelation, whose\ngrowth at large supercooling is responsible for the apparent divergence of the\nshear viscosity, is a direct result of a residual shear stress in the\nstructures associated with the local potential minima. We argue that the\nessential mechanical transition experienced by a liquid on cooling occurs at a\ntemperature well above the glass transition temperature and corresponds to the\ncrossover from the high temperature liquid to the viscous liquid, the latter\ncharacterised by stress relaxation dominated by the residual stress. Following\non from this observation, as the density is decreased, the local potential\nminima become unable to sustain any persistent stress (and, hence, support a\nglass transition), in a manner that can be explicitly connected to the\ninteractions between atoms. The reported crossover implies an associated change\nin the mechanism of dissipation in liquids and, hence, raises the prospect of a\ncoherent microscopic treatment of nonlinear rheology and the relationship\nbetween self diffusion and viscosity in supercooled liquids.", "category": "cond-mat_soft" }, { "text": "Active Viscoelastic Matter: from Bacterial Drag Reduction to Turbulent\n Solids: A paradigm for internally driven matter is the active nematic liquid crystal,\nwhereby the equations of a conventional nematic are supplemented by a minimal\nactive stress that violates time reversal symmetry. In practice, active fluids\nmay have not only liquid crystalline but also viscoelastic polymer degrees of\nfreedom. Here we explore the resulting interplay by coupling an active nematic\nto a minimal model of polymer rheology. We find that adding polymer can greatly\nincrease the complexity of spontaneous flow, but can also have calming effects,\nthereby increasing the net throughput of spontaneous flow along a pipe (a\n'drag-reduction' effect). Remarkably, active turbulence can also arise after\nswitching on activity in a sufficiently soft elastomeric solid.", "category": "cond-mat_soft" }, { "text": "Swimming statistics of cargo-loaded single bacteria: Burgeoning interest in the area of bacteria-powered micro robotic systems\nprompted us to study the dynamics of cargo transport by single bacteria. In\nthis paper, we have studied the swimming behaviour of oil-droplets attached as\na cargo to the cell bodies of single bacteria. The oil-droplet loaded bacteria\nexhibit super-diffusive motion which is characterized by high degree of\ndirectional persistence. Interestingly, bacteria could navigate even when\nloaded with oil-droplets as large as 8 microns with an effective increase in\nrotational drag by more than 2 orders when compared to free bacteria. Further,\nthe directional persistence of oil-droplet loaded bacteria was independent of\nthe cargo size.", "category": "cond-mat_soft" }, { "text": "Liquid-Gas phase transition in Bose-Einstein Condensates with time\n evolution: We study the effects of a repulsive three-body interaction on a system of\ntrapped ultra-cold atoms in Bose-Einstein condensed state. The stationary\nsolutions of the corresponding $s-$wave non-linear Schr\\\"{o}dinger equation\nsuggest a scenario of first-order liquid-gas phase transition in the condensed\nstate up to a critical strength of the effective three-body force. The time\nevolution of the condensate with feeding process and three-body recombination\nlosses has a new characteristic pattern. Also, the decay time of the dense\n(liquid) phase is longer than expected due to strong oscillations of the\nmean-square-radius.", "category": "cond-mat_soft" }, { "text": "An adaptive hierarchical domain decomposition method for parallel\n contact dynamics simulations of granular materials: A fully parallel version of the contact dynamics (CD) method is presented in\nthis paper. For large enough systems, 100% efficiency has been demonstrated for\nup to 256 processors using a hierarchical domain decomposition with dynamic\nload balancing. The iterative scheme to calculate the contact forces is left\ndomain-wise sequential, with data exchange after each iteration step, which\nensures its stability. The number of additional iterations required for\nconvergence by the partially parallel updates at the domain boundaries becomes\nnegligible with increasing number of particles, which allows for an effective\nparallelization. Compared to the sequential implementation, we found no\ninfluence of the parallelization on simulation results.", "category": "cond-mat_soft" }, { "text": "Novel self-assembled morphologies from isotropic interactions: We present results from particle simulations with isotropic medium range\ninteractions in two dimensions. At low temperature novel types of aggregated\nstructures appear. We show that these structures can be explained by\nspontaneous symmetry breaking in analytic solutions to an adaptation of the\nspherical spin model. We predict the critical particle number where the\nsymmetry breaking occurs and show that the resulting phase diagram agrees well\nwith results from particle simulations.", "category": "cond-mat_soft" }, { "text": "Interaction between Nearly Hard Colloidal Spheres at an Oil-Water\n Interface: We show that the interaction potential between sterically stabilized, nearly\nhard-sphere [poly(methylmethacrylate)-poly(lauryl methacrylate) (PMMA-PLMA)]\ncolloids at a water-oil interface has a negligible unscreened-dipole\ncontribution, suggesting that models previously developed for charged particles\nat liquid interfaces are not necessarily applicable to sterically stabilized\nparticles. Interparticle potentials, $U(r)$, are extracted from radial\ndistribution functions [$g(r)$, measured by fluorescence microscopy] via\nOrnstein-Zernike inversion and via a reverse Monte Carlo scheme. The results\nare then validated by particle tracking in a blinking optical trap. Using a\nBayesian model comparison, we find that our PMMA-PLMA data is better described\nby a screened monopole only rather than a functional form having a screened\nmonopole plus an unscreened dipole term. We postulate that the long range\nrepulsion we observe arises mainly through interactions between neutral holes\non a charged interface, i.e., the charge of the liquid interface cannot, in\ngeneral, be ignored. In agreement with this interpretation, we find that the\ninteraction can be tuned by varying salt concentration in the aqueous phase.\nInspired by recent theoretical work on point charges at dielectric interfaces,\nwhich we explain is relevant here, we show that a screened $\\frac{1}{r^2}$ term\ncan also be used to fit our data. Finally, we present measurements for\npoly(methyl methacrylate)-poly(12-hydroxystearic acid) (PMMA-PHSA) particles at\na water-oil interface. These suggest that, for PMMA-PHSA particles, there is an\nadditional contribution to the interaction potential. This is in line with our\noptical-tweezer measurements for PMMA-PHSA colloids in bulk oil, which indicate\nthat they are slightly charged.", "category": "cond-mat_soft" }, { "text": "Complex Memory Formation in Frictional Granular Media: Using numerical simulations it is shown that a jammed, random pack of soft\nfrictional grains can store an arbitrary waveform that is applied as a small\ntime-dependent shear while the system is slowly compressed. When the system is\ndecompressed at a later time, an approximation of the input waveform is\nrecalled in time-reversed order as shear stresses on the system boundaries.\nThis effect depends on friction between the grains, and is independent of some\naspects of the friction model. This type of memory could potentially be\nobservable in other types of random media that form internal contacts when\ncompressed.", "category": "cond-mat_soft" }, { "text": "Smectic-A and Smectic-C Phases and Phase Transitions in Liquid\n Crystal-Aerosil Gels: High-resolution X-ray scattering studies of the nonpolar thermotropic liquid\ncrystal 4-n-pentylphenylthiol-4'-n-octyloxybenzoate (\\bar{8}S5) in aerosil gel\nnano-networks reveal that the aerosil-induced disorder significantly alters\nboth the nematic to Smectic-A and Smectic-A to Smectic-C phase transitions. The\nlimiting Smectic-A correlation length follows a power-law dependence on the\naerosil density in quantitative agreement with the limiting lengths measured\npreviously in other Smectic-A liquid crystal gels. The Smectic-A to Smectic-C\nliquid crystalline phase transition is altered fundamentally by the presence of\nthe aerosil gel. The onset of the Smectic-C phase remains relatively sharp but\nthere is an extended coexistence region where Smectic-A and Smectic-C domains\ncan exist.", "category": "cond-mat_soft" }, { "text": "Experimental verification of Arcsine laws in mesoscopic non-equilibrium\n and active systems: A large number of processes in the mesoscopic world occur out of equilibrium,\nwhere the time course of a system evolution becomes immensely important since\nit is driven principally by dissipative effects. Non-equilibrium steady states\n(NESS) represent a crucial category in such systems, where relaxation\ntimescales are comparable to the operational timescales. In this study, we\nemploy a model NESS stochastic system which comprises of a colloidal\nmicroparticle, optically trapped in a viscous fluid, externally driven by a\ntemporally correlated noise, and show that time-integrated observables such as\nthe entropic current, the work done on the system or the work dissipated by it,\nfollow the three Levy arcsine laws [1], in the large time limit. We discover\nthat cumulative distributions converge faster to arcsine distributions when it\nis near equilibrium and the rate of entropy production is small, because in\nthat case the entropic current has weaker temporal autocorrelation. We study\nthis phenomenon changing the strength of the added noise or by perturbing our\nsystem with a flow field produced by a microbubble at close proximity to the\ntrapped particle. We confirm our experimental findings with theoretical\nsimulations of the systems. Our work provides an interesting insight into the\nNESS statistics of the meso-regime, where stochastic fluctuations play a\npivotal role.", "category": "cond-mat_soft" }, { "text": "Sensitivity of the stress response function to packing preparation: A granular assembly composed of a collection of identical grains may pack\nunder different microscopic configurations with microscopic features that are\nsensitive to the preparation history. A given configuration may also change in\nresponse to external actions such as compression, shearing etc. We show using a\nmechanical response function method developed experimentally and numerically,\nthat the macroscopic stress profiles are strongly dependent on these\npreparation procedures. These results were obtained for both two and three\ndimensions. The method reveals that, under a given preparation history, the\nmacroscopic symmetries of the granular material is affected and in most cases\nsignificant departures from isotropy should be observed. This suggests a new\npath toward a non-intrusive test of granular material constitutive properties.", "category": "cond-mat_soft" }, { "text": "Bending and Twisting Elasticity: a Revised Marko-Siggia Model on DNA\n Chirality: A revised Marko-Siggia elastic model for DNA double helix [Macromolecules 27,\n981 (1994)] is proposed, which includes the WLC bending energy and a new chiral\ntwisting energy term. It is predicted that the mean helical repeat length (HRL)\nfor short DNA rings increases with the decreasing of chain length; while for\nvery long chains, their mean HRL is the same, independent of both the chain\nlength and whether the ends are closed, it is longer than the value for\nrectilinear DNAs. Our results are in good agreement with experiments.", "category": "cond-mat_soft" }, { "text": "Dynamical properties of densely packed confined hard-sphere fluids: Numerical solutions of the mode-coupling theory (MCT) equations for a\nhard-sphere fluid confined between two parallel hard walls are elaborated. The\ngoverning equations feature multiple parallel relaxation channels which\nsignificantly complicate their numerical integration. We investigate the\nintermediate scattering functions and the susceptibility spectra close to\nstructural arrest and compare to an asymptotic analysis of the MCT equations.\nWe corroborate that the data converge in the $\\beta$-scaling regime to two\nasymptotic power laws, viz. the critical decay and the von Schweidler law. The\nnumerical results reveal a non-monotonic dependence of the power-law exponents\non the slab width and a non-trivial kink in the low-frequency susceptibility\nspectra. We also find qualitative agreement of these theoretical results to\nevent-driven molecular-dynamics simulations of polydisperse hard-sphere system.\nIn particular, the non-trivial dependence of the dynamical properties on the\nslab width is well reproduced.", "category": "cond-mat_soft" }, { "text": "The effect of chain polydispersity on the elasticity of disordered\n polymer networks: Due to their unique structural and mechanical properties,\nrandomly-crosslinked polymer networks play an important role in many different\nfields, ranging from cellular biology to industrial processes. In order to\nelucidate how these properties are controlled by the physical details of the\nnetwork (\\textit{e.g.} chain-length and end-to-end distributions), we generate\ndisordered phantom networks with different crosslinker concentrations $C$ and\ninitial density $\\rho_{\\rm init}$ and evaluate their elastic properties. We\nfind that the shear modulus computed at the same strand concentration for\nnetworks with the same $C$, which determines the number of chains and the\nchain-length distribution, depends strongly on the preparation protocol of the\nnetwork, here controlled by $\\rho_{\\rm init}$. We rationalise this dependence\nby employing a generic stress-strain relation for polymer networks that does\nnot rely on the specific form of the polymer end-to-end distance distribution.\nWe find that the shear modulus of the networks is a non-monotonic function of\nthe density of elastically-active strands, and that this behaviour has a purely\nentropic origin. Our results show that if short chains are abundant, as it is\nalways the case for randomly-crosslinked polymer networks, the knowledge of the\nexact chain conformation distribution is essential for predicting correctly the\nelastic properties. Finally, we apply our theoretical approach to published\nexperimental data, qualitatively confirming our interpretations.", "category": "cond-mat_soft" }, { "text": "Mechanics and force transmission in soft composites of rods in elastic\n gels: We report detailed theoretical investigations of the micro-mechanics and bulk\nelastic properties of composites consisting of randomly distributed stiff\nfibers embedded in an elastic matrix in two and three dimensions. Recent\nexperiments published in Physical Review Letters [102, 188303 (2009)] have\nsuggested that the inclusion of stiff microtubules in a softer, nearly\nincompressible biopolymer matrix can lead to emergent compressibility. This can\nbe understood in terms of the enhancement of the compressibility of the\ncomposite relative to its shear compliance as a result of the addition of stiff\nrod-like inclusions. We show that the Poisson's ratio $\\nu$ of such a composite\nevolves with increasing rod density towards a particular value, or {\\em fixed\npoint}, independent of the material properties of the matrix, so long as it has\na finite initial compressibility. This fixed point is $\\nu=1/4$ in three\ndimensions and $\\nu=1/3$ in two dimensions. Our results suggest an important\nrole for stiff filaments such as microtubules and stress fibers in cell\nmechanics. At the same time, our work has a wider elasticity context, with\npotential applications to composite elastic media with a wide separation of\nscales in stiffness of its constituents such as carbon nanotube-polymer\ncomposites, which have been shown to have highly tunable mechanics.", "category": "cond-mat_soft" }, { "text": "Dynamic correlations in Brownian many-body systems: For classical Brownian systems driven out of equilibrium we derive\ninhomogeneous two-time correlation functions from functional differentiation of\nthe one-body density and current with respect to external fields. In order to\nallow for appropriate freedom upon building the derivatives, we formally\nsupplement the Smoluchowski dynamics by a source term, which vanishes at the\nphysical solution. These techniques are applied to obtain a complete set of\ndynamic Ornstein-Zernike equations, which serve for the development of\napproximation schemes. The rules of functional calculus lead naturally to\nnon-Markovian equations of motion for the two-time correlators. Memory\nfunctions are identified as functional derivatives of a unique space- and\ntime-nonlocal dissipation power functional.", "category": "cond-mat_soft" }, { "text": "Localization transition of random copolymers at interfaces: We consider adsorption of random copolymer chains onto an interface within\nthe model of Garel et al. Europhysics Letters 8, 9 (1989). By using the replica\nmethod the adsorption of the copolymer at the interface is mapped onto the\nproblem of finding the ground state of a quantum mechanical Hamiltonian. To\nstudy this ground state we introduce a novel variational principle for the\nGreen's function, which generalizes the well-known Rayleigh-Ritz method of\nQuantum Mechanics to nonstationary states. Minimization with an appropriate\ntrial Green's function enables us to find the phase diagram for the\nlocalization-delocalization transition for an ideal random copolymer at the\ninterface.", "category": "cond-mat_soft" }, { "text": "Determining the Anchoring Strength of a Capillary Using Topological\n Defects: We consider a smectic-A* in a capillary with surface anchoring that favors\nparallel alignment. If the bulk phase of the smectic is the standard\ntwist-grain-boundary phase of chiral smectics, then there will be a critical\nradius below which the smectic will not have any topological defects. Above\nthis radius a single screw dislocation in the center of the capillary will be\nfavored. Along with surface anchoring, a magnetic field will also suppress the\nformation of a screw dislocation. In this note, we calculate the critical field\nat which a defect is energetically preferred as a function of the surface\nanchoring strength and the capillary radius. Experiments at a few different\nradii could thus determine the anchoring strength.", "category": "cond-mat_soft" }, { "text": "Shapes enhancing the propulsion of multiflagellated helical\n microswimmers: In this paper we are interested in optimizing the shape of multi-flagellated\nhelical microswimmers. Mimicking the propagation of helical waves along the\nflagella, they self-propel by rotating their tails. The swimmer's dynamics is\ncomputed using the Boundary Element Method, implemented in the open source\nMatlab library $Gypsilab$. We exploit a Bayesian optimization algorithm to\nmaximize the swimmer's speeds through their shape optimization. Our results\nshow that the optimal tail shapes are helices with large wavelength, such that\nthe shape periodicity is disregarded. Moreover, the best propulsion speed is\nachieved for elongated heads when the swimmer has one or two flagella.\nSurprisingly, a round head is obtained when more flagella are considered. Our\nresults indicate that the position and number of flagella modify the propulsion\npattern and play a significant role in the optimal design of the head. It\nappears that Bayesian optimization is a promising method for performance\nimprovement in microswimming.", "category": "cond-mat_soft" }, { "text": "Surface relaxation of lyotropic lamellar phases: We study the relaxation modes of an interface between a lyotropic lamellar\nphase and a gas or a simple liquid. The response is found to be qualitatively\ndifferent from those of both simple liquids and single-component smectic-A\nliquid crystals. At low rates it is governed by a non-inertial, diffusive mode\nwhose decay rate increases quadratically with wavenumber, $|\\omega|=Aq^2$. The\ncoefficient $A$ depends on the restoring forces of surface tension,\ncompressibility and bending, while the dissipation is dominated by the\nso-called slip mechanism, i.e, relative motion of the two components of the\nphase parallel to the lamellae. This surface mode has a large penetration depth\nwhich, for sterically stabilised phases, is of order $(dq^2)^{-1}$, where $d$\nis the microscopic lamellar spacing.", "category": "cond-mat_soft" }, { "text": "Thermal fluctuations of an interface near a contact line: The effect of thermal fluctuations near a contact line of a liquid interface\npartially wetting an impenetrable substrate is studied analytically and\nnumerically. Promoting both the interface profile and the contact line position\nto random variables, we explore the equilibrium properties of the corresponding\nfluctuating contact line problem based on an interfacial Hamiltonian involving\na \"contact\" binding potential. To facilitate an analytical treatment we\nconsider the case of a one-dimensional interface. The effective boundary\ncondition at the contact line is determined by a dimensionless parameter that\nencodes the relative importance of thermal energy and substrate energy at the\nmicroscopic scale. We find that this parameter controls the transition from a\npartially wetting to a pseudo-partial wetting state, the latter being\ncharacterized by a thin prewetting film of fixed thickness. In the partial\nwetting regime, instead, the profile typically approaches the substrate via an\nexponentially thinning prewetting film. We show that, independently of the\nphysics at the microscopic scale, Young's angle is recovered sufficiently far\nfrom the substrate. The fluctuations of the interface and of the contact line\ngive rise to an effective disjoining pressure, exponentially decreasing with\nheight. Fluctuations therefore provide a regularization of the singular contact\nforces occurring in the corresponding deterministic problem.", "category": "cond-mat_soft" }, { "text": "Dancing disclinations in confined active nematics: The spontaneous emergence of collective flows is a generic property of active\nfluids and often leads to chaotic flow patterns characterised by swirls, jets,\nand topological disclinations in their orientation field. However, the ability\nto achieve structured flows and ordered disclinations is of particular\nimportance in the design and control of active systems. By confining an active\nnematic fluid within a channel, we find a regular motion of disclinations, in\nconjunction with a well defined and dynamic vortex lattice. As pairs of moving\ndisclinations travel through the channel, they continually exchange partners\nproducing a dynamic ordered state, reminiscent of Ceilidh dancing. We\nanticipate that this biomimetic ability to self-assemble organised topological\ndisclinations and dynamically structured flow fields in engineered geometries\nwill pave the road towards establishing new active topological microfluidic\ndevices.", "category": "cond-mat_soft" }, { "text": "Neural Network Model for Structure Factor of Polymer Systems: As an important physical quantity to understand the internal structure of\npolymer chains, the structure factor is being studied both in theory and\nexperiment. Theoretically, the structure factor of Gaussian chains have been\nsolved analytically, but for wormlike chains, numerical approaches are often\nused, such as Monte Carlo (MC) simulations, solving modified diffusion equation\n(MDE), etc. In those works, the structure factor needs to be calculated\ndifferently for different regions of the wave vector and chain rigidity, and\nsome calculation processes are resource consuming. In this work, by training a\ndeep neural network (NN), we obtained an efficient model to calculate the\nstructure factor of polymer chains, without considering different regions of\nwavenumber and chain rigidity. Furthermore, based on the trained neural network\nmodel, we predicted the contour and Kuhn length of some polymer chains by using\nscattering experimental data, and we found our model can get pretty reasonable\npredictions. This work provides a method to obtain structure factor for polymer\nchains, which is as good as previous, and with a more computationally\nefficient. Also, it provides a potential way for the experimental researchers\nto measure the contour and Kuhn length of polymer chains.", "category": "cond-mat_soft" }, { "text": "A molecular dynamics study of chemical gelation in a patchy particle\n model: We report event-driven molecular dynamics simulations of the irreversible\ngelation of hard ellipsoids of revolution containing several associating\ngroups, characterizing how the cluster size distribution evolves as a function\nof the extent of reaction, both below and above the gel point. We find that in\na very large interval of values of the extent of reaction, parameter-free\nmean-field predictions are extremely accurate, providing evidence that in this\nmodel the Ginzburg zone near the gel point, where non-mean field effects are\nimportant, is very limited. We also find that the Flory's hypothesis for the\npost-gelation regime properly describes the connectivity of the clusters even\nif the long-time limit of the extent of reaction does not reach the fully\nreacted state. This study shows that irreversibly aggregating asymmetric\nhard-core patchy particles may provide a close realization of the mean-field\nmodel, for which available theoretical predictions may help control the\nstructure and the connectivity of the gel state. Besides chemical gels, the\nmodel is relevant to network-forming soft materials like systems with\nbioselective interactions, functionalized molecules and patchy colloids.", "category": "cond-mat_soft" }, { "text": "Curvature Dependence of Hydrophobic Hydration Dynamics: We investigate the curvature-dependence of water dynamics in the vicinity of\nhydrophobic spherical solutes using molecular dynamics simulations. For both,\nthe lateral and perpendicular diffusivity as well as for H-bond kinetics of\nwater in the first hydration shell, we find a non-monotonic solute-size\ndependence, exhibiting extrema close to the well-known structural crossover\nlength scale for hydrophobic hydration. Additionally, we find an apparently\nanomalous diffusion for water moving parallel to the surface of small solutes,\nwhich, however, can be explained by topology effects. The intimate connection\nbetween solute curvature, water structure and dynamics has implications for our\nunderstanding of hydration dynamics at heterogeneous biomolecular surfaces.", "category": "cond-mat_soft" }, { "text": "Phase diagram of heteronuclear Janus dumbbells: Using Aggregation-Volume-Bias Monte Carlo simulations along with Successive\nUmbrella Sampling and Histogram Re-weighting, we study the phase diagram of a\nsystem of dumbbells formed by two touching spheres having variable sizes, as\nwell as different interaction properties. The first sphere ($h$) interacts with\nall other spheres belonging to different dumbbells with a hard-sphere\npotential. The second sphere ($s$) interacts via a square-well interaction with\nother $s$ spheres belonging to different dumbbells and with a hard-sphere\npotential with all remaining $h$ spheres. We focus on the region where the $s$\nsphere is larger than the $h$ sphere, as measured by a parameter $1\\le\n\\alpha\\le 2 $ controlling the relative size of the two spheres.\n As $\\alpha \\to 2$ a simple fluid of square-well spheres is recovered, whereas\n$\\alpha \\to 1$ corresponds to the Janus dumbbell limit, where the $h$ and $s$\nspheres have equal sizes. Many phase diagrams falling into three classes are\nobserved, depending on the value of $\\alpha$. The $1.8 \\le \\alpha \\le 2$ is\ndominated by a gas-liquid phase separation very similar to that of a pure\nsquare-well fluid with varied critical temperature and density. When $1.3 \\le\n\\alpha \\le 1.8$ we find a progressive destabilization of the gas-liquid phase\ndiagram by the onset of self-assembled structures, that eventually lead to a\nmetastability of the gas-liquid transition below $\\alpha=1.2$.", "category": "cond-mat_soft" }, { "text": "Local Cooperativity Mechanism in the DNA Melting Transition: We propose a new statistical mechanics model for the melting transition of\nDNA. Base pairing and stacking are treated as separate degrees of freedom, and\nthe interplay between pairing and stacking is described by a set of local rules\nwhich mimic the geometrical constraints in the real molecule. This microscopic\nmechanism intrinsically accounts for the cooperativity related to the free\nenergy penalty of bubble nucleation. The model describes both the unpairing and\nunstacking parts of the spectroscopically determined experimental melting\ncurves. Furthermore, the model explains the observed temperature dependence of\nthe effective thermodynamic parameters used in models of the nearest neighbor\n(NN) type. We compute the partition function for the model through the transfer\nmatrix formalism, which we also generalize to include non local chain entropy\nterms. This part introduces a new parametrization of the Yeramian-like transfer\nmatrix approach to the Poland-Scheraga description of DNA melting. The model is\nexactly solvable in the homogeneous thermodynamic limit, and we calculate all\nobservables without use of the grand partition function. As is well known,\nmodels of this class have a first order or continuous phase transition at the\ntemperature of complete strand separation depending on the value of the\nexponent of the bubble entropy.", "category": "cond-mat_soft" }, { "text": "Heterogeneous Solvent Dissipation Coupled with Particle Rearrangement in\n Shear Thinning Non-Brownian Suspensions: Dense non-Brownian suspensions exhibit significant shear thinning, although a\ncomprehensive understanding of the full scope of this phenomenon remains\nelusive. This study numerically reveals intimate heterogenous coupled dynamics\nbetween many-body particle motions and solvent hydrodynamics in shear-thinning\nnon-Brownian suspensions. We demonstrate the spatially correlated viscous\ndissipation and particle motions; they share the same characteristic length,\nwhich decreases with increasing shear rate. We further show that, at lower\nshear rates, significant particle density changes are induced against the\nincompressibility of the solvent, suggesting the cooperative creation and\nannihilation of gaps and flow channels. We discuss that hydrodynamic\ninteractions may substantially restrict particle rearrangements even in highly\ndense suspensions, influencing the quantitative aspects of macroscopic\nrheology.", "category": "cond-mat_soft" }, { "text": "Role of the glassy dynamics and thermal mixing in the dynamic nuclear\n polarization and relaxation mechanisms of pyruvic acid: The temperature dependence of $^1$H and $^{13}$C nuclear spin-lattice\nrelaxation rate $1/T_1$ has been studied in the 1.6 K - 4.2 K temperature range\nin pure pyruvic acid and in pyruvic acid containing trityl radicals at a\nconcentration of 15 mM. The temperature dependence of $1/T_1$ is found to\nfollow a quadratic power law for both nuclei in the two samples. Remarkably the\nsame temperature dependence is displayed also by the electron spin-lattice\nrelaxation rate $1/T_{1e}$ in the sample containing radicals. These results are\nexplained by considering the effect of the structural dynamics on the\nrelaxation rates in pyruvic acid. Dynamic nuclear polarization experiments show\nthat below 4 K the $^{13}$C build up rate scales with $1/T_{\\text{1e}}$, in\nanalogy to $^{13}$C $1/T_1$ and consistently with a thermal mixing scenario\nwhere all the electrons are collectively involved in the dynamic nuclear\npolarization process and the nuclear spin reservoir is in good thermal contact\nwith the electron spin system.", "category": "cond-mat_soft" }, { "text": "Wall slip and flow of concentrated hard-sphere colloidal suspensions: We present a comprehensive study of the slip and flow of concentrated\ncolloidal suspensions using cone-plate rheometry and simultaneous confocal\nimaging. In the colloidal glass regime, for smooth, non-stick walls, the solid\nnature of the suspension causes a transition in the rheology from\nHerschel-Bulkley (HB) bulk flow behavior at large stress to a Bingham-like slip\nbehavior at low stress, which is suppressed for sufficient colloid-wall\nattraction or colloid-scale wall roughness. Visualization shows how the\nslip-shear transition depends on gap size and the boundary conditions at both\nwalls and that partial slip persist well above the yield stress. A\nphenomenological model, incorporating the Bingham slip law and HB bulk flow,\nfully accounts for the behavior. Microscopically, the Bingham law is related to\na thin (sub-colloidal) lubrication layer at the wall, giving rise to a\ncharacteristic dependence of slip parameters on particle size and\nconcentration. We relate this to the suspension's osmotic pressure and yield\nstress and also analyze the influence of van der Waals interaction. For the\nlargest concentrations, we observe non-uniform flow around the yield stress, in\nline with recent work on bulk shear-banding of concentrated pastes. We also\ndescribe residual slip in concentrated liquid suspensions, where the vanishing\nyield stress causes coexistence of (weak) slip and bulk shear flow for all\nmeasured rates.", "category": "cond-mat_soft" }, { "text": "Charged dendrimers revisited: Effective charge and surface potential of\n dendritic polyglycerol sulfate: We investigate key electrostatic features of charged dendrimers at hand of\nthe biomedically important dendritic polyglycerol sulfate (dPGS) macromolecule\nusing multi-scale computer simulations and Zetasizer experiments. In our\nsimulation study, we first develop an effective mesoscale Hamiltonian specific\nto dPGS based on input from all-atom, explicit-water simulations of dPGS of low\ngeneration. Employing this in coarse-grained, implicit-solvent/explicit-salt\nLangevin dynamics simulations, we then study dPGS structural and electrostatic\nproperties up to the sixth generation. By systematically mapping then the\ncalculated electrostatic potential onto the Debye-H\\\"uckel form -- that serves\nas a basic defining equation for the effective charge -- we determine\nwell-defined effective net charges and corresponding radii, surface charge\ndensities, and surface potentials of dPGS. The latter are found to be up to one\norder of magnitude smaller than the bare values and consistent with previously\nderived theories on charge renormalization and weak saturation for high\ndendrimer generations (charges). Finally, we find that the surface potential of\nthe dendrimers estimated from the simulations compare very well with our new\nelectrophoretic experiments.", "category": "cond-mat_soft" }, { "text": "Versatile coating platform for metal oxide nanoparticles: applications\n to materials and biological science: In this feature article, we provide an overview of our research on\nstatistical copolymers as a coating material for metal oxide nanoparticles and\nsurfaces. These copolymers contain functional groups enabling non-covalent\nbinding to oxide surfaces and poly(ethylene glycol) (PEG) polymers for\ncolloidal stability and stealthiness. The functional groups are organic\nderivatives of phosphorous acid compounds R-H$_2$PO$_3$, also known as\nphosphonic acids that have been screened for their strong affinity to metals\nand their ability to build multidentate binding. Herein we develop a\npolymer-based coating platform that shares features with the techniques of\nself-assembled monolayers (SAM) and Layer-by-Layer (L-b-L) deposition. The\nmilestones of this endeavor are the synthesis of PEG-based copolymers\ncontaining multiple phosphonic acid groups, the implementation of simple\nprotocols combining versatility with high particle production yields and the\nexperimental demonstration of the colloidal stability of the coated particles.\nAs a demonstration, coating studies are conducted on cerium (CeO$_2$), iron\n($\\gamma$-Fe$_2$O$_3$), aluminum (Al$_2$O$_3$) and titanium (TiO$_2$) oxides of\ndifferent sizes and morphologies. We finally discuss applications in the domain\nof nanomaterials and nanomedicine. We evaluate the beneficial effects of\ncoating on redispersible nanopowders, contrast agents for In Vitro/Vivo assays\nand stimuli-responsive particles.", "category": "cond-mat_soft" }, { "text": "Intra-Globular Structures in Multiblock Copolymer Chains from a Monte\n Carlo Simulation: Multiblock copolymer chains in implicit nonselective solvents are studied by\nMonte Carlo method which employs a parallel tempering algorithm. Chains\nconsisting of 120 $A$ and 120 $B$ monomers, arranged in three distinct\nmicroarchitectures: $(10-10)_{12}$, $(6-6)_{20}$, and $(3-3)_{40}$, collapse to\nglobular states upon cooling, as expected. By varying both the reduced\ntemperature $T^*$ and compatibility between monomers $\\omega$, numerous\nintra-globular structures are obtained: diclusters (handshake, spiral, torus\nwith a core, etc.), triclusters, and $n$-clusters with $n>3$ (lamellar and\nother), which are reminiscent of the block copolymer nanophases for spherically\nconfined geometries. Phase diagrams for various chains in the $(T^*,\n\\omega)$-space are mapped. The structure factor $S(k)$, for a selected\nmicroarchitecture and $\\omega$, is calculated. Since $S(k)$ can be measured in\nscattering experiments, it can be used to relate simulation results to an\nexperiment. Self-assembly in those systems is interpreted in term of\ncompetition between minimization of the interfacial area separating different\ntypes of monomers and minimization of contacts between chain and solvent.\nFinally, the relevance of this model to the protein folding is addressed.", "category": "cond-mat_soft" }, { "text": "Surprising simplicity in the modeling of dynamic granular intrusion: Granular intrusions, such as dynamic impact or wheel locomotion, are complex\nmultiphase phenomena where the grains exhibit solid-like and fluid-like\ncharacteristics together with an ejected gas-like phase. Despite decades of\nmodeling efforts, a unified description of the physics in such intrusions is as\nyet unknown. Here we show that a continuum model based on the simple notions of\nfrictional flow and tension-free separation describes complex granular\nintrusions near free surfaces. This model captures dynamics in a variety of\nexperiments including wheel locomotion, plate intrusions, and running legged\nrobots. The model reveals that three effects (a static contribution and two\ndynamic ones) primarily give rise to intrusion forces in such scenarios.\nIdentification of these effects enables the development of a further\nreduced-order technique (Dynamic Resistive Force Theory) for rapid modeling of\ngranular locomotion of arbitrarily shaped intruders. The continuum-motivated\nstrategy we propose for identifying physical mechanisms and corresponding\nreduced-order relations has potential use for a variety of other materials.", "category": "cond-mat_soft" }, { "text": "Micelle formation, gelation and phase separation of amphiphilic\n multiblock copolymers: The phase behaviour of amphiphilic multiblock copolymers with a large number\nof blocks in semidilute solutions is studied by lattice Monte Carlo\nsimulations. The influence on the resulting structures of the concentration,\nthe solvent quality and the ratio of hydrophobic to hydrophilic monomers in the\nchains has been assessed explicitely. Several distinct regimes are put in\nevidence. For poorly substituted (mainly hydrophilic) copolymers formation of\nmicelles is observed, either isolated or connected by the hydrophilic moieties,\ndepending on concentration and chain length. For more highly substituted chains\nlarger tubular hydrophobic structures appear which, at higher concentration,\njoin to form extended hydrophobic cores. For both substitution ratios gelation\nis observed, but with a very different gel network structure. For the poorly\nsubstituted chains the gel consists of micelles cross-linked by hydrophilic\nblocks whereas for the highly substituted copolymers the extended hydrophobic\ncores form the gelling network. The interplay between gelation and phase\nseparation clearly appears in the phase diagram. In particular, for poorly\nsubstituted copolymers and in a narrow concentration range, we observe a\nsol-gel transition followed by an inverse gel-sol transition when increasing\nthe interaction energy. The simulation results are discussed in the context of\nthe experimentally observed phase properties of methylcellulose, a\nhydrophobically substituted polysaccharide.", "category": "cond-mat_soft" }, { "text": "Force spectroscopy of polymer desorption: Theory and Molecular Dynamics\n simulation: Forced detachment of a single polymer chain, strongly-adsorbed on a solid\nsubstrate, is investigated by two complementary methods: a coarse-grained\nanalytical dynamical model, based on the Onsager stochastic equation, and\nMolecular Dynamics (MD) simulations with Langevin thermostat. The suggested\napproach makes it possible to go beyond the limitations of the conventional\nBell-Evans model. We observe a series of characteristic force spikes when the\npulling force is measured against the cantilever displacement during detachment\nat constant velocity $v_c$ (displacement control mode) and find that the\naverage magnitude of this force increases as $v_c$ grows. The probability\ndistributions of the pulling force and the end-monomer distance from the\nsurface at the moment of final detachment are investigated for different\nadsorption energy $\\epsilon$ and pulling velocity $v_c$. Our extensive\nMD-simulations validate and support the main theoretical findings. Moreover,\nthe simulation reveals a novel behavior: for a strong-friction and massive\ncantilever the force spikes pattern is smeared out at large $v_c$. As a\nchallenging task for experimental bio-polymers sequencing in future we suggest\nthe fabrication of stiff, super-light, nanometer-sized AFM probe.", "category": "cond-mat_soft" }, { "text": "Fundamental measure theory for the electric double layer: implications\n for blue-energy harvesting and water desalination: Capacitive mixing (CAPMIX) and capacitive deionization (CDI) are promising\ncandidates for harvesting clean, renewable energy and for the energy efficient\nproduction of potable water, respectively. Both CAPMIX and CDI involve\nwater-immersed porous carbon (supercapacitors) electrodes at voltages of the\norder of hundreds of millivolts, such that counter-ionic packing is important\nfor the electric double layer (EDL) which forms near the surface of these\nporous materials. Thus, we propose a density functional theory (DFT) to model\nthe EDL, where the White-Bear mark II fundamental measure theory functional is\ncombined with a mean-field Coulombic and a mean spherical approximation-type\ncorrection to describe the interplay between dense packing and electrostatics,\nin good agreement with molecular dynamics simulations. We discuss the\nconcentration-dependent potential rise due to changes in the chemical potential\nin capacitors in the context of an over-ideal theoretical description and its\nimpact on energy harvesting and water desalination. Compared to less elaborate\nmean-field models our DFT calculations reveal a higher work output for\nblue-energy cycles and a higher energy demand for desalination cycles.", "category": "cond-mat_soft" }, { "text": "Deformation and motion of giant unilamellar vesicles loaded with gold\n nanoparticles driven by induced charge electro-osmotic flow: A vesicle is a spherical structure composed of a phospholipid bilayer that is\nused as a container for chemicals, both it in vivo and it in vitro systems. In\nboth cases, the vesicles can be passively moved using external molecular motors\nor flows. The active motion of the vesicles can potentially expand their\napplications in microfluid devices. In this study, we created giant unilamellar\nvesicles (GUVs) that loads dodecanethiol-functionalized gold nanoparticles\n(AuNPs) using natural swelling method. An external alternating current (AC)\nelectric field was applied to the sample to drive the system. A flow was\nconfirmed with dense optical flow method around GUVs, even in the absence of\nAuNPs. The quadratic dependence of the flow on applied elecric fields confirms\nthat the flow is due to induced charge electro-osmotic (ICEO) mechanism.\nFurthermore, the GUVs containing AuNPs moved and deformed significantly under\nexternal AC electric fields compared with those without AuNPs. We also\nconfirmed that the translational speed of GUVs was positively correlated with\nthe volume ratio of AuNPs. These experimental results suggest that the motion\nand deformation of GUVs were cause by ICEO flow, which was unbalanced owing to\nthe presence of localized AuNPs on the membrane.", "category": "cond-mat_soft" }, { "text": "Some comments on the fracture of viscoelastic solids: Crack propagation in viscoelastic solids like rubber is of great practical\nimportance. Shrimali and Lopez-Pamies have proposed a new interesting approach\nfor the crack propagation in viscoelastic solids. We give comments on the\nvalidity of the theory and point out some effects not included in the theory.", "category": "cond-mat_soft" }, { "text": "Withdrawing a solid from a bath: how much liquid is coated?: A solid withdrawn from a liquid bath entrains a film. In this review, after\nrecalling the predictions and results for pure Newtonian liquids coated on\nsimple solids, we analyze the deviations to this ideal case exploring\nsuccessively three potential sources of complexity: the liquid-air interface,\nthe bulk rheological properties of the liquid and the mechanical or chemical\nproperties of the solid. For these different complexities, we show that\nsignificant effects on the film thickness are observed experimentally and we\nsummarize the theoretical analysis presented in the literature, which attempt\nto rationalize these measurements.", "category": "cond-mat_soft" }, { "text": "Lift force on an asymmetrical obstacle immersed in a dilute granular\n flow: This paper investigates the lift force exerted on an elliptical obstacle\nimmersed in a granular flow through analytical calculations and computer\nsimulations. The results are shown as a function of the obstacle size,\norientation with respect to the flow direction (tilt angle), the restitution\ncoefficient and ellipse eccentricity. The theoretical argument, based on the\nforce exerted on the obstacle due to inelastic, frictionless collisions of a\nvery dilute flow, captures the qualitative features of the lift, but fails to\nreproduce the data quantitatively. The reason behind this disagreement is that\nthe dilute flow assumption on which this argument is built breaks down as a\ngranular shock wave forms in front of the obstacle. More specifically, the\nshock wave change the grains impact velocity at the obstacle, decreasing the\noverall net lift obtained from a very dilute flow.", "category": "cond-mat_soft" }, { "text": "Anisotropic Characteristic Lengths of Colloidal Monolayers Near a\n Water-Air Interface: Near-interface colloidal monolayers have often been used as model systems for\nresearch on hydrodynamics in biophysics and microfluidic systems. Using optical\nmicroscopy and multiparticle tracking techniques, the correlated diffusion of\nparticles is experimentally measured in colloidal monolayers near a water-air\ninterface. It is found that the characteristic lengths X1 and X2 of such a\ncolloidal monolayer are anisotropic in these two perpendicular directions. The\nformer (X1)is equal to the Saffman length of the monolayer and reflects the\ncontinuous nature of the system in the longitudinal direction. The latter\n(X2)is a function of both the Saffman length and the radius of the colloids and\nreflects the discrete nature of the system in the transverse direction. This\ndiscovery demonstrates that the hydrodynamics intrinsically follow different\nrules in these two directions in this system.", "category": "cond-mat_soft" }, { "text": "Physics of suction cups in air and in water: We present experimental results for the dependency of the pull-off time\n(failure time) on the pull-off force for suction cups in the air and in water.\nThe results are analyzed using a theory we have developed for the contact\nbetween suction cups and randomly rough surfaces. The theory predicts the\ndependency of the pull-off time (failure time) on the pull-off force, and is\ntested with measurements performed on suction cups made from a soft polyvinyl\nchloride (PVC). As substrates we used sandblasted poly(methyl methacrylate)\n(PMMA). The theory is in good agreement with the experiments in air, except for\nsurfaces with the root-mean-square (rms) roughness below $\\approx 1 \\ {\\rm \\mu\nm}$, where we observed lifetimes much longer than predicted by the theory. We\nshow that this is due to out-diffusion of plasticizer from the soft PVC, which\nblock the critical constrictions along the air flow channels. In water some\ndeviation between theory and experiments is observed which may be due to\ncapillary forces. We discuss the role of cavitation for the failure time of\nsuction cups in water.", "category": "cond-mat_soft" }, { "text": "Global perspectives on the energy landscapes of liquids, supercooled\n liquids, and glassy systems: The potential energy landscape ensemble: In principle, all of the dynamical complexities of many-body systems are\nencapsulated in the potential energy landscapes on which the atoms move - an\nobservation that suggests that the essentials of the dynamics ought to be\ndetermined by the geometry of those landscapes. But what are the principal\ngeometric features that control the long-time dynamics? We suggest that the key\nlies not in the local minima and saddles of the landscape, but in a more global\nproperty of the surface: its accessible pathways. In order to make this notion\nmore precise we introduce two ideas: (1) a switch to a new ensemble that\nremoves the concept of potential barriers from the problem, and (2) a way of\nfinding optimum pathways within this new ensemble. The potential energy\nlandscape ensemble, which we describe in the current paper, regards the maximum\naccessible potential energy, rather than the temperature, as a control\nvariable. We show here that while this approach is thermodynamically equivalent\nto the canonical ensemble, it not only sidesteps the idea of barriers, it\nallows us to be quantitative about the connectivity of a landscape. We\nillustrate these ideas with calculations on a simple atomic liquid and on the\nKob-Andersen model of a glass-forming liquid, showing, in the process, that the\nlandscape of the Kob-Anderson model appears to have a connectivity transition\nat the landscape energy associated with its mode-coupling transition. We turn\nto the problem of finding the most efficient pathways through potential energy\nlandscapes in our companion paper.", "category": "cond-mat_soft" }, { "text": "Temperature as an external field for colloid-polymer mixtures :\n \"quenching\" by heating and \"melting\" by cooling: We investigate the response to temperature of a well-known colloid-polymer\nmixture. At room temperature, the critical value of the second virial\ncoefficient of the effective interaction for the Asakura-Oosawa model predicts\nthe onset of gelation with remarkable accuracy. Upon cooling the system, the\neffective attractions between colloids induced by polymer depletion are\nreduced, because the polymer radius of gyration is decreases as the\ntheta-temperature is approached. Paradoxically, this raises the effective\ntemperature, leading to \"melting\" of colloidal gels. We find the Asakura-Oosawa\nmodel of effective colloid interactions with a simple description of the\npolymer temperature response provides a quantitative description of the\nfluid-gel transition. Further we present evidence for enhancement of\ncrystallisation rates near the metastable critical point.", "category": "cond-mat_soft" }, { "text": "Helix formation in linear achiral dendronized polymers. A computer\n simulation study: We present a molecular simulation study of the structure of linear\ndendronized polymers. We use excluded volume interactions in the context of a\ngeneric coarse-grained molecular model whose geometrical parameters are tuned\nto represent a poly(para-phenylene) backbone with benzyl ether, Frechet type\ndendrons. We apply Monte Carlo sampling in order to investigate the formation\nof packing-induced chiral structures along the polymer backbone of these\nchemically non-chiral systems. We find that helical structures can be formed,\nusually with defects consisting of domains with reversed helical handedness.\nClear signs of helical arrangements of the dendrons begin to appear for\ndendritic generation g=4, while for g=5 these arrangements dominate and perfect\nhelices can even be observed as equilibrium structures obtained from certain\ntypes of starting configurations.", "category": "cond-mat_soft" }, { "text": "Parametric excitation of wrinkles in elastic sheets on elastic and\n viscoelastic substrates: Thin elastic sheets supported on compliant media form wrinkles under lateral\ncompression. Since the lateral pressure is coupled to the sheet's deformation,\nvarying it periodically in time creates a parametric excitation. We study the\nresulting parametric resonance of wrinkling modes in sheets supported on\nsemi-infinite elastic or viscoelastic media, at pressures smaller than the\ncritical pressure of static wrinkling. We find distinctive behaviors as a\nfunction of excitation amplitude and frequency, including (a) a different\ndependence of the dynamic wrinkle wavelength on sheet thickness compared to the\nstatic wavelength; and (b) a discontinuous decrease of the wrinkle wavelength\nupon increasing excitation frequency at sufficiently large pressures. In the\ncase of a viscoelastic substrate, resonant wrinkling requires crossing a\nthreshold of excitation amplitude. The frequencies for observing these\nphenomena in relevant experimental systems are of the order of a kilohertz and\nabove. We discuss experimental implications of the results.", "category": "cond-mat_soft" }, { "text": "Superfast collective motion of magnetic particles: It is well-known that magnetic forces can induce a formation of densely\npacked strings of magnetic particles or even sheafs of several strings\n(spindles). Here we show that in a sufficiently strong magnetic field, more\ncomplex aggregates of particles, translating with a much faster speed than\nwould be for a single particle or even a spindle, can be assembled at the\nwater-air interface. Such a superfast flotilla is composed of many distant\nstrings or spindles, playing a role of its vessels, and moves, practically, as\na whole. We provide theoretical results to interpret the effect of a collective\nmotion of such magnetic vessels. Our theory shows that, in contrast to an\nisolated chain or spindle, which velocity grows logarithmically with the number\nof magnetic particles, the speed of the interface flotilla becomes much higher,\nbeing proportional to the square root of their number. These results may guide\nthe design of magnetic systems for extremely fast controlled delivery.", "category": "cond-mat_soft" }, { "text": "Saffman-Taylor instability in a non-Brownian suspension: finger\n selection and destabilization: We study the Saffman-Taylor instability in a non-Brownian suspension by\ninjection of air. We find that flow structuration in the Hele-Shaw cell can be\ndescribed by an effective viscosity depending on the volume fraction. When this\nviscosity is used to define the control parameter of the instability, the\nclassical finger selection for Newtonian fluids is recovered. However, this\npicture breaks down when the cell thickness is decreased below approximatively\n10 grain sizes. The discrete nature of the grains plays also a determinant role\nin the the early destabilization of the fingers observed. The grains produce a\nperturbation at the interface proportional to the grain size and can thus be\nconsidered as a \"controlled noise\". The finite amplitude instability mechanism\nproposed earlier by Bensimon et al. allows to link this perturbation to the\nactual values of the destabilization threshold.", "category": "cond-mat_soft" }, { "text": "Interfacial Reactions: Mixed Order Kinetics and Segregation Effects: We study A-B reaction kinetics at a fixed interface separating A and B bulks.\nInitially, the number of reactions ${\\cal R}_t \\sim t n_A^\\infty n_B^\\infty$ is\n2nd order in the far-field densities $n_A^\\infty,n_B^\\infty$. First order\nkinetics, governed by diffusion from the dilute bulk, onset at long times:\n${\\cal R}_t\\approx x_t n_A^\\infty$ where $x_t\\sim t^{1/z}$ is the rms molecular\ndisplacement. Below a critical dimension, $d