Physics - Soft Condensed Matter Publications (50)

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Physics - Soft Condensed Matter Publications

We develop two-dimensional Brownian dynamics simulations to examine the motion of disks under thermal fluctuations and Hookean forces. Our simulations are designed to be experimental-like, since the experimental conditions define the available time-scales which characterize the solution of Langevin equations. To define the fluid model and methodology, we explain the basics of the theory of Brownian motion applicable to quasi-twodimensional diffusion of optically-trapped microspheres. Read More


Rheology of cohesive dilute granular gases is theoretically and numerically studied. The flow curve between the shear viscosity and the shear rate is derived from the inelastic Boltzmann equation for particles under the influence of square-well potentials in a simple uniform shear state. It is found that the stable uniformly sheared state only exists above a critical shear rate in which the viscosity is almost identical to that for uniformly sheared hard core granular particles. Read More


Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, 1D supramolecular twisted ribbons and 2D colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Read More


We study the quantum phase transition between a paramagnetic and ferromagnetic metal in the presence of Rashba spin-orbit coupling in one dimension. Using bosonization, we analyze the transition by means of renormalization group, controlled by an $\varepsilon$-expansion around the upper critical dimension of two. We show that the presence of Rashba spin-orbit coupling allows for a new nonlinear term in the bosonized action, which generically leads to a fluctuation driven first-order transition. Read More


A Grand-canonical Monte-Carlo simulation method extended to simulate a mixture of salts is presented. Due to charge neutrality requirement of electrolyte solutions, ions must be added to or removed from the system in groups. This leads to some complications compared to regular Grand Canonical simulation. Read More


Fish, birds, insects and robots frequently swim or fly in groups. During their 3 dimensional collective motion, these agents do not stop, they avoid collisions by strong short-range repulsion, and achieve group cohesion by weak long-range attraction. In a minimal model that is isotropic, and continuous in both space and time, we demonstrate that (i) adjusting speed to a preferred value, combined with (ii) radial repulsion and an (iii) effective long-range attraction are sufficient for the stable ordering of autonomously moving agents in space. Read More


Starting from a Langevin formulation of a thermally perturbed nonlinear elastic model of the ferroelectric smectic-C$^*$ (SmC${*}$) liquid crystals in the presence of an electric field, this article characterizes the hitherto unexplored dynamical phase transition from a thermo-electrically forced ferroelectric SmC${}^{*}$ phase to a chiral nematic liquid crystalline phase and vice versa. The theoretical analysis is based on a combination of dynamic renormalization (DRG) and numerical simulation of the emergent model. While the DRG architecture predicts a generic transition to the Kardar-Parisi-Zhang (KPZ) universality class at dynamic equilibrium, in agreement with recent experiments, the numerical simulations of the model show simultaneous existence of two phases, one a "subdiffusive" (SD) phase characterized by a dynamical exponent value of 1, and the other a KPZ phase, characterized by a dynamical exponent value of 1. Read More


Recent experiments on mixed liquid crystals have highlighted the hugely significant role of ferromagnetic nanoparticle impurities in defining the nematic-smectic-A phase transition point. Structured around a Flory-Huggins free energy of isotropic mixing and Landau-de Gennes free energy, this article presents a phenomenological mean-field model that quantifies the role of such impurities in analyzing thermodynamic phases, in a mixture of thermotropic smectic liquid crystal and ferromagnetic nanoparticles. First we discuss the impact of ferromagnetic nanoparticles on the isotropic-ferronematic and ferronematic-ferrosmectic phase transitions and their transition temperatures. Read More


Biochemical networks play a crucial role in biological systems, implementing a broad range of vital functions. They normally operate at low copy numbers and in spatial settings, but this is often ignored and well-stirred conditions are assumed. Yet, it is increasingly becoming clear that even microscopic spatial inhomogeneities oftentimes can induce significant differences on the macroscopic level. Read More


This Letter introduces unexpected diffusion properties in dense granular flows, and shows that they result from the development of partially jammed clusters of grains, or granular vortices. Transverse diffusion coefficients $D$ and average vortex sizes $\ell$ are systematically measured in simulated plane shear flows at differing internal numbers $I$ revealing (i) a strong deviation from the expected scaling $D\propto d^2 \dot \gamma$ involving the grain size $d$ and shear rate $\dot \gamma$ and (ii) an increase in average vortex size $\ell$ at low $I$, following $\ell\propto dI^{-\frac{1}{2}}$ but limited by the system size. A general scaling $D\propto \ell d \dot \gamma $ is introduced that captures all the measurements and highlights the key role of vortex size. Read More


In this work, the Quasi-Random Lattice (QRL) model is summarized and critically discussed, in order to outline its potentialities and limitations, in perspective of future developments. QRL primarily focuses on the mean activity coefficient of ionic solutions, the model having first been developed in order to provide practical equations, able to involve a minimal number of unknown or unpredictable quantities. QRL at present depends on one adjustable parameter (at given pressure and temperature), experimentally known for many common salts either symmetric or asymmetric, and corresponding to a well-defined concentration, which also sets the upper limit of applicability of the model. Read More


Current understanding of how contractility emerges in disordered actomyosin networks of non-muscle cells is still largely based on the intuition derived from earlier works on muscle contractility. This view, however, largely overlooks the free energy gain following passive cross-linker binding, which, even in the absence of active fluctuations, provides a thermodynamic drive towards highly overlapping filamentous states. In this work, we shed light on this phenomenon, showing that passive cross-linkers, when considered in the context of two anti-parallel filaments, generate noticeable contractile forces. Read More


Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic mechanisms underlying spatial organisation in cells. In this work, we use a continuum model of membrane and protein dynamics to study the behaviour of curvature-inducing proteins on membranes of spherical shape, such as living cells or lipid vesicles. Read More


In a recent work on fluid infiltration in a Hele-Shaw cell with the pore-block geometry of Sierpinski carpets (SCs), the area filled by the invading fluid was shown to scale as F~t^n, with n<1/2, thus providing a macroscopic realization of anomalous diffusion [Filipovitch et al, Water Resour. Res. 52 5167 (2016)]. Read More


Granular materials are an important physical realization of active matter. In vibration-fluidized granular matter, both diffusion and self-propulsion derive from the same collisional forcing, unlike many other active systems where there is a clean separation between the origin of single-particle mobility and the coupling to noise. Here we present experimental studies of single-particle motion in a vibrated granular monolayer, along with theoretical analysis that compares grain motion at short and long time scales to the assumptions and predictions, respectively, of the active Brownian particle (ABP) model. Read More


Athermal disordered systems can exhibit a remarkable response to an applied oscillatory shear: after a relatively few shearing cycles, the system falls into a configuration that had already been visited in a previous cycle. After this point the system repeats its dynamics periodically despite undergoing many particle rearrangements during each cycle. We study the behavior of orbits as we approach the jamming point in simulations of jammed particles subject to oscillatory shear at fixed pressure and zero temperature. Read More


Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined morphologies. This is the case in numerous medical conditions where normally soluble proteins aggregate into fibers. Read More


I describe the manifestation of the non-Euclidean geometry in the behavior of collective observables of some complex physical systems. Specifically, I consider the formation of equilibrium shapes of plants and statistics of sparse random graphs. For these systems I discuss the following interlinked questions: (i) the optimal embedding of plants leaves in the three-dimensional space, (ii) the spectral statistics of sparse random matrix ensembles. Read More


A longstanding, and still present, proposal relates the activation of collective intramolecular oscillations of biomolecules with their biological functioning. These collective oscillations are predicted to occur in the THz frequency domain. Collective oscillations of an entire molecule, or of a substantial fraction of its atoms, are essential to generate giant oscillating molecular dipole moments. Read More


We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structures out of patchy particles, and investigate it with Brownian Dynamics (BD) simulations. Its first element is the use of specific patch-patch and shell-shell interactions between the particles, that can be implemented through differential functionalization of patched and shell regions with specific DNA strands. The other key element of our approach is the use of layer-by-layer protocol that allows to avoid a formations of undesired random aggregates. Read More


Particle tracking, which is an essential tool in many fields of scientific research, uses algorithms that retrieve the centroid of tracked particles with sub-pixel accuracy. However, images in which the particles occupy a small number of pixels on the detector, are in close proximity to other particles or suffer from background noise, show a systematic error in which the particle sub-pixel positions are biased towards the center of the pixel. This pixel locking effect greatly reduces particle tracking accuracy. Read More


Wet granular aggregates are common precursors of construction materials, food, and health care products. The physical mechanisms involved in the mixing of dry grains with a wet substrate are not well understood and difficult to control. Here, we study experimentally the accretion of dry grains on a wet granular substrate by measuring the growth dynamics of the wet aggregate. Read More


We establish a comprehensive description of the patterns formed when a wetting liquid displaces a viscous fluid confined in a porous medium. Building on model microfluidic experiments, we evidence four imbibition scenarios all yielding different large-scale morphologies. Combining high-resolution imaging and confocal microscopy, we show that they originate from two liquid-entrainment transitions and a Rayleigh-Plateau instability at the pore scale. Read More


In an emulsion system, emulsifier is one of the most important substances as it determines the formation, stability and physicochemical properties of emulsions. In this study, the effects of emulsifier concentration, type of hydrophilic emulsifier, as well as portions of primary emulsion (weight) on the stability of W/O/W emulsions were investigated. Microscopy images of W/O/W emulsions indicated that the emulsions prepared with 0. Read More


We develop a mesoscopic field theory for the collective nonequilibrium dynamics of multicomponent mixtures of interacting active (i.e., motile) and passive (i. Read More


Thermalized elastic membranes without distant self-avoidance are believed to undergo a crumpling transition when the microscopic bending stiffness is comparable to $kT$. Most potential physical realizations of such membranes have a bending stiffness well in excess of experimentally achievable temperatures and are therefore unlikely ever to access the crumpling regime. We propose a mechanism to tune the onset of the crumpling transition by altering the geometry and topology of the sheet itself. Read More


Disordered many-particle hyperuniform systems are exotic amorphous states of matter that lie between crystals and liquids. Hyperuniform systems have attracted recent attention because they are endowed with novel transport and optical properties. Recently, the hyperuniformity concept has been generalized to characterize scalar fields, two-phase media and random vector fields. Read More


The "double diffusivity" model was proposed in the late 1970s, and reworked in the early 1980s, as a continuum counterpart to existing discrete models of diffusion corresponding to high diffusivity paths, such as grain boundaries and dislocation lines. Technically, the model pans out as a system of coupled {\it Fick type} diffusion equations to represent "regular" and "high" diffusivity paths with "source terms" accounting for the mass exchange between the two paths. The model remit was extended by analogy to describe flow in porous media with double porosity, as well as to model heat conduction in media with two non-equilibrium local temperature baths e. Read More


We develop an elasto-plastic description for the transient dynamics prior to steady flow of athermally yielding materials. Our mean-field model not only reproduces the experimentally observed non-linear time dependence of the shear-rate response to an external shear-stress, but also allows for the determination of the different physical processes involved in the onset of the re-acceleration phase after the initial critical slowing down and a distinct well defined fluidization phase. The evidenced power-law dependence of the fluidization time on the distance of the applied to an age dependent static yield stress is not universal but strongly dependent on initial conditions. Read More


Recent diffraction experiments on metallic glasses have unveiled an unexpected non-cubic scaling law between density and average interatomic distance, which lead to the speculations on the presence of fractal glass order. Using X-ray tomography we identify here a similar non-cubic scaling law in disordered granular packing of spherical particles. We find that the scaling law is directly related to the contact neighbors within first nearest neighbor shell, and therefore is closely connected to the phenomenon of jamming. Read More


Crystal plasticity is mediated through dislocations, which form knotted configurations in a complex energy landscape. Once they disentangle and move, they may also be impeded by permanent obstacles with finite energy barriers or frustrating long-range interactions. The outcome of such complexity is the emergence of dislocation avalanches as the basic mechanism of plastic flow in solids at the nanoscale. Read More


We report that the lift force on a single large particle segregating in a monodisperse dense granular flow is correlated with a downstream velocity lag. This correlation suggests a viscous-inertial origin for the lift force, similar to the Saffman lift force in (micro) fluids. This insight is relevant for modelling of particle-size segregation and our approach opens up a new avenue for the numerical study of granular flows. Read More


Thin rigid sheets floating on a liquid substrate appear, for example, in coatings and surfactant monolayers. Upon uniaxial compression the sheet undergoes transitions from a compressed flat state to a periodic wrinkled pattern to a localized folded pattern. The stability of these states is determined by the in-plane elasticity of the sheet, its bending rigidity, and the hydrostatics of the underlying liquid. Read More


Amorphous materials such as metallic, polymeric, and colloidal glasses, exhibit complex preparation-dependent mechanical response to applied shear. We perform numerical simulations to investigate the mechanical response of binary Lennard-Jones glasses undergoing athermal, quasistatic pure shear as a function of the cooling rate $R$ used to prepare them. The ensemble-averaged stress versus strain curve $\langle\sigma(\gamma)\rangle$ resembles the spatial average in the large size limit, which appears smooth and displays a putative elastic regime at small strains, a yielding-related peak at intermediate strain, and a plastic flow regime at large strains. Read More


A recent version of statistical associating fluid theory (SAFT), namely SAFT2, is coupled with the van der Waals and Platteeuw theory to study the alkane hydrate phase equilibrium conditions. The model is found to provide an accurate representation of the alkane hydrate dissociation conditions with and without inhibitors, such as salts, alcohols, as well as mixed salts and alcohol. Based on SAFT2, a heterosegmented SAFT equation of state is developed to model the thermodynamic properties of aqueous ionic liquid (IL) solutions, which is recently discovered as dual function gas hydrate inhibitors. Read More


Understanding how nanostructure and nanomechanics influence physical material properties on the micro- and macroscale is an essential goal in soft condensed matter research. Mechanisms governing fragmentation and chirality inversion of filamentous colloids are of specific interest because of their critical role in load-bearing and self-organizing functionalities of soft nanomaterials. Here we provide a fundamental insight into the self-organization across several length scales of nanocellulose, an important bio-colloid system with wide-ranging applications as structural, insulating and functional material. Read More


A key process in the life of any multicellular organism is its development from a single fertilized egg into a full grown adult. Naturally, this process has been studied in great detail, with particular focus on its biochemical and genetic aspects. However, the mechanics of development have gained much less attention. Read More


The surface shear viscosity of an insoluble surfactant monolayer often depends strongly on its surface pressure. Here, we show that a particle moving within a bounded monolayer breaks the kinematic reversibility of low-Reynolds-number flows. The Lorentz reciprocal theorem allows such irreversibilities to be computed without solving the full nonlinear equations, giving the leading-order contribution of surface-pressure-dependent surface viscosity. Read More


The propagation of sound waves on lipid monolayers supported on water has been studied during the melting transition. Since changes in volume, area, and compressibility in lipid membranes have biological relevance, the observed sound propagation is of paramount importance. However, it is unknown what would occur on a lipid bilayer, which is a more approximate model of a cell membrane. Read More


Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While previous theoretical studies of particle diffusion have typically assumed either impenetrable obstacles or binding interactions that immobilize the particle, in many cellular contexts bound particles remain mobile. Read More


The charge transfer integral, site energy and the stacking angle fluctuations are used to study the hole and electron transport in recently synthesized dialkyl substituted thienothiophene caped benzobisthiazole (BDHTT-BBT) and methyl-substituted dicyanovinyl-capped quinquethiophene (DCV5T-Me) molecules. The charge transfer parameters, such as coherent and incoherent rate coefficients, hopping conductivity, mobility, disorder drift time, drift force, potential equilibrium rate and density flux rate are calculated and discussed. It has been observed that the charge decay up to the crossover point (or disorder drift time) is exponential, non-dispersive and charge transport follows the band-like transport. Read More


Spectra of thermal fluctuations of a wide range of interfaces, from liquid/air, viscoelastic material/air, liquid/liquid, to liquid/viscoelastic material interfaces, were measured over 100 Hz to 10 MHz frequency range. The obtained spectra were compared with the fluctuation theory of interfaces, and found to be mostly in quite good agreement, when the theory was generalized to apply to thermal fluctuations of liquid/viscoelastic material interfaces. The spectra were measured using a system that combines light reflection, statistical noise reduction through averaged correlations, and confocal microscopy. Read More


We report on the self-assembly of inverse patchy colloids (IPC) using Monte Carlo simulations in two-dimensions. The IPC model considered in this work corresponds to either bipolar colloids or colloids decorated with complementary DNA on their surfaces, where only patch and non-patch parts attract. The patch coverage is found to be a dominant factor in deciding equilibrium self-assembled structures. Read More


We present thermophoretic measurements in aqueous suspensions of three different polystyrene (PS) particles of varying negative charge, size and surface coating. Our measurement technique is based on the observation of the colloidal steady-state distribution using conventional bright-field microscopy, which avoids undesirable effects such as laser-induced convection or local heating. We find that the colloids with the weakest zeta potential exhibit the strongest thermophoretic effect, suggesting that surface functionality leads to a more intricate dependence of the Soret coefficient on hydrodynamic boundary conditions than predicted by existing theoretical approaches. Read More


Two-dimensionally nanoconfined water between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water under a periodic confining potential by means of computer simulations, both using empirical potentials and from first-principles. We propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude of the oscillation. Read More


Biocompatible microencapsulation is of widespread interest for the targeted delivery of active species in fields such as pharmaceuticals, cosmetics and agro-chemistry. Capsules obtained by the self-assembly of polymers at interfaces enable the combination of responsiveness to stimuli, biocompatibility and scaled up production. Here, we present a one-step method to produce in situ membranes at oil-water interfaces, based on the hydrogen bond complexation of polymers between H-bond acceptor and donor in the oil and aqueous phases, respectively. Read More


In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a fixed amount of time, while it waits for an ATP molecule binding and triggering the impulse, during an exponentially distributed time lapse. The polymer is modelled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment modelled with a Langevin dynamics at fixed temperature. Read More


Using agent-based simulations of self-propelled particles subject to short-range repulsion and nematic alignment we explore the dynamical phases of a dense active material confined to the surface of a sphere. We map the dynamical phase diagram as a function of curvature, alignment strength and activity and reproduce phases seen in recent experiments on active microtubules moving on the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1/2 defects. Read More


We investigate crack propagation in a simple two-dimensional visco-elastic model and find a scaling regime in the relation between the propagation velocity and energy release rate or fracture energy, together with lower and upper bounds of the scaling regime. On the basis of our result, the existence of the lower and upper bounds is expected to be universal or model-independent: the present simple simulation model provides generic insight into the physics of crack propagation, and the model will be a first step towards the development of a more refined coarse-grained model. Relatively abrupt changes of velocity are predicted near the lower and upper bounds for the scaling regime and the positions of the bounds could be good markers for the development of tough polymers, for which we provide simple views that could be useful as guiding principles for toughening polymer-based materials. Read More


Exploiting the energy of randomly moving active agents such as bacteria is a fascinating way to power a microdevice. Here we show, by simulations, that a chain-grafted disk-like colloid can rotate unidirectionally when immersed in a thin film of active particle suspension. The spontaneous symmetry breaking of chain configurations is the origin of the unidirectional rotation. Read More