Physics - Soft Condensed Matter Publications (50)

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Physics - Soft Condensed Matter Publications

Many amorphous materials show spatially heterogenous dynamics, as different regions of the same system relax at different rates. Such a signature, known as Dynamic Heterogeneity, has been crucial to understand the jamming transition in simple model systems and, currently, is considered very promising to characterize more complex fluids of industrial and biological relevance. Unfortunately, measurements of dynamic heterogeneities typically require sophysticated experimental set-ups and are performed by few specialized groups. Read More


Non-neutrally buoyant soft particles in vertical microflows are investigated. We find, soft particles lighter than the liquid migrate to off-center streamlines in a downward Poiseuille flow (buoyancy-force antiparallel to flow). In contrast, heavy soft particles migrate to the center of the downward (and vanishing) Poiseuille flow. Read More


Mechanical systems can display topological characteristics similar to that of topological insulators. Here we report a large class of topological mechanical systems related to the BDI symmetry class. These are self-assembled chains of rigid bodies with an inversion center and no reflection planes. Read More


We relate the breakdown of equations of states for the mechanical pressure of generic dry active systems to the lack of momentum conservation in such systems. We show how sources and sinks of momentum arise generically close to confining walls. These typically depend on the interactions of the container with the particles, which makes the mechanical pressure a container-dependent quantity. Read More


Artificially synthesized Janus particles have tremendous prospective as in-vivo drug-delivery agents due to the possibility of self-propulsion by external stimuli. Here we report the first ever computational study of translational and rotational motion of self-propelled Janus tracers in a het- erogeneous polymeric environment. The presence of polymers makes the translational mean square displacement (MSD) of the Janus tracer to grow very slowly as compared to that of a free Janus tracer, but surprisingly the mean square angular displacement (MSAD) is significantly increased as observed in a recent experiment. Read More


We study triangulated surface models with nontrivial surface metrices for membranes. The surface model is defined by a mapping ${\bf r}$ from a two dimensional parameter space $M$ to the three dimensional Euclidean space ${\bf R}^3$. The metric variable $g_{ab}$, which is always fixed to the Euclidean metric $\delta_{ab}$, can be extended to a more general non-Euclidean metric on $M$ in the continuous model. Read More


Collective cell migration is a highly regulated process involved in wound healing, cancer metastasis and morphogenesis. Mechanical interactions among cells provide an important regulatory mechanism to coordinate such collective motion. Using a Self-Propelled Voronoi (SPV) model that links cell mechanics to cell shape and cell motility, we formulate a generalized mechanical inference method to obtain the spatio-temporal distribution of cellular stresses from measured traction forces in motile tissues and show that such traction-based stresses match those calculated from instantaneous cell shapes. Read More


When a droplet (which size is characterized by R) is confined between two parallel planes, its morphology will change accordingly to either varying the volume of the droplet or the separation (characterized by h) between the planes. We are aiming at investigating how such geometric confinement affects the wetting behaviours of a droplet. Our focus lies on two distinguished regimes: (1) a pancake shape in a Hele-Shaw cell when the droplet is highly compressed (i. Read More


We analyze the statistics of loops formation in $f$-branched star polymers in an environment with structural defects, correlated at large distances $r$ according to a power law $\sim r^{-a}$. Applying the direct polymer renormalization approach, we found the values of the set of universal exponents, governing the scaling of probabilities of various types of loops in macromolecules. Read More


The salt-induced microheterogeneity (MH) formation in binary liquid mixtures is studied by small-angle X-ray scattering (SAXS) and liquid state theory. Previous experiments have shown that this phenomenon occurs for antagonistic salts, whose cations and anions prefer different components of the solvent mixture. However, so far the precise mechanism leading to the characteristic length scale of MHs remained unclear. Read More


The viscoelastic behavior of composites consisting of spindle-shaped hematite particles in poly-N-isopropylacrylamide hydrogels is investigated both, by means of rheological oscillatory shear experiments, and the field-induced alignment of these mesoscale, anisotropic particles in external magnetic fields. Due to their magnetic moment and magnetic anisotropy hematite spindles align with their long axis perpendicular to the direction of an external magnetic field. The field induced torque acting on the magnetic particles leads to an elastic deformation of the hydrogel matrix. Read More


We study frictionless and non-adhesive contact between elastic half-spaces with self-affine surfaces. Using a recently suggested corrective technique, we ensure an unprecedented accuracy in computation of the true contact area evolution under increasing pressure. This accuracy enables us to draw conclusions on the role of the surface's spectrum breadth (Nayak parameter) in the contact area evolution. Read More


We theoretically investigate the coexistences of lamellar phases both in binary and ternary surfactant solutions. The previous free energy of a lamellar stack is extended to take into account the translational entropy of membrane segments. The obtained phase diagram for binary surfactant solutions (surfactant/water mixtures) shows a phase separation between two lamellar phases and also exhibits a critical point. Read More


Active systems on curved geometries are ubiquitous in the living world. In the presence of curvature orientationally ordered polar flocks are forced to be inhomogeneous, often requiring the presence of topological defects even in the steady state due to the constraints imposed by the topology of the underlying surface. In the presence of spontaneous flow the system additionally supports long-wavelength propagating sound modes which get gapped by the curvature of the underlying substrate. Read More


The flow of water confined to nanometer-sized pores is central to a wide range of subjects from biology to nanofluidic devices. Despite its importance, a clear picture about nanoscale fluid dynamics is yet to emerge. Here we measured dissipation in less than 20 nm thick water films and it was found to decrease for both wetting and non-wetting confining surfaces. Read More


In this paper, we proposed a stochastic model which describes two species of particles moving in counterflow. The model generalizes the theoretical framework describing the transport in random systems since particles can work as mobile obstacles, whereas particles of one species move in opposite direction to the particles of the other species, or they can work as fixed obstacles remaining in their places during the time evolution. We conducted a detailed study about the statistics concerning the crossing time of particles, as well as the effects of the lateral transitions on the time required to the system reaches a state of complete geographic separation of species. Read More


The diffusion of a Janus rod-shaped nanoparticle in a dense Lennard-Jones fluid is studied using molecular dynamics (MD) simulations. The Janus particle is modeled as a rigid cylinder whose atoms on each half-side have different interaction energies with fluid molecules, thus comprising wetting and nonwetting surfaces. We found that both rotational and translational diffusion coefficients are larger for Janus particles with higher wettability contrast, and these values are bound between the two limiting cases of uniformly wetting and nonwetting particles. Read More


In this work, we use flow visualization and rheometry techniques to study the dynamics and evolution of secondary flows in a model wormlike micellar solution sheared between concentric cylinders, i.e., in a Taylor-Couette (TC) cell. Read More


Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We perform measurements on the endothermic and relatively slow enzyme aldolase, which also shows substrate-induced enhanced diffusion. We propose a new physical paradigm, which reveals that the diffusion coefficient of a model enzyme hydrodynamically coupled to its environment increases significantly when undergoing changes in conformational fluctuations in a substrate-dependent manner, and is independent of the overall turnover rate of the underlying enzymatic reaction. Read More


We present parallel version of Rosenbluth Self-Avoiding Walk generation method implemented on Graphics Processing Units (GPUs) using CUDA libraries. The method scales almost linearly with the number of CUDA cores and the method efficiency has only hardware limitations. The method is introduced in two realizations: on a cubic lattice and in real space. Read More


We revisit the celebrated Wilemski-Fixman (WF) treatment for the looping time of a free-draining polymer. The WF theory introduces a sink term into the Fokker-Planck equation for the $3(N+1)$-dimensional Ornstein-Uhlenbeck process of the polymer dynamics, which accounts for the appropriate boundary condition due to the formation of a loop. The assumption for WF theory is considerably relaxed. Read More


We present a high accuracy Monte Carlo simulation study of the Isotropic - Nematic phase transition of a lattice dispersion model of biaxial liquid crystals. The NI coexistence curve terminating at the Landau critical point have been determined using multiple histogram reweighting technique. A close investigation reveals a sharp departure in the nature of the $N$-$I$ coexistence curve in temperature- biaxiality parameter phase diagram in comparison to the earlier theoretical (either mean-field or computer simulation) predictions. Read More


Capillary forces acting at the surface of a liquid drop can be strong enough to deform small objects and recent studies have provided several examples of elastic instabilities induced by surface tension. We present such an example where a liquid drop sits on a straight fiber, and we show that the liquid attracts the fiber which thereby coils inside the drop. We derive the equilibrium equations for the system, compute bifurcation curves, and show the packed fiber may adopt several possible configurations inside the drop. Read More


We discuss instabilities of fluid films of nanoscale thickness, with a particular focus on films where the destabilising mechanism allows for linear instability, metastability, and absolute stability. Our study is motivated by nematic liquid crystal films; however we note that similar instability mechanisms, and forms of the effective disjoining pressure, appear in other contexts, such as the well-studied problem of polymeric films on two-layered substrates. The analysis is carried out within the framework of the long-wave approximation, which leads to a fourth order nonlinear partial different equation for the film thickness. Read More


Friction in ordered atomistic layers plays a central role in various nanoscale systems ranging from nanomachines to biological systems. It governs transport properties, wear and dissipation. Defects and incommensurate lattice constants dramatically change these properties. Read More


Gene drives have the potential to rapidly replace a harmful wild-type allele with a gene drive allele engineered to have desired functionalities. However, an accidental or premature release of a gene drive construct to the natural environment could damage an ecosystem irreversibly. Thus, it is important to understand the spatiotemporal consequences of the super-Mendelian population genetics prior to potential applications. Read More


Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule is denaturated. It is known that the extension and shape of the SR depend on i) the specific protein residue-residue interactions in the native state of the amino acids sequence and ii) the water properties at the hydration interface. Read More


We present a study of the dynamics of small solute particles in a solvent medium where the solute is much smaller in size, mimicking the diffusion of small particles in crowded environment. The solute exhibits Fickian diffusion arising from non-Gaussian Van Hove correlation function. Our study shows that there are at least two possible origins of this non-Gaussian behaviour: the decoupling of the solute-solvent dynamics and the intermittency in the solute motion, the latter playing a dominant role. Read More


We study different types of microswimmers moving in channels with varying cross section and thereby interacting hydrodynamically with the channel walls. Starting from the Smoluchowski equation for a dilute suspension, for which interactions among swimmers can be neglected, we derive analytic expressions for the lateral probability distribution between plane channel walls. For weakly corrugated channels we extend the Fick--Jacobs approach to microswimmers and thereby derive an effective equation for the probability distribution along the channel axis. Read More


We apply second order Andersen-Weeks-Chandler perturbation theory to the one-component sticky-hard-spheres fluid. We compare the results with the mean spherical approximation, the Percus-Yevick approximation, two generalized Percus-Yevick approximations, and the Monte Carlo simulations. Read More


We investigate the elastic wave propagation in various hyperelastic materials which subjected to simple-shear deformation. Two compressible types of three conventional hyperelastic models are considered. We found pure elastic wave modes can be obtained in compressible neo-Hookean materials constructed by adding a bulk strain energy term to the incompressible strain energy function. Read More


The biophysical analysis of dynamically formed multi-protein complexes in solution presents a formidable technical challenge. Sedimentation velocity (SV) analytical ultracentrifugation achieves strongly size-dependent hydrodynamic resolution of different size species, and can be combined with multi-component detection by exploiting different spectral properties or temporally modulated signals from photoswitchable proteins. Coexisting complexes arising from self- or hetero-associations that can be distinguished in SV allow measurement of their stoichiometry, affinity, and cooperativity. Read More


Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective variables has proven challenging. Here we suggest that the NMR $S^2$ order parameter can be used to this effect. Read More


Elasticity of soft materials can be greatly influenced by the presence of air bubbles. Such a capillary effect is expected for a wide range of materials, from polymer gels to concentrated emulsions and colloidal suspensions. Whereas experimental results and theory exist for describing the elasto-capillary behavior of bubbly materials (i. Read More


The slip behavior of polydimethylsiloxane (PDMS) polymer melts flowing on non-adsorbing surfaces made of short non-entangled PDMS chains densely end-grafted to silica has been characterized. For high enough shear rates, constant slip lengths proportional to the bulk fluid viscosity have been observed, in agreement with Navier's interfacial equation, and demonstrating that the interfacial Navier's friction coefficient is a local quantity, independent of the polymer molecular weight. Comparing the interfacial shear stresses deduced from these measured slip lengths to available friction stress measured for crosslinked PDMS elastomers, we directly compared the interfacial melt or elastomer friction coefficient to the monomer-monomer friction. Read More


Viscous flows in a quasi-two-dimensional Hele-Shaw geometry can lead to an interfacial instability when one fluid, of viscosity $\eta_{in}$ displaces another of higher viscosity, $\eta_{out}$. Recent studies have shown that there is a delay in the onset of fingering in miscible fluids as the viscosity ratio, $\eta_{in}/\eta_{out}$, increases and approaches unity; the interface can remain stable even though the displacing liquid is less viscous. This paper shows that a delayed onset and stable pattern can occur in immiscible fluids as well. Read More


The observed spatio-temporal ciliary beat patterns on multiciliated epithelia are suspected to be the result of self-organizing processes on various levels. Here, we present an abstract epithelium model at the pluricellular level, which intends to make the self-organization of ciliary beating patterns as well as of the associated fluid transport across the airway epithelium plausible. Ciliated cells are modeled in terms of locally interacting oscillating two-state actuators. Read More


We report a novel form of convection in suspensions of the bioluminiscent marine bacterium $Photobacterium~phosphoreum$. Suspensions of these bacteria placed in a chamber open to the air create persistent luminiscent plumes most easily visible when observed in the dark. These flows are strikingly similar to the classical bioconvection pattern of aerotactic swimming bacteria, which create an unstable stratification by swimming upwards to an air-water interface, but they are a puzzle since the strain of $P. Read More


Influence of magnitude and direction of static magnetic field applied on a drying drop of a laboratory synthesized water base ferrofluid placed on a plane glass plate is investigated. Like all other multi-component fluid this drop also exhibited familiar coffee ring pattern in absence of field while, this pattern is modulated by applying magnetic field and thickness of the ring modulated by the applied field and thickness of the ring decreases exponentially with increase in field when direction of field is normal to the plane of the substrate. Effect of the field on the evaporation rate and temporal variation of contact angle is also studied. Read More


When dense granular systems are exposed to external forcing, they evolve on the time scale that is typically related to the externally imposed one (shear or compression rate, for example). This evolution could be characterized by observing temporal evolution of contact networks. However, it is not immediately clear whether the force networks, defined on contact networks by considering force interactions between the particles, evolve on a similar time scale. Read More


Active biological systems reside far from equilibrium, dissipating heat even in their steady state, thus requiring an extension of conventional equilibrium thermodynamics and statistical mechanics. In this Letter, we have extended the emerging framework of stochastic thermodynamics to active matter. In particular, for the active Ornstein-Uhlenbeck model, we have provided consistent definitions of thermodynamic quantities such as work, energy, heat, entropy, and entropy production at the level of single, stochastic trajectories and derived related fluctuation relations. Read More


We present Monte Carlo data of the stress-strain diagrams obtained using two different triangulated surface models. The first is the canonical surface model of Helfrich and Polyakov (HP), and the second is a Finsler geometry (FG) model. The shape of the experimentally observed stress-strain diagram is called J-shaped. Read More


Spin-coating technique is very fast, cheap, reproducible, simple and needs less material to fabricate films of particulate systems/colloids. Their thickness and uniformity may be controlled by means of external fields. We apply magnetic fields during the spin-coating of a moderately concentrated superparamagnetic colloid (made of silica coated magnetite particles). Read More


Population annealing is a hybrid of sequential and Markov chain Monte Carlo methods geared towards the efficient parallel simulation of systems with complex free-energy landscapes. Systems with first-order phase transitions are among the problems in computational physics that are difficult to tackle with standard methods such as local-update simulations in the canonical ensemble, for example with the Metropolis algorithm. It is hence interesting to see whether such transitions can be more easily studied using population annealing. Read More


The J-integral is recognized as a fundamental parameter in fracture mechanics that characterizes the inherent resistance of materials to crack growth. However, the conventional methods to calculate the J-integral, which require knowledge of the exact position of a crack tip and the continuum fields around it, are unable to precisely measure the J-integral of polymer composites at the nanoscale. This work aims to propose an effective calculation method based on coarse-grained (CG) simulations for predicting the J-integral of carbon nanotube (CNT)/polymer composites. Read More


Recent experiments have shown that liquid drops on highly deformable substrates exhibit mutual interactions. This is similar to the Cheerios effect, the capillary interaction of solid particles at a liquid interface, but now the roles of solid and liquid are reversed. Here we present a dynamical theory for this inverted Cheerios effect, taking into account elasticity, capillarity and the viscoelastic rheology of the substrate. Read More


Machine elements and mechanical components have often surfaces with anisotropic roughness, which may result from the machining processes, e.g. grinding, or from wear. Read More


We propose a stochastic method to generate exactly the overdamped Langevin dynamics of semi-flexible Gaussian chains, conditioned to evolve between given initial and final conformations in a preassigned time. The initial and final conformations have no restrictions, and hence can be in any knotted state. Our method allows to generate statistically independent paths in a computationally efficient manner. Read More


Investigating microstructure of suspensions with particles having anisotropic shape that share complex interactions is a challenging task leading to competing claims. This work investigates phase behavior of one such system: aqueous Laponite suspension, which is highly contested in the literature, using rheological and microscopic tools. Remarkably, we observe that over a broad range of Laponite (1. Read More