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Catalytic swimmers have attracted much attention as alternatives to biological systems for examining collective microscopic dynamics and the response to physico-chemical signals. Yet, understanding and predicting even the most fundamental characteristics of their individual propulsion still raises important challenges...
A constitutive model is presented for brittle granular materials based on a recent reformulation of the breakage mechanics theory. Compared with previous breakage mechanics-based models, the proposed model is improved to capture strain softening towards the critical state following the peak stress observed in dense sp...
We perform systematic simulation experiments on model systems with soft-sphere repulsive interactions to test the predicted dynamic equivalence between soft-sphere liquids with similar static structure. For this we compare the simulated dynamics (mean squared displacement, intermediate scattering function, {\alpha}-re...
The transport of sediment by a fluid along the surface is responsible for dune formation, dust entrainment and for a rich diversity of patterns on the bottom of oceans, rivers, and planetary surfaces. Most previous models of sediment transport have focused on the equilibrium (or saturated) particle flux.
Velocity jumps observed for crack propagation under a static boundary condition have been used as a controlling factor in developing tough rubbers. However, the static test requires many samples to detect the velocity jump.
We demonstrated recently that polyelectrolytes with cationic moieties along the chain and a single anionic head are able to form physical hydrogels due to the reversible nature of the head-to-body ionic bond. Here we generate a variety of such polyelectrolytes with various cationic moieties and counterion combinations...
Using nonequilibrium computer simulations, we study the response of ferromagnetic nanofilaments, consisting of stabilized onedimensional chains of ferromagnetic nanoparticles, under external rotating magnetic fields. In difference with their analogous microscale and stiff counterparts, which have been actively studied...
Networks of semiflexible or stiff polymers such as most biopolymers are known to deform inhomogeneously when sheared. The effects of such non-affine deformation have been shown to be much stronger than for flexible polymers.
We propose a generalization of stochastic thermodynamics to systems of active particles, which move under the combined influence of stochastic internal self-propulsions (activity) and a heat bath. The main idea is to consider joint trajectories of particles' positions and self-propulsions.
Microscopic relaxation timescales are estimated from the autocorrelation functions obtained by dynamic light scattering experiments for Laponite suspensions with different concentrations ($C_{L}$), added salt concentrations ($C_{S}$) and temperatures ($T$). It has been shown in an earlier work [Soft Matter, 10, 3292-3...
Both non-neural and neural biological systems can learn. So rather than focusing on purely brain-like learning, efforts are underway to study learning in physical systems.
Recent experiments have shown that surface stresses in soft materials can have a significant strain-dependence. Here we explore the implications of this surface elasticity to show how, and when, we expect it to arise.
We compare two recently developed mesoscale models of binary immiscible and ternary amphiphilic fluids. We describe and compare the algorithms in detail and discuss their stability properties.
Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other...
Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. <br>Motivated by these questions we construct a generic hydrodynamic theory for lipid membranes {that are active, due for instance...
Molecular dynamics simulations are used to demonstrate that a binary solvent can be used to stratify colloidal mixtures when the suspension is rapidly dried. The solvent consists of two components, one more volatile than the other.
Experimental measurements of contact forces are limited to spheres and disks in three and two dimensions, making the evaluation of the shape effect and universality of force distributions and the comparison between experiments and theories extremely difficult. Here we present precise measurements of vector contact for...
We simulate a densely jammed, athermal assembly of repulsive soft particles immersed in a solvent. Starting from an initial condition corresponding to a quench from a high temperature, we find non-trivial slow dynamics driven by a gradual release of stored elastic energy, with the root mean squared particle speed deca...
This article is aimed at studying the effects of the dimensional crossover (DC) on physical properties of condensed systems near phase transition and critical points. Here we consider the following problems: (1) the theoretical provisions that allow to study the effect of spatial confinement on DC near phase transitio...
We present a hybrid method for the simulation of colloidal systems, that combines molecular dynamics (MD) with the Lattice-Boltzmann (LB) scheme. The LB method is used as a model for the solvent in order to take into account the hydrodynamic mass and momentum transport through the solvent.
Despite the extensive research that has been conducted for decades on the behavior of confined liquids, detailed knowledge of this phenomenon, particularly in the mixed/boundary lubrication regime, remains limited. This can be attributed to several factors including the difficulty of direct experimental observations o...
Liquid crystal elastomers (LCEs) marry the large deformation response of a cross-linked polymer network with the nematic order of liquid crystals pendent to the network. Of particular interest is the actuation of LCE sheets where the nematic order, modeled by a unit vector called the director, is specified heterogeneo...
We present a numerical method that consistently implements thermal fluctuations and hydrodynamic interactions to the motion of Brownian particles dispersed in incompressible host fluids. In this method, the thermal fluctuations are introduced as random forces acting on the Brownian particles.
Amorphous solids exhibit an excess of low-frequency vibrational modes beyond the Debye prediction, contributing to their anomalous mechanical and thermal properties. Although a $\omega^4$ power-law scaling is often proposed for the distribution of these modes, the precise exponent remains a subject of debate.
Disordered solids respond to quasistatic shear with intermittent avalanches of plastic activity, an example of the crackling noise observed in many nonequilibrium critical systems. The temporal power spectrum of activity within disordered solids consists of three distinct domains: a novel power-law rise with frequency...
We examine sedimentation density profiles of star polymer solutions as an example of colloidal systems in sedimentation equilibrium which exhibit reentrant melting in their bulk phase diagram. Phase transitions between a fluid and a fluid with an intercalated solid are observed below a critical gravitational strength ...
One approach to the understanding of fusion in cells and model membranes involves stalk formation and expansion of the hemifusion diaphragm. We predict theoretically the initiation of hemifusion by stalk expansion and the dynamics of mesoscopic hemifusion diaphragm expansion in the light of recent experiments and theo...
We show by means of continuum theory and simulations that geometric percolation in uniaxial nematics of hard slender particles is fundamentally different from that in isotropic dispersions. In the nematic, percolation depends only very weakly on the density and is, in essence, determined by a distance criterion that d...
Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized macromolecular and colloidal systems. Here we consider a simple aggregation model which di...
We explore the possibility that hyperfine interaction causes the recently discovered organic magnetoresistance (OMAR) effect. Our study employs both experiment and theoretical modelling.
The spreading of a cap-shaped spherical droplet of non-Newtonian power-law liquids on a completely wettable spherical substrate is theoretically studied. Both convex spherical substrates and concave spherical cavities with smooth or rough surfaces are considered.
The age-old idea of "like dissolves like" requires a notion of "likeness" that is hard to quantify for polymers. We revisit the concepts of pure component cohesive energy density $c^{\text{P}}$ and mutual cohesive energy density $c_{12}$ so that they can be extended to polymers.
Self-assembly of nanoparticles at fluid-fluid interfaces is a promising route to fabricate functional materials from the bottom-up. However, directing and controlling particles into highly tunable and predictable structures -- while essential -- is a challenge.
We use self-consistent field theory to determine structural and energetic properties of intermediates and transition states involved in bilayer membrane fusion. In particular, we extend our original calculations from those of the standard hemifusion mechanism, which was studied in detail in the first paper of this ser...
We formulate the dynamical theory of nematic polymers, starting from a microscopic Poisson bracket approach. We find that the Poisson bracket between the nematic director and momentum depends on the (Maier-Saupe) order parameter of the nematic phase.
We investigate the effects of cell division and apopotosis on collective dynamics in two-dimensional epithelial tissues. Our model includes three key ingredients observed across many epithelia, namely cell-cell adhesion, cell death and a cell division process that depends on the surrounding environment.
We use computer simulations to study the existence and stability of a biaxial nematic $N_b$ phase in systems of hard polyhedral cuboids, triangular prisms, and rhombic platelets, characterized by a long ($L$), medium ($M$), and short ($S$) particle axis. For all three shape families, we find stable $N_b$ states provid...
Multitime correlation functions provide useful probes for the ensembles of trajectories underlying the stochastic dynamics of complex systems. These can be obtained by measuring their optical response to sequences of ultrashort optical pulse.
We investigate the dynamics of granular columns of point particles that interact via long-range hydrodynamic interactions and fall under the action of gravity. We investigate the influence of inertia using the Green's function for the Oseen equation.
We have investigated dynamical heterogeneity in a highly supercooled liquid using molecular-dynamics simulations in three dimensions. Dynamical heterogeneity can be characterized by three quantities: correlation length $\xi_4$, intensity $\chi_4$, and lifetime $\tau_{\text{hetero}}$.
Particle shape is a critical parameter that plays an important role in self-assembly, for example, in designing targeted complex structures with desired properties. In the last decades an unprecedented range of monodisperse nanoparticle systems with control over the shape of the particles have become available.
Based on a microscopic density functional theory we investigate the morphology of thin liquidlike wetting films adsorbed on substrates endowed with well-defined chemical heterogeneities. As paradigmatic cases we focus on a single chemical step and on a single stripe.
Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above...
Despite many attempts, the relation between fracture and structure of polymer networks is yet to be clarified. For this problem, a recent study for phantom chain simulations [Macromolecules, 56, 9359 (2023)] has demonstrated that the fracture characteristics obtained for polymer networks with various node functionalit...
Based on numerical simulations of a lattice kinetic model for soft-glassy materials, we characterize the global rheology of a dense emulsion-like system, under three representative load conditions: Couette flow, time-oscillating Strain and Kolmogorov flow. It is found that in all cases the rheology is described by a H...
We study the structure of complexes formed between ionic surfactants (SF) and a single oppositely charged polyelectrolyte (PE) chain. For our computer simulation we use the ``primitive'' electrolyte model: while the polyelectrolyte is modeled by a tethered chain of charged hard sphere beads, the surfactant mol...
Recently, we proposed a method that converts the force between two-large colloids into the pressure on the surface element (FPSE conversion) in a system of a colloidal solution. Using it, the density distribution of the small colloids around the large colloid is calculated.
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by a special three body interaction and impacts on the behaviour both locally and ...
As a method for controlling active materials, researchers have suggested designing patterns of activity on a substrate, which should guide the motion of topological defects. To investigate this concept, we model the behavior of a single defect of topological charge $+1/2$, moving in an activity gradient.
We study the Plateau-Rayleigh instability of a viscoelastic soft solid layer coated on a rigid cylinder i.e., a soft fibre with a rigid core. The onset of instability is examined using a linear stability analysis.
The collective diffusion effects in system of a colloidal particles in a liquid crystal has been proposed. In this article described peculiarity of collective diffusion colloidal particles in a liquid crystal, which can be observe experimentally.
The study of liquid crystals at equilibrium has led to fundamental insights into the nature of ordered materials, as well as to practical applications such as display technologies. Active nematics are a fundamentally different class of liquid crystals, driven away from equilibrium by the autonomous motion of their con...
Insight in the structure of nanoparticle assemblies up to a single particle level is key to understand the collective properties of these assemblies, which critically depend on the individual particle positions and orientations. However, the characterization of large, micron sized assemblies containing small, 10-500 n...
Viral fibers play a central role in many virus infection mechanisms since they recognize the corresponding host and establish a mechanical link to its surface. Specifically, bacteriophages have to anchor to bacteria through the fibers surrounding the tail before starting the viral DNA translocation into the host.
Due to the potential impact on the diagnosis and treatment of various cardiovascular diseases, work on the rheology of blood has significantly expanded in the last decade, both experimentally and theoretically. Experimentally, blood has been confirmed to demonstrate a variety of non-Newtonian rheological characteristi...
Naturally occurring protein fibers often undergo anisotropic swelling when hydrated. Within a tendon, a hydrated collagen fibril's radius expands by 40% but its length only increases by 5%.
In the present work, we developed a sustainable and effective antimicrobial surface film based on Micro-Fibrillated Cellulose. The resulting porous cellulose thin film is barely noticeable to human eyes due to its sub-micron thickness, of which the coverage, porosity and microstructure can be modulated by the formulat...
The parametrically driven, damped Gross-Pitaevskii equation, which models Bose-Einstein condensates in which the interatomic s-wave scattering length is modulated in time, is shown to support spatially modulated states in the form of rolls. A Landau equation with broken phase symmetry is derived, which governs the dyn...
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the development of catalytic surfaces, a number of existing computational and experimental...
In the mimetic membrane system of phosphatidylcholine bilayers, thickening (pre-critical behavior, anomalous swelling) of the bilayers is observed, in the vicinity of the main transition, which is non-linear with temperature. The sterols cholesterol and androsten are used as sensors in a time-resolved simultaneous sma...
In this paper we demonstrate a quantitative way to measure the membrane potential of live cells by dielectric spectroscopy. We also show that the values of the membrane potential obtained using our technique are in good agreement with those obtained using traditional methods-voltage sensitive dyes.
We demonstrate a technique for simultaneously measuring each component of the force vectors and mobility tensor of a small collection of colloidal particles based on observing a set of particle trajectories. For a few-body system of micron-sized polymer beads in oil separated by several particle radii, we find that th...
The nucleation field for infinite magnetic nanotubes, in the case of a magnetic field applied parallel to the long axis of the tubes, is calculated as a function of their geometric parameters and compared with those produced inside the pores of anodic alumina membranes by atomic layer deposition. We also extended this...
Self-dual structures whose dual counterparts are themselves possess unique hidden symmetry, beyond the description of classical spatial symmetry groups. Here we propose a strategy based on { a nematic monolayer of} attractive half-cylindrical colloids to self-assemble these exotic structures.
In this work we develop a theoretical framework for the localization of flow in the steadily flowing regime of sheared disordered solids with inertial dynamics on a microscopic scale. To this aim we perform rheology studies at fixed shear rate on a 3D model of dense disordered solid.
We analyze the dynamics of Brownian ratchets in a confined environment. The motion of the particles is described by a Fick-Jakobs kinetic equation in which the presence of boundaries is modeled by means of an entropic potential.
We present a phenomenological time-dependent Ginzburg-Landau theory of nonlinear plastic deformations in solids. Because the problem is very complex, we first give models in one and two dimensions without vacancies and interstitials, where large strains produce densely distributed slips but the mass density deviations...
A simple kinetic model of a two-component deformable and reactive bilayer is presented. The two differently shaped components are interconverted by a nonequilibrium reaction, and a phenomenological coupling between local composition and curvature is proposed.
The propulsion direction of active particles is a key feature in self-propelled systems and depends on the propulsion mechanism and environmental conditions. Here, using 3D micro-printed catalytically active particles, we experimentally show that the propulsion direction can change with increasing fuel concentration w...
The onset and growth of rigid clusters in a two-dimensional (2D) suspension in shear flow are studied by numerical simulations. The suspension exhibits the lubricated-to-frictional rheology transition, but the key results here are for stresses above the levels that cause extreme shear-thickening.
We propose a method to parameterize a coarse grained model for the hydrodynamic friction between nearly touching rough spheres in suspension flows. The frictional resistance due to surface roughness primarily alters the sliding and rolling modes of motion of rough particles.
An analytic solution for Helfrich spontaneous curvature membrane model (H. Naito, <a href="http://M.Okuda" rel="external noopener nofollow" class="link-external link-http">this http URL</a> and Ou-Yang Zhong-Can, Phys.
Nanodroplets on chemically structured substrates move under the action of disjoining pressure induced forces. A detailed analysis of them shows that even in the absence of long-ranged lateral variations of the effective interface potential, already the fact, that due their small size nano-droplets do not sample the di...
It is known from the wave-like motion of microtubules in motility assays that the piconewton forces that motors produce can be sufficient to bend the filaments. In cellular phenomena such as cytosplasmic streaming, molecular motors translocate along cytoskeletal filaments, carrying cargo which entrains fluid.
An approximative method for solving the Bloch-Torrey equation in general porous media is presented. The method expand the boundaries defining the porous media using electrostatic charges.
We investigate the two-dimensional melting of deformable polymeric particles with multi-body interactions described by the Voronoi model. We report machine learning evidence for the existence of the intermediate hexatic phase in this system, and extract the critical exponent $\nu\approx0.65$ for the divergence of the ...
We present a combined x-ray and neutron reflectivity study characterizing the interface between polystyrene (PS) and silanized surfaces. Motivated by the large difference in slip velocity of PS on top of dodecyl-trichlorosilane (DTS) and octadecyl-trichlorosilane (OTS) found in previous studies, these two systems were...
We investigate the universal orientation-dependent interactions between non-spherical colloidal particles immersed in a critical solvent by studying the instructive paradigm of a needle embedded in bounded two-dimensional Ising models at bulk criticality. For a needle in an Ising strip the interaction on mesoscopic sc...
Ethanol injection and variations of it are a class of methods where two miscible phases---one of which contains dissolved lipids---are mixed together leading to the self-assembly of lipid molecules to form liposomes. This method has been suggested, among other applications, for in-situ synthesis of liposomes as drug d...
In this work, we discuss the connection between the anomalies of the thermodynamic properties, experimentally observed in tertiary butyl alcohol (TBA) and water solutions, and the molecular clustering in these solutions, as revealed by molecular dynamics (MD) simulations. These anomalies are observed in relatively dil...
We present a comprehensive study of a model system of repulsive self-propelled disks in two dimensions with ferromagnetic and nematic velocity alignment interactions. We characterize the phase behavior of the system as a function of the alignment and self-propulsion strength, featuring orientational order for strong a...
In this topical review, we give an overview of the structure and dynamics of a single polymer chain in active baths, Gaussian or non-Gaussian. The review begins with the discussion of single flexible or semiflexible linear polymer chains subjected to two noises, thermal and active.
Chemotaxis allows single cells to self-organize at the population level, as classically described by Keller-Segel models. We show that chemotactic aggregation can be understood using a generalized Maxwell construction based on the balance of density fluxes and reactive turnover.
Diffusive properties of interacting magnetic dipoles confined in a parabolic narrow channel and in the presence of a periodic modulated (corrugated) potential along the unconfined direction are studied using Brownian dynamics simulations. We compare our simulation results with the analytical result for the effective d...
We consider an inextensible, semiflexible polymer or worm-like chain, with persistence length $P$ and contour length $L$, fluctuating in a cylindrical channel of diameter $D$. In the regime $D\ll P\ll L$, corresponding to a long, tightly confined polymer, the average length of the channel $<R_\parallel>$ occupie...
The two-dimensional ordering of bacteriorhodopsins in a lipid bilayer was studied using a binary hard-disk model. The phase diagrams were calculated, taking into account the lateral depletion effects.
We extend our exact reformulation of the bosonic many-body problem in terms of a stochastic Hartree ansatz to a stochastic Gutzwiller ansatz for the Bose Hubbard model. This makes the corresponding Monte Carlo method more efficient for strongly correlated bosonic phases like the Mott insulator phase or the Tonks phase...
Using event-driven molecular dynamics simulations, we quantify how the self diffusivity of confined hard-sphere fluids depends on the nature of the confining boundaries. We explore systems with featureless confining boundaries that treat particle-boundary collisions in different ways and also various types of physical...
Slow flow of a single fluid through a porous medium is well understood on a macroscopic level through Darcy's law, a linear relation between flow rate and a combination of pressure differences, viscosity, and gravitational forces. Two-phase flow is complicated by the interface separating the fluids, but understand...
We study the freezing kinetics of colloidal polycrystals made of micelles of Pluronic F108, a thermosensitive copolymer, to which a small amount of silica nanoparticles of size comparable to that of the micelles are added. We use rheology and calorimetry to measure Tc, the crystallization temperature, and find that Tc...
Membrane-type Acoustic Metamaterials (MAMs) have demonstrated unusual capacity in controlling low-frequency sound transmission/reflection. In this paper, an analytical vibroacoustic membrane model is developed to study sound transmission behavior of the MAM under a normal incidence.
We identify a class of composite membranes: fluid bilayers coupled to an elastic meshwork, that are such that the meshwork's energy is a function $F_\mathrm{el}[A_\xi]$ \textit{not} of the real microscopic membrane area $A$, but of a \textit{smoothed} membrane's area $A_\xi$, which corresponds to the area of th...
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the ...
The deformation of an elastic micro-capsule in an infinite shear flow is studied numerically using a spectral method. The shape of the capsule and the hydrodynamic flow field are expanded into smooth basis functions.
Inspired by recent experiments and simulations on pattern formation in biomolecules by optical tweezers, a theoretical description based on reference interaction site model (RISM) integral equation method is developed to calculate the equilibrium density profiles of small polyelectrolytes in an external potential. The...
In this thesis I present most of the results obtained during my PhD, where I worked on different subjects regarding jamming in systems of frictionless spheres. In particular, I focused on microscopic properties of jammed packings, such as the distribution of contact forces and interparticle gaps, as well as the single...
A variety of self-consistent (SC) equations have been proposed for non-uniform states of liquid particles under external fields, including adsorbed states at solid substrates and confined states in pores. External fields represent not only confining geometries but also fixed solutes.
For amorphous solids, it has been intensely debated whether the traditional view on solids, in terms of the ground state and harmonic low energy excitations on top of it, such as phonons, is still valid. Recent theoretical developments of amorphous solids revealed the possibility of unexpectedly complex free energy la...
We quantify, within mode coupling theory, how changes in the liquid structure affect that of the glass. Apart from the known sensitivity to the structure factor $S(q)$ at wavevectors around the first sharp diffraction peak $q_0$, we find a strong (and inverted) response to structure at wavevectors \emph{below} this pe...
Fingering instabilities akin to the Rayleigh-Taylor (RT) instability in fluids have been observed in a binary granular system consisting of dense and small particles layered on top of lighter and larger particles, when the system is subjected to vertical vibration and fluidizing gas flow. Using observations from exper...

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