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Colloidal gels are elasto-plastic materials composed of an out-of-equilibrium, self-assembled network of micron-sized (solid) particles suspended in a fluid. Recent work has shown that far-field hydrodynamic interactions do not change gel structure, only the rate at which the network forms and ages.
One possibility to adjust material properties to a specific need is to embed units of one substance into a matrix of another substance. Even materials that are readily tunable during operation can be generated in this way.
We propose a reaction-diffusion system that converts topological information of an active nematic into chemical signals. We show that a curvature-activated reaction dipole is sufficient for creating a system that dynamically senses topology by producing a concentration field possessing local extrema coinciding with $\...
We present mesoscale numerical simulations based on the coupling of the fluctuating lattice Boltzmann method (FLBM) for multicomponent systems with a wetted finite-size particle model. This newly coupled methodologies are used to study the motion of a spherical particle driven by a constant body force in a confined ch...
The dynamics of ring polymer melts are studied via molecular dynamics simulations of the Kremer-Grest bead-spring model. Rouse mode analysis is performed in comparison with linear polymers by changing the chain length.
We investigate the influence of confinement on phase separation in colloid-polymer mixtures. To describe the particle interactions, the colloid-polymer model of Asakura and Oosawa [J. Chem. Phys. 22, 1255 (1954)] is used.
We develop a theoretical and computational approach to deal with systems that involve a disparate range of spatio-temporal scales, such as those comprised of colloidal particles or polymers moving in a fluidic molecular environment. Our approach is based on a multiscale modeling that combines the slow dynamics of the ...
In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias,...
In this work we compare and characterize the behavior of Langevin and Dissipative Particle Dynamics (DPD) thermostats in a broad range of non-equilibrium simulations of polymeric systems. Polymer brushes in relative sliding motion, polymeric liquids in Poiseuille and Couette flows, and brush-melt interfaces are used a...
This paper summarizes the properties of strongly correlating liquids, i.e., liquids with strong correlations between virial and potential energy equilibrium fluctuations at constant volume. We proceed to focus on the experimental predictions for strongly correlating glass-forming liquids.
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membr...
In this article, we develop a Bayesian approach to estimate parameters from time traces that originate from an overdamped Brownian particle in a harmonic potential, or Ornstein-Uhlenbeck process (OU). We show that least-square fitting the autocorrelation function, which is often the standard way of analyzing such data...
The shape of the cross section of a dense fiber bundle is related to the symmetry of its molecular packing. However, this statement might be belied by type I collagen fibrils which have a rounded section of high symmetry while structural studies suggest that their molecules are assembled with a long range lateral orde...
We present a new method based on the scattering technique to investigate fluctuation-induced forces at a fluid interface. The scattering approach, well suited to the study of many body systems of arbitrary geometries, is augmented to include boundary fluctuations.
Sessile drying droplets in various bio-relevant systems, encompassing passive bio-colloids like DNA, proteins, and blood to active microbes, gain considerable attention due to intricate interplay among different convective flows, droplet pinning, mechanical stress, wettability, and the emergence of distinctive patterns...
Polymer droplets subjected to a heated environment have significance in several fields ranging from spray drying and powder formation to surface coating. In the present work, we investigate the evaporation of a high viscoelastic modulus aqueous polymeric droplet in an acoustically levitated environment.
Near field hydrodynamic interactions are essential to determine many important emergent behaviors observed in active suspensions, but have not been successfully modeled so far. In this work we propose an effective model capable of efficiently capturing the essence of the near field hydrodynamic interactions, validated...
We examine analytically equilibrium conformations of elastic chains of paramagnetic beads in the presence of a precessing magnetic field. Conformations of these filaments are determined by minimizing their total energy, given in the harmonic approximation by the sum of the bending energy, quadratic in its curvature, a...
We perform extensive Monte Carlo simulations to investigate the phase behaviour of colloidal suspensions of hard board-like particles (HBPs). While theories restricting particle orientation or ignoring higher ordered phases suggest the existence of a stable biaxial nematic phase, our recent simulation results on monod...
In this study, we implement the deviatoric curvature model to examine dynamically triangulated surfaces with anisotropic membrane inclusions. The Monte-Carlo numerical scheme is devised to not only minimize the total bending energy of the membrane but also the in-plane nematic order of the inclusions by considering th...
Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling.
Granular flows in small-outlet hoppers exhibit several characteristic but poorly understood behaviors: temporary clogs (pauses) where flow stops before later spontaneously restarting, permanent clogs that last indefinitely, and non-Gaussian, non-monotonic flow-rate statistics. These aspects have been studied independe...
Incompressibility is established for three-dimensional and two-dimensional deformations of an anisotropic linearly elastic material, as conditions to be satisfied by the elastic compliances. These conditions make it straightforward to derive results for incompressible materials from those established for the compressi...
The interfacial behavior of active Brownian polymer (ABPO) is studied by Langevin dynamics simulations. On the dependence of adsorption strength and activity characterized by Peclet number (Pe), the polymer displays two typical states on the surface: adsorption and desorption states.
Conical microfluidic channels filled with electrolytes exhibit volatile memristive behavior, offering a promising platform for energy-efficient, neuromorphic computing. Here, we integrate these iontronic channels as additional nonlinear elements in nonlinear Shinriki-inspired oscillators and demonstrate that they exhi...
This study uses advanced numerical methods to estimate the mean force potential (PMF) between charged, polarizable colloidal particles in dense electrolytes. We observe that when the Debye screening length, $\lambda_{\mathrm{D}}$, is below the hydrated ion size, the PMF shows discernible oscillations of purely electro...
We study the deformation of soft solid layers in the presence of sessile droplets or capillary bridges. By incorporating the surface tension balance at the contact line, we examine the rotation of the wetting ridge and the corresponding change in the contact angle.
Quantized vortex states of weakly interacting Bose-Einstein condensate of atoms with attractive interatomic interaction in an axially symmetric harmonic oscillator trap are investigated using the numerical solution of the time-dependent Gross-Pitaevskii (GP) equation obtained by the semi-implicit Crank-Nicholson method...
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to non-trivial mechanical responses.
We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from th...
Collective cellular movement plays a crucial role in many processes fundamental to health, including development, reproduction, infection, wound healing, and cancer. The emergent dynamics that arise in these systems are typically thought to depend on how cells interact with one another and the mechanisms used to drive...
Recent literature indicates that attractive interactions between particles of a dense liquid play a secondary role in determining its bulk mechanical properties. Here we show that, in contrast with their apparent unimportance to the bulk mechanics of dense liquids, attractive interactions can have a major effect on ma...
This paper aims to provide an introduction to a basic form of the ${\bf Q}$-tensor approach to modelling liquid crystals, which has seen increased interest in recent years. The increase in interest in this type of modelling approach has been driven by investigations into the fundamental nature of defects and new appli...
We present results from Langevin dynamics simulations of a glassy active-passive mixture of soft-repulsive binary colloidal disks. Activity on the smaller particles is applied according to the quorum sensing scheme, in which a smaller particle will be active for a persistence time if its local nearest neighbors are eq...
We consider a simple model of an internally driven self-rotating object; a rotor, confined to two dimensions by a thin film of low Reynolds number fluid. We undertake a detailed study of the hydrodynamic interactions between a pair of rotors and find that their effect on the resulting dynamics is a combination of fast...
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully upon binding.
Thermo-osmotic flows, generated by applying a thermal gradient along a liquid-solid interface, could be harnessed to convert waste heat into electricity. While this phenomenon has been known for almost a century, there is a crucial need to gain a better understanding of the molecular origins of thermo-osmosis.
The sudden arrest of flow by formation of a stable arch over an outlet is a unique and characteristic feature of granular materials. Previous work suggests that grains near the outlet randomly sample configurational flow microstates until a clog-causing flow microstate is reached.
In this paper, an exact unitary transformation is examined that allows for the construction of solutions of coupled nonlinear Schr{ö}dinger equations with additional linear field coupling, from solutions of the problem where this linear coupling is absent. The most general case where the transformation is applicable i...
We suppose and develop a simple quantitative model of polymer film conductivity. This model can be seen as a further development of the ideas of Vlasov, Apresyan et al.
Cosmic large-scale structures, animal flocks, and living tissues are non-equilibrium organized systems created by dissipative processes. Despite the uniqueness, the realization of dissipative structures is still difficult.
In three-dimensional discrete element method (DEM) simulations, the particle motions within a granular assembly can produce bewildering sequences of movements at the contacts between particle pairs. With frictional contacts, the relationship between contact movement and force is non-linear and path-dependent, requirin...
In this article, we present a mathematical model that answers a classical question concerning how much force, which is generally called static friction force, will it require to initiate the motion of a soft solid block such as gel, rubber or elastomer on a hard surface for instance glass surface. The model uses popul...
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is hereby recognized as a nontrivial heteropolymer property capable of providing fundam...
Interfacial polar molecules feature a strongly anisotropic response to applied electric field, favoring dipole orientations parallel to the interface. In water, in particular, this effect combines with generic orientational preferences induced by spatial asymmetry of water hydrogen bonding under confined geometry, whi...
Solid-state superconducting circuits are versatile systems in which quantum states can be engineered and controlled. Recent progress in this area has opened up exciting possibilities for exploring fundamental physics as well as applications in quantum information technology; in a series of experiments it was shown tha...
Bond-orientational order in DNA-assembled nanoparticle lattices is explored with the help of recently introduced Symmetry-specific Bond Order Parameters (SymBOPs). This approach provides a more sensitive analysis of local order than traditional scalar Bond Order Parameters, facilitating the identification of coherent ...
Understanding the organization of matter under the long-range electrostatic force is a fundamental problem in multiple fields. In this work, based on the electrically charged tethered membrane model, we reveal regular structures underlying the lowest-energy states of inhomogeneously stretched planar lattices by a comb...
The structural properties of static, jammed packings of monodisperse spheres in the vicinity of the jamming transition are investigated using large-scale computer simulations. At small wavenumber $k$, we argue that the anomalous behavior in the static structure factor, $S(k) \sim k$, is consequential of an excess of l...
Recent magnetic tweezers experiments have reported systematic deviations of the twist response of double-stranded DNA from the predictions of the twistable worm-like chain model. Here we show, by means of analytical results and computer simulations, that these discrepancies can be resolved if a coupling between twist ...
We consider the sedimentation of a colloidal gel under confinement in the direction of gravity. The confinement allows us to compare directly experiments and computer simulations, for the same system size in the vertical direction.
In recent experiments [M. Dubois, B. Demé, T. Gulik-Krzywicki, J.-C. Dedieu, C. Vautrin, S. Désert, E. Perez, and T. Zemb, Nature (London) Vol. 411, 672 (2001)] the spontaneous formation of hollow bilayer vesicles with polyhedral symmetry has been observed. On the basis of the experimental phenomenology it was suggest...
Osmosis is a universal phenomenon occurring in a broad variety of processes and fields. It is the archetype of entropic forces, both trivial in its fundamental expression - the van 't Hoff perfect gas law - and highly subtle in its physical roots.
Langevin dynamics is used to study equilibrium properties of the suspension of magnetic filaments (chains of nanoparticles permanently crosslinked with polymers). It is shown that the filament suspension generally has a larger magnetic susceptibility than the system of unlinked nanoparticles with the same average part...
A novel polar coordinate lattice Boltzmann kinetic model for detonation phenomena is presented and applied to investigate typical implosion and explosion processes. In this model, the change of discrete distribution function due to local chemical reaction is dynamically coupled into in the modified lattice Boltzmann e...
We prepare a degenerate Fermi gas of potassium atoms by sympathetic cooling with rubidium atoms in a one-dimensional optical lattice. In a tight lattice we observe a change of the density of states of the system, which is a signature of quasi two dimensional confinement.
Unstable growth of cracks (rough crack surface and crack branching) in dynamic fracture has long been observed in various materials. Until now, there was no universally agreed upon explanation for these instabilities.
As a first step to understanding the role of molecular or chemical polydispersity in self-assembly, we put forward a coarse-grained model that describes the spontaneous formation of quasi-linear polymers in solutions containing two self-assembling species. Our theoretical framework is based on a two-component self-ass...
We study the transport of Brownian particles under a constant driving force and moving in channels that present a varying centerline but have constant aperture width. We investigate two types of channels, {\it solid} channels in which the particles are geometrically confined between walls and {\em soft} channels in wh...
Using an athermal quasistatic simulation protocol, we study the distribution of free volumes in sheared hard-particle packings close to, but below, the random-close packing threshold. We show that under shear, and independent of volume fraction, the free volumes develop features similar to close-packed systems -- part...
Although ubiquitous in nature and industrial processes, transport processes at the interface during evaporation and condensation are still poorly understood. Experiments have shown temperature discontinuities at the interface during evaporation and condensation but the experimentally reported interface temperature jum...
We investigate the nonequilibrium dynamics of spherical active Brownian particles in three spatial dimensions that interact via a pair potential. The investigation is based on a predictive local field theory that is derived by a rigorous coarse-graining starting from the overdamped Langevin dynamics of the particles.
We use computer simulations to study highly dense systems of granular particles that are driven by oscillating forces. We implement different dissipation mechanisms that are used to extract the injected energy.
Condensation of objects into stable clusters occurs naturally in equilibrium and driven systems. It is commonly held that potential interactions, depletion forces, or sensing are the only mechanisms which can create long-lived compact structures.
Applying very small purely radial strains on amorphous solids in radial geometry one observes elastic responses that break the radial symmetry. Without any plasticity involved, the responses indicate nonlinear mode coupling contributions even for minute strains.
We study the linearized hydrodynamics of a two-component fluid membrane near a repulsive wall, via a model which incorporates curvature- concentration coupling as well as hydrodynamic interactions. This model is a simplified version of a recently proposed one [J.-B. Manneville et al. Phys. Rev. E, 64, 021908 (2001)] f...
Inevitably, almost all cancer patients develop resistance to targeted therapy. Intratumor heterogeneity (ITH) is a major cause of drug resistance.
We numerically study the dynamics of a polydisperse double emulsion under a symmetric shear flow. We show that both dispersity and shear rate crucially affect the behavior of the innermost drops and of the surrounding shell.
We construct a coupled map lattice model for the spontaneous pore formation in anodic oxidation in two dimensions and perform numerical simulations, after we explain steady flat solutions, their linear stability and a single pore solution for a model of Parkhutik and Shershulsky.
We perform local measurements of both the shear rate and the particle fraction to study viscous resuspension in non-Brownian suspensions. A suspension of PMMA spherical particles dispersed in a lighter Newtonian fluid (Triton X100) is sheared in a vertical Couette cell.
Elastic membranes composed of paramagnetic beads offer the possibility of assembling versatile actuators operated autonomously by external magnetic fields. Here we develop a theoretical framework to study shapes of such paramagnetic membranes under the influence of a fast precessing magnetic field.
We investigate the desiccation crack patterns on the surface of a drying paste made of calcium carbonate (CaCO$_3$) powder and distilled water. Forced vibration of the CaCO$_3$ paste prior to drying results in an anisotropic crack pattern, in which many long cracks develop along a specific preferred direction.
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this important material parameter.
An important task in the simulation of hard spheres and other hard particles is structure prediction via equilibration. Event-driven molecular dynamics is efficient because its Newtonian dynamics equilibrates fluctuations with the speed of sound.
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal filaments over artificial and biological swimmers on microscopic to groups of a...
We perform molecular-dynamics simulations of the vibrational and the elasto-plastic properties of polymeric glasses and crystals and corresponding atomic systems. We evidence that the elastic scaling of the density of states in the low-frequency boson peak (BP) region is different in crystals and glasses.
The transition from a nematic to an isotropic state in a self-closing spherical liquid crystal shell with tangential alignment is a stimulating phenomenon to investigate, as the topology dictates that the shell exhibits local isotropic points at all temperatures in the nematic phase range, in the form of topological de...
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.
We report numerical results for velocity correlations in dense, gravity-driven granular flow down an inclined plane. For the grains on the surface layer, our results are consistent with experimental measurements reported by Pouliquen.
We extend the Doering-Constantin approach to upper bounds on energy dissipation in turbulent flows by introducing a balance parameter into the variational principle. This parameter governs the relative weight of different contributions to the dissipation rate.
Nanoparticle self-assembly is an efficient bottom-up strategy for the creation of nanostructures. In the standard approach, ligands are grafted on the surfaces of nanoparticles to keep them separated and control interparticle interactions.
A straightforward analytical scheme is proposed for computing the long-time, asymptotic mean velocity and dispersivity (effective diffusivity) of a particle undergoing a discrete biased random walk on a periodic lattice amongst an array of immobile, impenetrable obstacles. The results of this Taylor-Aris dispersion-ba...
Non-equilibrium molecular dynamics simulations were performed to study the thermodynamic, structural, and dynamical properties of the single-component Lennard-Jones and the Kob-Andersen binary Lennard-Jones liquids. Both systems are known to be strongly correlating, i.e., have strong correlations between equilibrium t...
We present a 2D lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single Oxygen at the center of a site and two Hydrogen atoms on each side.
We propose an alternative mechanism for the gating of biological membrane channels in response to membrane tension that involves a change in the slope of the membrane near the channel. Under biological membrane tensions we show that the energy difference between the closed (tilted) and open (untilted) states can far e...
The variation of energies associated with soft matter interfaces where surface inhomogeneities are present. These energies include the total bending and splay energy, the variable surface tension energy, a coupling energy between the total curvature and an underlying surface concentration field, the energy due to an e...
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctuation relation, the system free energy landscape is evaluated.
Sufficiently dense intrinsically out-of-equilibrium suspensions, such as those observed in biological systems, can be modelled as active fluids characterised by their orientational symmetry. While mesoscale numerical approaches to active nematic fluids have been developed, polar fluids are simulated as either ensemble...
We consider a model mixture of hard colloidal spheres and non-adsorbing polymer chains in a theta solvent. The polymer component is modelled as a polydisperse mixture of effective spheres, mutually noninteracting but excluded from the colloids, with radii that are free to adjust to allow for colloid-induced compressio...
We demonstrate that a discontinuous shear thickening (DST) can take place even in a moderately dense inertial suspension consisting of frictionless soft particles. This DST can be regarded as an ignited-quenched transition in the inertial suspension.
Liquid marbles, droplets coated with a granular layer, are highly mobile as particles prevent capillary adhesion with the substrate. Yet, they exhibit static friction due to their granular shell, which resists rolling until it yields.
Myelin figures (MFs) -- cylindrical lyotropic liquid crystalline structures consisting of concentric arrays of bilayers and aqueous media -- arise from the hydration of the bulk lamellar phase of many common amphiphiles. Prior efforts have concentrated on the formation, structure, and dynamics of myelin produced by ph...
Glasses are structurally liquid-like, but mechanically solid-like. Most attempts to understand glasses start from liquid state theory.
Sub-nanometer aqueous clusters containing a single trivalent metal cation can exhibit charge-induced structural instabilities. Here, we present computational evidence that clusters containing a single \ce{Fe^{3+}}, \ce{Lu^{3+}}, or \ce{La^{3+}} ion undergo continuous geometric transformations as a consequence of this ...
We investigate the onset of the wall-induced convection in vertically vibrated granular matter by means of experiments and two-dimensional computer simulations. In both simulations and experiments we find that the wall-induced convection occurs inside the bouncing bed region of the parameter space in which the granula...
Capturing the correct dynamics at the Coarse-Grained (CG) scale remains a central challenge in the advancement of systematic CG models for soft matter simulations. The Generalized Langevin Equation (GLE), rooted in the Mori-Zwanzig formalism, provides a robust framework for incorporating friction and stochastic forces...
The reorientation behaviour of a smectic-A (SmA) elastomer deformed parallel to the smectic layer normal has been interpreted as a Sm-C like transition by Stenull and Lubensky. Experiments, however, prove that such a transition does not occur.
We propose a theoretical framework for dealing with a transient polymer network undergoing small deformations, based on the rate of breaking and re-forming of network crosslinks and the evolving elastic reference state. In this framework, the characteristics of the deformed transient network at microscopic and macrosc...
To further understand the complex behavior of swimming microorganisms, the spontaneous motion of nonliving matter provides essential insights. While substantial research has focused on quantitatively analyzing complex behavioral patterns, characterizing these dynamics aiming for inclusive comparison to the behavior of...
We perform molecular dynamics simulations to characterize the occurrence of inhomogeneous shear flows in soft jammed materials. We use rough walls to impose a simple shear flow and study the athermal motion of jammed assemblies of soft particles, both for purely repulsive interactions and in the presence of an additio...

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