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We present a method of calculating the electric charge density of glass and silica surfaces in contact with aqueous electrolytes for two cases of practical relevance that are not amenable to standard techniques: surfaces of low specific area at low ionic strength and surfaces interacting strongly with a second anionic ... |
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. |
``Pasta alla Cacio e pepe'' is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. |
In jamming systems like colloids, emulsions, foams, and biological tissues, significant deformation is essential for processes such as material scraping or wound self-healing. To adequately spread a foam or cream over a surface, external force must be applied to artificially scrape it. |
Fatigue refers to the changes in material properties caused by repeatedly applied loads. It has been widely studied for, e.g., construction materials, but much less has been done on soft materials. |
Monte Carlo simulations of protein folding show the emergence of a strong correlation between the relative contact order parameter, CO, and the folding time, t, of two-state folding proteins for longer chains with number of amino acids, N>=54, and higher contact order, CO > 0.17. The correlation is particularly ... |
We apply a phenomenological theory of polar liquids to calculate the interaction energy between two plane surfaces at nm-distances. We show that depending on the properties of the surface-liquid interfaces, the interacting surfaces induce polarization of the liquid in different ways. |
We utilize total-internal reflection to isolate the two-dimensional `surface foam' formed at the planar boundary of a three-dimensional sample. The resulting images of surface Plateau borders are consistent with Plateau's laws for a truly two-dimensional foam. |
Mechanically stable sphere packings are generated in three-dimensional space using the discrete element method, which span a wide range in structural order, ranging from fully amorphous to quasi-ordered structures, as characterized by the bond orientational order parameter. As the packing pressure, $p$, varies from th... |
A simplistic model, based on the concept of anankeon, is proposed to predict the value of the viscosity of a material in its liquid phase. As a result, within the simplifications and hypothesis made to define the model, it is possible to predict |
The structure of spherical micelles of the diblock poly(styrene-block-acrylic acid) [PS-b-PA] copolymer in water was investigated up to concentrations where the polyelectrolyte coronal layers have to shrink and/or interpenetrate in order to accommodate the micelles in the increasingly crowded volume. We obtained the p... |
Starting from the physics on the grain scale, we develop a simple continuum description of aeolian sand transport. Beyond popular mean-field models, but without sacrificing their computational efficiency, it accounts for both dominant grain populations, hopping (or "saltating") and creeping (or "reptating&... |
We present an automated procedure to assign CATH and SCOP classifications to proteins whose FSSP score is available. CATH classification is assigned down to the topology level and SCOP classification to the fold level. |
We study four double-gyroid (DG) grain boundaries (GBs) with different orientations numerically using the Landau--Brazovskii free energy, including the (422) twin boundary studied recently, a network switching GB, and two tilt GBs. Topological variations and geometric deformations are investigated. |
We develop a analytical and quantitative theory of the tube model concept for entangled networks of semiflexible polymers. The absolute value of the tube diameter L_perp is derived as a function of the polymers' persistence length l_p and mesh size xi of the network. |
We present a series of experiments investigating the flow regimes and repose angles of highly concave particle packings in a rotating drum. By varying grain geometry from spherical to highly non-convex shapes, adjusting frictional properties and the particle number of branches, we examine how these parameters and the ... |
We study numerically the critical behavior and marginal stability of the shear jamming transition for frictionless soft spheres, observed to occur over a finite range of densities, associated with isotropic jamming for densities above the minimum jamming (J-point) density. Several quantities are shown to scale near th... |
In the paper we investigate statistical and topological properties of fractional Brownian polymer chains, equipped with the short-range volume interactions. The attention is paid to statistical properties of collapsed conformations with the fractal dimension $D_f\ge 2$ in the three-dimensional space, which are analyze... |
We investigate the contact of a rigid cylindrical punch with an adhesive beam mounted on flexible end supports. Adhesion is modeled through an adhesive zone model. |
We propose a novel design paradigm for multistate machines where transitions from one state to another are organized by bifurcations of multiple equilibria of the energy landscape describing the collective interactions of the machine components. This design paradigm is attractive since, near bifurcations, small variat... |
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. |
We show that charge inversion, i.e. interfacial charges attracting counterions in excess of their own nominal charge, is a general effect that takes place in most charged systems next to aqueous solutions with multivalent ions and identify three different electrostatic origins for this effect 1) counterion-counterion ... |
We study crystal nucleation under the influence of sedimentation in a model of colloidal hard spheres via Brownian Dynamics simulations. We introduce two external fields acting on the colloidal fluid: a uniform gravitational field (body force), and a surface field imposed by pinning a layer of equilibrium particles (r... |
Brownian diffusion of rod-like polymers in the presence of randomly distributed spherical obstacles is studied using molecular dynamics (MD) simulations. It is observed that dependence of the reduced diffusion coefficient of these macromolecules on the available volume fraction can be described reasonably by a power l... |
We predict the possible existence of a new phase of liquid crystals near the nematic-isotropic ($ NI $) transition. This phase is an achiral, tilt-analogue of the blue phase and is composed of a lattice of {\em double-tilt}, escape-configuration cylinders. |
We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with a modified method of ... |
This paper is an expanded edition of the rapid communication published several years ago by the author (Phys. Rev. B, v76, 041402(R), 2007) on the simulation of wetting transition of water on graphite, aiming to provide more details on the methodology, parameters, and results of the study which might be of interest to... |
We develop and harness a phase field simulation method to study liquid filling on grooved surfaces. We consider both short-range and long-range liquid-solid interactions, with the latter including purely attractive and repulsive interactions, as well as those with short-range attraction and long-range repulsion. |
In low Reynolds number swimming and pumping, differently to everyday experience, a net motion (or flow) can be achieved only if the constructing parts of the swimmer (or pump) follow a non-trivial pattern of motion, in order to break time reciprocity. The case of a driven fan, which spins to create a flow of air, but ... |
We present a theoretical and computational model for the behavior of a porous solid undergoing two interdependent processes, the finite deformation of a solid and species migration through the solid, which are distinct in bulk and on surface. Nonlinear theories allow us to systematically study porous solids in a wide ... |
We derive the Frank elastic constants for nematic solutions of semiflexible polymers. We plot these results as a function of the coarse-grained Maier-Saupe quadrupole aligning strength and polymer stiffness ranging from rigid to highly flexible. |
Deterministic positioning and assembly of colloidal nanoparticles (NPs) onto substrates is a core requirement and a promising alternative to top down lithography to create functional nanostructures and nanodevices with intriguing optical, electrical, and catalytic features. Capillary-assisted particle assembly (CAPA) ... |
In a recent paper [S. Khrapak, Molecules {\bf 25}, 3498 (2000)] the longitudinal and transverse sound velocities of conventional Lennard-Jones systems at the liquid-solid coexistence were calculated. |
We study experimentally statistical properties of the opening times of knots in vertically vibrated granular chains. Our measurements are in good qualitative and quantitative agreement with a theoretical model involving three random walks interacting via hard core exclusion in one spatial dimension. |
A simple criterion for melting of two-dimensional crystals with soft long-ranged interactions is proposed. It states that the ratio of the transverse sound velocity of an ideal crystalline lattice to the thermal velocity is a quasi-universal number close to $4.3$ at melting. |
In this Letter we present evidences of the occurrence of a tricritical filling transition for an Ising model in a linear wedge. We perform Monte Carlo simulations in a double wedge where antisymmetric fields act at the top and bottom wedges, decorated with specific field acting only along the wegde axes. |
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this... |
A fundamental problem of glass transition is to explain the jump of heat capacity at the glass transition temperature $T_g$ without asserting the existence of a distinct solid glass phase. This problem is also common to other disordered systems, including spin glasses. |
We study the scattering of solitons in the nonlinear Schroedinger equation on local inhomogeneities which may give rise to resonant transmission and reflection. In both cases, we derive resonance conditions for the soliton's velocity. |
The dynamics of a spherical chemically-powered synthetic colloidal motor that operates by a self-diffusiophoretic mechanism and has a catalytic domain of arbitrary shape is studied using both continuum theory and particle-based simulations. The motor executes active rotational motion when self-generated concentration ... |
An incremental evolution equation, i.e. a Master equation in statistical mechanics, is introduced for force distributions in polydisperse frictional particle packings. As basic ingredients of the Master equation, the conditional probability distributions of particle overlaps are determined by molecular dynamics simula... |
We study a set of models of self-propelled particles that achieve collective motion through similar alignment-based dynamics, considering versions with and without repulsive interactions that do not affect the heading directions. We explore their phase space within a broad range of values of two nondimensional paramet... |
We study the motion of a sphere of diameter 330 $\mu$m embedded in a Carbopol microgel under the effect of the acoustic radiation pressure exerted by a focused ultrasonic field. The sphere motion within the microgel is tracked using videomicroscopy and compared to conventional creep and recovery measurements performed... |
Cell spreading and motility on an adhesive substrate are driven by the active physical forces generated by the actin cytoskeleton. We have recently shown that coupling curved membrane complexes to protrusive forces, exerted by the actin polymerization that they recruit, provides a mechanism that can give rise to spont... |
The industrial implementation of biofuel production from lignocellulosic biomass faces a number of economic obstacles. One of these is the cost of enzymes, typically used for cellulose hydrolysis. |
Lipid rafts are hypothesized to facilitate protein interaction, tension regulation, and trafficking in biological membranes, but the mechanisms responsible for their formation and maintenance are not clear. Insights into many other condensed matter phenomena have come from colloidal systems, whose micron-scale particl... |
We performed small-angle X-ray scattering measurements of liquid Te using a synchrotron radiation facility and observed the maximum scattering intensity near 620 K in the supercooled region (melting temperature 723 K). This result is an experimental observation of the ridge line of the critical density fluctuation ass... |
We report temperature-responsive soft composites of semiflexible biopolymer networks (fibrin) containing dispersed microgel colloidal particles of poly(N-isopropylacrylamide) (pNIPAM) that undergo a thermodynamically driven de-swelling transition above a Lower Critical Solution Temperature (LCST). Unlike standard poly... |
Directed assembly of colloids is an exciting field in materials science to form structures with new symmetries and responses. Fluid interfaces have been widely exploited to make densely packed ordered structures. |
We consider a minimal computational model of tissue dynamics with two active ingredients: local particle division and apoptosis. We neglect other non-equilibrium effects such as self-propulsion. |
Polymer matrix fiber composites often suffer from residual stresses due to differences in coefficients of thermal expansion between the fibers and resins, as well as contractile strain of the resins during curing. To address residual stress driven composite failure, we propose the use of vitrimers as composite resins,... |
A highly sheared dense aqueous suspension of granular cornstarch particles displays rich nonlinear rheology. We had previously demonstrated the growth and onset of interfacial instabilities when shear-thinning cornstarch suspensions were displaced by a Newtonian fluid, and had suggested methods to maximise displacemen... |
By means of molecular dynamics, we study a model system for colloidal suspensions where the interaction is based on a competition between attraction and repulsion. At low temperatures the relaxation time $\tau$ first increases as a power law as a function of the volume fraction $\phi$ and then, due to the finite lifet... |
Three dimensional calculations of ductile crack growth under mode I plane strain, small scale yielding conditions are carried out using an elastic-viscoplastic constitutive relation for a progres- sively cavitating plastic solid with two populations of void nucleating second phase particles. Full field solutions are o... |
The square-gradient density-functional model with triple-parabolic free energy, that was used previously to study the homogeneous bubble nucleation [J. Chem. Phys. 129, 104508 (2008)], is used to study the stability of the critical bubble nucleated within the bulk under-saturated stretched fluid. The stability of the ... |
We study the transport of paramagnetic colloidal particles on a patterned magnetic substrate with kinetic Monte Carlo and Brownian dynamics computer simulations. The planar substrate is decorated with point dipoles in either parallel or zigzag stripe arrangements and exposed to an additional external magnetic field th... |
Quantifying local structures in self-assembled systems is a central challenge in soft matter and materials science. When no a priori knowledge of the relevant structures is available, traditional order parameters often fall short. |
We discuss aging and localization in a simple "Eshelby" mesoscopic model of amorphous plasticity. Plastic deformation is assumed to occur through a series of local reorganizations. |
Catalytic colloidal swimmers that propel due to self-generated fluid flows exhibit strong affinity for surfaces. We here report experimental measurements of significantly different velocities of such microswimmers in the vicinity of substrates made from different materials. |
Self-organization of active matter as well as driven granular matter in non-equilibrium dynamical states has attracted considerable attention not only from the fundamental and application viewpoints but also as a model to understand the occurrence of such phenomena in nature. These systems share common features origin... |
We have investigated the motion characteristics of a movable piston immersed in a one dimensional gas of hard rods by event-oriented molecular dynamics in the absence of thermal noise. Periodic and reflecting boundary conditions are explored. |
Structure-dynamics correlation is one of the major ongoing debates in the glass transition, although a number of structural features have been found connected to the dynamic heterogeneity in different glass-forming colloidal systems. Here using colloidal experiments combined with coarse-grained molecular dynamics simu... |
The objective of this paper is to correct an error in analyses of quasielastic scattering spectra. The error invokes a valid calculation under conditions in which its primary assumptions are incorrect, resulting in misleading interpretations of spectra. |
Many biological and synthetic systems are suspensions of oriented, actively-moving components. Unlike in passive suspensions, the interplay between orientational order, active flows, and interactions with boundaries gives rise to fascinating new phenomena in such active suspensions. |
We examine the jamming transition in a two-dimensional granular polymer system using compressional simulations. The jamming density \phi_c decreases with increasing length of the granular chain due to the formation of loop structures, in excellent agreement with recent experiments. |
We consider the relationship between the temperature at which averaged energy landscape properties change sharply ($T_{o}$), and the breakdown of mean-field treatments of the dynamics of supercooled liquids. First, we show that the solution of the wavevector dependent mode-coupling equations undergoes an ergodic-noner... |
The insertion of solvent particles in molecular dynamics simulations of complex fluids is required in many situations involving open systems, but this challenging task has been scarcely explored in the literature. We propose a simple and fast algorithm (USHER) that inserts the new solvent particles at locations where ... |
Electrical signals in excitable cells involve spatially localized ionic fluxes through ion channels and pumps on cellular lipid membranes. Common approaches to understand how these localized fluxes spread assume that the membrane and the surrounding electrolyte comprise an equivalent circuit of capacitors and resistor... |
Convincing evidence of domain growth in the heating of ultrastable glasses suggests that the equilibration dynamics of super-cooled liquids could be driven by a nucleation and growth mechanism. We investigate this possibility by simulating the equilibration dynamics of a model glass during both heating and cooling bet... |
We have investigated controversial issues regarding the mesoscale behavior of 3-methylpyridine (3MP), heavy water, and sodium tetraphenylborate (NaBPh4) solutions by combining results obtained from dynamic light scattering (DLS) and small-angle neutron scattering (SANS). We have addressed three questions: |
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. |
A simulation model is presented, comprising elastic spheres with a short range attraction. Besides conservative forces, radial- and shear friction, and radial noise are added. |
Jammed particulate systems, such as granular media, colloids, and foams, interact via one-sided forces that are nonzero only when particles overlap. We find that systems with one-sided repulsive interactions possess no linear response regime in the large system limit ($N\rightarrow \infty$) for all pressures $p$ (or c... |
By performing lattice Boltzmann simulations of a binary mixture, we scrutinize the dynamical scaling hypothesis for the spinodal decomposition of binary mixtures for the crossover region, i.e. the region of parameters in the growth curve where neither inertia nor viscous forces dominate the coarsening process. Our res... |
In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs: GROMACS and LAMMPS. |
Soft particles display highly versatile properties with respect to hard colloids, even more so at fluid-fluid interfaces. In particular, microgels, consisting of a cross-linked polymer network, are able to deform and flatten upon adsorption at the interface due to the balance between surface tension and internal elast... |
At low volume fraction, disordered arrangements of frictionless spheres are found in un--jammed states unable to support applied stresses, while at high volume fraction they are found in jammed states with mechanical strength. Here we show, focusing on the hard sphere zero pressure limit, that the transition between u... |
There has been much recent interest in the chiral motion of achiral particles that sediment in a viscous fluid in a regime where inertial effects can be neglected. This occurs in a broad range of applications such as those involving biological objects like algae, ultra-thin graphene flakes, or colloidal suspensions. |
Predicting the macroscopic chiral behaviour of cholesteric liquid crystals from the microscopic chirality of the particles is highly non-trivial, even when the chiral interactions are purely entropic in nature. Here we introduce a novel chiral hard-particle model, namely particles with a twisted polyhedral shape and o... |
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have territorial organization with signatures pointing to metastability, we analyzed the b... |
Cellular locomotion often involves the motion of thin, elastic filaments, such as cilia and flagella, in viscous environments. The manuscript serves as a general introduction to the topic of modelling microscale elastohydrodynamics. |
For various species of biological cells, experimental observations indicate the existence of universal distributions of the cellular size, scaling relations between the cell-size moments and simple rules for the cell-size control. We address a class of models for the control of cell division, and present the steady st... |
We answer the questions raised by Donev, Torquato, Stillinger, and Connelly in their "Comment on "Jamming at zero temperature and zero applied stress: The epitome of disorder. ' " We emphasize that we follow a fundamentally different approach than they have done to reinterpret random close packing in te... |
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is determined by the denatured bubbles for a continuous transition, e.g., when the two st... |
We determine the quantitative effect, in the maximum number of particles and other static observables, due to small anharmonic terms added to the confining potential of an atomic condensed system with negative two-body interaction. As an example of how a cubic or quartic anharmonic term can affect the maximum number o... |
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. |
This article presents a new force model for performing quantitative simulations of dense granular materials. Interactions between multiple contacts (MC) on the same grain are explicitly taken into account. |
Machine learning offers promising tools to develop surrogate models for polymer structure-property relations. Surrogate models can be built upon existing polymer data and are useful for rapidly predicting the properties of unknown polymers. |
In this paper we formulate a nonlocal density functional theory of inhomogeneous water. We model a water molecule as a couple of oppositely charged sites. |
Counterion distributions and effective electrostatic interactions between spherical macroions in polyelectrolyte solutions are calculated via second-order perturbation (linear response) theory. By modelling the macroions as continuous charge distributions that are permeable to counterions, analytical expressions are o... |
Controlling the assembly of polyelectrolytes and surfactant at liquid-liquid interfaces offers new ways to fabricate soft materials with specific physical properties. However, little is known of the relationships between the kinetics of interfacial assembly, structural and rheological properties of such interfaces. |
Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. |
The structure of spherical micelles of the diblock copolymer poly(styrene-block-acrylic acid) in water was investigated with small angle neutron scattering (SANS) and contrast matching. We have monitored inter-micelle correlation and the extension of the polyelectrolyte chains in the coronal layer through the overlap ... |
Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight backbone, both radial density profiles of monomers and side chain ends are obtained, as... |
We introduce Spiral, a third-order integration algorithm for the rotational motion of extended bodies. It requires only one force calculation per time step, does not require quaternion normalization at each time step, and can be formulated for both leapfrog and synchronous integration schemes, making it compatible wit... |
We investigate the wormlike polymer chains using self-consistent field theory and take into account the Onsager excluded-volume interaction between polymer segments. The propagator of polymer chain is one of the essential physical quantities used to study the conformation of polymers, which satisfies the modified diff... |
We study the immersion of a ferromagnetic nanowire within a nematic liquid crystal using a lattice Boltzmann algorithm to solve the full three-dimensional equations of hydrodynamics. We present an algorithm for including a moving boundary, to simulate a nanowire, in a lattice Boltzmann simulation. |
2H NMR spin-lattice relaxation and line-shape analyses are performed to study the temperature-dependent dynamics of water in the hydration shells of myoglobin, elastin, and collagen. |
In this paper, we review the computational aspects of a multiscale dissipative particle dynamics model for complex fluid simulations based on the feature-rich geometry of the Voronoi tessellation. The geometrical features of the model are critical since the mesh is directly connected to the physics by the interpretati... |
The entrapment of bacteria near boundary surfaces is of biological and practical importance, yet the underlying physics is still not well understood. We demonstrate that it is crucial to include a commonly neglected entropic effect arising from the spatial variation of hydrodynamic interactions, through a model that p... |
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