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Diffusion-driven patterns appear on curved surfaces in many settings, initiated by unstable modes of an underlying Laplacian operator. On a flat surface or perfect sphere, the patterns are degenerate, reflecting translational/rotational symmetry. |
A theory is presented to account for the increase in surface tension of water in the presence of electrolyte. Unlike the original ``grand-canonical'' calculation of Onsager and Samaras, which relied on the Gibbs adsorption isotherm and lead to a result which could only be expressed as an infinite series, our a... |
Investigating thermodynamic properties of liquid-solid transitions of flexible homopolymers with elastic bonds by means of multicanonical Monte Carlo simulations, we find crystalline conformations that resemble ground-state structures of Lennard-Jones clusters. This allows us to set up a structural classification sche... |
The properties of surfaces with charge-regulated patches are studied using non-linear Poisson-Boltzmann theory. Using a mode expansion to solve the non-linear problem efficiently, we reveal the charging behaviour of Debye-length sized patches. |
Stealthy hyperuniform (SHU) many-particle systems are distinguished by a structure factor that vanishes not only at zero wavenumber (as in ``standard'' hyperuniform systems) but also across an extended range of wavenumbers near the origin. We generate disordered SHU packings of identical and `nonoverlapping... |
Dense bacterial suspensions display collective motion exhibiting coherent flow structures reminiscent of turbulent flows. In contrast to inertial turbulence, understanding the microscopic dynamics of bacterial fluid elements undergoing collective motion is in its incipient stages. |
We numerically studied active Brownian particles with attractive interactions. Contrary to our intuition, the attractive force between particles disrupts the formation of a single cluster observed in motility-induced phase separation, giving rise to a multi-cluster state characterized by a power-law distribution of cl... |
Most organic and inorganic surfaces (e.g., glass, nucleic acids or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces. |
The electrostatic double layer force is key to determining the stability and self-assembly of charged colloids and many other soft matter systems. Fully understanding the attractive force between two like-charged surfaces remains a great challenge. |
We present a detailed numerical study of multi-component colloidal gels interacting sterically and obtained by arrested phase separation. Under deformation, we found that the interplay between the different intertwined networks is key. |
We present an integrated experimental and quantitative theoretical study of the mechanics of self-crosslinked, neutral, repulsive pNIPAM microgel suspensions over concentration (c) range spanning the fluid, glassy and putative "soft jammed" regimes. In the glassy regime we measure a linear elastic dynamic shea... |
We report the observation of a novel isotropic phase of amphiphile bilayers in a mixed system consisting of the ionic surfactant, sodium docecylsulphate (SDS), and the organic salt p-toludine hydrochloride (PTHC). This system forms a collapsed lamellar ($L_\alpha$) phase over a wide range of water content, which trans... |
The relative stability of two-dimensional soft quasicrystals is examined using a recently developed projection method which provides a unified numerical framework to compute the free energy of periodic crystal and quasicrystals. Accurate free energies of numerous ordered phases, including dodecagonal, decagonal and oc... |
We show by inherent structure (IS) analysis that the sharp composition dependent breakdown of the Stokes-Einstein relation correlates surprisingly well with an equally sharp non-monotonic variation in the average inherent structure (IS) energy of these mixtures. Further IS analysis reveals the existence of a unique gr... |
In this article we consider systems of parallel hard {\it superellipsoids}, which can be viewed as a possible interpolation between ellipsoids of revolution and cylinders. Superellipsoids are characterized by an aspect ratio and an exponent $\alpha$ (shape parameter) which takes care of the geometry, with $\alpha=1$ c... |
We present an experimental demonstration of a deterministic optical rocking ratchet. A periodic and asymmetric light pattern is created to interact with dielectric microparticles in water, giving rise to a ratchet potential. |
Large scale molecular dynamics simulations are used to study drying suspensions of a binary mixture of large and small particles in explicit and implicit solvents. The solvent is first modeled explicitly and then mapped to a uniform viscous medium by matching the diffusion coefficients and the pair correlation functio... |
We review recent theoretical advances on controlling the fluid-fluid phase transition with electric fields. Using a mean-field approach, we compare the effects of uniform versus non-uniform electric fields, and show how non-uniform fields are better at altering the phase diagram. |
The ground state polaron potential of 1D lattice of two-level molecules with spinless electrons and two Einstein phonon modes with quantum phonon-assisted transitions between the levels is found anharmonic in phonon displacements. The potential shows a crossover from two nonequivalent broad minima to a single narrow m... |
There is significant interest in modelling the mechanics and physics of growth of soft biological systems such as tumors and bacterial biofilms. Solid tumors account for more than 85% of cancer mortality and bacterial biofilms account for a significant part of all human microbial <a href="http://infections.These" rel=... |
To reach a deeper understanding of fluid interfaces it is necessary to identify a meaningful coarse-graining length that separates intrinsic fluctuations from capillary ones, given the lack of a proper statistical mechanical definition of the latter. Here, with the help of unsupervised learning techniques, we introduc... |
Dense particulate suspensions often become more dilute as they move downstream through a constriction. We find that as a shear-thickening suspension is extruded through a narrow die and undergoes such liquid migration, the extrudate maintains a steady concentration $\phi_c$, independent of time or initial concentratio... |
We study the spontaneous charging and the crystallization of spherical micron-sized water-droplets dispersed in oil by numerically solving, within a Poisson-Boltzmann theory in the geometry of a spherical cell, for the density profiles of the cations and anions in the system. We take into account screening, ionic Born... |
Characterization of medium-range order in amorphous materials and its relation to short-range order is discussed. A new topological approach is presented here to extract a hierarchical structure of amorphous materials, which is robust against small perturbations and allows us to distinguish it from periodic or random ... |
The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. |
Different compaction processes of the nanosized granular system, which is a prototype of an alumina nanopowder, are studied by the granular dynamics method. For all processes: compaction curves ''density vs. pressure'' of the powder compact are calculated, the elastic and the plastic parts are extracte... |
The correct description of the ionic interaction and stable equilibrium of the simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model of the monovalent ions is very important. The force field needs to reproduce coincident many properties of ions, like their structure, solv... |
The effect of evaporation on droplet sedimentation times is crucial for estimating the risk of infection from virus-containing airborne droplets. For droplet radii in the range 100 nm < R < 60 {\mu}m, evaporation can be described in the stagnant-flow approximation and is diffusion limited. |
A panoptic view of architectured planar lattices based on star-polygon tilings was developed. Four star-polygon-based lattice sub-families, formed of systematically arranged triangles, squares, or hexagons, were investigated numerically and experimentally. |
While the behavior of active colloidal molecules is well studied by now for a constant activity, the effect of activity gradients is much less understood. Here we explore one of the simplest molecules in activity gradients, namely active chiral dimers composed of two particles with opposite active torques of the same ... |
We employ molecular dynamics simulations to investigate ion and water transport driven by an electric field through quasi-two-dimensional nanoslits with a tapered geometry. Despite the absence of surface charge on the channel walls and the associated electric double layer, we do observe a robust ion selectivity. |
We reconsider the electrostatic contribution to the persistence length, $\ell_e$, of a single, infinitely long charged polymer in the presence of screening. A Gaussian variational method is employed, taking $\ell_e$ as the only variational parameter. |
The folding mechanism of the Villin headpiece (HP36) is studied by means of a novel approach which entails an initial coarse-grained Monte Carlo (MC) scheme followed by all-atom molecular dynamics (MD) simulations in explicit solvent. The MC evolution occurs in a simplified free-energy landscape and allows an efficien... |
Structural correlations between colloids in a binary mixture of charged and uncharged spheres are calculated using computer simulations of the primitive model with explicit microions. For aqueous suspensions in a solvent of large dielectric constant, the traditional Derjaguin-Landau-Vervey-Overbeek (DLVO) theory of li... |
We synthesize thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) colloidal microgel particles of different stiffnesses by controlling the concentration of crosslinker in a one-pot synthesis method. We employ oscillatory rheology and cryogenic scanning electron microscopy to study the temperature and stiffness-induc... |
Artificial microswimmers, nano and microrobots, are essential in many applications from engineering to biology and medicine. We present a Stokesian Dynamics study of the dynamical properties and efficiency of one of the simplest artificial swimmer, the three linked spheres swimmer (TLS), extensively shown to be an exc... |
Water drops spontaneously accumulate charges when they move on hydrophobic dielectric surfaces by slide electrification. On the one hand, slide electrification generates electricity with possible applications on tiny devices. |
As a model for a suspension of hard-sphere like colloidal particles where small nonadsorbing dissolved polymers create a depletion attraction, we introduce an effective colloid-colloid potential closely related to the Asakura-Oosawa model but that does not have any discontinuities. In simulations, this model straightf... |
We explain theoretically peculiarities of the smectic A -- hexatic B equilibrium phase coexistence in a finite temperature range recently observed experimentally in free standing smectic films [<a href="http://I.A.Zaluzhnyy" rel="external noopener nofollow" class="link-external link-http">this http URL</a> et al., Phys... |
We demonstrate how to generalize two of the most well-known random graph models, the classic random graph, and random graphs with a given degree distribution, by the introduction of hidden variables in the form of extra degrees of freedom, color, applied to vertices or stubs (half-edges). The color is assumed unobserv... |
It is shown that structuring at the microlevel, a previously not described in detail phenomenon, is the intrinsic property of water and aqueous solutions. At room conditions water (including "ultrapure" one) and aqueous solutions are dispersed systems in which microcrystals of NaCl, surrounded by a layer of hy... |
We introduce a model of friction between two contacting (stationary or co-sliding) rough surfaces, each comprising a random ensemble of polydisperse hemispherical bumps. In the simplest version of the model, the bumps experience on contact with each other only pairwise elastic repulsion and dissipative drag. |
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks and three-dimensional genome folding. |
A new mathematical representation for nonlinear viscoelasticity is presented based on application of the Volterra series expansion to the general nonlinear relationship between shear stress and shear strain history. This theoretical and experimental framework, which we call Medium Amplitude Parallel Superposition (MAP... |
The calculation of the interfacial free energy between two thermodynamic phases is crucial across various fields, including materials science, chemistry, and condensed matter physics. In this study, we apply an existing thermodynamic approach, the Gibbs-Cahn integration method, to determine the interfacial free energy... |
Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations reveal that the presence of magnesium chloride (MgCl$_2$) induces perturbations in... |
Impurity-induced defects play a crucial role for the properties of crystals, but little is known about impurities with anisotropic shape. Here, we study how colloidal dumbbells distort and interact with a hexagonal crystal of charged colloidal spheres at a fluid interface. |
We study the effect of mergers in the force chain model describing the stress profile in static granular materials. Combining numerical and analytical calculations we show that granular materials do not generally behave in an elastic-like manner, however they may under specific conditions, which are elaborated. |
In amorphous solids subject to shear or thermal excitation, so-called structural indicators have been developed that predict locations of future plasticity or particle rearrangements. An open question is whether similar tools can be used in dense active materials, but a challenge is that under most circumstances, acti... |
In this work we presented a novel computational model of precipitation polymerization allowing one to obtain core-shell microgels via a realistic cross-linking process based on the experimental procedure. We showed that the cross-linker-monomer reactivity ratios r are responsible for the microgel internal structure. |
We develop our recently proposed lattice-Boltzmann method for the non-equilibrium dynamics of amphiphilic fluids (Chen, Boghosian, Coveney and Nekovee, Proc. Roy. |
We study a classical model of thermally fluctuating polymers confined to two dimensions, experiencing a grooved periodic potential, and subject to pulling forces both along and transverse to the grooves. The equilibrium polymer conformations are described by a mapping to a quantum system with a non-Hermitian Hamiltoni... |
Acetaminophen (APAP) or Paracetamol, despite its wide and common use for pain and fever symptoms, shows a variety of side effects, toxic effects, and overdose effects. The most common form of toxic effects of APAP is in the liver where phosphatidylcholine is the major component of the cell membrane with additional ass... |
We solve numerically the nonlinear differential equation for the Hele-Shaw, Saffman-Taylor problem derived in the preceding work. Stationary solutions with no free phenomenological parameters are found to fit the measured patterns. |
When we place conducting bodies in electrolyte solutions, their surface potential $\Phi_s$ appears to be much smaller in magnitude than the intrinsic one $\Phi_0$ and normally does not obey the classical electrostatic boundary condition of a constant surface potential expected for conductors. In this paper, we demonst... |
A recent granular rheology based on an implicit `granular fluidity' field has been shown to quantitatively predict many nonlocal phenomena. However, the physical nature of the field has not been identified. |
We examine the statistics of conformations of a linear polymer in a solvent. The polymer is allowed to form double polymers. |
Analytical expressions for the osmotic pressure of electrolytes confined within electrolyte-filled, hollow, charged nanoparticles are studied using contact theorems for cavity nanoshells immersed in a low-concentration electrolyte. Three shell geometries are considered: planar, cylindrical, and spherical. |
In many scenarios -- when we bite food or during a crash -- fracture is inevitable. Finding solutions to steer fracture to mitigate its impact or turn it into a purposeful functionality, is therefore crucial. |
Based on a collective description of electrolytes composed of charge-regulated macro-ions and simple salt ions, we analyze their equilibrium charge state in the bulk and their behavior in the vicinity of an external electrified surface. The mean-field formulation of mobile macro-ions in an electrolyte bathing solution... |
Here we show that in ultrasonic fields the phenomenon of reconversion of shear-modes into an effective compressional wave has a significant effect for bubbles in a medium viscosity liquid or weak gel. We present the consequent extra terms in the effective wavenumber and find the changes in sound velocity for different... |
We use an analogue of nanoindentation on a colloidal glass to elucidate the incipient plastic deformation of glasses. By tracking the motion of the individual particles in three dimensions, we visualize the strain field and glass structure during the emerging deformation. |
Dynamics is central to living systems. In the last two decades, experiments have revealed that the dynamics in diverse biological systems - from intracellular cytoplasm to cellular and organismal aggregates - are remarkably similar to that in dense systems of inanimate particles in equilibrium. |
We investigate the steady state properties of an active fluid modeled as an assembly of soft repulsive spheres subjected to Gaussian colored noise. Such a noise captures one of the salient aspects of active particles, namely the persistence of their motion and determines a variety of novel features with respect to fam... |
Thermal fluctuations of microtubules (MTs) and other cytoskeletal filaments govern to a great extent the complex rheological properties of the cytoskeleton in eukaryotic cells. In recent years, much effort has been put into capturing the dynamics of these fluctuations by means of analytical and numerical models. |
Molecular dynamics simulations are used to investigate the connection between thermal history and physical aging in polymer glasses, in particular the effects of a temperature square step. Measurements of two-time correlation functions show that a negative temperature step causes "rejuvenation" of the sample: ... |
Morphologies of a vesicle confined in a spherical vesicle were explored experimentally by fast confocal laser microscopy and numerically by a dynamically-triangulated membrane model with area-difference elasticity. The confinement was found to induce several novel shapes of the inner vesicles, that had been never obse... |
We prepare packings of frictional tetrahedra with volume fractions {\phi} ranging from 0.469 to 0.622 using three different experimental protocols under isobaric conditions. Analysis via X-ray micro-tomography reveals that the contact number Z grows with {\phi}, but does depend on the preparation protocol. |
The excess entropy, Se, defined as the difference between the entropies of the liquid and the ideal gas under identical density and temperature conditions, is shown to be the critical quantity connecting the structural, diffusional and density anomalies in water-like liquids. Based on simulations of silica and the two... |
A study of the gas dynamics of a dilute collection of the inelastically colliding hard spheres is presented. When diffusive processes are neglected the gas density blows up in a finite time. |
The structure and stresses of static granular packs in cylindrical containers are studied using large-scale discrete element molecular dynamics simulations in three dimensions. We generate packings by both pouring and sedimentation and examine how the final state depends on the method of construction. |
We investigate the granular temperatures in force-free granular gases under exponential resetting. When a resetting event occurs, the granular temperature attains its initial value, whereas it decreases because of the inelastic collisions between the resetting events. |
The influence of the finite sizes on the coherent properties of 3D Bose systems is considered. As is shown, the correlation functions of a Bose gas in a trap have essential differences from analogous correlation functions in an infinite system. |
We study the assembling of P3HT chains in vacuo by means of a combination of first principles density functional theory and model potential molecular dynamics. We find that, in the absence of any external constraints, the pi-pi interchain interaction between thiophenes is the major driving force for the assembling. |
For many biotechnological applications it would be useful to better understand the effects produced by electric fields on lipid membranes. This review discusses several aspects of the electrostatic properties of a planar lipid membrane with its surrounding electrolyte in a normal DC or AC electric field. |
Most theoretical descriptions of lyotropic cholesteric liquid crystals to date focus on homogeneous systems in which the rod concentration, as opposed to the rod orientation, is uniform. In this work, we build upon the Onsager-Straley theory for twisted nematics and study the effect of weak concentration gradients, ge... |
Polyhedral vesicles with a large bending modulus of the membrane such as the gel phase lipid membrane were studied using a Brownian dynamics simulation. The vesicles exhibit various polyhedral morphologies such as tetrahedron and cube shapes. |
Ionic liquids (ILs) are appealing electrolytes for their favorable physicochemical properties. However, despite their longstanding use, understanding the capacitive behavior of ILs remains challenging. |
Using a 2D lattice model, we conduct Monte Carlo simulations of micellar aggregation of linear-chain amphiphiles having two solvophilic head groups. In the context of this simple model, we quantify how the amphiphile architecture influences the critical micelle concentration (CMC), with a particular focus on the role ... |
We use machine learning methods to approximate a classical density functional. As a study case, we choose the model problem of a Lennard Jones fluid in one dimension where there is no exact solution available and training data sets must be obtained from simulations. |
The ability to control wettability is important for a wide range of technological applications in which precise microfluidic handling is required. It is known that predesigned roughness at a micro- or nano- scale enhances the wetting properties of solid materials giving rise to super-hydrophobic or super-hydrophilic b... |
The fluctuation-induced interaction between two rod-like, rigid inclusions in a fluid vesicle is studied by means of canonical ensemble Monte Carlo simulations. The vesicle membrane is represented by a triangulated network of hard spheres. |
The molecular mobility of glass and supercooled liquid states of nilutamide has been studied with broadband dielectric spectroscopy for a wide range of temperature and frequency. Besides primary $\alpha$-relaxation an excess wing like secondary relaxation is observed. |
For the first time the electrohydrodynamic convection (EHC) of nematic liquid crystals is studied via fully nonlinear simulation. As a system of rich pattern-formation the EHC is mostly studied with negative nematic liquid crystals experimentally, and sometimes with the help of theoretical instability analysis in the ... |
We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin filaments with branching due to the Arp2/3 complex. |
Ultrasound scattered by a dense shoal of fish undergoes mesoscopic interference, as is typical of low-temperature electrical transport in metals or light scattering in colloidal suspensions. Through large-scale measurements in open sea, we show a set of striking deviations from classical wave diffusion making fish sho... |
Knowledge of relaxation processes is fundamental in glass science and technology because relaxation is intrinsically related to vitrification, tempering as well as to annealing and sev-eral applications of glasses. However, there are conflicting reports -- summarized here for different glasses -- on whether the struct... |
We show that a fluid under strong spatially periodic confinement displays a glass transition within mode-coupling theory (MCT) at a much lower density than the corresponding bulk system. We use fluctuating hydrodynamics, with confinement imposed through a periodic potential whose wavelength plays an important role in ... |
An experimental apparatus measuring free-surface deformation of a centrifuged granular pile is developed. By horizontally rotating a quasi two-dimensional granular pile whose apex is located at the vertical rotation axis, the resultant force of gravity and centrifuge yields the deformation of the granular pile. |
We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (Pfold = 0.5). Using results for the force... |
The overall goal of this thesis is to investigate the connection between the dynamics and structure of molecular glass formers, by testing different scaling laws for both. The inspiration for this work is the Isomorph theory because it predicts a connection between structure and dynamics. |
Crystallization represents the prime example of a disorder order transition. In realistic situations, however, container walls and impurities are frequently present and hence crystallization is heterogeneously seeded. |
Electronic transport through DNA wires in the presence of a strong dissipative environment is investigated. We show that new bath-induced electronic states are formed within the bandgap. |
Inspired by recent publications doubtful of the FCS technique, we scrutinize how irreversible (static) and reversible (dynamic) quenching can influence the interpretation of such data. We consider intermediate cases where the assessment of photophysics (static quenching, blinking-like triplet state relaxation) influen... |
Mixtures of lipids and cholesterol are commonly used as model systems for studying the formation of liquid-ordered ($L_o$) domains in heterogeneous biological membranes. The simplest model system exhibiting coexistence between $L_o$ domains and a liquid-disordered ($L_d$) matrix is that of a binary mixture of saturate... |
Using collision driven discrete molecular dynamics (DMD), we investigate the thermodynamics and dynamics of systems of 500 dumbbell molecules interacting by a purely repulsive ramp-like discretized potential, consisting of $n$ steps of equal size. We compare the behavior of the two systems, with $n = 18$ and $n = 144$... |
A tethered surface model is investigated by using the canonical Monte Carlo simulation technique on a torus with an intrinsic curvature. We find that the model undergoes a first-order phase transition between the smooth phase and the crumpled one. |
Various soft materials share some common features, such as significant entropic effect, large fluctuations, sensitivity to thermodynamic conditions, and mesoscopic characteristic spatial and temporal scales. However, no quantitative definitions have yet been provided for soft matter, and the intrinsic mechanisms leadi... |
This work investigates how a thermal diode can be designed from a nematic liquid crystal confined inside a cylindrical capillary. In the case of homeotropic anchoring, a defect structure called escaped radial disclination arises. |
We analyse scaling laws that govern macromolecules of different topology: polymer chains, homogeneous and miktoarm star polymers in a good solvent possibly constrained by a porous medium. The latter is modelled by long-range-correlated disorder with a pair correlation function g(r) that decays with a power law g(r) r^... |
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