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arXiv2020

Testing the isomorph invariance of the bridge functions of Yukawa one-component plasmas. I. Intermediate and long range

It has been recently conjectured that bridge functions remain nearly invariant along phase diagram lines of constant excess entropy for the broad class of R-simple liquids. To test this hypothesis, the bridge functions of Yukawa systems are computed outside the correlation void with the Ornstein-Zernike inversion method and structural input from ultra-accurate molecular dynamics simulations. The effect of statistical, grid, finite-size, tail and isomorphic errors is quantified. Uncertainty propagation analysis is complemented with a detailed investigation of the sensitivity of the bridge function to periodic and aperiodic multiplicative perturbations in the radial distribution function. In the long and intermediate range, bridge functions are demonstrated to be approximately isomorph invariant.

cond-mat.soft↗

arXiv2017

The alignment of nematic liquid crystal by the Ti layer processed by nonlinear laser lithography

It is well known that the alignment of liquid crystals can be realized by rubbing or photoalignment technologies. Recently nonlinear laser lithography was introduced as a fast, relatively low-cost method for large area nano-grating fabrication based on laser-induced periodic surface structuring. In this letter for the first time the usage of the nonlinear laser lithography as a perspective method of the alignment of nematics was presented. By nonlinear laser lithography, microgrooves with about 1 μm period were formed on Ti layer. The microstructured Ti layer was coated with oxidianiline-polyimide film with annealing of the polymer followed without any further processing. Aligning properties of microstructured Ti layers were examined with combined twist LC cell. The dependencies of the twist angle of LC cells and azimuthal anchoring energy of layers on scanning speed and power of laser beam during processing of the Ti layer were the focus of our studies as well. The maximum azimuthal anchoring energy, obtained for pure microstructured Ti layer, is comparable with photoalignment technology. It was found that the deposition of polyimide film on microstructured Ti layer leads to the gain effect of the azimuthal anchoring energy. Also, AFM study of aligning surfaces was carried out.

cond-mat.soft↗

arXiv2009

Ions in mixed dielectric solvents: density profiles and osmotic pressure between charged interfaces

The forces between charged macromolecules, usually given in terms of osmotic pressure, are highly affected by the intervening ionic solution. While in most theoretical studies the solution is treated as a homogeneous structureless dielectric medium, recent experimental studies concluded that, for a bathing solution composed of two solvents (binary mixture), the osmotic pressure between charged macromolecules is affected by the binary solvent composition. By adding local solvent composition terms to the free energy, we obtain a general expression for the osmotic pressure, in planar geometry and within the mean-field framework. The added effect is due to the permeability inhomogeneity and nonelectrostatic short-range interactions between the ions and solvents (preferential solvation). This effect is mostly pronounced at small distances and leads to a reduction in the osmotic pressure for macromolecular separations of the order 1--2 nm. Furthermore, it leads to a depletion of one of the two solvents from the charged macromolecules (modeled as planar interfaces). Lastly, by comparing the theoretical results with experimental ones, an explanation based on preferential solvation is offered for recent experiments on the osmotic pressure of DNA solutions.

cond-mat.soft↗

arXiv2013

Small-amplitude inhomogeneous plane waves in a deformed Mooney-Rivlin material

The propagation of small-amplitude inhomogeneous plane waves in an isotropic homogeneous incompressible Mooney--Rivlin material is considered when the material is maintained in a state of finite static homogeneous deformation. Disturbances of complex exponential type are sought and all propagating inhomogeneous solutions to the equations of motion are given, as well as the conditions for linear, elliptical, or circular polarization. % It is seen that a great variety of solutions arises. These include some original solutions, such as circularly-polarized plane waves which propagate with an arbitrary complex scalar slowness, or linearly-polarized waves for which the direction of propagation is not necessarily orthogonal to the direction of attenuation. % Throughout the paper, geometrical interpretations and explicit examples are presented.

cond-mat.soft↗

arXiv2018

Densest vs. jammed packings of 2D bent-core trimers

We identify the maximally dense lattice packings of tangent-disk trimers with fixed bond angles ($θ= θ_0$) and contrast them to both their nonmaximally-dense-but-strictly-jammed lattice packings as well as the disordered jammed states they form for a range of compression protocols. While only $θ_0 = 0,\ 60^\circ,\ \rm{and}\ 120^\circ$ trimers can form the triangular lattice, maximally-dense maximally-symmetric packings for all $θ_0$ fall into just two categories distinguished by their bond topologies: half-elongated-triangular for $0 < θ_0 < 60^\circ$ and elongated-snub-square for $60^\circ < θ_0 < 120^\circ$. The presence of degenerate, lower-symmetry versions of these densest packings combined with several families of less-dense-but-strictly-jammed lattice packings act in concert to promote jamming.

cond-mat.soft↗

arXiv2019

Transport coefficients of self-propelled particles: Reverse perturbations and transverse current correlations

The reverse perturbation method [Phys. Rev. E 59, 4894 (1999)] for shearing simple liquids and measuring their viscosity is extended to the Vicsek-model (VM) of active particles [Phys. Rev. Lett. 75, 1226 (1995)] and its metric-free version. The sheared systems exhibit a phenomenon that is similar to the skin effect of an alternating electric current: momentum that is fed into the boundaries of a layer decays mostly exponentially towards the center of the layer. It is shown how two transport coefficients, i.e. the shear viscosity $ν$ and the momentum amplification coefficient $λ$, can be obtained by fitting this decay with an analytical solution of the hydrodynamic equations for the VM. The viscosity of the VM consists of two parts, a kinetic and a collisional contribution. While analytical predictions already exist for the former, a novel expression for the collisional part is derived by an Enskog-like kinetic theory. To verify the predictions for the transport coefficients, Green-Kubo relations were evaluated and transverse current correlations were measured in independent simulations. Not too far to the transition to collective motion, we find excellent agreement between the different measurements of the transport coefficients. However, the measured values of $ν$ and $1-λ$ are always slightly higher than the mean-field predictions, even at large mean free paths and at state points quite far from the threshold to collective motion, that is, far in the disordered phase. These findings seem to indicate that the mean-field assumption of molecular chaos is much less reliable in systems with velocity-alignment rules such as the VM, compared to models obeying detailed balance such as Multi-Particle Collision Dynamics.

cond-mat.soft↗

arXiv2016

Asymmetric exchange in flocks

As the constituents of a flock are polar, one expects a fore-aft asymmetry in their interactions. We show here that the resulting antisymmetric part of the "exchange coupling" between a bird and its neighbours, if large enough, destabilizes the flock through spontaneous turning of the birds. The same asymmetry also yields a natural mechanism for a difference between the speed of advection of information along the flock and the speed of the flock itself. We show that the absence of detailed balance, and not merely the breaking of Galilean invariance, is responsible for this difference. We delineate the conditions on parameters and wavenumber for the existence of the turning instability. Lastly we present an alternative perspective based on flow-alignment effects in an active liquid crystal with turning inertia in contact with a momentum sink.

cond-mat.stat-mech↗

arXiv2001

Using Nonlinear Response to Estimate the Strength of an Elastic Network

Disordered networks of fragile elastic elements have been proposed as a model of inner porous regions of large bones [Gunaratne et.al., cond-mat/0009221, http://xyz.lanl.gov]. It is shown that the ratio $Γ$ of responses of such a network to static and periodic strain can be used to estimate its ultimate (or breaking) stress. Since bone fracture in older adults results from the weakening of porous bone, we discuss the possibility of using $Γ$ as a non-invasive diagnostic of osteoporotic bone.

cond-mat.soft↗

arXiv2003

Field theoretic calculation of the surface tension for a model electrolyte system

We carry out the calculation of the surface tension for a model electrolyte to first order in a cumulant expansion about a free field theory equivalent to the Debye-Hückel approximation. In contrast with previous calculations, the surface tension is calculated directly without recourse to integrating thermodynamic relations. The system considered is a monovalent electrolyte with a region at the interface, of width h, from which the ionic species are excluded. In the case where the external dielectric constant epsilon_0 is smaller than the electrolyte solution's dielectric constant epsilon we show that the calculation at this order can be fully regularized. In the case where h is taken to be zero the Onsager-Samaras limiting law for the excess surface tension of dilute electrolyte solutions is recovered, with corrections coming from a non-zero value of epsilon_0/epsilon.

cond-mat.soft↗

arXiv2007

Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''

One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $τ$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte Carlo and Molecular Dynamics methods confirm the original prediction $τ\sim N^{2ν+1}$, which scales in the same manner as the Rouse relaxation time of the chain except for a larger prefactor, and invalidates other scaling claims.

cond-mat.soft↗

arXiv2008

Density scaling as a property of strongly correlating viscous liquids

We address a recent conjecture according to which the relaxation time $τ$ of a viscous liquid obeys density scaling ($τ=F(ρ^γ/T)$ where $ρ$ is density) if the liquid is ``strongly correlating,'' i.e., has almost 100% correlation between equilibrium virial and potential-energy fluctuations [Pedersen {\it et al.}, PRL {\bf 100}, 011201 (2008)]. Computer simulations of two model liquids - an asymmetric dumbbell model and the Lewis-Wahnström OTP model - confirm the conjecture and demonstrate that the scaling exponent $γ$ can be accurately predicted from equilibrium fluctuations.

cond-mat.soft↗

arXiv2017

Paramagnetic response of muscle-type systems

We provide a prototypical description of mechanically-induced collective conformational change (folding), relevant in a variety of biological contexts from muscle contraction to hair cell gating and integrin binding. Our study is inspired by the seminal Huxley-Simmons (HS) model which we reinterpret from the perspective of stochastic dynamics involving rigidly coupled bi-stable elements. In this interpretation the HS model can be mapped to a paramagnetic Ising model, however, the equivalence is not complete due to the presence of elastic elements responsible for negative susceptibility and quasi-critical behavior. We go beyond the conventional chemo-mechanical description of such systems, revealing both its strengths and its limitations.

physics.bio-ph↗

arXiv2016

Sorting motile rods by activity

We show, through experiments and simulations, that geometrically polar granular rods, rendered active by the transduction of vertical vibration, undergo a collective trapping phase transition in the presence of a V-shaped obstacle when the opening angle drops below a threshold value. We propose a mechanism that accounts qualitatively for the transition, based on the cooperative reduction of angular noise with increasing area fraction. We exploit the sensitivity of trapping to the persistence of directed motion to sort particles based on the statistical properties of their activity.

cond-mat.soft↗

arXiv2018

Predicting optimal hematocrit in silico

Optimal hematocrit $H_o$ maximizes oxygen transport. In healthy humans, the average hematocrit $H$ is in the range of 40-45$\%$, but it can significantly change in blood pathologies such as severe anemia (low $H$) and polycythemia (high $H$). Whether the hematocrit level in humans corresponds to the optimal one is a long standing physiological question. Here, using numerical simulations with the Lattice Boltzmann method and two mechanical models of the red blood cell (RBC) we predict the optimal hematocrit, and explore how altering the mechanical properties of RBCs affects $H_o$. We develop a simplified analytical theory that accounts for results obtained from numerical simulations and provides insight into the physical mechanisms determining $H_o$. Our numerical and analytical models can easily be modified to incorporate a wide range of mechanical properties of RBCs as well as other soft particles thereby providing means for the rational design of blood substitutes. Our work lays the foundations for systematic theoretical study of the optimal hematocrit and its link with pathological RBCs associated with various diseases (e.g. sickle cell anemia, diabetes mellitus, malaria, elliptocytosis).

cond-mat.soft↗

arXiv2018

Magnetic Polymer Models for Epigenomic Organisation and Phase Separation

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. Yet, the physical principles underlying the dynamical coupling between three-dimensional genomic organisation and one-dimensional epigenetic patterns remain elusive. To shed light on this issue, here we study by mean field theory and Brownian dynamics simulations a magnetic polymer model for chromosomes, where each monomer carries a dynamic epigenetic mark. At the single chromosome level, we show that a first order transition describes the unlimited spreading of epigenetic marks, a phenomenon that is often observed in vivo. At the level of the whole nucleus, experiments suggest chromosomes form micro-phase separated compartments with distinct epigenetic marks. We here discover that for a melt of magnetic polymers such a morphology is thermodynamically unstable, but can be stabilised by a non- equilibrium and ATP-mediated epigenetic switch between different monomer states.

cond-mat.soft↗

arXiv2017

Creeping Avalanches of Brownian Granular Suspensions

We study the avalanche dynamics of a pile of micron-sized silica grains in miniaturized rotating drums filled with water. Contrary to what is expected for classical granular materials, the avalanches do not stop at a finite angle of repose. Below an angle $θ$\_c, we observe a creep regime where the piles slowly flow until they become flat. In this regime, the relaxation is logarithmic in time and is slower when the ratio between the weight of the grains and the thermal agitation is increased. We propose a simple 1D model based on Kramer's escape rate to describe this flow.

cond-mat.soft↗

arXiv2007

Growing smooth interfaces with inhomogeneous, moving external fields: dynamical transitions, devil's staircases and self-assembled ripples

We study the steady state structure and dynamics of an interface in a pure Ising system on a square lattice placed in an inhomogeneous external field. The field has a profile with a fixed shape designed to stabilize a flat interface, and is translated with velocity v_e. For small v_e, the interface is stuck to the profile, is macroscopically smooth, and is rippled with a periodicity in general incommensurate with the lattice parameter. For arbitrary orientations of the profile, the local slope of the interface locks in to one of infinitely many rational values (devil's staircase) which most closely approximates the profile. These ``lock-in'' structures and ripples dissappear as v_e increases. For still larger v_e the profile detaches from the interface which is now characterized by standard Kardar-Parisi-Zhang (KPZ) exponents.

cond-mat.soft↗

arXiv2005

Nonuniversality of the dispersion interaction: analytic benchmarks for van der Waals energy functionals

We highlight the non-universality of the asymptotic behavior of dispersion forces, such that a sum of inverse sixth power contributions is often inadequate. We analytically evaluate the cross-correlation energy Ec between two pi-conjugated layers separated by a large distance D within the electromagnetically non-retarded Random Phase Approximation, via a tight-binding model. For two perfect semimetallic graphene sheets at T=0K we find Ec = C D^{-3}, in contrast to the "insulating" D^{-4} dependence predicted by currently accepted approximations. We also treat the case where one graphene layer is replaced by a thin metal, a model relevant to the exfoliation of graphite. Our general considerations also apply to nanotubes, nanowires and layered metals.

cond-mat.soft↗