Structural Properties of the Sliding Columnar Phase in Layered Liquid Crystalline Systems

Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These lamellar DNA-cationic-lipid complexes can in principle exhibit a variety of equilibrium phases, including a columnar phase in which parallel DNA strands from a 2D lattice, a nematic lamellar phase in which DNA strands align along a common direction but exhibit no long-range positional order, and a possible new intermediate phase, the sliding columnar (SC) phase, characterized by a vanishing shear modulus for relative displacement of DNA lattices but a nonvanishing modulus for compressing these lattices. We develop a model capable of describing all phases and transitions among them and use it to calculate structural properties of the sliding columnar phase. We calculate displacement and density correlation functions and x-ray scattering intensities in this phase and show, in particular, that density correlations within a layer have an unusual $\exp(- {\rm const.} \ln^2 r)$ dependence on separation r. We investigate the stability of the SC phase with respect to shear couplings leading to the columnar phase and dislocation unbinding leading to the lamellar nematic phase. For models with interactions only between nearest neighbor planes, we conclude that the SC phase is not thermodynamically stable. Correlation functions in the nematic lamellar phase, however, exhibit SC behavior over a range of length scalesComment: 28 pages, 4 figure

Tuning Jammed Frictionless Disk Packings from Isostatic to Hyperstatic

We perform extensive computational studies of two-dimensional static bidisperse disk packings using two distinct packing-generation protocols. The first involves thermally quenching equilibrated liquid configurations to zero temperature over a range of thermal quench rates $r$ and initial packing fractions followed by compression and decompression in small steps to reach packing fractions $\phi_J$ at jamming onset. For the second, we seed the system with initial configurations that promote micro- and macrophase-separated packings followed by compression and decompression to $\phi_J$. We find that amorphous, isostatic packings exist over a finite range of packing fractions from $\phi_{\rm min} \le \phi_J \le \phi_{\rm max}$ in the large-system limit, with $\phi_{\rm max} \approx 0.853$. In agreement with previous calculations, we obtain $\phi_{\rm min} \approx 0.84$ for $r > r^*$, where $r^*$ is the rate above which $\phi_J$ is insensitive to rate. We further compare the structural and mechanical properties of isostatic versus hyperstatic packings. The structural characterizations include the contact number, bond orientational order, and mixing ratios of the large and small particles. We find that the isostatic packings are positionally and compositionally disordered, whereas bond-orientational and compositional order increase with contact number for hyperstatic packings. In addition, we calculate the static shear modulus and normal mode frequencies of the static packings to understand the extent to which the mechanical properties of amorphous, isostatic packings are different from partially ordered packings. We find that the mechanical properties of the packings change continuously as the contact number increases from isostatic to hyperstatic.Comment: 11 pages, 15 figure

Entropy and Temperature of a Static Granular Assembly

Granular matter is comprised of a large number of particles whose collective behavior determines macroscopic properties such as flow and mechanical strength. A comprehensive theory of the properties of granular matter, therefore, requires a statistical framework. In molecular matter, equilibrium statistical mechanics, which is founded on the principle of conservation of energy, provides this framework. Grains, however, are small but macroscopic objects whose interactions are dissipative since energy can be lost through excitations of the internal degrees of freedom. In this work, we construct a statistical framework for static, mechanically stable packings of grains, which parallels that of equilibrium statistical mechanics but with conservation of energy replaced by the conservation of a function related to the mechanical stress tensor. Our analysis demonstrates the existence of a state function that has all the attributes of entropy. In particular, maximizing this state function leads to a well-defined granular temperature for these systems. Predictions of the ensemble are verified against simulated packings of frictionless, deformable disks. Our demonstration that a statistical ensemble can be constructed through the identification of conserved quantities other than energy is a new approach that is expected to open up avenues for statistical descriptions of other non-equilibrium systems.Comment: 5 pages, 4 figure

Elastic Correlations in Nucleosomal DNA Structure

The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J. Richmond and C.A. Davey, Nature {\bf 423}, 145 (2003)], it is shown that elastic correlations exist between twist, roll, tilt, and stretching of DNA, as well as the distance between phosphate groups. The twist-bend coupling term is shown to be able to capture these correlations to a large extent, and a fit to the experimental data yields a new estimate of G=25 nm for the value of the twist-bend coupling constant

Nonlinear Elasticity of the Sliding Columnar Phase

The sliding columnar phase is a new liquid-crystalline phase of matter composed of two-dimensional smectic lattices stacked one on top of the other. This phase is characterized by strong orientational but weak positional correlations between lattices in neighboring layers and a vanishing shear modulus for sliding lattices relative to each other. A simplified elasticity theory of the phase only allows intralayer fluctuations of the columns and has three important elastic constants: the compression, rotation, and bending moduli, $B$, $K_y$, and $K$. The rotationally invariant theory contains anharmonic terms that lead to long wavelength renormalizations of the elastic constants similar to the Grinstein-Pelcovits renormalization of the elastic constants in smectic liquid crystals. We calculate these renormalizations at the critical dimension $d=3$ and find that $K_y(q) \sim K^{1/2}(q) \sim B^{-1/3}(q) \sim (\ln(1/q))^{1/4}$, where $q$ is a wavenumber. The behavior of $B$, $K_y$, and $K$ in a model that includes fluctuations perpendicular to the layers is identical to that of the simple model with rigid layers. We use dimensional regularization rather than a hard-cutoff renormalization scheme because ambiguities arise in the one-loop integrals with a finite cutoff.Comment: This file contains 18 pages of double column text in REVTEX format and 6 postscript figure

A minimal model for kinetic arrest

To elucidate slow dynamics in glassy materials, we introduce the {\it Figure-8 model} in which $N$ hard blocks undergo Brownian motion around a circuit in the shape of a figure-8. This system undergoes kinetic arrest at a critical packing fraction $\phi=\phi_g < 1$, and for $\phi\approx\phi_g$ long-time diffusion is controlled by rare, cooperative `junction-crossing' particle rearrangements. We find that the average time between junction crossings $\tau_{JC}$, and hence the structural relaxation time, does not simply scale with the configurational volume \OmegaLow of transition states, because $\tau_{JC}$ also depends on the time to complete a junction crossing. The importance of these results in understanding cage-breaking dynamics in glassy systems is discussed.Comment: 4 pages, 4 figure

Jamming transition in emulsions and granular materials

We investigate the jamming transition in packings of emulsions and granular materials via molecular dynamics simulations. The emulsion model is composed of frictionless droplets interacting via nonlinear normal forces obtained using experimental data acquired by confocal microscopy of compressed emulsions systems. Granular materials are modeled by Hertz-Mindlin deformable spherical grains with Coulomb friction. In both cases, we find power-law scaling for the vanishing of pressure and excess number of contacts as the system approaches the jamming transition from high volume fractions. We find that the construction history parametrized by the compression rate during the preparation protocol has a strong effect on the micromechanical properties of granular materials but not on emulsions. This leads the granular system to jam at different volume fractions depending on the histories. Isostaticity is found in the packings close to the jamming transition in emulsions and in granular materials at slow compression rates and infinite friction. Heterogeneity of interparticle forces increases as the packings approach the jamming transition which is demonstrated by the exponential tail in force distributions and the small values of the participation number measuring spatial localization of the forces. However, no signatures of the jamming transition are observed in structural properties, like the radial distribution functions and the distributions of contacts.Comment: Submitted to PR

Organization of atomic bond tensions in model glasses

In order to understand whether internal stresses in glasses are correlated or randomly distributed, we study the organization of atomic bond tensions (normal forces between pairs of atoms). Measurements of the invariants of the atomic bond tension tensor in simulated 2D and 3D binary Lennard-Jones glasses, reveal new and unexpected correlations and provide support for Alexander's conjecture about the non-random character of internal stresses in amorphous solids

Effective Temperatures of a Driven System Near Jamming

Fluctuations in a model of a sheared, zero-temperature foam are studied numerically. Five different quantities that reduce to the true temperature in an equilibrium thermal system are calculated. All five have the same shear-rate dependence, and three have the same value. Near the onset of jamming, the relaxation time is the same function of these three temperatures in the sheared system as of the true temperature in an unsheared system. These results imply that statistical mechanics is useful for the system and provide strong support for the concept of jamming.Comment: 4 pages, 4 postscript figure

Effect of boundaries on the force distributions in granular media

The effect of boundaries on the force distributions in granular media is illustrated by simulations of 2D packings of frictionless, Hertzian spheres. To elucidate discrepancies between experimental observations and theoretical predictions, we distinguish between the weight distribution {\cal P} (w) measured in experiments and analyzed in the q-model, and the distribution of interparticle forces P(f). The latter one is robust, while {\cal P}(w) can be obtained once the local packing geometry and P(f) are known. By manipulating the (boundary) geometry, we show that {\cal P}(w) can be varied drastically.Comment: 4 pages, 4 figure