Collective Molecular Dynamics in Proteins and Membranes

The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of membrane composition and properties and of structure and dynamics of the surrounding hydration water on protein function is an upcoming hot topic, which can be addressed by modern experimental and computational techniques. Correlated molecular motions might play a crucial role for the understanding of, for instance, transport processes and elastic properties, and might be relevant for protein function. Experimentally that involves determining dispersion relations for the different molecular components, i.e., the length scale dependent excitation frequencies and relaxation rates. Only very few experimental techniques can access dynamical properties in biological materials on the nanometer scale, and resolve dynamics of lipid molecules, hydration water molecules and proteins and the interaction between them. In this context, inelastic neutron scattering turned out to be a very powerful tool to study dynamics and interactions in biomolecular materials up to relevant nanosecond time scales and down to the nanometer length scale. We review and discuss inelastic neutron scattering experiments to study membrane elasticity and protein-protein interactions of membrane embedded proteins

Thermal Fluctuations in a Lamellar Phase of a Binary Amphiphile-Solvent Mixture: A Molecular Dynamics Study

We investigate thermal fluctuations in a smectic A phase of an amphiphile-solvent mixture with molecular dynamics simulations. We use an idealized model system, where solvent particles are represented by simple beads, and amphiphiles by bead-and-spring tetramers. At a solvent bead fraction of 20 % and sufficiently low temperature, the amphiphiles self-assemble into a highly oriented lamellar phase. Our study aims at comparing the structure of this phase with the predictions of the elastic theory of thermally fluctuating fluid membrane stacks [Lei et al., J. Phys. II 5, 1155 (1995)]. We suggest a method which permits to calculate the bending rigidity and compressibility modulus of the lamellar stack from the simulation data. The simulation results are in reasonable agreement with the theory

Smectic order, pinning, and phase transition in a smectic liquid crystal cell with a random substrate

We study smectic-liquid-crystal order in a cell with a heterogeneous substrate imposing surface random positional and orientational pinnings. Proposing a minimal random elastic model, we demonstrate that, for a thick cell, the smectic state without a rubbed substrate is always unstable at long scales and, for weak random pinning, is replaced by a smectic glass state. We compute the statistics of the associated substrate-driven distortions and the characteristic smectic domain size on the heterogeneous substrate and in the bulk. We find that for weak disorder, the system exhibits a three-dimensional temperature-controlled phase transition between a weakly and strongly pinned smectic glass states akin to the Cardy-Ostlund phase transition. We explore experimental implications of the predicted phenomenology and suggest that it provides a plausible explanation for the experimental observations on polarized light microscopy and x-ray scattering.Comment: 30 pages, 11 figures, Published in PRE, with minor typos correcte

Relative Chirality Of Octupolar Columns In A Triangular Array

The relative chirality of helical columns of planar disks having threefold symmetry,is studied using a model Hamiltonian derived from symmetry arguments that describe low-order octupole interactions. The columns are assumed to pack in a triangular array perpendicular to the columnar axes. Ground-state and finite-temperature mean-field phase diagrams are obtained as functions of interaction parameters. Due to the structure of the disks, there appears a term in the Hamiltonian that is not present for systems with lower internal symmetry, such as classical spin systems. This interaction is responsible for the stabilization of phases in which one third of the columns have a chirality opposite to the others. Such a phase has been observed in the discotic liquid crystal hexa-hexylthiotriphenylene

Thermal phase diagrams of columnar liquid crystals

In order to understand the possible sequence of transitions from the disordered columnar phase to the helical phase in hexa(hexylthio)triphenylene (HHTT), we study a three-dimensional planar model with octupolar interactions inscribed on a triangular lattice of columns. We obtain thermal phase diagrams using a mean-field approximation and Monte Carlo simulations. These two approaches give similar results, namely, in the quasi one-dimensional regime, as the temperature is lowered, the columns order with a linear polarization, whereas helical phases develop at lower temperatures. The helicity patterns of the helical phases are determined by the exact nature of the frustration in the system, itself related to the octupolar nature of the molecules.Comment: 12 pages, 9 figures, ReVTe

The Smectic AA-CC Phase Transition in Biaxial Disordered Environments

We study the smectic $A$-$C$ phase transition in biaxial disordered environments, e.g. fully anisotropic aerogel. We find that both the $A$ and $C$ phases belong to the universality class of the "XY Bragg glass", and therefore have quasi-long-ranged translational smectic order. The phase transition itself belongs to a new universality class, which we study using an $\epsilon=7/2-d$ expansion. We find a stable fixed point, which implies a continuous transition, the critical exponents of which we calculate

First order isotropic - smectic-A transition in liquid crystal-aerosil gels

The short-range order which remains when the isotropic to smectic-A transition is perturbed by a gel of silica nanoparticles (aerosils) has been studied using high-resolution synchrotron x-ray diffraction. The gels have been created \textit{in situ} in decylcyanobiphenyl (10CB), which has a strongly first-order isotropic to smectic-A transition. The effects are determined by detailed analysis of the temperature and gel density dependence of the smectic structure factor. In previous studies of the continuous nematic to smectic-A transition in a variety of thermotropic liquid crystals the aerosil gel appeared to pin, at random, the phase of the smectic density modulation. For the isotropic to smectic-A transition the same gel perturbation yields different results. The smectic correlation length decreases more slowly with increasing random field variance in good quantitative agreement with the effect of a random pinning field at a transition from a uniform phase directly to a phase with one-dimensional translational order. We thus compare the influence of random fields on a \textit{freezing} transition with and without an intervening orientationally ordered phase.Comment: 8 pages, 8 figure

Nonequilibrium steady states in a vibrated-rod monolayer: tetratic, nematic and smectic correlations

We study experimentally the nonequilibrium phase behaviour of a horizontal monolayer of macroscopic rods. The motion of the rods in two dimensions is driven by vibrations in the vertical direction. Aside from the control variables of packing fraction and aspect ratio that are typically explored in molecular liquid crystalline systems, due to the macroscopic size of the particles we are also able to investigate the effect of the precise shape of the particle on the steady states of this driven system. We find that the shape plays an important role in determining the nature of the orientational ordering at high packing fraction. Cylindrical particles show substantial tetratic correlations over a range of aspect ratios where spherocylinders have previously been shown by Bates et al (JCP 112, 10034 (2000)) to undergo transitions between isotropic and nematic phases. Particles that are thinner at the ends (rolling pins or bails) show nematic ordering over the same range of aspect ratios, with a well-established nematic phase at large aspect ratio and a defect-ridden nematic state with large-scale swirling motion at small aspect ratios. Finally, long-grain, basmati rice, whose geometry is intermediate between the two shapes above, shows phases with strong indications of smectic order.Comment: 18 pages and 13 eps figures, references adde

Fluctuations and phase transitions in Larkin-Ovchinnikov liquid crystal states of population-imbalanced resonant Fermi gas

Motivated by a realization of imbalanced Feshbach-resonant atomic Fermi gases, we formulate a low-energy theory of the Fulde-Ferrell and the Larkin-Ovchinnikov (LO) states and use it to analyze fluctuations, stability, and phase transitions in these enigmatic finite momentum-paired superfluids. Focusing on the unidirectional LO pair-density wave state, that spontaneously breaks the continuous rotational and translational symmetries, we show that it is characterized by two Goldstone modes, corresponding to a superfluid phase and a smectic phonon. Because of the liquid-crystalline "softness" of the latter, at finite temperature the 3d state is characterized by a vanishing LO order parameter, quasi-Bragg peaks in the structure and momentum distribution functions, and a "charge"-4, paired Cooper-pairs, off-diagonal-long-range order, with a superfluid-stiffness anisotropy that diverges near a transition into a nonsuperfluid state. In addition to conventional integer vortices and dislocations the LO superfluid smectic exhibits composite half-integer vortex-dislocation defects. A proliferation of defects leads to a rich variety of descendant states, such as the "charge"-4 superfluid and Fermi-liquid nematics and topologically ordered nonsuperfluid states, that generically intervene between the LO state and the conventional superfluid and the polarized Fermi-liquid at low and high imbalance, respectively. The fermionic sector of the LO gapless superconductor is also quite unique, exhibiting a Fermi surface of Bogoliubov quasiparticles associated with the Andreev band of states, localized on the array of the LO domain-walls.Comment: 56 pages, 21 figure

Magnetic Phase Diagram of the Ferromagnetically Stacked Triangular XY Antiferromagnet: A Finite-Size Scaling Study

Histogram Monte-Carlo simulation results are presented for the magnetic-field -- temperature phase diagram of the XY model on a stacked triangular lattice with antiferromagnetic intraplane and ferromagnetic interplane interactions. Finite-size scaling results at the various transition boundaries are consistent with expectations based on symmetry arguments. Although a molecular-field treatment of the Hamiltonian fails to reproduce the correct structure for the phase diagram, it is demonstrated that a phenomenological Landau-type free-energy model contains all the esstential features. These results serve to complement and extend our earlier work [Phys. Rev. B {\bf 48}, 3840 (1993)].Comment: 5 pages (RevTex 3.0), 6 figures available upon request, CRPS 93-