Lattice Glass Models

Motivated by the concept of geometrical frustration, we introduce a class of statistical mechanics lattice models for the glass transition. Monte Carlo simulations in three dimensions show that they display a dynamical glass transition which is very similar to that observed in other off-lattice systems and which does not depend on a specific dynamical rule. Whereas their analytic solution within the Bethe approximation shows that they do have a discontinuous glass transition compatible with the numerical observations.Comment: 4 pages, 2 figures; minor change

Critical and Tricritical Hard Objects on Bicolorable Random Lattices: Exact Solutions

We address the general problem of hard objects on random lattices, and emphasize the crucial role played by the colorability of the lattices to ensure the existence of a crystallization transition. We first solve explicitly the naive (colorless) random-lattice version of the hard-square model and find that the only matter critical point is the non-unitary Lee-Yang edge singularity. We then show how to restore the crystallization transition of the hard-square model by considering the same model on bicolored random lattices. Solving this model exactly, we show moreover that the crystallization transition point lies in the universality class of the Ising model coupled to 2D quantum gravity. We finally extend our analysis to a new two-particle exclusion model, whose regular lattice version involves hard squares of two different sizes. The exact solution of this model on bicolorable random lattices displays a phase diagram with two (continuous and discontinuous) crystallization transition lines meeting at a higher order critical point, in the universality class of the tricritical Ising model coupled to 2D quantum gravity.Comment: 48 pages, 13 figures, tex, harvmac, eps

Density functional theory for nearest-neighbor exclusion lattice gasses in two and three dimensions

To speak about fundamental measure theory obliges to mention dimensional crossover. This feature, inherent to the systems themselves, was incorporated in the theory almost from the beginning. Although at first it was thought to be a consistency check for the theory, it rapidly became its fundamental pillar, thus becoming the only density functional theory which possesses such a property. It is straightforward that dimensional crossover connects, for instance, the parallel hard cube system (three-dimensional) with that of squares (two-dimensional) and rods (one-dimensional). We show here that there are many more connections which can be established in this way. Through them we deduce from the functional for parallel hard (hyper)cubes in the simple (hyper)cubic lattice the corresponding functionals for the nearest-neighbor exclusion lattice gases in the square, triangular, simple cubic, face-centered cubic, and body-centered cubic lattices. As an application, the bulk phase diagram for all these systems is obtained.Comment: 13 pages, 13 figures; needs revtex

First- and second-order phase transitions in a driven lattice gas with nearest-neighbor exclusion

A lattice gas with infinite repulsion between particles separated by $\leq 1$ lattice spacing, and nearest-neighbor hopping dynamics, is subject to a drive favoring movement along one axis of the square lattice. The equilibrium (zero drive) transition to a phase with sublattice ordering, known to be continuous, shifts to lower density, and becomes discontinuous for large bias. In the ordered nonequilibrium steady state, both the particle and order-parameter densities are nonuniform, with a large fraction of the particles occupying a jammed strip oriented along the drive. The relaxation exhibits features reminiscent of models of granular and glassy materials.Comment: 8 pages, 5 figures; results due to bad random number generator corrected; significantly revised conclusion

The repulsive lattice gas, the independent-set polynomial, and the Lov\'asz local lemma

We elucidate the close connection between the repulsive lattice gas in equilibrium statistical mechanics and the Lovasz local lemma in probabilistic combinatorics. We show that the conclusion of the Lovasz local lemma holds for dependency graph G and probabilities {p_x} if and only if the independent-set polynomial for G is nonvanishing in the polydisc of radii {p_x}. Furthermore, we show that the usual proof of the Lovasz local lemma -- which provides a sufficient condition for this to occur -- corresponds to a simple inductive argument for the nonvanishing of the independent-set polynomial in a polydisc, which was discovered implicitly by Shearer and explicitly by Dobrushin. We also present some refinements and extensions of both arguments, including a generalization of the Lovasz local lemma that allows for "soft" dependencies. In addition, we prove some general properties of the partition function of a repulsive lattice gas, most of which are consequences of the alternating-sign property for the Mayer coefficients. We conclude with a brief discussion of the repulsive lattice gas on countably infinite graphs.Comment: LaTex2e, 97 pages. Version 2 makes slight changes to improve clarity. To be published in J. Stat. Phy

Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer

The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells

Blockade of TRPM7 Channel Activity and Cell Death by Inhibitors of 5-Lipoxygenase

TRPM7 is a ubiquitous divalent-selective ion channel with its own kinase domain. Recent studies have shown that suppression of TRPM7 protein expression by RNA interference increases resistance to ischemia-induced neuronal cell death in vivo and in vitro, making the channel a potentially attractive pharmacological target for molecular intervention. Here, we report the identification of the 5-lipoxygenase inhibitors, NDGA, AA861, and MK886, as potent blockers of the TRPM7 channel. Using a cell-based assay, application of these compounds prevented cell rounding caused by overexpression of TRPM7 in HEK-293 cells, whereas inhibitors of 12-lipoxygenase and 15-lipoxygenase did not prevent the change in cell morphology. Application of the 5-lipoxygenase inhibitors blocked heterologously expressed TRPM7 whole-cell currents without affecting the protein's expression level or its cell surface concentration. All three inhibitors were also effective in blocking the native TRPM7 current in HEK-293 cells. However, two other 5-lipoxygenase specific inhibitors, 5,6-dehydro-arachidonic acid and zileuton, were ineffective in suppressing TRPM7 channel activity. Targeted knockdown of 5-lipoxygenase did not reduce TRPM7 whole-cell currents. In addition, application of 5-hydroperoxyeicosatetraenoic acid (5-HPETE), the product of 5-lipoxygenase, or 5-HPETE's downstream metabolites, leukotriene B4 and leukotriene D4, did not stimulate TRPM7 channel activity. These data suggested that NDGA, AA861, and MK886 reduced the TRPM7 channel activity independent of their effect on 5-lipoxygenase activity. Application of AA861 and NDGA reduced cell death for cells overexpressing TRPM7 cultured in low extracellular divalent cations. Moreover, treatment of HEK-293 cells with AA861 increased cell resistance to apoptotic stimuli to a level similar to that obtained for cells in which TRPM7 was knocked down by RNA interference. In conclusion, NDGA, AA861, and MK886 are potent blockers of the TRPM7 channel capable of attenuating TRPM7's function during cell stress, making them effective tools for the biophysical characterization and suppression of TRPM7 channel conductance in vivo

Adsorption of Reactive Particles on a Random Catalytic Chain: An Exact Solution

We study equilibrium properties of a catalytically-activated annihilation $A + A \to 0$ reaction taking place on a one-dimensional chain of length $N$ ($N \to \infty$) in which some segments (placed at random, with mean concentration $p$) possess special, catalytic properties. Annihilation reaction takes place, as soon as any two $A$ particles land onto two vacant sites at the extremities of the catalytic segment, or when any $A$ particle lands onto a vacant site on a catalytic segment while the site at the other extremity of this segment is already occupied by another $A$ particle. Non-catalytic segments are inert with respect to reaction and here two adsorbed $A$ particles harmlessly coexist. For both "annealed" and "quenched" disorder in placement of the catalytic segments, we calculate exactly the disorder-average pressure per site. Explicit asymptotic formulae for the particle mean density and the compressibility are also presented.Comment: AMSTeX, 27 pages + 4 figure