Approach to hyperuniformity of steady states of facilitated exclusion processes.

We consider the fluctuations in the number of particles in a box of sizeLdinZd,d⩾1, in the (infinite volume) translation invariant stationary states of the facilitated exclusion process, also called the conserved lattice gas model. When started in a Bernoulli (product) measure at densityρ, these systems approach, ast→∞, a 'frozen' state forρ⩽ρc, withρc=1/2ford = 1 andρc<1/2ford⩾2. Atρ=ρcthe limiting state is, as observed by Hexner and Levine, hyperuniform, that is, the variance of the number of particles in the box grows slower thanLd. We give a general description of how the variances at different scales ofLbehave asρ↗ρc. On the largest scale,L≫L2, the fluctuations are normal (in fact the same as in the original product measure), while in a regionL1≪L≪L2, with bothL1andL2going to infinity asρ↗ρc, the variance grows faster than normal. For1≪L≪L1the variance is the same as in the hyperuniform system. (All results discussed are rigorous ford = 1 and based on simulations ford⩾2.).

Kardar-Parisi-Zhang universality class and the anchored Toom interface.

We revisit the anchored Toom interface and use Kardar-Parisi-Zhang scaling theory to argue that the interface fluctuations are governed by the Airy1 process with the role of space and time interchanged. The predictions, which contain no free parameter, are numerically well confirmed for space-time statistics in the stationary state. In particular, the spatial fluctuations of the interface computed numerically agree well with those given by the GOE edge distribution of Tracy and Widom [Commun. Math. Phys. 177, 727 (1996)].

Sarcoidosis within a renal allograft: a case report and review of the literature.

Sarcoidosis is an unusual disorder of unknown etiology. Clinically apparent renal involvement is rare in sarcoidosis. The incidence of recurrence in transplant recipients is unknown with few cases having been reported previously. Herein we report a case of sarcoidosis involving a renal allograft that occurred 3 years after transplantation and provide a literature review.

Nonequilibrium stationary state of a harmonic crystal with alternating masses.

We analyze the nonequilibrium steady states (NESS) of a one-dimensional harmonic chain of N atoms with alternating masses connected to heat reservoirs at unequal temperatures. We find that the temperature profile defined through the local kinetic energy T(j)≡/mj oscillates with period two in the bulk of the system. Depending on boundary conditions, either the heavier or the lighter particles in the bulk are hotter. We obtain explicit integral expressions for the bulk temperature profile and steady state current in the limit N→∞. These depend on whether N is odd or even. We also study similar temperature oscillations in the NESS of systems with noise in the dynamics. These die out as N→∞.

Heat conduction in disordered harmonic lattices with energy-conserving noise.

We study heat conduction in a harmonic crystal whose bulk dynamics is supplemented by random reversals (flips) of the velocity of each particle at a rate λ. The system is maintained in a nonequilibrium stationary state (NESS) by contacts with white-noise Langevin reservoirs at different temperatures. We show that the one-body and pair correlations in this system are the same (after an appropriate mapping of parameters) as those obtained for a model with self-consistent reservoirs. This is true both for the case of equal and random (quenched) masses. While the heat conductivity in the NESS of the ordered system is known explicitly, much less is known about the random mass case. Here we investigate the random system with velocity flips. We improve the bounds on the Green-Kubo conductivity obtained by Bernardin [J. Stat. Phys. 133, 417 (2008)]. The conductivity of the one-dimensional system is then studied both numerically and analytically. This sheds some light on the effect of noise on the transport properties of systems with localized states caused by quenched disorder.

Effect of phonon-phonon interactions on localization.

We study the heat current J in a classical one-dimensional disordered chain with on-site pinning and with ends connected to stochastic thermal reservoirs at different temperatures. In the absence of anharmonicity all modes are localized and there is a gap in the spectrum. Consequently J decays exponentially with system size N. Using simulations we find that even a small amount of anharmonicity leads to a J approximately 1/N dependence, implying diffusive transport of energy.

Protective immunogenicity of the paraflagellar rod protein 2 of Leishmania mexicana.

Paraflagellar rod proteins (PFR) are a potent immunogen against experimental Trypanosoma cruzi infection. PFR are highly conserved among kinetoplastid parasites. We therefore evaluated the immunogenicity of the Leishmania mexicana pfr-2 gene and protein product in the hamster model of American cutaneous leishmaniasis. Immunization with pfr-2 DNA-induced specific antibody, confirming immunogenicity. Subsequent challenge with 10,000 and 500 stationary phase L. mexicana promastigotes respectively, resulted in delayed appearance of lesions, and significant reduction in lesions post infection in male hamsters, yet exacerbated lesions in female hamsters. Immunization with recombinant PFR-2 protein (rPFR-2) prevented lesion development in female hamsters challenged with L. panamensis, but was ineffective against L. mexicana. Nevertheless, prime boost immunization of female hamsters with rPFR and pfr-2 DNA significantly reduced lesion size following challenge with 500 L. mexicana promastigotes, supporting the relevance of PFR-2 as a potential vaccine constituent.

Boltzmann entropy for dense fluids not in local equilibrium.

Using computer simulations, we investigate the time evolution of the (Boltzmann) entropy of a dense fluid not in local equilibrium. The macrovariables M describing the system are the (empirical) particle density f=[f(x,v)] and the total energy E. We find that S(f(t),E) is a monotone increasing in time even when its kinetic part is decreasing. We argue that for isolated Hamiltonian systems monotonicity of S(M(t))=S(M(X(t))) should hold generally for "typical" (the overwhelming majority of) initial microstates (phase points) X0 belonging to the initial macrostate M0, satisfying M(X0)=M(0). This is a consequence of Liouville's theorem when M(t) evolves according to an autonomous deterministic law.

Space-charge-limited 2D electron flow between two flat electrodes in a strong magnetic field.

An approximate analytic solution is constructed for the 2D space-charge-limited emission by a cathode surrounded by nonemitting conducting ledges of width Lambda. An essentially exact solution (via conformal mapping) of the electrostatic problem in vacuum is matched to the solution of a linearized problem in the space charge region whose boundaries are sharp due to the presence of a strong magnetic field. The current density growth in a narrow interval near the edges of the cathode depends strongly on Lambda. We obtain an empirical formula for the total current as a function of Lambda which extends to more general cathode geometries.

Exact free energy functional for a driven diffusive open stationary nonequilibrium system.

We obtain the exact probability exp[-LF([rho(x)])] of finding a macroscopic density profile rho(x) in the stationary nonequilibrium state of an open driven diffusive system, when the size of the system L-->infinity. F, which plays the role of a nonequilibrium free energy, has a very different structure from that found in the purely diffusive case. As there, F is nonlocal, but the shocks and dynamic phase transitions of the driven system are reflected in nonconvexity of F, in discontinuities in its second derivatives, and in non-Gaussian fluctuations in the steady state.

Properties of stationary nonequilibrium states in the thermostatted periodic Lorentz gas: the multiparticle system.

We study the stationary nonequilibrium states of N-point particles moving under the influence of an electric field E among fixed obstacles (disk) in a two-dimensional torus. The total kinetic energy of the system is kept constant through a Gaussian thermostat that produces a velocity dependent mean field interaction between the particles. The current and the particle distribution functions are obtained numerically and compared for small /E/ with analytic solutions of a Boltzmann-type equation obtained by treating the collisions with the obstacles as random independent scatterings. The agreement is surprisingly good for both small and large N. The latter system in turn agrees with a self-consistent one-particle evolution expected to hold in the N-->infinity limit.

Thermodynamic entropy production fluctuation in a two-dimensional shear flow model.

We investigate fluctuations in the momentum flux across a surface perpendicular to the velocity gradient in a stationary shear flow maintained by either thermostated deterministic or by stochastic boundary conditions. In the deterministic system the fluctuation relation for the probability of large deviations, which holds for the phase space volume contraction giving the Gibbs ensemble entropy production, never seems to hold for the flux which gives the hydrodynamic entropy production. In the stochastic case the fluctuation relation is found to hold for the total flux, as predicted by various exact results, but not for the flux across part of the surface. The latter appear to satisfy a modified fluctuation relation. Similar results are obtained for the heat flux in a steady state produced by stochastic boundaries at different temperatures.

Oligomeric structure of virion-associated and soluble forms of the simian immunodeficiency virus envelope protein in the prefusion activated conformation.

The envelope proteins (env) of simian immunodeficiency virus (SIV) and HIV type 1 assemble to form noncovalently associated oligomers in the endoplasmic reticulum. After cleavage in a Golgi compartment, oligomeric env complexes are transported to the surface of infected cells, where incorporation into budding virions can occur. Difficulties in obtaining adequate quantities of virions retaining env, as well as the unstable nature and hydrophobicity of the oligomer, may account for the absence of previous biophysical studies to determine the oligomeric valency of membrane-associated env. The aim of this study was to evaluate the oligomeric state of SIV env before membrane-fusion activation. Virion-associated env, obtained by crosslinking and detergent extraction, and non-crosslinked secreted env ectodomain (recombinant gp140) were purified by lentil-lectin chromatography and gel filtration as single predominant species. Sedimentation equilibrium-derived mass values for both forms of SIV env were close to those predicted for trimeric assemblies. Determination of the mass of individual molecules by scanning transmission electron microscopy confirmed that SIV virion-associated env and gp140 formed largely homogeneous populations of trimers. Furthermore, a triangular or tri-lobed morphology was clearly visualized in a subset of the trimers.

Free energy functional for nonequilibrium systems: an exactly solvable case.

We consider the steady state of an open system in which there is a flux of matter between two reservoirs at different chemical potentials. For a large system of size N, the probability of any macroscopic density profile rho(x) is exp[-NF([rho])]; F thus generalizes to nonequilibrium systems the notion of free energy density for equilibrium systems. Our exact expression for F is a nonlocal functional of rho, which yields the macroscopically long range correlations in the nonequilibrium steady state previously predicted by fluctuating hydrodynamics and observed experimentally.

SmtB-DNA and protein-protein interactions in the formation of the cyanobacterial metallothionein repression complex: Zn2+ does not dissociate the protein-DNA complex in vitro.

The synechococcal metallothionein locus smt consists of two divergent genes: smtA coding for the metallothionein SmtA, and smtB coding for the trans-acting regulator SmtB. The latter binds at two inverted repeats, designated S1/S2 and S3/S4, in the overlapping promoter/operator sites between the two genes. We have determined the binding stoichiometries to the entire operator/promoter DNA and to the separate S1/S2 and S3/S4 half-operator oligonucleotides using sedimentation equilibrium and sedimentation velocity measurements. The full promoter/operator DNA binds two SmtB dimers. The hydrodynamic behavior of this complex supports a compact nucleoprotein structure. Each separate S1/S2 and S3/S4 operator sequence also binds two dimers. An equal molar mixture of separate S1/S2 and S3/S4 operator sequences, in excess SmtB, forms a S1/S2-SmtB:SmtB-S3/S4 bridge complex. Combining these results with previously published binding interference data, which showed consecutive S1/S2 and S3/S4 SmtB occupancy on the operator/promoter DNA, we have developed a model for the establishment of the repression complex that appears to involve significant DNA compaction, presumably DNA bending, stabilized by SmtB-SmtB bridge interactions. DNase I footprinting titrations also showed consecutive S1/S2 and S3/S4 SmtB occupancy. The footprints expand considerably in the presence of Zn2+. Hence, SmtB remains bound to the operator sites when Zn2+ ions are present. This result is further supported by gel retardation assay. Failure of the metal ions to dissociate SmtB from the DNA points to a hitherto unknown function of SmtB in the regulation of the smt locus.

Surface-directed spinodal decomposition in binary fluid mixtures.

We consider the phase separation of binary fluids in contact with a surface, which is preferentially wetted by one of the components of the mixture. We review the results available for this problem and present numerical results obtained using a mesoscopic level simulation technique for the three-dimensional problem.

Study of the assembly of vesicular stomatitis virus N protein: role of the P protein.

To derive structural information about the vesicular stomatitis virus (VSV) nucleocapsid (N) protein, the N protein and the VSV phosphoprotein (P protein) were expressed together in Escherichia coli. The N and P proteins formed soluble protein complexes of various molar ratios when coexpressed. The major N/P protein complex was composed of 10 molecules of the N protein, 5 molecules of the P protein, and an RNA. A soluble N protein-RNA oligomer free of the P protein was isolated from the N/P protein-RNA complex using conditions of lowered pH. The molecular weight of the N protein-RNA oligomer, 513,879, as determined by analytical ultracentrifugation, showed that it was composed of 10 molecules of the N protein and an RNA of approximately 90 nucleotides. The N protein-RNA oligomer had the appearance of a disk with outer diameter, inner diameter, and thickness of 148 +/- 10 A, 78 +/- 9 A, and 83 +/- 8 A, respectively, as determined by electron microscopy. RNA in the complexes was protected from RNase digestion and was stable at pH 11. This verified that N/P protein complexes expressed in E. coli were competent for encapsidation. In addition to coexpression with the full-length P protein, the N protein was expressed with the C-terminal 72 amino acids of the P protein. This portion of the P protein was sufficient for binding to the N protein, maintaining it in a soluble state, and for assembly of N protein-RNA oligomers. With the results provided in this report, we propose a model for the assembly of an N/P protein-RNA oligomer.