Chapman-Enskog expansion about nonequilibrium states: the sheared granular fluid

The Chapman-Enskog method of solution of kinetic equations, such as the Boltzmann equation, is based on an expansion in gradients of the deviations fo the hydrodynamic fields from a uniform reference state (e.g., local equilibrium). This paper presents an extension of the method so as to allow for expansions about \emph{arbitrary}, far-from equilibrium reference states. The primary result is a set of hydrodynamic equations for studying variations from the arbitrary reference state which, unlike the usual Navier-Stokes hydrodynamics, does not restrict the reference state in any way. The method is illustrated by application to a sheared granular gas which cannot be studied using the usual Navier-Stokes hydrodynamics.Comment: 23 pages, no figures. Submited to PRE Replaced to correct misc. errors Replaced to correct misc. errors, make notation more consistant, extend discussio

Field-test of a robust, portable, frequency-stable laser

We operate a frequency-stable laser in a non-laboratory environment where the test platform is a passenger vehicle. We measure the acceleration experienced by the laser and actively correct for it to achieve a system acceleration sensitivity of $\Delta f / f$ = $11(2) \times 10^{-12}$/g, $6(2) \times 10^{-12}$/g, and $4(1) \times 10^{-12}$/g for accelerations in three orthogonal directions at 1 Hz. The acceleration spectrum and laser performance are evaluated with the vehicle both stationary and moving. The laser linewidth in the stationary vehicle with engine idling is 1.7(1) Hz

Proton Association Constants of His 37 in the Influenza-A M218–60 Dimer-of-Dimers

National Institute of Biomedical Imaging and Bioengineering (U.S.) (EB001960)National Institute of Biomedical Imaging and Bioengineering (U.S.) (EB002026)National Institute of Biomedical Imaging and Bioengineering (U.S.) (GM094648

Inherent Rheology of a Granular Fluid in Uniform Shear Flow

In contrast to normal fluids, a granular fluid under shear supports a steady state with uniform temperature and density since the collisional cooling can compensate locally for viscous heating. It is shown that the hydrodynamic description of this steady state is inherently non-Newtonian. As a consequence, the Newtonian shear viscosity cannot be determined from experiments or simulation of uniform shear flow. For a given degree of inelasticity, the complete nonlinear dependence of the shear viscosity on the shear rate requires the analysis of the unsteady hydrodynamic behavior. The relationship to the Chapman-Enskog method to derive hydrodynamics is clarified using an approximate Grad's solution of the Boltzmann kinetic equationComment: 10 pages, 4 figures; substantially enlarged version; to be published in PR

Unusual architecture of the p7 channel from hepatitis C virus

The Hepatitis C virus (HCV) has developed a small membrane protein, p7, which remarkably can self-assemble into a large channel complex that selectively conducts cations1-4. We are curious as to what structural solution has the viroporin adopted to afford selective cation conduction because p7 has no homology with any of the known prokaryotic or eukaryotic channel proteins. The p7 activity can be inhibited by amantadine and rimantadine2,5, which also happen to be potent blockers of the influenza M2 channel6 and licensed drugs against influenza infections7. The adamantane derivatives were subjects of HCV clinical trials8, but large variation in drug efficacy among the various HCV genotypes has been difficult to explain without detailed molecular structures. Here, we determined the structures of this HCV viroporin as well as its drug-binding site using the latest nuclear magnetic resonance (NMR) technologies. The structure exhibits an unusual mode of hexameric assembly, where the individual p7 monomers, i, not only interact with their immediate neighbors, but also reach farther to associate with the i+2 and i+3 monomers, forming a sophisticated, funnel-like architecture. The structure also alludes to a mechanism of cation selection: an asparagine/histidine ring that constricts the narrow end of the funnel serves as a broad cation selectivity filter while an arginine/lysine ring that defines the wide end of the funnel may selectively allow cation diffusion into the channel. Our functional investigation using whole-cell channel recording showed that these residues are indeed critical for channel activity. NMR measurements of the channel-drug complex revealed six equivalent hydrophobic pockets between the peripheral and pore-forming helices to which amantadine or rimantadine binds, and compound binding specifically to this position may allosterically inhibit cation conduction by preventing the channel from opening. Our data provide molecular explanation for p7-mediated cation conductance and its inhibition by adamantane derivatives

Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org

In-situ strain tuning of the Dirac surface states in Bi2Se3 films

Elastic strain has the potential for a controlled manipulation of the band gap and spin-polarized Dirac states of topological materials, which can lead to pseudo-magnetic-field effects, helical flat bands and topological phase transitions. However, practical realization of these exotic phenomena is challenging and yet to be achieved. Here, we show that the Dirac surface states of the topological insulator Bi2Se3 can be reversibly tuned by an externally applied elastic strain. Performing in-situ x-ray diffraction and in-situ angle-resolved photoemission spectroscopy measurements during tensile testing of epitaxial Bi2Se3 films bonded onto a flexible substrate, we demonstrate elastic strains of up to 2.1% and quantify the resulting reversible changes in the topological surface state. Our study establishes the functional relationship between the lattice and electronic structures of Bi2Se3 and, more generally, demonstrates a new route toward momentum-resolved mapping of strain-induced band structure changes