Sequence composition and environment effects on residue fluctuations in protein structures

The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per residue elastic network model accounting for the nonhomogeneous protein mass distribution and the inter-atomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues, showing agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.Comment: 8 pages, 4 figure

Slow-string limit and "antiferromagnetic" state in AdS/CFT

We discuss a slow-moving limit of a rigid circular equal-spin solution on R x S^3. We suggest that the solution with the winding number equal to the total spin approximates the quantum string state dual to the maximal-dimension ``antiferromagnetic'' state of the SU(2) spin chain on the gauge theory side. An expansion of the string action near this solution leads to a weakly coupled system of a sine-Gordon model and a free field. We show that a similar effective Hamiltonian appears in a certain continuum limit from the half-filled Hubbard model that was recently suggested to describe the all-order dilatation operator of the dual gauge theory in the SU(2) sector. We also discuss some other slow-string solutions with one spin component in AdS_5 and one in S^5.Comment: 32 pages, Latex v2: one footnote and references adde

Breadboard stellar tracker system test report, volume 1

The performance of a star tracker equipped with a focal plane detector was evaluated. The CID board is an array of 256 x 256 pixels which are 20 x 20 micrometers in dimension. The tracker used for test was a breadboard tracker system developed by BASD. Unique acquisition and tracking algorithms are employed to enhance performance. A pattern recognition process is used to test for proper image spread function and to avoid false acquisition on noise. A very linear, high gain, interpixel transfer function is derived for interpolating star position. The lens used in the tracker has an EFL of 100 mm. The tracker has an FOV of 2.93 degrees resulting in a pixel angular subtense of 41.253 arc sec in each axis. The test procedure used for the program presented a star to the tracker in a circular pattern of positions; the pattern was formed by projecting a simulated star through a rotatable deviation wedge. Further tests determined readout noise, Noise Equivalent Displacement during track, and spatial noise during acquisition by taking related data and reducing it

The influence of local field corrections on Thomson scattering in non-ideal two-component plasmas

Thomson scattering in non-ideal (collision-dominated) two-component plasmas is calculated accounting for electron-ion collisions as well as electron-electron correlations. This is achieved by using a novel interpolation scheme for the electron-electron response function generalizing the traditional Mermin approach. Also, ions are treated as randomly distributed inert scattering centers. The collision frequency is taken as a dynamic and complex quantity and is calculated from a microscopic quantum-statistical approach. Implications due to different approximations for the electron-electron correlation, i.e. different forms of the OCP local field correction, are discussed

Buoyancy waves in Pluto's high atmosphere: Implications for stellar occultations

We apply scintillation theory to stellar signal fluctuations in the high-resolution, high signal/noise, dual-wavelength data from the MMT observation of the 2007 March 18 occultation of P445.3 by Pluto. A well-defined high wavenumber cutoff in the fluctuations is consistent with viscous-thermal dissipation of buoyancy waves (internal gravity waves) in Pluto's high atmosphere, and provides strong evidence that the underlying density fluctuations are governed by the gravity-wave dispersion relation.Comment: Accepted 18 June 2009 for publication in Icaru

Temperature Fluctuations driven by Magnetorotational Instability in Protoplanetary Disks

The magnetorotational instability (MRI) drives magnetized turbulence in sufficiently ionized regions of protoplanetary disks, leading to mass accretion. The dissipation of the potential energy associated with this accretion determines the thermal structure of accreting regions. Until recently, the heating from the turbulence has only been treated in an azimuthally averaged sense, neglecting local fluctuations. However, magnetized turbulence dissipates its energy intermittently in current sheet structures. We study this intermittent energy dissipation using high resolution numerical models including a treatment of radiative thermal diffusion in an optically thick regime. Our models predict that these turbulent current sheets drive order unity temperature variations even where the MRI is damped strongly by Ohmic resistivity. This implies that the current sheet structures where energy dissipation occurs must be well resolved to correctly capture the flow structure in numerical models. Higher resolutions are required to resolve energy dissipation than to resolve the magnetic field strength or accretion stresses. The temperature variations are large enough to have major consequences for mineral formation in disks, including melting chondrules, remelting calcium-aluminum rich inclusions, and annealing silicates; and may drive hysteresis: current sheets in MRI active regions could be significantly more conductive than the remainder of the disk.Comment: 16 pages, 13 figures, ApJ In Press, updated to match proof

Ferromagnetism in the Periodic Anderson Model - a Modified Alloy Analogy

We introduce a new aproximation scheme for the periodic Anderson model (PAM). The modified alloy approximation represents an optimum alloy approximation for the strong coupling limit, which can be solved within the CPA-formalism. Zero-temperature and finite-temperature phase diagrams are presented for the PAM in the intermediate-valence regime. The diversity of magnetic properties accessible by variation of the system parameters can be studied by means of quasiparticle densities of states: The conduction band couples either ferro- or antiferromagneticaly to the f-levels. A finite hybridization is a necessary precondition for ferromagnetism. However, too strong hybridization generally suppresses ferromagnetism, but can for certain system parameters also lead to a semi-metallic state with unusual magnetic properties. By comparing with the spectral density approximation, the influence of quasiparticle damping can be examined.Comment: 20 pages, 13 figure

Many-body approach to the nonlinear interaction of charged particles with an interacting free electron gas

We report various many-body theoretical approaches to the nonlinear decay rate and energy loss of charged particles moving in an interacting free electron gas. These include perturbative formulations of the scattering matrix, the self-energy, and the induced electron density. Explicit expressions for these quantities are obtained, with inclusion of exchange and correlation effects.Comment: 11 pages, 5 figures. To appear in Journal of Physics