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

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

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

Exact Solution of a Electron System Combining Two Different t-J Models

A new strongly correlated electron model is presented. This is formed by two types of sites: one where double occupancy is forbidden, as in the t-J model, and the other where double occupancy is allowed but vacancy is not allowed, as an inverse t-J model. The Hamiltonian shows nearest and next-to-nearest neighbour interactions and it is solved by means of a modified algebraic nested Bethe Ansatz. The number of sites where vacancy is not allowed, may be treated as a new parameter if the model is looked at as a t-J model with impurities. The ground and excited states are described in the thermodynamic limit.Comment: Some corrections and references added. To be published in J. Phys.

Strong-Coupling Expansion for the Hubbard Model

A strong-coupling expansion for models of correlated electrons in any dimension is presented. The method is applied to the Hubbard model in $d$ dimensions and compared with numerical results in $d=1$. Third order expansion of the Green function suffices to exhibit both the Mott metal-insulator transition and a low-temperature regime where antiferromagnetic correlations are strong. It is predicted that some of the weak photoemission signals observed in one-dimensional systems such as $SrCuO_2$ should become stronger as temperature increases away from the spin-charge separated state.Comment: 4 pages, RevTex, 3 epsf figures include

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