Properties of contact matrices induced by pairwise interactions in proteins

The total conformational energy is assumed to consist of pairwise interaction energies between atoms or residues, each of which is expressed as a product of a conformation-dependent function (an element of a contact matrix, C-matrix) and a sequence-dependent energy parameter (an element of a contact energy matrix, E-matrix). Such pairwise interactions in proteins force native C-matrices to be in a relationship as if the interactions are a Go-like potential [N. Go, Annu. Rev. Biophys. Bioeng. 12. 183 (1983)] for the native C-matrix, because the lowest bound of the total energy function is equal to the total energy of the native conformation interacting in a Go-like pairwise potential. This relationship between C- and E-matrices corresponds to (a) a parallel relationship between the eigenvectors of the C- and E-matrices and a linear relationship between their eigenvalues, and (b) a parallel relationship between a contact number vector and the principal eigenvectors of the C- and E-matrices; the E-matrix is expanded in a series of eigenspaces with an additional constant term, which corresponds to a threshold of contact energy that approximately separates native contacts from non-native ones. These relationships are confirmed in 182 representatives from each family of the SCOP database by examining inner products between the principal eigenvector of the C-matrix, that of the E-matrix evaluated with a statistical contact potential, and a contact number vector. In addition, the spectral representation of C- and E-matrices reveals that pairwise residue-residue interactions, which depends only on the types of interacting amino acids but not on other residues in a protein, are insufficient and other interactions including residue connectivities and steric hindrance are needed to make native structures the unique lowest energy conformations.Comment: Errata in DOI:10.1103/PhysRevE.77.051910 has been corrected in the present versio

Estimation of the mean of a discrete parameter, covariance stationary, stochastic process in rotation sampling

Constrained optimization procedure for deriving linear estimator of population mean in rotation samplin

Reversion phenomena of Cu-Cr alloys

Cu-Cr alloys which were given various aging and reversion treatments were investigated in terms of electrical resistivity and hardness. Transmission electron microscopy was one technique employed. Some results obtained are as follows: the increment of electrical resistivity after the reversion at a constant temperature decreases as the aging temperature rises. In a constant aging condition, the increment of electrical resistivity after the reversion increases, and the time required for a maximum reversion becomes shorter as the reversion temperature rises. The reversion phenomena can be repeated, but its amount decreases rapidly by repetition. At first, the amount of reversion increases with aging time and reaches its maximum, and then tends to decrease again. Hardness changes by the reversion are very small, but the hardness tends to soften slightly. Any changes in transmission electron micrographs by the reversion treatment cannot be detected

Weibel instability and associated strong fields in a fully 3D simulation of a relativistic shock

Plasma instabilities (e.g., Buneman, Weibel and other two-stream instabilities) excited in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a new 3-D relativistic particle-in-cell code, we have investigated the particle acceleration and shock structure associated with an unmagnetized relativistic electron-positron jet propagating into an unmagnetized electron-positron plasma. The simulation has been performed using a long simulation system in order to study the nonlinear stages of the Weibel instability, the particle acceleration mechanism, and the shock structure. Cold jet electrons are thermalized and slowed while the ambient electrons are swept up to create a partially developed hydrodynamic (HD) like shock structure. In the leading shock, electron density increases by a factor of 3.5 in the simulation frame. Strong electromagnetic fields are generated in the trailing shock and provide an emission site. We discuss the possible implication of our simulation results within the AGN and GRB context.Comment: 4 pages, 3 figures, ApJ Letters, in pres

3-D General Relativistic MHD Simulations of Generating Jets

We have performed a first fully 3-D GRMHD simulation with Schwarzschild black hole with a free falling corona. The initial simulation results show that a jet is created as in previous axisymmetric simulations. However, the time to generate the jet is longer than in the 2-D simulations. We expect that due to the additional azimuthal dimension the dynamics of jet formation can be modified.Comment: 4 pages Proc. Oxford Radio Galaxy Workshop ed. R. Laing & K. Blundell (San Francisco: PASP) in press (revised

Results from K2K and status of T2K

Results from the K2K experiment and status of the T2K experiment are reported.Comment: 9 pages, 6 figures. Talk at International Conference on New Trends in High-Energy Physics (Crimea2005), Yalta, Ukraine, September 10-17, 200

Long baseline accelerator neutrino experiments

Neutrino oscillation has been observed and shown to be consistent with the idea that the oscillations are due to the co-existence of three mass and three flavor eigen-states. This is confirmed by the dependence on L/E and the observation of the explicit flavor changes associated with the oscillations in νμ → ντ and νμ → νe. The three mixing angles, which corresponds to the mixing of the three neutrino states, have been measured. They are large compared to those of quarks, especially the mixing of second and third generation is almost maximal. Reactor and accelerator data are consistent with three-neutrino framework at 10% level. Next generation long baseline neutrino experiments will clarify the mass hierarchy, relation of νμ, ντ and second, third mass states and may discover CP violation in neutrino oscillation. However, to investigate the structure of flavor physics further, it will be necessary to have critical tests of the three-neutrino framework itself and the origin of possible CP violation in lepton

The emission of energetic electrons from the complex streamer corona adjacent to leader stepping

We here propose a model to capture the complexity of the streamer corona adjacent to leader stepping and relate it to the production of energetic electrons serving as a source of X-rays and $\gamma$-rays, manifesting in terrestrial gamma-ray flashes (TGFs). During its stepping, the leader tip is accompanied by a corona consisting of multitudinous streamers perturbing the air in its vicinity and leaving residual charge behind. We explore the relative importance of air perturbations and preionization on the production of energetic run-away electrons by 2.5D cylindrical Monte Carlo particle simulations of streamers in ambient fields of 16 kV cm$^{-1}$ and 50 kV cm$^{-1}$ at ground pressure. We explore preionization levels between $10^{10}$ m$^{-3}$ and $10^{13}$ m$^{-3}$, channel widths between 0.5 and 1.5 times the original streamer widths and air perturbation levels between 0\% and 50\% of ambient air. We observe that streamers in preionized and perturbed air accelerate more efficiently than in non-ionized and uniform air with air perturbation dominating the streamer acceleration. We find that in unperturbed air preionization levels of $10^{11}$ m$^{-3}$ are sufficient to explain run-away electron rates measured in conjunction with terrestrial gamma-ray flashes. In perturbed air, the production rate of runaway electrons varies from $10^{10}$ s$^{-1}$ to $10^{17}$ s$^{-1}$ with maximum electron energies from some hundreds of eV up to some hundreds of keV in fields above and below the breakdown strength. In the presented simulations the number of runaway electrons matches with the number of energetic electrons measured in alignment with the observations of terrestrial gamma-ray flashes. Conclusively, the complexity of the streamer zone ahead of leader tips allows explaining the emission of energetic electrons and photons from streamer discharges.Comment: 29 pages, 11 figures, 2 table

Particle Acceleration, Magnetic Field Generation, and Emission in Relativistic Shocks

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet front propagating into an ambient plasma. We find small differences in the results for no ambient and modest ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. The small scale magnetic field structure generated by the Weibel instability is appropriate to the generation of ``jitter'' radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation resulting from small scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.Comment: 6 pages, 1 figure, revised and accepted for Advances in Space Research (35th COSPAR Scientific Assembly, Paris, 18-25 July 2004

Acceleration Mechanics in Relativistic Shocks by the Weibel Instability

Plasma instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks may be responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated long-term particle acceleration associated with relativistic electron-ion or electron-positron jet fronts propagating into an unmagnetized ambient electron-ion or electron-positron plasma. These simulations have been performed with a longer simulation system than our previous simulations in order to investigate the nonlinear stage of the Weibel instability and its particle acceleration mechanism. The current channels generated by the Weibel instability are surrounded by toroidal magnetic fields and radial electric fields. This radial electric field is quasi stationary and accelerates particles which are then deflected by the magnetic field.Comment: 17 pages, 5 figures, accepted for publication in ApJ, A full resolution ot the paper can be found at http://gammaray.nsstc.nasa.gov/~nishikawa/accmec.pd