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

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

Particle Acceleration in Relativistic Jets due to Weibel Instability

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the 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 through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. While some Fermi acceleration may occur at the jet front, the majority of electron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron's transverse deflection behind the jet head. The ``jitter'' radiation (Medvedev 2000) from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.Comment: ApJ, in press, Sept. 20, 2003 (figures with better resolution: http://gammaray.nsstc.nasa.gov/~nishikawa/apjweib.pdf

Particle Acceleration and Magnetic Field Generation in Electron-Positron 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 electron-positron jet front propagating into an ambient electron-positron plasma with and without initial magnetic fields. We find small differences in the results for no ambient and modest ambient magnetic fields. New 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. Furthermore, the non-linear fluctuation amplitudes of densities, currents, electric, and magnetic fields in the electron-positron shock are larger than those found in the electron-ion shock studied in a previous paper at the comparable simulation time. This comes from the fact that both electrons and positrons contribute to generation of the Weibel instability. Additionally, we have performed simulations with different electron skin depths. We find that growth times scale inversely with the plasma frequency, and the sizes of structures created by the Weibel instability scale proportional to the electron skin depth. This is the expected result and indicates that the simulations have sufficient grid resolution. The simulation results show that the Weibel instability is responsible for generating and amplifying nonuniform, small-scale magnetic fields which contribute to the electron's (positron's) transverse deflection behind the jet head.Comment: 18 pages, 8 figures, revised and accepted for ApJ, A full resolution of the paper can be found at http://gammaray.nsstc.nasa.gov/~nishikawa/apjep1.pd

Particle Acceleration and Radiation associated with Magnetic Field Generation from Relativistic Collisionless Shocks

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the 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 through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron's transverse deflection behind the jet head. The ``jitter'' radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.Comment: 4 pages, 1 figure, submitted to Proceedings of 2003 Gamma Ray Burst Conferenc

Renormalized parameters and perturbation theory for an n-channel Anderson model with Hund's rule coupling: Asymmetric case

We explore the predictions of the renormalized perturbation theory for an n-channel Anderson model, both with and without Hund's rule coupling, in the regime away from particle-hole symmetry. For the model with n=2 we deduce the renormalized parameters from numerical renormalization group calculations, and plot them as a function of the occupation at the impurity site, nd. From these we deduce the spin, orbital and charge susceptibilities, Wilson ratios and quasiparticle density of states at T=0, in the different parameter regimes, which gives a comprehensive overview of the low energy behavior of the model. We compare the difference in Kondo behaviors at the points where nd=1 and nd=2. One unexpected feature of the results is the suppression of the charge susceptibility in the strong correlation regime over the occupation number range 1 <nd <3.Comment: 9 pages, 17 figure

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