Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry

An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is important. Such a simplified model is essential for efficient search of conformational space. In this work, we present a formulation of potential function for simplified representations of protein structures. It is based on the combination of descriptors derived from residue-residue contact and sequence-dependent local geometry. The optimal weight coefficients for contact and local geometry is obtained through optimization by maximizing margins among native and decoy structures. The latter are generated by chain growth and by gapless threading. The performance of the potential function in blind test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. This potential function have comparable or better performance than several residue-based potential functions that require in addition coordinates of side chain centers or coordinates of all side chain atoms.Comment: 4 pages, 2 figures, Accepted by 26th IEEE-EMBS Conference, San Francisc

Statistical Properties of Multiple Optical Emission Components in Gamma-Ray Bursts and Implications

Well-sampled optical lightcurves of 146 gamma-ray bursts (GRBs) are complied from the literature. Multiple optical emission components are extracted with power-law function fits to these lightcurves. We present a systematical analysis for statistical properties and their relations to prompt gamma-ray emission and X-ray afterglow for each component. We show that peak luminosity in the prompt and late flares are correlated and the evolution of the peak luminosity may signal the evolution of the accretion rate. No tight correlation between the shallow decay phase/plateau and prompt gamma-ray emission is found. Assuming that they are due to a long-lasting wind injected by a compact object, we show that the injected behavior favors the scenarios of a long-lasting wind after the main burst episode. The peak luminosity of the afterglow onset is tightly correlated with Eiso, and it is dimmer as peaking later. Assuming that the onset bump is due to the fireball deceleration by the external medium, we examine the Gamma_0-Eiso relation and find that it is confirmed with the current sample. Optical re-brightening is observed in 30 GRBs in our sample. It shares the same relation between the width and the peak time as found in the onset bump, but no clear correlation between the peak luminosity and Eiso as observed in the onset bumps is found. Although its peak luminosity also decays with time, the slope is much shallower than that of the onset peak. We get L t^{-1}_{p}$, being consistent with off-axis observations to an expanding external fireball in a wind-like circum medium. The late re-brightening may signal another jet component. Mixing of different emission components may be the reason for the observed chromatic breaks in different energy bands.Comment: 10 pages, 5 figures, to be published by IJMPD (Proceedings of "The Third Galileo - Xu Guangqi meeting", Beijing, October 11-15, 2011

Effects of tensor forces in nuclear spin-orbit splittings from ab initio calculations

A systematic and specific pattern due to the effects of the tensor forces is found in the evolution of spin-orbit splittings in neutron drops. This result is obtained from relativistic Brueckner-Hartree-Fock theory using the bare nucleon-nucleon interaction. It forms an important guide for future microscopic derivations of relativistic and nonrelativistic nuclear energy density functionals.Comment: 14 pages, 3 figure

Fully self-consistent relativistic Brueckner-Hartree-Fock theory for finite nuclei

Starting from the relativistic form of the Bonn potential as a bare nucleon-nucleon interaction, the full Relativistic Brueckner-Hartree-Fock (RBHF) equations are solved for finite nuclei in a fully self-consistent basis. This provides a relativistic ab initio calculation of the ground state properties of finite nuclei without any free parameters and without three-body forces. The convergence properties for the solutions of these coupled equations are discussed in detail at the example of the nucleus $^{16}$O. The binding energies, radii, and spin-orbit splittings of the doubly magic nuclei $^{4}$He, $^{16}$O, and $^{40}$Ca are calculated and compared with the earlier RBHF calculated results in a fixed Dirac Woods-Saxon basis and other non-relativistic ab initio calculated results based on pure two-body forces.Comment: 22 pages, 13 figure