On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse grained energy function to describe the ensuing side-chain geometry in terms of the C$_\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\alpha$-C$_\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \.A in root-mean-square distance from the experimental X-ray structure

Dual Superconductors and SU(2) Yang-Mills

We propose that the SU(2) Yang-Mills theory can be interpreted as a two-band dual superconductor with an interband Josephson coupling. We discuss various consequences of this interpretation including electric flux quantization, confinement of vortices with fractional flux, and the possibility that a closed vortex loop exhibits exotic exchange statistics

Elastic Energy and Phase Structure in a Continuous Spin Ising Chain with Applications to the Protein Folding Problem

We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three known nontrivial phases of polymers: At low temperatures the model is in a collapsed phase, at medium temperatures it is in a random walk phase, and at high temperatures it enters the self-avoiding random walk phase. By investigating the temperature dependence of the specific energy we confirm that the transition between the collapsed phase and the random walk phase is a phase transition, while the random walk phase and self-avoiding random walk phase are separated from each other by a cross-over transition. We also compare the predictions of the model to a phenomenological elastic energy formula, proposed by Huang and Lei to describe folded proteins.Comment: 12 pages, 23 figures, RevTeX 4.

On the Point-Splitting Method of the Commutator Anomaly of the Gauss Law Operators

We analyze the generalized point-splitting method and Jo's result for the commutator anomaly. We find that certain classes of general regularization kernels satisfying integral conditions provide a unique result, which, however differs from Faddeev's cohomological result.Comment: 16 pages, RevTex, 1 figure + 1 table, uses psbox.te

Induced Parity Breaking Term at Finite Temperature

We compute the exact induced parity-breaking part of the effective action for 2+1 massive fermions in $QED_3$ at finite temperature by calculating the fermion determinant in a particular background. The result confirms that gauge invariance of the effective action is respected even when large gauge transformations are considered.Comment: to be published in Physical Review Letters. 5 pages, Revtex, no figure

Shafranov's virial theorem and magnetic plasma confinement

Shafranov's virial theorem implies that nontrivial magnetohydrodynamical equilibrium configurations must be supported by externally supplied currents. Here we extend the virial theorem to field theory, where it relates to Derrick's scaling argument on soliton stability. We then employ virial arguments to investigate a realistic field theory model of a two-component plasma, and conclude that stable localized solitons can exist in the bulk of a finite density plasma. These solitons entail a nontrivial electric field which implies that purely magnetohydrodynamical arguments are insufficient for describing stable, nontrivial structures within the bulk of a plasma.Comment: 9 pages no figure

Influence of a temperature-dependent shear viscosity on the azimuthal asymmetries of transverse momentum spectra in ultrarelativistic heavy-ion collisions

We study the influence of a temperature-dependent shear viscosity over entropy density ratio $\eta/s$, different shear relaxation times $\tau_\pi$, as well as different initial conditions on the transverse momentum spectra of charged hadrons and identified particles. We investigate the azimuthal flow asymmetries as a function of both collision energy and centrality. The elliptic flow coefficient turns out to be dominated by the hadronic viscosity at RHIC energies. Only at higher collision energies the impact of the viscosity in the QGP phase is visible in the flow asymmetries. Nevertheless, the shear viscosity near the QCD transition region has the largest impact on the collective flow of the system. We also find that the centrality dependence of the elliptic flow is sensitive to the temperature dependence of $\eta/s$.Comment: 13 pages, 20 figure