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

BRST extension of the Faddeev model

The Faddeev model is a second class constrained system. Here we construct its nilpotent BRST operator and derive the ensuing manifestly BRST invariant Lagrangian. Our construction employs the structure of Stuckelberg fields in a nontrivial fashion.Comment: 4 pages, new references adde

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.

Hadron multiplicities, pT-spectra and net-baryon number in central Pb+Pb collisions at the LHC

We compute the initial energy density and net baryon number density in 5% most central Pb+Pb collisions at $\sqrt s=5.5$ TeV from pQCD + (final state) saturation, and describe the evolution of the produced system with boost-invariant transversely expanding hydrodynamics. In addition to the total multiplicity at midrapidity, we give predictions for the multiplicity of charged hadrons, pions, kaons and (anti)protons, for the total transverse energy and net-baryon number, as well as for the $p_T$-spectrum of charged hadrons, pions and kaons. We also predict the region of applicability of hydrodynamics by comparing these results with high-$p_T$ hadron spectra computed from pQCD and energy losses.Comment: 2 pages, 2 figures, to be presented at the workshop "Heavy Ion Collisions at the LHC: Last Call for Predictions" at CERN 29 May - 2 Jun

Dynamical freeze-out condition in ultrarelativistic heavy ion collisions

We determine the decoupling surfaces for the hydrodynamic description of heavy ion collisions at RHIC and LHC by comparing the local hydrodynamic expansion rate with the microscopic pion-pion scattering rate. The pion $p_T$ spectra for nuclear collisions at RHIC and LHC are computed by applying the Cooper-Frye procedure on the dynamical-decoupling surfaces, and compared with those obtained from the constant-temperature freeze-out surfaces. Comparison with RHIC data shows that the system indeed decouples when the expansion rate becomes comparable with the pion scattering rate. The dynamical decoupling based on the rates comparison also suggests that the effective decoupling temperature in central heavy ion collisions remains practically unchanged from RHIC to LHC.Comment: 7 pages, 9 figure

On quantum cohomology and dynamical systems

We investigate aspects of quantum cohomology and Floer cohomology in the context of a generic classical Hamiltonian system. In particular, we show that Floer's instanton equation is related to a quantum Euler character in the quantum cohomology defined by topological nonlinear \sigma-model. This relation is an infinite dimensional analogy with the relation between Poincar\'e-Hopf and Gauss-Bonnet-Chern formulae in classical Morse theory. By applying localization techniques to functional integrals we then show that for a K\"ahler manifold this quantum Euler character also coincides with the Euler character determined by the deRham cohomology of the target space. Our results are consistent with the Arnold conjecture which estimates periodic solutions to classical Hamilton's equations in terms of deRham cohomology of the phase space

Splitting The Gluon?

In the strongly correlated environment of high-temperature cuprate superconductors, the spin and charge degrees of freedom of an electron seem to separate from each other. A similar phenomenon may be present in the strong coupling phase of Yang-Mills theories, where a separation between the color charge and the spin of a gluon could play a role in a mass gap formation. Here we study the phase structure of a decomposed SU(2) Yang-Mills theory in a mean field approximation, by inspecting quantum fluctuations in the condensate which is formed by the color charge component of the gluon field. Our results suggest that the decomposed theory has an involved phase structure. In particular, there appears to be a phase which is quite reminiscent of the superconducting phase in cuprates. We also find evidence that this phase is separated from the asymptotically free theory by an intermediate pseudogap phase.Comment: Improved discussion of magnetic nature of phases; removed unsubstantiated speculation about color confinemen

Transverse Spectra of Hadrons in Central AAAA Collisions at RHIC and LHC from pQCD+Saturation+Hydrodynamics and from pQCD+Energy Losses

We study the transverse spectra of hadrons in nearly central $AA$ collisions at RHIC and LHC in a broad transverse momentum range Low-$p_T$ spectra are calculated by using boost-invariant hydrodynamics with initial energy and net-baryon densities from the EKRT pQCD+saturation model. High-$p_T$ spectra are obtained from pQCD jet calculation including the energy loss of the parton in the matter prior to its fragmentation to final hadrons.Comment: 4 pages, 2 figures, proceedings for Quark Matter 200

Elliptic flow in nuclear collisions at the Large Hadron Collider

We use perfect-fluid hydrodynamical model to predict the elliptic flow coefficients in Pb + Pb collisions at the Large Hadron Collider (LHC). The initial state for the hydrodynamical calculation for central $A + A$ collisions is obtained from the perturbative QCD + saturation (EKRT) model. The centrality dependence of the initial state is modeled by the optical Glauber model. We show that the baseline results obtained from the framework are in good agreement with the data from the Relativistic Heavy Ion Collider (RHIC), and show predictions for the $p_T$ spectra and elliptic flow of pions in Pb + Pb collisions at the LHC. Also mass and multiplicity effects are discussed.Comment: 11 pages, 10 figure