2,736 research outputs found
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 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 carbon orientations. The
energy function can model the side-chain geometry with a sub-atomic precision.
As an example we construct the C-C 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 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 -spectrum of charged
hadrons, pions and kaons. We also predict the region of applicability of
hydrodynamics by comparing these results with high- 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
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 Collisions at RHIC and LHC from pQCD+Saturation+Hydrodynamics and from pQCD+Energy Losses
We study the transverse spectra of hadrons in nearly central collisions
at RHIC and LHC in a broad transverse momentum range Low- spectra are
calculated by using boost-invariant hydrodynamics with initial energy and
net-baryon densities from the EKRT pQCD+saturation model. High- 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 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 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
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