2,097 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
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 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 , different shear relaxation times , 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 .Comment: 13 pages, 20 figure
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