7,066 research outputs found
Properties of contact matrices induced by pairwise interactions in proteins
The total conformational energy is assumed to consist of pairwise interaction
energies between atoms or residues, each of which is expressed as a product of
a conformation-dependent function (an element of a contact matrix, C-matrix)
and a sequence-dependent energy parameter (an element of a contact energy
matrix, E-matrix). Such pairwise interactions in proteins force native
C-matrices to be in a relationship as if the interactions are a Go-like
potential [N. Go, Annu. Rev. Biophys. Bioeng. 12. 183 (1983)] for the native
C-matrix, because the lowest bound of the total energy function is equal to the
total energy of the native conformation interacting in a Go-like pairwise
potential. This relationship between C- and E-matrices corresponds to (a) a
parallel relationship between the eigenvectors of the C- and E-matrices and a
linear relationship between their eigenvalues, and (b) a parallel relationship
between a contact number vector and the principal eigenvectors of the C- and
E-matrices; the E-matrix is expanded in a series of eigenspaces with an
additional constant term, which corresponds to a threshold of contact energy
that approximately separates native contacts from non-native ones. These
relationships are confirmed in 182 representatives from each family of the SCOP
database by examining inner products between the principal eigenvector of the
C-matrix, that of the E-matrix evaluated with a statistical contact potential,
and a contact number vector. In addition, the spectral representation of C- and
E-matrices reveals that pairwise residue-residue interactions, which depends
only on the types of interacting amino acids but not on other residues in a
protein, are insufficient and other interactions including residue
connectivities and steric hindrance are needed to make native structures the
unique lowest energy conformations.Comment: Errata in DOI:10.1103/PhysRevE.77.051910 has been corrected in the
present versio
Face- and Cell-Averaged Nodal-Gradient Approach to Cell-Centered Finite-Volume Method on Mixed Grids
In this paper, the averaged nodal-gradient approach previously developed for triangular grids is extended to mixed triangular-quadrilateral grids. It is shown that the face- averaged approach leads to deteriorated iterative convergence on quadrilateral grids. To develop a convergent solver, we consider cell-averaging instead of face-averaging for quadri- lateral cells. We show that the cell-averaged approach leads to a convergent solver and can be efficiently combined with the face-averaged approach on mixed grids. The method is demonstrated for various inviscid and viscous problems from low to high Mach numbers on two-dimensional mixed grids
Efficient and Robust Weighted Least-Squares Cell-Average Gradient Construction Methods for the Simulation of Scramjet Flows
The ability to solve the equations governing the hypersonic turbulent flow of a real gas on unstructured grids using a spatially-elliptic, 2nd-order accurate, cell-centered, finite-volume method has been recently implemented in the VULCAN-CFD code. The construction of cell-average gradients using a weighted linear least-squares method and the use of these gradients in the construction of the inviscid fluxes is the focus of this paper. A comparison of least-squares stencil construction methodologies is presented and approaches designed to minimize the number of cells used to augment/stabilize the least-squares stencil while preserving accuracy are explored. Due to our interest in hypersonic flow, a robust multidimensional cell-average gradient limiter procedure that is consistent with the stencil used to construct the cellaverage gradients is described. Canonical problems are computed to illustrate the challenges and investigate the accuracy, robustness and convergence behavior of the cell-average gradient methods on unstructured cell-centered finite-volume grids. Finally, thermally perfect, chemically frozen, Mach 7.8 turbulent flow of air through a scramjet engine flowpath is computed and compared with experimental data to demonstrate the robustness, accuracy and convergence behavior of the preferred gradient method for a realistic 3-D geometry on a non-hex-dominant grid
Renormalized parameters and perturbation theory for an n-channel Anderson model with Hund's rule coupling: Asymmetric case
We explore the predictions of the renormalized perturbation theory for an
n-channel Anderson model, both with and without Hund's rule coupling, in the
regime away from particle-hole symmetry. For the model with n=2 we deduce the
renormalized parameters from numerical renormalization group calculations, and
plot them as a function of the occupation at the impurity site, nd. From these
we deduce the spin, orbital and charge susceptibilities, Wilson ratios and
quasiparticle density of states at T=0, in the different parameter regimes,
which gives a comprehensive overview of the low energy behavior of the model.
We compare the difference in Kondo behaviors at the points where nd=1 and nd=2.
One unexpected feature of the results is the suppression of the charge
susceptibility in the strong correlation regime over the occupation number
range 1 <nd <3.Comment: 9 pages, 17 figure
Fermi Liquids and the Luttinger Integral
The Luttinger Theorem, which relates the electron density to the volume of
the Fermi surface in an itinerant electron system, is taken to be one of the
essential features of a Fermi liquid. The microscopic derivation of this result
depends on the vanishing of a certain integral, the Luttinger integral , which is also the basis of the Friedel sum rule for impurity models,
relating the impurity occupation number to the scattering phase shift of the
conduction electrons. It is known that non-zero values of with
, occur in impurity models in phases with non-analytic low
energy scattering, classified as singular Fermi liquids. Here we show the same
values, , occur in an impurity model in phases with regular
low energy Fermi liquid behavior. Consequently the Luttinger integral can be
taken to characterize these phases, and the quantum critical points separating
them interpreted as topological.Comment: 5 pages 7 figure
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