One way to Characterize the compact structures of lattice protein model

On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact structure. The Partnum is compared with the concept Designability of protein structures emerged recently. It is shown that the highly designable structures have, on average, an atypical number of local degree of freedom. The statistical property of Partnum and its dependence on sequence length is also studied.Comment: 10 pages, 5 figure

Hopping conductivity in heavily doped n-type GaAs layers in the quantum Hall effect regime

We investigate the magnetoresistance of epitaxially grown, heavily doped n-type GaAs layers with thickness (40-50 nm) larger than the electronic mean free path (23 nm). The temperature dependence of the dissipative resistance R_{xx} in the quantum Hall effect regime can be well described by a hopping law (R_{xx} \propto exp{-(T_0/T)^p}) with p=0.6. We discuss this result in terms of variable range hopping in a Coulomb gap together with a dependence of the electron localization length on the energy in the gap. The value of the exponent p>0.5 shows that electron-electron interactions have to be taken into account in order to explain the occurrence of the quantum Hall effect in these samples, which have a three-dimensional single electron density of states.Comment: 5 pages, 2 figures, 1 tabl

Quantum Hall Effect induced by electron-electron interaction in disordered GaAs layers with 3D spectrum

It is shown that the observed Quantum Hall Effect in epitaxial layers of heavily doped n-type GaAs with thickness (50-140 nm) larger the mean free path of the conduction electrons (15-30 nm) and, therefore, with a three-dimensional single-particle spectrum is induced by the electron-electron interaction. The Hall resistance R_xy of the thinnest sample reveals a wide plateau at small activation energy E_a=0.4 K found in the temperature dependence of the transverse resistance R_xx. The different minima in the transverse conductance G_xx of the different samples show a universal temperature dependence (logarithmic in a large range of rescaled temperatures T/T_0) which is reminiscent of electron-electron-interaction effects in coherent diffusive transport.Comment: 6 pages, 3 figures, 1 tabl

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

Origin of Scaling Behavior of Protein Packing Density: A Sequential Monte Carlo Study of Compact Long Chain Polymers

Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find that the radius of gyration provides poor description of protein packing but the alpha contact number we introduce here characterize proteins well. We further demonstrate that protein-like scaling relationship between packing density and chain length is observed in off-lattice self-avoiding walks. A key problem in studying compact chain polymer is the attrition problem: It is difficult to generate independent samples of compact long self-avoiding walks. We develop an algorithm based on the framework of sequential Monte Carlo and succeed in generating populations of compact long chain off-lattice polymers up to length $N=2,000$. Results based on analysis of these chain polymers suggest that maintaining high packing density is only characteristic of short chain proteins. We found that the scaling behavior of packing density with chain length of proteins is a generic feature of random polymers satisfying loose constraint in compactness. We conclude that proteins are not optimized by evolution to eliminate packing voids.Comment: 9 pages, 10 figures. Accepted by J. Chem. Phy

Topological oscillations of the magnetoconductance in disordered GaAs layers

Oscillatory variations of the diagonal ($G_{xx}$) and Hall ($G_{xy}$) magnetoconductances are discussed in view of topological scaling effects giving rise to the quantum Hall effect. They occur in a field range without oscillations of the density of states due to Landau quantization, and are, therefore, totally different from the Shubnikov-de Haas oscillations. Such oscillations are experimentally observed in disordered GaAs layers in the extreme quantum limit of applied magnetic field with a good description by the unified scaling theory of the integer and fractional quantum Hall effect.Comment: 4 pages, 4 figure

Improvement in steel smelting by studying melt behavior

Analysis shows that the disequilibrium of melts may be used to characterize metal quality and to optimize smelting technology. For the production of pipe steel by means of a superpowerful DSP-135 arc furnace, a ladle-furnace unit, a vacuum-treatment system, and a continuous-casting machine, the sources of melt disequilibrium are studied in relation to the properties of the final steel. That provides the basis for the development of parameters characterizing different stages of the process. The proposed improvements in smelting technology are shown to be very efficient. © 2013 Allerton Press, Inc