Introduction to Protein Structure Prediction

This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global com- munity, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a sin- gle fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated

HOT SCALAR ELECTRODYNAMICS AS A TOY MODEL FOR HOT QCD

Hot scalar electrodynamics is adopted as a toy model for a hot gluon plasma to display some aspects of the compulsory resummation of hard thermal loops when next-to-leading order quantities at soft momentum scales are to be calculated. [Talk given by A.K.R. at a one-day meeting dedicated to the memory of Tanguy ALTHERR, held on November 4, 1994 at CERN, Geneva. To appear in a Gedenkschrift published by World Scientific.]Comment: 11 pages, LaTeX, uses epsf.sty, 1 uuencoded postscript figur

A Dyson-Schwinger study of the four-gluon vertex

We present a self-consistent calculation of the four-gluon vertex of Landau gauge Yang--Mills theory from a truncated Dyson--Schwinger equation. The equation contains the leading diagrams in the ultraviolet and is solved using as the only input results for lower Green functions from previous Dyson--Schwinger calculations that are in good agreement with lattice data. All quantities are therefore fixed and no higher Green functions enter within this truncation. Our self-consistent solution resolves the full momentum dependence of the vertex but is limited to the tree-level tensor structure at the moment. Calculations of selected dressing functions for other tensor structures from this solution are used to exemplify that they are suppressed compared to the tree-level structure except for possible logarithmic enhancements in the deep infrared. Our results furthermore allow one to extract a qualitative fit for the vertex and a running coupling.Comment: 23 pages, 14 figs.; more detailed discussion of renormalization, version accepted by EPJ

Violation of the Holographic Viscosity Bound in a Strongly Coupled Anisotropic Plasma

We study the conductivity and shear viscosity tensors of a strongly coupled N=4 super-Yang-Mills plasma which is kept anisotropic by a theta parameter that depends linearly on one of the spatial dimensions. Its holographic dual is given by an anisotropic axion-dilaton-gravity background and has recently been proposed by Mateos and Trancanelli as a model for the pre-equilibrium stage of quark-gluon plasma in heavy-ion collisions. By applying the membrane paradigm which we also check by numerical evaluation of Kubo formula and lowest lying quasinormal modes, we find that the shear viscosity purely transverse to the direction of anisotropy saturates the holographic viscosity bound, whereas longitudinal shear viscosities are smaller, providing the first such example not involving higher-derivative theories of gravity and, more importantly, with fully known gauge-gravity correspondence.Comment: 4 pages, 2 figures; v3: references added, version to appear in Phys. Rev. Let

Spatial Analysis of Market Linkages in North Carolina Using Threshold Autoregression Models with Variable Transaction Costs

In North Carolina, where soybeans and corn are the two primary crops, the recent increase in the demand for U.S. corn has triggered a shift of farm acreage from soybeans to corn, leading to a rapid rise in prices of both commodities. However, the rate of the price changes, as well as the price level, is significantly different in markets that are located in different parts of the state. This study extends the literature that examines linkages between spatially separated markets by using a threshold autoregressive model with a less restrictive assumption for estimating the transaction cost neutral band -- the band within which trade is not profitable. This generalization allows the neutral band of transactions costs to change according to various external factors, including fuel costs and seasonality. The estimation results indicate that for longer time series data, variable thresholds models statistically outperform the constant thresholds specification, and may provide a better representation of corn and soybean price data. Additionally, impulse response functions that use the asymmetric variable threshold model parameters indicate that the magnitude of the shock as well as the time-to-price-parity-equilibrium in the linked markets may be underestimated if a constant thresholds specification is implemented.threshold autoregression, spatially separated markets, impulse response, neutral band, Demand and Price Analysis, Marketing, Q11, Q13,