Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures

For successful ab initio protein structure prediction, a method is needed to identify native-like structures from a set containing both native and non-native protein-like conformations. In this regard, the use of distance geometry has shown promise when accurate inter-residue distances are available. We describe a method by which distance geometry restraints are culled from sets of 500 protein-like conformations for four small helical proteins generated by the method of Simons et al. (1997). A consensus-based approach was applied in which every inter-Calpha distance was measured, and the most frequently occurring distances were used as input restraints for distance geometry. For each protein, a structure with lower coordinate root-mean-square (RMS) error than the mean of the original set was constructed; in three cases the topology of the fold resembled that of the native protein. When the fold sets were filtered for the best scoring conformations with respect to an all-atom knowledge-based scoring function, the remaining subset of 50 structures yielded restraints of higher accuracy. A second round of distance geometry using these restraints resulted in an average coordinate RMS error of 4.38 A.     

The Design of a New Policy Model to Support Ontology-Driven Reasoning for Autonomic Networking

The purpose of autonomic networking is to manage the business and technical complexity of networked components and systems. However, the lack of a common lingua franca makes it impossible to use vendor-specific network management data to ascertain the state of the network at any given time. Furthermore, the tools used to analyze management data, which include information and data models, ontologies, machine learning algorithms, and policy languages, are all different, and hence require different data in different formats. This paper describes a new version of the Directory Enabled Networks next generation (DEN-ng) policy model, which is part of the FOCALE autonomic network architecture. This new policy model has been built using three guiding principles: (1) the policy model is rooted in information models, so that it can govern managed entities, (2) the model is expressly constructed to facilitate the generation of ontologies, so that reasoning about policies constructed from the model may be done, and (3) the model is expressly constructed so that a policy language can be developed from it.     

A 200-MHz 64-b dual-issue CMOS microprocessor

A 400-MIPS/200-MFLOPS (peak) custom 64-b VLSI CPU is described. The chip is fabricated in a 0.75-μm CMOS technology utilizing three levels of metalization and optimized for 3.3-V operation. The die size is 16.8 mm×13.9 mm and contains 1.68 M transistors. The chip includes separate 8-kbyte instruction and data caches and a fully pipelined floating-point unit (FPU) that can handle both IEEE and VAX standard floating-point data types. It is designed to execute two instructions per cycle among scoreboarded integer, floating-point, address, and branch execution units. Power dissipation is 30 W at 200-MHz operation     

Intersonic shear crack growth along weak planes

Classical dynamic fracture theories predict the Rayleigh surface wave speed (c _R ) to be the limiting speed of propagation for mode-I cracks in constitutively homogeneous, isotropic, linear elastic materials subjected to remote loading. For mode-II cracks, propagating along prescribed straight line paths, the same theories, while excluding the possibility of crack growth in the speed regime between c _R and the shear wave speed, c _s , do not exclude intersonic (c _s <υ<c _l ) crack tip speeds. In the present study, we provide the first experimental evidence of intersonic crack growth in such constitutively homogeneous and isotropic solids, ever recorded in a laboratory setting. Intersonic shear dominated crack growth, featuring shear shock waves, was observed along weak planes in a brittle polyester resin under far-field asymmetric loading. The shear cracks initially propagate at speeds just above c _s and subsequently accelerate rapidly to the longitudinal wave speed (c _l ) of the solid. At longer times, when steady state conditions are attained, they propagate at speeds slightly higher than √2–c _s . The experimental results compare well with existing asymptotic theories of intersonic crack growth, and the significance of the preferred speed of √2–c _s is discussed. Received: 13 September 1999 / Reviewed and occerted: 19 November 1999     

The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection

The key to an accurate method of protein structure prediction is the development of an effective discriminatory function. Knowledge-based discriminatory functions extract parameters from statistical analysis of experimentally determined protein structures. We assess how the quality of the protein structures used for compiling statistics affects the performance of a residue-specific all-atom probability discriminatory function (RAPDF). We find that the discriminatory power correlates with the quality of the structural dataset on which the RAPDF is parameterized in a statistically significant manner. The overrepresentation of unfavorable contacts in the low-resolution and NMR structures contributes to the major errors in the compilation of the conditional probabilities. Such errors weaken the discriminatory power of the function, especially when decoy conformations also contain considerable numbers of unfavorable contacts. This indicates that using high-resolution structural datasets after filtering out unfavorable contacts can improve the performance of knowledge-based discriminatory functions.     

A pipelined 50-MHz CMOS 64-bit floating-point arithmetic processor

A 135K transistor, uniformly pipelined 50-MHz CMOS 64-bit floating-point arithmetic processor chip is described. The execution unit is capable of sustaining pipelined performance of one 32-bit or 64-bit result every 20 ns for all operations except double-precision multiply (40 ns) and divide. The chip employs an exponent difference prediction scheme and a unified leading-one and sticky-bit computation logic for the addition and subtraction operations. A hardware multiplier using a radix-8 modified Booth algorithm and a divider using a radix-2 SRT algorithm are employed.<>     

Characterization of Edge Contact: Atomically Resolved Semiconductor–Metal Lateral Boundary in MoS2

Despite recent efforts for the development of transition‐metal‐dichalcogenide‐based high‐performance thin‐film transistors, device performance has not improved much, mainly because of the high contact resistance at the interface between the 2D semiconductor and the metal electrode. Edge contact has been proposed for the fabrication of a high‐quality electrical contact; however, the complete electronic properties for the contact resistance have not been elucidated in detail. Using the scanning tunneling microscopy/spectroscopy and scanning transmission electron microscopy techniques, the edge contact, as well as the lateral boundary between the 2D semiconducting layer and the metalized interfacial layer, are investigated, and their electronic properties and the energy band profile across the boundary are shown. The results demonstrate a possible mechanism for the formation of an ohmic contact in homojunctions of the transition‐metal dichalcogenides semiconductor–metal layers and suggest a new device scheme utilizing the low‐resistance edge contact.     

Determinants of side chain conformational preferences in protein structures

A discriminatory function based on a statistical analysis of atomic contacts in protein structures is used for selecting side chain rotamers given a peptide main chain. The function allows us to rank different possible side chain conformations on the basis of contacts between side chain atoms and atoms in the environment. We compare the differences in constructing side chain conformations using contacts with only the local main chain, using the entire main chain, and by building pairs of side chains simultaneously with local main chain information. Using only the local main chain allows us to construct side chains with approximately 75% of the chi1 angles within 30 degrees of the experimental value, and an average side chain atom r.m.s.d. of 1.72 A in a set of 10 proteins. The results of constructing side chains for the 10 proteins are compared with the results of other side chain building methods previously published. The comparison shows similar accuracies. An advantage of the present method is that it can be used to select a small number of likely side chain conformations for each residue, thus permitting limited combinatorial searches for building multiple protein side chains simultaneously.     

The effect of adding whey protein particles as inert filler on thermophysical properties of fat‐reduced semihard cheese type Gouda

The effect of added microparticulated whey protein (Simplesse^®) on textural and thermophysical properties of fat‐reduced semihard cheese type Gouda was investigated. Full‐fat, reduced‐fat and low‐fat cheeses were manufactured of comparable moisture content, each made of control milk and milk systems containing 1% Simplesse^®, respectively. Whey protein particles improved textural properties of reduced‐fat and low‐fat cheese. Meltability and flowability were significantly enhanced by an increased fat level, Simplesse^® addition and ripening time. The results emphasise the role of microparticulated whey proteins acting as an inert filler within the composite cheese matrix and allow textural and thermophysical properties of fat‐reduced cheeses to be adjusted towards cheese with higher fat content.