Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics

Unlike homopolymers, biopolymers are composed of specific sequences of different types of monomers. In proteins and RNA molecules, one-dimensional sequence information encodes a three-dimensional fold, leading to a corresponding molecular function. Such folded structures are not treated adequately through traditional methods of polymer statistical mechanics. A promising new way to solve problems of the statistical mechanics of biomolecules comes from computational linguistics, the field that uses computers to parse and understand the sentences in natural languages. Here, we give two examples. First, we show that a dynamic programming method of computational linguistics gives a fast way to search protein models for native structures. Interestingly, the computational search process closely resembles the physical folding process. Second, linguistics-based dynamic programming methods are also useful for computing partition functions and densities of states for some foldable biopolymers - helix-bundle proteins are reviewed here. In these ways, computational linguistics is helping to solve problems of the searching and counting of biopolymer conformations.     

Specification and automatic verification of self-timed queues

Speed-independent circuit design is of increasing interest because of global timing problems in VLSI. Unfortunately, speed-independent design is very subtle. We propose the use of statemachine verification tools to ameliorate this problem. This article illustrates issues in the modeling, specification, and verification of speed-independent circuits through consideration of self-timed queues. User-level specifications are given as Petri nets, which are translated into trace structures for automatic processing. Three different implementations of queues are considered: a chain of queue cells, two parallel chains, and a circular buffer example using a separate RAM.     

Picogram detection levels of asialofetuin via the carbohydrate moieties using the light addressable potentiometric sensor

Fetal calf serum asialofetuin was assayed in the sandwich format using biotinylated and fluoresceinated ricin toxin (B-RCA and F-RCA). The sandwiched species was captured on a biotin-BSA coated nitrocellulose membrane with streptavidin. Anti-fluorescein antibody-urease conjugate was bound to the complex, and detected and quantitated under microvolume conditions using the light addressable potentiometric sensor. As little as 250 pg of asialofetuin was detectable whereas fetuin gave no response at conditions as high as 32 ng. Using a competitive inhibition assay, we established that the binding constant for the asialofetuin-ricin complex was 3.6 x 10(8) M-1. This is in good agreement with data published using glycopeptides derived from asialofetuin, and RCA and the ricin agglutinin, RCA-120.     

Social modeling films to deter smoking in adolescents: Results of a three-year field investigation.

Developed a smoking deterrence strategy within a social-learning and persuasive-communication framework consisting principally of a series of films. In the films, detailed techniques for coping with social influences on smoking are depicted. Dependent measures of knowledge gained from the films, of intentions to smoke, and of smoking behavior utilizing a novel nicotine-in-saliva analysis were administered. Students in 13 junior high schools were assigned to 3 experimental and 4 control groups. Seventh- through 9th-grade smoking deterrence interventions and dependent measures were administered in the experimental schools, and the dependent measures only were administered in the control schools. At the end of the 8th and 9th grades, analyses of the data reveal that experimental Ss smoked less frequently and intended to smoke less frequently than did controls and that knowledge generated by the films was significantly related to smoking intention and behavior. (20 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Tradeoffs between noise, distortion and fibre length for multichannel analogue TV transmission over graded index fibres at 0.83 ?m

The tradeoffs between noise, distortion and fibre length allowing multichannel TV transmission by analogue modulation over kilometer lengths have been investigated experimentally. Two and four VHF TV channels have been transmitted using linearly driven diode lasers at 0.83 ?m and multimode fibres over four and one kilometer, respectively, with signal/noise ratios above 40 dB (video unweighted) and intermodulation distortions below ?65 dB.     

BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions

We present here a freely available web-based database, called BioMThermDB 1.0, of thermophysical and dynamic properties of various proteins and their aqueous solutions. It contains the hydrodynamic radius, electrophoretic mobility, zeta potential, self-diffusion coefficient, solution viscosity, and cloud-point temperature, as well as the conditions for those determinations and details of the experimental method. It can facilitate the meta-analysis and visualization of data, can enable comparisons, and may be useful for comparing theoretical model predictions with experiments.     

A System for Viscosity Measurements at Pressures up to 3 GPa and Elevated Temperatures

A falling body viscometer was developed to measure viscosity of lubricants between 10^-1 to 10⁵ Pa.s at high pressures (up to 3 GPa) and temperatures of 20–200°C. The viscometer was incorporated into a variable-support pressure vessel mounted in an O-frame press. A solenoid is used to raise the falling soft iron plunger to its upper position, where it closes a pair of contacts. On deactivating the upper solenoid, the plunger, falls to the lower position to close a second pair of contacts. Fall times are measured by a timer in 0.1s increments. Viscosity of a few fluids, namely a synthetic turbine engine oil, a mineral oil, white gasoline and a 1:1 mixture of the mineral oil and white gasoline were measured to demonstrate capability of the system. For the synthetic turbine engine oil, isoviscous curves for 10², 10³ and 10⁴ Pa.s are presented on a P–T diagram and estimates are made of the viscosity at which dynamic effects can be expected.     

Traction Characteristics of High-Temperature Powder-Lubricated Ceramics (Si3N4/αSiC)

As part of a high-temperature, dry-lubricated bearing technology and lubricant system development program, a high-speed, high-temperature disk-on-disk tribometer was utilized and a matrix of traction data covering a range of load, speed and temperature was obtained. The influence of dry powder lubricants, TiO₂ and MoS₂, on the traction coefficients between two ceramic materials, Si₃N₄ and SiC, was investigated. The most important results of this investigation are characteristic curves for the traction coefficient vs. the slide/roll ratio with dry powders which are reminiscent of fluids, and the observation of dry powder lubricants' lower traction coefficients and wear. Measured tractions are found to be a strong function of powder lubricant type and values decrease moderately with slide-to-roll ratio and load. The data, show a weak sensitivity to temperature.     

A Practical Approach to Partial Functions in CVC Lite

Most verification approaches assume a mathematical formalism in which functions are total, even though partial functions occur naturally in many applications. Furthermore, although there have been various proposals for logics of partial functions, there is no consensus on which is “the right” logic to use for verification applications. In this paper, we propose using a three-valued Kleene logic, where partial functions return the “undefined” value when applied outside of their domains. The particular semantics are chosen according to the principle of least surprise to the user; if there is disagreement among the various approaches on what the value of the formula should be, its evaluation is undefined. We show that the problem of checking validity in the three-valued logic can be reduced to checking validity in a standard two-valued logic, and describe how this approach has been successfully implemented in our tool, CVC Lite.