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Selecting a processor for computations in molecular biophysics.

A number of relatively low-cost processors are now available which employ architectural features previously found only on very expensive supercomputers. The speed of these computers makes it possible to reduce the time to solution of certain problems and to resolve large problems that previously were too time consuming to perform locally. A brief overview of this type of processor is given and the implications for computations in molecular biophysics are discussed in reference to the results of a benchmark that uses the refinement of a protein structure from X-ray crystallographic data.

Computers

A CPU benchmark for protein crystallographic refinement.

The CPU time required to complete a cycle of restrained least-squares refinement of a protein structure from X-ray crystallographic data using the FORTRAN codes PROTIN and PROLSQ are reported for 48 different processors, ranging from single-user workstations to supercomputers. Sequential, vector, VLIW, multiprocessor, and RISC hardware architectures are compared using both a small and a large protein structure. Representative compile times for each hardware type are also given, and the improvement in run-time when coding for a specific hardware architecture considered. The benchmarks involve scalar integer and vector floating point arithmetic and are representative of the calculations performed in many scientific disciplines.

Computers

Note on wave propagation in a thin elastic tube containing a viscous fluid.

This paper deals with the theoretical and experimental investigation of the propagation of pressure waves through a straight thin-walled elastic tube, filled with a streaming Newtonian fluid. The tube used was of silicon rubber and measured 200 mm in length, 8 mm in internal diameter and 1 mm in wall thickness. The velocity profiles across the diameter of the tube were measured at the beginning, at the middle and the end of the elastic pipe and compared with the results of a mathematical-computational model. The test data agree fairly well with the calculated values.

Diffusion

A useful method for determining class-specific rheumatoid factors with computerized analyses of data.

A simple and sensitive enzyme-linked immunosorbent assay (ELISA) was developed to determine rheumatoid factors (RFs) of IgG, IgA and IgM class. Standardisation was performed with a standard reference serum for IgM-RF, calibrated according to the WHO preparation, and with the serum of a patient containing high levels of IgA- and IgG-RF. The sigmoidal shaped calibration curve was fitted with a computerized four parameter logistic model with simplified mathematical computations. This method provided to be more accurate for measuring RF levels, as judged by the smaller residuals, than logit or log-linear transformations. The considerable reduction in processing time, which is obtained by the computerized analysis of data, makes this method of class-specific RF determination suitable for routine analysis.

Enzyme-Linked Immunosorbent Assay

BACTID: a microcomputer implementation of a PASCAL program for bacterial identification based on Bayesean probability.

A computer program (BACTID) is described which enables the identification of bacteria based on a priori data and Bayesean probability testing. The program is not limited to a specific format, has a short execution time, can be easily applied to a variety of situations, and can be run on almost any microcomputer system operating under either 8-bit CP/M or 16-bit MS-DOS or PC-DOS. Additionally, BACTID is not limited to one type of computer (hardware independent); is not limited by size of the computer's random access memory (RAM independent); can recognize various database matrices (format independent); is able to compensate for missing data; and allows for various methods of data entry. The efficacy of the program was checked against a commercially available test system and a 99.34% agreement was obtained. Also, the execution time for a 46 x 21 data matrix was as little as 3.5 seconds. These results show that microcomputer identification programs not only are viable alternatives to code-book registers, but also offer flexibility which is not found in commercial systems.

Bacteria

From simple to complex oscillatory behaviour: analysis of bursting in a multiply regulated biochemical system.

We analyze the transition from simple to complex oscillatory behaviour in a three-variable biochemical system that consists of the coupling in series of two autocatalytic enzyme reactions. Complex periodic behaviour occurs in the form of bursting in which clusters of spikes are separated by phases of relative quiescence. The generation of such temporal patterns is investigated by a series of complementary approaches. The dynamics of the system is first cast into two different time-scales, and one of the variables is taken as a slowly-varying parameter influencing the behaviour of the two remaining variables. This analysis shows how complex oscillations develop from simple periodic behaviour and accounts for the existence of various modes of bursting as well as for the dependence of the number of spikes per period on key parameters of the model. We further reduce the number of variables by analyzing bursting by means of one-dimensional return maps obtained from the time evolution of the three-dimensional system. The analysis of a related piecewise linear map allows for a detailed understanding of the complex sequence leading from a bursting pattern with p spikes to a pattern with p + 1 spikes per period. We show that this transition possesses properties of self-similarity associated with the occurrence of more and more complex patterns of bursting. In addition to bursting, period-doubling bifurcations leading to chaos are observed, as in the differential system, when the piecewise-linear map becomes nonlinear.

Catalysis

METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer.

METAMOD, a BBC microcomputer-based software package for steady-state modelling and control analysis of model metabolic pathways, is described, The package consists of two programs. METADEF allows the user to define the pathway in terms of reactions, rate equations and initial concentrations of metabolites. METACAL uses one of two algorithms to calculate the steady-state concentrations and fluxes. One algorithm uses the current ratio of production and consumption rates of variable metabolites to adjust iteratively their concentrations in such a way that they converge towards the steady state. The other algorithm solves the roots of the system equations by means of a quasi-Newtonian procedure. Control analysis allows the calculation of elasticity, control and response coefficients, by means of finite difference approximation. METAMOD is interactive and easy to use, and suitable for teaching and research purposes.

Algorithms

A demonstration of pharmacokinetics and physiological modelling using a microcomputer for data capture and analysis.

We describe a simple and inexpensive demonstration of mass transport and exchange using dye clearance from a hydrodynamic model. A microcomputer was used for data acquisition and storage, non-linear least squares curve fitting, compartmental analysis and parameter estimation. The system is useful for demonstrating the indicator-dilution technique for fluid volume measurement and compartmental analysis in pharmacokinetics.

Algorithms

Microcomputer package for statistical analysis of microbial populations.

We have developed a Pascal system to compare microbial populations from different ecological sites using microcomputers. The values calculated are: the coverage value and its standard error, the minimum similarity and the geometric similarity between two biological samples, and the Lambda test consisting of calculating the ratio of the mean similarity between two subsets by the mean similarity within subsets. This system is written for Apple II, IBM or compatible computers, but it can work for any computer which can use CP/M, if the programs are recompiled for such a system.

Algorithms

Matrix algebra routines for the Acorn Archimedes microcomputer: example applications.

A set of matrix algebra routines have been written, as BASICV procedures, for the Acorn Archimedes microcomputer. It is shown that these procedures are executed so quickly that programs, which require matrix algebra computations, can be written in interpreted BASIC. Two example applications, reciprocal averaging and principal components analysis, are demonstrated.

Computers

Use of simultaneous curve fitting and a four-parameter logistic model to evaluate the nutritional quality of protein sources at growth rates of rats from maintenance to maximum gain.

A four-parameter logistic model was used to describe the dose-response relationship of rats fed diets containing 12 levels of casein, peanut meal or wheat gluten. The model was capable of accurately describing the entire response curve of rats fed diets containing each of the three protein sources. Incorporation of a technique known as parameter sharing into the curve-fitting process facilitated convergence of the parameter estimates for b (the response of rats fed a protein-free diet) and Rmax (maximum response) for all curves when compared with the values observed experimentally. Parameter sharing also provided a method by which the curves could be differentiated on a statistical basis. These data indicate that the relative value of a protein source is dependent on the concentration of the protein in the diet. The application of nonlinear models combined with parameter sharing provides a technique by which protein values can be evaluated at levels of animal response from maintenance to maximum growth.

Animals

Cognitive remediation in pediatric head injury: a case study.

Little work has been done in delineating cognitive remediation approaches for pediatric survivors of head injury. The use of a cognitive remediation approach is described in a case study of a 16-year-old male, who was 1 1/2 years post severe traumatic brain injury. Specific techniques and treatment course are outlined to demonstrate the model offered as one meeting the unique needs of the pediatric survivor. This model emphasizes a behavioral, individually tailored approach with clear delineation of a functional academic skill goal of competence in mathematical computation. Results indicate accomplishment of goals and some generalization of skills obtained to a math domain that was not the major focus of the remediation attempts.

Achievement

Electron dose-rate conversion factors for external exposure of the skin from uniformly deposited activity on the body surface.

Dose-rate conversion factors have been calculated for external exposure of the skin from electrons emitted by sources that are deposited uniformly on the body surface. The dose-rate factors are obtained from electron scaled point kernels developed by Berger (Be71; Be73; Be74). The dose-rate factors are calculated at depths of 4, 8, and 40 mg cm-2 below the body surface as recommended by Whitton (Wh73), and at a depth of 7 mg cm-2 as recommended in ICRP Publication 26 (ICRP77). The dependence of the dose-rate factors at selected depths on the energy of the emitted electrons is displayed. The dose-rate factors for selected radionuclides of potential importance in radiological assessments are tabulated.

Beta Particles

The realization of a pulsatile implantable impeller pump with low hemolysis.

A pulsatile implantable impeller pump with low hemolysis was developed without markedly increasing the complexity of the system compared with the nonpulsatile pump. The key to the question is to design a three-dimensional impeller with twisted vanes, compacted by an axial helical spiral and a radial logarithmic spiral so as to reduce the turbulent shear in the pump as the impeller changes its rotations per minute periodically to generate a physiologic pulsatile flow. Both mathematic computation of velocity distribution in the impeller and geometric illustration of the velocity triangle at the top of the vane have demonstrated that the peripheral velocity variation of blood cells in a twisted impeller will be less than that in an untwisted impeller. Thus, the main mechanical factor of hemolysis in the impeller pump, namely, the turbulent shear, should be reduced because it is proportional to the product of velocity variations measured in two perpendicular directions. In the in vitro experiments, the pump delivered 4 L/min mean flow at 100 mm Hg mean pressure (pulsed between 80-120 mm Hg) for more than 3 h in a circulatory model containing 700 ml of fresh citrated porcine blood. Every half hour, the free hemoglobin level in the plasma was tested, and the resulting index of hemolysis was about 0.020, slightly more than that of a nonpulsatile impeller pump developed in Shanghai. To compare hemolysis, the index of hemolysis of this pump is about 1/6 of that of the self-made diaphragm pump and 1/13 of that of the Polystan Pulsatile Pump.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals