Biomedical subjects
Publications and source records attributed to A N Barrett.
Computational sequencing of nucleic acid and amino acid sequences is placing increasing demands on computer resources. The use of prime numbers is explored as a convenient means of improving program speed and reducing storage requirements. It is concluded that the application of the prime number approach leads to significant increases in speed and some reduction in storage requirements.
This paper illustrates how a simple geometric model resembling the shape of the chick wing bud at an early growth stage can be mathematically expanded to simulate subsequent growth characteristics of the developing bud. The model was tested against several sets of experimental data and gave an acceptable representation of growth over the range considered. Representing growth patterns in this form enables the determination of differential growth characteristics in different parts of the bud and provides boundary constraints which will play an important part in the eventual evaluation of internal growth mechanisms.
Ab initio molecular orbital calculations of electron distribution in tetramethylammonium ion and its uncharged isoelectronic analogue, neopentane, have been carried out. Comparison of the two compounds permits a detailed description of the delocalization of the positive charge of tetramethylammonium ion. The van der Waals surface of this ion is found to be characterized by "patches" of positive charge associated with the methyl groups, interspersed with essentially neutral regions. The consequences of this nonspherical charge distribution for interaction with anions have been explored by calculations of the interaction energy of fluoride ion with tetramethylammonium ion and neopentane in several mutual orientations. The lowest-energy orientation is found to be one in which the anion approaches a "face" of the tetrahedral cation (opposite to a C--N bond direction). The origins of this preference and the electron redistribution produced by the interaction with fluoride are discussed. The tetramethylammonium ion is clearly not a featureless positively charged sphere but will have appreciable geometrical specificity in its interaction with a presumed anionic group on the acetylcholine receptor.
An optical 'flicker' method is described for the precise azimuthal and translational co-registration of many noisy but identical molecular images. Starting with a real micrograph of known biological objects showing no visible detail below 4 nm, a lattice of images of individual objects was synthesized by computer and translationally filtered, using real experimental data throughout. Detail was recovered conforming with known structural features of the object down to about 1.5 nm, and rotational analysis showed that the registration accuracy of the lattice elements was better than 0.5 nm on the object. Application to the straightening of real two-dimensional lattices with long-range distortion is discussed.
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A system is described for building up serial sections into a three dimensional structure, incorporating density, that can be displayed and then further manipulated by rotation about three orthogonal axes. The initial application was to produce a computer model of a protein structure and to compare the diverse images obtained from rotation with the two dimensional images observed in related electron micrographs. To obtain sufficient contrast in the electron microscope images of protein structures, the specimens need to be stained and since this can cause some deformation of the observed images, it is also necessary to simulate ths possible effects of stain on the protein model. Because of the need to compare numerous orientations of the combined model, techniques are available either for speeding up the comparison or for obtaining better accuracy. The methods have been applied to the interpretation of electron micrograph images of microbiological specimens, where the three dimensional structure of the specimen is an important aid in understanding its biological function, but the techniques are also applicable to more general serial reconstruction requirements.
This paper describes a technique for obtaining values of the width and variation in optical density of sectioned bacterial cell walls by interactive computational methods. Background 'noise' prevents accurate determination of cell wall boundaries from the data in a single scan line but the noise may be suppressed by averaging several consecutive scan lines. although application of the technique is explained for sectioned bacterial cell walls, it is equally valid for similar situations where single line scans of electron micrographs are inadequate for precise determination of measurement.
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