THEORETICAL STUDIES ON THE METHODS OF RECONSTRUCTING PHYLOGENETIC TREES FROM DNA SEQUENCE DATA (MOLECULAR EVOLUTION, HOMINOID EVOLUTION, COMPUTER SIMULATION)

(1) A mathematical theory for computing the probabilities of various nucleotide configurations is developed, and the probability of obtaining the correct phylogenetic tree (model tree) from sequence data is evaluated for six phylogenetic tree-making methods (UPGMA, distance Wagner method, transformed distance method, Fitch-Margoliash's method, maximum parsimony method, and compatibility method). The number of nucleotides (m*) necessary to obtain the correct tree with a probability of 95% is estimated with special reference to the human, chimpanzee, and gorilla divergence. m* is at least 4,200, but the availability of outgroup species greatly reduces m* for all methods except UPGMA. m* increases if transitions occur more frequently than transversions as in the case of mitochondrial DNA. (2) A new tree-making method called the neighbor-joining method is proposed. This method is applicable either for distance data or character state data. Computer simulation has shown that the neighbor-joining method is generally better than UPGMA, Farris' method, Li's method, and modified Farris method on recovering the true topology when distance data are used. A related method, the simultaneous partitioning method, is also discussed. (3) The maximum likelihood (ML) method for phylogeny reconstruction under the assumption of both constant and varying evolutionary rates is studied, and a new algorithm for obtaining the ML tree is presented. This method gives a tree similar to that obtained by UPGMA when constant evolutionary rate is assumed, whereas it gives a tree similar to that obtained by the maximum parsimony tree and the neighbor-joining method when varying evolutionary rate is assumed. ^

Theoretical studies of the mid-latitude ionosphere

Following a brief description of the atmosphere and ionosphere in Chapter I we describe how the equations of continuity and momentum for 0+, H+, He+, 0++ are derived from the formulations of St-Maurice and Schunk(1977) and Quegan et al.(1981) in Chapter II. In Chapter III we investigate the nature of the downward flow of protons in a collapsing post-sunset ionosphere. We derive an analytical form for the limiting temperature, we also note the importance of the polarization field term and concluded that the flow will remain subsonic for realistic conditions. The time-dependent behaviour of He+ under sunspot minimum conditions is investigated in Chapter IV. This is achieved by numerical solution of the 0+, H+ and,He+ continuity and momentum equations, treating He+ as a minor ion with 0+ , H+ as major ions. We found that He+ flows upwards during the day-time and downwards during the nighttime. He+ flux tube content reached a maximum on the 8th day of the integration period and started to decreasing. This is due to the large amount of H+ present at the late stages of the integration period which makes He+ unable to diffuse through the H+ layer away from the loss region. In Chapter V we investigate the behaviour of 0++ using sunspot maximum parameters. Although our results support the findings of Geis and Young (1981) that the large amounts of 0++ at the equator are caused mainly by thermal diffusion, the model used by Geis and Young overemphesizes the effect of thermal diffusion. The importance of 0++ - 0+ collision frequency is also noted. In Chapter VI we extend the work of Chapter IV, presenting a comparative study of H and He at sunspot minimum and sunspot maximum.In this last Chapter all three ions, O+ ,H+ and He+ , are treated theoretically as major ions and we concentrate mainly on light ion contents and fluxes. The results of this Chapter indicate that by assuming He+ as a minor ion we under-estimate He+ and over-estimate. H+. Some interesting features concerning the day to day behaviour of the light ion fluxes arise. In particular the day-time H+ fluxes decrease from day to day in contrast to the work of Murphy et al.(1976). In appendix.A we derive some analytical forms for the optical depth so that the models can include a realistic description of photoionization.

Experimental and theoretical studies on a distributed temperature sensor based on Brillouin scattering

Results are reported from recent research on the use of the Brillouin gain/loss mechanism for distributed sensing. A theoretical model of the interaction of the pulsed and CW beams is described and compared with experiments. Results from a system with a 51 km sensing length are presented. We finally investigate issues related to the variation within the sensing fiber of the polarizations of the two beams.

Experimental and theoretical studies on six-membered ring hydrogen bond systems in crystalline drug substances

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

Experimental and theoretical studies on molecular geometry and polymorphism in crystalline drug substances

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

Experimental and theoretical studies on a distributed temperature sensor based on Brillouin scattering

Results are reported from recent research on the use of the Brillouin gain/loss mechanism for distributed sensing. A theoretical model of the interaction of the pulsed and CW beams is described and compared with experiments. Results from a system with a 51 km sensing length are presented. We finally investigate issues related to the variation within the sensing fiber of the polarizations of the two beams.

Experimental and theoretical studies on a distributed temperature sensor based on Brillouin scattering

Results are reported from recent research on the use of the Brillouin gain/loss mechanism for distributed sensing. A theoretical model of the interaction of the pulsed and CW beams is described and compared with experiments. Results from a system with a 51 km sensing length are presented. We finally investigate issues related to the variation within the sensing fiber of the polarizations of the two beams.

X-ray crystallographic and theoretical studies of an anticonvulsant enaminone:methyl 4-(4'-bromophenyl)amino-6-methyl-2-oxocyclohex-3-en-1-oate

Objective: The aims of this study were to establish the structure of the potent anticonvulsant enaminone methyl 4-(4′-bromophenyl)amino-6-methyl-2- oxocyclohex-3-en-1-oate (E139), and to determine the energetically preferred conformation of the molecule, which is responsible for the biological activity. Materials and Methods: The structure of the molecule was determined by X-ray crystallography. Theoretical ab initio calculations with different basis sets were used to compare the energies of the different enantiomers and to other structurally related compounds. Results: The X-ray crystal structure revealed two independent molecules of E139, both with absolute configuration C11(S), C12(R), and their inverse. Ab initio calculations with the 6-31G, 3-21G and STO-3G basis sets confirmed that the C11(S), C12(R) enantiomer with both substituents equatorial had the lowest energy. Compared to relevant crystal structures, the geometry of the theoretical structures shows a longer C-N and shorter C=O distance with more cyclohexene ring puckering in the isolated molecule. Conclusion: Based on a pharmacophoric model it is suggested that the enaminone system HN-C=C-C=O and the 4-bromophenyl group in E139 are necessary to confer anticonvulsant property that could lead to the design of new and improved anticonvulsant agents. Copyright © 2003 S. Karger AG, Basel.

Evolutionary games with two timescales

We consider a two timescale model of learning by economic agents wherein active or 'ontogenetic' learning by individuals takes place on a fast scale and passive or 'phylogenetic' learning by society as a whole on a slow scale, each affecting the evolution of the other. The former is modelled by the Monte Carlo dynamics of physics, while the latter is modelled by the replicator dynamics of evolutionary biology. Various qualitative aspects of the dynamics are studied in some simple cases, both analytically and numerically, and its role as a useful modelling device is emphasized.

Twist phase in Gaussian-beam optics

The recently discovered twist phase is studied in the context of the full ten-parameter family of partially coherent general anisotropic Gaussian Schell-model beams. It is shown that the nonnegativity requirement on the cross-spectral density of the beam demands that the strength of the twist phase be bounded from above by the inverse of the transverse coherence area of the beam. The twist phase as a two-point function is shown to have the structure of the generalized Huygens kernel or Green's function of a first-order system. The ray-transfer matrix of this system is exhibited. Wolf-type coherent-mode decomposition of the twist phase is carried out. Imposition of the twist phase on an otherwise untwisted beam is shown to result in a linear transformation in the ray phase space of the Wigner distribution. Though this transformation preserves the four-dimensional phase-space volume, it is not symplectic and hence it can, when impressed on a Wigner distribution, push it out of the convex set of all bona fide Wigner distributions unless the original Wigner distribution was sufficiently deep into the interior of the set.

Gaussian Schell-model beams and general shape invariance

We present two six-parameter families of anisotropic Gaussian Schell-model beams that propagate in a shape-invariant manner, with the intensity distribution continuously twisting about the beam axis. The two families differ in the sense or helicity of this beam twist. The propagation characteristics of these shape-invariant beams are studied, and the restrictions on the beam parameters that arise from the optical uncertainty principle are brought out. Shape invariance is traced to a fundamental dynamical symmetry that underlies these beams. This symmetry is the product of spatial rotation and fractional Fourier transformation.