LinkFinder: An expert system that constructs phylogenic trees

An expert system has been developed using the C Language Integrated Production System (CLIPS) that automates the process of constructing DNA sequence based phylogenies (trees or lineages) that indicate evolutionary relationships. LinkFinder takes as input homologous DNA sequences from distinct individual organisms. It measures variations between the sequences, selects appropriate proportionality constants, and estimates the time that has passed since each pair of organisms diverged from a common ancestor. It then designs and outputs a phylogenic map summarizing these results. LinkFinder can find genetic relationships between different species, and between individuals of the same species, including humans. It was designed to take advantage of the vast amount of sequence data being produced by the Genome Project, and should be of value to evolution theorists who wish to utilize this data, but who have no formal training in molecular genetics. Evolutionary theory holds that distinct organisms carrying a common gene inherited that gene from a common ancestor. Homologous genes vary from individual to individual and species to species, and the amount of variation is now believed to be directly proportional to the time that has passed since divergence from a common ancestor. The proportionality constant must be determined experimentally; it varies considerably with the types of organisms and DNA molecules under study. Given an appropriate constant, and the variation between two DNA sequences, a simple linear equation gives the divergence time

Monitoring and Research on Wading Birds in the Water Conservation Areas ofthe Everglades: The 1996 Nesting season

This project was initiated to continue monitoring reproductive responses of wading birds in the central Everglades, and to investigate two areas of research considered key to understanding and managing wading birds: nestling energetics, and factors affecting food availability. This report summarizes the first of two years of work. (101 page document

System identification, time series analysis and forecasting:The Captain Toolbox handbook.

CAPTAIN is a MATLAB compatible toolbox for non stationary time series analysis, system identification, signal processing and forecasting, using unobserved components models, time variable parameter models, state dependent parameter models and multiple input transfer function models. CAPTAIN also includes functions for true digital control

Nonminimal state space approach to multivariable ramp metering control of motorway bottlenecks

The paper discusses the automatic control of motorway traffic flows utilising ramp metering, i.e. traffic lights on the on-ramp entrances. A multivariable ramp metering system is developed, based on the nonminimal state space (NMSS) approach to control system design using adaptive proportional-integral-plus, linear quadratic (PIP–LQ) optimal controllers. The controller is evaluated on a nonlinear statistical traffic model (STM) simulation of the Amsterdam motorway ring road near the Coen Tunnel

Super- and subradiant emission of two-level systems in the near-Dicke limit

We analyze the stability of super- and subradiant states in a system of identical two-level atoms in the near-Dicke limit, i.e., when the atoms are very close to each other compared to the wavelength of resonant light. The dynamics of the system are studied using a renormalized master equation, both with multipolar and minimal-coupling interaction schemes. We show that both models lead to the same result and, in contrast to unrenormalized models, predict that the relative orientation of the (co-aligned) dipoles is unimportant in the Dicke limit. Our master equation is of relevance to any system of dipole-coupled two-level atoms, and gives bounds on the strength of the dipole-dipole interaction for closely spaced atoms. Exact calculations for small atom systems in the near-Dicke limit show the increased emission times resulting from the evolution generated by the strong dipole-dipole interaction. However, for large numbers of atoms in the near-Dicke limit, it is shown that as the number of atoms increases, the effect of the dipole-dipole interaction on collective emission is reduced.Comment: 14 pages, 6 figures, published versio

Proportional-integral-plus (PIP) control of the ALSTOM gasifier problem

Although it is able to exploit the full power of optimal state variable feedback within a non-minimum state-space (NMSS) setting, the proportional-integral-plus (PIP) controller is simple to implement and provides a logical extension of conventional proportional-integral and proportional-integral-derivative (PI/PID) controllers, with additional dynamic feedback and input compensators introduced automatically by the NMSS formulation of the problem when the process is of greater than first order or has appreciable pure time delays. The present paper applies the PIP methodology to the ALSTOM benchmark challenge, which takes the form of a highly coupled multi-variable linear model, representing the gasifier system of an integrated gasification combined cycle (IGCC) power plant. In particular, a straightforwardly tuned discrete-time PIP control system based on a reduced-order backward-shift model of the gasifier is found to yield good control of the benchmark, meeting most of the specified performance requirements at three different operating points

Budding and Domain Shape Transformations in Mixed Lipid Films and Bilayer Membranes

We study the stability and shapes of domains with spontaneous curvature in fluid films and membranes, embedded in a surrounding membrane with zero spontaneous curvature. These domains can result from the inclusion of an impurity in a fluid membrane, or from phase separation within the membrane. We show that for small but finite line and surface tensions and for finite spontaneous curvatures, an equilibrium phase of protruding circular domains is obtained at low impurity concentrations. At higher concentrations, we predict a transition from circular domains, or "caplets", to stripes. In both cases, we calculate the shapes of these domains within the Monge representation for the membrane shape. With increasing line tension, we show numerically that there is a budding transformation from stable protruding circular domains to spherical buds. We calculate the full phase diagram, and demonstrate a two triple points, of respectively bud-flat-caplet and flat-stripe-caplet coexistence.Comment: 14 pages, to appear in Phys Rev

Planar micromachined glass cantilevers utilising integrated Bragg Fabry-Perot cavities

Here we demonstrate a glass cantilever based on a unique micromachining and etching approach, combined with UV written Bragg gratings. We shall also discuss the increase in sensitivity by using two Bragg gratings to form Fabry-Pérot cavity. Cantilevers are in ultra sensitive force sensors used in applications such as Atomic Force Microscopy, mass sensing and acoustic transducers

Method and apparatus for analyzing material properties using ultrasound

Apparatus is disclosed for investigating the mechanical properties of a solid material such as bone, including means for positioning the apparatus in proximity to a surface of the material, at least one emitting ultrasound transducer, at least one receiving ultrasound transducer positioned to received ultrasound waves that have been emitted and have contacted the surface of the material, means for varying the angle of incidence of the emitted ultrasound wave towards the material, means for determining the alignment of the surface of the material with respect to the emitting and receiving ultrasound transdsucers, and signal analyzer means coupled to the receiving transducer for determining at least one characteristic of the received ultrasound wave which is indicative of a mechanical property of the material. A method is also disclosed of using such apparatus. The present invention permits the quick and efficient evaluation of treatment for osteoporosis, and whether that treatment has in fact reduced the tendency of a patient's bones to fracture.Board of Regents, University of Texas Syste

Cost effective combined axial fan and throttling valve control of ventilation rate

This paper is concerned with Proportional-Integral-Plus (PIP) control of ventilation rate in mechanically ventilated agricultural buildings. In particular, it develops a unique fan and throttling valve control system for a 22m3 test chamber, representing a section of a livestock building or glasshouse, at the Katholieke Universiteit Leuven. Here, the throttling valve is employed to restrict airflow at the outlet, so generating a higher static pressure difference over the control fan. In contrast with previous approaches, however, the throttling valve is directly employed as a second control actuator, utilising airflow from either the axial fan or natural ventilation. The new combined fan/valve configuration is compared with a commercially available PID-based controller and a previously developed scheduled PIP design, yielding a reduction in power consumption in both cases of up to 45%