Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “evolutionary optimization”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11

The damper placement problem for large flexible space structures

The damper placement problem for large flexible space truss structures is formulated as a combinatorial optimization problem. The objective is to determine the p truss members of the structure to replace with active (or passive) dampers so that the modal damping ratio is as large as possible for all significant modes of vibration. Equivalently, given a strain energy matrix with rows indexed on the modes and the columns indexed on the truss members, we seek to find the set of p columns such that the smallest row sum, over the p columns, is maximized. We develop a tabu search heuristic for the damper placement problems on the Controls Structures Interaction (CSI) Phase 1 Evolutionary Model (10 modes and 1507 truss members). The resulting solutions are shown to be of high quality.

Kincaid, Rex K.↗

Space Station Freedom Integrated Research and Development Growth

Space Station Freedom is designed to be an Earth-orbiting, multidiscipline research and development (R&D) facility capable of evolution to accomodate a variety of potential uses. One evolution scenario is growth to an enhanced R&D facility. In support of the Space Station Freedom Program Preliminary Design Review (PDR), the NASA Langley Research Center Space Station Office is analyzing growth requirements and evaluating configurations for this R&D utilization. This paper presents a summary of FY1989 study results including time-phased growth plans, R&D growth issues and configurations, and recommendations for the program baseline design which will facilitate evolutionary R&D growth. This study consisted of three major areas of concentration: mission requirements analysis; Space Station Freedom systems growth analysis; and growth accomodations and trades. Mission requirements analysis was performed to develop a realistic mission model of post-Phase 1 R&D missions. A systems-level analysis was performed to project incremental growth requirements of Space Station Freedom needed to support these R&D missions. Identification of growth requirements and specific growth elements led to the need for special accomodations analyses and trades. These studies included identification of hooks and scars on the baseline design, determination of an optimal module growth pattern, analysis of the dual keel length, and determination of an optimal locaton for the customer servicing facility. Results of this study show that Space Station Freedom must be capable of evolving to a dual keel, eight pressurized module configuration (two growth habs and two growth labs); providing 275 kW power (for experimenters and station housekeeping); accomodating a crew of 24; and supporting other growth structures and special facilities to meet projected R&D mission requirements.

Meredith, Barry D.↗

The experience factory: Can it make you a 5? or what is its relationship to other quality and improvement concepts?

The concepts of quality improvements have permeated many businesses. It is clear that the nineties will be the quality era for software and there is a growing need to develop or adapt quality improvement approaches to the software business. Thus we must understand software as an artifact and software as a business. Since the business we are dealing with is software, we must understand the nature of software and software development. The software discipline is evolutionary and experimental; it is a laboratory science. Software is development not production. The technologies of the discipline are human based. There is a lack of models that allow us to reason about the process and the product. All software is not the same; process is a variable, goals are variable, etc. Packaged, reusable, experiences require additional resources in the form of organization, processes, people, etc. There have been a variety of organizational frameworks proposed to improve quality for various businesses. The ones discussed in this presentation include: Plan-Do-Check-Act, a quality improvement process based upon a feedback cycle for optimizing a single process model/production line; the Experience Factory/Quality Improvement Paradigm, continuous improvements through the experimentation, packaging, and reuse of experiences based upon a business's needs; Total Quality Management, a management approach to long term success through customer satisfaction based on the participation of all members of an organization; the SEI capability maturity model, a staged process improvement based upon assessment with regard to a set of key process areas until you reach a level 5 which represents a continuous process improvement; and Lean (software) Development, a principle supporting the concentration of the production on 'value added' activities and the elimination of reduction of 'not value added' activities.

Basili, Victor R.↗

Experiments with a Parallel Multi-Objective Evolutionary Algorithm for Scheduling

Evolutionary multi-objective algorithms have great potential for scheduling in those situations where tradeoffs among competing objectives represent a key requirement. One challenge, however, is runtime performance, as a consequence of evolving not just a single schedule, but an entire population, while attempting to sample the Pareto frontier as accurately and uniformly as possible. The growing availability of multi-core processors in end user workstations, and even laptops, has raised the question of the extent to which such hardware can be used to speed up evolutionary algorithms. In this paper we report on early experiments in parallelizing a Generalized Differential Evolution (GDE) algorithm for scheduling long-range activities on NASA's Deep Space Network. Initial results show that significant speedups can be achieved, but that performance does not necessarily improve as more cores are utilized. We describe our preliminary results and some initial suggestions from parallelizing the GDE algorithm. Directions for future work are outlined.

scheduling↗

Karhunen-Loeve Estimation of the Power Spectrum Parameters from the Angular Distribution of Galaxies in Early Sloan Digital Sky Survey Data

We present measurements of parameters of the three-dimensional power spectrum of galaxy clustering from 222 square degrees of early imaging data in the Sloan Digital Sky Survey (SDSS). The projected galaxy distribution on the sky is expanded over a set of Karhunen-Loeve (KL) eigenfunctions, which optimize the signal-to-noise ratio in our analysis. A maximum likelihood analysis is used to estimate parameters that set the shape and amplitude of the three-dimensional power spectrum of galaxies in the SDSS magnitude-limited sample with r* less than 21. Our best estimates are gamma = 0.188 +/- 0.04 and sigma(sub 8L) = 0.915 +/- 0.06 (statistical errors only), for a flat universe with a cosmological constant. We demonstrate that our measurements contain signal from scales at or beyond the peak of the three-dimensional power spectrum. We discuss how the results scale with systematic uncertainties, like the radial selection function. We find that the central values satisfy the analytically estimated scaling relation. We have also explored the effects of evolutionary corrections, various truncations of the KL basis, seeing, sample size, and limiting magnitude. We find that the impact of most of these uncertainties stay within the 2 sigma uncertainties of our fiducial result.

Szalay, Alexander S.↗

Launch vehicle and power level impacts on electric GEO insertion

Solar Electric Propulsion (SEP) has been shown to increase net geosynchronous spacecraft mass when used for station keeping and final orbit insertion. The impact of launch vehicle selection and power level on the benefits of this approach were examined for 20 and 25 kW systems launched using the Ariane 5, Atlas IIAR, Long March, Proton, and Sea Launch vehicles. Two advanced on-board propulsion technologies, 5 kW ion and Hall thruster systems, were used to establish the relative merits of the technologies and launch vehicles. GaAs solar arrays were assumed. The analysis identifies the optimal starting orbits for the SEP orbit raising/plane changing while considering the impacts of radiation degradation in the Van Allen belts, shading, power degradation, and oblateness. This use of SEP to provide part of the orbit insertion results in net mass increases of 15 - 38% and 18 - 46% for one to two month trip times, respectively, over just using SEP for 15 years of north/south station keeping. SEP technology was shown to have a greater impact on net masses of launch vehicles with higher launch latitudes when avoidance of solar array and payload degradation is desired. This greater impact of SEP could help reduce the plane changing disadvantage of high latitude launch sites. Comparison with results for 10 and 15 kW systems show clear benefits of incremental increases in SEP power level, suggesting that an evolutionary approach to high power SEP for geosynchronous spacecraft is possible.

Oleson, Steven R.↗

Agent Based Modeling of Air Carrier Behavior for Evaluation of Technology Equipage and Adoption

As part of ongoing research, the National Aeronautics and Space Administration (NASA) and LMI developed a research framework to assist policymakers in identifying impacts on the U.S. air transportation system (ATS) of potential policies and technology related to the implementation of the Next Generation Air Transportation System (NextGen). This framework, called the Air Transportation System Evolutionary Simulation (ATS-EVOS), integrates multiple models into a single process flow to best simulate responses by U.S. commercial airlines and other ATS stakeholders to NextGen-related policies, and in turn, how those responses impact the ATS. Development of this framework required NASA and LMI to create an agent-based model of airline and passenger behavior. This Airline Evolutionary Simulation (AIRLINE-EVOS) models airline decisions about tactical airfare and schedule adjustments, and strategic decisions related to fleet assignments, market prices, and equipage. AIRLINE-EVOS models its own heterogeneous population of passenger agents that interact with airlines; this interaction allows the model to simulate the cycle of action-reaction as airlines compete with each other and engage passengers. We validated a baseline configuration of AIRLINE-EVOS against Airline Origin and Destination Survey (DB1B) data and subject matter expert opinion, and we verified the ATS-EVOS framework and agent behavior logic through scenario-based experiments. These experiments demonstrated AIRLINE-EVOS's capabilities in responding to an input price shock in fuel prices, and to equipage challenges in a series of analyses based on potential incentive policies for best equipped best served, optimal-wind routing, and traffic management initiative exemption concepts..

Horio, Brant M.↗

The Pheno-Evo Model: Evolution of Microbial Phenotypic Diversity in 2D Space

Biologists appreciate microbes for their simplicity and predictability: we assume that a population of genetically identical cells in a uniform environment will all behave the same way. While this assumption is often useful, it is also often wrong. Not only might microbes in a clonal population act differently from one another, the differences may be categorical (growing v. non-growing; toxin-sensitive v. tolerant), and this diversity might be an evolved trait conferring increased fitness on the population. How does such phenotypic heterogeneity evolve? And how does a population find the optimal distribution of phenotypes for a given environment? Efforts at modeling microbial phenotypic heterogeneity often focus on populations with two discrete phenotypic types; phenotypes in continuous distributions remain poorly explored. To address this gap and to explore the role of spatial relationships, we use agent-based modeling to simulate a phenotypically diverse population of microbial cells evolving in the presence of periodic toxic stress. Cells on patches in a 2D grid may degrade toxin, suffer damage from toxin, switch phenotype, and reproduce. An individual's phenotype its toxin degradation rate-- for which there is a tradeoff with reproduction-- and the genotype encodes the distribution of phenotypic values in the population. The rate of toxin diffusion determines how individuals influence their neighbors' environments. We examine the effects of toxin concentration, diffusion rate, and environmental predictability on the survival success of populations with different phenotype distributions, and populations' evolutionary trajectories when phenotype distribution is allowed to evolve. We conduct all simulations on the platform NetLogo, which provides a friendly interface allowing users of any experience level to tweak parameters and run their own simulations. We have also created custom tools in R for analyzing and visualizing the results of multiple runs.

microbial evolution↗

Asymptotic Giant Branch stars as a source of short-lived radioactive nuclei in the solar nebula

We carried out a theoretical evaluation of the contribution of Asymptotic Giant Branch (AGB) stars to some short-lived (10(exp 6) less than or equal to Tau-bar less than or equal to 2 x 10(exp 7) yr) isotopes in the Interstellar Medium (ISM) and in the early solar system using stellar model calculations for thermally pulsing evolutionary phases of low-mass stars. The yields of s-process nuclei in the convective He-shell for different neutron exposures tau(sub 0) were obtained, and AGB stars were shown to produce several radioactive nuclei (especially Pd-107, Pb-205, Fe-60, Zr-93, Tc-99, Cs-135, and Hf-182) in diferent amounts. Assuming either contamination of the solar nebula from a single AGB star or models for continuous injection and mixing from many stars into the ISM, we calculate the ratios of radioactive to stable nuclei at the epoch of the Sun's formation. The dilution factor between the AGB ejecta and the early solar system matter is obtained by matching the observed Pd-107/Pd-108 and depends on the value of tau(sub 0). It is found that small masses M(sub He) of He-shell material (10(exp -4)-10(exp -7) solar mass) enriched in s-process nuclei are sufficient to contaminate 1 solar mass of the ISM to produce the Pd-107 found in the early solar system. Predictions are made for all of the other radioactive isotopes. The optimal model to explain several observed radioactive species at different states of the proto-solar nebula involves a single AGB star with a low neutron exposure (tau(sub 0) = 0.03 mbarn(sup -1)) which contaminated the cloud with a dilution factor of M(sub He)/solar mass approximately 1.5 x 10(exp -4). This will also contribute newly synthesized stable s-process nuclei in the amount of approximately 10(exp -4) of their abundances already present in the proto-solar cloud. Variations in the degree of homogenization (approximately 30%) of the injected material may account for some of the small general isotopic anomalies found in meteorites. It is also found that Fe-60 is produced in small but significant quantities that may be sufficient to explain the observations if the time elapsed delta from the contamination of the ISM to the formation of protoplanetary bodies is not higher than delta = 5 x 10(exp 6) yr. If delta is longer, up to 10 x 10(exp 6) yr, this would require the single AGB star to experience enhanced neutron densities (n(sub n) approximately 3 x 10(exp 9)n/cu cm) in the s-processing zone in order to compensate for the branching at Fe-59. The alternative model of long-term continuous ejection of matter from many AGB stars does not appear to match the observations. We also estimate the Al-26 production from the H-shell and find that the Al-26 abundance in the early solar system may be readily explained in a self-consistent manner. Moreover, Al-26 from AGB stars may contribute substantially to the galactic Al-26 gamma-source, while no significant gamma-flux from Co-60 (deriving from Fe-60 decay) is to be expected.

Wasserburg, G. J.↗

Space transfer vehicle concepts and requirements. Volume 1: Executive summary

The objectives of the Space Transfer Vehicle (STV) Concepts and Requirements studies were to provide sensitivity data on usage, economics, and technology associated with new space transportation systems. The study was structured to utilize data on the emerging launch vehicles, the latest mission scenarios, and Space Exploration Initiative (SEI) payload manifesting and schedules, to define a flexible, high performance, cost effective, evolutionary space transportation system for NASA. Initial activities were to support the MSFC effort in the preparation of inputs to the 90 Day Report to the National Space Council (NSC). With the results of this study establishing a point-of-departure for continuing the STV studies in 1990, additional options and mission architectures were defined. The continuing studies will update and expand the parametrics, assess new cargo and manned ETO vehicles, determine impacts on the redefined Phase 0 Space Station Freedom, and to develop a design that encompasses adequate configuration flexibility to ensure compliance with on-going NASA study recommendations with major system disconnects. In terms of general requirements, the objectives of the STV system and its mission profiles will address crew safety and mission success through a failure-tolerant and forgiving design approach. These objectives were addressed through the following: engine-out capability for all mission phases; built-in-test for vehicle health monitoring to allow testing of all critical functions such as, verification of lunar landing and ascent engines before initiating the landing sequence; critical subsystems will have multiple strings for redundancy plus adequate supplies of onboard spares for removal and replacement of failed items; crew radiation protection; and trajectories that optimize lunar and Mars performance and flyby abort capabilities.

Source record↗

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones. c2002 The Willi Hennig Society.

NASA Discipline Evolutionary Biology↗

Aircraft integrated design and analysis: A classroom experience

AAE 451 is the capstone course required of all senior undergraduates in the School of Aeronautics and Astronautics at Purdue University. During the past year the first steps of a long evolutionary process were taken to change the content and expectations of this course. These changes are the result of the availability of advanced computational capabilities and sophisticated electronic media availability at Purdue. This presentation will describe both the long range objectives and this year's experience using the High Speed Commercial Transport (HSCT) design, the AIAA Long Duration Aircraft design and a Remotely Piloted Vehicle (RPV) design proposal as project objectives. The central goal of these efforts was to provide a user-friendly, computer-software-based, environment to supplement traditional design course methodology. The Purdue University Computer Center (PUCC), the Engineering Computer Network (ECN), and stand-alone PC's were used for this development. This year's accomplishments centered primarily on aerodynamics software obtained from the NASA Langley Research Center and its integration into the classroom. Word processor capability for oral and written work and computer graphics were also blended into the course. A total of 10 HSCT designs were generated, ranging from twin-fuselage and forward-swept wing aircraft, to the more traditional delta and double-delta wing aircraft. Four Long Duration Aircraft designs were submitted, together with one RPV design tailored for photographic surveillance. Supporting these activities were three video satellite lectures beamed from NASA/Langley to Purdue. These lectures covered diverse areas such as an overview of HSCT design, supersonic-aircraft stability and control, and optimization of aircraft performance. Plans for next year's effort will be reviewed, including dedicated computer workstation utilization, remote satellite lectures, and university/industrial cooperative efforts.

Source record↗

Report of the Panel on Aerodynamics

Progress in aerodynamics over the past 50 years has been evidenced by the development of increasingly sophisticated and efficient flight vehicles throughout the flight spectrum. Advances have generally arisen in an evolutionary manner from experience gained in wind tunnel testing, flight testing, and improvements in analytical and computational capabilities. As a result of this evolutionary development, both military and commercial vehicles operate at a relatively high efficiency level. This observation plus the fact that airplanes have not changed appreciably in outward appearance over recent years has led some skeptics to conclude incorrectly that aerodynamics is a mature technology, with little to be gained from further developments in the field. It is of interest to note that progress in aerodynamics has occurred without a thorough understanding of the fundamental physics of flow, turbulence, vortex dynamics, and separated flow, for example. The present understanding of transition, turbulence, and boundary layer separation is actually very limited. However, these fundamental flow phenomena provide the key to reducing the viscous drag of aircraft. Drag reduction provides the greatest potential for increased flight efficiency from the standpoint of both saving energy and maximizing performance. Recent advances have led to innovative concepts for reducing turbulent friction drag by modifying the turbulent structure within the boundary layer. Further advances in this basic area should lead to methods for reducing skin friction drag significantly. The current challenges for military aircraft open entirely new fields of investigation for the aerodynamicist. The ability through very high speed information processing technology to totally integrate the flight and propulsion controls can permit an aircraft to fly with "complete abandon," avoiding departure, buffet, and other undesirable characteristics. To utilize these new control concepts, complex aerodynamic phenomena will have to be understood, predicted, and controlled. Current requirements for military aircraft include configuration optimization through a widened envelope from subsonic to supersonic and from low to high angles of attack. This task is further complicated by requirements for control of observables. These challenging new designs do not have the luxury of a large experimental data base from which to optimize for various parameter combinations. Consequently, there exists a strong need for better techniques, both experimental and computational, to permit design optimization in a complete sense.

Bradley, Richard G.↗

NASA Tech Briefs, July 2009

Topics covered include: Dual Cryogenic Capacitive Density Sensor; Hail Monitor Sensor; Miniature Six-Axis Load Sensor for Robotic Fingertip; Improved Blackbody Temperature Sensors for a Vacuum Furnace; Wrap-Around Out-the-Window Sensor Fusion System; Wide-Range Temperature Sensors with High-Level Pulse Train Output; Terminal Descent Sensor Simulation; A Robust Mechanical Sensing System for Unmanned Sea Surface Vehicles; Additive for Low-Temperature Operation of Li-(CF)n Cells; Li/CFx Cells Optimized for Low-Temperature Operation; Number Codes Readable by Magnetic-Field-Response Recorders; Determining Locations by Use of Networks of Passive Beacons; Superconducting Hot-Electron Submillimeter-Wave Detector; Large-Aperture Membrane Active Phased-Array Antennas; Optical Injection Locking of a VCSEL in an OEO; Measuring Multiple Resistances Using Single-Point Excitation; Improved-Bandwidth Transimpedance Amplifier; Inter-Symbol Guard Time for Synchronizing Optical PPM; Novel Materials Containing Single-Wall Carbon Nanotubes Wrapped in Polymer Molecules; Light-Curing Adhesive Repair Tapes; Thin-Film Solid Oxide Fuel Cells; Zinc Alloys for the Fabrication of Semiconductor Devices; Small, Lightweight, Collapsible Glove Box; Radial Halbach Magnetic Bearings; Aerial Deployment and Inflation System for Mars Helium Balloons; Steel Primer Chamber Assemblies for Dual Initiated Pyrovalves; Voice Coil Percussive Mechanism Concept for Hammer Drill; Inherently Ducted Propfans and Bi-Props; Silicon Nanowire Growth at Chosen Positions and Orientations; Detecting Airborne Mercury by Use of Gold Nanowires; Detecting Airborne Mercury by Use of Palladium Chloride; Micro Electron MicroProbe and Sample Analyzer; Nanowire Electron Scattering Spectroscopy; Electron-Spin Filters Would Offer Spin Polarization Greater than 1; Subcritical-Water Extraction of Organics from Solid Matrices; A Model for Predicting Thermoelectric Properties of Bi2Te3; Integrated Miniature Arrays of Optical Biomolecule Detectors; A Software Rejuvenation Framework for Distributed Computing; Kurtosis Approach to Solution of a Nonlinear ICA Problem; Robust Software Architecture for Robots; R4SA for Controlling Robots; Bio-Inspired Neural Model for Learning Dynamic Models; Evolutionary Computing Methods for Spectral Retrieval; Monitoring Disasters by Use of Instrumented Robotic Aircraft; Complexity for Survival of Living Systems; Using Drained Spacecraft Propellant Tanks for Habitation; Connecting Node; and Electrolytes for Low-Temperature Operation of Li-CFx Cells.

Source record↗

Integrated Modeling Tools for Thermal Analysis and Applications

Integrated modeling of spacecraft systems is a rapidly evolving area in which multidisciplinary models are developed to design and analyze spacecraft configurations. These models are especially important in the early design stages where rapid trades between subsystems can substantially impact design decisions. Integrated modeling is one of the cornerstones of two of NASA's planned missions in the Origins Program -- the Next Generation Space Telescope (NGST) and the Space Interferometry Mission (SIM). Common modeling tools for control design and opto-mechanical analysis have recently emerged and are becoming increasingly widely used. A discipline that has been somewhat less integrated, but is nevertheless of critical concern for high precision optical instruments, is thermal analysis and design. A major factor contributing to this mild estrangement is that the modeling philosophies and objectives for structural and thermal systems typically do not coincide. Consequently the tools that are used in these discplines suffer a degree of incompatibility, each having developed along their own evolutionary path. Although standard thermal tools have worked relatively well in the past. integration with other disciplines requires revisiting modeling assumptions and solution methods. Over the past several years we have been developing a MATLAB based integrated modeling tool called IMOS (Integrated Modeling of Optical Systems) which integrates many aspects of structural, optical, control and dynamical analysis disciplines. Recent efforts have included developing a thermal modeling and analysis capability, which is the subject of this article. Currently, the IMOS thermal suite contains steady state and transient heat equation solvers, and the ability to set up the linear conduction network from an IMOS finite element model. The IMOS code generates linear conduction elements associated with plates and beams/rods of the thermal network directly from the finite element structural model. Conductances for temperature varying materials are accommodated. This capability both streamlines the process of developing the thermal model from the finite element model, and also makes the structural and thermal models compatible in the sense that each structural node is associated with a thermal node. This is particularly useful when the purpose of the analysis is to predict structural deformations due to thermal loads. The steady state solver uses a restricted step size Newton method, and the transient solver is an adaptive step size implicit method applicable to general differential algebraic systems. Temperature dependent conductances and capacitances are accommodated by the solvers. In addition to discussing the modeling and solution methods. applications where the thermal modeling is "in the loop" with sensitivity analysis, optimization and optical performance drawn from our experiences with the Space Interferometry Mission (SIM), and the Next Generation Space Telescope (NGST) are presented.

Milman, Mark H.↗

Efficiency of parallel direct optimization

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size. c2001 The Willi Hennig Society.

NASA Discipline Evolutionary Biology↗

PheniX: A New Vision for the Hard X-ray Sky

We are proposing a mission devoted to high energy X-ray astronomy that is based on a focusing telescope operating in the 1-200 keV energy range but optimized for the hard X-ray range. The main scientific topics concern: Physics of compact objects: The proximity of compact objects provides a unique laboratory to study matter and radiation in extreme conditions of temperature and density in strong gravitational environment. The emission of high energy photons from these objects is far from being understood. The unprecedented sensitivity in the high energy domain will allow a precise determination of the non-thermal processes at work in the vicinity of compact objects. The full 1-200 keV energy coverage will be ideal to disentangle the emission processes produced in the spacetime regions most affected by strong-gravity, as well as the physical links: disk-thermal emission-iron line-comptonisation-reflection-non-thermal emission-jets. Neutron stars-magnetic field-cyclotron lines: Time resolved spectroscopy (and polarimetry) at ultra-high sensitivity of AXP, milliseconds pulsars and magnetars will give new tools to study the role of the synchrotron processes at work in these objects. Cyclotron lines-direct measurement of magnetic filed-equation of state constraints-short bursts-giant flares could all be studied with great details. AGN: The large sensitivity improvement will provide detailed spectral properties of the high energy emission of AGN's. This will give a fresh look to the connection between accretion and jet emission and will provide a new understanding of the physical processes at work. Detection of high-redshift active nuclei in this energy range will allow to introduce an evolutionary aspect to high-energy studies of AGN, probing directly the origin of the Cosmic X-ray Background also in the non-thermal range (> 20 keV). Element formation-Supernovae: The energy resolution achievable for this mission (<0.5 keV) and a large high energy effective area are ideally suited for the 44Ti line study (68 and 78 keV). This radioactive nuclei emission will give an estimate of their quantities and speed in their environment. In addition the study of the spatial structure and spectral emission of SNR will advance our knowledge of the dynamics of supernovae explosions, of particles acceleration mechanisms and how the elements are released in the interstellar medium. Instrumental design: The progress of X-ray focusing optics techniques allows a major step in the instrumental design: the collecting area becomes independent of the detection area. This drastically reduces the instrumental background and will open a new era. The optics will be based on depth-graded multi-layer mirrors in a Wolter I configuration. To obtain a significant effective area in the hundred of keV range a focal length in the 40-50 meters range (attainable with a deployable mast) is needed. In addition such a mission could benefit from recent progress made on mirror coating. We propose to cover the 1-200 keV energy range with a single detector, a double-sided Germanium strip detector operating at 80 K. The main features will be: (a) good energy resolution (.150 keV at 5 keV and <.5 keV at 100 keV), (b) 3 dimensional event localization with a low number of electronic chains, (c) background rejection by the 3D localization, (d) polarisation capabilities in the Compton regime.

PHENIX↗

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Non-NASA Center↗