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At least 145 records · Page 8

Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

Rodriquez-Gomez, D.

The evolutionary stage of an RRs star SX Phe

The evolutionary stage for a short period variable SX Phe was investigated. It was assumed that SX Phe is a mixed star with low metal abundance in which the material was mixed after the star evolved off the main sequence, and is in the second hydrogen burning stage. The validity of this hypothesis was examined by constructing two evolutionary sequences with (X,Z,M/solar mass) = (0.5,0.004,0.75) and (0.5,0.001,0.70) in the hydrogen burning phase and computed the pulsation period. Agreement between theoretical results and observational data was sufficient to conclude that the mixed model is actually adequate for SX Phe. The applicability of this model to other RRs stars is briefly discussed.

Saio, H.

ARES I Aerodynamic Testing at the NASA Langley Unitary Plan Wind Tunnel

Small-scale force and moment and pressure models based on the outer mold lines of the Ares I design analysis cycle crew launch vehicle were tested in the NASA Langley Research Center Unitary Plan Wind Tunnel from May 2006 to September 2009. The test objectives were to establish supersonic ascent aerodynamic databases and to obtain force and moment, surface pressure, and longitudinal line-load distributions for comparison to computational predictions. Test data were obtained at low through high supersonic Mach numbers for ranges of the Reynolds number, angle of attack, and roll angle. This paper focuses on (1) the sensitivity of the supersonic aerodynamic characteristics to selected protuberances, outer mold line changes, and wind tunnel boundary layer transition techniques, (2) comparisons of experimental data to computational predictions, and (3) data reproducibility. The experimental data obtained in the Unitary Plan Wind Tunnel captured the effects of evolutionary changes to the Ares I crew launch vehicle, exhibited good agreement with predictions, and displayed satisfactory within-test and tunnel-to-tunnel data reproducibility.

Erickson, Gary E.

A Petaflops Era Computing Analysis

This report covers a study of the potential for petaflops (1O(exp 15) floating point operations per second) computing. This study was performed within the year 1996 and should be considered as the first step in an on-going effort. 'Me analysis concludes that a petaflop system is technically feasible but not feasible with today's state-of-the-art. Since the computer arena is now a commodity business, most experts expect that a petaflops system will evolve from current technology in an evolutionary fashion. To meet the price expectations of users waiting for petaflop performance, great improvements in lowering component costs will be required. Lower power consumption is also a must. The present rate of progress in improved performance places the date of introduction of petaflop systems at about 2010. Several years before that date, it is projected that the resolution limit of chips will reach the now known resolution limit. Aside from the economic problems and constraints, software is identified as the major problem. The tone of this initial study is more pessimistic than most of the Super-published material available on petaflop systems. Workers in the field are expected to generate more data which could serve to provide a basis for a more informed projection. This report includes an annotated bibliography.

Preston, Frank S.

Automated Design of Quantum Circuits

In order to design a quantum circuit that performs a desired quantum computation, it is necessary to find a decomposition of the unitary matrix that represents that computation in terms of a sequence of quantum gate operations.

evolutionary programming

Evolutionary models of halo stars with rotation. II - Effects of metallicity on lithium depletion, and possible implications for the primordial lithium abundance

Models of metal-poor stars with rotation were computed and their lithium depletion was compared with observations of halo stars. The models that have turn-off ages compatible with the observations have a nearly flat Li-T(eff) relationship in the region of the Spite lithium 'plateau'. Depending on the initial angular momentum, the models have a depletion factor ranging between a factor of 5 and a factor of 10 at fixed T(eff), implying a maximum initial lithium abundance of 3.1. Both the dispersion and the overall depletion factor are much smaller for metal-poor models than for solar metallicity ones. The factors that determine lithium depletion in rotational models are discussed and the different depletion patterns in solar metallicity and metal-poor models are traced to differences in their structure and evolution. The dependence of the lithium depletion on age, mass, initial angular momentum, and metallicity is also discussed. The dispersion predicted from these models is not inconsistent with the observations.

Pinsonneault, M. H.

Evolutionary problems of Cepheids and other giants investigated with new radiative opacities

Comparison of evolutionary tracks, pulsation constants, and linearized pulsational-stability coefficients for stellar models applicable to the problems of classical Cepheids, whose structures were calculated using the Cox-Stewart (1965) opacities and a recently computed set of opacities. The latter are based on the hot 'Thomas-Fermi' statistical model of the atom for all elements heavier than hydrogen and helium; they contain larger helium and metals contributions, but a smaller hydrogen contribution than the former ones for the same chemical composition. The difference in metals contribution affects mainly the location and shape of the evolutionary tracks on the H-R diagram, while the difference in hydrogen and helium contributions has its greatest effect on the pulsational properties of the Cepheid models. From the comparison of evolutionary tracks it is concluded that: (1) the theoretical M/L relation for evolved giants is changed very little by using the second set of opacities; (2) Q-values for the fundamental mode of radial pulsation in Cepheid envelope models increase if the second set is used, but the classical mass discrepancy remains; and (3) the second set leads to pulsational-instability.

Carson, T. R.

Exhaustive Versus Randomized Searchers for Nonlinear Optimization in 21st Century Computing: Solar Application

We present a simple multi-dimensional exhaustive search method to obtain, in a reasonable time, the optimal solution of a nonlinear programming problem. It is more relevant in the present day non-mainframe computing scenario where an estimated 95% computing resources remains unutilized and computing speed touches petaflops. While the processor speed is doubling every 18 months, the band width is doubling every 12 months, and the hard disk space is doubling every 9 months. A randomized search algorithm or, equivalently, an evolutionary search method is often used instead of an exhaustive search algorithm. The reason is that a randomized approach is usually polynomial-time, i.e., fast while an exhaustive search method is exponential-time i.e., slow. We discuss the increasing importance of exhaustive search in optimization with the steady increase of computing power for solving many real-world problems of reasonable size. We also discuss the computational error and complexity of the search algorithm focusing on the fact that no measuring device can usually measure a quantity with an accuracy greater than 0.005%. We stress the fact that the quality of solution of the exhaustive search - a deterministic method - is better than that of randomized search. In 21 st century computing environment, exhaustive search cannot be left aside as an untouchable and it is not always exponential. We also describe a possible application of these algorithms in improving the efficiency of solar cells - a real hot topic - in the current energy crisis. These algorithms could be excellent tools in the hands of experimentalists and could save not only large amount of time needed for experiments but also could validate the theory against experimental results fast.

Sen, Syamal K.

Computer-Automated Evolution of Spacecraft X-Band Antennas

A document discusses the use of computer- aided evolution in arriving at a design for X-band communication antennas for NASA s three Space Technology 5 (ST5) satellites, which were launched on March 22, 2006. Two evolutionary algorithms, incorporating different representations of the antenna design and different fitness functions, were used to automatically design and optimize an X-band antenna design. A set of antenna designs satisfying initial ST5 mission requirements was evolved by use these algorithms. The two best antennas - one from each evolutionary algorithm - were built. During flight-qualification testing of these antennas, the mission requirements were changed. After minimal changes in the evolutionary algorithms - mostly in the fitness functions - new antenna designs satisfying the changed mission requirements were evolved and within one month of this change, two new antennas were designed and prototypes of the antennas were built and tested. One of these newly evolved antennas was approved for deployment on the ST5 mission, and flight-qualified versions of this design were built and installed on the spacecraft. At the time of writing the document, these antennas were the first computer-evolved hardware in outer space.

Lohn, Jason D.

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 design, the AIAA Long Duration Aircraft design and RPV design proposal as project objectives. The central goal of these efforts is 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 are being used for this development. This year's accomplishments center primarily on aerodynamics software obtained from NASA/Langley 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 ten HSCT designs were generated, ranging from twin-fuselage aircraft, 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.

Weisshaar, Terrence A.

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

On the theory of thermal runaway in the hydrogen envelope of a white dwarf

An evolutionary sequence was calculated for a white dwarf on which a hydrogen rich envelope is assumed to increase with time. The stellar models were computed by integrating numerically the system of stellar structure equations by means of the Henyey method. The accretion of matter was assumed to be quasi-static. Near the point of the chemical discontinuity, a temperature maximum is shown to arise, and hydrogen ignites; a thin shell energy source is formed which is thermally unstable. The resulting thermal runaway was investigated numerically and by means of a simple approximation based on the energy balance in the hydrogen burning shell source.

Redkoborodyy, Y. N.

Nuclear fusion and carbon flashes on neutron stars

This paper reports on detailed calculations of the thermal evolution of the carbon-burning shells in the envelopes of accreting neutron stars for mass-accretion rates of 1 hundred-billionth to 2 billionths of a solar mass per yr and neutron-star masses of 0.56 and 1.41 solar masses. The work of Hansen and Van Horn (1975) is extended to higher densities, and a more detailed treatment of nuclear processing in the hydrogen- and helium-burning regions is included. Results of steady-state calculations are presented, and results of time-dependent computations are examined for accretion rates of 3 ten-billionths and 1 billionth of solar mass per yr. It is found that two evolutionary sequences lead to carbon flashes and that the carbon abundance at the base of the helium shell is a strong function of accretion rate. Upper limits are placed on the accretion rates at which carbon flashes will be important.

Taam, R. E.

Search-based optimization

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed-state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed-state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost-efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP-complete phylogenetic optimization problems such as genomic break-point analysis. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Non-NASA Center

Recent Progress in OVERFLOW Convergence Improvements

Improvements have been made to the implicit symmetric successive overrelaxation algorithm in the OVERFLOW 2.3 structured, overset grid, computational fluid dynamics flow solver. These improvements, consisting of implicit boundary conditions, improved flux Jacobian linearizations, and CFL number ramping, are a series of evolutionary changes to the linear solver that have resulted in increased nonlinear convergence rates and faster time to solution. A series of test cases are presented that demonstrate the effect of the changes through comparison with the original SSOR path and other linear solver implementations within OVERFLOW.

Joseph M Derlaga

Functional characteristics of the calcium modulated proteins seen from an evolutionary perspective

We have constructed dendrograms relating 173 EF-hand proteins of known amino acid sequence. We aligned all of these proteins by their EF-hand domains, omitting interdomain regions. Initial dendrograms were computed by minimum mutation distance methods. Using these as starting points, we determined the best dendrogram by the method of maximum parsimony, scored by minimum mutation distance. We identified 14 distinct subfamilies as well as 6 unique proteins that are perhaps the sole representatives of other subfamilies. This information is given in tabular form. Within subfamilies one can easily align interdomain regions. The resulting dendrograms are very similar to those computed using domains only. Dendrograms constructed using pairs of domains show general congruence. However, there are enough exceptions to caution against an overly simple scheme in which one pair of gene duplications leads from one domain precurser to a four domain prototype from which all other forms evolved. The ability to bind calcium was lost and acquired several times during evolution. The distribution of introns does not conform to the dendrogram based on amino acid sequences. The rates of evolution appear to be much slower within subfamilies, especially within calmodulin, than those prior to the definition of subfamily.

Kretsinger, R. H.

Design Space Issues for Intrinsic Evolvable Hardware

This paper discuss the problem of increased programming time for intrinsic evolvable hardware (EHW) as the complexity of the circuit grows. We develop equations for the size of the population, n, and the number of generations required for the population to converge, ngen, based on L, the length of the programming string. We show that the processing time of the computer becomes negligible for intrinsic EHW since the selection/crossover/mutation steps are only done once per generation, suggesting there is room for use of more complex evolutionary algorithms m intrinsic EHW. F i y , we review the state of the practice and discuss the notion of a system design approach for intrinsic EHW.

Hereford, James

Feature Learning for Multispectral Satellite Imagery Classification Using Neural Architecture Search

Automated classification of remote sensing data is an integral tool for earth scientists, and deep learning has proven very successful at solving such problems. However, building deep learning models to process the data requires expert knowledge of machine learning. We introduce DELTA, a software toolkit to bridge this technical gap and make deep learning easily accessible to earth scientists. Visual feature engineering is a critical part of the machine learning lifecycle, and hence is a key area that will be automated by DELTA. Hand-engineered features can perform well, but require a cross functional team with expertise in both machine learning and the specific problem domain, which is costly in both researcher time and labor. The problem is more acute with multispectral satellite imagery, which requires considerable computational resources to process. In order to automate the feature learning process, a neural architecture search samples the space of asymmetric and symmetric autoencoders using evolutionary algorithms. Since denoising autoencoders have been shown to perform well for feature learning, the autoencoders are trained on various levels of noise and the features generated by the best performing autoencoders evaluated according to their performance on image classification tasks. The resulting features are demonstrated to be effective for Landsat-8 flood mapping, as well as benchmark datasets CIFAR10 and SVHN.

Robert Campbell