Evolutionary Computing Methods for Spectral Retrieval
NASA Technical Reports Server (NTRS)
Terrile, Richard; Fink, Wolfgang; Huntsberger, Terrance; Lee, Seugwon; Tisdale, Edwin; VonAllmen, Paul; Tinetti, Geivanna
2009-01-01
A methodology for processing spectral images to retrieve information on underlying physical, chemical, and/or biological phenomena is based on evolutionary and related computational methods implemented in software. In a typical case, the solution (the information that one seeks to retrieve) consists of parameters of a mathematical model that represents one or more of the phenomena of interest. The methodology was developed for the initial purpose of retrieving the desired information from spectral image data acquired by remote-sensing instruments aimed at planets (including the Earth). Examples of information desired in such applications include trace gas concentrations, temperature profiles, surface types, day/night fractions, cloud/aerosol fractions, seasons, and viewing angles. The methodology is also potentially useful for retrieving information on chemical and/or biological hazards in terrestrial settings. In this methodology, one utilizes an iterative process that minimizes a fitness function indicative of the degree of dissimilarity between observed and synthetic spectral and angular data. The evolutionary computing methods that lie at the heart of this process yield a population of solutions (sets of the desired parameters) within an accuracy represented by a fitness-function value specified by the user. The evolutionary computing methods (ECM) used in this methodology are Genetic Algorithms and Simulated Annealing, both of which are well-established optimization techniques and have also been described in previous NASA Tech Briefs articles. These are embedded in a conceptual framework, represented in the architecture of the implementing software, that enables automatic retrieval of spectral and angular data and analysis of the retrieved solutions for uniqueness.
Patton, Robert M; Cui, Xiaohui; Jiao, Yu; Potok, Thomas E
2008-01-01
The rate at which information overwhelms humans is significantly more than the rate at which humans have learned to process, analyze, and leverage this information. To overcome this challenge, new methods of computing must be formulated, and scientist and engineers have looked to nature for inspiration in developing these new methods. Consequently, evolutionary computing has emerged as new paradigm for computing, and has rapidly demonstrated its ability to solve real-world problems where traditional techniques have failed. This field of work has now become quite broad and encompasses areas ranging from artificial life to neural networks. This chapter focuses specifically on two sub-areas of nature-inspired computing: Evolutionary Algorithms and Swarm Intelligence.
Evolutionary Computational Methods for Identifying Emergent Behavior in Autonomous Systems
NASA Technical Reports Server (NTRS)
Terrile, Richard J.; Guillaume, Alexandre
2011-01-01
A technique based on Evolutionary Computational Methods (ECMs) was developed that allows for the automated optimization of complex computationally modeled systems, such as autonomous systems. The primary technology, which enables the ECM to find optimal solutions in complex search spaces, derives from evolutionary algorithms such as the genetic algorithm and differential evolution. These methods are based on biological processes, particularly genetics, and define an iterative process that evolves parameter sets into an optimum. Evolutionary computation is a method that operates on a population of existing computational-based engineering models (or simulators) and competes them using biologically inspired genetic operators on large parallel cluster computers. The result is the ability to automatically find design optimizations and trades, and thereby greatly amplify the role of the system engineer.
Evolutionary computational methods to predict oral bioavailability QSPRs.
Bains, William; Gilbert, Richard; Sviridenko, Lilya; Gascon, Jose-Miguel; Scoffin, Robert; Birchall, Kris; Harvey, Inman; Caldwell, John
2002-01-01
This review discusses evolutionary and adaptive methods for predicting oral bioavailability (OB) from chemical structure. Genetic Programming (GP), a specific form of evolutionary computing, is compared with some other advanced computational methods for OB prediction. The results show that classifying drugs into 'high' and 'low' OB classes on the basis of their structure alone is solvable, and initial models are already producing output that would be useful for pharmaceutical research. The results also suggest that quantitative prediction of OB will be tractable. Critical aspects of the solution will involve the use of techniques that can: (i) handle problems with a very large number of variables (high dimensionality); (ii) cope with 'noisy' data; and (iii) implement binary choices to sub-classify molecules with behavior that are qualitatively different. Detailed quantitative predictions will emerge from more refined models that are hybrids derived from mechanistic models of the biology of oral absorption and the power of advanced computing techniques to predict the behavior of the components of those models in silico. PMID:11865672
NASA Astrophysics Data System (ADS)
Piotrowski, Adam P.; Napiorkowski, Jarosław J.
2011-09-01
SummaryAlthough neural networks have been widely applied to various hydrological problems, including river flow forecasting, for at least 15 years, they have usually been trained by means of gradient-based algorithms. Recently nature inspired Evolutionary Computation algorithms have rapidly developed as optimization methods able to cope not only with non-differentiable functions but also with a great number of local minima. Some of proposed Evolutionary Computation algorithms have been tested for neural networks training, but publications which compare their performance with gradient-based training methods are rare and present contradictory conclusions. The main goal of the present study is to verify the applicability of a number of recently developed Evolutionary Computation optimization methods, mostly from the Differential Evolution family, to multi-layer perceptron neural networks training for daily rainfall-runoff forecasting. In the present paper eight Evolutionary Computation methods, namely the first version of Differential Evolution (DE), Distributed DE with Explorative-Exploitative Population Families, Self-Adaptive DE, DE with Global and Local Neighbors, Grouping DE, JADE, Comprehensive Learning Particle Swarm Optimization and Efficient Population Utilization Strategy Particle Swarm Optimization are tested against the Levenberg-Marquardt algorithm - probably the most efficient in terms of speed and success rate among gradient-based methods. The Annapolis River catchment was selected as the area of this study due to its specific climatic conditions, characterized by significant seasonal changes in runoff, rapid floods, dry summers, severe winters with snowfall, snow melting, frequent freeze and thaw, and presence of river ice - conditions which make flow forecasting more troublesome. The overall performance of the Levenberg-Marquardt algorithm and the DE with Global and Local Neighbors method for neural networks training turns out to be superior to other
Algorithmic Mechanism Design of Evolutionary Computation
Pei, Yan
2015-01-01
We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777
Algorithmic Mechanism Design of Evolutionary Computation.
Pei, Yan
2015-01-01
We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777
Statistical Methods for Evolutionary Trees
Edwards, A. W. F.
2009-01-01
In 1963 and 1964, L. L. Cavalli-Sforza and A. W. F. Edwards introduced novel methods for computing evolutionary trees from genetical data, initially for human populations from blood-group gene frequencies. The most important development was their introduction of statistical methods of estimation applied to stochastic models of evolution. PMID:19797062
Evolutionary computation method for pattern recognition of cis-acting sites.
Howard, Daniel; Benson, Karl
2003-11-01
This paper develops an evolutionary method that learns inductively to recognize the makeup and the position of very short consensus sequences, cis-acting sites, which are a typical feature of promoters in genomes. The method combines a Finite State Automata (FSA) and Genetic Programming (GP) to discover candidate promoter sequences in primary sequence data. An experiment measures the success of the method for promoter prediction in the human genome. This class of method can take large base pair jumps and this may enable it to process very long genomic sequences to discover gene specific cis-acting sites, and genes which are regulated together. PMID:14642656
EVOLUTIONARY COMPUTING PROJECT
C. BARRETT; C. REIDYS
2000-09-01
This report summarizes LDRD-funded mathematical research related to computer simulation, inspired in part by combinatorial analysis of sequence to structure relationships of bio-molecules. Computer simulations calculate the interactions among many individual, local entities, thereby generating global dynamics. The objective of this project was to establish a mathematical basis for a comprehensive theory of computer simulations. This mathematical theory is intended to rigorously underwrite very large complex simulations, including simulation of bio- and socio-technical systems. We believe excellent progress has been made. Abstraction of three main ingredients of simulation forms the mathematical setting, called Sequential Dynamical Systems (SDS): (1) functions realized as data-local procedures represent entity state transformations, (2) a graph that expresses locality of the functions and which represents the dependencies among entities, and (3) an ordering, or schedule according to which the entities are evaluated, e.g., up-dated. The research spans algebraic foundations, formal dynamical systems, computer simulation, and theoretical computer science. The theoretical approach is also deeply related to theoretical issues in parallel compilation. Numerous publications were produced, follow-on projects have been identified and are being developed programmatically, and a new area in computational algebra, SDS, was produced.
NASA Astrophysics Data System (ADS)
Hortos, William S.
2011-06-01
Published studies have focused on the application of one bio-inspired or evolutionary computational method to the functions of a single protocol layer in a wireless ad hoc sensor network (WSN). For example, swarm intelligence in the form of ant colony optimization (ACO), has been repeatedly considered for the routing of data/information among nodes, a network-layer function, while genetic algorithms (GAs) have been used to select transmission frequencies and power levels, physical-layer functions. Similarly, artificial immune systems (AISs) as well as trust models of quantized data reputation have been invoked for detection of network intrusions that cause anomalies in data and information; these act on the application and presentation layers. Most recently, a self-organizing scheduling scheme inspired by frog-calling behavior for reliable data transmission in wireless sensor networks, termed anti-phase synchronization, has been applied to realize collision-free transmissions between neighboring nodes, a function of the MAC layer. In a novel departure from previous work, the cross-layer approach to WSN protocol design suggests applying more than one evolutionary computational method to the functions of the appropriate layers to improve the QoS performance of the cross-layer design beyond that of one method applied to a single layer's functions. A baseline WSN protocol design, embedding GAs, anti-phase synchronization, ACO, and a trust model based on quantized data reputation at the physical, MAC, network, and application layers, respectively, is constructed. Simulation results demonstrate the synergies among the bioinspired/ evolutionary methods of the proposed baseline design improve the overall QoS performance of networks over that of a single computational method.
Computational Physics and Evolutionary Dynamics
NASA Astrophysics Data System (ADS)
Fontana, Walter
2000-03-01
One aspect of computational physics deals with the characterization of statistical regularities in materials. Computational physics meets biology when these materials can evolve. RNA molecules are a case in point. The folding of RNA sequences into secondary structures (shapes) inspires a simple biophysically grounded genotype-phenotype map that can be explored computationally and in the laboratory. We have identified some statistical regularities of this map and begin to understand their evolutionary consequences. (1) ``typical shapes'': Only a small subset of shapes realized by the RNA folding map is typical, in the sense of containing shapes that are realized significantly more often than others. Consequence: evolutionary histories mostly involve typical shapes, and thus exhibit generic properties. (2) ``neutral networks'': Sequences folding into the same shape are mutationally connected into a network that reaches across sequence space. Consequence: Evolutionary transitions between shapes reflect the fraction of boundary shared by the corresponding neutral networks in sequence space. The notion of a (dis)continuous transition can be made rigorous. (3) ``shape space covering'': Given a random sequence, a modest number of mutations suffices to reach a sequence realizing any typical shape. Consequence: The effective search space for evolutionary optimization is greatly reduced, and adaptive success is less dependent on initial conditions. (4) ``plasticity mirrors variability'': The repertoire of low energy shapes of a sequence is an indicator of how much and in which ways its energetically optimal shape can be altered by a single point mutation. Consequence: (i) Thermodynamic shape stability and mutational robustness are intimately linked. (ii) When natural selection favors the increase of stability, extreme mutational robustness -- to the point of an evolutionary dead-end -- is produced as a side effect. (iii) The hallmark of robust shapes is modularity.
Scalable computing for evolutionary genomics.
Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert
2012-01-01
Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project
NASA Astrophysics Data System (ADS)
Burman, Jerry A.
1999-12-01
Hyperspectral image sets are three dimensional data volumes that are difficult to exploit by manual means because they are comprised of multiple bands of image data that are not easily visualized or assessed. GTE Government Systems Corporation has developed a system that utilizes Evolutionary Computing techniques to automatically identify materials in terrain hyperspectral imagery. The system employs sophisticated signature preprocessing and a unique combination of non- parametric search algorithms guided by a model based cost function to achieve rapid convergence and pattern recognition. The system is scaleable and is capable of discriminating and identifying pertinent materials that comprise a specific object of interest in the terrain and estimating the percentage of materials present within a pixel of interest (spectral unmixing). The method has been applied and evaluated against real hyperspectral imagery data from the AVIRIS sensor. In addition, the process has been applied to remotely sensed infrared spectra collected at the microscopic level to assess the amounts of DNA, RNA and protein present in human tissue samples as an aid to the early detection of cancer.
Optimizing a reconfigurable material via evolutionary computation
NASA Astrophysics Data System (ADS)
Wilken, Sam; Miskin, Marc Z.; Jaeger, Heinrich M.
2015-08-01
Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6 ×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 1010 possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions.
Optimizing a reconfigurable material via evolutionary computation.
Wilken, Sam; Miskin, Marc Z; Jaeger, Heinrich M
2015-08-01
Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 10^{10} possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions. PMID:26382399
From computers to cultivation: reconceptualizing evolutionary psychology
Barrett, Louise; Pollet, Thomas V.; Stulp, Gert
2014-01-01
Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school) is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific) computational mechanisms, or modules (the massive modularity hypothesis). Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive) represent a true alternative to standard computational approaches, with an emphasis on “cognitive integration” or the “extended mind hypothesis” in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human “mind-making” within an evolutionarily informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach. PMID:25161633
From computers to cultivation: reconceptualizing evolutionary psychology.
Barrett, Louise; Pollet, Thomas V; Stulp, Gert
2014-01-01
Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school) is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific) computational mechanisms, or modules (the massive modularity hypothesis). Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive) represent a true alternative to standard computational approaches, with an emphasis on "cognitive integration" or the "extended mind hypothesis" in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human "mind-making" within an evolutionarily informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach. PMID:25161633
Integrated evolutionary computation neural network quality controller for automated systems
Patro, S.; Kolarik, W.J.
1999-06-01
With increasing competition in the global market, more and more stringent quality standards and specifications are being demands at lower costs. Manufacturing applications of computing power are becoming more common. The application of neural networks to identification and control of dynamic processes has been discussed. The limitations of using neural networks for control purposes has been pointed out and a different technique, evolutionary computation, has been discussed. The results of identifying and controlling an unstable, dynamic process using evolutionary computation methods has been presented. A framework for an integrated system, using both neural networks and evolutionary computation, has been proposed to identify the process and then control the product quality, in a dynamic, multivariable system, in real-time.
Parallel evolutionary computation in bioinformatics applications.
Pinho, Jorge; Sobral, João Luis; Rocha, Miguel
2013-05-01
A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. PMID:23127284
A Bright Future for Evolutionary Methods in Drug Design.
Le, Tu C; Winkler, David A
2015-08-01
Most medicinal chemists understand that chemical space is extremely large, essentially infinite. Although high-throughput experimental methods allow exploration of drug-like space more rapidly, they are still insufficient to fully exploit the opportunities that such large chemical space offers. Evolutionary methods can synergistically blend automated synthesis and characterization methods with computational design to identify promising regions of chemical space more efficiently. We describe how evolutionary methods are implemented, and provide examples of published drug development research in which these methods have generated molecules with increased efficacy. We anticipate that evolutionary methods will play an important role in future drug discovery. PMID:26059362
García, Liliana Torcoroma; Cristancho, Laura Maritza; Vera, Erika Patricia; Begambre, Oscar
2015-10-28
This work describes a new strategy for optimal design of Multiplex-PCR primer sequences. The process is based on the Particle Swarm Optimization-Simplex algorithm (Mult-PSOS). Diverging from previous solutions centered on heuristic tools, the Mult-PSOS is selfconfigured because it does not require the definition of the algorithm's initial search parameters. The successful performance of this method was validated in vitro using Multiplex- PCR assays. For this validation, seven gene sequences of the most prevalent bacteria implicated in urinary tract infections were taken as DNA targets. The in vitro tests confirmed the good performance of the Mult-PSOS, with respect to infectious disease diagnosis, in the rapid and efficient selection of the optimal oligonucleotide sequences for Multiplex-PCRs. The predicted sequences allowed the adequate amplification of all amplicons in a single step (with the correct amount of DNA template and primers), reducing significantly the need for trial and error experiments. In addition, owing to its independence from the initial selection of the heuristic constants, the Mult-PSOS can be employed by non-expert users in computational techniques or in primer design problems. PMID:26059514
NASA Astrophysics Data System (ADS)
Hortos, William S.
2012-06-01
In the author's previous work, a cross-layer protocol approach to wireless sensor network (WSN) intrusion detection an identification is created with multiple bio-inspired/evolutionary computational methods applied to the functions of the protocol layers, a single method to each layer, to improve the intrusion-detection performance of the protocol over that of one method applied to only a single layer's functions. The WSN cross-layer protocol design embeds GAs, anti-phase synchronization, ACO, and a trust model based on quantized data reputation at the physical, MAC, network, and application layer, respectively. The construct neglects to assess the net effect of the combined bioinspired methods on the quality-of-service (QoS) performance for "normal" data streams, that is, streams without intrusions. Analytic expressions of throughput, delay, and jitter, coupled with simulation results for WSNs free of intrusion attacks, are the basis for sensitivity analyses of QoS metrics for normal traffic to the bio-inspired methods.
Evolutionary Computation Applied to the Tuning of MEMS Gyroscopes
NASA Technical Reports Server (NTRS)
Keymeulen, Didier; Fink, Wolfgang; Ferguson, Michael I.; Peay, Chris; Oks, Boris; Terrile, Richard; Yee, Karl
2005-01-01
We propose a tuning method for MEMS gyroscopes based on evolutionary computation to efficiently increase the sensitivity of MEMS gyroscopes through tuning and, furthermore, to find the optimally tuned configuration for this state of increased sensitivity. The tuning method was tested for the second generation JPL/Boeing Post-resonator MEMS gyroscope using the measurement of the frequency response of the MEMS device in open-loop operation.
Using Evolutionary Computation on GPS Position Correction
2014-01-01
More and more devices are equipped with global positioning system (GPS). However, those handheld devices with consumer-grade GPS receivers usually have low accuracy in positioning. A position correction algorithm is therefore useful in this case. In this paper, we proposed an evolutionary computation based technique to generate a correction function by two GPS receivers and a known reference location. Locating one GPS receiver on the known location and combining its longitude and latitude information and exact poisoning information, the proposed technique is capable of evolving a correction function by such. The proposed technique can be implemented and executed on handheld devices without hardware reconfiguration. Experiments are conducted to demonstrate performance of the proposed technique. Positioning error could be significantly reduced from the order of 10 m to the order of 1 m. PMID:24578657
Airlines Network Optimization using Evolutionary Computation
NASA Astrophysics Data System (ADS)
Inoue, Hiroki; Kato, Yasuhiko; Sakagami, Tomoya
In recent years, various networks have come to exist in our surroundings. Not only the internet and airline routes can be thought of as networks: protein interactions are also networks. An “economic network design problem” can be discussed by assuming that a vertex is an economic player and that a link represents some connection between economic players. In this paper, the Airlines network is taken up as an example of an “economic network design problem”, and the Airlines network which the profit of the entire Airlines industry is maximized is clarified. The Airlines network is modeled based on connections models proposed by Jackson and Wolinsky, and the utility function of the network is defined. In addition, the optimization simulation using the evolutionary computation is shown for a domestic airline in Japan.
Development of X-TOOLSS: Preliminary Design of Space Systems Using Evolutionary Computation
NASA Technical Reports Server (NTRS)
Schnell, Andrew R.; Hull, Patrick V.; Turner, Mike L.; Dozier, Gerry; Alverson, Lauren; Garrett, Aaron; Reneau, Jarred
2008-01-01
Evolutionary computational (EC) techniques such as genetic algorithms (GA) have been identified as promising methods to explore the design space of mechanical and electrical systems at the earliest stages of design. In this paper the authors summarize their research in the use of evolutionary computation to develop preliminary designs for various space systems. An evolutionary computational solver developed over the course of the research, X-TOOLSS (Exploration Toolset for the Optimization of Launch and Space Systems) is discussed. With the success of early, low-fidelity example problems, an outline of work involving more computationally complex models is discussed.
Evolutionary Cell Computing: From Protocells to Self-Organized Computing
NASA Technical Reports Server (NTRS)
Colombano, Silvano; New, Michael H.; Pohorille, Andrew; Scargle, Jeffrey; Stassinopoulos, Dimitris; Pearson, Mark; Warren, James
2000-01-01
On the path from inanimate to animate matter, a key step was the self-organization of molecules into protocells - the earliest ancestors of contemporary cells. Studies of the properties of protocells and the mechanisms by which they maintained themselves and reproduced are an important part of astrobiology. These studies also have the potential to greatly impact research in nanotechnology and computer science. Previous studies of protocells have focussed on self-replication. In these systems, Darwinian evolution occurs through a series of small alterations to functional molecules whose identities are stored. Protocells, however, may have been incapable of such storage. We hypothesize that under such conditions, the replication of functions and their interrelationships, rather than the precise identities of the functional molecules, is sufficient for survival and evolution. This process is called non-genomic evolution. Recent breakthroughs in experimental protein chemistry have opened the gates for experimental tests of non-genomic evolution. On the basis of these achievements, we have developed a stochastic model for examining the evolutionary potential of non-genomic systems. In this model, the formation and destruction (hydrolysis) of bonds joining amino acids in proteins occur through catalyzed, albeit possibly inefficient, pathways. Each protein can act as a substrate for polymerization or hydrolysis, or as a catalyst of these chemical reactions. When a protein is hydrolyzed to form two new proteins, or two proteins are joined into a single protein, the catalytic abilities of the product proteins are related to the catalytic abilities of the reactants. We will demonstrate that the catalytic capabilities of such a system can increase. Its evolutionary potential is dependent upon the competition between the formation of bond-forming and bond-cutting catalysts. The degree to which hydrolysis preferentially affects bonds in less efficient, and therefore less well
NASA Astrophysics Data System (ADS)
Christober, C.; Rajan, Asir
2011-01-01
This paper presents a new approach to solve the short-term unit commitment problem using An Evolutionary Programming Based tabu search method with cooling and banking constraints. Numerical results are shown comparing the cost solutions and computation time obtained by using the evolutionary programming method and other conventional methods like dynamic programming, lagrangian relaxation.
Creative Conceptual Design Based on Evolutionary DNA Computing Technique
NASA Astrophysics Data System (ADS)
Liu, Xiyu; Liu, Hong; Zheng, Yangyang
Creative conceptual design is an important area in computer aided innovation. Typical design methodology includes exploration and optimization by evolutionary techniques such as EC and swarm intelligence. Although there are many proposed algorithms and applications for creative design by these techniques, the computing models are implemented mostly by traditional von Neumann’s architecture. On the other hand, the possibility of using DNA as a computing technique arouses wide interests in recent years with huge built-in parallel computing nature and ability to solve NP complete problems. This new computing technique is performed by biological operations on DNA molecules rather than chips. The purpose of this paper is to propose a simulated evolutionary DNA computing model and integrate DNA computing with creative conceptual design. The proposed technique will apply for large scale, high parallel design problems potentially.
Bi-directional evolutionary level set method for topology optimization
NASA Astrophysics Data System (ADS)
Zhu, Benliang; Zhang, Xianmin; Fatikow, Sergej; Wang, Nianfeng
2015-03-01
A bi-directional evolutionary level set method for solving topology optimization problems is presented in this article. The proposed method has three main advantages over the standard level set method. First, new holes can be automatically generated in the design domain during the optimization process. Second, the dependency of the obtained optimized configurations upon the initial configurations is eliminated. Optimized configurations can be obtained even being started from a minimum possible initial guess. Third, the method can be easily implemented and is computationally more efficient. The validity of the proposed method is tested on the mean compliance minimization problem and the compliant mechanisms topology optimization problem.
Topological evolutionary computing in the optimal design of 2D and 3D structures
NASA Astrophysics Data System (ADS)
Burczynski, T.; Poteralski, A.; Szczepanik, M.
2007-10-01
An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.
Protein 3D Structure Computed from Evolutionary Sequence Variation
Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris
2011-01-01
The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein
Studying Collective Human Decision Making and Creativity with Evolutionary Computation.
Sayama, Hiroki; Dionne, Shelley D
2015-01-01
We report a summary of our interdisciplinary research project "Evolutionary Perspective on Collective Decision Making" that was conducted through close collaboration between computational, organizational, and social scientists at Binghamton University. We redefined collective human decision making and creativity as evolution of ecologies of ideas, where populations of ideas evolve via continual applications of evolutionary operators such as reproduction, recombination, mutation, selection, and migration of ideas, each conducted by participating humans. Based on this evolutionary perspective, we generated hypotheses about collective human decision making, using agent-based computer simulations. The hypotheses were then tested through several experiments with real human subjects. Throughout this project, we utilized evolutionary computation (EC) in non-traditional ways-(1) as a theoretical framework for reinterpreting the dynamics of idea generation and selection, (2) as a computational simulation model of collective human decision-making processes, and (3) as a research tool for collecting high-resolution experimental data on actual collaborative design and decision making from human subjects. We believe our work demonstrates untapped potential of EC for interdisciplinary research involving human and social dynamics. PMID:26280078
Computationally mapping sequence space to understand evolutionary protein engineering.
Armstrong, Kathryn A; Tidor, Bruce
2008-01-01
Evolutionary protein engineering has been dramatically successful, producing a wide variety of new proteins with altered stability, binding affinity, and enzymatic activity. However, the success of such procedures is often unreliable, and the impact of the choice of protein, engineering goal, and evolutionary procedure is not well understood. We have created a framework for understanding aspects of the protein engineering process by computationally mapping regions of feasible sequence space for three small proteins using structure-based design protocols. We then tested the ability of different evolutionary search strategies to explore these sequence spaces. The results point to a non-intuitive relationship between the error-prone PCR mutation rate and the number of rounds of replication. The evolutionary relationships among feasible sequences reveal hub-like sequences that serve as particularly fruitful starting sequences for evolutionary search. Moreover, genetic recombination procedures were examined, and tradeoffs relating sequence diversity and search efficiency were identified. This framework allows us to consider the impact of protein structure on the allowed sequence space and therefore on the challenges that each protein presents to error-prone PCR and genetic recombination procedures. PMID:18020358
An evolutionary method to achieve stable superpixel tracking
NASA Astrophysics Data System (ADS)
Xi, Wenxing; Tang, Xinyi
2014-11-01
Object tracking is a hot and hard problem in the computer vision study area.We deal with large objects,which are challenged in many aspects,such as the factors of lighting, size, posture, disturbance, occlusion, and so on.The superpixel tracking method has been proposed to deal with this problem. Unlike many other approaches, it is robust in all the mentioned aspects to some extent. It is very flexible to deal with non-rigid objects just like the meanshift of color histogram does,but can be more advanced, since it takes advantage of the segmented local color histogram. Here we first introduce the adaptive superpixel tracking algorithm, which is comprised by two parts, modeling and confidence mapping using the color features of superpixels.We model them by clustering, just like the "bags of words" method does, and build the cluster confidence.The model is adaptive since it just learns from some latest tracked frames, which can accumulate errors and lead to drift easily. So we propose a refined model, which incorporates the kalman filter's ideas to this problem, by integrating the current model and the new model as an evolutionary one, to better adapt to the object variation and disturbance in subsequent frames, thus achieve more stable tracking. The evolutionary model is achieved by reclustering the cluster centers of the two models, to make new cluster centers and new cluster confidences. We allocate different weight to them, if the current model gets more weight, then the evolutionary model will be more stable, otherwise it will be more adaptive. Finally we give some experiment comparisons between the evolutionary model and the adaptive one. For most cases, when the scene of the object is stable, namely there is no big sudden light change or color change, the evolutionary model outperforms the adaptive one. The reason is that the adaptive one easily learns from other objects. But when the scene suffers big sudden change, the evolutionary model can't quickly adapt
Gene expression: The missing link in evolutionary computation
Kargupta, H.
1997-09-01
This paper points out that the traditional perspective of evolutionary computation may not provide the complete picture of evolutionary search. This paper focuses on gene expression-- transformations of representation (DNA->RNA->Protein) from a the perspective of relation construction. It decomposes the complex process of gene expression into several steps, namely (1) expression control of DNA base pairs, (2) alphabet transformations during transcription and translation, and (3) folding of the proteins from sequence representation to Euclidean space. Each of these steps is investigated on grounds of relation construction and search efficiency. At the end these pieces of the puzzle are put together to develope a possibly crude and cartoon computational description of gene expression.
2014-01-01
Background To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. Results This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Conclusions Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel
Predicting land cover using GIS, Bayesian and evolutionary algorithm methods.
Aitkenhead, M J; Aalders, I H
2009-01-01
Modelling land cover change from existing land cover maps is a vital requirement for anyone wishing to understand how the landscape may change in the future. In order to test any land cover change model, existing data must be used. However, often it is not known which data should be applied to the problem, or whether relationships exist within and between complex datasets. Here we have developed and tested a model that applied evolutionary processes to Bayesian networks. The model was developed and tested on a dataset containing land cover information and environmental data, in order to show that decisions about which datasets should be used could be made automatically. Bayesian networks are amenable to evolutionary methods as they can be easily described using a binary string to which crossover and mutation operations can be applied. The method, developed to allow comparison with standard Bayesian network development software, was proved capable of carrying out a rapid and effective search of the space of possible networks in order to find an optimal or near-optimal solution for the selection of datasets that have causal links with one another. Comparison of land cover mapping in the North-East of Scotland was made with a commercial Bayesian software package, with the evolutionary method being shown to provide greater flexibility in its ability to adapt to incorporate/utilise available evidence/knowledge and develop effective and accurate network structures, at the cost of requiring additional computer programming skills. The dataset used to develop the models included GIS-based data taken from the Land Cover for Scotland 1988 (LCS88), Land Capability for Forestry (LCF), Land Capability for Agriculture (LCA), the soil map of Scotland and additional climatic variables. PMID:18079039
Generative Representations for Computer-Automated Evolutionary Design
NASA Technical Reports Server (NTRS)
Hornby, Gregory S.
2006-01-01
With the increasing computational power of computers, software design systems are progressing from being tools for architects and designers to express their ideas to tools capable of creating designs under human guidance. One of the main limitations for these computer-automated design systems is the representation with which they encode designs. If the representation cannot encode a certain design, then the design system cannot produce it. To be able to produce new types of designs, and not just optimize pre-defined parameterizations, evolutionary design systems must use generative representations. Generative representations are assembly procedures, or algorithms, for constructing a design thereby allowing for truly novel design solutions to be encoded. In addition, by enabling modularity, regularity and hierarchy, the level of sophistication that can be evolved is increased. We demonstrate the advantages of generative representations on two different design domains: the evolution of spacecraft antennas and the evolution of 3D objects.
Tuning of MEMS Devices using Evolutionary Computation and Open-loop Frequency Response
NASA Technical Reports Server (NTRS)
Keymeulen, Didier; Fink, Wolfgang; Ferguson, Michael I.; Peay, Chris; Oks, Boris; Terrile, Richard; Yee, Karl
2005-01-01
We propose a tuning method for MEMS gyroscopes based on evolutionary computation that has the capacity to efficiently increase the sensitivity of MEMS gyroscopes through tuning and, furthermore, to find the optimally tuned configuration for this state of increased sensitivity. The tuning method was tested for the second generation JPL/Boeing Post-resonator MEMS gyroscope using the measurement of the frequency response of the MEMS device in open-loop operation.
Supporting Air-Conditioning Controller Design Using Evolutionary Computation
NASA Astrophysics Data System (ADS)
Kojima, Kazuyuki; Watanuki, Keiichi
In recent years, as part of the remarkable development of electronic techniques, electronic control has been applied to various systems. Many sensors and actuators have been implemented into those systems, and energy efficiency and performance have been greatly improved. However, these systems have been complicated, and much time has been required to develop system controllers. In this paper, a method of automatic controller design for those systems is described. In order to automate the design of an electronic controller, an evolutionary hardware is applied. First, the framework for applying the genetic algorithm to the automation of controller design is described. In particular, the coding of a chromosome is shown in detail. Then, how to make a fitness function is represented, with an air conditioner as an example, and the controller of the air conditioner is developed automatically using our proposed framework. Finally, an evolutionary simulation is performed to confirm our framework.
Evolutionary Computation for the Identification of Emergent Behavior in Autonomous Systems
NASA Technical Reports Server (NTRS)
Terrile, Richard J.; Guillaume, Alexandre
2009-01-01
Over the past several years the Center for Evolutionary Computation and Automated Design at the Jet Propulsion Laboratory has developed a technique based on Evolutionary Computational Methods (ECM) that allows for the automated optimization of complex computationally modeled systems. An important application of this technique is for the identification of emergent behaviors in autonomous systems. Mobility platforms such as rovers or airborne vehicles are now being designed with autonomous mission controllers that can find trajectories over a solution space that is larger than can reasonably be tested. It is critical to identify control behaviors that are not predicted and can have surprising results (both good and bad). These emergent behaviors need to be identified, characterized and either incorporated into or isolated from the acceptable range of control characteristics. We use cluster analysis of automatically retrieved solutions to identify isolated populations of solutions with divergent behaviors.
Computational complexity of ecological and evolutionary spatial dynamics
Ibsen-Jensen, Rasmus; Chatterjee, Krishnendu; Nowak, Martin A.
2015-01-01
There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP). PMID:26644569
Computational complexity of ecological and evolutionary spatial dynamics.
Ibsen-Jensen, Rasmus; Chatterjee, Krishnendu; Nowak, Martin A
2015-12-22
There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP). PMID:26644569
Evolutionary adaptive eye tracking for low-cost human computer interaction applications
NASA Astrophysics Data System (ADS)
Shen, Yan; Shin, Hak Chul; Sung, Won Jun; Khim, Sarang; Kim, Honglak; Rhee, Phill Kyu
2013-01-01
We present an evolutionary adaptive eye-tracking framework aiming for low-cost human computer interaction. The main focus is to guarantee eye-tracking performance without using high-cost devices and strongly controlled situations. The performance optimization of eye tracking is formulated into the dynamic control problem of deciding on an eye tracking algorithm structure and associated thresholds/parameters, where the dynamic control space is denoted by genotype and phenotype spaces. The evolutionary algorithm is responsible for exploring the genotype control space, and the reinforcement learning algorithm organizes the evolved genotype into a reactive phenotype. The evolutionary algorithm encodes an eye-tracking scheme as a genetic code based on image variation analysis. Then, the reinforcement learning algorithm defines internal states in a phenotype control space limited by the perceived genetic code and carries out interactive adaptations. The proposed method can achieve optimal performance by compromising the difficulty in the real-time performance of the evolutionary algorithm and the drawback of the huge search space of the reinforcement learning algorithm. Extensive experiments were carried out using webcam image sequences and yielded very encouraging results. The framework can be readily applied to other low-cost vision-based human computer interactions in solving their intrinsic brittleness in unstable operational environments.
Kernel Method Based Human Model for Enhancing Interactive Evolutionary Optimization
Zhao, Qiangfu; Liu, Yong
2015-01-01
A fitness landscape presents the relationship between individual and its reproductive success in evolutionary computation (EC). However, discrete and approximate landscape in an original search space may not support enough and accurate information for EC search, especially in interactive EC (IEC). The fitness landscape of human subjective evaluation in IEC is very difficult and impossible to model, even with a hypothesis of what its definition might be. In this paper, we propose a method to establish a human model in projected high dimensional search space by kernel classification for enhancing IEC search. Because bivalent logic is a simplest perceptual paradigm, the human model is established by considering this paradigm principle. In feature space, we design a linear classifier as a human model to obtain user preference knowledge, which cannot be supported linearly in original discrete search space. The human model is established by this method for predicting potential perceptual knowledge of human. With the human model, we design an evolution control method to enhance IEC search. From experimental evaluation results with a pseudo-IEC user, our proposed model and method can enhance IEC search significantly. PMID:25879050
Crowd Computing as a Cooperation Problem: An Evolutionary Approach
NASA Astrophysics Data System (ADS)
Christoforou, Evgenia; Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Sánchez, Angel
2013-05-01
Cooperation is one of the socio-economic issues that has received more attention from the physics community. The problem has been mostly considered by studying games such as the Prisoner's Dilemma or the Public Goods Game. Here, we take a step forward by studying cooperation in the context of crowd computing. We introduce a model loosely based on Principal-agent theory in which people (workers) contribute to the solution of a distributed problem by computing answers and reporting to the problem proposer (master). To go beyond classical approaches involving the concept of Nash equilibrium, we work on an evolutionary framework in which both the master and the workers update their behavior through reinforcement learning. Using a Markov chain approach, we show theoretically that under certain----not very restrictive—conditions, the master can ensure the reliability of the answer resulting of the process. Then, we study the model by numerical simulations, finding that convergence, meaning that the system reaches a point in which it always produces reliable answers, may in general be much faster than the upper bounds given by the theoretical calculation. We also discuss the effects of the master's level of tolerance to defectors, about which the theory does not provide information. The discussion shows that the system works even with very large tolerances. We conclude with a discussion of our results and possible directions to carry this research further.
Exploring Evolutionary Patterns in Genetic Sequence: A Computer Exercise
ERIC Educational Resources Information Center
Shumate, Alice M.; Windsor, Aaron J.
2010-01-01
The increase in publications presenting molecular evolutionary analyses and the availability of comparative sequence data through resources such as NCBI's GenBank underscore the necessity of providing undergraduates with hands-on sequence analysis skills in an evolutionary context. This need is particularly acute given that students have been…
Visser, Marco D.; McMahon, Sean M.; Merow, Cory; Dixon, Philip M.; Record, Sydne; Jongejans, Eelke
2015-01-01
Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research. PMID:25811842
An Evolutionary Computation Approach to Examine Functional Brain Plasticity.
Roy, Arnab; Campbell, Colin; Bernier, Rachel A; Hillary, Frank G
2016-01-01
One common research goal in systems neurosciences is to understand how the functional relationship between a pair of regions of interest (ROIs) evolves over time. Examining neural connectivity in this way is well-suited for the study of developmental processes, learning, and even in recovery or treatment designs in response to injury. For most fMRI based studies, the strength of the functional relationship between two ROIs is defined as the correlation between the average signal representing each region. The drawback to this approach is that much information is lost due to averaging heterogeneous voxels, and therefore, the functional relationship between a ROI-pair that evolve at a spatial scale much finer than the ROIs remain undetected. To address this shortcoming, we introduce a novel evolutionary computation (EC) based voxel-level procedure to examine functional plasticity between an investigator defined ROI-pair by simultaneously using subject-specific BOLD-fMRI data collected from two sessions seperated by finite duration of time. This data-driven procedure detects a sub-region composed of spatially connected voxels from each ROI (a so-called sub-regional-pair) such that the pair shows a significant gain/loss of functional relationship strength across the two time points. The procedure is recursive and iteratively finds all statistically significant sub-regional-pairs within the ROIs. Using this approach, we examine functional plasticity between the default mode network (DMN) and the executive control network (ECN) during recovery from traumatic brain injury (TBI); the study includes 14 TBI and 12 healthy control subjects. We demonstrate that the EC based procedure is able to detect functional plasticity where a traditional averaging based approach fails. The subject-specific plasticity estimates obtained using the EC-procedure are highly consistent across multiple runs. Group-level analyses using these plasticity estimates showed an increase in the strength
An Evolutionary Computation Approach to Examine Functional Brain Plasticity
Roy, Arnab; Campbell, Colin; Bernier, Rachel A.; Hillary, Frank G.
2016-01-01
One common research goal in systems neurosciences is to understand how the functional relationship between a pair of regions of interest (ROIs) evolves over time. Examining neural connectivity in this way is well-suited for the study of developmental processes, learning, and even in recovery or treatment designs in response to injury. For most fMRI based studies, the strength of the functional relationship between two ROIs is defined as the correlation between the average signal representing each region. The drawback to this approach is that much information is lost due to averaging heterogeneous voxels, and therefore, the functional relationship between a ROI-pair that evolve at a spatial scale much finer than the ROIs remain undetected. To address this shortcoming, we introduce a novel evolutionary computation (EC) based voxel-level procedure to examine functional plasticity between an investigator defined ROI-pair by simultaneously using subject-specific BOLD-fMRI data collected from two sessions seperated by finite duration of time. This data-driven procedure detects a sub-region composed of spatially connected voxels from each ROI (a so-called sub-regional-pair) such that the pair shows a significant gain/loss of functional relationship strength across the two time points. The procedure is recursive and iteratively finds all statistically significant sub-regional-pairs within the ROIs. Using this approach, we examine functional plasticity between the default mode network (DMN) and the executive control network (ECN) during recovery from traumatic brain injury (TBI); the study includes 14 TBI and 12 healthy control subjects. We demonstrate that the EC based procedure is able to detect functional plasticity where a traditional averaging based approach fails. The subject-specific plasticity estimates obtained using the EC-procedure are highly consistent across multiple runs. Group-level analyses using these plasticity estimates showed an increase in the strength
De-Hazing of Multi-Spectral Images with Evolutionary Computing
NASA Astrophysics Data System (ADS)
von Allmen, P.; Lee, S.; Diner, D. J.; Martonchik, J.; Davis, A. B.
2009-12-01
We developed an algorithm that allows for removing haze from a digital picture by numerically subtracting the contribution of optical scattering by aerosols. The scene is modeled by defining a reflectance function for each pixel, which describes the angular dependence of light scattering at the surface, and by describing the scattering from aerosols with a set of models of varying complexity. An optimization algorithm that mixes downhill methods with evolutionary computing approaches was used to fit the observed image to the model of the scene. The contribution of the aerosol scattering is then removed to obtain a de-hazed image. We will present results for multispectral images taken by NASA’s Multi-angle Imaging SpectroRadiometer and we will discuss the numerical efficiency of the algorithm implemented on a multi-node quadcore cluster computer.
Proposal of Evolutionary Simplex Method for Global Optimization Problem
NASA Astrophysics Data System (ADS)
Shimizu, Yoshiaki
To make an agile decision in a rational manner, role of optimization engineering has been notified increasingly under diversified customer demand. With this point of view, in this paper, we have proposed a new evolutionary method serving as an optimization technique in the paradigm of optimization engineering. The developed method has prospects to solve globally various complicated problem appearing in real world applications. It is evolved from the conventional method known as Nelder and Mead’s Simplex method by virtue of idea borrowed from recent meta-heuristic method such as PSO. Mentioning an algorithm to handle linear inequality constraints effectively, we have validated effectiveness of the proposed method through comparison with other methods using several benchmark problems.
Computational Methods for Crashworthiness
NASA Technical Reports Server (NTRS)
Noor, Ahmed K. (Compiler); Carden, Huey D. (Compiler)
1993-01-01
Presentations and discussions from the joint UVA/NASA Workshop on Computational Methods for Crashworthiness held at Langley Research Center on 2-3 Sep. 1992 are included. The presentations addressed activities in the area of impact dynamics. Workshop attendees represented NASA, the Army and Air Force, the Lawrence Livermore and Sandia National Laboratories, the aircraft and automotive industries, and academia. The workshop objectives were to assess the state-of-technology in the numerical simulation of crash and to provide guidelines for future research.
Barrett, Nathaniel F
2010-01-01
Cognitive science of the last half-century has been dominated by the computational theory of mind and its picture of thought as information processing. Taking this picture for granted, the most prominent evolutionary theories of religion of the last fifteen years have sought to understand human religiosity as the product or by-product of universal information processing mechanisms that were adaptive in our ancestral environment. The rigidity of such explanations is at odds with the highly context-sensitive nature of historical studies of religion, and thus contributes to the apparent tug-of-war between scientific and humanistic perspectives. This essay argues that this antagonism stems in part from a deep flaw of computational theory, namely its notion of information as pre-given and context-free. In contrast, non-computational theories that picture mind as an adaptive, interactive process in which information is jointly constructed by organism and environment offer an alternative approach to an evolutionary understanding of human religiosity, one that is compatible with historical studies and amenable to a wide range of inquiries, including some limited kinds of theological inquiry. PMID:20879191
A novel fitness evaluation method for evolutionary algorithms
NASA Astrophysics Data System (ADS)
Wang, Ji-feng; Tang, Ke-zong
2013-03-01
Fitness evaluation is a crucial task in evolutionary algorithms because it can affect the convergence speed and also the quality of the final solution. But these algorithms may require huge computation power for solving nonlinear programming problems. This paper proposes a novel fitness evaluation approach which employs similarity-base learning embedded in a classical differential evolution (SDE) to evaluate all new individuals. Each individual consists of three elements: parameter vector (v), a fitness value (f), and a reliability value(r). The f is calculated using NFEA, and only when the r is below a threshold is the f calculated using true fitness function. Moreover, applying error compensation system to the proposed algorithm further enhances the performance of the algorithm to make r much closer to true fitness value for each new child. Simulation results over a comprehensive set of benchmark functions show that the convergence rate of the proposed algorithm is much faster than much that of the compared algorithms.
Bi-Directional Evolutionary Topology Optimization Using Element Replaceable Method
NASA Astrophysics Data System (ADS)
Zhu, J. H.; Zhang, W. H.; Qiu, K. P.
2007-06-01
In the present paper, design problems of maximizing the structural stiffness or natural frequency are considered subject to the material volume constraint. A new element replaceable method (ERPM) is proposed for evolutionary topology optimization of structures. Compared with existing versions of evolutionary structural optimization methods, contributions are twofold. On the one hand, a new automatic element deletion/growth procedure is established. The deletion of a finite element means that a solid element is replaced with an orthotropic cellular microstructure (OCM) element. The growth of an element means that an OCM element is replaced with a solid element of full materials. In fact, both operations are interchangeable depending upon how the value of element sensitivity is with respect to the objective function. The OCM design strategy is beneficial in preventing artificial modes for dynamic problems. Besides, the iteration validity is greatly improved with the introduction of a check position (CP) technique. On the other hand, a new checkerboard control algorithm is proposed to work together with the above procedure. After the identification of local checkerboards and detailed structures over the entire design domain, the algorithm will fill or delete elements depending upon the prescribed threshold of sensitivity values. Numerical results show that the ERPM is efficient and a clear and valuable material pattern can be achieved for both static and dynamic problems.
NASA Astrophysics Data System (ADS)
Rao, Dhananjai M.; Chernyakhovsky, Alexander; Rao, Victoria
2008-05-01
Humanity is facing an increasing number of highly virulent and communicable diseases such as avian influenza. Researchers believe that avian influenza has potential to evolve into one of the deadliest pandemics. Combating these diseases requires in-depth knowledge of their epidemiology. An effective methodology for discovering epidemiological knowledge is to utilize a descriptive, evolutionary, ecological model and use bio-simulations to study and analyze it. These types of bio-simulations fall under the category of computational evolutionary methods because the individual entities participating in the simulation are permitted to evolve in a natural manner by reacting to changes in the simulated ecosystem. This work describes the application of the aforementioned methodology to discover epidemiological knowledge about avian influenza using a novel eco-modeling and bio-simulation environment called SEARUMS. The mathematical principles underlying SEARUMS, its design, and the procedure for using SEARUMS are discussed. The bio-simulations and multi-faceted case studies conducted using SEARUMS elucidate its ability to pinpoint timelines, epicenters, and socio-economic impacts of avian influenza. This knowledge is invaluable for proactive deployment of countermeasures in order to minimize negative socioeconomic impacts, combat the disease, and avert a pandemic.
Rao, Dhananjai M.; Chernyakhovsky, Alexander; Rao, Victoria
2008-05-08
Humanity is facing an increasing number of highly virulent and communicable diseases such as avian influenza. Researchers believe that avian influenza has potential to evolve into one of the deadliest pandemics. Combating these diseases requires in-depth knowledge of their epidemiology. An effective methodology for discovering epidemiological knowledge is to utilize a descriptive, evolutionary, ecological model and use bio-simulations to study and analyze it. These types of bio-simulations fall under the category of computational evolutionary methods because the individual entities participating in the simulation are permitted to evolve in a natural manner by reacting to changes in the simulated ecosystem. This work describes the application of the aforementioned methodology to discover epidemiological knowledge about avian influenza using a novel eco-modeling and bio-simulation environment called SEARUMS. The mathematical principles underlying SEARUMS, its design, and the procedure for using SEARUMS are discussed. The bio-simulations and multi-faceted case studies conducted using SEARUMS elucidate its ability to pinpoint timelines, epicenters, and socio-economic impacts of avian influenza. This knowledge is invaluable for proactive deployment of countermeasures in order to minimize negative socioeconomic impacts, combat the disease, and avert a pandemic.
Tuning of MEMS Gyroscope using Evolutionary Algorithm and "Switched Drive-Angle" Method
NASA Technical Reports Server (NTRS)
Keymeulen, Didier; Ferguson, Michael I.; Breuer, Luke; Peay, Chris; Oks, Boris; Cheng, Yen; Kim, Dennis; MacDonald, Eric; Foor, David; Terrile, Rich; Yee, Karl
2006-01-01
We propose a tuning method for Micro-Electro-Mechanical Systems (MEMS) gyroscopes based on evolutionary computation that has the capacity to efficiently increase the sensitivity of MEMS gyroscopes through tuning and, furthermore, to find the optimally tuned configuration for this state of increased sensitivity. We present the results of an experiment to determine the speed and efficiency of an evolutionary algorithm applied to electrostatic tuning of MEMS micro gyros. The MEMS gyro used in this experiment is a pyrex post resonator gyro (PRG) in a closed-loop control system. A measure of the quality of tuning is given by the difference in resonant frequencies, or frequency split, for the two orthogonal rocking axes. The current implementation of the closed-loop platform is able to measure and attain a relative stability in the sub-millihertz range, leading to a reduction of the frequency split to less than 100 mHz.
Supervised and unsupervised discretization methods for evolutionary algorithms
Cantu-Paz, E
2001-01-24
This paper introduces simple model-building evolutionary algorithms (EAs) that operate on continuous domains. The algorithms are based on supervised and unsupervised discretization methods that have been used as preprocessing steps in machine learning. The basic idea is to discretize the continuous variables and use the discretization as a simple model of the solutions under consideration. The model is then used to generate new solutions directly, instead of using the usual operators based on sexual recombination and mutation. The algorithms presented here have fewer parameters than traditional and other model-building EAs. They expect that the proposed algorithms that use multivariate models scale up better to the dimensionality of the problem than existing EAs.
Scalable Evolutionary Computation for Efficient Information Extraction from Remote Sensed Imagery
NASA Astrophysics Data System (ADS)
Almutairi, L. M.; Shetty, S.; Momm, H. G.
2014-11-01
Evolutionary computation, in the form of genetic programming, is used to aid information extraction process from high-resolution satellite imagery in a semi-automatic fashion. Distributing and parallelizing the task of evaluating all candidate solutions during the evolutionary process could significantly reduce the inherent computational cost of evolving solutions that are composed of multichannel large images. In this study, we present the design and implementation of a system that leverages cloud-computing technology to expedite supervised solution development in a centralized evolutionary framework. The system uses the MapReduce programming model to implement a distributed version of the existing framework in a cloud-computing platform. The proposed system has two major subsystems; (i) data preparation: the generation of random spectral indices; and (ii) distributed processing: the distributed implementation of genetic programming, which is used to spectrally distinguish the features of interest from the remaining image background in the cloud computing environment in order to improve scalability. The proposed system reduces response time by leveraging the vast computational and storage resources in a cloud computing environment. The results demonstrate that distributing the candidate solutions reduces the execution time by 91.58%. These findings indicate that such technology could be applied to more complex problems that involve a larger population size and number of generations.
Learning Evolution and the Nature of Science Using Evolutionary Computing and Artificial Life
ERIC Educational Resources Information Center
Pennock, Robert T.
2007-01-01
Because evolution in natural systems happens so slowly, it is difficult to design inquiry-based labs where students can experiment and observe evolution in the way they can when studying other phenomena. New research in evolutionary computation and artificial life provides a solution to this problem. This paper describes a new A-Life software…
Evolutionary computing for the design search and optimization of space vehicle power subsystems
NASA Technical Reports Server (NTRS)
Kordon, M.; Klimeck, G.; Hanks, D.
2004-01-01
Evolutionary computing has proven to be a straightforward and robust approach for optimizing a wide range of difficult analysis and design problems. This paper discusses the application of these techniques to an existing space vehicle power subsystem resource and performance analysis simulation in a parallel processing environment.
On computational methods for crashworthiness
NASA Technical Reports Server (NTRS)
Belytschko, T.
1992-01-01
The evolution of computational methods for crashworthiness and related fields is described and linked with the decreasing cost of computational resources and with improvements in computation methodologies. The latter includes more effective time integration procedures and more efficient elements. Some recent developments in methodologies and future trends are also summarized. These include multi-time step integration (or subcycling), further improvements in elements, adaptive meshes, and the exploitation of parallel computers.
Nguyen, Thi-Hau; Ranwez, Vincent; Berry, Vincent; Scornavacca, Celine
2013-01-01
The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree-gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations. PMID:24124449
Nguyen, Thi-Hau; Ranwez, Vincent; Berry, Vincent; Scornavacca, Celine
2013-01-01
The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree–gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations. PMID:24124449
Wayne F. Boyer; Gurdeep S. Hura
2005-09-01
The Problem of obtaining an optimal matching and scheduling of interdependent tasks in distributed heterogeneous computing (DHC) environments is well known to be an NP-hard problem. In a DHC system, task execution time is dependent on the machine to which it is assigned and task precedence constraints are represented by a directed acyclic graph. Recent research in evolutionary techniques has shown that genetic algorithms usually obtain more efficient schedules that other known algorithms. We propose a non-evolutionary random scheduling (RS) algorithm for efficient matching and scheduling of inter-dependent tasks in a DHC system. RS is a succession of randomized task orderings and a heuristic mapping from task order to schedule. Randomized task ordering is effectively a topological sort where the outcome may be any possible task order for which the task precedent constraints are maintained. A detailed comparison to existing evolutionary techniques (GA and PSGA) shows the proposed algorithm is less complex than evolutionary techniques, computes schedules in less time, requires less memory and fewer tuning parameters. Simulation results show that the average schedules produced by RS are approximately as efficient as PSGA schedules for all cases studied and clearly more efficient than PSGA for certain cases. The standard formulation for the scheduling problem addressed in this paper is Rm|prec|Cmax.,
Evolutionary method for finding communities in bipartite networks
NASA Astrophysics Data System (ADS)
Zhan, Weihua; Zhang, Zhongzhi; Guan, Jihong; Zhou, Shuigeng
2011-06-01
An important step in unveiling the relation between network structure and dynamics defined on networks is to detect communities, and numerous methods have been developed separately to identify community structure in different classes of networks, such as unipartite networks, bipartite networks, and directed networks. Here, we show that the finding of communities in such networks can be unified in a general framework—detection of community structure in bipartite networks. Moreover, we propose an evolutionary method for efficiently identifying communities in bipartite networks. To this end, we show that both unipartite and directed networks can be represented as bipartite networks, and their modularity is completely consistent with that for bipartite networks, the detection of modular structure on which can be reformulated as modularity maximization. To optimize the bipartite modularity, we develop a modified adaptive genetic algorithm (MAGA), which is shown to be especially efficient for community structure detection. The high efficiency of the MAGA is based on the following three improvements we make. First, we introduce a different measure for the informativeness of a locus instead of the standard deviation, which can exactly determine which loci mutate. This measure is the bias between the distribution of a locus over the current population and the uniform distribution of the locus, i.e., the Kullback-Leibler divergence between them. Second, we develop a reassignment technique for differentiating the informative state a locus has attained from the random state in the initial phase. Third, we present a modified mutation rule which by incorporating related operations can guarantee the convergence of the MAGA to the global optimum and can speed up the convergence process. Experimental results show that the MAGA outperforms existing methods in terms of modularity for both bipartite and unipartite networks.
NASA Astrophysics Data System (ADS)
Shahrokhi, Ava; Jahangirian, Alireza
2010-06-01
A multi-layer perceptron neural network (NN) method is used for efficient estimation of the expensive objective functions in the evolutionary optimization with the genetic algorithm (GA). The estimation capability of the NN is improved by dynamic retraining using the data from successive generations. In addition, the normal distribution of the training data variables is used to determine well-trained parts of the design space for the NN approximation. The efficiency of the method is demonstrated by two transonic airfoil design problems considering inviscid and viscous flow solvers. Results are compared with those of the simple GA and an alternative surrogate method. The total number of flow solver calls is reduced by about 40% using this fitness approximation technique, which in turn reduces the total computational time without influencing the convergence rate of the optimization algorithm. The accuracy of the NN estimation is considerably improved using the normal distribution approach compared with the alternative method.
Spirov, Alexander; Holloway, David
2013-01-01
This paper surveys modeling approaches for studying the evolution of gene regulatory networks (GRNs). Modeling of the design or ‘wiring’ of GRNs has become increasingly common in developmental and medical biology, as a means of quantifying gene-gene interactions, the response to perturbations, and the overall dynamic motifs of networks. Drawing from developments in GRN ‘design’ modeling, a number of groups are now using simulations to study how GRNs evolve, both for comparative genomics and to uncover general principles of evolutionary processes. Such work can generally be termed evolution in silico. Complementary to these biologically-focused approaches, a now well-established field of computer science is Evolutionary Computations (EC), in which highly efficient optimization techniques are inspired from evolutionary principles. In surveying biological simulation approaches, we discuss the considerations that must be taken with respect to: a) the precision and completeness of the data (e.g. are the simulations for very close matches to anatomical data, or are they for more general exploration of evolutionary principles); b) the level of detail to model (we proceed from ‘coarse-grained’ evolution of simple gene-gene interactions to ‘fine-grained’ evolution at the DNA sequence level); c) to what degree is it important to include the genome’s cellular context; and d) the efficiency of computation. With respect to the latter, we argue that developments in computer science EC offer the means to perform more complete simulation searches, and will lead to more comprehensive biological predictions. PMID:23726941
Peptide design by artificial neural networks and computer-based evolutionary search
Schneider, Gisbert; Schrödl, Wieland; Wallukat, Gerd; Müller, Johannes; Nissen, Eberhard; Rönspeck, Wolfgang; Wrede, Paul; Kunze, Rudolf
1998-01-01
A technique for systematic peptide variation by a combination of rational and evolutionary approaches is presented. The design scheme consists of five consecutive steps: (i) identification of a “seed peptide” with a desired activity, (ii) generation of variants selected from a physicochemical space around the seed peptide, (iii) synthesis and testing of this biased library, (iv) modeling of a quantitative sequence-activity relationship by an artificial neural network, and (v) de novo design by a computer-based evolutionary search in sequence space using the trained neural network as the fitness function. This strategy was successfully applied to the identification of novel peptides that fully prevent the positive chronotropic effect of anti-β1-adrenoreceptor autoantibodies from the serum of patients with dilated cardiomyopathy. The seed peptide, comprising 10 residues, was derived by epitope mapping from an extracellular loop of human β1-adrenoreceptor. A set of 90 peptides was synthesized and tested to provide training data for neural network development. De novo design revealed peptides with desired activities that do not match the seed peptide sequence. These results demonstrate that computer-based evolutionary searches can generate novel peptides with substantial biological activity. PMID:9770460
Spirov, Alexander V; Holloway, David M
2010-05-01
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolutionary computations is proposed. The approach is based on Genetic Algorithms (GA), with new crossover operators especially designed for these purposes. The new operators use local homology between parental strings to preserve building blocks found by the algorithm. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. This architecture is significant for Royal Road class fitness functions. Two real-life Systems Biology problems with such fitness functions are implemented here: evolution of the bacterial promoter rrnPl and of the enhancer of the Drosophila even-skipped gene. The effectiveness of the approach compared to standard GA is demonstrated on several benchmark and real-life tasks. PMID:20930945
Spirov, Alexander V.; Holloway, David M.
2010-01-01
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolutionary computations is proposed. The approach is based on Genetic Algorithms (GA), with new crossover operators especially designed for these purposes. The new operators use local homology between parental strings to preserve building blocks found by the algorithm. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. This architecture is significant for Royal Road class fitness functions. Two real-life Systems Biology problems with such fitness functions are implemented here: evolution of the bacterial promoter rrnPl and of the enhancer of the Drosophila even-skipped gene. The effectiveness of the approach compared to standard GA is demonstrated on several benchmark and real-life tasks. PMID:20930945
Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.
Pérez-Losada, Marcos; Arenas, Miguel; Galán, Juan Carlos; Palero, Ferran; González-Candelas, Fernando
2015-03-01
Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure. PMID:25541518
Computational Methods Development at Ames
NASA Technical Reports Server (NTRS)
Kwak, Dochan; Smith, Charles A. (Technical Monitor)
1998-01-01
This viewgraph presentation outlines the development at Ames Research Center of advanced computational methods to provide appropriate fidelity computational analysis/design capabilities. Current thrusts of the Ames research include: 1) methods to enhance/accelerate viscous flow simulation procedures, and the development of hybrid/polyhedral-grid procedures for viscous flow; 2) the development of real time transonic flow simulation procedures for a production wind tunnel, and intelligent data management technology; and 3) the validation of methods and the flow physics study gives historical precedents to above research, and speculates on its future course.
Computational Methods For Composite Structures
NASA Technical Reports Server (NTRS)
Chamis, Christos C.
1988-01-01
Selected methods of computation for simulation of mechanical behavior of fiber/matrix composite materials described in report. For each method, report describes significance of behavior to be simulated, procedure for simulation, and representative results. Following applications discussed: effects of progressive degradation of interply layers on responses of composite structures, dynamic responses of notched and unnotched specimens, interlaminar fracture toughness, progressive fracture, thermal distortions of sandwich composite structure, and metal-matrix composite structures for use at high temperatures. Methods demonstrate effectiveness of computational simulation as applied to complex composite structures in general and aerospace-propulsion structural components in particular.
Computational Methods in Drug Discovery
Sliwoski, Gregory; Kothiwale, Sandeepkumar; Meiler, Jens
2014-01-01
Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature. PMID:24381236
Computational Modeling Method for Superalloys
NASA Technical Reports Server (NTRS)
Bozzolo, Guillermo; Noebe, Ronald D.; Gayda, John
1997-01-01
Computer modeling based on theoretical quantum techniques has been largely inefficient due to limitations on the methods or the computer needs associated with such calculations, thus perpetuating the notion that little help can be expected from computer simulations for the atomistic design of new materials. In a major effort to overcome these limitations and to provide a tool for efficiently assisting in the development of new alloys, we developed the BFS method for alloys, which together with the experimental results from previous and current research that validate its use for large-scale simulations, provide the ideal grounds for developing a computationally economical and physically sound procedure for supplementing the experimental work at great cost and time savings.
Evolutionary computing for the design search and optimization of space vehicle power subsystems
NASA Technical Reports Server (NTRS)
Kordon, Mark; Klimeck, Gerhard; Hanks, David; Hua, Hook
2004-01-01
Evolutionary computing has proven to be a straightforward and robust approach for optimizing a wide range of difficult analysis and design problems. This paper discusses the application of these techniques to an existing space vehicle power subsystem resource and performance analysis simulation in a parallel processing environment. Out preliminary results demonstrate that this approach has the potential to improve the space system trade study process by allowing engineers to statistically weight subsystem goals of mass, cost and performance then automatically size power elements based on anticipated performance of the subsystem rather than on worst-case estimates.
NASA Astrophysics Data System (ADS)
MacDonald, Ronald Douglas
The primary goal of this study was to explore how the use of a computer simulation of basic evolutionary processes, in combination with small-group discussions, affected Intermediate/Senior pre-service science teachers' perspectives of basic evolutionary concepts. Qualitative and quantitative methods were used in a case study approach with 19 pre-service Intermediate/Senior science teachers at an Ontario university. Several sub-goals were explored. The first sub-goal was to assess Intermediate/Senior pre-service science teachers' current conceptions of evolution. The results indicated that approximately two-thirds of the participants had a poor understanding of basic evolutionary concepts, with only 2 of the 19 participants demonstrating a strong comprehension. These results were found to be very similar to comparable samples of subjects from other research. The second sub-goal was to explore the relationships among Intermediate/Senior pre-service science teachers' understanding of contemporary evolutionary concepts, their perspectives of the nature of science, and their intentions to teach evolutionary concepts in the classroom. Participants' knowledge of evolutionary concepts was found to be associated strongly with their intentions to teach evolution by natural selection (r = .42). However, knowledge of evolutionary concepts was not found to be associated with any particular science epistemology perspective. The third sub-goal was to analyze and to interpret the small-group discussions as members interacted with the simulation. The simulation was found to be highly engaging and a very effective method of encouraging participants to speculate, question, discuss and learn about important evolutionary concepts. Analyses of the discussions revealed that the simulation evoked a wide array of correct conceptions as well as misconceptions. The fourth sub-goal was to assess the extent to which creating a lesson plan on the topic of natural selection could affect
NASA Technical Reports Server (NTRS)
Keymeulen, Didier; Ferguson, Michael I.; Fink, Wolfgang; Oks, Boris; Peay, Chris; Terrile, Richard; Cheng, Yen; Kim, Dennis; MacDonald, Eric; Foor, David
2005-01-01
We propose a tuning method for MEMS gyroscopes based on evolutionary computation to efficiently increase the sensitivity of MEMS gyroscopes through tuning. The tuning method was tested for the second generation JPL/Boeing Post-resonator MEMS gyroscope using the measurement of the frequency response of the MEMS device in open-loop operation. We also report on the development of a hardware platform for integrated tuning and closed loop operation of MEMS gyroscopes. The control of this device is implemented through a digital design on a Field Programmable Gate Array (FPGA). The hardware platform easily transitions to an embedded solution that allows for the miniaturization of the system to a single chip.
Cepstral methods in computational vision
NASA Astrophysics Data System (ADS)
Bandari, Esfandiar; Little, James J.
1993-05-01
Many computational vision routines can be regarded as recognition and retrieval of echoes in space or time. Cepstral analysis is a powerful nonlinear adaptive signal processing methodology widely used in many areas such as: echo retrieval and removal, speech processing and phoneme chunking, radar and sonar processing, seismology, medicine, image deblurring and restoration, and signal recovery. The aim of this paper is: (1) To provide a brief mathematical and historical review of cepstral techniques. (2) To introduce computational and performance improvements to power and differential cepstrum for use in detection of echoes; and to provide a comparison between these methods and the traditional cepstral techniques. (3) To apply cepstrum to visual tasks such as motion analysis and trinocular vision. And (4) to draw a brief comparison between cepstrum and other matching techniques. The computational and performance improvements introduced in this paper can e applied in other areas that frequently utilize cepstrum.
Optimal Navier-Stokes Design of Compressor Impellers Using Evolutionary Computation
NASA Astrophysics Data System (ADS)
Benini, Ernesto
2003-09-01
In the design of modern centrifugal compressor impellers, it is fundamental to account for three-dimensional effects and to use an optimization strategy that helps the designer to achieve the required objectives with the presence of constraints. In this paper, a fully three-dimensional optimization method is described that combines a CFD code and an evolutionary algorithm. The design scenario contemplated here involves the maximization of impeller peak efficiency with constraints on the impeller pressure ratio and operating range. The method is used to improve the performances of a baseline impeller of known characteristics. An optimal solution is proposed and compared to the original configuration.
Hybrid evolutionary computing model for mobile agents of wireless Internet multimedia
NASA Astrophysics Data System (ADS)
Hortos, William S.
2001-03-01
The ecosystem is used as an evolutionary paradigm of natural laws for the distributed information retrieval via mobile agents to allow the computational load to be added to server nodes of wireless networks, while reducing the traffic on communication links. Based on the Food Web model, a set of computational rules of natural balance form the outer stage to control the evolution of mobile agents providing multimedia services with a wireless Internet protocol WIP. The evolutionary model shows how mobile agents should behave with the WIP, in particular, how mobile agents can cooperate, compete and learn from each other, based on an underlying competition for radio network resources to establish the wireless connections to support the quality of service QoS of user requests. Mobile agents are also allowed to clone themselves, propagate and communicate with other agents. A two-layer model is proposed for agent evolution: the outer layer is based on the law of natural balancing, the inner layer is based on a discrete version of a Kohonen self-organizing feature map SOFM to distribute network resources to meet QoS requirements. The former is embedded in the higher OSI layers of the WIP, while the latter is used in the resource management procedures of Layer 2 and 3 of the protocol. Algorithms for the distributed computation of mobile agent evolutionary behavior are developed by adding a learning state to the agent evolution state diagram. When an agent is in an indeterminate state, it can communicate to other agents. Computing models can be replicated from other agents. Then the agents transitions to the mutating state to wait for a new information-retrieval goal. When a wireless terminal or station lacks a network resource, an agent in the suspending state can change its policy to submit to the environment before it transitions to the searching state. The agents learn the facts of agent state information entered into an external database. In the cloning process, two
Deep Space Network Scheduling Using Evolutionary Computational Methods
NASA Technical Reports Server (NTRS)
Guillaume, Alexandre; Lee, Seugnwon; Wang, Yeou-Fang; Terrile, Richard J.
2007-01-01
The paper presents the specific approach taken to formulate the problem in terms of gene encoding, fitness function, and genetic operations. The genome is encoded such that a subset of the scheduling constraints is automatically satisfied. Several fitness functions are formulated to emphasize different aspects of the scheduling problem. The optimal solutions of the different fitness functions demonstrate the trade-off of the scheduling problem and provide insight into a conflict resolution process.
Computational methods for stellerator configurations
NASA Astrophysics Data System (ADS)
Betancourt, O.
This project had two main objectives. The first one was to continue to develop computational methods for the study of three dimensional magnetic confinement configurations. The second one was to collaborate and interact with researchers in the field who can use these techniques to study and design fusion experiments. The first objective has been achieved with the development of the spectral code BETAS and the formulation of a new variational approach for the study of magnetic island formation in a self consistent fashion. The code can compute the correct island width corresponding to the saturated island, a result shown by comparing the computed island with the results of unstable tearing modes in Tokamaks and with experimental results in the IMS Stellarator. In addition to studying three dimensional nonlinear effects in Tokamaks configurations, these self consistent computed island equilibria will be used to study transport effects due to magnetic island formation and to nonlinearly bifurcated equilibria. The second objective was achieved through direct collaboration with Steve Hirshman at Oak Ridge, D. Anderson and R. Talmage at Wisconsin as well as through participation in the Sherwood and APS meetings.
An evolutionary method for synthesizing technological planning and architectural advance
NASA Astrophysics Data System (ADS)
Cole, Bjorn Forstrom
the appropriate technological antecedents are accounted for in developing the projection. The third chapter of the thesis compiles a series of observations and philosophical considerations into a series of research questions. Some research questions are then answered with further thought, observation, and reading, leading to conjectures on the problem. The remainder require some form of experimentation, and so are used to formulate hypotheses. Falsifiability conditions are then generated from those hypotheses, and used to get the development of experiments to be performed, in this case on a computer upon various conditions of use of a genetic algorithm. The fourth chapter of the thesis walks through the formulation of a method to attack the problem of strategically choosing an architecture. This method is designed to find the optimum architecture under multiple conditions, which is required for the ability to play the "what if" games typically undertaken in strategic situations. The chapter walks through a graph-based representation of architecture, provides the rationale for choosing a given technology forecasting technique, and lays out the implementation of the optimization algorithm, named Sindri, within a commercial analysis code, Pacelab. The fifth chapter of the thesis then tests the Sindri code. The first test applied is a series of standardized combinatorial spaces, which are meant to be analogous to test problems traditionally posed to optimizers (e.g., Rosenbrock's valley function). The results from this test assess the value of various operators used to transform the architecture graph in the course of conducting a genetic search. Finally, this method is employed on a test case involving the transition of a miniature helicopter from glow engine to battery propulsion, and finally to a design where the battery functions as both structure and power source. The final two chapters develop conclusions based on the body of work conducted within this thesis and
Breen, Gerald-Mark; Matusitz, Jonathan
2009-01-01
Telemedicine, the use of advanced communication technologies in the healthcare context, has a rich history and a clear evolutionary course. In this paper, the authors identify telemedicine as operationally defined, the services and technologies it comprises, the direction telemedicine has taken, along with its increased acceptance in the healthcare communities. The authors also describe some of the key pitfalls warred with by researchers and activists to advance telemedicine to its full potential and lead to an unobstructed team of technicians to identify telemedicine’s diverse utilities. A discussion and future directions section is included to provide fresh ideas to health communication and computer-mediated scholars wishing to delve into this area and make a difference to enhance public understanding of this field. PMID:20300559
5D parameter estimation of near-field sources using hybrid evolutionary computational techniques.
Zaman, Fawad; Qureshi, Ijaz Mansoor
2014-01-01
Hybrid evolutionary computational technique is developed to jointly estimate the amplitude, frequency, range, and 2D direction of arrival (elevation and azimuth angles) of near-field sources impinging on centrosymmetric cross array. Specifically, genetic algorithm is used as a global optimizer, whereas pattern search and interior point algorithms are employed as rapid local search optimizers. For this, a new multiobjective fitness function is constructed, which is the combination of mean square error and correlation between the normalized desired and estimated vectors. The performance of the proposed hybrid scheme is compared not only with the individual responses of genetic algorithm, interior point algorithm, and pattern search, but also with the existing traditional techniques. The proposed schemes produced fairly good results in terms of estimation accuracy, convergence rate, and robustness against noise. A large number of Monte-Carlo simulations are carried out to test out the validity and reliability of each scheme. PMID:24701156
Development of a multisegment coal mill model using an evolutionary computation technique
Wei, J.L.; Wang, J.; Wu, Q.H.
2007-09-15
This paper presents a multisegment coal mill model that covers the whole milling process from mill startup to shutdown. This multisegment mathematical model is derived through analysis of energy transferring, heat exchange, and mass flow balances. The work presented in the paper focuses on modeling E-type vertical spindle coal mills that are widely used in coal-fired power plants. An evolutionary computation technique is adopted to identify the unknown model parameters using the on-site measurement data. The identified parameters are then validated with different sets of online measured data. Validation results indicate that the model is accurate enough to represent the whole process of coal mill dynamics and can be used for prediction of the mill dynamic performance. Therefore, the model can be used for online monitoring, fault detection, and control to improve the efficiency of combustion.
How quickly do brains catch up with bodies? A comparative method for detecting evolutionary lag.
Deaner, R O; Nunn, C L
1999-01-01
A trait may be at odds with theoretical expectation because it is still in the process of responding to a recent selective force. Such a situation can be termed evolutionary lag. Although many cases of evolutionary lag have been suggested, almost all of the arguments have focused on trait fitness. An alternative approach is to examine the prediction that trait expression is a function of the time over which the trait could evolve. Here we present a phylogenetic comparative method for using this 'time' approach and we apply the method to a long-standing lag hypothesis: evolutionary changes in brain size lag behind evolutionary changes in body size. We tested the prediction in primates that brain mass contrast residuals, calculated from a regression of pairwise brain mass contrasts on positive pairwise body mass contrasts, are correlated with the time since the paired species diverged. Contrary to the brain size lag hypothesis, time since divergence was not significantly correlated with brain mass contrast residuals. We found the same result when we accounted for socioecology, used alternative body mass estimates and used male rather than female values. These tests do not support the brain size lag hypothesis. Therefore, body mass need not be viewed as a suspect variable in comparative neuroanatomical studies and relative brain size should not be used to infer recent evolutionary changes in body size. PMID:10331289
Ishibuchi, Hisao; Sudo, Takahiko; Nojima, Yusuke
2016-01-01
In interactive evolutionary computation (IEC), each solution is evaluated by a human user. Usually the total number of examined solutions is very small. In some applications such as hearing aid design and music composition, only a single solution can be evaluated at a time by a human user. Moreover, accurate and precise numerical evaluation is difficult. Based on these considerations, we formulated an IEC model with the minimum requirement for fitness evaluation ability of human users under the following assumptions: They can evaluate only a single solution at a time, they can memorize only a single previous solution they have just evaluated, their evaluation result on the current solution is whether it is better than the previous one or not, and the best solution among the evaluated ones should be identified after a pre-specified number of evaluations. In this paper, we first explain our IEC model in detail. Next we propose a ([Formula: see text])ES-style algorithm for our IEC model. Then we propose an offline meta-level approach to automated algorithm design for our IEC model. The main feature of our approach is the use of a different mechanism (e.g., mutation, crossover, random initialization) to generate each solution to be evaluated. Through computational experiments on test problems, our approach is compared with the ([Formula: see text])ES-style algorithm where a solution generation mechanism is pre-specified and fixed throughout the execution of the algorithm. PMID:27026888
An evolutionary computational theory of prefrontal executive function in decision-making.
Koechlin, Etienne
2014-11-01
The prefrontal cortex subserves executive control and decision-making, that is, the coordination and selection of thoughts and actions in the service of adaptive behaviour. We present here a computational theory describing the evolution of the prefrontal cortex from rodents to humans as gradually adding new inferential Bayesian capabilities for dealing with a computationally intractable decision problem: exploring and learning new behavioural strategies versus exploiting and adjusting previously learned ones through reinforcement learning (RL). We provide a principled account identifying three inferential steps optimizing this arbitration through the emergence of (i) factual reactive inferences in paralimbic prefrontal regions in rodents; (ii) factual proactive inferences in lateral prefrontal regions in primates and (iii) counterfactual reactive and proactive inferences in human frontopolar regions. The theory clarifies the integration of model-free and model-based RL through the notion of strategy creation. The theory also shows that counterfactual inferences in humans yield to the notion of hypothesis testing, a critical reasoning ability for approximating optimal adaptive processes and presumably endowing humans with a qualitative evolutionary advantage in adaptive behaviour. PMID:25267817
Mean protein evolutionary distance: a method for comparative protein evolution and its application.
Wise, Michael J
2013-01-01
Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins' roles. Different species' proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz. PMID:23613826
O'Hagan, Steve; Knowles, Joshua; Kell, Douglas B.
2012-01-01
Comparatively few studies have addressed directly the question of quantifying the benefits to be had from using molecular genetic markers in experimental breeding programmes (e.g. for improved crops and livestock), nor the question of which organisms should be mated with each other to best effect. We argue that this requires in silico modelling, an approach for which there is a large literature in the field of evolutionary computation (EC), but which has not really been applied in this way to experimental breeding programmes. EC seeks to optimise measurable outcomes (phenotypic fitnesses) by optimising in silico the mutation, recombination and selection regimes that are used. We review some of the approaches from EC, and compare experimentally, using a biologically relevant in silico landscape, some algorithms that have knowledge of where they are in the (genotypic) search space (G-algorithms) with some (albeit well-tuned ones) that do not (F-algorithms). For the present kinds of landscapes, F- and G-algorithms were broadly comparable in quality and effectiveness, although we recognise that the G-algorithms were not equipped with any ‘prior knowledge’ of epistatic pathway interactions. This use of algorithms based on machine learning has important implications for the optimisation of experimental breeding programmes in the post-genomic era when we shall potentially have access to the full genome sequence of every organism in a breeding population. The non-proprietary code that we have used is made freely available (via Supplementary information). PMID:23185279
Using evolutionary computation to optimize an SVM used in detecting buried objects in FLIR imagery
NASA Astrophysics Data System (ADS)
Paino, Alex; Popescu, Mihail; Keller, James M.; Stone, Kevin
2013-06-01
In this paper we describe an approach for optimizing the parameters of a Support Vector Machine (SVM) as part of an algorithm used to detect buried objects in forward looking infrared (FLIR) imagery captured by a camera installed on a moving vehicle. The overall algorithm consists of a spot-finding procedure (to look for potential targets) followed by the extraction of several features from the neighborhood of each spot. The features include local binary pattern (LBP) and histogram of oriented gradients (HOG) as these are good at detecting texture classes. Finally, we project and sum each hit into UTM space along with its confidence value (obtained from the SVM), producing a confidence map for ROC analysis. In this work, we use an Evolutionary Computation Algorithm (ECA) to optimize various parameters involved in the system, such as the combination of features used, parameters on the Canny edge detector, the SVM kernel, and various HOG and LBP parameters. To validate our approach, we compare results obtained from an SVM using parameters obtained through our ECA technique with those previously selected by hand through several iterations of "guess and check".
Computational methods for stealth design
Cable, V.P. )
1992-08-01
A review is presented of the utilization of computer models for stealth design toward the ultimate goal of designing and fielding an aircraft that remains undetected at any altitude and any range. Attention is given to the advancements achieved in computational tools and their utilization. Consideration is given to the development of supercomputers for large-scale scientific computing and the development of high-fidelity, 3D, radar-signature-prediction tools for complex shapes with nonmetallic and radar-penetrable materials.
Sarkar, Kanchan; Sharma, Rahul; Bhattacharyya, S P
2010-03-01
A density matrix based soft-computing solution to the quantum mechanical problem of computing the molecular electronic structure of fairly long polythiophene (PT) chains is proposed. The soft-computing solution is based on a "random mutation hill climbing" scheme which is modified by blending it with a deterministic method based on a trial single-particle density matrix [P((0))(R)] for the guessed structural parameters (R), which is allowed to evolve under a unitary transformation generated by the Hamiltonian H(R). The Hamiltonian itself changes as the geometrical parameters (R) defining the polythiophene chain undergo mutation. The scale (λ) of the transformation is optimized by making the energy [E(λ)] stationary with respect to λ. The robustness and the performance levels of variants of the algorithm are analyzed and compared with those of other derivative free methods. The method is further tested successfully with optimization of the geometry of bipolaron-doped long PT chains. PMID:26613302
Optimization Methods for Computer Animation.
ERIC Educational Resources Information Center
Donkin, John Caldwell
Emphasizing the importance of economy and efficiency in the production of computer animation, this master's thesis outlines methodologies that can be used to develop animated sequences with the highest quality images for the least expenditure. It is assumed that if computer animators are to be able to fully exploit the available resources, they…
Evolutionary topology optimization using the extended finite element method and isolines
NASA Astrophysics Data System (ADS)
Abdi, Meisam; Wildman, Ricky; Ashcroft, Ian
2014-05-01
This study presents a new algorithm for structural topological optimization of two-dimensional continuum structures by combining the extended finite element method (X-FEM) with an evolutionary optimization algorithm. Taking advantage of an isoline design approach for boundary representation in a fixed grid domain, X-FEM can be implemented to improve the accuracy of finite element solutions on the boundary during the optimization process. Although this approach does not use any remeshing or moving mesh algorithms, final topologies have smooth and clearly defined boundaries which need no further interpretation. Numerical comparisons of the converged solutions with standard bi-directional evolutionary structural optimization solutions show the efficiency of the proposed method, and comparison with the converged solutions using MSC NASTRAN confirms the high accuracy of this method.
Computational methods for probability of instability calculations
NASA Technical Reports Server (NTRS)
Wu, Y.-T.; Burnside, O. H.
1990-01-01
This paper summarizes the development of the methods and a computer program to compute the probability of instability of a dynamic system than can be represented by a system of second-order ordinary linear differential equations. Two instability criteria based upon the roots of the characteristics equation or Routh-Hurwitz test functions are investigated. Computational methods based on system reliability analysis methods and importance sampling concepts are proposed to perform efficient probabilistic analysis. Numerical examples are provided to demonstrate the methods.
An improved approximate-Bayesian model-choice method for estimating shared evolutionary history
2014-01-01
Background To understand biological diversification, it is important to account for large-scale processes that affect the evolutionary history of groups of co-distributed populations of organisms. Such events predict temporally clustered divergences times, a pattern that can be estimated using genetic data from co-distributed species. I introduce a new approximate-Bayesian method for comparative phylogeographical model-choice that estimates the temporal distribution of divergences across taxa from multi-locus DNA sequence data. The model is an extension of that implemented in msBayes. Results By reparameterizing the model, introducing more flexible priors on demographic and divergence-time parameters, and implementing a non-parametric Dirichlet-process prior over divergence models, I improved the robustness, accuracy, and power of the method for estimating shared evolutionary history across taxa. Conclusions The results demonstrate the improved performance of the new method is due to (1) more appropriate priors on divergence-time and demographic parameters that avoid prohibitively small marginal likelihoods for models with more divergence events, and (2) the Dirichlet-process providing a flexible prior on divergence histories that does not strongly disfavor models with intermediate numbers of divergence events. The new method yields more robust estimates of posterior uncertainty, and thus greatly reduces the tendency to incorrectly estimate models of shared evolutionary history with strong support. PMID:24992937
Numerical simulation of evolutionary erodible bedforms using the particle finite element method
NASA Astrophysics Data System (ADS)
Bravo, Rafael; Becker, Pablo; Ortiz, Pablo
2016-07-01
This paper presents a numerical strategy for the simulation of flows with evolutionary erodible boundaries. The fluid equations are fully resolved in 3D, while the sediment transport is modelled using the Exner equation and solved with an explicit Lagrangian procedure based on a fixed 2D mesh. Flow and sediment are coupled in geometry by deforming the fluid mesh in the vertical direction and in velocities with the experimental sediment flux computed using the Meyer Peter Müller model. A comparison with real experiments on channels is performed, giving good agreement.
Computational methods for unsteady transonic flows
NASA Technical Reports Server (NTRS)
Edwards, John W.; Thomas, James L.
1987-01-01
Computational methods for unsteady transonic flows are surveyed with emphasis upon applications to aeroelastic analysis and flutter prediction. Computational difficulty is discussed with respect to type of unsteady flow; attached, mixed (attached/separated) and separated. Significant early computations of shock motions, aileron buzz and periodic oscillations are discussed. The maturation of computational methods towards the capability of treating complete vehicles with reasonable computational resources is noted and a survey of recent comparisons with experimental results is compiled. The importance of mixed attached and separated flow modeling for aeroelastic analysis is discussed and recent calculations of periodic aerodynamic oscillations for an 18 percent thick circular arc airfoil are given.
Computational methods for unsteady transonic flows
NASA Technical Reports Server (NTRS)
Edwards, John W.; Thomas, J. L.
1987-01-01
Computational methods for unsteady transonic flows are surveyed with emphasis on prediction. Computational difficulty is discussed with respect to type of unsteady flow; attached, mixed (attached/separated) and separated. Significant early computations of shock motions, aileron buzz and periodic oscillations are discussed. The maturation of computational methods towards the capability of treating complete vehicles with reasonable computational resources is noted and a survey of recent comparisons with experimental results is compiled. The importance of mixed attached and separated flow modeling for aeroelastic analysis is discussed, and recent calculations of periodic aerodynamic oscillations for an 18 percent thick circular arc airfoil are given.
Multiprocessor computer overset grid method and apparatus
Barnette, Daniel W.; Ober, Curtis C.
2003-01-01
A multiprocessor computer overset grid method and apparatus comprises associating points in each overset grid with processors and using mapped interpolation transformations to communicate intermediate values between processors assigned base and target points of the interpolation transformations. The method allows a multiprocessor computer to operate with effective load balance on overset grid applications.
Computational Methods in Nanostructure Design
NASA Astrophysics Data System (ADS)
Bellesia, Giovanni; Lampoudi, Sotiria; Shea, Joan-Emma
Self-assembling peptides can serve as building blocks for novel biomaterials. Replica exchange molecular dynamics simulations are a powerful means to probe the conformational space of these peptides. We discuss the theoretical foundations of this enhanced sampling method and its use in biomolecular simulations. We then apply this method to determine the monomeric conformations of the Alzheimer amyloid-β(12-28) peptide that can serve as initiation sites for aggregation.
Squires, R Burke; Pickett, Brett E; Das, Sajal; Scheuermann, Richard H
2014-12-01
In 2009 a novel pandemic H1N1 influenza virus (H1N1pdm09) emerged as the first official influenza pandemic of the 21st century. Early genomic sequence analysis pointed to the swine origin of the virus. Here we report a novel computational approach to determine the evolutionary trajectory of viral sequences that uses data-driven estimations of nucleotide substitution rates to track the gradual accumulation of observed sequence alterations over time. Phylogenetic analysis and multiple sequence alignments show that sequences belonging to the resulting evolutionary trajectory of the H1N1pdm09 lineage exhibit a gradual accumulation of sequence variations and tight temporal correlations in the topological structure of the phylogenetic trees. These results suggest that our evolutionary trajectory analysis (ETA) can more effectively pinpoint the evolutionary history of viruses, including the host and geographical location traversed by each segment, when compared against either BLAST or traditional phylogenetic analysis alone. PMID:25064525
Combinatorial protein design strategies using computational methods.
Kono, Hidetoshi; Wang, Wei; Saven, Jeffery G
2007-01-01
Computational methods continue to facilitate efforts in protein design. Most of this work has focused on searching sequence space to identify one or a few sequences compatible with a given structure and functionality. Probabilistic computational methods provide information regarding the range of amino acid variability permitted by desired functional and structural constraints. Such methods may be used to guide the construction of both individual sequences and combinatorial libraries of proteins. PMID:17041256
Computational Methods to Model Persistence.
Vandervelde, Alexandra; Loris, Remy; Danckaert, Jan; Gelens, Lendert
2016-01-01
Bacterial persister cells are dormant cells, tolerant to multiple antibiotics, that are involved in several chronic infections. Toxin-antitoxin modules play a significant role in the generation of such persister cells. Toxin-antitoxin modules are small genetic elements, omnipresent in the genomes of bacteria, which code for an intracellular toxin and its neutralizing antitoxin. In the past decade, mathematical modeling has become an important tool to study the regulation of toxin-antitoxin modules and their relation to the emergence of persister cells. Here, we provide an overview of several numerical methods to simulate toxin-antitoxin modules. We cover both deterministic modeling using ordinary differential equations and stochastic modeling using stochastic differential equations and the Gillespie method. Several characteristics of toxin-antitoxin modules such as protein production and degradation, negative autoregulation through DNA binding, toxin-antitoxin complex formation and conditional cooperativity are gradually integrated in these models. Finally, by including growth rate modulation, we link toxin-antitoxin module expression to the generation of persister cells. PMID:26468111
Computational Methods for Ideal Magnetohydrodynamics
NASA Astrophysics Data System (ADS)
Kercher, Andrew D.
Numerical schemes for the ideal magnetohydrodynamics (MHD) are widely used for modeling space weather and astrophysical flows. They are designed to resolve the different waves that propagate through a magnetohydro fluid, namely, the fast, Alfven, slow, and entropy waves. Numerical schemes for ideal magnetohydrodynamics that are based on the standard finite volume (FV) discretization exhibit pseudo-convergence in which non-regular waves no longer exist only after heavy grid refinement. A method is described for obtaining solutions for coplanar and near coplanar cases that consist of only regular waves, independent of grid refinement. The method, referred to as Compound Wave Modification (CWM), involves removing the flux associated with non-regular structures and can be used for simulations in two- and three-dimensions because it does not require explicitly tracking an Alfven wave. For a near coplanar case, and for grids with 213 points or less, we find root-mean-square-errors (RMSEs) that are as much as 6 times smaller. For the coplanar case, in which non-regular structures will exist at all levels of grid refinement for standard FV schemes, the RMSE is as much as 25 times smaller. A multidimensional ideal MHD code has been implemented for simulations on graphics processing units (GPUs). Performance measurements were conducted for both the NVIDIA GeForce GTX Titan and Intel Xeon E5645 processor. The GPU is shown to perform one to two orders of magnitude greater than the CPU when using a single core, and two to three times greater than when run in parallel with OpenMP. Performance comparisons are made for two methods of storing data on the GPU. The first approach stores data as an Array of Structures (AoS), e.g., a point coordinate array of size 3 x n is iterated over. The second approach stores data as a Structure of Arrays (SoA), e.g. three separate arrays of size n are iterated over simultaneously. For an AoS, coalescing does not occur, reducing memory efficiency
NASA Astrophysics Data System (ADS)
Brintaki, Athina N.
Modeling molecular structures is critical for understanding the principles that govern the behavior of molecules and for facilitating the exploration of potential pharmaceutical drugs and nanoscale designs. Biological molecules are flexible bodies that can adopt many different shapes (or conformations) until they reach a stable molecular state that is usually described by the minimum internal energy. A major challenge in modeling flexible molecules is the exponential explosion in computational complexity as the molecular size increases and many degrees of freedom are considered to represent the molecules' flexibility. This research work proposes a novel generic computational geometric approach called enhanced BioGeoFilter (g.eBGF) that geometrically interprets inter-atomic interactions to impose geometric constraints during molecular conformational search to reduce the time for identifying chemically-feasible conformations. Two new methods called Kinematics-Based Differential Evolution ( kDE) and Biological Differential Evolution ( BioDE) are also introduced to direct the molecular conformational search towards low energy (stable) conformations. The proposed kDE method kinematically describes a molecule's deformation mechanism while it uses differential evolution to minimize the intra-molecular energy. On the other hand, the proposed BioDE utilizes our developed g.eBGF data structure as a surrogate approximation model to reduce the number of exact evaluations and to speed the molecular conformational search. This research work will be extremely useful in enabling the modeling of flexible molecules and in facilitating the exploration of nanoscale designs through the virtual assembly of molecules. Our research work can also be used in areas such as molecular docking, protein folding, and nanoscale computer-aided design where rapid collision detection scheme for highly deformable objects is essential.
Xulvi-Brunet, Ramon; Campbell, Gregory W; Rajamani, Sudha; Jiménez, José I; Chen, Irene A
2016-08-15
In vitro selection experiments in biochemistry allow for the discovery of novel molecules capable of specific desired biochemical functions. However, this is not the only benefit we can obtain from such selection experiments. Since selection from a random library yields an unprecedented, and sometimes comprehensive, view of how a particular biochemical function is distributed across sequence space, selection experiments also provide data for creating and analyzing molecular fitness landscapes, which directly map function (phenotypes) to sequence information (genotypes). Given the importance of understanding the relationship between sequence and functional activity, reliable methods to build and analyze fitness landscapes are needed. Here, we present some statistical methods to extract this information from pools of RNA molecules. We also provide new computational tools to construct and study molecular fitness landscapes. PMID:27211010
Transonic wing analysis using advanced computational methods
NASA Technical Reports Server (NTRS)
Henne, P. A.; Hicks, R. M.
1978-01-01
This paper discusses the application of three-dimensional computational transonic flow methods to several different types of transport wing designs. The purpose of these applications is to evaluate the basic accuracy and limitations associated with such numerical methods. The use of such computational methods for practical engineering problems can only be justified after favorable evaluations are completed. The paper summarizes a study of both the small-disturbance and the full potential technique for computing three-dimensional transonic flows. Computed three-dimensional results are compared to both experimental measurements and theoretical results. Comparisons are made not only of pressure distributions but also of lift and drag forces. Transonic drag rise characteristics are compared. Three-dimensional pressure distributions and aerodynamic forces, computed from the full potential solution, compare reasonably well with experimental results for a wide range of configurations and flow conditions.
Spectral Methods for Computational Fluid Dynamics
NASA Technical Reports Server (NTRS)
Zang, T. A.; Streett, C. L.; Hussaini, M. Y.
1994-01-01
As a tool for large-scale computations in fluid dynamics, spectral methods were prophesized in 1944, born in 1954, virtually buried in the mid-1960's, resurrected in 1969, evangalized in the 1970's, and catholicized in the 1980's. The use of spectral methods for meteorological problems was proposed by Blinova in 1944 and the first numerical computations were conducted by Silberman (1954). By the early 1960's computers had achieved sufficient power to permit calculations with hundreds of degrees of freedom. For problems of this size the traditional way of computing the nonlinear terms in spectral methods was expensive compared with finite-difference methods. Consequently, spectral methods fell out of favor. The expense of computing nonlinear terms remained a severe drawback until Orszag (1969) and Eliasen, Machenauer, and Rasmussen (1970) developed the transform methods that still form the backbone of many large-scale spectral computations. The original proselytes of spectral methods were meteorologists involved in global weather modeling and fluid dynamicists investigating isotropic turbulence. The converts who were inspired by the successes of these pioneers remained, for the most part, confined to these and closely related fields throughout the 1970's. During that decade spectral methods appeared to be well-suited only for problems governed by ordinary diSerential eqllations or by partial differential equations with periodic boundary conditions. And, of course, the solution itself needed to be smooth. Some of the obstacles to wider application of spectral methods were: (1) poor resolution of discontinuous solutions; (2) inefficient implementation of implicit methods; and (3) drastic geometric constraints. All of these barriers have undergone some erosion during the 1980's, particularly the latter two. As a result, the applicability and appeal of spectral methods for computational fluid dynamics has broadened considerably. The motivation for the use of spectral
Computational Chemistry Using Modern Electronic Structure Methods
ERIC Educational Resources Information Center
Bell, Stephen; Dines, Trevor J.; Chowdhry, Babur Z.; Withnall, Robert
2007-01-01
Various modern electronic structure methods are now days used to teach computational chemistry to undergraduate students. Such quantum calculations can now be easily used even for large size molecules.
Computational methods for global/local analysis
NASA Technical Reports Server (NTRS)
Ransom, Jonathan B.; Mccleary, Susan L.; Aminpour, Mohammad A.; Knight, Norman F., Jr.
1992-01-01
Computational methods for global/local analysis of structures which include both uncoupled and coupled methods are described. In addition, global/local analysis methodology for automatic refinement of incompatible global and local finite element models is developed. Representative structural analysis problems are presented to demonstrate the global/local analysis methods.
Detection and characterization of flaws in CFRP by SQUID gradiometer using evolutionary computation
NASA Astrophysics Data System (ADS)
Kojima, F.; Kawai, R.; Kasai, N.; Hatsukade, H.
2002-05-01
This paper is concerned with a quantitative nondestructive evaluation of a carbon fiberglass reinforced plastic (CFRP) using the low temperature superconductor (LTS) SQUID gradiometer. The evaluation can be implemented by applying the alternative current injection to the CFRP with a defect. A 3D finite element code is developed for analyzing the SQUID based nondestructive system. Using the evolutionary programming, an efficient inverse scheme is proposed for recovering flaws in CFRP. The proposed algorithm is tested for the detection and characterization of flaws in the CFRP samples.
Afreen, Nazia; Naqvi, Irshad H; Broor, Shobha; Ahmed, Anwar; Kazim, Syed Naqui; Dohare, Ravins; Kumar, Manoj; Parveen, Shama
2016-03-01
Dengue fever is the most important arboviral disease in the tropical and sub-tropical countries of the world. Delhi, the metropolitan capital state of India, has reported many dengue outbreaks, with the last outbreak occurring in 2013. We have recently reported predominance of dengue virus serotype 2 during 2011-2014 in Delhi. In the present study, we report molecular characterization and evolutionary analysis of dengue serotype 2 viruses which were detected in 2011-2014 in Delhi. Envelope genes of 42 DENV-2 strains were sequenced in the study. All DENV-2 strains grouped within the Cosmopolitan genotype and further clustered into three lineages; Lineage I, II and III. Lineage III replaced lineage I during dengue fever outbreak of 2013. Further, a novel mutation Thr404Ile was detected in the stem region of the envelope protein of a single DENV-2 strain in 2014. Nucleotide substitution rate and time to the most recent common ancestor were determined by molecular clock analysis using Bayesian methods. A change in effective population size of Indian DENV-2 viruses was investigated through Bayesian skyline plot. The study will be a vital road map for investigation of epidemiology and evolutionary pattern of dengue viruses in India. PMID:26977703
Afreen, Nazia; Naqvi, Irshad H.; Broor, Shobha; Ahmed, Anwar; Kazim, Syed Naqui; Dohare, Ravins; Kumar, Manoj; Parveen, Shama
2016-01-01
Dengue fever is the most important arboviral disease in the tropical and sub-tropical countries of the world. Delhi, the metropolitan capital state of India, has reported many dengue outbreaks, with the last outbreak occurring in 2013. We have recently reported predominance of dengue virus serotype 2 during 2011–2014 in Delhi. In the present study, we report molecular characterization and evolutionary analysis of dengue serotype 2 viruses which were detected in 2011–2014 in Delhi. Envelope genes of 42 DENV-2 strains were sequenced in the study. All DENV-2 strains grouped within the Cosmopolitan genotype and further clustered into three lineages; Lineage I, II and III. Lineage III replaced lineage I during dengue fever outbreak of 2013. Further, a novel mutation Thr404Ile was detected in the stem region of the envelope protein of a single DENV-2 strain in 2014. Nucleotide substitution rate and time to the most recent common ancestor were determined by molecular clock analysis using Bayesian methods. A change in effective population size of Indian DENV-2 viruses was investigated through Bayesian skyline plot. The study will be a vital road map for investigation of epidemiology and evolutionary pattern of dengue viruses in India. PMID:26977703
Dehzangi, Abdollah; Paliwal, Kuldip; Lyons, James; Sharma, Alok; Sattar, Abdul
2014-01-01
Protein fold recognition (PFR) is considered as an important step towards the protein structure prediction problem. Despite all the efforts that have been made so far, finding an accurate and fast computational approach to solve the PFR still remains a challenging problem for bioinformatics and computational biology. In this study, we propose the concept of segmented-based feature extraction technique to provide local evolutionary information embedded in position specific scoring matrix (PSSM) and structural information embedded in the predicted secondary structure of proteins using SPINE-X. We also employ the concept of occurrence feature to extract global discriminatory information from PSSM and SPINE-X. By applying a support vector machine (SVM) to our extracted features, we enhance the protein fold prediction accuracy for 7.4 percent over the best results reported in the literature. We also report 73.8 percent prediction accuracy for a data set consisting of proteins with less than 25 percent sequence similarity rates and 80.7 percent prediction accuracy for a data set with proteins belonging to 110 folds with less than 40 percent sequence similarity rates. We also investigate the relation between the number of folds and the number of features being used and show that the number of features should be increased to get better protein fold prediction results when the number of folds is relatively large. PMID:26356019
Belciug, Smaranda; Gorunescu, Florin
2015-02-01
Scarce healthcare resources require carefully made policies ensuring optimal bed allocation, quality healthcare service, and adequate financial support. This paper proposes a complex analysis of the resource allocation in a hospital department by integrating in the same framework a queuing system, a compartmental model, and an evolutionary-based optimization. The queuing system shapes the flow of patients through the hospital, the compartmental model offers a feasible structure of the hospital department in accordance to the queuing characteristics, and the evolutionary paradigm provides the means to optimize the bed-occupancy management and the resource utilization using a genetic algorithm approach. The paper also focuses on a "What-if analysis" providing a flexible tool to explore the effects on the outcomes of the queuing system and resource utilization through systematic changes in the input parameters. The methodology was illustrated using a simulation based on real data collected from a geriatric department of a hospital from London, UK. In addition, the paper explores the possibility of adapting the methodology to different medical departments (surgery, stroke, and mental illness). Moreover, the paper also focuses on the practical use of the model from the healthcare point of view, by presenting a simulated application. PMID:25433363
Computational Methods for Rough Classification and Discovery.
ERIC Educational Resources Information Center
Bell, D. A.; Guan, J. W.
1998-01-01
Rough set theory is a new mathematical tool to deal with vagueness and uncertainty. Computational methods are presented for using rough sets to identify classes in datasets, finding dependencies in relations, and discovering rules which are hidden in databases. The methods are illustrated with a running example from a database of car test results.…
Updated Panel-Method Computer Program
NASA Technical Reports Server (NTRS)
Ashby, Dale L.
1995-01-01
Panel code PMARC_12 (Panel Method Ames Research Center, version 12) computes potential-flow fields around complex three-dimensional bodies such as complete aircraft models. Contains several advanced features, including internal mathematical modeling of flow, time-stepping wake model for simulating either steady or unsteady motions, capability for Trefftz computation of drag induced by plane, and capability for computation of off-body and on-body streamlines, and capability of computation of boundary-layer parameters by use of two-dimensional integral boundary-layer method along surface streamlines. Investigators interested in visual representations of phenomena, may want to consider obtaining program GVS (ARC-13361), General visualization System. GVS is Silicon Graphics IRIS program created to support scientific-visualization needs of PMARC_12. GVS available separately from COSMIC. PMARC_12 written in standard FORTRAN 77, with exception of NAMELIST extension used for input.
Computing discharge using the index velocity method
Levesque, Victor A.; Oberg, Kevin A.
2012-01-01
Application of the index velocity method for computing continuous records of discharge has become increasingly common, especially since the introduction of low-cost acoustic Doppler velocity meters (ADVMs) in 1997. Presently (2011), the index velocity method is being used to compute discharge records for approximately 470 gaging stations operated and maintained by the U.S. Geological Survey. The purpose of this report is to document and describe techniques for computing discharge records using the index velocity method. Computing discharge using the index velocity method differs from the traditional stage-discharge method by separating velocity and area into two ratings—the index velocity rating and the stage-area rating. The outputs from each of these ratings, mean channel velocity (V) and cross-sectional area (A), are then multiplied together to compute a discharge. For the index velocity method, V is a function of such parameters as streamwise velocity, stage, cross-stream velocity, and velocity head, and A is a function of stage and cross-section shape. The index velocity method can be used at locations where stage-discharge methods are used, but it is especially appropriate when more than one specific discharge can be measured for a specific stage. After the ADVM is selected, installed, and configured, the stage-area rating and the index velocity rating must be developed. A standard cross section is identified and surveyed in order to develop the stage-area rating. The standard cross section should be surveyed every year for the first 3 years of operation and thereafter at a lesser frequency, depending on the susceptibility of the cross section to change. Periodic measurements of discharge are used to calibrate and validate the index rating for the range of conditions experienced at the gaging station. Data from discharge measurements, ADVMs, and stage sensors are compiled for index-rating analysis. Index ratings are developed by means of regression
Computational stoning method for surface defect detection
NASA Astrophysics Data System (ADS)
Ma, Ninshu; Zhu, Xinhai
2013-12-01
Surface defects on outer panels of automotive bodies must be controlled in order to improve the surface quality. The detection and quantitative evaluation of surface defects are quite difficult because the deflection of surface defects is very small. One of detecting methods for surface defects used in factories is a stoning method in which a stone block is moved on the surface of a stamped panel. The computational stoning method was developed to detect surface low defect by authors based on a geometry contact algorithm between a stone block and a stamped panel. If the surface is convex, the stone block always contacts with the convex surface of a stamped panel and the contact gap between them is zero. If there is a surface low, the stone block does not contact to the surface and the contact gap can be computed based on contact algorithm. The convex surface defect can also be detected by applying computational stoning method to the back surface of a stamped panel. By performing two way stoning computations from both the normal surface and the back surface, not only the depth of surface low defect but also the height of convex surface defect can be detected. The surface low defect and convex surface defect can also be detected through multi-directions. Surface defects on the handle emboss of outer panels were accurately detected using the computational stoning method and compared with the real shape. A very good accuracy was obtained.
Method and system for benchmarking computers
Gustafson, John L.
1993-09-14
A testing system and method for benchmarking computer systems. The system includes a store containing a scalable set of tasks to be performed to produce a solution in ever-increasing degrees of resolution as a larger number of the tasks are performed. A timing and control module allots to each computer a fixed benchmarking interval in which to perform the stored tasks. Means are provided for determining, after completion of the benchmarking interval, the degree of progress through the scalable set of tasks and for producing a benchmarking rating relating to the degree of progress for each computer.
Computational Analysis of the Predicted Evolutionary Conservation of Human Phosphorylation Sites
Trost, Brett; Kusalik, Anthony; Napper, Scott
2016-01-01
Protein kinase-mediated phosphorylation is among the most important post-translational modifications. However, few phosphorylation sites have been experimentally identified for most species, making it difficult to determine the degree to which phosphorylation sites are conserved. The goal of this study was to use computational methods to characterize the conservation of human phosphorylation sites in a wide variety of eukaryotes. Using experimentally-determined human sites as input, homologous phosphorylation sites were predicted in all 432 eukaryotes for which complete proteomes were available. For each pair of species, we calculated phosphorylation site conservation as the number of phosphorylation sites found in both species divided by the number found in at least one of the two species. A clustering of the species based on this conservation measure was concordant with phylogenies based on traditional genomic measures. For a subset of the 432 species, phosphorylation site conservation was compared to conservation of both protein kinases and proteins in general. Protein kinases exhibited the highest degree of conservation, while general proteins were less conserved and phosphorylation sites were least conserved. Although preliminary, these data tentatively suggest that variation in phosphorylation sites may play a larger role in explaining phenotypic differences among organisms than differences in the complements of protein kinases or general proteins. PMID:27046079
Rogers, S W
1999-10-15
Because the brain does not usually leave direct evidence of its existence in the fossil record, our view of this structure in extinct species has relied upon inferences drawn from comparisons between parts of the skeleton that do fossilize or with modern-day relatives that survived extinction. However, soft-tissue structure preservation may indeed occasionally occur, particularly in the endocranial space. By applying modern imaging and analysis methods to such natural cranial "endocasts," we can now learn more than ever thought possible about the brains of extinct species. I will discuss one such example in which spiral computed tomography (CT) scanning analysis has been successfully applied to reveal preserved internal structures of a naturally occurring endocranial cast of Allosaurus fragilis, the dominant carnivorous dinosaur of the late Jurassic period. The ability to directly examine the neuroanatomy of an extinct dinosaur, whose modern-day relatives are birds and crocodiles, has exciting implications about Allosaurus' behavior, its adaptive responses to its environment, and its eventual extinction. PMID:10597341
NASA Technical Reports Server (NTRS)
Pulliam, T. H.; Nemec, M.; Holst, T.; Zingg, D. W.; Kwak, Dochan (Technical Monitor)
2002-01-01
A comparison between an Evolutionary Algorithm (EA) and an Adjoint-Gradient (AG) Method applied to a two-dimensional Navier-Stokes code for airfoil design is presented. Both approaches use a common function evaluation code, the steady-state explicit part of the code,ARC2D. The parameterization of the design space is a common B-spline approach for an airfoil surface, which together with a common griding approach, restricts the AG and EA to the same design space. Results are presented for a class of viscous transonic airfoils in which the optimization tradeoff between drag minimization as one objective and lift maximization as another, produces the multi-objective design space. Comparisons are made for efficiency, accuracy and design consistency.
Kerf modelling in abrasive waterjet milling using evolutionary computation and ANOVA techniques
NASA Astrophysics Data System (ADS)
Alberdi, A.; Rivero, A.; Carrascal, A.; Lamikiz, A.
2012-04-01
Many researchers demonstrated the capability of Abrasive Waterjet (AWJ) technology for precision milling operations. However, the concurrence of several input parameters along with the stochastic nature of this technology leads to a complex process control, which requires a work focused in process modelling. This research work introduces a model to predict the kerf shape in AWJ slot milling in Aluminium 7075-T651 in terms of four important process parameters: the pressure, the abrasive flow rate, the stand-off distance and the traverse feed rate. A hybrid evolutionary approach was employed for kerf shape modelling. This technique allowed characterizing the profile through two parameters: the maximum cutting depth and the full width at half maximum. On the other hand, based on ANOVA and regression techniques, these two parameters were also modelled as a function of process parameters. Combination of both models resulted in an adequate strategy to predict the kerf shape for different machining conditions.
Computational toxicology (CompTox) leverages the significant gains in computing power and computational techniques (e.g., numerical approaches, structure-activity relationships, bioinformatics) realized over the last few years, thereby reducing costs and increasing efficiency i...
Semiempirical methods for computing turbulent flows
NASA Technical Reports Server (NTRS)
Belov, I. A.; Ginzburg, I. P.
1986-01-01
Two semiempirical theories which provide a basis for determining the turbulent friction and heat exchange near a wall are presented: (1) the Prandtl-Karman theory, and (2) the theory utilizing an equation for the energy of turbulent pulsations. A comparison is made between exact numerical methods and approximate integral methods for computing the turbulent boundary layers in the presence of pressure, blowing, or suction gradients. Using the turbulent flow around a plate as an example, it is shown that, when computing turbulent flows with external turbulence, it is preferable to construct a turbulence model based on the equation for energy of turbulent pulsations.
An Efficient Method for Computing All Reducts
NASA Astrophysics Data System (ADS)
Bao, Yongguang; Du, Xiaoyong; Deng, Mingrong; Ishii, Naohiro
In the process of data mining of decision table using Rough Sets methodology, the main computational effort is associated with the determination of the reducts. Computing all reducts is a combinatorial NP-hard computational problem. Therefore the only way to achieve its faster execution is by providing an algorithm, with a better constant factor, which may solve this problem in reasonable time for real-life data sets. The purpose of this presentation is to propose two new efficient algorithms to compute reducts in information systems. The proposed algorithms are based on the proposition of reduct and the relation between the reduct and discernibility matrix. Experiments have been conducted on some real world domains in execution time. The results show it improves the execution time when compared with the other methods. In real application, we can combine the two proposed algorithms.
Evolutionary methods for multidisciplinary optimization applied to the design of UAV systems†
NASA Astrophysics Data System (ADS)
Gonzalez, L. F.; Periaux, J.; Damp, L.; Srinivas, K.
2007-10-01
The implementation and use of a framework in which engineering optimization problems can be analysed are described. In the first part, the foundations of the framework and the hierarchical asynchronous parallel multi-objective evolutionary algorithms (HAPMOEAs) are presented. These are based upon evolution strategies and incorporate the concepts of multi-objective optimization, hierarchical topology, asynchronous evaluation of candidate solutions, and parallel computing. The methodology is presented first and the potential of HAPMOEAs for solving multi-criteria optimization problems is demonstrated on test case problems of increasing difficulty. In the second part of the article several recent applications of multi-objective and multidisciplinary optimization (MO) are described. These illustrate the capabilities of the framework and methodology for the design of UAV and UCAV systems. The application presented deals with a two-objective (drag and weight) UAV wing plan-form optimization. The basic concepts are refined and more sophisticated software and design tools with low- and high-fidelity CFD and FEA models are introduced. Various features described in the text are used to meet the challenge in optimization presented by these test cases.
Applying Human Computation Methods to Information Science
ERIC Educational Resources Information Center
Harris, Christopher Glenn
2013-01-01
Human Computation methods such as crowdsourcing and games with a purpose (GWAP) have each recently drawn considerable attention for their ability to synergize the strengths of people and technology to accomplish tasks that are challenging for either to do well alone. Despite this increased attention, much of this transformation has been focused on…
Efficient Methods to Compute Genomic Predictions
Technology Transfer Automated Retrieval System (TEKTRAN)
Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and simultaneously estimate thousands of marker effects. Algorithms were derived and computer programs tested on simulated data for 50,000 markers and 2,967 bulls. Accurate estimates of ...
Computational Methods for Structural Mechanics and Dynamics
NASA Technical Reports Server (NTRS)
Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)
1989-01-01
Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.
Computational methods for inlet airframe integration
NASA Technical Reports Server (NTRS)
Towne, Charles E.
1988-01-01
Fundamental equations encountered in computational fluid dynamics (CFD), and analyses used for internal flow are introduced. Irrotational flow; Euler equations; boundary layers; parabolized Navier-Stokes equations; and time averaged Navier-Stokes equations are treated. Assumptions made and solution methods are outlined, with examples. The overall status of CFD in propulsion is indicated.
Borg: an auto-adaptive many-objective evolutionary computing framework.
Hadka, David; Reed, Patrick
2013-01-01
This study introduces the Borg multi-objective evolutionary algorithm (MOEA) for many-objective, multimodal optimization. The Borg MOEA combines ε-dominance, a measure of convergence speed named ε-progress, randomized restarts, and auto-adaptive multioperator recombination into a unified optimization framework. A comparative study on 33 instances of 18 test problems from the DTLZ, WFG, and CEC 2009 test suites demonstrates Borg meets or exceeds six state of the art MOEAs on the majority of the tested problems. The performance for each test problem is evaluated using a 1,000 point Latin hypercube sampling of each algorithm's feasible parameterization space. The statistical performance of every sampled MOEA parameterization is evaluated using 50 replicate random seed trials. The Borg MOEA is not a single algorithm; instead it represents a class of algorithms whose operators are adaptively selected based on the problem. The adaptive discovery of key operators is of particular importance for benchmarking how variation operators enhance search for complex many-objective problems. PMID:22385134
McCorkle, Douglas S.; Bryden, Kenneth M.
2011-01-01
Several recent reports and workshops have identified integrated computational engineering as an emerging technology with the potential to transform engineering design. The goal is to integrate geometric models, analyses, simulations, optimization and decision-making tools, and all other aspects of the engineering process into a shared, interactive computer-generated environment that facilitates multidisciplinary and collaborative engineering. While integrated computational engineering environments can be constructed from scratch with high-level programming languages, the complexity of these proposed environments makes this type of approach prohibitively slow and expensive. Rather, a high-level software framework is needed to provide the user with the capability to construct an application in an intuitive manner using existing models and engineering tools with minimal programming. In this paper, we present an exploratory open source software framework that can be used to integrate the geometric models, computational fluid dynamics (CFD), and optimization tools needed for shape optimization of complex systems. This framework is demonstrated using the multiphase flow analysis of a complete coal transport system for an 800 MW pulverized coal power station. The framework uses engineering objects and three-dimensional visualization to enable the user to interactively design and optimize the performance of the coal transport system.
Shifted power method for computing tensor eigenvalues.
Mayo, Jackson R.; Kolda, Tamara Gibson
2010-07-01
Recent work on eigenvalues and eigenvectors for tensors of order m >= 3 has been motivated by applications in blind source separation, magnetic resonance imaging, molecular conformation, and more. In this paper, we consider methods for computing real symmetric-tensor eigenpairs of the form Ax{sup m-1} = lambda x subject to ||x||=1, which is closely related to optimal rank-1 approximation of a symmetric tensor. Our contribution is a shifted symmetric higher-order power method (SS-HOPM), which we show is guaranteed to converge to a tensor eigenpair. SS-HOPM can be viewed as a generalization of the power iteration method for matrices or of the symmetric higher-order power method. Additionally, using fixed point analysis, we can characterize exactly which eigenpairs can and cannot be found by the method. Numerical examples are presented, including examples from an extension of the method to finding complex eigenpairs.
Shifted power method for computing tensor eigenpairs.
Mayo, Jackson R.; Kolda, Tamara Gibson
2010-10-01
Recent work on eigenvalues and eigenvectors for tensors of order m {>=} 3 has been motivated by applications in blind source separation, magnetic resonance imaging, molecular conformation, and more. In this paper, we consider methods for computing real symmetric-tensor eigenpairs of the form Ax{sup m-1} = {lambda}x subject to {parallel}x{parallel} = 1, which is closely related to optimal rank-1 approximation of a symmetric tensor. Our contribution is a novel shifted symmetric higher-order power method (SS-HOPM), which we showis guaranteed to converge to a tensor eigenpair. SS-HOPM can be viewed as a generalization of the power iteration method for matrices or of the symmetric higher-order power method. Additionally, using fixed point analysis, we can characterize exactly which eigenpairs can and cannot be found by the method. Numerical examples are presented, including examples from an extension of the method to fnding complex eigenpairs.
Computational Thermochemistry and Benchmarking of Reliable Methods
Feller, David F.; Dixon, David A.; Dunning, Thom H.; Dupuis, Michel; McClemore, Doug; Peterson, Kirk A.; Xantheas, Sotiris S.; Bernholdt, David E.; Windus, Theresa L.; Chalasinski, Grzegorz; Fosada, Rubicelia; Olguim, Jorge; Dobbs, Kerwin D.; Frurip, Donald; Stevens, Walter J.; Rondan, Nelson; Chase, Jared M.; Nichols, Jeffrey A.
2006-06-20
During the first and second years of the Computational Thermochemistry and Benchmarking of Reliable Methods project, we completed several studies using the parallel computing capabilities of the NWChem software and Molecular Science Computing Facility (MSCF), including large-scale density functional theory (DFT), second-order Moeller-Plesset (MP2) perturbation theory, and CCSD(T) calculations. During the third year, we continued to pursue the computational thermodynamic and benchmarking studies outlined in our proposal. With the issues affecting the robustness of the coupled cluster part of NWChem resolved, we pursued studies of the heats-of-formation of compounds containing 5 to 7 first- and/or second-row elements and approximately 10 to 14 hydrogens. The size of these systems, when combined with the large basis sets (cc-pVQZ and aug-cc-pVQZ) that are necessary for extrapolating to the complete basis set limit, creates a formidable computational challenge, for which NWChem on NWMPP1 is well suited.
Computational methods for industrial radiation measurement applications
Gardner, R.P.; Guo, P.; Ao, Q.
1996-12-31
Computational methods have been used with considerable success to complement radiation measurements in solving a wide range of industrial problems. The almost exponential growth of computer capability and applications in the last few years leads to a {open_quotes}black box{close_quotes} mentality for radiation measurement applications. If a black box is defined as any radiation measurement device that is capable of measuring the parameters of interest when a wide range of operating and sample conditions may occur, then the development of computational methods for industrial radiation measurement applications should now be focused on the black box approach and the deduction of properties of interest from the response with acceptable accuracy and reasonable efficiency. Nowadays, increasingly better understanding of radiation physical processes, more accurate and complete fundamental physical data, and more advanced modeling and software/hardware techniques have made it possible to make giant strides in that direction with new ideas implemented with computer software. The Center for Engineering Applications of Radioisotopes (CEAR) at North Carolina State University has been working on a variety of projects in the area of radiation analyzers and gauges for accomplishing this for quite some time, and they are discussed here with emphasis on current accomplishments.
NASA Astrophysics Data System (ADS)
Tuller, Tamir; Birin, Hadas; Kupiec, Martin; Ruppin, Eytan
The inference of ancestral genomes is a fundamental problem in molecular evolution. Due to the statistical nature of this problem, the most likely or the most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In recent studies we showed that co-evolution is an important force that can be used for significantly improving the inference of ancestral genome content.
Computational methods for ideal compressible flow
NASA Technical Reports Server (NTRS)
Vanleer, B.
1983-01-01
Conservative dissipative difference schemes for computing one dimensional flow are introduced, and the recognition and representation of flow discontinuities are discussed. Multidimensional methods are outlined. Second order finite volume schemes are introduced. Conversion of difference schemes for a single linear convection equation into schemes for the hyperbolic system of the nonlinear conservation laws of ideal compressible flow is explained. Approximate Riemann solvers are presented. Monotone initial value interpolation; and limiters, switches, and artificial dissipation are considered.
Computational methods for vortex dominated compressible flows
NASA Technical Reports Server (NTRS)
Murman, Earll M.
1987-01-01
The principal objectives were to: understand the mechanisms by which Euler equation computations model leading edge vortex flows; understand the vortical and shock wave structures that may exist for different wing shapes, angles of incidence, and Mach numbers; and compare calculations with experiments in order to ascertain the limitations and advantages of Euler equation models. The initial approach utilized the cell centered finite volume Jameson scheme. The final calculation utilized a cell vertex finite volume method on an unstructured grid. Both methods used Runge-Kutta four stage schemes for integrating the equations. The principal findings are briefly summarized.
Analytic Method for Computing Instrument Pointing Jitter
NASA Technical Reports Server (NTRS)
Bayard, David
2003-01-01
A new method of calculating the root-mean-square (rms) pointing jitter of a scientific instrument (e.g., a camera, radar antenna, or telescope) is introduced based on a state-space concept. In comparison with the prior method of calculating the rms pointing jitter, the present method involves significantly less computation. The rms pointing jitter of an instrument (the square root of the jitter variance shown in the figure) is an important physical quantity which impacts the design of the instrument, its actuators, controls, sensory components, and sensor- output-sampling circuitry. Using the Sirlin, San Martin, and Lucke definition of pointing jitter, the prior method of computing the rms pointing jitter involves a frequency-domain integral of a rational polynomial multiplied by a transcendental weighting function, necessitating the use of numerical-integration techniques. In practice, numerical integration complicates the problem of calculating the rms pointing error. In contrast, the state-space method provides exact analytic expressions that can be evaluated without numerical integration.
Probabilistic Computational Methods in Structural Failure Analysis
NASA Astrophysics Data System (ADS)
Krejsa, Martin; Kralik, Juraj
2015-12-01
Probabilistic methods are used in engineering where a computational model contains random variables. Each random variable in the probabilistic calculations contains uncertainties. Typical sources of uncertainties are properties of the material and production and/or assembly inaccuracies in the geometry or the environment where the structure should be located. The paper is focused on methods for the calculations of failure probabilities in structural failure and reliability analysis with special attention on newly developed probabilistic method: Direct Optimized Probabilistic Calculation (DOProC), which is highly efficient in terms of calculation time and the accuracy of the solution. The novelty of the proposed method lies in an optimized numerical integration that does not require any simulation technique. The algorithm has been implemented in mentioned software applications, and has been used several times in probabilistic tasks and probabilistic reliability assessments.
NASA Technical Reports Server (NTRS)
Elliott, Kenny B.; Ugoletti, Roberto; Sulla, Jeff
1992-01-01
The evolution and optimization of a real-time digital control system is presented. The control system is part of a testbed used to perform focused technology research on the interactions of spacecraft platform and instrument controllers with the flexible-body dynamics of the platform and platform appendages. The control system consists of Computer Automated Measurement and Control (CAMAC) standard data acquisition equipment interfaced to a workstation computer. The goal of this work is to optimize the control system's performance to support controls research using controllers with up to 50 states and frame rates above 200 Hz. The original system could support a 16-state controller operating at a rate of 150 Hz. By using simple yet effective software improvements, Input/Output (I/O) latencies and contention problems are reduced or eliminated in the control system. The final configuration can support a 16-state controller operating at 475 Hz. Effectively the control system's performance was increased by a factor of 3.
Numerical methods for problems in computational aeroacoustics
NASA Astrophysics Data System (ADS)
Mead, Jodi Lorraine
1998-12-01
A goal of computational aeroacoustics is the accurate calculation of noise from a jet in the far field. This work concerns the numerical aspects of accurately calculating acoustic waves over large distances and long time. More specifically, the stability, efficiency, accuracy, dispersion and dissipation in spatial discretizations, time stepping schemes, and absorbing boundaries for the direct solution of wave propagation problems are determined. Efficient finite difference methods developed by Tam and Webb, which minimize dispersion and dissipation, are commonly used for the spatial and temporal discretization. Alternatively, high order pseudospectral methods can be made more efficient by using the grid transformation introduced by Kosloff and Tal-Ezer. Work in this dissertation confirms that the grid transformation introduced by Kosloff and Tal-Ezer is not spectrally accurate because, in the limit, the grid transformation forces zero derivatives at the boundaries. If a small number of grid points are used, it is shown that approximations with the Chebyshev pseudospectral method with the Kosloff and Tal-Ezer grid transformation are as accurate as with the Chebyshev pseudospectral method. This result is based on the analysis of the phase and amplitude errors of these methods, and their use for the solution of a benchmark problem in computational aeroacoustics. For the grid transformed Chebyshev method with a small number of grid points it is, however, more appropriate to compare its accuracy with that of high- order finite difference methods. This comparison, for an order of accuracy 10-3 for a benchmark problem in computational aeroacoustics, is performed for the grid transformed Chebyshev method and the fourth order finite difference method of Tam. Solutions with the finite difference method are as accurate. and the finite difference method is more efficient than, the Chebyshev pseudospectral method with the grid transformation. The efficiency of the Chebyshev
Delamination detection using methods of computational intelligence
NASA Astrophysics Data System (ADS)
Ihesiulor, Obinna K.; Shankar, Krishna; Zhang, Zhifang; Ray, Tapabrata
2012-11-01
Abstract Reliable delamination prediction scheme is indispensable in order to prevent potential risks of catastrophic failures in composite structures. The existence of delaminations changes the vibration characteristics of composite laminates and hence such indicators can be used to quantify the health characteristics of laminates. An approach for online health monitoring of in-service composite laminates is presented in this paper that relies on methods based on computational intelligence. Typical changes in the observed vibration characteristics (i.e. change in natural frequencies) are considered as inputs to identify the existence, location and magnitude of delaminations. The performance of the proposed approach is demonstrated using numerical models of composite laminates. Since this identification problem essentially involves the solution of an optimization problem, the use of finite element (FE) methods as the underlying tool for analysis turns out to be computationally expensive. A surrogate assisted optimization approach is hence introduced to contain the computational time within affordable limits. An artificial neural network (ANN) model with Bayesian regularization is used as the underlying approximation scheme while an improved rate of convergence is achieved using a memetic algorithm. However, building of ANN surrogate models usually requires large training datasets. K-means clustering is effectively employed to reduce the size of datasets. ANN is also used via inverse modeling to determine the position, size and location of delaminations using changes in measured natural frequencies. The results clearly highlight the efficiency and the robustness of the approach.
Review of Computational Stirling Analysis Methods
NASA Technical Reports Server (NTRS)
Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.
2004-01-01
Nuclear thermal to electric power conversion carries the promise of longer duration missions and higher scientific data transmission rates back to Earth for both Mars rovers and deep space missions. A free-piston Stirling convertor is a candidate technology that is considered an efficient and reliable power conversion device for such purposes. While already very efficient, it is believed that better Stirling engines can be developed if the losses inherent its current designs could be better understood. However, they are difficult to instrument and so efforts are underway to simulate a complete Stirling engine numerically. This has only recently been attempted and a review of the methods leading up to and including such computational analysis is presented. And finally it is proposed that the quality and depth of Stirling loss understanding may be improved by utilizing the higher fidelity and efficiency of recently developed numerical methods. One such method, the Ultra HI-Fl technique is presented in detail.
Computational Statistical Methods for Social Network Models
Hunter, David R.; Krivitsky, Pavel N.; Schweinberger, Michael
2013-01-01
We review the broad range of recent statistical work in social network models, with emphasis on computational aspects of these methods. Particular focus is applied to exponential-family random graph models (ERGM) and latent variable models for data on complete networks observed at a single time point, though we also briefly review many methods for incompletely observed networks and networks observed at multiple time points. Although we mention far more modeling techniques than we can possibly cover in depth, we provide numerous citations to current literature. We illustrate several of the methods on a small, well-known network dataset, Sampson’s monks, providing code where possible so that these analyses may be duplicated. PMID:23828720
Computational Fluid Dynamics-Based Design Optimization Method for Archimedes Screw Blood Pumps.
Yu, Hai; Janiga, Gábor; Thévenin, Dominique
2016-04-01
An optimization method suitable for improving the performance of Archimedes screw axial rotary blood pumps is described in the present article. In order to achieve a more robust design and to save computational resources, this method combines the advantages of the established pump design theory with modern computer-aided, computational fluid dynamics (CFD)-based design optimization (CFD-O) relying on evolutionary algorithms and computational fluid dynamics. The main purposes of this project are to: (i) integrate pump design theory within the already existing CFD-based optimization; (ii) demonstrate that the resulting procedure is suitable for optimizing an Archimedes screw blood pump in terms of efficiency. Results obtained in this study demonstrate that the developed tool is able to meet both objectives. Finally, the resulting level of hemolysis can be numerically assessed for the optimal design, as hemolysis is an issue of overwhelming importance for blood pumps. PMID:26526039
NASA Astrophysics Data System (ADS)
Shahamatnia, Ehsan; Dorotovič, Ivan; Fonseca, Jose M.; Ribeiro, Rita A.
2016-03-01
Developing specialized software tools is essential to support studies of solar activity evolution. With new space missions such as Solar Dynamics Observatory (SDO), solar images are being produced in unprecedented volumes. To capitalize on that huge data availability, the scientific community needs a new generation of software tools for automatic and efficient data processing. In this paper a prototype of a modular framework for solar feature detection, characterization, and tracking is presented. To develop an efficient system capable of automatic solar feature tracking and measuring, a hybrid approach combining specialized image processing, evolutionary optimization, and soft computing algorithms is being followed. The specialized hybrid algorithm for tracking solar features allows automatic feature tracking while gathering characterization details about the tracked features. The hybrid algorithm takes advantages of the snake model, a specialized image processing algorithm widely used in applications such as boundary delineation, image segmentation, and object tracking. Further, it exploits the flexibility and efficiency of Particle Swarm Optimization (PSO), a stochastic population based optimization algorithm. PSO has been used successfully in a wide range of applications including combinatorial optimization, control, clustering, robotics, scheduling, and image processing and video analysis applications. The proposed tool, denoted PSO-Snake model, was already successfully tested in other works for tracking sunspots and coronal bright points. In this work, we discuss the application of the PSO-Snake algorithm for calculating the sidereal rotational angular velocity of the solar corona. To validate the results we compare them with published manual results performed by an expert.
Priedigkeit, Nolan; Wolfe, Nicholas; Clark, Nathan L.
2015-01-01
Genes involved in the same function tend to have similar evolutionary histories, in that their rates of evolution covary over time. This coevolutionary signature, termed Evolutionary Rate Covariation (ERC), is calculated using only gene sequences from a set of closely related species and has demonstrated potential as a computational tool for inferring functional relationships between genes. To further define applications of ERC, we first established that roughly 55% of genetic diseases posses an ERC signature between their contributing genes. At a false discovery rate of 5% we report 40 such diseases including cancers, developmental disorders and mitochondrial diseases. Given these coevolutionary signatures between disease genes, we then assessed ERC's ability to prioritize known disease genes out of a list of unrelated candidates. We found that in the presence of an ERC signature, the true disease gene is effectively prioritized to the top 6% of candidates on average. We then apply this strategy to a melanoma-associated region on chromosome 1 and identify MCL1 as a potential causative gene. Furthermore, to gain global insight into disease mechanisms, we used ERC to predict molecular connections between 310 nominally distinct diseases. The resulting “disease map” network associates several diseases with related pathogenic mechanisms and unveils many novel relationships between clinically distinct diseases, such as between Hirschsprung's disease and melanoma. Taken together, these results demonstrate the utility of molecular evolution as a gene discovery platform and show that evolutionary signatures can be used to build informative gene-based networks. PMID:25679399
Computational methods for optical molecular imaging
Chen, Duan; Wei, Guo-Wei; Cong, Wen-Xiang; Wang, Ge
2010-01-01
Summary A new computational technique, the matched interface and boundary (MIB) method, is presented to model the photon propagation in biological tissue for the optical molecular imaging. Optical properties have significant differences in different organs of small animals, resulting in discontinuous coefficients in the diffusion equation model. Complex organ shape of small animal induces singularities of the geometric model as well. The MIB method is designed as a dimension splitting approach to decompose a multidimensional interface problem into one-dimensional ones. The methodology simplifies the topological relation near an interface and is able to handle discontinuous coefficients and complex interfaces with geometric singularities. In the present MIB method, both the interface jump condition and the photon flux jump conditions are rigorously enforced at the interface location by using only the lowest-order jump conditions. This solution near the interface is smoothly extended across the interface so that central finite difference schemes can be employed without the loss of accuracy. A wide range of numerical experiments are carried out to validate the proposed MIB method. The second-order convergence is maintained in all benchmark problems. The fourth-order convergence is also demonstrated for some three-dimensional problems. The robustness of the proposed method over the variable strength of the linear term of the diffusion equation is also examined. The performance of the present approach is compared with that of the standard finite element method. The numerical study indicates that the proposed method is a potentially efficient and robust approach for the optical molecular imaging. PMID:20485461
Computational electromagnetic methods for transcranial magnetic stimulation
NASA Astrophysics Data System (ADS)
Gomez, Luis J.
Transcranial magnetic stimulation (TMS) is a noninvasive technique used both as a research tool for cognitive neuroscience and as a FDA approved treatment for depression. During TMS, coils positioned near the scalp generate electric fields and activate targeted brain regions. In this thesis, several computational electromagnetics methods that improve the analysis, design, and uncertainty quantification of TMS systems were developed. Analysis: A new fast direct technique for solving the large and sparse linear system of equations (LSEs) arising from the finite difference (FD) discretization of Maxwell's quasi-static equations was developed. Following a factorization step, the solver permits computation of TMS fields inside realistic brain models in seconds, allowing for patient-specific real-time usage during TMS. The solver is an alternative to iterative methods for solving FD LSEs, often requiring run-times of minutes. A new integral equation (IE) method for analyzing TMS fields was developed. The human head is highly-heterogeneous and characterized by high-relative permittivities (107). IE techniques for analyzing electromagnetic interactions with such media suffer from high-contrast and low-frequency breakdowns. The novel high-permittivity and low-frequency stable internally combined volume-surface IE method developed. The method not only applies to the analysis of high-permittivity objects, but it is also the first IE tool that is stable when analyzing highly-inhomogeneous negative permittivity plasmas. Design: TMS applications call for electric fields to be sharply focused on regions that lie deep inside the brain. Unfortunately, fields generated by present-day Figure-8 coils stimulate relatively large regions near the brain surface. An optimization method for designing single feed TMS coil-arrays capable of producing more localized and deeper stimulation was developed. Results show that the coil-arrays stimulate 2.4 cm into the head while stimulating 3
Evolutionary stability on graphs
Ohtsuki, Hisashi; Nowak, Martin A.
2008-01-01
Evolutionary stability is a fundamental concept in evolutionary game theory. A strategy is called an evolutionarily stable strategy (ESS), if its monomorphic population rejects the invasion of any other mutant strategy. Recent studies have revealed that population structure can considerably affect evolutionary dynamics. Here we derive the conditions of evolutionary stability for games on graphs. We obtain analytical conditions for regular graphs of degree k > 2. Those theoretical predictions are compared with computer simulations for random regular graphs and for lattices. We study three different update rules: birth-death (BD), death-birth (DB), and imitation (IM) updating. Evolutionary stability on sparse graphs does not imply evolutionary stability in a well-mixed population, nor vice versa. We provide a geometrical interpretation of the ESS condition on graphs. PMID:18295801
Computational predictive methods for fracture and fatigue
NASA Astrophysics Data System (ADS)
Cordes, J.; Chang, A. T.; Nelson, N.; Kim, Y.
1994-09-01
The damage-tolerant design philosophy as used by aircraft industries enables aircraft components and aircraft structures to operate safely with minor damage, small cracks, and flaws. Maintenance and inspection procedures insure that damages developed during service remain below design values. When damage is found, repairs or design modifications are implemented and flight is resumed. Design and redesign guidelines, such as military specifications MIL-A-83444, have successfully reduced the incidence of damage and cracks. However, fatigue cracks continue to appear in aircraft well before the design life has expired. The F16 airplane, for instance, developed small cracks in the engine mount, wing support, bulk heads, the fuselage upper skin, the fuel shelf joints, and along the upper wings. Some cracks were found after 600 hours of the 8000 hour design service life and design modifications were required. Tests on the F16 plane showed that the design loading conditions were close to the predicted loading conditions. Improvements to analytic methods for predicting fatigue crack growth adjacent to holes, when multiple damage sites are present, and in corrosive environments would result in more cost-effective designs, fewer repairs, and fewer redesigns. The overall objective of the research described in this paper is to develop, verify, and extend the computational efficiency of analysis procedures necessary for damage tolerant design. This paper describes an elastic/plastic fracture method and an associated fatigue analysis method for damage tolerant design. Both methods are unique in that material parameters such as fracture toughness, R-curve data, and fatigue constants are not required. The methods are implemented with a general-purpose finite element package. Several proof-of-concept examples are given. With further development, the methods could be extended for analysis of multi-site damage, creep-fatigue, and corrosion fatigue problems.
Computational predictive methods for fracture and fatigue
NASA Technical Reports Server (NTRS)
Cordes, J.; Chang, A. T.; Nelson, N.; Kim, Y.
1994-01-01
The damage-tolerant design philosophy as used by aircraft industries enables aircraft components and aircraft structures to operate safely with minor damage, small cracks, and flaws. Maintenance and inspection procedures insure that damages developed during service remain below design values. When damage is found, repairs or design modifications are implemented and flight is resumed. Design and redesign guidelines, such as military specifications MIL-A-83444, have successfully reduced the incidence of damage and cracks. However, fatigue cracks continue to appear in aircraft well before the design life has expired. The F16 airplane, for instance, developed small cracks in the engine mount, wing support, bulk heads, the fuselage upper skin, the fuel shelf joints, and along the upper wings. Some cracks were found after 600 hours of the 8000 hour design service life and design modifications were required. Tests on the F16 plane showed that the design loading conditions were close to the predicted loading conditions. Improvements to analytic methods for predicting fatigue crack growth adjacent to holes, when multiple damage sites are present, and in corrosive environments would result in more cost-effective designs, fewer repairs, and fewer redesigns. The overall objective of the research described in this paper is to develop, verify, and extend the computational efficiency of analysis procedures necessary for damage tolerant design. This paper describes an elastic/plastic fracture method and an associated fatigue analysis method for damage tolerant design. Both methods are unique in that material parameters such as fracture toughness, R-curve data, and fatigue constants are not required. The methods are implemented with a general-purpose finite element package. Several proof-of-concept examples are given. With further development, the methods could be extended for analysis of multi-site damage, creep-fatigue, and corrosion fatigue problems.
Computational Methods for Domain Partitioning of Protein Structures
NASA Astrophysics Data System (ADS)
Veretnik, Stella; Shindyalov, Ilya
Analysis of protein structures typically begins with decomposition of structure into more basic units, called "structural domains". The underlying goal is to reduce a complex protein structure to a set of simpler yet structurally meaningful units, each of which can be analyzed independently. Structural semi-independence of domains is their hallmark: domains often have compact structure and can fold or function independently. Domains can undergo so-called "domain shuffling"when they reappear in different combinations in different proteins thus implementing different biological functions (Doolittle, 1995). Proteins can then be conceived as being built of such basic blocks: some, especially small proteins, consist usually of just one domain, while other proteins possess a more complex architecture containing multiple domains. Therefore, the methods for partitioning a structure into domains are of critical importance: their outcome defines the set of basic units upon which structural classifications are built and evolutionary analysis is performed. This is especially true nowadays in the era of structural genomics. Today there are many methods that decompose the structure into domains: some of them are manual (i.e., based on human judgment), others are semiautomatic, and still others are completely automatic (based on algorithms implemented as software). Overall there is a high level of consistency and robustness in the process of partitioning a structure into domains (for ˜80% of proteins); at least for structures where domain location is obvious. The picture is less bright when we consider proteins with more complex architectures—neither human experts nor computational methods can reach consistent partitioning in many such cases. This is a rather accurate reflection of biological phenomena in general since domains are formed by different mechanisms, hence it is nearly impossible to come up with a set of well-defined rules that captures all of the observed cases.
Domain decomposition methods in computational fluid dynamics
NASA Technical Reports Server (NTRS)
Gropp, William D.; Keyes, David E.
1992-01-01
The divide-and-conquer paradigm of iterative domain decomposition, or substructuring, has become a practical tool in computational fluid dynamic applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. These features are illustrated on the classic model problem of flow over a backstep using Newton's method as the nonlinear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately, and they can be combined synergistically. Sample performance results are included from an Intel iPSC/860 hypercube implementation.
Domain decomposition methods in computational fluid dynamics
NASA Technical Reports Server (NTRS)
Gropp, William D.; Keyes, David E.
1991-01-01
The divide-and-conquer paradigm of iterative domain decomposition, or substructuring, has become a practical tool in computational fluid dynamic applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. These features are illustrated on the classic model problem of flow over a backstep using Newton's method as the nonlinear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately, and they can be combined synergistically. Sample performance results are included from an Intel iPSC/860 hypercube implementation.
Computational simulation methods for composite fracture mechanics
NASA Technical Reports Server (NTRS)
Murthy, Pappu L. N.
1988-01-01
Structural integrity, durability, and damage tolerance of advanced composites are assessed by studying damage initiation at various scales (micro, macro, and global) and accumulation and growth leading to global failure, quantitatively and qualitatively. In addition, various fracture toughness parameters associated with a typical damage and its growth must be determined. Computational structural analysis codes to aid the composite design engineer in performing these tasks were developed. CODSTRAN (COmposite Durability STRuctural ANalysis) is used to qualitatively and quantitatively assess the progressive damage occurring in composite structures due to mechanical and environmental loads. Next, methods are covered that are currently being developed and used at Lewis to predict interlaminar fracture toughness and related parameters of fiber composites given a prescribed damage. The general purpose finite element code MSC/NASTRAN was used to simulate the interlaminar fracture and the associated individual as well as mixed-mode strain energy release rates in fiber composites.
Modules and methods for all photonic computing
Schultz, David R.; Ma, Chao Hung
2001-01-01
A method for all photonic computing, comprising the steps of: encoding a first optical/electro-optical element with a two dimensional mathematical function representing input data; illuminating the first optical/electro-optical element with a collimated beam of light; illuminating a second optical/electro-optical element with light from the first optical/electro-optical element, the second optical/electro-optical element having a characteristic response corresponding to an iterative algorithm useful for solving a partial differential equation; iteratively recirculating the signal through the second optical/electro-optical element with light from the second optical/electro-optical element for a predetermined number of iterations; and, after the predetermined number of iterations, optically and/or electro-optically collecting output data representing an iterative optical solution from the second optical/electro-optical element.
47 CFR 80.771 - Method of computing coverage.
Code of Federal Regulations, 2011 CFR
2011-10-01
... 47 Telecommunication 5 2011-10-01 2011-10-01 false Method of computing coverage. 80.771 Section 80... STATIONS IN THE MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.771 Method of computing coverage. Compute the +17 dBu contour as follows: (a) Determine the effective...
47 CFR 80.771 - Method of computing coverage.
Code of Federal Regulations, 2010 CFR
2010-10-01
... 47 Telecommunication 5 2010-10-01 2010-10-01 false Method of computing coverage. 80.771 Section 80... STATIONS IN THE MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.771 Method of computing coverage. Compute the +17 dBu contour as follows: (a) Determine the effective...
Rivera-Rivera, Carlos J; Montoya-Burgos, Juan I
2016-06-01
Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Locus Specific Sequence Subsampling (LS³), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS³ sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software implementation provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS³ with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS³. PMID:26912812
Rivera-Rivera, Carlos J.; Montoya-Burgos, Juan I.
2016-01-01
Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Locus Specific Sequence Subsampling (LS³), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS³ sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software implementation provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS³ with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS³. PMID:26912812
Computational Evaluation of the Traceback Method
ERIC Educational Resources Information Center
Kol, Sheli; Nir, Bracha; Wintner, Shuly
2014-01-01
Several models of language acquisition have emerged in recent years that rely on computational algorithms for simulation and evaluation. Computational models are formal and precise, and can thus provide mathematically well-motivated insights into the process of language acquisition. Such models are amenable to robust computational evaluation,…
Pinheiro, Ana; Woof, Jenny M.; Abi-Rached, Laurent; Parham, Peter; Esteves, Pedro J.
2013-01-01
IgA is the predominant immunoglobulin isotype in mucosal tissues and external secretions, playing important roles both in defense against pathogens and in maintenance of commensal microbiota. Considering the complexity of its interactions with the surrounding environment, IgA is a likely target for diversifying or positive selection. To investigate this possibility, the action of natural selection on IgA was examined in depth with six different methods: CODEML from the PAML package and the SLAC, FEL, REL, MEME and FUBAR methods implemented in the Datamonkey webserver. In considering just primate IgA, these analyses show that diversifying selection targeted five positions of the Cα1 and Cα2 domains of IgA. Extending the analysis to include other mammals identified 18 positively selected sites: ten in Cα1, five in Cα2 and three in Cα3. All but one of these positions display variation in polarity and charge. Their structural locations suggest they indirectly influence the conformation of sites on IgA that are critical for interaction with host IgA receptors and also with proteins produced by mucosal pathogens that prevent their elimination by IgA-mediated effector mechanisms. Demonstrating the plasticity of IgA in the evolution of different groups of mammals, only two of the eighteen selected positions in all mammals are included in the five selected positions in primates. That IgA residues subject to positive selection impact sites targeted both by host receptors and subversive pathogen ligands highlights the evolutionary arms race playing out between mammals and pathogens, and further emphasizes the importance of IgA in protection against mucosal pathogens. PMID:24019941
Pinheiro, Ana; Woof, Jenny M; Abi-Rached, Laurent; Parham, Peter; Esteves, Pedro J
2013-01-01
IgA is the predominant immunoglobulin isotype in mucosal tissues and external secretions, playing important roles both in defense against pathogens and in maintenance of commensal microbiota. Considering the complexity of its interactions with the surrounding environment, IgA is a likely target for diversifying or positive selection. To investigate this possibility, the action of natural selection on IgA was examined in depth with six different methods: CODEML from the PAML package and the SLAC, FEL, REL, MEME and FUBAR methods implemented in the Datamonkey webserver. In considering just primate IgA, these analyses show that diversifying selection targeted five positions of the Cα1 and Cα2 domains of IgA. Extending the analysis to include other mammals identified 18 positively selected sites: ten in Cα1, five in Cα2 and three in Cα3. All but one of these positions display variation in polarity and charge. Their structural locations suggest they indirectly influence the conformation of sites on IgA that are critical for interaction with host IgA receptors and also with proteins produced by mucosal pathogens that prevent their elimination by IgA-mediated effector mechanisms. Demonstrating the plasticity of IgA in the evolution of different groups of mammals, only two of the eighteen selected positions in all mammals are included in the five selected positions in primates. That IgA residues subject to positive selection impact sites targeted both by host receptors and subversive pathogen ligands highlights the evolutionary arms race playing out between mammals and pathogens, and further emphasizes the importance of IgA in protection against mucosal pathogens. PMID:24019941
Object Orientated Methods in Computational Fluid Dynamics.
NASA Astrophysics Data System (ADS)
Tabor, Gavin; Weller, Henry; Jasak, Hrvoje; Fureby, Christer
1997-11-01
We outline the aims of the FOAM code, a Finite Volume Computational Fluid Dynamics code written in C++, and discuss the use of Object Orientated Programming (OOP) methods to achieve these aims. The intention when writing this code was to make it as easy as possible to alter the modelling : this was achieved by making the top level syntax of the code as close as possible to conventional mathematical notation for tensors and partial differential equations. Object orientation enables us to define classes for both types of objects, and the operator overloading possible in C++ allows normal symbols to be used for the basic operations. The introduction of features such as automatic dimension checking of equations helps to enforce correct coding of models. We also discuss the use of OOP techniques such as data encapsulation and code reuse. As examples of the flexibility of this approach, we discuss the implementation of turbulence modelling using RAS and LES. The code is used to simulate turbulent flow for a number of test cases, including fully developed channel flow and flow around obstacles. We also demonstrate the use of the code for solving structures calculations and magnetohydrodynamics.
ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING
The overall goal of the EPA-ORD NERL research program on Computational Toxicology (CompTox) is to provide the Agency with the tools of modern chemistry, biology, and computing to improve quantitative risk assessments and reduce uncertainties in the source-to-adverse outcome conti...
Methods for Improving the User-Computer Interface. Technical Report.
ERIC Educational Resources Information Center
McCann, Patrick H.
This summary of methods for improving the user-computer interface is based on a review of the pertinent literature. Requirements of the personal computer user are identified and contrasted with computer designer perspectives towards the user. The user's psychological needs are described, so that the design of the user-computer interface may be…
Valavanis, Ioannis; Pilalis, Eleftherios; Georgiadis, Panagiotis; Kyrtopoulos, Soterios; Chatziioannou, Aristotelis
2015-01-01
DNA methylation profiling exploits microarray technologies, thus yielding a wealth of high-volume data. Here, an intelligent framework is applied, encompassing epidemiological genome-scale DNA methylation data produced from the Illumina’s Infinium Human Methylation 450K Bead Chip platform, in an effort to correlate interesting methylation patterns with cancer predisposition and, in particular, breast cancer and B-cell lymphoma. Feature selection and classification are employed in order to select, from an initial set of ~480,000 methylation measurements at CpG sites, predictive cancer epigenetic biomarkers and assess their classification power for discriminating healthy versus cancer related classes. Feature selection exploits evolutionary algorithms or a graph-theoretic methodology which makes use of the semantics information included in the Gene Ontology (GO) tree. The selected features, corresponding to methylation of CpG sites, attained moderate-to-high classification accuracies when imported to a series of classifiers evaluated by resampling or blindfold validation. The semantics-driven selection revealed sets of CpG sites performing similarly with evolutionary selection in the classification tasks. However, gene enrichment and pathway analysis showed that it additionally provides more descriptive sets of GO terms and KEGG pathways regarding the cancer phenotypes studied here. Results support the expediency of this methodology regarding its application in epidemiological studies.
Tseng, Z. Jack; Flynn, John J.
2015-01-01
Morphology serves as a ubiquitous proxy in macroevolutionary studies to identify potential adaptive processes and patterns. Inferences of functional significance of phenotypes or their evolution are overwhelmingly based on data from living taxa. Yet, correspondence between form and function has been tested in only a few model species, and those linkages are highly complex. The lack of explicit methodologies to integrate form and function analyses within a deep-time and phylogenetic context weakens inferences of adaptive morphological evolution, by invoking but not testing form–function linkages. Here, we provide a novel approach to test mechanical properties at reconstructed ancestral nodes/taxa and the strength and direction of evolutionary pathways in feeding biomechanics, in a case study of carnivorous mammals. Using biomechanical profile comparisons that provide functional signals for the separation of feeding morphologies, we demonstrate, using experimental optimization criteria on estimation of strength and direction of functional changes on a phylogeny, that convergence in mechanical properties and degree of evolutionary optimization can be decoupled. This integrative approach is broadly applicable to other clades, by using quantitative data and model-based tests to evaluate interpretations of function from morphology and functional explanations for observed macroevolutionary pathways. PMID:25994295
Tseng, Z Jack; Flynn, John J
2015-06-01
Morphology serves as a ubiquitous proxy in macroevolutionary studies to identify potential adaptive processes and patterns. Inferences of functional significance of phenotypes or their evolution are overwhelmingly based on data from living taxa. Yet, correspondence between form and function has been tested in only a few model species, and those linkages are highly complex. The lack of explicit methodologies to integrate form and function analyses within a deep-time and phylogenetic context weakens inferences of adaptive morphological evolution, by invoking but not testing form-function linkages. Here, we provide a novel approach to test mechanical properties at reconstructed ancestral nodes/taxa and the strength and direction of evolutionary pathways in feeding biomechanics, in a case study of carnivorous mammals. Using biomechanical profile comparisons that provide functional signals for the separation of feeding morphologies, we demonstrate, using experimental optimization criteria on estimation of strength and direction of functional changes on a phylogeny, that convergence in mechanical properties and degree of evolutionary optimization can be decoupled. This integrative approach is broadly applicable to other clades, by using quantitative data and model-based tests to evaluate interpretations of function from morphology and functional explanations for observed macroevolutionary pathways. PMID:25994295
Computational methods in sequence and structure prediction
NASA Astrophysics Data System (ADS)
Lang, Caiyi
This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter sequence structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the upstream of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the upstream regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the upstream regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed
Reliability of cephalometric analysis using manual and interactive computer methods.
Davis, D N; Mackay, F
1991-05-01
This study compares the results of cephalometric analyses using manual and interactive computer graphics methods. Results are statistically in favour of the interactive computer system. This study provides a basis for ongoing research into alternative methods of cephalometric analyses, such as digitization and automatic landmark identification using sophisticated computer vision systems. PMID:1911687
Evolutionary enhancement of the SLIM-MAUD method of estimating human error rates
Zamanali, J.H. ); Hubbard, F.R. ); Mosleh, A. ); Waller, M.A. )
1992-01-01
The methodology described in this paper assigns plant-specific dynamic human error rates (HERs) for individual plant examinations based on procedural difficulty, on configuration features, and on the time available to perform the action. This methodology is an evolutionary improvement of the success likelihood index methodology (SLIM-MAUD) for use in systemic scenarios. It is based on the assumption that the HER in a particular situation depends of the combined effects of a comprehensive set of performance-shaping factors (PSFs) that influence the operator's ability to perform the action successfully. The PSFs relate the details of the systemic scenario in which the action must be performed according to the operator's psychological and cognitive condition.
Computational structural mechanics methods research using an evolving framework
NASA Technical Reports Server (NTRS)
Knight, N. F., Jr.; Lotts, C. G.; Gillian, R. E.
1990-01-01
Advanced structural analysis and computational methods that exploit high-performance computers are being developed in a computational structural mechanics research activity sponsored by the NASA Langley Research Center. These new methods are developed in an evolving framework and applied to representative complex structural analysis problems from the aerospace industry. An overview of the methods development environment is presented, and methods research areas are described. Selected application studies are also summarized.
The causal pie model: an epidemiological method applied to evolutionary biology and ecology.
Wensink, Maarten; Westendorp, Rudi G J; Baudisch, Annette
2014-05-01
A general concept for thinking about causality facilitates swift comprehension of results, and the vocabulary that belongs to the concept is instrumental in cross-disciplinary communication. The causal pie model has fulfilled this role in epidemiology and could be of similar value in evolutionary biology and ecology. In the causal pie model, outcomes result from sufficient causes. Each sufficient cause is made up of a "causal pie" of "component causes". Several different causal pies may exist for the same outcome. If and only if all component causes of a sufficient cause are present, that is, a causal pie is complete, does the outcome occur. The effect of a component cause hence depends on the presence of the other component causes that constitute some causal pie. Because all component causes are equally and fully causative for the outcome, the sum of causes for some outcome exceeds 100%. The causal pie model provides a way of thinking that maps into a number of recurrent themes in evolutionary biology and ecology: It charts when component causes have an effect and are subject to natural selection, and how component causes affect selection on other component causes; which partitions of outcomes with respect to causes are feasible and useful; and how to view the composition of a(n apparently homogeneous) population. The diversity of specific results that is directly understood from the causal pie model is a test for both the validity and the applicability of the model. The causal pie model provides a common language in which results across disciplines can be communicated and serves as a template along which future causal analyses can be made. PMID:24963386
Dembo, Mana; Radovčić, Davorka; Garvin, Heather M; Laird, Myra F; Schroeder, Lauren; Scott, Jill E; Brophy, Juliet; Ackermann, Rebecca R; Musiba, Chares M; de Ruiter, Darryl J; Mooers, Arne Ø; Collard, Mark
2016-08-01
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: "Where does H. naledi fit in the hominin evolutionary tree?" and "How old is it?" We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out three analyses. First, we performed a dated Bayesian analysis to generate estimates of the evolutionary relationships of fossil hominins including H. naledi. Then we employed Bayes factor tests to compare the strength of support for hypotheses about the relationships of H. naledi suggested by the best-estimate trees. Lastly, we carried out a resampling analysis to assess the accuracy of the age estimate for H. naledi yielded by the dated Bayesian analysis. The analyses strongly supported the hypothesis that H. naledi forms a clade with the other Homo species and Australopithecus sediba. The analyses were more ambiguous regarding the position of H. naledi within the (Homo, Au. sediba) clade. A number of hypotheses were rejected, but several others were not. Based on the available craniodental data, Homo antecessor, Asian Homo erectus, Homo habilis, Homo floresiensis, Homo sapiens, and Au. sediba could all be the sister taxon of H. naledi. According to the dated Bayesian analysis, the most likely age for H. naledi is 912 ka. This age estimate was supported by the resampling analysis. Our findings have a number of implications. Most notably, they support the assignment of the new specimens to Homo, cast doubt on the claim that H. naledi is simply a variant of H. erectus, and suggest H. naledi is younger than has been previously proposed. PMID:27457542
Method of performing computational aeroelastic analyses
NASA Technical Reports Server (NTRS)
Silva, Walter A. (Inventor)
2011-01-01
Computational aeroelastic analyses typically use a mathematical model for the structural modes of a flexible structure and a nonlinear aerodynamic model that can generate a plurality of unsteady aerodynamic responses based on the structural modes for conditions defining an aerodynamic condition of the flexible structure. In the present invention, a linear state-space model is generated using a single execution of the nonlinear aerodynamic model for all of the structural modes where a family of orthogonal functions is used as the inputs. Then, static and dynamic aeroelastic solutions are generated using computational interaction between the mathematical model and the linear state-space model for a plurality of periodic points in time.
Wing analysis using a transonic potential flow computational method
NASA Technical Reports Server (NTRS)
Henne, P. A.; Hicks, R. M.
1978-01-01
The ability of the method to compute wing transonic performance was determined by comparing computed results with both experimental data and results computed by other theoretical procedures. Both pressure distributions and aerodynamic forces were evaluated. Comparisons indicated that the method is a significant improvement in transonic wing analysis capability. In particular, the computational method generally calculated the correct development of three-dimensional pressure distributions from subcritical to transonic conditions. Complicated, multiple shocked flows observed experimentally were reproduced computationally. The ability to identify the effects of design modifications was demonstrated both in terms of pressure distributions and shock drag characteristics.
A method of billing third generation computer users
NASA Technical Reports Server (NTRS)
Anderson, P. N.; Hyter, D. R.
1973-01-01
A method is presented for charging users for the processing of their applications on third generation digital computer systems is presented. For background purposes, problems and goals in billing on third generation systems are discussed. Detailed formulas are derived based on expected utilization and computer component cost. These formulas are then applied to a specific computer system (UNIVAC 1108). The method, although possessing some weaknesses, is presented as a definite improvement over use of second generation billing methods.
Soft computing methods for geoidal height transformation
NASA Astrophysics Data System (ADS)
Akyilmaz, O.; Özlüdemir, M. T.; Ayan, T.; Çelik, R. N.
2009-07-01
Soft computing techniques, such as fuzzy logic and artificial neural network (ANN) approaches, have enabled researchers to create precise models for use in many scientific and engineering applications. Applications that can be employed in geodetic studies include the estimation of earth rotation parameters and the determination of mean sea level changes. Another important field of geodesy in which these computing techniques can be applied is geoidal height transformation. We report here our use of a conventional polynomial model, the Adaptive Network-based Fuzzy (or in some publications, Adaptive Neuro-Fuzzy) Inference System (ANFIS), an ANN and a modified ANN approach to approximate geoid heights. These approximation models have been tested on a number of test points. The results obtained through the transformation processes from ellipsoidal heights into local levelling heights have also been compared.
Computational Methods to Predict Protein Interaction Partners
NASA Astrophysics Data System (ADS)
Valencia, Alfonso; Pazos, Florencio
In the new paradigm for studying biological phenomena represented by Systems Biology, cellular components are not considered in isolation but as forming complex networks of relationships. Protein interaction networks are among the first objects studied from this new point of view. Deciphering the interactome (the whole network of interactions for a given proteome) has been shown to be a very complex task. Computational techniques for detecting protein interactions have become standard tools for dealing with this problem, helping and complementing their experimental counterparts. Most of these techniques use genomic or sequence features intuitively related with protein interactions and are based on "first principles" in the sense that they do not involve training with examples. There are also other computational techniques that use other sources of information (i.e. structural information or even experimental data) or are based on training with examples.
Cao, Buwen; Luo, Jiawei; Liang, Cheng; Wang, Shulin; Song, Dan
2015-10-01
The identification of protein complexes in protein-protein interaction (PPI) networks has greatly advanced our understanding of biological organisms. Existing computational methods to detect protein complexes are usually based on specific network topological properties of PPI networks. However, due to the inherent complexity of the network structures, the identification of protein complexes may not be fully addressed by using single network topological property. In this study, we propose a novel MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. Our approach first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally we describe our algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of our method, we compared MOEPGA with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, our approach can cover a certain number of proteins in the input PPI network in terms of the normalized clustering score. Taken together, our method can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions. PMID:26298638
Integrative tracking methods elucidate the evolutionary dynamics of a migratory divide
Alvarado, Allison H; Fuller, Trevon L; Smith, Thomas B
2014-01-01
Migratory divides, the boundary between adjacent bird populations that migrate in different directions, are of considerable interest to evolutionary biologists because of their alleged role in speciation of migratory birds. However, the small size of many passerines has traditionally limited the tools available to track populations and as a result, restricted our ability to study how reproductive isolation might occur across a divide. Here, we integrate multiple approaches by using genetic, geolocator, and morphological data to investigate a migratory divide in hermit thrushes (Catharus guttatus). First, high genetic divergence between migratory groups indicates the divide is a region of secondary contact between historically isolated populations. Second, despite low sample sizes, geolocators reveal dramatic differences in overwintering locations and migratory distance of individuals from either side of the divide. Third, a diagnostic genetic marker that proved useful for tracking a key population suggests a likely intermediate nonbreeding location of birds from the hybrid zone. This finding, combined with lower return rates from this region, is consistent with comparatively lower fitness of hybrids, which is possibly due to this intermediate migration pattern. We discuss our results in the context of reproductive isolating mechanisms associated with migration patterns that have long been hypothesized to promote divergence across migratory divides. PMID:25535561
Soft Computing Methods in Design of Superalloys
NASA Technical Reports Server (NTRS)
Cios, K. J.; Berke, L.; Vary, A.; Sharma, S.
1996-01-01
Soft computing techniques of neural networks and genetic algorithms are used in the design of superalloys. The cyclic oxidation attack parameter K(sub a), generated from tests at NASA Lewis Research Center, is modelled as a function of the superalloy chemistry and test temperature using a neural network. This model is then used in conjunction with a genetic algorithm to obtain an optimized superalloy composition resulting in low K(sub a) values.
Computational methods for physical mapping of chromosomes
Torney, D.C.; Schenk, K.R. ); Whittaker, C.C. Los Alamos National Lab., NM ); White, S.W. )
1990-01-01
A standard technique for mapping a chromosome is to randomly select pieces, to use restriction enzymes to cut these pieces into fragments, and then to use the fragments for estimating the probability of overlap of these pieces. Typically, the order of the fragments within a piece is not determined, and the observed fragment data from each pair of pieces must be permuted N1 {times} N2 ways to evaluate the probability of overlap, N1 and N2 being the observed number of fragments in the two selected pieces. We will describe computational approaches used to substantially reduce the computational complexity of the calculation of overlap probability from fragment data. Presently, about 10{sup {minus}4} CPU seconds on one processor of an IBM 3090 is required for calculation of overlap probability from the fragment data of two randomly selected pieces, with an average of ten fragments per piece. A parallel version has been written using IBM clustered FORTRAN. Parallel measurements for 1, 6, and 12 processors will be presented. This approach has proven promising in the mapping of chromosome 16 at Los Alamos National Laboratory. We will also describe other computational challenges presented by physical mapping. 4 refs., 4 figs., 1 tab.
Computational Methods for Analyzing Health News Coverage
ERIC Educational Resources Information Center
McFarlane, Delano J.
2011-01-01
Researchers that investigate the media's coverage of health have historically relied on keyword searches to retrieve relevant health news coverage, and manual content analysis methods to categorize and score health news text. These methods are problematic. Manual content analysis methods are labor intensive, time consuming, and inherently…
Integral Deferred Correction methods for scientific computing
NASA Astrophysics Data System (ADS)
Morton, Maureen Marilla
Since high order numerical methods frequently can attain accurate solutions more efficiently than low order methods, we develop and analyze new high order numerical integrators for the time discretization of ordinary and partial differential equations. Our novel methods address some of the issues surrounding high order numerical time integration, such as the difficulty of many popular methods' construction and handling the effects of disparate behaviors produce by different terms in the equations to be solved. We are motivated by the simplicity of how Deferred Correction (DC) methods achieve high order accuracy [72, 27]. DC methods are numerical time integrators that, rather than calculating tedious coefficients for order conditions, instead construct high order accurate solutions by iteratively improving a low order preliminary numerical solution. With each iteration, an error equation is solved, the error decreases, and the order of accuracy increases. Later, DC methods were adjusted to include an integral formulation of the residual, which stabilizes the method. These Spectral Deferred Correction (SDC) methods [25] motivated Integral Deferred Corrections (IDC) methods. Typically, SDC methods are limited to increasing the order of accuracy by one with each iteration due to smoothness properties imposed by the gridspacing. However, under mild assumptions, explicit IDC methods allow for any explicit rth order Runge-Kutta (RK) method to be used within each iteration, and then an order of accuracy increase of r is attained after each iteration [18]. We extend these results to the construction of implicit IDC methods that use implicit RK methods, and we prove analogous results for order of convergence. One means of solving equations with disparate parts is by semi-implicit integrators, handling a "fast" part implicitly and a "slow" part explicitly. We incorporate additive RK (ARK) integrators into the iterations of IDC methods in order to construct new arbitrary order
Holmes, Tim; Zanker, Johannes M.
2013-01-01
Studying aesthetic preference is notoriously difficult because it targets individual experience. Eye movements provide a rich source of behavioral measures that directly reflect subjective choice. To determine individual preferences for simple composition rules we here use fixation duration as the fitness measure in a Gaze Driven Evolutionary Algorithm (GDEA), which has been demonstrated as a tool to identify aesthetic preferences (Holmes and Zanker, 2012). In the present study, the GDEA was used to investigate the preferred combination of color and shape which have been promoted in the Bauhaus arts school. We used the same three shapes (square, circle, triangle) used by Kandinsky (1923), with the three color palette from the original experiment (A), an extended seven color palette (B), and eight different shape orientation (C). Participants were instructed to look for their preferred circle, triangle or square in displays with eight stimuli of different shapes, colors and rotations, in an attempt to test for a strong preference for red squares, yellow triangles and blue circles in such an unbiased experimental design and with an extended set of possible combinations. We Tested six participants extensively on the different conditions and found consistent preferences for color-shape combinations for individuals, but little evidence at the group level for clear color/shape preference consistent with Kandinsky's claims, apart from some weak link between yellow and triangles. Our findings suggest substantial inter-individual differences in the presence of stable individual associations of color and shapes, but also that these associations are robust within a single individual. These individual differences go some way toward challenging the claims of the universal preference for color/shape combinations proposed by Kandinsky, but also indicate that a much larger sample size would be needed to confidently reject that hypothesis. Moreover, these experiments highlight the
Meiklejohn, Kelly A; Faircloth, Brant C; Glenn, Travis C; Kimball, Rebecca T; Braun, Edward L
2016-07-01
Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10-15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences
Computation of Transonic Flows Using Potential Methods
NASA Technical Reports Server (NTRS)
Hoist, Terry L.; Kwak, Dochan (Technical Monitor)
1997-01-01
The proposed paper will describe the state of the art associated with numerical solution of the full or exact velocity potential equation for solving transonic, external-aerodynamic flows. The presentation will begin with a review of the literature emphasizing research activities of the past decade. Next, the various forms of the full or exact velocity potential equation, the equation's corresponding mathematical characteristics, and the derivation assumptions will be presented and described in detail. Impact of the derivation assumptions on simulation accuracy, especially with respect to shock wave capture, will be presented and discussed relative to the more complete Euler or Navier-Stokes formulations. The technical presentation will continue with a description of recently developed full potential numerical approach characteristics. This description will include governing equation nondimensionalization, physical-to-computational-domain mapping procedures, a limited description of grid generation requirements, the spatial discretization scheme, numerical implementation of boundary conditions, and the iteration scheme. The next portion of the presentation will present and discuss numerical results for several two- and three-dimensional aerodynamic applications. Included in the results section will be a discussion and demonstration of a typical grid refinement analysis for determining spatial convergence of the numerical solution and level of solution accuracy. Computer timings for a variety of full potential applications will be compared and contrasted with similar results for the Euler equation formulation. Finally. the presentation will end with concluding remarks and recommendations for future work.
Computational Methods for Jet Noise Simulation
NASA Technical Reports Server (NTRS)
Goodrich, John W. (Technical Monitor); Hagstrom, Thomas
2003-01-01
The purpose of our project is to develop, analyze, and test novel numerical technologies central to the long term goal of direct simulations of subsonic jet noise. Our current focus is on two issues: accurate, near-field domain truncations and high-order, single-step discretizations of the governing equations. The Direct Numerical Simulation (DNS) of jet noise poses a number of extreme challenges to computational technique. In particular, the problem involves multiple temporal and spatial scales as well as flow instabilities and is posed on an unbounded spatial domain. Moreover, the basic phenomenon of interest, the radiation of acoustic waves to the far field, involves only a minuscule fraction of the total energy. The best current simulations of jet noise are at low Reynolds number. It is likely that an increase of one to two orders of magnitude will be necessary to reach a regime where the separation between the energy-containing and dissipation scales is sufficient to make the radiated noise essentially independent of the Reynolds number. Such an increase in resolution cannot be obtained in the near future solely through increases in computing power. Therefore, new numerical methodologies of maximal efficiency and accuracy are required.
Discontinuous Galerkin Methods: Theory, Computation and Applications
Cockburn, B.; Karniadakis, G. E.; Shu, C-W
2000-12-31
This volume contains a survey article for Discontinuous Galerkin Methods (DGM) by the editors as well as 16 papers by invited speakers and 32 papers by contributed speakers of the First International Symposium on Discontinuous Galerkin Methods. It covers theory, applications, and implementation aspects of DGM.
Computational methods for aerodynamic design using numerical optimization
NASA Technical Reports Server (NTRS)
Peeters, M. F.
1983-01-01
Five methods to increase the computational efficiency of aerodynamic design using numerical optimization, by reducing the computer time required to perform gradient calculations, are examined. The most promising method consists of drastically reducing the size of the computational domain on which aerodynamic calculations are made during gradient calculations. Since a gradient calculation requires the solution of the flow about an airfoil whose geometry was slightly perturbed from a base airfoil, the flow about the base airfoil is used to determine boundary conditions on the reduced computational domain. This method worked well in subcritical flow.
Three parallel computation methods for structural vibration analysis
NASA Technical Reports Server (NTRS)
Storaasli, Olaf; Bostic, Susan; Patrick, Merrell; Mahajan, Umesh; Ma, Shing
1988-01-01
The Lanczos (1950), multisectioning, and subspace iteration sequential methods for vibration analysis presently used as bases for three parallel algorithms are noted, in the aftermath of three example problems, to maintain reasonable accuracy in the computation of vibration frequencies. Significant computation time reductions are obtained as the number of processors increases. An analysis is made of the performance of each method, in order to characterize relative strengths and weaknesses as well as to identify those parameters that most strongly affect computation efficiency.
Domain identification in impedance computed tomography by spline collocation method
NASA Technical Reports Server (NTRS)
Kojima, Fumio
1990-01-01
A method for estimating an unknown domain in elliptic boundary value problems is considered. The problem is formulated as an inverse problem of integral equations of the second kind. A computational method is developed using a splice collocation scheme. The results can be applied to the inverse problem of impedance computed tomography (ICT) for image reconstruction.
12 CFR 227.25 - Unfair balance computation method.
Code of Federal Regulations, 2010 CFR
2010-01-01
... under 12 CFR 226.12 or 12 CFR 226.13; or (2) Adjustments to finance charges as a result of the return of... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Unfair balance computation method. 227.25... Practices Rule § 227.25 Unfair balance computation method. (a) General rule. Except as provided in...
Overview of computational structural methods for modern military aircraft
NASA Technical Reports Server (NTRS)
Kudva, J. N.
1992-01-01
Computational structural methods are essential for designing modern military aircraft. This briefing deals with computational structural methods (CSM) currently used. First a brief summary of modern day aircraft structural design procedures is presented. Following this, several ongoing CSM related projects at Northrop are discussed. Finally, shortcomings in this area, future requirements, and summary remarks are given.
Classical versus Computer Algebra Methods in Elementary Geometry
ERIC Educational Resources Information Center
Pech, Pavel
2005-01-01
Computer algebra methods based on results of commutative algebra like Groebner bases of ideals and elimination of variables make it possible to solve complex, elementary and non elementary problems of geometry, which are difficult to solve using a classical approach. Computer algebra methods permit the proof of geometric theorems, automatic…
Method and device for computed tomography
Lux, P.W.; Op De Beek, J.C.A.; Van Leiden, H.F.
1983-09-06
A computer tomography device in which the detectors are asymmetrically arranged with respect to the connecting line between the X-ray source, the center of rotation of the source, and the detectors is disclosed. The detector device produces an incomplete profile of measuring values which are supplemented with ''zeros'' during processing in order to form a number of measuring values of a complete profile. In order to avoid artefacts which are produced by the acute transients between measuring values and ''zeros'', a number of measuring values adjoining the acute transients are projected around the center of rotation and multipled by a factor so that from the zeros a smoothly increasing series of adapted measuring values is obtained.
Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin.
Bhutoria, Savita; Kalpana, Ganjam V; Acharya, Seetharama A
2016-09-01
The structure of a protein can be very informative of its function. However, determining protein structures experimentally can often be very challenging. Computational methods have been used successfully in modeling structures with sufficient accuracy. Here we have used computational tools to predict the structure of an evolutionarily conserved and functionally significant domain of Integrase interactor (INI)1/hSNF5 protein. INI1 is a component of the chromatin remodeling SWI/SNF complex, a tumor suppressor and is involved in many protein-protein interactions. It belongs to SNF5 family of proteins that contain two conserved repeat (Rpt) domains. Rpt1 domain of INI1 binds to HIV-1 Integrase, and acts as a dominant negative mutant to inhibit viral replication. Rpt1 domain also interacts with oncogene c-MYC and modulates its transcriptional activity. We carried out an ab initio modeling of a segment of INI1 protein containing the Rpt1 domain. The structural model suggested the presence of a compact and well defined ββαα topology as core structure in the Rpt1 domain of INI1. This topology in Rpt1 was similar to PFU domain of Phospholipase A2 Activating Protein, PLAA. Interestingly, PFU domain shares similarity with Ubiquitin and has ubiquitin binding activity. Because of the structural similarity between Rpt1 domain of INI1 and PFU domain of PLAA, we propose that Rpt1 domain of INI1 may participate in ubiquitin recognition or binding with ubiquitin or ubiquitin related proteins. This modeling study may shed light on the mode of interactions of Rpt1 domain of INI1 and is likely to facilitate future functional studies of INI1. PMID:27261671
COMSAC: Computational Methods for Stability and Control. Part 1
NASA Technical Reports Server (NTRS)
Fremaux, C. Michael (Compiler); Hall, Robert M. (Compiler)
2004-01-01
Work on stability and control included the following reports:Introductory Remarks; Introduction to Computational Methods for Stability and Control (COMSAC); Stability & Control Challenges for COMSAC: a NASA Langley Perspective; Emerging CFD Capabilities and Outlook A NASA Langley Perspective; The Role for Computational Fluid Dynamics for Stability and Control:Is it Time?; Northrop Grumman Perspective on COMSAC; Boeing Integrated Defense Systems Perspective on COMSAC; Computational Methods in Stability and Control:WPAFB Perspective; Perspective: Raytheon Aircraft Company; A Greybeard's View of the State of Aerodynamic Prediction; Computational Methods for Stability and Control: A Perspective; Boeing TacAir Stability and Control Issues for Computational Fluid Dynamics; NAVAIR S&C Issues for CFD; An S&C Perspective on CFD; Issues, Challenges & Payoffs: A Boeing User s Perspective on CFD for S&C; and Stability and Control in Computational Simulations for Conceptual and Preliminary Design: the Past, Today, and Future?
Marcé-Nogué, Jordi; Fortuny, Josep; De Esteban-Trivigno, Soledad; Sánchez, Montserrat; Gil, Lluís; Galobart, Àngel
2015-01-01
For the first time in vertebrate palaeontology, the potential of joining Finite Element Analysis (FEA) and Parametrical Analysis (PA) is used to shed new light on two different cranial parameters from the orbits to evaluate their biomechanical role and evolutionary patterns. The early tetrapod group of Stereospondyls, one of the largest groups of Temnospondyls is used as a case study because its orbits position and size vary hugely within the members of this group. An adult skull of Edingerella madagascariensis was analysed using two different cases of boundary and loading conditions in order to quantify stress and deformation response under a bilateral bite and during skull raising. Firstly, the variation of the original geometry of its orbits was introduced in the models producing new FEA results, allowing the exploration of the ecomorphology, feeding strategy and evolutionary patterns of these top predators. Secondly, the quantitative results were analysed in order to check if the orbit size and position were correlated with different stress patterns. These results revealed that in most of the cases the stress distribution is not affected by changes in the size and position of the orbit. This finding supports the high mechanical plasticity of this group during the Triassic period. The absence of mechanical constraints regarding the orbit probably promoted the ecomorphological diversity acknowledged for this group, as well as its ecological niche differentiation in the terrestrial Triassic ecosystems in clades as lydekkerinids, trematosaurs, capitosaurs or metoposaurs. PMID:26107295
Marcé-Nogué, Jordi; Fortuny, Josep; De Esteban-Trivigno, Soledad; Sánchez, Montserrat; Gil, Lluís; Galobart, Àngel
2015-01-01
For the first time in vertebrate palaeontology, the potential of joining Finite Element Analysis (FEA) and Parametrical Analysis (PA) is used to shed new light on two different cranial parameters from the orbits to evaluate their biomechanical role and evolutionary patterns. The early tetrapod group of Stereospondyls, one of the largest groups of Temnospondyls is used as a case study because its orbits position and size vary hugely within the members of this group. An adult skull of Edingerella madagascariensis was analysed using two different cases of boundary and loading conditions in order to quantify stress and deformation response under a bilateral bite and during skull raising. Firstly, the variation of the original geometry of its orbits was introduced in the models producing new FEA results, allowing the exploration of the ecomorphology, feeding strategy and evolutionary patterns of these top predators. Secondly, the quantitative results were analysed in order to check if the orbit size and position were correlated with different stress patterns. These results revealed that in most of the cases the stress distribution is not affected by changes in the size and position of the orbit. This finding supports the high mechanical plasticity of this group during the Triassic period. The absence of mechanical constraints regarding the orbit probably promoted the ecomorphological diversity acknowledged for this group, as well as its ecological niche differentiation in the terrestrial Triassic ecosystems in clades as lydekkerinids, trematosaurs, capitosaurs or metoposaurs. PMID:26107295
Computational method for analysis of polyethylene biodegradation
NASA Astrophysics Data System (ADS)
Watanabe, Masaji; Kawai, Fusako; Shibata, Masaru; Yokoyama, Shigeo; Sudate, Yasuhiro
2003-12-01
In a previous study concerning the biodegradation of polyethylene, we proposed a mathematical model based on two primary factors: the direct consumption or absorption of small molecules and the successive weight loss of large molecules due to β-oxidation. Our model is an initial value problem consisting of a differential equation whose independent variable is time. Its unknown variable represents the total weight of all the polyethylene molecules that belong to a molecular-weight class specified by a parameter. In this paper, we describe a numerical technique to introduce experimental results into analysis of our model. We first establish its mathematical foundation in order to guarantee its validity, by showing that the initial value problem associated with the differential equation has a unique solution. Our computational technique is based on a linear system of differential equations derived from the original problem. We introduce some numerical results to illustrate our technique as a practical application of the linear approximation. In particular, we show how to solve the inverse problem to determine the consumption rate and the β-oxidation rate numerically, and illustrate our numerical technique by analyzing the GPC patterns of polyethylene wax obtained before and after 5 weeks cultivation of a fungus, Aspergillus sp. AK-3. A numerical simulation based on these degradation rates confirms that the primary factors of the polyethylene biodegradation posed in modeling are indeed appropriate.
A Novel College Network Resource Management Method using Cloud Computing
NASA Astrophysics Data System (ADS)
Lin, Chen
At present information construction of college mainly has construction of college networks and management information system; there are many problems during the process of information. Cloud computing is development of distributed processing, parallel processing and grid computing, which make data stored on the cloud, make software and services placed in the cloud and build on top of various standards and protocols, you can get it through all kinds of equipments. This article introduces cloud computing and function of cloud computing, then analyzes the exiting problems of college network resource management, the cloud computing technology and methods are applied in the construction of college information sharing platform.
Transonic Flow Computations Using Nonlinear Potential Methods
NASA Technical Reports Server (NTRS)
Holst, Terry L.; Kwak, Dochan (Technical Monitor)
2000-01-01
This presentation describes the state of transonic flow simulation using nonlinear potential methods for external aerodynamic applications. The presentation begins with a review of the various potential equation forms (with emphasis on the full potential equation) and includes a discussion of pertinent mathematical characteristics and all derivation assumptions. Impact of the derivation assumptions on simulation accuracy, especially with respect to shock wave capture, is discussed. Key characteristics of all numerical algorithm types used for solving nonlinear potential equations, including steady, unsteady, space marching, and design methods, are described. Both spatial discretization and iteration scheme characteristics are examined. Numerical results for various aerodynamic applications are included throughout the presentation to highlight key discussion points. The presentation ends with concluding remarks and recommendations for future work. Overall. nonlinear potential solvers are efficient, highly developed and routinely used in the aerodynamic design environment for cruise conditions. Published by Elsevier Science Ltd. All rights reserved.
Eco-Evo PVAs: Incorporating Eco-Evolutionary Processes into Population Viability Models
We synthesize how advances in computational methods and population genomics can be combined within an Ecological-Evolutionary (Eco-Evo) PVA model. Eco-Evo PVA models are powerful new tools for understanding the influence of evolutionary processes on plant and animal population pe...
Method for transferring data from an unsecured computer to a secured computer
Nilsen, Curt A.
1997-01-01
A method is described for transferring data from an unsecured computer to a secured computer. The method includes transmitting the data and then receiving the data. Next, the data is retransmitted and rereceived. Then, it is determined if errors were introduced when the data was transmitted by the unsecured computer or received by the secured computer. Similarly, it is determined if errors were introduced when the data was retransmitted by the unsecured computer or rereceived by the secured computer. A warning signal is emitted from a warning device coupled to the secured computer if (i) an error was introduced when the data was transmitted or received, and (ii) an error was introduced when the data was retransmitted or rereceived.
Statistical and Computational Methods for Genetic Diseases: An Overview
Di Taranto, Maria Donata
2015-01-01
The identification of causes of genetic diseases has been carried out by several approaches with increasing complexity. Innovation of genetic methodologies leads to the production of large amounts of data that needs the support of statistical and computational methods to be correctly processed. The aim of the paper is to provide an overview of statistical and computational methods paying attention to methods for the sequence analysis and complex diseases. PMID:26106440
Hybrid evolutionary programming for heavily constrained problems.
Myung, H; Kim, J H
1996-01-01
A hybrid of evolutionary programming (EP) and a deterministic optimization procedure is applied to a series of non-linear and quadratic optimization problems. The hybrid scheme is compared with other existing schemes such as EP alone, two-phase (TP) optimization, and EP with a non-stationary penalty function (NS-EP). The results indicate that the hybrid method can outperform the other methods when addressing heavily constrained optimization problems in terms of computational efficiency and solution accuracy. PMID:8833746
Multiscale methods for computational RNA enzymology
Panteva, Maria T.; Dissanayake, Thakshila; Chen, Haoyuan; Radak, Brian K.; Kuechler, Erich R.; Giambaşu, George M.; Lee, Tai-Sung; York, Darrin M.
2016-01-01
RNA catalysis is of fundamental importance to biology and yet remains ill-understood due to its complex nature. The multi-dimensional “problem space” of RNA catalysis includes both local and global conformational rearrangements, changes in the ion atmosphere around nucleic acids and metal ion binding, dependence on potentially correlated protonation states of key residues and bond breaking/forming in the chemical steps of the reaction. The goal of this article is to summarize and apply multiscale modeling methods in an effort to target the different parts of the RNA catalysis problem space while also addressing the limitations and pitfalls of these methods. Classical molecular dynamics (MD) simulations, reference interaction site model (RISM) calculations, constant pH molecular dynamics (CpHMD) simulations, Hamiltonian replica exchange molecular dynamics (HREMD) and quantum mechanical/molecular mechanical (QM/MM) simulations will be discussed in the context of the study of RNA backbone cleavage transesterification. This reaction is catalyzed by both RNA and protein enzymes, and here we examine the different mechanistic strategies taken by the hepatitis delta virus ribozyme (HDVr) and RNase A. PMID:25726472
Coarse-graining methods for computational biology.
Saunders, Marissa G; Voth, Gregory A
2013-01-01
Connecting the molecular world to biology requires understanding how molecular-scale dynamics propagate upward in scale to define the function of biological structures. To address this challenge, multiscale approaches, including coarse-graining methods, become necessary. We discuss here the theoretical underpinnings and history of coarse-graining and summarize the state of the field, organizing key methodologies based on an emerging paradigm for multiscale theory and modeling of biomolecular systems. This framework involves an integrated, iterative approach to couple information from different scales. The primary steps, which coincide with key areas of method development, include developing first-pass coarse-grained models guided by experimental results, performing numerous large-scale coarse-grained simulations, identifying important interactions that drive emergent behaviors, and finally reconnecting to the molecular scale by performing all-atom molecular dynamics simulations guided by the coarse-grained results. The coarse-grained modeling can then be extended and refined, with the entire loop repeated iteratively if necessary. PMID:23451897
A Method for Fast Computation of FTLE Fields
NASA Astrophysics Data System (ADS)
Brunton, Steven; Rowley, Clarence
2008-11-01
An efficient method for computing finite time Lyapunov exponent (FTLE) fields is investigated. FTLE fields, which measure the stretching between nearby particles, are important in determining transport mechanisms in unsteady flows. Ridges of the FTLE field are Lagrangian Coherent Structures (LCS) and provide an unsteady analogue of invariant manifolds from dynamical systems theory. FTLE field computations are expensive because of the large number of particle trajectories which must be integrated. However, when computing a time series of fields, it is possible to use the integrated trajectories at a previous time to compute an approximation of the integrated trajectories initialized at a later time, resulting in significant computational savings. This work provides analytic estimates for accumulated error and computation time as well as simulations comparing exact results with the approximate method for a number of interesting flows.
Testing and Validation of Computational Methods for Mass Spectrometry.
Gatto, Laurent; Hansen, Kasper D; Hoopmann, Michael R; Hermjakob, Henning; Kohlbacher, Oliver; Beyer, Andreas
2016-03-01
High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets ( http://compms.org/RefData ) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods. PMID:26549429
Computational Simulations and the Scientific Method
NASA Technical Reports Server (NTRS)
Kleb, Bil; Wood, Bill
2005-01-01
As scientific simulation software becomes more complicated, the scientific-software implementor's need for component tests from new model developers becomes more crucial. The community's ability to follow the basic premise of the Scientific Method requires independently repeatable experiments, and model innovators are in the best position to create these test fixtures. Scientific software developers also need to quickly judge the value of the new model, i.e., its cost-to-benefit ratio in terms of gains provided by the new model and implementation risks such as cost, time, and quality. This paper asks two questions. The first is whether other scientific software developers would find published component tests useful, and the second is whether model innovators think publishing test fixtures is a feasible approach.
Computer systems and methods for visualizing data
Stolte, Chris; Hanrahan, Patrick
2010-07-13
A method for forming a visual plot using a hierarchical structure of a dataset. The dataset comprises a measure and a dimension. The dimension consists of a plurality of levels. The plurality of levels form a dimension hierarchy. The visual plot is constructed based on a specification. A first level from the plurality of levels is represented by a first component of the visual plot. A second level from the plurality of levels is represented by a second component of the visual plot. The dataset is queried to retrieve data in accordance with the specification. The data includes all or a portion of the dimension and all or a portion of the measure. The visual plot is populated with the retrieved data in accordance with the specification.
Low-Rank Incremental Methods for Computing Dominant Singular Subspaces
Baker, Christopher G; Gallivan, Dr. Kyle A; Van Dooren, Dr. Paul
2012-01-01
Computing the singular values and vectors of a matrix is a crucial kernel in numerous scientific and industrial applications. As such, numerous methods have been proposed to handle this problem in a computationally efficient way. This paper considers a family of methods for incrementally computing the dominant SVD of a large matrix A. Specifically, we describe a unification of a number of previously disparate methods for approximating the dominant SVD via a single pass through A. We tie the behavior of these methods to that of a class of optimization-based iterative eigensolvers on A'*A. An iterative procedure is proposed which allows the computation of an accurate dominant SVD via multiple passes through A. We present an analysis of the convergence of this iteration, and provide empirical demonstration of the proposed method on both synthetic and benchmark data.
Developing a multimodal biometric authentication system using soft computing methods.
Malcangi, Mario
2015-01-01
Robust personal authentication is becoming ever more important in computer-based applications. Among a variety of methods, biometric offers several advantages, mainly in embedded system applications. Hard and soft multi-biometric, combined with hard and soft computing methods, can be applied to improve the personal authentication process and to generalize the applicability. This chapter describes the embedded implementation of a multi-biometric (voiceprint and fingerprint) multimodal identification system based on hard computing methods (DSP) for feature extraction and matching, an artificial neural network (ANN) for soft feature pattern matching, and a fuzzy logic engine (FLE) for data fusion and decision. PMID:25502384
Review - Computational methods for internal flows with emphasis on turbomachinery
NASA Technical Reports Server (NTRS)
Mcnally, W. D.; Sockol, P. M.
1985-01-01
Current computational methods for analyzing flows in turbomachinery and other related internal propulsion components are presented. The methods are divided into two classes. The inviscid methods deal specifically with turbomachinery applications. Viscous methods, deal with generalized duct flows as well as flows in turbomachinery passages. Inviscid methods are categorized into the potential, stream function, and Euler approaches. Viscous methods are treated in terms of parabolic, partially parabolic, and elliptic procedures. Various grids used in association with these procedures are also discussed.
Computational methods for internal flows with emphasis on turbomachinery
NASA Technical Reports Server (NTRS)
Mcnally, W. D.; Sockol, P. M.
1981-01-01
Current computational methods for analyzing flows in turbomachinery and other related internal propulsion components are presented. The methods are divided into two classes. The inviscid methods deal specifically with turbomachinery applications. Viscous methods, deal with generalized duct flows as well as flows in turbomachinery passages. Inviscid methods are categorized into the potential, stream function, and Euler aproaches. Viscous methods are treated in terms of parabolic, partially parabolic, and elliptic procedures. Various grids used in association with these procedures are also discussed.
Hunt, Tam
2014-01-01
Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766
GAP Noise Computation By The CE/SE Method
NASA Technical Reports Server (NTRS)
Loh, Ching Y.; Chang, Sin-Chung; Wang, Xiao Y.; Jorgenson, Philip C. E.
2001-01-01
A typical gap noise problem is considered in this paper using the new space-time conservation element and solution element (CE/SE) method. Implementation of the computation is straightforward. No turbulence model, LES (large eddy simulation) or a preset boundary layer profile is used, yet the computed frequency agrees well with the experimental one.
47 CFR 80.771 - Method of computing coverage.
Code of Federal Regulations, 2012 CFR
2012-10-01
... 47 Telecommunication 5 2012-10-01 2012-10-01 false Method of computing coverage. 80.771 Section 80.771 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES STATIONS IN THE MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.771...
Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods.
Ogilvie, Huw A; Heled, Joseph; Xie, Dong; Drummond, Alexei J
2016-05-01
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent. PMID:26821913
Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods
Ogilvie, Huw A.; Heled, Joseph; Xie, Dong; Drummond, Alexei J.
2016-01-01
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent. PMID:26821913
Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods.
Benevides, Leandro de Jesus; Carvalho, Daniel Santana de; Andrade, Roberto Fernandes Silva; Bomfim, Gilberto Cafezeiro; Fernandes, Flora Maria de Campos
2016-07-14
Apolipoprotein E (apo E) is a human glycoprotein with 299 amino acids, and it is a major component of very low density lipoproteins (VLDL) and a group of high-density lipoproteins (HDL). Phylogenetic studies are important to clarify how various apo E proteins are related in groups of organisms and whether they evolved from a common ancestor. Here, we aimed at performing a phylogenetic study on apo E carrying organisms. We employed a classical and robust method, such as Maximum Likelihood (ML), and compared the results using a more recent approach based on complex networks. Thirty-two apo E amino acid sequences were downloaded from NCBI. A clear separation could be observed among three major groups: mammals, fish and amphibians. The results obtained from ML method, as well as from the constructed networks showed two different groups: one with mammals only (C1) and another with fish (C2), and a single node with the single sequence available for an amphibian. The accordance in results from the different methods shows that the complex networks approach is effective in phylogenetic studies. Furthermore, our results revealed the conservation of apo E among animal groups. PMID:27419397
Job-shop scheduling with a combination of evolutionary and heuristic methods
NASA Astrophysics Data System (ADS)
Patkai, Bela; Torvinen, Seppo
1999-08-01
Since almost all of the scheduling problems are NP-hard-- cannot be solved in polynomial time--those companies that need a realistic scheduling system face serious limitations of available methods for finding an optimal schedule, especially if the given environment requires adaptation to dynamic variations. Exact methods do find an optimal schedule, but the size of the problem they can solve is very limited, excluding this way the required scalability. The solution presented in this paper is a simple, multi-pass heuristic method, which aims to avoid the limitations of other well-known formulations. Even though the dispatching rules are fast and provide near-optimal solutions in most cases, they are severely limited in efficiency--especially in case the schedule builder satisfies a significant number of constraints. That is the main motivation for adding a simplified genetic algorithm to the dispatching rules, which--due to its stochastic nature--belongs to heuristic, too. The scheduling problem is of a middle size Finnish factory, throughout the investigations their up-to-date manufacturing data has been used for the sake of realistic calculations.
Woods, Kristina N.; Pfeffer, Juergen
2016-01-01
It is now widely accepted that protein function is intimately tied with the navigation of energy landscapes. In this framework, a protein sequence is not described by a distinct structure but rather by an ensemble of conformations. And it is through this ensemble that evolution is able to modify a protein’s function by altering its landscape. Hence, the evolution of protein functions involves selective pressures that adjust the sampling of the conformational states. In this work, we focus on elucidating the evolutionary pathway that shaped the function of individual proteins that make-up the mammalian c-type lysozyme subfamily. Using both experimental and computational methods, we map out specific intermolecular interactions that direct the sampling of conformational states and accordingly, also underlie shifts in the landscape that are directly connected with the formation of novel protein functions. By contrasting three representative proteins in the family we identify molecular mechanisms that are associated with the selectivity of enhanced antimicrobial properties and consequently, divergent protein function. Namely, we link the extent of localized fluctuations involving the loop separating helices A and B with shifts in the equilibrium of the ensemble of conformational states that mediate interdomain coupling and concurrently moderate substrate binding affinity. This work reveals unique insights into the molecular level mechanisms that promote the progression of interactions that connect the immune response to infection with the nutritional properties of lactation, while also providing a deeper understanding about how evolving energy landscapes may define present-day protein function. PMID:26337549
Platform-independent method for computer aided schematic drawings
Vell, Jeffrey L.; Siganporia, Darius M.; Levy, Arthur J.
2012-02-14
A CAD/CAM method is disclosed for a computer system to capture and interchange schematic drawing and associated design information. The schematic drawing and design information are stored in an extensible, platform-independent format.
Computer method for identification of boiler transfer functions
NASA Technical Reports Server (NTRS)
Miles, J. H.
1972-01-01
Iterative computer aided procedure was developed which provides for identification of boiler transfer functions using frequency response data. Method uses frequency response data to obtain satisfactory transfer function for both high and low vapor exit quality data.
Computer Simulation Methods for Defect Configurations and Nanoscale Structures
Gao, Fei
2010-01-01
This chapter will describe general computer simulation methods, including ab initio calculations, molecular dynamics and kinetic Monte-Carlo method, and their applications to the calculations of defect configurations in various materials (metals, ceramics and oxides) and the simulations of nanoscale structures due to ion-solid interactions. The multiscale theory, modeling, and simulation techniques (both time scale and space scale) will be emphasized, and the comparisons between computer simulation results and exprimental observations will be made.
Panel-Method Computer Code For Potential Flow
NASA Technical Reports Server (NTRS)
Ashby, Dale L.; Dudley, Michael R.; Iguchi, Steven K.
1992-01-01
Low-order panel method used to reduce computation time. Panel code PMARC (Panel Method Ames Research Center) numerically simulates flow field around or through complex three-dimensional bodies such as complete aircraft models or wind tunnel. Based on potential-flow theory. Facilitates addition of new features to code and tailoring of code to specific problems and computer-hardware constraints. Written in standard FORTRAN 77.
Method and computer program product for maintenance and modernization backlogging
Mattimore, Bernard G; Reynolds, Paul E; Farrell, Jill M
2013-02-19
According to one embodiment, a computer program product for determining future facility conditions includes a computer readable medium having computer readable program code stored therein. The computer readable program code includes computer readable program code for calculating a time period specific maintenance cost, for calculating a time period specific modernization factor, and for calculating a time period specific backlog factor. Future facility conditions equal the time period specific maintenance cost plus the time period specific modernization factor plus the time period specific backlog factor. In another embodiment, a computer-implemented method for calculating future facility conditions includes calculating a time period specific maintenance cost, calculating a time period specific modernization factor, and calculating a time period specific backlog factor. Future facility conditions equal the time period specific maintenance cost plus the time period specific modernization factor plus the time period specific backlog factor. Other embodiments are also presented.
Automated Antenna Design with Evolutionary Algorithms
NASA Technical Reports Server (NTRS)
Linden, Derek; Hornby, Greg; Lohn, Jason; Globus, Al; Krishunkumor, K.
2006-01-01
Current methods of designing and optimizing antennas by hand are time and labor intensive, and limit complexity. Evolutionary design techniques can overcome these limitations by searching the design space and automatically finding effective solutions. In recent years, evolutionary algorithms have shown great promise in finding practical solutions in large, poorly understood design spaces. In particular, spacecraft antenna design has proven tractable to evolutionary design techniques. Researchers have been investigating evolutionary antenna design and optimization since the early 1990s, and the field has grown in recent years as computer speed has increased and electromagnetic simulators have improved. Two requirements-compliant antennas, one for ST5 and another for TDRS-C, have been automatically designed by evolutionary algorithms. The ST5 antenna is slated to fly this year, and a TDRS-C phased array element has been fabricated and tested. Such automated evolutionary design is enabled by medium-to-high quality simulators and fast modern computers to evaluate computer-generated designs. Evolutionary algorithms automate cut-and-try engineering, substituting automated search though millions of potential designs for intelligent search by engineers through a much smaller number of designs. For evolutionary design, the engineer chooses the evolutionary technique, parameters and the basic form of the antenna, e.g., single wire for ST5 and crossed-element Yagi for TDRS-C. Evolutionary algorithms then search for optimal configurations in the space defined by the engineer. NASA's Space Technology 5 (ST5) mission will launch three small spacecraft to test innovative concepts and technologies. Advanced evolutionary algorithms were used to automatically design antennas for ST5. The combination of wide beamwidth for a circularly-polarized wave and wide impedance bandwidth made for a challenging antenna design problem. From past experience in designing wire antennas, we chose to
Methods for operating parallel computing systems employing sequenced communications
Benner, R.E.; Gustafson, J.L.; Montry, G.R.
1999-08-10
A parallel computing system and method are disclosed having improved performance where a program is concurrently run on a plurality of nodes for reducing total processing time, each node having a processor, a memory, and a predetermined number of communication channels connected to the node and independently connected directly to other nodes. The present invention improves performance of the parallel computing system by providing a system which can provide efficient communication between the processors and between the system and input and output devices. A method is also disclosed which can locate defective nodes with the computing system. 15 figs.
Methods for operating parallel computing systems employing sequenced communications
Benner, Robert E.; Gustafson, John L.; Montry, Gary R.
1999-01-01
A parallel computing system and method having improved performance where a program is concurrently run on a plurality of nodes for reducing total processing time, each node having a processor, a memory, and a predetermined number of communication channels connected to the node and independently connected directly to other nodes. The present invention improves performance of performance of the parallel computing system by providing a system which can provide efficient communication between the processors and between the system and input and output devices. A method is also disclosed which can locate defective nodes with the computing system.
Convergence acceleration of the Proteus computer code with multigrid methods
NASA Technical Reports Server (NTRS)
Demuren, A. O.; Ibraheem, S. O.
1992-01-01
Presented here is the first part of a study to implement convergence acceleration techniques based on the multigrid concept in the Proteus computer code. A review is given of previous studies on the implementation of multigrid methods in computer codes for compressible flow analysis. Also presented is a detailed stability analysis of upwind and central-difference based numerical schemes for solving the Euler and Navier-Stokes equations. Results are given of a convergence study of the Proteus code on computational grids of different sizes. The results presented here form the foundation for the implementation of multigrid methods in the Proteus code.
Evolutionary behavioral genetics
Zietsch, Brendan P.; de Candia, Teresa R; Keller, Matthew C.
2014-01-01
We describe the scientific enterprise at the intersection of evolutionary psychology and behavioral genetics—a field that could be termed Evolutionary Behavioral Genetics—and how modern genetic data is revolutionizing our ability to test questions in this field. We first explain how genetically informative data and designs can be used to investigate questions about the evolution of human behavior, and describe some of the findings arising from these approaches. Second, we explain how evolutionary theory can be applied to the investigation of behavioral genetic variation. We give examples of how new data and methods provide insight into the genetic architecture of behavioral variation and what this tells us about the evolutionary processes that acted on the underlying causal genetic variants. PMID:25587556
An efficient method for computation of the manipulator inertia matrix
NASA Technical Reports Server (NTRS)
Fijany, Amir; Bejczy, Antal K.
1989-01-01
An efficient method of computation of the manipulator inertia matrix is presented. Using spatial notations, the method leads to the definition of the composite rigid-body spatial inertia, which is a spatial representation of the notion of augmented body. The previously proposed methods, the physical interpretations leading to their derivation, and their redundancies are analyzed. The proposed method achieves a greater efficiency by eliminating the redundancy in the intrinsic equations as well as by a better choice of coordinate frame for their projection. In this case, removing the redundancy leads to greater efficiency of the computation in both serial and parallel senses.
A Hybrid Soft-computing Method for Image Analysis of Digital Plantar Scanners
Razjouyan, Javad; Khayat, Omid; Siahi, Mehdi; Mansouri, Ali Alizadeh
2013-01-01
Digital foot scanners have been developed in recent years to yield anthropometrists digital image of insole with pressure distribution and anthropometric information. In this paper, a hybrid algorithm containing gray level spatial correlation (GLSC) histogram and Shanbag entropy is presented for analysis of scanned foot images. An evolutionary algorithm is also employed to find the optimum parameters of GLSC and transform function of the membership values. Resulting binary images as the thresholded images are undergone anthropometric measurements taking in to account the scale factor of pixel size to metric scale. The proposed method is finally applied to plantar images obtained through scanning feet of randomly selected subjects by a foot scanner system as our experimental setup described in the paper. Running computation time and the effects of GLSC parameters are investigated in the simulation results. PMID:24083133
Testing for Independence between Evolutionary Processes.
Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume
2016-09-01
Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens. PMID:27208890
Method for computing the optimal signal distribution and channel capacity.
Shapiro, E G; Shapiro, D A; Turitsyn, S K
2015-06-15
An iterative method for computing the channel capacity of both discrete and continuous input, continuous output channels is proposed. The efficiency of new method is demonstrated in comparison with the classical Blahut - Arimoto algorithm for several known channels. Moreover, we also present a hybrid method combining advantages of both the Blahut - Arimoto algorithm and our iterative approach. The new method is especially efficient for the channels with a priory unknown discrete input alphabet. PMID:26193496
Gorelik, Gregory; Shackelford, Todd K
2014-01-01
In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment. PMID:25300054
Comparison of methods for computing streamflow statistics for Pennsylvania streams
Ehlke, Marla H.; Reed, Lloyd A.
1999-01-01
Methods for computing streamflow statistics intended for use on ungaged locations on Pennsylvania streams are presented and compared to frequency distributions of gaged streamflow data. The streamflow statistics used in the comparisons include the 7-day 10-year low flow, 50-year flood flow, and the 100-year flood flow; additional statistics are presented. Streamflow statistics for gaged locations on streams in Pennsylvania were computed using three methods for the comparisons: 1) Log-Pearson type III frequency distribution (Log-Pearson) of continuous-record streamflow data, 2) regional regression equations developed by the U.S. Geological Survey in 1982 (WRI 82-21), and 3) regional regression equations developed by the Pennsylvania State University in 1981 (PSU-IV). Log-Pearson distribution was considered the reference method for evaluation of the regional regression equations. Low-flow statistics were computed using the Log-Pearson distribution and WRI 82-21, whereas flood-flow statistics were computed using all three methods. The urban adjustment for PSU-IV was modified from the recommended computation to exclude Philadelphia and the surrounding areas (region 1) from the adjustment. Adjustments for storage area for PSU-IV were also slightly modified. A comparison of the 7-day 10-year low flow computed from Log-Pearson distribution and WRI-82- 21 showed that the methods produced significantly different values for about 7 percent of the state. The same methods produced 50-year and 100-year flood flows that were significantly different for about 24 percent of the state. Flood-flow statistics computed using Log-Pearson distribution and PSU-IV were not significantly different in any regions of the state. These findings are based on a statistical comparison using the t-test on signed ranks and graphical methods.
Evolutionary model with Turing machines
NASA Astrophysics Data System (ADS)
Feverati, Giovanni; Musso, Fabio
2008-06-01
The development of a large noncoding fraction in eukaryotic DNA and the phenomenon of the code bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code growth) the evolution of a complex code cannot be attained without maintaining a large inactive fraction. To test this hypothesis we performed computer simulations of an evolutionary toy model for Turing machines, studying the relations among fitness and coding versus noncoding ratio while varying mutation and code growth rates. The results suggest that, in our model, having a large reservoir of noncoding states constitutes a great (long term) evolutionary advantage.
Computational Methods for Protein Identification from Mass Spectrometry Data
McHugh, Leo; Arthur, Jonathan W
2008-01-01
Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology. PMID:18463710
Method for implementation of recursive hierarchical segmentation on parallel computers
NASA Technical Reports Server (NTRS)
Tilton, James C. (Inventor)
2005-01-01
A method, computer readable storage, and apparatus for implementing a recursive hierarchical segmentation algorithm on a parallel computing platform. The method includes setting a bottom level of recursion that defines where a recursive division of an image into sections stops dividing, and setting an intermediate level of recursion where the recursive division changes from a parallel implementation into a serial implementation. The segmentation algorithm is implemented according to the set levels. The method can also include setting a convergence check level of recursion with which the first level of recursion communicates with when performing a convergence check.
Artificial Intelligence Methods: Challenge in Computer Based Polymer Design
NASA Astrophysics Data System (ADS)
Rusu, Teodora; Pinteala, Mariana; Cartwright, Hugh
2009-08-01
This paper deals with the use of Artificial Intelligence Methods (AI) in the design of new molecules possessing desired physical, chemical and biological properties. This is an important and difficult problem in the chemical, material and pharmaceutical industries. Traditional methods involve a laborious and expensive trial-and-error procedure, but computer-assisted approaches offer many advantages in the automation of molecular design.
Solution-adaptive finite element method in computational fracture mechanics
NASA Technical Reports Server (NTRS)
Min, J. B.; Bass, J. M.; Spradley, L. W.
1993-01-01
Some recent results obtained using solution-adaptive finite element method in linear elastic two-dimensional fracture mechanics problems are presented. The focus is on the basic issue of adaptive finite element method for validating the applications of new methodology to fracture mechanics problems by computing demonstration problems and comparing the stress intensity factors to analytical results.
Calculating PI Using Historical Methods and Your Personal Computer.
ERIC Educational Resources Information Center
Mandell, Alan
1989-01-01
Provides a software program for determining PI to the 15th place after the decimal. Explores the history of determining the value of PI from Archimedes to present computer methods. Investigates Wallis's, Liebniz's, and Buffon's methods. Written for Tandy GW-BASIC (IBM compatible) with 384K. Suggestions for Apple II's are given. (MVL)
Probability computations using the SIGMA-PI method on a personal computer
Haskin, F.E.; Lazo, M.S.; Heger, A.S.
1990-09-30
The SIGMA-PI ({Sigma}{Pi}) method as implemented in the SIGPI computer code, is designed to accurately and efficiently evaluate the probability of Boolean expressions in disjunctive normal form given the base event probabilities. The method is not limited to problems in which base event probabilities are small, nor to Boolean expressions that exclude the compliments of base events, nor to problems in which base events are independent. The feasibility of implementing the {Sigma}{Pi} method on a personal computer has been evaluated, and a version of the SIGPI code capable of quantifying simple Boolean expressions with independent base events on the personal computer has been developed. Tasks required for a fully functional personal computer version of SIGPI have been identified together with enhancements that could be implemented to improve the utility and efficiency of the code.
Methods and systems for providing reconfigurable and recoverable computing resources
NASA Technical Reports Server (NTRS)
Stange, Kent (Inventor); Hess, Richard (Inventor); Kelley, Gerald B (Inventor); Rogers, Randy (Inventor)
2010-01-01
A method for optimizing the use of digital computing resources to achieve reliability and availability of the computing resources is disclosed. The method comprises providing one or more processors with a recovery mechanism, the one or more processors executing one or more applications. A determination is made whether the one or more processors needs to be reconfigured. A rapid recovery is employed to reconfigure the one or more processors when needed. A computing system that provides reconfigurable and recoverable computing resources is also disclosed. The system comprises one or more processors with a recovery mechanism, with the one or more processors configured to execute a first application, and an additional processor configured to execute a second application different than the first application. The additional processor is reconfigurable with rapid recovery such that the additional processor can execute the first application when one of the one more processors fails.
Computational methods for structural load and resistance modeling
NASA Technical Reports Server (NTRS)
Thacker, B. H.; Millwater, H. R.; Harren, S. V.
1991-01-01
An automated capability for computing structural reliability considering uncertainties in both load and resistance variables is presented. The computations are carried out using an automated Advanced Mean Value iteration algorithm (AMV +) with performance functions involving load and resistance variables obtained by both explicit and implicit methods. A complete description of the procedures used is given as well as several illustrative examples, verified by Monte Carlo Analysis. In particular, the computational methods described in the paper are shown to be quite accurate and efficient for a material nonlinear structure considering material damage as a function of several primitive random variables. The results show clearly the effectiveness of the algorithms for computing the reliability of large-scale structural systems with a maximum number of resolutions.
Fortune, E S; Rose, G J
1997-01-01
Weakly electric fish have parallel electrosensory systems, the phylogenetically older ampullary system and the novel tuberous system. The tuberous system is an adaptation related to the evolution of active electrolocation. To examine the evolutionary relationship of the ampullary and tuberous systems, the temporal filtering properties of ampullary neurons in the dorsal torus semicircularis of Eigenmannia were studied. 'Whole-cell' recordings were made in vivo using patch-type pipettes. The responses of 19 neurons to sinusoidal electric signals (< 40 Hz) were recorded and the anatomy of these neurons demonstrated by injection of biocytin. All eight low-pass ampullary neurons had broad, relatively smooth post-synaptic potentials (psps) that at low frequencies nicely reflected the sinusoidal stimuli. These neurons had somata of 10-14 microns diameter and thick, spiny dendrites. Eight high-pass neurons were recorded, representing three physiological classes. The first class (3 neurons) had psps that roughly followed the sinusoidal time course of the stimulus; the psp morphology was similar to low-pass neurons. The second class had many small, fast, individual psps; their rate of occurrence varied with the stimulus. Finally, four neurons showed psps that were of constant width across stimulus frequencies. All three classes of high-pass neurons had small somata (8-10 microns diameter) with thin dendrites and either few or no spines. Some of these neurons had large varicosities on the dendrites. Three neurons had band-pass filtering properties: neurons that showed strong band-pass properties were morphologically similar to low-pass neurons. Comparisons of the temporal filtering, shapes of post-synaptic potentials, and anatomy of ampullary and tuberous neurons in the torus suggest that the circuitry for tuberous processing in the torus may have evolved as an elaboration or duplication of the ampullary system. The mechanisms underlying the low-pass filtering characteristics
A Lanczos eigenvalue method on a parallel computer
NASA Technical Reports Server (NTRS)
Bostic, Susan W.; Fulton, Robert E.
1987-01-01
Eigenvalue analyses of complex structures is a computationally intensive task which can benefit significantly from new and impending parallel computers. This study reports on a parallel computer implementation of the Lanczos method for free vibration analysis. The approach used here subdivides the major Lanczos calculation tasks into subtasks and introduces parallelism down to the subtask levels such as matrix decomposition and forward/backward substitution. The method was implemented on a commercial parallel computer and results were obtained for a long flexible space structure. While parallel computing efficiency for the Lanczos method was good for a moderate number of processors for the test problem, the greatest reduction in time was realized for the decomposition of the stiffness matrix, a calculation which took 70 percent of the time in the sequential program and which took 25 percent of the time on eight processors. For a sample calculation of the twenty lowest frequencies of a 486 degree of freedom problem, the total sequential computing time was reduced by almost a factor of ten using 16 processors.
Computational methods to obtain time optimal jet engine control
NASA Technical Reports Server (NTRS)
Basso, R. J.; Leake, R. J.
1976-01-01
Dynamic Programming and the Fletcher-Reeves Conjugate Gradient Method are two existing methods which can be applied to solve a general class of unconstrained fixed time, free right end optimal control problems. New techniques are developed to adapt these methods to solve a time optimal control problem with state variable and control constraints. Specifically, they are applied to compute a time optimal control for a jet engine control problem.
A stochastic method for computing hadronic matrix elements
Alexandrou, Constantia; Constantinou, Martha; Dinter, Simon; Drach, Vincent; Jansen, Karl; Hadjiyiannakou, Kyriakos; Renner, Dru B.
2014-01-24
In this study, we present a stochastic method for the calculation of baryon 3-point functions which is an alternative to the typically used sequential method offering more versatility. We analyze the scaling of the error of the stochastically evaluated 3-point function with the lattice volume and find a favorable signal to noise ratio suggesting that the stochastic method can be extended to large volumes providing an efficient approach to compute hadronic matrix elements and form factors.
Fully consistent CFD methods for incompressible flow computations
NASA Astrophysics Data System (ADS)
Kolmogorov, D. K.; Shen, W. Z.; Sørensen, N. N.; Sørensen, J. N.
2014-06-01
Nowadays collocated grid based CFD methods are one of the most efficient tools for computations of the flows past wind turbines. To ensure the robustness of the methods they require special attention to the well-known problem of pressure-velocity coupling. Many commercial codes to ensure the pressure-velocity coupling on collocated grids use the so-called momentum interpolation method of Rhie and Chow [1]. As known, the method and some of its widely spread modifications result in solutions, which are dependent of time step at convergence. In this paper the magnitude of the dependence is shown to contribute about 0.5% into the total error in a typical turbulent flow computation. Nevertheless if coarse grids are used, the standard interpolation methods result in much higher non-consistent behavior. To overcome the problem, a recently developed interpolation method, which is independent of time step, is used. It is shown that in comparison to other time step independent method, the method may enhance the convergence rate of the SIMPLEC algorithm up to 25 %. The method is verified using turbulent flow computations around a NACA 64618 airfoil and the roll-up of a shear layer, which may appear in wind turbine wake.
Practical Use of Computationally Frugal Model Analysis Methods
Hill, Mary C.; Kavetski, Dmitri; Clark, Martyn; Ye, Ming; Arabi, Mazdak; Lu, Dan; Foglia, Laura; Mehl, Steffen
2015-03-21
Computationally frugal methods of model analysis can provide substantial benefits when developing models of groundwater and other environmental systems. Model analysis includes ways to evaluate model adequacy and to perform sensitivity and uncertainty analysis. Frugal methods typically require 10s of parallelizable model runs; their convenience allows for other uses of the computational effort. We suggest that model analysis be posed as a set of questions used to organize methods that range from frugal to expensive (requiring 10,000 model runs or more). This encourages focus on method utility, even when methods have starkly different theoretical backgrounds. We note that many frugalmore » methods are more useful when unrealistic process-model nonlinearities are reduced. Inexpensive diagnostics are identified for determining when frugal methods are advantageous. Examples from the literature are used to demonstrate local methods and the diagnostics. We suggest that the greater use of computationally frugal model analysis methods would allow questions such as those posed in this work to be addressed more routinely, allowing the environmental sciences community to obtain greater scientific insight from the many ongoing and future modeling efforts« less
Practical Use of Computationally Frugal Model Analysis Methods
Hill, Mary C.; Kavetski, Dmitri; Clark, Martyn; Ye, Ming; Arabi, Mazdak; Lu, Dan; Foglia, Laura; Mehl, Steffen
2015-03-21
Computationally frugal methods of model analysis can provide substantial benefits when developing models of groundwater and other environmental systems. Model analysis includes ways to evaluate model adequacy and to perform sensitivity and uncertainty analysis. Frugal methods typically require 10s of parallelizable model runs; their convenience allows for other uses of the computational effort. We suggest that model analysis be posed as a set of questions used to organize methods that range from frugal to expensive (requiring 10,000 model runs or more). This encourages focus on method utility, even when methods have starkly different theoretical backgrounds. We note that many frugal methods are more useful when unrealistic process-model nonlinearities are reduced. Inexpensive diagnostics are identified for determining when frugal methods are advantageous. Examples from the literature are used to demonstrate local methods and the diagnostics. We suggest that the greater use of computationally frugal model analysis methods would allow questions such as those posed in this work to be addressed more routinely, allowing the environmental sciences community to obtain greater scientific insight from the many ongoing and future modeling efforts
Geometrical MTF computation method based on the irradiance model
NASA Astrophysics Data System (ADS)
Lin, P.-D.; Liu, C.-S.
2011-01-01
The Modulation Transfer Function (MTF) is a measure of an optical system's ability to transfer contrast from the specimen to the image plane at a specific resolution. It can be computed either numerically by geometrical optics or measured experimentally by imaging a knife edge or a bar-target pattern of varying spatial frequency. Previously, MTF accuracy was generally affected by the size of the mesh on the image plane. This paper presents a new MTF computation method based on the irradiance model, without counting the number of rays hitting each grid. To verify the method, the MTF in the sagittal and meridional directions of an axis-symmetrical optical system is computed by both the ray-counting and the proposed methods. It is found that the grid size meshed on the image plane significantly affects the MTF of the ray-counting method, sometimes with significantly negative results. The proposed irradiance method is immune to issues of grid size. The CPU computation time for the two methods is approximately the same.
Applications of computer-intensive statistical methods to environmental research.
Pitt, D G; Kreutzweiser, D P
1998-02-01
Conventional statistical approaches rely heavily on the properties of the central limit theorem to bridge the gap between the characteristics of a sample and some theoretical sampling distribution. Problems associated with nonrandom sampling, unknown population distributions, heterogeneous variances, small sample sizes, and missing data jeopardize the assumptions of such approaches and cast skepticism on conclusions. Conventional nonparametric alternatives offer freedom from distribution assumptions, but design limitations and loss of power can be serious drawbacks. With the data-processing capacity of today's computers, a new dimension of distribution-free statistical methods has evolved that addresses many of the limitations of conventional parametric and nonparametric methods. Computer-intensive statistical methods involve reshuffling, resampling, or simulating a data set thousands of times to empirically define a sampling distribution for a chosen test statistic. The only assumption necessary for valid results is the random assignment of experimental units to the test groups or treatments. Application to a real data set illustrates the advantages of these methods, including freedom from distribution assumptions without loss of power, complete choice over test statistics, easy adaptation to design complexities and missing data, and considerable intuitive appeal. The illustrations also reveal that computer-intensive methods can be more time consuming than conventional methods and the amount of computer code required to orchestrate reshuffling, resampling, or simulation procedures can be appreciable. PMID:9515080
A Fast and Reliable Computational Method for Estimating Population Genetic Parameters
Vasco, Daniel A.
2008-01-01
The estimation of ancestral and current effective population sizes in expanding populations is a fundamental problem in population genetics. Recently it has become possible to scan entire genomes of several individuals within a population. These genomic data sets can be used to estimate basic population parameters such as the effective population size and population growth rate. Full-data-likelihood methods potentially offer a powerful statistical framework for inferring population genetic parameters. However, for large data sets, computationally intensive methods based upon full-likelihood estimates may encounter difficulties. First, the computational method may be prohibitively slow or difficult to implement for large data. Second, estimation bias may markedly affect the accuracy and reliability of parameter estimates, as suggested from past work on coalescent methods. To address these problems, a fast and computationally efficient least-squares method for estimating population parameters from genomic data is presented here. Instead of modeling genomic data using a full likelihood, this new approach uses an analogous function, in which the full data are replaced with a vector of summary statistics. Furthermore, these least-squares estimators may show significantly less estimation bias for growth rate and genetic diversity than a corresponding maximum-likelihood estimator for the same coalescent process. The least-squares statistics also scale up to genome-sized data sets with many nucleotides and loci. These results demonstrate that least-squares statistics will likely prove useful for nonlinear parameter estimation when the underlying population genomic processes have complex evolutionary dynamics involving interactions between mutation, selection, demography, and recombination. PMID:18505868
Software for computing eigenvalue bounds for iterative subspace matrix methods
NASA Astrophysics Data System (ADS)
Shepard, Ron; Minkoff, Michael; Zhou, Yunkai
2005-07-01
This paper describes software for computing eigenvalue bounds to the standard and generalized hermitian eigenvalue problem as described in [Y. Zhou, R. Shepard, M. Minkoff, Computing eigenvalue bounds for iterative subspace matrix methods, Comput. Phys. Comm. 167 (2005) 90-102]. The software discussed in this manuscript applies to any subspace method, including Lanczos, Davidson, SPAM, Generalized Davidson Inverse Iteration, Jacobi-Davidson, and the Generalized Jacobi-Davidson methods, and it is applicable to either outer or inner eigenvalues. This software can be applied during the subspace iterations in order to truncate the iterative process and to avoid unnecessary effort when converging specific eigenvalues to a required target accuracy, and it can be applied to the final set of Ritz values to assess the accuracy of the converged results. Program summaryTitle of program: SUBROUTINE BOUNDS_OPT Catalogue identifier: ADVE Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVE Computers: any computer that supports a Fortran 90 compiler Operating systems: any computer that supports a Fortran 90 compiler Programming language: Standard Fortran 90 High speed storage required:5m+5 working-precision and 2m+7 integer for m Ritz values No. of bits in a word: The floating point working precision is parameterized with the symbolic constant WP No. of lines in distributed program, including test data, etc.: 2452 No. of bytes in distributed program, including test data, etc.: 281 543 Distribution format: tar.gz Nature of physical problem: The computational solution of eigenvalue problems using iterative subspace methods has widespread applications in the physical sciences and engineering as well as other areas of mathematical modeling (economics, social sciences, etc.). The accuracy of the solution of such problems and the utility of those errors is a fundamental problem that is of
Integration of computational methods into automotive wind tunnel testing
Katz, J.
1989-01-01
This paper discusses the aerodynamics of a generic, enclosed-wheel racing-car shape without wheels investigated numerically and compared with one-quarter scale wind-tunnel data. Because both methods lack perfection in simulating actual road conditions, a complementary application of these methods was studied. The computations served for correcting the high-blockage wind-tunnel results and provided detailed pressure data which improved the physical understanding of the flow field. The experimental data was used here mainly to provide information on the location of flow-separation lines and on the aerodynamic loads; these in turn were used to validate and to calibrate the computations.
NASA Technical Reports Server (NTRS)
Elliott, Kenny B.; Ugoletti, Roberto; Sulla, Jeff
1992-01-01
The evolution and optimization of a real-time digital control system is presented. The control system is part of a testbed used to perform focused technology research on the interactions of spacecraft platform and instrument controllers with the flexible-body dynamics of the platform and platform appendages. The control system consists of Computer Automated Measurement and Control (CAMAC) standard data acquisition equipment interfaced to a workstation computer. The goal of this work is to optimize the control system's performance to support controls research using controllers with up to 50 states and frame rates above 200 Hz. The original system could support a 16-state controller operating at a rate of 150 Hz. By using simple yet effective software improvements, Input/Output (I/O) latencies and contention problems are reduced or eliminated in the control system. The final configuration can support a 16-state controller operating at 475 Hz. Effectively the control system's performance was increased by a factor of 3.
Practical Use of Computationally Frugal Model Analysis Methods.
Hill, Mary C; Kavetski, Dmitri; Clark, Martyn; Ye, Ming; Arabi, Mazdak; Lu, Dan; Foglia, Laura; Mehl, Steffen
2016-03-01
Three challenges compromise the utility of mathematical models of groundwater and other environmental systems: (1) a dizzying array of model analysis methods and metrics make it difficult to compare evaluations of model adequacy, sensitivity, and uncertainty; (2) the high computational demands of many popular model analysis methods (requiring 1000's, 10,000 s, or more model runs) make them difficult to apply to complex models; and (3) many models are plagued by unrealistic nonlinearities arising from the numerical model formulation and implementation. This study proposes a strategy to address these challenges through a careful combination of model analysis and implementation methods. In this strategy, computationally frugal model analysis methods (often requiring a few dozen parallelizable model runs) play a major role, and computationally demanding methods are used for problems where (relatively) inexpensive diagnostics suggest the frugal methods are unreliable. We also argue in favor of detecting and, where possible, eliminating unrealistic model nonlinearities-this increases the realism of the model itself and facilitates the application of frugal methods. Literature examples are used to demonstrate the use of frugal methods and associated diagnostics. We suggest that the strategy proposed in this paper would allow the environmental sciences community to achieve greater transparency and falsifiability of environmental models, and obtain greater scientific insight from ongoing and future modeling efforts. PMID:25810333
A comparative study of computational methods in cosmic gas dynamics
NASA Technical Reports Server (NTRS)
Van Albada, G. D.; Van Leer, B.; Roberts, W. W., Jr.
1982-01-01
Many theoretical investigations of fluid flows in astrophysics require extensive numerical calculations. The selection of an appropriate computational method is, therefore, important for the astronomer who has to solve an astrophysical flow problem. The present investigation has the objective to provide an informational basis for such a selection by comparing a variety of numerical methods with the aid of a test problem. The test problem involves a simple, one-dimensional model of the gas flow in a spiral galaxy. The numerical methods considered include the beam scheme, Godunov's method (G), the second-order flux-splitting method (FS2), MacCormack's method, and the flux corrected transport methods of Boris and Book (1973). It is found that the best second-order method (FS2) outperforms the best first-order method (G) by a huge margin.
Evolutionary Design in Embryogeny
NASA Astrophysics Data System (ADS)
Ashlock, Daniel
In biology texts embryogeny is defined as "the development or production of an embryo." An embryo is a living creature in its first stage of life, from the fertilized egg cell through the initial development of its morphology and its chemical networks. The study of embryogeny is part of developmental biology [1, 2]. The reader may wonder why a book on evolutionary design should have a section on embryogeny. Computational embryogeny is the study of representations for evolutionary computation that mimic biological embryogeny. These representations contain analogs to the complex biological processes that steer a single cell to become a rose, a mouse, or a man. The advantage of using embryogenic representations is their richness of expression. A small seed of information can be expanded, through a developmental process, into a complex and potentially useful object. This richness of expression comes at a substantial price: the developmental process is sufficiently complex to be unpredictable.
Computer controlled fluorometer device and method of operating same
Kolber, Z.; Falkowski, P.
1990-07-17
A computer controlled fluorometer device and method of operating same, said device being made to include a pump flash source and a probe flash source and one or more sample chambers in combination with a light condenser lens system and associated filters and reflectors and collimators, as well as signal conditioning and monitoring means and a programmable computer means and a software programmable source of background irradiance that is operable according to the method of the invention to rapidly, efficiently and accurately measure photosynthetic activity by precisely monitoring and recording changes in fluorescence yield produced by a controlled series of predetermined cycles of probe and pump flashes from the respective probe and pump sources that are controlled by the computer means. 13 figs.
Computer controlled fluorometer device and method of operating same
Kolber, Zbigniew; Falkowski, Paul
1990-01-01
A computer controlled fluorometer device and method of operating same, said device being made to include a pump flash source and a probe flash source and one or more sample chambers in combination with a light condenser lens system and associated filters and reflectors and collimators, as well as signal conditioning and monitoring means and a programmable computer means and a software programmable source of background irradiance that is operable according to the method of the invention to rapidly, efficiently and accurately measure photosynthetic activity by precisely monitoring and recording changes in fluorescence yield produced by a controlled series of predetermined cycles of probe and pump flashes from the respective probe and pump sources that are controlled by the computer means.
Computational Methods for Dynamic Stability and Control Derivatives
NASA Technical Reports Server (NTRS)
Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.
2003-01-01
Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.
Computational Methods for Dynamic Stability and Control Derivatives
NASA Technical Reports Server (NTRS)
Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.
2004-01-01
Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.
A computational method for automated characterization of genetic components.
Yordanov, Boyan; Dalchau, Neil; Grant, Paul K; Pedersen, Michael; Emmott, Stephen; Haseloff, Jim; Phillips, Andrew
2014-08-15
The ability to design and construct synthetic biological systems with predictable behavior could enable significant advances in medical treatment, agricultural sustainability, and bioenergy production. However, to reach a stage where such systems can be reliably designed from biological components, integrated experimental and computational techniques that enable robust component characterization are needed. In this paper we present a computational method for the automated characterization of genetic components. Our method exploits a recently developed multichannel experimental protocol and integrates bacterial growth modeling, Bayesian parameter estimation, and model selection, together with data processing steps that are amenable to automation. We implement the method within the Genetic Engineering of Cells modeling and design environment, which enables both characterization and design to be integrated within a common software framework. To demonstrate the application of the method, we quantitatively characterize a synthetic receiver device that responds to the 3-oxohexanoyl-homoserine lactone signal, across a range of experimental conditions. PMID:24628037
PSD computations using Welch's method. [Power Spectral Density (PSD)
Solomon, Jr, O M
1991-12-01
This report describes Welch's method for computing Power Spectral Densities (PSDs). We first describe the bandpass filter method which uses filtering, squaring, and averaging operations to estimate a PSD. Second, we delineate the relationship of Welch's method to the bandpass filter method. Third, the frequency domain signal-to-noise ratio for a sine wave in white noise is derived. This derivation includes the computation of the noise floor due to quantization noise. The signal-to-noise ratio and noise flood depend on the FFT length and window. Fourth, the variance the Welch's PSD is discussed via chi-square random variables and degrees of freedom. This report contains many examples, figures and tables to illustrate the concepts. 26 refs.
Decluttering Methods for Computer-Generated Graphic Displays
NASA Technical Reports Server (NTRS)
Schultz, E. Eugene, Jr.
1986-01-01
Symbol simplification and contrasting enhance viewer's ability to detect particular symbol. Report describes experiments designed to indicate how various decluttering methods affect viewer's abilities to distinguish essential from nonessential features on computer-generated graphic displays. Results indicate partial removal of nonessential graphic features through symbol simplification effective in decluttering as total removal of nonessential graphic features.
A Probabilistic Method for Computing Term-by-Term Relationships.
ERIC Educational Resources Information Center
Wong, S. K. M.; Yao, Y. Y.
1993-01-01
Suggests a probabilistic method to compute the term relationships from relevance information, which complements the studies on a nonprobabilistic technique called pseudo-classification. A quadratic ranking function is derived by incorporating the term-by-term relationships. Procedures for estimating the required parameters are provided by…
Convergence acceleration of the Proteus computer code with multigrid methods
NASA Technical Reports Server (NTRS)
Demuren, A. O.; Ibraheem, S. O.
1995-01-01
This report presents the results of a study to implement convergence acceleration techniques based on the multigrid concept in the two-dimensional and three-dimensional versions of the Proteus computer code. The first section presents a review of the relevant literature on the implementation of the multigrid methods in computer codes for compressible flow analysis. The next two sections present detailed stability analysis of numerical schemes for solving the Euler and Navier-Stokes equations, based on conventional von Neumann analysis and the bi-grid analysis, respectively. The next section presents details of the computational method used in the Proteus computer code. Finally, the multigrid implementation and applications to several two-dimensional and three-dimensional test problems are presented. The results of the present study show that the multigrid method always leads to a reduction in the number of iterations (or time steps) required for convergence. However, there is an overhead associated with the use of multigrid acceleration. The overhead is higher in 2-D problems than in 3-D problems, thus overall multigrid savings in CPU time are in general better in the latter. Savings of about 40-50 percent are typical in 3-D problems, but they are about 20-30 percent in large 2-D problems. The present multigrid method is applicable to steady-state problems and is therefore ineffective in problems with inherently unstable solutions.
Micro-computed tomography: an alternative method for shark ageing.
Geraghty, P T; Jones, A S; Stewart, J; Macbeth, W G
2012-04-01
Micro-computed tomography (microCT) produced 3D reconstructions of shark Carcharhinus brevipinna vertebrae that could be virtually sectioned along any desired plane, and upon which growth bands were readily visible. When compared to manual sectioning, it proved to be a valid and repeatable means of ageing and offers several distinct advantages over other ageing methods. PMID:22497384
pyro: Python-based tutorial for computational methods for hydrodynamics
NASA Astrophysics Data System (ADS)
Zingale, Michael
2015-07-01
pyro is a simple python-based tutorial on computational methods for hydrodynamics. It includes 2-d solvers for advection, compressible, incompressible, and low Mach number hydrodynamics, diffusion, and multigrid. It is written with ease of understanding in mind. An extensive set of notes that is part of the Open Astrophysics Bookshelf project provides details of the algorithms.
EQUILIBRIUM AND NONEQUILIBRIUM FOUNDATIONS OF FREE ENERGY COMPUTATIONAL METHODS
C. JARZYNSKI
2001-03-01
Statistical mechanics provides a rigorous framework for the numerical estimation of free energy differences in complex systems such as biomolecules. This paper presents a brief review of the statistical mechanical identities underlying a number of techniques for computing free energy differences. Both equilibrium and nonequilibrium methods are covered.
Trajectory optimization using parallel shooting method on parallel computer
Wirthman, D.J.; Park, S.Y.; Vadali, S.R.
1995-03-01
The efficiency of a parallel shooting method on a parallel computer for solving a variety of optimal control guidance problems is studied. Several examples are considered to demonstrate that a speedup of nearly 7 to 1 is achieved with the use of 16 processors. It is suggested that further improvements in performance can be achieved by parallelizing in the state domain. 10 refs.
A Higher Order Iterative Method for Computing the Drazin Inverse
Soleymani, F.; Stanimirović, Predrag S.
2013-01-01
A method with high convergence rate for finding approximate inverses of nonsingular matrices is suggested and established analytically. An extension of the introduced computational scheme to general square matrices is defined. The extended method could be used for finding the Drazin inverse. The application of the scheme on large sparse test matrices alongside the use in preconditioning of linear system of equations will be presented to clarify the contribution of the paper. PMID:24222747
Method and system for environmentally adaptive fault tolerant computing
NASA Technical Reports Server (NTRS)
Copenhaver, Jason L. (Inventor); Jeremy, Ramos (Inventor); Wolfe, Jeffrey M. (Inventor); Brenner, Dean (Inventor)
2010-01-01
A method and system for adapting fault tolerant computing. The method includes the steps of measuring an environmental condition representative of an environment. An on-board processing system's sensitivity to the measured environmental condition is measured. It is determined whether to reconfigure a fault tolerance of the on-board processing system based in part on the measured environmental condition. The fault tolerance of the on-board processing system may be reconfigured based in part on the measured environmental condition.
Stress intensity estimates by a computer assisted photoelastic method
NASA Technical Reports Server (NTRS)
Smith, C. W.
1977-01-01
Following an introductory history, the frozen stress photoelastic method is reviewed together with analytical and experimental aspects of cracks in photoelastic models. Analytical foundations are then presented upon which a computer assisted frozen stress photoelastic technique is based for extracting estimates of stress intensity factors from three-dimensional cracked body problems. The use of the method is demonstrated for two currently important three-dimensional crack problems.
A Parallel Iterative Method for Computing Molecular Absorption Spectra.
Koval, Peter; Foerster, Dietrich; Coulaud, Olivier
2010-09-14
We describe a fast parallel iterative method for computing molecular absorption spectra within TDDFT linear response and using the LCAO method. We use a local basis of "dominant products" to parametrize the space of orbital products that occur in the LCAO approach. In this basis, the dynamic polarizability is computed iteratively within an appropriate Krylov subspace. The iterative procedure uses a matrix-free GMRES method to determine the (interacting) density response. The resulting code is about 1 order of magnitude faster than our previous full-matrix method. This acceleration makes the speed of our TDDFT code comparable with codes based on Casida's equation. The implementation of our method uses hybrid MPI and OpenMP parallelization in which load balancing and memory access are optimized. To validate our approach and to establish benchmarks, we compute spectra of large molecules on various types of parallel machines. The methods developed here are fairly general, and we believe they will find useful applications in molecular physics/chemistry, even for problems that are beyond TDDFT, such as organic semiconductors, particularly in photovoltaics. PMID:26616067
Three-dimensional cardiac computational modelling: methods, features and applications.
Lopez-Perez, Alejandro; Sebastian, Rafael; Ferrero, Jose M
2015-01-01
The combination of computational models and biophysical simulations can help to interpret an array of experimental data and contribute to the understanding, diagnosis and treatment of complex diseases such as cardiac arrhythmias. For this reason, three-dimensional (3D) cardiac computational modelling is currently a rising field of research. The advance of medical imaging technology over the last decades has allowed the evolution from generic to patient-specific 3D cardiac models that faithfully represent the anatomy and different cardiac features of a given alive subject. Here we analyse sixty representative 3D cardiac computational models developed and published during the last fifty years, describing their information sources, features, development methods and online availability. This paper also reviews the necessary components to build a 3D computational model of the heart aimed at biophysical simulation, paying especial attention to cardiac electrophysiology (EP), and the existing approaches to incorporate those components. We assess the challenges associated to the different steps of the building process, from the processing of raw clinical or biological data to the final application, including image segmentation, inclusion of substructures and meshing among others. We briefly outline the personalisation approaches that are currently available in 3D cardiac computational modelling. Finally, we present examples of several specific applications, mainly related to cardiac EP simulation and model-based image analysis, showing the potential usefulness of 3D cardiac computational modelling into clinical environments as a tool to aid in the prevention, diagnosis and treatment of cardiac diseases. PMID:25928297
Using diagnostic radiology in human evolutionary studies
SPOOR, FRED; JEFFERY, NATHAN; ZONNEVELD, FRANS
2000-01-01
This paper reviews the application of medical imaging and associated computer graphics techniques to the study of human evolutionary history, with an emphasis on basic concepts and on the advantages and limitations of each method. Following a short discussion of plain film radiography and pluridirectional tomography, the principles of computed tomography (CT) and magnetic resonance imaging (MRI) and their role in the investigation of extant and fossil morphology are considered in more detail. The second half of the paper deals with techniques of 3-dimensional visualisation based on CT and MRI and with quantitative analysis of digital images. PMID:10999271
Analysis and optimization of cyclic methods in orbit computation
NASA Technical Reports Server (NTRS)
Pierce, S.
1973-01-01
The mathematical analysis and computation of the K=3, order 4; K=4, order 6; and K=5, order 7 cyclic methods and the K=5, order 6 Cowell method and some results of optimizing the 3 backpoint cyclic multistep methods for solving ordinary differential equations are presented. Cyclic methods have the advantage over traditional methods of having higher order for a given number of backpoints while at the same time having more free parameters. After considering several error sources the primary source for the cyclic methods has been isolated. The free parameters for three backpoint methods were used to minimize the effects of some of these error sources. They now yield more accuracy with the same computing time as Cowell's method on selected problems. This work is being extended to the five backpoint methods. The analysis and optimization are more difficult here since the matrices are larger and the dimension of the optimizing space is larger. Indications are that the primary error source can be reduced. This will still leave several parameters free to minimize other sources.
Computational Methods for Structural Mechanics and Dynamics, part 1
NASA Technical Reports Server (NTRS)
Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)
1989-01-01
The structural analysis methods research has several goals. One goal is to develop analysis methods that are general. This goal of generality leads naturally to finite-element methods, but the research will also include other structural analysis methods. Another goal is that the methods be amenable to error analysis; that is, given a physical problem and a mathematical model of that problem, an analyst would like to know the probable error in predicting a given response quantity. The ultimate objective is to specify the error tolerances and to use automated logic to adjust the mathematical model or solution strategy to obtain that accuracy. A third goal is to develop structural analysis methods that can exploit parallel processing computers. The structural analysis methods research will focus initially on three types of problems: local/global nonlinear stress analysis, nonlinear transient dynamics, and tire modeling.
Applying Evolutionary Anthropology
Gibson, Mhairi A; Lawson, David W
2015-01-01
Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561
NASA Astrophysics Data System (ADS)
Kanta, L.; Berglund, E. Z.
2015-12-01
Urban water supply systems may be managed through supply-side and demand-side strategies, which focus on water source expansion and demand reductions, respectively. Supply-side strategies bear infrastructure and energy costs, while demand-side strategies bear costs of implementation and inconvenience to consumers. To evaluate the performance of demand-side strategies, the participation and water use adaptations of consumers should be simulated. In this study, a Complex Adaptive Systems (CAS) framework is developed to simulate consumer agents that change their consumption to affect the withdrawal from the water supply system, which, in turn influences operational policies and long-term resource planning. Agent-based models are encoded to represent consumers and a policy maker agent and are coupled with water resources system simulation models. The CAS framework is coupled with an evolutionary computation-based multi-objective methodology to explore tradeoffs in cost, inconvenience to consumers, and environmental impacts for both supply-side and demand-side strategies. Decisions are identified to specify storage levels in a reservoir that trigger (1) increases in the volume of water pumped through inter-basin transfers from an external reservoir and (2) drought stages, which restrict the volume of water that is allowed for residential outdoor uses. The proposed methodology is demonstrated for Arlington, Texas, water supply system to identify non-dominated strategies for an historic drought decade. Results demonstrate that pumping costs associated with maximizing environmental reliability exceed pumping costs associated with minimizing restrictions on consumer water use.
Open Issues in Evolutionary Robotics.
Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne
2016-01-01
One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots. PMID:26581015
A computationally efficient particle-simulation method suited to vector-computer architectures
McDonald, J.D.
1990-01-01
Recent interest in a National Aero-Space Plane (NASP) and various Aero-assisted Space Transfer Vehicles (ASTVs) presents the need for a greater understanding of high-speed rarefied flight conditions. Particle simulation techniques such as the Direct Simulation Monte Carlo (DSMC) method are well suited to such problems, but the high cost of computation limits the application of the methods to two-dimensional or very simple three-dimensional problems. This research re-examines the algorithmic structure of existing particle simulation methods and re-structures them to allow efficient implementation on vector-oriented supercomputers. A brief overview of the DSMC method and the Cray-2 vector computer architecture are provided, and the elements of the DSMC method that inhibit substantial vectorization are identified. One such element is the collision selection algorithm. A complete reformulation of underlying kinetic theory shows that this may be efficiently vectorized for general gas mixtures. The mechanics of collisions are vectorizable in the DSMC method, but several optimizations are suggested that greatly enhance performance. Also this thesis proposes a new mechanism for the exchange of energy between vibration and other energy modes. The developed scheme makes use of quantized vibrational states and is used in place of the Borgnakke-Larsen model. Finally, a simplified representation of physical space and boundary conditions is utilized to further reduce the computational cost of the developed method. Comparison to solutions obtained from the DSMC method for the relaxation of internal energy modes in a homogeneous gas, as well as single and multiple specie shock wave profiles, are presented. Additionally, a large scale simulation of the flow about the proposed Aeroassisted Flight Experiment (AFE) vehicle is included as an example of the new computational capability of the developed particle simulation method.
Investigating human evolutionary history
WOOD, BERNARD
2000-01-01
We rely on fossils for the interpretation of more than 95% of our evolutionary history. Fieldwork resulting in the recovery of fresh fossil evidence is an important component of reconstructing human evolutionary history, but advances can also be made by extracting additional evidence for the existing fossil record, and by improving the methods used to interpret the fossil evidence. This review shows how information from imaging and dental microstructure has contributed to improving our understanding of the hominin fossil record. It also surveys recent advances in the use of the fossil record for phylogenetic inference. PMID:10999269
Computing the Casimir energy using the point-matching method
Lombardo, F. C.; Mazzitelli, F. D.; Vazquez, M.; Villar, P. I.
2009-09-15
We use a point-matching approach to numerically compute the Casimir interaction energy for a two perfect-conductor waveguide of arbitrary section. We present the method and describe the procedure used to obtain the numerical results. At first, our technique is tested for geometries with known solutions, such as concentric and eccentric cylinders. Then, we apply the point-matching technique to compute the Casimir interaction energy for new geometries such as concentric corrugated cylinders and cylinders inside conductors with focal lines.
The ensemble switch method for computing interfacial tensions.
Schmitz, Fabian; Virnau, Peter
2015-04-14
We present a systematic thermodynamic integration approach to compute interfacial tensions for solid-liquid interfaces, which is based on the ensemble switch method. Applying Monte Carlo simulations and finite-size scaling techniques, we obtain results for hard spheres, which are in agreement with previous computations. The case of solid-liquid interfaces in a variant of the effective Asakura-Oosawa model and of liquid-vapor interfaces in the Lennard-Jones model are discussed as well. We demonstrate that a thorough finite-size analysis of the simulation data is required to obtain precise results for the interfacial tension. PMID:25877563
Digital data storage systems, computers, and data verification methods
Groeneveld, Bennett J.; Austad, Wayne E.; Walsh, Stuart C.; Herring, Catherine A.
2005-12-27
Digital data storage systems, computers, and data verification methods are provided. According to a first aspect of the invention, a computer includes an interface adapted to couple with a dynamic database; and processing circuitry configured to provide a first hash from digital data stored within a portion of the dynamic database at an initial moment in time, to provide a second hash from digital data stored within the portion of the dynamic database at a subsequent moment in time, and to compare the first hash and the second hash.
The ensemble switch method for computing interfacial tensions
Schmitz, Fabian; Virnau, Peter
2015-04-14
We present a systematic thermodynamic integration approach to compute interfacial tensions for solid-liquid interfaces, which is based on the ensemble switch method. Applying Monte Carlo simulations and finite-size scaling techniques, we obtain results for hard spheres, which are in agreement with previous computations. The case of solid-liquid interfaces in a variant of the effective Asakura-Oosawa model and of liquid-vapor interfaces in the Lennard-Jones model are discussed as well. We demonstrate that a thorough finite-size analysis of the simulation data is required to obtain precise results for the interfacial tension.
Methods for the computation of detailed geoids and their accuracy
NASA Technical Reports Server (NTRS)
Rapp, R. H.; Rummel, R.
1975-01-01
Two methods for the computation of geoid undulations using potential coefficients and 1 deg x 1 deg terrestrial anomaly data are examined. It was found that both methods give the same final result but that one method allows a more simplified error analysis. Specific equations were considered for the effect of the mass of the atmosphere and a cap dependent zero-order undulation term was derived. Although a correction to a gravity anomaly for the effect of the atmosphere is only about -0.87 mgal, this correction causes a fairly large undulation correction that was not considered previously. The accuracy of a geoid undulation computed by these techniques was estimated considering anomaly data errors, potential coefficient errors, and truncation (only a finite set of potential coefficients being used) errors. It was found that an optimum cap size of 20 deg should be used. The geoid and its accuracy were computed in the Geos 3 calibration area using the GEM 6 potential coefficients and 1 deg x 1 deg terrestrial anomaly data. The accuracy of the computed geoid is on the order of plus or minus 2 m with respect to an unknown set of best earth parameter constants.
An effective method for computing the noise in biochemical networks
NASA Astrophysics Data System (ADS)
Zhang, Jiajun; Nie, Qing; He, Miao; Zhou, Tianshou
2013-02-01
We present a simple yet effective method, which is based on power series expansion, for computing exact binomial moments that can be in turn used to compute steady-state probability distributions as well as the noise in linear or nonlinear biochemical reaction networks. When the method is applied to representative reaction networks such as the ON-OFF models of gene expression, gene models of promoter progression, gene auto-regulatory models, and common signaling motifs, the exact formulae for computing the intensities of noise in the species of interest or steady-state distributions are analytically given. Interestingly, we find that positive (negative) feedback does not enlarge (reduce) noise as claimed in previous works but has a counter-intuitive effect and that the multi-OFF (or ON) mechanism always attenuates the noise in contrast to the common ON-OFF mechanism and can modulate the noise to the lowest level independently of the mRNA mean. Except for its power in deriving analytical expressions for distributions and noise, our method is programmable and has apparent advantages in reducing computational cost.
A Computationally Efficient Method for Polyphonic Pitch Estimation
NASA Astrophysics Data System (ADS)
Zhou, Ruohua; Reiss, Joshua D.; Mattavelli, Marco; Zoia, Giorgio
2009-12-01
This paper presents a computationally efficient method for polyphonic pitch estimation. The method employs the Fast Resonator Time-Frequency Image (RTFI) as the basic time-frequency analysis tool. The approach is composed of two main stages. First, a preliminary pitch estimation is obtained by means of a simple peak-picking procedure in the pitch energy spectrum. Such spectrum is calculated from the original RTFI energy spectrum according to harmonic grouping principles. Then the incorrect estimations are removed according to spectral irregularity and knowledge of the harmonic structures of the music notes played on commonly used music instruments. The new approach is compared with a variety of other frame-based polyphonic pitch estimation methods, and results demonstrate the high performance and computational efficiency of the approach.
Computation of Pressurized Gas Bearings Using CE/SE Method
NASA Technical Reports Server (NTRS)
Cioc, Sorin; Dimofte, Florin; Keith, Theo G., Jr.; Fleming, David P.
2003-01-01
The space-time conservation element and solution element (CE/SE) method is extended to compute compressible viscous flows in pressurized thin fluid films. This numerical scheme has previously been used successfully to solve a wide variety of compressible flow problems, including flows with large and small discontinuities. In this paper, the method is applied to calculate the pressure distribution in a hybrid gas journal bearing. The formulation of the problem is presented, including the modeling of the feeding system. the numerical results obtained are compared with experimental data. Good agreement between the computed results and the test data were obtained, and thus validate the CE/SE method to solve such problems.
Method of computer-aided measurement in a shooting range
NASA Astrophysics Data System (ADS)
Liu, Chanlao; Zhang, Yun; Xiong, Rensheng; Sun, Yishang
2000-10-01
In the view of the blindness of photoelectric measurement scheme argument and the danger of live shell measurement in shooting range, this paper provided a computer aided measurement method guiding the measurement scheme argument and equipment researching and producing and driving the measurement process visiblization and standardization. The computer aided measurement in shooting range can be divided into the mathematical simulation of targets moving, the mathematical simulation of measurement method, the mathematical simulation of photoelectric system, the animated displaying of measurement process, and so on. By adding random jamming, Gaussian white noise and so on, the live measurement environment and condition was built. By using mathematical discretization, the time series pictures was obtained. By controlling the time changing and time unifying of several equipment, the animated displaying of measurement process was built. The programming language was MATLAB. The method was proved through simulating the intersection measurement trajectory of antiaircraft gun's shell successfully.
Computer-aided methods of determining thyristor thermal transients
Lu, E.; Bronner, G.
1988-08-01
An accurate tracing of the thyristor thermal response is investigated. This paper offers several alternatives for thermal modeling and analysis by using an electrical circuit analog: topological method, convolution integral method, etc. These methods are adaptable to numerical solutions and well suited to the use of the digital computer. The thermal analysis of thyristors was performed for the 1000 MVA converter system at the Princeton Plasma Physics Laboratory. Transient thermal impedance curves for individual thyristors in a given cooling arrangement were known from measurements and from manufacturer's data. The analysis pertains to almost any loading case, and the results are obtained in a numerical or a graphical format. 6 refs., 9 figs.
HOLM,ELIZABETH A.; BATTAILE,CORBETT C.; BUCHHEIT,THOMAS E.; FANG,HUEI ELIOT; RINTOUL,MARK DANIEL; VEDULA,VENKATA R.; GLASS,S. JILL; KNOROVSKY,GERALD A.; NEILSEN,MICHAEL K.; WELLMAN,GERALD W.; SULSKY,DEBORAH; SHEN,YU-LIN; SCHREYER,H. BUCK
2000-04-01
Computational materials simulations have traditionally focused on individual phenomena: grain growth, crack propagation, plastic flow, etc. However, real materials behavior results from a complex interplay between phenomena. In this project, the authors explored methods for coupling mesoscale simulations of microstructural evolution and micromechanical response. In one case, massively parallel (MP) simulations for grain evolution and microcracking in alumina stronglink materials were dynamically coupled. In the other, codes for domain coarsening and plastic deformation in CuSi braze alloys were iteratively linked. this program provided the first comparison of two promising ways to integrate mesoscale computer codes. Coupled microstructural/micromechanical codes were applied to experimentally observed microstructures for the first time. In addition to the coupled codes, this project developed a suite of new computational capabilities (PARGRAIN, GLAD, OOF, MPM, polycrystal plasticity, front tracking). The problem of plasticity length scale in continuum calculations was recognized and a solution strategy was developed. The simulations were experimentally validated on stockpile materials.
Computational methods in metabolic engineering for strain design.
Long, Matthew R; Ong, Wai Kit; Reed, Jennifer L
2015-08-01
Metabolic engineering uses genetic approaches to control microbial metabolism to produce desired compounds. Computational tools can identify new biological routes to chemicals and the changes needed in host metabolism to improve chemical production. Recent computational efforts have focused on exploring what compounds can be made biologically using native, heterologous, and/or enzymes with broad specificity. Additionally, computational methods have been developed to suggest different types of genetic modifications (e.g. gene deletion/addition or up/down regulation), as well as suggest strategies meeting different criteria (e.g. high yield, high productivity, or substrate co-utilization). Strategies to improve the runtime performances have also been developed, which allow for more complex metabolic engineering strategies to be identified. Future incorporation of kinetic considerations will further improve strain design algorithms. PMID:25576846
Evolutionary development of tensegrity structures.
Lobo, Daniel; Vico, Francisco J
2010-09-01
Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering. PMID:20619314
Evolutionary Strategies for Protein Folding
NASA Astrophysics Data System (ADS)
Murthy Gopal, Srinivasa; Wenzel, Wolfgang
2006-03-01
The free energy approach for predicting the protein tertiary structure describes the native state of a protein as the global minimum of an appropriate free-energy forcefield. The low-energy region of the free-energy landscape of a protein is extremely rugged. Efficient optimization methods must therefore speed up the search for the global optimum by avoiding high energy transition states, adapt large scale moves or accept unphysical intermediates. Here we investigate an evolutionary strategies(ES) for optimizing a protein conformation in our all-atom free-energy force field([1],[2]). A set of random conformations is evolved using an ES to get a diverse population containing low energy structure. The ES is shown to balance energy improvement and yet maintain diversity in structures. The ES is implemented as a master-client model for distributed computing. Starting from random structures and by using this optimization technique, we were able to fold a 20 amino-acid helical protein and 16 amino-acid beta hairpin[3]. We compare ES to basin hopping method. [1]T. Herges and W. Wenzel,Biophys.J. 87,3100(2004) [2] A. Verma and W. Wenzel Stabilization and folding of beta-sheet and alpha-helical proteins in an all-atom free energy model(submitted)(2005) [3] S. M. Gopal and W. Wenzel Evolutionary Strategies for Protein Folding (in preparation)
Practical methods to improve the development of computational software
Osborne, A. G.; Harding, D. W.; Deinert, M. R.
2013-07-01
The use of computation has become ubiquitous in science and engineering. As the complexity of computer codes has increased, so has the need for robust methods to minimize errors. Past work has show that the number of functional errors is related the number of commands that a code executes. Since the late 1960's, major participants in the field of computation have encouraged the development of best practices for programming to help reduce coder induced error, and this has lead to the emergence of 'software engineering' as a field of study. Best practices for coding and software production have now evolved and become common in the development of commercial software. These same techniques, however, are largely absent from the development of computational codes by research groups. Many of the best practice techniques from the professional software community would be easy for research groups in nuclear science and engineering to adopt. This paper outlines the history of software engineering, as well as issues in modern scientific computation, and recommends practices that should be adopted by individual scientific programmers and university research groups. (authors)
NASA Astrophysics Data System (ADS)
Zare Hosseinzadeh, Ali; Ghodrati Amiri, Gholamreza; Koo, Ki-Young
2016-04-01
This article presents an effective method for structural damage identification. The damage diagnosis problem is introduced as an optimization problem which is based on computing static displacements by the flexibility matrix. By utilizing this matrix, the complexity of the static displacement measurements in real cases can be overcome. The optimization problem is solved by a fast evolutionary optimization strategy, named the cuckoo optimization algorithm. The performance of the presented method was demonstrated by studying the benchmark problem provided by the IASC-ASCE Task Group on Structural Health Monitoring, and a numerical example of a frame. Moreover, the robustness of the presented approach was investigated in the presence of some prevalent modelling errors, and also when noisy and incomplete modal data are available. Finally, the efficiency of the proposed method was verified by an experimental study of a five-storey shear building structure. All the obtained results show the good performance of the presented method.
Domain decomposition methods for the parallel computation of reacting flows
NASA Technical Reports Server (NTRS)
Keyes, David E.
1988-01-01
Domain decomposition is a natural route to parallel computing for partial differential equation solvers. Subdomains of which the original domain of definition is comprised are assigned to independent processors at the price of periodic coordination between processors to compute global parameters and maintain the requisite degree of continuity of the solution at the subdomain interfaces. In the domain-decomposed solution of steady multidimensional systems of PDEs by finite difference methods using a pseudo-transient version of Newton iteration, the only portion of the computation which generally stands in the way of efficient parallelization is the solution of the large, sparse linear systems arising at each Newton step. For some Jacobian matrices drawn from an actual two-dimensional reacting flow problem, comparisons are made between relaxation-based linear solvers and also preconditioned iterative methods of Conjugate Gradient and Chebyshev type, focusing attention on both iteration count and global inner product count. The generalized minimum residual method with block-ILU preconditioning is judged the best serial method among those considered, and parallel numerical experiments on the Encore Multimax demonstrate for it approximately 10-fold speedup on 16 processors.
Advanced Computational Aeroacoustics Methods for Fan Noise Prediction
NASA Technical Reports Server (NTRS)
Envia, Edmane (Technical Monitor); Tam, Christopher
2003-01-01
Direct computation of fan noise is presently not possible. One of the major difficulties is the geometrical complexity of the problem. In the case of fan noise, the blade geometry is critical to the loading on the blade and hence the intensity of the radiated noise. The precise geometry must be incorporated into the computation. In computational fluid dynamics (CFD), there are two general ways to handle problems with complex geometry. One way is to use unstructured grids. The other is to use body fitted overset grids. In the overset grid method, accurate data transfer is of utmost importance. For acoustic computation, it is not clear that the currently used data transfer methods are sufficiently accurate as not to contaminate the very small amplitude acoustic disturbances. In CFD, low order schemes are, invariably, used in conjunction with unstructured grids. However, low order schemes are known to be numerically dispersive and dissipative. dissipative errors are extremely undesirable for acoustic wave problems. The objective of this project is to develop a high order unstructured grid Dispersion-Relation-Preserving (DRP) scheme. would minimize numerical dispersion and dissipation errors. contains the results of the funded portion of the project. scheme on an unstructured grid has been developed. constructed in the wave number space. The characteristics of the scheme can be improved by the inclusion of additional constraints. Stability of the scheme has been investigated. Stability can be improved by adopting the upwinding strategy.
A random walk method for computing genetic location scores.
Lange, K; Sobel, E
1991-01-01
Calculation of location scores is one of the most computationally intensive tasks in modern genetics. Since these scores are crucial in placing disease loci on marker maps, there is ample incentive to pursue such calculations with large numbers of markers. However, in contrast to the simple, standardized pedigrees used in making marker maps, disease pedigrees are often graphically complex and sparsely phenotyped. These complications can present insuperable barriers to exact likelihood calculations with more than a few markers simultaneously. To overcome these barriers we introduce in the present paper a random walk method for computing approximate location scores with large numbers of biallelic markers. Sufficient mathematical theory is developed to explain the method. Feasibility is checked by small-scale simulations for two applications permitting exact calculation of location scores. PMID:1746559
Computational methods. [Calculation of dynamic loading to offshore platforms
Maeda, H. . Inst. of Industrial Science)
1993-02-01
With regard to the computational methods for hydrodynamic forces, first identification of marine hydrodynamics in offshore technology is discussed. Then general computational methods, the state of the arts and uncertainty on flow problems in offshore technology in which developed, developing and undeveloped problems are categorized and future works follow. Marine hydrodynamics consists of water surface and underwater fluid dynamics. Marine hydrodynamics covers, not only hydro, but also aerodynamics such as wind load or current-wave-wind interaction, hydrodynamics such as cavitation, underwater noise, multi-phase flow such as two-phase flow in pipes or air bubble in water or surface and internal waves, and magneto-hydrodynamics such as propulsion due to super conductivity. Among them, two key words are focused on as the identification of marine hydrodynamics in offshore technology; they are free surface and vortex shedding.
Computational methods for efficient structural reliability and reliability sensitivity analysis
NASA Technical Reports Server (NTRS)
Wu, Y.-T.
1993-01-01
This paper presents recent developments in efficient structural reliability analysis methods. The paper proposes an efficient, adaptive importance sampling (AIS) method that can be used to compute reliability and reliability sensitivities. The AIS approach uses a sampling density that is proportional to the joint PDF of the random variables. Starting from an initial approximate failure domain, sampling proceeds adaptively and incrementally with the goal of reaching a sampling domain that is slightly greater than the failure domain to minimize over-sampling in the safe region. Several reliability sensitivity coefficients are proposed that can be computed directly and easily from the above AIS-based failure points. These probability sensitivities can be used for identifying key random variables and for adjusting design to achieve reliability-based objectives. The proposed AIS methodology is demonstrated using a turbine blade reliability analysis problem.
Characterization of Meta-Materials Using Computational Electromagnetic Methods
NASA Technical Reports Server (NTRS)
Deshpande, Manohar; Shin, Joon
2005-01-01
An efficient and powerful computational method is presented to synthesize a meta-material to specified electromagnetic properties. Using the periodicity of meta-materials, the Finite Element Methodology (FEM) is developed to estimate the reflection and transmission through the meta-material structure for a normal plane wave incidence. For efficient computations of the reflection and transmission over a wide band frequency range through a meta-material a Finite Difference Time Domain (FDTD) approach is also developed. Using the Nicholson-Ross method and the Genetic Algorithms, a robust procedure to extract electromagnetic properties of meta-material from the knowledge of its reflection and transmission coefficients is described. Few numerical examples are also presented to validate the present approach.
Computer processing improves hydraulics optimization with new methods
Gavignet, A.A.; Wick, C.J.
1987-12-01
In current practice, pressure drops in the mud circulating system and the settling velocity of cuttings are calculated with simple rheological models and simple equations. Wellsite computers now allow more sophistication in drilling computations. In this paper, experimental results on the settling velocity of spheres in drilling fluids are reported, along with rheograms done over a wide range of shear rates. The flow curves are fitted to polynomials and general methods are developed to predict friction losses and settling velocities as functions of the polynomial coefficients. These methods were incorporated in a software package that can handle any rig configuration system, including riser booster. Graphic displays show the effect of each parameter on the performance of the circulating system.
Experiences using DAKOTA stochastic expansion methods in computational simulations.
Templeton, Jeremy Alan; Ruthruff, Joseph R.
2012-01-01
Uncertainty quantification (UQ) methods bring rigorous statistical connections to the analysis of computational and experiment data, and provide a basis for probabilistically assessing margins associated with safety and reliability. The DAKOTA toolkit developed at Sandia National Laboratories implements a number of UQ methods, which are being increasingly adopted by modeling and simulation teams to facilitate these analyses. This report disseminates results as to the performance of DAKOTA's stochastic expansion methods for UQ on a representative application. Our results provide a number of insights that may be of interest to future users of these methods, including the behavior of the methods in estimating responses at varying probability levels, and the expansion levels for the methodologies that may be needed to achieve convergence.
A hierarchical method for molecular docking using cloud computing.
Kang, Ling; Guo, Quan; Wang, Xicheng
2012-11-01
Discovering small molecules that interact with protein targets will be a key part of future drug discovery efforts. Molecular docking of drug-like molecules is likely to be valuable in this field; however, the great number of such molecules makes the potential size of this task enormous. In this paper, a method to screen small molecular databases using cloud computing is proposed. This method is called the hierarchical method for molecular docking and can be completed in a relatively short period of time. In this method, the optimization of molecular docking is divided into two subproblems based on the different effects on the protein-ligand interaction energy. An adaptive genetic algorithm is developed to solve the optimization problem and a new docking program (FlexGAsDock) based on the hierarchical docking method has been developed. The implementation of docking on a cloud computing platform is then discussed. The docking results show that this method can be conveniently used for the efficient molecular design of drugs. PMID:23017886
A survey of synchronization methods for parallel computers
Dinning, A. )
1989-07-01
This article examines how traditional synchronization methods influence the design of MIMD multiprocessors. This particular class of architectures is one in which high-level synchronization plays an important role. Although vector processors, dataflow machines, and single instruction, multiple-data (SIMD) computers are highly synchronized, their synchronization is generally an explicit part of the control flow and is executed as part of every instruction. In MIMD multiprocessors, synchronization must occur on demand, so more sophisticated schemes are needed.
Computational Methods for Failure Analysis and Life Prediction
NASA Technical Reports Server (NTRS)
Noor, Ahmed K. (Compiler); Harris, Charles E. (Compiler); Housner, Jerrold M. (Compiler); Hopkins, Dale A. (Compiler)
1993-01-01
This conference publication contains the presentations and discussions from the joint UVA/NASA Workshop on Computational Methods for Failure Analysis and Life Prediction held at NASA Langley Research Center 14-15 Oct. 1992. The presentations focused on damage failure and life predictions of polymer-matrix composite structures. They covered some of the research activities at NASA Langley, NASA Lewis, Southwest Research Institute, industry, and universities. Both airframes and propulsion systems were considered.
Computational Catalysis Using the Artificial Force Induced Reaction Method.
Sameera, W M C; Maeda, Satoshi; Morokuma, Keiji
2016-04-19
The artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy is an automatic approach to explore all important reaction paths of complex reactions. Most traditional methods in computational catalysis require guess reaction paths. On the other hand, the AFIR approach locates local minima (LMs) and transition states (TSs) of reaction paths without a guess, and therefore finds unanticipated as well as anticipated reaction paths. The AFIR method has been applied for multicomponent organic reactions, such as the aldol reaction, Passerini reaction, Biginelli reaction, and phase-transfer catalysis. In the presence of several reactants, many equilibrium structures are possible, leading to a number of reaction pathways. The AFIR method in the GRRM strategy determines all of the important equilibrium structures and subsequent reaction paths systematically. As the AFIR search is fully automatic, exhaustive trial-and-error and guess-and-check processes by the user can be eliminated. At the same time, the AFIR search is systematic, and therefore a more accurate and comprehensive description of the reaction mechanism can be determined. The AFIR method has been used for the study of full catalytic cycles and reaction steps in transition metal catalysis, such as cobalt-catalyzed hydroformylation and iron-catalyzed carbon-carbon bond formation reactions in aqueous media. Some AFIR applications have targeted the selectivity-determining step of transition-metal-catalyzed asymmetric reactions, including stereoselective water-tolerant lanthanide Lewis acid-catalyzed Mukaiyama aldol reactions. In terms of establishing the selectivity of a reaction, systematic sampling of the transition states is critical. In this direction, AFIR is very useful for performing a systematic and automatic determination of TSs. In the presence of a comprehensive description of the transition states, the selectivity of the reaction can be calculated more accurately
Computer method for identification of boiler transfer functions
NASA Technical Reports Server (NTRS)
Miles, J. H.
1971-01-01
An iterative computer method is described for identifying boiler transfer functions using frequency response data. An objective penalized performance measure and a nonlinear minimization technique are used to cause the locus of points generated by a transfer function to resemble the locus of points obtained from frequency response measurements. Different transfer functions can be tried until a satisfactory empirical transfer function to the system is found. To illustrate the method, some examples and some results from a study of a set of data consisting of measurements of the inlet impedance of a single tube forced flow boiler with inserts are given.
Integration of viscous effects into inviscid computational methods
NASA Technical Reports Server (NTRS)
Katz, Joseph
1990-01-01
A variety of practical fluid dynamic problems related to the low-speed, high Reynolds number flow over aircraft and ground vehicles fall in a category where some simplified mathematical models become applicable. This provides the fluid dynamicists with a more economical computational tool, compared to the alternative solution of the Navier Stokes equations. The objective was to provide a brief survey of some of the viscous boundary layer solution methods and to propose a method for coupling between the inviscid outer flow and the viscous boundary layer solutions. Results of this survey and details of the viscous/inviscid flow coupling efforts are presented.
Graphics processing unit acceleration of computational electromagnetic methods
NASA Astrophysics Data System (ADS)
Inman, Matthew
The use of Graphical Processing Units (GPU's) for scientific applications has been evolving and expanding for the decade. GPU's provide an alternative to the CPU in the creation and execution of the numerical codes that are often relied upon in to perform simulations in computational electromagnetics. While originally designed purely to display graphics on the users monitor, GPU's today are essentially powerful floating point co-processors that can be programmed not only to render complex graphics, but also perform the complex mathematical calculations often encountered in scientific computing. Currently the GPU's being produced often contain hundreds of separate cores able to access large amounts of high-speed dedicated memory. By utilizing the power offered by such a specialized processor, it is possible to drastically speed up the calculations required in computational electromagnetics. This increase in speed allows for the use of GPU based simulations in a variety of situations that the computational time has heretofore been a limiting factor in, such as in educational courses. Many situations in teaching electromagnetics often rely upon simple examples of problems due to the simulation times needed to analyze more complex problems. The use of GPU based simulations will be shown to allow demonstrations of more advanced problems than previously allowed by adapting the methods for use on the GPU. Modules will be developed for a wide variety of teaching situations utilizing the speed of the GPU to demonstrate various techniques and ideas previously unrealizable.
Automated uncertainty analysis methods in the FRAP computer codes. [PWR
Peck, S O
1980-01-01
A user oriented, automated uncertainty analysis capability has been incorporated in the Fuel Rod Analysis Program (FRAP) computer codes. The FRAP codes have been developed for the analysis of Light Water Reactor fuel rod behavior during steady state (FRAPCON) and transient (FRAP-T) conditions as part of the United States Nuclear Regulatory Commission's Water Reactor Safety Research Program. The objective of uncertainty analysis of these codes is to obtain estimates of the uncertainty in computed outputs of the codes is to obtain estimates of the uncertainty in computed outputs of the codes as a function of known uncertainties in input variables. This paper presents the methods used to generate an uncertainty analysis of a large computer code, discusses the assumptions that are made, and shows techniques for testing them. An uncertainty analysis of FRAP-T calculated fuel rod behavior during a hypothetical loss-of-coolant transient is presented as an example and carried through the discussion to illustrate the various concepts.
On a method computing transient wave propagation in ionospheric regions
NASA Technical Reports Server (NTRS)
Gray, K. G.; Bowhill, S. A.
1978-01-01
A consequence of an exoatmospheric nuclear burst is an electromagnetic pulse (EMP) radiated from it. In a region far enough away from the burst, where nonlinear effects can be ignored, the EMP can be represented by a large-amplitude narrow-time-width plane-wave pulse. If the ionosphere intervenes the origin and destination of the EMP, frequency dispersion can cause significant changes in the original pulse upon reception. A method of computing these dispersive effects of transient wave propagation is summarized. The method described is different from the standard transform techniques and provides physical insight into the transient wave process. The method, although exact, can be used in approximating the early-time transient response of an ionospheric region by a simple integration with only explicit knowledge of the electron density, electron collision frequency, and electron gyrofrequency required. As an illustration of the method, it is applied to a simple example and contrasted with the corresponding transform solution.
ALFRED: A Practical Method for Alignment-Free Distance Computation.
Thankachan, Sharma V; Chockalingam, Sriram P; Liu, Yongchao; Apostolico, Alberto; Aluru, Srinivas
2016-06-01
Alignment-free approaches are gaining persistent interest in many sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, especially for large-scale sequence datasets. Besides the widely used k-mer methods, the average common substring (ACS) approach has emerged to be one of the well-known alignment-free approaches. Two recent works further generalize this ACS approach by allowing a bounded number k of mismatches in the common substrings, relying on approximation (linear time) and exact computation, respectively. Albeit having a good worst-case time complexity [Formula: see text], the exact approach is complex and unlikely to be efficient in practice. Herein, we present ALFRED, an alignment-free distance computation method, which solves the generalized common substring search problem via exact computation. Compared to the theoretical approach, our algorithm is easier to implement and more practical to use, while still providing highly competitive theoretical performances with an expected run-time of [Formula: see text]. By applying our program to phylogenetic inference as a case study, we find that our program facilitates to exactly reconstruct the topology of the reference phylogenetic tree for a set of 27 primate mitochondrial genomes, at reasonably acceptable speed. ALFRED is implemented in C++ programming language and the source code is freely available online. PMID:27138275
Optimum threshold selection method of centroid computation for Gaussian spot
NASA Astrophysics Data System (ADS)
Li, Xuxu; Li, Xinyang; Wang, Caixia
2015-10-01
Centroid computation of Gaussian spot is often conducted to get the exact position of a target or to measure wave-front slopes in the fields of target tracking and wave-front sensing. Center of Gravity (CoG) is the most traditional method of centroid computation, known as its low algorithmic complexity. However both electronic noise from the detector and photonic noise from the environment reduces its accuracy. In order to improve the accuracy, thresholding is unavoidable before centroid computation, and optimum threshold need to be selected. In this paper, the model of Gaussian spot is established to analyze the performance of optimum threshold under different Signal-to-Noise Ratio (SNR) conditions. Besides, two optimum threshold selection methods are introduced: TmCoG (using m % of the maximum intensity of spot as threshold), and TkCoG ( usingμn +κσ n as the threshold), μn and σn are the mean value and deviation of back noise. Firstly, their impact on the detection error under various SNR conditions is simulated respectively to find the way to decide the value of k or m. Then, a comparison between them is made. According to the simulation result, TmCoG is superior over TkCoG for the accuracy of selected threshold, and detection error is also lower.
Approximation method to compute domain related integrals in structural studies
NASA Astrophysics Data System (ADS)
Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.
2015-11-01
Various engineering calculi use integral calculus in theoretical models, i.e. analytical and numerical models. For usual problems, integrals have mathematical exact solutions. If the domain of integration is complicated, there may be used several methods to calculate the integral. The first idea is to divide the domain in smaller sub-domains for which there are direct calculus relations, i.e. in strength of materials the bending moment may be computed in some discrete points using the graphical integration of the shear force diagram, which usually has a simple shape. Another example is in mathematics, where the surface of a subgraph may be approximated by a set of rectangles or trapezoids used to calculate the definite integral. The goal of the work is to introduce our studies about the calculus of the integrals in the transverse section domains, computer aided solutions and a generalizing method. The aim of our research is to create general computer based methods to execute the calculi in structural studies. Thus, we define a Boolean algebra which operates with ‘simple’ shape domains. This algebraic standpoint uses addition and subtraction, conditioned by the sign of every ‘simple’ shape (-1 for the shapes to be subtracted). By ‘simple’ shape or ‘basic’ shape we define either shapes for which there are direct calculus relations, or domains for which their frontiers are approximated by known functions and the according calculus is carried out using an algorithm. The ‘basic’ shapes are linked to the calculus of the most significant stresses in the section, refined aspect which needs special attention. Starting from this idea, in the libraries of ‘basic’ shapes, there were included rectangles, ellipses and domains whose frontiers are approximated by spline functions. The domain triangularization methods suggested that another ‘basic’ shape to be considered is the triangle. The subsequent phase was to deduce the exact relations for the
Wang, Shuai; Luo, Xuenong; Wei, Wei; Zheng, Yadong; Dou, Yongxi; Cai, Xuepeng
2013-01-01
Individual genes or regions are still commonly used to estimate the phylogenetic relationships among viral isolates. The genomic regions that can faithfully provide assessments consistent with those predicted with full-length genome sequences would be preferable to serve as good candidates of the phylogenetic markers for molecular epidemiological studies of many viruses. Here we employed a statistical method to evaluate the evolutionary relationships between individual viral genes and full-length genomes without tree construction as a way to determine which gene can match the genome well in phylogenetic analyses. This method was performed by calculation of linear correlations between the genetic distance matrices of aligned individual gene sequences and aligned genome sequences. We applied this method to the phylogenetic analyses of porcine circovirus 2 (PCV2), measles virus (MV), hepatitis E virus (HEV) and Japanese encephalitis virus (JEV). Phylogenetic trees were constructed for comparisons and the possible factors affecting the method accuracy were also discussed in the calculations. The results revealed that this method could produce results consistent with those of previous studies about the proper consensus sequences that could be successfully used as phylogenetic markers. And our results also suggested that these evolutionary correlations could provide useful information for identifying genes that could be used effectively to infer the genetic relationships. PMID:24312527
Tensor product decomposition methods for plasmas physics computations
NASA Astrophysics Data System (ADS)
Del-Castillo-Negrete, D.
2012-03-01
Tensor product decomposition (TPD) methods are a powerful linear algebra technique for the efficient representation of high dimensional data sets. In the simplest 2-dimensional case, TPD reduces to the singular value decomposition (SVD) of matrices. These methods, which are closely related to proper orthogonal decomposition techniques, have been extensively applied in signal and image processing, and to some fluid mechanics problems. However, their use in plasma physics computation is relatively new. Some recent applications include: data compression of 6-dimensional gyrokinetic plasma turbulence data sets,footnotetextD. R. Hatch, D. del-Castillo-Negrete, and P. W. Terry. Submitted to Journal Comp. Phys. (2011). noise reduction in particle methods,footnotetextR. Nguyen, D. del-Castillo-Negrete, K. Schneider, M. Farge, and G. Chen: Journal of Comp. Phys. 229, 2821-2839 (2010). and multiscale analysis of plasma turbulence.footnotetextS. Futatani, S. Benkadda, and D. del-Castillo-Negrete: Phys. of Plasmas, 16, 042506 (2009) The goal of this presentation is to discuss a novel application of TPD methods to projective integration of particle-based collisional plasma transport computations.
New developments in the multiscale hybrid energy density computational method
NASA Astrophysics Data System (ADS)
Min, Sun; Shanying, Wang; Dianwu, Wang; Chongyu, Wang
2016-01-01
Further developments in the hybrid multiscale energy density method are proposed on the basis of our previous papers. The key points are as follows. (i) The theoretical method for the determination of the weight parameter in the energy coupling equation of transition region in multiscale model is given via constructing underdetermined equations. (ii) By applying the developed mathematical method, the weight parameters have been given and used to treat some problems in homogeneous charge density systems, which are directly related with multiscale science. (iii) A theoretical algorithm has also been presented for treating non-homogeneous systems of charge density. The key to the theoretical computational methods is the decomposition of the electrostatic energy in the total energy of density functional theory for probing the spanning characteristic at atomic scale, layer by layer, by which the choice of chemical elements and the defect complex effect can be understood deeply. (iv) The numerical computational program and design have also been presented. Project supported by the National Basic Research Program of China (Grant No. 2011CB606402) and the National Natural Science Foundation of China (Grant No. 51071091).
COMSAC: Computational Methods for Stability and Control. Part 2
NASA Technical Reports Server (NTRS)
Fremaux, C. Michael (Compiler); Hall, Robert M. (Compiler)
2004-01-01
The unprecedented advances being made in computational fluid dynamic (CFD) technology have demonstrated the powerful capabilities of codes in applications to civil and military aircraft. Used in conjunction with wind-tunnel and flight investigations, many codes are now routinely used by designers in diverse applications such as aerodynamic performance predictions and propulsion integration. Typically, these codes are most reliable for attached, steady, and predominantly turbulent flows. As a result of increasing reliability and confidence in CFD, wind-tunnel testing for some new configurations has been substantially reduced in key areas, such as wing trade studies for mission performance guarantees. Interest is now growing in the application of computational methods to other critical design challenges. One of the most important disciplinary elements for civil and military aircraft is prediction of stability and control characteristics. CFD offers the potential for significantly increasing the basic understanding, prediction, and control of flow phenomena associated with requirements for satisfactory aircraft handling characteristics.
An analytical method for computing atomic contact areas in biomolecules.
Mach, Paul; Koehl, Patrice
2013-01-15
We propose a new analytical method for detecting and computing contacts between atoms in biomolecules. It is based on the alpha shape theory and proceeds in three steps. First, we compute the weighted Delaunay triangulation of the union of spheres representing the molecule. In the second step, the Delaunay complex is filtered to derive the dual complex. Finally, contacts between spheres are collected. In this approach, two atoms i and j are defined to be in contact if their centers are connected by an edge in the dual complex. The contact areas between atom i and its neighbors are computed based on the caps formed by these neighbors on the surface of i; the total area of all these caps is partitioned according to their spherical Laguerre Voronoi diagram on the surface of i. This method is analytical and its implementation in a new program BallContact is fast and robust. We have used BallContact to study contacts in a database of 1551 high resolution protein structures. We show that with this new definition of atomic contacts, we generate realistic representations of the environments of atoms and residues within a protein. In particular, we establish the importance of nonpolar contact areas that complement the information represented by the accessible surface areas. This new method bears similarity to the tessellation methods used to quantify atomic volumes and contacts, with the advantage that it does not require the presence of explicit solvent molecules if the surface of the protein is to be considered. © 2012 Wiley Periodicals, Inc. PMID:22965816
Domain decomposition methods for the parallel computation of reacting flows
NASA Astrophysics Data System (ADS)
Keyes, David E.
1989-05-01
Domain decomposition is a natural route to parallel computing for partial differential equation solvers. In this procedure, subdomains of which the original domain of definition is comprised are assigned to independent processors at the price of periodic coordination between processors to compute global parameters and maintain the requisite degree of continuity of the solution at the subdomain interfaces. In the domain-decomposed solution of steady multidimensional systems of PDEs by finite difference methods using a pseudo-transient version of Newton iteration, the only portion of the computation which generally stands in the way of efficient parallelization is the solution of the large, sparse linear systems arising at each Newton step. For some Jacobian matrices drawn from an actual two-dimensional reacting flow problem, we make comparisons between relaxation-based linear solvers and also preconditioned iterative methods of Conjugate Gradient and Chebyshev type, focusing attention on both iteration count and global inner product count. The generalized minimum residual method with block-ILU preconditioning is judged the best serial method among those considered, and parallel numerical experiments on the Encore Multimax demostrate for it approximately 10-fold speedup on 16 processsors. The three special features of reacting flow models in relation to these linear systems are: the possibly large number of degrees of freedom per gridpoint, the dominance of dense intra-point source-term coupling over inter-point convective-diffusive coupling throughout significant portions of the flow-field and strong nonlinearities which restrict the time step to small values (independent of linear algebraic considerations) throughout significant portions of the iteration history. Though these features are exploited to advantage herein, many aspects of the paper are applicable to the modeling of general convective-diffusive systems.
Computation of multi-material interactions using point method
Zhang, Duan Z; Ma, Xia; Giguere, Paul T
2009-01-01
Calculations of fluid flows are often based on Eulerian description, while calculations of solid deformations are often based on Lagrangian description of the material. When the Eulerian descriptions are used to problems of solid deformations, the state variables, such as stress and damage, need to be advected, causing significant numerical diffusion error. When Lagrangian methods are used to problems involving large solid deformat ions or fluid flows, mesh distortion and entanglement are significant sources of error, and often lead to failure of the calculation. There are significant difficulties for either method when applied to problems involving large deformation of solids. To address these difficulties, particle-in-cell (PIC) method is introduced in the 1960s. In the method Eulerian meshes stay fixed and the Lagrangian particles move through the Eulerian meshes during the material deformation. Since its introduction, many improvements to the method have been made. The work of Sulsky et al. (1995, Comput. Phys. Commun. v. 87, pp. 236) provides a mathematical foundation for an improved version, material point method (MPM) of the PIC method. The unique advantages of the MPM method have led to many attempts of applying the method to problems involving interaction of different materials, such as fluid-structure interactions. These problems are multiphase flow or multimaterial deformation problems. In these problems pressures, material densities and volume fractions are determined by satisfying the continuity constraint. However, due to the difference in the approximations between the material point method and the Eulerian method, erroneous results for pressure will be obtained if the same scheme used in Eulerian methods for multiphase flows is used to calculate the pressure. To resolve this issue, we introduce a numerical scheme that satisfies the continuity requirement to higher order of accuracy in the sense of weak solutions for the continuity equations
Turbopump Performance Improved by Evolutionary Algorithms
NASA Technical Reports Server (NTRS)
Oyama, Akira; Liou, Meng-Sing
2002-01-01
The development of design optimization technology for turbomachinery has been initiated using the multiobjective evolutionary algorithm under NASA's Intelligent Synthesis Environment and Revolutionary Aeropropulsion Concepts programs. As an alternative to the traditional gradient-based methods, evolutionary algorithms (EA's) are emergent design-optimization algorithms modeled after the mechanisms found in natural evolution. EA's search from multiple points, instead of moving from a single point. In addition, they require no derivatives or gradients of the objective function, leading to robustness and simplicity in coupling any evaluation codes. Parallel efficiency also becomes very high by using a simple master-slave concept for function evaluations, since such evaluations often consume the most CPU time, such as computational fluid dynamics. Application of EA's to multiobjective design problems is also straightforward because EA's maintain a population of design candidates in parallel. Because of these advantages, EA's are a unique and attractive approach to real-world design optimization problems.
PREFACE: Theory, Modelling and Computational methods for Semiconductors
NASA Astrophysics Data System (ADS)
Migliorato, Max; Probert, Matt
2010-04-01
These conference proceedings contain the written papers of the contributions presented at the 2nd International Conference on: Theory, Modelling and Computational methods for Semiconductors. The conference was held at the St Williams College, York, UK on 13th-15th Jan 2010. The previous conference in this series took place in 2008 at the University of Manchester, UK. The scope of this conference embraces modelling, theory and the use of sophisticated computational tools in Semiconductor science and technology, where there is a substantial potential for time saving in R&D. The development of high speed computer architectures is finally allowing the routine use of accurate methods for calculating the structural, thermodynamic, vibrational and electronic properties of semiconductors and their heterostructures. This workshop ran for three days, with the objective of bringing together UK and international leading experts in the field of theory of group IV, III-V and II-VI semiconductors together with postdocs and students in the early stages of their careers. The first day focused on providing an introduction and overview of this vast field, aimed particularly at students at this influential point in their careers. We would like to thank all participants for their contribution to the conference programme and these proceedings. We would also like to acknowledge the financial support from the Institute of Physics (Computational Physics group and Semiconductor Physics group), the UK Car-Parrinello Consortium, Accelrys (distributors of Materials Studio) and Quantumwise (distributors of Atomistix). The Editors Acknowledgements Conference Organising Committee: Dr Matt Probert (University of York) and Dr Max Migliorato (University of Manchester) Programme Committee: Dr Marco Califano (University of Leeds), Dr Jacob Gavartin (Accelrys Ltd, Cambridge), Dr Stanko Tomic (STFC Daresbury Laboratory), Dr Gabi Slavcheva (Imperial College London) Proceedings edited and compiled by Dr
Pande, Paritosh; Liu, Yuan-Zhi; South, Fredrick A; Boppart, Stephen A
2016-07-15
Numerical correction of optical aberrations provides an inexpensive and simpler alternative to the traditionally used hardware-based adaptive optics techniques. In this Letter, we present an automated computational aberration correction method for broadband interferometric imaging techniques. In the proposed method, the process of aberration correction is modeled as a filtering operation on the aberrant image using a phase filter in the Fourier domain. The phase filter is expressed as a linear combination of Zernike polynomials with unknown coefficients, which are estimated through an iterative optimization scheme based on maximizing an image sharpness metric. The method is validated on both simulated data and experimental data obtained from a tissue phantom, an ex vivo tissue sample, and an in vivo photoreceptor layer of the human retina. PMID:27420526
On implicit Runge-Kutta methods for parallel computations
NASA Technical Reports Server (NTRS)
Keeling, Stephen L.
1987-01-01
Implicit Runge-Kutta methods which are well-suited for parallel computations are characterized. It is claimed that such methods are first of all, those for which the associated rational approximation to the exponential has distinct poles, and these are called multiply explicit (MIRK) methods. Also, because of the so-called order reduction phenomenon, there is reason to require that these poles be real. Then, it is proved that a necessary condition for a q-stage, real MIRK to be A sub 0-stable with maximal order q + 1 is that q = 1, 2, 3, or 5. Nevertheless, it is shown that for every positive integer q, there exists a q-stage, real MIRK which is I-stable with order q. Finally, some useful examples of algebraically stable MIRKs are given.
Multiscale Methods, Parallel Computation, and Neural Networks for Real-Time Computer Vision.
NASA Astrophysics Data System (ADS)
Battiti, Roberto
1990-01-01
This thesis presents new algorithms for low and intermediate level computer vision. The guiding ideas in the presented approach are those of hierarchical and adaptive processing, concurrent computation, and supervised learning. Processing of the visual data at different resolutions is used not only to reduce the amount of computation necessary to reach the fixed point, but also to produce a more accurate estimation of the desired parameters. The presented adaptive multiple scale technique is applied to the problem of motion field estimation. Different parts of the image are analyzed at a resolution that is chosen in order to minimize the error in the coefficients of the differential equations to be solved. Tests with video-acquired images show that velocity estimation is more accurate over a wide range of motion with respect to the homogeneous scheme. In some cases introduction of explicit discontinuities coupled to the continuous variables can be used to avoid propagation of visual information from areas corresponding to objects with different physical and/or kinematic properties. The human visual system uses concurrent computation in order to process the vast amount of visual data in "real -time." Although with different technological constraints, parallel computation can be used efficiently for computer vision. All the presented algorithms have been implemented on medium grain distributed memory multicomputers with a speed-up approximately proportional to the number of processors used. A simple two-dimensional domain decomposition assigns regions of the multiresolution pyramid to the different processors. The inter-processor communication needed during the solution process is proportional to the linear dimension of the assigned domain, so that efficiency is close to 100% if a large region is assigned to each processor. Finally, learning algorithms are shown to be a viable technique to engineer computer vision systems for different applications starting from
Review methods for image segmentation from computed tomography images
Mamat, Nurwahidah; Rahman, Wan Eny Zarina Wan Abdul; Soh, Shaharuddin Cik; Mahmud, Rozi
2014-12-04
Image segmentation is a challenging process in order to get the accuracy of segmentation, automation and robustness especially in medical images. There exist many segmentation methods that can be implemented to medical images but not all methods are suitable. For the medical purposes, the aims of image segmentation are to study the anatomical structure, identify the region of interest, measure tissue volume to measure growth of tumor and help in treatment planning prior to radiation therapy. In this paper, we present a review method for segmentation purposes using Computed Tomography (CT) images. CT images has their own characteristics that affect the ability to visualize anatomic structures and pathologic features such as blurring of the image and visual noise. The details about the methods, the goodness and the problem incurred in the methods will be defined and explained. It is necessary to know the suitable segmentation method in order to get accurate segmentation. This paper can be a guide to researcher to choose the suitable segmentation method especially in segmenting the images from CT scan.
Numerical Methods of Computational Electromagnetics for Complex Inhomogeneous Systems
Cai, Wei
2014-05-15
Understanding electromagnetic phenomena is the key in many scientific investigation and engineering designs such as solar cell designs, studying biological ion channels for diseases, and creating clean fusion energies, among other things. The objectives of the project are to develop high order numerical methods to simulate evanescent electromagnetic waves occurring in plasmon solar cells and biological ion-channels, where local field enhancement within random media in the former and long range electrostatic interactions in the latter are of major challenges for accurate and efficient numerical computations. We have accomplished these objectives by developing high order numerical methods for solving Maxwell equations such as high order finite element basis for discontinuous Galerkin methods, well-conditioned Nedelec edge element method, divergence free finite element basis for MHD, and fast integral equation methods for layered media. These methods can be used to model the complex local field enhancement in plasmon solar cells. On the other hand, to treat long range electrostatic interaction in ion channels, we have developed image charge based method for a hybrid model in combining atomistic electrostatics and continuum Poisson-Boltzmann electrostatics. Such a hybrid model will speed up the molecular dynamics simulation of transport in biological ion-channels.
Atomistic Method Applied to Computational Modeling of Surface Alloys
NASA Technical Reports Server (NTRS)
Bozzolo, Guillermo H.; Abel, Phillip B.
2000-01-01
The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on
A Novel Automated Method for Analyzing Cylindrical Computed Tomography Data
NASA Technical Reports Server (NTRS)
Roth, D. J.; Burke, E. R.; Rauser, R. W.; Martin, R. E.
2011-01-01
A novel software method is presented that is applicable for analyzing cylindrical and partially cylindrical objects inspected using computed tomography. This method involves unwrapping and re-slicing data so that the CT data from the cylindrical object can be viewed as a series of 2-D sheets in the vertical direction in addition to volume rendering and normal plane views provided by traditional CT software. The method is based on interior and exterior surface edge detection and under proper conditions, is FULLY AUTOMATED and requires no input from the user except the correct voxel dimension from the CT scan. The software is available from NASA in 32- and 64-bit versions that can be applied to gigabyte-sized data sets, processing data either in random access memory or primarily on the computer hard drive. Please inquire with the presenting author if further interested. This software differentiates itself in total from other possible re-slicing software solutions due to complete automation and advanced processing and analysis capabilities.
A multigrid nonoscillatory method for computing high speed flows
NASA Technical Reports Server (NTRS)
Li, C. P.; Shieh, T. H.
1993-01-01
A multigrid method using different smoothers has been developed to solve the Euler equations discretized by a nonoscillatory scheme up to fourth order accuracy. The best smoothing property is provided by a five-stage Runge-Kutta technique with optimized coefficients, yet the most efficient smoother is a backward Euler technique in factored and diagonalized form. The singlegrid solution for a hypersonic, viscous conic flow is in excellent agreement with the solution obtained by the third order MUSCL and Roe's method. Mach 8 inviscid flow computations for a complete entry probe have shown that the accuracy is at least as good as the symmetric TVD scheme of Yee and Harten. The implicit multigrid method is four times more efficient than the explicit multigrid technique and 3.5 times faster than the single-grid implicit technique. For a Mach 8.7 inviscid flow over a blunt delta wing at 30 deg incidence, the CPU reduction factor from the three-level multigrid computation is 2.2 on a grid of 37 x 41 x 73 nodes.
Combustor flow computations in general coordinates with a multigrid method
NASA Astrophysics Data System (ADS)
Shyy, Wei; Braaten, Mark E.
The computational approach presented for single-phase combusting turbulent flowfields balances the requirements of complex physical and chemical flow interactions with those of resolving the three-dimensional geometrical constraints of the combustor contours, film cooling slots, and circular dilution holes. Attention is given to the three-dimensional grid-generation algorithm, the two-dimensional adaptive grid method applied to recirculating turbulent reacting flows, and theory/data assessments for three-dimensional combusting flows in an annular gas turbine combustor.
Assessment of nonequilibrium radiation computation methods for hypersonic flows
NASA Technical Reports Server (NTRS)
Sharma, Surendra
1993-01-01
The present understanding of shock-layer radiation in the low density regime, as appropriate to hypersonic vehicles, is surveyed. Based on the relative importance of electron excitation and radiation transport, the hypersonic flows are divided into three groups: weakly ionized, moderately ionized, and highly ionized flows. In the light of this division, the existing laboratory and flight data are scrutinized. Finally, an assessment of the nonequilibrium radiation computation methods for the three regimes in hypersonic flows is presented. The assessment is conducted by comparing experimental data against the values predicted by the physical model.
Experiences with the Lanczos method on a parallel computer
NASA Technical Reports Server (NTRS)
Bostic, Susan W.; Fulton, Robert E.
1987-01-01
A parallel computer implementation of the Lanczos method for the free-vibration analysis of structures is considered, and results for two example problems show substantial time-reduction over the sequential solutions. The major Lanczos calculation tasks are subdivided into subtasks, and parallelism is introduced at the subtask level. A speedup of 7.8 on eight processors was obtained for the decomposition step of the problem involving a 60-m three-longeron space mast, and a speedup of 14.6 on 16 processors was obtained for the decomposition step of the problem involving a blade-stiffened graphite-epoxy panel.
Computational Studies of Protein Aggregation: Methods and Applications
NASA Astrophysics Data System (ADS)
Morriss-Andrews, Alex; Shea, Joan-Emma
2015-04-01
Protein aggregation involves the self-assembly of normally soluble proteins into large supramolecular assemblies. The typical end product of aggregation is the amyloid fibril, an extended structure enriched in Î²-sheet content. The aggregation process has been linked to a number of diseases, most notably Alzheimer's disease, but fibril formation can also play a functional role in certain organisms. This review focuses on theoretical studies of the process of fibril formation, with an emphasis on the computational models and methods commonly used to tackle this problem.
Computational methods for improving thermal imaging for consumer devices
NASA Astrophysics Data System (ADS)
Lynch, Colm N.; Devaney, Nicholas; Drimbarean, Alexandru
2015-05-01
In consumer imaging, the spatial resolution of thermal microbolometer arrays is limited by the large physical size of the individual detector elements. This also limits the number of pixels per image. If thermal sensors are to find a place in consumer imaging, as the newly released FLIR One would suggest, this resolution issue must be addressed. Our work focuses on improving the output quality of low resolution thermal cameras through computational means. The method we propose utilises sub-pixel shifts and temporal variations in the scene, using information from thermal and visible channels. Results from simulations and lab experiments are presented.
Fan Flutter Computations Using the Harmonic Balance Method
NASA Technical Reports Server (NTRS)
Bakhle, Milind A.; Thomas, Jeffrey P.; Reddy, T.S.R.
2009-01-01
An experimental forward-swept fan encountered flutter at part-speed conditions during wind tunnel testing. A new propulsion aeroelasticity code, based on a computational fluid dynamics (CFD) approach, was used to model the aeroelastic behavior of this fan. This threedimensional code models the unsteady flowfield due to blade vibrations using a harmonic balance method to solve the Navier-Stokes equations. This paper describes the flutter calculations and compares the results to experimental measurements and previous results from a time-accurate propulsion aeroelasticity code.
Method and apparatus for managing transactions with connected computers
Goldsmith, Steven Y.; Phillips, Laurence R.; Spires, Shannon V.
2003-01-01
The present invention provides a method and apparatus that make use of existing computer and communication resources and that reduce the errors and delays common to complex transactions such as international shipping. The present invention comprises an agent-based collaborative work environment that assists geographically distributed commercial and government users in the management of complex transactions such as the transshipment of goods across the U.S.-Mexico border. Software agents can mediate the creation, validation and secure sharing of shipment information and regulatory documentation over the Internet, using the World-Wide Web to interface with human users.
A new method to compute lunisolar perturbations in satellite motions
NASA Technical Reports Server (NTRS)
Kozai, Y.
1973-01-01
A new method to compute lunisolar perturbations in satellite motion is proposed. The disturbing function is expressed by the orbital elements of the satellite and the geocentric polar coordinates of the moon and the sun. The secular and long periodic perturbations are derived by numerical integrations, and the short periodic perturbations are derived analytically. The perturbations due to the tides can be included in the same way. In the Appendix, the motion of the orbital plane for a synchronous satellite is discussed; it is concluded that the inclination cannot stay below 7 deg.
Spore: Spawning Evolutionary Misconceptions?
NASA Astrophysics Data System (ADS)
Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.
2010-10-01
The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.
Deterministic point inclusion methods for computational applications with complex geometry
Khamayseh, Ahmed; Kuprat, Andrew P.
2008-11-21
A fundamental problem in computation is finding practical and efficient algorithms for determining if a query point is contained within a model of a three-dimensional solid. The solid is modeled using a general boundary representation that can contain polygonal elements and/or parametric patches.We have developed two such algorithms: the first is based on a global closest feature query, and the second is based on a local intersection query. Both algorithms work for two- and three-dimensional objects. This paper presents both algorithms, as well as the spatial data structures and queries required for efficient implementation of the algorithms. Applications for these algorithms include computational geometry, mesh generation, particle simulation, multiphysics coupling, and computer graphics. These methods are deterministic in that they do not involve random perturbations of diagnostic rays cast from the query point in order to avoid ‘unclean’ or ‘singular’ intersections of the rays with the geometry. Avoiding the necessity of such random perturbations will become increasingly important as geometries become more convoluted and complex.
DETERMINISTIC POINT INCLUSION METHODS FOR COMPUTATIONAL APPLICATIONS WITH COMPLEX GEOMETRY.
Khamayseh, Ahmed K; Kuprat, Andrew
2008-01-01
A fundamental problem in computation is finding practical and efficient algorithms for determining if a query point is contained within a model of a three-dimensional solid. The solid is modeled using a general boundary representation that can contain polygonal elements and/or parametric patches. We have developed two such algorithms: the first is based on a global closest feature query, and the second is based on a local intersection query. Both algorithms work for two- and three-dimensional objects. This paper presents both algorithms, as well as the spatial data structures and queries required for efficient implementation of the algorithms. Applications for these algorithms include computational geometry, mesh generation, particle simulation, multiphysics coupling, and computer graphics. These methods are deterministic in that they do not involve random perturbations of diagnostic rays cast from the query point in order to avoid "unclean" or "singular" intersections of the rays with the geometry. Avoiding the necessity of such random perturbations will become increasingly important as geometries become more convoluted and complex.
Applications of Computational Methods for Dynamic Stability and Control Derivatives
NASA Technical Reports Server (NTRS)
Green, Lawrence L.; Spence, Angela M.
2004-01-01
Initial steps in the application o f a low-order panel method computational fluid dynamic (CFD) code to the calculation of aircraft dynamic stability and control (S&C) derivatives are documented. Several capabilities, unique to CFD but not unique to this particular demonstration, are identified and demonstrated in this paper. These unique capabilities complement conventional S&C techniques and they include the ability to: 1) perform maneuvers without the flow-kinematic restrictions and support interference commonly associated with experimental S&C facilities, 2) easily simulate advanced S&C testing techniques, 3) compute exact S&C derivatives with uncertainty propagation bounds, and 4) alter the flow physics associated with a particular testing technique from those observed in a wind or water tunnel test in order to isolate effects. Also presented are discussions about some computational issues associated with the simulation of S&C tests and selected results from numerous surface grid resolution studies performed during the course of the study.
Computational methods for studying G protein-coupled receptors (GPCRs).
Kaczor, Agnieszka A; Rutkowska, Ewelina; Bartuzi, Damian; Targowska-Duda, Katarzyna M; Matosiuk, Dariusz; Selent, Jana
2016-01-01
The functioning of GPCRs is classically described by the ternary complex model as the interplay of three basic components: a receptor, an agonist, and a G protein. According to this model, receptor activation results from an interaction with an agonist, which translates into the activation of a particular G protein in the intracellular compartment that, in turn, is able to initiate particular signaling cascades. Extensive studies on GPCRs have led to new findings which open unexplored and exciting possibilities for drug design and safer and more effective treatments with GPCR targeting drugs. These include discovery of novel signaling mechanisms such as ligand promiscuity resulting in multitarget ligands and signaling cross-talks, allosteric modulation, biased agonism, and formation of receptor homo- and heterodimers and oligomers which can be efficiently studied with computational methods. Computer-aided drug design techniques can reduce the cost of drug development by up to 50%. In particular structure- and ligand-based virtual screening techniques are a valuable tool for identifying new leads and have been shown to be especially efficient for GPCRs in comparison to water-soluble proteins. Modern computer-aided approaches can be helpful for the discovery of compounds with designed affinity profiles. Furthermore, homology modeling facilitated by a growing number of available templates as well as molecular docking supported by sophisticated techniques of molecular dynamics and quantitative structure-activity relationship models are an excellent source of information about drug-receptor interactions at the molecular level. PMID:26928552
An experiment in hurricane track prediction using parallel computing methods
NASA Technical Reports Server (NTRS)
Song, Chang G.; Jwo, Jung-Sing; Lakshmivarahan, S.; Dhall, S. K.; Lewis, John M.; Velden, Christopher S.
1994-01-01
The barotropic model is used to explore the advantages of parallel processing in deterministic forecasting. We apply this model to the track forecasting of hurricane Elena (1985). In this particular application, solutions to systems of elliptic equations are the essence of the computational mechanics. One set of equations is associated with the decomposition of the wind into irrotational and nondivergent components - this determines the initial nondivergent state. Another set is associated with recovery of the streamfunction from the forecasted vorticity. We demonstrate that direct parallel methods based on accelerated block cyclic reduction (BCR) significantly reduce the computational time required to solve the elliptic equations germane to this decomposition and forecast problem. A 72-h track prediction was made using incremental time steps of 16 min on a network of 3000 grid points nominally separated by 100 km. The prediction took 30 sec on the 8-processor Alliant FX/8 computer. This was a speed-up of 3.7 when compared to the one-processor version. The 72-h prediction of Elena's track was made as the storm moved toward Florida's west coast. Approximately 200 km west of Tampa Bay, Elena executed a dramatic recurvature that ultimately changed its course toward the northwest. Although the barotropic track forecast was unable to capture the hurricane's tight cycloidal looping maneuver, the subsequent northwesterly movement was accurately forecasted as was the location and timing of landfall near Mobile Bay.
Open Rotor Computational Aeroacoustic Analysis with an Immersed Boundary Method
NASA Technical Reports Server (NTRS)
Brehm, Christoph; Barad, Michael F.; Kiris, Cetin C.
2016-01-01
Reliable noise prediction capabilities are essential to enable novel fuel efficient open rotor designs that can meet the community and cabin noise standards. Toward this end, immersed boundary methods have reached a level of maturity so that they are being frequently employed for specific real world applications within NASA. This paper demonstrates that our higher-order immersed boundary method provides the ability for aeroacoustic analysis of wake-dominated flow fields generated by highly complex geometries. This is the first of a kind aeroacoustic simulation of an open rotor propulsion system employing an immersed boundary method. In addition to discussing the peculiarities of applying the immersed boundary method to this moving boundary problem, we will provide a detailed aeroacoustic analysis of the noise generation mechanisms encountered in the open rotor flow. The simulation data is compared to available experimental data and other computational results employing more conventional CFD methods. The noise generation mechanisms are analyzed employing spectral analysis, proper orthogonal decomposition and the causality method.
Computation of Sound Propagation by Boundary Element Method
NASA Technical Reports Server (NTRS)
Guo, Yueping
2005-01-01
This report documents the development of a Boundary Element Method (BEM) code for the computation of sound propagation in uniform mean flows. The basic formulation and implementation follow the standard BEM methodology; the convective wave equation and the boundary conditions on the surfaces of the bodies in the flow are formulated into an integral equation and the method of collocation is used to discretize this equation into a matrix equation to be solved numerically. New features discussed here include the formulation of the additional terms due to the effects of the mean flow and the treatment of the numerical singularities in the implementation by the method of collocation. The effects of mean flows introduce terms in the integral equation that contain the gradients of the unknown, which is undesirable if the gradients are treated as additional unknowns, greatly increasing the sizes of the matrix equation, or if numerical differentiation is used to approximate the gradients, introducing numerical error in the computation. It is shown that these terms can be reformulated in terms of the unknown itself, making the integral equation very similar to the case without mean flows and simple for numerical implementation. To avoid asymptotic analysis in the treatment of numerical singularities in the method of collocation, as is conventionally done, we perform the surface integrations in the integral equation by using sub-triangles so that the field point never coincide with the evaluation points on the surfaces. This simplifies the formulation and greatly facilitates the implementation. To validate the method and the code, three canonic problems are studied. They are respectively the sound scattering by a sphere, the sound reflection by a plate in uniform mean flows and the sound propagation over a hump of irregular shape in uniform flows. The first two have analytical solutions and the third is solved by the method of Computational Aeroacoustics (CAA), all of which
Immersed boundary conditions method for computational fluid dynamics problems
NASA Astrophysics Data System (ADS)
Husain, Syed Zahid
This dissertation presents implicit spectrally-accurate algorithms based on the concept of immersed boundary conditions (IBC) for solving a range of computational fluid dynamics (CFD) problems where the physical domains involve boundary irregularities. Both fixed and moving irregularities are considered with particular emphasis placed on the two-dimensional moving boundary problems. The physical model problems considered are comprised of the Laplace operator, the biharmonic operator and the Navier-Stokes equations, and thus cover the most commonly encountered types of operators in CFD analyses. The IBC algorithm uses a fixed and regular computational domain with flow domain immersed inside the computational domain. Boundary conditions along the edges of the time-dependent flow domain enter the algorithm in the form of internal constraints. Spectral spatial discretization for two-dimensional problems is based on Fourier expansions in the stream-wise direction and Chebyshev expansions in the normal-to-the-wall direction. Up to fourth-order implicit temporal discretization methods have been implemented. The IBC algorithm is shown to deliver the theoretically predicted accuracy in both time and space. Construction of the boundary constraints in the IBC algorithm provides degrees of freedom in excess of that required to formulate a closed system of algebraic equations. The 'classical IBC formulation' works by retaining number boundary constraints that are just sufficient to form a closed system of equations. The use of additional boundary constraints leads to the 'over-determined formulation' of the IBC algorithm. Over-determined systems are explored in order to improve the accuracy of the IBC method and to expand its applicability to more extreme geometries. Standard direct over-determined solvers based on evaluation of pseudo-inverses of the complete coefficient matrices have been tested on three model problems, namely, the Laplace equation, the biharmonic equation
Computational analysis of methods for reduction of induced drag
NASA Technical Reports Server (NTRS)
Janus, J. M.; Chatterjee, Animesh; Cave, Chris
1993-01-01
The purpose of this effort was to perform a computational flow analysis of a design concept centered around induced drag reduction and tip-vortex energy recovery. The flow model solves the unsteady three-dimensional Euler equations, discretized as a finite-volume method, utilizing a high-resolution approximate Riemann solver for cell interface flux definitions. The numerical scheme is an approximately-factored block LU implicit Newton iterative-refinement method. Multiblock domain decomposition is used to partition the field into an ordered arrangement of blocks. Three configurations are analyzed: a baseline fuselage-wing, a fuselage-wing-nacelle, and a fuselage-wing-nacelle-propfan. Aerodynamic force coefficients, propfan performance coefficients, and flowfield maps are used to qualitatively access design efficacy. Where appropriate, comparisons are made with available experimental data.
A computational design method for transonic turbomachinery cascades
NASA Technical Reports Server (NTRS)
Sobieczky, H.; Dulikravich, D. S.
1982-01-01
This paper describes a systematical computational procedure to find configuration changes necessary to modify the resulting flow past turbomachinery cascades, channels and nozzles, to be shock-free at prescribed transonic operating conditions. The method is based on a finite area transonic analysis technique and the fictitious gas approach. This design scheme has two major areas of application. First, it can be used for design of supercritical cascades, with applications mainly in compressor blade design. Second, it provides subsonic inlet shapes including sonic surfaces with suitable initial data for the design of supersonic (accelerated) exits, like nozzles and turbine cascade shapes. This fast, accurate and economical method with a proven potential for applications to three-dimensional flows is illustrated by some design examples.
Radiation Transport Computation in Stochastic Media: Method and Application
NASA Astrophysics Data System (ADS)
Liang, Chao
Stochastic media, characterized by the stochastic distribution of inclusions in a background medium, are typical radiation transport media encountered in natural or engineering systems. In the community of radiation transport computation, there is always a demand of accurate and efficient methods that can account for the nature of the stochastic distribution. In this dissertation, we focus on methodology development for the radiation transport computation that is applied to neutronic analyses of nuclear reactor designs characterized by the stochastic distribution of particle fuel. Reactor concepts with the employment of a fuel design consisting of a random heterogeneous mixture of fissile material and non-fissile moderator are constantly proposed. Key physical quantities such as core criticality and power distribution, reactivity control design parameters, depletion and fuel burn-up need to be carefully evaluated. In order to meet these practical requirements, we first need to develop accurate and fast computational methods that can effectively account for the stochastic nature of double heterogeneity configuration. A Monte Carlo based method called Chord Length Sampling (CLS) method is considered to be a promising method for analyzing those TRISO-type fueled reactors. Although the CLS method has been proposed for more than two decades and much research has been conducted to enhance its applicability, further efforts are still needed to address some key research gaps that exist for the CLS method. (1) There is a general lack of thorough investigation of the factors that give rise to the inaccuracy of the CLS method found by many researchers. The accuracy of the CLS method depends on the optical and geometric properties of the system. In some specific scenarios, considerable inaccuracies have been reported. However, no research has been providing a clear interpretation of the reasons responsible for the inaccuracy in the reported scenarios. Furthermore, no any
Implicit extrapolation methods for multilevel finite element computations
Jung, M.; Ruede, U.
1994-12-31
The finite element package FEMGP has been developed to solve elliptic and parabolic problems arising in the computation of magnetic and thermomechanical fields. FEMGP implements various methods for the construction of hierarchical finite element meshes, a variety of efficient multilevel solvers, including multigrid and preconditioned conjugate gradient iterations, as well as pre- and post-processing software. Within FEMGP, multigrid {tau}-extrapolation can be employed to improve the finite element solution iteratively to higher order. This algorithm is based on an implicit extrapolation, so that the algorithm differs from a regular multigrid algorithm only by a slightly modified computation of the residuals on the finest mesh. Another advantage of this technique is, that in contrast to explicit extrapolation methods, it does not rely on the existence of global error expansions, and therefore neither requires uniform meshes nor global regularity assumptions. In the paper the authors will analyse the {tau}-extrapolation algorithm and present experimental results in the context of the FEMGP package. Furthermore, the {tau}-extrapolation results will be compared to higher order finite element solutions.
Matrix element method for high performance computing platforms
NASA Astrophysics Data System (ADS)
Grasseau, G.; Chamont, D.; Beaudette, F.; Bianchini, L.; Davignon, O.; Mastrolorenzo, L.; Ochando, C.; Paganini, P.; Strebler, T.
2015-12-01
Lot of efforts have been devoted by ATLAS and CMS teams to improve the quality of LHC events analysis with the Matrix Element Method (MEM). Up to now, very few implementations try to face up the huge computing resources required by this method. We propose here a highly parallel version, combining MPI and OpenCL, which makes the MEM exploitation reachable for the whole CMS datasets with a moderate cost. In the article, we describe the status of two software projects under development, one focused on physics and one focused on computing. We also showcase their preliminary performance obtained with classical multi-core processors, CUDA accelerators and MIC co-processors. This let us extrapolate that with the help of 6 high-end accelerators, we should be able to reprocess the whole LHC run 1 within 10 days, and that we have a satisfying metric for the upcoming run 2. The future work will consist in finalizing a single merged system including all the physics and all the parallelism infrastructure, thus optimizing implementation for best hardware platforms.
Recent advances in computer camera methods for machine vision
NASA Astrophysics Data System (ADS)
Olson, Gaylord G.; Walker, Jo N.
1998-10-01
During the past year, several new computer camera methods (hardware and software) have been developed which have applications in machine vision. These are described below, along with some test results. The improvements are generally in the direction of higher speed and greater parallelism. A PCI interface card has been designed which is adaptable to multiple CCD types, both color and monochrome. A newly designed A/D converter allows for a choice of 8 or 10-bit conversion resolution and a choice of two different analog inputs. Thus, by using four of these converters feeding the 32-bit PCI data bus, up to 8 camera heads can be used with a single PCI card, and four camera heads can be operated in parallel. The card has been designed so that any of 8 different CCD types can be used with it (6 monochrome and 2 color CCDs) ranging in resolution from 192 by 165 pixels up to 1134 by 972 pixels. In the area of software, a method has been developed to better utilize the decision-making capability of the computer along with the sub-array scan capabilities of many CCDs. Specifically, it is shown below how to achieve a dual scan mode camera system wherein one scan mode is a low density, high speed scan of a complete image area, and a higher density sub-array scan is used in those areas where changes have been observed. The name given to this technique is adaptive sub-array scanning.
Open Rotor Computational Aeroacoustic Analysis with an Immersed Boundary Method
NASA Technical Reports Server (NTRS)
Brehm, Christoph; Barad, Michael F.; Kiris, Cetin C.
2016-01-01
Reliable noise prediction capabilities are essential to enable novel fuel efficient open rotor designs that can meet the community and cabin noise standards. Toward this end, immersed boundary methods have reached a level of maturity where more and more complex flow problems can be tackled with this approach. This paper demonstrates that our higher-order immersed boundary method provides the ability for aeroacoustic analysis of wake-dominated flow fields generated by a contra-rotating open rotor. This is the first of a kind aeroacoustic simulation of an open rotor propulsion system employing an immersed boundary method. In addition to discussing the methodologies of how to apply the immersed boundary method to this moving boundary problem, we will provide a detailed validation of the aeroacoustic analysis approach employing the Launch Ascent and Vehicle Aerodynamics (LAVA) solver. Two free-stream Mach numbers with M=0.2 and M=0.78 are considered in this analysis that are based on the nominally take-off and cruise flow conditions. The simulation data is compared to available experimental data and other computational results employing more conventional CFD methods. Spectral analysis is used to determine the dominant wave propagation pattern in the acoustic near-field.
Parallel computation of multigroup reactivity coefficient using iterative method
Susmikanti, Mike; Dewayatna, Winter
2013-09-09
One of the research activities to support the commercial radioisotope production program is a safety research target irradiation FPM (Fission Product Molybdenum). FPM targets form a tube made of stainless steel in which the nuclear degrees of superimposed high-enriched uranium. FPM irradiation tube is intended to obtain fission. The fission material widely used in the form of kits in the world of nuclear medicine. Irradiation FPM tube reactor core would interfere with performance. One of the disorders comes from changes in flux or reactivity. It is necessary to study a method for calculating safety terrace ongoing configuration changes during the life of the reactor, making the code faster became an absolute necessity. Neutron safety margin for the research reactor can be reused without modification to the calculation of the reactivity of the reactor, so that is an advantage of using perturbation method. The criticality and flux in multigroup diffusion model was calculate at various irradiation positions in some uranium content. This model has a complex computation. Several parallel algorithms with iterative method have been developed for the sparse and big matrix solution. The Black-Red Gauss Seidel Iteration and the power iteration parallel method can be used to solve multigroup diffusion equation system and calculated the criticality and reactivity coeficient. This research was developed code for reactivity calculation which used one of safety analysis with parallel processing. It can be done more quickly and efficiently by utilizing the parallel processing in the multicore computer. This code was applied for the safety limits calculation of irradiated targets FPM with increment Uranium.
Parallel computation of multigroup reactivity coefficient using iterative method
NASA Astrophysics Data System (ADS)
Susmikanti, Mike; Dewayatna, Winter
2013-09-01
One of the research activities to support the commercial radioisotope production program is a safety research target irradiation FPM (Fission Product Molybdenum). FPM targets form a tube made of stainless steel in which the nuclear degrees of superimposed high-enriched uranium. FPM irradiation tube is intended to obtain fission. The fission material widely used in the form of kits in the world of nuclear medicine. Irradiation FPM tube reactor core would interfere with performance. One of the disorders comes from changes in flux or reactivity. It is necessary to study a method for calculating safety terrace ongoing configuration changes during the life of the reactor, making the code faster became an absolute necessity. Neutron safety margin for the research reactor can be reused without modification to the calculation of the reactivity of the reactor, so that is an advantage of using perturbation method. The criticality and flux in multigroup diffusion model was calculate at various irradiation positions in some uranium content. This model has a complex computation. Several parallel algorithms with iterative method have been developed for the sparse and big matrix solution. The Black-Red Gauss Seidel Iteration and the power iteration parallel method can be used to solve multigroup diffusion equation system and calculated the criticality and reactivity coeficient. This research was developed code for reactivity calculation which used one of safety analysis with parallel processing. It can be done more quickly and efficiently by utilizing the parallel processing in the multicore computer. This code was applied for the safety limits calculation of irradiated targets FPM with increment Uranium.
Computer Anxiety and Students' Preferred Feedback Methods in EFL Writing
ERIC Educational Resources Information Center
Matsumura, Shoichi; Hann, George
2004-01-01
Computer-mediated instruction plays a significant role in foreign language education. The incorporation of computer technology into the classroom has also been accompanied by an increasing number of students who experience anxiety when interacting with computers. This study examined the effects of computer anxiety on students' choice of feedback…
A computational method to predict carbonylation sites in yeast proteins.
Lv, H Q; Liu, J; Han, J Q; Zheng, J G; Liu, R L
2016-01-01
Several post-translational modifications (PTM) have been discussed in literature. Among a variety of oxidative stress-induced PTM, protein carbonylation is considered a biomarker of oxidative stress. Only certain proteins can be carbonylated because only four amino acid residues, namely lysine (K), arginine (R), threonine (T) and proline (P), are susceptible to carbonylation. The yeast proteome is an excellent model to explore oxidative stress, especially protein carbonylation. Current experimental approaches in identifying carbonylation sites are expensive, time-consuming and limited in their abilities to process proteins. Furthermore, there is no bioinformational method to predict carbonylation sites in yeast proteins. Therefore, we propose a computational method to predict yeast carbonylation sites. This method has total accuracies of 86.32, 85.89, 84.80, and 86.80% in predicting the carbonylation sites of K, R, T, and P, respectively. These results were confirmed by 10-fold cross-validation. The ability to identify carbonylation sites in different kinds of features was analyzed and the position-specific composition of the modification site-flanking residues was discussed. Additionally, a software tool has been developed to help with the calculations in this method. Datasets and the software are available at https://sourceforge.net/projects/hqlstudio/ files/CarSpred.Y/. PMID:27420944
Matching wind turbine rotors and loads: computational methods for designers
Seale, J.B.
1983-04-01
This report provides a comprehensive method for matching wind energy conversion system (WECS) rotors with the load characteristics of common electrical and mechanical applications. The user must supply: (1) turbine aerodynamic efficiency as a function of tipspeed ratio; (2) mechanical load torque as a function of rotation speed; (3) useful delivered power as a function of incoming mechanical power; (4) site average windspeed and, for maximum accuracy, distribution data. The description of the data includes governing limits consistent with the capacities of components. The report develops, a step-by-step method for converting the data into useful results: (1) from turbine efficiency and load torque characteristics, turbine power is predicted as a function of windspeed; (2) a decision is made how turbine power is to be governed (it may self-govern) to insure safety of all components; (3) mechanical conversion efficiency comes into play to predict how useful delivered power varies with windspeed; (4) wind statistics come into play to predict longterm energy output. Most systems can be approximated by a graph-and-calculator approach: Computer-generated families of coefficient curves provide data for algebraic scaling formulas. The method leads not only to energy predictions, but also to insight into the processes being modeled. Direct use of a computer program provides more sophisticated calculations where a highly unusual system is to be modeled, where accuracy is at a premium, or where error analysis is required. The analysis is fleshed out witn in-depth case studies for induction generator and inverter utility systems; battery chargers; resistance heaters; positive displacement pumps, including three different load-compensation strategies; and centrifugal pumps with unregulated electric power transmission from turbine to pump.
Ab initio methods for nuclear properties - a computational physics approach
NASA Astrophysics Data System (ADS)
Maris, Pieter
2011-04-01
A microscopic theory for the structure and reactions of light nuclei poses formidable challenges for high-performance computing. Several ab-initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab-initio no-core full configuration (NCFC) approach is based on basis space expansion methods and uses Slater determinants of single-nucleon basis functions to express the nuclear wave function. In this approach, the quantum many-particle problem becomes a large sparse matrix eigenvalue problem. The eigenvalues of this matrix give us the binding energies, and the corresponding eigenvectors the nuclear wave functions. These wave functions can be employed to evaluate experimental quantities. In order to reach numerical convergence for fundamental problems of interest, the matrix dimension often exceeds 1 billion, and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. I discuss different strategies for distributing and solving this large sparse matrix on current multicore computer architectures, including methods to deal with with memory bottleneck. Several of these strategies have been implemented in the code MFDn, which is a parallel fortran code for nuclear structure calculations. I will show scaling behavior and compare the performance of the pure MPI version with the hybrid MPI/OpenMP code on Cray XT4 and XT5 platforms. For large core counts (typically 5,000 and above), the hybrid version is more efficient than pure MPI. With this code, we have been able to predict properties of the unstable nucleus 14F, which have since been confirmed by experiments. I will also give an overview of other recent results for nuclei in the A = 6 to 16 range with 2- and 3-body interactions. Supported in part by US DOE Grant DE-FC02-09ER41582.
Computational modeling of multicellular constructs with the material point method.
Guilkey, James E; Hoying, James B; Weiss, Jeffrey A
2006-01-01
Computational modeling of the mechanics of cells and multicellular constructs with standard numerical discretization techniques such as the finite element (FE) method is complicated by the complex geometry, material properties and boundary conditions that are associated with such systems. The objectives of this research were to apply the material point method (MPM), a meshless method, to the modeling of vascularized constructs by adapting the algorithm to accurately handle quasi-static, large deformation mechanics, and to apply the modified MPM algorithm to large-scale simulations using a discretization that was obtained directly from volumetric confocal image data. The standard implicit time integration algorithm for MPM was modified to allow the background computational grid to remain fixed with respect to the spatial distribution of material points during the analysis. This algorithm was used to simulate the 3D mechanics of a vascularized scaffold under tension, consisting of growing microvascular fragments embedded in a collagen gel, by discretizing the construct with over 13.6 million material points. Baseline 3D simulations demonstrated that the modified MPM algorithm was both more accurate and more robust than the standard MPM algorithm. Scaling studies demonstrated the ability of the parallel code to scale to 200 processors. Optimal discretization was established for the simulations of the mechanics of vascularized scaffolds by examining stress distributions and reaction forces. Sensitivity studies demonstrated that the reaction force during simulated extension was highly sensitive to the modulus of the microvessels, despite the fact that they comprised only 10.4% of the volume of the total sample. In contrast, the reaction force was relatively insensitive to the effective Poisson's ratio of the entire sample. These results suggest that the MPM simulations could form the basis for estimating the modulus of the embedded microvessels through a parameter
ERIC Educational Resources Information Center
Bessey, Barbara L.; And Others
Graphical methods for displaying data, as well as available computer software and hardware, are reviewed. The authors have emphasized the types of graphs which are most relevant to the needs of the National Center for Education Statistics (NCES) and its readers. The following types of graphs are described: tabulations, stem-and-leaf displays,…
Orr, Caley M; Leventhal, Evan L; Chivers, Spencer F; Marzke, Mary W; Wolfe, Scott W; Crisco, Joseph J
2010-04-01
The functional morphology of the wrist pertains to a number of important questions in primate evolutionary biology, including that of hominins. Reconstructing locomotor and manipulative capabilities of the wrist in extinct species requires a detailed understanding of wrist biomechanics in extant primates and the relationship between carpal form and function. The kinematics of carpal movement, and the role individual joints play in providing mobility and stability of the wrist, is central to such efforts. However, there have been few detailed biomechanical studies of the nonhuman primate wrist. This is largely because of the complexity of wrist morphology and the considerable technical challenges involved in tracking the movements of the many small bones that compose the carpus. The purpose of this article is to introduce and outline a method adapted from human clinical studies of three-dimensional (3D) carpal kinematics for use in a comparative context. The method employs computed tomography of primate cadaver forelimbs in increments throughout the wrist's range of motion, coupled with markerless registration of 3D polygon models based on inertial properties of each bone. The 3D kinematic principles involved in extracting motion axis parameters that describe bone movement are reviewed. In addition, a set of anatomically based coordinate systems embedded in the radius, capitate, hamate, lunate, and scaphoid is presented for the benefit of other primate functional morphologists interested in studying carpal kinematics. Finally, a brief demonstration of how the application of these methods can elucidate the mechanics of the wrist in primates illustrates the closer-packing of carpals in chimpanzees than in orangutans, which may help to stabilize the midcarpus and produce a more rigid wrist beneficial for efficient hand posturing during knuckle-walking locomotion. PMID:20235325
Novel computational methods to design protein-protein interactions
NASA Astrophysics Data System (ADS)
Zhou, Alice Qinhua; O'Hern, Corey; Regan, Lynne
2014-03-01
Despite the abundance of structural data, we still cannot accurately predict the structural and energetic changes resulting from mutations at protein interfaces. The inadequacy of current computational approaches to the analysis and design of protein-protein interactions has hampered the development of novel therapeutic and diagnostic agents. In this work, we apply a simple physical model that includes only a minimal set of geometrical constraints, excluded volume, and attractive van der Waals interactions to 1) rank the binding affinity of mutants of tetratricopeptide repeat proteins with their cognate peptides, 2) rank the energetics of binding of small designed proteins to the hydrophobic stem region of the influenza hemagglutinin protein, and 3) predict the stability of T4 lysozyme and staphylococcal nuclease mutants. This work will not only lead to a fundamental understanding of protein-protein interactions, but also to the development of efficient computational methods to rationally design protein interfaces with tunable specificity and affinity, and numerous applications in biomedicine. NSF DMR-1006537, PHY-1019147, Raymond and Beverly Sackler Institute for Biological, Physical and Engineering Sciences, and Howard Hughes Medical Institute.
Inter-Domain Redundancy Path Computation Methods Based on PCE
NASA Astrophysics Data System (ADS)
Hayashi, Rie; Oki, Eiji; Shiomoto, Kohei
This paper evaluates three inter-domain redundancy path computation methods based on PCE (Path Computation Element). Some inter-domain paths carry traffic that must be assured of high quality and high reliability transfer such as telephony over IP and premium virtual private networks (VPNs). It is, therefore, important to set inter-domain redundancy paths, i. e. primary and secondary paths. The first scheme utilizes an existing protocol and the basic PCE implementation. It does not need any extension or modification. In the second scheme, PCEs make a virtual shortest path tree (VSPT) considering the candidates of primary paths that have corresponding secondary paths. The goal is to reduce blocking probability; corresponding secondary paths may be found more often after a primary path is decided; no protocol extension is necessary. In the third scheme, PCEs make a VSPT considering all candidates of primary and secondary paths. Blocking probability is further decreased since all possible candidates are located, and the sum of primary and secondary path cost is reduced by choosing the pair with minimum cost among all path pairs. Numerical evaluations show that the second and third schemes offer only a few percent reduction in blocking probability and path pair total cost, while the overheads imposed by protocol revision and increase of the amount of calculation and information to be exchanged are large. This suggests that the first scheme, the most basic and simple one, is the best choice.
Methods for increased computational efficiency of multibody simulations
NASA Astrophysics Data System (ADS)
Epple, Alexander
This thesis is concerned with the efficient numerical simulation of finite element based flexible multibody systems. Scaling operations are systematically applied to the governing index-3 differential algebraic equations in order to solve the problem of ill conditioning for small time step sizes. The importance of augmented Lagrangian terms is demonstrated. The use of fast sparse solvers is justified for the solution of the linearized equations of motion resulting in significant savings of computational costs. Three time stepping schemes for the integration of the governing equations of flexible multibody systems are discussed in detail. These schemes are the two-stage Radau IIA scheme, the energy decaying scheme, and the generalized-a method. Their formulations are adapted to the specific structure of the governing equations of flexible multibody systems. The efficiency of the time integration schemes is comprehensively evaluated on a series of test problems. Formulations for structural and constraint elements are reviewed and the problem of interpolation of finite rotations in geometrically exact structural elements is revisited. This results in the development of a new improved interpolation algorithm, which preserves the objectivity of the strain field and guarantees stable simulations in the presence of arbitrarily large rotations. Finally, strategies for the spatial discretization of beams in the presence of steep variations in cross-sectional properties are developed. These strategies reduce the number of degrees of freedom needed to accurately analyze beams with discontinuous properties, resulting in improved computational efficiency.
Methods and computer readable medium for improved radiotherapy dosimetry planning
Wessol, Daniel E.; Frandsen, Michael W.; Wheeler, Floyd J.; Nigg, David W.
2005-11-15
Methods and computer readable media are disclosed for ultimately developing a dosimetry plan for a treatment volume irradiated during radiation therapy with a radiation source concentrated internally within a patient or incident from an external beam. The dosimetry plan is available in near "real-time" because of the novel geometric model construction of the treatment volume which in turn allows for rapid calculations to be performed for simulated movements of particles along particle tracks therethrough. The particles are exemplary representations of alpha, beta or gamma emissions emanating from an internal radiation source during various radiotherapies, such as brachytherapy or targeted radionuclide therapy, or they are exemplary representations of high-energy photons, electrons, protons or other ionizing particles incident on the treatment volume from an external source. In a preferred embodiment, a medical image of a treatment volume irradiated during radiotherapy having a plurality of pixels of information is obtained.
Search systems and computer-implemented search methods
Payne, Deborah A.; Burtner, Edwin R.; Bohn, Shawn J.; Hampton, Shawn D.; Gillen, David S.; Henry, Michael J.
2015-12-22
Search systems and computer-implemented search methods are described. In one aspect, a search system includes a communications interface configured to access a plurality of data items of a collection, wherein the data items include a plurality of image objects individually comprising image data utilized to generate an image of the respective data item. The search system may include processing circuitry coupled with the communications interface and configured to process the image data of the data items of the collection to identify a plurality of image content facets which are indicative of image content contained within the images and to associate the image objects with the image content facets and a display coupled with the processing circuitry and configured to depict the image objects associated with the image content facets.
Modern wing flutter analysis by computational fluid dynamics methods
NASA Technical Reports Server (NTRS)
Cunningham, Herbert J.; Batina, John T.; Bennett, Robert M.
1988-01-01
The application and assessment of the recently developed CAP-TSD transonic small-disturbance code for flutter prediction is described. The CAP-TSD code has been developed for aeroelastic analysis of complete aircraft configurations and was previously applied to the calculation of steady and unsteady pressures with favorable results. Generalized aerodynamic forces and flutter characteristics are calculated and compared with linear theory results and with experimental data for a 45 deg sweptback wing. These results are in good agreement with the experimental flutter data which is the first step toward validating CAP-TSD for general transonic aeroelastic applications. The paper presents these results and comparisons along with general remarks regarding modern wing flutter analysis by computational fluid dynamics methods.
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.
Wagner, Jeffrey R; Lee, Christopher T; Durrant, Jacob D; Malmstrom, Robert D; Feher, Victoria A; Amaro, Rommie E
2016-06-01
Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening. Over the past decade, structural data has become more readily available for larger protein systems and more membrane protein classes (e.g., GPCRs and ion channels), which are common allosteric drug targets. In parallel, improved simulation methods now provide better atomistic understanding of the protein dynamics and cooperative motions that are critical to allosteric mechanisms. As a result of these advances, the field of predictive allosteric drug development is now on the cusp of a new era of rational structure-based computational methods. Here, we review algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations, describe tools that assess the druggability of these pockets, and discuss how Markov state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding. In each section, we first provide an overview of the various method classes before describing relevant algorithms and software packages. PMID:27074285
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs
2016-01-01
Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening. Over the past decade, structural data has become more readily available for larger protein systems and more membrane protein classes (e.g., GPCRs and ion channels), which are common allosteric drug targets. In parallel, improved simulation methods now provide better atomistic understanding of the protein dynamics and cooperative motions that are critical to allosteric mechanisms. As a result of these advances, the field of predictive allosteric drug development is now on the cusp of a new era of rational structure-based computational methods. Here, we review algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations, describe tools that assess the druggability of these pockets, and discuss how Markov state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding. In each section, we first provide an overview of the various method classes before describing relevant algorithms and software packages. PMID:27074285
Computational method for transmission eigenvalues for a spherically stratified medium.
Cheng, Xiaoliang; Yang, Jing
2015-07-01
We consider a computational method for the interior transmission eigenvalue problem that arises in acoustic and electromagnetic scattering. The transmission eigenvalues contain useful information about some physical properties, such as the index of refraction. Instead of the existence and estimation of the spectral property of the transmission eigenvalues, we focus on the numerical calculation, especially for spherically stratified media in R^{3}. Due to the nonlinearity and the special structure of the interior transmission eigenvalue problem, there are not many numerical methods to date. First, we reduce the problem into a second-order ordinary differential equation. Then, we apply the Hermite finite element to the weak formulation of the equation. With proper rewriting of the matrix-vector form, we change the original nonlinear eigenvalue problem into a quadratic eigenvalue problem, which can be written as a linear system and solved by the eigs function in MATLAB. This numerical method is fast, effective, and can calculate as many transmission eigenvalues as needed at a time. PMID:26367151
Mohamad, Saharuddin Bin; Ong, Ai Ling; Khairuddin, Raja Farhana; Ripen, Adiratna Mat
2010-01-01
Laccases are industrially attractive enzymes and their applications have expanded to the field of bioremediation. The challenge of today's biotechnology in enzymatic studies is to design enzymes that not only have a higher activity but are also more stable and could fit well with the condition requirements. Laccases are known to oxidize non-natural substrates like polycyclic aromatic hydrocarbons (PAHs). We suppose by increasing the hydrophobicity of laccase, it would increase the chance of the enzyme to meet the hydrophobic substrates in a contamination site, therefore increasing the bioremediation efficacy of PAHs from environment. In this attempt, the applications of evolutionary trace (ET), molecular surface accessibility and hydrophobicity analysis on laccase sequences and laccase's crystal structure (1KYA) are described for optimal design of an enzyme with higher hydrophobicity. Our analysis revealed that Q23A, Q45I, N141A, Q237V, N262L, N301V, N331A, Q360L and Q482A could be promising exchanges to be tested in mutagenesis experiments. PMID:22430288
ERIC Educational Resources Information Center
Jairam, Dharmananda; Kiewra, Kenneth A.
2010-01-01
This study used self-report and observation techniques to investigate how students study computer-based materials. In addition, it examined if a study method called SOAR can facilitate computer-based learning. SOAR is an acronym that stands for the method's 4 theoretically driven and empirically supported components: select (S), organize (O),…
29 CFR 779.266 - Methods of computing annual volume of sales or business.
Code of Federal Regulations, 2014 CFR
2014-07-01
... 29 Labor 3 2014-07-01 2014-07-01 false Methods of computing annual volume of sales or business... Apply; Enterprise Coverage Computing the Annual Volume § 779.266 Methods of computing annual volume of sales or business. (a) No computations of annual gross dollar volume are necessary to determine...
29 CFR 779.266 - Methods of computing annual volume of sales or business.
Code of Federal Regulations, 2012 CFR
2012-07-01
... 29 Labor 3 2012-07-01 2012-07-01 false Methods of computing annual volume of sales or business... Apply; Enterprise Coverage Computing the Annual Volume § 779.266 Methods of computing annual volume of sales or business. (a) No computations of annual gross dollar volume are necessary to determine...
29 CFR 779.266 - Methods of computing annual volume of sales or business.
Code of Federal Regulations, 2013 CFR
2013-07-01
... 29 Labor 3 2013-07-01 2013-07-01 false Methods of computing annual volume of sales or business... Apply; Enterprise Coverage Computing the Annual Volume § 779.266 Methods of computing annual volume of sales or business. (a) No computations of annual gross dollar volume are necessary to determine...
47 CFR 80.771 - Method of computing coverage.
Code of Federal Regulations, 2013 CFR
2013-10-01
... of computing coverage. Compute the +17 dBu contour as follows: (a) Determine the effective antenna... each point of +17 dBu field strength for all radials and draw the contour by connecting the...
47 CFR 80.771 - Method of computing coverage.
Code of Federal Regulations, 2014 CFR
2014-10-01
... of computing coverage. Compute the +17 dBu contour as follows: (a) Determine the effective antenna... each point of +17 dBu field strength for all radials and draw the contour by connecting the...
Theoretical and computational methods for three-body processes
NASA Astrophysics Data System (ADS)
Blandon Zapata, Juan David
This thesis discusses the development and application of theoretical and computational methods to study three-body processes. The main focus is on the calculation of three-body resonances and bound states. This broadly includes the study of Efimov states and resonances, three-body shape resonances, three- body Feshbach resonances, three-body pre-dissociated states in systems with a conical intersection, and the calculation of three-body recombination rate coefficients. The method was applied to a number of systems. A chapter of the thesis is dedicated to the related study of deriving correlation diagrams for three-body states before and after a three-body collision. More specifically, the thesis discusses the calculation of the H+H+H three-body recombination rate coefficient using the developed method. Additionally, we discuss a conceptually simple and effective diabatization procedure for the calculation of pre-dissociated vibrational states for a system with a conical intersection. We apply the method to H 3 , where the quantum molecular dynamics are notoriously difficult and where non-adiabatic couplings are important, and a correct description of the geometric phase associated with the diabatic representation is crucial for an accurate representation of these couplings. With our approach, we were also able to calculate Efimov-type resonances. The calculations of bound states and resonances were performed by formulating the problem in hyperspherical coordinates, and obtaining three-body eigenstates and eigen-energies by applying the hyperspherical adiabatic separation and the slow variable discretization. We employed the complex absorbing potential to calculate resonance energies and lifetimes, and introduce an uniquely defined diabatization procedure to treat X 3 molecules with a conical intersection. The proposed approach is general enough to be applied to problems in nuclear, atomic, molecular and astrophysics.
Evolutionary dynamics in set structured populations
Tarnita, Corina E.; Antal, Tibor; Ohtsuki, Hisashi; Nowak, Martin A.
2009-01-01
Evolutionary dynamics are strongly affected by population structure. The outcome of an evolutionary process in a well-mixed population can be very different from that in a structured population. We introduce a powerful method to study dynamical population structure: evolutionary set theory. The individuals of a population are distributed over sets. Individuals interact with others who are in the same set. Any 2 individuals can have several sets in common. Some sets can be empty, whereas others have many members. Interactions occur in terms of an evolutionary game. The payoff of the game is interpreted as fitness. Both the strategy and the set memberships change under evolutionary updating. Therefore, the population structure itself is a consequence of evolutionary dynamics. We construct a general mathematical approach for studying any evolutionary game in set structured populations. As a particular example, we study the evolution of cooperation and derive precise conditions for cooperators to be selected over defectors. PMID:19433793
Evolutionary Dynamics of Biological Games
NASA Astrophysics Data System (ADS)
Nowak, Martin A.; Sigmund, Karl
2004-02-01
Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.
Studying allosteric regulation in metal sensor proteins using computational methods.
Chakravorty, Dhruva K; Merz, Kenneth M
2014-01-01
In this chapter, we describe advances made in understanding the mechanism of allosteric regulation of DNA operator binding in the ArsR/SmtB family of metal-sensing proteins using computational methods. The paradigm, zinc-sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Here, we discuss studies that helped to characterize a metal ion-mediated hydrogen-bonding pathway (HBP) that plays a dominant role in the allosteric mechanism of DNA operator binding in these proteins. The chapter discusses computational methods used to provide a molecular basis for the large conformational motions and allosteric coupling free energy (~6kcal/mol) associated with Zn(II) binding in CzrA. We present an accurate and convenient means by which to include metal ions in the nuclear magnetic resonance (NMR) structure determination process using molecular dynamics (MD) constrained by NMR-derived data. The method provides a realistic and physically viable description of the metal-binding site(s) and has potentially broad applicability in the structure determination of metal ion-bound proteins, protein folding, and metal template protein-design studies. Finally, our simulations provide strong support for a proposed HBP that physically connects the metal-binding residue, His97, to the DNA-binding interface through the αR helix that is present only in the Zn(II)-bound state. We find the interprotomer hydrogen bond interaction to be significantly stronger (~8kcal/mol) at functional allosteric metal-binding sites compared to the apo proteins. This interaction works to overcome the considerable disorder at these hydrogen-bonding sites in apo protein and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. This interaction is found to be considerably weaker in nonresponsive metal-binding sites. These findings suggest a conserved functional
NASA Astrophysics Data System (ADS)
Szabó, György; Fáth, Gábor
2007-07-01
Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.
A Computational Method for Materials Design of New Interfaces
NASA Astrophysics Data System (ADS)
Kaminski, Jakub; Ratsch, Christian; Weber, Justin; Haverty, Michael; Shankar, Sadasivan
2015-03-01
We propose a novel computational approach to explore the broad configurational space of possible interfaces formed from known crystal structures to find new heterostructure materials with potentially interesting properties. In a series of steps with increasing complexity and accuracy, the vast number of possible combinations is narrowed down to a limited set of the most promising and chemically compatible candidates. This systematic screening encompasses (i) establishing the geometrical compatibility along multiple crystallographic orientations of two materials, (ii) simple functions eliminating configurations with unfavorable interatomic steric conflicts, (iii) application of empirical and semi-empirical potentials estimating approximate energetics and structures, (iv) use of DFT based quantum-chemical methods to ascertain the final optimal geometry and stability of the interface in question. For efficient high-throughput screening we have developed a new method to calculate surface energies, which allows for fast and systematic treatment of materials terminated with non-polar surfaces. We show that our approach leads to a maximum error around 3% from the exact reference. The representative results from our search protocol will be presented for selected materials including semiconductors and oxides.
Semi-coarsening multigrid methods for parallel computing
Jones, J.E.
1996-12-31
Standard multigrid methods are not well suited for problems with anisotropic coefficients which can occur, for example, on grids that are stretched to resolve a boundary layer. There are several different modifications of the standard multigrid algorithm that yield efficient methods for anisotropic problems. In the paper, we investigate the parallel performance of these multigrid algorithms. Multigrid algorithms which work well for anisotropic problems are based on line relaxation and/or semi-coarsening. In semi-coarsening multigrid algorithms a grid is coarsened in only one of the coordinate directions unlike standard or full-coarsening multigrid algorithms where a grid is coarsened in each of the coordinate directions. When both semi-coarsening and line relaxation are used, the resulting multigrid algorithm is robust and automatic in that it requires no knowledge of the nature of the anisotropy. This is the basic multigrid algorithm whose parallel performance we investigate in the paper. The algorithm is currently being implemented on an IBM SP2 and its performance is being analyzed. In addition to looking at the parallel performance of the basic semi-coarsening algorithm, we present algorithmic modifications with potentially better parallel efficiency. One modification reduces the amount of computational work done in relaxation at the expense of using multiple coarse grids. This modification is also being implemented with the aim of comparing its performance to that of the basic semi-coarsening algorithm.
Development of computational methods for heavy lift launch vehicles
NASA Technical Reports Server (NTRS)
Yoon, Seokkwan; Ryan, James S.
1993-01-01
The research effort has been focused on the development of an advanced flow solver for complex viscous turbulent flows with shock waves. The three-dimensional Euler and full/thin-layer Reynolds-averaged Navier-Stokes equations for compressible flows are solved on structured hexahedral grids. The Baldwin-Lomax algebraic turbulence model is used for closure. The space discretization is based on a cell-centered finite-volume method augmented by a variety of numerical dissipation models with optional total variation diminishing limiters. The governing equations are integrated in time by an implicit method based on lower-upper factorization and symmetric Gauss-Seidel relaxation. The algorithm is vectorized on diagonal planes of sweep using two-dimensional indices in three dimensions. A new computer program named CENS3D has been developed for viscous turbulent flows with discontinuities. Details of the code are described in Appendix A and Appendix B. With the developments of the numerical algorithm and dissipation model, the simulation of three-dimensional viscous compressible flows has become more efficient and accurate. The results of the research are expected to yield a direct impact on the design process of future liquid fueled launch systems.
Non-unitary probabilistic quantum computing circuit and method
NASA Technical Reports Server (NTRS)
Williams, Colin P. (Inventor); Gingrich, Robert M. (Inventor)
2009-01-01
A quantum circuit performing quantum computation in a quantum computer. A chosen transformation of an initial n-qubit state is probabilistically obtained. The circuit comprises a unitary quantum operator obtained from a non-unitary quantum operator, operating on an n-qubit state and an ancilla state. When operation on the ancilla state provides a success condition, computation is stopped. When operation on the ancilla state provides a failure condition, computation is performed again on the ancilla state and the n-qubit state obtained in the previous computation, until a success condition is obtained.
Computational Methods for Analyzing Fluid Flow Dynamics from Digital Imagery
Luttman, A.
2012-03-30
The main goal (long term) of this work is to perform computational dynamics analysis and quantify uncertainty from vector fields computed directly from measured data. Global analysis based on observed spatiotemporal evolution is performed by objective function based on expected physics and informed scientific priors, variational optimization to compute vector fields from measured data, and transport analysis proceeding with observations and priors. A mathematical formulation for computing flow fields is set up for computing the minimizer for the problem. An application to oceanic flow based on sea surface temperature is presented.
A stoichiometric calibration method for dual energy computed tomography.
Bourque, Alexandra E; Carrier, Jean-François; Bouchard, Hugo
2014-04-21
The accuracy of radiotherapy dose calculation relies crucially on patient composition data. The computed tomography (CT) calibration methods based on the stoichiometric calibration of Schneider et al (1996 Phys. Med. Biol. 41 111-24) are the most reliable to determine electron density (ED) with commercial single energy CT scanners. Along with the recent developments in dual energy CT (DECT) commercial scanners, several methods were published to determine ED and the effective atomic number (EAN) for polyenergetic beams without the need for CT calibration curves. This paper intends to show that with a rigorous definition of the EAN, the stoichiometric calibration method can be successfully adapted to DECT with significant accuracy improvements with respect to the literature without the need for spectrum measurements or empirical beam hardening corrections. Using a theoretical framework of ICRP human tissue compositions and the XCOM photon cross sections database, the revised stoichiometric calibration method yields Hounsfield unit (HU) predictions within less than ±1.3 HU of the theoretical HU calculated from XCOM data averaged over the spectra used (e.g., 80 kVp, 100 kVp, 140 kVp and 140/Sn kVp). A fit of mean excitation energy (I-value) data as a function of EAN is provided in order to determine the ion stopping power of human tissues from ED-EAN measurements. Analysis of the calibration phantom measurements with the Siemens SOMATOM Definition Flash dual source CT scanner shows that the present formalism yields mean absolute errors of (0.3 ± 0.4)% and (1.6 ± 2.0)% on ED and EAN, respectively. For ion therapy, the mean absolute errors for calibrated I-values and proton stopping powers (216 MeV) are (4.1 ± 2.7)% and (0.5 ± 0.4)%, respectively. In all clinical situations studied, the uncertainties in ion ranges in water for therapeutic energies are found to be less than 1.3 mm, 0.7 mm and 0.5 mm for protons, helium and carbon ions respectively, using a
A stoichiometric calibration method for dual energy computed tomography
NASA Astrophysics Data System (ADS)
Bourque, Alexandra E.; Carrier, Jean-François; Bouchard, Hugo
2014-04-01
The accuracy of radiotherapy dose calculation relies crucially on patient composition data. The computed tomography (CT) calibration methods based on the stoichiometric calibration of Schneider et al (1996 Phys. Med. Biol. 41 111-24) are the most reliable to determine electron density (ED) with commercial single energy CT scanners. Along with the recent developments in dual energy CT (DECT) commercial scanners, several methods were published to determine ED and the effective atomic number (EAN) for polyenergetic beams without the need for CT calibration curves. This paper intends to show that with a rigorous definition of the EAN, the stoichiometric calibration method can be successfully adapted to DECT with significant accuracy improvements with respect to the literature without the need for spectrum measurements or empirical beam hardening corrections. Using a theoretical framework of ICRP human tissue compositions and the XCOM photon cross sections database, the revised stoichiometric calibration method yields Hounsfield unit (HU) predictions within less than ±1.3 HU of the theoretical HU calculated from XCOM data averaged over the spectra used (e.g., 80 kVp, 100 kVp, 140 kVp and 140/Sn kVp). A fit of mean excitation energy (I-value) data as a function of EAN is provided in order to determine the ion stopping power of human tissues from ED-EAN measurements. Analysis of the calibration phantom measurements with the Siemens SOMATOM Definition Flash dual source CT scanner shows that the present formalism yields mean absolute errors of (0.3 ± 0.4)% and (1.6 ± 2.0)% on ED and EAN, respectively. For ion therapy, the mean absolute errors for calibrated I-values and proton stopping powers (216 MeV) are (4.1 ± 2.7)% and (0.5 ± 0.4)%, respectively. In all clinical situations studied, the uncertainties in ion ranges in water for therapeutic energies are found to be less than 1.3 mm, 0.7 mm and 0.5 mm for protons, helium and carbon ions respectively, using a generic
26 CFR 1.167(b)-0 - Methods of computing depreciation.
Code of Federal Regulations, 2010 CFR
2010-04-01
... 26 Internal Revenue 2 2010-04-01 2010-04-01 false Methods of computing depreciation. 1.167(b)-0....167(b)-0 Methods of computing depreciation. (a) In general. Any reasonable and consistently applied method of computing depreciation may be used or continued in use under section 167. Regardless of...
34 CFR 682.304 - Methods for computing interest benefits and special allowance.
Code of Federal Regulations, 2011 CFR
2011-07-01
... 34 Education 4 2011-07-01 2011-07-01 false Methods for computing interest benefits and special... LOAN (FFEL) PROGRAM Federal Payments of Interest and Special Allowance § 682.304 Methods for computing... shall use the average daily balance method to determine the balance on which the Secretary computes...
26 CFR 1.669(a)-3 - Tax computed by the exact throwback method.
Code of Federal Regulations, 2010 CFR
2010-04-01
... 26 Internal Revenue 8 2010-04-01 2010-04-01 false Tax computed by the exact throwback method. 1... Taxable Years Beginning Before January 1, 1969 § 1.669(a)-3 Tax computed by the exact throwback method. (a... compute the tax, on amounts deemed distributed under section 666, by the exact throwback method...
34 CFR 682.304 - Methods for computing interest benefits and special allowance.
Code of Federal Regulations, 2010 CFR
2010-07-01
... 34 Education 3 2010-07-01 2010-07-01 false Methods for computing interest benefits and special...) PROGRAM Federal Payments of Interest and Special Allowance § 682.304 Methods for computing interest... shall use the average daily balance method to determine the balance on which the Secretary computes...
26 CFR 1.167(b)-0 - Methods of computing depreciation.
Code of Federal Regulations, 2011 CFR
2011-04-01
... 26 Internal Revenue 2 2011-04-01 2011-04-01 false Methods of computing depreciation. 1.167(b)-0....167(b)-0 Methods of computing depreciation. (a) In general. Any reasonable and consistently applied method of computing depreciation may be used or continued in use under section 167. Regardless of...
34 CFR 682.304 - Methods for computing interest benefits and special allowance.
Code of Federal Regulations, 2013 CFR
2013-07-01
... 34 Education 4 2013-07-01 2013-07-01 false Methods for computing interest benefits and special... LOAN (FFEL) PROGRAM Federal Payments of Interest and Special Allowance § 682.304 Methods for computing... shall use the average daily balance method to determine the balance on which the Secretary computes...
34 CFR 682.304 - Methods for computing interest benefits and special allowance.
Code of Federal Regulations, 2012 CFR
2012-07-01
... 34 Education 4 2012-07-01 2012-07-01 false Methods for computing interest benefits and special... LOAN (FFEL) PROGRAM Federal Payments of Interest and Special Allowance § 682.304 Methods for computing... shall use the average daily balance method to determine the balance on which the Secretary computes...
34 CFR 682.304 - Methods for computing interest benefits and special allowance.
Code of Federal Regulations, 2014 CFR
2014-07-01
... 34 Education 4 2014-07-01 2014-07-01 false Methods for computing interest benefits and special... LOAN (FFEL) PROGRAM Federal Payments of Interest and Special Allowance § 682.304 Methods for computing... shall use the average daily balance method to determine the balance on which the Secretary computes...
Methodical Approaches to Teaching of Computer Modeling in Computer Science Course
ERIC Educational Resources Information Center
Rakhimzhanova, B. Lyazzat; Issabayeva, N. Darazha; Khakimova, Tiyshtik; Bolyskhanova, J. Madina
2015-01-01
The purpose of this study was to justify of the formation technique of representation of modeling methodology at computer science lessons. The necessity of studying computer modeling is that the current trends of strengthening of general education and worldview functions of computer science define the necessity of additional research of the…
Understanding evolutionary potential in virtual CPU instruction set architectures.
Bryson, David M; Ofria, Charles
2013-01-01
We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements in the majority of test environments, along with versions of each of the remaining architecture modifications that show significant improvements in multiple environments. However, some tested modifications were detrimental, though most exhibit no systematic effects on evolutionary potential, highlighting the robustness of digital evolution. Combined, these observations enhance our understanding of how instruction architecture impacts evolutionary potential, enabling the creation of architectures that support more rapid evolution of complex solutions to a
Validation of viscous and inviscid computational methods for turbomachinery components
NASA Technical Reports Server (NTRS)
Povinelli, L. A.
1986-01-01
An assessment of several three-dimensional computer codes used at the NASA Lewis Research Center is presented. Four flow situations are examined, for which both experimental data and computational results are available. The four flows form a basis for the evaluation of the computational procedures. It is concluded that transonic rotor flow at peak efficiency conditions may be calculated with a reasonable degree of accuracy, whereas, off-design conditions are not accurately determined. Duct flows and turbine cascade flows may also be computed with reasonable accuracy whereas radial inflow turbine flow remains a challenging problem.
Recent advances in computational structural reliability analysis methods
NASA Technical Reports Server (NTRS)
Thacker, Ben H.; Wu, Y.-T.; Millwater, Harry R.; Torng, Tony Y.; Riha, David S.
1993-01-01
The goal of structural reliability analysis is to determine the probability that the structure will adequately perform its intended function when operating under the given environmental conditions. Thus, the notion of reliability admits the possibility of failure. Given the fact that many different modes of failure are usually possible, achievement of this goal is a formidable task, especially for large, complex structural systems. The traditional (deterministic) design methodology attempts to assure reliability by the application of safety factors and conservative assumptions. However, the safety factor approach lacks a quantitative basis in that the level of reliability is never known and usually results in overly conservative designs because of compounding conservatisms. Furthermore, problem parameters that control the reliability are not identified, nor their importance evaluated. A summary of recent advances in computational structural reliability assessment is presented. A significant level of activity in the research and development community was seen recently, much of which was directed towards the prediction of failure probabilities for single mode failures. The focus is to present some early results and demonstrations of advanced reliability methods applied to structural system problems. This includes structures that can fail as a result of multiple component failures (e.g., a redundant truss), or structural components that may fail due to multiple interacting failure modes (e.g., excessive deflection, resonate vibration, or creep rupture). From these results, some observations and recommendations are made with regard to future research needs.
A Computational Method for Materials Design of Interfaces
NASA Astrophysics Data System (ADS)
Kaminski, Jakub; Ratsch, Christian; Shankar, Sadasivan
2014-03-01
In the present work we propose a novel computational approach to explore the broad configurational space of possible interfaces formed from known crystal structures to find new hetrostructure materials with potentially interesting properties. In the series of subsequent steps with increasing complexity and accuracy, the vast number of possible combinations is narrowed down to a limited set of the most promising and chemically compatible candidates. This systematic screening encompasses (i) establishing the geometrical compatibility along multiple crystallographic orientations of two (or more) materials, (ii) simple functions eliminating configurations with unfavorable interatomic steric conflicts, (iii) application of empirical and semi-empirical potentials estimating approximate energetics and structures, (iv) use of DFT based quantum-chemical methods to ascertain the final optimal geometry and stability of the interface in question. We also demonstrate the flexibility and efficiency of our approach depending on the size of the investigated structures and size of the search space. The representative results from our search protocol will be presented for selected materials including semiconductors, transition metal systems, and oxides.
Established and emerging dose reduction methods in cardiac computed tomography.
Small, Gary R; Kazmi, Mustapha; Dekemp, Robert A; Chow, Benjamin J W
2011-08-01
Cardiac computed tomography (CT) is a non-invasive modality that is commonly used as an alternative to invasive coronary angiography for the investigation of coronary artery disease. The enthusiasm for this technology has been tempered by a growing appreciation of the potential risks of malignancy associated with the use of ionising radiation. In the spirit of minimizing patient risk, the medical profession and industry have worked hard to developed methods and protocols to reduce patient radiation exposure while maintaining excellent diagnostic accuracy. A complete understanding of radiation reduction techniques will allow clinicians to reduce patient risk while providing an important diagnostic service. This review will consider the established and emerging techniques that may be adopted to reduce patient absorbed doses from x-ray CT. By modifying (1) x-ray tube output, (2) imaging time (scan duration), (3) imaging distance (scan length) and (4) the appropriate use of shielding, clinicians will be able to adhere to the 'as low as reasonably achievable (ALARA)' principle. PMID:21630110
Computational Methods for RNA Structure Validation and Improvement.
Jain, Swati; Richardson, David C; Richardson, Jane S
2015-01-01
With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. To make clean biological interpretations from three-dimensional structures, it is imperative to have high-quality, accurate RNA crystal structures available, and the community has thoroughly embraced that goal. However, due to the many degrees of freedom inherent in RNA structure (especially for the backbone), it is a significant challenge to succeed in building accurate experimental models for RNA structures. This chapter describes the tools and techniques our research group and our collaborators have developed over the years to help RNA structural biologists both evaluate and achieve better accuracy. Expert analysis of large, high-resolution, quality-conscious RNA datasets provides the fundamental information that enables automated methods for robust and efficient error diagnosis in validating RNA structures at all resolutions. The even more crucial goal of correcting the diagnosed outliers has steadily developed toward highly effective, computationally based techniques. Automation enables solving complex issues in large RNA structures, but cannot circumvent the need for thoughtful examination of local details, and so we also provide some guidance for interpreting and acting on the results of current structure validation for RNA. PMID:26068742
Improved computational methods for simulating inertial confinement fusion
NASA Astrophysics Data System (ADS)
Fatenejad, Milad
This dissertation describes the development of two multidimensional Lagrangian code for simulating inertial confinement fusion (ICF) on structured meshes. The first is DRACO, a production code primarily developed by the Laboratory for Laser Energetics. Several significant new capabilities were implemented including the ability to model radiative transfer using Implicit Monte Carlo [Fleck et al., JCP 8, 313 (1971)]. DRACO was also extended to operate in 3D Cartesian geometry on hexahedral meshes. Originally the code was only used in 2D cylindrical geometry. This included implementing thermal conduction and a flux-limited multigroup diffusion model for radiative transfer. Diffusion equations are solved by extending the 2D Kershaw method [Kershaw, JCP 39, 375 (1981)] to three dimensions. The second radiation-hydrodynamics code developed as part of this thesis is Cooper, a new 3D code which operates on structured hexahedral meshes. Cooper supports the compatible hydrodynamics framework [Caramana et al., JCP 146, 227 (1998)] to obtain round-off error levels of global energy conservation. This level of energy conservation is maintained even when two temperature thermal conduction, ion/electron equilibration, and multigroup diffusion based radiative transfer is active. Cooper is parallelized using domain decomposition, and photon energy group decomposition. The Mesh Oriented datABase (MOAB) computational library is used to exchange information between processes when domain decomposition is used. Cooper's performance is analyzed through direct comparisons with DRACO. Cooper also contains a method for preserving spherical symmetry during target implosions [Caramana et al., JCP 157, 89 (1999)]. Several deceleration phase implosion simulations were used to compare instability growth using traditional hydrodynamics and compatible hydrodynamics with/without symmetry modification. These simulations demonstrate increased symmetry preservation errors when traditional hydrodynamics
Evolutionary status of Polaris
NASA Astrophysics Data System (ADS)
Fadeyev, Yu. A.
2015-05-01
Hydrodynamic models of short-period Cepheids were computed to determine the pulsation period as a function of evolutionary time during the first and third crossings of the instability strip. The equations of radiation hydrodynamics and turbulent convection for radial stellar pulsations were solved with the initial conditions obtained from the evolutionary models of Population I stars (X = 0.7, Z = 0.02) with masses from 5.2 to 6.5 M⊙ and the convective core overshooting parameter 0.1 ≤ αov ≤ 0.3. In Cepheids with period of 4 d the rate of pulsation period change during the first crossing of the instability strip is over 50 times larger than that during the third crossing. Polaris is shown to cross the instability strip for the first time and to be the fundamental mode pulsator. The best agreement between the predicted and observed rates of period change was obtained for the model with mass of 5.4 M⊙ and the overshooting parameter αov = 0.25. The bolometric luminosity and radius are L = 1.26 × 103 L⊙ and R = 37.5 R⊙, respectively. In the HR diagram, Polaris is located at the red edge of the instability strip.
Parallel Computing Environments and Methods for Power Distribution System Simulation
Lu, Ning; Taylor, Zachary T.; Chassin, David P.; Guttromson, Ross T.; Studham, Scott S.
2005-11-10
The development of cost-effective high-performance parallel computing on multi-processor super computers makes it attractive to port excessively time consuming simulation software from personal computers (PC) to super computes. The power distribution system simulator (PDSS) takes a bottom-up approach and simulates load at appliance level, where detailed thermal models for appliances are used. This approach works well for a small power distribution system consisting of a few thousand appliances. When the number of appliances increases, the simulation uses up the PC memory and its run time increases to a point where the approach is no longer feasible to model a practical large power distribution system. This paper presents an effort made to port a PC-based power distribution system simulator (PDSS) to a 128-processor shared-memory super computer. The paper offers an overview of the parallel computing environment and a description of the modification made to the PDSS model. The performances of the PDSS running on a standalone PC and on the super computer are compared. Future research direction of utilizing parallel computing in the power distribution system simulation is also addressed.
Students' Attitudes towards Control Methods in Computer-Assisted Instruction.
ERIC Educational Resources Information Center
Hintze, Hanne; And Others
1988-01-01
Describes study designed to investigate dental students' attitudes toward computer-assisted teaching as applied in programs for oral radiology in Denmark. Programs using personal computers and slide projectors with varying degrees of learner and teacher control are described, and differences in attitudes between male and female students are…
NASA Astrophysics Data System (ADS)
Healy, Thomas J.
1993-04-01
The paper describes an evolutionary approach to the development of aerospace systems, represented by the introduction of integrated product teams (IPTs), which are now used at Rockwell's Space Systems Division on all new programs and are introduced into existing projects after demonstrations of increases in quality and reductions in cost and schedule due to IPTs. Each IPT is unique and reflects its own program and lasts for the life of the program. An IPT includes customers, suppliers, subcontractors, and associate contractors, and have a charter, mission, scope of authority, budget, and schedule. Functional management is responsible for the staffing, training, method development, and generic technology development.
Sanfilippo, Antonio P [Richland, WA; Tratz, Stephen C [Richland, WA; Gregory, Michelle L [Richland, WA; Chappell, Alan R [Seattle, WA; Whitney, Paul D [Richland, WA; Posse, Christian [Seattle, WA; Baddeley, Robert L [Richland, WA; Hohimer, Ryan E [West Richland, WA
2011-10-11
Methods of defining ontologies, word disambiguation methods, computer systems, and articles of manufacture are described according to some aspects. In one aspect, a word disambiguation method includes accessing textual content to be disambiguated, wherein the textual content comprises a plurality of words individually comprising a plurality of word senses, for an individual word of the textual content, identifying one of the word senses of the word as indicative of the meaning of the word in the textual content, for the individual word, selecting one of a plurality of event classes of a lexical database ontology using the identified word sense of the individual word, and for the individual word, associating the selected one of the event classes with the textual content to provide disambiguation of a meaning of the individual word in the textual content.
29 CFR 779.342 - Methods of computing annual volume of sales.
Code of Federal Regulations, 2013 CFR
2013-07-01
... 29 Labor 3 2013-07-01 2013-07-01 false Methods of computing annual volume of sales. 779.342... Establishments Computing Annual Dollar Volume and Combination of Exemptions § 779.342 Methods of computing annual volume of sales. The tests as to whether an establishment qualifies for exemption under section...
29 CFR 779.342 - Methods of computing annual volume of sales.
Code of Federal Regulations, 2011 CFR
2011-07-01
... 29 Labor 3 2011-07-01 2011-07-01 false Methods of computing annual volume of sales. 779.342... Establishments Computing Annual Dollar Volume and Combination of Exemptions § 779.342 Methods of computing annual volume of sales. The tests as to whether an establishment qualifies for exemption under section...
29 CFR 779.342 - Methods of computing annual volume of sales.
Code of Federal Regulations, 2012 CFR
2012-07-01
... 29 Labor 3 2012-07-01 2012-07-01 false Methods of computing annual volume of sales. 779.342... Establishments Computing Annual Dollar Volume and Combination of Exemptions § 779.342 Methods of computing annual volume of sales. The tests as to whether an establishment qualifies for exemption under section...
29 CFR 779.342 - Methods of computing annual volume of sales.
Code of Federal Regulations, 2014 CFR
2014-07-01
... 29 Labor 3 2014-07-01 2014-07-01 false Methods of computing annual volume of sales. 779.342... Establishments Computing Annual Dollar Volume and Combination of Exemptions § 779.342 Methods of computing annual volume of sales. The tests as to whether an establishment qualifies for exemption under section...
29 CFR 779.342 - Methods of computing annual volume of sales.
Code of Federal Regulations, 2010 CFR
2010-07-01
... 29 Labor 3 2010-07-01 2010-07-01 false Methods of computing annual volume of sales. 779.342... Establishments Computing Annual Dollar Volume and Combination of Exemptions § 779.342 Methods of computing annual volume of sales. The tests as to whether an establishment qualifies for exemption under section...
Asronomical refraction: Computational methods for all zenith angles
NASA Technical Reports Server (NTRS)
Auer, L. H.; Standish, E. M.
2000-01-01
It is shown that the problem of computing astronomical refraction for any value of the zenith angle may be reduced to a simple, nonsingular, numerical quadrature when the proper choice is made for the independent variable of integration.
Computational Fluid Dynamics. [numerical methods and algorithm development
NASA Technical Reports Server (NTRS)
1992-01-01
This collection of papers was presented at the Computational Fluid Dynamics (CFD) Conference held at Ames Research Center in California on March 12 through 14, 1991. It is an overview of CFD activities at NASA Lewis Research Center. The main thrust of computational work at Lewis is aimed at propulsion systems. Specific issues related to propulsion CFD and associated modeling will also be presented. Examples of results obtained with the most recent algorithm development will also be presented.
The repeated replacement method: a pure Lagrangian meshfree method for computational fluid dynamics.
Walker, Wade A
2012-01-01
In this paper we describe the repeated replacement method (RRM), a new meshfree method for computational fluid dynamics (CFD). RRM simulates fluid flow by modeling compressible fluids' tendency to evolve towards a state of constant density, velocity, and pressure. To evolve a fluid flow simulation forward in time, RRM repeatedly "chops out" fluid from active areas and replaces it with new "flattened" fluid cells with the same mass, momentum, and energy. We call the new cells "flattened" because we give them constant density, velocity, and pressure, even though the chopped-out fluid may have had gradients in these primitive variables. RRM adaptively chooses the sizes and locations of the areas it chops out and replaces. It creates more and smaller new cells in areas of high gradient, and fewer and larger new cells in areas of lower gradient. This naturally leads to an adaptive level of accuracy, where more computational effort is spent on active areas of the fluid, and less effort is spent on inactive areas. We show that for common test problems, RRM produces results similar to other high-resolution CFD methods, while using a very different mathematical framework. RRM does not use Riemann solvers, flux or slope limiters, a mesh, or a stencil, and it operates in a purely Lagrangian mode. RRM also does not evaluate numerical derivatives, does not integrate equations of motion, and does not solve systems of equations. PMID:22866175
ERIC Educational Resources Information Center
Fritsch, Helmut; And Others
1989-01-01
The authors present reports of current research on distance education at the FernUniversitat in West Germany. Fritsch discusses adapting distance education techniques for small classes. Kuffner describes procedures for providing feedback to students using personalized computer-generated letters. Klute discusses using a computer with tutorial…
ERIC Educational Resources Information Center
Starkweather, John A.
During the exploratory phase of this two-year project, 234 instructional computer programs were written by 167 junior and senior high school students, instructed as individuals, in small groups, and in whole classes. Then a doctoral study investigated the effectiveness of computer-assisted instruction in the development of problem solving skills.…
Do Examinees Understand Score Reports for Alternate Methods of Scoring Computer Based Tests?
ERIC Educational Resources Information Center
Whittaker, Tiffany A.; Williams, Natasha J.; Dodd, Barbara G.
2011-01-01
This study assessed the interpretability of scaled scores based on either number correct (NC) scoring for a paper-and-pencil test or one of two methods of scoring computer-based tests: an item pattern (IP) scoring method and a method based on equated NC scoring. The equated NC scoring method for computer-based tests was proposed as an alternative…
The evolution of emergent computation.
Crutchfield, J P; Mitchell, M
1995-01-01
A simple evolutionary process can discover sophisticated methods for emergent information processing in decentralized spatially extended systems. The mechanisms underlying the resulting emergent computation are explicated by a technique for analyzing particle-based logic embedded in pattern-forming systems. Understanding how globally coordinated computation can emerge in evolution is relevant both for the scientific understanding of natural information processing and for engineering new forms of parallel computing systems. PMID:11607588
Evolutionary Optimization of a Geometrically Refined Truss
NASA Technical Reports Server (NTRS)
Hull, P. V.; Tinker, M. L.; Dozier, G. V.
2007-01-01
Structural optimization is a field of research that has experienced noteworthy growth for many years. Researchers in this area have developed optimization tools to successfully design and model structures, typically minimizing mass while maintaining certain deflection and stress constraints. Numerous optimization studies have been performed to minimize mass, deflection, and stress on a benchmark cantilever truss problem. Predominantly traditional optimization theory is applied to this problem. The cross-sectional area of each member is optimized to minimize the aforementioned objectives. This Technical Publication (TP) presents a structural optimization technique that has been previously applied to compliant mechanism design. This technique demonstrates a method that combines topology optimization, geometric refinement, finite element analysis, and two forms of evolutionary computation: genetic algorithms and differential evolution to successfully optimize a benchmark structural optimization problem. A nontraditional solution to the benchmark problem is presented in this TP, specifically a geometrically refined topological solution. The design process begins with an alternate control mesh formulation, multilevel geometric smoothing operation, and an elastostatic structural analysis. The design process is wrapped in an evolutionary computing optimization toolset.
Evolutionary optimization of a Genetically Refined Truss
NASA Technical Reports Server (NTRS)
Hull, Patrick V.; Tinker, Michael L.; Dozier, Gerry
2005-01-01
Structural optimization is a field of research that has experienced noteworthy growth for many years. Researchers in this area have developed optimization tools to successfully design and model structures, typically minimizing mass while maintaining certain deflection and stress constraints. Numerous optimization studies have been performed to minimize mass, deflection and stress on a benchmark cantilever truss problem. Predominantly traditional optimization theory is applied to this problem. The cross-sectional area of each member is optimized to minimize the aforementioned objectives. This paper will present a structural optimization technique that has been previously applied to compliant mechanism design. This technique demonstrates a method that combines topology optimization, geometric refinement, finite element analysis, and two forms of evolutionary computation: Genetic Algorithms and Differential Evolution to successfully optimize a benchmark structural optimization problem. An non-traditional solution to the benchmark problem is presented in this paper, specifically a geometrically refined topological solution. The design process begins with an alternate control mesh formulation, multilevel geometric smoothing operation, and an elastostatic structural analysis. The design process is wrapped in an evolutionary computing optimization toolset.
NASA Astrophysics Data System (ADS)
Shimizu, Yoshiaki; Sakaguchi, Tatsuhiko; Pralomkarn, Theerayoth
To meet higher customer satisfaction and shorter production lead time, assembly lines are shifting to mixed-model assembly lines. Accordingly, sequencing is becoming an increasingly important operation scheduling that directly affects on efficiency of the entire process. In this study, such sequencing problem at the mixed-model assembly line has been formulated as a bi-objective integer programming problem so that decision making through trade-off analysis can bring about significant production improvements. Then we have developed a multi-objective analysis method by hybridizing conventional and recent meta-heuristic methods. After showing its generic idea, the car mixed-model assembly line sequencing problem is concerned as a case study. Certain measures are also introduced to quantitatively evaluate the performances of the method through comparison.
An alternative computational method for finding the minimum-premium insurance portfolio
NASA Astrophysics Data System (ADS)
Katsikis, Vasilios N.
2016-06-01
In this article, we design a computational method, which differs from the standard linear programming techniques, for computing the minimum-premium insurance portfolio. The corresponding algorithm as well as a Matlab implementation are provided.
NASA Astrophysics Data System (ADS)
Shen, Xin; Zhang, Jing; Yao, Huang
2015-12-01
Remote sensing satellites play an increasingly prominent role in environmental monitoring and disaster rescue. Taking advantage of almost the same sunshine condition to same place and global coverage, most of these satellites are operated on the sun-synchronous orbit. However, it brings some problems inevitably, the most significant one is that the temporal resolution of sun-synchronous orbit satellite can't satisfy the demand of specific region monitoring mission. To overcome the disadvantages, two methods are exploited: the first one is to build satellite constellation which contains multiple sunsynchronous satellites, just like the CHARTER mechanism has done; the second is to design non-predetermined orbit based on the concrete mission demand. An effective method for remote sensing satellite orbit design based on multiobjective evolution algorithm is presented in this paper. Orbit design problem is converted into a multi-objective optimization problem, and a fast and elitist multi-objective genetic algorithm is utilized to solve this problem. Firstly, the demand of the mission is transformed into multiple objective functions, and the six orbit elements of the satellite are taken as genes in design space, then a simulate evolution process is performed. An optimal resolution can be obtained after specified generation via evolution operation (selection, crossover, and mutation). To examine validity of the proposed method, a case study is introduced: Orbit design of an optical satellite for regional disaster monitoring, the mission demand include both minimizing the average revisit time internal of two objectives. The simulation result shows that the solution for this mission obtained by our method meet the demand the users' demand. We can draw a conclusion that the method presented in this paper is efficient for remote sensing orbit design.
Progress Towards Computational Method for Circulation Control Airfoils
NASA Technical Reports Server (NTRS)
Swanson, R. C.; Rumsey, C. L.; Anders, S. G.
2005-01-01
The compressible Reynolds-averaged Navier-Stokes equations are solved for circulation control airfoil flows. Numerical solutions are computed with both structured and unstructured grid solvers. Several turbulence models are considered, including the Spalart-Allmaras model with and without curvature corrections, the shear stress transport model of Menter, and the k-enstrophy model. Circulation control flows with jet momentum coefficients of 0.03, 0.10, and 0.226 are considered. Comparisons are made between computed and experimental pressure distributions, velocity profiles, Reynolds stress profiles, and streamline patterns. Including curvature effects yields the closest agreement with the measured data.
Panigrahi, Priyabrata; Sule, Manas; Sharma, Ranu; Ramasamy, Sureshkumar; Suresh, C G
2014-06-01
Bile salt hydrolases (BSHs) are gut microbial enzymes that play a significant role in the bile acid modification pathway. Penicillin V acylases (PVAs) are enzymes produced by environmental microbes, having a possible role in pathogenesis or scavenging of phenolic compounds in their microbial habitats. The correct annotation of such physiologically and industrially important enzymes is thus vital. The current methods relying solely on sequence homology do not always provide accurate annotations for these two members of the cholylglycine hydrolase (CGH) family as BSH/PVA enzymes. Here, we present an improved method [binding site similarity (BSS)-based scoring system] for the correct annotation of the CGH family members as BSH/PVA enzymes, which along with the phylogenetic information incorporates the substrate specificity as well as the binding site information. The BSS scoring system was developed through the analysis of the binding sites and binding modes of the available BSH/PVA structures with substrates glycocholic acid and penicillin V. The 198 sequences in the dataset were then annotated accurately using BSS scores as BSH/PVA enzymes. The dataset presented contained sequences from Gram-positive bacteria, Gram-negative bacteria and archaea. The clustering obtained for the dataset using the method described above showed a clear distinction in annotation of Gram-positive bacteria and Gram-negative bacteria. Based on this clustering and a detailed analysis of the sequences of the CGH family in the dataset, we could infer that the CGH genes might have evolved in accordance with the hypothesis stating the evolution of diderms and archaea from the monoderms. PMID:24644246
Computer-Graphics and the Literary Construct: A Learning Method.
ERIC Educational Resources Information Center
Henry, Avril
2002-01-01
Describes an undergraduate student module that was developed at the University of Exeter (United Kingdom) in which students made their own computer graphics to discover and to describe literary structures in texts of their choice. Discusses learning outcomes and refers to the Web site that shows students' course work. (Author/LRW)
New Methods of Mobile Computing: From Smartphones to Smart Education
ERIC Educational Resources Information Center
Sykes, Edward R.
2014-01-01
Every aspect of our daily lives has been touched by the ubiquitous nature of mobile devices. We have experienced an exponential growth of mobile computing--a trend that seems to have no limit. This paper provides a report on the findings of a recent offering of an iPhone Application Development course at Sheridan College, Ontario, Canada. It…
All for One: Integrating Budgetary Methods by Computer.
ERIC Educational Resources Information Center
Herman, Jerry J.
1994-01-01
With the advent of high speed and sophisticated computer programs, all budgetary systems can be combined in one fiscal management information system. Defines and provides examples for the four budgeting systems: (1) function/object; (2) planning, programming, budgeting system; (3) zero-based budgeting; and (4) site-based budgeting. (MLF)
Simple computer method provides contours for radiological images
NASA Technical Reports Server (NTRS)
Newell, J. D.; Keller, R. A.; Baily, N. A.
1975-01-01
Computer is provided with information concerning boundaries in total image. Gradient of each point in digitized image is calculated with aid of threshold technique; then there is invoked set of algorithms designed to reduce number of gradient elements and to retain only major ones for definition of contour.
Optical Design Methods: Your Head As A Personal Computer
NASA Astrophysics Data System (ADS)
Shafer, David
1985-07-01
Several design approaches are described which feature the use of your head as a design tool. This involves thinking about the design task at hand, trying to break it into separate, easily understood subtasks, and approaching these in a creative and intelligent fashion, as only humans can do. You and your computer can become a very powerful team when this design philosophy is adopted.
[Computation method for optimization of recipes for protein content].
Kovalev, N I; Karzeva, N J; Fiterer, V O
1987-01-01
The authors propose a calculated protein utilization coefficient. This coefficient considers the difference between the utilization rates of the proteins being contained in the mixture and their amino-acid composition. The proposed formula allows calculations by computer. The data obtained show high correlations with the results received by biological tests with Tetrahymena cultures. PMID:3431579
Computer Facilitated Mathematical Methods in Chemical Engineering--Similarity Solution
ERIC Educational Resources Information Center
Subramanian, Venkat R.
2006-01-01
High-performance computers coupled with highly efficient numerical schemes and user-friendly software packages have helped instructors to teach numerical solutions and analysis of various nonlinear models more efficiently in the classroom. One of the main objectives of a model is to provide insight about the system of interest. Analytical…
Computed radiography imaging plates and associated methods of manufacture
Henry, Nathaniel F.; Moses, Alex K.
2015-08-18
Computed radiography imaging plates incorporating an intensifying material that is coupled to or intermixed with the phosphor layer, allowing electrons and/or low energy x-rays to impart their energy on the phosphor layer, while decreasing internal scattering and increasing resolution. The radiation needed to perform radiography can also be reduced as a result.
29 CFR 548.500 - Methods of computation.
Code of Federal Regulations, 2010 CFR
2010-07-01
... computing overtime compensation for a piece worker for hours of work in excess of 8 in each day is the employee's average hourly earnings for all work performed during that day. 23 The employee is entitled to one-half the basic rate for each daily overtime hour in addition to the total piece work earnings...
Verifying a computational method for predicting extreme ground motion
Harris, R.A.; Barall, M.; Andrews, D.J.; Duan, B.; Ma, S.; Dunham, E.M.; Gabriel, A.-A.; Kaneko, Y.; Kase, Y.; Aagaard, B.T.; Oglesby, D.D.; Ampuero, J.-P.; Hanks, T.C.; Abrahamson, N.
2011-01-01
In situations where seismological data is rare or nonexistent, computer simulations may be used to predict ground motions caused by future earthquakes. This is particularly practical in the case of extreme ground motions, where engineers of special buildings may need to design for an event that has not been historically observed but which may occur in the far-distant future. Once the simulations have been performed, however, they still need to be tested. The SCEC-USGS dynamic rupture code verification exercise provides a testing mechanism for simulations that involve spontaneous earthquake rupture. We have performed this examination for the specific computer code that was used to predict maximum possible ground motion near Yucca Mountain. Our SCEC-USGS group exercises have demonstrated that the specific computer code that was used for the Yucca Mountain simulations produces similar results to those produced by other computer codes when tackling the same science problem. We also found that the 3D ground motion simulations produced smaller ground motions than the 2D simulations.
Evolutionary foundations for cancer biology
Aktipis, C Athena; Nesse, Randolph M
2013-01-01
New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles—cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations—provide a foundation for understanding, preventing, and treating cancer. PMID:23396885
Toward a unifying framework for evolutionary processes
Paixão, Tiago; Badkobeh, Golnaz; Barton, Nick; Çörüş, Doğan; Dang, Duc-Cuong; Friedrich, Tobias; Lehre, Per Kristian; Sudholt, Dirk; Sutton, Andrew M.; Trubenová, Barbora
2015-01-01
The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. PMID:26215686
A method for computing the leading-edge suction in a higher-order panel method
NASA Technical Reports Server (NTRS)
Ehlers, F. E.; Manro, M. E.
1984-01-01
Experimental data show that the phenomenon of a separation induced leading edge vortex is influenced by the wing thickness and the shape of the leading edge. Both thickness and leading edge shape (rounded rather than point) delay the formation of a vortex. Existing computer programs used to predict the effect of a leading edge vortex do not include a procedure for determining whether or not a vortex actually exists. Studies under NASA Contract NAS1-15678 have shown that the vortex development can be predicted by using the relationship between the leading edge suction coefficient and the parabolic nose drag. The linear theory FLEXSTAB was used to calculate the leading edge suction coefficient. This report describes the development of a method for calculating leading edge suction using the capabilities of the higher order panel methods (exact boundary conditions). For a two dimensional case, numerical methods were developed using the double strength and downwash distribution along the chord. A Gaussian quadrature formula that directly incorporates the logarithmic singularity in the downwash distribution, at all panel edges, was found to be the best method.
Minimizing the Free Energy: A Computer Method for Teaching Chemical Equilibrium Concepts.
ERIC Educational Resources Information Center
Heald, Emerson F.
1978-01-01
Presents a computer method for teaching chemical equilibrium concepts using material balance conditions and the minimization of the free energy. Method for the calculation of chemical equilibrium, the computer program used to solve equilibrium problems and applications of the method are also included. (HM)
29 CFR 4011.9 - Method and date of issuance of notice; computation of time.
Code of Federal Regulations, 2010 CFR
2010-07-01
... 29 Labor 9 2010-07-01 2010-07-01 false Method and date of issuance of notice; computation of time... CORPORATION CERTAIN REPORTING AND DISCLOSURE REQUIREMENTS DISCLOSURE TO PARTICIPANTS § 4011.9 Method and date of issuance of notice; computation of time. (a) Method of issuance. The PBGC applies the rules...
3D modeling method for computer animate based on modified weak structured light method
NASA Astrophysics Data System (ADS)
Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei
2010-11-01
A simple and affordable 3D scanner is designed in this paper. Three-dimensional digital models are playing an increasingly important role in many fields, such as computer animate, industrial design, artistic design and heritage conservation. For many complex shapes, optical measurement systems are indispensable to acquiring the 3D information. In the field of computer animate, such an optical measurement device is too expensive to be widely adopted, and on the other hand, the precision is not as critical a factor in that situation. In this paper, a new cheap 3D measurement system is implemented based on modified weak structured light, using only a video camera, a light source and a straight stick rotating on a fixed axis. For an ordinary weak structured light configuration, one or two reference planes are required, and the shadows on these planes must be tracked in the scanning process, which destroy the convenience of this method. In the modified system, reference planes are unnecessary, and size range of the scanned objects is expanded widely. A new calibration procedure is also realized for the proposed method, and points cloud is obtained by analyzing the shadow strips on the object. A two-stage ICP algorithm is used to merge the points cloud from different viewpoints to get a full description of the object, and after a series of operations, a NURBS surface model is generated in the end. A complex toy bear is used to verify the efficiency of the method, and errors range from 0.7783mm to 1.4326mm comparing with the ground truth measurement.
An evolutionary approach to simulated football free kick optimisation
NASA Astrophysics Data System (ADS)
Rhodes, Martin; Coupland, Simon
We present a genetic algorithm-based evolutionary computing approach to the optimisation of simulated football free kick situations. A detailed physics model is implemented in order to apply evolutionary computing techniques to the creation of strategic offensive shots and defensive player locations.
On multigrid methods for the Navier-Stokes Computer
NASA Technical Reports Server (NTRS)
Nosenchuck, D. M.; Krist, S. E.; Zang, T. A.
1988-01-01
The overall architecture of the multipurpose parallel-processing Navier-Stokes Computer (NSC) being developed by Princeton and NASA Langley (Nosenchuck et al., 1986) is described and illustrated with extensive diagrams, and the NSC implementation of an elementary multigrid algorithm for simulating isotropic turbulence (based on solution of the incompressible time-dependent Navier-Stokes equations with constant viscosity) is characterized in detail. The present NSC design concept calls for 64 nodes, each with the performance of a class VI supercomputer, linked together by a fiber-optic hypercube network and joined to a front-end computer by a global bus. In this configuration, the NSC would have a storage capacity of over 32 Gword and a peak speed of over 40 Gflops. The multigrid Navier-Stokes code discussed would give sustained operation rates of about 25 Gflops.
Parallel computation with adaptive methods for elliptic and hyperbolic systems
Benantar, M.; Biswas, R.; Flaherty, J.E.; Shephard, M.S.
1990-01-01
We consider the solution of two dimensional vector systems of elliptic and hyperbolic partial differential equations on a shared memory parallel computer. For elliptic problems, the spatial domain is discretized using a finite quadtree mesh generation procedure and the differential system is discretized by a finite element-Galerkin technique with a piecewise linear polynomial basis. Resulting linear algebraic systems are solved using the conjugate gradient technique with element-by-element and symmetric successive over-relaxation preconditioners. Stiffness matrix assembly and linear system solutions are processed in parallel with computations scheduled on noncontiguous quadrants of the tree in order to minimize process synchronization. Determining noncontiguous regions by coloring the regular finite quadtree structure is far simpler than coloring elements of the unstructured mesh that the finite quadtree procedure generates. We describe linear-time complexity coloring procedures that use six and eight colors.
Application of traditional CFD methods to nonlinear computational aeroacoustics problems
NASA Technical Reports Server (NTRS)
Chyczewski, Thomas S.; Long, Lyle N.
1995-01-01
This paper describes an implementation of a high order finite difference technique and its application to the category 2 problems of the ICASE/LaRC Workshop on Computational Aeroacoustics (CAA). Essentially, a popular Computational Fluid Dynamics (CFD) approach (central differencing, Runge-Kutta time integration and artificial dissipation) is modified to handle aeroacoustic problems. The changes include increasing the order of the spatial differencing to sixth order and modifying the artificial dissipation so that it does not significantly contaminate the wave solution. All of the results were obtained from the CM5 located at the Numerical Aerodynamic Simulation Laboratory. lt was coded in CMFortran (very similar to HPF), using programming techniques developed for communication intensive large stencils, and ran very efficiently.
Multi-Level iterative methods in computational plasma physics
Knoll, D.A.; Barnes, D.C.; Brackbill, J.U.; Chacon, L.; Lapenta, G.
1999-03-01
Plasma physics phenomena occur on a wide range of spatial scales and on a wide range of time scales. When attempting to model plasma physics problems numerically the authors are inevitably faced with the need for both fine spatial resolution (fine grids) and implicit time integration methods. Fine grids can tax the efficiency of iterative methods and large time steps can challenge the robustness of iterative methods. To meet these challenges they are developing a hybrid approach where multigrid methods are used as preconditioners to Krylov subspace based iterative methods such as conjugate gradients or GMRES. For nonlinear problems they apply multigrid preconditioning to a matrix-few Newton-GMRES method. Results are presented for application of these multilevel iterative methods to the field solves in implicit moment method PIC, multidimensional nonlinear Fokker-Planck problems, and their initial efforts in particle MHD.
Managing expectations when publishing tools and methods for computational proteomics.
Martens, Lennart; Kohlbacher, Oliver; Weintraub, Susan T
2015-05-01
Computational tools are pivotal in proteomics because they are crucial for identification, quantification, and statistical assessment of data. The gateway to finding the best choice of a tool or approach for a particular problem is frequently journal articles, yet there is often an overwhelming variety of options that makes it hard to decide on the best solution. This is particularly difficult for nonexperts in bioinformatics. The maturity, reliability, and performance of tools can vary widely because publications may appear at different stages of development. A novel idea might merit early publication despite only offering proof-of-principle, while it may take years before a tool can be considered mature, and by that time it might be difficult for a new publication to be accepted because of a perceived lack of novelty. After discussions with members of the computational mass spectrometry community, we describe here proposed recommendations for organization of informatics manuscripts as a way to set the expectations of readers (and reviewers) through three different manuscript types that are based on existing journal designations. Brief Communications are short reports describing novel computational approaches where the implementation is not necessarily production-ready. Research Articles present both a novel idea and mature implementation that has been suitably benchmarked. Application Notes focus on a mature and tested tool or concept and need not be novel but should offer advancement from improved quality, ease of use, and/or implementation. Organizing computational proteomics contributions into these three manuscript types will facilitate the review process and will also enable readers to identify the maturity and applicability of the tool for their own workflows. PMID:25764342
Two methods of computing molecular dipole and quadrupole derivatives
NASA Astrophysics Data System (ADS)
Lazzeretti, P.; Zanasi, R.; Fowler, P. W.
1988-01-01
Polarized basis sets are used to compute dipole and quadrupole derivatives of the hydrides LiH, CH4, NH3, H2O, and HF. Analytic calculation of derivatives is compared with calculation via the dipole and quadrupole electric shielding tensors. With these basis sets, violation of the Hellmann-Feynman theorem is only about 0.01 a.u. in dipole derivatives and 0.02 a.u. in quadrupole derivatives.
Computational Methods for the Analysis of Array Comparative Genomic Hybridization
Chari, Raj; Lockwood, William W.; Lam, Wan L.
2006-01-01
Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development. PMID:17992253
Knowledge Guided Evolutionary Algorithms in Financial Investing
ERIC Educational Resources Information Center
Wimmer, Hayden
2013-01-01
A large body of literature exists on evolutionary computing, genetic algorithms, decision trees, codified knowledge, and knowledge management systems; however, the intersection of these computing topics has not been widely researched. Moving through the set of all possible solutions--or traversing the search space--at random exhibits no control…
Unconventional methods of imaging: computational microscopy and compact implementations
NASA Astrophysics Data System (ADS)
McLeod, Euan; Ozcan, Aydogan
2016-07-01
In the past two decades or so, there has been a renaissance of optical microscopy research and development. Much work has been done in an effort to improve the resolution and sensitivity of microscopes, while at the same time to introduce new imaging modalities, and make existing imaging systems more efficient and more accessible. In this review, we look at two particular aspects of this renaissance: computational imaging techniques and compact imaging platforms. In many cases, these aspects go hand-in-hand because the use of computational techniques can simplify the demands placed on optical hardware in obtaining a desired imaging performance. In the first main section, we cover lens-based computational imaging, in particular, light-field microscopy, structured illumination, synthetic aperture, Fourier ptychography, and compressive imaging. In the second main section, we review lensfree holographic on-chip imaging, including how images are reconstructed, phase recovery techniques, and integration with smart substrates for more advanced imaging tasks. In the third main section we describe how these and other microscopy modalities have been implemented in compact and field-portable devices, often based around smartphones. Finally, we conclude with some comments about opportunities and demand for better results, and where we believe the field is heading.
Computational Systems Biology in Cancer: Modeling Methods and Applications
Materi, Wayne; Wishart, David S.
2007-01-01
In recent years it has become clear that carcinogenesis is a complex process, both at the molecular and cellular levels. Understanding the origins, growth and spread of cancer, therefore requires an integrated or system-wide approach. Computational systems biology is an emerging sub-discipline in systems biology that utilizes the wealth of data from genomic, proteomic and metabolomic studies to build computer simulations of intra and intercellular processes. Several useful descriptive and predictive models of the origin, growth and spread of cancers have been developed in an effort to better understand the disease and potential therapeutic approaches. In this review we describe and assess the practical and theoretical underpinnings of commonly-used modeling approaches, including ordinary and partial differential equations, petri nets, cellular automata, agent based models and hybrid systems. A number of computer-based formalisms have been implemented to improve the accessibility of the various approaches to researchers whose primary interest lies outside of model development. We discuss several of these and describe how they have led to novel insights into tumor genesis, growth, apoptosis, vascularization and therapy. PMID:19936081
Frequency response modeling and control of flexible structures: Computational methods
NASA Technical Reports Server (NTRS)
Bennett, William H.
1989-01-01
The dynamics of vibrations in flexible structures can be conventiently modeled in terms of frequency response models. For structural control such models capture the distributed parameter dynamics of the elastic structural response as an irrational transfer function. For most flexible structures arising in aerospace applications the irrational transfer functions which arise are of a special class of pseudo-meromorphic functions which have only a finite number of right half place poles. Computational algorithms are demonstrated for design of multiloop control laws for such models based on optimal Wiener-Hopf control of the frequency responses. The algorithms employ a sampled-data representation of irrational transfer functions which is particularly attractive for numerical computation. One key algorithm for the solution of the optimal control problem is the spectral factorization of an irrational transfer function. The basis for the spectral factorization algorithm is highlighted together with associated computational issues arising in optimal regulator design. Options for implementation of wide band vibration control for flexible structures based on the sampled-data frequency response models is also highlighted. A simple flexible structure control example is considered to demonstrate the combined frequency response modeling and control algorithms.
Unconventional methods of imaging: computational microscopy and compact implementations.
McLeod, Euan; Ozcan, Aydogan
2016-07-01
In the past two decades or so, there has been a renaissance of optical microscopy research and development. Much work has been done in an effort to improve the resolution and sensitivity of microscopes, while at the same time to introduce new imaging modalities, and make existing imaging systems more efficient and more accessible. In this review, we look at two particular aspects of this renaissance: computational imaging techniques and compact imaging platforms. In many cases, these aspects go hand-in-hand because the use of computational techniques can simplify the demands placed on optical hardware in obtaining a desired imaging performance. In the first main section, we cover lens-based computational imaging, in particular, light-field microscopy, structured illumination, synthetic aperture, Fourier ptychography, and compressive imaging. In the second main section, we review lensfree holographic on-chip imaging, including how images are reconstructed, phase recovery techniques, and integration with smart substrates for more advanced imaging tasks. In the third main section we describe how these and other microscopy modalities have been implemented in compact and field-portable devices, often based around smartphones. Finally, we conclude with some comments about opportunities and demand for better results, and where we believe the field is heading. PMID:27214407
Advanced Computational Methods for Security Constrained Financial Transmission Rights
Kalsi, Karanjit; Elbert, Stephen T.; Vlachopoulou, Maria; Zhou, Ning; Huang, Zhenyu
2012-07-26
Financial Transmission Rights (FTRs) are financial insurance tools to help power market participants reduce price risks associated with transmission congestion. FTRs are issued based on a process of solving a constrained optimization problem with the objective to maximize the FTR social welfare under power flow security constraints. Security constraints for different FTR categories (monthly, seasonal or annual) are usually coupled and the number of constraints increases exponentially with the number of categories. Commercial software for FTR calculation can only provide limited categories of FTRs due to the inherent computational challenges mentioned above. In this paper, first an innovative mathematical reformulation of the FTR problem is presented which dramatically improves the computational efficiency of optimization problem. After having re-formulated the problem, a novel non-linear dynamic system (NDS) approach is proposed to solve the optimization problem. The new formulation and performance of the NDS solver is benchmarked against widely used linear programming (LP) solvers like CPLEX™ and tested on both standard IEEE test systems and large-scale systems using data from the Western Electricity Coordinating Council (WECC). The performance of the NDS is demonstrated to be comparable and in some cases is shown to outperform the widely used CPLEX algorithms. The proposed formulation and NDS based solver is also easily parallelizable enabling further computational improvement.
26 CFR 1.669(a)-3 - Tax computed by the exact throwback method.
Code of Federal Regulations, 2011 CFR
2011-04-01
... 26 Internal Revenue 8 2011-04-01 2011-04-01 false Tax computed by the exact throwback method. 1... Applicable to Taxable Years Beginning Before January 1, 1969 § 1.669(a)-3 Tax computed by the exact throwback... elects to compute the tax, on amounts deemed distributed under section 666, by the exact throwback...
26 CFR 1.669(a)-3 - Tax computed by the exact throwback method.
Code of Federal Regulations, 2013 CFR
2013-04-01
... 26 Internal Revenue 8 2013-04-01 2013-04-01 false Tax computed by the exact throwback method. 1... Applicable to Taxable Years Beginning Before January 1, 1969 § 1.669(a)-3 Tax computed by the exact throwback... elects to compute the tax, on amounts deemed distributed under section 666, by the exact throwback...
An historical survey of computational methods in optimal control.
NASA Technical Reports Server (NTRS)
Polak, E.
1973-01-01
Review of some of the salient theoretical developments in the specific area of optimal control algorithms. The first algorithms for optimal control were aimed at unconstrained problems and were derived by using first- and second-variation methods of the calculus of variations. These methods have subsequently been recognized as gradient, Newton-Raphson, or Gauss-Newton methods in function space. A much more recent addition to the arsenal of unconstrained optimal control algorithms are several variations of conjugate-gradient methods. At first, constrained optimal control problems could only be solved by exterior penalty function methods. Later algorithms specifically designed for constrained problems have appeared. Among these are methods for solving the unconstrained linear quadratic regulator problem, as well as certain constrained minimum-time and minimum-energy problems. Differential-dynamic programming was developed from dynamic programming considerations. The conditional-gradient method, the gradient-projection method, and a couple of feasible directions methods were obtained as extensions or adaptations of related algorithms for finite-dimensional problems. Finally, the so-called epsilon-methods combine the Ritz method with penalty function techniques.
Methods for Computationally Efficient Structured CFD Simulations of Complex Turbomachinery Flows
NASA Technical Reports Server (NTRS)
Herrick, Gregory P.; Chen, Jen-Ping
2012-01-01
This research presents more efficient computational methods by which to perform multi-block structured Computational Fluid Dynamics (CFD) simulations of turbomachinery, thus facilitating higher-fidelity solutions of complicated geometries and their associated flows. This computational framework offers flexibility in allocating resources to balance process count and wall-clock computation time, while facilitating research interests of simulating axial compressor stall inception with more complete gridding of the flow passages and rotor tip clearance regions than is typically practiced with structured codes. The paradigm presented herein facilitates CFD simulation of previously impractical geometries and flows. These methods are validated and demonstrate improved computational efficiency when applied to complicated geometries and flows.
Alex J. Dragt
2012-08-31
Since 1980, under the grant DEFG02-96ER40949, the Department of Energy has supported the educational and research work of the University of Maryland Dynamical Systems and Accelerator Theory (DSAT) Group. The primary focus of this educational/research group has been on the computation and analysis of charged-particle beam transport using Lie algebraic methods, and on advanced methods for the computation of electromagnetic fields and multiparticle phenomena. This Final Report summarizes the accomplishments of the DSAT Group from its inception in 1980 through its end in 2011.
A method of computational magnetohydrodynamics defining stable Scyllac equilibria
Betancourt, Octavio; Garabedian, Paul
1977-01-01
A computer code has been developed for the numerical calculation of sharp boundary equilibria of a toroidal plasma with diffuse pressure profile. This generalizes earlier work that was done separately on the sharp boundary and diffuse models, and it allows for large amplitude distortions of the plasma in three-dimensional space. By running the code, equilibria that are stable to the so-called m = 1, k = 0 mode have been found for Scyllac, which is a high beta toroidal confinement device of very large aspect ratio. PMID:16592383
Shielding analysis methods available in the scale computational system
Parks, C.V.; Tang, J.S.; Hermann, O.W.; Bucholz, J.A.; Emmett, M.B.
1986-01-01
Computational tools have been included in the SCALE system to allow shielding analysis to be performed using both discrete-ordinates and Monte Carlo techniques. One-dimensional discrete ordinates analyses are performed with the XSDRNPM-S module, and point dose rates outside the shield are calculated with the XSDOSE module. Multidimensional analyses are performed with the MORSE-SGC/S Monte Carlo module. This paper will review the above modules and the four Shielding Analysis Sequences (SAS) developed for the SCALE system. 7 refs., 8 figs.
Computation of nonparametric convex hazard estimators via profile methods
Jankowski, Hanna K.; Wellner, Jon A.
2010-01-01
This paper proposes a profile likelihood algorithm to compute the nonparametric maximum likelihood estimator of a convex hazard function. The maximisation is performed in two steps: First the support reduction algorithm is used to maximise the likelihood over all hazard functions with a given point of minimum (or antimode). Then it is shown that the profile (or partially maximised) likelihood is quasi-concave as a function of the antimode, so that a bisection algorithm can be applied to find the maximum of the profile likelihood, and hence also the global maximum. The new algorithm is illustrated using both artificial and real data, including lifetime data for Canadian males and females. PMID:20300560