Economics of hardwood silviculture using skyline and conventional logging

Treesearch

John E. Baumgras; Gary W. Miller; Chris B. LeDoux

1995-01-01

Managing Appalachian hardwood forests to satisfy the growing and diverse demands on this resource will require alternatives to traditional silvicultural methods and harvesting systems. Determining the relative economic efficiency of these alternative methods and systems with respect to harvest cash flows is essential. The effects of silvicultural methods and roundwood...

Operational test of the prototype peewee yarder.

Treesearch

Charles N. Mann; Ronald W. Mifflin

1979-01-01

An operational test of a small, prototype running skyline yarder was conducted early in 1978. Test results indicate that this yarder concept promises a low cost, high performance system for harvesting small logs where skyline methods are indicated. Timber harvest by thinning took place on 12 uphill and 2 downhill skyline roads, and clearcut harvesting was performed on...

The SKYTOWER and SKYMOBILE programs for locating and designing skyline harvest units.

Treesearch

R.H. Twito; R.J. McGaughey; S.E. Reutebuch

1988-01-01

PLANS, a software package for integrated timber-harvest planning, uses digital terrain models to provide the topographic data needed to fit harvest and transportation designs to specific terrain. SKYTOWER and SKYMOBILE are integral programs in the PLANS package and are used to design the timber-harvest units for skyline systems. SKYTOWER determines skyline payloads and...

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. PMID:25102069

Registration of Panoramic/Fish-Eye Image Sequence and LiDAR Points Using Skyline Features

PubMed Central

Zhu, Ningning; Jia, Yonghong; Ji, Shunping

2018-01-01

We propose utilizing a rigorous registration model and a skyline-based method for automatic registration of LiDAR points and a sequence of panoramic/fish-eye images in a mobile mapping system (MMS). This method can automatically optimize original registration parameters and avoid the use of manual interventions in control point-based registration methods. First, the rigorous registration model between the LiDAR points and the panoramic/fish-eye image was built. Second, skyline pixels from panoramic/fish-eye images and skyline points from the MMS’s LiDAR points were extracted, relying on the difference in the pixel values and the registration model, respectively. Third, a brute force optimization method was used to search for optimal matching parameters between skyline pixels and skyline points. In the experiments, the original registration method and the control point registration method were used to compare the accuracy of our method with a sequence of panoramic/fish-eye images. The result showed: (1) the panoramic/fish-eye image registration model is effective and can achieve high-precision registration of the image and the MMS’s LiDAR points; (2) the skyline-based registration method can automatically optimize the initial attitude parameters, realizing a high-precision registration of a panoramic/fish-eye image and the MMS’s LiDAR points; and (3) the attitude correction values of the sequences of panoramic/fish-eye images are different, and the values must be solved one by one. PMID:29883431

Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation.

PubMed

Schilling, Birgit; Rardin, Matthew J; MacLean, Brendan X; Zawadzka, Anna M; Frewen, Barbara E; Cusack, Michael P; Sorensen, Dylan J; Bereman, Michael S; Jing, Enxuan; Wu, Christine C; Verdin, Eric; Kahn, C Ronald; Maccoss, Michael J; Gibson, Bradford W

2012-05-01

Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models.

Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline

PubMed Central

Schilling, Birgit; Rardin, Matthew J.; MacLean, Brendan X.; Zawadzka, Anna M.; Frewen, Barbara E.; Cusack, Michael P.; Sorensen, Dylan J.; Bereman, Michael S.; Jing, Enxuan; Wu, Christine C.; Verdin, Eric; Kahn, C. Ronald; MacCoss, Michael J.; Gibson, Bradford W.

2012-01-01

Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models. PMID:22454539

Analysis of terrain map matching using multisensing techniques for applications to autonomous vehicle navigation

NASA Technical Reports Server (NTRS)

Page, Lance; Shen, C. N.

1991-01-01

This paper describes skyline-based terrain matching, a new method for locating the vantage point of laser range-finding measurements on a global map previously prepared by satellite or aerial mapping. Skylines can be extracted from the range-finding measurements and modelled from the global map, and are represented in parametric, cylindrical form with azimuth angle as the independent variable. The three translational parameters of the vantage point are determined with a three-dimensional matching of these two sets of skylines.

3. ENVIRONMENT, FROM NORTH, SHOWING RICHMOND SKYLINE, BRIDGE DECK AND ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

3. ENVIRONMENT, FROM NORTH, SHOWING RICHMOND SKYLINE, BRIDGE DECK AND ROADWAY, AND NORTH APPROACH - Fifth Street Viaduct, Spanning Bacon's Quarter Branch Valley on Fifth Street, Richmond, Independent City, VA

Tsugaru Iwaki Skyline, Japan

NASA Image and Video Library

2018-05-03

The Tsugaru Iwaki Skyline is a toll road in northern Japan, which partially ascends Mount Iwaki stratovolcano, and is notable for its steep gradient and 69 hairpin turns. The road ascends 806 meters over an average gradient of 8.66%, with some sections going up to 10%. The Tsugaru Iwaki Skyline has been considered one of the most dangerous mountain roads in the world. (Wikipedia) The image was acquired May 26, 2015, and is located at 40.6 degrees north, 140.3 degrees east. https://photojournal.jpl.nasa.gov/catalog/PIA22385

Limiting Index Sort: A New Non-Dominated Sorting Algorithm and its Comparison to the State-of-the-Art

DTIC Science & Technology

2010-05-01

Skyline Algorithms 2.2.1 Block-Nested Loops A simple way to find the skyline is to use the block-nested loops ( BNL ) algorithm [3], which is the algorithm...by an NDS member are discarded. After every individual has been compared with the NDS, the NDS is the dataset’s skyline. In the best case for BNL ...SFS) algorithm [4] is a variation on BNL that first introduces the idea of initially ordering the individuals by a monotonically increasing scoring

77 FR 15118 - Buy American Exceptions Under the American Recovery and Reinvestment Act of 2009

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-14

... heat pumps for the Skyline Crest Sustainability Upgrade project. FOR FURTHER INFORMATION CONTACT... Skyline Crest Sustainability Upgrade project. The exception was granted by HUD on the basis that the...

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

PubMed

Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

2016-07-01

Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Block 2. Photograph represents general view taken from the north/west ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Block 2. Photograph represents general view taken from the north/west region of the May D & F Tower. Photograph shows the main public gathering space for Skyline Park and depicts a light feature and an “Information” sign - Skyline Park, 1500-1800 Arapaho Street, Denver, Denver County, CO

Toyota/Skyline Technical Education Network. Cooperative Demonstration Program. Final Performance Report.

ERIC Educational Resources Information Center

Skyline Coll., San Bruno, CA.

A joint project was conducted between Toyota Motor Sales and Skyline College (in the San Francisco, California, area) to create an automotive technician training program that would serve the needs of working adults. During the project, a model high technology curriculum suitable for adults was developed, the quality of instruction available for…

A Skyline Plugin for Pathway-Centric Data Browsing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Degan, Michael G.; Ryadinskiy, Lillian; Fujimoto, Grant M.

For targeted proteomics to be broadly adopted in biological laboratories as a routine experimental protocol, wet-bench biologists must be able to approach SRM assay design in the same way they approach biological experimental design. Most often, biological hypotheses are envisioned in a set of protein interactions, networks and pathways. We present a plugin for the popular Skyline tool that presents public mass spectrometry data in a pathway-centric view to assist users in browsing available data and determining how to design quantitative experiments. Selected proteins and their underlying mass spectra are imported to Skyline for further assay design (transition selection). Themore » same plugin can be used for hypothesis-drive DIA data analysis, again utilizing the pathway view to help narrow down the set of proteins which will be investigated. The plugin is backed by the PNNL Biodiversity Library, a corpus of 3 million peptides from >100 organisms, and the draft human proteome. Users can upload personal data to the plugin to use the pathway navigation prior to importing their own data into Skyline.« less

A Skyline Plugin for Pathway-Centric Data Browsing

NASA Astrophysics Data System (ADS)

Degan, Michael G.; Ryadinskiy, Lillian; Fujimoto, Grant M.; Wilkins, Christopher S.; Lichti, Cheryl F.; Payne, Samuel H.

2016-11-01

For targeted proteomics to be broadly adopted in biological laboratories as a routine experimental protocol, wet-bench biologists must be able to approach selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) assay design in the same way they approach biological experimental design. Most often, biological hypotheses are envisioned in a set of protein interactions, networks, and pathways. We present a plugin for the popular Skyline tool that presents public mass spectrometry data in a pathway-centric view to assist users in browsing available data and determining how to design quantitative experiments. Selected proteins and their underlying mass spectra are imported to Skyline for further assay design (transition selection). The same plugin can be used for hypothesis-driven data-independent acquisition (DIA) data analysis, again utilizing the pathway view to help narrow down the set of proteins that will be investigated. The plugin is backed by the Pacific Northwest National Laboratory (PNNL) Biodiversity Library, a corpus of 3 million peptides from >100 organisms, and the draft human proteome. Users can upload personal data to the plugin to use the pathway navigation prior to importing their own data into Skyline.

Spectral Skyline Separation: Extended Landmark Databases and Panoramic Imaging

PubMed Central

Differt, Dario; Möller, Ralf

2016-01-01

Evidence from behavioral experiments suggests that insects use the skyline as a cue for visual navigation. However, changes of lighting conditions, over hours, days or possibly seasons, significantly affect the appearance of the sky and ground objects. One possible solution to this problem is to extract the “skyline” by an illumination-invariant classification of the environment into two classes, ground objects and sky. In a previous study (Insect models of illumination-invariant skyline extraction from UV (ultraviolet) and green channels), we examined the idea of using two different color channels available for many insects (UV and green) to perform this segmentation. We found out that for suburban scenes in temperate zones, where the skyline is dominated by trees and artificial objects like houses, a “local” UV segmentation with adaptive thresholds applied to individual images leads to the most reliable classification. Furthermore, a “global” segmentation with fixed thresholds (trained on an image dataset recorded over several days) using UV-only information is only slightly worse compared to using both the UV and green channel. In this study, we address three issues: First, to enhance the limited range of environments covered by the dataset collected in the previous study, we gathered additional data samples of skylines consisting of minerals (stones, sand, earth) as ground objects. We could show that also for mineral-rich environments, UV-only segmentation achieves a quality comparable to multi-spectral (UV and green) segmentation. Second, we collected a wide variety of ground objects to examine their spectral characteristics under different lighting conditions. On the one hand, we found that the special case of diffusely-illuminated minerals increases the difficulty to reliably separate ground objects from the sky. On the other hand, the spectral characteristics of this collection of ground objects covers well with the data collected in the skyline databases, increasing, due to the increased variety of ground objects, the validity of our findings for novel environments. Third, we collected omnidirectional images, as often used for visual navigation tasks, of skylines using an UV-reflective hyperbolic mirror. We could show that “local” separation techniques can be adapted to the use of panoramic images by splitting the image into segments and finding individual thresholds for each segment. Contrarily, this is not possible for ‘global’ separation techniques. PMID:27690053

Harvesting costs and environmental impacts associated with skyline yarding shelterwood harvests and thinning in Appalachian hardwoods

Treesearch

J. E. Baumgras; C. B. LeDoux; J. R. Sherar

1993-01-01

To evaluate the potential for moderating the visual impact and soil disturbance associated with timber harvesting on steep-slope hardwood sites, thinning and shelterwood harvests were conducted with a skyline yarding system. Operations were monitored to document harvesting production, residual stand damage, soil disturbance, and visual quality. Yarding costs for...

Skyline Gathers K-12 Together Under One Roof.

ERIC Educational Resources Information Center

American School Board Journal, 1968

1968-01-01

Skyline School is a flexible and economical elementary and high school design for 400 pupils. The library, a large resource center serving all ages, and the administration offices are accented by landscaped courts. There are two instructional material centers per grade grouping of K-6 and 7-12. Grades 1-6 surround the kindergarten, which has…

Evaluation of out-of-core computer programs for the solution of symmetric banded linear equations. [simultaneous equations

NASA Technical Reports Server (NTRS)

Dunham, R. S.

1976-01-01

FORTRAN coded out-of-core equation solvers that solve using direct methods symmetric banded systems of simultaneous algebraic equations. Banded, frontal and column (skyline) solvers were studied as well as solvers that can partition the working area and thus could fit into any available core. Comparison timings are presented for several typical two dimensional and three dimensional continuum type grids of elements with and without midside nodes. Extensive conclusions are also given.

Parallel-Vector Algorithm For Rapid Structural Anlysis

NASA Technical Reports Server (NTRS)

Agarwal, Tarun R.; Nguyen, Duc T.; Storaasli, Olaf O.

1993-01-01

New algorithm developed to overcome deficiency of skyline storage scheme by use of variable-band storage scheme. Exploits both parallel and vector capabilities of modern high-performance computers. Gives engineers and designers opportunity to include more design variables and constraints during optimization of structures. Enables use of more refined finite-element meshes to obtain improved understanding of complex behaviors of aerospace structures leading to better, safer designs. Not only attractive for current supercomputers but also for next generation of shared-memory supercomputers.

Skyline Wide Educational Plan (SWEP) Product Evaluation Report: Educational Goals for the Future (1980's). SWEP Evaluation Report No. 2.

ERIC Educational Resources Information Center

Burns, Robert J.

The major purpose of this evaluation report is to scrutinize the Skyline Wide Educational Plan (SWEP) research methods and analytical schemes and to communicate the project's constituency priorities relative to the educational programs and processes of the future. A Delphi technique was used as the primary mechanism for gathering and scrutinizing…

Tree damage from skyline logging in a western larch/Douglas-fir stand

Treesearch

Robert E. Benson; Michael J. Gonsior

1981-01-01

Damage to shelterwood leave trees and to understory trees in shelterwood and clearcut logging units logged with skyline yarders was measured, and related to stand conditions, harvesting specifications, and yarding system-terrain interactions. About 23 percent of the marked leave trees in the shelterwood units were killed in logging, and about 10 percent had moderate to...

A new method for estimating the demographic history from DNA sequences: an importance sampling approach

PubMed Central

Ait Kaci Azzou, Sadoune; Larribe, Fabrice; Froda, Sorana

2015-01-01

The effective population size over time (demographic history) can be retraced from a sample of contemporary DNA sequences. In this paper, we propose a novel methodology based on importance sampling (IS) for exploring such demographic histories. Our starting point is the generalized skyline plot with the main difference being that our procedure, skywis plot, uses a large number of genealogies. The information provided by these genealogies is combined according to the IS weights. Thus, we compute a weighted average of the effective population sizes on specific time intervals (epochs), where the genealogies that agree more with the data are given more weight. We illustrate by a simulation study that the skywis plot correctly reconstructs the recent demographic history under the scenarios most commonly considered in the literature. In particular, our method can capture a change point in the effective population size, and its overall performance is comparable with the one of the bayesian skyline plot. We also introduce the case of serially sampled sequences and illustrate that it is possible to improve the performance of the skywis plot in the case of an exponential expansion of the effective population size. PMID:26300910

Camera Geolocation From Mountain Images

DTIC Science & Technology

2015-09-17

be reliably extracted from query images. However, in real-life scenarios the skyline in a query image may be blurred or invisible , due to occlusions...extracted from multiple mountain ridges is critical to reliably geolocating challenging real-world query images with blurred or invisible mountain skylines...Buddemeier, A. Bissacco, F. Brucher, T. Chua, H. Neven, and J. Yagnik, “Tour the world: building a web -scale landmark recognition engine,” in Proc. of

Mountain Logging Symposium Proceedings Held in West Virginia on Jun 5-7, 1984

DTIC Science & Technology

1984-06-07

and board" analysis ( Lysons and Mann 1967) provided a method to make skyline payload determination feasible using topographic maps or field run... Lysons , Hilton H.; Mann, Charles N. Skyline tension and deflection handbook. Res. Pap. PNW-39. Portland, OR: U.S. Department of Agriculture, Forest...those described by Mifflin and Lysons (1978)and Miyata (1980). The estimated cost for the Clearwater Yarder and a four-man crew was $48.27 per

Skyline Wide Educational Plan (SWEP) Planning Project. Volume 2 -- Appendices. Combined Quarterly Report No. 4 (April 1 to June 30, 1974) and Final Report (July 1973 to August 1974).

ERIC Educational Resources Information Center

Dallas Independent School District, TX. Dept. of Research and Evaluation.

This volume consists of a number of appendixes containing data and analyses that were compiled to aid administrators of the Skyline Wide Educational Plan (SWEP) in their efforts to develop a comprehensive secondary school plan for the Dallas-Fort Worth metroplex in the 1970's. Much of the volume is devoted to various facility considerations…

Reliable Execution Based on CPN and Skyline Optimization for Web Service Composition

PubMed Central

Ha, Weitao; Zhang, Guojun

2013-01-01

With development of SOA, the complex problem can be solved by combining available individual services and ordering them to best suit user's requirements. Web services composition is widely used in business environment. With the features of inherent autonomy and heterogeneity for component web services, it is difficult to predict the behavior of the overall composite service. Therefore, transactional properties and nonfunctional quality of service (QoS) properties are crucial for selecting the web services to take part in the composition. Transactional properties ensure reliability of composite Web service, and QoS properties can identify the best candidate web services from a set of functionally equivalent services. In this paper we define a Colored Petri Net (CPN) model which involves transactional properties of web services in the composition process. To ensure reliable and correct execution, unfolding processes of the CPN are followed. The execution of transactional composition Web service (TCWS) is formalized by CPN properties. To identify the best services of QoS properties from candidate service sets formed in the TCSW-CPN, we use skyline computation to retrieve dominant Web service. It can overcome that the reduction of individual scores to an overall similarity leads to significant information loss. We evaluate our approach experimentally using both real and synthetically generated datasets. PMID:23935431

Reliable execution based on CPN and skyline optimization for Web service composition.

PubMed

Chen, Liping; Ha, Weitao; Zhang, Guojun

2013-01-01

With development of SOA, the complex problem can be solved by combining available individual services and ordering them to best suit user's requirements. Web services composition is widely used in business environment. With the features of inherent autonomy and heterogeneity for component web services, it is difficult to predict the behavior of the overall composite service. Therefore, transactional properties and nonfunctional quality of service (QoS) properties are crucial for selecting the web services to take part in the composition. Transactional properties ensure reliability of composite Web service, and QoS properties can identify the best candidate web services from a set of functionally equivalent services. In this paper we define a Colored Petri Net (CPN) model which involves transactional properties of web services in the composition process. To ensure reliable and correct execution, unfolding processes of the CPN are followed. The execution of transactional composition Web service (TCWS) is formalized by CPN properties. To identify the best services of QoS properties from candidate service sets formed in the TCSW-CPN, we use skyline computation to retrieve dominant Web service. It can overcome that the reduction of individual scores to an overall similarity leads to significant information loss. We evaluate our approach experimentally using both real and synthetically generated datasets.

Specialist and generalist symbionts show counterintuitive levels of genetic diversity and discordant demographic histories along the Florida Reef Tract

NASA Astrophysics Data System (ADS)

Titus, Benjamin M.; Daly, Marymegan

2017-03-01

Specialist and generalist life histories are expected to result in contrasting levels of genetic diversity at the population level, and symbioses are expected to lead to patterns that reflect a shared biogeographic history and co-diversification. We test these assumptions using mtDNA sequencing and a comparative phylogeographic approach for six co-occurring crustacean species that are symbiotic with sea anemones on western Atlantic coral reefs, yet vary in their host specificities: four are host specialists and two are host generalists. We first conducted species discovery analyses to delimit cryptic lineages, followed by classic population genetic diversity analyses for each delimited taxon, and then reconstructed the demographic history for each taxon using traditional summary statistics, Bayesian skyline plots, and approximate Bayesian computation to test for signatures of recent and concerted population expansion. The genetic diversity values recovered here contravene the expectations of the specialist-generalist variation hypothesis and classic population genetics theory; all specialist lineages had greater genetic diversity than generalists. Demography suggests recent population expansions in all taxa, although Bayesian skyline plots and approximate Bayesian computation suggest the timing and magnitude of these events were idiosyncratic. These results do not meet the a priori expectation of concordance among symbiotic taxa and suggest that intrinsic aspects of species biology may contribute more to phylogeographic history than extrinsic forces that shape whole communities. The recovery of two cryptic specialist lineages adds an additional layer of biodiversity to this symbiosis and contributes to an emerging pattern of cryptic speciation in the specialist taxa. Our results underscore the differences in the evolutionary processes acting on marine systems from the terrestrial processes that often drive theory. Finally, we continue to highlight the Florida Reef Tract as an important biodiversity hotspot.

Using a multifrontal sparse solver in a high performance, finite element code

NASA Technical Reports Server (NTRS)

King, Scott D.; Lucas, Robert; Raefsky, Arthur

1990-01-01

We consider the performance of the finite element method on a vector supercomputer. The computationally intensive parts of the finite element method are typically the individual element forms and the solution of the global stiffness matrix both of which are vectorized in high performance codes. To further increase throughput, new algorithms are needed. We compare a multifrontal sparse solver to a traditional skyline solver in a finite element code on a vector supercomputer. The multifrontal solver uses the Multiple-Minimum Degree reordering heuristic to reduce the number of operations required to factor a sparse matrix and full matrix computational kernels (e.g., BLAS3) to enhance vector performance. The net result in an order-of-magnitude reduction in run time for a finite element application on one processor of a Cray X-MP.

Comparison of two matrix data structures for advanced CSM testbed applications

NASA Technical Reports Server (NTRS)

Regelbrugge, M. E.; Brogan, F. A.; Nour-Omid, B.; Rankin, C. C.; Wright, M. A.

1989-01-01

The first section describes data storage schemes presently used by the Computational Structural Mechanics (CSM) testbed sparse matrix facilities and similar skyline (profile) matrix facilities. The second section contains a discussion of certain features required for the implementation of particular advanced CSM algorithms, and how these features might be incorporated into the data storage schemes described previously. The third section presents recommendations, based on the discussions of the prior sections, for directing future CSM testbed development to provide necessary matrix facilities for advanced algorithm implementation and use. The objective is to lend insight into the matrix structures discussed and to help explain the process of evaluating alternative matrix data structures and utilities for subsequent use in the CSM testbed.

Rapid Assessment of Contaminants and Interferences in Mass Spectrometry Data Using Skyline

NASA Astrophysics Data System (ADS)

Rardin, Matthew J.

2018-04-01

Proper sample preparation in proteomic workflows is essential to the success of modern mass spectrometry experiments. Complex workflows often require reagents which are incompatible with MS analysis (e.g., detergents) necessitating a variety of sample cleanup procedures. Efforts to understand and mitigate sample contamination are a continual source of disruption with respect to both time and resources. To improve the ability to rapidly assess sample contamination from a diverse array of sources, I developed a molecular library in Skyline for rapid extraction of contaminant precursor signals using MS1 filtering. This contaminant template library is easily managed and can be modified for a diverse array of mass spectrometry sample preparation workflows. Utilization of this template allows rapid assessment of sample integrity and indicates potential sources of contamination. [Figure not available: see fulltext.

The impact of warming on greenhouse gas fluxes: an experimental comparison which reveals the varied response of ecosystems to climate change.

NASA Astrophysics Data System (ADS)

Stockdale, James; Ineson, Philip

2016-04-01

Modelled predictions of the response of terrestrial systems to climate change are highly variable, yet the response of net ecosystem exchange (NEE) is a vital ecosystem behaviour to understand due to its inherent feedback to the carbon cycle. The establishment and subsequent monitoring of replicated experimental manipulations are a direct method to reveal these responses, yet are difficult to achieve as they typically resource-heavy and labour intensive. We actively manipulated the temperature at three agricultural grasslands in southern England and deployed novel 'SkyLine' systems, recently developed at the University of York, to continuously monitor GHG fluxes. Each 'SkyLine' is a low-cost and fully autonomous technology yet produces fluxes at a near-continuous temporal frequency and across a wide spatial area. The results produced by 'SkyLine' enable the detail response of each system to increased temperature over diurnal and seasonal timescales. Unexpected differences in NEE are shown between superficially similar ecosystems which, upon investigation, suggest that interactions between a variety of environmental variables are key and that knowledge of pre-existing environmental conditions help to predict a systems response to future climate. For example, the prevailing hydrological conditions at each site appear to affect its response to changing temperature. The high-frequency data shown here, combined with the fully-replicated experimental design reveal complex interactions which must be understood to improve predictions of ecosystem response to a changing climate.

Data-Independent MS/MS Quantification of Neuropeptides for Determination of Putative Feeding-Related Neurohormones in Microdialysate

PubMed Central

2015-01-01

Food consumption is an important behavior that is regulated by an intricate array of neuropeptides (NPs). Although many feeding-related NPs have been identified in mammals, precise mechanisms are unclear and difficult to study in mammals, as current methods are not highly multiplexed and require extensive a priori knowledge about analytes. New advances in data-independent acquisition (DIA) MS/MS and the open-source quantification software Skyline have opened up the possibility to identify hundreds of compounds and quantify them from a single DIA MS/MS run. An untargeted DIA MSE quantification method using Skyline software for multiplexed, discovery-driven quantification was developed and found to produce linear calibration curves for peptides at physiologically relevant concentrations using a protein digest as internal standard. By using this method, preliminary relative quantification of the crab Cancer borealis neuropeptidome (<2 kDa, 137 peptides from 18 families) was possible in microdialysates from 8 replicate feeding experiments. Of these NPs, 55 were detected with an average mass error below 10 ppm. The time-resolved profiles of relative concentration changes for 6 are shown, and there is great potential for the use of this method in future experiments to aid in correlation of NP changes with behavior. This work presents an unbiased approach to winnowing candidate NPs related to a behavior of interest in a functionally relevant manner, and demonstrates the success of such a UPLC-MSE quantification method using the open source software Skyline. PMID:25552291

Data-independent MS/MS quantification of neuropeptides for determination of putative feeding-related neurohormones in microdialysate.

PubMed

Schmerberg, Claire M; Liang, Zhidan; Li, Lingjun

2015-01-21

Food consumption is an important behavior that is regulated by an intricate array of neuropeptides (NPs). Although many feeding-related NPs have been identified in mammals, precise mechanisms are unclear and difficult to study in mammals, as current methods are not highly multiplexed and require extensive a priori knowledge about analytes. New advances in data-independent acquisition (DIA) MS/MS and the open-source quantification software Skyline have opened up the possibility to identify hundreds of compounds and quantify them from a single DIA MS/MS run. An untargeted DIA MS(E) quantification method using Skyline software for multiplexed, discovery-driven quantification was developed and found to produce linear calibration curves for peptides at physiologically relevant concentrations using a protein digest as internal standard. By using this method, preliminary relative quantification of the crab Cancer borealis neuropeptidome (<2 kDa, 137 peptides from 18 families) was possible in microdialysates from 8 replicate feeding experiments. Of these NPs, 55 were detected with an average mass error below 10 ppm. The time-resolved profiles of relative concentration changes for 6 are shown, and there is great potential for the use of this method in future experiments to aid in correlation of NP changes with behavior. This work presents an unbiased approach to winnowing candidate NPs related to a behavior of interest in a functionally relevant manner, and demonstrates the success of such a UPLC-MS(E) quantification method using the open source software Skyline.

8. Engineering Drawing of Panama Gun Mount by U.S. Engineering ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

8. Engineering Drawing of Panama Gun Mount by U.S. Engineering Office, San Francisco, California - Fort Funston, Panama Mounts for 155mm Guns, Skyline Boulevard & Great Highway, San Francisco, San Francisco County, CA

Photogrammetric mobile satellite service prediction

NASA Technical Reports Server (NTRS)

Akturan, Riza; Vogel, Wolfhard J.

1994-01-01

Photographic images of the sky were taken with a camera through a fisheye lens with a 180 deg field-of-view. The images of rural, suburban, and urban scenes were analyzed on a computer to derive quantitative information about the elevation angles at which the sky becomes visible. Such knowledge is needed by designers of mobile and personal satellite communications systems and is desired by customers of these systems. The 90th percentile elevation angle of the skyline was found to be 10 deg, 17 deg, and 51 deg in the three environments. At 8 deg, 75 percent, 75 percent, and 35 percent of the sky was visible, respectively. The elevation autocorrelation fell to zero with a 72 deg lag in the rural and urban environment and a 40 deg lag in the suburb. Mean estimation errors are below 4 deg.

ORD BROWNFIELDS RESEARCH

EPA Science Inventory

The exhibit is a 10'x10' skyline truss which will be used to highlight the activities of the U.S.-German Bilateral Working Group in the area of brownfields revitalization. The U.S. product, Sustainable Management Approaches and Revitalization Tools - electronic (SMARTe) will be d...

Implementation of precast concrete deck system NUDECK (2nd generation).

DOT National Transportation Integrated Search

2013-12-01

The first generation of precast concrete deck system, NUDECK, developed by the University of NebraskaLincoln (UNL) for Nebraska Department of Roads (NDOR), was implemented on the Skyline Bridge, : Omaha, NE in 2004. The project was highly successful ...

STS-119 Launch Skyline

NASA Image and Video Library

2009-03-15

STS119-S-025 (15 March 2009) --- The setting sun paints the clouds over NASA's Kennedy Space Center in Florida before the launch of Space Shuttle Discovery on the STS-119 mission. Liftoff is scheduled for 7:43 p.m. (EDT) on March 15, 2009.

4. A river level view of the Broad Street bridge ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. A river level view of the Broad Street bridge and Columbus skyline from the railroad truss north of the bridge. - Broad Street Bridge, Spanning Scioto River at U.S. Route 40 (Broad Street), Columbus, Franklin County, OH

Deadly Everest Avalanche Site Spotted by NASA Spacecraft

NASA Image and Video Library

2014-04-28

On Friday, April 26, 2014, an avalanche on Mount Everest killed at least 13 Sherpa guides. NASA Terra spacecraft looked toward the northeast, with Mount Everest center, and Lhotse, the fourth-highest mountain on Earth, on the skyline to right center.

101. Catalog HHistory 1, C.C.C., 34 Landscaping, Negative No. 1340 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

101. Catalog H-History 1, C.C.C., 34 Landscaping, Negative No. 1340 (Photographer and date unknown) BANK BLENDING WORK BY CCC. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

98. Catalog HHistory 1, C.C.C., 19 Tree Planting, Negative No. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

98. Catalog H-History 1, C.C.C., 19 Tree Planting, Negative No. P 474c (Photographer and date unknown) TRANSPLANTING TREE. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

Evaluating the constructability of NUDECK precast concrete deck panels for Kearney Bypass Project.

DOT National Transportation Integrated Search

2015-02-01

The first generation of precast concrete deck system, NUDECK, was implemented on the Skyline Bridge, : Omaha, NE in 2004. The second generation of NUDECK system was developed to further simplify the : system and improve its constructability and durab...

66. BIG MEADOWS. VIEW OF PARKING AREA AT THE GATED ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

66. BIG MEADOWS. VIEW OF PARKING AREA AT THE GATED ENTRANCE TO RAPIDAN FIRE ROAD, THE ACCESS ROAD TO CAMP HOOVER. LOOKING SOUTH, MILE 51.3. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

2. VIEW OF PARK SIGNAGE AT FRONT ROYAL. SIGN SAYS: ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. VIEW OF PARK SIGNAGE AT FRONT ROYAL. SIGN SAYS: "NORTH ENTRANCE SHENANDOAH NATIONAL PARK." LOCATED ON EXIT SIDE OF ROAD. LOOKING SOUTHWEST, MILE 0.0. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

100. Catalog HHistory 1, C.C.C., 34 Landscaping, Negative No. P ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

100. Catalog H-History 1, C.C.C., 34 Landscaping, Negative No. P 733c (Photographer and date unknown) SLOPE MAINTENANCE WORK BY CCC. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

99. Catalog HHistory 1, C.C.C., 23 Guard Rail Construction, Negative ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

99. Catalog H-History 1, C.C.C., 23 Guard Rail Construction, Negative No. P455e (Photographer and date unknown) GUARD RAIL INSTALLATION. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

3D exploitation of large urban photo archives

NASA Astrophysics Data System (ADS)

Cho, Peter; Snavely, Noah; Anderson, Ross

2010-04-01

Recent work in computer vision has demonstrated the potential to automatically recover camera and scene geometry from large collections of uncooperatively-collected photos. At the same time, aerial ladar and Geographic Information System (GIS) data are becoming more readily accessible. In this paper, we present a system for fusing these data sources in order to transfer 3D and GIS information into outdoor urban imagery. Applying this system to 1000+ pictures shot of the lower Manhattan skyline and the Statue of Liberty, we present two proof-of-concept examples of geometry-based photo enhancement which are difficult to perform via conventional image processing: feature annotation and image-based querying. In these examples, high-level knowledge projects from 3D world-space into georegistered 2D image planes and/or propagates between different photos. Such automatic capabilities lay the groundwork for future real-time labeling of imagery shot in complex city environments by mobile smart phones.

10. Detail of map showing Battery Davis and Panama Gun ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. Detail of map showing Battery Davis and Panama Gun Mounts at right, by U.S. Engineering Office, San Francisco, California, August 5, 1934. - Fort Funston, Panama Mounts for 155mm Guns, Skyline Boulevard & Great Highway, San Francisco, San Francisco County, CA

5. VIEW LOOKING NORTHEAST INTO CENTRAL COURTYARD OF TECHWOOD DORMITORY, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. VIEW LOOKING NORTHEAST INTO CENTRAL COURTYARD OF TECHWOOD DORMITORY, SHOWING WEST FRONT OF CENTER WING AND PART OF SOUTH SIDE OF NORTH WING. MIDTOWN SKYLINE VISIBLE IN BACKGROUND. - Techwood Homes, McDaniel Dormitory, 581-587 Techwood Drive, Atlanta, Fulton County, GA

Skyline logging productivity under alternative harvesting prescriptions and levels of utilization in larch-fir stands

Treesearch

Rulon B. Gardner

1980-01-01

Larch-fir stands in northwest Montana were experimentally logged to determine the influence of increasingly intensive levels of utilization upon rates of yarding production, under three different silvicultural prescriptions. Variables influencing rate of production were also identified.

Research on the Intensity Analysis and Result Visualization of Construction Land in Urban Planning

NASA Astrophysics Data System (ADS)

Cui, J.; Dong, B.; Li, J.; Li, L.

2017-09-01

As a fundamental work of urban planning, the intensity analysis of construction land involves many repetitive data processing works that are prone to cause errors or data precision loss, and the lack of efficient methods and tools to visualizing the analysis results in current urban planning. In the research a portable tool is developed by using the Model Builder technique embedded in ArcGIS to provide automatic data processing and rapid result visualization for the works. A series of basic modules provided by ArcGIS are linked together to shape a whole data processing chain in the tool. Once the required data is imported, the analysis results and related maps and graphs including the intensity values and zoning map, the skyline analysis map etc. are produced automatically. Finally the tool is installation-free and can be dispatched quickly between planning teams.

High Rise Building: The Mega Sculpture Made Of Steel, Concrete and Glass

NASA Astrophysics Data System (ADS)

Stefańska, Alicja; Załuski, Daniel

2017-10-01

High rise building has transformed from providing not only the expansion of floor space but functioning as mega sculpture in the city. The shift away from economic efficiency driven need is only expected to grow in the future. Based on literature studies; after analysing planning documents and case studies, it was examined whether the presumption that gaining the maximum amount of usable area is the only driving factor; or if the need for the creation of an image for the city provided a supplementary reason. The results showed that forming high rise buildings as three-dimensional sculptures is influenced not only by aesthetics, but also marketing. Visual distinction in the city skyline is economically beneficial for investors gaining not only functionality but art, enriching the cultural landscape. Organizing architectural competitions, public debates and following the latest art trends is therefore possible due to large budgets of such projects.

TCA precipitation and ethanol/HCl single-step purification evaluation: One-dimensional gel electrophoresis, bradford assays, spectrofluorometry and Raman spectroscopy data on HSA, Rnase, lysozyme - Mascots and Skyline data.

PubMed

Eddhif, Balkis; Guignard, Nadia; Batonneau, Yann; Clarhaut, Jonathan; Papot, Sébastien; Geffroy-Rodier, Claude; Poinot, Pauline

2018-04-01

The data presented here are related to the research paper entitled "Study of a Novel Agent for TCA Precipitated Proteins Washing - Comprehensive Insights into the Role of Ethanol/HCl on Molten Globule State by Multi-Spectroscopic Analyses" (Eddhif et al., submitted for publication) [1]. The suitability of ethanol/HCl for the washing of TCA-precipitated proteins was first investigated on standard solution of HSA, cellulase, ribonuclease and lysozyme. Recoveries were assessed by one-dimensional gel electrophoresis, Bradford assays and UPLC-HRMS. The mechanistic that triggers protein conformational changes at each purification stage was then investigated by Raman spectroscopy and spectrofluorometry. Finally, the efficiency of the method was evaluated on three different complex samples (mouse liver, river biofilm, loamy soil surface). Proteins profiling was assessed by gel electrophoresis and by UPLC-HRMS.

75 FR 5289 - Defense Health Board (DHB) Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-02

... DEPARTMENT OF DEFENSE Office of the Secretary Defense Health Board (DHB) Meeting AGENCY... announces that the Defense Health Board (DHB or Board) will meet on March 1-2, 2010, to address and.... Feeks, Executive Secretary, Defense Health Board, Five Skyline Place, 5111 Leesburg Pike, Suite 810...

3 CFR 8410 - Proclamation 8410 of September 3, 2009. National Days of Prayer and Remembrance, 2009

Code of Federal Regulations, 2010 CFR

2010-01-01

... struck the skyline of New York City, the structure of the Pentagon, and the grass of Pennsylvania. In the... world. They have left the safety of home so that our Nation might be more secure. They have endured...

Extract useful knowledge from agro-hydrological simulations data for decision making

NASA Astrophysics Data System (ADS)

Gascuel-odoux, C.; Bouadi, T.; Cordier, M.; Quiniou, R.

2013-12-01

In recent years, models have been developed and used to test the effect of scenarios and help stakeholders in decision making. Agro-hydrological models have guided agricultural water management by testing the effect of landscape structure and farming system changes on water quantity and quality. Such models generate a large amount of data but few are stored and are often not customized for stakeholders, so that a great amount of information is lost from the simulation process or not transformed in a usable format. A first approach, already published (Trepos et al., 2012), has been developed to identify object oriented tree patterns, that represent surface flow and pollutant pathways from plot to plot, involved in water pollution by herbicides. A simulation model (Gascuel-odoux et al., 2009) predicted herbicide transfer rate, defined as the proportion of applied herbicide that reaches water courses. The predictions were used as a set of learning examples for symbolic learning techniques to induce rules based on qualitative and quantitative attributes and explain two extreme classes in transfer rate. Two automatic symbolic learning techniques were used: the inductive logic programming approach to induce spatial tree patterns, and an attribute-value method to induce aggregated attributes of the trees. A visualization interface allows the users to identify rules explaining contamination and mitigation measures improving the current situation. A second approach has been recently developed to analyse directly the simulated data (Bouadi et al, submitted). A data warehouse called N-catch has been built to store and manage simulation data from the agro-hydrological model TNT2 (Beaujouan et al., 2002). 44 output key simulated variables are stored per plot and at a daily time step on a 50 squared km area, i.e, 8 GB of storage size. After identifying the set of multileveled dimensions integrating hierarchical structures and relationships among related dimension levels, N-Catch has been designed using the open source Business Intelligence Platform Pentaho. We show how to use online analytical processing (OLAP) to access and exploit, intuitively and quickly, the multidimensional and aggregated data from the N-Catch data warehouse. We illustrate how the data warehouse can be used to explore spatio-temporal dimensions efficiently and to discover new knowledge at multiple levels of simulation. OLAP tool can be used to synthesize environmental information and understand nitrogen emissions in water bodies by generating comparative and personalized views of historical data. This DWH is currently extended with data mining or information retrieval methods as Skyline queries to perform advanced analyses (Bouadi et al., 2012). Bouadi et al. N-Catch: A Data Warehouse for Multilevel Analysis of Simulated Nitrogen Data from an Agro-hydrological Model. Submitted. Bouadi et al., 2012) Bouadi, T., Cordier, M., and Quiniou, R. (2012). Incremental computation of skyline queries with dynamic preferences. In DEXA (1), pages 219-233. Trepos et al. 2012. Mining simulation data by rule induction to determine critical source areas of stream water pollution by herbicides. Computers and Electronics in Agriculture 86, 75-88.

75 FR 25198 - Intermountain Region, Boise National Forest, Emmett Ranger District; Idaho Scriver Creek...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... commercial and noncommercial vegetation management and road system modifications and maintenance. DATES... stands and old forest habitat; (2) improve watershed conditions and reduce road- related impacts to... commercial timber harvest on about 3,265 acres utilizing tractor/off-road jammer (1,124 acres), skyline (926...

Block 3. Central view of Block 3 observed from the ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Block 3. Central view of Block 3 observed from the west to the east. This photograph reveals the alignment of trees within the central path of the park. In addition, this photograph exposes broken bricks aligning tree beds - Skyline Park, 1500-1800 Arapaho Street, Denver, Denver County, CO

SIMYAR: a cable-yarding simulation model.

Treesearch

R.J. McGaughey; R.H. Twito

1987-01-01

A skyline-logging simulation model designed to help planners evaluate potential yarding options and alternative harvest plans is presented. The model, called SIMYAR, uses information about the timber stand, yarding equipment, and unit geometry to estimate yarding co stand productivity for a particular operation. The costs of felling, bucking, loading, and hauling are...

Balloon logging with the inverted skyline

NASA Technical Reports Server (NTRS)

Mosher, C. F.

1975-01-01

There is a gap in aerial logging techniques that has to be filled. The need for a simple, safe, sizeable system has to be developed before aerial logging will become effective and accepted in the logging industry. This paper presents such a system designed on simple principles with realistic cost and ecological benefits.

97. Catalog B, Higher Plants, 200 2 American Chestnut Tree, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

97. Catalog B, Higher Plants, 200 2 American Chestnut Tree, Negative No. 6032 (Photographer and date unknown) THIS GHOST FOREST OF BLIGHTED CHESTNUTS ONCE STOOD APPROXIMATELY AT THE LOCATION OF THE BYRD VISITOR CENTER. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

A Spoonful of Sugar

ERIC Educational Resources Information Center

Fedore, Heidi

2005-01-01

In 2002, with pressure on students and educators mounting regarding performance on standardized tests, the author, who is an assistant principal at Skyline High School in Issaquah, Washington, and some staff members decided to have a little fun in the midst of the preparation for the state's high-stakes test, the Washington Assessment of Student…

PHOTOGRAPH NUMBERS 40, 39, 38 FORM A 189 DEGREE PANORAMA ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

PHOTOGRAPH NUMBERS 40, 39, 38 FORM A 189 DEGREE PANORAMA FROM LEFT TO RIGHT. PHOTOGRAPH NUMBER 38 LOOKING NORTHEAST TO SKYLINE FROM ROOF OF POLSON BUILDING; PHOTOGRAPH NUMBER 39 VIEW NORTH; PHOTOGRAPH NUMBER 40 VIEW NORTHWEST. - Alaskan Way Viaduct and Battery Street Tunnel, Seattle, King County, WA

The trustworthy digital camera: Restoring credibility to the photographic image

NASA Technical Reports Server (NTRS)

Friedman, Gary L.

1994-01-01

The increasing sophistication of computers has made digital manipulation of photographic images, as well as other digitally-recorded artifacts such as audio and video, incredibly easy to perform and increasingly difficult to detect. Today, every picture appearing in newspapers and magazines has been digitally altered to some degree, with the severity varying from the trivial (cleaning up 'noise' and removing distracting backgrounds) to the point of deception (articles of clothing removed, heads attached to other people's bodies, and the complete rearrangement of city skylines). As the power, flexibility, and ubiquity of image-altering computers continues to increase, the well-known adage that 'the photography doesn't lie' will continue to become an anachronism. A solution to this problem comes from a concept called digital signatures, which incorporates modern cryptographic techniques to authenticate electronic mail messages. 'Authenticate' in this case means one can be sure that the message has not been altered, and that the sender's identity has not been forged. The technique can serve not only to authenticate images, but also to help the photographer retain and enforce copyright protection when the concept of 'electronic original' is no longer meaningful.

77 FR 9624 - Narrow Woven Ribbons With Woven Selvedge From Taiwan: Rescission, in Part, of Antidumping Duty...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-17

...) Multicolor Inc.; (7) Novelty Handicrafts Co., Ltd.; (8) Pacific Imports; (9) Papillon Ribbon & Bow (Canada... Lion Ribbon Company, Inc., for the following companies: (1) Apex Ribbon; (2) Apex Trimmings; (3) FinerRibbon.com ; (4) Hsien Chan Enterprise Co., Ltd.; (5) Hubschercorp; (6) Intercontinental Skyline; (7...

Nutrient losses from timber harvesting in a larch/ Douglas-fir forest

Treesearch

Nellie M. Stark

1979-01-01

Nutrient levels as a result of experimental clearcutting, shelterwood cutting, and group selection cutting - each with three levels of harvesting intensity - were studied in a larchfir forest in northwest Montana, experimentally logged with a skyline system. None of the treatments altered nutrient levels in an intermittent stream, nor were excessive amounts of...

Trends in streamflow and suspended sediment after logging, North Fork Caspar Creek

Treesearch

Jack Lewis; Elizabeth T. Keppeler

2007-01-01

Streamflow and suspended sediment were intensively monitored at fourteen gaging stations before and after logging a second-growth redwood (Sequoia sempervirens) forest. About 50 percent of the watershed was harvested, primarily by clear-cutting with skyline-cable systems. New road construction and tractor skidding were restricted to gently-sloping...

102. Catalog HHistory 1, C.C.C., 34 Landscaping, Negative No. 6040a ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

102. Catalog H-History 1, C.C.C., 34 Landscaping, Negative No. 6040a (Photographer and date unknown) BEAUTIFICATION PROGRAM STARTED AS SOON AS GRADING ALONG THE DRIVE WAS COMPLETED. CCC CAMP 3 SHOWN PLANTING LAUREL. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

Smith Assists in Superstorm Sandy Relief Efforts | Poster

Cancer.gov

By Cathy McClintock, Guest Writer It should have been routine by now for a 30-year volunteer firefighter/ emergency medical technician from Thurmont, Md., but it wasn’t. That first night, as Ross Smith, IT security, looked across the Hudson River from Jersey City, N.J., he saw an unusually dark New York skyline.

Building high-quality assay libraries for targeted analysis of SWATH MS data.

PubMed

Schubert, Olga T; Gillet, Ludovic C; Collins, Ben C; Navarro, Pedro; Rosenberger, George; Wolski, Witold E; Lam, Henry; Amodei, Dario; Mallick, Parag; MacLean, Brendan; Aebersold, Ruedi

2015-03-01

Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus spectra and compilation of MS coordinates that uniquely define each targeted peptide. Crucial steps such as false discovery rate (FDR) control, retention time normalization and handling of post-translationally modified peptides are detailed. Finally, we show how to use the library to extract SWATH data with the open-source software Skyline. The protocol takes 2-3 d to complete, depending on the extent of the library and the computational resources available.

Bayesian inference of a historical bottleneck in a heavily exploited marine mammal.

PubMed

Hoffman, J I; Grant, S M; Forcada, J; Phillips, C D

2011-10-01

Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and Approximate Bayesian Computation, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important problems in conservation and evolutionary biology. © 2011 Blackwell Publishing Ltd.

Model for Evaluating the Cost Consequences of Deferring New System Acquisition Through Upgrades

DTIC Science & Technology

1999-07-01

Analysis & Evaluation The Pentagon Washington, DC 20301 Attn: Mr. Eric Coulter, Director Projection Forces Division, Room 2E314 Lt Col Kathleen Conley...1034 Office of the Air National Guard ANG/AQM 5109 Leesburg Pike Skyline VI, Suite 302A Falls Church, VA 22041-3201 Attn: Col Brent Marler 1 Lt Col

Installation and use of epoxy-grouted rock anchors for skyline logging in southeast Alaska.

Treesearch

W.L. Schroeder; D.N. Swanston

1992-01-01

Field tests of the load-carrying capacity of epoxy-grouted rock anchors in poor quality bedrock on Wrangel Island in southeast Alaska demonstrated the effectiveness of rock anchors as substitutes for stump anchors for logging system guylines. Ultimate capacity depends mainly on rock hardness or strength and length of the imbedded anchor.

An earth anchor system: installation and design guide.

Treesearch

R.L. Copstead; D.D. Studier

1990-01-01

A system for anchoring the guylines and skylines of cable yarding equipment is presented. A description of three types of tipping plate anchors is given. Descriptions of the installation equipment and methods specific to each type are given. Procedures for determining the correct number of anchors to install are included, as are guidelines for installing the anchors so...

Production and cost of a live skyline cable yarder tested in Appalachia

Treesearch

Edward L. Fisher; Harry G. Gibson; Cleveland J. Biller

1980-01-01

Logging systems that are profitable and environmentally acceptable are needed in Appalachian hardwood forests. Small, mobile cable yarders show promise in meeting both economic and environmental objectives. One such yarder, the Ecologger, was tested on the Jefferson National Forest near Marion, Virginia. Production rates and costs are presented for the system along...

103. Catalog HHistory 1, C.C.C., 58 Landscaping, Negative No. 870 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

103. Catalog H-History 1, C.C.C., 58 Landscaping, Negative No. 870 10 ca. 1936 PROPAGATION AND PLANTING. ROOTED PLANTS TRANSPLANTED FROM HOT BEDS TO CANS TO SHADED BEDS IN PREPARATION FOR PLANTING ON ROAD SLOPES. NURSERY AT NORTH ENTRANCE. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

Cost and production analysis of the Bitterroot Miniyarder on an Appalachian hardwood site

Treesearch

John E. Baumgras; Penn A. Peters; Penn A. Peters

1985-01-01

An 18-horsepower skyline yarder was studied on a steep slope clearcut, yarding small hardwood trees uphill for fuelwood. Yarding cycle characteristics sampled include: total cycle time including delays, 5.20 minutes; yarding distance, 208 feet (350 feet maximum); turn volume, 11.6 cubic feet (24 cubic feet maximum); pieces per turn, 2.3. Cost analysis shows yarding...

Predicting the payload capability of cable logging systems including the effect of partial suspension

Treesearch

Gary D. Falk

1981-01-01

A systematic procedure for predicting the payload capability of running, live, and standing skylines is presented. Three hand-held calculator programs are used to predict payload capability that includes the effect of partial suspension. The programs allow for predictions for downhill yarding and for yarding away from the yarder. The equations and basic principles...

A second look at cable logging in the Appalachians

Treesearch

Harry G. Gibson; Cleveland J. Biller

1975-01-01

Cable logging, once used extensively in the Appalachians, is being re-examined to see if smaller, more mobile systems can help solve some of the timber-managment problems on steep slopes. A small Austrian skyline was tested in West Virginia to determine its feasibility for harvesting enstern hardwoods. The short-term test included both selection and clearcut harvesting...

Gods of the City? Reflecting on City Building Games as an Early Introduction to Urban Systems

ERIC Educational Resources Information Center

Bereitschaft, Bradley

2016-01-01

For millions of gamers and students alike, city building games (CBGs) like SimCity and the more recent Cities: Skylines present a compelling initial introduction to the world of urban planning and development. As such, these games have great potential to shape players' understanding and expectations of real urban patterns and processes. In this…

DNA breaks and end resection measured genome-wide by end sequencing | Center for Cancer Research

Cancer.gov

About the Cover The cover depicts a ribbon of DNA portrayed as a city skyline. The central gap in the landscape localizes to the precise site of the DNA break. The features surrounding the break denote the processing of DNA-end structures (end-resection) emanating from the break location. Cover artwork by Ethan Tyler, NIH. Abstract

The California Community College Baccalaureate Degree Pilot Program: A Case Study of Baccalaureate Degree Implementation

ERIC Educational Resources Information Center

Yeager, Susan Cadavid

2017-01-01

This case study examined the implementation of a baccalaureate degree at Skyline Community College--one of the 15 California community colleges authorized to offer baccalaureate degrees established as part of a pilot program enacted by the California Legislature via Senate Bill 850 (2014). The study explored the policies and procedures in place at…

High gain solar photovoltaics

NASA Astrophysics Data System (ADS)

MacDonald, B.; Finot, M.; Heiken, B.; Trowbridge, T.; Ackler, H.; Leonard, L.; Johnson, E.; Chang, B.; Keating, T.

2009-08-01

Skyline Solar Inc. has developed a novel silicon-based PV system to simultaneously reduce energy cost and improve scalability of solar energy. The system achieves high gain through a combination of high capacity factor and optical concentration. The design approach drives innovation not only into the details of the system hardware, but also into manufacturing and deployment-related costs and bottlenecks. The result of this philosophy is a modular PV system whose manufacturing strategy relies only on currently existing silicon solar cell, module, reflector and aluminum parts supply chains, as well as turnkey PV module production lines and metal fabrication industries that already exist at enormous scale. Furthermore, with a high gain system design, the generating capacity of all components is multiplied, leading to a rapidly scalable system. The product design and commercialization strategy cooperate synergistically to promise dramatically lower LCOE with substantially lower risk relative to materials-intensive innovations. In this paper, we will present the key design aspects of Skyline's system, including aspects of the optical, mechanical and thermal components, revealing the ease of scalability, low cost and high performance. Additionally, we will present performance and reliability results on modules and the system, using ASTM and UL/IEC methodologies.

Upscaling of greenhouse gas emissions in upland forestry following clearfell

NASA Astrophysics Data System (ADS)

Toet, Sylvia; Keane, Ben; Yamulki, Sirwan; Blei, Emanuel; Gibson-Poole, Simon; Xenakis, Georgios; Perks, Mike; Morison, James; Ineson, Phil

2016-04-01

Data on greenhouse gas (GHG) emissions caused by forest management activities are limited. Management such as clearfelling may, however, have major impacts on the GHG balance of forests through effects of soil disturbance, increased water table, and brash and root inputs. Besides carbon dioxide (CO2), the biogenic GHGs nitrous oxide (N2O) and methane (CH4) may also contribute to GHG emissions from managed forests. Accurate flux estimates of all three GHGs are therefore necessary, but, since GHG emissions usually show large spatial and temporal variability, in particular CH4 and N2O fluxes, high-frequency GHG flux measurements and better understanding of their controls are central to improve process-based flux models and GHG budgets at multiple scales. In this study, we determined CO2, CH4 and N2O emissions following felling in a mature Sitka spruce (Picea sitchensis) stand in an upland forest in northern England. High-frequency measurements were made along a transect using a novel, automated GHG chamber flux system ('SkyLine') developed at the University of York. The replicated, linear experiment aimed (1) to quantify GHG emissions from three main topographical features at the clearfell site, i.e. the ridges on which trees had been planted, the hollows in between and the drainage ditches, and (2) to determine the effects of the green-needle component of the discarded brash. We also measured abiotic soil and climatic factors alongside the 'SkyLine' GHG flux measurements to identify drivers of the observed GHG emissions. All three topographic features were overall sources of GHG emissions (in CO2 equivalents), and, although drainage ditches are often not included in studies, GHG emissions per unit area were highest from ditches, followed by ridges and lowest in hollows. The CO2 emissions were most important in the GHG balance of ridges and hollows, but CH4 emissions were very high from the drainage ditches, contributing to over 50% of their overall net GHG emissions. Ridges usually emitted N2O, whilst N2O emissions from hollows and ditches were very low. As much as 25% of the total GHG flux resulted from large intermittent emissions from the ditches following rainfall. Addition of green needles from the brash immediately increased soil respiration and reduced CH4 emission in comparison to controls. To upscale our high-frequency 'SkyLine' GHG flux measurements at the different topographic features to the field scale, we collected high resolution imagery from unmanned aerial vehicle (UAV) flights. We will compare results using this upscaling technique to GHG emissions simultaneously measured by eddy covariance with the 'SkyLine' system in the predominant footprint. This detailed knowledge of the spatial and temporal distribution of GHG emissions in an upland forest after felling and their drivers, and development of robust upscaling techniques can provide important tools to improve GHG flux models and to design appropriate management practices in upland forestry to mitigate GHG emissions following clearfell.

Predicting bunching costs for the Radio Horse 9 winch

Treesearch

Chris B. LeDoux; Bruce W. Kling; Patrice A. Harou; Patrice A. Harou

1987-01-01

Data from field studies and a prebunching cost simulator have been assembled and converted into a general equation that can be used to estimate the prebunching cost of the Radio Horse 9 winch. The methods can be used to estimate prebunching cost for bunching under the skyline corridor for swinging with cable systems, for bunching to skid trail edge to be picked up by a...

A topographic index to quantify the effect of mesoscale and form on site productivity

Treesearch

W. Henry McNab

1992-01-01

Landform is related to environmental factorsthat affectsite productivity in mountainous areas. I devised a simple index of landform and tested this index as a predictor of site index ín the Blue Ridge physiographic province. The landform index is the mean of eight slope gradients from plot center to skyline. A preliminary test indicated that the index was...

76 FR 76684 - Idaho: Tentative Approval of State Underground Storage Tank Program

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-08

.... Skyline, Suite B, Idaho Falls, ID 83402 from 10 a.m. to 12 p.m. and 1 p.m. to 4 p.m.; and 6. IDEQ Lewiston... ENVIRONMENTAL PROTECTION AGENCY 40 CFR Part 281 [EPA-R10-UST-2011-0896; FRL-9502-6] Idaho...). ACTION: Proposed rule. SUMMARY: The State of Idaho has applied for final approval of its Underground...

104. Catalog HHistory 1, C.C.C., 73 Picnic Furniture Construction, Negative ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

104. Catalog H-History 1, C.C.C., 73 Picnic Furniture Construction, Negative No. 8821 ca. 1936 WOOD UTILIZATION. COMPLETED RUSTIC BENCH MADE BY CCC ENROLLEES AT CAMP NP-3 FOR USE AT PARKING OVERLOOKS AND PICNIC GROUNDS. NOTE SAW IN BACKGROUND USED FOR HALVING CHESTNUT. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA

Cycle-time equation for the Koller K300 cable yarder operating on steep slopes in the Northeast

Treesearch

Neil K. Huyler; Chris B. LeDoux

1997-01-01

Describes a delay-free-cycle time equation for the Koller K300 skyline yarder operating on steep slopes in the Northeast. Using the equation, the average delay-free-cycle time was 5.72 minutes. This means that about 420 cubic feet of material per hour can be produced. The important variables used in the equation were slope yarding distance, lateral yarding distance,...

Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.

PubMed

Maclean, Brendan; Tomazela, Daniela M; Abbatiello, Susan E; Zhang, Shucha; Whiteaker, Jeffrey R; Paulovich, Amanda G; Carr, Steven A; Maccoss, Michael J

2010-12-15

Proteomics experiments based on Selected Reaction Monitoring (SRM, also referred to as Multiple Reaction Monitoring or MRM) are being used to target large numbers of protein candidates in complex mixtures. At present, instrument parameters are often optimized for each peptide, a time and resource intensive process. Large SRM experiments are greatly facilitated by having the ability to predict MS instrument parameters that work well with the broad diversity of peptides they target. For this reason, we investigated the impact of using simple linear equations to predict the collision energy (CE) on peptide signal intensity and compared it with the empirical optimization of the CE for each peptide and transition individually. Using optimized linear equations, the difference between predicted and empirically derived CE values was found to be an average gain of only 7.8% of total peak area. We also found that existing commonly used linear equations fall short of their potential, and should be recalculated for each charge state and when introducing new instrument platforms. We provide a fully automated pipeline for calculating these equations and individually optimizing CE of each transition on SRM instruments from Agilent, Applied Biosystems, Thermo-Scientific and Waters in the open source Skyline software tool ( http://proteome.gs.washington.edu/software/skyline ).

Implementation of statistical process control for proteomic experiments via LC MS/MS.

PubMed

Bereman, Michael S; Johnson, Richard; Bollinger, James; Boss, Yuval; Shulman, Nick; MacLean, Brendan; Hoofnagle, Andrew N; MacCoss, Michael J

2014-04-01

Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software. It monitors five quality control metrics in a shotgun or targeted proteomic workflow. None of these metrics require peptide identification. The source code, written in the R statistical language, runs directly from the Skyline interface, which supports the use of raw data files from several of the mass spectrometry vendors. It provides real time evaluation of the chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution), and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts. Thresholds are experiment- and instrument-specific and are determined empirically from user-defined quality control standards that enable the separation of random noise and systematic error. Finally, Pareto analysis provides a summary of performance metrics and guides the user to metrics with high variance. The utility of these charts to evaluate proteomic experiments is illustrated in two case studies.

surf3d: A 3-D finite-element program for the analysis of surface and corner cracks in solids subjected to mode-1 loadings

NASA Technical Reports Server (NTRS)

Raju, I. S.; Newman, J. C., Jr.

1993-01-01

A computer program, surf3d, that uses the 3D finite-element method to calculate the stress-intensity factors for surface, corner, and embedded cracks in finite-thickness plates with and without circular holes, was developed. The cracks are assumed to be either elliptic or part eliptic in shape. The computer program uses eight-noded hexahedral elements to model the solid. The program uses a skyline storage and solver. The stress-intensity factors are evaluated using the force method, the crack-opening displacement method, and the 3-D virtual crack closure methods. In the manual the input to and the output of the surf3d program are described. This manual also demonstrates the use of the program and describes the calculation of the stress-intensity factors. Several examples with sample data files are included with the manual. To facilitate modeling of the user's crack configuration and loading, a companion program (a preprocessor program) that generates the data for the surf3d called gensurf was also developed. The gensurf program is a three dimensional mesh generator program that requires minimal input and that builds a complete data file for surf3d. The program surf3d is operational on Unix machines such as CRAY Y-MP, CRAY-2, and Convex C-220.

Costs of harvesting forest biomass on steep slopes with a small cable yarder: results from field trials and simulations

Treesearch

John E. Baumgras; Chris B. LeDoux

1986-01-01

Cable yarding can reduce the environmental impact of timber harvesting on steep slopes by increasing road spacing and reducing soil disturbance. To determine the cost of harvesting forest biomass with a small cable yarder, a 13.4 kW (18 hp) skyline yarder was tested on two southern Appalachian sites. At both sites, fuelwood was harvested from the boles of hardwood...

2. A panoramic view of the historical district as seen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. A panoramic view of the historical district as seen from the top of the Waterford Towers. This picture shows the Town Street bridge in the foreground, the Broad Street bridge in the background, Central High School on the left and the Columbus skyline on the right (facing north), and Bicentennial Park just below. - Broad Street Bridge, Spanning Scioto River at U.S. Route 40 (Broad Street), Columbus, Franklin County, OH

User-Driven Geolocation of Untagged Desert Imagery Using Digital Elevation Models (Open Access)

DTIC Science & Technology

2013-09-12

IEEE International Conference on, pages 3677–3680. IEEE, 2011. [13] W. Zhang and J. Kosecka. Image based localization in urban environments. In 3D ...non- urban environments such as deserts. Our system generates synthetic skyline views from a DEM and extracts stable concavity-based features from these...fine as 100m2. 1. Introduction Automatic geolocation of imagery has many exciting use cases. For example, such a tool could semantically orga- nize

User-Driven Geolocation of Untagged Desert Imagery Using Digital Elevation Models

DTIC Science & Technology

2013-01-01

Conference on, pages 3677–3680. IEEE, 2011. [13] W. Zhang and J. Kosecka. Image based localization in urban environments. In 3D Data Processing...non- urban environments such as deserts. Our system generates synthetic skyline views from a DEM and extracts stable concavity-based features from these...fine as 100m2. 1. Introduction Automatic geolocation of imagery has many exciting use cases. For example, such a tool could semantically orga- nize

Pre-Whaling Genetic Diversity and Population Ecology in Eastern Pacific Gray Whales: Insights from Ancient DNA and Stable Isotopes

PubMed Central

Alter, S. Elizabeth; Newsome, Seth D.; Palumbi, Stephen R.

2012-01-01

Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ∼5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size. PMID:22590499

Lustration: Transitional Justice in Poland and Its Continuous Struggle to Make Means With the Past

DTIC Science & Technology

2008-06-01

Warsaw, just as the secret police did over its citizens. The skyline of Warsaw, dominated by this building, offers a daily reminder of life under the...the communist regime (especially acts of collaboration with the secret police) and in turn disqualifying members of these groups from holding high...Ministry of Interior for their name to be vetted through the Secret Police files of the former regime.3 A similar approach was adopted in Poland, but due

Ancient Chinese Astronomy - An Overview

NASA Astrophysics Data System (ADS)

Shi, Yunli

Documentary and archaeological evidence testifies the early origin and continuous development of ancient Chinese astronomy to meet both the ideological and practical needs of a society largely based on agriculture. There was a long period when the beginning of the year, month, and season was determined by direct observation of celestial phenomena, including their alignments with respect to the local skyline. As the need for more exact study arose, new instruments for more exact observation were invented and the system of calendrical astronomy became entirely mathematized.

Development and Evaluation of a Parallel Reaction Monitoring Strategy for Large-Scale Targeted Metabolomics Quantification.

PubMed

Zhou, Juntuo; Liu, Huiying; Liu, Yang; Liu, Jia; Zhao, Xuyang; Yin, Yuxin

2016-04-19

Recent advances in mass spectrometers which have yielded higher resolution and faster scanning speeds have expanded their application in metabolomics of diverse diseases. Using a quadrupole-Orbitrap LC-MS system, we developed an efficient large-scale quantitative method targeting 237 metabolites involved in various metabolic pathways using scheduled, parallel reaction monitoring (PRM). We assessed the dynamic range, linearity, reproducibility, and system suitability of the PRM assay by measuring concentration curves, biological samples, and clinical serum samples. The quantification performances of PRM and MS1-based assays in Q-Exactive were compared, and the MRM assay in QTRAP 6500 was also compared. The PRM assay monitoring 237 polar metabolites showed greater reproducibility and quantitative accuracy than MS1-based quantification and also showed greater flexibility in postacquisition assay refinement than the MRM assay in QTRAP 6500. We present a workflow for convenient PRM data processing using Skyline software which is free of charge. In this study we have established a reliable PRM methodology on a quadrupole-Orbitrap platform for evaluation of large-scale targeted metabolomics, which provides a new choice for basic and clinical metabolomics study.

The connection between landscapes and the solar ephemeris in honeybees.

PubMed

Towne, William F; Moscrip, Heather

2008-12-01

Honeybees connect the sun's daily pattern of azimuthal movement to some aspect of the landscape around their nests. In the present study, we ask what aspect of the landscape is used in this context--the entire landscape panorama or only sectors seen along familiar flight routes. Previous studies of the solar ephemeris memory in bees have generally used bees that had experience flying a specific route, usually along a treeline, to a feeder. When such bees were moved to a differently oriented treeline on overcast days, the bees oriented their communicative dances as if they were still at the first treeline, based on a memory of the sun's course in relation to some aspect of the site, possibly the familiar route along the treeline or possibly the entire landscape or skyline panorama. Our results show that bees lacking specific flight-route training can nonetheless recall the sun's compass bearing relative to novel flight routes in their natal landscape. Specifically, we moved a hive from one landscape to a differently oriented twin landscape, and only after transplantation under overcast skies did we move a feeder away from the hive. These bees nonetheless danced accurately by memory of the sun's course in relation to their natal landscape. The bees' knowledge of the relationship between the sun and landscape, therefore, is not limited to familiar flight routes and so may encompass, at least functionally, the entire panorama. Further evidence suggests that the skyline in particular may be the bees' preferred reference in this context.

Enhanced HIV-1 surveillance using molecular epidemiology to study and monitor HIV-1 outbreaks among intravenous drug users (IDUs) in Athens and Bucharest.

PubMed

Paraskevis, Dimitrios; Paraschiv, Simona; Sypsa, Vana; Nikolopoulos, Georgios; Tsiara, Chryssa; Magiorkinis, Gkikas; Psichogiou, Mina; Flampouris, Andreas; Mardarescu, Mariana; Niculescu, Iulia; Batan, Ionelia; Malliori, Meni; Otelea, Dan; Hatzakis, Angelos

2015-10-01

A significant increase in HIV-1 diagnoses was reported among Injecting Drug Users (IDUs) in the Athens (17-fold) and Bucharest (9-fold) metropolitan areas starting 2011. Molecular analyses were conducted on HIV-1 sequences from IDUs comprising 51% and 20% of the diagnosed cases among IDUs during 2011-2013 for Greece and Romania, respectively. Phylodynamic analyses were performed using the newly developed birth-death serial skyline model which allows estimating of important epidemiological parameters, as implemented in BEAST programme. Most infections (>90%) occurred within four and three IDU local transmission networks in Athens and Bucharest, respectively. For all Romanian clusters, the viral strains originated from local circulating strains, whereas in Athens, the local strains seeded only two of the four sub-outbreaks. Birth-death skyline plots suggest a more explosive nature for sub-outbreaks in Bucharest than in Athens. In Athens, two sub-outbreaks had been controlled (Re<1.0) by 2013 and two appeared to be endemic (Re∼1). In Bucharest one outbreak continued to expand (Re>1.0) and two had been controlled (Re<1.0). The lead times were shorter for the outbreak in Athens than in Bucharest. Enhanced molecular surveillance proved useful to gain information about the origin, causal pathways, dispersal patterns and transmission dynamics of the outbreaks that can be useful in a public health setting. Copyright © 2015 Elsevier B.V. All rights reserved.

Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS

NASA Astrophysics Data System (ADS)

Ashwood, Christopher; Lin, Chi-Hung; Thaysen-Andersen, Morten; Packer, Nicolle H.

2018-03-01

Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers. [Figure not available: see fulltext.

Phylogeography of the Rock Shell Thais clavigera (Mollusca): Evidence for Long-Distance Dispersal in the Northwestern Pacific

PubMed Central

Jung, Daewui; Li, Qi; Kong, Ling-Feng; Ni, Gang; Nakano, Tomoyuki; Matsukuma, Akihiko; Kim, Sanghee; Park, Chungoo; Lee, Hyuk Je; Park, Joong-Ki

2015-01-01

The present-day genetic structure of a species reflects both historical demography and patterns of contemporary gene flow among populations. To precisely understand how these factors shape current population structure of the northwestern (NW) Pacific marine gastropod, Thais clavigera, we determined the partial nucleotide sequences of the mitochondrial COI gene for 602 individuals sampled from 29 localities spanning almost the whole distribution of T. clavigera in the NW Pacific Ocean (~3,700 km). Results from population genetic and demographic analyses (AMOVA, ΦST-statistics, haplotype networks, Tajima’s D, Fu’s FS, mismatch distribution, and Bayesian skyline plots) revealed a lack of genealogical branches or geographical clusters, and a high level of genetic (haplotype) diversity within each of studied population. Nevertheless, low but significant genetic structuring was detected among some geographical populations separated by the Changjiang River, suggesting the presence of geographical barriers to larval dispersal around this region. Several lines of evidence including significant negative Tajima’s D and Fu’s FS statistics values, the unimodally shaped mismatch distribution, and Bayesian skyline plots suggest a population expansion at marine isotope stage 11 (MIS 11; 400 ka), the longest and warmest interglacial interval during the Pleistocene epoch. The lack of genetic structure among the great majority of the NW Pacific T. clavigera populations may be attributable to high gene flow by current-driven long-distance dispersal of prolonged planktonic larval phase of this species. PMID:26171966

Using Data Warehouses to extract knowledge from Agro-Hydrological simulations

NASA Astrophysics Data System (ADS)

Bouadi, Tassadit; Gascuel-Odoux, Chantal; Cordier, Marie-Odile; Quiniou, René; Moreau, Pierre

2013-04-01

In recent years, simulation models have been used more and more in hydrology to test the effect of scenarios and help stakeholders in decision making. Agro-hydrological models have oriented agricultural water management, by testing the effect of landscape structure and farming system changes on water and chemical emission in rivers. Such models generate a large amount of data while few of them, such as daily concentrations at the outlet of the catchment, or annual budgets regarding soil, water and atmosphere emissions, are stored and analyzed. Thus, a great amount of information is lost from the simulation process. This is due to the large volumes of simulated data, but also to the difficulties in analyzing and transforming the data in an usable information. In this talk we illustrate a data warehouse which has been built to store and manage simulation data coming from the agro-hydrological model TNT (Topography-based nitrogen transfer and transformations, (Beaujouan et al., 2002)). This model simulates the transfer and transformation of nitrogen in agricultural catchments. TNT was used over 10 years on the Yar catchment (western France), a 50 km2 square area which present a detailed data set and have to facing to environmental issue (coastal eutrophication). 44 output key simulated variables are stored at a daily time step, i.e, 8 GB of storage size, which allows the users to explore the N emission in space and time, to quantify all the processes of transfer and transformation regarding the cropping systems, their location within the catchment, the emission in water and atmosphere, and finally to get new knowledge and help in making specific and detailed decision in space and time. We present the dimensional modeling process of the Nitrogen in catchment data warehouse (i.e. the snowflake model). After identifying the set of multileveled dimensions with complex hierarchical structures and relationships among related dimension levels, we chose the snowflake model to design our agri-environmental data warehouse. The snowflake schema is required for flexible querying complex dimension relationships. We have designed the Nitrogen in catchment data warehouse using the open source Business Intelligence Platform Pentaho Version 3.5. We use the online analytical processing (OLAP) to access and exploit, intuitively and quickly, the multidimensional and aggregated data from the Nitrogen in catchment data warehouse. We illustrate how the data warehouse can be efficiently used to explore spatio-temporal dimensions and to discover new knowledge and enrich the exploitation level of simulations. We show how the OLAP tool can be used to provide the user with the ability to synthesize environmental information and to understand nitrates emission in surface water by using comparative, personalized views on historical data. To perform advanced analyses that aim to find meaningful patterns and relationships in the data, the Nitrogen in catchment data warehouse should be extended with data mining or information retrieval methods as Skyline queries (Bouadi et al., 2012). (Beaujouan et al., 2002) Beaujouan, V., Durand, P., Ruiz, L., Aurousseau, P., and Cotteret, G. (2002). A hydrological model dedicated to topography-based simulation of nitrogen transfer and transformation: rationale and application to the geomorphology denitrification relationship. Hydrological Processes, pages 493-507. (Bouadi et al., 2012) Bouadi, T., Cordier, M., and Quiniou, R. (2012). Incremental computation of skyline queries with dynamic preferences. In DEXA (1), pages 219-233.

Open Source Software Tool Skyline Reaches Key Agreement with Mass Spectrometer Vendors | Office of Cancer Clinical Proteomics Research

Cancer.gov

The full proteomics analysis of a small tumor sample (similar in mass to a few grains of rice) produces well over 500 megabytes of unprocessed "raw" data when analyzed on a mass spectrometer (MS). Thus, for every proteomics experiment there is a vast amount of raw data that must be analyzed and interrogated in order to extract biological information. Moreover, the raw data output from different MS vendors are generally in different formats inhibiting the ability of labs to productively work together.

Space Shuttle Discovery DC Fly-Over

NASA Image and Video Library

2012-04-17

Space shuttle Discovery, mounted atop a NASA 747 Shuttle Carrier Aircraft (SCA), flies over the Washington skyline as seen from a NASA T-38 aircraft, Tuesday, April 17, 2012. Discovery, the first orbiter retired from NASA’s shuttle fleet, completed 39 missions, spent 365 days in space, orbited the Earth 5,830 times, and traveled 148,221,675 miles. NASA will transfer Discovery to the National Air and Space Museum to begin its new mission to commemorate past achievements in space and to educate and inspire future generations of explorers. Photo Credit: (NASA/Robert Markowitz)

Unique patellofemoral alignment in a patient with a symptomatic bipartite patella.

PubMed

Ishikawa, Masakazu; Adachi, Nobuo; Deie, Masataka; Nakamae, Atsuo; Nakasa, Tomoyuki; Kamei, Goki; Takazawa, Kobun; Ochi, Mitsuo

2016-01-01

A symptomatic bipartite patella is rarely seen in athletic adolescents or young adults in daily clinical practice. To date, only a limited number of studies have focused on patellofemoral alignment. The current study revealed a unique patellofemoral alignment in a patient with a symptomatic bipartite patella. Twelve patients with 12 symptomatic bipartite patellae who underwent arthroscopic vastus lateralis release (VLR) were investigated (10 males and two females, age: 15.7±4.4years). The radiographic data of contralateral intact and affected knees were reviewed retrospectively. From the lateral- and skyline-view imaging, the following parameters were measured: the congruence angle (CA), the lateral patellofemoral angle (LPA), and the Caton-Deschamps index (CDI). As an additional parameter, the bipartite fragment angle (BFA) was evaluated against the main part of the patella in the skyline view. Compared with the contralateral side, the affected patellae were significantly medialized and laterally tilted (CA: P=0.019; LPA: P=0.016), although there was no significant difference in CDI (P=0.877). This patellar malalignment was found to significantly change after VLR (CA: P=0.001; LPA: P=0.003) and the patellar height was significantly lower than in the preoperative condition (P=0.016). In addition, the BFA significantly shifted to a higher degree after operation (P=0.001). Patients with symptomatic bipartite patellae presented significantly medialized and laterally tilted patellae compared with the contralateral intact side. This malalignment was corrected by VLR, and the alignment of the bipartite fragment was also significantly changed. Level IV, case series. Copyright © 2015 Elsevier B.V. All rights reserved.

Viking Lander imaging investigation: Picture catalog of primary mission experiment data record

NASA Technical Reports Server (NTRS)

Tucker, R. B.

1978-01-01

All the images returned by the two Viking Landers during the primary phase of the Viking Mission are presented. Listings of supplemental information which described the conditions under which the images were acquired are included together with skyline drawings which show where the images are positioned in the field of view of the cameras. Subsets of the images are listed in a variety of sequences to aid in locating images of interest. The format and organization of the digital magnetic tape storage of the images are described. The mission and the camera system are briefly described.

Shuttle Enterprise Flight to New York

NASA Image and Video Library

2012-04-27

Space shuttle Enterprise, mounted atop a NASA 747 Shuttle Carrier Aircraft (SCA), is seen as it flies over the Manhattan Skyline with Freedom Tower in the background, Friday, April 27, 2012, in New York. Enterprise was the first shuttle orbiter built for NASA performing test flights in the atmosphere and was incapable of spaceflight. Originally housed at the Smithsonian's Steven F. Udvar-Hazy Center, Enterprise will be demated from the SCA and placed on a barge that will eventually be moved by tugboat up the Hudson River to the Intrepid Sea, Air & Space Museum in June. Photo Credit: (NASA/Robert Markowitz)

Shuttle Enterprise Flight to New York

NASA Image and Video Library

2012-04-27

Space shuttle Enterprise, mounted atop a NASA 747 Shuttle Carrier Aircraft (SCA), is seen as it flies near the Statue of Liberty and the Manhattan skyline, Friday, April 27, 2012, in New York. Enterprise was the first shuttle orbiter built for NASA performing test flights in the atmosphere and was incapable of spaceflight. Originally housed at the Smithsonian's Steven F. Udvar-Hazy Center, Enterprise will be demated from the SCA and placed on a barge that will eventually be moved by tugboat up the Hudson River to the Intrepid Sea, Air & Space Museum in June. Photo Credit: (NASA/Robert Markowitz)

An integrated strategy for the quantitative analysis of endogenous proteins: A case of gender-dependent expression of P450 enzymes in rat liver microsome.

PubMed

Shao, Yuhao; Yin, Xiaoxi; Kang, Dian; Shen, Boyu; Zhu, Zhangpei; Li, Xinuo; Li, Haofeng; Xie, Lin; Wang, Guangji; Liang, Yan

2017-08-01

Liquid chromatography mass spectrometry based methods provide powerful tools for protein analysis. Cytochromes P450 (CYPs), the most important drug metabolic enzymes, always exhibit sex-dependent expression patterns and metabolic activities. To date, analysis of CYPs based on mass spectrometry is still facing critical technical challenges due to the complexity and diversity of CYP isoforms besides lack of corresponding standards. The aim of present work consisted in developing a label-free qualitative and quantitative strategy for endogenous proteins, and then applying to the gender-difference study for CYPs in rat liver microsomes (RLMs). Initially, trypsin digested RLM specimens were analyzed by the nanoLC-LTQ-Orbitrap MS/MS. Skyline, an open source and freely available software for targeted proteomics research, was then used to screen the main CYP isoforms in RLMs under a series of criteria automatically, and a total of 40 and 39 CYP isoforms were identified in male and female RLMs, respectively. More importantly, a robust quantitative method in a tandem mass spectrometry-multiple reaction mode (MS/MS-MRM) was built and optimized under the help of Skyline, and successfully applied into the CYP gender difference study in RLMs. In this process, a simple and accurate approach named 'Standard Curve Slope" (SCS) was established based on the difference of standard curve slopes of CYPs between female and male RLMs in order to assess the gender difference of CYPs in RLMs. This presently developed methodology and approach could be widely used in the protein regulation study during drug pharmacological mechanism research. Copyright © 2017 Elsevier B.V. All rights reserved.

High prevalence of HBV/A1 subgenotype in native south Americans may be explained by recent economic developments in the Amazon.

PubMed

Godoy, Bibiane A; Gomes-Gouvêa, Michele S; Zagonel-Oliveira, Marcelo; Alvarado-Mora, Mónica V; Salzano, Francisco M; Pinho, João R R; Fagundes, Nelson J R

2016-09-01

Native American populations present the highest prevalence of Hepatitis B Virus (HBV) infection in the Americas, which may be associated to severe disease outcomes. Ten HBV genotypes (A–J) have been described, displaying a remarkable geographic structure, which most likely reflects historic patterns of human migrations. In this study, we characterize the HBV strains circulating in a historical sample of Native South Americans to characterize the historical viral dynamics in this population. The sample consisted of 1070 individuals belonging to 38 populations collected between 1965 and 1997. Presence of HBV DNA was checked by quantitative real-time PCR, and determination of HBV genotypes and subgenotypes was performed through sequencing and phylogenetic analysis of a fragment including part of HBsAg and Pol coding regions (S/Pol). A Bayesian Skyline Plot analysis was performed to compare the viral population dynamics of HBV/A1 strains found in Native Americans and in the general Brazilian population. A total of 109 individuals were positive for HBV DNA (~ 10%), and 70 samples were successfully sequenced and genotyped. Subgenotype A1 (HBV/A1), related to African populations and the African slave trade, was the most prevalent (66–94%). The Skyline Plot analysis showed a marked population expansion of HBV/A1 in Native Americans occurring more recently (1945–1965) than in the general Brazilian population. Our results suggest that historic processes that contributed to formation of HBV/A1 circulating in Native American are related with more recent migratory waves towards the Amazon basin, which generated a different viral dynamics in this region.

Beyond context to the skyline: thinking in 3D.

PubMed

Hoagwood, Kimberly; Olin, Serene; Cleek, Andrew

2013-01-01

Sweeping and profound structural, regulatory, and fiscal changes are rapidly reshaping the contours of health and mental health practice. The community-based practice contexts described in the excellent review by Garland and colleagues are being fundamentally altered with different business models, regional networks, accountability standards, and incentive structures. If community-based mental health services are to remain viable, the two-dimensional and flat research and practice paradigm has to be replaced with three-dimensional thinking. Failure to take seriously the changes that are happening to the larger healthcare context and respond actively through significant system redesign will lead to the demise of specialty mental health services.

Viking lander imaging investigation during extended and continuation automatic missions. Volume 2: Lander 2 picture catalog of experiment data record

NASA Technical Reports Server (NTRS)

Jones, K. L.; Henshaw, M.; Mcmenomy, C.; Robles, A.; Scribner, P. C.; Wall, S. D.; Wilson, J. W.

1981-01-01

Images returned by the two Viking landers during the extended and continuation automatic phases of the Viking Mission are presented. Information describing the conditions under which the images were acquired is included with skyline drawings showing the images positioned in the field of view of the cameras. Subsets of the images are listed in a variety of sequences to aid in locating images of interest. The format and organization of the digital magnetic tape storage of the images are described. A brief description of the mission and the camera system is also included.

Viking lander imaging investigation during extended and continuation automatic missions. Volume 1: Lander 1 picture catalog of experiment data record

NASA Technical Reports Server (NTRS)

Jones, K. L.; Henshaw, M.; Mcmenomy, C.; Robles, A.; Scribner, P. C.; Wall, S. D.; Wilson, J. W.

1981-01-01

All images returned by Viking Lander 1 during the extended and continuation automatic phases of the Viking Mission are presented. Listings of supplemental information which describe the conditions under which the images were acquired are included together with skyline drawings which show where the images are positioned in the field of view of the cameras. Subsets of the images are listed in a variety of sequences to aid in locating images of interest. The format and organization of the digital magnetic tape storage of the images are described as well as the mission and the camera system.

Computationally efficient multibody simulations

NASA Technical Reports Server (NTRS)

Ramakrishnan, Jayant; Kumar, Manoj

1994-01-01

Computationally efficient approaches to the solution of the dynamics of multibody systems are presented in this work. The computational efficiency is derived from both the algorithmic and implementational standpoint. Order(n) approaches provide a new formulation of the equations of motion eliminating the assembly and numerical inversion of a system mass matrix as required by conventional algorithms. Computational efficiency is also gained in the implementation phase by the symbolic processing and parallel implementation of these equations. Comparison of this algorithm with existing multibody simulation programs illustrates the increased computational efficiency.

Phylodynamics of classical swine fever virus with emphasis on Ecuadorian strains.

PubMed

Garrido Haro, A D; Barrera Valle, M; Acosta, A; J Flores, F

2018-06-01

Classic swine fever virus (CSFV) is a Pestivirus from the Flaviviridae family that affects pigs worldwide and is endemic in several Latin American countries. However, there are still some countries in the region, including Ecuador, for which CSFV molecular information is lacking. To better understand the epidemiology of CSFV in the Americas, sequences from CSFVs from Ecuador were generated and a phylodynamic analysis of the virus was performed. Sequences for the full-length glycoprotein E2 gene of twenty field isolates were obtained and, along with sequences from strains previously described in the Americas and from the most representative strains worldwide, were used to analyse the phylodynamics of the virus. Bayesian methods were used to test several molecular clock and demographic models. A calibrated ultrametric tree and a Bayesian skyline were constructed, and codons associated with positive selection involving immune scape were detected. The best model according to Bayes factors was the strict molecular clock and Bayesian skyline model, which shows that CSFV has an evolution rate of 3.2 × 10 -4 substitutions per site per year. The model estimates the origin of CSFV in the mid-1500s. There is a strong spatial structure for CSFV in the Americas, indicating that the virus is moving mainly through neighbouring countries. The genetic diversity of CSFV has increased constantly since its appearance, with a slight decrease in mid-twentieth century, which coincides, with eradication campaigns in North America. Even though there is no evidence of strong directional evolution of the E2 gene in CSFV, codons 713, 761, 762 and 975 appear to be selected positively and could be related to virulence or pathogenesis. These results reveal how CSFV has spread and evolved since it first appeared in the Americas and provide important information for attaining the goal of eradication of this virus in Latin America. © 2018 Blackwell Verlag GmbH.

Putting humans in the loop: Using crowdsourced snow information to inform water management

NASA Astrophysics Data System (ADS)

Fedorov, Roman; Giuliani, Matteo; Castelletti, Andrea; Fraternali, Piero

2016-04-01

The unprecedented availability of user generated data on the Web due to the advent of online services, social networks, and crowdsourcing, is opening new opportunities for enhancing real-time monitoring and modeling of environmental systems based on data that are public, low-cost, and spatio-temporally dense, possibly contributing to our ability of making better decisions. In this work, we contribute a novel crowdsourcing procedure for computing virtual snow indexes from public web images, either produced by users or generated by touristic webcams, which is based on a complex architecture designed for automatically crawling content from multiple web data sources. The procedure retains only geo-tagged images containing a mountain skyline, identifies the visible peaks in each image using a public online digital terrain model, and classifies the mountain image pixels as snow or no-snow. This operation yields a snow mask per image, from which it is possible to extract time series of virtual snow indexes representing a proxy of the snow covered area. The value of the obtained virtual snow indexes is estimated in a real world water management problem. We consider the snow-dominated catchment of Lake Como, a regulated lake in Northern Italy, where snowmelt represents the most important contribution to seasonal lake storage, and we used the virtual snow indexes for informing the daily operation of the lake's dam. Numerical results show that such information is effective in extending the anticipation capacity of the lake operations, ultimately improving the system performance.

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.

PubMed

Schönberg, Anna; Theunert, Christoph; Li, Mingkun; Stoneking, Mark; Nasidze, Ivan

2011-09-01

To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used high-throughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the Caucasus (Armenians, Azeri and Georgians), and one group each from Iran and Turkey. Overall diversity is very high, with 144 different sequences that fall into 97 different haplogroups found among the 147 individuals. Bayesian skyline plots (BSPs) of population size change through time show a population expansion around 40-50 kya, followed by a constant population size, and then another expansion around 15-18 kya for the groups from the Caucasus and Iran. The BSP for Turkey differs the most from the others, with an increase from 35 to 50 kya followed by a prolonged period of constant population size, and no indication of a second period of growth. An approximate Bayesian computation approach was used to estimate divergence times between each pair of populations; the oldest divergence times were between Turkey and the other four groups from the South Caucasus and Iran (~400-600 generations), while the divergence time of the three Caucasus groups from each other was comparable to their divergence time from Iran (average of ~360 generations). These results illustrate the value of random sampling of complete mtDNA genome sequences that can be obtained with high-throughput sequencing platforms.

Benchmark Lisp And Ada Programs

NASA Technical Reports Server (NTRS)

Davis, Gloria; Galant, David; Lim, Raymond; Stutz, John; Gibson, J.; Raghavan, B.; Cheesema, P.; Taylor, W.

1992-01-01

Suite of nonparallel benchmark programs, ELAPSE, designed for three tests: comparing efficiency of computer processing via Lisp vs. Ada; comparing efficiencies of several computers processing via Lisp; or comparing several computers processing via Ada. Tests efficiency which computer executes routines in each language. Available for computer equipped with validated Ada compiler and/or Common Lisp system.

Efficient Numeric and Geometric Computations using Heterogeneous Shared Memory Architectures

DTIC Science & Technology

2017-10-04

Report: Efficient Numeric and Geometric Computations using Heterogeneous Shared Memory Architectures The views, opinions and/or findings contained in this...Chapel Hill Title: Efficient Numeric and Geometric Computations using Heterogeneous Shared Memory Architectures Report Term: 0-Other Email: dm...algorithms for scientific and geometric computing by exploiting the power and performance efficiency of heterogeneous shared memory architectures . These

Complex Population Dynamics and the Coalescent Under Neutrality

PubMed Central

Volz, Erik M.

2012-01-01

Estimates of the coalescent effective population size Ne can be poorly correlated with the true population size. The relationship between Ne and the population size is sensitive to the way in which birth and death rates vary over time. The problem of inference is exacerbated when the mechanisms underlying population dynamics are complex and depend on many parameters. In instances where nonparametric estimators of Ne such as the skyline struggle to reproduce the correct demographic history, model-based estimators that can draw on prior information about population size and growth rates may be more efficient. A coalescent model is developed for a large class of populations such that the demographic history is described by a deterministic nonlinear dynamical system of arbitrary dimension. This class of demographic model differs from those typically used in population genetics. Birth and death rates are not fixed, and no assumptions are made regarding the fraction of the population sampled. Furthermore, the population may be structured in such a way that gene copies reproduce both within and across demes. For this large class of models, it is shown how to derive the rate of coalescence, as well as the likelihood of a gene genealogy with heterochronous sampling and labeled taxa, and how to simulate a coalescent tree conditional on a complex demographic history. This theoretical framework encapsulates many of the models used by ecologists and epidemiologists and should facilitate the integration of population genetics with the study of mathematical population dynamics. PMID:22042576

The Effect of Computer Automation on Institutional Review Board (IRB) Office Efficiency

ERIC Educational Resources Information Center

Oder, Karl; Pittman, Stephanie

2015-01-01

Companies purchase computer systems to make their processes more efficient through automation. Some academic medical centers (AMC) have purchased computer systems for their institutional review boards (IRB) to increase efficiency and compliance with regulations. IRB computer systems are expensive to purchase, deploy, and maintain. An AMC should…

A second level of the Saint Petersburg skyline

NASA Astrophysics Data System (ADS)

Krasnopolsky, Andrey; Bolotin, Sergey

2018-03-01

The article considers the history of the residential development in Saint Petersburg and states corresponding landmark dates. In recent years, changes in the altitude range of the residential development are noted, the influence of this factor on the formation of the city's silhouette is assessed. Reasons for such changes are identified. Attractiveness of high-rise residential complexes for living is assessed. Conclusions are made of tendencies in further housing construction development in terms of its altitude range. It is noted that it is possible to locate multi-storied buildings in the periphery of the city, taking into account specific visual characteristics of the construction site and silhouette of erected buildings; as for central districts, strict regulations regarding the altitude range are needed.

Interpreting megalithic tomb orientation and siting within broader cultural contexts

NASA Astrophysics Data System (ADS)

Prendergast, Frank

2016-02-01

This paper assesses the measured axial orientations and siting of Irish passage tombs. The distribution of monuments with passages/entrances directed at related tombs/cairns is shown. Where this phenomenon occurs, the targeted structure is invariably located at a higher elevation on the skyline and this could suggest a symbolic and hierarchical relationship in their relative siting in the landscape. Additional analysis of astronomical declinations at a national scale has identified tombs with an axial alignment towards the rising and setting positions of the Sun at the winter and summer solstices. A criteria-based framework is developed which potentially allows for these types of data to be more meaningfully considered and culturally interpreted within broader archaeological and social anthropological contexts.

On efficiency of fire simulation realization: parallelization with greater number of computational meshes

NASA Astrophysics Data System (ADS)

Valasek, Lukas; Glasa, Jan

2017-12-01

Current fire simulation systems are capable to utilize advantages of high-performance computer (HPC) platforms available and to model fires efficiently in parallel. In this paper, efficiency of a corridor fire simulation on a HPC computer cluster is discussed. The parallel MPI version of Fire Dynamics Simulator is used for testing efficiency of selected strategies of allocation of computational resources of the cluster using a greater number of computational cores. Simulation results indicate that if the number of cores used is not equal to a multiple of the total number of cluster node cores there are allocation strategies which provide more efficient calculations.

Analytical Cost Metrics : Days of Future Past

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prajapati, Nirmal; Rajopadhye, Sanjay; Djidjev, Hristo Nikolov

As we move towards the exascale era, the new architectures must be capable of running the massive computational problems efficiently. Scientists and researchers are continuously investing in tuning the performance of extreme-scale computational problems. These problems arise in almost all areas of computing, ranging from big data analytics, artificial intelligence, search, machine learning, virtual/augmented reality, computer vision, image/signal processing to computational science and bioinformatics. With Moore’s law driving the evolution of hardware platforms towards exascale, the dominant performance metric (time efficiency) has now expanded to also incorporate power/energy efficiency. Therefore the major challenge that we face in computing systems researchmore » is: “how to solve massive-scale computational problems in the most time/power/energy efficient manner?”« less

Experimental Realization of High-Efficiency Counterfactual Computation.

PubMed

Kong, Fei; Ju, Chenyong; Huang, Pu; Wang, Pengfei; Kong, Xi; Shi, Fazhan; Jiang, Liang; Du, Jiangfeng

2015-08-21

Counterfactual computation (CFC) exemplifies the fascinating quantum process by which the result of a computation may be learned without actually running the computer. In previous experimental studies, the counterfactual efficiency is limited to below 50%. Here we report an experimental realization of the generalized CFC protocol, in which the counterfactual efficiency can break the 50% limit and even approach unity in principle. The experiment is performed with the spins of a negatively charged nitrogen-vacancy color center in diamond. Taking advantage of the quantum Zeno effect, the computer can remain in the not-running subspace due to the frequent projection by the environment, while the computation result can be revealed by final detection. The counterfactual efficiency up to 85% has been demonstrated in our experiment, which opens the possibility of many exciting applications of CFC, such as high-efficiency quantum integration and imaging.

Experimental Realization of High-Efficiency Counterfactual Computation

NASA Astrophysics Data System (ADS)

Kong, Fei; Ju, Chenyong; Huang, Pu; Wang, Pengfei; Kong, Xi; Shi, Fazhan; Jiang, Liang; Du, Jiangfeng

2015-08-01

Counterfactual computation (CFC) exemplifies the fascinating quantum process by which the result of a computation may be learned without actually running the computer. In previous experimental studies, the counterfactual efficiency is limited to below 50%. Here we report an experimental realization of the generalized CFC protocol, in which the counterfactual efficiency can break the 50% limit and even approach unity in principle. The experiment is performed with the spins of a negatively charged nitrogen-vacancy color center in diamond. Taking advantage of the quantum Zeno effect, the computer can remain in the not-running subspace due to the frequent projection by the environment, while the computation result can be revealed by final detection. The counterfactual efficiency up to 85% has been demonstrated in our experiment, which opens the possibility of many exciting applications of CFC, such as high-efficiency quantum integration and imaging.

Experimental evaluation of certification trails using abstract data type validation

NASA Technical Reports Server (NTRS)

Wilson, Dwight S.; Sullivan, Gregory F.; Masson, Gerald M.

1993-01-01

Certification trails are a recently introduced and promising approach to fault-detection and fault-tolerance. Recent experimental work reveals many cases in which a certification-trail approach allows for significantly faster program execution time than a basic time-redundancy approach. Algorithms for answer-validation of abstract data types allow a certification trail approach to be used for a wide variety of problems. An attempt to assess the performance of algorithms utilizing certification trails on abstract data types is reported. Specifically, this method was applied to the following problems: heapsort, Hullman tree, shortest path, and skyline. Previous results used certification trails specific to a particular problem and implementation. The approach allows certification trails to be localized to 'data structure modules,' making the use of this technique transparent to the user of such modules.

VizieR Online Data Catalog: Investigating Tully-Fisher relation with KMOS3D (Ubler+,

NASA Astrophysics Data System (ADS)

Ubler, H.; Forster Schreiber, N. M.; Genzel, R.; Wisnioski, E.; Wuyts, S.; Lang, P.; Naab, T.; Burkert, A.; van Dokkum, P. G.; Tacconi, L. J.; Wilman, D. J.; Fossati, M.; Mendel, J. T.; Beifiori, A.; Belli, S.; Bender, R.; Brammer, G. B.; Chan, J.; Davies, R.; Fabricius, M.; Galametz, A.; Lutz, D.; Momcheva, I. G.; Nelson, E. J.; Saglia, R. P.; Seitz, S.; Tadaki, K.

2018-02-01

This work is based on the first 3yr of observations of KMOS3D multiyear near-infrared (near-IR) IFS survey of more than 600 mass-selected star-forming galaxies (SFGs) at 0.6<~z<~2.6 with the K-band Multi Object Spectrograph (KMOS; Sharples+ 2013Msngr.151...21S) on the Very Large Telescope. The KMOS3D survey and data reduction are described in detail by Wisnioski et al. 2015ApJ...799..209W The results presented in this paper build on the KMOS3D sample as of 2016 January, with 536 observed galaxies. Of these, 316 are detected in, and have spatially resolved, Hα emission free from skyline contamination from which two-dimensional velocity and dispersion maps are produced. (1 data file).

Closer Look: Majestic Mountains and Frozen Plains

NASA Image and Video Library

2015-09-17

Just 15 minutes after its closest approach to Pluto on July 14, 2015, NASA's New Horizons spacecraft looked back toward the sun and captured a near-sunset view of the rugged, icy mountains and flat ice plains extending to Pluto's horizon. The smooth expanse of the informally named Sputnik Planum (right) is flanked to the west (left) by rugged mountains up to 11,000 feet (3,500 meters) high, including the informally named Norgay Montes in the foreground and Hillary Montes on the skyline. The backlighting highlights more than a dozen layers of haze in Pluto's tenuous but distended atmosphere. The image was taken from a distance of 11,000 miles (18,000 kilometers) to Pluto; the scene is 230 miles (380 kilometers) across. http://photojournal.jpl.nasa.gov/catalog/PIA19947

Preparing to Test for Deep Space

NASA Image and Video Library

2015-07-15

A structural steel section is lifted into place atop the B-2 Test Stand at NASA’s Stennis Space Center as part of modification work to prepare for testing the core stage of NASA’s new Space Launch System. The section is part of the Main Propulsion Test Article (MPTA) framework, which will support the SLS core stage for testing. The existing framework was installed on the stand in the late 1970s to test the shuttle MPTA. However, that framework had to be repositioned and modified to accommodate the larger SLS stage. About 1 million pounds of structural steel has been added, extending the framework about 100 feet higher and providing a new look to the Stennis skyline. Stennis will test the actual flight core stage for the first uncrewed SLS mission, Exploration Mission-1.

A computable expression of closure to efficient causation.

PubMed

Mossio, Matteo; Longo, Giuseppe; Stewart, John

2009-04-07

In this paper, we propose a mathematical expression of closure to efficient causation in terms of lambda-calculus; we argue that this opens up the perspective of developing principled computer simulations of systems closed to efficient causation in an appropriate programming language. An important implication of our formulation is that, by exhibiting an expression in lambda-calculus, which is a paradigmatic formalism for computability and programming, we show that there are no conceptual or principled problems in realizing a computer simulation or model of closure to efficient causation. We conclude with a brief discussion of the question whether closure to efficient causation captures all relevant properties of living systems. We suggest that it might not be the case, and that more complex definitions could indeed create crucial some obstacles to computability.

Diversification in the South American Pampas: the genetic and morphological variation of the widespread Petunia axillaris complex (Solanaceae).

PubMed

Turchetto, Caroline; Fagundes, Nelson J R; Segatto, Ana L A; Kuhlemeier, Cris; Solís Neffa, Viviana G; Speranza, Pablo R; Bonatto, Sandro L; Freitas, Loreta B

2014-02-01

Understanding the spatiotemporal distribution of genetic variation and the ways in which this distribution is connected to the ecological context of natural populations is fundamental for understanding the nature and mode of intraspecific and, ultimately, interspecific differentiation. The Petunia axillaris complex is endemic to the grasslands of southern South America and includes three subspecies: P. a. axillaris, P. a. parodii and P. a. subandina. These subspecies are traditionally delimited based on both geography and floral morphology, although the latter is highly variable. Here, we determined the patterns of genetic (nuclear and cpDNA), morphological and ecological (bioclimatic) variation of a large number of P. axillaris populations and found that they are mostly coincident with subspecies delimitation. The nuclear data suggest that the subspecies are likely independent evolutionary units, and their morphological differences may be associated with local adaptations to diverse climatic and/or edaphic conditions and population isolation. The demographic dynamics over time estimated by skyline plot analyses showed different patterns for each subspecies in the last 100 000 years, which is compatible with a divergence time between 35 000 and 107 000 years ago between P. a. axillaris and P. a. parodii, as estimated with the IMa program. Coalescent simulation tests using Approximate Bayesian Computation do not support previous suggestions of extensive gene flow between P. a. axillaris and P. a. parodii in their contact zone. © 2013 John Wiley & Sons Ltd.

Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices

PubMed Central

Phillips, C D; Hoffman, J I; George, J C; Suydam, R S; Huebinger, R M; Patton, J C; Bickham, J W

2013-01-01

Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography. PMID:23403722

Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA.

PubMed

Rosvold, Jørgen; Røed, Knut H; Hufthammer, Anne Karin; Andersen, Reidar; Stenøien, Hans K

2012-09-26

Red deer (Cervus elaphus) have been an important human resource for millennia, experiencing intensive human influence through habitat alterations, hunting and translocation of animals. In this study we investigate a time series of ancient and contemporary DNA from Norwegian red deer spanning about 7,000 years. Our main aim was to investigate how increasing agricultural land use, hunting pressure and possibly human mediated translocation of animals have affected the genetic diversity on a long-term scale. We obtained mtDNA (D-loop) sequences from 73 ancient specimens. These show higher genetic diversity in ancient compared to extant samples, with the highest diversity preceding the onset of agricultural intensification in the Early Iron Age. Using standard diversity indices, Bayesian skyline plot and approximate Bayesian computation, we detected a population reduction which was more prolonged than, but not as severe as, historic documents indicate. There are signs of substantial changes in haplotype frequencies primarily due to loss of haplotypes through genetic drift. There is no indication of human mediated translocations into the Norwegian population. All the Norwegian sequences show a western European origin, from which the Norwegian lineage diverged approximately 15,000 years ago. Our results provide direct insight into the effects of increasing habitat fragmentation and human hunting pressure on genetic diversity and structure of red deer populations. They also shed light on the northward post-glacial colonisation process of red deer in Europe and suggest increased precision in inferring past demographic events when including both ancient and contemporary DNA.

Recovery Act - CAREER: Sustainable Silicon -- Energy-Efficient VLSI Interconnect for Extreme-Scale Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiang, Patrick

2014-01-31

The research goal of this CAREER proposal is to develop energy-efficient, VLSI interconnect circuits and systems that will facilitate future massively-parallel, high-performance computing. Extreme-scale computing will exhibit massive parallelism on multiple vertical levels, from thou­ sands of computational units on a single processor to thousands of processors in a single data center. Unfortunately, the energy required to communicate between these units at every level (on­ chip, off-chip, off-rack) will be the critical limitation to energy efficiency. Therefore, the PI's career goal is to become a leading researcher in the design of energy-efficient VLSI interconnect for future computing systems.

The thermodynamic efficiency of computations made in cells across the range of life

NASA Astrophysics Data System (ADS)

Kempes, Christopher P.; Wolpert, David; Cohen, Zachary; Pérez-Mercader, Juan

2017-11-01

Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size and converges to the polymerization cost of the ribosome. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. However, the rates of total computation per unit mass are non-monotonic in bacteria with increasing cell size, and also change across different biological architectures, including the shift from unicellular to multicellular eukaryotes. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Evaluation of the discrete vortex wake cross flow model using vector computers. Part 1: Theory and application

NASA Technical Reports Server (NTRS)

1979-01-01

The current program had the objective to modify a discrete vortex wake method to efficiently compute the aerodynamic forces and moments on high fineness ratio bodies (f approximately 10.0). The approach is to increase computational efficiency by structuring the program to take advantage of new computer vector software and by developing new algorithms when vector software can not efficiently be used. An efficient program was written and substantial savings achieved. Several test cases were run for fineness ratios up to f = 16.0 and angles of attack up to 50 degrees.

Curiosity Self-Portrait at Murray Buttes.

NASA Image and Video Library

2016-10-03

This self-portrait of NASA's Curiosity Mars rover shows the vehicle at the "Quela" drilling location in the "Murray Buttes" area on lower Mount Sharp. Key features on the skyline of this panorama are the dark mesa called "M12" to the left of the rover's mast and pale, upper Mount Sharp to the right of the mast. The top of M12 stands about 23 feet (7 meters) above the base of the sloping piles of rocks just behind Curiosity. The scene combines approximately 60 images taken by the Mars Hand Lens Imager (MAHLI) camera at the end of the rover's robotic arm. Most of the component images were taken on Sept. 17, 2016, during the 1,463rd Martian day, or sol, of Curiosity's work on Mars. Two component images of the drill-hole area in front of the rover were taken on Sol 1466 (Sept. 20) to show the hole created by collecting a drilled sample at Quela on Sol 1464 (Sept. 18). The skyline sweeps from west on the left to south-southwest on the right, with the rover's mast at northeast. The rover's location when it recorded this scene was where it ended a drive on Sol 1455, mapped at http://mars.nasa.gov/msl/multimedia/images/?ImageID=8029. The view does not include the rover's arm nor the MAHLI camera itself, except in the miniature scene reflected upside down in the parabolic mirror at the top of the mast. That mirror is part of Curiosity's Chemistry and Camera (ChemCam) instrument. MAHLI appears in the center of the mirror. Wrist motions and turret rotations on the arm allowed MAHLI to acquire the mosaic's component images. The arm was positioned out of the shot in the images, or portions of images, that were used in this mosaic. This process was used previously in acquiring and assembling Curiosity self-portraits taken at other sample-collection sites, including "Rocknest" (PIA16468), "Windjana" (PIA18390"), "Buckskin" (PIA19808) and "Gobabeb" (PIA20316). For scale, the rover's wheels are 20 inches (50 centimeters) in diameter and about 16 inches (40 centimeters) wide. http://photojournal.jpl.nasa.gov/catalog/PIA20844

The Impact of the Tree Prior on Molecular Dating of Data Sets Containing a Mixture of Inter- and Intraspecies Sampling.

PubMed

Ritchie, Andrew M; Lo, Nathan; Ho, Simon Y W

2017-05-01

In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analyzed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling. [Bayesian phylogenetic methods; model testing; molecular dating; node time; tree prior.]. © The authors 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

CCOMP: An efficient algorithm for complex roots computation of determinantal equations

NASA Astrophysics Data System (ADS)

Zouros, Grigorios P.

2018-01-01

In this paper a free Python algorithm, entitled CCOMP (Complex roots COMPutation), is developed for the efficient computation of complex roots of determinantal equations inside a prescribed complex domain. The key to the method presented is the efficient determination of the candidate points inside the domain which, in their close neighborhood, a complex root may lie. Once these points are detected, the algorithm proceeds to a two-dimensional minimization problem with respect to the minimum modulus eigenvalue of the system matrix. In the core of CCOMP exist three sub-algorithms whose tasks are the efficient estimation of the minimum modulus eigenvalues of the system matrix inside the prescribed domain, the efficient computation of candidate points which guarantee the existence of minima, and finally, the computation of minima via bound constrained minimization algorithms. Theoretical results and heuristics support the development and the performance of the algorithm, which is discussed in detail. CCOMP supports general complex matrices, and its efficiency, applicability and validity is demonstrated to a variety of microwave applications.

Memristive Mixed-Signal Neuromorphic Systems: Energy-Efficient Learning at the Circuit-Level

DOE PAGES

Chakma, Gangotree; Adnan, Md Musabbir; Wyer, Austin R.; ...

2017-11-23

Neuromorphic computing is non-von Neumann computer architecture for the post Moore’s law era of computing. Since a main focus of the post Moore’s law era is energy-efficient computing with fewer resources and less area, neuromorphic computing contributes effectively in this research. Here in this paper, we present a memristive neuromorphic system for improved power and area efficiency. Our particular mixed-signal approach implements neural networks with spiking events in a synchronous way. Moreover, the use of nano-scale memristive devices saves both area and power in the system. We also provide device-level considerations that make the system more energy-efficient. The proposed systemmore » additionally includes synchronous digital long term plasticity, an online learning methodology that helps the system train the neural networks during the operation phase and improves the efficiency in learning considering the power consumption and area overhead.« less

Memristive Mixed-Signal Neuromorphic Systems: Energy-Efficient Learning at the Circuit-Level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakma, Gangotree; Adnan, Md Musabbir; Wyer, Austin R.

Neuromorphic computing is non-von Neumann computer architecture for the post Moore’s law era of computing. Since a main focus of the post Moore’s law era is energy-efficient computing with fewer resources and less area, neuromorphic computing contributes effectively in this research. Here in this paper, we present a memristive neuromorphic system for improved power and area efficiency. Our particular mixed-signal approach implements neural networks with spiking events in a synchronous way. Moreover, the use of nano-scale memristive devices saves both area and power in the system. We also provide device-level considerations that make the system more energy-efficient. The proposed systemmore » additionally includes synchronous digital long term plasticity, an online learning methodology that helps the system train the neural networks during the operation phase and improves the efficiency in learning considering the power consumption and area overhead.« less

Geospatial Representation, Analysis and Computing Using Bandlimited Functions

DTIC Science & Technology

2010-02-19

navigation of aircraft and missiles require detailed representations of gravity and efficient methods for determining orbits and trajectories. However, many...efficient on today’s computers. Under this grant new, computationally efficient, localized representations of gravity have been developed and tested. As a...step in developing a new approach to estimating gravitational potentials, a multiresolution representation for gravity estimation has been proposed

Efficient Computational Prototyping of Mixed Technology Microfluidic Components and Systems

DTIC Science & Technology

2002-08-01

AFRL-IF-RS-TR-2002-190 Final Technical Report August 2002 EFFICIENT COMPUTATIONAL PROTOTYPING OF MIXED TECHNOLOGY MICROFLUIDIC...SUBTITLE EFFICIENT COMPUTATIONAL PROTOTYPING OF MIXED TECHNOLOGY MICROFLUIDIC COMPONENTS AND SYSTEMS 6. AUTHOR(S) Narayan R. Aluru, Jacob White...Aided Design (CAD) tools for microfluidic components and systems were developed in this effort. Innovative numerical methods and algorithms for mixed

Exact and efficient simulation of concordant computation

NASA Astrophysics Data System (ADS)

Cable, Hugo; Browne, Daniel E.

2015-11-01

Concordant computation is a circuit-based model of quantum computation for mixed states, that assumes that all correlations within the register are discord-free (i.e. the correlations are essentially classical) at every step of the computation. The question of whether concordant computation always admits efficient simulation by a classical computer was first considered by Eastin in arXiv:quant-ph/1006.4402v1, where an answer in the affirmative was given for circuits consisting only of one- and two-qubit gates. Building on this work, we develop the theory of classical simulation of concordant computation. We present a new framework for understanding such computations, argue that a larger class of concordant computations admit efficient simulation, and provide alternative proofs for the main results of arXiv:quant-ph/1006.4402v1 with an emphasis on the exactness of simulation which is crucial for this model. We include detailed analysis of the arithmetic complexity for solving equations in the simulation, as well as extensions to larger gates and qudits. We explore the limitations of our approach, and discuss the challenges faced in developing efficient classical simulation algorithms for all concordant computations.

Efficient computation of the Grünwald-Letnikov fractional diffusion derivative using adaptive time step memory

NASA Astrophysics Data System (ADS)

MacDonald, Christopher L.; Bhattacharya, Nirupama; Sprouse, Brian P.; Silva, Gabriel A.

2015-09-01

Computing numerical solutions to fractional differential equations can be computationally intensive due to the effect of non-local derivatives in which all previous time points contribute to the current iteration. In general, numerical approaches that depend on truncating part of the system history while efficient, can suffer from high degrees of error and inaccuracy. Here we present an adaptive time step memory method for smooth functions applied to the Grünwald-Letnikov fractional diffusion derivative. This method is computationally efficient and results in smaller errors during numerical simulations. Sampled points along the system's history at progressively longer intervals are assumed to reflect the values of neighboring time points. By including progressively fewer points backward in time, a temporally 'weighted' history is computed that includes contributions from the entire past of the system, maintaining accuracy, but with fewer points actually calculated, greatly improving computational efficiency.

Modelling UV irradiances on arbitrarily oriented surfaces: effects of sky obstructions

NASA Astrophysics Data System (ADS)

Hess, M.; Koepke, P.

2008-02-01

A method is presented to calculate UV irradiances on inclined surfaces that additionally takes into account the influence of sky obstructions caused by obstacles such as mountains, houses, trees, or umbrellas. Thus the method allows calculating the impact of UV radiation on biological systems, such as for instance the human skin or eye, in any natural or artificial environment. The method, a combination of radiation models, is explained and the correctness of its results is demonstrated. The effect of a natural skyline is shown for an Alpine ski area, where the UV irradiance even on a horizontal surface may increase due to reflection at snow by more than 10%. In contrast in a street canyon the irradiance on a horizontal surface is reduced down to 30% in shadow and to about 75% for a position in the sun.

Progress made in understanding Mount Rainier's hazards

USGS Publications Warehouse

Sisson, T.W.; Vallance, J.W.; Pringle, P.T.

2001-01-01

At 4392 m high, glacier-clad Mount Rainier dominates the skyline of the southern Puget Sound region and is the centerpiece of Mount Rainier National Park. About 2.5 million people of the greater Seattle-Tacoma metropolitan area can see Mount Rainier on clear days, and 150,000 live in areas swept by lahars and floods that emanated from the volcano during the last 6,000 years (Figure 1). These lahars include the voluminous Osceola Mudflow that floors the lowlands south of Seattle and east of Tacoma, and which was generated by massive volcano flank-collapse. Mount Rainier's last eruption was a light dusting of ash in 1894; minor pumice last erupted between 1820 and 1854; and the most recent large eruptions we know of were about 1100 and 2300 years ago, according to reports from the U.S. Geological Survey.

An efficient algorithm to compute marginal posterior genotype probabilities for every member of a pedigree with loops

PubMed Central

2009-01-01

Background Marginal posterior genotype probabilities need to be computed for genetic analyses such as geneticcounseling in humans and selective breeding in animal and plant species. Methods In this paper, we describe a peeling based, deterministic, exact algorithm to compute efficiently genotype probabilities for every member of a pedigree with loops without recourse to junction-tree methods from graph theory. The efficiency in computing the likelihood by peeling comes from storing intermediate results in multidimensional tables called cutsets. Computing marginal genotype probabilities for individual i requires recomputing the likelihood for each of the possible genotypes of individual i. This can be done efficiently by storing intermediate results in two types of cutsets called anterior and posterior cutsets and reusing these intermediate results to compute the likelihood. Examples A small example is used to illustrate the theoretical concepts discussed in this paper, and marginal genotype probabilities are computed at a monogenic disease locus for every member in a real cattle pedigree. PMID:19958551

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.

High Performance Computing Meets Energy Efficiency - Continuum Magazine |

Science.gov Websites

NREL High Performance Computing Meets Energy Efficiency High Performance Computing Meets Energy turbines. Simulation by Patrick J. Moriarty and Matthew J. Churchfield, NREL The new High Performance Computing Data Center at the National Renewable Energy Laboratory (NREL) hosts high-speed, high-volume data

Propulsive efficiency of frog swimming with different feet and swimming patterns

PubMed Central

Jizhuang, Fan; Wei, Zhang; Bowen, Yuan; Gangfeng, Liu

2017-01-01

ABSTRACT Aquatic and terrestrial animals have different swimming performances and mechanical efficiencies based on their different swimming methods. To explore propulsion in swimming frogs, this study calculated mechanical efficiencies based on data describing aquatic and terrestrial webbed-foot shapes and swimming patterns. First, a simplified frog model and dynamic equation were established, and hydrodynamic forces on the foot were computed according to computational fluid dynamic calculations. Then, a two-link mechanism was used to stand in for the diverse and complicated hind legs found in different frog species, in order to simplify the input work calculation. Joint torques were derived based on the virtual work principle to compute the efficiency of foot propulsion. Finally, two feet and swimming patterns were combined to compute propulsive efficiency. The aquatic frog demonstrated a propulsive efficiency (43.11%) between those of drag-based and lift-based propulsions, while the terrestrial frog efficiency (29.58%) fell within the range of drag-based propulsion. The results illustrate the main factor of swimming patterns for swimming performance and efficiency. PMID:28302669

An efficient formulation of robot arm dynamics for control and computer simulation

NASA Astrophysics Data System (ADS)

Lee, C. S. G.; Nigam, R.

This paper describes an efficient formulation of the dynamic equations of motion of industrial robots based on the Lagrange formulation of d'Alembert's principle. This formulation, as applied to a PUMA robot arm, results in a set of closed form second order differential equations with cross product terms. They are not as efficient in computation as those formulated by the Newton-Euler method, but provide a better analytical model for control analysis and computer simulation. Computational complexities of this dynamic model together with other models are tabulated for discussion.

Correction of Patellofemoral Malalignment With Patellofemoral Arthroplasty.

PubMed

Valoroso, Marco; Saffarini, Mo; La Barbera, Giuseppe; Toanen, Cécile; Hannink, Gerjon; Nover, Luca; Dejour, David H

2017-12-01

The goal of patellofemoral arthroplasty (PFA) is to replace damaged cartilage and correct underlying deformities to reduce pain and prevent maltracking. We aimed to determine how PFA modifies patellar height, tilt, and tibial tuberosity-trochlear groove (TT-TG) distance. The hypothesis was that PFA would correct trochlear dysplasia or extensor mechanism malalignment. The authors prospectively studied a series of 16 patients (13 women and 3 men) aged 64.9 ± 16.3 years (range 41-86 years) who received PFA. All knees were assessed preoperatively and 6 months postoperatively using frontal, lateral, and "skyline" x-rays, and computed tomography scans to calculate patellar tilt, patellar height, and TT-TG distance. The interobserver agreement was excellent for all parameters (intraclass correlation coefficient >0.95). Preoperatively, the median patellar tilt without quadriceps contraction (QC) was 17.5° (range 5.3°-33.4°) and with QC was 19.8° (range 0°-52.0°). The median Caton-Deschamps index was 0.91 (range 0.80-1.22) and TT-TG distance was 14.5 mm (range 4.0-22.0 mm). Postoperatively, the median patellar tilt without QC was 0.3° (range -15.3° to 9.5°) and with QC was 6.1° (range -11.5° to 13.3°). The median Caton-Deschamps index was 1.11 (range 0.81-1.20) and TT-TG distance was 10.1 mm (range 1.8-13.8 mm). The present study demonstrates that beyond replacing arthritic cartilage, trochlear-cutting PFA improves patellofemoral congruence by correcting trochlear dysplasia and standardizing radiological measurements as patellar tilt and TT-TG. The association of lateral patellar facetectomy improves patellar tracking by reducing the patellar tilt. Copyright © 2017 Elsevier Inc. All rights reserved.

Extinction and recolonization of maritime Antarctica in the limpet Nacella concinna (Strebel, 1908) during the last glacial cycle: toward a model of Quaternary biogeography in shallow Antarctic invertebrates.

PubMed

González-Wevar, C A; Saucède, T; Morley, S A; Chown, S L; Poulin, E

2013-10-01

Quaternary glaciations in Antarctica drastically modified geographical ranges and population sizes of marine benthic invertebrates and thus affected the amount and distribution of intraspecific genetic variation. Here, we present new genetic information in the Antarctic limpet Nacella concinna, a dominant Antarctic benthic species along shallow ice-free rocky ecosystems. We examined the patterns of genetic diversity and structure in this broadcast spawner along maritime Antarctica and from the peri-Antarctic island of South Georgia. Genetic analyses showed that N. concinna represents a single panmictic unit in maritime Antarctic. Low levels of genetic diversity characterized this population; its median-joining haplotype network revealed a typical star-like topology with a short genealogy and a dominant haplotype broadly distributed. As previously reported with nuclear markers, we detected significant genetic differentiation between South Georgia Island and maritime Antarctica populations. Higher levels of genetic diversity, a more expanded genealogy and the presence of more private haplotypes support the hypothesis of glacial persistence in this peri-Antarctic island. Bayesian Skyline plot and mismatch distribution analyses recognized an older demographic history in South Georgia. Approximate Bayesian computations did not support the persistence of N. concinna along maritime Antarctica during the last glacial period, but indicated the resilience of the species in peri-Antarctic refugia (South Georgia Island). We proposed a model of Quaternary Biogeography for Antarctic marine benthic invertebrates with shallow and narrow bathymetric ranges including (i) extinction of maritime Antarctic populations during glacial periods; (ii) persistence of populations in peri-Antarctic refugia; and (iii) recolonization of maritime Antarctica following the deglaciation process. © 2013 John Wiley & Sons Ltd.

Comparative phylogeography highlights the double-edged sword of climate change faced by arctic- and alpine-adapted mammals.

PubMed

Lanier, Hayley C; Gunderson, Aren M; Weksler, Marcelo; Fedorov, Vadim B; Olson, Link E

2015-01-01

Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity.

Comparative Phylogeography Highlights the Double-Edged Sword of Climate Change Faced by Arctic- and Alpine-Adapted Mammals

PubMed Central

Lanier, Hayley C.; Gunderson, Aren M.; Weksler, Marcelo; Fedorov, Vadim B.; Olson, Link E.

2015-01-01

Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity. PMID:25734275

Efficient universal blind quantum computation.

PubMed

Giovannetti, Vittorio; Maccone, Lorenzo; Morimae, Tomoyuki; Rudolph, Terry G

2013-12-06

We give a cheat sensitive protocol for blind universal quantum computation that is efficient in terms of computational and communication resources: it allows one party to perform an arbitrary computation on a second party's quantum computer without revealing either which computation is performed, or its input and output. The first party's computational capabilities can be extremely limited: she must only be able to create and measure single-qubit superposition states. The second party is not required to use measurement-based quantum computation. The protocol requires the (optimal) exchange of O(Jlog2(N)) single-qubit states, where J is the computational depth and N is the number of qubits needed for the computation.

Computational efficiency for the surface renewal method

NASA Astrophysics Data System (ADS)

Kelley, Jason; Higgins, Chad

2018-04-01

Measuring surface fluxes using the surface renewal (SR) method requires programmatic algorithms for tabulation, algebraic calculation, and data quality control. A number of different methods have been published describing automated calibration of SR parameters. Because the SR method utilizes high-frequency (10 Hz+) measurements, some steps in the flux calculation are computationally expensive, especially when automating SR to perform many iterations of these calculations. Several new algorithms were written that perform the required calculations more efficiently and rapidly, and that tested for sensitivity to length of flux averaging period, ability to measure over a large range of lag timescales, and overall computational efficiency. These algorithms utilize signal processing techniques and algebraic simplifications that demonstrate simple modifications that dramatically improve computational efficiency. The results here complement efforts by other authors to standardize a robust and accurate computational SR method. Increased speed of computation time grants flexibility to implementing the SR method, opening new avenues for SR to be used in research, for applied monitoring, and in novel field deployments.

Energy Efficiency Challenges of 5G Small Cell Networks.

PubMed

Ge, Xiaohu; Yang, Jing; Gharavi, Hamid; Sun, Yang

2017-05-01

The deployment of a large number of small cells poses new challenges to energy efficiency, which has often been ignored in fifth generation (5G) cellular networks. While massive multiple-input multiple outputs (MIMO) will reduce the transmission power at the expense of higher computational cost, the question remains as to which computation or transmission power is more important in the energy efficiency of 5G small cell networks. Thus, the main objective in this paper is to investigate the computation power based on the Landauer principle. Simulation results reveal that more than 50% of the energy is consumed by the computation power at 5G small cell base stations (BSs). Moreover, the computation power of 5G small cell BS can approach 800 watt when the massive MIMO (e.g., 128 antennas) is deployed to transmit high volume traffic. This clearly indicates that computation power optimization can play a major role in the energy efficiency of small cell networks.

Energy Efficiency Challenges of 5G Small Cell Networks

PubMed Central

Ge, Xiaohu; Yang, Jing; Gharavi, Hamid; Sun, Yang

2017-01-01

The deployment of a large number of small cells poses new challenges to energy efficiency, which has often been ignored in fifth generation (5G) cellular networks. While massive multiple-input multiple outputs (MIMO) will reduce the transmission power at the expense of higher computational cost, the question remains as to which computation or transmission power is more important in the energy efficiency of 5G small cell networks. Thus, the main objective in this paper is to investigate the computation power based on the Landauer principle. Simulation results reveal that more than 50% of the energy is consumed by the computation power at 5G small cell base stations (BSs). Moreover, the computation power of 5G small cell BS can approach 800 watt when the massive MIMO (e.g., 128 antennas) is deployed to transmit high volume traffic. This clearly indicates that computation power optimization can play a major role in the energy efficiency of small cell networks. PMID:28757670

Efficient computation of photonic crystal waveguide modes with dispersive material.

PubMed

Schmidt, Kersten; Kappeler, Roman

2010-03-29

The optimization of PhC waveguides is a key issue for successfully designing PhC devices. Since this design task is computationally expensive, efficient methods are demanded. The available codes for computing photonic bands are also applied to PhC waveguides. They are reliable but not very efficient, which is even more pronounced for dispersive material. We present a method based on higher order finite elements with curved cells, which allows to solve for the band structure taking directly into account the dispersiveness of the materials. This is accomplished by reformulating the wave equations as a linear eigenproblem in the complex wave-vectors k. For this method, we demonstrate the high efficiency for the computation of guided PhC waveguide modes by a convergence analysis.

Analytical prediction with multidimensional computer programs and experimental verification of the performance, at a variety of operating conditions, of two traveling wave tubes with depressed collectors

NASA Technical Reports Server (NTRS)

Dayton, J. A., Jr.; Kosmahl, H. G.; Ramins, P.; Stankiewicz, N.

1979-01-01

Experimental and analytical results are compared for two high performance, octave bandwidth TWT's that use depressed collectors (MDC's) to improve the efficiency. The computations were carried out with advanced, multidimensional computer programs that are described here in detail. These programs model the electron beam as a series of either disks or rings of charge and follow their multidimensional trajectories from the RF input of the ideal TWT, through the slow wave structure, through the magnetic refocusing system, to their points of impact in the depressed collector. Traveling wave tube performance, collector efficiency, and collector current distribution were computed and the results compared with measurements for a number of TWT-MDC systems. Power conservation and correct accounting of TWT and collector losses were observed. For the TWT's operating at saturation, very good agreement was obtained between the computed and measured collector efficiencies. For a TWT operating 3 and 6 dB below saturation, excellent agreement between computed and measured collector efficiencies was obtained in some cases but only fair agreement in others. However, deviations can largely be explained by small differences in the computed and actual spent beam energy distributions. The analytical tools used here appear to be sufficiently refined to design efficient collectors for this class of TWT. However, for maximum efficiency, some experimental optimization (e.g., collector voltages and aperture sizes) will most likely be required.

An efficient and accurate 3D displacements tracking strategy for digital volume correlation

NASA Astrophysics Data System (ADS)

Pan, Bing; Wang, Bo; Wu, Dafang; Lubineau, Gilles

2014-07-01

Owing to its inherent computational complexity, practical implementation of digital volume correlation (DVC) for internal displacement and strain mapping faces important challenges in improving its computational efficiency. In this work, an efficient and accurate 3D displacement tracking strategy is proposed for fast DVC calculation. The efficiency advantage is achieved by using three improvements. First, to eliminate the need of updating Hessian matrix in each iteration, an efficient 3D inverse compositional Gauss-Newton (3D IC-GN) algorithm is introduced to replace existing forward additive algorithms for accurate sub-voxel displacement registration. Second, to ensure the 3D IC-GN algorithm that converges accurately and rapidly and avoid time-consuming integer-voxel displacement searching, a generalized reliability-guided displacement tracking strategy is designed to transfer accurate and complete initial guess of deformation for each calculation point from its computed neighbors. Third, to avoid the repeated computation of sub-voxel intensity interpolation coefficients, an interpolation coefficient lookup table is established for tricubic interpolation. The computational complexity of the proposed fast DVC and the existing typical DVC algorithms are first analyzed quantitatively according to necessary arithmetic operations. Then, numerical tests are performed to verify the performance of the fast DVC algorithm in terms of measurement accuracy and computational efficiency. The experimental results indicate that, compared with the existing DVC algorithm, the presented fast DVC algorithm produces similar precision and slightly higher accuracy at a substantially reduced computational cost.

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

PubMed

Wan, Shixiang; Zou, Quan

2017-01-01

Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene

PubMed Central

Barlow, Axel; Cooper, Alan; Hou, Xin-Dong; Ji, Xue-Ping; Zhong, Bo-Jian; Liu, Hong; Flynn, Lawrence J.; Yuan, Jun-Xia; Wang, Li-Rui; Basler, Nikolas; Westbury, Michael V.; Hofreiter, Michael; Lai, Xu-Long

2018-01-01

The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential. PMID:29642393

Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene.

PubMed

Sheng, Gui-Lian; Barlow, Axel; Cooper, Alan; Hou, Xin-Dong; Ji, Xue-Ping; Jablonski, Nina G; Zhong, Bo-Jian; Liu, Hong; Flynn, Lawrence J; Yuan, Jun-Xia; Wang, Li-Rui; Basler, Nikolas; Westbury, Michael V; Hofreiter, Michael; Lai, Xu-Long

2018-04-06

The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cyt b and 12s rRNA, partial 16s rRNA and ND1 , and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

Efficient computation of hashes

NASA Astrophysics Data System (ADS)

Lopes, Raul H. C.; Franqueira, Virginia N. L.; Hobson, Peter R.

2014-06-01

The sequential computation of hashes at the core of many distributed storage systems and found, for example, in grid services can hinder efficiency in service quality and even pose security challenges that can only be addressed by the use of parallel hash tree modes. The main contributions of this paper are, first, the identification of several efficiency and security challenges posed by the use of sequential hash computation based on the Merkle-Damgard engine. In addition, alternatives for the parallel computation of hash trees are discussed, and a prototype for a new parallel implementation of the Keccak function, the SHA-3 winner, is introduced.

Scientific Discovery through Advanced Computing (SciDAC-3) Partnership Project Annual Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoffman, Forest M.; Bochev, Pavel B.; Cameron-Smith, Philip J..

The Applying Computationally Efficient Schemes for BioGeochemical Cycles ACES4BGC Project is advancing the predictive capabilities of Earth System Models (ESMs) by reducing two of the largest sources of uncertainty, aerosols and biospheric feedbacks, with a highly efficient computational approach. In particular, this project is implementing and optimizing new computationally efficient tracer advection algorithms for large numbers of tracer species; adding important biogeochemical interactions between the atmosphere, land, and ocean models; and applying uncertainty quanti cation (UQ) techniques to constrain process parameters and evaluate uncertainties in feedbacks between biogeochemical cycles and the climate system.

Projected role of advanced computational aerodynamic methods at the Lockheed-Georgia company

NASA Technical Reports Server (NTRS)

Lores, M. E.

1978-01-01

Experience with advanced computational methods being used at the Lockheed-Georgia Company to aid in the evaluation and design of new and modified aircraft indicates that large and specialized computers will be needed to make advanced three-dimensional viscous aerodynamic computations practical. The Numerical Aerodynamic Simulation Facility should be used to provide a tool for designing better aerospace vehicles while at the same time reducing development costs by performing computations using Navier-Stokes equations solution algorithms and permitting less sophisticated but nevertheless complex calculations to be made efficiently. Configuration definition procedures and data output formats can probably best be defined in cooperation with industry, therefore, the computer should handle many remote terminals efficiently. The capability of transferring data to and from other computers needs to be provided. Because of the significant amount of input and output associated with 3-D viscous flow calculations and because of the exceedingly fast computation speed envisioned for the computer, special attention should be paid to providing rapid, diversified, and efficient input and output.

Texture functions in image analysis: A computationally efficient solution

NASA Technical Reports Server (NTRS)

Cox, S. C.; Rose, J. F.

1983-01-01

A computationally efficient means for calculating texture measurements from digital images by use of the co-occurrence technique is presented. The calculation of the statistical descriptors of image texture and a solution that circumvents the need for calculating and storing a co-occurrence matrix are discussed. The results show that existing efficient algorithms for calculating sums, sums of squares, and cross products can be used to compute complex co-occurrence relationships directly from the digital image input.

Robust efficient video fingerprinting

NASA Astrophysics Data System (ADS)

Puri, Manika; Lubin, Jeffrey

2009-02-01

We have developed a video fingerprinting system with robustness and efficiency as the primary and secondary design criteria. In extensive testing, the system has shown robustness to cropping, letter-boxing, sub-titling, blur, drastic compression, frame rate changes, size changes and color changes, as well as to the geometric distortions often associated with camcorder capture in cinema settings. Efficiency is afforded by a novel two-stage detection process in which a fast matching process first computes a number of likely candidates, which are then passed to a second slower process that computes the overall best match with minimal false alarm probability. One key component of the algorithm is a maximally stable volume computation - a three-dimensional generalization of maximally stable extremal regions - that provides a content-centric coordinate system for subsequent hash function computation, independent of any affine transformation or extensive cropping. Other key features include an efficient bin-based polling strategy for initial candidate selection, and a final SIFT feature-based computation for final verification. We describe the algorithm and its performance, and then discuss additional modifications that can provide further improvement to efficiency and accuracy.

Parallel Computation of Unsteady Flows on a Network of Workstations

NASA Technical Reports Server (NTRS)

1997-01-01

Parallel computation of unsteady flows requires significant computational resources. The utilization of a network of workstations seems an efficient solution to the problem where large problems can be treated at a reasonable cost. This approach requires the solution of several problems: 1) the partitioning and distribution of the problem over a network of workstation, 2) efficient communication tools, 3) managing the system efficiently for a given problem. Of course, there is the question of the efficiency of any given numerical algorithm to such a computing system. NPARC code was chosen as a sample for the application. For the explicit version of the NPARC code both two- and three-dimensional problems were studied. Again both steady and unsteady problems were investigated. The issues studied as a part of the research program were: 1) how to distribute the data between the workstations, 2) how to compute and how to communicate at each node efficiently, 3) how to balance the load distribution. In the following, a summary of these activities is presented. Details of the work have been presented and published as referenced.

Modelling UV irradiances on arbitrarily oriented surfaces: effects of sky obstructions

NASA Astrophysics Data System (ADS)

Hess, M.; Koepke, P.

2008-07-01

A method is presented to calculate UV irradiances on inclined surfaces that additionally takes into account the influence of sky obstructions caused by obstacles such as mountains, houses, trees, or umbrellas. With this method it is thus possible to calculate the impact of UV radiation on biological systems, such as, for instance, the human skin or eye, in any natural or artificial environment. The method, which consists of a combination of radiation models, is explained here and the accuracy of its results is demonstrated. The effect of a natural skyline is shown for an Alpine ski area, where the UV irradiance even on a horizontal surface may increase due to reflection from snow by more than 10 percent. In contrast, in a street canyon the irradiance on a horizontal surface is reduced to 30% in shadow and to about 75% for a position in the sun.

Pluto Majestic Mountains, Frozen Plains and Foggy Hazes

NASA Image and Video Library

2015-09-17

Just 15 minutes after its closest approach to Pluto on July 14, 2015, NASA's New Horizons spacecraft looked back toward the sun and captured this near-sunset view of the rugged, icy mountains and flat ice plains extending to Pluto's horizon. The smooth expanse of the informally named icy plain Sputnik Planum (right) is flanked to the west (left) by rugged mountains up to 11,000 feet (3,500 meters) high, including the informally named Norgay Montes in the foreground and Hillary Montes on the skyline. To the right, east of Sputnik, rougher terrain is cut by apparent glaciers. The backlighting highlights more than a dozen layers of haze in Pluto's tenuous but distended atmosphere. The image was taken from a distance of 11,000 miles (18,000 kilometers) to Pluto; the scene is 780 miles (1,250 kilometers) wide. http://photojournal.jpl.nasa.gov/catalog/PIA19948

Population genetic structure of critically endangered salamander (Hynobius amjiensis) in China: recommendations for conservation.

PubMed

Yang, J; Chen, C S; Chen, S H; Ding, P; Fan, Z Y; Lu, Y W; Yu, L P; Lin, H D

2016-06-10

Amji's salamander (Hynobius amjiensis) is a critically endangered species (IUCN Red List), which is endemic to mainland China. In the present study, five haplotypes were genotyped for the mtDNA cyt b gene in 45 specimens from three populations. Relatively low levels of haplotype diversity (h = 0.524) and nucleotide diversity (π = 0.00532) were detected. Analyses of the phylogenic structure of H. amjiensis showed no evidence of major geographic partitions or substantial barriers to historical gene flow throughout the species' range. Two major phylogenetic haplotype groups were revealed, and were estimated to have diverged about 1.262 million years ago. Mismatch distribution analysis, neutrality tests, and Bayesian skyline plots revealed no evidence of dramatic changes in the effective population size. According to the SAMOVA and STRUCTURE analyses, H. amjiensis should be regarded as two different management units.

Computational performance of a smoothed particle hydrodynamics simulation for shared-memory parallel computing

NASA Astrophysics Data System (ADS)

Nishiura, Daisuke; Furuichi, Mikito; Sakaguchi, Hide

2015-09-01

The computational performance of a smoothed particle hydrodynamics (SPH) simulation is investigated for three types of current shared-memory parallel computer devices: many integrated core (MIC) processors, graphics processing units (GPUs), and multi-core CPUs. We are especially interested in efficient shared-memory allocation methods for each chipset, because the efficient data access patterns differ between compute unified device architecture (CUDA) programming for GPUs and OpenMP programming for MIC processors and multi-core CPUs. We first introduce several parallel implementation techniques for the SPH code, and then examine these on our target computer architectures to determine the most effective algorithms for each processor unit. In addition, we evaluate the effective computing performance and power efficiency of the SPH simulation on each architecture, as these are critical metrics for overall performance in a multi-device environment. In our benchmark test, the GPU is found to produce the best arithmetic performance as a standalone device unit, and gives the most efficient power consumption. The multi-core CPU obtains the most effective computing performance. The computational speed of the MIC processor on Xeon Phi approached that of two Xeon CPUs. This indicates that using MICs is an attractive choice for existing SPH codes on multi-core CPUs parallelized by OpenMP, as it gains computational acceleration without the need for significant changes to the source code.

Application of microarray analysis on computer cluster and cloud platforms.

PubMed

Bernau, C; Boulesteix, A-L; Knaus, J

2013-01-01

Analysis of recent high-dimensional biological data tends to be computationally intensive as many common approaches such as resampling or permutation tests require the basic statistical analysis to be repeated many times. A crucial advantage of these methods is that they can be easily parallelized due to the computational independence of the resampling or permutation iterations, which has induced many statistics departments to establish their own computer clusters. An alternative is to rent computing resources in the cloud, e.g. at Amazon Web Services. In this article we analyze whether a selection of statistical projects, recently implemented at our department, can be efficiently realized on these cloud resources. Moreover, we illustrate an opportunity to combine computer cluster and cloud resources. In order to compare the efficiency of computer cluster and cloud implementations and their respective parallelizations we use microarray analysis procedures and compare their runtimes on the different platforms. Amazon Web Services provide various instance types which meet the particular needs of the different statistical projects we analyzed in this paper. Moreover, the network capacity is sufficient and the parallelization is comparable in efficiency to standard computer cluster implementations. Our results suggest that many statistical projects can be efficiently realized on cloud resources. It is important to mention, however, that workflows can change substantially as a result of a shift from computer cluster to cloud computing.

Dynamic Load-Balancing for Distributed Heterogeneous Computing of Parallel CFD Problems

NASA Technical Reports Server (NTRS)

Ecer, A.; Chien, Y. P.; Boenisch, T.; Akay, H. U.

2000-01-01

The developed methodology is aimed at improving the efficiency of executing block-structured algorithms on parallel, distributed, heterogeneous computers. The basic approach of these algorithms is to divide the flow domain into many sub- domains called blocks, and solve the governing equations over these blocks. Dynamic load balancing problem is defined as the efficient distribution of the blocks among the available processors over a period of several hours of computations. In environments with computers of different architecture, operating systems, CPU speed, memory size, load, and network speed, balancing the loads and managing the communication between processors becomes crucial. Load balancing software tools for mutually dependent parallel processes have been created to efficiently utilize an advanced computation environment and algorithms. These tools are dynamic in nature because of the chances in the computer environment during execution time. More recently, these tools were extended to a second operating system: NT. In this paper, the problems associated with this application will be discussed. Also, the developed algorithms were combined with the load sharing capability of LSF to efficiently utilize workstation clusters for parallel computing. Finally, results will be presented on running a NASA based code ADPAC to demonstrate the developed tools for dynamic load balancing.

Efficient conjugate gradient algorithms for computation of the manipulator forward dynamics

NASA Technical Reports Server (NTRS)

Fijany, Amir; Scheid, Robert E.

1989-01-01

The applicability of conjugate gradient algorithms for computation of the manipulator forward dynamics is investigated. The redundancies in the previously proposed conjugate gradient algorithm are analyzed. A new version is developed which, by avoiding these redundancies, achieves a significantly greater efficiency. A preconditioned conjugate gradient algorithm is also presented. A diagonal matrix whose elements are the diagonal elements of the inertia matrix is proposed as the preconditioner. In order to increase the computational efficiency, an algorithm is developed which exploits the synergism between the computation of the diagonal elements of the inertia matrix and that required by the conjugate gradient algorithm.

Least squares QR-based decomposition provides an efficient way of computing optimal regularization parameter in photoacoustic tomography.

PubMed

Shaw, Calvin B; Prakash, Jaya; Pramanik, Manojit; Yalavarthy, Phaneendra K

2013-08-01

A computationally efficient approach that computes the optimal regularization parameter for the Tikhonov-minimization scheme is developed for photoacoustic imaging. This approach is based on the least squares-QR decomposition which is a well-known dimensionality reduction technique for a large system of equations. It is shown that the proposed framework is effective in terms of quantitative and qualitative reconstructions of initial pressure distribution enabled via finding an optimal regularization parameter. The computational efficiency and performance of the proposed method are shown using a test case of numerical blood vessel phantom, where the initial pressure is exactly known for quantitative comparison.

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.

I/O-Efficient Scientific Computation Using TPIE

NASA Technical Reports Server (NTRS)

Vengroff, Darren Erik; Vitter, Jeffrey Scott

1996-01-01

In recent years, input/output (I/O)-efficient algorithms for a wide variety of problems have appeared in the literature. However, systems specifically designed to assist programmers in implementing such algorithms have remained scarce. TPIE is a system designed to support I/O-efficient paradigms for problems from a variety of domains, including computational geometry, graph algorithms, and scientific computation. The TPIE interface frees programmers from having to deal not only with explicit read and write calls, but also the complex memory management that must be performed for I/O-efficient computation. In this paper we discuss applications of TPIE to problems in scientific computation. We discuss algorithmic issues underlying the design and implementation of the relevant components of TPIE and present performance results of programs written to solve a series of benchmark problems using our current TPIE prototype. Some of the benchmarks we present are based on the NAS parallel benchmarks while others are of our own creation. We demonstrate that the central processing unit (CPU) overhead required to manage I/O is small and that even with just a single disk, the I/O overhead of I/O-efficient computation ranges from negligible to the same order of magnitude as CPU time. We conjecture that if we use a number of disks in parallel this overhead can be all but eliminated.

Computer-Based Learning: Interleaving Whole and Sectional Representation of Neuroanatomy

ERIC Educational Resources Information Center

Pani, John R.; Chariker, Julia H.; Naaz, Farah

2013-01-01

The large volume of material to be learned in biomedical disciplines requires optimizing the efficiency of instruction. In prior work with computer-based instruction of neuroanatomy, it was relatively efficient for learners to master whole anatomy and then transfer to learning sectional anatomy. It may, however, be more efficient to continuously…

Gradient gravitational search: An efficient metaheuristic algorithm for global optimization.

PubMed

Dash, Tirtharaj; Sahu, Prabhat K

2015-05-30

The adaptation of novel techniques developed in the field of computational chemistry to solve the concerned problems for large and flexible molecules is taking the center stage with regard to efficient algorithm, computational cost and accuracy. In this article, the gradient-based gravitational search (GGS) algorithm, using analytical gradients for a fast minimization to the next local minimum has been reported. Its efficiency as metaheuristic approach has also been compared with Gradient Tabu Search and others like: Gravitational Search, Cuckoo Search, and Back Tracking Search algorithms for global optimization. Moreover, the GGS approach has also been applied to computational chemistry problems for finding the minimal value potential energy of two-dimensional and three-dimensional off-lattice protein models. The simulation results reveal the relative stability and physical accuracy of protein models with efficient computational cost. © 2015 Wiley Periodicals, Inc.

Efficient convolutional sparse coding

DOEpatents

Wohlberg, Brendt

2017-06-20

Computationally efficient algorithms may be applied for fast dictionary learning solving the convolutional sparse coding problem in the Fourier domain. More specifically, efficient convolutional sparse coding may be derived within an alternating direction method of multipliers (ADMM) framework that utilizes fast Fourier transforms (FFT) to solve the main linear system in the frequency domain. Such algorithms may enable a significant reduction in computational cost over conventional approaches by implementing a linear solver for the most critical and computationally expensive component of the conventional iterative algorithm. The theoretical computational cost of the algorithm may be reduced from O(M.sup.3N) to O(MN log N), where N is the dimensionality of the data and M is the number of elements in the dictionary. This significant improvement in efficiency may greatly increase the range of problems that can practically be addressed via convolutional sparse representations.

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists

PubMed Central

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

3-D Perspective View, Kamchatka Peninsula, Russia

NASA Technical Reports Server (NTRS)

2000-01-01

This perspective view shows the western side of the volcanically active Kamchatka Peninsula in eastern Russia. The image was generated using the first data collected during the Shuttle Radar Topography Mission (SRTM). In the foreground is the Sea of Okhotsk. Inland from the coast, vegetated floodplains and low relief hills rise toward snow capped peaks. The topographic effects on snow and vegetation distribution are very clear in this near-horizontal view. Forming the skyline is the Sredinnyy Khrebet, the volcanic mountain range that makes up the spine of the peninsula. High resolution SRTM topographic data will be used by geologists to study how volcanoes form and to understand the hazards posed by future eruptions.

This image was generated using topographic data from SRTM and an enhanced true-color image from the Landsat 7 satellite. This image contains about 2,400 meters (7,880 feet) of total relief. The topographic expression was enhanced by adding artificial shading as calculated from the SRTM elevation model. The Landsat data was provided by the United States Geological Survey's Earth Resources Observations Systems (EROS) Data Center, Sioux Falls, South Dakota.

SRTM, launched on February 11, 2000, used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar(SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. To collect the 3-D SRTM data, engineers added a 60-meter-long (200-foot) mast, installed additional C-band and X-band antennas, and improved tracking and navigation devices. SRTM collected three-dimensional measurements of nearly 80 percent of the Earth's surface. SRTM is a cooperative project between NASA, the National Imagery and Mapping Agency (NIMA) of the U.S. Department of Defense, and the German and Italian space agencies. It is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Earth Science Enterprise, Washington, D.C.

Size: 33.3 km (20.6 miles) wide x 136 km (84 miles) coast to skyline Location: 58.3 deg. North lat., 160 deg. East long. Orientation: Easterly view, 2 degrees down from horizontal Original Data Resolution: 30 meters (99 feet) Vertical Exaggeration: 3 times Date Acquired: February 12, 2000 (SRTM) August 1, 1999 (Landsat) Image: NASA/JPL/NIMA

Graeco-Roman Astro-Architecture: The Temples of Pompeii

NASA Astrophysics Data System (ADS)

Tiede, Vance R.

2014-01-01

Roman architect Marcus Vetruvius Pollio (ca. 75-15 BC) wrote, “[O]ne who professes himself as an architect should be…acquainted with astronomy and the theory of the heavens…. From astronomy we find the east, west, south, and north, as well as the theory of the heavens, the Equinox, Solstice and courses of the Stars.” (De Architectura Libri Decem I:i:3,10). In order to investigate the role of astronomy in temple orientation, the author conducted a preliminary GIS DEM/Satellite Imaging survey of 11 temples at Pompeii, Italy (N 40d 45', E 14d 29'). The GIS survey measured the true azimuth and horizon altitude of each temple’s major axis and was field checked by a Ground Truth survey with theodolite and GPS, 5-18 April 2013. The resulting 3D vector data was analyzed with Program STONEHENGE (Hawkins 1983, 328) to identify the local skyline declinations aligned with the temple major axes. Analysis suggests that the major axes of the temples of Apollo, Jupiter and Venus are equally as likely to have been oriented to Pompeii’s urban grid, itself oriented NW-SE on Mt. Vesuvius’ slope and hydraulic gradient to optimize urban sewer/street drainage (cf. Hodge 1992). However, the remaining nine temples appear to be oriented to astronomical targets on the local horizon associated with Graeco-Roman calendrics and mythology. TEMPLE/ DATE/ MAJOR AXIS ASTRO-TARGET (Skyline Declination in degrees) Public Lares/AD 50/ Cross-Quarter 7 Nov/3 Feb Sun Set, Last Gleam (-16.5) Vespsian/ AD 69-79/ Cross-Quarter 7 Nov/3 Feb Sun Set, LG (-16.2) Fortuna Augusta/ AD 1/ Winter Solstice Sun Set, LG (-22.9) Aesculapius/ 100 BC/ Perseus Rise (β Persei-Algol = +33.0) & Midsummer Moon Major Stand Still Set, LG (-28.1) Isis/ 100 BC/ Midwinter Moon Major Stand Still Rise, Tangent (+28.5) & Equinox Sun Set, Tangent (-0.3) Jupiter/ 150 BC/ Θ Scorpionis-Sargas Rise (-38.0) Apollo/ 550 (rebuilt 70 BC)/ α Columbae-Phact Rise (-37.1) Venus/ 150 BC (rebuilt 70 BC)/ α Columbae-Phact Rise (-37.7) Ceres/ 250 BC/ Midsummer Moon Major Stand Still Set, LG (-27.9) Dioysyus/ 250 BC/ Equinox Sun Set, LG (+0.3) Doric/ 550 BC/ β Orionis-Rigel Rise (-14.6)

Efficiently modeling neural networks on massively parallel computers

NASA Technical Reports Server (NTRS)

Farber, Robert M.

1993-01-01

Neural networks are a very useful tool for analyzing and modeling complex real world systems. Applying neural network simulations to real world problems generally involves large amounts of data and massive amounts of computation. To efficiently handle the computational requirements of large problems, we have implemented at Los Alamos a highly efficient neural network compiler for serial computers, vector computers, vector parallel computers, and fine grain SIMD computers such as the CM-2 connection machine. This paper describes the mapping used by the compiler to implement feed-forward backpropagation neural networks for a SIMD (Single Instruction Multiple Data) architecture parallel computer. Thinking Machines Corporation has benchmarked our code at 1.3 billion interconnects per second (approximately 3 gigaflops) on a 64,000 processor CM-2 connection machine (Singer 1990). This mapping is applicable to other SIMD computers and can be implemented on MIMD computers such as the CM-5 connection machine. Our mapping has virtually no communications overhead with the exception of the communications required for a global summation across the processors (which has a sub-linear runtime growth on the order of O(log(number of processors)). We can efficiently model very large neural networks which have many neurons and interconnects and our mapping can extend to arbitrarily large networks (within memory limitations) by merging the memory space of separate processors with fast adjacent processor interprocessor communications. This paper will consider the simulation of only feed forward neural network although this method is extendable to recurrent networks.

Efficient and Flexible Computation of Many-Electron Wave Function Overlaps.

PubMed

Plasser, Felix; Ruckenbauer, Matthias; Mai, Sebastian; Oppel, Markus; Marquetand, Philipp; González, Leticia

2016-03-08

A new algorithm for the computation of the overlap between many-electron wave functions is described. This algorithm allows for the extensive use of recurring intermediates and thus provides high computational efficiency. Because of the general formalism employed, overlaps can be computed for varying wave function types, molecular orbitals, basis sets, and molecular geometries. This paves the way for efficiently computing nonadiabatic interaction terms for dynamics simulations. In addition, other application areas can be envisaged, such as the comparison of wave functions constructed at different levels of theory. Aside from explaining the algorithm and evaluating the performance, a detailed analysis of the numerical stability of wave function overlaps is carried out, and strategies for overcoming potential severe pitfalls due to displaced atoms and truncated wave functions are presented.

A POSTERIORI ERROR ANALYSIS OF TWO STAGE COMPUTATION METHODS WITH APPLICATION TO EFFICIENT DISCRETIZATION AND THE PARAREAL ALGORITHM.

PubMed

Chaudhry, Jehanzeb Hameed; Estep, Don; Tavener, Simon; Carey, Varis; Sandelin, Jeff

2016-01-01

We consider numerical methods for initial value problems that employ a two stage approach consisting of solution on a relatively coarse discretization followed by solution on a relatively fine discretization. Examples include adaptive error control, parallel-in-time solution schemes, and efficient solution of adjoint problems for computing a posteriori error estimates. We describe a general formulation of two stage computations then perform a general a posteriori error analysis based on computable residuals and solution of an adjoint problem. The analysis accommodates various variations in the two stage computation and in formulation of the adjoint problems. We apply the analysis to compute "dual-weighted" a posteriori error estimates, to develop novel algorithms for efficient solution that take into account cancellation of error, and to the Parareal Algorithm. We test the various results using several numerical examples.

Developing an Efficient Computational Method that Estimates the Ability of Students in a Web-Based Learning Environment

ERIC Educational Resources Information Center

Lee, Young-Jin

2012-01-01

This paper presents a computational method that can efficiently estimate the ability of students from the log files of a Web-based learning environment capturing their problem solving processes. The computational method developed in this study approximates the posterior distribution of the student's ability obtained from the conventional Bayes…

Development of a Compact Eleven Feed Cryostat for the Patriot 12-m Antenna System

NASA Technical Reports Server (NTRS)

Beaudoin, Christopher; Kildal, Per-Simon; Yang, Jian; Pantaleev, Miroslav

2010-01-01

The Eleven antenna has constant beam width, constant phase center location, and low spillover over a decade bandwidth. Therefore, it can feed a reflector for high aperture efficiency (also called feed efficiency). It is equally important that the feed efficiency and its subefficiencies not be degraded significantly by installing the feed in a cryostat. The MIT Haystack Observatory, with guidance from Onsala Space Observatory and Chalmers University, has been working to integrate the Eleven antenna into a compact cryostat suitable for the Patriot 12-m antenna. Since the analysis of the feed efficiencies in this presentation is purely computational, we first demonstrate the validity of the computed results by comparing them to measurements. Subsequently, we analyze the dependence of the cryostat size on the feed efficiencies, and, lastly, the Patriot 12-m subreflector is incorporated into the computational model to assess the overall broadband efficiency of the antenna system.

Determination of efficiency of an aged HPGe detector for gaseous sources by self absorption correction and point source methods

NASA Astrophysics Data System (ADS)

Sarangapani, R.; Jose, M. T.; Srinivasan, T. K.; Venkatraman, B.

2017-07-01

Methods for the determination of efficiency of an aged high purity germanium (HPGe) detector for gaseous sources have been presented in the paper. X-ray radiography of the detector has been performed to get detector dimensions for computational purposes. The dead layer thickness of HPGe detector has been ascertained from experiments and Monte Carlo computations. Experimental work with standard point and liquid sources in several cylindrical geometries has been undertaken for obtaining energy dependant efficiency. Monte Carlo simulations have been performed for computing efficiencies for point, liquid and gaseous sources. Self absorption correction factors have been obtained using mathematical equations for volume sources and MCNP simulations. Self-absorption correction and point source methods have been used to estimate the efficiency for gaseous sources. The efficiencies determined from the present work have been used to estimate activity of cover gas sample of a fast reactor.

Efficiency of including first-generation information in second-generation ranking and selection: results of computer simulation.

Treesearch

T.Z. Ye; K.J.S. Jayawickrama; G.R. Johnson

2006-01-01

Using computer simulation, we evaluated the impact of using first-generation information to increase selection efficiency in a second-generation breeding program. Selection efficiency was compared in terms of increase in rank correlation between estimated and true breeding values (i.e., ranking accuracy), reduction in coefficient of variation of correlation...

High-Performance Computing Data Center Efficiency Dashboard | Computational

Science.gov Websites

recovery water (ERW) loop Heat exchanger for energy recovery Thermosyphon Heat exchanger between ERW loop and cooling tower loop Evaporative cooling towers Learn more about our energy-efficient facility

Parallel implementation of geometrical shock dynamics for two dimensional converging shock waves

NASA Astrophysics Data System (ADS)

Qiu, Shi; Liu, Kuang; Eliasson, Veronica

2016-10-01

Geometrical shock dynamics (GSD) theory is an appealing method to predict the shock motion in the sense that it is more computationally efficient than solving the traditional Euler equations, especially for converging shock waves. However, to solve and optimize large scale configurations, the main bottleneck is the computational cost. Among the existing numerical GSD schemes, there is only one that has been implemented on parallel computers, with the purpose to analyze detonation waves. To extend the computational advantage of the GSD theory to more general applications such as converging shock waves, a numerical implementation using a spatial decomposition method has been coupled with a front tracking approach on parallel computers. In addition, an efficient tridiagonal system solver for massively parallel computers has been applied to resolve the most expensive function in this implementation, resulting in an efficiency of 0.93 while using 32 HPCC cores. Moreover, symmetric boundary conditions have been developed to further reduce the computational cost, achieving a speedup of 19.26 for a 12-sided polygonal converging shock.

An Initial Multi-Domain Modeling of an Actively Cooled Structure

NASA Technical Reports Server (NTRS)

Steinthorsson, Erlendur

1997-01-01

A methodology for the simulation of turbine cooling flows is being developed. The methodology seeks to combine numerical techniques that optimize both accuracy and computational efficiency. Key components of the methodology include the use of multiblock grid systems for modeling complex geometries, and multigrid convergence acceleration for enhancing computational efficiency in highly resolved fluid flow simulations. The use of the methodology has been demonstrated in several turbo machinery flow and heat transfer studies. Ongoing and future work involves implementing additional turbulence models, improving computational efficiency, adding AMR.

Efficient calibration for imperfect computer models

DOE PAGES

Tuo, Rui; Wu, C. F. Jeff

2015-12-01

Many computer models contain unknown parameters which need to be estimated using physical observations. Furthermore, the calibration method based on Gaussian process models may lead to unreasonable estimate for imperfect computer models. In this work, we extend their study to calibration problems with stochastic physical data. We propose a novel method, called the L 2 calibration, and show its semiparametric efficiency. The conventional method of the ordinary least squares is also studied. Theoretical analysis shows that it is consistent but not efficient. Here, numerical examples show that the proposed method outperforms the existing ones.

Research related to improved computer aided design software package. [comparative efficiency of finite, boundary, and hybrid element methods in elastostatics

NASA Technical Reports Server (NTRS)

Walston, W. H., Jr.

1986-01-01

The comparative computational efficiencies of the finite element (FEM), boundary element (BEM), and hybrid boundary element-finite element (HVFEM) analysis techniques are evaluated for representative bounded domain interior and unbounded domain exterior problems in elastostatics. Computational efficiency is carefully defined in this study as the computer time required to attain a specified level of solution accuracy. The study found the FEM superior to the BEM for the interior problem, while the reverse was true for the exterior problem. The hybrid analysis technique was found to be comparable or superior to both the FEM and BEM for both the interior and exterior problems.

A Simple and Resource-efficient Setup for the Computer-aided Drug Design Laboratory.

PubMed

Moretti, Loris; Sartori, Luca

2016-10-01

Undertaking modelling investigations for Computer-Aided Drug Design (CADD) requires a proper environment. In principle, this could be done on a single computer, but the reality of a drug discovery program requires robustness and high-throughput computing (HTC) to efficiently support the research. Therefore, a more capable alternative is needed but its implementation has no widespread solution. Here, the realization of such a computing facility is discussed, from general layout to technical details all aspects are covered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secure Multiparty Quantum Computation for Summation and Multiplication.

PubMed

Shi, Run-hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2016-01-21

As a fundamental primitive, Secure Multiparty Summation and Multiplication can be used to build complex secure protocols for other multiparty computations, specially, numerical computations. However, there is still lack of systematical and efficient quantum methods to compute Secure Multiparty Summation and Multiplication. In this paper, we present a novel and efficient quantum approach to securely compute the summation and multiplication of multiparty private inputs, respectively. Compared to classical solutions, our proposed approach can ensure the unconditional security and the perfect privacy protection based on the physical principle of quantum mechanics.

Secure Multiparty Quantum Computation for Summation and Multiplication

PubMed Central

Shi, Run-hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2016-01-01

As a fundamental primitive, Secure Multiparty Summation and Multiplication can be used to build complex secure protocols for other multiparty computations, specially, numerical computations. However, there is still lack of systematical and efficient quantum methods to compute Secure Multiparty Summation and Multiplication. In this paper, we present a novel and efficient quantum approach to securely compute the summation and multiplication of multiparty private inputs, respectively. Compared to classical solutions, our proposed approach can ensure the unconditional security and the perfect privacy protection based on the physical principle of quantum mechanics. PMID:26792197

Parallel Domain Decomposition Formulation and Software for Large-Scale Sparse Symmetrical/Unsymmetrical Aeroacoustic Applications

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Watson, Willie R. (Technical Monitor)

2005-01-01

The overall objectives of this research work are to formulate and validate efficient parallel algorithms, and to efficiently design/implement computer software for solving large-scale acoustic problems, arised from the unified frameworks of the finite element procedures. The adopted parallel Finite Element (FE) Domain Decomposition (DD) procedures should fully take advantages of multiple processing capabilities offered by most modern high performance computing platforms for efficient parallel computation. To achieve this objective. the formulation needs to integrate efficient sparse (and dense) assembly techniques, hybrid (or mixed) direct and iterative equation solvers, proper pre-conditioned strategies, unrolling strategies, and effective processors' communicating schemes. Finally, the numerical performance of the developed parallel finite element procedures will be evaluated by solving series of structural, and acoustic (symmetrical and un-symmetrical) problems (in different computing platforms). Comparisons with existing "commercialized" and/or "public domain" software are also included, whenever possible.

An approximate solution to improve computational efficiency of impedance-type payload load prediction

NASA Technical Reports Server (NTRS)

White, C. W.

1981-01-01

The computational efficiency of the impedance type loads prediction method was studied. Three goals were addressed: devise a method to make the impedance method operate more efficiently in the computer; assess the accuracy and convenience of the method for determining the effect of design changes; and investigate the use of the method to identify design changes for reduction of payload loads. The method is suitable for calculation of dynamic response in either the frequency or time domain. It is concluded that: the choice of an orthogonal coordinate system will allow the impedance method to operate more efficiently in the computer; the approximate mode impedance technique is adequate for determining the effect of design changes, and is applicable for both statically determinate and statically indeterminate payload attachments; and beneficial design changes to reduce payload loads can be identified by the combined application of impedance techniques and energy distribution review techniques.

Efficient modeling of vector hysteresis using a novel Hopfield neural network implementation of Stoner–Wohlfarth-like operators

PubMed Central

Adly, Amr A.; Abd-El-Hafiz, Salwa K.

2012-01-01

Incorporation of hysteresis models in electromagnetic analysis approaches is indispensable to accurate field computation in complex magnetic media. Throughout those computations, vector nature and computational efficiency of such models become especially crucial when sophisticated geometries requiring massive sub-region discretization are involved. Recently, an efficient vector Preisach-type hysteresis model constructed from only two scalar models having orthogonally coupled elementary operators has been proposed. This paper presents a novel Hopfield neural network approach for the implementation of Stoner–Wohlfarth-like operators that could lead to a significant enhancement in the computational efficiency of the aforementioned model. Advantages of this approach stem from the non-rectangular nature of these operators that substantially minimizes the number of operators needed to achieve an accurate vector hysteresis model. Details of the proposed approach, its identification and experimental testing are presented in the paper. PMID:25685446

Entanglement negativity bounds for fermionic Gaussian states

NASA Astrophysics Data System (ADS)

Eisert, Jens; Eisler, Viktor; Zimborás, Zoltán

2018-04-01

The entanglement negativity is a versatile measure of entanglement that has numerous applications in quantum information and in condensed matter theory. It can not only efficiently be computed in the Hilbert space dimension, but for noninteracting bosonic systems, one can compute the negativity efficiently in the number of modes. However, such an efficient computation does not carry over to the fermionic realm, the ultimate reason for this being that the partial transpose of a fermionic Gaussian state is no longer Gaussian. To provide a remedy for this state of affairs, in this work, we introduce efficiently computable and rigorous upper and lower bounds to the negativity, making use of techniques of semidefinite programming, building upon the Lagrangian formulation of fermionic linear optics, and exploiting suitable products of Gaussian operators. We discuss examples in quantum many-body theory and hint at applications in the study of topological properties at finite temperature.

HPC on Competitive Cloud Resources

NASA Astrophysics Data System (ADS)

Bientinesi, Paolo; Iakymchuk, Roman; Napper, Jeff

Computing as a utility has reached the mainstream. Scientists can now easily rent time on large commercial clusters that can be expanded and reduced on-demand in real-time. However, current commercial cloud computing performance falls short of systems specifically designed for scientific applications. Scientific computing needs are quite different from those of the web applications that have been the focus of cloud computing vendors. In this chapter we demonstrate through empirical evaluation the computational efficiency of high-performance numerical applications in a commercial cloud environment when resources are shared under high contention. Using the Linpack benchmark as a case study, we show that cache utilization becomes highly unpredictable and similarly affects computation time. For some problems, not only is it more efficient to underutilize resources, but the solution can be reached sooner in realtime (wall-time). We also show that the smallest, cheapest (64-bit) instance on the studied environment is the best for price to performance ration. In light of the high-contention we witness, we believe that alternative definitions of efficiency for commercial cloud environments should be introduced where strong performance guarantees do not exist. Concepts like average, expected performance and execution time, expected cost to completion, and variance measures--traditionally ignored in the high-performance computing context--now should complement or even substitute the standard definitions of efficiency.

A synthetic visual plane algorithm for visibility computation in consideration of accuracy and efficiency

NASA Astrophysics Data System (ADS)

Yu, Jieqing; Wu, Lixin; Hu, Qingsong; Yan, Zhigang; Zhang, Shaoliang

2017-12-01

Visibility computation is of great interest to location optimization, environmental planning, ecology, and tourism. Many algorithms have been developed for visibility computation. In this paper, we propose a novel method of visibility computation, called synthetic visual plane (SVP), to achieve better performance with respect to efficiency, accuracy, or both. The method uses a global horizon, which is a synthesis of line-of-sight information of all nearer points, to determine the visibility of a point, which makes it an accurate visibility method. We used discretization of horizon to gain a good performance in efficiency. After discretization, the accuracy and efficiency of SVP depends on the scale of discretization (i.e., zone width). The method is more accurate at smaller zone widths, but this requires a longer operating time. Users must strike a balance between accuracy and efficiency at their discretion. According to our experiments, SVP is less accurate but more efficient than R2 if the zone width is set to one grid. However, SVP becomes more accurate than R2 when the zone width is set to 1/24 grid, while it continues to perform as fast or faster than R2. Although SVP performs worse than reference plane and depth map with respect to efficiency, it is superior in accuracy to these other two algorithms.

Green's function methods in heavy ion shielding

NASA Technical Reports Server (NTRS)

Wilson, John W.; Costen, Robert C.; Shinn, Judy L.; Badavi, Francis F.

1993-01-01

An analytic solution to the heavy ion transport in terms of Green's function is used to generate a highly efficient computer code for space applications. The efficiency of the computer code is accomplished by a nonperturbative technique extending Green's function over the solution domain. The computer code can also be applied to accelerator boundary conditions to allow code validation in laboratory experiments.

Application of the MacCormack scheme to overland flow routing for high-spatial resolution distributed hydrological model

NASA Astrophysics Data System (ADS)

Zhang, Ling; Nan, Zhuotong; Liang, Xu; Xu, Yi; Hernández, Felipe; Li, Lianxia

2018-03-01

Although process-based distributed hydrological models (PDHMs) are evolving rapidly over the last few decades, their extensive applications are still challenged by the computational expenses. This study attempted, for the first time, to apply the numerically efficient MacCormack algorithm to overland flow routing in a representative high-spatial resolution PDHM, i.e., the distributed hydrology-soil-vegetation model (DHSVM), in order to improve its computational efficiency. The analytical verification indicates that both the semi and full versions of the MacCormack schemes exhibit robust numerical stability and are more computationally efficient than the conventional explicit linear scheme. The full-version outperforms the semi-version in terms of simulation accuracy when a same time step is adopted. The semi-MacCormack scheme was implemented into DHSVM (version 3.1.2) to solve the kinematic wave equations for overland flow routing. The performance and practicality of the enhanced DHSVM-MacCormack model was assessed by performing two groups of modeling experiments in the Mercer Creek watershed, a small urban catchment near Bellevue, Washington. The experiments show that DHSVM-MacCormack can considerably improve the computational efficiency without compromising the simulation accuracy of the original DHSVM model. More specifically, with the same computational environment and model settings, the computational time required by DHSVM-MacCormack can be reduced to several dozen minutes for a simulation period of three months (in contrast with one day and a half by the original DHSVM model) without noticeable sacrifice of the accuracy. The MacCormack scheme proves to be applicable to overland flow routing in DHSVM, which implies that it can be coupled into other PHDMs for watershed routing to either significantly improve their computational efficiency or to make the kinematic wave routing for high resolution modeling computational feasible.

Cost Considerations in Nonlinear Finite-Element Computing

NASA Technical Reports Server (NTRS)

Utku, S.; Melosh, R. J.; Islam, M.; Salama, M.

1985-01-01

Conference paper discusses computational requirements for finiteelement analysis using quasi-linear approach to nonlinear problems. Paper evaluates computational efficiency of different computer architecturtural types in terms of relative cost and computing time.

Enhancing battery efficiency for pervasive health-monitoring systems based on electronic textiles.

PubMed

Zheng, Nenggan; Wu, Zhaohui; Lin, Man; Yang, Laurence Tianruo

2010-03-01

Electronic textiles are regarded as one of the most important computation platforms for future computer-assisted health-monitoring applications. In these novel systems, multiple batteries are used in order to prolong their operational lifetime, which is a significant metric for system usability. However, due to the nonlinear features of batteries, computing systems with multiple batteries cannot achieve the same battery efficiency as those powered by a monolithic battery of equal capacity. In this paper, we propose an algorithm aiming to maximize battery efficiency globally for the computer-assisted health-care systems with multiple batteries. Based on an accurate analytical battery model, the concept of weighted battery fatigue degree is introduced and the novel battery-scheduling algorithm called predicted weighted fatigue degree least first (PWFDLF) is developed. Besides, we also discuss our attempts during search PWFDLF: a weighted round-robin (WRR) and a greedy algorithm achieving highest local battery efficiency, which reduces to the sequential discharging policy. Evaluation results show that a considerable improvement in battery efficiency can be obtained by PWFDLF under various battery configurations and current profiles compared to conventional sequential and WRR discharging policies.

Fuel Injector Design Optimization for an Annular Scramjet Geometry

NASA Technical Reports Server (NTRS)

Steffen, Christopher J., Jr.

2003-01-01

A four-parameter, three-level, central composite experiment design has been used to optimize the configuration of an annular scramjet injector geometry using computational fluid dynamics. The computational fluid dynamic solutions played the role of computer experiments, and response surface methodology was used to capture the simulation results for mixing efficiency and total pressure recovery within the scramjet flowpath. An optimization procedure, based upon the response surface results of mixing efficiency, was used to compare the optimal design configuration against the target efficiency value of 92.5%. The results of three different optimization procedures are presented and all point to the need to look outside the current design space for different injector geometries that can meet or exceed the stated mixing efficiency target.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

PubMed

Duan, Lili; Liu, Xiao; Zhang, John Z H

2016-05-04

Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

[Economic efficiency of computer monitoring of health].

PubMed

Il'icheva, N P; Stazhadze, L L

2001-01-01

Presents the method of computer monitoring of health, based on utilization of modern information technologies in public health. The method helps organize preventive activities of an outpatient clinic at a high level and essentially decrease the time and money loss. Efficiency of such preventive measures, increased number of computer and Internet users suggests that such methods are promising and further studies in this field are needed.

ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING: APPLICATION OF COMPUTATIONAL BIOPHYSICAL TRANSPORT, COMPUTATIONAL CHEMISTRY, AND COMPUTATIONAL BIOLOGY

EPA Science Inventory

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...

Computing Interactions Of Free-Space Radiation With Matter

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Cucinotta, F. A.; Shinn, J. L.; Townsend, L. W.; Badavi, F. F.; Tripathi, R. K.; Silberberg, R.; Tsao, C. H.; Badwar, G. D.

1995-01-01

High Charge and Energy Transport (HZETRN) computer program computationally efficient, user-friendly package of software adressing problem of transport of, and shielding against, radiation in free space. Designed as "black box" for design engineers not concerned with physics of underlying atomic and nuclear radiation processes in free-space environment, but rather primarily interested in obtaining fast and accurate dosimetric information for design and construction of modules and devices for use in free space. Computational efficiency achieved by unique algorithm based on deterministic approach to solution of Boltzmann equation rather than computationally intensive statistical Monte Carlo method. Written in FORTRAN.

Computational strategies for three-dimensional flow simulations on distributed computer systems. Ph.D. Thesis Semiannual Status Report, 15 Aug. 1993 - 15 Feb. 1994

NASA Technical Reports Server (NTRS)

Weed, Richard Allen; Sankar, L. N.

1994-01-01

An increasing amount of research activity in computational fluid dynamics has been devoted to the development of efficient algorithms for parallel computing systems. The increasing performance to price ratio of engineering workstations has led to research to development procedures for implementing a parallel computing system composed of distributed workstations. This thesis proposal outlines an ongoing research program to develop efficient strategies for performing three-dimensional flow analysis on distributed computing systems. The PVM parallel programming interface was used to modify an existing three-dimensional flow solver, the TEAM code developed by Lockheed for the Air Force, to function as a parallel flow solver on clusters of workstations. Steady flow solutions were generated for three different wing and body geometries to validate the code and evaluate code performance. The proposed research will extend the parallel code development to determine the most efficient strategies for unsteady flow simulations.

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data

PubMed Central

Serang, Oliver; MacCoss, Michael J.; Noble, William Stafford

2010-01-01

The problem of identifying proteins from a shotgun proteomics experiment has not been definitively solved. Identifying the proteins in a sample requires ranking them, ideally with interpretable scores. In particular, “degenerate” peptides, which map to multiple proteins, have made such a ranking difficult to compute. The problem of computing posterior probabilities for the proteins, which can be interpreted as confidence in a protein’s presence, has been especially daunting. Previous approaches have either ignored the peptide degeneracy problem completely, addressed it by computing a heuristic set of proteins or heuristic posterior probabilities, or by estimating the posterior probabilities with sampling methods. We present a probabilistic model for protein identification in tandem mass spectrometry that recognizes peptide degeneracy. We then introduce graph-transforming algorithms that facilitate efficient computation of protein probabilities, even for large data sets. We evaluate our identification procedure on five different well-characterized data sets and demonstrate our ability to efficiently compute high-quality protein posteriors. PMID:20712337

Efficient path-based computations on pedigree graphs with compact encodings

PubMed Central

2012-01-01

A pedigree is a diagram of family relationships, and it is often used to determine the mode of inheritance (dominant, recessive, etc.) of genetic diseases. Along with rapidly growing knowledge of genetics and accumulation of genealogy information, pedigree data is becoming increasingly important. In large pedigree graphs, path-based methods for efficiently computing genealogical measurements, such as inbreeding and kinship coefficients of individuals, depend on efficient identification and processing of paths. In this paper, we propose a new compact path encoding scheme on large pedigrees, accompanied by an efficient algorithm for identifying paths. We demonstrate the utilization of our proposed method by applying it to the inbreeding coefficient computation. We present time and space complexity analysis, and also manifest the efficiency of our method for evaluating inbreeding coefficients as compared to previous methods by experimental results using pedigree graphs with real and synthetic data. Both theoretical and experimental results demonstrate that our method is more scalable and efficient than previous methods in terms of time and space requirements. PMID:22536898

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

PubMed

Thijssen, Bram; Dijkstra, Tjeerd M H; Heskes, Tom; Wessels, Lodewyk F A

2016-10-21

Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calculating Bayesian statistical estimates are computationally demanding, and each algorithm has unique advantages and disadvantages. It is typically unclear, before starting an analysis, which algorithm will perform well on a given computational model. We present BCM, a toolkit for the Bayesian analysis of Computational Models using samplers. It provides efficient, multithreaded implementations of eleven algorithms for sampling from posterior probability distributions and for calculating marginal likelihoods. BCM includes tools to simplify the process of model specification and scripts for visualizing the results. The flexible architecture allows it to be used on diverse types of biological computational models. In an example inference task using a model of the cell cycle based on ordinary differential equations, BCM is significantly more efficient than existing software packages, allowing more challenging inference problems to be solved. BCM represents an efficient one-stop-shop for computational modelers wishing to use sampler-based Bayesian statistics.

Efficient computation of kinship and identity coefficients on large pedigrees.

PubMed

Cheng, En; Elliott, Brendan; Ozsoyoglu, Z Meral

2009-06-01

With the rapidly expanding field of medical genetics and genetic counseling, genealogy information is becoming increasingly abundant. An important computation on pedigree data is the calculation of identity coefficients, which provide a complete description of the degree of relatedness of a pair of individuals. The areas of application of identity coefficients are numerous and diverse, from genetic counseling to disease tracking, and thus, the computation of identity coefficients merits special attention. However, the computation of identity coefficients is not done directly, but rather as the final step after computing a set of generalized kinship coefficients. In this paper, we first propose a novel Path-Counting Formula for calculating generalized kinship coefficients, which is motivated by Wright's path-counting method for computing inbreeding coefficient. We then present an efficient and scalable scheme for calculating generalized kinship coefficients on large pedigrees using NodeCodes, a special encoding scheme for expediting the evaluation of queries on pedigree graph structures. Furthermore, we propose an improved scheme using Family NodeCodes for the computation of generalized kinship coefficients, which is motivated by the significant improvement of using Family NodeCodes for inbreeding coefficient over the use of NodeCodes. We also perform experiments for evaluating the efficiency of our method, and compare it with the performance of the traditional recursive algorithm for three individuals. Experimental results demonstrate that the resulting scheme is more scalable and efficient than the traditional recursive methods for computing generalized kinship coefficients.

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads.

PubMed

Stone, John E; Hallock, Michael J; Phillips, James C; Peterson, Joseph R; Luthey-Schulten, Zaida; Schulten, Klaus

2016-05-01

Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers.

Technical Note: scuda: A software platform for cumulative dose assessment.

PubMed

Park, Seyoun; McNutt, Todd; Plishker, William; Quon, Harry; Wong, John; Shekhar, Raj; Lee, Junghoon

2016-10-01

Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (scuda) that can be seamlessly integrated into the clinical workflow. scuda consists of deformable image registration (DIR), segmentation, dose computation modules, and a graphical user interface. It is connected to our image PACS and radiotherapy informatics databases from which it automatically queries/retrieves patient images, radiotherapy plan, beam data, and daily treatment information, thus providing an efficient and unified workflow. For accurate registration of the planning CT and daily CBCTs, the authors iteratively correct CBCT intensities by matching local intensity histograms during the DIR process. Contours of the target tumor and critical structures are then propagated from the planning CT to daily CBCTs using the computed deformations. The actual delivered daily dose is computed using the registered CT and patient setup information by a superposition/convolution algorithm, and accumulated using the computed deformation fields. Both DIR and dose computation modules are accelerated by a graphics processing unit. The cumulative dose computation process has been validated on 30 head and neck (HN) cancer cases, showing 3.5 ± 5.0 Gy (mean±STD) absolute mean dose differences between the planned and the actually delivered doses in the parotid glands. On average, DIR, dose computation, and segmentation take 20 s/fraction and 17 min for a 35-fraction treatment including additional computation for dose accumulation. The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.

Technical Note: SCUDA: A software platform for cumulative dose assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Seyoun; McNutt, Todd; Quon, Harry

Purpose: Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (SCUDA) that can be seamlessly integrated into the clinical workflow. Methods: SCUDA consists of deformable image registration (DIR), segmentation, dose computation modules, and a graphical user interface. It is connected to our imagemore » PACS and radiotherapy informatics databases from which it automatically queries/retrieves patient images, radiotherapy plan, beam data, and daily treatment information, thus providing an efficient and unified workflow. For accurate registration of the planning CT and daily CBCTs, the authors iteratively correct CBCT intensities by matching local intensity histograms during the DIR process. Contours of the target tumor and critical structures are then propagated from the planning CT to daily CBCTs using the computed deformations. The actual delivered daily dose is computed using the registered CT and patient setup information by a superposition/convolution algorithm, and accumulated using the computed deformation fields. Both DIR and dose computation modules are accelerated by a graphics processing unit. Results: The cumulative dose computation process has been validated on 30 head and neck (HN) cancer cases, showing 3.5 ± 5.0 Gy (mean±STD) absolute mean dose differences between the planned and the actually delivered doses in the parotid glands. On average, DIR, dose computation, and segmentation take 20 s/fraction and 17 min for a 35-fraction treatment including additional computation for dose accumulation. Conclusions: The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.« less

Analog synthetic biology.

PubMed

Sarpeshkar, R

2014-03-28

We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.

Analog synthetic biology

PubMed Central

Sarpeshkar, R.

2014-01-01

We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog–digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA–protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations. PMID:24567476

Spin-neurons: A possible path to energy-efficient neuromorphic computers

NASA Astrophysics Data System (ADS)

Sharad, Mrigank; Fan, Deliang; Roy, Kaushik

2013-12-01

Recent years have witnessed growing interest in the field of brain-inspired computing based on neural-network architectures. In order to translate the related algorithmic models into powerful, yet energy-efficient cognitive-computing hardware, computing-devices beyond CMOS may need to be explored. The suitability of such devices to this field of computing would strongly depend upon how closely their physical characteristics match with the essential computing primitives employed in such models. In this work, we discuss the rationale of applying emerging spin-torque devices for bio-inspired computing. Recent spin-torque experiments have shown the path to low-current, low-voltage, and high-speed magnetization switching in nano-scale magnetic devices. Such magneto-metallic, current-mode spin-torque switches can mimic the analog summing and "thresholding" operation of an artificial neuron with high energy-efficiency. Comparison with CMOS-based analog circuit-model of a neuron shows that "spin-neurons" (spin based circuit model of neurons) can achieve more than two orders of magnitude lower energy and beyond three orders of magnitude reduction in energy-delay product. The application of spin-neurons can therefore be an attractive option for neuromorphic computers of future.

Spin-neurons: A possible path to energy-efficient neuromorphic computers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharad, Mrigank; Fan, Deliang; Roy, Kaushik

Recent years have witnessed growing interest in the field of brain-inspired computing based on neural-network architectures. In order to translate the related algorithmic models into powerful, yet energy-efficient cognitive-computing hardware, computing-devices beyond CMOS may need to be explored. The suitability of such devices to this field of computing would strongly depend upon how closely their physical characteristics match with the essential computing primitives employed in such models. In this work, we discuss the rationale of applying emerging spin-torque devices for bio-inspired computing. Recent spin-torque experiments have shown the path to low-current, low-voltage, and high-speed magnetization switching in nano-scale magnetic devices.more » Such magneto-metallic, current-mode spin-torque switches can mimic the analog summing and “thresholding” operation of an artificial neuron with high energy-efficiency. Comparison with CMOS-based analog circuit-model of a neuron shows that “spin-neurons” (spin based circuit model of neurons) can achieve more than two orders of magnitude lower energy and beyond three orders of magnitude reduction in energy-delay product. The application of spin-neurons can therefore be an attractive option for neuromorphic computers of future.« less

Computation of unsteady transonic aerodynamics with steady state fixed by truncation error injection

NASA Technical Reports Server (NTRS)

Fung, K.-Y.; Fu, J.-K.

1985-01-01

A novel technique is introduced for efficient computations of unsteady transonic aerodynamics. The steady flow corresponding to body shape is maintained by truncation error injection while the perturbed unsteady flows corresponding to unsteady body motions are being computed. This allows the use of different grids comparable to the characteristic length scales of the steady and unsteady flows and, hence, allows efficient computation of the unsteady perturbations. An example of typical unsteady computation of flow over a supercritical airfoil shows that substantial savings in computation time and storage without loss of solution accuracy can easily be achieved. This technique is easy to apply and requires very few changes to existing codes.

A parallel computing engine for a class of time critical processes.

PubMed

Nabhan, T M; Zomaya, A Y

1997-01-01

This paper focuses on the efficient parallel implementation of systems of numerically intensive nature over loosely coupled multiprocessor architectures. These analytical models are of significant importance to many real-time systems that have to meet severe time constants. A parallel computing engine (PCE) has been developed in this work for the efficient simplification and the near optimal scheduling of numerical models over the different cooperating processors of the parallel computer. First, the analytical system is efficiently coded in its general form. The model is then simplified by using any available information (e.g., constant parameters). A task graph representing the interconnections among the different components (or equations) is generated. The graph can then be compressed to control the computation/communication requirements. The task scheduler employs a graph-based iterative scheme, based on the simulated annealing algorithm, to map the vertices of the task graph onto a Multiple-Instruction-stream Multiple-Data-stream (MIMD) type of architecture. The algorithm uses a nonanalytical cost function that properly considers the computation capability of the processors, the network topology, the communication time, and congestion possibilities. Moreover, the proposed technique is simple, flexible, and computationally viable. The efficiency of the algorithm is demonstrated by two case studies with good results.

A flexible and accurate digital volume correlation method applicable to high-resolution volumetric images

NASA Astrophysics Data System (ADS)

Pan, Bing; Wang, Bo

2017-10-01

Digital volume correlation (DVC) is a powerful technique for quantifying interior deformation within solid opaque materials and biological tissues. In the last two decades, great efforts have been made to improve the accuracy and efficiency of the DVC algorithm. However, there is still a lack of a flexible, robust and accurate version that can be efficiently implemented in personal computers with limited RAM. This paper proposes an advanced DVC method that can realize accurate full-field internal deformation measurement applicable to high-resolution volume images with up to billions of voxels. Specifically, a novel layer-wise reliability-guided displacement tracking strategy combined with dynamic data management is presented to guide the DVC computation from slice to slice. The displacements at specified calculation points in each layer are computed using the advanced 3D inverse-compositional Gauss-Newton algorithm with the complete initial guess of the deformation vector accurately predicted from the computed calculation points. Since only limited slices of interest in the reference and deformed volume images rather than the whole volume images are required, the DVC calculation can thus be efficiently implemented on personal computers. The flexibility, accuracy and efficiency of the presented DVC approach are demonstrated by analyzing computer-simulated and experimentally obtained high-resolution volume images.

Multiphysics Computational Analysis of a Solid-Core Nuclear Thermal Engine Thrust Chamber

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Canabal, Francisco; Cheng, Gary; Chen, Yen-Sen

2007-01-01

The objective of this effort is to develop an efficient and accurate computational heat transfer methodology to predict thermal, fluid, and hydrogen environments for a hypothetical solid-core, nuclear thermal engine - the Small Engine. In addition, the effects of power profile and hydrogen conversion on heat transfer efficiency and thrust performance were also investigated. The computational methodology is based on an unstructured-grid, pressure-based, all speeds, chemically reacting, computational fluid dynamics platform, while formulations of conjugate heat transfer were implemented to describe the heat transfer from solid to hydrogen inside the solid-core reactor. The computational domain covers the entire thrust chamber so that the afore-mentioned heat transfer effects impact the thrust performance directly. The result shows that the computed core-exit gas temperature, specific impulse, and core pressure drop agree well with those of design data for the Small Engine. Finite-rate chemistry is very important in predicting the proper energy balance as naturally occurring hydrogen decomposition is endothermic. Locally strong hydrogen conversion associated with centralized power profile gives poor heat transfer efficiency and lower thrust performance. On the other hand, uniform hydrogen conversion associated with a more uniform radial power profile achieves higher heat transfer efficiency, and higher thrust performance.

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.

PubMed

Drawert, Brian; Lawson, Michael J; Petzold, Linda; Khammash, Mustafa

2010-02-21

We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.

Dendritic Properties Control Energy Efficiency of Action Potentials in Cortical Pyramidal Cells

PubMed Central

Yi, Guosheng; Wang, Jiang; Wei, Xile; Deng, Bin

2017-01-01

Neural computation is performed by transforming input signals into sequences of action potentials (APs), which is metabolically expensive and limited by the energy available to the brain. The metabolic efficiency of single AP has important consequences for the computational power of the cell, which is determined by its biophysical properties and morphologies. Here we adopt biophysically-based two-compartment models to investigate how dendrites affect energy efficiency of APs in cortical pyramidal neurons. We measure the Na+ entry during the spike and examine how it is efficiently used for generating AP depolarization. We show that increasing the proportion of dendritic area or coupling conductance between two chambers decreases Na+ entry efficiency of somatic AP. Activating inward Ca2+ current in dendrites results in dendritic spike, which increases AP efficiency. Activating Ca2+-activated outward K+ current in dendrites, however, decreases Na+ entry efficiency. We demonstrate that the active and passive dendrites take effects by altering the overlap between Na+ influx and internal current flowing from soma to dendrite. We explain a fundamental link between dendritic properties and AP efficiency, which is essential to interpret how neural computation consumes metabolic energy and how biophysics and morphologies contribute to such consumption. PMID:28919852

Dendritic Properties Control Energy Efficiency of Action Potentials in Cortical Pyramidal Cells.

PubMed

Yi, Guosheng; Wang, Jiang; Wei, Xile; Deng, Bin

2017-01-01

Neural computation is performed by transforming input signals into sequences of action potentials (APs), which is metabolically expensive and limited by the energy available to the brain. The metabolic efficiency of single AP has important consequences for the computational power of the cell, which is determined by its biophysical properties and morphologies. Here we adopt biophysically-based two-compartment models to investigate how dendrites affect energy efficiency of APs in cortical pyramidal neurons. We measure the Na + entry during the spike and examine how it is efficiently used for generating AP depolarization. We show that increasing the proportion of dendritic area or coupling conductance between two chambers decreases Na + entry efficiency of somatic AP. Activating inward Ca 2+ current in dendrites results in dendritic spike, which increases AP efficiency. Activating Ca 2+ -activated outward K + current in dendrites, however, decreases Na + entry efficiency. We demonstrate that the active and passive dendrites take effects by altering the overlap between Na + influx and internal current flowing from soma to dendrite. We explain a fundamental link between dendritic properties and AP efficiency, which is essential to interpret how neural computation consumes metabolic energy and how biophysics and morphologies contribute to such consumption.

Computer-based learning: interleaving whole and sectional representation of neuroanatomy.

PubMed

Pani, John R; Chariker, Julia H; Naaz, Farah

2013-01-01

The large volume of material to be learned in biomedical disciplines requires optimizing the efficiency of instruction. In prior work with computer-based instruction of neuroanatomy, it was relatively efficient for learners to master whole anatomy and then transfer to learning sectional anatomy. It may, however, be more efficient to continuously integrate learning of whole and sectional anatomy. A study of computer-based learning of neuroanatomy was conducted to compare a basic transfer paradigm for learning whole and sectional neuroanatomy with a method in which the two forms of representation were interleaved (alternated). For all experimental groups, interactive computer programs supported an approach to instruction called adaptive exploration. Each learning trial consisted of time-limited exploration of neuroanatomy, self-timed testing, and graphical feedback. The primary result of this study was that interleaved learning of whole and sectional neuroanatomy was more efficient than the basic transfer method, without cost to long-term retention or generalization of knowledge to recognizing new images (Visible Human and MRI). Copyright © 2012 American Association of Anatomists.

Convolutional networks for fast, energy-efficient neuromorphic computing

PubMed Central

Esser, Steven K.; Merolla, Paul A.; Arthur, John V.; Cassidy, Andrew S.; Appuswamy, Rathinakumar; Andreopoulos, Alexander; Berg, David J.; McKinstry, Jeffrey L.; Melano, Timothy; Barch, Davis R.; di Nolfo, Carmelo; Datta, Pallab; Amir, Arnon; Taba, Brian; Flickner, Myron D.; Modha, Dharmendra S.

2016-01-01

Deep networks are now able to achieve human-level performance on a broad spectrum of recognition tasks. Independently, neuromorphic computing has now demonstrated unprecedented energy-efficiency through a new chip architecture based on spiking neurons, low precision synapses, and a scalable communication network. Here, we demonstrate that neuromorphic computing, despite its novel architectural primitives, can implement deep convolution networks that (i) approach state-of-the-art classification accuracy across eight standard datasets encompassing vision and speech, (ii) perform inference while preserving the hardware’s underlying energy-efficiency and high throughput, running on the aforementioned datasets at between 1,200 and 2,600 frames/s and using between 25 and 275 mW (effectively >6,000 frames/s per Watt), and (iii) can be specified and trained using backpropagation with the same ease-of-use as contemporary deep learning. This approach allows the algorithmic power of deep learning to be merged with the efficiency of neuromorphic processors, bringing the promise of embedded, intelligent, brain-inspired computing one step closer. PMID:27651489

Convolutional networks for fast, energy-efficient neuromorphic computing.

PubMed

Esser, Steven K; Merolla, Paul A; Arthur, John V; Cassidy, Andrew S; Appuswamy, Rathinakumar; Andreopoulos, Alexander; Berg, David J; McKinstry, Jeffrey L; Melano, Timothy; Barch, Davis R; di Nolfo, Carmelo; Datta, Pallab; Amir, Arnon; Taba, Brian; Flickner, Myron D; Modha, Dharmendra S

2016-10-11

Deep networks are now able to achieve human-level performance on a broad spectrum of recognition tasks. Independently, neuromorphic computing has now demonstrated unprecedented energy-efficiency through a new chip architecture based on spiking neurons, low precision synapses, and a scalable communication network. Here, we demonstrate that neuromorphic computing, despite its novel architectural primitives, can implement deep convolution networks that (i) approach state-of-the-art classification accuracy across eight standard datasets encompassing vision and speech, (ii) perform inference while preserving the hardware's underlying energy-efficiency and high throughput, running on the aforementioned datasets at between 1,200 and 2,600 frames/s and using between 25 and 275 mW (effectively >6,000 frames/s per Watt), and (iii) can be specified and trained using backpropagation with the same ease-of-use as contemporary deep learning. This approach allows the algorithmic power of deep learning to be merged with the efficiency of neuromorphic processors, bringing the promise of embedded, intelligent, brain-inspired computing one step closer.

Positive Wigner functions render classical simulation of quantum computation efficient.

PubMed

Mari, A; Eisert, J

2012-12-07

We show that quantum circuits where the initial state and all the following quantum operations can be represented by positive Wigner functions can be classically efficiently simulated. This is true both for continuous-variable as well as discrete variable systems in odd prime dimensions, two cases which will be treated on entirely the same footing. Noting the fact that Clifford and Gaussian operations preserve the positivity of the Wigner function, our result generalizes the Gottesman-Knill theorem. Our algorithm provides a way of sampling from the output distribution of a computation or a simulation, including the efficient sampling from an approximate output distribution in the case of sampling imperfections for initial states, gates, or measurements. In this sense, this work highlights the role of the positive Wigner function as separating classically efficiently simulable systems from those that are potentially universal for quantum computing and simulation, and it emphasizes the role of negativity of the Wigner function as a computational resource.

Computer-Based Learning: Interleaving Whole and Sectional Representation of Neuroanatomy

PubMed Central

Pani, John R.; Chariker, Julia H.; Naaz, Farah

2015-01-01

The large volume of material to be learned in biomedical disciplines requires optimizing the efficiency of instruction. In prior work with computer-based instruction of neuroanatomy, it was relatively efficient for learners to master whole anatomy and then transfer to learning sectional anatomy. It may, however, be more efficient to continuously integrate learning of whole and sectional anatomy. A study of computer-based learning of neuroanatomy was conducted to compare a basic transfer paradigm for learning whole and sectional neuroanatomy with a method in which the two forms of representation were interleaved (alternated). For all experimental groups, interactive computer programs supported an approach to instruction called adaptive exploration. Each learning trial consisted of time-limited exploration of neuroanatomy, self-timed testing, and graphical feedback. The primary result of this study was that interleaved learning of whole and sectional neuroanatomy was more efficient than the basic transfer method, without cost to long-term retention or generalization of knowledge to recognizing new images (Visible Human and MRI). PMID:22761001

CFD Analysis and Design Optimization Using Parallel Computers

NASA Technical Reports Server (NTRS)

Martinelli, Luigi; Alonso, Juan Jose; Jameson, Antony; Reuther, James

1997-01-01

A versatile and efficient multi-block method is presented for the simulation of both steady and unsteady flow, as well as aerodynamic design optimization of complete aircraft configurations. The compressible Euler and Reynolds Averaged Navier-Stokes (RANS) equations are discretized using a high resolution scheme on body-fitted structured meshes. An efficient multigrid implicit scheme is implemented for time-accurate flow calculations. Optimum aerodynamic shape design is achieved at very low cost using an adjoint formulation. The method is implemented on parallel computing systems using the MPI message passing interface standard to ensure portability. The results demonstrate that, by combining highly efficient algorithms with parallel computing, it is possible to perform detailed steady and unsteady analysis as well as automatic design for complex configurations using the present generation of parallel computers.

Energy 101: Energy Efficient Data Centers

ScienceCinema

None

2018-04-16

Data centers provide mission-critical computing functions vital to the daily operation of top U.S. economic, scientific, and technological organizations. These data centers consume large amounts of energy to run and maintain their computer systems, servers, and associated high-performance components—up to 3% of all U.S. electricity powers data centers. And as more information comes online, data centers will consume even more energy. Data centers can become more energy efficient by incorporating features like power-saving "stand-by" modes, energy monitoring software, and efficient cooling systems instead of energy-intensive air conditioners. These and other efficiency improvements to data centers can produce significant energy savings, reduce the load on the electric grid, and help protect the nation by increasing the reliability of critical computer operations.

Smart integrated microsystems: the energy efficiency challenge (Conference Presentation) (Plenary Presentation)

NASA Astrophysics Data System (ADS)

Benini, Luca

2017-06-01

The "internet of everything" envisions trillions of connected objects loaded with high-bandwidth sensors requiring massive amounts of local signal processing, fusion, pattern extraction and classification. From the computational viewpoint, the challenge is formidable and can be addressed only by pushing computing fabrics toward massive parallelism and brain-like energy efficiency levels. CMOS technology can still take us a long way toward this goal, but technology scaling is losing steam. Energy efficiency improvement will increasingly hinge on architecture, circuits, design techniques such as heterogeneous 3D integration, mixed-signal preprocessing, event-based approximate computing and non-Von-Neumann architectures for scalable acceleration.

An Adaptive Evolutionary Algorithm for Traveling Salesman Problem with Precedence Constraints

PubMed Central

Sung, Jinmo; Jeong, Bongju

2014-01-01

Traveling sales man problem with precedence constraints is one of the most notorious problems in terms of the efficiency of its solution approach, even though it has very wide range of industrial applications. We propose a new evolutionary algorithm to efficiently obtain good solutions by improving the search process. Our genetic operators guarantee the feasibility of solutions over the generations of population, which significantly improves the computational efficiency even when it is combined with our flexible adaptive searching strategy. The efficiency of the algorithm is investigated by computational experiments. PMID:24701158

An adaptive evolutionary algorithm for traveling salesman problem with precedence constraints.

PubMed

Sung, Jinmo; Jeong, Bongju

2014-01-01

Traveling sales man problem with precedence constraints is one of the most notorious problems in terms of the efficiency of its solution approach, even though it has very wide range of industrial applications. We propose a new evolutionary algorithm to efficiently obtain good solutions by improving the search process. Our genetic operators guarantee the feasibility of solutions over the generations of population, which significantly improves the computational efficiency even when it is combined with our flexible adaptive searching strategy. The efficiency of the algorithm is investigated by computational experiments.

Interhemispheric Resource Sharing: Decreasing Benefits with Increasing Processing Efficiency

ERIC Educational Resources Information Center

Maertens, M.; Pollmann, S.

2005-01-01

Visual matches are sometimes faster when stimuli are presented across visual hemifields, compared to within-field matching. Using a cued geometric figure matching task, we investigated the influence of computational complexity vs. processing efficiency on this bilateral distribution advantage (BDA). Computational complexity was manipulated by…

The Improvement of Efficiency in the Numerical Computation of Orbit Trajectories

NASA Technical Reports Server (NTRS)

Dyer, J.; Danchick, R.; Pierce, S.; Haney, R.

1972-01-01

An analysis, system design, programming, and evaluation of results are described for numerical computation of orbit trajectories. Evaluation of generalized methods, interaction of different formulations for satellite motion, transformation of equations of motion and integrator loads, and development of efficient integrators are also considered.

Framework for computationally efficient optimal irrigation scheduling using ant colony optimization

USDA-ARS?s Scientific Manuscript database

A general optimization framework is introduced with the overall goal of reducing search space size and increasing the computational efficiency of evolutionary algorithm application for optimal irrigation scheduling. The framework achieves this goal by representing the problem in the form of a decisi...

DANoC: An Efficient Algorithm and Hardware Codesign of Deep Neural Networks on Chip.

PubMed

Zhou, Xichuan; Li, Shengli; Tang, Fang; Hu, Shengdong; Lin, Zhi; Zhang, Lei

2017-07-18

Deep neural networks (NNs) are the state-of-the-art models for understanding the content of images and videos. However, implementing deep NNs in embedded systems is a challenging task, e.g., a typical deep belief network could exhaust gigabytes of memory and result in bandwidth and computational bottlenecks. To address this challenge, this paper presents an algorithm and hardware codesign for efficient deep neural computation. A hardware-oriented deep learning algorithm, named the deep adaptive network, is proposed to explore the sparsity of neural connections. By adaptively removing the majority of neural connections and robustly representing the reserved connections using binary integers, the proposed algorithm could save up to 99.9% memory utility and computational resources without undermining classification accuracy. An efficient sparse-mapping-memory-based hardware architecture is proposed to fully take advantage of the algorithmic optimization. Different from traditional Von Neumann architecture, the deep-adaptive network on chip (DANoC) brings communication and computation in close proximity to avoid power-hungry parameter transfers between on-board memory and on-chip computational units. Experiments over different image classification benchmarks show that the DANoC system achieves competitively high accuracy and efficiency comparing with the state-of-the-art approaches.

Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-03-01

Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

Computer-intensive simulation of solid-state NMR experiments using SIMPSON.

PubMed

Tošner, Zdeněk; Andersen, Rasmus; Stevensson, Baltzar; Edén, Mattias; Nielsen, Niels Chr; Vosegaard, Thomas

2014-09-01

Conducting large-scale solid-state NMR simulations requires fast computer software potentially in combination with efficient computational resources to complete within a reasonable time frame. Such simulations may involve large spin systems, multiple-parameter fitting of experimental spectra, or multiple-pulse experiment design using parameter scan, non-linear optimization, or optimal control procedures. To efficiently accommodate such simulations, we here present an improved version of the widely distributed open-source SIMPSON NMR simulation software package adapted to contemporary high performance hardware setups. The software is optimized for fast performance on standard stand-alone computers, multi-core processors, and large clusters of identical nodes. We describe the novel features for fast computation including internal matrix manipulations, propagator setups and acquisition strategies. For efficient calculation of powder averages, we implemented interpolation method of Alderman, Solum, and Grant, as well as recently introduced fast Wigner transform interpolation technique. The potential of the optimal control toolbox is greatly enhanced by higher precision gradients in combination with the efficient optimization algorithm known as limited memory Broyden-Fletcher-Goldfarb-Shanno. In addition, advanced parallelization can be used in all types of calculations, providing significant time reductions. SIMPSON is thus reflecting current knowledge in the field of numerical simulations of solid-state NMR experiments. The efficiency and novel features are demonstrated on the representative simulations. Copyright © 2014 Elsevier Inc. All rights reserved.

Heterogeneous High Throughput Scientific Computing with APM X-Gene and Intel Xeon Phi

NASA Astrophysics Data System (ADS)

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; Eulisse, Giulio; Knight, Robert; Muzaffar, Shahzad

2015-05-01

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. We report our experience on software porting, performance and energy efficiency and evaluate the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).

Efficient implementation of multidimensional fast fourier transform on a distributed-memory parallel multi-node computer

DOEpatents

Bhanot, Gyan V [Princeton, NJ; Chen, Dong [Croton-On-Hudson, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Steinmacher-Burow, Burkhard D [Mount Kisco, NY; Vranas, Pavlos M [Bedford Hills, NY

2012-01-10

The present in invention is directed to a method, system and program storage device for efficiently implementing a multidimensional Fast Fourier Transform (FFT) of a multidimensional array comprising a plurality of elements initially distributed in a multi-node computer system comprising a plurality of nodes in communication over a network, comprising: distributing the plurality of elements of the array in a first dimension across the plurality of nodes of the computer system over the network to facilitate a first one-dimensional FFT; performing the first one-dimensional FFT on the elements of the array distributed at each node in the first dimension; re-distributing the one-dimensional FFT-transformed elements at each node in a second dimension via "all-to-all" distribution in random order across other nodes of the computer system over the network; and performing a second one-dimensional FFT on elements of the array re-distributed at each node in the second dimension, wherein the random order facilitates efficient utilization of the network thereby efficiently implementing the multidimensional FFT. The "all-to-all" re-distribution of array elements is further efficiently implemented in applications other than the multidimensional FFT on the distributed-memory parallel supercomputer.

Efficient implementation of a multidimensional fast fourier transform on a distributed-memory parallel multi-node computer

DOEpatents

Bhanot, Gyan V [Princeton, NJ; Chen, Dong [Croton-On-Hudson, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Steinmacher-Burow, Burkhard D [Mount Kisco, NY; Vranas, Pavlos M [Bedford Hills, NY

2008-01-01

The present in invention is directed to a method, system and program storage device for efficiently implementing a multidimensional Fast Fourier Transform (FFT) of a multidimensional array comprising a plurality of elements initially distributed in a multi-node computer system comprising a plurality of nodes in communication over a network, comprising: distributing the plurality of elements of the array in a first dimension across the plurality of nodes of the computer system over the network to facilitate a first one-dimensional FFT; performing the first one-dimensional FFT on the elements of the array distributed at each node in the first dimension; re-distributing the one-dimensional FFT-transformed elements at each node in a second dimension via "all-to-all" distribution in random order across other nodes of the computer system over the network; and performing a second one-dimensional FFT on elements of the array re-distributed at each node in the second dimension, wherein the random order facilitates efficient utilization of the network thereby efficiently implementing the multidimensional FFT. The "all-to-all" re-distribution of array elements is further efficiently implemented in applications other than the multidimensional FFT on the distributed-memory parallel supercomputer.

Edge-Based Efficient Search over Encrypted Data Mobile Cloud Storage

PubMed Central

Liu, Fang; Cai, Zhiping; Xiao, Nong; Zhao, Ziming

2018-01-01

Smart sensor-equipped mobile devices sense, collect, and process data generated by the edge network to achieve intelligent control, but such mobile devices usually have limited storage and computing resources. Mobile cloud storage provides a promising solution owing to its rich storage resources, great accessibility, and low cost. But it also brings a risk of information leakage. The encryption of sensitive data is the basic step to resist the risk. However, deploying a high complexity encryption and decryption algorithm on mobile devices will greatly increase the burden of terminal operation and the difficulty to implement the necessary privacy protection algorithm. In this paper, we propose ENSURE (EfficieNt and SecURE), an efficient and secure encrypted search architecture over mobile cloud storage. ENSURE is inspired by edge computing. It allows mobile devices to offload the computation intensive task onto the edge server to achieve a high efficiency. Besides, to protect data security, it reduces the information acquisition of untrusted cloud by hiding the relevance between query keyword and search results from the cloud. Experiments on a real data set show that ENSURE reduces the computation time by 15% to 49% and saves the energy consumption by 38% to 69% per query. PMID:29652810

Edge-Based Efficient Search over Encrypted Data Mobile Cloud Storage.

PubMed

Guo, Yeting; Liu, Fang; Cai, Zhiping; Xiao, Nong; Zhao, Ziming

2018-04-13

Smart sensor-equipped mobile devices sense, collect, and process data generated by the edge network to achieve intelligent control, but such mobile devices usually have limited storage and computing resources. Mobile cloud storage provides a promising solution owing to its rich storage resources, great accessibility, and low cost. But it also brings a risk of information leakage. The encryption of sensitive data is the basic step to resist the risk. However, deploying a high complexity encryption and decryption algorithm on mobile devices will greatly increase the burden of terminal operation and the difficulty to implement the necessary privacy protection algorithm. In this paper, we propose ENSURE (EfficieNt and SecURE), an efficient and secure encrypted search architecture over mobile cloud storage. ENSURE is inspired by edge computing. It allows mobile devices to offload the computation intensive task onto the edge server to achieve a high efficiency. Besides, to protect data security, it reduces the information acquisition of untrusted cloud by hiding the relevance between query keyword and search results from the cloud. Experiments on a real data set show that ENSURE reduces the computation time by 15% to 49% and saves the energy consumption by 38% to 69% per query.

Efficient computation of the genomic relationship matrix and other matrices used in single-step evaluation.

PubMed

Aguilar, I; Misztal, I; Legarra, A; Tsuruta, S

2011-12-01

Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40 K SNPs, with the number of genotyped animals up to 30 000. Matrix multiplication in the computation of the genomic relationship was by a simple 'do' loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30 000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries. © 2011 Blackwell Verlag GmbH.

An efficient sparse matrix multiplication scheme for the CYBER 205 computer

NASA Technical Reports Server (NTRS)

Lambiotte, Jules J., Jr.

1988-01-01

This paper describes the development of an efficient algorithm for computing the product of a matrix and vector on a CYBER 205 vector computer. The desire to provide software which allows the user to choose between the often conflicting goals of minimizing central processing unit (CPU) time or storage requirements has led to a diagonal-based algorithm in which one of four types of storage is selected for each diagonal. The candidate storage types employed were chosen to be efficient on the CYBER 205 for diagonals which have nonzero structure which is dense, moderately sparse, very sparse and short, or very sparse and long; however, for many densities, no diagonal type is most efficient with respect to both resource requirements, and a trade-off must be made. For each diagonal, an initialization subroutine estimates the CPU time and storage required for each storage type based on results from previously performed numerical experimentation. These requirements are adjusted by weights provided by the user which reflect the relative importance the user places on the two resources. The adjusted resource requirements are then compared to select the most efficient storage and computational scheme.

Multiscale Space-Time Computational Methods for Fluid-Structure Interactions

DTIC Science & Technology

2015-09-13

prescribed fully or partially, is from an actual locust, extracted from high-speed, multi-camera video recordings of the locust in a wind tunnel . We use...With creative methods for coupling the fluid and structure, we can increase the scope and efficiency of the FSI modeling . Multiscale methods, which now...play an important role in computational mathematics, can also increase the accuracy and efficiency of the computer modeling techniques. The main

Certification trails and software design for testability

NASA Technical Reports Server (NTRS)

Sullivan, Gregory F.; Wilson, Dwight S.; Masson, Gerald M.

1993-01-01

Design techniques which may be applied to make program testing easier were investigated. Methods for modifying a program to generate additional data which we refer to as a certification trail are presented. This additional data is designed to allow the program output to be checked more quickly and effectively. Certification trails were described primarily from a theoretical perspective. A comprehensive attempt to assess experimentally the performance and overall value of the certification trail method is reported. The method was applied to nine fundamental, well-known algorithms for the following problems: convex hull, sorting, huffman tree, shortest path, closest pair, line segment intersection, longest increasing subsequence, skyline, and voronoi diagram. Run-time performance data for each of these problems is given, and selected problems are described in more detail. Our results indicate that there are many cases in which certification trails allow for significantly faster overall program execution time than a 2-version programming approach, and also give further evidence of the breadth of applicability of this method.

A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva

PubMed Central

Kawahara, Rebeca; Bollinger, James G.; Rivera, César; Ribeiro, Ana Carolina P.; Brandão, Thaís Bianca; Paes Leme, Adriana F.; MacCoss, Michael J.

2015-01-01

Head and neck cancers, including oral squamous cell carcinoma (OSCC), are the sixth most common malignancy in the world and are characterized by poor prognosis and a low survival rate. Saliva is oral fluid with intimate contact with OSCC. Besides non-invasive, simple, and rapid to collect, saliva is a potential source of biomarkers. In this study, we build an SRM assay that targets fourteen OSCC candidate biomarker proteins, which were evaluated in a set of clinically-derived saliva samples. Using Skyline software package, we demonstrated a statistically significant higher abundance of the C1R, LCN2, SLPI, FAM49B, TAGLN2, CFB, C3, C4B, LRG1, SERPINA1 candidate biomarkers in the saliva of OSCC patients. Furthermore, our study also demonstrated that CFB, C3, C4B, SERPINA1 and LRG1 are associated with the risk of developing OSCC. Overall, this study successfully used targeted proteomics to measure in saliva a panel of biomarker candidates for OSCC. PMID:26552850

A multi-center study benchmarks software tools for label-free proteome quantification

PubMed Central

Gillet, Ludovic C; Bernhardt, Oliver M.; MacLean, Brendan; Röst, Hannes L.; Tate, Stephen A.; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I.; Aebersold, Ruedi; Tenzer, Stefan

2016-01-01

The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics. PMID:27701404

A multicenter study benchmarks software tools for label-free proteome quantification.

PubMed

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

Using iRT, a normalized retention time for more targeted measurement of peptides

PubMed Central

Escher, Claudia; Reiter, Lukas; MacLean, Brendan; Ossola, Reto; Herzog, Franz; Chilton, John; MacCoss, Michael J.; Rinner, Oliver

2014-01-01

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than 4 times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments. PMID:22577012

Emerging Coxsackievirus A6 Causing Hand, Foot and Mouth Disease, Vietnam

PubMed Central

Anh, Nguyen To; Nhu, Le Nguyen Truc; Van, Hoang Minh Tu; Hong, Nguyen Thi Thu; Thanh, Tran Tan; Hang, Vu Thi Ty; Ny, Nguyen Thi Han; Nguyet, Lam Anh; Phuong, Tran Thi Lan; Nhan, Le Nguyen Thanh; Hung, Nguyen Thanh; Khanh, Truong Huu; Tuan, Ha Manh; Viet, Ho Lu; Nam, Nguyen Tran; Viet, Do Chau; Qui, Phan Tu; Wills, Bridget; Sabanathan, Sarawathy; Chau, Nguyen Van Vinh; Thwaites, Louise; Rogier van Doorn, H.; Thwaites, Guy; Rabaa, Maia A.

2018-01-01

Hand, foot and mouth disease (HFMD) is a major public health issue in Asia and has global pandemic potential. Coxsackievirus A6 (CV-A6) was detected in 514/2,230 (23%) of HFMD patients admitted to 3 major hospitals in southern Vietnam during 2011–2015. Of these patients, 93 (18%) had severe HFMD. Phylogenetic analysis of 98 genome sequences revealed they belonged to cluster A and had been circulating in Vietnam for 2 years before emergence. CV-A6 movement among localities within Vietnam occurred frequently, whereas viral movement across international borders appeared rare. Skyline plots identified fluctuations in the relative genetic diversity of CV-A6 corresponding to large CV-A6–associated HFMD outbreaks worldwide. These data show that CV-A6 is an emerging pathogen and emphasize the necessity of active surveillance and understanding the mechanisms that shape the pathogen evolution and emergence, which is essential for development and implementation of intervention strategies. PMID:29553326

Population dynamics and in vitro antibody pressure of porcine parvovirus indicate a decrease in variability.

PubMed

Streck, André Felipe; Homeier, Timo; Foerster, Tessa; Truyen, Uwe

2013-09-01

To estimate the impact of porcine parvovirus (PPV) vaccines on the emergence of new phenotypes, the population dynamic history of the virus was calculated using the Bayesian Markov chain Monte Carlo method with a Bayesian skyline coalescent model. Additionally, an in vitro model was performed with consecutive passages of the 'Challenge' strain (a virulent field strain) and NADL2 strain (a vaccine strain) in a PK-15 cell line supplemented with polyclonal antibodies raised against the vaccine strain. A decrease in genetic diversity was observed in the presence of antibodies in vitro or after vaccination (as estimated by the in silico model). We hypothesized that the antibodies induced a selective pressure that may reduce the incidence of neutral selection, which should play a major role in the emergence of new mutations. In this scenario, vaccine failures and non-vaccinated populations (e.g. wild boars) may have an important impact in the emergence of new phenotypes.

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…

Cognitive Load Theory vs. Constructivist Approaches: Which Best Leads to Efficient, Deep Learning?

ERIC Educational Resources Information Center

Vogel-Walcutt, J. J.; Gebrim, J. B.; Bowers, C.; Carper, T. M.; Nicholson, D.

2011-01-01

Computer-assisted learning, in the form of simulation-based training, is heavily focused upon by the military. Because computer-based learning offers highly portable, reusable, and cost-efficient training options, the military has dedicated significant resources to the investigation of instructional strategies that improve learning efficiency…

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

PubMed Central

Stone, John E.; Hallock, Michael J.; Phillips, James C.; Peterson, Joseph R.; Luthey-Schulten, Zaida; Schulten, Klaus

2016-01-01

Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers. PMID:27516922

Computational Properties of the Hippocampus Increase the Efficiency of Goal-Directed Foraging through Hierarchical Reinforcement Learning

PubMed Central

Chalmers, Eric; Luczak, Artur; Gruber, Aaron J.

2016-01-01

The mammalian brain is thought to use a version of Model-based Reinforcement Learning (MBRL) to guide “goal-directed” behavior, wherein animals consider goals and make plans to acquire desired outcomes. However, conventional MBRL algorithms do not fully explain animals' ability to rapidly adapt to environmental changes, or learn multiple complex tasks. They also require extensive computation, suggesting that goal-directed behavior is cognitively expensive. We propose here that key features of processing in the hippocampus support a flexible MBRL mechanism for spatial navigation that is computationally efficient and can adapt quickly to change. We investigate this idea by implementing a computational MBRL framework that incorporates features inspired by computational properties of the hippocampus: a hierarchical representation of space, “forward sweeps” through future spatial trajectories, and context-driven remapping of place cells. We find that a hierarchical abstraction of space greatly reduces the computational load (mental effort) required for adaptation to changing environmental conditions, and allows efficient scaling to large problems. It also allows abstract knowledge gained at high levels to guide adaptation to new obstacles. Moreover, a context-driven remapping mechanism allows learning and memory of multiple tasks. Simulating dorsal or ventral hippocampal lesions in our computational framework qualitatively reproduces behavioral deficits observed in rodents with analogous lesions. The framework may thus embody key features of how the brain organizes model-based RL to efficiently solve navigation and other difficult tasks. PMID:28018203

Polynomial-time quantum algorithm for the simulation of chemical dynamics

PubMed Central

Kassal, Ivan; Jordan, Stephen P.; Love, Peter J.; Mohseni, Masoud; Aspuru-Guzik, Alán

2008-01-01

The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can be applied only to small systems. By contrast, we demonstrate that quantum computers could exactly simulate chemical reactions in polynomial time. Our algorithm uses the split-operator approach and explicitly simulates all electron-nuclear and interelectronic interactions in quadratic time. Surprisingly, this treatment is not only more accurate than the Born–Oppenheimer approximation but faster and more efficient as well, for all reactions with more than about four atoms. This is the case even though the entire electronic wave function is propagated on a grid with appropriately short time steps. Although the preparation and measurement of arbitrary states on a quantum computer is inefficient, here we demonstrate how to prepare states of chemical interest efficiently. We also show how to efficiently obtain chemically relevant observables, such as state-to-state transition probabilities and thermal reaction rates. Quantum computers using these techniques could outperform current classical computers with 100 qubits. PMID:19033207

Computationally efficient algorithm for Gaussian Process regression in case of structured samples

NASA Astrophysics Data System (ADS)

Belyaev, M.; Burnaev, E.; Kapushev, Y.

2016-04-01

Surrogate modeling is widely used in many engineering problems. Data sets often have Cartesian product structure (for instance factorial design of experiments with missing points). In such case the size of the data set can be very large. Therefore, one of the most popular algorithms for approximation-Gaussian Process regression-can be hardly applied due to its computational complexity. In this paper a computationally efficient approach for constructing Gaussian Process regression in case of data sets with Cartesian product structure is presented. Efficiency is achieved by using a special structure of the data set and operations with tensors. Proposed algorithm has low computational as well as memory complexity compared to existing algorithms. In this work we also introduce a regularization procedure allowing to take into account anisotropy of the data set and avoid degeneracy of regression model.

Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

NASA Astrophysics Data System (ADS)

Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

2016-07-01

Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

Parallel scalability and efficiency of vortex particle method for aeroelasticity analysis of bluff bodies

NASA Astrophysics Data System (ADS)

Tolba, Khaled Ibrahim; Morgenthal, Guido

2018-01-01

This paper presents an analysis of the scalability and efficiency of a simulation framework based on the vortex particle method. The code is applied for the numerical aerodynamic analysis of line-like structures. The numerical code runs on multicore CPU and GPU architectures using OpenCL framework. The focus of this paper is the analysis of the parallel efficiency and scalability of the method being applied to an engineering test case, specifically the aeroelastic response of a long-span bridge girder at the construction stage. The target is to assess the optimal configuration and the required computer architecture, such that it becomes feasible to efficiently utilise the method within the computational resources available for a regular engineering office. The simulations and the scalability analysis are performed on a regular gaming type computer.

A Computationally Efficient Parallel Levenberg-Marquardt Algorithm for Large-Scale Big-Data Inversion

NASA Astrophysics Data System (ADS)

Lin, Y.; O'Malley, D.; Vesselinov, V. V.

2015-12-01

Inverse modeling seeks model parameters given a set of observed state variables. However, for many practical problems due to the facts that the observed data sets are often large and model parameters are often numerous, conventional methods for solving the inverse modeling can be computationally expensive. We have developed a new, computationally-efficient Levenberg-Marquardt method for solving large-scale inverse modeling. Levenberg-Marquardt methods require the solution of a dense linear system of equations which can be prohibitively expensive to compute for large-scale inverse problems. Our novel method projects the original large-scale linear problem down to a Krylov subspace, such that the dimensionality of the measurements can be significantly reduced. Furthermore, instead of solving the linear system for every Levenberg-Marquardt damping parameter, we store the Krylov subspace computed when solving the first damping parameter and recycle it for all the following damping parameters. The efficiency of our new inverse modeling algorithm is significantly improved by using these computational techniques. We apply this new inverse modeling method to invert for a random transitivity field. Our algorithm is fast enough to solve for the distributed model parameters (transitivity) at each computational node in the model domain. The inversion is also aided by the use regularization techniques. The algorithm is coded in Julia and implemented in the MADS computational framework (http://mads.lanl.gov). Julia is an advanced high-level scientific programing language that allows for efficient memory management and utilization of high-performance computational resources. By comparing with a Levenberg-Marquardt method using standard linear inversion techniques, our Levenberg-Marquardt method yields speed-up ratio of 15 in a multi-core computational environment and a speed-up ratio of 45 in a single-core computational environment. Therefore, our new inverse modeling method is a powerful tool for large-scale applications.

Evaluation of reinitialization-free nonvolatile computer systems for energy-harvesting Internet of things applications

NASA Astrophysics Data System (ADS)

Onizawa, Naoya; Tamakoshi, Akira; Hanyu, Takahiro

2017-08-01

In this paper, reinitialization-free nonvolatile computer systems are designed and evaluated for energy-harvesting Internet of things (IoT) applications. In energy-harvesting applications, as power supplies generated from renewable power sources cause frequent power failures, data processed need to be backed up when power failures occur. Unless data are safely backed up before power supplies diminish, reinitialization processes are required when power supplies are recovered, which results in low energy efficiencies and slow operations. Using nonvolatile devices in processors and memories can realize a faster backup than a conventional volatile computer system, leading to a higher energy efficiency. To evaluate the energy efficiency upon frequent power failures, typical computer systems including processors and memories are designed using 90 nm CMOS or CMOS/magnetic tunnel junction (MTJ) technologies. Nonvolatile ARM Cortex-M0 processors with 4 kB MRAMs are evaluated using a typical computing benchmark program, Dhrystone, which shows a few order-of-magnitude reductions in energy in comparison with a volatile processor with SRAM.

Unified treatment of microscopic boundary conditions and efficient algorithms for estimating tangent operators of the homogenized behavior in the computational homogenization method

NASA Astrophysics Data System (ADS)

Nguyen, Van-Dung; Wu, Ling; Noels, Ludovic

2017-03-01

This work provides a unified treatment of arbitrary kinds of microscopic boundary conditions usually considered in the multi-scale computational homogenization method for nonlinear multi-physics problems. An efficient procedure is developed to enforce the multi-point linear constraints arising from the microscopic boundary condition either by the direct constraint elimination or by the Lagrange multiplier elimination methods. The macroscopic tangent operators are computed in an efficient way from a multiple right hand sides linear system whose left hand side matrix is the stiffness matrix of the microscopic linearized system at the converged solution. The number of vectors at the right hand side is equal to the number of the macroscopic kinematic variables used to formulate the microscopic boundary condition. As the resolution of the microscopic linearized system often follows a direct factorization procedure, the computation of the macroscopic tangent operators is then performed using this factorized matrix at a reduced computational time.

Probabilistic methods for rotordynamics analysis

NASA Technical Reports Server (NTRS)

Wu, Y.-T.; Torng, T. Y.; Millwater, H. R.; Fossum, A. F.; Rheinfurth, M. H.

1991-01-01

This paper summarizes the development of the methods and a computer program to compute the probability of instability of dynamic systems that can be represented by a system of second-order ordinary linear differential equations. Two instability criteria based upon the eigenvalues or Routh-Hurwitz test functions are investigated. Computational methods based on a fast probability integration concept and an efficient adaptive importance sampling method are proposed to perform efficient probabilistic analysis. A numerical example is provided to demonstrate the methods.

Efficient shortest-path-tree computation in network routing based on pulse-coupled neural networks.

PubMed

Qu, Hong; Yi, Zhang; Yang, Simon X

2013-06-01

Shortest path tree (SPT) computation is a critical issue for routers using link-state routing protocols, such as the most commonly used open shortest path first and intermediate system to intermediate system. Each router needs to recompute a new SPT rooted from itself whenever a change happens in the link state. Most commercial routers do this computation by deleting the current SPT and building a new one using static algorithms such as the Dijkstra algorithm at the beginning. Such recomputation of an entire SPT is inefficient, which may consume a considerable amount of CPU time and result in a time delay in the network. Some dynamic updating methods using the information in the updated SPT have been proposed in recent years. However, there are still many limitations in those dynamic algorithms. In this paper, a new modified model of pulse-coupled neural networks (M-PCNNs) is proposed for the SPT computation. It is rigorously proved that the proposed model is capable of solving some optimization problems, such as the SPT. A static algorithm is proposed based on the M-PCNNs to compute the SPT efficiently for large-scale problems. In addition, a dynamic algorithm that makes use of the structure of the previously computed SPT is proposed, which significantly improves the efficiency of the algorithm. Simulation results demonstrate the effective and efficient performance of the proposed approach.

Distributing and storing data efficiently by means of special datasets in the ATLAS collaboration

NASA Astrophysics Data System (ADS)

Köneke, Karsten; ATLAS Collaboration

2011-12-01

With the start of the LHC physics program, the ATLAS experiment started to record vast amounts of data. This data has to be distributed and stored on the world-wide computing grid in a smart way in order to enable an effective and efficient analysis by physicists. This article describes how the ATLAS collaboration chose to create specialized reduced datasets in order to efficiently use computing resources and facilitate physics analyses.

High-Performance Computing for the Electromagnetic Modeling and Simulation of Interconnects

NASA Technical Reports Server (NTRS)

Schutt-Aine, Jose E.

1996-01-01

The electromagnetic modeling of packages and interconnects plays a very important role in the design of high-speed digital circuits, and is most efficiently performed by using computer-aided design algorithms. In recent years, packaging has become a critical area in the design of high-speed communication systems and fast computers, and the importance of the software support for their development has increased accordingly. Throughout this project, our efforts have focused on the development of modeling and simulation techniques and algorithms that permit the fast computation of the electrical parameters of interconnects and the efficient simulation of their electrical performance.

Facilitating NASA Earth Science Data Processing Using Nebula Cloud Computing

NASA Technical Reports Server (NTRS)

Pham, Long; Chen, Aijun; Kempler, Steven; Lynnes, Christopher; Theobald, Michael; Asghar, Esfandiari; Campino, Jane; Vollmer, Bruce

2011-01-01

Cloud Computing has been implemented in several commercial arenas. The NASA Nebula Cloud Computing platform is an Infrastructure as a Service (IaaS) built in 2008 at NASA Ames Research Center and 2010 at GSFC. Nebula is an open source Cloud platform intended to: a) Make NASA realize significant cost savings through efficient resource utilization, reduced energy consumption, and reduced labor costs. b) Provide an easier way for NASA scientists and researchers to efficiently explore and share large and complex data sets. c) Allow customers to provision, manage, and decommission computing capabilities on an as-needed bases

A class of parallel algorithms for computation of the manipulator inertia matrix

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1989-01-01

Parallel and parallel/pipeline algorithms for computation of the manipulator inertia matrix are presented. An algorithm based on composite rigid-body spatial inertia method, which provides better features for parallelization, is used for the computation of the inertia matrix. Two parallel algorithms are developed which achieve the time lower bound in computation. Also described is the mapping of these algorithms with topological variation on a two-dimensional processor array, with nearest-neighbor connection, and with cardinality variation on a linear processor array. An efficient parallel/pipeline algorithm for the linear array was also developed, but at significantly higher efficiency.

Heterogeneous high throughput scientific computing with APM X-Gene and Intel Xeon Phi

DOE PAGES

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; ...

2015-05-22

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. As a result, we report our experience on software porting, performance and energy efficiency and evaluatemore » the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).« less

Efficient storage, computation, and exposure of computer-generated holograms by electron-beam lithography.

PubMed

Newman, D M; Hawley, R W; Goeckel, D L; Crawford, R D; Abraham, S; Gallagher, N C

1993-05-10

An efficient storage format was developed for computer-generated holograms for use in electron-beam lithography. This method employs run-length encoding and Lempel-Ziv-Welch compression and succeeds in exposing holograms that were previously infeasible owing to the hologram's tremendous pattern-data file size. These holograms also require significant computation; thus the algorithm was implemented on a parallel computer, which improved performance by 2 orders of magnitude. The decompression algorithm was integrated into the Cambridge electron-beam machine's front-end processor.Although this provides much-needed ability, some hardware enhancements will be required in the future to overcome inadequacies in the current front-end processor that result in a lengthy exposure time.

High-Performance Computing Systems and Operations | Computational Science |

Science.gov Websites

NREL Systems and Operations High-Performance Computing Systems and Operations NREL operates high-performance computing (HPC) systems dedicated to advancing energy efficiency and renewable energy technologies. Capabilities NREL's HPC capabilities include: High-Performance Computing Systems We operate

Crowd Sensing-Enabling Security Service Recommendation for Social Fog Computing Systems

PubMed Central

Wu, Jun; Su, Zhou; Li, Jianhua

2017-01-01

Fog computing, shifting intelligence and resources from the remote cloud to edge networks, has the potential of providing low-latency for the communication from sensing data sources to users. For the objects from the Internet of Things (IoT) to the cloud, it is a new trend that the objects establish social-like relationships with each other, which efficiently brings the benefits of developed sociality to a complex environment. As fog service become more sophisticated, it will become more convenient for fog users to share their own services, resources, and data via social networks. Meanwhile, the efficient social organization can enable more flexible, secure, and collaborative networking. Aforementioned advantages make the social network a potential architecture for fog computing systems. In this paper, we design an architecture for social fog computing, in which the services of fog are provisioned based on “friend” relationships. To the best of our knowledge, this is the first attempt at an organized fog computing system-based social model. Meanwhile, social networking enhances the complexity and security risks of fog computing services, creating difficulties of security service recommendations in social fog computing. To address this, we propose a novel crowd sensing-enabling security service provisioning method to recommend security services accurately in social fog computing systems. Simulation results show the feasibilities and efficiency of the crowd sensing-enabling security service recommendation method for social fog computing systems. PMID:28758943

Crowd Sensing-Enabling Security Service Recommendation for Social Fog Computing Systems.

PubMed

Wu, Jun; Su, Zhou; Wang, Shen; Li, Jianhua

2017-07-30

Fog computing, shifting intelligence and resources from the remote cloud to edge networks, has the potential of providing low-latency for the communication from sensing data sources to users. For the objects from the Internet of Things (IoT) to the cloud, it is a new trend that the objects establish social-like relationships with each other, which efficiently brings the benefits of developed sociality to a complex environment. As fog service become more sophisticated, it will become more convenient for fog users to share their own services, resources, and data via social networks. Meanwhile, the efficient social organization can enable more flexible, secure, and collaborative networking. Aforementioned advantages make the social network a potential architecture for fog computing systems. In this paper, we design an architecture for social fog computing, in which the services of fog are provisioned based on "friend" relationships. To the best of our knowledge, this is the first attempt at an organized fog computing system-based social model. Meanwhile, social networking enhances the complexity and security risks of fog computing services, creating difficulties of security service recommendations in social fog computing. To address this, we propose a novel crowd sensing-enabling security service provisioning method to recommend security services accurately in social fog computing systems. Simulation results show the feasibilities and efficiency of the crowd sensing-enabling security service recommendation method for social fog computing systems.

A fast indirect method to compute functions of genomic relationships concerning genotyped and ungenotyped individuals, for diversity management.

PubMed

Colleau, Jean-Jacques; Palhière, Isabelle; Rodríguez-Ramilo, Silvia T; Legarra, Andres

2017-12-01

Pedigree-based management of genetic diversity in populations, e.g., using optimal contributions, involves computation of the [Formula: see text] type yielding elements (relationships) or functions (usually averages) of relationship matrices. For pedigree-based relationships [Formula: see text], a very efficient method exists. When all the individuals of interest are genotyped, genomic management can be addressed using the genomic relationship matrix [Formula: see text]; however, to date, the computational problem of efficiently computing [Formula: see text] has not been well studied. When some individuals of interest are not genotyped, genomic management should consider the relationship matrix [Formula: see text] that combines genotyped and ungenotyped individuals; however, direct computation of [Formula: see text] is computationally very demanding, because construction of a possibly huge matrix is required. Our work presents efficient ways of computing [Formula: see text] and [Formula: see text], with applications on real data from dairy sheep and dairy goat breeding schemes. For genomic relationships, an efficient indirect computation with quadratic instead of cubic cost is [Formula: see text], where Z is a matrix relating animals to genotypes. For the relationship matrix [Formula: see text], we propose an indirect method based on the difference between vectors [Formula: see text], which involves computation of [Formula: see text] and of products such as [Formula: see text] and [Formula: see text], where [Formula: see text] is a working vector derived from [Formula: see text]. The latter computation is the most demanding but can be done using sparse Cholesky decompositions of matrix [Formula: see text], which allows handling very large genomic and pedigree data files. Studies based on simulations reported in the literature show that the trends of average relationships in [Formula: see text] and [Formula: see text] differ as genomic selection proceeds. When selection is based on genomic relationships but management is based on pedigree data, the true genetic diversity is overestimated. However, our tests on real data from sheep and goat obtained before genomic selection started do not show this. We present efficient methods to compute elements and statistics of the genomic relationships [Formula: see text] and of matrix [Formula: see text] that combines ungenotyped and genotyped individuals. These methods should be useful to monitor and handle genomic diversity.

A method to efficiently apply a biogeochemical model to a landscape.

Treesearch

Robert E. Kennedy; David P. Turner; Warren B. Cohen; Michael Guzy

2006-01-01

Biogeochemical models offer an important means of understanding carbon dynamics, but the computational complexity of many models means that modeling all grid cells on a large landscape is computationally burdensome. Because most biogeochemical models ignore adjacency effects between cells, however, a more efficient approach is possible. Recognizing that spatial...

Time and Learning Efficiency in Internet-Based Learning: A Systematic Review and Meta-Analysis

ERIC Educational Resources Information Center

Cook, David A.; Levinson, Anthony J.; Garside, Sarah

2010-01-01

Authors have claimed that Internet-based instruction promotes greater learning efficiency than non-computer methods. Objectives Determine, through a systematic synthesis of evidence in health professions education, how Internet-based instruction compares with non-computer instruction in time spent learning, and what features of Internet-based…

Solving wood chip transport problems with computer simulation.

Treesearch

Dennis P. Bradley; Sharon A. Winsauer

1976-01-01

Efficient chip transport operations are difficult to achieve due to frequent and often unpredictable changes in distance to market, chipping rate, time spent at the mill, and equipment costs. This paper describes a computer simulation model that allows a logger to design an efficient transport system in response to these changing factors.

Multiscale Reactive Molecular Dynamics

DTIC Science & Technology

2012-08-15

biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system ...coupling to slower, cooperative motions of the system . These inherently multiscale problems require computationally efficient and accurate methods to...condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus

Efficient Stochastic Inversion Using Adjoint Models and Kernel-PCA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thimmisetty, Charanraj A.; Zhao, Wenju; Chen, Xiao

2017-10-18

Performing stochastic inversion on a computationally expensive forward simulation model with a high-dimensional uncertain parameter space (e.g. a spatial random field) is computationally prohibitive even when gradient information can be computed efficiently. Moreover, the ‘nonlinear’ mapping from parameters to observables generally gives rise to non-Gaussian posteriors even with Gaussian priors, thus hampering the use of efficient inversion algorithms designed for models with Gaussian assumptions. In this paper, we propose a novel Bayesian stochastic inversion methodology, which is characterized by a tight coupling between the gradient-based Langevin Markov Chain Monte Carlo (LMCMC) method and a kernel principal component analysis (KPCA). Thismore » approach addresses the ‘curse-of-dimensionality’ via KPCA to identify a low-dimensional feature space within the high-dimensional and nonlinearly correlated parameter space. In addition, non-Gaussian posterior distributions are estimated via an efficient LMCMC method on the projected low-dimensional feature space. We will demonstrate this computational framework by integrating and adapting our recent data-driven statistics-on-manifolds constructions and reduction-through-projection techniques to a linear elasticity model.« less

Bringing the CMS distributed computing system into scalable operations

NASA Astrophysics Data System (ADS)

Belforte, S.; Fanfani, A.; Fisk, I.; Flix, J.; Hernández, J. M.; Kress, T.; Letts, J.; Magini, N.; Miccio, V.; Sciabà, A.

2010-04-01

Establishing efficient and scalable operations of the CMS distributed computing system critically relies on the proper integration, commissioning and scale testing of the data and workload management tools, the various computing workflows and the underlying computing infrastructure, located at more than 50 computing centres worldwide and interconnected by the Worldwide LHC Computing Grid. Computing challenges periodically undertaken by CMS in the past years with increasing scale and complexity have revealed the need for a sustained effort on computing integration and commissioning activities. The Processing and Data Access (PADA) Task Force was established at the beginning of 2008 within the CMS Computing Program with the mandate of validating the infrastructure for organized processing and user analysis including the sites and the workload and data management tools, validating the distributed production system by performing functionality, reliability and scale tests, helping sites to commission, configure and optimize the networking and storage through scale testing data transfers and data processing, and improving the efficiency of accessing data across the CMS computing system from global transfers to local access. This contribution reports on the tools and procedures developed by CMS for computing commissioning and scale testing as well as the improvements accomplished towards efficient, reliable and scalable computing operations. The activities include the development and operation of load generators for job submission and data transfers with the aim of stressing the experiment and Grid data management and workload management systems, site commissioning procedures and tools to monitor and improve site availability and reliability, as well as activities targeted to the commissioning of the distributed production, user analysis and monitoring systems.

TDat: An Efficient Platform for Processing Petabyte-Scale Whole-Brain Volumetric Images.

PubMed

Li, Yuxin; Gong, Hui; Yang, Xiaoquan; Yuan, Jing; Jiang, Tao; Li, Xiangning; Sun, Qingtao; Zhu, Dan; Wang, Zhenyu; Luo, Qingming; Li, Anan

2017-01-01

Three-dimensional imaging of whole mammalian brains at single-neuron resolution has generated terabyte (TB)- and even petabyte (PB)-sized datasets. Due to their size, processing these massive image datasets can be hindered by the computer hardware and software typically found in biological laboratories. To fill this gap, we have developed an efficient platform named TDat, which adopts a novel data reformatting strategy by reading cuboid data and employing parallel computing. In data reformatting, TDat is more efficient than any other software. In data accessing, we adopted parallelization to fully explore the capability for data transmission in computers. We applied TDat in large-volume data rigid registration and neuron tracing in whole-brain data with single-neuron resolution, which has never been demonstrated in other studies. We also showed its compatibility with various computing platforms, image processing software and imaging systems.

Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

1991-01-01

Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

Efficient quantum walk on a quantum processor

PubMed Central

Qiang, Xiaogang; Loke, Thomas; Montanaro, Ashley; Aungskunsiri, Kanin; Zhou, Xiaoqi; O'Brien, Jeremy L.; Wang, Jingbo B.; Matthews, Jonathan C. F.

2016-01-01

The random walk formalism is used across a wide range of applications, from modelling share prices to predicting population genetics. Likewise, quantum walks have shown much potential as a framework for developing new quantum algorithms. Here we present explicit efficient quantum circuits for implementing continuous-time quantum walks on the circulant class of graphs. These circuits allow us to sample from the output probability distributions of quantum walks on circulant graphs efficiently. We also show that solving the same sampling problem for arbitrary circulant quantum circuits is intractable for a classical computer, assuming conjectures from computational complexity theory. This is a new link between continuous-time quantum walks and computational complexity theory and it indicates a family of tasks that could ultimately demonstrate quantum supremacy over classical computers. As a proof of principle, we experimentally implement the proposed quantum circuit on an example circulant graph using a two-qubit photonics quantum processor. PMID:27146471

Efficient Computation of Difference Vibrational Spectra in Isothermal-Isobaric Ensemble.

PubMed

Joutsuka, Tatsuya; Morita, Akihiro

2016-11-03

Difference spectroscopy between two close systems is widely used to augment its selectivity to the different parts of the observed system, though the molecular dynamics calculation of tiny difference spectra would be computationally extraordinary demanding by subtraction of two spectra. Therefore, we have proposed an efficient computational algorithm of difference spectra without resorting to the subtraction. The present paper reports our extension of the theoretical method in the isothermal-isobaric (NPT) ensemble. The present theory expands our applications of analysis including pressure dependence of the spectra. We verified that the present theory yields accurate difference spectra in the NPT condition as well, with remarkable computational efficiency over the straightforward subtraction by several orders of magnitude. This method is further applied to vibrational spectra of liquid water with varying pressure and succeeded in reproducing tiny difference spectra by pressure change. The anomalous pressure dependence is elucidated in relation to other properties of liquid water.

An efficient method for hybrid density functional calculation with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Wang, Maoyuan; Liu, Gui-Bin; Guo, Hong; Yao, Yugui

2018-03-01

In first-principles calculations, hybrid functional is often used to improve accuracy from local exchange correlation functionals. A drawback is that evaluating the hybrid functional needs significantly more computing effort. When spin-orbit coupling (SOC) is taken into account, the non-collinear spin structure increases computing effort by at least eight times. As a result, hybrid functional calculations with SOC are intractable in most cases. In this paper, we present an approximate solution to this problem by developing an efficient method based on a mixed linear combination of atomic orbital (LCAO) scheme. We demonstrate the power of this method using several examples and we show that the results compare very well with those of direct hybrid functional calculations with SOC, yet the method only requires a computing effort similar to that without SOC. The presented technique provides a good balance between computing efficiency and accuracy, and it can be extended to magnetic materials.

Image restoration for three-dimensional fluorescence microscopy using an orthonormal basis for efficient representation of depth-variant point-spread functions

PubMed Central

Patwary, Nurmohammed; Preza, Chrysanthe

2015-01-01

A depth-variant (DV) image restoration algorithm for wide field fluorescence microscopy, using an orthonormal basis decomposition of DV point-spread functions (PSFs), is investigated in this study. The efficient PSF representation is based on a previously developed principal component analysis (PCA), which is computationally intensive. We present an approach developed to reduce the number of DV PSFs required for the PCA computation, thereby making the PCA-based approach computationally tractable for thick samples. Restoration results from both synthetic and experimental images show consistency and that the proposed algorithm addresses efficiently depth-induced aberration using a small number of principal components. Comparison of the PCA-based algorithm with a previously-developed strata-based DV restoration algorithm demonstrates that the proposed method improves performance by 50% in terms of accuracy and simultaneously reduces the processing time by 64% using comparable computational resources. PMID:26504634

Development and Applications of a Modular Parallel Process for Large Scale Fluid/Structures Problems

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.; Byun, Chansup; Kwak, Dochan (Technical Monitor)

2001-01-01

A modular process that can efficiently solve large scale multidisciplinary problems using massively parallel super computers is presented. The process integrates disciplines with diverse physical characteristics by retaining the efficiency of individual disciplines. Computational domain independence of individual disciplines is maintained using a meta programming approach. The process integrates disciplines without affecting the combined performance. Results are demonstrated for large scale aerospace problems on several supercomputers. The super scalability and portability of the approach is demonstrated on several parallel computers.

Efficient quantum circuits for one-way quantum computing.

PubMed

Tanamoto, Tetsufumi; Liu, Yu-Xi; Hu, Xuedong; Nori, Franco

2009-03-13

While Ising-type interactions are ideal for implementing controlled phase flip gates in one-way quantum computing, natural interactions between solid-state qubits are most often described by either the XY or the Heisenberg models. We show an efficient way of generating cluster states directly using either the imaginary SWAP (iSWAP) gate for the XY model, or the sqrt[SWAP] gate for the Heisenberg model. Our approach thus makes one-way quantum computing more feasible for solid-state devices.

Printed Multi-Turn Loop Antenna for RF Bio-Telemetry

NASA Technical Reports Server (NTRS)

Simons, Rainee N.; Hall, David G.; Miranda, Felix A.

2004-01-01

In this paper, a novel printed multi-turn loop antenna for contact-less powering and RF telemetry from implantable bio- MEMS sensors at a design frequency of 300 MHz is demonstrated. In addition, computed values of input reactance, radiation resistance, skin effect resistance, and radiation efficiency for the printed multi-turn loop antenna are presented. The computed input reactance is compared with the measured values and shown to be in fair agreement. The computed radiation efficiency at the design frequency is about 24 percent.

Computationally Efficient Clustering of Audio-Visual Meeting Data

NASA Astrophysics Data System (ADS)

Hung, Hayley; Friedland, Gerald; Yeo, Chuohao

This chapter presents novel computationally efficient algorithms to extract semantically meaningful acoustic and visual events related to each of the participants in a group discussion using the example of business meeting recordings. The recording setup involves relatively few audio-visual sensors, comprising a limited number of cameras and microphones. We first demonstrate computationally efficient algorithms that can identify who spoke and when, a problem in speech processing known as speaker diarization. We also extract visual activity features efficiently from MPEG4 video by taking advantage of the processing that was already done for video compression. Then, we present a method of associating the audio-visual data together so that the content of each participant can be managed individually. The methods presented in this article can be used as a principal component that enables many higher-level semantic analysis tasks needed in search, retrieval, and navigation.

Image detection and compression for memory efficient system analysis

NASA Astrophysics Data System (ADS)

Bayraktar, Mustafa

2015-02-01

The advances in digital signal processing have been progressing towards efficient use of memory and processing. Both of these factors can be utilized efficiently by using feasible techniques of image storage by computing the minimum information of image which will enhance computation in later processes. Scale Invariant Feature Transform (SIFT) can be utilized to estimate and retrieve of an image. In computer vision, SIFT can be implemented to recognize the image by comparing its key features from SIFT saved key point descriptors. The main advantage of SIFT is that it doesn't only remove the redundant information from an image but also reduces the key points by matching their orientation and adding them together in different windows of image [1]. Another key property of this approach is that it works on highly contrasted images more efficiently because it`s design is based on collecting key points from the contrast shades of image.

Efficient GW calculations using eigenvalue-eigenvector decomposition of the dielectric matrix

NASA Astrophysics Data System (ADS)

Nguyen, Huy-Viet; Pham, T. Anh; Rocca, Dario; Galli, Giulia

2011-03-01

During the past 25 years, the GW method has been successfully used to compute electronic quasi-particle excitation spectra of a variety of materials. It is however a computationally intensive technique, as it involves summations over occupied and empty electronic states, to evaluate both the Green function (G) and the dielectric matrix (DM) entering the expression of the screened Coulomb interaction (W). Recent developments have shown that eigenpotentials of DMs can be efficiently calculated without any explicit evaluation of empty states. In this work, we will present a computationally efficient approach to the calculations of GW spectra by combining a representation of DMs in terms of its eigenpotentials and a recently developed iterative algorithm. As a demonstration of the efficiency of the method, we will present calculations of the vertical ionization potentials of several systems. Work was funnded by SciDAC-e DE-FC02-06ER25777.

Implementing Parquet equations using HPX

NASA Astrophysics Data System (ADS)

Kellar, Samuel; Wagle, Bibek; Yang, Shuxiang; Tam, Ka-Ming; Kaiser, Hartmut; Moreno, Juana; Jarrell, Mark

A new C++ runtime system (HPX) enables simulations of complex systems to run more efficiently on parallel and heterogeneous systems. This increased efficiency allows for solutions to larger simulations of the parquet approximation for a system with impurities. The relevancy of the parquet equations depends upon the ability to solve systems which require long runs and large amounts of memory. These limitations, in addition to numerical complications arising from stability of the solutions, necessitate running on large distributed systems. As the computational resources trend towards the exascale and the limitations arising from computational resources vanish efficiency of large scale simulations becomes a focus. HPX facilitates efficient simulations through intelligent overlapping of computation and communication. Simulations such as the parquet equations which require the transfer of large amounts of data should benefit from HPX implementations. Supported by the the NSF EPSCoR Cooperative Agreement No. EPS-1003897 with additional support from the Louisiana Board of Regents.

hp-Adaptive time integration based on the BDF for viscous flows

NASA Astrophysics Data System (ADS)

Hay, A.; Etienne, S.; Pelletier, D.; Garon, A.

2015-06-01

This paper presents a procedure based on the Backward Differentiation Formulas of order 1 to 5 to obtain efficient time integration of the incompressible Navier-Stokes equations. The adaptive algorithm performs both stepsize and order selections to control respectively the solution accuracy and the computational efficiency of the time integration process. The stepsize selection (h-adaptivity) is based on a local error estimate and an error controller to guarantee that the numerical solution accuracy is within a user prescribed tolerance. The order selection (p-adaptivity) relies on the idea that low-accuracy solutions can be computed efficiently by low order time integrators while accurate solutions require high order time integrators to keep computational time low. The selection is based on a stability test that detects growing numerical noise and deems a method of order p stable if there is no method of lower order that delivers the same solution accuracy for a larger stepsize. Hence, it guarantees both that (1) the used method of integration operates inside of its stability region and (2) the time integration procedure is computationally efficient. The proposed time integration procedure also features a time-step rejection and quarantine mechanisms, a modified Newton method with a predictor and dense output techniques to compute solution at off-step points.

GPU-accelerated element-free reverse-time migration with Gauss points partition

NASA Astrophysics Data System (ADS)

Zhou, Zhen; Jia, Xiaofeng; Qiang, Xiaodong

2018-06-01

An element-free method (EFM) has been demonstrated successfully in elasticity, heat conduction and fatigue crack growth problems. We present the theory of EFM and its numerical applications in seismic modelling and reverse time migration (RTM). Compared with the finite difference method and the finite element method, the EFM has unique advantages: (1) independence of grids in computation and (2) lower expense and more flexibility (because only the information of the nodes and the boundary of the concerned area is required). However, in EFM, due to improper computation and storage of some large sparse matrices, such as the mass matrix and the stiffness matrix, the method is difficult to apply to seismic modelling and RTM for a large velocity model. To solve the problem of storage and computation efficiency, we propose a concept of Gauss points partition and utilise the graphics processing unit to improve the computational efficiency. We employ the compressed sparse row format to compress the intermediate large sparse matrices and attempt to simplify the operations by solving the linear equations with CULA solver. To improve the computation efficiency further, we introduce the concept of the lumped mass matrix. Numerical experiments indicate that the proposed method is accurate and more efficient than the regular EFM.

Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP

NASA Astrophysics Data System (ADS)

Hofierka, Jaroslav; Lacko, Michal; Zubal, Stanislav

2017-10-01

In this paper, we describe the parallelization of three complex and computationally intensive modules of GRASS GIS using the OpenMP application programming interface for multi-core computers. These include the v.surf.rst module for spatial interpolation, the r.sun module for solar radiation modeling and the r.sim.water module for water flow simulation. We briefly describe the functionality of the modules and parallelization approaches used in the modules. Our approach includes the analysis of the module's functionality, identification of source code segments suitable for parallelization and proper application of OpenMP parallelization code to create efficient threads processing the subtasks. We document the efficiency of the solutions using the airborne laser scanning data representing land surface in the test area and derived high-resolution digital terrain model grids. We discuss the performance speed-up and parallelization efficiency depending on the number of processor threads. The study showed a substantial increase in computation speeds on a standard multi-core computer while maintaining the accuracy of results in comparison to the output from original modules. The presented parallelization approach showed the simplicity and efficiency of the parallelization of open-source GRASS GIS modules using OpenMP, leading to an increased performance of this geospatial software on standard multi-core computers.

Convergence Acceleration of a Navier-Stokes Solver for Efficient Static Aeroelastic Computations

NASA Technical Reports Server (NTRS)

Obayashi, Shigeru; Guruswamy, Guru P.

1995-01-01

New capabilities have been developed for a Navier-Stokes solver to perform steady-state simulations more efficiently. The flow solver for solving the Navier-Stokes equations is based on a combination of the lower-upper factored symmetric Gauss-Seidel implicit method and the modified Harten-Lax-van Leer-Einfeldt upwind scheme. A numerically stable and efficient pseudo-time-marching method is also developed for computing steady flows over flexible wings. Results are demonstrated for transonic flows over rigid and flexible wings.

High-efficiency AlGaAs-GaAs Cassegrainian concentrator cells

NASA Technical Reports Server (NTRS)

Werthen, J. G.; Hamaker, H. C.; Virshup, G. F.; Lewis, C. R.; Ford, C. W.

1985-01-01

AlGaAs-GaAs heteroface space concentrator solar cells have been fabricated by metalorganic chemical vapor deposition. AMO efficiencies as high as 21.1% have been observed both for p-n and np structures under concentration (90 to 100X) at 25 C. Both cell structures are characterized by high quantum efficiencies and their performances are close to those predicted by a realistic computer model. In agreement with the computer model, the n-p cell exhibits a higher short-circuit current density.

Solving groundwater flow problems by conjugate-gradient methods and the strongly implicit procedure

USGS Publications Warehouse

Hill, Mary C.

1990-01-01

The performance of the preconditioned conjugate-gradient method with three preconditioners is compared with the strongly implicit procedure (SIP) using a scalar computer. The preconditioners considered are the incomplete Cholesky (ICCG) and the modified incomplete Cholesky (MICCG), which require the same computer storage as SIP as programmed for a problem with a symmetric matrix, and a polynomial preconditioner (POLCG), which requires less computer storage than SIP. Although POLCG is usually used on vector computers, it is included here because of its small storage requirements. In this paper, published comparisons of the solvers are evaluated, all four solvers are compared for the first time, and new test cases are presented to provide a more complete basis by which the solvers can be judged for typical groundwater flow problems. Based on nine test cases, the following conclusions are reached: (1) SIP is actually as efficient as ICCG for some of the published, linear, two-dimensional test cases that were reportedly solved much more efficiently by ICCG; (2) SIP is more efficient than other published comparisons would indicate when common convergence criteria are used; and (3) for problems that are three-dimensional, nonlinear, or both, and for which common convergence criteria are used, SIP is often more efficient than ICCG, and is sometimes more efficient than MICCG.

Investigating power capping toward energy-efficient scientific applications: Investigating Power Capping toward Energy-Efficient Scientific Applications

DOE PAGES

Haidar, Azzam; Jagode, Heike; Vaccaro, Phil; ...

2018-03-22

The emergence of power efficiency as a primary constraint in processor and system design poses new challenges concerning power and energy awareness for numerical libraries and scientific applications. Power consumption also plays a major role in the design of data centers, which may house petascale or exascale-level computing systems. At these extreme scales, understanding and improving the energy efficiency of numerical libraries and their related applications becomes a crucial part of the successful implementation and operation of the computing system. In this paper, we study and investigate the practice of controlling a compute system's power usage, and we explore howmore » different power caps affect the performance of numerical algorithms with different computational intensities. Further, we determine the impact, in terms of performance and energy usage, that these caps have on a system running scientific applications. This analysis will enable us to characterize the types of algorithms that benefit most from these power management schemes. Our experiments are performed using a set of representative kernels and several popular scientific benchmarks. Lastly, we quantify a number of power and performance measurements and draw observations and conclusions that can be viewed as a roadmap to achieving energy efficiency in the design and execution of scientific algorithms.« less

Investigating power capping toward energy-efficient scientific applications: Investigating Power Capping toward Energy-Efficient Scientific Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haidar, Azzam; Jagode, Heike; Vaccaro, Phil

The emergence of power efficiency as a primary constraint in processor and system design poses new challenges concerning power and energy awareness for numerical libraries and scientific applications. Power consumption also plays a major role in the design of data centers, which may house petascale or exascale-level computing systems. At these extreme scales, understanding and improving the energy efficiency of numerical libraries and their related applications becomes a crucial part of the successful implementation and operation of the computing system. In this paper, we study and investigate the practice of controlling a compute system's power usage, and we explore howmore » different power caps affect the performance of numerical algorithms with different computational intensities. Further, we determine the impact, in terms of performance and energy usage, that these caps have on a system running scientific applications. This analysis will enable us to characterize the types of algorithms that benefit most from these power management schemes. Our experiments are performed using a set of representative kernels and several popular scientific benchmarks. Lastly, we quantify a number of power and performance measurements and draw observations and conclusions that can be viewed as a roadmap to achieving energy efficiency in the design and execution of scientific algorithms.« less

Reducing Vehicle Weight and Improving U.S. Energy Efficiency Using Integrated Computational Materials Engineering

NASA Astrophysics Data System (ADS)

Joost, William J.

2012-09-01

Transportation accounts for approximately 28% of U.S. energy consumption with the majority of transportation energy derived from petroleum sources. Many technologies such as vehicle electrification, advanced combustion, and advanced fuels can reduce transportation energy consumption by improving the efficiency of cars and trucks. Lightweight materials are another important technology that can improve passenger vehicle fuel efficiency by 6-8% for each 10% reduction in weight while also making electric and alternative vehicles more competitive. Despite the opportunities for improved efficiency, widespread deployment of lightweight materials for automotive structures is hampered by technology gaps most often associated with performance, manufacturability, and cost. In this report, the impact of reduced vehicle weight on energy efficiency is discussed with a particular emphasis on quantitative relationships determined by several researchers. The most promising lightweight materials systems are described along with a brief review of the most significant technical barriers to their implementation. For each material system, the development of accurate material models is critical to support simulation-intensive processing and structural design for vehicles; improved models also contribute to an integrated computational materials engineering (ICME) approach for addressing technical barriers and accelerating deployment. The value of computational techniques is described by considering recent ICME and computational materials science success stories with an emphasis on applying problem-specific methods.

The Effects of Computer Instruction on College Students' Reading Skills.

ERIC Educational Resources Information Center

Kuehner, Alison V.

1999-01-01

Reviews research concerning computer-based reading instruction for college students. Finds that most studies suggest that computers can provide motivating and efficient learning, but it is not clear whether the computer, or the instruction via computer, accounts for student gains. Notes many methodological flaws in the studies. Suggests…

Facilitating higher-fidelity simulations of axial compressor instability and other turbomachinery flow conditions

NASA Astrophysics Data System (ADS)

Herrick, Gregory Paul

The quest to accurately capture flow phenomena with length-scales both short and long and to accurately represent complex flow phenomena within disparately sized geometry inspires a need for an efficient, high-fidelity, multi-block structured computational fluid dynamics (CFD) parallel computational scheme. This research presents and demonstrates a more efficient computational method by which to perform multi-block structured CFD parallel computational simulations, thus facilitating higher-fidelity solutions of complicated geometries (due to the inclusion of grids for "small'' flow areas which are often merely modeled) and their associated flows. This computational framework offers greater flexibility and user-control in allocating the resource balance between process count and wall-clock computation time. The principal modifications implemented in this revision consist of a "multiple grid block per processing core'' software infrastructure and an analytic computation of viscous flux Jacobians. The development of this scheme is largely motivated by the desire to simulate axial compressor stall inception with more complete gridding of the flow passages (including rotor tip clearance regions) than has been previously done while maintaining high computational efficiency (i.e., minimal consumption of computational resources), and thus this paradigm shall be demonstrated with an examination of instability in a transonic axial compressor. However, the paradigm presented herein facilitates CFD simulation of myriad previously impractical geometries and flows and is not limited to detailed analyses of axial compressor flows. While the simulations presented herein were technically possible under the previous structure of the subject software, they were much less computationally efficient and thus not pragmatically feasible; the previous research using this software to perform three-dimensional, full-annulus, time-accurate, unsteady, full-stage (with sliding-interface) simulations of rotating stall inception in axial compressors utilized tip clearance periodic models, while the scheme here is demonstrated by a simulation of axial compressor stall inception utilizing gridded rotor tip clearance regions. As will be discussed, much previous research---experimental, theoretical, and computational---has suggested that understanding clearance flow behavior is critical to understanding stall inception, and previous computational research efforts which have used tip clearance models have begged the question, "What about the clearance flows?''. This research begins to address that question.

A Secure and Verifiable Outsourced Access Control Scheme in Fog-Cloud Computing.

PubMed

Fan, Kai; Wang, Junxiong; Wang, Xin; Li, Hui; Yang, Yintang

2017-07-24

With the rapid development of big data and Internet of things (IOT), the number of networking devices and data volume are increasing dramatically. Fog computing, which extends cloud computing to the edge of the network can effectively solve the bottleneck problems of data transmission and data storage. However, security and privacy challenges are also arising in the fog-cloud computing environment. Ciphertext-policy attribute-based encryption (CP-ABE) can be adopted to realize data access control in fog-cloud computing systems. In this paper, we propose a verifiable outsourced multi-authority access control scheme, named VO-MAACS. In our construction, most encryption and decryption computations are outsourced to fog devices and the computation results can be verified by using our verification method. Meanwhile, to address the revocation issue, we design an efficient user and attribute revocation method for it. Finally, analysis and simulation results show that our scheme is both secure and highly efficient.

Elastic Cloud Computing Architecture and System for Heterogeneous Spatiotemporal Computing

NASA Astrophysics Data System (ADS)

Shi, X.

2017-10-01

Spatiotemporal computation implements a variety of different algorithms. When big data are involved, desktop computer or standalone application may not be able to complete the computation task due to limited memory and computing power. Now that a variety of hardware accelerators and computing platforms are available to improve the performance of geocomputation, different algorithms may have different behavior on different computing infrastructure and platforms. Some are perfect for implementation on a cluster of graphics processing units (GPUs), while GPUs may not be useful on certain kind of spatiotemporal computation. This is the same situation in utilizing a cluster of Intel's many-integrated-core (MIC) or Xeon Phi, as well as Hadoop or Spark platforms, to handle big spatiotemporal data. Furthermore, considering the energy efficiency requirement in general computation, Field Programmable Gate Array (FPGA) may be a better solution for better energy efficiency when the performance of computation could be similar or better than GPUs and MICs. It is expected that an elastic cloud computing architecture and system that integrates all of GPUs, MICs, and FPGAs could be developed and deployed to support spatiotemporal computing over heterogeneous data types and computational problems.

Comparing Server Energy Use and Efficiency Using Small Sample Sizes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coles, Henry C.; Qin, Yong; Price, Phillip N.

This report documents a demonstration that compared the energy consumption and efficiency of a limited sample size of server-type IT equipment from different manufacturers by measuring power at the server power supply power cords. The results are specific to the equipment and methods used. However, it is hoped that those responsible for IT equipment selection can used the methods described to choose models that optimize energy use efficiency. The demonstration was conducted in a data center at Lawrence Berkeley National Laboratory in Berkeley, California. It was performed with five servers of similar mechanical and electronic specifications; three from Intel andmore » one each from Dell and Supermicro. Server IT equipment is constructed using commodity components, server manufacturer-designed assemblies, and control systems. Server compute efficiency is constrained by the commodity component specifications and integration requirements. The design freedom, outside of the commodity component constraints, provides room for the manufacturer to offer a product with competitive efficiency that meets market needs at a compelling price. A goal of the demonstration was to compare and quantify the server efficiency for three different brands. The efficiency is defined as the average compute rate (computations per unit of time) divided by the average energy consumption rate. The research team used an industry standard benchmark software package to provide a repeatable software load to obtain the compute rate and provide a variety of power consumption levels. Energy use when the servers were in an idle state (not providing computing work) were also measured. At high server compute loads, all brands, using the same key components (processors and memory), had similar results; therefore, from these results, it could not be concluded that one brand is more efficient than the other brands. The test results show that the power consumption variability caused by the key components as a group is similar to all other components as a group. However, some differences were observed. The Supermicro server used 27 percent more power at idle compared to the other brands. The Intel server had a power supply control feature called cold redundancy, and the data suggest that cold redundancy can provide energy savings at low power levels. Test and evaluation methods that might be used by others having limited resources for IT equipment evaluation are explained in the report.« less

Improving the Efficiency and Effectiveness of Grading through the Use of Computer-Assisted Grading Rubrics

ERIC Educational Resources Information Center

Anglin, Linda; Anglin, Kenneth; Schumann, Paul L.; Kaliski, John A.

2008-01-01

This study tests the use of computer-assisted grading rubrics compared to other grading methods with respect to the efficiency and effectiveness of different grading processes for subjective assignments. The test was performed on a large Introduction to Business course. The students in this course were randomly assigned to four treatment groups…

The Goal Specificity Effect on Strategy Use and Instructional Efficiency during Computer-Based Scientific Discovery Learning

ERIC Educational Resources Information Center

Kunsting, Josef; Wirth, Joachim; Paas, Fred

2011-01-01

Using a computer-based scientific discovery learning environment on buoyancy in fluids we investigated the "effects of goal specificity" (nonspecific goals vs. specific goals) for two goal types (problem solving goals vs. learning goals) on "strategy use" and "instructional efficiency". Our empirical findings close an important research gap,…

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.

Simple formalism for efficient derivatives and multi-determinant expansions in quantum Monte Carlo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippi, Claudia, E-mail: c.filippi@utwente.nl; Assaraf, Roland, E-mail: assaraf@lct.jussieu.fr; Moroni, Saverio, E-mail: moroni@democritos.it

2016-05-21

We present a simple and general formalism to compute efficiently the derivatives of a multi-determinant Jastrow-Slater wave function, the local energy, the interatomic forces, and similar quantities needed in quantum Monte Carlo. Through a straightforward manipulation of matrices evaluated on the occupied and virtual orbitals, we obtain an efficiency equivalent to algorithmic differentiation in the computation of the interatomic forces and the optimization of the orbital parameters. Furthermore, for a large multi-determinant expansion, the significant computational gain afforded by a recently introduced table method is here extended to the local value of any one-body operator and to its derivatives, inmore » both all-electron and pseudopotential calculations.« less

Information processing using a single dynamical node as complex system

PubMed Central

Appeltant, L.; Soriano, M.C.; Van der Sande, G.; Danckaert, J.; Massar, S.; Dambre, J.; Schrauwen, B.; Mirasso, C.R.; Fischer, I.

2011-01-01

Novel methods for information processing are highly desired in our information-driven society. Inspired by the brain's ability to process information, the recently introduced paradigm known as 'reservoir computing' shows that complex networks can efficiently perform computation. Here we introduce a novel architecture that reduces the usually required large number of elements to a single nonlinear node with delayed feedback. Through an electronic implementation, we experimentally and numerically demonstrate excellent performance in a speech recognition benchmark. Complementary numerical studies also show excellent performance for a time series prediction benchmark. These results prove that delay-dynamical systems, even in their simplest manifestation, can perform efficient information processing. This finding paves the way to feasible and resource-efficient technological implementations of reservoir computing. PMID:21915110

Influence of computational fluid dynamics on experimental aerospace facilities: A fifteen year projection

NASA Technical Reports Server (NTRS)

1983-01-01

An assessment was made of the impact of developments in computational fluid dynamics (CFD) on the traditional role of aerospace ground test facilities over the next fifteen years. With improvements in CFD and more powerful scientific computers projected over this period it is expected to have the capability to compute the flow over a complete aircraft at a unit cost three orders of magnitude lower than presently possible. Over the same period improvements in ground test facilities will progress by application of computational techniques including CFD to data acquisition, facility operational efficiency, and simulation of the light envelope; however, no dramatic change in unit cost is expected as greater efficiency will be countered by higher energy and labor costs.

Adjoint-Based Aerodynamic Design of Complex Aerospace Configurations

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.

2016-01-01

An overview of twenty years of adjoint-based aerodynamic design research at NASA Langley Research Center is presented. Adjoint-based algorithms provide a powerful tool for efficient sensitivity analysis of complex large-scale computational fluid dynamics (CFD) simulations. Unlike alternative approaches for which computational expense generally scales with the number of design parameters, adjoint techniques yield sensitivity derivatives of a simulation output with respect to all input parameters at the cost of a single additional simulation. With modern large-scale CFD applications often requiring millions of compute hours for a single analysis, the efficiency afforded by adjoint methods is critical in realizing a computationally tractable design optimization capability for such applications.

A learnable parallel processing architecture towards unity of memory and computing

NASA Astrophysics Data System (ADS)

Li, H.; Gao, B.; Chen, Z.; Zhao, Y.; Huang, P.; Ye, H.; Liu, L.; Liu, X.; Kang, J.

2015-08-01

Developing energy-efficient parallel information processing systems beyond von Neumann architecture is a long-standing goal of modern information technologies. The widely used von Neumann computer architecture separates memory and computing units, which leads to energy-hungry data movement when computers work. In order to meet the need of efficient information processing for the data-driven applications such as big data and Internet of Things, an energy-efficient processing architecture beyond von Neumann is critical for the information society. Here we show a non-von Neumann architecture built of resistive switching (RS) devices named “iMemComp”, where memory and logic are unified with single-type devices. Leveraging nonvolatile nature and structural parallelism of crossbar RS arrays, we have equipped “iMemComp” with capabilities of computing in parallel and learning user-defined logic functions for large-scale information processing tasks. Such architecture eliminates the energy-hungry data movement in von Neumann computers. Compared with contemporary silicon technology, adder circuits based on “iMemComp” can improve the speed by 76.8% and the power dissipation by 60.3%, together with a 700 times aggressive reduction in the circuit area.

A learnable parallel processing architecture towards unity of memory and computing.

PubMed

Li, H; Gao, B; Chen, Z; Zhao, Y; Huang, P; Ye, H; Liu, L; Liu, X; Kang, J

2015-08-14

Developing energy-efficient parallel information processing systems beyond von Neumann architecture is a long-standing goal of modern information technologies. The widely used von Neumann computer architecture separates memory and computing units, which leads to energy-hungry data movement when computers work. In order to meet the need of efficient information processing for the data-driven applications such as big data and Internet of Things, an energy-efficient processing architecture beyond von Neumann is critical for the information society. Here we show a non-von Neumann architecture built of resistive switching (RS) devices named "iMemComp", where memory and logic are unified with single-type devices. Leveraging nonvolatile nature and structural parallelism of crossbar RS arrays, we have equipped "iMemComp" with capabilities of computing in parallel and learning user-defined logic functions for large-scale information processing tasks. Such architecture eliminates the energy-hungry data movement in von Neumann computers. Compared with contemporary silicon technology, adder circuits based on "iMemComp" can improve the speed by 76.8% and the power dissipation by 60.3%, together with a 700 times aggressive reduction in the circuit area.

Acceleration of FDTD mode solver by high-performance computing techniques.

PubMed

Han, Lin; Xi, Yanping; Huang, Wei-Ping

2010-06-21

A two-dimensional (2D) compact finite-difference time-domain (FDTD) mode solver is developed based on wave equation formalism in combination with the matrix pencil method (MPM). The method is validated for calculation of both real guided and complex leaky modes of typical optical waveguides against the bench-mark finite-difference (FD) eigen mode solver. By taking advantage of the inherent parallel nature of the FDTD algorithm, the mode solver is implemented on graphics processing units (GPUs) using the compute unified device architecture (CUDA). It is demonstrated that the high-performance computing technique leads to significant acceleration of the FDTD mode solver with more than 30 times improvement in computational efficiency in comparison with the conventional FDTD mode solver running on CPU of a standard desktop computer. The computational efficiency of the accelerated FDTD method is in the same order of magnitude of the standard finite-difference eigen mode solver and yet require much less memory (e.g., less than 10%). Therefore, the new method may serve as an efficient, accurate and robust tool for mode calculation of optical waveguides even when the conventional eigen value mode solvers are no longer applicable due to memory limitation.

Coalescent: an open-science framework for importance sampling in coalescent theory.

PubMed

Tewari, Susanta; Spouge, John L

2015-01-01

Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner. Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable. Conclusions. In coalescent theory, many studies of computational efficiency consider only effective sample size. Here, we evaluate proposals in the coalescent literature, to discover that the order of efficiency among the three importance sampling schemes changes when one considers running time as well as effective sample size. We also describe a computational technique called "just-in-time delegation" available to improve the trade-off between running time and precision by constructing improved importance sampling schemes from existing ones. Thus, our systems approach is a potential solution to the "2(8) programs problem" highlighted by Felsenstein, because it provides the flexibility to include or exclude various features of similar coalescent models or importance sampling schemes.

Simple proof of equivalence between adiabatic quantum computation and the circuit model.

PubMed

Mizel, Ari; Lidar, Daniel A; Mitchell, Morgan

2007-08-17

We prove the equivalence between adiabatic quantum computation and quantum computation in the circuit model. An explicit adiabatic computation procedure is given that generates a ground state from which the answer can be extracted. The amount of time needed is evaluated by computing the gap. We show that the procedure is computationally efficient.

Optimizing Cubature for Efficient Integration of Subspace Deformations

PubMed Central

An, Steven S.; Kim, Theodore; James, Doug L.

2009-01-01

We propose an efficient scheme for evaluating nonlinear subspace forces (and Jacobians) associated with subspace deformations. The core problem we address is efficient integration of the subspace force density over the 3D spatial domain. Similar to Gaussian quadrature schemes that efficiently integrate functions that lie in particular polynomial subspaces, we propose cubature schemes (multi-dimensional quadrature) optimized for efficient integration of force densities associated with particular subspace deformations, particular materials, and particular geometric domains. We support generic subspace deformation kinematics, and nonlinear hyperelastic materials. For an r-dimensional deformation subspace with O(r) cubature points, our method is able to evaluate subspace forces at O(r2) cost. We also describe composite cubature rules for runtime error estimation. Results are provided for various subspace deformation models, several hyperelastic materials (St.Venant-Kirchhoff, Mooney-Rivlin, Arruda-Boyce), and multimodal (graphics, haptics, sound) applications. We show dramatically better efficiency than traditional Monte Carlo integration. CR Categories: I.6.8 [Simulation and Modeling]: Types of Simulation—Animation, I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—Physically based modeling G.1.4 [Mathematics of Computing]: Numerical Analysis—Quadrature and Numerical Differentiation PMID:19956777

Propulsive efficiency of the underwater dolphin kick in humans.

PubMed

von Loebbecke, Alfred; Mittal, Rajat; Fish, Frank; Mark, Russell

2009-05-01

Three-dimensional fully unsteady computational fluid dynamic simulations of five Olympic-level swimmers performing the underwater dolphin kick are used to estimate the swimmer's propulsive efficiencies. These estimates are compared with those of a cetacean performing the dolphin kick. The geometries of the swimmers and the cetacean are based on laser and CT scans, respectively, and the stroke kinematics is based on underwater video footage. The simulations indicate that the propulsive efficiency for human swimmers varies over a relatively wide range from about 11% to 29%. The efficiency of the cetacean is found to be about 56%, which is significantly higher than the human swimmers. The computed efficiency is found not to correlate with either the slender body theory or with the Strouhal number.

Marc Henry de Frahan | NREL

Science.gov Websites

Computing Project, Marc develops high-fidelity turbulence models to enhance simulation accuracy and efficient numerical algorithms for future high performance computing hardware architectures. Research Interests High performance computing High order numerical methods for computational fluid dynamics Fluid

High-efficiency photorealistic computer-generated holograms based on the backward ray-tracing technique

NASA Astrophysics Data System (ADS)

Wang, Yuan; Chen, Zhidong; Sang, Xinzhu; Li, Hui; Zhao, Linmin

2018-03-01

Holographic displays can provide the complete optical wave field of a three-dimensional (3D) scene, including the depth perception. However, it often takes a long computation time to produce traditional computer-generated holograms (CGHs) without more complex and photorealistic rendering. The backward ray-tracing technique is able to render photorealistic high-quality images, which noticeably reduce the computation time achieved from the high-degree parallelism. Here, a high-efficiency photorealistic computer-generated hologram method is presented based on the ray-tracing technique. Rays are parallelly launched and traced under different illuminations and circumstances. Experimental results demonstrate the effectiveness of the proposed method. Compared with the traditional point cloud CGH, the computation time is decreased to 24 s to reconstruct a 3D object of 100 ×100 rays with continuous depth change.

PRESAGE: Protecting Structured Address Generation against Soft Errors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Vishal C.; Gopalakrishnan, Ganesh; Krishnamoorthy, Sriram

Modern computer scaling trends in pursuit of larger component counts and power efficiency have, unfortunately, lead to less reliable hardware and consequently soft errors escaping into application data ("silent data corruptions"). Techniques to enhance system resilience hinge on the availability of efficient error detectors that have high detection rates, low false positive rates, and lower computational overhead. Unfortunately, efficient detectors to detect faults during address generation (to index large arrays) have not been widely researched. We present a novel lightweight compiler-driven technique called PRESAGE for detecting bit-flips affecting structured address computations. A key insight underlying PRESAGE is that any addressmore » computation scheme that flows an already incurred error is better than a scheme that corrupts one particular array access but otherwise (falsely) appears to compute perfectly. Enabling the flow of errors allows one to situate detectors at loop exit points, and helps turn silent corruptions into easily detectable error situations. Our experiments using PolyBench benchmark suite indicate that PRESAGE-based error detectors have a high error-detection rate while incurring low overheads.« less

PRESAGE: Protecting Structured Address Generation against Soft Errors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Vishal C.; Gopalakrishnan, Ganesh; Krishnamoorthy, Sriram

Modern computer scaling trends in pursuit of larger component counts and power efficiency have, unfortunately, lead to less reliable hardware and consequently soft errors escaping into application data ("silent data corruptions"). Techniques to enhance system resilience hinge on the availability of efficient error detectors that have high detection rates, low false positive rates, and lower computational overhead. Unfortunately, efficient detectors to detect faults during address generation have not been widely researched (especially in the context of indexing large arrays). We present a novel lightweight compiler-driven technique called PRESAGE for detecting bit-flips affecting structured address computations. A key insight underlying PRESAGEmore » is that any address computation scheme that propagates an already incurred error is better than a scheme that corrupts one particular array access but otherwise (falsely) appears to compute perfectly. Ensuring the propagation of errors allows one to place detectors at loop exit points and helps turn silent corruptions into easily detectable error situations. Our experiments using the PolyBench benchmark suite indicate that PRESAGE-based error detectors have a high error-detection rate while incurring low overheads.« less

Hamiltonian Monte Carlo acceleration using surrogate functions with random bases.

PubMed

Zhang, Cheng; Shahbaba, Babak; Zhao, Hongkai

2017-11-01

For big data analysis, high computational cost for Bayesian methods often limits their applications in practice. In recent years, there have been many attempts to improve computational efficiency of Bayesian inference. Here we propose an efficient and scalable computational technique for a state-of-the-art Markov chain Monte Carlo methods, namely, Hamiltonian Monte Carlo. The key idea is to explore and exploit the structure and regularity in parameter space for the underlying probabilistic model to construct an effective approximation of its geometric properties. To this end, we build a surrogate function to approximate the target distribution using properly chosen random bases and an efficient optimization process. The resulting method provides a flexible, scalable, and efficient sampling algorithm, which converges to the correct target distribution. We show that by choosing the basis functions and optimization process differently, our method can be related to other approaches for the construction of surrogate functions such as generalized additive models or Gaussian process models. Experiments based on simulated and real data show that our approach leads to substantially more efficient sampling algorithms compared to existing state-of-the-art methods.

Efficient classical simulation of the Deutsch-Jozsa and Simon's algorithms

NASA Astrophysics Data System (ADS)

Johansson, Niklas; Larsson, Jan-Åke

2017-09-01

A long-standing aim of quantum information research is to understand what gives quantum computers their advantage. This requires separating problems that need genuinely quantum resources from those for which classical resources are enough. Two examples of quantum speed-up are the Deutsch-Jozsa and Simon's problem, both efficiently solvable on a quantum Turing machine, and both believed to lack efficient classical solutions. Here we present a framework that can simulate both quantum algorithms efficiently, solving the Deutsch-Jozsa problem with probability 1 using only one oracle query, and Simon's problem using linearly many oracle queries, just as expected of an ideal quantum computer. The presented simulation framework is in turn efficiently simulatable in a classical probabilistic Turing machine. This shows that the Deutsch-Jozsa and Simon's problem do not require any genuinely quantum resources, and that the quantum algorithms show no speed-up when compared with their corresponding classical simulation. Finally, this gives insight into what properties are needed in the two algorithms and calls for further study of oracle separation between quantum and classical computation.

Higher-order adaptive finite-element methods for Kohn–Sham density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Motamarri, P.; Nowak, M.R.; Leiter, K.

2013-11-15

We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposedmore » solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using modest computational resources, and good scalability of the present implementation up to 192 processors.« less

Energy efficiency indicators for high electric-load buildings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aebischer, Bernard; Balmer, Markus A.; Kinney, Satkartar

2003-06-01

Energy per unit of floor area is not an adequate indicator for energy efficiency in high electric-load buildings. For two activities, restaurants and computer centres, alternative indicators for energy efficiency are discussed.

Design synthesis and optimization of permanent magnet synchronous machines based on computationally-efficient finite element analysis

NASA Astrophysics Data System (ADS)

Sizov, Gennadi Y.

In this dissertation, a model-based multi-objective optimal design of permanent magnet ac machines, supplied by sine-wave current regulated drives, is developed and implemented. The design procedure uses an efficient electromagnetic finite element-based solver to accurately model nonlinear material properties and complex geometric shapes associated with magnetic circuit design. Application of an electromagnetic finite element-based solver allows for accurate computation of intricate performance parameters and characteristics. The first contribution of this dissertation is the development of a rapid computational method that allows accurate and efficient exploration of large multi-dimensional design spaces in search of optimum design(s). The computationally efficient finite element-based approach developed in this work provides a framework of tools that allow rapid analysis of synchronous electric machines operating under steady-state conditions. In the developed modeling approach, major steady-state performance parameters such as, winding flux linkages and voltages, average, cogging and ripple torques, stator core flux densities, core losses, efficiencies and saturated machine winding inductances, are calculated with minimum computational effort. In addition, the method includes means for rapid estimation of distributed stator forces and three-dimensional effects of stator and/or rotor skew on the performance of the machine. The second contribution of this dissertation is the development of the design synthesis and optimization method based on a differential evolution algorithm. The approach relies on the developed finite element-based modeling method for electromagnetic analysis and is able to tackle large-scale multi-objective design problems using modest computational resources. Overall, computational time savings of up to two orders of magnitude are achievable, when compared to current and prevalent state-of-the-art methods. These computational savings allow one to expand the optimization problem to achieve more complex and comprehensive design objectives. The method is used in the design process of several interior permanent magnet industrial motors. The presented case studies demonstrate that the developed finite element-based approach practically eliminates the need for using less accurate analytical and lumped parameter equivalent circuit models for electric machine design optimization. The design process and experimental validation of the case-study machines are detailed in the dissertation.

Developing a Computer Workshop To Facilitate Computer Skills and Minimize Anxiety for Early Childhood Educators.

ERIC Educational Resources Information Center

Wood, Eileen; Willoughby, Teena; Specht, Jacqueline; Stern-Cavalcante, Wilma; Child, Carol

2002-01-01

Early childhood educators were assigned to one of three instructional conditions to assess the impact of computer workshops on their level of computer anxiety, knowledge, and comfort with technology. Overall, workshops provided gains that could translate into more effective and efficient computer use in the classroom. (Author)

LaRC local area networks to support distributed computing

NASA Technical Reports Server (NTRS)

Riddle, E. P.

1984-01-01

The Langley Research Center's (LaRC) Local Area Network (LAN) effort is discussed. LaRC initiated the development of a LAN to support a growing distributed computing environment at the Center. The purpose of the network is to provide an improved capability (over inteactive and RJE terminal access) for sharing multivendor computer resources. Specifically, the network will provide a data highway for the transfer of files between mainframe computers, minicomputers, work stations, and personal computers. An important influence on the overall network design was the vital need of LaRC researchers to efficiently utilize the large CDC mainframe computers in the central scientific computing facility. Although there was a steady migration from a centralized to a distributed computing environment at LaRC in recent years, the work load on the central resources increased. Major emphasis in the network design was on communication with the central resources within the distributed environment. The network to be implemented will allow researchers to utilize the central resources, distributed minicomputers, work stations, and personal computers to obtain the proper level of computing power to efficiently perform their jobs.

On the impact of approximate computation in an analog DeSTIN architecture.

PubMed

Young, Steven; Lu, Junjie; Holleman, Jeremy; Arel, Itamar

2014-05-01

Deep machine learning (DML) holds the potential to revolutionize machine learning by automating rich feature extraction, which has become the primary bottleneck of human engineering in pattern recognition systems. However, the heavy computational burden renders DML systems implemented on conventional digital processors impractical for large-scale problems. The highly parallel computations required to implement large-scale deep learning systems are well suited to custom hardware. Analog computation has demonstrated power efficiency advantages of multiple orders of magnitude relative to digital systems while performing nonideal computations. In this paper, we investigate typical error sources introduced by analog computational elements and their impact on system-level performance in DeSTIN--a compositional deep learning architecture. These inaccuracies are evaluated on a pattern classification benchmark, clearly demonstrating the robustness of the underlying algorithm to the errors introduced by analog computational elements. A clear understanding of the impacts of nonideal computations is necessary to fully exploit the efficiency of analog circuits.

A hydrological emulator for global applications - HE v1.0.0

NASA Astrophysics Data System (ADS)

Liu, Yaling; Hejazi, Mohamad; Li, Hongyi; Zhang, Xuesong; Leng, Guoyong

2018-03-01

While global hydrological models (GHMs) are very useful in exploring water resources and interactions between the Earth and human systems, their use often requires numerous model inputs, complex model calibration, and high computation costs. To overcome these challenges, we construct an efficient open-source and ready-to-use hydrological emulator (HE) that can mimic complex GHMs at a range of spatial scales (e.g., basin, region, globe). More specifically, we construct both a lumped and a distributed scheme of the HE based on the monthly abcd model to explore the tradeoff between computational cost and model fidelity. Model predictability and computational efficiency are evaluated in simulating global runoff from 1971 to 2010 with both the lumped and distributed schemes. The results are compared against the runoff product from the widely used Variable Infiltration Capacity (VIC) model. Our evaluation indicates that the lumped and distributed schemes present comparable results regarding annual total quantity, spatial pattern, and temporal variation of the major water fluxes (e.g., total runoff, evapotranspiration) across the global 235 basins (e.g., correlation coefficient r between the annual total runoff from either of these two schemes and the VIC is > 0.96), except for several cold (e.g., Arctic, interior Tibet), dry (e.g., North Africa) and mountainous (e.g., Argentina) regions. Compared against the monthly total runoff product from the VIC (aggregated from daily runoff), the global mean Kling-Gupta efficiencies are 0.75 and 0.79 for the lumped and distributed schemes, respectively, with the distributed scheme better capturing spatial heterogeneity. Notably, the computation efficiency of the lumped scheme is 2 orders of magnitude higher than the distributed one and 7 orders more efficient than the VIC model. A case study of uncertainty analysis for the world's 16 basins with top annual streamflow is conducted using 100 000 model simulations, and it demonstrates the lumped scheme's extraordinary advantage in computational efficiency. Our results suggest that the revised lumped abcd model can serve as an efficient and reasonable HE for complex GHMs and is suitable for broad practical use, and the distributed scheme is also an efficient alternative if spatial heterogeneity is of more interest.

TU-AB-303-08: GPU-Based Software Platform for Efficient Image-Guided Adaptive Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, S; Robinson, A; McNutt, T

2015-06-15

Purpose: In this study, we develop an integrated software platform for adaptive radiation therapy (ART) that combines fast and accurate image registration, segmentation, and dose computation/accumulation methods. Methods: The proposed system consists of three key components; 1) deformable image registration (DIR), 2) automatic segmentation, and 3) dose computation/accumulation. The computationally intensive modules including DIR and dose computation have been implemented on a graphics processing unit (GPU). All required patient-specific data including the planning CT (pCT) with contours, daily cone-beam CTs, and treatment plan are automatically queried and retrieved from their own databases. To improve the accuracy of DIR between pCTmore » and CBCTs, we use the double force demons DIR algorithm in combination with iterative CBCT intensity correction by local intensity histogram matching. Segmentation of daily CBCT is then obtained by propagating contours from the pCT. Daily dose delivered to the patient is computed on the registered pCT by a GPU-accelerated superposition/convolution algorithm. Finally, computed daily doses are accumulated to show the total delivered dose to date. Results: Since the accuracy of DIR critically affects the quality of the other processes, we first evaluated our DIR method on eight head-and-neck cancer cases and compared its performance. Normalized mutual-information (NMI) and normalized cross-correlation (NCC) computed as similarity measures, and our method produced overall NMI of 0.663 and NCC of 0.987, outperforming conventional methods by 3.8% and 1.9%, respectively. Experimental results show that our registration method is more consistent and roust than existing algorithms, and also computationally efficient. Computation time at each fraction took around one minute (30–50 seconds for registration and 15–25 seconds for dose computation). Conclusion: We developed an integrated GPU-accelerated software platform that enables accurate and efficient DIR, auto-segmentation, and dose computation, thus supporting an efficient ART workflow. This work was supported by NIH/NCI under grant R42CA137886.« less

Fast sweeping methods for hyperbolic systems of conservation laws at steady state II

NASA Astrophysics Data System (ADS)

Engquist, Björn; Froese, Brittany D.; Tsai, Yen-Hsi Richard

2015-04-01

The idea of using fast sweeping methods for solving stationary systems of conservation laws has previously been proposed for efficiently computing solutions with sharp shocks. We further develop these methods to allow for a more challenging class of problems including problems with sonic points, shocks originating in the interior of the domain, rarefaction waves, and two-dimensional systems. We show that fast sweeping methods can produce higher-order accuracy. Computational results validate the claims of accuracy, sharp shock curves, and optimal computational efficiency.

Multiple multicontrol unitary operations: Implementation and applications

NASA Astrophysics Data System (ADS)

Lin, Qing

2018-04-01

The efficient implementation of computational tasks is critical to quantum computations. In quantum circuits, multicontrol unitary operations are important components. Here, we present an extremely efficient and direct approach to multiple multicontrol unitary operations without decomposition to CNOT and single-photon gates. With the proposed approach, the necessary two-photon operations could be reduced from O( n 3) with the traditional decomposition approach to O( n), which will greatly relax the requirements and make large-scale quantum computation feasible. Moreover, we propose the potential application to the ( n- k)-uniform hypergraph state.

A non-linear programming approach to the computer-aided design of regulators using a linear-quadratic formulation

NASA Technical Reports Server (NTRS)

Fleming, P.

1985-01-01

A design technique is proposed for linear regulators in which a feedback controller of fixed structure is chosen to minimize an integral quadratic objective function subject to the satisfaction of integral quadratic constraint functions. Application of a non-linear programming algorithm to this mathematically tractable formulation results in an efficient and useful computer-aided design tool. Particular attention is paid to computational efficiency and various recommendations are made. Two design examples illustrate the flexibility of the approach and highlight the special insight afforded to the designer.

STAR adaptation of QR algorithm. [program for solving over-determined systems of linear equations

NASA Technical Reports Server (NTRS)

Shah, S. N.

1981-01-01

The QR algorithm used on a serial computer and executed on the Control Data Corporation 6000 Computer was adapted to execute efficiently on the Control Data STAR-100 computer. How the scalar program was adapted for the STAR-100 and why these adaptations yielded an efficient STAR program is described. Program listings of the old scalar version and the vectorized SL/1 version are presented in the appendices. Execution times for the two versions applied to the same system of linear equations, are compared.

Secure and Efficient Network Fault Localization

DTIC Science & Technology

2012-02-27

ORGANIZATION NAME(S) AND ADDRESS (ES) Carnegie Mellon University,School of Computer Science,Computer Science Department,Pittsburgh,PA,15213 8. PERFORMING...ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS (ES) 10. SPONSOR/MONITOR’S ACRONYM(S) 11. SPONSOR/MONITOR’S REPORT...efficiency than previously known protocols for fault localization. Our proposed fault localization protocols also address the security threats that

Using Neural Net Technology To Enhance the Efficiency of a Computer Adaptive Testing Application.

ERIC Educational Resources Information Center

Van Nelson, C.; Henriksen, Larry W.

The potential for computer adaptive testing (CAT) has been well documented. In order to improve the efficiency of this process, it may be possible to utilize a neural network, or more specifically, a back propagation neural network. The paper asserts that in order to accomplish this end, it must be shown that grouping examinees by ability as…

The Application of Multiobjective Evolutionary Algorithms to an Educational Computational Model of Science Information Processing: A Computational Experiment in Science Education

ERIC Educational Resources Information Center

Lamb, Richard L.; Firestone, Jonah B.

2017-01-01

Conflicting explanations and unrelated information in science classrooms increase cognitive load and decrease efficiency in learning. This reduced efficiency ultimately limits one's ability to solve reasoning problems in the science. In reasoning, it is the ability of students to sift through and identify critical pieces of information that is of…

Center for Efficient Exascale Discretizations Software Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolev, Tzanio; Dobrev, Veselin; Tomov, Vladimir

The CEED Software suite is a collection of generally applicable software tools focusing on the following computational motives: PDE discretizations on unstructured meshes, high-order finite element and spectral element methods and unstructured adaptive mesh refinement. All of this software is being developed as part of CEED, a co-design Center for Efficient Exascale Discretizations, within DOE's Exascale Computing Project (ECP) program.

Efficient Algorithms for Estimating the Absorption Spectrum within Linear Response TDDFT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brabec, Jiri; Lin, Lin; Shao, Meiyue

We present two iterative algorithms for approximating the absorption spectrum of molecules within linear response of time-dependent density functional theory (TDDFT) framework. These methods do not attempt to compute eigenvalues or eigenvectors of the linear response matrix. They are designed to approximate the absorption spectrum as a function directly. They take advantage of the special structure of the linear response matrix. Neither method requires the linear response matrix to be constructed explicitly. They only require a procedure that performs the multiplication of the linear response matrix with a vector. These methods can also be easily modified to efficiently estimate themore » density of states (DOS) of the linear response matrix without computing the eigenvalues of this matrix. We show by computational experiments that the methods proposed in this paper can be much more efficient than methods that are based on the exact diagonalization of the linear response matrix. We show that they can also be more efficient than real-time TDDFT simulations. We compare the pros and cons of these methods in terms of their accuracy as well as their computational and storage cost.« less

Automated Measurement of Patient-Specific Tibial Slopes from MRI

PubMed Central

Amerinatanzi, Amirhesam; Summers, Rodney K.; Ahmadi, Kaveh; Goel, Vijay K.; Hewett, Timothy E.; Nyman, Edward

2017-01-01

Background: Multi-planar proximal tibial slopes may be associated with increased likelihood of osteoarthritis and anterior cruciate ligament injury, due in part to their role in checking the anterior-posterior stability of the knee. Established methods suffer repeatability limitations and lack computational efficiency for intuitive clinical adoption. The aims of this study were to develop a novel automated approach and to compare the repeatability and computational efficiency of the approach against previously established methods. Methods: Tibial slope geometries were obtained via MRI and measured using an automated Matlab-based approach. Data were compared for repeatability and evaluated for computational efficiency. Results: Mean lateral tibial slope (LTS) for females (7.2°) was greater than for males (1.66°). Mean LTS in the lateral concavity zone was greater for females (7.8° for females, 4.2° for males). Mean medial tibial slope (MTS) for females was greater (9.3° vs. 4.6°). Along the medial concavity zone, female subjects demonstrated greater MTS. Conclusion: The automated method was more repeatable and computationally efficient than previously identified methods and may aid in the clinical assessment of knee injury risk, inform surgical planning, and implant design efforts. PMID:28952547

A new framework for comprehensive, robust, and efficient global sensitivity analysis: 1. Theory

NASA Astrophysics Data System (ADS)

Razavi, Saman; Gupta, Hoshin V.

2016-01-01

Computer simulation models are continually growing in complexity with increasingly more factors to be identified. Sensitivity Analysis (SA) provides an essential means for understanding the role and importance of these factors in producing model responses. However, conventional approaches to SA suffer from (1) an ambiguous characterization of sensitivity, and (2) poor computational efficiency, particularly as the problem dimension grows. Here, we present a new and general sensitivity analysis framework (called VARS), based on an analogy to "variogram analysis," that provides an intuitive and comprehensive characterization of sensitivity across the full spectrum of scales in the factor space. We prove, theoretically, that Morris (derivative-based) and Sobol (variance-based) methods and their extensions are special cases of VARS, and that their SA indices can be computed as by-products of the VARS framework. Synthetic functions that resemble actual model response surfaces are used to illustrate the concepts, and show VARS to be as much as two orders of magnitude more computationally efficient than the state-of-the-art Sobol approach. In a companion paper, we propose a practical implementation strategy, and demonstrate the effectiveness, efficiency, and reliability (robustness) of the VARS framework on real-data case studies.

Energy Efficient Engine (E3) controls and accessories detail design report

NASA Technical Reports Server (NTRS)

Beitler, R. S.; Lavash, J. P.

1982-01-01

An Energy Efficient Engine program has been established by NASA to develop technology for improving the energy efficiency of future commercial transport aircraft engines. As part of this program, a new turbofan engine was designed. This report describes the fuel and control system for this engine. The system design is based on many of the proven concepts and component designs used on the General Electric CF6 family of engines. One significant difference is the incorporation of digital electronic computation in place of the hydromechanical computation currently used.

Improvements in the efficiency of turboexpanders in cryogenic applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agahi, R.R.; Lin, M.C.; Ershaghi, B.

1996-12-31

Process designers have utilized turboexpanders in cryogenic processes because of their higher thermal efficiencies when compared with conventional refrigeration cycles. Process design and equipment performance have improved substantially through the utilization of modern technologies. Turboexpander manufacturers have also adopted Computational Fluid Dynamic Software, Computer Numerical Control Technology and Holography Techniques to further improve an already impressive turboexpander efficiency performance. In this paper, the authors explain the design process of the turboexpander utilizing modern technology. Two cases of turboexpanders processing helium (4.35{degrees}K) and hydrogen (56{degrees}K) will be presented.

Virtualization and cloud computing in dentistry.

PubMed

Chow, Frank; Muftu, Ali; Shorter, Richard

2014-01-01

The use of virtualization and cloud computing has changed the way we use computers. Virtualization is a method of placing software called a hypervisor on the hardware of a computer or a host operating system. It allows a guest operating system to run on top of the physical computer with a virtual machine (i.e., virtual computer). Virtualization allows multiple virtual computers to run on top of one physical computer and to share its hardware resources, such as printers, scanners, and modems. This increases the efficient use of the computer by decreasing costs (e.g., hardware, electricity administration, and management) since only one physical computer is needed and running. This virtualization platform is the basis for cloud computing. It has expanded into areas of server and storage virtualization. One of the commonly used dental storage systems is cloud storage. Patient information is encrypted as required by the Health Insurance Portability and Accountability Act (HIPAA) and stored on off-site private cloud services for a monthly service fee. As computer costs continue to increase, so too will the need for more storage and processing power. Virtual and cloud computing will be a method for dentists to minimize costs and maximize computer efficiency in the near future. This article will provide some useful information on current uses of cloud computing.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Lattice Boltzmann Method for 3-D Flows with Curved Boundary

NASA Technical Reports Server (NTRS)

Mei, Renwei; Shyy, Wei; Yu, Dazhi; Luo, Li-Shi

2002-01-01

In this work, we investigate two issues that are important to computational efficiency and reliability in fluid dynamics applications of the lattice, Boltzmann equation (LBE): (1) Computational stability and accuracy of different lattice Boltzmann models and (2) the treatment of the boundary conditions on curved solid boundaries and their 3-D implementations. Three athermal 3-D LBE models (D3QI5, D3Ql9, and D3Q27) are studied and compared in terms of efficiency, accuracy, and robustness. The boundary treatment recently developed by Filippova and Hanel and Met et al. in 2-D is extended to and implemented for 3-D. The convergence, stability, and computational efficiency of the 3-D LBE models with the boundary treatment for curved boundaries were tested in simulations of four 3-D flows: (1) Fully developed flows in a square duct, (2) flow in a 3-D lid-driven cavity, (3) fully developed flows in a circular pipe, and (4) a uniform flow over a sphere. We found that while the fifteen-velocity 3-D (D3Ql5) model is more prone to numerical instability and the D3Q27 is more computationally intensive, the 63Q19 model provides a balance between computational reliability and efficiency. Through numerical simulations, we demonstrated that the boundary treatment for 3-D arbitrary curved geometry has second-order accuracy and possesses satisfactory stability characteristics.

Development of Efficient Real-Fluid Model in Simulating Liquid Rocket Injector Flows

NASA Technical Reports Server (NTRS)

Cheng, Gary; Farmer, Richard

2003-01-01

The characteristics of propellant mixing near the injector have a profound effect on the liquid rocket engine performance. However, the flow features near the injector of liquid rocket engines are extremely complicated, for example supercritical-pressure spray, turbulent mixing, and chemical reactions are present. Previously, a homogeneous spray approach with a real-fluid property model was developed to account for the compressibility and evaporation effects such that thermodynamics properties of a mixture at a wide range of pressures and temperatures can be properly calculated, including liquid-phase, gas- phase, two-phase, and dense fluid regions. The developed homogeneous spray model demonstrated a good success in simulating uni- element shear coaxial injector spray combustion flows. However, the real-fluid model suffered a computational deficiency when applied to a pressure-based computational fluid dynamics (CFD) code. The deficiency is caused by the pressure and enthalpy being the independent variables in the solution procedure of a pressure-based code, whereas the real-fluid model utilizes density and temperature as independent variables. The objective of the present research work is to improve the computational efficiency of the real-fluid property model in computing thermal properties. The proposed approach is called an efficient real-fluid model, and the improvement of computational efficiency is achieved by using a combination of a liquid species and a gaseous species to represent a real-fluid species.

Multi-GPU hybrid programming accelerated three-dimensional phase-field model in binary alloy

NASA Astrophysics Data System (ADS)

Zhu, Changsheng; Liu, Jieqiong; Zhu, Mingfang; Feng, Li

2018-03-01

In the process of dendritic growth simulation, the computational efficiency and the problem scales have extremely important influence on simulation efficiency of three-dimensional phase-field model. Thus, seeking for high performance calculation method to improve the computational efficiency and to expand the problem scales has a great significance to the research of microstructure of the material. A high performance calculation method based on MPI+CUDA hybrid programming model is introduced. Multi-GPU is used to implement quantitative numerical simulations of three-dimensional phase-field model in binary alloy under the condition of multi-physical processes coupling. The acceleration effect of different GPU nodes on different calculation scales is explored. On the foundation of multi-GPU calculation model that has been introduced, two optimization schemes, Non-blocking communication optimization and overlap of MPI and GPU computing optimization, are proposed. The results of two optimization schemes and basic multi-GPU model are compared. The calculation results show that the use of multi-GPU calculation model can improve the computational efficiency of three-dimensional phase-field obviously, which is 13 times to single GPU, and the problem scales have been expanded to 8193. The feasibility of two optimization schemes is shown, and the overlap of MPI and GPU computing optimization has better performance, which is 1.7 times to basic multi-GPU model, when 21 GPUs are used.

Efficiency of parallel direct optimization

NASA Technical Reports Server (NTRS)

Janies, D. A.; Wheeler, W. C.

2001-01-01

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

Introduction to Computer Aided Instruction in the Language Laboratory.

ERIC Educational Resources Information Center

Hughett, Harvey L.

The first half of this book focuses on the rationale, ideas, and information for the use of technology, including microcomputers, to improve language teaching efficiency. Topics discussed include foreign language computer assisted instruction (CAI), hardware and software selection, computer literacy, educational computing organizations, ease of…

Notification: Fieldwork for CIGIE Cloud Computing Initiative – Status of Cloud-Computing Within the Federal Government

EPA Pesticide Factsheets

Project #OA-FY14-0126, January 15, 2014. The EPA OIG is starting fieldwork on the Council of the Inspectors General on Integrity and Efficiency (CIGIE) Cloud Computing Initiative – Status of Cloud-Computing Environments Within the Federal Government.

Laboratory Mathematics

ERIC Educational Resources Information Center

de Mestre, Neville

2004-01-01

Computers were invented to help mathematicians perform long and complicated calculations more efficiently. By the time that a computing area became a familiar space in primary and secondary schools, the initial motivation for computer use had been submerged in the many other functions that modern computers now accomplish. Not only the mathematics…

Proceedings of the Workshop on Computational Aspects in the Control of Flexible Systems, part 1

NASA Technical Reports Server (NTRS)

Taylor, Lawrence W., Jr. (Compiler)

1989-01-01

Control/Structures Integration program software needs, computer aided control engineering for flexible spacecraft, computer aided design, computational efficiency and capability, modeling and parameter estimation, and control synthesis and optimization software for flexible structures and robots are among the topics discussed.

Computational multicore on two-layer 1D shallow water equations for erodible dambreak

NASA Astrophysics Data System (ADS)

Simanjuntak, C. A.; Bagustara, B. A. R. H.; Gunawan, P. H.

2018-03-01

The simulation of erodible dambreak using two-layer shallow water equations and SCHR scheme are elaborated in this paper. The results show that the two-layer SWE model in a good agreement with the data experiment which is performed by Louvain-la-Neuve Université Catholique de Louvain. Moreover, the parallel algorithm with multicore architecture are given in the results. The results show that Computer I with processor Intel(R) Core(TM) i5-2500 CPU Quad-Core has the best performance to accelerate the computational time. Moreover, Computer III with processor AMD A6-5200 APU Quad-Core is observed has higher speedup and efficiency. The speedup and efficiency of Computer III with number of grids 3200 are 3.716050530 times and 92.9% respectively.

An Assessment of Artificial Compressibility and Pressure Projection Methods for Incompressible Flow Simulations

NASA Technical Reports Server (NTRS)

Kwak, Dochan; Kiris, C.; Smith, Charles A. (Technical Monitor)

1998-01-01

Performance of the two commonly used numerical procedures, one based on artificial compressibility method and the other pressure projection method, are compared. These formulations are selected primarily because they are designed for three-dimensional applications. The computational procedures are compared by obtaining steady state solutions of a wake vortex and unsteady solutions of a curved duct flow. For steady computations, artificial compressibility was very efficient in terms of computing time and robustness. For an unsteady flow which requires small physical time step, pressure projection method was found to be computationally more efficient than an artificial compressibility method. This comparison is intended to give some basis for selecting a method or a flow solution code for large three-dimensional applications where computing resources become a critical issue.

An efficient coordinate transformation technique for unsteady, transonic aerodynamic analysis of low aspect-ratio wings

NASA Technical Reports Server (NTRS)

Guruswamy, G. P.; Goorjian, P. M.

1984-01-01

An efficient coordinate transformation technique is presented for constructing grids for unsteady, transonic aerodynamic computations for delta-type wings. The original shearing transformation yielded computations that were numerically unstable and this paper discusses the sources of those instabilities. The new shearing transformation yields computations that are stable, fast, and accurate. Comparisons of those two methods are shown for the flow over the F5 wing that demonstrate the new stability. Also, comparisons are made with experimental data that demonstrate the accuracy of the new method. The computations were made by using a time-accurate, finite-difference, alternating-direction-implicit (ADI) algorithm for the transonic small-disturbance potential equation.

Efficient computation of aerodynamic influence coefficients for aeroelastic analysis on a transputer network

NASA Technical Reports Server (NTRS)

Janetzke, David C.; Murthy, Durbha V.

1991-01-01

Aeroelastic analysis is multi-disciplinary and computationally expensive. Hence, it can greatly benefit from parallel processing. As part of an effort to develop an aeroelastic capability on a distributed memory transputer network, a parallel algorithm for the computation of aerodynamic influence coefficients is implemented on a network of 32 transputers. The aerodynamic influence coefficients are calculated using a 3-D unsteady aerodynamic model and a parallel discretization. Efficiencies up to 85 percent were demonstrated using 32 processors. The effect of subtask ordering, problem size, and network topology are presented. A comparison to results on a shared memory computer indicates that higher speedup is achieved on the distributed memory system.

Construction and application of Red5 cluster based on OpenStack

NASA Astrophysics Data System (ADS)

Wang, Jiaqing; Song, Jianxin

2017-08-01

With the application and development of cloud computing technology in various fields, the resource utilization rate of the data center has been improved obviously, and the system based on cloud computing platform has also improved the expansibility and stability. In the traditional way, Red5 cluster resource utilization is low and the system stability is poor. This paper uses cloud computing to efficiently calculate the resource allocation ability, and builds a Red5 server cluster based on OpenStack. Multimedia applications can be published to the Red5 cloud server cluster. The system achieves the flexible construction of computing resources, but also greatly improves the stability of the cluster and service efficiency.

An efficient method to compute spurious end point contributions in PO solutions. [Physical Optics

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.; Pistorius, Carl W. I.

1987-01-01

A method is given to compute the spurious endpoint contributions in the physical optics solution for electromagnetic scattering from conducting bodies. The method is applicable to general three-dimensional structures. The only information required to use the method is the radius of curvature of the body at the shadow boundary. Thus, the method is very efficient for numerical computations. As an illustration, the method is applied to several bodies of revolution to compute the endpoint contributions for backscattering in the case of axial incidence. It is shown that in high-frequency situations, the endpoint contributions obtained using the method are equal to the true endpoint contributions.

Parallel computation using boundary elements in solid mechanics

NASA Technical Reports Server (NTRS)

Chien, L. S.; Sun, C. T.

1990-01-01

The inherent parallelism of the boundary element method is shown. The boundary element is formulated by assuming the linear variation of displacements and tractions within a line element. Moreover, MACSYMA symbolic program is employed to obtain the analytical results for influence coefficients. Three computational components are parallelized in this method to show the speedup and efficiency in computation. The global coefficient matrix is first formed concurrently. Then, the parallel Gaussian elimination solution scheme is applied to solve the resulting system of equations. Finally, and more importantly, the domain solutions of a given boundary value problem are calculated simultaneously. The linear speedups and high efficiencies are shown for solving a demonstrated problem on Sequent Symmetry S81 parallel computing system.

LOCAL ORTHOGONAL CUTTING METHOD FOR COMPUTING MEDIAL CURVES AND ITS BIOMEDICAL APPLICATIONS

PubMed Central

Einstein, Daniel R.; Dyedov, Vladimir

2010-01-01

Medial curves have a wide range of applications in geometric modeling and analysis (such as shape matching) and biomedical engineering (such as morphometry and computer assisted surgery). The computation of medial curves poses significant challenges, both in terms of theoretical analysis and practical efficiency and reliability. In this paper, we propose a definition and analysis of medial curves and also describe an efficient and robust method called local orthogonal cutting (LOC) for computing medial curves. Our approach is based on three key concepts: a local orthogonal decomposition of objects into substructures, a differential geometry concept called the interior center of curvature (ICC), and integrated stability and consistency tests. These concepts lend themselves to robust numerical techniques and result in an algorithm that is efficient and noise resistant. We illustrate the effectiveness and robustness of our approach with some highly complex, large-scale, noisy biomedical geometries derived from medical images, including lung airways and blood vessels. We also present comparisons of our method with some existing methods. PMID:20628546

Efficient parallel resolution of the simplified transport equations in mixed-dual formulation

NASA Astrophysics Data System (ADS)

Barrault, M.; Lathuilière, B.; Ramet, P.; Roman, J.

2011-03-01

A reactivity computation consists of computing the highest eigenvalue of a generalized eigenvalue problem, for which an inverse power algorithm is commonly used. Very fine modelizations are difficult to treat for our sequential solver, based on the simplified transport equations, in terms of memory consumption and computational time. A first implementation of a Lagrangian based domain decomposition method brings to a poor parallel efficiency because of an increase in the power iterations [1]. In order to obtain a high parallel efficiency, we improve the parallelization scheme by changing the location of the loop over the subdomains in the overall algorithm and by benefiting from the characteristics of the Raviart-Thomas finite element. The new parallel algorithm still allows us to locally adapt the numerical scheme (mesh, finite element order). However, it can be significantly optimized for the matching grid case. The good behavior of the new parallelization scheme is demonstrated for the matching grid case on several hundreds of nodes for computations based on a pin-by-pin discretization.

Inverse targeting —An effective immunization strategy

NASA Astrophysics Data System (ADS)

Schneider, C. M.; Mihaljev, T.; Herrmann, H. J.

2012-05-01

We propose a new method to immunize populations or computer networks against epidemics which is more efficient than any continuous immunization method considered before. The novelty of our method resides in the way of determining the immunization targets. First we identify those individuals or computers that contribute the least to the disease spreading measured through their contribution to the size of the largest connected cluster in the social or a computer network. The immunization process follows the list of identified individuals or computers in inverse order, immunizing first those which are most relevant for the epidemic spreading. We have applied our immunization strategy to several model networks and two real networks, the Internet and the collaboration network of high-energy physicists. We find that our new immunization strategy is in the case of model networks up to 14%, and for real networks up to 33% more efficient than immunizing dynamically the most connected nodes in a network. Our strategy is also numerically efficient and can therefore be applied to large systems.

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

NREL's Building-Integrated Supercomputer Provides Heating and Efficient Computing (Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2014-09-01

NREL's Energy Systems Integration Facility (ESIF) is meant to investigate new ways to integrate energy sources so they work together efficiently, and one of the key tools to that investigation, a new supercomputer, is itself a prime example of energy systems integration. NREL teamed with Hewlett-Packard (HP) and Intel to develop the innovative warm-water, liquid-cooled Peregrine supercomputer, which not only operates efficiently but also serves as the primary source of building heat for ESIF offices and laboratories. This innovative high-performance computer (HPC) can perform more than a quadrillion calculations per second as part of the world's most energy-efficient HPC datamore » center.« less

A Survey of Methods for Analyzing and Improving GPU Energy Efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mittal, Sparsh; Vetter, Jeffrey S

2014-01-01

Recent years have witnessed a phenomenal growth in the computational capabilities and applications of GPUs. However, this trend has also led to dramatic increase in their power consumption. This paper surveys research works on analyzing and improving energy efficiency of GPUs. It also provides a classification of these techniques on the basis of their main research idea. Further, it attempts to synthesize research works which compare energy efficiency of GPUs with other computing systems, e.g. FPGAs and CPUs. The aim of this survey is to provide researchers with knowledge of state-of-the-art in GPU power management and motivate them to architectmore » highly energy-efficient GPUs of tomorrow.« less

Are Heavy Users of Computer Games and Social Media More Computer Literate?

ERIC Educational Resources Information Center

Appel, Markus

2012-01-01

Adolescents spend a substantial part of their leisure time with playing games and using social media such as Facebook. The present paper examines the link between adolescents' computer and Internet activities and computer literacy (defined as the ability to work with a computer efficiently). A cross-sectional study with N = 200 adolescents, aged…

Tensor Factorization for Low-Rank Tensor Completion.

PubMed

Zhou, Pan; Lu, Canyi; Lin, Zhouchen; Zhang, Chao

2018-03-01

Recently, a tensor nuclear norm (TNN) based method was proposed to solve the tensor completion problem, which has achieved state-of-the-art performance on image and video inpainting tasks. However, it requires computing tensor singular value decomposition (t-SVD), which costs much computation and thus cannot efficiently handle tensor data, due to its natural large scale. Motivated by TNN, we propose a novel low-rank tensor factorization method for efficiently solving the 3-way tensor completion problem. Our method preserves the low-rank structure of a tensor by factorizing it into the product of two tensors of smaller sizes. In the optimization process, our method only needs to update two smaller tensors, which can be more efficiently conducted than computing t-SVD. Furthermore, we prove that the proposed alternating minimization algorithm can converge to a Karush-Kuhn-Tucker point. Experimental results on the synthetic data recovery, image and video inpainting tasks clearly demonstrate the superior performance and efficiency of our developed method over state-of-the-arts including the TNN and matricization methods.

Design and Verification of Remote Sensing Image Data Center Storage Architecture Based on Hadoop

NASA Astrophysics Data System (ADS)

Tang, D.; Zhou, X.; Jing, Y.; Cong, W.; Li, C.

2018-04-01

The data center is a new concept of data processing and application proposed in recent years. It is a new method of processing technologies based on data, parallel computing, and compatibility with different hardware clusters. While optimizing the data storage management structure, it fully utilizes cluster resource computing nodes and improves the efficiency of data parallel application. This paper used mature Hadoop technology to build a large-scale distributed image management architecture for remote sensing imagery. Using MapReduce parallel processing technology, it called many computing nodes to process image storage blocks and pyramids in the background to improve the efficiency of image reading and application and sovled the need for concurrent multi-user high-speed access to remotely sensed data. It verified the rationality, reliability and superiority of the system design by testing the storage efficiency of different image data and multi-users and analyzing the distributed storage architecture to improve the application efficiency of remote sensing images through building an actual Hadoop service system.

Word aligned bitmap compression method, data structure, and apparatus

DOEpatents

Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

2004-12-14

The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

Efficient Parallelization of a Dynamic Unstructured Application on the Tera MTA

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak

1999-01-01

The success of parallel computing in solving real-life computationally-intensive problems relies on their efficient mapping and execution on large-scale multiprocessor architectures. Many important applications are both unstructured and dynamic in nature, making their efficient parallel implementation a daunting task. This paper presents the parallelization of a dynamic unstructured mesh adaptation algorithm using three popular programming paradigms on three leading supercomputers. We examine an MPI message-passing implementation on the Cray T3E and the SGI Origin2OOO, a shared-memory implementation using cache coherent nonuniform memory access (CC-NUMA) of the Origin2OOO, and a multi-threaded version on the newly-released Tera Multi-threaded Architecture (MTA). We compare several critical factors of this parallel code development, including runtime, scalability, programmability, and memory overhead. Our overall results demonstrate that multi-threaded systems offer tremendous potential for quickly and efficiently solving some of the most challenging real-life problems on parallel computers.

Use of parallel computing in mass processing of laser data

NASA Astrophysics Data System (ADS)

Będkowski, J.; Bratuś, R.; Prochaska, M.; Rzonca, A.

2015-12-01

The first part of the paper includes a description of the rules used to generate the algorithm needed for the purpose of parallel computing and also discusses the origins of the idea of research on the use of graphics processors in large scale processing of laser scanning data. The next part of the paper includes the results of an efficiency assessment performed for an array of different processing options, all of which were substantially accelerated with parallel computing. The processing options were divided into the generation of orthophotos using point clouds, coloring of point clouds, transformations, and the generation of a regular grid, as well as advanced processes such as the detection of planes and edges, point cloud classification, and the analysis of data for the purpose of quality control. Most algorithms had to be formulated from scratch in the context of the requirements of parallel computing. A few of the algorithms were based on existing technology developed by the Dephos Software Company and then adapted to parallel computing in the course of this research study. Processing time was determined for each process employed for a typical quantity of data processed, which helped confirm the high efficiency of the solutions proposed and the applicability of parallel computing to the processing of laser scanning data. The high efficiency of parallel computing yields new opportunities in the creation and organization of processing methods for laser scanning data.

Usability of an Adaptive Computer Assistant that Improves Self-care and Health Literacy of Older Adults

PubMed Central

Blanson Henkemans, O. A.; Rogers, W. A.; Fisk, A. D.; Neerincx, M. A.; Lindenberg, J.; van der Mast, C. A. P. G.

2014-01-01

Summary Objectives We developed an adaptive computer assistant for the supervision of diabetics’ self-care, to support limiting illness and need for acute treatment, and improve health literacy. This assistant monitors self-care activities logged in the patient’s electronic diary. Accordingly, it provides context-aware feedback. The objective was to evaluate whether older adults in general can make use of the computer assistant and to compare an adaptive computer assistant with a fixed one, concerning its usability and contribution to health literacy. Methods We conducted a laboratory experiment in the Georgia Tech Aware Home wherein 28 older adults participated in a usability evaluation of the computer assistant, while engaged in scenarios reflecting normal and health-critical situations. We evaluated the assistant on effectiveness, efficiency, satisfaction, and educational value. Finally, we studied the moderating effects of the subjects’ personal characteristics. Results Logging self-care tasks and receiving feedback from the computer assistant enhanced the subjects’ knowledge of diabetes. The adaptive assistant was more effective in dealing with normal and health-critical situations, and, generally, it led to more time efficiency. Subjects’ personal characteristics had substantial effects on the effectiveness and efficiency of the two computer assistants. Conclusions Older adults were able to use the adaptive computer assistant. In addition, it had a positive effect on the development of health literacy. The assistant has the potential to support older diabetics’ self care while maintaining quality of life. PMID:18213433

Microprogramming Handbook. Second Edition.

ERIC Educational Resources Information Center

Microdata Corp., Santa Ana, CA.

Instead of instructions residing in the main memory as in a fixed instruction computer, a micro-programable computer has a separete read-only memory which is alterable so that the system can be efficiently adapted to the application at hand. Microprogramable computers are faster than fixed instruction computers for several reasons: instruction…

High-Performance Computing Data Center Warm-Water Liquid Cooling |

Science.gov Websites

Computational Science | NREL Warm-Water Liquid Cooling High-Performance Computing Data Center Warm-Water Liquid Cooling NREL's High-Performance Computing Data Center (HPC Data Center) is liquid water Liquid cooling technologies offer a more energy-efficient solution that also allows for effective

Building Efficient Wireless Infrastructures for Pervasive Computing Environments

ERIC Educational Resources Information Center

Sheng, Bo

2010-01-01

Pervasive computing is an emerging concept that thoroughly brings computing devices and the consequent technology into people's daily life and activities. Most of these computing devices are very small, sometimes even "invisible", and often embedded into the objects surrounding people. In addition, these devices usually are not isolated, but…

[Correlation of codon biases and potential secondary structures with mRNA translation efficiency in unicellular organisms].

PubMed

Vladimirov, N V; Likhoshvaĭ, V A; Matushkin, Iu G

2007-01-01

Gene expression is known to correlate with degree of codon bias in many unicellular organisms. However, such correlation is absent in some organisms. Recently we demonstrated that inverted complementary repeats within coding DNA sequence must be considered for proper estimation of translation efficiency, since they may form secondary structures that obstruct ribosome movement. We have developed a program for estimation of potential coding DNA sequence expression in defined unicellular organism using its genome sequence. The program computes elongation efficiency index. Computation is based on estimation of coding DNA sequence elongation efficiency, taking into account three key factors: codon bias, average number of inverted complementary repeats, and free energy of potential stem-loop structures formed by the repeats. The influence of these factors on translation is numerically estimated. An optimal proportion of these factors is computed for each organism individually. Quantitative translational characteristics of 384 unicellular organisms (351 bacteria, 28 archaea, 5 eukaryota) have been computed using their annotated genomes from NCBI GenBank. Five potential evolutionary strategies of translational optimization have been determined among studied organisms. A considerable difference of preferred translational strategies between Bacteria and Archaea has been revealed. Significant correlations between elongation efficiency index and gene expression levels have been shown for two organisms (S. cerevisiae and H. pylori) using available microarray data. The proposed method allows to estimate numerically the coding DNA sequence translation efficiency and to optimize nucleotide composition of heterologous genes in unicellular organisms. http://www.mgs.bionet.nsc.ru/mgs/programs/eei-calculator/.

Parallel high-performance grid computing: capabilities and opportunities of a novel demanding service and business class allowing highest resource efficiency.

PubMed

Kepper, Nick; Ettig, Ramona; Dickmann, Frank; Stehr, Rene; Grosveld, Frank G; Wedemann, Gero; Knoch, Tobias A

2010-01-01

Especially in the life-science and the health-care sectors the huge IT requirements are imminent due to the large and complex systems to be analysed and simulated. Grid infrastructures play here a rapidly increasing role for research, diagnostics, and treatment, since they provide the necessary large-scale resources efficiently. Whereas grids were first used for huge number crunching of trivially parallelizable problems, increasingly parallel high-performance computing is required. Here, we show for the prime example of molecular dynamic simulations how the presence of large grid clusters including very fast network interconnects within grid infrastructures allows now parallel high-performance grid computing efficiently and thus combines the benefits of dedicated super-computing centres and grid infrastructures. The demands for this service class are the highest since the user group has very heterogeneous requirements: i) two to many thousands of CPUs, ii) different memory architectures, iii) huge storage capabilities, and iv) fast communication via network interconnects, are all needed in different combinations and must be considered in a highly dedicated manner to reach highest performance efficiency. Beyond, advanced and dedicated i) interaction with users, ii) the management of jobs, iii) accounting, and iv) billing, not only combines classic with parallel high-performance grid usage, but more importantly is also able to increase the efficiency of IT resource providers. Consequently, the mere "yes-we-can" becomes a huge opportunity like e.g. the life-science and health-care sectors as well as grid infrastructures by reaching higher level of resource efficiency.

Manyscale Computing for Sensor Processing in Support of Space Situational Awareness

NASA Astrophysics Data System (ADS)

Schmalz, M.; Chapman, W.; Hayden, E.; Sahni, S.; Ranka, S.

2014-09-01

Increasing image and signal data burden associated with sensor data processing in support of space situational awareness implies continuing computational throughput growth beyond the petascale regime. In addition to growing applications data burden and diversity, the breadth, diversity and scalability of high performance computing architectures and their various organizations challenge the development of a single, unifying, practicable model of parallel computation. Therefore, models for scalable parallel processing have exploited architectural and structural idiosyncrasies, yielding potential misapplications when legacy programs are ported among such architectures. In response to this challenge, we have developed a concise, efficient computational paradigm and software called Manyscale Computing to facilitate efficient mapping of annotated application codes to heterogeneous parallel architectures. Our theory, algorithms, software, and experimental results support partitioning and scheduling of application codes for envisioned parallel architectures, in terms of work atoms that are mapped (for example) to threads or thread blocks on computational hardware. Because of the rigor, completeness, conciseness, and layered design of our manyscale approach, application-to-architecture mapping is feasible and scalable for architectures at petascales, exascales, and above. Further, our methodology is simple, relying primarily on a small set of primitive mapping operations and support routines that are readily implemented on modern parallel processors such as graphics processing units (GPUs) and hybrid multi-processors (HMPs). In this paper, we overview the opportunities and challenges of manyscale computing for image and signal processing in support of space situational awareness applications. We discuss applications in terms of a layered hardware architecture (laboratory > supercomputer > rack > processor > component hierarchy). Demonstration applications include performance analysis and results in terms of execution time as well as storage, power, and energy consumption for bus-connected and/or networked architectures. The feasibility of the manyscale paradigm is demonstrated by addressing four principal challenges: (1) architectural/structural diversity, parallelism, and locality, (2) masking of I/O and memory latencies, (3) scalability of design as well as implementation, and (4) efficient representation/expression of parallel applications. Examples will demonstrate how manyscale computing helps solve these challenges efficiently on real-world computing systems.

An accurate, compact and computationally efficient representation of orbitals for quantum Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Luo, Ye; Esler, Kenneth; Kent, Paul; Shulenburger, Luke

Quantum Monte Carlo (QMC) calculations of giant molecules, surface and defect properties of solids have been feasible recently due to drastically expanding computational resources. However, with the most computationally efficient basis set, B-splines, these calculations are severely restricted by the memory capacity of compute nodes. The B-spline coefficients are shared on a node but not distributed among nodes, to ensure fast evaluation. A hybrid representation which incorporates atomic orbitals near the ions and B-spline ones in the interstitial regions offers a more accurate and less memory demanding description of the orbitals because they are naturally more atomic like near ions and much smoother in between, thus allowing coarser B-spline grids. We will demonstrate the advantage of hybrid representation over pure B-spline and Gaussian basis sets and also show significant speed-up like computing the non-local pseudopotentials with our new scheme. Moreover, we discuss a new algorithm for atomic orbital initialization which used to require an extra workflow step taking a few days. With this work, the highly efficient hybrid representation paves the way to simulate large size even in-homogeneous systems using QMC. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Computational Materials Sciences Program.

Optimal Computing Budget Allocation for Particle Swarm Optimization in Stochastic Optimization.

PubMed

Zhang, Si; Xu, Jie; Lee, Loo Hay; Chew, Ek Peng; Wong, Wai Peng; Chen, Chun-Hung

2017-04-01

Particle Swarm Optimization (PSO) is a popular metaheuristic for deterministic optimization. Originated in the interpretations of the movement of individuals in a bird flock or fish school, PSO introduces the concept of personal best and global best to simulate the pattern of searching for food by flocking and successfully translate the natural phenomena to the optimization of complex functions. Many real-life applications of PSO cope with stochastic problems. To solve a stochastic problem using PSO, a straightforward approach is to equally allocate computational effort among all particles and obtain the same number of samples of fitness values. This is not an efficient use of computational budget and leaves considerable room for improvement. This paper proposes a seamless integration of the concept of optimal computing budget allocation (OCBA) into PSO to improve the computational efficiency of PSO for stochastic optimization problems. We derive an asymptotically optimal allocation rule to intelligently determine the number of samples for all particles such that the PSO algorithm can efficiently select the personal best and global best when there is stochastic estimation noise in fitness values. We also propose an easy-to-implement sequential procedure. Numerical tests show that our new approach can obtain much better results using the same amount of computational effort.

FastMag: Fast micromagnetic simulator for complex magnetic structures (invited)

NASA Astrophysics Data System (ADS)

Chang, R.; Li, S.; Lubarda, M. V.; Livshitz, B.; Lomakin, V.

2011-04-01

A fast micromagnetic simulator (FastMag) for general problems is presented. FastMag solves the Landau-Lifshitz-Gilbert equation and can handle multiscale problems with a high computational efficiency. The simulator derives its high performance from efficient methods for evaluating the effective field and from implementations on massively parallel graphics processing unit (GPU) architectures. FastMag discretizes the computational domain into tetrahedral elements and therefore is highly flexible for general problems. The magnetostatic field is computed via the superposition principle for both volume and surface parts of the computational domain. This is accomplished by implementing efficient quadrature rules and analytical integration for overlapping elements in which the integral kernel is singular. Thus, discretized superposition integrals are computed using a nonuniform grid interpolation method, which evaluates the field from N sources at N collocated observers in O(N) operations. This approach allows handling objects of arbitrary shape, allows easily calculating of the field outside the magnetized domains, does not require solving a linear system of equations, and requires little memory. FastMag is implemented on GPUs with ?> GPU-central processing unit speed-ups of 2 orders of magnitude. Simulations are shown of a large array of magnetic dots and a recording head fully discretized down to the exchange length, with over a hundred million tetrahedral elements on an inexpensive desktop computer.

Optimal Computing Budget Allocation for Particle Swarm Optimization in Stochastic Optimization

PubMed Central

Zhang, Si; Xu, Jie; Lee, Loo Hay; Chew, Ek Peng; Chen, Chun-Hung

2017-01-01

Particle Swarm Optimization (PSO) is a popular metaheuristic for deterministic optimization. Originated in the interpretations of the movement of individuals in a bird flock or fish school, PSO introduces the concept of personal best and global best to simulate the pattern of searching for food by flocking and successfully translate the natural phenomena to the optimization of complex functions. Many real-life applications of PSO cope with stochastic problems. To solve a stochastic problem using PSO, a straightforward approach is to equally allocate computational effort among all particles and obtain the same number of samples of fitness values. This is not an efficient use of computational budget and leaves considerable room for improvement. This paper proposes a seamless integration of the concept of optimal computing budget allocation (OCBA) into PSO to improve the computational efficiency of PSO for stochastic optimization problems. We derive an asymptotically optimal allocation rule to intelligently determine the number of samples for all particles such that the PSO algorithm can efficiently select the personal best and global best when there is stochastic estimation noise in fitness values. We also propose an easy-to-implement sequential procedure. Numerical tests show that our new approach can obtain much better results using the same amount of computational effort. PMID:29170617

An efficient numerical technique for calculating thermal spreading resistance

NASA Technical Reports Server (NTRS)

Gale, E. H., Jr.

1977-01-01

An efficient numerical technique for solving the equations resulting from finite difference analyses of fields governed by Poisson's equation is presented. The method is direct (noniterative)and the computer work required varies with the square of the order of the coefficient matrix. The computational work required varies with the cube of this order for standard inversion techniques, e.g., Gaussian elimination, Jordan, Doolittle, etc.

Parallel CE/SE Computations via Domain Decomposition

NASA Technical Reports Server (NTRS)

Himansu, Ananda; Jorgenson, Philip C. E.; Wang, Xiao-Yen; Chang, Sin-Chung

2000-01-01

This paper describes the parallelization strategy and achieved parallel efficiency of an explicit time-marching algorithm for solving conservation laws. The Space-Time Conservation Element and Solution Element (CE/SE) algorithm for solving the 2D and 3D Euler equations is parallelized with the aid of domain decomposition. The parallel efficiency of the resultant algorithm on a Silicon Graphics Origin 2000 parallel computer is checked.

Efficient computation of turbulent flow in ribbed passages using a non-overlapping near-wall domain decomposition method

NASA Astrophysics Data System (ADS)

Jones, Adam; Utyuzhnikov, Sergey

2017-08-01

Turbulent flow in a ribbed channel is studied using an efficient near-wall domain decomposition (NDD) method. The NDD approach is formulated by splitting the computational domain into an inner and outer region, with an interface boundary between the two. The computational mesh covers the outer region, and the flow in this region is solved using the open-source CFD code Code_Saturne with special boundary conditions on the interface boundary, called interface boundary conditions (IBCs). The IBCs are of Robin type and incorporate the effect of the inner region on the flow in the outer region. IBCs are formulated in terms of the distance from the interface boundary to the wall in the inner region. It is demonstrated that up to 90% of the region between the ribs in the ribbed passage can be removed from the computational mesh with an error on the friction factor within 2.5%. In addition, computations with NDD are faster than computations based on low Reynolds number (LRN) models by a factor of five. Different rib heights can be studied with the same mesh in the outer region without affecting the accuracy of the friction factor. This is tested with six different rib heights in an example of a design optimisation study. It is found that the friction factors computed with NDD are almost identical to the fully-resolved results. When used for inverse problems, NDD is considerably more efficient than LRN computations because only one computation needs to be performed and only one mesh needs to be generated.

An efficient implementation of 3D high-resolution imaging for large-scale seismic data with GPU/CPU heterogeneous parallel computing

NASA Astrophysics Data System (ADS)

Xu, Jincheng; Liu, Wei; Wang, Jin; Liu, Linong; Zhang, Jianfeng

2018-02-01

De-absorption pre-stack time migration (QPSTM) compensates for the absorption and dispersion of seismic waves by introducing an effective Q parameter, thereby making it an effective tool for 3D, high-resolution imaging of seismic data. Although the optimal aperture obtained via stationary-phase migration reduces the computational cost of 3D QPSTM and yields 3D stationary-phase QPSTM, the associated computational efficiency is still the main problem in the processing of 3D, high-resolution images for real large-scale seismic data. In the current paper, we proposed a division method for large-scale, 3D seismic data to optimize the performance of stationary-phase QPSTM on clusters of graphics processing units (GPU). Then, we designed an imaging point parallel strategy to achieve an optimal parallel computing performance. Afterward, we adopted an asynchronous double buffering scheme for multi-stream to perform the GPU/CPU parallel computing. Moreover, several key optimization strategies of computation and storage based on the compute unified device architecture (CUDA) were adopted to accelerate the 3D stationary-phase QPSTM algorithm. Compared with the initial GPU code, the implementation of the key optimization steps, including thread optimization, shared memory optimization, register optimization and special function units (SFU), greatly improved the efficiency. A numerical example employing real large-scale, 3D seismic data showed that our scheme is nearly 80 times faster than the CPU-QPSTM algorithm. Our GPU/CPU heterogeneous parallel computing framework significant reduces the computational cost and facilitates 3D high-resolution imaging for large-scale seismic data.

An Efficiency Analysis of U.S. Business Schools

ERIC Educational Resources Information Center

Sexton, Thomas R.

2010-01-01

In the current economic climate, business schools face crucial decisions. As resources become scarcer, schools must either streamline operations or limit them. An efficiency analysis of U.S. business schools is presented that computes, for each business school, an overall efficiency score and provides separate factor efficiency scores, indicating…

Efficient Transition Probability Computation for Continuous-Time Branching Processes via Compressed Sensing.

PubMed

Xu, Jason; Minin, Vladimir N

2015-07-01

Branching processes are a class of continuous-time Markov chains (CTMCs) with ubiquitous applications. A general difficulty in statistical inference under partially observed CTMC models arises in computing transition probabilities when the discrete state space is large or uncountable. Classical methods such as matrix exponentiation are infeasible for large or countably infinite state spaces, and sampling-based alternatives are computationally intensive, requiring integration over all possible hidden events. Recent work has successfully applied generating function techniques to computing transition probabilities for linear multi-type branching processes. While these techniques often require significantly fewer computations than matrix exponentiation, they also become prohibitive in applications with large populations. We propose a compressed sensing framework that significantly accelerates the generating function method, decreasing computational cost up to a logarithmic factor by only assuming the probability mass of transitions is sparse. We demonstrate accurate and efficient transition probability computations in branching process models for blood cell formation and evolution of self-replicating transposable elements in bacterial genomes.

A Secure and Verifiable Outsourced Access Control Scheme in Fog-Cloud Computing

PubMed Central

Fan, Kai; Wang, Junxiong; Wang, Xin; Li, Hui; Yang, Yintang

2017-01-01

With the rapid development of big data and Internet of things (IOT), the number of networking devices and data volume are increasing dramatically. Fog computing, which extends cloud computing to the edge of the network can effectively solve the bottleneck problems of data transmission and data storage. However, security and privacy challenges are also arising in the fog-cloud computing environment. Ciphertext-policy attribute-based encryption (CP-ABE) can be adopted to realize data access control in fog-cloud computing systems. In this paper, we propose a verifiable outsourced multi-authority access control scheme, named VO-MAACS. In our construction, most encryption and decryption computations are outsourced to fog devices and the computation results can be verified by using our verification method. Meanwhile, to address the revocation issue, we design an efficient user and attribute revocation method for it. Finally, analysis and simulation results show that our scheme is both secure and highly efficient. PMID:28737733

Efficient Transition Probability Computation for Continuous-Time Branching Processes via Compressed Sensing

PubMed Central

Xu, Jason; Minin, Vladimir N.

2016-01-01

Branching processes are a class of continuous-time Markov chains (CTMCs) with ubiquitous applications. A general difficulty in statistical inference under partially observed CTMC models arises in computing transition probabilities when the discrete state space is large or uncountable. Classical methods such as matrix exponentiation are infeasible for large or countably infinite state spaces, and sampling-based alternatives are computationally intensive, requiring integration over all possible hidden events. Recent work has successfully applied generating function techniques to computing transition probabilities for linear multi-type branching processes. While these techniques often require significantly fewer computations than matrix exponentiation, they also become prohibitive in applications with large populations. We propose a compressed sensing framework that significantly accelerates the generating function method, decreasing computational cost up to a logarithmic factor by only assuming the probability mass of transitions is sparse. We demonstrate accurate and efficient transition probability computations in branching process models for blood cell formation and evolution of self-replicating transposable elements in bacterial genomes. PMID:26949377

Multiresolution molecular mechanics: Implementation and efficiency

NASA Astrophysics Data System (ADS)

Biyikli, Emre; To, Albert C.

2017-01-01

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3-8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

An efficient parallel termination detection algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, A. H.; Crivelli, S.; Jessup, E. R.

2004-05-27

Information local to any one processor is insufficient to monitor the overall progress of most distributed computations. Typically, a second distributed computation for detecting termination of the main computation is necessary. In order to be a useful computational tool, the termination detection routine must operate concurrently with the main computation, adding minimal overhead, and it must promptly and correctly detect termination when it occurs. In this paper, we present a new algorithm for detecting the termination of a parallel computation on distributed-memory MIMD computers that satisfies all of those criteria. A variety of termination detection algorithms have been devised. Ofmore » these, the algorithm presented by Sinha, Kale, and Ramkumar (henceforth, the SKR algorithm) is unique in its ability to adapt to the load conditions of the system on which it runs, thereby minimizing the impact of termination detection on performance. Because their algorithm also detects termination quickly, we consider it to be the most efficient practical algorithm presently available. The termination detection algorithm presented here was developed for use in the PMESC programming library for distributed-memory MIMD computers. Like the SKR algorithm, our algorithm adapts to system loads and imposes little overhead. Also like the SKR algorithm, ours is tree-based, and it does not depend on any assumptions about the physical interconnection topology of the processors or the specifics of the distributed computation. In addition, our algorithm is easier to implement and requires only half as many tree traverses as does the SKR algorithm. This paper is organized as follows. In section 2, we define our computational model. In section 3, we review the SKR algorithm. We introduce our new algorithm in section 4, and prove its correctness in section 5. We discuss its efficiency and present experimental results in section 6.« less

Computation in generalised probabilisitic theories

NASA Astrophysics Data System (ADS)

Lee, Ciarán M.; Barrett, Jonathan

2015-08-01

From the general difficulty of simulating quantum systems using classical systems, and in particular the existence of an efficient quantum algorithm for factoring, it is likely that quantum computation is intrinsically more powerful than classical computation. At present, the best upper bound known for the power of quantum computation is that {{BQP}}\\subseteq {{AWPP}}, where {{AWPP}} is a classical complexity class (known to be included in {{PP}}, hence {{PSPACE}}). This work investigates limits on computational power that are imposed by simple physical, or information theoretic, principles. To this end, we define a circuit-based model of computation in a class of operationally-defined theories more general than quantum theory, and ask: what is the minimal set of physical assumptions under which the above inclusions still hold? We show that given only an assumption of tomographic locality (roughly, that multipartite states and transformations can be characterized by local measurements), efficient computations are contained in {{AWPP}}. This inclusion still holds even without assuming a basic notion of causality (where the notion is, roughly, that probabilities for outcomes cannot depend on future measurement choices). Following Aaronson, we extend the computational model by allowing post-selection on measurement outcomes. Aaronson showed that the corresponding quantum complexity class, {{PostBQP}}, is equal to {{PP}}. Given only the assumption of tomographic locality, the inclusion in {{PP}} still holds for post-selected computation in general theories. Hence in a world with post-selection, quantum theory is optimal for computation in the space of all operational theories. We then consider whether one can obtain relativized complexity results for general theories. It is not obvious how to define a sensible notion of a computational oracle in the general framework that reduces to the standard notion in the quantum case. Nevertheless, it is possible to define computation relative to a ‘classical oracle’. Then, we show there exists a classical oracle relative to which efficient computation in any theory satisfying the causality assumption does not include {{NP}}.

The efficiency of geophysical adjoint codes generated by automatic differentiation tools

NASA Astrophysics Data System (ADS)

Vlasenko, A. V.; Köhl, A.; Stammer, D.

2016-02-01

The accuracy of numerical models that describe complex physical or chemical processes depends on the choice of model parameters. Estimating an optimal set of parameters by optimization algorithms requires knowledge of the sensitivity of the process of interest to model parameters. Typically the sensitivity computation involves differentiation of the model, which can be performed by applying algorithmic differentiation (AD) tools to the underlying numerical code. However, existing AD tools differ substantially in design, legibility and computational efficiency. In this study we show that, for geophysical data assimilation problems of varying complexity, the performance of adjoint codes generated by the existing AD tools (i) Open_AD, (ii) Tapenade, (iii) NAGWare and (iv) Transformation of Algorithms in Fortran (TAF) can be vastly different. Based on simple test problems, we evaluate the efficiency of each AD tool with respect to computational speed, accuracy of the adjoint, the efficiency of memory usage, and the capability of each AD tool to handle modern FORTRAN 90-95 elements such as structures and pointers, which are new elements that either combine groups of variables or provide aliases to memory addresses, respectively. We show that, while operator overloading tools are the only ones suitable for modern codes written in object-oriented programming languages, their computational efficiency lags behind source transformation by orders of magnitude, rendering the application of these modern tools to practical assimilation problems prohibitive. In contrast, the application of source transformation tools appears to be the most efficient choice, allowing handling even large geophysical data assimilation problems. However, they can only be applied to numerical models written in earlier generations of programming languages. Our study indicates that applying existing AD tools to realistic geophysical problems faces limitations that urgently need to be solved to allow the continuous use of AD tools for solving geophysical problems on modern computer architectures.

Low-Energy Truly Random Number Generation with Superparamagnetic Tunnel Junctions for Unconventional Computing

NASA Astrophysics Data System (ADS)

Vodenicarevic, D.; Locatelli, N.; Mizrahi, A.; Friedman, J. S.; Vincent, A. F.; Romera, M.; Fukushima, A.; Yakushiji, K.; Kubota, H.; Yuasa, S.; Tiwari, S.; Grollier, J.; Querlioz, D.

2017-11-01

Low-energy random number generation is critical for many emerging computing schemes proposed to complement or replace von Neumann architectures. However, current random number generators are always associated with an energy cost that is prohibitive for these computing schemes. We introduce random number bit generation based on specific nanodevices: superparamagnetic tunnel junctions. We experimentally demonstrate high-quality random bit generation that represents an orders-of-magnitude improvement in energy efficiency over current solutions. We show that the random generation speed improves with nanodevice scaling, and we investigate the impact of temperature, magnetic field, and cross talk. Finally, we show how alternative computing schemes can be implemented using superparamagentic tunnel junctions as random number generators. These results open the way for fabricating efficient hardware computing devices leveraging stochasticity, and they highlight an alternative use for emerging nanodevices.

An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology.

PubMed

Macías-Díaz, J E; Macías, Siegfried; Medina-Ramírez, I E

2013-12-01

In this manuscript, we present a computational model to approximate the solutions of a partial differential equation which describes the growth dynamics of microbial films. The numerical technique reported in this work is an explicit, nonlinear finite-difference methodology which is computationally implemented using Newton's method. Our scheme is compared numerically against an implicit, linear finite-difference discretization of the same partial differential equation, whose computer coding requires an implementation of the stabilized bi-conjugate gradient method. Our numerical results evince that the nonlinear approach results in a more efficient approximation to the solutions of the biofilm model considered, and demands less computer memory. Moreover, the positivity of initial profiles is preserved in the practice by the nonlinear scheme proposed. Copyright © 2013 Elsevier Ltd. All rights reserved.

Future computing platforms for science in a power constrained era

DOE PAGES

Abdurachmanov, David; Elmer, Peter; Eulisse, Giulio; ...

2015-12-23

Power consumption will be a key constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics (HEP). This makes performance-per-watt a crucial metric for selecting cost-efficient computing solutions. For this paper, we have done a wide survey of current and emerging architectures becoming available on the market including x86-64 variants, ARMv7 32-bit, ARMv8 64-bit, Many-Core and GPU solutions, as well as newer System-on-Chip (SoC) solutions. We compare performance and energy efficiency using an evolving set of standardized HEP-related benchmarks and power measurement techniques we have been developing. In conclusion, we evaluate the potentialmore » for use of such computing solutions in the context of DHTC systems, such as the Worldwide LHC Computing Grid (WLCG).« less

ClimateSpark: An in-memory distributed computing framework for big climate data analytics

NASA Astrophysics Data System (ADS)

Hu, Fei; Yang, Chaowei; Schnase, John L.; Duffy, Daniel Q.; Xu, Mengchao; Bowen, Michael K.; Lee, Tsengdar; Song, Weiwei

2018-06-01

The unprecedented growth of climate data creates new opportunities for climate studies, and yet big climate data pose a grand challenge to climatologists to efficiently manage and analyze big data. The complexity of climate data content and analytical algorithms increases the difficulty of implementing algorithms on high performance computing systems. This paper proposes an in-memory, distributed computing framework, ClimateSpark, to facilitate complex big data analytics and time-consuming computational tasks. Chunking data structure improves parallel I/O efficiency, while a spatiotemporal index is built for the chunks to avoid unnecessary data reading and preprocessing. An integrated, multi-dimensional, array-based data model (ClimateRDD) and ETL operations are developed to address big climate data variety by integrating the processing components of the climate data lifecycle. ClimateSpark utilizes Spark SQL and Apache Zeppelin to develop a web portal to facilitate the interaction among climatologists, climate data, analytic operations and computing resources (e.g., using SQL query and Scala/Python notebook). Experimental results show that ClimateSpark conducts different spatiotemporal data queries/analytics with high efficiency and data locality. ClimateSpark is easily adaptable to other big multiple-dimensional, array-based datasets in various geoscience domains.

A LSQR-type method provides a computationally efficient automated optimal choice of regularization parameter in diffuse optical tomography.

PubMed

Prakash, Jaya; Yalavarthy, Phaneendra K

2013-03-01

Developing a computationally efficient automated method for the optimal choice of regularization parameter in diffuse optical tomography. The least-squares QR (LSQR)-type method that uses Lanczos bidiagonalization is known to be computationally efficient in performing the reconstruction procedure in diffuse optical tomography. The same is effectively deployed via an optimization procedure that uses the simplex method to find the optimal regularization parameter. The proposed LSQR-type method is compared with the traditional methods such as L-curve, generalized cross-validation (GCV), and recently proposed minimal residual method (MRM)-based choice of regularization parameter using numerical and experimental phantom data. The results indicate that the proposed LSQR-type and MRM-based methods performance in terms of reconstructed image quality is similar and superior compared to L-curve and GCV-based methods. The proposed method computational complexity is at least five times lower compared to MRM-based method, making it an optimal technique. The LSQR-type method was able to overcome the inherent limitation of computationally expensive nature of MRM-based automated way finding the optimal regularization parameter in diffuse optical tomographic imaging, making this method more suitable to be deployed in real-time.

On the study of control effectiveness and computational efficiency of reduced Saint-Venant model in model predictive control of open channel flow

NASA Astrophysics Data System (ADS)

Xu, M.; van Overloop, P. J.; van de Giesen, N. C.

2011-02-01

Model predictive control (MPC) of open channel flow is becoming an important tool in water management. The complexity of the prediction model has a large influence on the MPC application in terms of control effectiveness and computational efficiency. The Saint-Venant equations, called SV model in this paper, and the Integrator Delay (ID) model are either accurate but computationally costly, or simple but restricted to allowed flow changes. In this paper, a reduced Saint-Venant (RSV) model is developed through a model reduction technique, Proper Orthogonal Decomposition (POD), on the SV equations. The RSV model keeps the main flow dynamics and functions over a large flow range but is easier to implement in MPC. In the test case of a modeled canal reach, the number of states and disturbances in the RSV model is about 45 and 16 times less than the SV model, respectively. The computational time of MPC with the RSV model is significantly reduced, while the controller remains effective. Thus, the RSV model is a promising means to balance the control effectiveness and computational efficiency.

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures.

PubMed

Stamatakis, Alexandros; Ott, Michael

2008-12-27

The continuous accumulation of sequence data, for example, due to novel wet-laboratory techniques such as pyrosequencing, coupled with the increasing popularity of multi-gene phylogenies and emerging multi-core processor architectures that face problems of cache congestion, poses new challenges with respect to the efficient computation of the phylogenetic maximum-likelihood (ML) function. Here, we propose two approaches that can significantly speed up likelihood computations that typically represent over 95 per cent of the computational effort conducted by current ML or Bayesian inference programs. Initially, we present a method and an appropriate data structure to efficiently compute the likelihood score on 'gappy' multi-gene alignments. By 'gappy' we denote sampling-induced gaps owing to missing sequences in individual genes (partitions), i.e. not real alignment gaps. A first proof-of-concept implementation in RAXML indicates that this approach can accelerate inferences on large and gappy alignments by approximately one order of magnitude. Moreover, we present insights and initial performance results on multi-core architectures obtained during the transition from an OpenMP-based to a Pthreads-based fine-grained parallelization of the ML function.

Efficient computation of the joint sample frequency spectra for multiple populations.

PubMed

Kamm, John A; Terhorst, Jonathan; Song, Yun S

2017-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity.

Carbon nanotube computer.

PubMed

Shulaker, Max M; Hills, Gage; Patil, Nishant; Wei, Hai; Chen, Hong-Yu; Wong, H-S Philip; Mitra, Subhasish

2013-09-26

The miniaturization of electronic devices has been the principal driving force behind the semiconductor industry, and has brought about major improvements in computational power and energy efficiency. Although advances with silicon-based electronics continue to be made, alternative technologies are being explored. Digital circuits based on transistors fabricated from carbon nanotubes (CNTs) have the potential to outperform silicon by improving the energy-delay product, a metric of energy efficiency, by more than an order of magnitude. Hence, CNTs are an exciting complement to existing semiconductor technologies. Owing to substantial fundamental imperfections inherent in CNTs, however, only very basic circuit blocks have been demonstrated. Here we show how these imperfections can be overcome, and demonstrate the first computer built entirely using CNT-based transistors. The CNT computer runs an operating system that is capable of multitasking: as a demonstration, we perform counting and integer-sorting simultaneously. In addition, we implement 20 different instructions from the commercial MIPS instruction set to demonstrate the generality of our CNT computer. This experimental demonstration is the most complex carbon-based electronic system yet realized. It is a considerable advance because CNTs are prominent among a variety of emerging technologies that are being considered for the next generation of highly energy-efficient electronic systems.

Efficient computation of the joint sample frequency spectra for multiple populations

PubMed Central

Kamm, John A.; Terhorst, Jonathan; Song, Yun S.

2016-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity. PMID:28239248

Computing rank-revealing QR factorizations of dense matrices.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bischof, C. H.; Quintana-Orti, G.; Mathematics and Computer Science

1998-06-01

We develop algorithms and implementations for computing rank-revealing QR (RRQR) factorizations of dense matrices. First, we develop an efficient block algorithm for approximating an RRQR factorization, employing a windowed version of the commonly used Golub pivoting strategy, aided by incremental condition estimation. Second, we develop efficiently implementable variants of guaranteed reliable RRQR algorithms for triangular matrices originally suggested by Chandrasekaran and Ipsen and by Pan and Tang. We suggest algorithmic improvements with respect to condition estimation, termination criteria, and Givens updating. By combining the block algorithm with one of the triangular postprocessing steps, we arrive at an efficient and reliablemore » algorithm for computing an RRQR factorization of a dense matrix. Experimental results on IBM RS/6000 SGI R8000 platforms show that this approach performs up to three times faster that the less reliable QR factorization with column pivoting as it is currently implemented in LAPACK, and comes within 15% of the performance of the LAPACK block algorithm for computing a QR factorization without any column exchanges. Thus, we expect this routine to be useful in may circumstances where numerical rank deficiency cannot be ruled out, but currently has been ignored because of the computational cost of dealing with it.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rebay, S.

This work is devoted to the description of an efficient unstructured mesh generation method entirely based on the Delaunay triangulation. The distinctive characteristic of the proposed method is that point positions and connections are computed simultaneously. This result is achieved by taking advantage of the sequential way in which the Bowyer-Watson algorithm computes the Delaunay triangulation. Two methods are proposed which have great geometrical flexibility, in that they allow us to treat domains of arbitrary shape and topology and to generate arbitrarily nonuniform meshes. The methods are computationally efficient and are applicable both in two and three dimensions. 11 refs.,more » 20 figs., 1 tab.« less

Efficient computation of PDF-based characteristics from diffusion MR signal.

PubMed

Assemlal, Haz-Edine; Tschumperlé, David; Brun, Luc

2008-01-01

We present a general method for the computation of PDF-based characteristics of the tissue micro-architecture in MR imaging. The approach relies on the approximation of the MR signal by a series expansion based on Spherical Harmonics and Laguerre-Gaussian functions, followed by a simple projection step that is efficiently done in a finite dimensional space. The resulting algorithm is generic, flexible and is able to compute a large set of useful characteristics of the local tissues structure. We illustrate the effectiveness of this approach by showing results on synthetic and real MR datasets acquired in a clinical time-frame.

Storage and computationally efficient permutations of factorized covariance and square-root information arrays

NASA Technical Reports Server (NTRS)

Muellerschoen, R. J.

1988-01-01

A unified method to permute vector stored Upper triangular Diagonal factorized covariance and vector stored upper triangular Square Root Information arrays is presented. The method involves cyclic permutation of the rows and columns of the arrays and retriangularization with fast (slow) Givens rotations (reflections). Minimal computation is performed, and a one dimensional scratch array is required. To make the method efficient for large arrays on a virtual memory machine, computations are arranged so as to avoid expensive paging faults. This method is potentially important for processing large volumes of radio metric data in the Deep Space Network.

Damsel: A Data Model Storage Library for Exascale Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koziol, Quincey

The goal of this project is to enable exascale computational science applications to interact conveniently and efficiently with storage through abstractions that match their data models. We will accomplish this through three major activities: (1) identifying major data model motifs in computational science applications and developing representative benchmarks; (2) developing a data model storage library, called Damsel, that supports these motifs, provides efficient storage data layouts, incorporates optimizations to enable exascale operation, and is tolerant to failures; and (3) productizing Damsel and working with computational scientists to encourage adoption of this library by the scientific community.

Novel scheme to compute chemical potentials of chain molecules on a lattice

NASA Astrophysics Data System (ADS)

Mooij, G. C. A. M.; Frenkel, D.

We present a novel method that allows efficient computation of the total number of allowed conformations of a chain molecule in a dense phase. Using this method, it is possible to estimate the chemical potential of such a chain molecule. We have tested the present method in simulations of a two-dimensional monolayer of chain molecules on a lattice (Whittington-Chapman model) and compared it with existing schemes to compute the chemical potential. We find that the present approach is two to three orders of magnitude faster than the most efficient of the existing methods.

An efficient parallel algorithm for the solution of a tridiagonal linear system of equations

NASA Technical Reports Server (NTRS)

Stone, H. S.

1971-01-01

Tridiagonal linear systems of equations are solved on conventional serial machines in a time proportional to N, where N is the number of equations. The conventional algorithms do not lend themselves directly to parallel computations on computers of the ILLIAC IV class, in the sense that they appear to be inherently serial. An efficient parallel algorithm is presented in which computation time grows as log sub 2 N. The algorithm is based on recursive doubling solutions of linear recurrence relations, and can be used to solve recurrence relations of all orders.

Model equations for the Eiffel Tower profile: historical perspective and new results

NASA Astrophysics Data System (ADS)

Weidman, Patrick; Pinelis, Iosif

2004-07-01

Model equations for the shape of the Eiffel Tower are investigated. One model purported to be based on Eiffel's writing does not give a tower with the correct curvature. A second popular model not connected with Eiffel's writings provides a fair approximation to the tower's skyline profile of 29 contiguous panels. Reported here is a third model derived from Eiffel's concern about wind loads on the tower, as documented in his communication to the French Civil Engineering Society on 30 March 1885. The result is a nonlinear, integro-differential equation which is solved to yield an exponential tower profile. It is further verified that, as Eiffel wrote, "in reality the curve exterior of the tower reproduces, at a determined scale, the same curve of the moments produced by the wind". An analysis of the actual tower profile shows that it is composed of two piecewise continuous exponentials with different growth rates. This is explained by specific safety factors for wind loading that Eiffel & Company incorporated in the design of the free-standing tower. To cite this article: P. Weidman, I. Pinelis, C. R. Mecanique 332 (2004).

Mitochondrial phylogeography of a Beringian relict: the endemic freshwater genus of blackfish Dallia (Esociformes).

PubMed

Campbell, M A; Lopéz, J A

2014-02-01

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median-joining haplotype networks, Bayesian skyline plots, mismatch analysis and spatial analysis of molecular variance (SAMOVA) to infer genealogical relationships and to assess patterns of phylogeography among extant mitochondrial lineages in populations of species of Dallia. The observed variation includes extensive standing mitochondrial genetic diversity and patterns of distinct spatial segregation corresponding to historical and contemporary barriers with minimal or no mixing of mitochondrial haplotypes between geographic areas. Mitochondrial diversity is highest in the common delta formed by the Yukon and Kuskokwim Rivers where they meet the Bering Sea. Other regions sampled in this study host comparatively low levels of mitochondrial diversity. The observed levels of mitochondrial diversity and the spatial distribution of that diversity are consistent with persistence of mitochondrial lineages in multiple refugia through the last glacial maximum. © 2014 The Fisheries Society of the British Isles.

Elemental composition and molecular structure of Botryococcus alginite in Westphalian cannel coals from Kentucky

USGS Publications Warehouse

Mastalerz, Maria; Hower, J.C.

1996-01-01

Botryococcus-derived alginites from the Westphalian Skyline, No. 5 Block, Leatherwood (eastern Kentucky) and Breckinridge (western Kentucky) coal beds have been analyzed for elemental composition and functional group distribution using an electron microprobe and micro-FTIR, respectively. The alginites from Kentucky show a carbon range of 81.6 to 92% and oxygen content of 3.5 to 9.5%. Sulphur content ranges from 0.66 to 0.84% and Fe, Si, Al and Ca occur in minor quantities. FTIR analysis demonstrates dominant CH2, CH3 bands and subordinate aromatic carbon in all alginites. The major differences between alginites are in the ratios of CH2 and CH3 groups and ratios between aromatic bands in the out-of-plane region. These differences suggest that, although the ancient Botryococcus derives from a selective preservation of a resistant polymer, it undergoes molecular and some elemental changes through the rank equivalent to vitrinite reflectance of 0.5-0.85%. Other differences, such as intensities of ether bridges and those of carboxyl/carbonyl groups, are attributed to differences in depositional environments.

Exploiting mineral data: applications to the diversity, distribution, and social networks of copper mineral

NASA Astrophysics Data System (ADS)

Morrison, S. M.; Downs, R. T.; Golden, J. J.; Pires, A.; Fox, P. A.; Ma, X.; Zednik, S.; Eleish, A.; Prabhu, A.; Hummer, D. R.; Liu, C.; Meyer, M.; Ralph, J.; Hystad, G.; Hazen, R. M.

2016-12-01

We have developed a comprehensive database of copper (Cu) mineral characteristics. These data include crystallographic, paragenetic, chemical, locality, age, structural complexity, and physical property information for the 689 Cu mineral species approved by the International Mineralogical Association (rruff.info/ima). Synthesis of this large, varied dataset allows for in-depth exploration of statistical trends and visualization techniques. With social network analysis (SNA) and cluster analysis of minerals, we create sociograms and chord diagrams. SNA visualizations illustrate the relationships and connectivity between mineral species, which often form cliques associated with rock type and/or geochemistry. Using mineral ecology statistics, we analyze mineral-locality frequency distribution and predict the number of missing mineral species, visualized with accumulation curves. By assembly of 2-dimensional KLEE diagrams of co-existing elements in minerals, we illustrate geochemical trends within a mineral system. To explore mineral age and chemical oxidation state, we create skyline diagrams and compare trends with varying chemistry. These trends illustrate mineral redox changes through geologic time and correlate with significant geologic occurrences, such as the Great Oxidation Event (GOE) or Wilson Cycles.

Performance Comparison of a Matrix Solver on a Heterogeneous Network Using Two Implementations of MPI: MPICH and LAM

NASA Technical Reports Server (NTRS)

Phillips, Jennifer K.

1995-01-01

Two of the current and most popular implementations of the Message-Passing Standard, Message Passing Interface (MPI), were contrasted: MPICH by Argonne National Laboratory, and LAM by the Ohio Supercomputer Center at Ohio State University. A parallel skyline matrix solver was adapted to be run in a heterogeneous environment using MPI. The Message-Passing Interface Forum was held in May 1994 which lead to a specification of library functions that implement the message-passing model of parallel communication. LAM, which creates it's own environment, is more robust in a highly heterogeneous network. MPICH uses the environment native to the machine architecture. While neither of these free-ware implementations provides the performance of native message-passing or vendor's implementations, MPICH begins to approach that performance on the SP-2. The machines used in this study were: IBM RS6000, 3 Sun4, SGI, and the IBM SP-2. Each machine is unique and a few machines required specific modifications during the installation. When installed correctly, both implementations worked well with only minor problems.

Using iRT, a normalized retention time for more targeted measurement of peptides.

PubMed

Escher, Claudia; Reiter, Lukas; MacLean, Brendan; Ossola, Reto; Herzog, Franz; Chilton, John; MacCoss, Michael J; Rinner, Oliver

2012-04-01

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

NASA Astrophysics Data System (ADS)

Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri

2018-02-01

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.

The history of aggregate development in the denver, Co area

USGS Publications Warehouse

Langer, W.H.

2009-01-01

At the start of the 20th century Denver's population was 203,795. Most streets were unpaved. Buildings were constructed of wood frame or masonry. Transport was by horse-drawn-wagon or rail. Statewide, aggregate consumption was less than 0.25 metric tons per person per year. One hundred years later Denver had a population of 2,365,345. Today Denver is a major metropolitan area at the crossroads of two interstates, home to a new international airport, and in the process of expanding its light rail transit system. The skyline is punctuated with skyscrapers. The urban center is surrounded with edge cities. These changes required huge amounts of aggregate. Statewide, aggregate consumption increased 50 fold to over 13 metric tons per person per year. Denver has a large potential supply of aggregate, but sand and gravel quality decreases downstream from the mountain front and potential sources of crushed stone occur in areas prized for their scenic beauty. These issues, along with urban encroachment and citizen opposition, have complicated aggregate development and have paved a new path for future aggregate development including sustainable resource management and reclamation techniques.

The genetic diversity and evolutionary history of hepatitis C virus in Vietnam

PubMed Central

Li, Chunhua; Yuan, Manqiong; Lu, Ling; Lu, Teng; Xia, Wenjie; Pham, Van H.; Vo, An X.D.; Nguyen, Mindie H.; Abe, Kenji

2014-01-01

Vietnam has a unique history in association with foreign countries, which may have resulted in multiple introductions of the alien HCV strains to mix with those indigenous ones. In this study, we characterized the HCV sequences in Core-E1 and NS5B regions from 236 Vietnamese individuals. We identified multiple HCV lineages; 6a, 6e, 6h, 6k, 6l, 6o, 6p, and two novel variants may represent the indigenous strains; 1a was probably introduced from the US; 1b and 2a possibly originated in East Asia; while 2i, 2j, and 2m were likely brought by French explorers. We inferred the evolutionary history for four major subtypes: 1a, 1b, 6a, and 6e. The obtained Bayesian Skyline Plots (BSPs) consistently showed the rapid HCV population growth from 1955-1963 until 1984 or after, corresponding to the era of the Vietnam War. We also estimated HCV growth rates and reconstructed phylogeographic trees for comparing subtypes 1a, 1b, and HCV-2. PMID:25193655

Information Extraction of Tourist Geological Resources Based on 3d Visualization Remote Sensing Image

NASA Astrophysics Data System (ADS)

Wang, X.

2018-04-01

Tourism geological resources are of high value in admiration, scientific research and universal education, which need to be protected and rationally utilized. In the past, most of the remote sensing investigations of tourism geological resources used two-dimensional remote sensing interpretation method, which made it difficult for some geological heritages to be interpreted and led to the omission of some information. This aim of this paper is to assess the value of a method using the three-dimensional visual remote sensing image to extract information of geological heritages. skyline software system is applied to fuse the 0.36 m aerial images and 5m interval DEM to establish the digital earth model. Based on the three-dimensional shape, color tone, shadow, texture and other image features, the distribution of tourism geological resources in Shandong Province and the location of geological heritage sites were obtained, such as geological structure, DaiGu landform, granite landform, Volcanic landform, sandy landform, Waterscapes, etc. The results show that using this method for remote sensing interpretation is highly recognizable, making the interpretation more accurate and comprehensive.

Fires in Shenandoah National Park

NASA Technical Reports Server (NTRS)

2002-01-01

A large smoke plume has been streaming eastward from Virginia's Shenandoah National Park near Old Rag Mountain. Based on satellite images, it appears the blaze started sometime between October 30 and 31. This true-color image of the fire was obtained on November 1, 2000 by the Moderate-resolution Imaging Spectroradiometer (MODIS), flying aboard NASA's Terra spacecraft. Thermal Infrared data, overlaid on the color image, reveals the presence of two active fires underneath the smoke plume. The northern fire (upper) is burning near the Pinnacles Picnic Area along Skyline Drive. The southern fire (lower) is on Old Rag Mountain. Old Rag is one of the most popular hikes in the Washington, DC area, and features extremely rugged terrain, with granite cliffs up to 90 feet high. This scene was produced using MODIS direct broadcast data received and processed at the Space Science and Engineering Center, University of Wisconsin-Madison. The smoke plume appears blue-grey while the red and yellow pixels show the locations of the smoldering and flaming portions of the fire, respectively. Image by Liam Gumley, Cooperative Institute for Meteorological Satellite Studies, and Robert Simmon, NASA GSFC

KSC-2014-3513

NASA Image and Video Library

2014-08-13

SAN DIEGO, Calif. – The USS Anchorage returns to Naval Base San Diego after completion of the Orion Underway Recovery Test 2 in the Pacific Ocean. The ship is framed by the skyline of the city of San Diego. NASA, Lockheed Martin and the U.S. Navy conducted the test on the Orion boilerplate test vehicle to prepare for recovery of the Orion crew module on its return from a deep space mission. The underway recovery test allowed the team to demonstrate and evaluate the recovery processes, procedures, new hardware and personnel in open waters. The Ground Systems Development and Operations Program conducted the underway recovery test. Orion is the exploration spacecraft designed to carry astronauts to destinations not yet explored by humans, including an asteroid and Mars. It will have emergency abort capability, sustain the crew during space travel and provide safe re-entry from deep space return velocities. The first unpiloted test flight of the Orion is scheduled to launch in 2014 atop a Delta IV rocket and in 2017 on NASA’s Space Launch System rocket. For more information, visit http://www.nasa.gov/orion. Photo credit: NASA/Kim Shiflett

KSC-2014-3514

NASA Image and Video Library

2014-08-13

SAN DIEGO, Calif. – The USS Anchorage returns to Naval Base San Diego after completion of the Orion Underway Recovery Test 2 in the Pacific Ocean. The ship is framed by the skyline of the city of San Diego. NASA, Lockheed Martin and the U.S. Navy conducted the test on the Orion boilerplate test vehicle to prepare for recovery of the Orion crew module on its return from a deep space mission. The underway recovery test allowed the team to demonstrate and evaluate the recovery processes, procedures, new hardware and personnel in open waters. The Ground Systems Development and Operations Program conducted the underway recovery test. Orion is the exploration spacecraft designed to carry astronauts to destinations not yet explored by humans, including an asteroid and Mars. It will have emergency abort capability, sustain the crew during space travel and provide safe re-entry from deep space return velocities. The first unpiloted test flight of the Orion is scheduled to launch in 2014 atop a Delta IV rocket and in 2017 on NASA’s Space Launch System rocket. For more information, visit http://www.nasa.gov/orion. Photo credit: NASA/Kim Shiflett

Accounting for rate variation among lineages in comparative demographic analyses

USGS Publications Warehouse

Hope, Andrew G.; Ho, Simon Y. W.; Malaney, Jason L.; Cook, Joseph A.; Talbot, Sandra L.

2014-01-01

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies.

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.

Irregular large-scale computed tomography on multiple graphics processors improves energy-efficiency metrics for industrial applications

NASA Astrophysics Data System (ADS)

Jimenez, Edward S.; Goodman, Eric L.; Park, Ryeojin; Orr, Laurel J.; Thompson, Kyle R.

2014-09-01

This paper will investigate energy-efficiency for various real-world industrial computed-tomography reconstruction algorithms, both CPU- and GPU-based implementations. This work shows that the energy required for a given reconstruction is based on performance and problem size. There are many ways to describe performance and energy efficiency, thus this work will investigate multiple metrics including performance-per-watt, energy-delay product, and energy consumption. This work found that irregular GPU-based approaches1 realized tremendous savings in energy consumption when compared to CPU implementations while also significantly improving the performance-per- watt and energy-delay product metrics. Additional energy savings and other metric improvement was realized on the GPU-based reconstructions by improving storage I/O by implementing a parallel MIMD-like modularization of the compute and I/O tasks.

Parallel discontinuous Galerkin FEM for computing hyperbolic conservation law on unstructured grids

NASA Astrophysics Data System (ADS)

Ma, Xinrong; Duan, Zhijian

2018-04-01

High-order resolution Discontinuous Galerkin finite element methods (DGFEM) has been known as a good method for solving Euler equations and Navier-Stokes equations on unstructured grid, but it costs too much computational resources. An efficient parallel algorithm was presented for solving the compressible Euler equations. Moreover, the multigrid strategy based on three-stage three-order TVD Runge-Kutta scheme was used in order to improve the computational efficiency of DGFEM and accelerate the convergence of the solution of unsteady compressible Euler equations. In order to make each processor maintain load balancing, the domain decomposition method was employed. Numerical experiment performed for the inviscid transonic flow fluid problems around NACA0012 airfoil and M6 wing. The results indicated that our parallel algorithm can improve acceleration and efficiency significantly, which is suitable for calculating the complex flow fluid.

Job Scheduling with Efficient Resource Monitoring in Cloud Datacenter

PubMed Central

Loganathan, Shyamala; Mukherjee, Saswati

2015-01-01

Cloud computing is an on-demand computing model, which uses virtualization technology to provide cloud resources to users in the form of virtual machines through internet. Being an adaptable technology, cloud computing is an excellent alternative for organizations for forming their own private cloud. Since the resources are limited in these private clouds maximizing the utilization of resources and giving the guaranteed service for the user are the ultimate goal. For that, efficient scheduling is needed. This research reports on an efficient data structure for resource management and resource scheduling technique in a private cloud environment and discusses a cloud model. The proposed scheduling algorithm considers the types of jobs and the resource availability in its scheduling decision. Finally, we conducted simulations using CloudSim and compared our algorithm with other existing methods, like V-MCT and priority scheduling algorithms. PMID:26473166

Job Scheduling with Efficient Resource Monitoring in Cloud Datacenter.

PubMed

Loganathan, Shyamala; Mukherjee, Saswati

2015-01-01

Cloud computing is an on-demand computing model, which uses virtualization technology to provide cloud resources to users in the form of virtual machines through internet. Being an adaptable technology, cloud computing is an excellent alternative for organizations for forming their own private cloud. Since the resources are limited in these private clouds maximizing the utilization of resources and giving the guaranteed service for the user are the ultimate goal. For that, efficient scheduling is needed. This research reports on an efficient data structure for resource management and resource scheduling technique in a private cloud environment and discusses a cloud model. The proposed scheduling algorithm considers the types of jobs and the resource availability in its scheduling decision. Finally, we conducted simulations using CloudSim and compared our algorithm with other existing methods, like V-MCT and priority scheduling algorithms.

Efficient FFT Algorithm for Psychoacoustic Model of the MPEG-4 AAC

NASA Astrophysics Data System (ADS)

Lee, Jae-Seong; Lee, Chang-Joon; Park, Young-Cheol; Youn, Dae-Hee

This paper proposes an efficient FFT algorithm for the Psycho-Acoustic Model (PAM) of MPEG-4 AAC. The proposed algorithm synthesizes FFT coefficients using MDCT and MDST coefficients through circular convolution. The complexity of the MDCT and MDST coefficients is approximately half of the original FFT. We also design a new PAM based on the proposed FFT algorithm, which has 15% lower computational complexity than the original PAM without degradation of sound quality. Subjective as well as objective test results are presented to confirm the efficiency of the proposed FFT computation algorithm and the PAM.

How to Compute a Slot Marker - Calculation of Controller Managed Spacing Tools for Efficient Descents with Precision Scheduling

NASA Technical Reports Server (NTRS)

Prevot, Thomas

2012-01-01

This paper describes the underlying principles and algorithms for computing the primary controller managed spacing (CMS) tools developed at NASA for precisely spacing aircraft along efficient descent paths. The trajectory-based CMS tools include slot markers, delay indications and speed advisories. These tools are one of three core NASA technologies integrated in NASAs ATM technology demonstration-1 (ATD-1) that will operationally demonstrate the feasibility of fuel-efficient, high throughput arrival operations using Automatic Dependent Surveillance Broadcast (ADS-B) and ground-based and airborne NASA technologies for precision scheduling and spacing.

An Efficient Identity-Based Key Management Scheme for Wireless Sensor Networks Using the Bloom Filter

PubMed Central

Qin, Zhongyuan; Zhang, Xinshuai; Feng, Kerong; Zhang, Qunfang; Huang, Jie

2014-01-01

With the rapid development and widespread adoption of wireless sensor networks (WSNs), security has become an increasingly prominent problem. How to establish a session key in node communication is a challenging task for WSNs. Considering the limitations in WSNs, such as low computing capacity, small memory, power supply limitations and price, we propose an efficient identity-based key management (IBKM) scheme, which exploits the Bloom filter to authenticate the communication sensor node with storage efficiency. The security analysis shows that IBKM can prevent several attacks effectively with acceptable computation and communication overhead. PMID:25264955

Leveraging Gibbs Ensemble Molecular Dynamics and Hybrid Monte Carlo/Molecular Dynamics for Efficient Study of Phase Equilibria.

PubMed

Gartner, Thomas E; Epps, Thomas H; Jayaraman, Arthi

2016-11-08

We describe an extension of the Gibbs ensemble molecular dynamics (GEMD) method for studying phase equilibria. Our modifications to GEMD allow for direct control over particle transfer between phases and improve the method's numerical stability. Additionally, we found that the modified GEMD approach had advantages in computational efficiency in comparison to a hybrid Monte Carlo (MC)/MD Gibbs ensemble scheme in the context of the single component Lennard-Jones fluid. We note that this increase in computational efficiency does not compromise the close agreement of phase equilibrium results between the two methods. However, numerical instabilities in the GEMD scheme hamper GEMD's use near the critical point. We propose that the computationally efficient GEMD simulations can be used to map out the majority of the phase window, with hybrid MC/MD used as a follow up for conditions under which GEMD may be unstable (e.g., near-critical behavior). In this manner, we can capitalize on the contrasting strengths of these two methods to enable the efficient study of phase equilibria for systems that present challenges for a purely stochastic GEMC method, such as dense or low temperature systems, and/or those with complex molecular topologies.

Efficient least angle regression for identification of linear-in-the-parameters models

PubMed Central

Beach, Thomas H.; Rezgui, Yacine

2017-01-01

Least angle regression, as a promising model selection method, differentiates itself from conventional stepwise and stagewise methods, in that it is neither too greedy nor too slow. It is closely related to L1 norm optimization, which has the advantage of low prediction variance through sacrificing part of model bias property in order to enhance model generalization capability. In this paper, we propose an efficient least angle regression algorithm for model selection for a large class of linear-in-the-parameters models with the purpose of accelerating the model selection process. The entire algorithm works completely in a recursive manner, where the correlations between model terms and residuals, the evolving directions and other pertinent variables are derived explicitly and updated successively at every subset selection step. The model coefficients are only computed when the algorithm finishes. The direct involvement of matrix inversions is thereby relieved. A detailed computational complexity analysis indicates that the proposed algorithm possesses significant computational efficiency, compared with the original approach where the well-known efficient Cholesky decomposition is involved in solving least angle regression. Three artificial and real-world examples are employed to demonstrate the effectiveness, efficiency and numerical stability of the proposed algorithm. PMID:28293140

The demodulated band transform

PubMed Central

Kovach, Christopher K.; Gander, Phillip E.

2016-01-01

Background Windowed Fourier decompositions (WFD) are widely used in measuring stationary and non-stationary spectral phenomena and in describing pairwise relationships among multiple signals. Although a variety of WFDs see frequent application in electrophysiological research, including the short-time Fourier transform, continuous wavelets, band-pass filtering and multitaper-based approaches, each carries certain drawbacks related to computational efficiency and spectral leakage. This work surveys the advantages of a WFD not previously applied in electrophysiological settings. New Methods A computationally efficient form of complex demodulation, the demodulated band transform (DBT), is described. Results DBT is shown to provide an efficient approach to spectral estimation with minimal susceptibility to spectral leakage. In addition, it lends itself well to adaptive filtering of non-stationary narrowband noise. Comparison with existing methods A detailed comparison with alternative WFDs is offered, with an emphasis on the relationship between DBT and Thomson's multitaper. DBT is shown to perform favorably in combining computational efficiency with minimal introduction of spectral leakage. Conclusion DBT is ideally suited to efficient estimation of both stationary and non-stationary spectral and cross-spectral statistics with minimal susceptibility to spectral leakage. These qualities are broadly desirable in many settings. PMID:26711370

Shared-Ride Taxi Computer Control System Requirements Study

DOT National Transportation Integrated Search

1977-08-01

The technical problem of scheduling and routing shared-ride taxi service is so great that only computers can handle it efficiently. This study is concerned with defining the requirements of such a computer system. The major objective of this study is...

Towards a Highly Efficient Meshfree Simulation of Non-Newtonian Free Surface Ice Flow: Application to the Haut Glacier d'Arolla

NASA Astrophysics Data System (ADS)

Shcherbakov, V.; Ahlkrona, J.

2016-12-01

In this work we develop a highly efficient meshfree approach to ice sheet modeling. Traditionally mesh based methods such as finite element methods are employed to simulate glacier and ice sheet dynamics. These methods are mature and well developed. However, despite of numerous advantages these methods suffer from some drawbacks such as necessity to remesh the computational domain every time it changes its shape, which significantly complicates the implementation on moving domains, or a costly assembly procedure for nonlinear problems. We introduce a novel meshfree approach that frees us from all these issues. The approach is built upon a radial basis function (RBF) method that, thanks to its meshfree nature, allows for an efficient handling of moving margins and free ice surface. RBF methods are also accurate and easy to implement. Since the formulation is stated in strong form it allows for a substantial reduction of the computational cost associated with the linear system assembly inside the nonlinear solver. We implement a global RBF method that defines an approximation on the entire computational domain. This method exhibits high accuracy properties. However, it suffers from a disadvantage that the coefficient matrix is dense, and therefore the computational efficiency decreases. In order to overcome this issue we also implement a localized RBF method that rests upon a partition of unity approach to subdivide the domain into several smaller subdomains. The radial basis function partition of unity method (RBF-PUM) inherits high approximation characteristics form the global RBF method while resulting in a sparse system of equations, which essentially increases the computational efficiency. To demonstrate the usefulness of the RBF methods we model the velocity field of ice flow in the Haut Glacier d'Arolla. We assume that the flow is governed by the nonlinear Blatter-Pattyn equations. We test the methods for different basal conditions and for a free moving surface. Both RBF methods are compared with a classical finite element method in terms of accuracy and efficiency. We find that the RBF methods are more efficient than the finite element method and well suited for ice dynamics modeling, especially the partition of unity approach.

Demystifying the GMAT: Computer-Based Testing Terms

ERIC Educational Resources Information Center

Rudner, Lawrence M.

2012-01-01

Computer-based testing can be a powerful means to make all aspects of test administration not only faster and more efficient, but also more accurate and more secure. While the Graduate Management Admission Test (GMAT) exam is a computer adaptive test, there are other approaches. This installment presents a primer of computer-based testing terms.

The Study of Surface Computer Supported Cooperative Work and Its Design, Efficiency, and Challenges

ERIC Educational Resources Information Center

Hwang, Wu-Yuin; Su, Jia-Han

2012-01-01

In this study, a Surface Computer Supported Cooperative Work paradigm is proposed. Recently, multitouch technology has become widely available for human-computer interaction. We found it has great potential to facilitate more awareness of human-to-human interaction than personal computers (PCs) in colocated collaborative work. However, other…

Case Studies of Auditing in a Computer-Based Systems Environment.

ERIC Educational Resources Information Center

General Accounting Office, Washington, DC.

In response to a growing need for effective and efficient means for auditing computer-based systems, a number of studies dealing primarily with batch-processing type computer operations have been conducted to explore the impact of computers on auditing activities in the Federal Government. This report first presents some statistical data on…

Working with Computers: Computer Orientation for Foreign Students.

ERIC Educational Resources Information Center

Barlow, Michael

Designed as a resource for foreign students, this book includes instructions not only on how to use computers, but also on how to use them to complete academic work more efficiently. Part I introduces the basic operations of mainframes and microcomputers and the major areas of computing, i.e., file management, editing, communications, databases,…

Individual Differences and Acquiring Computer Literacy: Are Women More Efficient Than Men?

ERIC Educational Resources Information Center

Gattiker, Urs E.

The training of computer users is becoming increasingly important to all industrialized nations. This study examined how individual differences (e.g. ability and gender) may affect learning outcomes when acquiring computer skills. Subjects (N=347) were college students who took a computer literacy course from a college of business administration…

Software Surface Modeling and Grid Generation Steering Committee

NASA Technical Reports Server (NTRS)

Smith, Robert E. (Editor)

1992-01-01

It is a NASA objective to promote improvements in the capability and efficiency of computational fluid dynamics. Grid generation, the creation of a discrete representation of the solution domain, is an essential part of computational fluid dynamics. However, grid generation about complex boundaries requires sophisticated surface-model descriptions of the boundaries. The surface modeling and the associated computation of surface grids consume an extremely large percentage of the total time required for volume grid generation. Efficient and user friendly software systems for surface modeling and grid generation are critical for computational fluid dynamics to reach its potential. The papers presented here represent the state-of-the-art in software systems for surface modeling and grid generation. Several papers describe improved techniques for grid generation.

Star adaptation for two-algorithms used on serial computers

NASA Technical Reports Server (NTRS)

Howser, L. M.; Lambiotte, J. J., Jr.

1974-01-01

Two representative algorithms used on a serial computer and presently executed on the Control Data Corporation 6000 computer were adapted to execute efficiently on the Control Data STAR-100 computer. Gaussian elimination for the solution of simultaneous linear equations and the Gauss-Legendre quadrature formula for the approximation of an integral are the two algorithms discussed. A description is given of how the programs were adapted for STAR and why these adaptations were necessary to obtain an efficient STAR program. Some points to consider when adapting an algorithm for STAR are discussed. Program listings of the 6000 version coded in 6000 FORTRAN, the adapted STAR version coded in 6000 FORTRAN, and the STAR version coded in STAR FORTRAN are presented in the appendices.

Redundancy management for efficient fault recovery in NASA's distributed computing system

NASA Technical Reports Server (NTRS)

Malek, Miroslaw; Pandya, Mihir; Yau, Kitty

1991-01-01

The management of redundancy in computer systems was studied and guidelines were provided for the development of NASA's fault-tolerant distributed systems. Fault recovery and reconfiguration mechanisms were examined. A theoretical foundation was laid for redundancy management by efficient reconfiguration methods and algorithmic diversity. Algorithms were developed to optimize the resources for embedding of computational graphs of tasks in the system architecture and reconfiguration of these tasks after a failure has occurred. The computational structure represented by a path and the complete binary tree was considered and the mesh and hypercube architectures were targeted for their embeddings. The innovative concept of Hybrid Algorithm Technique was introduced. This new technique provides a mechanism for obtaining fault tolerance while exhibiting improved performance.

Provable classically intractable sampling with measurement-based computation in constant time

NASA Astrophysics Data System (ADS)

Sanders, Stephen; Miller, Jacob; Miyake, Akimasa

We present a constant-time measurement-based quantum computation (MQC) protocol to perform a classically intractable sampling problem. We sample from the output probability distribution of a subclass of the instantaneous quantum polynomial time circuits introduced by Bremner, Montanaro and Shepherd. In contrast with the usual circuit model, our MQC implementation includes additional randomness due to byproduct operators associated with the computation. Despite this additional randomness we show that our sampling task cannot be efficiently simulated by a classical computer. We extend previous results to verify the quantum supremacy of our sampling protocol efficiently using only single-qubit Pauli measurements. Center for Quantum Information and Control, Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA.