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At least 487 records · Page 27

A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies

Researchers are perpetually amassing biological sequence data. The computational approaches employed by ecologists for organizing this data (e.g. alignment, phylogeny, etc.) typically scale nonlinearly in execution time with the size of the dataset. This often serves as a bottleneck for processing experimental data since many molecular studies are characterized by massive datasets. To keep up with experimental data demands, ecologists are forced to choose between continually upgrading expensive in-house computer hardware or outsourcing the most demanding computations to the cloud. Outsourcing is attractive since it is the least expensive option, but does not necessarily allow direct user interaction with the data for exploratory analysis. Desktop analytical tools such as ARB are indispensable for this purpose, but they do not necessarily offer a convenient solution for the coordination and integration of datasets between local and outsourced destinations. Therefore, researchers are currently left with an undesirable tradeoff between computational throughput and analytical capability. To mitigate this tradeoff we introduce a software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Our pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database. Furthermore, a tutorial implementation of the toolkit is provided in the supporting information, S1 Tutorial.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Aerosol and cloud microphysics covariability in the northeast Pacific boundary layer estimated with ship-based and satellite remote sensing observations: NE Pacific Aerosol-Cloud Interactions

Ship measurements collected over the northeast Pacific along transects between the port of Los Angeles (33.7°N, 118.2°W) and Honolulu (21.3°N, 157.8°W) during May to August 2013 were utilized to investigate the covariability between marine low cloud microphysical and aerosol properties. Ship-based retrievals of cloud optical depth (τ) from a Sun photometer and liquid water path (LWP) from a microwave radiometer were combined to derive cloud droplet number concentration Nd and compute a cloud-aerosol interaction (ACI) metric defined as ACICCN = ∂ ln(Nd)/∂ ln(CCN), with CCN denoting the cloud condensation nuclei concentration measured at 0.4% (CCN0.4) and 0.3% (CCN0.3) supersaturation. Analysis of CCN0.4, accumulation mode aerosol concentration (Na), and extinction coefficient (σext) indicates that Na and σext can be used as CCN0.4 proxies for estimating ACI. ACICCN derived from 10 min averaged Nd and CCN0.4 and CCN0.3, and CCN0.4 regressions using Na and σext, produce high ACICCN: near 1.0, that is, a fractional change in aerosols is associated with an equivalent fractional change in Nd. ACICCN computed in deep boundary layers was small (ACICCN = 0.60), indicating that surface aerosol measurements inadequately represent the aerosol variability below clouds. Satellite cloud retrievals from MODerate-resolution Imaging Spectroradiometer and GOES-15 data were compared against ship-based retrievals and further analyzed to compute a satellite-based ACICCN. Satellite data correlated well with their ship-based counterparts with linear correlation coefficients equal to or greater than 0.78. Combined satellite Nd and ship-based CCN0.4 and Na yielded a maximum ACICCN = 0.88–0.92, a value slightly less than the ship-based ACICCN, but still consistent with aircraft-based studies in the eastern Pacific.

Painemal, David↗

Molecular Hydrogen in Diffuse Interstellar Clouds of Arbitrary Three-Dimensional Geometry

We have constructed three-dimensional models for the equilibrium abundance of molecular hydrogen in diffuse interstellar clouds of arbitrary geometry that are illuminated by ultraviolet radiation. The position-dependent photodissociation rate of H2 in such clouds was computed with a 26 ray approximation to model the attenuation of the incident ultraviolet radiation field by dust and by H2 line absorption. We have applied our modeling technique to the isolated diffuse cloud G236+39, assuming that the cloud has a constant density and that the thickness of the cloud along the line of sight is at every point proportional to the 100 micron continuum intensity measured by IRAS. We find that our model can successfully account for observed variations in the ratio of 100 micron continuum intensity to H I column density, with larger values of that ratio occurring along lines of sight in which the molecular hydrogen fraction is expected to be the largest. Using a standard chi square analysis to assess the goodness of fit of our models, we find (at the 60 a level) that a three-dimensional model is more successful in matching the observational data than a one-dimensional model in which the geometrical extent of the cloud along the line of sight is assumed to be much smaller than its extent in the plane of the sky. If D is the distance to G236 + 39, and given standard assumptions about the rate of grain-catalyzed H2 formation, we find that the cloud has an extent along the line of sight that is 0.9 +/- 0.1 times its mean extent projected onto the plane of the sky and a gas density of 53 +/- 8 (100 pc/D) H nuclei/cc and is illuminated by a radiation field of 1.1 +/- 0.2 (100 pc/D) times the mean interstellar radiation field. The derived 100 micron emissivity per nucleon is 1.13 +/- 0.06 x 10(exp -20) MJy/sr sq cm.

Spaans, Marco↗

Retrieving Point Cloud of Cloud Points (PCCP) Value-Added Product from Stereo Cameras

In this report, we refer to a pair of cameras that capture synchronized pictures with overlapping fields of view (FOV) as a stereo pair. Each stereo pair independently performs a stereo reconstruction of cloud points. Currently, there are three U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility stereo pairs (six cameras in total) positioned around the Southern Great Plains (SGP) observatory’s Central Facility (CF; Romps and Oktem 2017). Time-synchronized pictures from the two cameras in a stereo pair can be paired together to obtain a three-dimensional (3D) reconstruction of feature points by triangulation. This document explains how we use ARM stereo cameras and stereophotogrammetric principles to generate the Point Cloud of Cloud Points (PCCP) Value-Added Product (VAP). The PCCP VAP is essentially a set of 3D positions representing the locations of cloud features in the sky. Thousands of cloud features can be reconstructed instantly in each stereo pair's FOV, which covers an area of tens of square kilometers. Cloud base and cloud top heights can be extracted from the PCCP product.

42 ENGINEERING↗

Lyman-alpha clouds as a relic of primordial density fluctuations

Primordial density fluctuations are studied using a CDM model and primordial clouds some of which are expanding, driven by pressure gradients created when the medium is photionized, and some of which are massive enough to continue collapsing in spite of the pressure. Normalization of CDM models to the clustering properties on large scales are used to predict the parameters of collapsing clouds of subgalactic mass at early epochs. It is shown that the abundance and dimensions of these clouds are comparable to those of the Lyman-alpha systems. The evolutionary history of the clouds is computed, utilizing a spherically symmetric hydrodynamics code with the dark matter treated as a collisionless fluid, and the H I column density distribution is evaluated as a function of N(H I) and redshift. The observed cloud parameters come out naturally in the CDM model and suggest that Lyman-alpha clouds are the missing link between primordial density fluctuations and the formation of galaxies.

Bond, J. R.↗

The Use of the Satellite Breakup Risk Assessment Model (SBRAM) to Characterize Collision Risk to Manned Spacecraft

NASA uses environment models such as ORDEM96 to characterize the long-term orbital debris collision hazard for spacecraft in LEO. Occasionally, however, there are breakups of satellites or rocket bodies that create enhanced collision hazard for a period of time. This enhanced collision hazard can pose increased risks to space operations - especially those involving manned missions where the tolerance for risk is very low. NASA has developed SBRAM to simulate the enhanced debris environment in the days and weeks that follow such a breakup. This simulation provides the kind of risk probabilities that can be used by mission planners to consider if changes are warranted for the mission. Announcements of breakups come to NASA from US Space Command as soon as they are identified. The pre-breakup orbit and time of breakup are used to determine the initial conditions of the explosion. SBRAM uses the latest explosion models developed at NASA to simulate a debris cloud for the breakup. The model uses a Monte Carlo technique to create a random debris cloud from the probability distributions in the breakup model. Each piece of debris randomly created in the cloud is propagated in a deterministic manner to include the effects of drag and other orbital perturbations. The detailed geometry of each simulated close approach to the target spacecraft is noted and logged and the collision probability is computed using an estimated probability density in down-range and cross-range positions of both the target spacecraft and debris object. The collision probability is computed from the overlap of these probability densities for each close-approach geometry and summed over all computed conjunctions. Cloud propagation runs over the desired time interval are then repeated until the scale of the collision risk can be estimated to a desired precision. This paper presents an overview of the SBRAM model and a number of examples, both real and hypothetical, to demonstrate its use. In addition, a number of different examples are shown how the data can be used by decision makers on issues such as spacecraft orientation and timing of EVAs.

Matney, Mark J.↗

Moving image analysis to the cloud: A case study with a genome-scale tomographic study

Over the last decade, the time required to measure a terabyte of microscopic imaging data has gone from years to minutes. This shift has moved many of the challenges away from experimental design and measurement to scalable storage, organization, and analysis. As many scientists and scientific institutions lack training and competencies in these areas, major bottlenecks have arisen and led to substantial delays and gaps between measurement, understanding, and dissemination. We present in this paper a framework for analyzing large 3D datasets using cloud-based computational and storage resources. We demonstrate its applicability by showing the setup and costs associated with the analysis of a genome-scale study of bone microstructure. We then evaluate the relative advantages and disadvantages associated with local versus cloud infrastructures.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Experimental Implementation of a Quantum Autoencoder via Quantum Adders

Abstract Quantum autoencoders allow for reducing the amount of resources in a quantum computation by mapping the original Hilbert space onto a reduced space with the relevant information. Recently, it is proposed to employ approximate quantum adders to implement quantum autoencoders in quantum technologies. Here, the experimental implementation of this proposal in the Rigetti cloud quantum computer is carried out employing up to three qubits. The experimental fidelities are in good agreement with the theoretical prediction, thus proving the feasibility to realize quantum autoencoders via quantum adders in state‐of‐the‐art superconducting quantum technologies.

Ding, Yongcheng↗

Quantum computing for heavy quarkonium spectroscopy

Here, we report a first demonstration for the application of quantum computing to heavy quarkonium spectroscopy study. Based on a Cornell-potential model for the heavy quark and antiquark system, we show how this Hamiltonian problem can be formulated and solved with the variational quantum eigensolver (VQE) approach on the IBM cloud quantum computing platform. Errors due to a global depolarizing noise channel are corrected with a zero-noise extrapolation method, resulting in good agreement with the expected value. We also generalize the VQE method for solving excited states by orthogonalization with respect to the ground state. This new approach is demonstrated to be successful for the quarkonium system on a noiseless quantum simulator and can easily be adapted for solving similar excited state problems in many other physical systems.

79 ASTRONOMY AND ASTROPHYSICS↗

A cylindrical shell model of the NASA-MPE barium ion cloud experiment.

A computer model is developed using infinitely long concentric cylindrical shells to represent the neutral atoms, ions and electrons in the barium cloud. The neutral shells are given a distribution of positions and velocities whose parameters are chosen to be consistent with the dynamics of the release. From this distribution, the ion and electron shells are generated at random using the observed time constant for photoionization. The ion and electron shells thus formed are followed using self-consistent equations of motion. Various averages which could be compared with observation of the actual cloud are calculated at regular time intervals. An unexpected result is the predicted very early return of the magnetic field within the cloud to its ambient value.

Grauer, A. D.↗

Evaluating Energy Differences on a Quantum Computer with Robust Phase Estimation

Here, we adapt the robust phase estimation algorithm to the evaluation of energy differences between two eigenstates using a quantum computer. This approach does not require controlled unitaries between auxiliary and system registers or even a single auxiliary qubit. As a proof of concept, we calculate the energies of the ground state and low-lying electronic excitations of a hydrogen molecule in a minimal basis on a cloud quantum computer. The denominative robustness of our approach is then quantified in terms of a high tolerance to coherent errors in the state preparation and measurement. Conceptually, we note that all quantum phase estimation algorithms ultimately evaluate eigenvalue differences.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Climate Model Diagnostic Analyzer

The comprehensive and innovative evaluation of climate models with newly available global observations is critically needed for the improvement of climate model current-state representation and future-state predictability. A climate model diagnostic evaluation process requires physics-based multi-variable analyses that typically involve large-volume and heterogeneous datasets, making them both computation- and data-intensive. With an exploratory nature of climate data analyses and an explosive growth of datasets and service tools, scientists are struggling to keep track of their datasets, tools, and execution/study history, let alone sharing them with others. In response, we have developed a cloud-enabled, provenance-supported, web-service system called Climate Model Diagnostic Analyzer (CMDA). CMDA enables the physics-based, multivariable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. At the same time, CMDA provides a crowd-sourcing space where scientists can organize their work efficiently and share their work with others. CMDA is empowered by many current state-of-the-art software packages in web service, provenance, and semantic search.

cloud computing↗

Computer tomography of large dust clouds in complex plasmas

The dust density is a central parameter of a dusty plasma. Here, a tomography setup for the determination of the three-dimensionally resolved density distribution of spatially extended dust clouds is presented. The dust clouds consist of micron-sized particles confined in a radio frequency argon plasma, where they fill almost the entire discharge volume. First, a line-of-sight integrated dust density is obtained from extinction measurements, where the incident light from an LED panel is scattered and absorbed by the dust. Performing these extinction measurements from many different angles allows the reconstruction of the 3D dust density distribution, analogous to a computer tomography in medical applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DIORAMA Nuclear Cloud Lofting Module Validity Range

This document investigates the region of validity of the DIORAMA nuclear cloud lofting module based on two separate factors: i) continuum fluid assumptions breaking down and ii) where ballistic effects become significant.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Experimental evaluation of a flexible I/O architecture for accelerating workflow engines in ultrascale environments

The increasing volume of scientific data and the limited scalability and performance of storage systems are currently presenting a significant limitation for the productivity of the scientific workflows running on both high-performance computing (HPC) and cloud platforms. Clearly needed is better integration of storage systems and workflow engines to address this problem. This paper presents and evaluates a novel solution that leverages codesign principles for integrating Hercules—an in-memory data store—with a workflow management system. We consider four main aspects: workflow representation, task scheduling, task placement, and task termination. As a result, the experimental evaluation on both cloud and HPC systems demonstrates significant performance and scalability improvements over existing state-of-the-art approaches.

97 MATHEMATICS AND COMPUTING↗

Failure prediction using machine learning in a virtualised HPC system and application

Failure is an increasingly important issue in high performance computing and cloud systems. As large-scale systems continue to grow in scale and complexity, mitigating the impact of failure and providing accurate predictions with sufficient lead time remains a challenging research problem. Traditional existing fault-tolerance strategies such as regular check-pointing and replication are not adequate because of the emerging complexities of high performance computing systems. This necessitates the importance of having an effective as well as proactive failure management approach in place aimed at minimizing the effect of failure within the system. With the advent of machine learning techniques, the ability to learn from past information to predict future pattern of behaviours makes it possible to predict potential system failure more accurately. Thus, in this paper, we explore the predictive abilities of machine learning by applying a number of algorithms to improve the accuracy of failure prediction. We have developed a failure prediction model using time series and machine learning, and performed comparison based tests on the prediction accuracy. The primary algorithms we considered are the support vector machine (SVM), random forest (RF), k-nearest neighbors (KNN), classification and regression trees (CART) and linear discriminant analysis (LDA). Experimental results indicates that the average prediction accuracy of our model using SVM when predicting failure is 90% accurate and effective compared to other algorithms. This finding implies that our method can effectively predict all possible future system and application failures within the system.

Mohammed, Bashir↗

The Medical Science DMZ

Objective We describe use cases and an institutional reference architecture for maintaining high-capacity, data-intensive network flows (e.g., 10, 40, 100 Gbpsþ) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods High-end networking, packet filter firewalls, network intrusion detection systems. Results We describe a “Medical Science DMZ” concept as an option for secure, high-volume transport of large, sensitive data sets between research institutions over national research networks. Discussion The exponentially increasing amounts of “omics” data, the rapid increase of high-quality imaging, and other rapidly growing clinical data sets have resulted in the rise of biomedical research “big data.” The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large data sets. Maintaining data-intensive flows that comply with HIPAA and other regulations presents a new challenge for biomedical research. Recognizing this, we describe a strategy that marries performance and security by borrowing from and redefining the concept of a “Science DMZ”—a framework that is used in physical sciences and engineering research to manage high-capacity data flows. Conclusion By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high-speed research networks while preserving privacy and meeting regulatory requirements.

97 MATHEMATICS AND COMPUTING↗