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A comprehensive collection of systems biology data characterizing the host response to viral infection

The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). As a result, by comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.

59 BASIC BIOLOGICAL SCIENCES↗

Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish

Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.

agrichemical↗

Natural and Engineered Features Supporting Environmental Performance of Idaho National Laboratory's Remote-Handled Low-Level Waste Disposal Facility - 19436

The Idaho National Laboratory's (INL's) Remote-Handled Low-Level Waste (RH LLW) Disposal Facility has been designed and constructed to receive waste generated at the INL site in support of the US DOE Office of Nuclear Energy (NE) and Naval Reactors (NR) missions. The facility has been designed to receive legacy RH LLW currently in storage at INL facilities and new waste generated by nuclear research programs. RH LLW to be received at the facility is solid waste consisting of surface contaminated materials; ion exchange resins used to purify cooling and canal water; and activated metal components generated during reactor core change outs and Naval spent fuel management; and nuclear R and D. Disposal of INL's RH LLW poses unique disposal challenges due to high radiation levels (contact rates up to 600 Sv/hr [60,000 Rem/hr]) that require remote handling and adequate shielding for transportation and disposal. The facility has been designed to meet the requirements of DOE Order 435.1, Radioactive Waste Management, including the all-pathways dose, air pathway dose, inadvertent intruder doses, and radon emissions limits. This paper presents an overview of natural and engineered design features that support the safety case and enhance the environmental performance of the facility. These features include location selection, use of reinforced pre-cast concrete vaults; a robust hydraulic drainage system; use of steel waste canisters for waste disposal; the facility monitoring system; facility layout; and crediting waste forms. The facility performance assessment (PA) developed to meet the requirements of DOE Order 435.1, credits each of these protective features. Releases from waste forms disposed of at this facility are limited by corrosion of the steel waste canisters which will ultimately allow contact with infiltrating water followed by transport of radionuclides from the vault system. The steel waste canisters were credited for their ability to limit water contact with the waste based on the demonstrated ability of the reinforced pre-caste concrete vaults to provide long-term structural protection of the steel waste canisters. Verification of hydraulic and concrete performance was conducted through laboratory data, field infiltration tests supported by a robust monitoring system, and numerical modeling. Releases into the vault system from activated metals are based on site-specific corrosion data. Radionuclide transport from the vault system from all waste forms is based on site-specific climatological, hydrologic, and stratigraphic data. At INL, the groundwater pathway historically and appropriately has received the most attention. By crediting aspects of the natural system, the engineered vault system, and the waste, estimated radiologic doses via the groundwater pathway are minimal. Air pathway doses were reduced by differentially crediting corrosion of aluminum and stainless steel activated metals resulting in the pathway being screened out of the PA. Groundwater and inadvertent intruder doses were reduced through selective facility layout. This paper provides an overview of the system-wide protective features incorporated into the facility design along with an extensive reference list to supporting technical papers and analyses that provide data and interpretation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Bit threads and holographic entanglement of purification

Generalizing the bit thread formalism, we use convex duality to derive dual flow programs to the bipartite and multipartite holographic entanglement of purification proposals and then prove several inequalities using these constructions. In the multipartite case we find the flows exhibit novel behavior which allows for a constrained flux on the boundary of the homology region. We show this flux can be made distinct from bi-partite terms and reflects the truly multipartite portion of the holographic entanglement of purification.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

THE MAGELLAN PFS PLANET SEARCH PROGRAM: RADIAL VELOCITY AND STELLAR ABUNDANCE ANALYSES OF THE 360 au, METAL-POOR BINARY “TWINS” HD 133131A and B

We present a new precision radial velocity (RV) data set that reveals multiple planets orbiting the stars in the ~360 au, G2+G2 “twin” binary HD 133131AB. Our six years of high-resolution echelle observations from MIKE and five years from the Planet Finder Spectrograph (PFS) on the Magellan telescopes indicate the presence of two eccentric planets around HD 133131A with minimum masses of 1.43 ± 0.03 and 0.63 ± 0.15 M{sub J} at 1.44 ± 0.005 and 4.79 ± 0.92 au, respectively. Additional PFS observations of HD 133131B spanning five years indicate the presence of one eccentric planet of minimum mass 2.50 ± 0.05 M{sub J} at 6.40 ± 0.59 au, making it one of the longest-period planets detected with RV to date. These planets are the first to be reported primarily based on data taken with the PFS on Magellan, demonstrating the instrument’s precision and the advantage of long-baseline RV observations. We perform a differential analysis between the Sun and each star, and between the stars themselves, to derive stellar parameters and measure a suite of 21 abundances across a wide range of condensation temperatures. The host stars are old (likely ~9.5 Gyr) and metal-poor ([Fe/H] ~ -0.30), and we detect a ~0.03 dex depletion in refractory elements in HD 133131A versus B (with standard errors ~0.017). This detection and analysis adds to a small but growing sample of binary “twin” exoplanet host stars with precise abundances measured, and represents the most metal-poor and likely oldest in that sample. Overall, the planets around HD 133131A and B fall in an unexpected regime in planet mass–host star metallicity space and will serve as an important benchmark for the study of long-period giant planets.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA Robotic Neurosurgery Testbed

The detection of tissue interface (e.g., normal tissue, cancer, tumor) has been limited clinically to tactile feedback, temperature monitoring, and the use of a miniature ultrasound probe for tissue differentiation during surgical operations. In neurosurgery, the needle used in the standard stereotactic CT (Computational Tomography) or MRI (Magnetic Resonance Imaging) guided brain biopsy provides no information about the tissue being sampled. The tissue sampled depends entirely upon the accuracy with which the localization provided by the preoperative CT or MRI scan is translated to the intracranial biopsy site. In addition, no information about the tissue being traversed by the needle (e.g., a blood vessel) is provided. Hemorrhage due to the biopsy needle tearing a blood vessel within the brain is the most devastating complication of stereotactic CT/MRI guided brain biopsy. A robotic neurosurgery testbed has been developed at NASA Ames Research Center as a spin-off of technologies from space, aeronautics and medical programs. The invention entitled 'Robotic Neurosurgery Leading to Multimodality Devices for Tissue Identification' is nearing a state ready for commercialization. The devices will: 1) improve diagnostic accuracy and precision of general surgery, with near term emphasis on stereotactic brain biopsy, 2) automate tissue identification, with near term emphasis on stereotactic brain biopsy, to permit remote control of the procedure, and 3) reduce morbidity for stereotactic brain biopsy. The commercial impact from this work is the potential development of a whole new generation of smart surgical tools to increase the safety, accuracy and efficiency of surgical procedures. Other potential markets include smart surgical tools for tumor ablation in neurosurgery, general exploratory surgery, prostate cancer surgery, and breast cancer surgery.

Mah, Robert↗

Attitude dynamics simulation subroutines for systems of hinge-connected rigid bodies with nonrigid appendages

Three computer subroutines designed to solve the vector-dyadic differential equations of rotational motion for systems that may be idealized as a collection of hinge-connected rigid bodies assembled in a tree topology, with an optional flexible appendage attached to each body are reported. Deformations of the appendages are mathematically represented by modal coordinates and are assumed small. Within these constraints, the subroutines provide equation solutions for (1) the most general case of unrestricted hinge rotations, with appendage base bodies nominally rotating at a constant speed, (2) the case of unrestricted hinge rotations between rigid bodies, with the restriction that those rigid bodies carrying appendages are nominally nonspinning, and (3) the case of small hinge rotations and nominally nonrotating appendages. Sample problems and their solutions are presented to illustrate the utility of the computer programs.

Fleischer, G. E.↗

Validation of Test Methods for Air Leak Rate Verification of Spaceflight Hardware

As deep space exploration continues to be the goal of NASAs human spaceflight program, verification of the performance of spaceflight hardware becomes increasingly critical. Suitable test methods for verifying the leak rate of sealing systems are identified in program qualification testing requirements. One acceptable method for verifying the air leak rate of gas pressure seals is the tracer gas leak detector method. In this method, a tracer gas (commonly helium) leaks past the test seal and is transported to the leak detector where the leak rate is quantified. To predict the air leak rate, a conversion factor of helium-to-air is applied depending on the magnitude of the helium flow rate. The conversion factor is based on either the molecular mass ratio or the ratio of the dynamic viscosities. The current work was aimed at validating this approach for permeation-level leak rates using a series of tests with a silicone elastomer O-ring. An established pressure decay method with constant differential pressure was used to evaluate both the air and helium leak rates of the O-ring under similar temperature and pressure conditions. The results from the pressure decay tests showed, for the elastomer O-ring, that neither the molecular flow nor the viscous flow helium-to-air conversion factors were applicable. Leak rate tests were also performed using nitrogen and argon as the test gas. Molecular mass and viscosity based helium-to-test gas conversion factors were applied, but did not correctly predict the measured leak rates of either gas. To further this study, the effect of pressure boundary conditions was investigated. Often, pressure decay leak rate tests are performed at a differential pressure of 101.3 kPa with atmospheric pressure on the downstream side of the test seal. In space applications, the differential pressure is similar, but with vacuum as the downstream pressure. The same O-ring was tested at four unique differential pressures ranging from 34.5 to 137.9 kPa. Up to six combinations of upstream and downstream pressures for each differential pressure were compared. For a given differential pressure, the various combinations of upstream and downstream dry air pressures did not significantly affect the leak rate. As expected, the leak rate of the O-ring increased with increasing differential pressure. The results suggested that the current leak test pressure conditions, used to verify spacecraft sealing systems with elastomer seals, produce accurate values even though the boundary conditions do not model the space application.

helium leak detector↗

Nuclear Data: From Measurement, Evaluation, Processing to Practical Applications [Slides]

Any analysis, design of a nuclear system will be as good as the knowledge of the nuclear data used whether differential and integral. ORNL is engaged in generating high level nuclear data for reactor, shielding, and safety applications. Nuclear data remains a major source of data uncertainties. Uncertainties on nuclear data rely upon measurements and evaluations. Tight connections with experimental facilities around the world have helped ORNL to address issues on ND and uncertainty. It is extremely important for ORNL to retain expertise on nuclear data in support of the research and expertise activities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Intracellular stress tomography reveals stress focusing and structural anisotropy in cytoskeleton of living cells

We describe a novel synchronous detection approach to map the transmission of mechanical stresses within the cytoplasm of an adherent cell. Using fluorescent protein-labeled mitochondria or cytoskeletal components as fiducial markers, we measured displacements and computed stresses in the cytoskeleton of a living cell plated on extracellular matrix molecules that arise in response to a small, external localized oscillatory load applied to transmembrane receptors on the apical cell surface. Induced synchronous displacements, stresses, and phase lags were found to be concentrated at sites quite remote from the localized load and were modulated by the preexisting tensile stress (prestress) in the cytoskeleton. Stresses applied at the apical surface also resulted in displacements of focal adhesion sites at the cell base. Cytoskeletal anisotropy was revealed by differential phase lags in X vs. Y directions. Displacements and stresses in the cytoskeleton of a cell plated on poly-L-lysine decayed quickly and were not concentrated at remote sites. These data indicate that mechanical forces are transferred across discrete cytoskeletal elements over long distances through the cytoplasm in the living adherent cell.

NASA Discipline Cell Biology↗

Hydrogen measurement during steam oxidation using coupled thermogravimetric analysis and quadrupole mass spectrometry

An analytical technique is presented with the goal of measuring reaction kinetics during steam oxidation reactions for three cases in which obtaining kinetics information often requires a prohibitive amount of time and cost. The technique presented relies on coupling thermogravimetric analysis (TGA) with a quantitative hydrogen measurement technique using quadrupole mass spectrometry (QMS). The first case considered is in differentiating between the kinetics of steam oxidation reactions and those for simultaneously reacting gaseous impurities such as nitrogen or oxygen. The second case allows one to independently measure the kinetics of oxide and hydride formation for systems in which both of these reactions are known to take place during steam oxidation. The third case deals with measuring the kinetics of formation for competing volatile and non-volatile oxides during certain steam oxidation reactions. In order to meet the requirements of the coupled technique, a methodology is presented which attempts to provide quantitative measurement of hydrogen generation using QMS in the presence of an interfering fragmentation species, namely water vapor. This is achieved such that all calibrations and corrections are performed during the TGA baseline and steam oxidation programs, making system operation virtually identical to standard TGA. Benchmarking results showed a relative error in hydrogen measurement of 5.7–8.4% following the application of a correction factor. Lastly, suggestions are made for possible improvements to the presented technique so that it may be better applied to the three cases presented.

36 MATERIALS SCIENCE↗

Airborne gravity and other geophysical techniques for understanding the lithosphere beneath the West Antarctic Ice Sheet

As part of a program entitled Corridor Aerogeophysics of the Southeastern Ross Transect Zone (CASERTZ), an aerogeophysical platform was developed to study the interaction of geological and glaciological processes in West Antarctica. A de Havilland Twin Otter was equipped with an ice-penetrating radar, a proton precession magnetometer, an airborne gravity system, and a laser altimeter. The 60-MHz ice-penetrating radar can recover sub-ice topography with an accuracy of about 10 m through 3 km of comparatively warm West Antarctic ice, while the laser altimeter profiling of the ice surface is accurate to approximately 1 m. The magnetic field observations are accurate to several nT, and the gravity measurements are accurate to better than 3 mGal. The aircraft is navigated by a local radio transponder network, while differential positioning techniques based on the Global Positioning System (GPS) satellites are used for recovering high-resolution horizontal and vertical positions. Attitude information from an inertial navigation system is used to correct the laser altimetry and a digital pressure transducer is used to recover vertical positions and accelerations in the absence of satellite positioning. Continuous base-station observations are made for the differential GPS positioning and the removal of ionospheric noise from the airborne magnetometer measurements.

Bell, Robin E.↗

Development of Multiobjective Optimization Techniques for Sonic Boom Minimization

A discrete, semi-analytical sensitivity analysis procedure has been developed for calculating aerodynamic design sensitivities. The sensitivities of the flow variables and the grid coordinates are numerically calculated using direct differentiation of the respective discretized governing equations. The sensitivity analysis techniques are adapted within a parabolized Navier Stokes equations solver. Aerodynamic design sensitivities for high speed wing-body configurations are calculated using the semi-analytical sensitivity analysis procedures. Representative results obtained compare well with those obtained using the finite difference approach and establish the computational efficiency and accuracy of the semi-analytical procedures. Multidisciplinary design optimization procedures have been developed for aerospace applications namely, gas turbine blades and high speed wing-body configurations. In complex applications, the coupled optimization problems are decomposed into sublevels using multilevel decomposition techniques. In cases with multiple objective functions, formal multiobjective formulation such as the Kreisselmeier-Steinhauser function approach and the modified global criteria approach have been used. Nonlinear programming techniques for continuous design variables and a hybrid optimization technique, based on a simulated annealing algorithm, for discrete design variables have been used for solving the optimization problems. The optimization procedure for gas turbine blades improves the aerodynamic and heat transfer characteristics of the blades. The two-dimensional, blade-to-blade aerodynamic analysis is performed using a panel code. The blade heat transfer analysis is performed using an in-house developed finite element procedure. The optimization procedure yields blade shapes with significantly improved velocity and temperature distributions. The multidisciplinary design optimization procedures for high speed wing-body configurations simultaneously improve the aerodynamic, the sonic boom and the structural characteristics of the aircraft. The flow solution is obtained using a comprehensive parabolized Navier Stokes solver. Sonic boom analysis is performed using an extrapolation procedure. The aircraft wing load carrying member is modeled as either an isotropic or a composite box beam. The isotropic box beam is analyzed using thin wall theory. The composite box beam is analyzed using a finite element procedure. The developed optimization procedures yield significant improvements in all the performance criteria and provide interesting design trade-offs. The semi-analytical sensitivity analysis techniques offer significant computational savings and allow the use of comprehensive analysis procedures within design optimization studies.

Chattopadhyay, Aditi↗

PETSc/TAO Users Manual (Rev. 3.19)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and opti mization that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than packages such as MATLAB or a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or lldb, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. There are several packages, built on PETSc, that may satisfy your needs without requiring directly using PETSc. We recommend reviewing these packages functionality before starting to code directly with PETSc. PETSc can be used to provide a “MPI parallel linear solver” in an otherwise sequential, or OpenMP parallel code. This approach cannot provide extremely large improvements in the application time by utilizing large numbers of MPI processes but can still improve the performance. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect true scalability to large numbers of MPI processes. See PCMPI for details on how to utilize the PETSc MPI linear solver server. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc has been supported for twenty-five years; see mailing list information on our website for information on contacting support.

97 MATHEMATICS AND COMPUTING↗

Observing strategy for the SDSS-IV/MaNGA IFU galaxy survey

Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) is an integral-field spectroscopic survey that is one of three core programs in the fourth-generation Sloan Digital Sky Survey (SDSS-IV). MaNGA’s 17 pluggable optical fiber-bundle integral field units (IFUs) will observe a sample of 10,000 nearby galaxies distributed throughout the SDSS imaging footprint (focusing particularly on the North Galactic Cap). In each pointing these IFUs are deployed across a 3° field; they yield spectral coverage 3600−10300 Å at a typical resolution R ∼ 2000, and sample the sky with 2″ diameter fiber apertures with a total bundle fill factor of 56%. Observing over such a large field and range of wavelengths is particularly challenging for obtaining uniform and integral spatial coverage and resolution at all wavelengths and across each entire fiber array. Data quality is affected by the IFU construction technique, chromatic and field differential refraction, the adopted dithering strategy, and many other effects. We use numerical simulations to constrain the hardware design and observing strategy for the survey with the aim of ensuring consistent data quality that meets the survey science requirements while permitting maximum observational flexibility. We find that MaNGA science goals are best achieved with IFUs composed of a regular hexagonal grid of optical fibers with rms displacement of 5 μm or less from their nominal packing position; this goal is met by the MaNGA hardware, which achieves 3 μm rms fiber placement. We further show that MaNGA observations are best obtained in sets of three 15 minute exposures dithered along the vertices of a 1.44 arcsec equilateral triangle; these sets form the minimum observational unit, and are repeated as needed to achieve a combined signal-to-noise ratio of 5 Å{sup −1} per fiber in the r-band continuum at a surface brightness of 23 AB arcsec{sup −2}. In order to ensure uniform coverage and delivered image quality, we require that the exposures in a given set be obtained within a 60 minute interval of each other in hour angle, and that all exposures be obtained at airmass ≲1.2 (i.e., within 1–3 hr of transit depending on the declination of a given field).

79 ASTRONOMY AND ASTROPHYSICS↗

A new method for the experimental heating of intact soil profiles for application to climate change experiments

Advanced facilities are needed to evaluate the response of complex ecosystems to projected unique climate conditions not observable in the context of current natural variation or through the use of climate gradients. A next-generation, experimental system for simulating future belowground temperature increases was conceived, simulated, constructed and tested in a temperate deciduous forest in Oak Ridge, Tennessee, USA. The new system uses low-wattage, 3-m deep, circumferentially-installed heaters surrounding a defined soil volume to both add the necessary energy to support a set-point soil temperature differential within the treatment area and to add exterior energy inputs equal to that which might be lost from lateral heat conduction. This approach, which is designed to work in conjunction with aboveground heated chambers, requires only two control positions, (1) aboveground air temperatures at 1 m and (2) belowground temperatures at 0.8 m. The approach is capable of achieving in situ target temperature differentials in the tested range of +4.0 0.5 C for soils to a measured depth of -2 m located within the aboveground boundary for air heating. These differentials were sustained throughout 2009, and both diurnal and seasonal cycles at all soil depths were retained using this simple heating approach. Measured mean energy inputs required to sustain the target heating level of +4 C over the 7.1 m2 target area were substantial: 21.1 kW h d-1 m-2 for aboveground heating but 16 times lower for belowground heaters at 1.3 kW h d-1 m-2. Observations of soil CO2 efflux from the surface of the target soil volumes showed CO2 losses throughout 2009 that were elevated above the temperature response curve for control CO2 losses at levels greater than have been reported in previous soil warming studies. Stimulation of biological activity of previously undisturbed deep-soil carbon stocks is the expected source. Long-term research programs may be able to apply similar experimental systems to address uncertainties in process-level responses of microbial, plant, and animal communities in whole, intact ecosystems using this new heating method that capture expected future warming and temperature dynamics throughout the soil profile.

54 ENVIRONMENTAL SCIENCES↗

Failure strength predictions for closed-cell polyvinyl chloride foams

This paper describes an effort to model mechanical strength of closed-cell polyvinyl chloride foams under static loading. The study presented here is a continuation of an earlier study to model elastic stiffness of closed-cell polyvinyl chloride foams as effective transversely isotropic materials. An engineering approach is used in the study and governing equations are developed for predicting the strength of polyvinyl chloride foams. To account for foam microstructure and cell-shape anisotropy on foam strength, a unit cell representation of the polyvinyl chloride foam microstructure is used to derive equations to assess tensile and shear strengths of polyvinyl chloride foams. The differential stretching of polyvinyl chloride foam cell walls (in the rise direction and in the in-plane directions) on the strength of the foam-matrix polymer is also taken into account in modeling the mechanical strength of polyvinyl chloride closed-cell foams. The behavior of closed-cell polyvinyl chloride foams under compression is different from that under tension. In the paper, the equations for predicting compressive strength of closed-cell polyvinyl chloride foams are based on an approximate theory developed in an earlier study of compressive strength of unidirectional composites. The validity of the foam strength predictive equations, derived in the paper, is first demonstrated through comparison of the predictions with the results on Divinycell H (DIAB) foams obtained from a systematic in-house test program. A comparison is also carried out between the strength predictions and the test results published by two polyvinyl chloride foam manufacturers for different density polyvinyl chloride foams. Good agreements are found for all the different density foams studied.

Lo, King H.↗

PETSc Users Manual (Rev. 3.13)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.

97 MATHEMATICS AND COMPUTING↗