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At least 199 records · Page 11

Agent-based modeling of microbes in space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal microgravity; however, much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER results agree with experimental data indicating that indirect effects of radiation (reactive oxygen species generation, metabolic impairment) have a greater impact on microorganisms than direct effects (DNA damage).

Jessica A Lee↗

Agent-Based Modeling of Microbes in Space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal gravity, and much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER growth curves recapitulate experimental results, and allow comparison between direct effects (DNA damage) and indirect effects (reactive oxygen species generation, metabolic impairment) of radiation.

microbiology↗

Synthesizing 3D Surfaces from Parameterized Strip Charts

We believe 3D information visualization has the power to unlock new levels of productivity in the monitoring and control of complex processes. Our goal is to provide visual methods to allow for rapid human insight into systems consisting of thousands to millions of parameters. We explore this hypothesis in two complex domains: NASA program management and NASA International Space Station (ISS) spacecraft computer operations. We seek to extend a common form of visualization called the strip chart from 2D to 3D. A strip chart can display the time series progression of a parameter and allows for trends and events to be identified. Strip charts can be overlayed when multiple parameters need to visualized in order to correlate their events. When many parameters are involved, the direct overlaying of strip charts can become confusing and may not fully utilize the graphing area to convey the relationships between the parameters. We provide a solution to this problem by generating 3D surfaces from parameterized strip charts. The 3D surface utilizes significantly more screen area to illustrate the differences in the parameters and the overlayed strip charts, and it can rapidly be scanned by humans to gain insight. The selection of the third dimension must be a parallel or parameterized homogenous resource in the target domain, defined using a finite, ordered, enumerated type, and not a heterogeneous type. We demonstrate our concepts with examples from the NASA program management domain (assessing the state of many plans) and the computers of the ISS (assessing the state of many computers). We identify 2D strip charts in each domain and show how to construct the corresponding 3D surfaces. The user can navigate the surface, zooming in on regions of interest, setting a mark and drilling down to source documents from which the data points have been derived. We close by discussing design issues, related work, and implementation challenges.

Robinson, Peter I.↗

Molecular Dynamics Investigation of the Structural and Mechanical Properties of Off-Stoichiometric Epoxy Resins

Molecular dynamic (MD) simulations were performed to compute the mechanical properties of off-stoichiometric epoxy resins as a function of hardener/epoxy mixture ratio (r). Properties were characterized in relation to their microscopic structures. Such resins have been used recently for adhesive-free bonding of large-scale composite structures using the co-curing-ply method. In this process, two partially precured composite panels with hardener-poor (HP) off-stoichiometric resins are coupled with ply(ies) of complementary hardener-rich (HR) formulations and then cured simultaneously. This bonding process has the potential to produce reliable and certifiable composite joints without the need for additional fasteners, which are often required for many conventional bonding methods because even small amounts of contamination can cause a weak bond. The reflow and mixing of the HP/HR resin in this bonding process result in a joint with no discernable interface that should not be susceptible to surface contamination. However, incomplete mixing of the two offset resins may result in chemical heterogeneity of the cured polymeric joint. Thus, different r values may be obtained across the joint. Classical MD simulations were performed to compute the Young’s modulus of polymers with different r values and correlate their properties to network structures. High stiffness was associated with molecular packing due to chemical crosslinking, leading to a single network structure. Moreover, the networks became denser as the ratio approached the stoichiometric value r = 1. Thus, the r = 1 systems were single clusters, with high stiffness, high molecular weight, and a high degree of crosslinking. Structural properties such as radius of gyration and mean square displacement were determined to investigate the variation in the stiffness with respect to r. This MD simulation study was validated with experimental measurements.

Chang Woon Jang↗

Atmospheric correction of high resolution land surface images

Algorithms to correct for atmospheric-scattering effects in high-spatial resolution land-surface images require the ability to perform rapid and accurate computations of the top-of-atmosphere diffuse radiance field for arbitrarily general surface reflectance distributions (which may be both heterogeneous and non-Lambertian) and atmospheric models. Using three-dimensional radiative transfer (3DRT) theory algorithms are being developed. The methodology used to perform the 3DRT calculations is described. It is shown how these calculations are used to perform atmospheric corrections, and the sensitivity of the retrieved surface reflectances to atmospheric structural parameters is illustrated.

Diner, D. J.↗

The chemistry of bromine in the stratosphere: Influence of a new rate constant for the reaction BrO + HO2

The impact of new laboratory data for the reaction BrO + HO2 yields HOBr + O2 in the depletion of global stratospheric ozone has been estimated using a one-dimensional photochemical model taking into account the heterogeneous reaction on sulphate aerosols which converts N2O5 into HNO3. Assuring an aerosol loading 2 times as large as the 'background' and a reaction probability of 0.1 for the above heterogeneous reaction, the 6 fold increase in the measured rate constant for the reaction of BrO with HO2 increases the computed depletion of global ozone produced by 20 ppt of total bromine from 2.01 percent to 2.36 percent. The use of the higher rate constant increases the HOBr mixing ratio and makes the bromine partitioning and the ozone depletion very sensitive to the branching ratio of the potential channel forming HBr in the BrO + HO2 reaction.

Pirre, Michel↗

Developing Information Power Grid Based Algorithms and Software

This was an exploratory study to enhance our understanding of problems involved in developing large scale applications in a heterogeneous distributed environment. It is likely that the large scale applications of the future will be built by coupling specialized computational modules together. For example, efforts now exist to couple ocean and atmospheric prediction codes to simulate a more complete climate system. These two applications differ in many respects. They have different grids, the data is in different unit systems and the algorithms for inte,-rating in time are different. In addition the code for each application is likely to have been developed on different architectures and tend to have poor performance when run on an architecture for which the code was not designed, if it runs at all. Architectural differences may also induce differences in data representation which effect precision and convergence criteria as well as data transfer issues. In order to couple such dissimilar codes some form of translation must be present. This translation should be able to handle interpolation from one grid to another as well as construction of the correct data field in the correct units from available data. Even if a code is to be developed from scratch, a modular approach will likely be followed in that standard scientific packages will be used to do the more mundane tasks such as linear algebra or Fourier transform operations. This approach allows the developers to concentrate on their science rather than becoming experts in linear algebra or signal processing. Problems associated with this development approach include difficulties associated with data extraction and translation from one module to another, module performance on different nodal architectures, and others. In addition to these data and software issues there exists operational issues such as platform stability and resource management.

Dongarra, Jack↗

XML-Based Visual Specification of Multidisciplinary Applications

The advancements in the Internet and Web technologies have fueled a growing interest in developing a web-based distributed computing environment. We have designed and developed Arcade, a web-based environment for designing, executing, monitoring, and controlling distributed heterogeneous applications, which is easy to use and access, portable, and provides support through all phases of the application development and execution. A major focus of the environment is the specification of heterogeneous, multidisciplinary applications. In this paper we focus on the visual and script-based specification interface of Arcade. The web/browser-based visual interface is designed to be intuitive to use and can also be used for visual monitoring during execution. The script specification is based on XML to: (1) make it portable across different frameworks, and (2) make the development of our tools easier by using the existing freely available XML parsers and editors. There is a one-to-one correspondence between the visual and script-based interfaces allowing users to go back and forth between the two. To support this we have developed translators that translate a script-based specification to a visual-based specification, and vice-versa. These translators are integrated with our tools and are transparent to users.

Al-Theneyan, Ahmed↗

Allowing for Horizontally Heterogeneous Clouds and Generalized Overlap in an Atmospheric GCM

While fully accounting for 3D effects in Global Climate Models (GCMs) appears not realistic at the present time for a variety of reasons such as computational cost and unavailability of 3D cloud structure in the models, incorporation in radiation schemes of subgrid cloud variability described by one-point statistics is now considered feasible and is being actively pursued. This development has gained momentum once it was demonstrated that CPU-intensive spectrally explicit Independent Column Approximation (lCA) can be substituted by stochastic Monte Carlo ICA (McICA) calculations where spectral integration is accomplished in a manner that produces relatively benign random noise. The McICA approach has been implemented in Goddard's GEOS-5 atmospheric GCM as part of the implementation of the RRTMG radiation package. GEOS-5 with McICA and RRTMG can handle horizontally variable clouds which can be set via a cloud generator to arbitrarily overlap within the full spectrum of maximum and random both in terms of cloud fraction and layer condensate distributions. In our presentation we will show radiative and other impacts of the combined horizontal and vertical cloud variability on multi-year simulations of an otherwise untuned GEOS-5 with fixed SSTs. Introducing cloud horizontal heterogeneity without changing the mean amounts of condensate reduces reflected solar and increases thermal radiation to space, but disproportionate changes may increase the radiative imbalance at TOA. The net radiation at TOA can be modulated by allowing the parameters of the generalized overlap and heterogeneity scheme to vary, a dependence whose behavior we will discuss. The sensitivity of the cloud radiative forcing to the parameters of cloud horizontal heterogeneity and comparisons of CERES-derived forcing will be shown.

Lee, D.↗

Orbital design strategy for domestic communication satellite systems.

Review of some of the considerations pertinent to efficient orbit utilization in the design of domestic communications satellite systems. A strategy is developed to efficiently locate a heterogeneous system of satellites within the available arc and provide room for future growth. A practical design is illustrated, using a computer simulation model, for the placement of 25 satellites within 73% of the available arc employing frequency and polarization coordination techniques. A number of widely variable factors that influence satellite spacing are examined. These factors include such critical system elements as telephony and television interference noise limits, frequency plan coordination, polarization plan coordination, ground antenna diameter, signal protection ratio, and satellite station keeping.

Ramji, S.↗

HEP - A semaphore-synchronized multiprocessor with central control

The paper describes the design concept of the Heterogeneous Element Processor (HEP), a system tailored to the special needs of scientific simulation. In order to achieve high-speed computation required by simulation, HEP features a hierarchy of processes executing in parallel on a number of processors, with synchronization being largely accomplished by hardware. A full-empty-reserve scheme of synchronization is realized by zero-one-valued hardware semaphores. A typical system has, besides the control computer and the scheduler, an algebraic module, a memory module, a first-in first-out (FIFO) module, an integrator module, and an I/O module. The architecture of the scheduler and the algebraic module is examined in detail.

Gilliland, M. C.↗

Experience with abstract notation one

The development of computer science has produced a vast number of machine architectures, programming languages, and compiler technologies. The cross product of these three characteristics defines the spectrum of previous and present data representation methodologies. With regard to computer networks, the uniqueness of these methodologies presents an obstacle when disparate host environments are to be interconnected. Interoperability within a heterogeneous network relies upon the establishment of data representation commonality. The International Standards Organization (ISO) is currently developing the abstract syntax notation one standard (ASN.1) and the basic encoding rules standard (BER) that collectively address this problem. When used within the presentation layer of the open systems interconnection reference model, these two standards provide the data representation commonality required to facilitate interoperability. The details of a compiler that was built to automate the use of ASN.1 and BER are described. From this experience, insights into both standards are given and potential problems relating to this development effort are discussed.

Harvey, James D.↗

Mapping Biophysical Parameters for Land Surface Modeling over the Continental US Using MODIS and Landsat

In terms of the space cities occupy, urbanization appears as a minor land transformation. However, it permanently modifies land's ecological functions, altering its carbon, energy, and water fluxes. It is therefore necessary to develop a land cover characterization at fine spatial and temporal scales to capture urbanization's effects on surface fluxes. We develop a series of biophysical vegetation parameters such as the fraction of photosynthetically active radiation, leaf area index, vegetation greenness fraction, and roughness length over the continental US using MODIS and Landsat products for 2001. A 13-class land cover map was developed at a climate modeling grid (CMG) merging the 500mMODIS land cover and the 30m impervious surface area from the National Land Cover Database. The landscape subgrid heterogeneity was preserved using fractions of each class from the 500 m and 30 m into the CMG. Biophysical parameters were computed using the 8-day composite Normalized Difference Vegetation Index produced by the North American Carbon Program. In addition to urban impact assessments, this dataset is useful for the computation of surface fluxes in land, vegetation, and urban models and is expected to be widely used in different land cover and land use change applications.

Biophysical↗

Distributed Quantum Processing via Integrated Regional Quantum Networks Using Free-Space Optical Links

The landscape for quantum computing is rapidly evolving with the development of quantum computers and the emergence of future science enabling applications being pursued in many areas, such as distributed quantum computing, hybrid computing scenarios that require cooperatively networked quantum and classical computing assets and more. Quantum networking is also advancing with multiple regional quantum networks and testbeds maturing across the nation. These quantum networking testbeds typically include multiple access points with a heterogeneous mixture of capabilities interconnected by fiber spanning anywhere from tens to hundreds of kilometers; many such networks incorporate a classical networking framework. Alongside these connectivity advancements in the infrastructure, there is quantum sensing device and component technology maturation that is serving to expand the body of quantum networking scenarios that are presently possible and redefining the quantum- enabled future. Bridging the present collective progress in quantum computing and quantum networking will enable the next era of purposeful advancements for national priority use-cases for the benefit of science. One such use-case is enabling future quantum computing applications via integrated regional quantum networking infrastructure in neighboring locations like New York and Maryland, both states are home to robust classical and quantum networking capabilities. To enable near-term distributed quantum computing applications via the practical integration of regional quantum networking infrastructure, free-space optical links via satellite communications will be essential to avoid the exponential loss commonly observed with fiber implementations. There is both an urgent need and a practical justification for pursuing such space-based integration scope now.

Harry Shaw↗

Validation and Scaling of Soil Moisture in a Semi-Arid Environment: SMAP Validation Experiment 2015 (SMAPVEX15)

The NASA SMAP (Soil Moisture Active Passive) mission conducted the SMAP Validation Experiment 2015 (SMAPVEX15) in order to support the calibration and validation activities of SMAP soil moisture data products. The main goals of the experiment were to address issues regarding the spatial disaggregation methodologies for improvement of soil moisture products and validation of the in situ measurement upscaling techniques. To support these objectives high-resolution soil moisture maps were acquired with the airborne PALS (Passive Active L-band Sensor) instrument over an area in southeast Arizona that includes the Walnut Gulch Experimental Watershed (WGEW), and intensive ground sampling was carried out to augment the permanent in situ instrumentation. The objective of the paper was to establish the correspondence and relationship between the highly heterogeneous spatial distribution of soil moisture on the ground and the coarse resolution radiometer-based soil moisture retrievals of SMAP. The high-resolution mapping conducted with PALS provided the required connection between the in situ measurements and SMAP retrievals. The in situ measurements were used to validate the PALS soil moisture acquired at 1-km resolution. Based on the information from a dense network of rain gauges in the study area, the in situ soil moisture measurements did not capture all the precipitation events accurately. That is, the PALS and SMAP soil moisture estimates responded to precipitation events detected by rain gauges, which were in some cases not detected by the in situ soil moisture sensors. It was also concluded that the spatial distribution of the soil moisture resulted from the relatively small spatial extents of the typical convective storms in this region was not completely captured with the in situ stations. After removing those cases (approximately10 of the observations) the following metrics were obtained: RMSD (root mean square difference) of0.016m3m3 and correlation of 0.83. The PALS soil moisture was also compared to SMAP and in situ soil moisture at the 36-km scale, which is the SMAP grid size for the standard product. PALS and SMAP soil moistures were found to be very similar owing to the close match of the brightness temperature measurements and the use of a common soil moisture retrieval algorithm. Spatial heterogeneity, which was identified using the high-resolution PALS soil moisture and the intensive ground sampling, also contributed to differences between the soil moisture estimates. In general, discrepancies found between the L-band soil moisture estimates and the 5-cm depth in situ measurements require methodologies to mitigate the impact on their interpretations in soil moisture validation and algorithm development. Specifically, the metrics computed for the SMAP radiometer-based soil moisture product over WGEW will include errors resulting from rainfall, particularly during the monsoon season when the spatial distribution of soil moisture is especially heterogeneous.

SMAPVEX15↗

Properties of the stratospheric aerosol layer studied with a one-dimensional computer model

Aerosol particle effects are often neglected in theoretical studies of stratospheric phenomena. In reality, the particulate matter normally found above the tropopause may influence the terrestrial radiation balance, catalyze heterogeneous chemical interactions, and serve as a tracer of atmospheric motions. The paper proposes a one-dimensional model of the stratospheric aerosol layer, and it is used to compare aerosol theory with observational data. The model considers gaseous sulfur photochemistry and the physical aerosol processes of nucleation, coagulation, sedimentation, and diffusion. Calculations of the effects on the aerosol layer of stratospheric injections of aluminum oxide particles by Space Shuttle engines and of sulfur dioxide molecules by volcanic activity are performed. The relation between measured aerosol variability and changes in stratospheric air temperatures and vertical transport rates are discussed.

Turco, R. P.↗

Coniferous Canopy BRF Simulation Based on 3-D Realistic Scene

It is difficulties for the computer simulation method to study radiation regime at large-scale. Simplified coniferous model was investigate d in the present study. It makes the computer simulation methods such as L-systems and radiosity-graphics combined method (RGM) more powerf ul in remote sensing of heterogeneous coniferous forests over a large -scale region. L-systems is applied to render 3-D coniferous forest scenarios: and RGM model was used to calculate BRF (bidirectional refle ctance factor) in visible and near-infrared regions. Results in this study show that in most cases both agreed well. Meanwhiie at a tree and forest level. the results are also good.

Wang, Xin-yun↗

Shape and Stress Sensing of Multilayered Composite and Sandwich Structures Using an Inverse Finite Element Method

The marked increase in the use of composite and sandwich material systems in aerospace, civil, and marine structures leads to the need for integrated Structural Health Management systems. A key capability to enable such systems is the real-time reconstruction of structural deformations, stresses, and failure criteria that are inferred from in-situ, discrete-location strain measurements. This technology is commonly referred to as shape- and stress-sensing. Presented herein is a computationally efficient shape- and stress-sensing methodology that is ideally suited for applications to laminated composite and sandwich structures. The new approach employs the inverse Finite Element Method (iFEM) as a general framework and the Refined Zigzag Theory (RZT) as the underlying plate theory. A three-node inverse plate finite element is formulated. The element formulation enables robust and efficient modeling of plate structures instrumented with strain sensors that have arbitrary positions. The methodology leads to a set of linear algebraic equations that are solved efficiently for the unknown nodal displacements. These displacements are then used at the finite element level to compute full-field strains, stresses, and failure criteria that are in turn used to assess structural integrity. Numerical results for multilayered, highly heterogeneous laminates demonstrate the unique capability of this new formulation for shape- and stress-sensing.

Cerracchio, Priscilla↗