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At least 1,567 records · Page 87

maranasgroup/yeastsMFA

The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and a few genetic perturbations thereof. Unlike stoichiometric models that are mostly invariant to the specific strain, it remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. This important question underpins the applicability range and prediction limits of kinetic reconstructions. To this end, herein we parameterize two separate large-scale kinetic models using K-FIT with genome-wide coverage corresponding to two distinct strains of Saccharomyces cerevisiae: CEN.PK 113-7D strain (model k-sacce306-CENPK), and growth-deficient BY4741 (isogenic to S288c; model k-sacce306-BY4741). The metabolic network for each model contains 306 reactions, 230 metabolites, and 119 substrate-level regulatory interactions. The two models (for CEN.PK and BY4741) recapitulate, within one standard deviation, 77% and 75% of the fitted dataset fluxes, respectively, determined by 13C metabolic flux analysis for wild-type and eight single-gene knockout mutants of each strain. Strain-specific kinetic parameterization results indicate that key enzymes in the TCA cycle, glycolysis, and arginine and proline metabolism drive the metabolic differences between these two strains of S. cerevisiae. Our results suggest that although kinetic models cannot be readily used across strains as stoichiometric models, they can capture species-specific information through the kinetic parameterization process.

Dinh, Hoang↗

maranasgroup/k-sacce306

The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and a few genetic perturbations thereof. Unlike stoichiometric models that are mostly invariant to the specific strain, it remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. This important question underpins the applicability range and prediction limits of kinetic reconstructions. To this end, herein we parameterize two separate large-scale kinetic models using K-FIT with genome-wide coverage corresponding to two distinct strains of Saccharomyces cerevisiae: CEN.PK 113-7D strain (model k-sacce306-CENPK), and growth-deficient BY4741 (isogenic to S288c; model k-sacce306-BY4741). The metabolic network for each model contains 306 reactions, 230 metabolites, and 119 substrate-level regulatory interactions. The two models (for CEN.PK and BY4741) recapitulate, within one standard deviation, 77% and 75% of the fitted dataset fluxes, respectively, determined by 13C metabolic flux analysis for wild-type and eight single-gene knockout mutants of each strain. Strain-specific kinetic parameterization results indicate that key enzymes in the TCA cycle, glycolysis, and arginine and proline metabolism drive the metabolic differences between these two strains of S. cerevisiae. Our results suggest that although kinetic models cannot be readily used across strains as stoichiometric models, they can capture species-specific information through the kinetic parameterization process.

Dinh, Hoang↗

Report on DOE support for GSC13 travel award

Consortium. The 3-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7th, 2012, and was hosted by the Beijing Genomics Institute (BGI). The meeting was entitled ‘From Genomes to Interactions to Communities to Models’ and aimed to be a scientific meeting that highlighted the role of data standards associated with genomic, metagenomic and amplicon sequence data, and the contextual information associated with the sample that data was generated from. To this end the meeting focused on genomic projects for animals, plants, fungi and viruses, metagenomic studies in host-microbe interactions, and community dynamics in microbial communities. In addition the meeting hosted a Genomic Observatories Network session, a GSC biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation. The meeting was very well organized by the local hosts at BGI, and all attendees reported that they were very happy with the outcome, service and quality of the science presented. Highlights were keynotes by Rita Colwell, Mitch Sogin and Jim Tiedje. The 5 attendees paid for by the DOE award were Daniel Smith and Jared Wilkening (University of Chicago); Patrick Chain (Los Alamos National Laboratory), Austin Davis-Richardson (University of Florida) and Greg Caporoaso (University of Northern Arizona). Each attendee was able to either present or become involved with the attending scientists, and each reported that they had got something significant out of the meeting. Here are detailed their personal accounts of the GSC13 meeting. We thank DOE for the helping to fund this valuable outreach initiative, and for supporting the attendance of these bright young scientists at this important meeting.

59 BASIC BIOLOGICAL SCIENCES↗

RAMSES II: RAMan Search for Extragalactic Symbiotic Stars Project Concept, Commissioning, and Early Results from the Science Verification Phase

Symbiotic stars (SySts) are long-period interacting binaries composed of a hot compact star, an evolved giant star, and a tangled network of gas and dust nebulae. They represent unique laboratories for studying a variety of important astrophysical problems, and have also been proposed as possible progenitors of SNIa. Presently, we know of 257 SySts in the Milky Way and 69 in external galaxies. However, these numbers are still in striking contrast with the predicted population of SySts in our Galaxy. Because of other astrophysical sources that mimic SySt colors, no photometric diagnostic tool has so far demonstrated the power to unambiguously identify a SySt, thus making the recourse to costly spectroscopic follow-up still inescapable. In this paper we present the concept, commissioning, and science verification phases, as well as the first scientific results, of RAMSES II—a Gemini Observatory Instrument Upgrade Project that has provided each GMOS instrument at both Gemini telescopes with a set of narrow-band filters centered on the Raman O vi 6830 Å band. Continuum-subtracted images using these new filters clearly revealed known SySts with a range of Raman O vi line strengths, even in crowed fields. RAMSES II observations also produced the first detection of Raman O vi emission from the SySt LMC 1 and confirmed Hen 3-1768 as a new SySt—the first photometric confirmation of a SySt. Via Raman O vi narrow-band imaging, RAMSES II provides the astronomical community with the first purely photometric tool for hunting SySts in the local universe.

79 ASTRONOMY AND ASTROPHYSICS↗

Report of the 13 th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012.

This report details the outcome of the 13 th Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5–7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.

59 BASIC BIOLOGICAL SCIENCES↗

Glassy interphases reinforce elastomeric nanocomposites by enhancing percolation-driven volume expansion under strain

For nearly a century, introduction of nanoparticles to elastomers has yielded extraordinarily tough nanocomposites that are critical to technologies from actuators to tires. The mechanisms by which this reinforcement occurs have nevertheless remained a central open question in material science. One widely debated hypothesis posits that strong interactions between polymer and particles induce "glassy bridges" that cement particles into a cohesive percolating network that resists elongation. Here, molecular dynamics simulations show that glassy particle shells do not primarily provide elongational cohesion. Instead, they amplify an underlying mechanism wherein competition between filler and elastomer networks causes the elastomer's volume to increase on deformation. This induces contributions from the elastomer's bulk modulus, which is of order 1000 times larger than its Young's modulus. These findings establish a unified understanding of low-strain reinforcement in filled elastomers as emanating from volumetric competition between coexisting particulate and elastomeric networks. This reframes and unifies our understanding of low-strain reinforcement, provides a clear-cut diagnostic for the presence of glassy bridging, and offers a new design principle for tough elastomeric nanocomposites.

Computational Physics (physics.comp-ph)↗

Computational models for the analysis of three-dimensional internal and exhaust plume flowfields

This paper describes computational procedures developed for the analysis of three-dimensional supersonic ducted flows and multinozzle exhaust plume flowfields. The models/codes embodying these procedures cater to a broad spectrum of geometric situations via the use of multiple reference plane grid networks in several coordinate systems. Shock capturing techniques are employed to trace the propagation and interaction of multiple shock surfaces while the plume interface, separating the exhaust and external flows, and the plume external shock are discretely analyzed. The computational grid within the reference planes follows the trace of streamlines to facilitate the incorporation of finite-rate chemistry and viscous computational capabilities. Exhaust gas properties consist of combustion products in chemical equilibrium. The computational accuracy of the models/codes is assessed via comparisons with exact solutions, results of other codes and experimental data. Results are presented for the flows in two-dimensional convergent and divergent ducts, expansive and compressive corner flows, flow in a rectangular nozzle and the plume flowfields for exhausts issuing out of single and multiple rectangular nozzles.

Dash, S. M.↗

Analysis of three-dimensional ducted and exhaust plume flowfields

Computational procedures are described for analyzing three-dimensional supersonic internal flows and multinozzle exhaust plume flowfields. The computer codes (BIGMAC and CHAR3D) embodying these procedures cater to a broad spectrum of geometric situations via the use of multiple reference plane grid networks in several coordinate systems. Shock capturing techniques are employed to trace the propagation and interaction of multiple shock surfaces. Gas properties consist of combustion products in chemical equilibrium. The computational accuracy of the codes is assessed via comparisons with the results of other codes and experimental data. Results are presented for the flows in two-dimensional ducts, corner flows, flow in a rectangular nozzle, and the plume flowfields for exhausts issuing out of single and multiple rectangular nozzles.

Dash, S. M.↗

The new space and Earth science information systems at NASA's archive

The on-line interactive systems of the National Space Science Data Center (NSSDC) are examined. The worldwide computer network connections that allow access to NSSDC users are outlined. The services offered by the NSSDC new technology on-line systems are presented, including the IUE request system, Total Ozone Mapping Spectrometer (TOMS) data, and data sets on astrophysics, atmospheric science, land sciences, and space plasma physics. Plans for future increases in the NSSDC data holdings are considered.

Green, James L.↗

The new space and earth science information systems at NASA's archive

The on-line interactive systems of the National Space Science Data Center (NSSDC) are examined. The worldwide computer network connections that allow access to NSSDC users are outlined. The services offered by the NSSDC new technology on-line systems are presented, including the IUE request system, ozone TOMS data, and data sets on astrophysics, atmospheric science, land sciences, and space plasma physics. Plans for future increases in the NSSDC data holdings are considered.

Green, James L.↗

SPACEWAY(TM) Providing Afordable and Versatile Telecommunication Solutions

This paper presents a summary description of SPACEWAY(TM), a network of Ka band geostationary satellites being developed by Hughes Communications, Inc. to provide worldwide interactive telecommunications services to small, low cost user terminals. By the end of this decade SPACEWAY(TM), using relatively few satellites and tightly focused spot beams, will provide affordable interactive 'bandwidth on demand' communication services on a global basis to consumer and commercial end users. This paper describes the system concept, details the space and ground segment characteristics, and discusses communication links.

Fitzpatrick, Edward James↗

Training Software in Artificial-Intelligence Computing Techniques

The Artificial Intelligence (AI) Toolkit is a computer program for training scientists, engineers, and university students in three soft-computing techniques (fuzzy logic, neural networks, and genetic algorithms) used in artificial-intelligence applications. The program promotes an easily understandable tutorial interface, including an interactive graphical component through which the user can gain hands-on experience in soft-computing techniques applied to realistic example problems. The tutorial provides step-by-step instructions on the workings of soft-computing technology, whereas the hands-on examples allow interaction and reinforcement of the techniques explained throughout the tutorial. In the fuzzy-logic example, a user can interact with a robot and an obstacle course to verify how fuzzy logic is used to command a rover traverse from an arbitrary start to the goal location. For the genetic algorithm example, the problem is to determine the minimum-length path for visiting a user-chosen set of planets in the solar system. For the neural-network example, the problem is to decide, on the basis of input data on physical characteristics, whether a person is a man, woman, or child. The AI Toolkit is compatible with the Windows 95,98, ME, NT 4.0, 2000, and XP operating systems. A computer having a processor speed of at least 300 MHz, and random-access memory of at least 56MB is recommended for optimal performance. The program can be run on a slower computer having less memory, but some functions may not be executed properly.

Howard, Ayanna↗

Emulation and Adversarial Analysis of EV Charging Networks

In the effort of decarbonization and evolution of the modern electrical grid, electric vehicles (EVs) play a key part to transform the grid. However, due to the rapid adoption of EVs and the demand of the charging infrastructure required to power said EVs, risk of a cyber-attack may impose serious consequences. There is a need to analyze and protect the charging ecosystem infrastructure from cyber threats before it reaches wide-scale deployment. In an effort to secure vehicle to grid (V2G) communications, standardization is necessary for continued reliable system operation. The protocol ISO 15118 outlines controls and practices that should be implemented for secure vehicle to grid (V2G) communications. The standard is gaining momentum for American markets as the demand for EV infrastructure grows. The adoption of ISO 15118 in American markets poses several challenges: the deployment of a public key infrastructure (PKI) as outlined within the standard, interoperability of charging different EVs with chargers from different manufactures using the PKI, and scaling the ecosystem to meet the demand while managing risks. This project was created to understand potential cyber and scaling challenges of PKI for EV infrastructure through utilizing a series of emulated components mapping to what exists in the EV ecosystem today, and the components of the PKI that are under development. The key nodes within the emulation that are under development are: electric vehicle (EV), electric vehicle supply equipment (EVSE), charge network operator (CNO), certificate authority (CA), and online certificate status protocol (OCSP) that must all interact using secure and trusted communications. With these emulated components and utilizing orchestration methods to rapidly deploy and scale the components, the ability to analyze risks of the ecosystem and address gaps before the PKI ecosystem is fully deployed to production should yield a more robust and mature production charging infrastructure. Our approach will use a modular architecture of virtual machines within an orchestration platform and will target scales of 100s, 1000s, and 10,000s of entities interacting. The core research questions trying to be answered with this scope of work are: what are the impacts of a rogue CA, what are the risks of certificate revocation list (CRL) management, what is the value of OCSP stapling, what components are vulnerable to DOS attacks, and what test effective payloads may impact the components.

charging ecosystem↗

A deep potential model with long-range electrostatic interactions

Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make molecular simulations with the accuracy of quantum mechanical density functional theory possible at a cost only moderately higher than that of empirical force fields. However, the majority of these models lack explicit long-range interactions and fail to describe properties that derive from the Coulombic tail of the forces. To overcome this limitation, we extend the DP model by approximating the long-range electrostatic interaction between ions (nuclei + core electrons) and valence electrons with that of distributions of spherical Gaussian charges located at ionic and electronic sites. The latter are rigorously defined in terms of the centers of the maximally localized Wannier distributions, whose dependence on the local atomic environment is modeled accurately by a deep neural network. In the DP long-range (DPLR) model, the electrostatic energy of the Gaussian charge system is added to short-range interactions that are represented as in the standard DP model. The resulting potential energy surface is smooth and possesses analytical forces and virial. Missing effects in the standard DP scheme are recovered, improving on accuracy and predictive power. By including long-range electrostatics, DPLR correctly extrapolates to large systems the potential energy surface learned from quantum mechanical calculations on smaller systems. We illustrate the approach with three examples: the potential energy profile of the water dimer, the free energy of interaction of a water molecule with a liquid water slab, and the phonon dispersion curves of the NaCl crystal.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Three-Dimensional Grid Visualization for Planning Activities: A Dubai Case Study

National Laboratory of the Rockies (NLR), in collaboration with the Dubai Electricity and Water Authority (DEWA) and Infra-X, has undertaken the Energy Visualization Analysis Project. The aim of this project is to enhance analytical and 3D visualization capabilities for distribution network planning and renewable energy integration. As modern grid continues to evolve with large-scale solar PV deployment and emerging distributed energy resources (DERs), the ability to effectively analyze, visualize, and communicate complex grid behaviors has become increasingly critical. The project focuses on developing empirical use cases based on real distribution feeder data and engineering workflows, ensuring the outcomes are directly aligned with operational environment. Through time-series power flow simulations and nodal hosting capacity analysis, the study quantifies the impacts of high PV penetration on voltage and thermal limits within representative 11 kV feeders. These analyses identify specific nodes and conditions where DER integration challenges arise. Furthermore, a Battery Energy Storage System (BESS) optimization algorithm was applied to determine the optimal size and placement of storage systems that can mitigate network constraints and enhance hosting capacity. The comparative results between base-case and BESS-augmented scenarios clearly demonstrate improvements in network stability and load management efficiency. In parallel, the NLR team developed an immersive 3D visualization framework, enabling interactive exploration of grid simulations using commodity head-mounted display (HMD) systems. This framework transforms conventional 2D simulation data into spatially intuitive visual environments - allowing engineers to analyze feeder conditions, PV hosting potential, and BESS effects in real time. This report represents the first foundational phase in establishing a visualization-driven analytical ecosystem. It provides a methodological foundation for data integration, visualization architecture, and simulation-based decision support, paving the way for large-scale adoption of immersive visualization across DEWA's Smart Grid Initiative, R&D activities, and future network resilience studies.

24 POWER TRANSMISSION AND DISTRIBUTION↗

EnviroNET: An on-line environment data base for LDEF data

EnviroNET is an on-line, free form data base intended to provide a centralized depository for a wide range of technical information on environmentally induced interactions of use to Space Shuttle customers and spacecraft designers. It provides a user friendly, menu driven format on networks that are connected globally and is available twenty-four hours a day, every day. The information updated regularly, includes expository text, tabular numerical data, charts and graphs, and models. The system pools space data collected over the years by NASA, USAF, other government facilities, industry, universities, and ESA. The models accept parameter input from the user and calculate and display the derived values corresponding to that input. In addition to the archive, interactive graphics programs are also available on space debris, the neutral atmosphere, radiation, magnetic field, and ionosphere. A user friendly informative interface is standard for all the models with a pop-up window, help window with information on inputs, outputs, and caveats. The system will eventually simplify mission analysis with analytical tools and deliver solution for computational intense graphical applications to do 'What if' scenarios. A proposed plan for developing a repository of LDEF information for a user group concludes the presentation.

Lauriente, Michael↗

Telemetry, tracking, and command consolidation in the Deep Space Network

Currently, in NASA's Deep Space Network (DSN), telemetry, tracking, and command (TT&C) functions are distributed between multiple subsystem computers. Control design of these subsystems did not consider the interaction necessary between the functions, which create opportunities for loss of data. Also, the current controller design can force the use of equipment that is not needed for the task at hand, to the detriment of others. As part of the Network Simplification Project (NSP), the TTC implementation has been re-examined, New telemetry and commanding equipment is being built, and the control of the TT&C functions is being consolidated into two controllers, Uplink and Downlink. The new equipment uses commercial components, as opposed to the custom built equipment it is replacing, which improves reliability and simplifies maintenance.

tracking↗

Connecting AmeriFlux to the Globe, Extending the Partnership with Global Flux Network FLUXNET

We propose a project that will extend and expand the activities and contributions of AmeriFlux, to the global stage by working with our international partners to continue operating and expand the functioning of global FLUXNET database. One goal is to produce the next-generation FLUXNET dataset. This will be an integrated dataset on carbon, water and energy fluxes, on meteorological conditions and on the structure and function of the ecosystems; we have to potential to construct a new database, double the size of the La Thuile dataset, with over 2000 site-years of trace gas flux measurements, and supporting meteorological and site meta-data from over 400 sites world-wide. The production of the next FLUXNET database is critical to the activities of this ROSE’s solicitation because these data will drive many of the carbon cycle synthesis activities and the model parameterization and validation activities. A second goal is to build the next-generation, data-system that will house, distribute and query data and discover new information by the broader biogeoscience user community. The third goal is to use these data in synthesis activities that improve our understanding on how climate, weather, ecological, physiological and soil factors govern the exchange of carbon, water and energy between vegetation and the atmosphere at multiple time and space scales. The fourth goal is to act as a coordinator of the project to recruit data, to organize a workshop/conference and to build a community of data sharing and interaction across vast cultural spectrum of participating scientists. The rationale for proposing this work is based on the fact that the vast databases that are produced by flux networks cannot perpetuate and evolve without continued support of the intellectual activities of scientists who produce data, expert in databases, and scientists who use data for modeling. The actuality of a flux network takes human intervention to recruit data from different countries and cultures, to build trust to share data in open-access format, to support data users, and to collaborate. Specifically, we will develop an updated data portal that is easy to navigate and conducive for distributing, visualization, evaluation and discovery of the multiple types of flux and environmental data and information. We will foster collaboration and interactions with our national and international partners and the recruitment of data by: 1) continuing the periodic publication of the newsletter, FLUXLETTER; 2) by hosting an international conference; 3) by coordinating and launching multi-investigator data synthesis activities; and 4) by developing tools that coordinate the development of research papers resulting from the dataset. Data products include raw and gap-filled data at their native time steps (30 minute averages), data products that are integrated on daily and annual time scales and value added products like ecosystem respiration and canopy photosynthesis. Uncertainty analysis and quality control metrics will be produced in coordination with AmeriFlux and ICOS. We will also work with colleagues to expand the scope of FLUXNET beyond carbon dioxide and water vapor, and start archiving the growing methane flux databases that are being collected, world-wide. The interpretation of the flux data relies on good meta-data. We will work with data providers to populate and expand the meta-data archives. We will also work with collaborators to incorporate data from remote sensing products such as MODIS and Landsat, from corresponding climate and weather stations. Another goal is to incorporate new data on canopy structure, with recent LIDAR acquisitions, to populate the data archive with automated soil respiration and understory flux measurements, where available and local climate records for corresponding sites. And, we will collaborate with the TRY database, by merging flux data with plant trait information.

54 ENVIRONMENTAL SCIENCES↗