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At least 1,657 records · Page 92
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks

Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. To illuminate these forces, we determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked β sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. By computationally threading the human proteome on our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such interactions. Finally, these segments are found in proteins as diverse as RNA binders, nuclear pore proteins, and keratins, which are known to form networks and localize to membraneless assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Characterizing 4-string contact interaction using machine learning

Abstract The geometry of 4-string contact interaction of closed string field theory is characterized using machine learning. We obtain Strebel quadratic differentials on 4-punctured spheres as a neural network by performing unsupervised learning with a custom-built loss function. This allows us to solve for local coordinates and compute their associated mapping radii numerically. We also train a neural network distinguishing vertex from Feynman region. As a check, 4-tachyon contact term in the tachyon potential is computed and a good agreement with the results in the literature is observed. We argue that our algorithm is manifestly independent of number of punctures and scaling it to characterize the geometry ofn-string contact interaction is feasible.

Physics↗
DOE OSTI2023

Elucidating the speciation of extracted lanthanides by diglycolamides

Many studies over the past few decades have been devoted to addressing the application of diglycolamides (DGAs) for hydrometallurgical-based, f-element separations. Work to date has shown the molecular structure of a DGA derivative can have a significant impact on intra-lanthanide partitioning patterns. More recent studies have pushed towards probing the structure function relationship of the lanthanide-DGA complex to enable the design of more efficient lanthanide separation systems. Spectroscopic techniques, such as UV–Visible, Fourier Transformed Infrared Spectroscopy (FT-IR), Nuclear Magnetic Resonance (NMR), and Extended X-ray Absorption Fine Structure (EXAFS), provide information regarding the inner-sphere coordination of a given lanthanide-DGA complex. Scattering techniques, such as Dynamic Light Scattering (DLS), Small-Angle X-ray Scattering (SAXS), and Small-Angle Neutron Scattering (SANS), address nanoscale structures including aggregate sizes and morphology. Here, this review assesses the current state-of-knowledge regarding lanthanide-DGA hydrometallurgical (i.e., solvent extraction systems) interrogated using spectroscopic and scattering techniques to characterize the extracted Ln 3+ DGA species. Of particular interest to this review is the impact of varied diluents, inclusion and variation of phase modifiers, and DGA derivatization on system characteristics. While there has been extensive literature on the application of DGAs for f-element separations, the literature lacks a collective assessment of the speciation of Ln 3+ in the organic phase. This review provides new insights into the field of DGA separations, explicitly with an application to intra-lanthanide separations. Specifically, this review illustrates the importance of both the co-extraction anion (Cl - , NO 3 - , or ClO 4 - ) as it pertains to both the aggregate size and Ln 3+ distribution coefficient. It is evident the ability of the anion to disrupt the hydrogen bonding network limits both aggregate size and distribution coefficients according to the Hoffmeister series. This suggests the importance of the large, softer anions with a low charge-to-surface area ratio on encouraging hydrogen bond interactions. In addition, the co-extracted cation (H + vs Na + ) is important for mitigating transfer of Ln 3+ from the aqueous to the organic phase through extensive hydrogen bonding networks. These networks are responsible for forming supramolecular aggregates where a change in morphology is observed with increasing concentrations of H + and/or Ln 3+ in the organic phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

LaserNetUS Collaboration Network—University of Rochester (Final Report)

LaserNetUS Collaborative Network established in 2018 is a network of high-power laser facilities supported by the Department of Energy (DOE) Office of Fusion Energy Sciences (FES) and operating effectively as a user facility. Its mission is to advance and promote intense laser science and applications by providing scientists and students with broad access to unique facilities and enabling technologies, advancing the frontiers of laser-science research, and fostering collaboration among researchers and networks from around the world. Users who submit proposals through an annual call are selected by an external and independent proposal review panel (PRP) not involving personnel from any of the facilities. Besides the Omega Laser Facility at the University of Rochester’s Laboratory for Laser Energetics (UR/LLE), the network during this project period includes high-intensity laser facilities from six other universities and three national laboratories, namely, the Colorado State University (CSU), the University of Michigan (UM), the University of Nebraska at Lincoln (UNL), The Ohio State University (OSU), Université du Québec, the University of Texas at Austin (UT Austin), Lawrence Berkeley National Laboratory (LBNL), SLAC National Accelerator Laboratory (SLAC) and Lawrence Livermore National Laboratory (LLNL), respectively. The network facilities span a wide range in laser pulse energy, pulse duration, repetition rate, and experimental diagnostic equipment enabling innovative research in a variety of exciting areas. Details of the LaserNetUS facilities, organization and committees, events, and accomplishments can be found at the network website (https://lasernetus.org/). A very important role that the LaserNetUS fulfills is the training of students and young scientists who will be key for the future development of laser-plasma science and high-power laser technology itself. The network provides these students not only with access to the most advanced instrumentation and laser facilities, but also the opportunities to interact and collaborate with students from other institutions and with a large group of experienced scientists. As the largest university-based laser users’ facility in the world, the Omega Laser Facility at the UR/LLE has served the high-energy-density physics (HEDP) and inertial fusion science community for nearly 40 years. The multi-beam multi-kJ OMEGA EP Laser System brings unique capabilities to the LaserNetUS network. The combination of high intensity and high energy in short- and long-pulse operation together with solid or gas-jet targets and externally applied magnetic fields provides users a wide domain of experimental conditions. This award provides a total of eight shot days on OMEGA EP for LaserNetUS users. During the award period of performance (June 2019–November 2021), seven teams have fully utilized the eight shot days for their unique science experiments on OMEGA EP with a total of 83 target shots. These experiments involve 13 graduate students, two undergraduate students and six postdoctoral researchers. Results have been widely disseminated at international conferences including LaserNetUS annual meeting (~20 presentations including three invited), and in peer-reviewed journal publications (three published with several manuscripts in preparation).

36 MATERIALS SCIENCE↗
DOE OSTI2020

3D Nanomagnetism in Low Density Interconnected Nanowire Networks

Free-standing, interconnected metallic nanowire networks with densities as low as 40 mg/cm 3 have been achieved over centimeter-scale areas, using electrodeposition into polycarbonate membranes that have been ion-tracked at multiple angles. Networks of interconnected magnetic nanowires further provide an exciting platform to explore 3-dimensional nanomagnetism, where their structure, topology, and frustration may be used as additional degrees of freedom to tailor the materials properties. New magnetization reversal mechanisms in cobalt networks are captured by the first-order reversal curve method, which demonstrate the evolution from strong demagnetizing dipolar interactions to intersection-mediated domain wall pinning and propagation, and eventually to shape-anisotropy dominated magnetization reversal. These findings open up new possibilities for 3-dimensional integrated magnetic devices for memory, complex computation, and neuromorphics.

36 MATERIALS SCIENCE↗
DOE OSTI2019

CO 3+1 network formation in ultra-high pressure carbonate liquids

Carbonate liquids are an important class of molten salts, not just for industrial applications, but also in geological processes. Carbonates are generally expected to be simple liquids, in terms of ionic interactions between the molecular carbonate anions and metal cations, and therefore relatively structureless compared to more “polymerized” silicate melts. But there is increasing evidence from phase relations, metal solubility, glass spectroscopy and simulations to suggest the emergence of carbonate “networks” at length scales longer than the component molecular anions. The stability of these emergent structures are known to be sensitive to temperature, but are also predicted to be favoured by pressure. This is important as a recent study suggests that subducted surface carbonate may melt near the Earth’s transition zone (~44 km), representing a barrier to the deep carbon cycle depending on the buoyancy and viscosity of these liquids. In this study we demonstrate a major advance in our understanding of carbonate liquids by combining simulations and high pressure measurements on a carbonate glass, (K 2 CO 3 -MgCO 3 ) to pressures in excess of 40 GPa, far higher than any previous in situ study. We show the clear formation of extended low-dimensional carbonate networks of close CO 3 2– pairs and the emergence of a “three plus one” local coordination environment, producing an unexpected increase in viscosity with pressure. Although carbonate melts may still be buoyant in the lower mantle, an increased viscosity by at least three orders of magnitude will restrict the upward mobility, possibly resulting in entrainment by the down-going slab.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Structurization of ferrofluids in the absence of an external magnetic field

Structural transformations in a model ferrofluid in the absence of an external magnetic field have been theoretically studied. The results agree with well-known laboratory experiments and computer simulations in showing that, if the concentration of particles and their magnetic interaction energy are below certain critical values, most particles form separate linear chains. If these parameters exceed the critical values, most particles concentrate so as to form branched network structures. The passage from chains to network has a continuous character rather than represents a discontinuous first-order phase transition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH (Session introduction)

Pathogenic infections are a major cause of both human disease and loss of crop yields and animal stocks and thus cause immense damage to the worldwide economy. The significance of infectious diseases is expected to increase in an ever more connected warming world, in which new viral, bacterial and fungal pathogens can find novel hosts and ecologic niches. At the same time, the complex and sophisticated mechanisms by which diverse pathogenic agents evade defense mechanisms and subvert their hosts networks to suit their lifestyle needs is still very incompletely understood especially from a systems perspective [1]. Thus, understanding host-pathogen interactions is both an important and a scientifically fascinating topic. Recently, technology has offered the opportunity to investigate host-pathogen interactions on a level of detail and scope that offers immense computational and analytical possibilities. Genome sequencing was pioneered on some of these pathogens, and the number of strains and variants of pathogens sequenced to date vastly outnumbers the number of host genomes available. At the same time, for both plant and human hosts more and more data on population level genomic variation becomes available and offers a rich field for analysis into the genetic interactions between host and pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

Proposed Development of NASA Glenn Research Center's Aeronautical Network Research Simulator

Accurate knowledge and understanding of data link traffic loads that will have an impact on the underlying communications infrastructure within the National Airspace System (NAS) is of paramount importance for planning, development and fielding of future airborne and ground-based communications systems. Attempting to better understand this impact, NASA Glenn Research Center (GRC), through its contractor Computer Networks & Software, Inc. (CNS, Inc.), has developed an emulation and test facility known as the Virtual Aircraft and Controller (VAC) to study data link interactions and the capacity of the NAS to support Controller Pilot Data Link Communications (CPDLC) traffic. The drawback of the current VAC test bed is that it does not allow the test personnel and researchers to present a real world RF environment to a complex airborne or ground system. Fortunately, the United States Air Force and Navy Avionics Test Commands, through its contractor ViaSat, Inc., have developed the Joint Communications Simulator (JCS) to provide communications band test and simulation capability for the RF spectrum through 18 GHz including Communications, Navigation, and Identification and Surveillance functions. In this paper, we are proposing the development of a new and robust test bed that will leverage on the existing NASA GRC's VAC and the Air Force and Navy Commands JCS systems capabilities and functionalities. The proposed NASA Glenn Research Center's Aeronautical Networks Research Simulator (ANRS) will combine current Air Traffic Control applications and physical RF stimulation into an integrated system capable of emulating data transmission behaviors including propagation delay, physical protocol delay, transmission failure and channel interference. The ANRS will provide a simulation/stimulation tool and test bed environment that allow the researcher to predict the performance of various aeronautical network protocol standards and their associated waveforms under varying density conditions. The system allows the user to define human-interactive and scripted aircraft and controller models of various standards, such as (but not limited to) Very High Frequency Digital Link (VDL) of various modes.

Nguyen, Thanh C.↗
DOE OSTI2015

Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data

Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.

Zhu, Yitan↗
DOE OSTI2023

IceNet for FireBox - A Berkeley Warehouse-Scale Computer

Berkeley’s FireBox is a next-generation warehouse-scale computer (WSC) that utilizes the energy-efficiency and bandwidth density of integrated silicon-photonic interconnects to enable a new high-bandwidth and low-latency network fabric connecting thousands of compute nodes to petabytes of DRAM and Flash storage. The high bandwidth, low latency and high connectivity of FireBox’s WSC network fabric (IceNet) will enable dramatic improvements in the overall system energy efficiency enabling fine-grain power control on system resources (processors, links and memory/storage components). IceNet is a special 3-stage photonic Clos network architected to achieve ultra-low-latency connectivity between processor nodes and memory, drastically cutting down on the energy wasted in resource idling (processors and memory stalled due to pending network requests). This is achieved by integration of the first and last switch stages into processor/memory hub clients and by heavy over-provisioning of the high-radix middle switches (FlareSwitches). A key hardware component developed in this program is an active laser power management photonic integrated circuits called LightSpark. It interacts with the FlareSwitch and provides laser power to a subset of occupied switch ports, increasing the utilization of laser light in the photonic network by an order of magnitude. In addition to guiding the laser power where it is needed, the laser-power management module enables both wavelength and laser redundancy, significantly increasing the robustness of the system. The goal of the IceNet fabric is to enable communication between 1000s of processor nodes and PBs of memory/storage with <100ns latency, <10pJ/b wall-plug energy cost at multiple Pb/s of available connectivity bandwidth. These metrics represent two-orders of magnitude improvement with respect to the status of current data-center technology.

42 ENGINEERING↗
DOE OSTI2026

Mechanics of pore array collapse and interaction in shock-compressed polymethyl methacrylate (PMMA)

Recent studies on dynamic pore collapse have revealed significant development of shear localization, which can lead to material failure in porous structures and hot spot generation in energetic materials. These findings have dramatically improved the understanding of failure mechanisms during pore collapse but also prompt further investigation of realistic porous materials. In particular, porous media consist of many pores and porous networks. Even in low-porosity materials, pores can form in close proximity during the manufacturing process, leading to the critical question of pore–pore interaction during collapse under dynamic loading conditions. This study investigates, via plate impact experiments coupled with high-speed internal digital image correlation and shadowgraphy techniques, the collapse of two pores in shock-compressed PMMA at stresses between 0.4 and 1 GPa. The results of these experiments provide new insights into shear localization in pore collapse, in addition to distinct interactions between pores. Shadowgraphy measurements reveal novel, direct visualization of shear band development and crack evolution from pore surfaces. Spacing between adiabatic shear bands is measured over a range of impact stresses and is predicted accurately by the Grady–Kipp model. Pore interactions are found to effect a transition in the impact stress threshold at which different failure mechanisms initiate and are also found to possibly influence preferential sites for shear cracking. Throughout the study, numerical and theoretical models are leveraged to understand shear localization behavior. The role of baroclinicity and wave interactions between the pores is used to elucidate interaction mechanisms between pores.

Lawlor, Barry P. [California Institute of Technolo↗
DOE OSTI2013

Multi-scale computational model of three-dimensional hemodynamics within a deformable full-body arterial network

In this article, we present a computational multi-scale model of fully three-dimensional and unsteady hemodynamics within the primary large arteries in the human. Computed tomography image data from two different patients were used to reconstruct a nearly complete network of the major arteries from head to foot. A linearized coupled-momentum method for fluid–structure-interaction was used to describe vessel wall deformability and a multi-domain method for outflow boundary condition specification was used to account for the distal circulation. We demonstrated that physiologically realistic results can be obtained from the model by comparing simulated quantities such as regional blood flow, pressure and flow waveforms, and pulse wave velocities to known values in the literature. We also simulated the impact of age-related arterial stiffening on wave propagation phenomena by progressively increasing the stiffness of the central arteries and found that the predicted effects on pressure amplification and pulse wave velocity are in agreement with findings in the clinical literature. This work demonstrates the feasibility of three-dimensional techniques for simulating hemodynamics in a full-body compliant arterial network.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1993

EnviroNET: On-line information for LDEF

EnviroNET is an on-line, free-form database intended to provide a centralized repository 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 research facilities, industry, universities, and the European Space Agency. The models accept parameter input from the user, then 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 fields, and the ionosphere. A user-friendly, informative interface is standard for all the models and includes a pop-up help window with information on inputs, outputs, and caveats. The system will eventually simplify mission analysis with analytical tools and deliver solutions for computationally intense graphical applications to do 'What if...' scenarios. A proposed plan for developing a repository of information from the Long Duration Exposure Facility (LDEF) for a user group is presented.

Lauriente, Michael↗
DOE OSTI2020

A transmission electron microscopy study of dislocation propagation and filtering in highly mismatched GaSb/GaAs heteroepitaxy

Monolithic integration of lattice-mismatched semiconductor materials opens up access to a wide range of bandgaps and new device functionalities. However, it is inevitably accompanied by defect formation. A thorough analysis of how these defects propagate and interact with interfaces is critical to understanding their effects on device parameters. In this study, we present a comprehensive study of dislocation networks in the GaSb/GaAs heteroepitaxial system using transmission electron microscopy (TEM). Specifically, the sample analyzed is a GaSb film grown on GaAs using dislocation–reduction strategies such as interfacial misfit array formation and introduction of a dislocation filtering layer. Using various TEM techniques, it is shown that such an analysis can reveal important information on the dislocation behavior including filtering mechanism, types of dislocation reactions, and other interactions with interfaces. A novel method that enables plan-view imaging of deeply embedded interfaces using TEM and a demonstration of independent imaging of different dislocation types are also presented. While clearly effective in characterizing dislocation behavior in GaSb/GaAs, we believe that the methods outlined in this article can be extended to study other heteroepitaxial material systems.

36 MATERIALS SCIENCE↗
NASA NTRS1994

Coordinating complex decision support activities across distributed applications

Knowledge-based technologies have been applied successfully to automate planning and scheduling in many problem domains. Automation of decision support can be increased further by integrating task-specific applications with supporting database systems, and by coordinating interactions between such tools to facilitate collaborative activities. Unfortunately, the technical obstacles that must be overcome to achieve this vision of transparent, cooperative problem-solving are daunting. Intelligent decision support tools are typically developed for standalone use, rely on incompatible, task-specific representational models and application programming interfaces (API's), and run on heterogeneous computing platforms. Getting such applications to interact freely calls for platform independent capabilities for distributed communication, as well as tools for mapping information across disparate representations. Symbiotics is developing a layered set of software tools (called NetWorks! for integrating and coordinating heterogeneous distributed applications. he top layer of tools consists of an extensible set of generic, programmable coordination services. Developers access these services via high-level API's to implement the desired interactions between distributed applications.

Adler, Richard M.↗
NASA NTRS1991

Robo-line storage: Low latency, high capacity storage systems over geographically distributed networks

Rapid advances in high performance computing are making possible more complete and accurate computer-based modeling of complex physical phenomena, such as weather front interactions, dynamics of chemical reactions, numerical aerodynamic analysis of airframes, and ocean-land-atmosphere interactions. Many of these 'grand challenge' applications are as demanding of the underlying storage system, in terms of their capacity and bandwidth requirements, as they are on the computational power of the processor. A global view of the Earth's ocean chlorophyll and land vegetation requires over 2 terabytes of raw satellite image data. In this paper, we describe our planned research program in high capacity, high bandwidth storage systems. The project has four overall goals. First, we will examine new methods for high capacity storage systems, made possible by low cost, small form factor magnetic and optical tape systems. Second, access to the storage system will be low latency and high bandwidth. To achieve this, we must interleave data transfer at all levels of the storage system, including devices, controllers, servers, and communications links. Latency will be reduced by extensive caching throughout the storage hierarchy. Third, we will provide effective management of a storage hierarchy, extending the techniques already developed for the Log Structured File System. Finally, we will construct a protototype high capacity file server, suitable for use on the National Research and Education Network (NREN). Such research must be a Cornerstone of any coherent program in high performance computing and communications.

Katz, Randy H.↗
DOE OSTI2023

LDRD23-0730: Invoking Multilayer Networks to Develop a Paradigm for Security Science—Summary Report

Current approaches to securing high consequence facilities (HCF) and critical assets are linear and static and therefore struggle to adapt to emerging threats (e.g., unmanned aerial systems) and changing environmental conditions (e.g., decreasing operational control). The pace of change in technological, organizational, societal, and political dynamics necessitates a move toward codifying underlying scientific principles to better characterize the rich interactions observed between HCF security technology, infrastructure, digital assets, and human or organizational components. The promising results of Laboratory Directed Research and Development (LDRD) 20-0373—“Developing a Resilient, Adaptive, and Systematic Paradigm for Security Analysis”—suggest that when compared to traditional security analysis, invoking multilayer network (MLN) modeling for HCF security system components captures unexpected failure cases and unanticipated interactions.

97 MATHEMATICS AND COMPUTING↗