Fusion barrier characteristics of actinides

NASA Astrophysics Data System (ADS)

Manjunatha, H. C.; Sridhar, K. N.

2018-03-01

We have studied fusion barrier characteristics of actinide compound nuclei with atomic number range 89 ≤ Z ≤ 103 for all projectile target combinations. After the calculation of fusion barrier heights and positions, we have searched for their parameterization. We have achieved the empirical formula for fusion barrier heights (VB), positions (RB), curvature of the inverted parabola (ħω) of actinide compound nuclei with atomic number range 89 ≤ Z ≤ 103 for all projectile target combinations (6

On genera of curves from high-loop generalized unitarity cuts

NASA Astrophysics Data System (ADS)

Huang, Rijun; Zhang, Yang

2013-04-01

Generalized unitarity cut of a Feynman diagram generates an algebraic system of polynomial equations. At high-loop levels, these equations may define a complex curve or a (hyper-)surface with complicated topology. We study the curve cases, i.e., a 4-dimensional L-loop diagram with (4 L-1) cuts. The topology of a complex curve is classified by its genus. Hence in this paper, we use computational algebraic geometry to calculate the genera of curves from two and three-loop unitarity cuts. The global structure of degenerate on-shell equations under some specific kinematic configurations is also sketched. The genus information can also be used to judge if a unitary cut solution could be rationally parameterized.

Heavy-quark production in gluon fusion at two loops in QCD

NASA Astrophysics Data System (ADS)

Czakon, M.; Mitov, A.; Moch, S.

2008-07-01

We present the two-loop virtual QCD corrections to the production of heavy quarks in gluon fusion. The results are exact in the limit when all kinematical invariants are large compared to the mass of the heavy quark up to terms suppressed by powers of the heavy-quark mass. Our derivation uses a simple relation between massless and massive QCD scattering amplitudes as well as a direct calculation of the massive amplitude at two loops. The results presented here together with those obtained previously for quark-quark scattering form important parts of the next-to-next-to-leading order QCD corrections to heavy-quark production in hadron-hadron collisions.

Interaction of 〈1 0 0〉 dislocation loops with dislocations studied by dislocation dynamics in α-iron

NASA Astrophysics Data System (ADS)

Shi, X. J.; Dupuy, L.; Devincre, B.; Terentyev, D.; Vincent, L.

2015-05-01

Interstitial dislocation loops with Burgers vector of 〈1 0 0〉 type are formed in α-iron under neutron or heavy ion irradiation. As the density and size of these loops increase with radiation dose and temperature, these defects are thought to play a key role in hardening and subsequent embrittlement of iron-based steels. The aim of the present work is to study the pinning strength of the loops on mobile dislocations. Prior to run massive Dislocation Dynamics (DD) simulations involving experimentally representative array of radiation defects and dislocations, the DD code and its parameterization are validated by comparing the individual loop-dislocation reactions with those obtained from direct atomistic Molecular Dynamics (MD) simulations. Several loop-dislocation reaction mechanisms are successfully reproduced as well as the values of the unpinning stress to detach mobile dislocations from the defects.

Iterative Bayesian Estimation of Travel Times on Urban Arterials: Fusing Loop Detector and Probe Vehicle Data.

PubMed

Liu, Kai; Cui, Meng-Ying; Cao, Peng; Wang, Jiang-Bo

2016-01-01

On urban arterials, travel time estimation is challenging especially from various data sources. Typically, fusing loop detector data and probe vehicle data to estimate travel time is a troublesome issue while considering the data issue of uncertain, imprecise and even conflicting. In this paper, we propose an improved data fusing methodology for link travel time estimation. Link travel times are simultaneously pre-estimated using loop detector data and probe vehicle data, based on which Bayesian fusion is then applied to fuse the estimated travel times. Next, Iterative Bayesian estimation is proposed to improve Bayesian fusion by incorporating two strategies: 1) substitution strategy which replaces the lower accurate travel time estimation from one sensor with the current fused travel time; and 2) specially-designed conditions for convergence which restrict the estimated travel time in a reasonable range. The estimation results show that, the proposed method outperforms probe vehicle data based method, loop detector based method and single Bayesian fusion, and the mean absolute percentage error is reduced to 4.8%. Additionally, iterative Bayesian estimation performs better for lighter traffic flows when the variability of travel time is practically higher than other periods.

Iterative Bayesian Estimation of Travel Times on Urban Arterials: Fusing Loop Detector and Probe Vehicle Data

PubMed Central

Cui, Meng-Ying; Cao, Peng; Wang, Jiang-Bo

2016-01-01

On urban arterials, travel time estimation is challenging especially from various data sources. Typically, fusing loop detector data and probe vehicle data to estimate travel time is a troublesome issue while considering the data issue of uncertain, imprecise and even conflicting. In this paper, we propose an improved data fusing methodology for link travel time estimation. Link travel times are simultaneously pre-estimated using loop detector data and probe vehicle data, based on which Bayesian fusion is then applied to fuse the estimated travel times. Next, Iterative Bayesian estimation is proposed to improve Bayesian fusion by incorporating two strategies: 1) substitution strategy which replaces the lower accurate travel time estimation from one sensor with the current fused travel time; and 2) specially-designed conditions for convergence which restrict the estimated travel time in a reasonable range. The estimation results show that, the proposed method outperforms probe vehicle data based method, loop detector based method and single Bayesian fusion, and the mean absolute percentage error is reduced to 4.8%. Additionally, iterative Bayesian estimation performs better for lighter traffic flows when the variability of travel time is practically higher than other periods. PMID:27362654

Structural and Functional Studies on the Marburg Virus GP2 Fusion Loop.

PubMed

Liu, Nina; Tao, Yisong; Brenowitz, Michael D; Girvin, Mark E; Lai, Jonathan R

2015-10-01

Marburg virus (MARV) and the ebolaviruses belong to the family Filoviridae (the members of which are filoviruses) that cause severe hemorrhagic fever. Infection requires fusion of the host and viral membranes, a process that occurs in the host cell endosomal compartment and is facilitated by the envelope glycoprotein fusion subunit, GP2. The N-terminal fusion loop (FL) of GP2 is a hydrophobic disulfide-bonded loop that is postulated to insert and disrupt the host endosomal membrane during fusion. Here, we describe the first structural and functional studies of a protein corresponding to the MARV GP2 FL. We found that this protein undergoes a pH-dependent conformational change, as monitored by circular dichroism and nuclear magnetic resonance. Furthermore, we report that, under low pH conditions, the MARV GP2 FL can induce content leakage from liposomes. The general aspects of this pH-dependent structure and lipid-perturbing behavior are consistent with previous reports on Ebola virus GP2 FL. However, nuclear magnetic resonance studies in lipid bicelles and mutational analysis indicate differences in structure exist between MARV and Ebola virus GP2 FL. These results provide new insight into the mechanism of MARV GP2-mediated cell entry. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

High Level Information Fusion (HLIF) with nested fusion loops

NASA Astrophysics Data System (ADS)

Woodley, Robert; Gosnell, Michael; Fischer, Amber

2013-05-01

Situation modeling and threat prediction require higher levels of data fusion in order to provide actionable information. Beyond the sensor data and sources the analyst has access to, the use of out-sourced and re-sourced data is becoming common. Through the years, some common frameworks have emerged for dealing with information fusion—perhaps the most ubiquitous being the JDL Data Fusion Group and their initial 4-level data fusion model. Since these initial developments, numerous models of information fusion have emerged, hoping to better capture the human-centric process of data analyses within a machine-centric framework. 21st Century Systems, Inc. has developed Fusion with Uncertainty Reasoning using Nested Assessment Characterizer Elements (FURNACE) to address challenges of high level information fusion and handle bias, ambiguity, and uncertainty (BAU) for Situation Modeling, Threat Modeling, and Threat Prediction. It combines JDL fusion levels with nested fusion loops and state-of-the-art data reasoning. Initial research has shown that FURNACE is able to reduce BAU and improve the fusion process by allowing high level information fusion (HLIF) to affect lower levels without the double counting of information or other biasing issues. The initial FURNACE project was focused on the underlying algorithms to produce a fusion system able to handle BAU and repurposed data in a cohesive manner. FURNACE supports analyst's efforts to develop situation models, threat models, and threat predictions to increase situational awareness of the battlespace. FURNACE will not only revolutionize the military intelligence realm, but also benefit the larger homeland defense, law enforcement, and business intelligence markets.

Design-Optimization Of Cylindrical, Layered Composite Structures Using Efficient Laminate Parameterization

NASA Astrophysics Data System (ADS)

Monicke, A.; Katajisto, H.; Leroy, M.; Petermann, N.; Kere, P.; Perillo, M.

2012-07-01

For many years, layered composites have proven essential for the successful design of high-performance space structures, such as launchers or satellites. A generic cylindrical composite structure for a launcher application was optimized with respect to objectives and constraints typical for space applications. The studies included the structural stability, laminate load response and failure analyses. Several types of cylinders (with and without stiffeners) were considered and optimized using different lay-up parameterizations. Results for the best designs are presented and discussed. The simulation tools, ESAComp [1] and modeFRONTIER [2], employed in the optimization loop are elucidated and their value for the optimization process is explained.

Antibodies to envelope glycoprotein of dengue virus during the natural course of infection are predominantly cross-reactive and recognize epitopes containing highly conserved residues at the fusion loop of domain II.

PubMed

Lai, Chih-Yun; Tsai, Wen-Yang; Lin, Su-Ru; Kao, Chuan-Liang; Hu, Hsien-Ping; King, Chwan-Chuen; Wu, Han-Chung; Chang, Gwong-Jen; Wang, Wei-Kung

2008-07-01

The antibody response to the envelope (E) glycoprotein of dengue virus (DENV) is known to play a critical role in both protection from and enhancement of disease, especially after primary infection. However, the relative amounts of homologous and heterologous anti-E antibodies and their epitopes remain unclear. In this study, we examined the antibody responses to E protein as well as to precursor membrane (PrM), capsid, and nonstructural protein 1 (NS1) of four serotypes of DENV by Western blot analysis of DENV serotype 2-infected patients with different disease severity and immune status during an outbreak in southern Taiwan in 2002. Based on the early-convalescent-phase sera tested, the rates of antibody responses to PrM and NS1 proteins were significantly higher in patients with secondary infection than in those with primary infection. A blocking experiment and neutralization assay showed that more than 90% of anti-E antibodies after primary infection were cross-reactive and nonneutralizing against heterologous serotypes and that only a minor proportion were type specific, which may account for the type-specific neutralization activity. Moreover, the E-binding activity in sera of 10 patients with primary infection was greatly reduced by amino acid replacements of three fusion loop residues, tryptophan at position 101, leucine at position 107, and phenylalanine at position 108, but not by replacements of those outside the fusion loop of domain II, suggesting that the predominantly cross-reactive anti-E antibodies recognized epitopes involving the highly conserved residues at the fusion loop of domain II. These findings have implications for our understanding of the pathogenesis of dengue and for the future design of subunit vaccine against DENV as well.

Direct simulation of amphiphilic nanoparticle mediated membrane interactions

NASA Astrophysics Data System (ADS)

Tahir, Mukarram; Alexander-Katz, Alfredo

Membrane fusion is a critical step in the transport of biological cargo through membrane-bound compartments like vesicles. Membrane proteins that alleviate energy barriers for initial stalk formation and eventual rupture of the hemifusion intermediate during fusion generally assist this process. Gold nanoparticles functionalized with a combination of hydrophobic and hydrophilic alkanethiol ligands have recently been shown to induce membrane re-arrangements that are similar to those associated with these fusion proteins. In this work, we utilize molecular dynamics simulation to systematically design nanoparticles that exhibit targeted interactions with membranes. We introduce a method for rapidly parameterizing nanoparticle topology for the MARTINI biomolecular force field to permit long timescale simulation of their interactions with lipid bilayers. We leverage this model to investigate how ligand chemistry governs the nanoparticle's insertion efficacy and the perturbations it generates in the membrane environment. We further demonstrate through unbiased simulations that these nanoparticles can direct the fusion of lipid assemblies such as micelles and vesicles in a manner that mimics the function of biological fusion peptides and SNARE proteins.

Closed Loop System Identification with Genetic Algorithms

NASA Technical Reports Server (NTRS)

Whorton, Mark S.

2004-01-01

High performance control design for a flexible space structure is challenging since high fidelity plant models are di.cult to obtain a priori. Uncertainty in the control design models typically require a very robust, low performance control design which must be tuned on-orbit to achieve the required performance. Closed loop system identi.cation is often required to obtain a multivariable open loop plant model based on closed-loop response data. In order to provide an accurate initial plant model to guarantee convergence for standard local optimization methods, this paper presents a global parameter optimization method using genetic algorithms. A minimal representation of the state space dynamics is employed to mitigate the non-uniqueness and over-parameterization of general state space realizations. This control-relevant system identi.cation procedure stresses the joint nature of the system identi.cation and control design problem by seeking to obtain a model that minimizes the di.erence between the predicted and actual closed-loop performance.

Fusion between perinuclear virions and the outer nuclear membrane requires the fusogenic activity of herpes simplex virus gB.

PubMed

Wright, Catherine C; Wisner, Todd W; Hannah, Brian P; Eisenberg, Roselyn J; Cohen, Gary H; Johnson, David C

2009-11-01

Herpesviruses cross nuclear membranes (NMs) in two steps, as follows: (i) capsids assemble and bud through the inner NM into the perinuclear space, producing enveloped virus particles, and (ii) the envelopes of these virus particles fuse with the outer NM. Two herpes simplex virus (HSV) glycoproteins, gB and gH (the latter, likely complexed as a heterodimer with gL), are necessary for the second step of this process. Mutants lacking both gB and gH accumulate in the perinuclear space or in herniations (membrane vesicles derived from the inner NM). Both gB and gH/gL are also known to act directly in fusing the virion envelope with host cell membranes during HSV entry into cells, i.e., both glycoproteins appear to function directly in different aspects of the membrane fusion process. We hypothesized that HSV gB and gH/gL also act directly in the membrane fusion that occurs during virus egress from the nucleus. Previous studies of the role of gB and gH/gL in nuclear egress involved HSV gB and gH null mutants that could potentially also possess gross defects in the virion envelope. Here, we produced recombinant HSV-expressing mutant forms of gB with single amino acid substitutions in the hydrophobic "fusion loops." These fusion loops are thought to play a direct role in membrane fusion by insertion into cellular membranes. HSV recombinants expressing gB with any one of four fusion loop mutations (W174R, W174Y, Y179K, and A261D) were unable to enter cells. Moreover, two of the mutants, W174Y and Y179K, displayed reduced abilities to mediate HSV cell-to-cell spread, and W174R and A261D exhibited no spread. All mutant viruses exhibited defects in nuclear egress, enveloped virions accumulated in herniations and in the perinuclear space, and fewer enveloped virions were detected on cell surfaces. These results support the hypothesis that gB functions directly to mediate the fusion between perinuclear virus particles and the outer NM.

Embedded Relative Navigation Sensor Fusion Algorithms for Autonomous Rendezvous and Docking Missions

NASA Technical Reports Server (NTRS)

DeKock, Brandon K.; Betts, Kevin M.; McDuffie, James H.; Dreas, Christine B.

2008-01-01

bd Systems (a subsidiary of SAIC) has developed a suite of embedded relative navigation sensor fusion algorithms to enable NASA autonomous rendezvous and docking (AR&D) missions. Translational and rotational Extended Kalman Filters (EKFs) were developed for integrating measurements based on the vehicles' orbital mechanics and high-fidelity sensor error models and provide a solution with increased accuracy and robustness relative to any single relative navigation sensor. The filters were tested tinough stand-alone covariance analysis, closed-loop testing with a high-fidelity multi-body orbital simulation, and hardware-in-the-loop (HWIL) testing in the Marshall Space Flight Center (MSFC) Flight Robotics Laboratory (FRL).

Design and Modeling of a Liquid Lithium LiMIT Loop

NASA Astrophysics Data System (ADS)

Szott, Matthew; Christenson, Michael; Stemmley, Steven; Ahn, Chisung; Andruczyk, Daniel; Ruzic, David

2017-10-01

The use of flowing liquid lithium in plasma facing components has been shown to reduce erosion and thermal stress damage, prolong device lifetime, decrease edge recycling, reduce impurities, and increase plasma performance, all while providing a clean and self-healing surface. The Liquid Metal Infused Trench (LiMIT) system has proven the concept of controlled thermoelectric magnetohydrodynamic-driven lithium flow for use in fusion relevant conditions, through tests at UIUC, HT-7, and Magnum PSI. As the use of liquid lithium in fusion devices progresses, emphasis must now be placed on full systems integration of flowing liquid metal concepts. The LiMIT system will be upgraded to include a full liquid lithium loop, which will pump lithium into the fusion device, utilize TEMHD to drive lithium through the vessel, and remove lithium for filtration and degassing. Flow control concepts recently developed at UIUC - including wetting control, dryout control, and flow velocity control - will be tested in conjunction in order to demonstrate a robust system. Lithium loop system requirements, designs, and modeling work will be presented, along with plans for installation and testing on the HIDRA device at UIUC. This work is supported by DOE/ALPS DE-FG02-99ER54515.

Gluon-fusion Higgs production in the Standard Model Effective Field Theory

NASA Astrophysics Data System (ADS)

Deutschmann, Nicolas; Duhr, Claude; Maltoni, Fabio; Vryonidou, Eleni

2017-12-01

We provide the complete set of predictions needed to achieve NLO accuracy in the Standard Model Effective Field Theory at dimension six for Higgs production in gluon fusion. In particular, we compute for the first time the contribution of the chromomagnetic operator {\\overline{Q}}_LΦ σ {q}_RG at NLO in QCD, which entails two-loop virtual and one-loop real contributions, as well as renormalisation and mixing with the Yukawa operator {Φ}^{\\dagger}Φ{\\overline{Q}}_LΦ {q}_R and the gluon-fusion operator Φ†Φ GG. Focusing on the top-quark-Higgs couplings, we consider the phenomenological impact of the NLO corrections in constraining the three relevant operators by implementing the results into the M adG raph5_ aMC@NLO frame-work. This allows us to compute total cross sections as well as to perform event generation at NLO that can be directly employed in experimental analyses.

Fusion Partner Toolchest for the Stabilization and Crystallization of G Protein-Coupled Receptors

PubMed Central

Chun, Eugene; Thompson, Aaron A.; Liu, Wei; Roth, Christopher B.; Griffith, Mark T.; Katritch, Vsevolod; Kunken, Joshua; Xu, Fei; Cherezov, Vadim; Hanson, Michael A.; Stevens, Raymond C.

2012-01-01

SUMMARY Structural studies of human G protein-coupled receptors (GPCRs) have recently been accelerated through the use of the T4 lysozyme fusion partner that was inserted into the third intracellular loop. Using chimeras of the human β2-adrenergic and human A2A adenosine receptors, we present the methodology and data for the selection of five new fusion partners for crystallizing GPCRs. In particular, the use of the thermostabilized apocytochrome b562RIL as a fusion partner displays certain advantages over the previously utilized T4 lysozyme, resulting in a significant improvement in stability and structure in GPCR-fusion constructs. PMID:22681902

Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity.

PubMed

Lee, Jinwoo; Nyenhuis, David A; Nelson, Elizabeth A; Cafiso, David S; White, Judith M; Tamm, Lukas K

2017-09-19

Ebolavirus (EBOV), an enveloped filamentous RNA virus causing severe hemorrhagic fever, enters cells by macropinocytosis and membrane fusion in a late endosomal compartment. Fusion is mediated by the EBOV envelope glycoprotein GP, which consists of subunits GP1 and GP2. GP1 binds to cellular receptors, including Niemann-Pick C1 (NPC1) protein, and GP2 is responsible for low pH-induced membrane fusion. Proteolytic cleavage and NPC1 binding at endosomal pH lead to conformational rearrangements of GP2 that include exposing the hydrophobic fusion loop (FL) for insertion into the cellular target membrane and forming a six-helix bundle structure. Although major portions of the GP2 structure have been solved in pre- and postfusion states and although current models place the transmembrane (TM) and FL domains of GP2 in close proximity at critical steps of membrane fusion, their structures in membrane environments, and especially interactions between them, have not yet been characterized. Here, we present the structure of the membrane proximal external region (MPER) connected to the TM domain: i.e., the missing parts of the EBOV GP2 structure. The structure, solved by solution NMR and EPR spectroscopy in membrane-mimetic environments, consists of a helix-turn-helix architecture that is independent of pH. Moreover, the MPER region is shown to interact in the membrane interface with the previously determined structure of the EBOV FL through several critical aromatic residues. Mutation of aromatic and neighboring residues in both binding partners decreases fusion and viral entry, highlighting the functional importance of the MPER/TM-FL interaction in EBOV entry and fusion.

NMR structure and localization of a large fragment of the SARS-CoV fusion protein: Implications in viral cell fusion.

PubMed

Mahajan, Mukesh; Chatterjee, Deepak; Bhuvaneswari, Kannaian; Pillay, Shubhadra; Bhattacharjya, Surajit

2018-02-01

The lethal Coronaviruses (CoVs), Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV) and most recently Middle East Respiratory Syndrome Coronavirus, (MERS-CoV) are serious human health hazard. A successful viral infection requires fusion between virus and host cells carried out by the surface spike glycoprotein or S protein of CoV. Current models propose that the S2 subunit of S protein assembled into a hexameric helical bundle exposing hydrophobic fusogenic peptides or fusion peptides (FPs) for membrane insertion. The N-terminus of S2 subunit of SARS-CoV reported to be active in cell fusion whereby FPs have been identified. Atomic-resolution structure of FPs derived either in model membranes or in membrane mimic environment would glean insights toward viral cell fusion mechanism. Here, we have solved 3D structure, dynamics and micelle localization of a 64-residue long fusion peptide or LFP in DPC detergent micelles by NMR methods. Micelle bound structure of LFP is elucidated by the presence of discretely folded helical and intervening loops. The C-terminus region, residues F42-Y62, displays a long hydrophobic helix, whereas the N-terminus is defined by a short amphipathic helix, residues R4-Q12. The intervening residues of LFP assume stretches of loops and helical turns. The N-terminal helix is sustained by close aromatic and aliphatic sidechain packing interactions at the non-polar face. 15 N{ 1 H}NOE studies indicated dynamical motion, at ps-ns timescale, of the helices of LFP in DPC micelles. PRE NMR showed that insertion of several regions of LFP into DPC micelle core. Together, the current study provides insights toward fusion mechanism of SARS-CoV. Copyright © 2017 Elsevier B.V. All rights reserved.

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor

PubMed Central

Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

2015-01-01

Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation. PMID:26061049

Combining Charge Couple Devices and Rate Sensors for the Feedforward Control System of a Charge Coupled Device Tracking Loop.

PubMed

Tang, Tao; Tian, Jing; Zhong, Daijun; Fu, Chengyu

2016-06-25

A rate feed forward control-based sensor fusion is proposed to improve the closed-loop performance for a charge couple device (CCD) tracking loop. The target trajectory is recovered by combining line of sight (LOS) errors from the CCD and the angular rate from a fiber-optic gyroscope (FOG). A Kalman filter based on the Singer acceleration model utilizes the reconstructive target trajectory to estimate the target velocity. Different from classical feed forward control, additive feedback loops are inevitably added to the original control loops due to the fact some closed-loop information is used. The transfer function of the Kalman filter in the frequency domain is built for analyzing the closed loop stability. The bandwidth of the Kalman filter is the major factor affecting the control stability and close-loop performance. Both simulations and experiments are provided to demonstrate the benefits of the proposed algorithm.

Fusion basis for lattice gauge theory and loop quantum gravity

NASA Astrophysics Data System (ADS)

Delcamp, Clement; Dittrich, Bianca; Riello, Aldo

2017-02-01

We introduce a new basis for the gauge-invariant Hilbert space of lattice gauge theory and loop quantum gravity in (2 + 1) dimensions, the fusion basis. In doing so, we shift the focus from the original lattice (or spin-network) structure directly to that of the magnetic (curvature) and electric (torsion) excitations themselves. These excitations are classified by the irreducible representations of the Drinfel'd double of the gauge group, and can be readily "fused" together by studying the tensor product of such representations. We will also describe in detail the ribbon operators that create and measure these excitations and make the quasi-local structure of the observable algebra explicit. Since the fusion basis allows for both magnetic and electric excitations from the onset, it turns out to be a precious tool for studying the large scale structure and coarse-graining flow of lattice gauge theories and loop quantum gravity. This is in neat contrast with the widely used spin-network basis, in which it is much more complicated to account for electric excitations, i.e. for Gauß constraint violations, emerging at larger scales. Moreover, since the fusion basis comes equipped with a hierarchical structure, it readily provides the language to design states with sophisticated multi-scale structures. Another way to employ this hierarchical structure is to encode a notion of subsystems for lattice gauge theories and (2 + 1) gravity coupled to point particles. In a follow-up work, we have exploited this notion to provide a new definition of entanglement entropy for these theories.

Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc.

PubMed

Guardado-Calvo, Pablo; Bignon, Eduardo A; Stettner, Eva; Jeffers, Scott Allen; Pérez-Vargas, Jimena; Pehau-Arnaudet, Gerard; Tortorici, M Alejandra; Jestin, Jean-Luc; England, Patrick; Tischler, Nicole D; Rey, Félix A

2016-10-01

Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic β-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha- and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single "fusion loop". We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal "tail" that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens.

Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1.

PubMed

Wang, Han; Shi, Yi; Song, Jian; Qi, Jianxun; Lu, Guangwen; Yan, Jinghua; Gao, George F

2016-01-14

Filoviruses, including Ebola and Marburg, cause fatal hemorrhagic fever in humans and primates. Understanding how these viruses enter host cells could help to develop effective therapeutics. An endosomal protein, Niemann-Pick C1 (NPC1), has been identified as a necessary entry receptor for this process, and priming of the viral glycoprotein (GP) to a fusion-competent state is a prerequisite for NPC1 binding. Here, we have determined the crystal structure of the primed GP (GPcl) of Ebola virus bound to domain C of NPC1 (NPC1-C) at a resolution of 2.3 Å. NPC1-C utilizes two protruding loops to engage a hydrophobic cavity on head of GPcl. Upon enzymatic cleavage and NPC1-C binding, conformational change in the GPcl further affects the state of the internal fusion loop, triggering membrane fusion. Our data therefore provide structural insights into filovirus entry in the late endosome and the molecular basis for design of therapeutic inhibitors of viral entry. Copyright © 2016 Elsevier Inc. All rights reserved.

Developing the Polynomial Expressions for Fields in the ITER Tokamak

NASA Astrophysics Data System (ADS)

Sharma, Stephen

2017-10-01

The two most important problems to be solved in the development of working nuclear fusion power plants are: sustained partial ignition and turbulence. These two phenomena are the subject of research and investigation through the development of analytic functions and computational models. Ansatz development through Gaussian wave-function approximations, dielectric quark models, field solutions using new elliptic functions, and better descriptions of the polynomials of the superconducting current loops are the critical theoretical developments that need to be improved. Euler-Lagrange equations of motion in addition to geodesic formulations generate the particle model which should correspond to the Dirac dispersive scattering coefficient calculations and the fluid plasma model. Feynman-Hellman formalism and Heaviside step functional forms are introduced to the fusion equations to produce simple expressions for the kinetic energy and loop currents. Conclusively, a polynomial description of the current loops, the Biot-Savart field, and the Lagrangian must be uncovered before there can be an adequate computational and iterative model of the thermonuclear plasma.

Expressions for Fields in the ITER Tokamak

NASA Astrophysics Data System (ADS)

Sharma, Stephen

2017-10-01

The two most important problems to be solved in the development of working nuclear fusion power plants are: sustained partial ignition and turbulence. These two phenomenon are the subject of research and investigation through the development of analytic functions and computational models. Ansatz development through Gaussian wave-function approximations, dielectric quark models, field solutions using new elliptic functions, and better descriptions of the polynomials of the superconducting current loops are the critical theoretical developments that need to be improved. Euler-Lagrange equations of motion in addition to geodesic formulations generate the particle model which should correspond to the Dirac dispersive scattering coefficient calculations and the fluid plasma model. Feynman-Hellman formalism and Heaviside step functional forms are introduced to the fusion equations to produce simple expressions for the kinetic energy and loop currents. Conclusively, a polynomial description of the current loops, the Biot-Savart field, and the Lagrangian must be uncovered before there can be an adequate computational and iterative model of the thermonuclear plasma.

The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1.

PubMed Central

Toczyski, D P; Steitz, J A

1993-01-01

EAP (EBER-associated protein) is an abundant, 15-kDa cellular RNA-binding protein which associates with certain herpesvirus small RNAs. We have raised polyclonal anti-EAP antibodies against a glutathione S-transferase-EAP fusion protein. Analysis of the RNA precipitated by these antibodies from Epstein-Barr virus (EBV)- or herpesvirus papio (HVP)-infected cells shows that > 95% of EBER 1 (EBV-encoded RNA 1) and the majority of HVP 1 (an HVP small RNA homologous to EBER 1) are associated with EAP. RNase protection experiments performed on native EBER 1 particles with affinity-purified anti-EAP antibodies demonstrate that EAP binds a stem-loop structure (stem-loop 3) of EBER 1. Since bacterially expressed glutathione S-transferase-EAP fusion protein binds EBER 1, we conclude that EAP binding is independent of any other cellular or viral protein. Detailed mutational analyses of stem-loop 3 suggest that EAP recognizes the majority of the nucleotides in this hairpin, interacting with both single-stranded and double-stranded regions in a sequence-specific manner. Binding studies utilizing EBER 1 deletion mutants suggest that there may also be a second, weaker EAP-binding site on stem-loop 4 of EBER 1. These data and the fact that stem-loop 3 represents the most highly conserved region between EBER 1 and HVP 1 suggest that EAP binding is a critical aspect of EBER 1 and HVP 1 function. Images PMID:8380232

Multi-sensor Improved Sea-Surface Temperature (MISST) for IOOS - Navy Component

DTIC Science & Technology

2013-09-30

application and data fusion techniques. 2. Parameterization of IR and MW retrieval differences, with consideration of diurnal warming and cool-skin effects...associated retrieval confidence, standard deviation (STD), and diurnal warming estimates to the application user community in the new GDS 2.0 GHRSST...including coral reefs, ocean modeling in the Gulf of Mexico, improved lake temperatures, numerical data assimilation by ocean models, numerical

Flexibility of the Head-Stalk Linker Domain of Paramyxovirus HN Glycoprotein Is Essential for Triggering Virus Fusion.

PubMed

Adu-Gyamfi, Emmanuel; Kim, Lori S; Jardetzky, Theodore S; Lamb, Robert A

2016-10-15

The Paramyxoviridae comprise a large family of enveloped, negative-sense, single-stranded RNA viruses with significant economic and public health implications. For nearly all paramyxoviruses, infection is initiated by fusion of the viral and host cell plasma membranes in a pH-independent fashion. Fusion is orchestrated by the receptor binding protein hemagglutinin-neuraminidase (HN; also called H or G depending on the virus type) protein and a fusion (F) protein, the latter undergoing a major refolding process to merge the two membranes. Mechanistic details regarding the coupling of receptor binding to F activation are not fully understood. Here, we have identified the flexible loop region connecting the bulky enzymatically active head and the four-helix bundle stalk to be essential for fusion promotion. Proline substitution in this region of HN of parainfluenza virus 5 (PIV5) and Newcastle disease virus HN abolishes cell-cell fusion, whereas HN retains receptor binding and neuraminidase activity. By using reverse genetics, we engineered recombinant PIV5-EGFP viruses with mutations in the head-stalk linker region of HN. Mutations in this region abolished virus recovery and infectivity. In sum, our data suggest that the loop region acts as a "hinge" around which the bulky head of HN swings to-and-fro to facilitate timely HN-mediate F-triggering, a notion consistent with the stalk-mediated activation model of paramyxovirus fusion. Paramyxovirus fusion with the host cell plasma membrane is essential for virus infection. Membrane fusion is orchestrated via interaction of the receptor binding protein (HN, H, or G) with the viral fusion glycoprotein (F). Two distinct models have been suggested to describe the mechanism of fusion: these include "the clamp" and the "provocateur" model of activation. By using biochemical and reverse genetics tools, we have obtained strong evidence in favor of the HN stalk-mediated activation of paramyxovirus fusion. Specifically, our data strongly support the notion that the short linker between the head and stalk plays a role in "conformational switching" of the head group to facilitate F-HN interaction and triggering. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Flexibility of the Head-Stalk Linker Domain of Paramyxovirus HN Glycoprotein Is Essential for Triggering Virus Fusion

PubMed Central

Adu-Gyamfi, Emmanuel; Kim, Lori S.; Jardetzky, Theodore S.

2016-01-01

ABSTRACT The Paramyxoviridae comprise a large family of enveloped, negative-sense, single-stranded RNA viruses with significant economic and public health implications. For nearly all paramyxoviruses, infection is initiated by fusion of the viral and host cell plasma membranes in a pH-independent fashion. Fusion is orchestrated by the receptor binding protein hemagglutinin-neuraminidase (HN; also called H or G depending on the virus type) protein and a fusion (F) protein, the latter undergoing a major refolding process to merge the two membranes. Mechanistic details regarding the coupling of receptor binding to F activation are not fully understood. Here, we have identified the flexible loop region connecting the bulky enzymatically active head and the four-helix bundle stalk to be essential for fusion promotion. Proline substitution in this region of HN of parainfluenza virus 5 (PIV5) and Newcastle disease virus HN abolishes cell-cell fusion, whereas HN retains receptor binding and neuraminidase activity. By using reverse genetics, we engineered recombinant PIV5-EGFP viruses with mutations in the head-stalk linker region of HN. Mutations in this region abolished virus recovery and infectivity. In sum, our data suggest that the loop region acts as a “hinge” around which the bulky head of HN swings to-and-fro to facilitate timely HN-mediate F-triggering, a notion consistent with the stalk-mediated activation model of paramyxovirus fusion. IMPORTANCE Paramyxovirus fusion with the host cell plasma membrane is essential for virus infection. Membrane fusion is orchestrated via interaction of the receptor binding protein (HN, H, or G) with the viral fusion glycoprotein (F). Two distinct models have been suggested to describe the mechanism of fusion: these include “the clamp” and the “provocateur” model of activation. By using biochemical and reverse genetics tools, we have obtained strong evidence in favor of the HN stalk-mediated activation of paramyxovirus fusion. Specifically, our data strongly support the notion that the short linker between the head and stalk plays a role in “conformational switching” of the head group to facilitate F-HN interaction and triggering. PMID:27489276

Impact of an integrated core/SOL description on the R and B T optimization of tokamak fusion reactors

NASA Astrophysics Data System (ADS)

Siccinio, M.; Fable, E.; Angioni, C.; Saarelma, S.; Scarabosio, A.; Zohm, H.

2018-01-01

An updated and improved version of the 0D divertor and scrape-off layer (SOL) model published in Siccinio et al (2016 Plasma Phys. Control. Fusion 58 125011) was coupled with the 1.5D transport code ASTRA (Pereverzev 1991 IPP Report 5/42, Pereverzev and Yushmanov 2002 IPP Report 5/98 and Fable et al 2013 Plasma Phys. Control. Fusion 55 124028). The resulting numerical tool was employed for various scans in the major radius R and in the toroidal magnetic field B T—for different safety factors q, allowable loop voltages V loop and H factors—in order to identify the most convenient choices for an electricity producing tokamak. Such a scenario analysis was carried out evaluating self-consistently, and simultaneously, the core profile and transport effects, which significantly impact on the fusion power outcome, and the divertor heat loads, which represent one of the most critical issues in view of the realization of fusion power plants (Zohm et al 2013 Nucl. Fusion 53 073019 and Wenninger et al 2017 Nucl. Fusion 57 046002). The main result is that, when divertor limits are enforced, the curves at constant electrical power output are closed on themselves in the R-BT plane, and a maximum achievable power exists—i.e. no benefits would be obtained from a further increase in R and B T once the optimum is reached. This result appears as an intrinsic physical limit for all those devices where a radiative SOL is needed to deal with the power exhaust, and where a lower limit on the power crossing the separatrix (e.g. because of the L-H transition) is present.

Numerical simulations and observations of surface wave fields under an extreme tropical cyclone

USGS Publications Warehouse

Fan, Y.; Ginis, I.; Hara, T.; Wright, C.W.; Walsh, E.J.

2009-01-01

The performance of the wave model WAVEWATCH III under a very strong, category 5, tropical cyclone wind forcing is investigated with different drag coefficient parameterizations and ocean current inputs. The model results are compared with field observations of the surface wave spectra from an airborne scanning radar altimeter, National Data Buoy Center (NDBC) time series, and satellite altimeter measurements in Hurricane Ivan (2004). The results suggest that the model with the original drag coefficient parameterization tends to overestimate the significant wave height and the dominant wavelength and produces a wave spectrum with narrower directional spreading. When an improved drag parameterization is introduced and the wave-current interaction is included, the model yields an improved forecast of significant wave height, but underestimates the dominant wavelength. When the hurricane moves over a preexisting mesoscale ocean feature, such as the Loop Current in the Gulf of Mexico or a warm-and cold-core ring, the current associated with the feature can accelerate or decelerate the wave propagation and significantly modulate the wave spectrum. ?? 2009 American Meteorological Society.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, J.L.; Jenkins, E.M.; Walthers, C.R.

Compound cryopumps have been added to the Tritium Systems Test Assembly (TSTA) integrated fusion fuel loop. Operations have been performed which closely simulate an actual fusion reactor pumping scenario. In addition, performance data have been taken that support the concept of using coconut charcoal as a sorbent at 4K for pumping helium. Later tests show that coconut charcoal may be used to co-pump D,T and He mixtures on a single 4K panel. Rotary spiral pumps have been used successfully in several applications at TSTA and have acquired more than 9000 hours of maintenance-free operation. Metal bellows pumps have been usedmore » to back the spiral pumps and have been relatively trouble free in loop operations. Bellows pumps also have more than 9000 hours of maintenance-free operation. 5 refs., 6 figs.« less

BOOTSTRAPPING THE CORONAL MAGNETIC FIELD WITH STEREO: UNIPOLAR POTENTIAL FIELD MODELING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aschwanden, Markus J.; Sandman, Anne W., E-mail: aschwanden@lmsal.co

We investigate the recently quantified misalignment of {alpha}{sub mis} {approx} 20{sup 0}-40{sup 0} between the three-dimensional geometry of stereoscopically triangulated coronal loops observed with STEREO/EUVI (in four active regions (ARs)) and theoretical (potential or nonlinear force-free) magnetic field models extrapolated from photospheric magnetograms. We develop an efficient method of bootstrapping the coronal magnetic field by forward fitting a parameterized potential field model to the STEREO-observed loops. The potential field model consists of a number of unipolar magnetic charges that are parameterized by decomposing a photospheric magnetogram from the Michelson Doppler Imager. The forward-fitting method yields a best-fit magnetic field modelmore » with a reduced misalignment of {alpha}{sub PF} {approx} 13{sup 0}-20{sup 0}. We also evaluate stereoscopic measurement errors and find a contribution of {alpha}{sub SE} {approx} 7{sup 0}-12{sup 0}, which constrains the residual misalignment to {alpha}{sub NP} {approx} 11{sup 0}-17{sup 0}, which is likely due to the nonpotentiality of the ARs. The residual misalignment angle, {alpha}{sub NP}, of the potential field due to nonpotentiality is found to correlate with the soft X-ray flux of the AR, which implies a relationship between electric currents and plasma heating.« less

Consistent Orientation of Moduli Spaces

NASA Astrophysics Data System (ADS)

Freed, Daniel S.; Hopkins, Michael J.; Teleman, Constantin

In a series of papers by Freed, Hopkins, and Teleman (2003, 2005, 2007a) the relationship between positive energy representations of the loop group of a compact Lie group G and the twisted equivariant K-theory Kτ+dimGG (G) was developed. Here G acts on itself by conjugation. The loop group representations depend on a choice of ‘level’, and the twisting τ is derived from the level. For all levels the main theorem is an isomorphism of abelian groups, and for special transgressed levels it is an isomorphism of rings: the fusion ring of the loop group andKτ+dimGG (G) as a ring. For G connected with π1G torsionfree, it has been proven that the ring Kτ+dimGG (G) is a quotient of the representation ring of G and can be calculated explicitly. In these cases it agrees with the fusion ring of the corresponding centrally extended loop group. This chapter explicates the multiplication on the twisted equivariant K-theory for an arbitrary compact Lie group G. It constructs a Frobenius ring structure on Kτ+dimGG (G). This is best expressed in the language of topological quantum field theory: a two-dimensional topological quantum field theory (TQFT) is constructed over the integers in which the abelian group attached to the circle is Kτ+dimGG (G).

Activation of Membrane Fusion by Murine Leukemia Viruses Is Controlled in cis or in trans by Interactions between the Receptor-Binding Domain and a Conserved Disulfide Loop of the Carboxy Terminus of the Surface Glycoprotein

PubMed Central

Lavillette, Dimitri; Boson, Bertrand; Russell, Stephen J.; Cosset, François-Loïc

2001-01-01

Cell entry of retroviruses is initiated by the recognition of cellular receptors and the subsequent membrane fusion between viral and cellular membranes. These two steps are mediated by the surface (SU) and transmembrane (TM) subunits of the retroviral envelope glycoprotein (Env), respectively. Determinants regulating membrane fusion have been described throughout SU and TM, but the processes coupling receptor recognition to fusion are still elusive. Here we establish that a critical interaction is formed between the receptor-binding domain (RBD) and the major disulfide loop of the carboxy-terminal domain (C domain) of the murine leukemia virus SU. Receptor binding causes an alteration of this interaction and, in turn, promotes further events of Env fusion activation. We characterize mutations which, by lowering this interaction and reducing the compatibility between the RBD and C domains of Env glycoprotein chimeras, affect both Env fusogenicity and sensitivity to receptor interference. Additionally, we demonstrate that suboptimal interactions in such mutant Env proteins can be compensated in trans by soluble RBDs in a manner that depends on their compatibility with the C domain. Our results therefore indicate that RBD/C domain interactions may occur in cis, via the proper RBD of the viral Env itself, or in trans, via a distinct RBD expressed by virion-free Env glycoproteins expressed endogenously by the infected cells or provided by neighboring Env trimers. PMID:11264358

Alternative ways of using field-based estimates to calibrate ecosystem models and their implications for carbon cycle studies

USGS Publications Warehouse

He, Yujie; Zhuang, Qianlai; McGuire, David; Liu, Yaling; Chen, Min

2013-01-01

Model-data fusion is a process in which field observations are used to constrain model parameters. How observations are used to constrain parameters has a direct impact on the carbon cycle dynamics simulated by ecosystem models. In this study, we present an evaluation of several options for the use of observations in modeling regional carbon dynamics and explore the implications of those options. We calibrated the Terrestrial Ecosystem Model on a hierarchy of three vegetation classification levels for the Alaskan boreal forest: species level, plant-functional-type level (PFT level), and biome level, and we examined the differences in simulated carbon dynamics. Species-specific field-based estimates were directly used to parameterize the model for species-level simulations, while weighted averages based on species percent cover were used to generate estimates for PFT- and biome-level model parameterization. We found that calibrated key ecosystem process parameters differed substantially among species and overlapped for species that are categorized into different PFTs. Our analysis of parameter sets suggests that the PFT-level parameterizations primarily reflected the dominant species and that functional information of some species were lost from the PFT-level parameterizations. The biome-level parameterization was primarily representative of the needleleaf PFT and lost information on broadleaf species or PFT function. Our results indicate that PFT-level simulations may be potentially representative of the performance of species-level simulations while biome-level simulations may result in biased estimates. Improved theoretical and empirical justifications for grouping species into PFTs or biomes are needed to adequately represent the dynamics of ecosystem functioning and structure.

Liquid lithium applications for solving challenging fusion reactor issues and NSTX-U contributions

DOE PAGES

Ono, M.; Jaworski, M. A.; Kaita, R.; ...

2016-08-05

Steady-state fusion reactor operation presents major divertor technology challenges, including high divertor heat flux both steady-state and transients. In addition to those issues, there are unresolved issues of long term dust accumulation and associated tritium inventory and safety issues. It has been suggested that radiative liquid lithium divertor concepts with a modest lithium-loop could provide a possible solution for these outstanding fusion reactor technology issues while potentially improving the reactor plasma performance. The application of lithium (Li) in NSTX resulted in improved H-mode confinement, H-mode power threshold reduction, and reduction in the divertor peak heat flux while maintaining essentially Li-freemore » core plasma operation even during H-modes. These promising results in NSTX and related modeling calculations motivated the radiative liquid lithium divertor (RLLD) concept and its variant, the active liquid lithium divertor concept (ARLLD), taking advantage of the enhanced Li radiation in relatively poorly confined divertor plasmas. It was estimated that only a few moles/sec of lithium injection would be needed to significantly reduce the divertor heat flux in a tokamak fusion power plant. By operating at lower temperatures ≤ 500°C than the first wall ~ 600 – 700°C, the LL-covered divertor chamber wall surfaces can serve as an effective particle pump, as impurities generally migrate toward lower temperature LL divertor surfaces. To maintain the LL purity, a closed LL loop system with a modest circulating capacity of ~ 1 liter/second (l/sec) is envisioned to sustain the steady-state operation of a 1 GW-electric class fusion power plant. By running the Li loop continuously, it can carry the dust particles and impurities generated in the vacuum vessel to outside where the dust / impurities are removed by relatively simple filter and cold/hot trap systems. Using a cold trap system, it can recover in tritium (T) in real time from LL at a rate of ~ 0.5 g / sec needed to sustain the fusion reaction while minimizing the T inventory issue. With an expected T fraction of ≤ 0.7 %, an acceptable level of T inventory can be achieved. In NSTX-U, preparations are now underway to elucidate the physics of Li plasma interactions with a number of Li application tools and Li radiation spectroscopic instruments. The NSTX-U Li evaporator which provides Li coating over the lower divertor plate, can offer important information on the RLLD concept, and the Li granule injector will test some of the key physics issue on the ARLLD concept. A LL-loop is also being prepared off line for prototyping future use on NSTX-U.« less

Robust lateral blended-wing-body aircraft feedback control design using a parameterized LFR model and DGK-iteration

NASA Astrophysics Data System (ADS)

Schirrer, A.; Westermayer, C.; Hemedi, M.; Kozek, M.

2013-12-01

This paper shows control design results, performance, and limitations of robust lateral control law designs based on the DGK-iteration mixed-μ-synthesis procedure for a large, flexible blended wing body (BWB) passenger aircraft. The aircraft dynamics is preshaped by a low-complexity inner loop control law providing stabilization, basic response shaping, and flexible mode damping. The μ controllers are designed to further improve vibration damping of the main flexible modes by exploiting the structure of the arising significant parameter-dependent plant variations. This is achieved by utilizing parameterized Linear Fractional Representations (LFR) of the aircraft rigid and flexible dynamics. Designs with various levels of LFR complexity are carried out and discussed, showing the achieved performance improvement over the initial controller and their robustness and complexity properties.

Polarimetric Intensity Parameterization of Radar and Other Remote Sensing Sources for Advanced Exploitation and Data Fusion: Theory

DTIC Science & Technology

2008-10-01

is theoretically similar to the concept of “partial or compact polarimetry”, yields comparable results to full or quadrature-polarized systems by...to the emerging “compact polarimetry” methodology [9]-[13] that exploits scattering system response to an incomplete set of input EM field components...a scattering operator or matrix. Although as theoretically discussed earlier, performance of such fully-polarized radar system (i.e., quadrature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ono, M.; Jaworski, M. A.; Kaita, R.

Steady-state fusion reactor operation presents major divertor technology challenges, including high divertor heat flux both steady-state and transients. In addition to those issues, there are unresolved issues of long term dust accumulation and associated tritium inventory and safety issues. It has been suggested that radiative liquid lithium divertor concepts with a modest lithium-loop could provide a possible solution for these outstanding fusion reactor technology issues while potentially improving the reactor plasma performance. The application of lithium (Li) in NSTX resulted in improved H-mode confinement, H-mode power threshold reduction, and reduction in the divertor peak heat flux while maintaining essentially Li-freemore » core plasma operation even during H-modes. These promising results in NSTX and related modeling calculations motivated the radiative liquid lithium divertor (RLLD) concept and its variant, the active liquid lithium divertor concept (ARLLD), taking advantage of the enhanced Li radiation in relatively poorly confined divertor plasmas. It was estimated that only a few moles/sec of lithium injection would be needed to significantly reduce the divertor heat flux in a tokamak fusion power plant. By operating at lower temperatures ≤ 500°C than the first wall ~ 600 – 700°C, the LL-covered divertor chamber wall surfaces can serve as an effective particle pump, as impurities generally migrate toward lower temperature LL divertor surfaces. To maintain the LL purity, a closed LL loop system with a modest circulating capacity of ~ 1 liter/second (l/sec) is envisioned to sustain the steady-state operation of a 1 GW-electric class fusion power plant. By running the Li loop continuously, it can carry the dust particles and impurities generated in the vacuum vessel to outside where the dust / impurities are removed by relatively simple filter and cold/hot trap systems. Using a cold trap system, it can recover in tritium (T) in real time from LL at a rate of ~ 0.5 g / sec needed to sustain the fusion reaction while minimizing the T inventory issue. With an expected T fraction of ≤ 0.7 %, an acceptable level of T inventory can be achieved. In NSTX-U, preparations are now underway to elucidate the physics of Li plasma interactions with a number of Li application tools and Li radiation spectroscopic instruments. The NSTX-U Li evaporator which provides Li coating over the lower divertor plate, can offer important information on the RLLD concept, and the Li granule injector will test some of the key physics issue on the ARLLD concept. A LL-loop is also being prepared off line for prototyping future use on NSTX-U.« less

Tritium Mitigation/Control for Advanced Reactor System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Xiaodong; Christensen, Richard; Saving, John P.

A tritium removal facility, which is similar to the design used for tritium recovery in fusion reactors, is proposed in this study for fluoride-salt-cooled high-temperature reactors (FHRs) to result in a two-loop FHR design with the elimination of an intermediate loop. Using this approach, an economic benefit can potentially be obtained by removing the intermediate loop, while the safety concern of tritium release can be mitigated. In addition, an intermediate heat exchanger (IHX) that can yield a similar tritium permeation rate to the production rate of 1.9 Ci/day in a 1,000 MWe PWR needs to be designed to prevent themore » residual tritium that is not captured in the tritium removal system from escaping into the power cycle and ultimately the environment. The main focus of this study is to aid the mitigation of tritium permeation issue from the FHR primary side to significantly reduce the concentration of tritium in the secondary side and the process heat application side (if applicable). The goal of the research is to propose a baseline FHR system without the intermediate loop. The specific objectives to accomplish the goals are: To estimate tritium permeation behavior in FHRs; To design a tritium removal system for FHRs; To meet the same tritium permeation level in FHRs as the tritium production rate of 1.9 Ci/day in 1,000 MWe PWRs; To demonstrate economic benefits of the proposed FHR system via comparing with the three-loop FHR system. The objectives were accomplished by designing tritium removal facilities, developing a tritium analysis code, and conducting an economic analysis. In the fusion reactor community, tritium extraction has been widely investigated and researched. Borrowing the experiences from the fusion reactor community, a tritium control and mitigation system was proposed. Based on mass transport theories, a tritium analysis code was developed, and the tritium behaviors were analyzed using the developed code. Tritium removal facilities were designed and laboratory-scale experiments were proposed for the validation of the proposed tritium removal facilities.« less

Phosphatidylinositol-3-kinase-dependent phosphorylation of SLP-76 by the lymphoma-associated ITK-SYK fusion-protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hussain, Alamdar, E-mail: alamdar.hussain@ki.se; Department of Biosciences, COMSATS Institute of Information Technology, Chak Shazad Campus, Islamabad; Faryal, Rani

Recurrent chromosomal translocations have long been implicated in various types of lymphomas and other malignancies. Novel recurrent t(5;9)(q33;q22) has been recently discovered in un-specified peripheral T-cell lymphoma. To elucidate the role of this translocation, the corresponding fusion construct encoding the N-terminal portion of the ITK kinase and the C-terminal catalytic region of the SYK kinase was generated. We herein show that the ITK-SYK fusion-protein is constitutively active. Moreover, we demonstrate that ITK-SYK is phosphorylated on key tyrosine residues and is capable of potently phosphorylating the related adapter proteins BLNK and SLP-76. In transiently transfected cells, SYK was phosphorylated at Y352more » but not detectably at the activation-loop tyrosines Y525/Y526. In contrast, ITK-SYK was phosphorylated both at Y212 and the activation-loop tyrosines Y385/Y386, corresponding to Y352 and Y525/Y526 in SYK, respectively. In resting primary lymphocytes, ITK-SYK predominantly localizes to the cell surface. In addition, we demonstrate that following stimulation, the ITK-SYK fusion-protein in cell lines translocates to the cell membrane and, moreover, that this phenomenon as well as SLP-76 phosphorylation are blocked upon phosphatidylinositol-3-kinase (PI3-kinase) inhibition.« less

Enzyme-linked immunosorbent assay for Escherichia coli heat-stable enterotoxin type II.

PubMed Central

Handl, C; Rönnberg, B; Nilsson, B; Olsson, E; Jonsson, H; Flock, J I

1988-01-01

The gene for Escherichia coli heat-stable enterotoxin type II (STII) was fused to the genes for protein A from Staphylococcus aureus and beta-galactosidase in two different expression systems. Antibodies raised in rabbits against the protein A-STII fusion protein recognized the beta-galactosidase-STII fusion protein. The latter fusion protein was used as the immobilized antigen in an enzyme-linked immunosorbent assay (ELISA) for detection of STII. The correlation between the results of the ELISA and the intestinal loop test in piglets was 95%, suggesting that the ELISA can be used to reliably detect STII. Images PMID:3049659

Quantum self-gravitating collapsing matter in a quantum geometry

NASA Astrophysics Data System (ADS)

Campiglia, Miguel; Gambini, Rodolfo; Olmedo, Javier; Pullin, Jorge

2016-09-01

The problem of how space-time responds to gravitating quantum matter in full quantum gravity has been one of the main questions that any program of quantization of gravity should address. Here we analyze this issue by considering the quantization of a collapsing null shell coupled to spherically symmetric loop quantum gravity. We show that the constraint algebra of canonical gravity is Abelian both classically and when quantized using loop quantum gravity techniques. The Hamiltonian constraint is well defined and suitable Dirac observables characterizing the problem were identified at the quantum level. We can write the metric as a parameterized Dirac observable at the quantum level and study the physics of the collapsing shell and black hole formation. We show how the singularity inside the black hole is eliminated by loop quantum gravity and how the shell can traverse it. The construction is compatible with a scenario in which the shell tunnels into a baby universe inside the black hole or one in which it could emerge through a white hole.

Exposure of Epitope Residues on the Outer Face of the Chikungunya Virus Envelope Trimer Determines Antibody Neutralizing Efficacy

PubMed Central

Fong, Rachel H.; Banik, Soma S. R.; Mattia, Kimberly; Barnes, Trevor; Tucker, David; Liss, Nathan; Lu, Kai; Selvarajah, Suganya; Srinivasan, Surabhi; Mabila, Manu; Miller, Adam; Muench, Marcus O.; Michault, Alain; Rucker, Joseph B.; Paes, Cheryl; Simmons, Graham; Kahle, Kristen M.

2014-01-01

ABSTRACT Chikungunya virus (CHIKV) is a reemerging alphavirus that causes a debilitating arthritic disease and infects millions of people and for which no specific treatment is available. Like many alphaviruses, the structural targets on CHIKV that elicit a protective humoral immune response in humans are poorly defined. Here we used phage display against virus-like particles (VLPs) to isolate seven human monoclonal antibodies (MAbs) against the CHIKV envelope glycoproteins E2 and E1. One MAb, IM-CKV063, was highly neutralizing (50% inhibitory concentration, 7.4 ng/ml), demonstrated high-affinity binding (320 pM), and was capable of therapeutic and prophylactic protection in multiple animal models up to 24 h postexposure. Epitope mapping using a comprehensive shotgun mutagenesis library of 910 mutants with E2/E1 alanine mutations demonstrated that IM-CKV063 binds to an intersubunit conformational epitope on domain A, a functionally important region of E2. MAbs against the highly conserved fusion loop have not previously been reported but were also isolated in our studies. Fusion loop MAbs were broadly cross-reactive against diverse alphaviruses but were nonneutralizing. Fusion loop MAb reactivity was affected by temperature and reactivity conditions, suggesting that the fusion loop is hidden in infectious virions. Visualization of the binding sites of 15 different MAbs on the structure of E2/E1 revealed that all epitopes are located at the membrane-distal region of the E2/E1 spike. Interestingly, epitopes on the exposed topmost and outer surfaces of the E2/E1 trimer structure were neutralizing, whereas epitopes facing the interior of the trimer were not, providing a rationale for vaccine design and therapeutic MAb development using the intact CHIKV E2/E1 trimer. IMPORTANCE CHIKV is the most important alphavirus affecting humans, resulting in a chronic arthritic condition that can persist for months or years. In recent years, millions of people have been infected globally, and the spread of CHIKV to the Americas is now beginning, with over 100,000 cases occurring in the Caribbean within 6 months of its arrival. Our study reports on seven human MAbs against the CHIKV envelope, including a highly protective MAb and rarely isolated fusion loop MAbs. Epitope mapping of these MAbs demonstrates how some E2/E1 epitopes are exposed or hidden from the human immune system and suggests a structural mechanism by which these MAbs protect (or fail to protect) against CHIKV infection. Our results suggest that the membrane-distal end of CHIKV E2/E1 is the primary target for the humoral immune response to CHIKV, and antibodies targeting the exposed topmost and outer surfaces of the E2/E1 trimer determine the neutralizing efficacy of this response. PMID:25275138

On Fusing Recursive Traversals of K-d Trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajbhandari, Samyam; Kim, Jinsung; Krishnamoorthy, Sriram

Loop fusion is a key program transformation for data locality optimization that is implemented in production compilers. But optimizing compilers currently cannot exploit fusion opportunities across a set of recursive tree traversal computations with producer-consumer relationships. In this paper, we develop a compile-time approach to dependence characterization and program transformation to enable fusion across recursively specified traversals over k-ary trees. We present the FuseT source-to-source code transformation framework to automatically generate fused composite recursive operators from an input program containing a sequence of primitive recursive operators. We use our framework to implement fused operators for MADNESS, Multiresolution Adaptive Numerical Environmentmore » for Scientific Simulation. We show that locality optimization through fusion can offer more than an order of magnitude performance improvement.« less

Distinguishing West Nile virus infection using a recombinant envelope protein with mutations in the conserved fusion-loop.

PubMed

Chabierski, Stefan; Barzon, Luisa; Papa, Anna; Niedrig, Matthias; Bramson, Jonathan L; Richner, Justin M; Palù, Giorgio; Diamond, Michael S; Ulbert, Sebastian

2014-05-09

West Nile Virus (WNV) is an emerging mosquito-transmitted flavivirus that continues to spread and cause disease throughout several parts of the world, including Europe and the Americas. Specific diagnosis of WNV infections using current serological testing is complicated by the high degree of cross-reactivity between antibodies against other clinically relevant flaviviruses, including dengue, tick-borne encephalitis (TBEV), Japanese encephalitis (JEV), and yellow fever (YFV) viruses. Cross-reactivity is particularly problematic in areas where different flaviviruses co-circulate or in populations that have been immunized with vaccines against TBEV, JEV, or YFV. The majority of cross-reactive antibodies against the immunodominant flavivirus envelope (E) protein target a conserved epitope in the fusion loop at the distal end of domain II. We tested a loss-of-function bacterially expressed recombinant WNV E protein containing mutations in the fusion loop and an adjacent loop domain as a possible diagnostic reagent. By comparing the binding of sera from humans infected with WNV or other flaviviruses to the wild type and the mutant E proteins, we analyzed the potential of this technology to specifically detect WNV antibodies. Using this system, we could reliably determine WNV infections. Antibodies from WNV-infected individuals bound equally well to the wild type and the mutant protein. In contrast, sera from persons infected with other flaviviruses showed significantly decreased binding to the mutant protein. By calculating the mean differences between antibody signals detected using the wild type and the mutant proteins, a value could be assigned for each of the flaviviruses, which distinguished their pattern of reactivity. Recombinant mutant E proteins can be used to discriminate infections with WNV from those with other flaviviruses. The data have important implications for the development of improved, specific serological assays for the detection of WNV antibodies in regions where other flaviviruses co-circulate or in populations that are immunized with other flavivirus vaccines.

HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop

PubMed Central

Eissmann, Kristin; Mueller, Sebastian; Sticht, Heinrich; Jung, Susan; Zou, Peng; Jiang, Shibo; Gross, Andrea; Eichler, Jutta; Fleckenstein, Bernhard; Reil, Heide

2013-01-01

A strategy for antiviral drug discovery is the elucidation and imitation of viral interference mechanisms. HIV-1 patients benefit from a coinfection with GB Virus C (GBV-C), since HIV-positive individuals with long-term GBV-C viraemia show better survival rates than HIV-1 patients without persisting GBV-C. A direct influence of GBV-C on HIV-1 replication has been shown in coinfection experiments. GBV-C is a human non-pathogenic member of the flaviviridae family that can replicate in T and B cells. Therefore, GBV-C shares partly the same ecological niche with HIV-1. In earlier work we have demonstrated that recombinant glycoprotein E2 of GBV-C and peptides derived from the E2 N-terminus interfere with HIV entry. In this study we investigated the underlying mechanism. Performing a virus-cell fusion assay and temperature-arrested HIV-infection kinetics, we provide evidence that the HIV-inhibitory E2 peptides interfere with late HIV-1 entry steps after the engagement of gp120 with CD4 receptor and coreceptor. Binding and competition experiments revealed that the N-terminal E2 peptides bind to the disulfide loop region of HIV-1 transmembrane protein gp41. In conjunction with computational analyses, we identified sequence similarities between the N-termini of GBV-C E2 and the HIV-1 glycoprotein gp120. This similarity appears to enable the GBV-C E2 N-terminus to interact with the HIV-1 gp41 disulfide loop, a crucial domain involved in the gp120-gp41 interface. Furthermore, the results of the present study provide initial proof of concept that peptides targeted to the gp41 disulfide loop are able to inhibit HIV fusion and should inspire the development of this new class of HIV-1 entry inhibitors. PMID:23349893

Attenuation of Recombinant Yellow Fever 17D Viruses Expressing Foreign Protein Epitopes at the Surface

PubMed Central

Bonaldo, Myrna C.; Garratt, Richard C.; Marchevsky, Renato S.; Coutinho, Evandro S. F.; Jabor, Alfredo V.; Almeida, Luís F. C.; Yamamura, Anna M. Y.; Duarte, Adriana S.; Oliveira, Prisciliana J.; Lizeu, Jackeline O. P.; Camacho, Luiz A. B.; Freire, Marcos S.; Galler, Ricardo

2005-01-01

The yellow fever (YF) 17D vaccine is a live attenuated virus. Three-dimensional (3D) homology modeling of the E protein structure from YF 17D virus and its comparison with that from tick-borne encephalitis virus revealed that it is possible to accommodate inserts of different sizes and amino acid compositions in the flavivirus E protein fg loop. This is consistent with the 3D structures of both the dimeric and trimeric forms in which the fg loop lies exposed to solvents. We demonstrate here that YF 17D viruses bearing foreign humoral (17D/8) and T-cell (17D/13) epitopes, which vary in sequence and length, displayed growth restriction. It is hypothesized that interference with the dimer-trimer transition and with the formation of a ring of such trimers in order to allow fusion compromises the capability of the E protein to induce fusion of viral and endosomal membranes, and a slower rate of fusion may delay the extent of virus production. This would account for the lower levels of replication in cultured cells and of viremia in monkeys, as well as for the more attenuated phenotype of the recombinant viruses in monkeys. Testing of both recombinant viruses (17D/8 and 17D/13) for monkey neurovirulence also suggests that insertion at the 17D E protein fg loop does not compromise the attenuated phenotype of YF 17D virus, further confirming the potential use of this site for the development of new live attenuated 17D virus-based vaccines. PMID:15956601

Model for the loop voltage of reversed field pinches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jarboe, T.R.; Alper, B.

1987-04-01

A simple model is presented that uses the concept of helicity balance to predict the toroidal loop voltage of reversed field pinches (RFP's). Data from the RFP's at Culham (Plasma Phys. Controlled Fusion 27, 1307 (1985)) are used to calibrate and verify the model. The model indicates that most of the helicity dissipation occurs in edge regions that are outside the limiters or in regions where field lines contact the walls. The value of this new interpretation to future RFP and spheromak experiments is discussed.

The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein.

PubMed

Fédry, Juliette; Liu, Yanjie; Péhau-Arnaudet, Gérard; Pei, Jimin; Li, Wenhao; Tortorici, M Alejandra; Traincard, François; Meola, Annalisa; Bricogne, Gérard; Grishin, Nick V; Snell, William J; Rey, Félix A; Krey, Thomas

2017-02-23

Sexual reproduction is almost universal in eukaryotic life and involves the fusion of male and female haploid gametes into a diploid cell. The sperm-restricted single-pass transmembrane protein HAP2-GCS1 has been postulated to function in membrane merger. Its presence in the major eukaryotic taxa-animals, plants, and protists (including important human pathogens like Plasmodium)-suggests that many eukaryotic organisms share a common gamete fusion mechanism. Here, we report combined bioinformatic, biochemical, mutational, and X-ray crystallographic studies on the unicellular alga Chlamydomonas reinhardtii HAP2 that reveal homology to class II viral membrane fusion proteins. We further show that targeting the segment corresponding to the fusion loop by mutagenesis or by antibodies blocks gamete fusion. These results demonstrate that HAP2 is the gamete fusogen and suggest a mechanism of action akin to viral fusion, indicating a way to block Plasmodium transmission and highlighting the impact of virus-cell genetic exchanges on the evolution of eukaryotic life. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

A New Hybrid BFOA-PSO Optimization Technique for Decoupling and Robust Control of Two-Coupled Distillation Column Process.

PubMed

Abdelkarim, Noha; Mohamed, Amr E; El-Garhy, Ahmed M; Dorrah, Hassen T

2016-01-01

The two-coupled distillation column process is a physically complicated system in many aspects. Specifically, the nested interrelationship between system inputs and outputs constitutes one of the significant challenges in system control design. Mostly, such a process is to be decoupled into several input/output pairings (loops), so that a single controller can be assigned for each loop. In the frame of this research, the Brain Emotional Learning Based Intelligent Controller (BELBIC) forms the control structure for each decoupled loop. The paper's main objective is to develop a parameterization technique for decoupling and control schemes, which ensures robust control behavior. In this regard, the novel optimization technique Bacterial Swarm Optimization (BSO) is utilized for the minimization of summation of the integral time-weighted squared errors (ITSEs) for all control loops. This optimization technique constitutes a hybrid between two techniques, which are the Particle Swarm and Bacterial Foraging algorithms. According to the simulation results, this hybridized technique ensures low mathematical burdens and high decoupling and control accuracy. Moreover, the behavior analysis of the proposed BELBIC shows a remarkable improvement in the time domain behavior and robustness over the conventional PID controller.

A New Hybrid BFOA-PSO Optimization Technique for Decoupling and Robust Control of Two-Coupled Distillation Column Process

PubMed Central

Mohamed, Amr E.; Dorrah, Hassen T.

2016-01-01

The two-coupled distillation column process is a physically complicated system in many aspects. Specifically, the nested interrelationship between system inputs and outputs constitutes one of the significant challenges in system control design. Mostly, such a process is to be decoupled into several input/output pairings (loops), so that a single controller can be assigned for each loop. In the frame of this research, the Brain Emotional Learning Based Intelligent Controller (BELBIC) forms the control structure for each decoupled loop. The paper's main objective is to develop a parameterization technique for decoupling and control schemes, which ensures robust control behavior. In this regard, the novel optimization technique Bacterial Swarm Optimization (BSO) is utilized for the minimization of summation of the integral time-weighted squared errors (ITSEs) for all control loops. This optimization technique constitutes a hybrid between two techniques, which are the Particle Swarm and Bacterial Foraging algorithms. According to the simulation results, this hybridized technique ensures low mathematical burdens and high decoupling and control accuracy. Moreover, the behavior analysis of the proposed BELBIC shows a remarkable improvement in the time domain behavior and robustness over the conventional PID controller. PMID:27807444

Modelling irradiation-induced softening in BCC iron by crystal plasticity approach

NASA Astrophysics Data System (ADS)

Xiao, Xiazi; Terentyev, Dmitry; Yu, Long; Song, Dingkun; Bakaev, A.; Duan, Huiling

2015-11-01

Crystal plasticity model (CPM) for BCC iron to account for radiation-induced strain softening is proposed. CPM is based on the plastically-driven and thermally-activated removal of dislocation loops. Atomistic simulations are applied to parameterize dislocation-defect interactions. Combining experimental microstructures, defect-hardening/absorption rules from atomistic simulations, and CPM fitted to properties of non-irradiated iron, the model achieves a good agreement with experimental data regarding radiation-induced strain softening and flow stress increase under neutron irradiation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Qianlong; Blissard, Gary W.; Liu, Tong-Xian

The Autographa californica multiple nucleopolyhedrovirus GP64 is a class III viral fusion protein. Although the post-fusion structure of GP64 has been solved, its pre-fusion structure and the detailed mechanism of conformational change are unknown. In GP64, domain V is predicted to interact with two domain I segments that flank fusion loop 2. To evaluate the significance of the amino acids involved in these interactions, we examined 24 amino acid positions that represent interacting and conserved residues within domains I and V. In several cases, substitution of a single amino acid involved in a predicted interaction disrupted membrane fusion activity, butmore » no single amino acid pair appears to be absolutely required. We identified 4 critical residues in domain V (G438, W439, T452, and T456) that are important for membrane fusion, and two residues (G438 and W439) that appear to be important for formation or stability of the pre-fusion conformation of GP64. - Highlights: • The baculovirus envelope glycoprotein GP64 is a class III viral fusion protein. • The detailed mechanism of conformational change of GP64 is unknown. • We analyzed 24 positions that might stabilize the post-fusion structure of GP64. • We identified 4 residues in domain V that were critical for membrane fusion. • Two residues are critical for formation of the pre-fusion conformation of GP64.« less

Rational Design of Dual Agonist-Antibody Fusions as Long-acting Therapeutic Hormones.

PubMed

Liu, Yan; Wang, Ying; Zhang, Yong; Liu, Tao; Jia, Haiqun; Zou, Huafei; Fu, Qiangwei; Zhang, Yuhan; Lu, Lucy; Chao, Elizabeth; Parker, Holly; Nguyen-Tran, Van; Shen, Weijun; Wang, Danling; Schultz, Peter G; Wang, Feng

2016-11-18

Recent studies have suggested that modulation of two or more signaling pathways can achieve substantial weight loss and glycemic stability. We have developed an approach to the generation of bifunctional antibody agonists that activate leptin receptor and GLP-1 receptor. Leptin was fused into the complementarity determining region 3 loop of the light chain alone, or in combination with exendin-4 (EX4) fused at the N-terminus of the heavy chain of Herceptin. The antibody fusions exhibit similar or increased in vitro activities on their cognate receptors, but 50-100-fold longer circulating half-lives in rodents compared to the corresponding native peptides/proteins. The efficacy of the leptin/EX4 dual antibody fusion on weight loss, especially fat mass loss, was enhanced in ob/ob mice and DIO mice compared to the antibody fusion of either EX4 or leptin alone. This work demonstrates the versatility of this combinatorial fusion strategy for generating dual antibody agonists with long half-lives.

Adaptive Neural Network Based Control of Noncanonical Nonlinear Systems.

PubMed

Zhang, Yanjun; Tao, Gang; Chen, Mou

2016-09-01

This paper presents a new study on the adaptive neural network-based control of a class of noncanonical nonlinear systems with large parametric uncertainties. Unlike commonly studied canonical form nonlinear systems whose neural network approximation system models have explicit relative degree structures, which can directly be used to derive parameterized controllers for adaptation, noncanonical form nonlinear systems usually do not have explicit relative degrees, and thus their approximation system models are also in noncanonical forms. It is well-known that the adaptive control of noncanonical form nonlinear systems involves the parameterization of system dynamics. As demonstrated in this paper, it is also the case for noncanonical neural network approximation system models. Effective control of such systems is an open research problem, especially in the presence of uncertain parameters. This paper shows that it is necessary to reparameterize such neural network system models for adaptive control design, and that such reparameterization can be realized using a relative degree formulation, a concept yet to be studied for general neural network system models. This paper then derives the parameterized controllers that guarantee closed-loop stability and asymptotic output tracking for noncanonical form neural network system models. An illustrative example is presented with the simulation results to demonstrate the control design procedure, and to verify the effectiveness of such a new design method.

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

PubMed

Olson, Mark A; Feig, Michael; Brooks, Charles L

2008-04-15

This article examines ab initio methods for the prediction of protein loops by a computational strategy of multiscale conformational sampling and physical energy scoring functions. Our approach consists of initial sampling of loop conformations from lattice-based low-resolution models followed by refinement using all-atom simulations. To allow enhanced conformational sampling, the replica exchange method was implemented. Physical energy functions based on CHARMM19 and CHARMM22 parameterizations with generalized Born (GB) solvent models were applied in scoring loop conformations extracted from the lattice simulations and, in the case of all-atom simulations, the ensemble of conformations were generated and scored with these models. Predictions are reported for 25 loop segments, each eight residues long and taken from a diverse set of 22 protein structures. We find that the simulations generally sampled conformations with low global root-mean-square-deviation (RMSD) for loop backbone coordinates from the known structures, whereas clustering conformations in RMSD space and scoring detected less favorable loop structures. Specifically, the lattice simulations sampled basins that exhibited an average global RMSD of 2.21 +/- 1.42 A, whereas clustering and scoring the loop conformations determined an RMSD of 3.72 +/- 1.91 A. Using CHARMM19/GB to refine the lattice conformations improved the sampling RMSD to 1.57 +/- 0.98 A and detection to 2.58 +/- 1.48 A. We found that further improvement could be gained from extending the upper temperature in the all-atom refinement from 400 to 800 K, where the results typically yield a reduction of approximately 1 A or greater in the RMSD of the detected loop. Overall, CHARMM19 with a simple pairwise GB solvent model is more efficient at sampling low-RMSD loop basins than CHARMM22 with a higher-resolution modified analytical GB model; however, the latter simulation method provides a more accurate description of the all-atom energy surface, yet demands a much greater computational cost. (c) 2007 Wiley Periodicals, Inc.

Development of emergent processing loops as a system of systems concept

NASA Astrophysics Data System (ADS)

Gainey, James C., Jr.; Blasch, Erik P.

1999-03-01

This paper describes an engineering approach toward implementing the current neuroscientific understanding of how the primate brain fuses, or integrates, 'information' in the decision-making process. We describe a System of Systems (SoS) design for improving the overall performance, capabilities, operational robustness, and user confidence in Identification (ID) systems and show how it could be applied to biometrics security. We use the Physio-associative temporal sensor integration algorithm (PATSIA) which is motivated by observed functions and interactions of the thalamus, hippocampus, and cortical structures in the brain. PATSIA utilizes signal theory mathematics to model how the human efficiently perceives and uses information from the environment. The hybrid architecture implements a possible SoS-level description of the Joint Directors of US Laboratories for Fusion Working Group's functional description involving 5 levels of fusion and their associated definitions. This SoS architecture propose dynamic sensor and knowledge-source integration by implementing multiple Emergent Processing Loops for predicting, feature extracting, matching, and Searching both static and dynamic database like MSTAR's PEMS loops. Biologically, this effort demonstrates these objectives by modeling similar processes from the eyes, ears, and somatosensory channels, through the thalamus, and to the cortices as appropriate while using the hippocampus for short-term memory search and storage as necessary. The particular approach demonstrated incorporates commercially available speaker verification and face recognition software and hardware to collect data and extract features to the PATSIA. The PATSIA maximizes the confidence levels for target identification or verification in dynamic situations using a belief filter. The proof of concept described here is easily adaptable and scaleable to other military and nonmilitary sensor fusion applications.

Passive tracking scheme for a single stationary observer

NASA Astrophysics Data System (ADS)

Chan, Y. T.; Rea, Terry

2001-08-01

While there are many techniques for Bearings-Only Tracking (BOT) in the ocean environment, they do not apply directly to the land situation. Generally, for tactical reasons, the land observer platform is stationary; but, it has two sensors, visual and infrared, for measuring bearings and a laser range finder (LRF) for measuring range. There is a requirement to develop a new BOT data fusion scheme that fuses the two sets of bearing readings, and together with a single LRF measurement, produces a unique track. This paper first develops a parameterized solution for the target speeds, prior to the occurrence of the LRF measurement, when the problem is unobservable. At, and after, the LRF measurement, a BOT formulated as a least squares (LS) estimator then produces a unique LS estimate of the target states. Bearing readings from the other sensor serve as instrumental variables in a data fusion setting to eliminate the bias in the BOT estimator. The result is recursive, unbiased and decentralized data fusion scheme. Results from two simulation experiments have corroborated the theoretical development and show that the scheme is optimal.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rudneva, Irina A.; Timofeeva, Tatiana A.; Ignatieva, Anna V.

In the present study we assessed pleiotropic characteristics of the antibody-selected mutations. We examined pH optimum of fusion, temperatures of HA heat inactivation, and in vitro and in vivo replication kinetics of the previously obtained influenza H5 escape mutants. Our results showed that HA1 N142K mutation significantly lowered the pH of fusion optimum. Mutations of the escape mutants located in the HA lateral loop significantly affected H5 HA thermostability (P<0.05). HA changes at positions 131, 144, 145, and 156 and substitutions at positions 131, 142, 145, and 156 affected the replicative ability of H5 escape mutants in vitro and inmore » vivo, respectively. Overall, a co-variation between antigenic specificity and different HA phenotypic properties has been demonstrated. We believe that the monitoring of pleiotropic effects of the HA mutations found in H5 escape mutants is essential for accurate prediction of mutants with pandemic potential. - Highlights: • HA1 N142K mutation significantly lowered the pH of fusion optimum. • Mutations located in the HA lateral loop significantly affected H5 HA thermostability. • HA changes at positions 131, 142, 144, 145, and 156 affected the replicative ability of H5 mutants. • Acquisition of glycosylation site could lead to the emergence of multiple pleiotropic effects.« less

Expression, purification and biochemical characterization of the cytoplasmic loop of PomA, a stator component of the Na+ driven flagellar motor

PubMed Central

Abe-Yoshizumi, Rei; Kobayashi, Shiori; Gohara, Mizuki; Hayashi, Kokoro; Kojima, Chojiro; Kojima, Seiji; Sudo, Yuki; Asami, Yasuo; Homma, Michio

2013-01-01

Flagellar motors embedded in bacterial membranes are molecular machines powered by specific ion flows. Each motor is composed of a stator and a rotor and the interactions of those components are believed to generate the torque. Na+ influx through the PomA/PomB stator complex of Vibrio alginolyticus is coupled to torque generation and is speculated to trigger structural changes in the cytoplasmic domain of PomA that interacts with a rotor protein in the C-ring, FliG, to drive the rotation. In this study, we tried to overproduce the cytoplasmic loop of PomA (PomA-Loop), but it was insoluble. Thus, we made a fusion protein with a small soluble tag (GB1) which allowed us to express and characterize the recombinant protein. The structure of the PomA-Loop seems to be very elongated or has a loose tertiary structure. When the PomA-Loop protein was produced in E. coli, a slight dominant effect was observed on motility. We conclude that the cytoplasmic loop alone retains a certain function. PMID:27493537

Dynamic Non-Rigid Objects Reconstruction with a Single RGB-D Sensor

PubMed Central

Zuo, Xinxin; Du, Chao; Wang, Runxiao; Zheng, Jiangbin; Yang, Ruigang

2018-01-01

This paper deals with the 3D reconstruction problem for dynamic non-rigid objects with a single RGB-D sensor. It is a challenging task as we consider the almost inevitable accumulation error issue in some previous sequential fusion methods and also the possible failure of surface tracking in a long sequence. Therefore, we propose a global non-rigid registration framework and tackle the drifting problem via an explicit loop closure. Our novel scheme starts with a fusion step to get multiple partial scans from the input sequence, followed by a pairwise non-rigid registration and loop detection step to obtain correspondences between neighboring partial pieces and those pieces that form a loop. Then, we perform a global registration procedure to align all those pieces together into a consistent canonical space as guided by those matches that we have established. Finally, our proposed model-update step helps fixing potential misalignments that still exist after the global registration. Both geometric and appearance constraints are enforced during our alignment; therefore, we are able to get the recovered model with accurate geometry as well as high fidelity color maps for the mesh. Experiments on both synthetic and various real datasets have demonstrated the capability of our approach to reconstruct complete and watertight deformable objects. PMID:29547562

Object kinetic Monte Carlo model for neutron and ion irradiation in tungsten: Impact of transmutation and carbon impurities

NASA Astrophysics Data System (ADS)

Castin, N.; Bonny, G.; Bakaev, A.; Ortiz, C. J.; Sand, A. E.; Terentyev, D.

2018-03-01

We upgrade our object kinetic Monte Carlo (OKMC) model, aimed at describing the microstructural evolution in tungsten (W) under neutron and ion irradiation. Two main improvements are proposed based on recently published atomistic data: (a) interstitial carbon impurities, and their interaction with radiation-induced defects (point defect clusters and loops), are more accurately parameterized thanks to ab initio findings; (b) W transmutation to rhenium (Re) upon neutron irradiation, impacting the diffusivity of radiation defects, is included, also relying on recent atomistic data. These essential amendments highly improve the portability of our OKMC model, providing a description for the formation of SIA-type loops under different irradiation conditions. The model is applied to simulate neutron and ion irradiation in pure W samples, in a wide range of fluxes and temperatures. We demonstrate that it performs a realistic prediction of the population of TEM-visible voids and loops, as compared to experimental evidence. The impact of the transmutation of W to Re, and of carbon trapping, is assessed.

Accurate predictor-corrector skip entry guidance for low lift-to-drag ratio spacecraft

NASA Astrophysics Data System (ADS)

Enmi, Y.; Qian, W.; He, K.; Di, D.

2018-06-01

This paper develops numerical predictor-corrector skip en try guidance for vehicles with low lift-to-drag L/D ratio during the skip entry phase of a Moon return mission. The guidance method is composed of two parts: trajectory planning before entry and closed-loop gu idance during skip entry. The result of trajectory planning before entry is able to present an initial value for predictor-corrector algorithm in closed-loop guidance for fast convergence. The magnitude of bank angle, which is parameterized as a linear function of the range-to-go, is modulated to satisfy the downrange requirements. The sign of the bank ang le is determined by the bank-reversal logic. The predictor-corrector algorithm repeatedly applied onboard in each guidance cycle to realize closed-loop guidance in the skip entry phase. The effectivity of the proposed guidance is validated by simulations in nominal conditions, including skip entry, loft entry, and direct entry, as well as simulations in dispersion conditions considering the combination disturbance of the entry interface, the aerodynamic coefficients, the air density, and the mass of the vehicle.

Immunization-elicited Broadly Protective Antibody Reveals Ebolavirus Fusion Loop as a Site of Vulnerability

PubMed Central

Zhao, Xuelian; Howell, Katie A.; He, Shihua; Brannan, Jennifer M.; Wec, Anna Z.; Davidson, Edgar; Turner, Hannah L.; Chiang, Chi-I; Lei, Lin; Fels, J. Maximilian; Vu, Hong; Shulenin, Sergey; Turonis, Ashley N.; Kuehne, Ana I.; Liu, Guodong; Ta, Mi; Wang, Yimeng; Sundling, Christopher; Xiao, Yongli; Spence, Jennifer S.; Doranz, Benjamin J.; Holtsberg, Frederick W.; Ward, Andrew B.; Chandran, Kartik; Dye, John M.; Qiu, Xiangguo; Li, Yuxing; Aman, M. Javad

2018-01-01

Summary While neutralizing antibodies are highly effective against ebolavirus infections, current experimental ebolavirus vaccines primarily elicit species-specific antibody responses. Here we describe an immunization-elicited macaque antibody (CA45) that clamps the internal fusion loop with the N-terminus of the ebolavirus glycoproteins (GP) and potently neutralizes Ebola, Sudan, Bundibugyo, and Reston viruses. CA45, alone or in combination with an antibody that blocks receptor binding, provided full protection against all pathogenic ebolaviruses in mice, guinea pigs, and ferrets. Analysis of memory B cells from the immunized macaque suggests that elicitation of broadly neutralizing antibodies (bNAbs) for ebolaviruses is possible but difficult, potentially due to the rarity of bNAb clones and their precursors. Unexpectedly, germline-reverted CA45, while exhibiting negligible binding to full-length GP, bound a proteolytically remodeled GP with picomolar affinity, suggesting that engineered ebolavirus vaccines could trigger rare bNAb precursors more robustly. These findings have important implications for developing pan-ebolavirus vaccine and immunotherapeutic cocktails. PMID:28525756

A non-planar two-loop three-point function beyond multiple polylogarithms

NASA Astrophysics Data System (ADS)

von Manteuffel, Andreas; Tancredi, Lorenzo

2017-06-01

We consider the analytic calculation of a two-loop non-planar three-point function which contributes to the two-loop amplitudes for t\\overline{t} production and γγ production in gluon fusion through a massive top-quark loop. All subtopology integrals can be written in terms of multiple polylogarithms over an irrational alphabet and we employ a new method for the integration of the differential equations which does not rely on the rationalization of the latter. The top topology integrals, instead, in spite of the absence of a massive three-particle cut, cannot be evaluated in terms of multiple polylogarithms and require the introduction of integrals over complete elliptic integrals and polylogarithms. We provide one-fold integral representations for the solutions and continue them analytically to all relevant regions of the phase space in terms of real functions, extracting all imaginary parts explicitly. The numerical evaluation of our expressions becomes straightforward in this way.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

NASA Astrophysics Data System (ADS)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

JET DT Scenario Extrapolation and Optimization with METIS

NASA Astrophysics Data System (ADS)

Urban, Jakub; Jaulmes, Fabien; Artaud, Jean-Francois

2017-10-01

Prospective JET (Joint European Torus) DT operation scenarios are modelled by the fast integrated code METIS. METIS combines scaling laws, e.g. for global and pedestal energy or density peaking, with simplified transport and source models, while retaining fundamental nonlinear couplings, in particular in the fusion power. We have tuned METIS parameters to match JET-ILW high performance experiments, including baseline and hybrid. Based on recent observations, we assume a weaker input power scaling than IPB98 and a 10% confinement improvement due to the higher ion mass. The rapidity of METIS is utilized to scan the performance of JET DT scenarios with respect to fundamental parameters, such as plasma current, magnetic field, density or heating power. Simplified, easily parameterized waveforms are used to study the effect the ramp-up speed or heating timing. Finally, an efficient Bayesian optimizer is employed to seek the most performant scenarios in terms of the fusion power or gain.

Investigation of the Solubility and Enzymatic Activity of a Thioredoxin-Gelonin Fusion Protein

DTIC Science & Technology

1997-05-01

1992). Figure lb is a diagram based on nuclear magnetic resonance data (NMR) of a 29-nucleotide RNA sequence containing the 17-nucleotide S/R loop and...Battalion Chemical Officer, Nuclear , Biological, Chancl Recoassanm Platoon Leader, Chemical Company Executive Officer, US Army Chemical Officer Advanced

Rubella virus: first calcium-requiring viral fusion protein.

PubMed

Dubé, Mathieu; Rey, Felix A; Kielian, Margaret

2014-12-01

Rubella virus (RuV) infection of pregnant women can cause fetal death, miscarriage, or severe fetal malformations, and remains a significant health problem in much of the underdeveloped world. RuV is a small enveloped RNA virus that infects target cells by receptor-mediated endocytosis and low pH-dependent membrane fusion. The structure of the RuV E1 fusion protein was recently solved in its postfusion conformation. RuV E1 is a member of the class II fusion proteins and is structurally related to the alphavirus and flavivirus fusion proteins. Unlike the other known class II fusion proteins, however, RuV E1 contains two fusion loops, with a metal ion complexed between them by the polar residues N88 and D136. Here we demonstrated that RuV infection specifically requires Ca(2+) during virus entry. Other tested cations did not substitute. Ca(2+) was not required for virus binding to cell surface receptors, endocytic uptake, or formation of the low pH-dependent E1 homotrimer. However, Ca(2+) was required for low pH-triggered E1 liposome insertion, virus fusion and infection. Alanine substitution of N88 or D136 was lethal. While the mutant viruses were efficiently assembled and endocytosed by host cells, E1-membrane insertion and fusion were specifically blocked. Together our data indicate that RuV E1 is the first example of a Ca(2+)-dependent viral fusion protein and has a unique membrane interaction mechanism.

On the two-loop virtual QCD corrections to Higgs boson pair production in the standard model

DOE PAGES

Degrassi, Giuseppe; Giardino, Pier Paolo; Gröber, Ramona

2016-07-21

Here, we compute the next-to-leading order virtual QCD corrections to Higgs-pair production via gluon fusion. We also present analytic results for the two-loop contributions to the spin-0 and spin-2 form factors in the amplitude. The reducible contributions, given by the double-triangle diagrams, are evaluated exactly while the two-loop irreducible diagrams are evaluated by an asymptotic expansion in heavy top-quark mass up to and including terms of O(1/mmore » $$8\\atop{t}$$). We estimate that mass effects can reduce the hadronic cross section by at most 10 %, assuming that the finite top-quark mass effects are of similar size in the entire range of partonic energies.« less

Combined line-of-sight error and angular position to generate feedforward control for a charge-coupled device-based tracking loop

NASA Astrophysics Data System (ADS)

Tang, Tao; Cai, Huaxiang; Huang, Yongmei; Ren, Ge

2015-10-01

A feedforward control based on data fusion is proposed to enhance closed-loop performance. The target trajectory as the observed value of a Kalman filter is recovered by synthesizing line-of-sight error and angular position from the encoder. A Kalman filter based on a Singer acceleration model is employed to estimate the target velocity. In this control scheme, the control stability is influenced by the bandwidth of the Kalman filter and time misalignment. The transfer function of the Kalman filter in the frequency domain is built for analyzing the closed loop stability, which shows that the Kalman filter is the major factor that affects the control stability. The feedforward control proposed here is verified through simulations and experiments.

Cheshire charge in (3+1)-dimensional topological phases

NASA Astrophysics Data System (ADS)

Else, Dominic V.; Nayak, Chetan

2017-07-01

We show that (3 +1 ) -dimensional topological phases of matter generically support loop excitations with topological degeneracy. The loops carry "Cheshire charge": topological charge that is not the integral of a locally defined topological charge density. Cheshire charge has previously been discussed in non-Abelian gauge theories, but we show that it is a generic feature of all (3+1)-D topological phases (even those constructed from an Abelian gauge group). Indeed, Cheshire charge is closely related to nontrivial three-loop braiding. We use a dimensional reduction argument to compute the topological degeneracy of loop excitations in the (3 +1 ) -dimensional topological phases associated with Dijkgraaf-Witten gauge theories. We explicitly construct membrane operators associated with such excitations in soluble microscopic lattice models in Z2×Z2 Dijkgraaf-Witten phases and generalize this construction to arbitrary membrane-net models. We explain why these loop excitations are the objects in the braided fusion 2-category Z (2 VectGω) , thereby supporting the hypothesis that 2-categories are the correct mathematical framework for (3 +1 ) -dimensional topological phases.

Analysis of Epitopes on Dengue Virus Envelope Protein Recognized by Monoclonal Antibodies and Polyclonal Human Sera by a High Throughput Assay

PubMed Central

Lin, Hong-En; Tsai, Wen-Yang; Liu, I-Ju; Li, Pi-Chun; Liao, Mei-Ying; Tsai, Jih-Jin; Wu, Yi-Chieh; Lai, Chih-Yun; Lu, Chih-Hsuan; Huang, Jyh-Hsiung; Chang, Gwong-Jen; Wu, Han-Chung; Wang, Wei-Kung

2012-01-01

Background The envelope (E) protein of dengue virus (DENV) is the major target of neutralizing antibodies and vaccine development. While previous studies on domain III or domain I/II alone have reported several epitopes of monoclonal antibodies (mAbs) against DENV E protein, the possibility of interdomain epitopes and the relationship between epitopes and neutralizing potency remain largely unexplored. Methodology/Principal Findings We developed a dot blot assay by using 67 alanine mutants of predicted surface-exposed E residues as a systematic approach to identify epitopes recognized by mAbs and polyclonal sera, and confirmed our findings using a capture-ELISA assay. Of the 12 mouse mAbs tested, three recognized a novel epitope involving residues (Q211, D215, P217) at the central interface of domain II, and three recognized residues at both domain III and the lateral ridge of domain II, suggesting a more frequent presence of interdomain epitopes than previously appreciated. Compared with mAbs generated by traditional protocols, the potent neutralizing mAbs generated by a new protocol recognized multiple residues in A strand or residues in C strand/CC′ loop of DENV2 and DENV1, and multiple residues in BC loop and residues in DE loop, EF loop/F strand or G strand of DENV1. The predominant epitopes of anti-E antibodies in polyclonal sera were found to include both fusion loop and non-fusion residues in the same or adjacent monomer. Conclusions/Significance Our analyses have implications for epitope-specific diagnostics and epitope-based dengue vaccines. This high throughput method has tremendous application for mapping both intra and interdomain epitopes recognized by human mAbs and polyclonal sera, which would further our understanding of humoral immune responses to DENV at the epitope level. PMID:22235356

Identification of Novel Fusion Inhibitors of Influenza A Virus by Chemical Genetics

PubMed Central

Lai, Kin Kui; Cheung, Nam Nam; Yang, Fang; Dai, Jun; Liu, Li; Chen, Zhiwei; Sze, Kong Hung; Chen, Honglin

2015-01-01

ABSTRACT A previous screening of more than 50,000 compounds led to the identification of a pool of bioactive small molecules with inhibitory effect on the influenza A virus. One of these compounds, now widely known as nucleozin, is a small molecule that targets the influenza A virus nucleoprotein. Here we identify and characterize two structurally different novel fusion inhibitors of the influenza A virus group 1 hemagglutinin (HA), FA-583 and FA-617, with low nanomolar activities. Escape mutants that are highly resistant to each of these compounds were generated, and both were found to carry mutations localized in close proximity to the B-loop of the hemagglutinin 2 protein, which plays a crucial role in the virion-host cell fusion process. Recombinant virus, generated through reverse genetics, confirmed the resistance phenotype. In addition, the proposed binding pockets predicted by molecular docking studies are in accordance with the resistance-bearing mutation sites. We show through mechanistic studies that FA-583 and FA-617 act as fusion inhibitors by prohibiting the low-pH-induced conformational change of hemagglutinin. Our study has offered concrete biological and mechanistic explorations for the strategic development of novel fusion inhibitors of influenza A viruses. IMPORTANCE Here we report two structurally distinctive novel fusion inhibitors of influenza A virus that act by interfering with the structural change of HA at acidic pH, a process necessary for successful entry of the virus. Mutational and molecular docking studies have identified their binding pockets situated in close proximity to the B-loop region of hemagglutinin 2. The reduced sensitivity of FA-583- or FA-617-associated mutants to another compound suggests a close proximity and even partial overlap of their binding sites on hemagglutinin. Amino acid sequence alignments and crystal structure analyses of group 1 and group 2 hemagglutinins have shed light on the possible binding mode of these two compounds. This report offers new lead compounds for the design of fusion inhibitors for influenza A viruses and further shows that analysis by forward chemical genetics is a highly effective approach for the identification of novel compounds that can perturb the infectivity of viruses and to probe new druggable targets or druggable domains in various viruses. PMID:26676787

Mutational analysis of the gag-pol junction of Moloney murine leukemia virus: requirements for expression of the gag-pol fusion protein.

PubMed Central

Felsenstein, K M; Goff, S P

1992-01-01

The gag-pol polyprotein of the murine and feline leukemia viruses is expressed by translational readthrough of a UAG terminator codon at the 3' end of the gag gene. To explore the cis-acting sequence requirements for the readthrough event in vivo, we generated a library of mutants of the Moloney murine leukemia virus with point mutations near the terminator codon and tested the mutant viral DNAs for the ability to direct synthesis of the gag-pol fusion protein and formation of infectious virus. The analysis showed that sequences 3' to the terminator are necessary and sufficient for the process. The results do not support a role for one proposed stem-loop structure that includes the terminator but are consistent with the involvement of another stem-loop 3' to the terminator. One mutant, containing two compensatory changes in this stem structure, was temperature sensitive for replication and for formation of the gag-pol protein. The results suggest that RNA sequence and structure are critical determinants of translational readthrough in vivo. Images PMID:1404606

Final Report on ITER Task Agreement 81-08

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richard L. Moore

As part of an ITER Implementing Task Agreement (ITA) between the ITER US Participant Team (PT) and the ITER International Team (IT), the INL Fusion Safety Program was tasked to provide the ITER IT with upgrades to the fusion version of the MELCOR 1.8.5 code including a beryllium dust oxidation model. The purpose of this model is to allow the ITER IT to investigate hydrogen production from beryllium dust layers on hot surfaces inside the ITER vacuum vessel (VV) during in-vessel loss-of-cooling accidents (LOCAs). Also included in the ITER ITA was a task to construct a RELAP5/ATHENA model of themore » ITER divertor cooling loop to model the draining of the loop during a large ex-vessel pipe break followed by an in-vessel divertor break and compare the results to a simular MELCOR model developed by the ITER IT. This report, which is the final report for this agreement, documents the completion of the work scope under this ITER TA, designated as TA 81-08.« less

Assessment of Closed-Loop Control Using Multi-Mode Sensor Fusion For a High Reynolds Number Transonic Jet

NASA Astrophysics Data System (ADS)

Low, Kerwin; Elhadidi, Basman; Glauser, Mark

2009-11-01

Understanding the different noise production mechanisms caused by the free shear flows in a turbulent jet flow provides insight to improve ``intelligent'' feedback mechanisms to control the noise. Towards this effort, a control scheme is based on feedback of azimuthal pressure measurements in the near field of the jet at two streamwise locations. Previous studies suggested that noise reduction can be achieved by azimuthal actuators perturbing the shear layer at the jet lip. The closed-loop actuation will be based on a low-dimensional Fourier representation of the hydrodynamic pressure measurements. Preliminary results show that control authority and reduction in the overall sound pressure level was possible. These results provide motivation to move forward with the overall vision of developing innovative multi-mode sensing methods to improve state estimation and derive dynamical systems. It is envisioned that estimating velocity-field and dynamic pressure information from various locations both local and in the far-field regions, sensor fusion techniques can be utilized to ascertain greater overall control authority.

Slope seeking for autonomous lift improvement by plasma surface discharge

NASA Astrophysics Data System (ADS)

Benard, Nicolas; Moreau, Eric; Griffin, John; Cattafesta, Louis N., III

2010-05-01

The present paper describes an experimental investigation of closed-loop separation control using plasma actuators. The post-stall-separated flow over a NACA 0015 airfoil is controlled using a single dielectric barrier discharge actuator located at the leading edge. Open-loop measurements are first performed to highlight the effects of the voltage amplitude on the control authority for freestream velocities of 10-30 m/s (chord Re = 1.3 × 105 to 4 × 105). The results indicate that partial or full reattachment can be achieved and motivate the choice of the slope seeking approach as the control algorithm. A single-input/single-output algorithm is used to autonomously seek the optimal voltage required to achieve the control objective (full flow reattachment associated with maximum lift). The paper briefly introduces the concept of slope seeking, and a detailed parameterization of the controller is considered. Static (fixed speed) closed-loop experiments are then discussed, which demonstrate the capability of the algorithm. In each case, the flow can be reattached in an autonomous fashion. The last part of the paper demonstrates the robustness of the gradient-based, model-free scheme for dynamic freestream conditions. This paper highlights the capability of slope seeking to autonomously achieve high lift when used to drive the voltage of a plasma actuator. It also describes the advantages and drawbacks of such a closed-loop approach.

Influence of minor displacements in loops of the porcine parvovirus VP2 capsid on virus-like particles assembly and the induction of antibody responses.

PubMed

Pan, Qunxing; He, Kongwang; Wang, Yongshan; Wang, Xiaoli; Ouyang, Wei

2013-06-01

An antigen-delivery system based on hybrid virus-like particles (VLPs) formed by the self-assembly of the capsid VP2 protein of porcine parvovirus (PPV) and expressing foreign peptides offers an alternative method for vaccination. In this study, the three-dimensional structure of the PPV capsid protein and surface loops deletion mutants were analyzed to define essential domains in PPV VP2 for the assembly of VLPs. Electron microscopic analysis and SDS-PAGE analysis confirmed the presence of abundant VLPs in a loop2 deletion mutant of expected size and appropriate morphology. Loop4 and loop2-loop4 deletion mutants, however, resulted in a lower number of particles and the morphology of the particles was not well preserved. Furthermore, the green fluorescent protein (gfp) gene was used as a model. GFP was observed at the same level in displacements mutants. However, GFP displacement mutants in loop2 construct allowed better adaptation for the fusion GFP to be further displayed on the surface of the capsid-like structure. Immunogenicity study showed that there is no obvious difference in mice inoculated with rAd-VP2(Δloop2), rAd-VP2(Δloop4), rAd-VP2(Δloop2-Δloop4), and PPV inactivated vaccine. The results suggested the possibility of inserting simultaneously B and T cell epitopes in the surface loop2 and the N-terminus. The combination of different types of epitopes (B, CD4+, and CD8+) in different positions of the PPV particles opens the way to the development of highly efficient vaccines, able to stimulate at the same time the different branches of the immune system.

Research on the Automatic Fusion Strategy of Fixed Value Boundary Based on the Weak Coupling Condition of Grid Partition

NASA Astrophysics Data System (ADS)

Wang, X. Y.; Dou, J. M.; Shen, H.; Li, J.; Yang, G. S.; Fan, R. Q.; Shen, Q.

2018-03-01

With the continuous strengthening of power grids, the network structure is becoming more and more complicated. An open and regional data modeling is used to complete the calculation of the protection fixed value based on the local region. At the same time, a high precision, quasi real-time boundary fusion technique is needed to seamlessly integrate the various regions so as to constitute an integrated fault computing platform which can conduct transient stability analysis of covering the whole network with high accuracy and multiple modes, deal with the impact results of non-single fault, interlocking fault and build “the first line of defense” of the power grid. The boundary fusion algorithm in this paper is an automatic fusion algorithm based on the boundary accurate coupling of the networking power grid partition, which takes the actual operation mode for qualification, complete the boundary coupling algorithm of various weak coupling partition based on open-loop mode, improving the fusion efficiency, truly reflecting its transient stability level, and effectively solving the problems of too much data, too many difficulties of partition fusion, and no effective fusion due to mutually exclusive conditions. In this paper, the basic principle of fusion process is introduced firstly, and then the method of boundary fusion customization is introduced by scene description. Finally, an example is given to illustrate the specific algorithm on how it effectively implements the boundary fusion after grid partition and to verify the accuracy and efficiency of the algorithm.

Structure of the Immature Dengue Virus at Low pH Primes Proteolytic Maturation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, I-Mei; Zhang, Wei; Holdaway, Heather A.

Intracellular cleavage of immature flaviviruses is a critical step in assembly that generates the membrane fusion potential of the E glycoprotein. With cryo-electron microscopy we show that the immature dengue particles undergo a reversible conformational change at low pH that renders them accessible to furin cleavage. At a pH of 6.0, the E proteins are arranged in a herringbone pattern with the pr peptides docked onto the fusion loops, a configuration similar to that of the mature virion. After cleavage, the dissociation of pr is pH-dependent, suggesting that in the acidic environment of the trans-Golgi network pr is retained onmore » the virion to prevent membrane fusion. These results suggest a mechanism by which flaviviruses are processed and stabilized in the host cell secretory pathway.« less

Transposon Mutagenesis of the Zika Virus Genome Highlights Regions Essential for RNA Replication and Restricted for Immune Evasion.

PubMed

Fulton, Benjamin O; Sachs, David; Schwarz, Megan C; Palese, Peter; Evans, Matthew J

2017-08-01

The molecular constraints affecting Zika virus (ZIKV) evolution are not well understood. To investigate ZIKV genetic flexibility, we used transposon mutagenesis to add 15-nucleotide insertions throughout the ZIKV MR766 genome and subsequently deep sequenced the viable mutants. Few ZIKV insertion mutants replicated, which likely reflects a high degree of functional constraints on the genome. The NS1 gene exhibited distinct mutational tolerances at different stages of the screen. This result may define regions of the NS1 protein that are required for the different stages of the viral life cycle. The ZIKV structural genes showed the highest degree of insertional tolerance. Although the envelope (E) protein exhibited particular flexibility, the highly conserved envelope domain II (EDII) fusion loop of the E protein was intolerant of transposon insertions. The fusion loop is also a target of pan-flavivirus antibodies that are generated against other flaviviruses and neutralize a broad range of dengue virus and ZIKV isolates. The genetic restrictions identified within the epitopes in the EDII fusion loop likely explain the sequence and antigenic conservation of these regions in ZIKV and among multiple flaviviruses. Thus, our results provide insights into the genetic restrictions on ZIKV that may affect the evolution of this virus. IMPORTANCE Zika virus recently emerged as a significant human pathogen. Determining the genetic constraints on Zika virus is important for understanding the factors affecting viral evolution. We used a genome-wide transposon mutagenesis screen to identify where mutations were tolerated in replicating viruses. We found that the genetic regions involved in RNA replication were mostly intolerant of mutations. The genes coding for structural proteins were more permissive to mutations. Despite the flexibility observed in these regions, we found that epitopes bound by broadly reactive antibodies were genetically constrained. This finding may explain the genetic conservation of these epitopes among flaviviruses. Copyright © 2017 American Society for Microbiology.

Dual Split Protein-Based Fusion Assay Reveals that Mutations to Herpes Simplex Virus (HSV) Glycoprotein gB Alter the Kinetics of Cell-Cell Fusion Induced by HSV Entry Glycoproteins

PubMed Central

Atanasiu, Doina; Saw, Wan Ting; Gallagher, John R.; Hannah, Brian P.; Matsuda, Zene; Whitbeck, J. Charles; Cohen, Gary H.

2013-01-01

Herpes simplex virus (HSV) entry and cell-cell fusion require glycoproteins gD, gH/gL, and gB. We propose that receptor-activated changes to gD cause it to activate gH/gL, which then triggers gB into an active form. We employed a dual split-protein (DSP) assay to monitor the kinetics of HSV glycoprotein-induced cell-cell fusion. This assay measures content mixing between two cells, i.e., fusion, within the same cell population in real time (minutes to hours). Titration experiments suggest that both gD and gH/gL act in a catalytic fashion to trigger gB. In fact, fusion rates are governed by the amount of gB on the cell surface. We then used the DSP assay to focus on mutants in two functional regions (FRs) of gB, FR1 and FR3. FR1 contains the fusion loops (FL1 and FL2), and FR3 encompasses the crown at the trimer top. All FL mutants initiated fusion very slowly, if at all. However, the fusion rates caused by some FL2 mutants increased over time, so that total fusion by 8 h looked much like that of the WT. Two distinct kinetic patterns, “slow and fast,” emerged for mutants in the crown of gB (FR3), again showing differences in initiation and ongoing fusion. Of note are the fusion kinetics of the gB syn mutant (LL871/872AA). Although this mutant was originally included as an ongoing high-rate-of-fusion control, its initiation of fusion is so rapid that it appears to be on a “hair trigger.” Thus, the DSP assay affords a unique way to examine the dynamics of HSV glycoprotein-induced cell fusion. PMID:23946457

Five Residues in the Apical Loop of the Respiratory Syncytial Virus Fusion Protein F2 Subunit are Critical for its Fusion Activity.

PubMed

Hicks, Stephanie N; Chaiwatpongsakorn, Supranee; Costello, Heather M; McLellan, Jason S; Ray, William; Peeples, Mark E

2018-05-09

The respiratory syncytial virus (RSV) fusion (F) protein is a trimeric, membrane-anchored glycoprotein capable of mediating both viral-target cell membrane fusion to initiate infection and cell-cell fusion, even in the absence of the attachment glycoprotein. The F protein is initially expressed in a precursor form, whose functional capabilities are activated by proteolysis at two sites between the F 1 and F 2 subunits. This cleavage results in expression of the metastable and high-energy prefusion conformation. To mediate fusion, the F protein is triggered by an unknown stimulus, causing the F 1 subunit to refold dramatically while F 2 changes minimally. Hypothesizing that the most likely site for interaction with a target-cell component would be the top, or apex, of the protein, we determined the importance of the residues in the apical loop of F 2 by scanning mutagenesis. Five residues were not important, two were of intermediate importance, and all four lysines and one isoleucine were essential. Alanine replacement did not result in the loss of pre-F conformation for any of these mutants. Each of the four lysines required its specific charge for fusion function. Alanine replacement of the three essential lysines on the ascent to the apex hindered fusion following a forced fusion event, suggesting they are involved in refolding. Alanine mutation at Ile64, also on the ascent to the apex, and Lys75, did not prevent fusion following forced triggering, suggesting they are not involved in refolding and may instead be involved in the natural triggering of the F protein. IMPORTANCE RSV infects virtually every child by the age of 3, causing nearly 33 million acute lower respiratory infections (ALRI) worldwide each year in children younger than 5 (Nair H, et al. 2010. Lancet 375:1545-55). RSV is also the second leading cause of respiratory related death in the elderly (Falsey AR, Walsh EE. 2005. Drugs Aging 22:577-87; Falsey AR, Hennessey PA, Formica MA, Cox C, Walsh EE. 2005. N Engl J Med 352:1749-1759). The monoclonal antibody palivizumab is approved for prophylactic use in some at-risk infants, but healthy infants remain unprotected. Furthermore, its expense limits its use primarily to developed countries. No vaccine or effective small-molecule drug is approved for preventing disease or treating infection (Costello HM, Ray W, Chaiwatpongsakorn S, Peeples ME. 2012. 12:110-128). The essential residues identified in the apical domain of F 2 are adjacent to the apical portion of F 1 which, upon triggering, refolds into the long heptad repeat A (HRA) with the fusion peptide at its N-terminus. These essential residues in F 2 are likely involved in triggering and/or refolding of the F protein and as such may be ideal targets for antiviral drug development. Copyright © 2018 American Society for Microbiology.

Control law parameterization for an aeroelastic wind-tunnel model equipped with an active roll control system and comparison with experiment

NASA Technical Reports Server (NTRS)

Perry, Boyd, III; Dunn, H. J.; Sandford, Maynard C.

1988-01-01

Nominal roll control laws were designed, implemented, and tested on an aeroelastically-scaled free-to-roll wind-tunnel model of an advanced fighter configuration. The tests were performed in the NASA Langley Transonic Dynamics Tunnel. A parametric study of the nominal roll control system was conducted. This parametric study determined possible control system gain variations which yielded identical closed-loop stability (roll mode pole location) and identical roll response but different maximum control-surface deflections. Comparison of analytical predictions with wind-tunnel results was generally very good.

Assessment of the MHD capability in the ATHENA code using data from the ALEX facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roth, P.A.

1989-03-01

The ATHENA (Advanced Thermal Hydraulic Energy Network Analyzer) code is a system transient analysis code with multi-loop, multi-fluid capabilities, which is available to the fusion community at the National Magnetic Fusion Energy Computing Center (NMFECC). The work reported here assesses the ATHENA magnetohydrodynamic (MHD) pressure drop model for liquid metals flowing through a strong magnetic field. An ATHENA model was developed for two simple geometry, adiabatic test sections used in the Argonne Liquid Metal Experiment (ALEX) at Argonne National Laboratory (ANL). The pressure drops calculated by ATHENA agreed well with the experimental results from the ALEX facility.

Very heavy MSSM higgs-bosson production at the linear collider

NASA Astrophysics Data System (ADS)

Hahn, T.; Heinemeyer, S.; Weiglein, G.

2003-03-01

In the Minimal Supersymmetric Standard Model (MSSM) we present the corrections to the heavy neutral CP-even Higgs-boson production in the WW-fusion and Higgs-strahlung channel, e +e - → overlinevv H , taking into account all O(α) corrections arising from loops of fermions and sfermions. While the H boson shows decoupling behavior at the tree-level, we find non-negligible loop corrections that can enhance the cross section considerably. At a center-of-mass energy of √ s = 1000 GeV, masses of up to MH ⪅ 750 GeV are accessible at the LC in favorable regions of the MSSM parameter space.

Dissection of the Role of the Stable Signal Peptide of the Arenavirus Envelope Glycoprotein in Membrane Fusion

PubMed Central

Messina, Emily L.; York, Joanne

2012-01-01

The arenavirus envelope glycoprotein (GPC) retains a stable signal peptide (SSP) as an essential subunit in the mature complex. The 58-amino-acid residue SSP comprises two membrane-spanning hydrophobic regions separated by a short ectodomain loop that interacts with the G2 fusion subunit to promote pH-dependent membrane fusion. Small-molecule compounds that target this unique SSP-G2 interaction prevent arenavirus entry and infection. The interaction between SSP and G2 is sensitive to the phylogenetic distance between New World (Junín) and Old World (Lassa) arenaviruses. For example, heterotypic GPC complexes are unable to support virion entry. In this report, we demonstrate that the hybrid GPC complexes are properly assembled, proteolytically cleaved, and transported to the cell surface but are specifically defective in their membrane fusion activity. Chimeric SSP constructs reveal that this incompatibility is localized to the first transmembrane segment of SSP (TM1). Genetic changes in TM1 also affect sensitivity to small-molecule fusion inhibitors, generating resistance in some cases and inhibitor dependence in others. Our studies suggest that interactions of SSP TM1 with the transmembrane domain of G2 may be important for GPC-mediated membrane fusion and its inhibition. PMID:22438561

High temperature annealing of ion irradiated tungsten

DOE PAGES

Ferroni, Francesco; Yi, Xiaoou; Arakawa, Kazuto; ...

2015-03-21

In this study, transmission electron microscopy of high temperature annealing of pure tungsten irradiated by self-ions was conducted to elucidate microstructural and defect evolution in temperature ranges relevant to fusion reactor applications (500–1200°C). Bulk isochronal and isothermal annealing of ion irradiated pure tungsten (2 MeV W + ions, 500°C, 1014 W +/cm 2) with temperatures of 800, 950, 1100 and 1400°C, from 0.5 to 8 h, was followed by ex situ characterization of defect size, number density, Burgers vector and nature. Loops with diameters larger than 2–3 nm were considered for detailed analysis, among which all loops had View themore » MathML source and were predominantly of interstitial nature. In situ annealing experiments from 300 up to 1200°C were also carried out, including dynamic temperature ramp-ups. These confirmed an acceleration of loop loss above 900°C. At different temperatures within this range, dislocations exhibited behaviour such as initial isolated loop hopping followed by large-scale rearrangements into loop chains, coalescence and finally line–loop interactions and widespread absorption by free-surfaces at increasing temperatures. An activation energy for the annealing of dislocation length was obtained, finding E a=1.34±0.2 eV for the 700–1100°C range.« less

Intelligent robust tracking control for a class of uncertain strict-feedback nonlinear systems.

PubMed

Chang, Yeong-Chan

2009-02-01

This paper addresses the problem of designing robust tracking controls for a large class of strict-feedback nonlinear systems involving plant uncertainties and external disturbances. The input and virtual input weighting matrices are perturbed by bounded time-varying uncertainties. An adaptive fuzzy-based (or neural-network-based) dynamic feedback tracking controller will be developed such that all the states and signals of the closed-loop system are bounded and the trajectory tracking error should be as small as possible. First, the adaptive approximators with linearly parameterized models are designed, and a partitioned procedure with respect to the developed adaptive approximators is proposed such that the implementation of the fuzzy (or neural network) basis functions depends only on the state variables but does not depend on the tuning approximation parameters. Furthermore, we extend to design the nonlinearly parameterized adaptive approximators. Consequently, the intelligent robust tracking control schemes developed in this paper possess the properties of computational simplicity and easy implementation. Finally, simulation examples are presented to demonstrate the effectiveness of the proposed control algorithms.

Optimizing the Four-Index Integral Transform Using Data Movement Lower Bounds Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajbhandari, Samyam; Rastello, Fabrice; Kowalski, Karol

The four-index integral transform is a fundamental and computationally demanding calculation used in many computational chemistry suites such as NWChem. It transforms a four-dimensional tensor from an atomic basis to a molecular basis. This transformation is most efficiently implemented as a sequence of four tensor contractions that each contract a four-dimensional tensor with a two-dimensional transformation matrix. Differing degrees of permutation symmetry in the intermediate and final tensors in the sequence of contractions cause intermediate tensors to be much larger than the final tensor and limit the number of electronic states in the modeled systems. Loop fusion, in conjunction withmore » tiling, can be very effective in reducing the total space requirement, as well as data movement. However, the large number of possible choices for loop fusion and tiling, and data/computation distribution across a parallel system, make it challenging to develop an optimized parallel implementation for the four-index integral transform. We develop a novel approach to address this problem, using lower bounds modeling of data movement complexity. We establish relationships between available aggregate physical memory in a parallel computer system and ineffective fusion configurations, enabling their pruning and consequent identification of effective choices and a characterization of optimality criteria. This work has resulted in the development of a significantly improved implementation of the four-index transform that enables higher performance and the ability to model larger electronic systems than the current implementation in the NWChem quantum chemistry software suite.« less

In Situ 3D Monitoring of Geometric Signatures in the Powder-Bed-Fusion Additive Manufacturing Process via Vision Sensing Methods

PubMed Central

Li, Zhongwei; Liu, Xingjian; Wen, Shifeng; He, Piyao; Zhong, Kai; Wei, Qingsong; Shi, Yusheng; Liu, Sheng

2018-01-01

Lack of monitoring of the in situ process signatures is one of the challenges that has been restricting the improvement of Powder-Bed-Fusion Additive Manufacturing (PBF AM). Among various process signatures, the monitoring of the geometric signatures is of high importance. This paper presents the use of vision sensing methods as a non-destructive in situ 3D measurement technique to monitor two main categories of geometric signatures: 3D surface topography and 3D contour data of the fusion area. To increase the efficiency and accuracy, an enhanced phase measuring profilometry (EPMP) is proposed to monitor the 3D surface topography of the powder bed and the fusion area reliably and rapidly. A slice model assisted contour detection method is developed to extract the contours of fusion area. The performance of the techniques is demonstrated with some selected measurements. Experimental results indicate that the proposed method can reveal irregularities caused by various defects and inspect the contour accuracy and surface quality. It holds the potential to be a powerful in situ 3D monitoring tool for manufacturing process optimization, close-loop control, and data visualization. PMID:29649171

Treatment of temporal aliasing effects in the context of next generation satellite gravimetry missions

NASA Astrophysics Data System (ADS)

Daras, Ilias; Pail, Roland

2017-09-01

Temporal aliasing effects have a large impact on the gravity field accuracy of current gravimetry missions and are also expected to dominate the error budget of Next Generation Gravimetry Missions (NGGMs). This paper focuses on aspects concerning their treatment in the context of Low-Low Satellite-to-Satellite Tracking NGGMs. Closed-loop full-scale simulations are performed for a two-pair Bender-type Satellite Formation Flight (SFF), by taking into account error models of new generation instrument technology. The enhanced spatial sampling and error isotropy enable a further reduction of temporal aliasing errors from the processing perspective. A parameterization technique is adopted where the functional model is augmented by low-resolution gravity field solutions coestimated at short time intervals, while the remaining higher-resolution gravity field solution is estimated at a longer time interval. Fine-tuning the parameterization choices leads to significant reduction of the temporal aliasing effects. The investigations reveal that the parameterization technique in case of a Bender-type SFF can successfully mitigate aliasing effects caused by undersampling of high-frequency atmospheric and oceanic signals, since their most significant variations can be captured by daily coestimated solutions. This amounts to a "self-dealiasing" method that differs significantly from the classical dealiasing approach used nowadays for Gravity Recovery and Climate Experiment processing, enabling NGGMs to retrieve the complete spectrum of Earth's nontidal geophysical processes, including, for the first time, high-frequency atmospheric and oceanic variations.

An intracellular motif of GLUT4 regulates fusion of GLUT4-containing vesicles.

PubMed

Heyward, Catherine A; Pettitt, Trevor R; Leney, Sophie E; Welsh, Gavin I; Tavaré, Jeremy M; Wakelam, Michael J O

2008-05-20

Insulin stimulates glucose uptake by adipocytes through increasing translocation of the glucose transporter GLUT4 from an intracellular compartment to the plasma membrane. Fusion of GLUT4-containing vesicles at the cell surface is thought to involve phospholipase D activity, generating the signalling lipid phosphatidic acid, although the mechanism of action is not yet clear. Here we report the identification of a putative phosphatidic acid-binding motif in a GLUT4 intracellular loop. Mutation of this motif causes a decrease in the insulin-induced exposure of GLUT4 at the cell surface of 3T3-L1 adipocytes via an effect on vesicle fusion. The potential phosphatidic acid-binding motif identified in this study is unique to GLUT4 among the sugar transporters, therefore this motif may provide a unique mechanism for regulating insulin-induced translocation by phospholipase D signalling.

Azimuthal Dependence of Intrinsic Top in Photon-Quark Scattering and Higgs Production in Boson-Gluon Fusion DIS

NASA Astrophysics Data System (ADS)

Boroun, G. R.; Khanehzar, A.; Boustanchi Kashan, M.

2017-11-01

In this paper, we study the top content of nucleon by analyzing azimuthal asymmetries in lepton-nucleon deep inelastic scattering (DIS), also we search for the Higgs boson associated production channel, t\\bar{t}H, at the large hadron-electron collider (LHeC) caused by boson-gluon fusion (BGF) contribution. We use azimuthal asymmetries in {γ }* Q cross sections in terms of helicity contributions to semi-inclusive deep inelastic scattering to investigate numerical properties of the \\cos 2φ distribution. We conclude that measuring azimuthal distributions caused by intrinsic heavy quark production can directly probe heavy quarks inside nucleon. Moreover, in order to estimate the probability of producing the Higgs boson, we suggest another approach in the framework of calculating t\\bar{t} cross section in boson-gluon fusion mechanism. Finally, we can confirm that this observed massive particle is referred to Higgs boson produced by fermion loop.

Varying self-inductance and energy storage in a sheared force-free arcade. [of coronal loops

NASA Technical Reports Server (NTRS)

Zuccarello, F.; Burm, H.; Kuperus, M.; Raadu, M.; Spicer, D. S.

1987-01-01

An electric circuit analogy is used to model the build-up and storage of magnetic energy in the coronal loops known to exist in the atmosphere of the sun. The present parameterization of magnetic energy storage in an electric circuit analog uses a bulk current I flowing in the circuit and a self-inductance L. Because the self-inductance is determined by the geometry of the magnetic configuration any change in its dimensions will change L. If L is increased, the amount of magnetic energy stored and the rate at which magnetic energy is stored are both increased. One way of increasing L is to shear the magnetic field lines and increase their effective geometrical length. Using the force-free field approximation for a magnetic arcade whose field lines are sheared by photospheric motions, it is demonstrated that the increase of magnetic energy is initially due to the increase of the current intensity I and later mainly due to the increase of the self-inductance.

Quantum Wronskian approach to six-point gluon scattering amplitudes at strong coupling

NASA Astrophysics Data System (ADS)

Hatsuda, Yasuyuki; Ito, Katsushi; Satoh, Yuji; Suzuki, Junji

2014-08-01

We study the six-point gluon scattering amplitudes in = 4 super Yang-Mills theory at strong coupling based on the twisted ℤ4-symmetric integrable model. The lattice regularization allows us to derive the associated thermodynamic Bethe ansatz (TBA) equations as well as the functional relations among the Q-/T-/Y-functions. The quantum Wronskian relation for the Q-/T-functions plays an important role in determining a series of the expansion coefficients of the T-/Y-functions around the UV limit, including the dependence on the twist parameter. Studying the CFT limit of the TBA equations, we derive the leading analytic expansion of the remainder function for the general kinematics around the limit where the dual Wilson loops become regular-polygonal. We also compare the rescaled remainder functions at strong coupling with those at two, three and four loops, and find that they are close to each other along the trajectories parameterized by the scale parameter of the integrable model.

PARP-1 inhibition as a targeted strategy to treat Ewing's sarcoma

PubMed Central

Brenner, J. Chad; Feng, Felix Y.; Han, Sumin; Patel, Sonam; Goyal, Siddharth V.; Bou-Maroun, Laura M.; Liu, Meilan; Lonigro, Robert; Prensner, John R.; Tomlins, Scott A.; Chinnaiyan, Arul M.

2012-01-01

Ewing's sarcoma family tumors (ESFTs) are aggressive malignancies which frequently harbor characteristic EWS-FLI1 or EWS-ERG genomic fusions. Here we report that these fusion products interact with the DNA damage response protein and transcriptional co-regulator PARP-1. ESFT cells, primary tumor xenografts and tumor metastases were all highly sensitive to PARP1 inhibition. Addition of a PARP1 inhibitor to the second-line chemotherapeutic agent temozolamide resulted in complete responses of all treated tumors in an EWS-FLI1-driven mouse xenograft model of ESFT. Mechanistic investigations revealed that DNA damage induced by expression of EWS-FLI1 or EWS-ERG fusion genes was potentiated by PARP1 inhibition in ESFT cell lines. Notably, EWS-FLI1 fusion genes acted in a positive feedback loop to maintain the expression of PARP1, which was required for EWS-FLI-mediated transcription, thereby enforcing oncogene-dependent sensitivity to PARP-1 inhibition. Together, our findings offer a strong preclinical rationale to target the EWS-FLI1: PARP1 intersection as a therapeutic strategy to improve the treatment of Ewing's sarcoma family tumors. PMID:22287547

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madu, Ikenna G.; Belouzard, Sandrine; Whittaker, Gary R., E-mail: grw7@cornell.ed

The S2 domain of the coronavirus spike (S) protein is known to be responsible for mediating membrane fusion. In addition to a well-recognized cleavage site at the S1-S2 boundary, a second proteolytic cleavage site has been identified in the severe acute respiratory syndrome coronavirus (SARS-CoV) S2 domain (R797). C-terminal to this S2 cleavage site is a conserved region flanked by cysteine residues C822 and C833. Here, we investigated the importance of this well conserved region for SARS-CoV S-mediated fusion activation. We show that the residues between C822-C833 are well conserved across all coronaviruses. Mutagenic analysis of SARS-CoV S, combined withmore » cell-cell fusion and pseudotyped virion infectivity assays, showed a critical role for the core-conserved residues C822, D830, L831, and C833. Based on available predictive models, we propose that the conserved domain flanked by cysteines 822 and 833 forms a loop structure that interacts with components of the SARS-CoV S trimer to control the activation of membrane fusion.« less

Posterior spinal osteosynthesis for cervical fracture/dislocation using a flexible multistrand cable system: technical note.

PubMed

Huhn, S L; Wolf, A L; Ecklund, J

1991-12-01

Cervical instability secondary to fracture/dislocation or traumatic subluxation involving the posterior elements may be treated by a variety of fusion techniques. The rigidity of the stainless steel wires used in posterior cervical fusions often leads to difficulty with insertion, adequate tension, and conformation of the graft construct. This report describes a technique of posterior cervical fusion employing a wire system using flexible stainless steel cables. The wire consists of a flexible, 49-strand, stainless steel cable connected on one end to a short, malleable, blunt leader with the opposite end connected to a small islet. The cable may be used in occipitocervical, atlantoaxial, facet-to-spinous process, and interspinous fusion techniques. The cable loop is secured by using a tension/crimper device that sets the desired tension in the cable. In addition to superior biomechanical strength, the flexibility of the cable allows greater ease of insertion and tension adjustment. In terms of direct operative instrumentation in posterior cervical arthrodesis, involving both the upper and lower cervical spine, the cable system appears to be a safe and efficient alternative to monofilament wires.

MagLIF scaling on Z and future machines

NASA Astrophysics Data System (ADS)

Slutz, Stephen; Stygar, William; Gomez, Matthew; Campbell, Edward; Peterson, Kyle; Sefkow, Adam; Sinars, Daniel; Vesey, Roger

2015-11-01

The MagLIF (Magnetized Liner Inertial Fusion) concept [S.A. Slutz et al Phys. Plasmas 17, 056303, 2010] has demonstrated [M.R. Gomez et al., PRL 113, 155003, 2014] fusion-relevant plasma conditions on the Z machine. We present 2D numerical simulations of the scaling of MagLIF on Z indicating that deuterium/tritium (DT) fusion yields greater than 100 kJ could be possible on Z when operated at a peak current of 25 MA. Much higher yields are predicted for MagLIF driven with larger peak currents. Two high performance pulsed-power machines (Z300 and Z800) have been designed based on Linear Transformer Driver (LTD) technology. The Z300 design would provide approximately 48 MA to a MagLIF load, while Z800 would provide about 66 MA. We used a parameterized Thevenin equivalent circuit to drive a series of 1D and 2D numerical simulations with currents between and beyond these two designs. Our simulations indicate that 5-10 MJ yields may be possible with Z300, while yields of about 1 GJ may be possible with Z800. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Double peak searches for scalar and pseudoscalar resonances at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carena, Marcela; Huang, Peisi; Ismail, Ahmed

2016-12-01

Many new physics models contain a neutral scalar resonance that can be predominantly produced via gluon fusion through loops. In such a case, there could be important effects of additional particles, that in turn may hadronize before decaying and form bound states. This interesting possibility may lead to novel signatures with double peaks that can be searched for at the LHC. We study the phenomenology of double peak searches in diboson final states from loop-induced production and decay of a new neutral spin-0 resonance at the LHC. The loop-induced couplings should be mediated by particles carrying color and electroweak chargemore » that after forming bound states will induce a second peak in the diboson invariant mass spectrum near twice their mass. A second peak could be present via loop-induced couplings into gg (dijet),gamma gamma and Z gamma final states as well as in the WW and ZZ channels for the case of a pseudoscalar resonance or for scalars with suppressed tree-level coupling to gauge bosons« less

Double peak searches for scalar and pseudoscalar resonances at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carena, Marcela; Huang, Peisi; Ismail, Ahmed

2016-12-01

Many new physics models contain a neutral scalar resonance that can be predominantly produced via gluon fusion through loops. In such a case, there could be important effects of additional particles, that in turn may hadronize before decaying and form bound states. This interesting possibility may lead to novel signatures with double peaks that can be searched for at the LHC. We study the phenomenology of double peak searches in diboson final states from loop induced production and decay of a new neutral spin-0 resonance at the LHC. The loop-induced couplings should be mediated by particles carrying color and electroweak charge that after forming bound states will induce a second peak in the diboson invariant mass spectrum near twice their mass. As a result, a second peak could be present via loop-induced couplings intomore » $gg$ (dijet), $$\\gamma\\gamma$$ and $$Z\\gamma$$ final states as well as in the $WW$ and $ZZ$ channels for the case of a pseudo-scalar resonance or for scalars with suppressed tree-level coupling to gauge bosons.« less

Higgs production via gluon fusion in k{sub T} factorisation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hautmann, F.; Jung, H.; Pandis, V.

2011-07-15

Theoretical studies of Higgs production via gluon fusion are frequently carried out in the limit where the top quark mass is much larger than the Higgs mass, an approximation which reduces the top quark loop to an effective vertex. We present a numerical analysis of the error thus introduced by performing a Monte Carlo calculation for gg{yields}h in k{sub T}-factorisation, using the parton shower generator CASCADE. By examining both inclusive and exclusive quantities, we find that retaining the top-mass dependence results in only a small enhancement of the cross-section. We then proceed to compare CASCADE to the collinear Monte Carlosmore » PYTHIA, MC-NLO and POWHEG.« less

A Broadly Flavivirus Cross-Neutralizing Monoclonal Antibody that Recognizes a Novel Epitope within the Fusion Loop of E Protein

PubMed Central

Jiang, Tao; Wang, Hua-Jing; Yang, Hai-ou; Tan, Weng-Long; Liu, Ran; Yu, Man; Ge, Bao-Xue; Zhu, Qing-Yu; Qin, E-De; Guo, Ya-Jun; Qin, Cheng-Feng

2011-01-01

Flaviviruses are a group of human pathogenic, enveloped RNA viruses that includes dengue (DENV), yellow fever (YFV), West Nile (WNV), and Japanese encephalitis (JEV) viruses. Cross-reactive antibodies against Flavivirus have been described, but most of them are generally weakly neutralizing. In this study, a novel monoclonal antibody, designated mAb 2A10G6, was determined to have broad cross-reactivity with DENV 1–4, YFV, WNV, JEV, and TBEV. Phage-display biopanning and structure modeling mapped 2A10G6 to a new epitope within the highly conserved flavivirus fusion loop peptide, the 98DRXW101 motif. Moreover, in vitro and in vivo experiments demonstrated that 2A10G6 potently neutralizes DENV 1–4, YFV, and WNV and confers protection from lethal challenge with DENV 1–4 and WNV in murine model. Furthermore, functional studies revealed that 2A10G6 blocks infection at a step after viral attachment. These results define a novel broadly flavivirus cross-reactive mAb with highly neutralizing activity that can be further developed as a therapeutic agent against severe flavivirus infections in humans. PMID:21264311

Multiscale integral analysis of a HT leakage in a fusion nuclear power plant

NASA Astrophysics Data System (ADS)

Velarde, M.; Fradera, J.; Perlado, J. M.; Zamora, I.; Martínez-Saban, E.; Colomer, C.; Briani, P.

2016-05-01

The present work presents an example of the application of an integral methodology based on a multiscale analysis that covers the whole tritium cycle within a nuclear fusion power plant, from a micro scale, analyzing key components where tritium is leaked through permeation, to a macro scale, considering its atmospheric transport. A leakage from the Nuclear Power Plants, (NPP) primary to the secondary side of a heat exchanger (HEX) is considered for the present example. Both primary and secondary loop coolants are assumed to be He. Leakage is placed inside the HEX, leaking tritium in elementary tritium (HT) form to the secondary loop where it permeates through the piping structural material to the exterior. The Heating Ventilation and Air Conditioning (HVAC) system removes the leaked tritium towards the NPP exhaust. The HEX is modelled with system codes and coupled to Computational Fluid Dynamic (CFD) to account for tritium dispersion inside the nuclear power plants buildings and in site environment. Finally, tritium dispersion is calculated with an atmospheric transport code and a dosimetry analysis is carried out. Results show how the implemented methodology is capable of assessing the impact of tritium from the microscale to the atmospheric scale including the dosimetric aspect.

HIT-SI Injector Voltage Measurements Using Injector Langmuir Probes

NASA Astrophysics Data System (ADS)

Aboul Hosn, Rabih; Smith, Roger; Jarboe, Thomas

2006-10-01

A pair of Langmuir probe arrays have been designed and built to measure floating potentials of the plasma at the injector mouth of the HIT-SI device. The Helicity Injected Torus using Steady Inductive Helicity Injection (HIT-SI) [1,2] is a ``bow tie'' spheromak using an electrodeless formation and sustainment concept. HIT-SI is powered by two inductive helicity injectors operated in quadrature to maintain a constant helicity injection rate. The electric probes consist of an array of four floating potential Langmuir probes measuring the voltage distribution in each injector from the shell to midpoint of the injector mouth. The probe measurements combine to determine the part of the injector loop voltage driving the n = 0 spheromak equilibrium region. Preliminary data suggest the spheromak voltage is the loop voltage minus the nearly constant injector voltage of 150-180 volts. These probe data will be used to calculate the helicity decay time of the spheromak. [1] T. R. Jarboe. Steady inductive helicity injection and its application to a high-beta spheromak. Fusion Technology, 36(1):85--91, July 1999. [2] P.E.Sieck et al., ``Demonstration of Steady Inductive Helicity Injection'', Nuc. Fusion, in press (2006).

Control of Warm Compression Stations Using Model Predictive Control: Simulation and Experimental Results

NASA Astrophysics Data System (ADS)

Bonne, F.; Alamir, M.; Bonnay, P.

2017-02-01

This paper deals with multivariable constrained model predictive control for Warm Compression Stations (WCS). WCSs are subject to numerous constraints (limits on pressures, actuators) that need to be satisfied using appropriate algorithms. The strategy is to replace all the PID loops controlling the WCS with an optimally designed model-based multivariable loop. This new strategy leads to high stability and fast disturbance rejection such as those induced by a turbine or a compressor stop, a key-aspect in the case of large scale cryogenic refrigeration. The proposed control scheme can be used to achieve precise control of pressures in normal operation or to avoid reaching stopping criteria (such as excessive pressures) under high disturbances (such as a pulsed heat load expected to take place in future fusion reactors, expected in the cryogenic cooling systems of the International Thermonuclear Experimental Reactor ITER or the Japan Torus-60 Super Advanced fusion experiment JT-60SA). The paper details the simulator used to validate this new control scheme and the associated simulation results on the SBTs WCS. This work is partially supported through the French National Research Agency (ANR), task agreement ANR-13-SEED-0005.

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web

USGS Publications Warehouse

Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.

2004-01-01

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

Lifting SU(2) spin networks to projected spin networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dupuis, Maiete; Livine, Etera R.

2010-09-15

Projected spin network states are the canonical basis of quantum states of geometry for the recent EPRL-FK spinfoam models for quantum gravity introduced by Engle-Pereira-Rovelli-Livine and Freidel-Krasnov. They are functionals of both the Lorentz connection and the time-normal field. We analyze in detail the map from these projected spin networks to the standard SU(2) spin networks of loop quantum gravity. We show that this map is not one to one and that the corresponding ambiguity is parameterized by the Immirzi parameter. We conclude with a comparison of the scalar products between projected spin networks and SU(2) spin network states.

A preference-ordered discrete-gaming approach to air-combat analysis

NASA Technical Reports Server (NTRS)

Kelley, H. J.; Lefton, L.

1978-01-01

An approach to one-on-one air-combat analysis is described which employs discrete gaming of a parameterized model featuring choice between several closed-loop control policies. A preference-ordering formulation due to Falco is applied to rational choice between outcomes: win, loss, mutual capture, purposeful disengagement, draw. Approximate optimization is provided by an active-cell scheme similar to Falco's obtained by a 'backing up' process similar to that of Kopp. The approach is designed primarily for short-duration duels between craft with large-envelope weaponry. Some illustrative computations are presented for an example modeled using constant-speed vehicles and very rough estimation of energy shifts.

New class of control laws for robotic manipulators. I - Nonadaptive case. II - Adaptive case

NASA Technical Reports Server (NTRS)

Wen, John T.; Bayard, David S.

1988-01-01

A new class of exponentially stabilizing control laws for joint level control of robot arms is discussed. Closed-loop exponential stability has been demonstrated for both the set point and tracking control problems by a slight modification of the energy Lyapunov function and the use of a lemma which handles third-order terms in the Lyapunov function derivatives. In the second part, these control laws are adapted in a simple fashion to achieve asymptotically stable adaptive control. The analysis addresses the nonlinear dynamics directly without approximation, linearization, or ad hoc assumptions, and uses a parameterization based on physical (time-invariant) quantities.

Developing Remote Sensing Products for Monitoring and Modeling Great Lakes Coastal Wetland Vulnerability to Climate Change and Land Use

NASA Astrophysics Data System (ADS)

Bourgeau-Chavez, L. L.; Miller, M. E.; Battaglia, M.; Banda, E.; Endres, S.; Currie, W. S.; Elgersma, K. J.; French, N. H. F.; Goldberg, D. E.; Hyndman, D. W.

2014-12-01

Spread of invasive plant species in the coastal wetlands of the Great Lakes is degrading wetland habitat, decreasing biodiversity, and decreasing ecosystem services. An understanding of the mechanisms of invasion is crucial to gaining control of this growing threat. To better understand the effects of land use and climatic drivers on the vulnerability of coastal zones to invasion, as well as to develop an understanding of the mechanisms of invasion, research is being conducted that integrates field studies, process-based ecosystem and hydrological models, and remote sensing. Spatial data from remote sensing is needed to parameterize the hydrological model and to test the outputs of the linked models. We will present several new remote sensing products that are providing important physiological, biochemical, and landscape information to parameterize and verify models. This includes a novel hybrid radar-optical technique to delineate stands of invasives, as well as natural wetland cover types; using radar to map seasonally inundated areas not hydrologically connected; and developing new algorithms to estimate leaf area index (LAI) using Landsat. A coastal map delineating wetland types including monocultures of the invaders (Typha spp. and Phragmites austrailis) was created using satellite radar (ALOS PALSAR, 20 m resolution) and optical data (Landsat 5, 30 m resolution) fusion from multiple dates in a Random Forests classifier. These maps provide verification of the integrated model showing areas at high risk of invasion. For parameterizing the hydrological model, maps of seasonal wetness are being developed using spring (wet) imagery and differencing that with summer (dry) imagery to detect the seasonally wet areas. Finally, development of LAI remote sensing high resolution algorithms for uplands and wetlands is underway. LAI algorithms for wetlands have not been previously developed due to the difficulty of a water background. These products are being used to improve the hydrological model through higher resolution products and parameterization of variables that have previously been largely unknown.

Model based multivariable controller for large scale compression stations. Design and experimental validation on the LHC 18KW cryorefrigerator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bonne, François; Bonnay, Patrick; Alamir, Mazen

2014-01-29

In this paper, a multivariable model-based non-linear controller for Warm Compression Stations (WCS) is proposed. The strategy is to replace all the PID loops controlling the WCS with an optimally designed model-based multivariable loop. This new strategy leads to high stability and fast disturbance rejection such as those induced by a turbine or a compressor stop, a key-aspect in the case of large scale cryogenic refrigeration. The proposed control scheme can be used to have precise control of every pressure in normal operation or to stabilize and control the cryoplant under high variation of thermal loads (such as a pulsedmore » heat load expected to take place in future fusion reactors such as those expected in the cryogenic cooling systems of the International Thermonuclear Experimental Reactor ITER or the Japan Torus-60 Super Advanced fusion experiment JT-60SA). The paper details how to set the WCS model up to synthesize the Linear Quadratic Optimal feedback gain and how to use it. After preliminary tuning at CEA-Grenoble on the 400W@1.8K helium test facility, the controller has been implemented on a Schneider PLC and fully tested first on the CERN's real-time simulator. Then, it was experimentally validated on a real CERN cryoplant. The efficiency of the solution is experimentally assessed using a reasonable operating scenario of start and stop of compressors and cryogenic turbines. This work is partially supported through the European Fusion Development Agreement (EFDA) Goal Oriented Training Program, task agreement WP10-GOT-GIRO.« less

Model based multivariable controller for large scale compression stations. Design and experimental validation on the LHC 18KW cryorefrigerator

NASA Astrophysics Data System (ADS)

Bonne, François; Alamir, Mazen; Bonnay, Patrick; Bradu, Benjamin

2014-01-01

In this paper, a multivariable model-based non-linear controller for Warm Compression Stations (WCS) is proposed. The strategy is to replace all the PID loops controlling the WCS with an optimally designed model-based multivariable loop. This new strategy leads to high stability and fast disturbance rejection such as those induced by a turbine or a compressor stop, a key-aspect in the case of large scale cryogenic refrigeration. The proposed control scheme can be used to have precise control of every pressure in normal operation or to stabilize and control the cryoplant under high variation of thermal loads (such as a pulsed heat load expected to take place in future fusion reactors such as those expected in the cryogenic cooling systems of the International Thermonuclear Experimental Reactor ITER or the Japan Torus-60 Super Advanced fusion experiment JT-60SA). The paper details how to set the WCS model up to synthesize the Linear Quadratic Optimal feedback gain and how to use it. After preliminary tuning at CEA-Grenoble on the 400W@1.8K helium test facility, the controller has been implemented on a Schneider PLC and fully tested first on the CERN's real-time simulator. Then, it was experimentally validated on a real CERN cryoplant. The efficiency of the solution is experimentally assessed using a reasonable operating scenario of start and stop of compressors and cryogenic turbines. This work is partially supported through the European Fusion Development Agreement (EFDA) Goal Oriented Training Program, task agreement WP10-GOT-GIRO.

Infection of CD4{sup +} T lymphocytes by the human T cell leukemia virus type 1 is mediated by the glucose transporter GLUT-1: Evidence using antibodies specific to the receptor's large extracellular domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Qingwen; Agrawal, Lokesh; VanHorn-Ali, Zainab

2006-05-25

To analyze HTLV-1 cytotropism, we developed a highly sensitive vaccinia virus-based assay measuring activation of a reporter gene upon fusion of two distinct cell populations. We used this system in a functional cDNA screening to isolate and confirm that the glucose transporter protein 1 (GLUT-1) is a receptor for HTLV-1. GLUT-1 is a ubiquitously expressed plasma membrane glycoprotein with 12 transmembrane domains and 6 extracellular loops (ECL). We demonstrate for the first time that peptide antibodies (GLUT-IgY) raised in chicken to the large extracellular loop (ECL1) detect GLUT-1 at the cell surface and inhibit envelope (Env)-mediated fusion and infection. Efficientmore » GLUT-IgY staining was detected with peripheral blood CD4{sup +} lymphocytes purified by positive selection. Further, GLUT-IgY caused efficient inhibition of Env-mediated fusion and infection of CD4{sup +} T and significantly lower inhibition of CD8{sup +} T lymphocytes. The specificity of GLUT-IgY antibodies to GLUT-1 was demonstrated by ECL1 peptide competition studies. Grafting ECL1 of GLUT-1 onto the receptor-negative GLUT-3 conferred significant receptor activity. In contrast, grafting ECL1 of GLUT-3 onto GLUT-1 resulted in a significant loss of the receptor activity. The ECL1-mediated receptor activity was efficiently blocked with four different human monoclonal antibody (HMab) to HTLV-1 Env. The ECL1-derived peptide blocked HTLV-1 Env-mediated fusion with several nonhuman mammalian cell lines. The results demonstrate the utilization of cell surface GLUT-1 in HTLV-1 infection of CD4{sup +} T lymphocytes and implicate a critical role for the ECL1 region in viral tropism.« less

Membrane-spanning lipids for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer

PubMed Central

Schwarzmann, Günter; Breiden, Bernadette; Sandhoff, Konrad

2015-01-01

A Förster resonance energy transfer-based fusion and transfer assay was developed to study, in model membranes, protein-mediated membrane fusion and intermembrane lipid transfer of fluorescent sphingolipid analogs. For this assay, it became necessary to apply labeled reporter molecules that are resistant to spontaneous as well as protein-mediated intermembrane transfer. The novelty of this assay is the use of nonextractable fluorescent membrane-spanning bipolar lipids. Starting from the tetraether lipid caldarchaeol, we synthesized fluorescent analogs with fluorophores at both polar ends. In addition, we synthesized radioactive glycosylated caldarchaeols. These labeled lipids were shown to stretch through bilayer membranes rather than to loop within a single lipid layer of liposomes. More important, the membrane-spanning lipids (MSLs) in contrast to phosphoglycerides proved to be nonextractable by proteins. We could show that the GM2 activator protein (GM2AP) is promiscuous with respect to glycero- and sphingolipid transfer. Saposin (Sap) B also transferred sphingolipids albeit with kinetics different from GM2AP. In addition, we could unambiguously show that the recombinant activator protein Sap C x His6 induced membrane fusion rather than intermembrane lipid transfer. These findings showed that these novel MSLs, in contrast with fluorescent phosphoglycerolipids, are well suited for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer. PMID:26269359

INFORM Lab: a testbed for high-level information fusion and resource management

NASA Astrophysics Data System (ADS)

Valin, Pierre; Guitouni, Adel; Bossé, Eloi; Wehn, Hans; Happe, Jens

2011-05-01

DRDC Valcartier and MDA have created an advanced simulation testbed for the purpose of evaluating the effectiveness of Network Enabled Operations in a Coastal Wide Area Surveillance situation, with algorithms provided by several universities. This INFORM Lab testbed allows experimenting with high-level distributed information fusion, dynamic resource management and configuration management, given multiple constraints on the resources and their communications networks. This paper describes the architecture of INFORM Lab, the essential concepts of goals and situation evidence, a selected set of algorithms for distributed information fusion and dynamic resource management, as well as auto-configurable information fusion architectures. The testbed provides general services which include a multilayer plug-and-play architecture, and a general multi-agent framework based on John Boyd's OODA loop. The testbed's performance is demonstrated on 2 types of scenarios/vignettes for 1) cooperative search-and-rescue efforts, and 2) a noncooperative smuggling scenario involving many target ships and various methods of deceit. For each mission, an appropriate subset of Canadian airborne and naval platforms are dispatched to collect situation evidence, which is fused, and then used to modify the platform trajectories for the most efficient collection of further situation evidence. These platforms are fusion nodes which obey a Command and Control node hierarchy.

Low-Power Embedded DSP Core for Communication Systems

NASA Astrophysics Data System (ADS)

Tsao, Ya-Lan; Chen, Wei-Hao; Tan, Ming Hsuan; Lin, Maw-Ching; Jou, Shyh-Jye

2003-12-01

This paper proposes a parameterized digital signal processor (DSP) core for an embedded digital signal processing system designed to achieve demodulation/synchronization with better performance and flexibility. The features of this DSP core include parameterized data path, dual MAC unit, subword MAC, and optional function-specific blocks for accelerating communication system modulation operations. This DSP core also has a low-power structure, which includes the gray-code addressing mode, pipeline sharing, and advanced hardware looping. Users can select the parameters and special functional blocks based on the character of their applications and then generating a DSP core. The DSP core has been implemented via a cell-based design method using a synthesizable Verilog code with TSMC 0.35[InlineEquation not available: see fulltext.]m SPQM and 0.25[InlineEquation not available: see fulltext.]m 1P5M library. The equivalent gate count of the core area without memory is approximately 50 k. Moreover, the maximum operating frequency of a[InlineEquation not available: see fulltext.] version is 100 MHz (0.35[InlineEquation not available: see fulltext.]m) and 140 MHz (0.25[InlineEquation not available: see fulltext.]m).

The anisotropic Wilson gauge action

NASA Astrophysics Data System (ADS)

Klassen, Timothy R.

1998-11-01

Anisotropic lattices, with a temporal lattice spacing smaller than the spatial one, allow precision Monte Carlo calculations of problems that are difficult to study otherwise: heavy quarks, glueballs, hybrids, and high temperature thermodynamics, for example. We here perform the first step required for such studies with the (quenched) Wilson gauge action, namely, the determination of the renormalized anisotropy Ξ as a function of the bare anisotropy Ξ0 and the coupling. By, essentially, comparing the finite-volume heavy quark potential where the quarks are separated along a spatial direction with that where they are separated along the time direction, we determine the relation between Ξ and Ξ0 to a fraction of 1% for weak and to 1% for strong coupling. We present a simple parameterization of this relation for 1 ⩽ Ξ ⩽ 6 and 5.5 ⩽ β ⩽ ∞, which incorporates the known one-loop result and reproduces our non-perturbative determinations within errors. Besides solving the problem of how to choose the bare anisotropies if one wants to take the continuum limit at fixed renormalized anisotropy, this parameterization also yields accurate estimates of the derivative {∂Ξ 0}/{∂Ξ} needed in thermodynamic studies.

Higher order corrections to mixed QCD-EW contributions to Higgs boson production in gluon fusion

NASA Astrophysics Data System (ADS)

Bonetti, Marco; Melnikov, Kirill; Tancredi, Lorenzo

2018-03-01

We present an estimate of the next-to-leading-order (NLO) QCD corrections to mixed QCD-electroweak contributions to the Higgs boson production cross section in gluon fusion, combining the recently computed three-loop virtual corrections and the approximate treatment of real emission in the soft approximation. We find that the NLO QCD corrections to the mixed QCD-electroweak contributions are nearly identical to NLO QCD corrections to QCD Higgs production. Our result confirms an earlier estimate of these O (α αs2) effects by Anastasiou et al. [J. High Energy Phys. 04 (2009) 003, 10.1088/1126-6708/2009/04/003] and provides further support for the factorization approximation of QCD and electroweak corrections.

Assessment of the MHD capability in the ATHENA code using data from the ALEX (Argonne Liquid Metal Experiment) facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roth, P.A.

1988-10-28

The ATHENA (Advanced Thermal Hydraulic Energy Network Analyzer) code is a system transient analysis code with multi-loop, multi-fluid capabilities, which is available to the fusion community at the National Magnetic Fusion Energy Computing Center (NMFECC). The work reported here assesses the ATHENA magnetohydrodynamic (MHD) pressure drop model for liquid metals flowing through a strong magnetic field. An ATHENA model was developed for two simple geometry, adiabatic test sections used in the Argonne Liquid Metal Experiment (ALEX) at Argonne National Laboratory (ANL). The pressure drops calculated by ATHENA agreed well with the experimental results from the ALEX facility. 13 refs., 4more » figs., 2 tabs.« less

Neutrino catalyzed diphoton excess

DOE PAGES

Chao, Wei

2016-08-16

In this paper we explain the 750 GeV diphoton resonance observed at the run-2 LHC as a scalar singlet S, that plays a key role in generating tiny but nonzero Majorana neutrino masses. The model contains four electroweak singlets: two leptoquarks, a singly charged scalar and a neutral scalar S. Majorana neutrino masses might be generated at the two-loop level as S gets nonzero vacuum expectation value. S can be produced at the LHC through the gluon fusion and decays into diphoton with charged scalars running in the loop. The model fits perfectly with a narrow width of the resonance.more » Finally, constraints on the model are investigated, which shows a negligible mixing between the resonance and the standard model Higgs boson.« less

Immunogenicity of a recombinant fusion protein of tandem repeat epitopes of foot-and-mouth disease virus type Asia 1 for guinea pigs.

PubMed

Zhang, Q; Yang, Y Q; Zhang, Z Y; Li, L; Yan, W Y; Jiang, W J; Xin, A G; Lei, C X; Zheng, Z X

2002-01-01

In this study, the sequences of capsid protein VPI regions of YNAs1.1 and YNAs1.2 isolates of foot-and-mouth disease virus (FMDV) were analyzed and a peptide containing amino acids (aa) 133-158 of VP1 and aa 20-34 of VP4 of FMDV type Asia I was assumed to contain B and T cell epitopes, because it is hypervariable and includes a cell attachment site RGD located in the G-H loop. The DNA fragments encoding aa 133-158 of VP1 and aa 20-34 of VP4 of FMDV type Asia 1 were chemically synthesized and ligated into a tandem repeat of aa 133-158-20 approximately 34-133-158. In order to enhance its immunogenicity, the tandem repeat was inserted downstream of the beta-galactosidase gene in the expression vector pWR590. This insertion yielded a recombinant expression vector pAS1 encoding the fusion protein. The latter reacted with sera from FMDV type Asia 1-infected animals in vitro and elicited high levels of neutralizing antibodies in guinea pigs. The T cell proliferation in immunized animals increased following stimulation with the fusion protein. It is reported for the first time that a recombinant fusion protein vaccine was produced using B and T cell epitopes of FMDV type Asia 1 and that this fusion protein was immunogenic. The fusion protein reported here can serve as a candidate of fusion epitopes for design of a vaccine against FMDV type Asia 1.

Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc

PubMed Central

Stettner, Eva; Jeffers, Scott Allen; Pérez-Vargas, Jimena; Pehau-Arnaudet, Gerard; Tortorici, M. Alejandra; Jestin, Jean-Luc; England, Patrick; Tischler, Nicole D.; Rey, Félix A.

2016-01-01

Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic β-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha- and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single “fusion loop”. We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal “tail” that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens. PMID:27783711

Type II integral membrane protein, TM of J paramyxovirus promotes cell-to-cell fusion.

PubMed

Li, Zhuo; Hung, Cher; Paterson, Reay G; Michel, Frank; Fuentes, Sandra; Place, Ryan; Lin, Yuan; Hogan, Robert J; Lamb, Robert A; He, Biao

2015-10-06

Paramyxoviruses include many important animal and human pathogens. Most paramyxoviruses have two integral membrane proteins: fusion protein (F) and attachment proteins hemagglutinin, hemagglutinin-neuraminidase, or glycoprotein (G), which are critical for viral entry into cells. J paramyxovirus (JPV) encodes four integral membrane proteins: F, G, SH, and transmembrane (TM). The function of TM is not known. In this work, we have generated a viable JPV lacking TM (JPV∆TM). JPV∆TM formed opaque plaques compared with JPV. Quantitative syncytia assays showed that JPV∆TM was defective in promoting cell-to-cell fusion (i.e., syncytia formation) compared with JPV. Furthermore, cells separately expressing F, G, TM, or F plus G did not form syncytia whereas cells expressing F plus TM formed some syncytia. However, syncytia formation was much greater with coexpression of F, G, and TM. Biochemical analysis indicates that F, G, and TM interact with each other. A small hydrophobic region in the TM ectodomain from amino acid residues 118 to 132, the hydrophobic loop (HL), was important for syncytial promotion, suggesting that the TM HL region plays a critical role in cell-to-cell fusion.

Sensor Fusion to Estimate the Depth and Width of the Weld Bead in Real Time in GMAW Processes

PubMed Central

Sampaio, Renato Coral; Vargas, José A. R.

2018-01-01

The arc welding process is widely used in industry but its automatic control is limited by the difficulty in measuring the weld bead geometry and closing the control loop on the arc, which has adverse environmental conditions. To address this problem, this work proposes a system to capture the welding variables and send stimuli to the Gas Metal Arc Welding (GMAW) conventional process with a constant voltage power source, which allows weld bead geometry estimation with an open-loop control. Dynamic models of depth and width estimators of the weld bead are implemented based on the fusion of thermographic data, welding current and welding voltage in a multilayer perceptron neural network. The estimators were trained and validated off-line with data from a novel algorithm developed to extract the features of the infrared image, a laser profilometer was implemented to measure the bead dimensions and an image processing algorithm that measures depth by making a longitudinal cut in the weld bead. These estimators are optimized for embedded devices and real-time processing and were implemented on a Field-Programmable Gate Array (FPGA) device. Experiments to collect data, train and validate the estimators are presented and discussed. The results show that the proposed method is useful in industrial and research environments. PMID:29570698

Sensor Fusion to Estimate the Depth and Width of the Weld Bead in Real Time in GMAW Processes.

PubMed

Bestard, Guillermo Alvarez; Sampaio, Renato Coral; Vargas, José A R; Alfaro, Sadek C Absi

2018-03-23

The arc welding process is widely used in industry but its automatic control is limited by the difficulty in measuring the weld bead geometry and closing the control loop on the arc, which has adverse environmental conditions. To address this problem, this work proposes a system to capture the welding variables and send stimuli to the Gas Metal Arc Welding (GMAW) conventional process with a constant voltage power source, which allows weld bead geometry estimation with an open-loop control. Dynamic models of depth and width estimators of the weld bead are implemented based on the fusion of thermographic data, welding current and welding voltage in a multilayer perceptron neural network. The estimators were trained and validated off-line with data from a novel algorithm developed to extract the features of the infrared image, a laser profilometer was implemented to measure the bead dimensions and an image processing algorithm that measures depth by making a longitudinal cut in the weld bead. These estimators are optimized for embedded devices and real-time processing and were implemented on a Field-Programmable Gate Array (FPGA) device. Experiments to collect data, train and validate the estimators are presented and discussed. The results show that the proposed method is useful in industrial and research environments.

IFMIF: overview of the validation activities

NASA Astrophysics Data System (ADS)

Knaster, J.; Arbeiter, F.; Cara, P.; Favuzza, P.; Furukawa, T.; Groeschel, F.; Heidinger, R.; Ibarra, A.; Matsumoto, H.; Mosnier, A.; Serizawa, H.; Sugimoto, M.; Suzuki, H.; Wakai, E.

2013-11-01

The Engineering Validation and Engineering Design Activities (EVEDA) for the International Fusion Materials Irradiation Facility (IFMIF), an international collaboration under the Broader Approach Agreement between Japan Government and EURATOM, aims at allowing a rapid construction phase of IFMIF in due time with an understanding of the cost involved. The three main facilities of IFMIF (1) the Accelerator Facility, (2) the Target Facility and (3) the Test Facility are the subject of validation activities that include the construction of either full scale prototypes or smartly devised scaled down facilities that will allow a straightforward extrapolation to IFMIF needs. By July 2013, the engineering design activities of IFMIF matured with the delivery of an Intermediate IFMIF Engineering Design Report (IIEDR) supported by experimental results. The installation of a Linac of 1.125 MW (125 mA and 9 MeV) of deuterons started in March 2013 in Rokkasho (Japan). The world's largest liquid Li test loop is running in Oarai (Japan) with an ambitious experimental programme for the years ahead. A full scale high flux test module that will house ∼1000 small specimens developed jointly in Europe and Japan for the Fusion programme has been constructed by KIT (Karlsruhe) together with its He gas cooling loop. A full scale medium flux test module to carry out on-line creep measurement has been validated by CRPP (Villigen).

Calcium-Dependent Rubella Virus Fusion Occurs in Early Endosomes.

PubMed

Dubé, Mathieu; Etienne, Loïc; Fels, Maximilian; Kielian, Margaret

2016-07-15

The E1 membrane protein of rubella virus (RuV) is a class II membrane fusion protein structurally related to the fusion proteins of the alphaviruses, flaviviruses, and phleboviruses. Virus entry is mediated by a low pH-dependent fusion reaction through E1's insertion into the cell membrane and refolding to a stable homotrimer. Unlike the other described class II proteins, RuV E1 contains 2 fusion loops, which complex a metal ion between them by interactions with residues N88 and D136. Insertion of the E1 protein into the target membrane, fusion, and infection require calcium and are blocked by alanine substitution of N88 or D136. Here we addressed the requirements of E1 for calcium binding and the intracellular location of the calcium requirement during virus entry. Our results demonstrated that N88 and D136 are optimally configured to support RuV fusion and are strongly selected for during the virus life cycle. While E1 has some similarities with cellular proteins that bind calcium and anionic lipids, RuV binding to the membrane was independent of anionic lipids. Virus fusion occurred within early endosomes, and chelation of intracellular calcium showed that calcium within the early endosome was required for virus fusion and infection. Calcium triggered the reversible insertion of E1 into the target membrane at neutral pH, but E1 homotrimer formation and fusion required a low pH. Thus, RuV E1, unlike other known class II fusion proteins, has distinct triggers for membrane insertion and fusion protein refolding mediated, respectively, by endosomal calcium and low pH. Rubella virus causes a mild disease of childhood, but infection of pregnant women frequently results in miscarriage or severe birth defects. In spite of an effective vaccine, RuV disease remains a serious problem in many developing countries. RuV infection of host cells involves endocytic uptake and low pH-triggered membrane fusion and is unusual in its requirement for calcium binding by the membrane fusion protein. Here we addressed the mechanism of the calcium requirement and the required location of calcium during virus entry. Both calcium and low pH were essential during the virus fusion reaction, which was shown to occur in the early endosome compartment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Calcium-Dependent Rubella Virus Fusion Occurs in Early Endosomes

PubMed Central

Dubé, Mathieu; Etienne, Loïc; Fels, Maximilian

2016-01-01

ABSTRACT The E1 membrane protein of rubella virus (RuV) is a class II membrane fusion protein structurally related to the fusion proteins of the alphaviruses, flaviviruses, and phleboviruses. Virus entry is mediated by a low pH-dependent fusion reaction through E1's insertion into the cell membrane and refolding to a stable homotrimer. Unlike the other described class II proteins, RuV E1 contains 2 fusion loops, which complex a metal ion between them by interactions with residues N88 and D136. Insertion of the E1 protein into the target membrane, fusion, and infection require calcium and are blocked by alanine substitution of N88 or D136. Here we addressed the requirements of E1 for calcium binding and the intracellular location of the calcium requirement during virus entry. Our results demonstrated that N88 and D136 are optimally configured to support RuV fusion and are strongly selected for during the virus life cycle. While E1 has some similarities with cellular proteins that bind calcium and anionic lipids, RuV binding to the membrane was independent of anionic lipids. Virus fusion occurred within early endosomes, and chelation of intracellular calcium showed that calcium within the early endosome was required for virus fusion and infection. Calcium triggered the reversible insertion of E1 into the target membrane at neutral pH, but E1 homotrimer formation and fusion required a low pH. Thus, RuV E1, unlike other known class II fusion proteins, has distinct triggers for membrane insertion and fusion protein refolding mediated, respectively, by endosomal calcium and low pH. IMPORTANCE Rubella virus causes a mild disease of childhood, but infection of pregnant women frequently results in miscarriage or severe birth defects. In spite of an effective vaccine, RuV disease remains a serious problem in many developing countries. RuV infection of host cells involves endocytic uptake and low pH-triggered membrane fusion and is unusual in its requirement for calcium binding by the membrane fusion protein. Here we addressed the mechanism of the calcium requirement and the required location of calcium during virus entry. Both calcium and low pH were essential during the virus fusion reaction, which was shown to occur in the early endosome compartment. PMID:27122589

A linear parameter-varying multiobjective control law design based on youla parametrization for a flexible blended wing body aircraft

NASA Astrophysics Data System (ADS)

Demourant, F.; Ferreres, G.

2013-12-01

This article presents a methodology for a linear parameter-varying (LPV) multiobjective flight control law design for a blended wing body (BWB) aircraft and results. So, the method is a direct design of a parametrized control law (with respect to some measured flight parameters) through a multimodel convex design to optimize a set of specifications on the full-flight domain and different mass cases. The methodology is based on the Youla parameterization which is very useful since closed loop specifications are affine with respect to Youla parameter. The LPV multiobjective design method is detailed and applied to the BWB flexible aircraft example.

A methodology for the synthesis of robust feedback systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Milich, David Albert

1988-01-01

A new methodology is developed for the synthesis of linear, time-variant (LTI) controllers for multivariable LTI systems. The resulting closed-loop system is nominally stable and exhibits a known level of performance. In addition, robustness of the feedback system is guaranteed, i.e., stability and performance are retained in the presence of multiple unstructured uncertainty blocks located at various points in the feedback loop. The design technique is referred to as the Causality Recovery Methodology (CRM). The CRM relies on the Youla parameterization of all stabilizing compensators to ensure nominal stability of the feedback system. A frequency-domain inequality in terms of the structured singular value mu defines the robustness specification. The optimal compensator, with respect to the mu condition, is shown to be noncausal in general. The aim of the CRM is to find a stable, causal transfer function matrix that approximates the robustness characteristics of the optimal solution. The CRM, via a series of infinite-dimensional convex programs, produces a closed-loop system whose performance robustness is at least as good as that of any initial design. The algorithm is approximated by a finite dimensional process for the purposes of implementation. Two numerical examples confirm the potential viability of the CRM concept; however, the robustness improvement comes at the expense of increased computational burden and compensator complexity.

Membrane-spanning lipids for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer.

PubMed

Schwarzmann, Günter; Breiden, Bernadette; Sandhoff, Konrad

2015-10-01

A Förster resonance energy transfer-based fusion and transfer assay was developed to study, in model membranes, protein-mediated membrane fusion and intermembrane lipid transfer of fluorescent sphingolipid analogs. For this assay, it became necessary to apply labeled reporter molecules that are resistant to spontaneous as well as protein-mediated intermembrane transfer. The novelty of this assay is the use of nonextractable fluorescent membrane-spanning bipolar lipids. Starting from the tetraether lipid caldarchaeol, we synthesized fluorescent analogs with fluorophores at both polar ends. In addition, we synthesized radioactive glycosylated caldarchaeols. These labeled lipids were shown to stretch through bilayer membranes rather than to loop within a single lipid layer of liposomes. More important, the membrane-spanning lipids (MSLs) in contrast to phosphoglycerides proved to be nonextractable by proteins. We could show that the GM2 activator protein (GM2AP) is promiscuous with respect to glycero- and sphingolipid transfer. Saposin (Sap) B also transferred sphingolipids albeit with kinetics different from GM2AP. In addition, we could unambiguously show that the recombinant activator protein Sap C x His6 induced membrane fusion rather than intermembrane lipid transfer. These findings showed that these novel MSLs, in contrast with fluorescent phosphoglycerolipids, are well suited for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer. Copyright © 2015 by the American Society for Biochemistry and Molecular Biology, Inc.

Synaptotagmin C2B Domain Regulates Ca2+-triggered Fusion in Vitro

PubMed Central

Gaffaney, Jon D.; Dunning, F. Mark; Wang, Zhao; Hui, Enfu; Chapman, Edwin R.

2008-01-01

Synaptotagmin (syt) 1 is localized to synaptic vesicles, binds Ca2+, and regulates neuronal exocytosis. Syt 1 harbors two Ca2+-binding motifs referred to as C2A and C2B. In this study we examine the function of the isolated C2 domains of Syt 1 using a reconstituted, SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor)-mediated, fusion assay. We report that inclusion of phosphatidylethanolamine into reconstituted SNARE vesicles enabled isolated C2B, but not C2A, to regulate Ca2+-triggered fusion. The isolated C2B domain had a 6-fold lower EC for Ca2+ 50-activated fusion than the intact cytosolic domain of Syt 1 (C2AB). Phosphatidylethanolamine increased both the rate and efficiency of C2AB- and C2B-regulated fusion without affecting their abilities to bind membrane-embedded syntaxin-SNAP-25 (t-SNARE) complexes. At equimolar concentrations, the isolated C2A domain was an effective inhibitor of C2B-, but not C2AB-regulated fusion; hence, C2A has markedly different effects in the fusion assay depending on whether it is tethered to C2B. Finally, scanning alanine mutagenesis of C2AB revealed four distinct groups of mutations within the C2B domain that play roles in the regulation of SNARE-mediated fusion. Surprisingly, substitution of Arg-398 with alanine, which lies on the opposite end of C2B from the Ca2+/membrane-binding loops, decreases C2AB t-SNARE binding and Ca2+-triggered fusion in vitro without affecting Ca2+-triggered interactions with phosphatidylserine or vesicle aggregation. In addition, some mutations uncouple the clamping and stimulatory functions of syt 1, suggesting that these two activities are mediated by distinct structural determinants in C2B. PMID:18784080

Vector-Boson Fusion Higgs Production at Three Loops in QCD.

PubMed

Dreyer, Frédéric A; Karlberg, Alexander

2016-08-12

We calculate the next-to-next-to-next-to-leading-order (N^{3}LO) QCD corrections to inclusive vector-boson fusion Higgs production at proton colliders, in the limit in which there is no color exchange between the hadronic systems associated with the two colliding protons. We also provide differential cross sections for the Higgs transverse momentum and rapidity distributions. We find that the corrections are at the 1‰-2‰ level, well within the scale uncertainty of the next-to-next-to-leading-order calculation. The associated scale uncertainty of the N^{3}LO calculation is typically found to be below the 2‰ level. We also consider theoretical uncertainties due to missing higher order parton distribution functions, and provide an estimate of their importance.

Novel design methods for magnetic flux loops in the National Compact Stellarator Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pomphrey, N.; Lazarus, E.; Zarnstorff, M.

2007-05-15

Magnetic pickup loops on the vacuum vessel (VV) can provide an abundance of equilibrium information for stellarators. A substantial effort has gone into designing flux loops for the National Compact Stellarator Experiment (NCSX) [Zarnstorff et al., Plasma Phys. Controlled Fusion 43, A237 (2001)], a three-field period quasi-axisymmetric stellarator under construction at the Princeton Plasma Physics Laboratory. The design philosophy, to measure all of the magnetic field distributions normal to the VV that can be measured, has necessitated the development of singular value decomposition algorithms for identifying efficient loop locations. Fields are expected to be predominantly stellarator symmetric (SS)--the symmetry ofmore » the machine design--with toroidal mode numbers per torus (n) equal to a multiple of 3 and possessing reflection symmetry in a period. However, plasma instabilities and coil imperfections will generate non-SS fields that must also be diagnosed. The measured symmetric fields will yield important information on the plasma current and pressure profile as well as on the plasma shape. All fields that obey the design symmetries could be measured by placing flux loops in a single half-period of the VV, but accurate resolution of nonsymmetric modes, quantified by the condition number of a matrix, requires repositioning loops to equivalent locations on the full torus. A subarray of loops located along the inside wall of the vertically elongated cross section was designed to detect n=3, m=5 or 6 resonant field perturbations that can cause important islands. Additional subarrays included are continuous in the toroidal and poloidal directions. Loops are also placed at symmetry points of the VV to obtain maximal sensitivity to asymmetric perturbations. Combining results from various calculations which have made extensive use of a database of 2500 free-boundary VMEC equilibria, has led to the choice of 225 flux loops for NCSX, of which 151 have distinct shapes.« less

Membrane topology analysis of Escherichia coli K-12 Mtr permease by alkaline phosphatase and beta-galactosidase fusions.

PubMed

Sarsero, J P; Pittard, A J

1995-01-01

The mtr gene of Escherichia coli K-12 encodes an inner membrane protein which is responsible for the active transport of trypotophan into the cell. It has been proposed that the Mtr permease has a novel structure consisting of 11 hydrophobic transmembrane spans, with a cytoplasmically disposed amino terminus and a carboxyl terminus located in the periplasmic space (J.P. Sarsero, P. J. Wookey, P. Gollnick, C. Yanofsky, and A.J. Pittard, J. Bacteriol. 173:3231-3234, 1991). The validity of this model was examined by the construction of fusion proteins between the Mtr permease and alkaline phosphatase or beta-galactosidase. In addition to the conventional methods, in which the reporter enzyme replaces a carboxyl-terminal portion of the membrane protein, the recently developed alkaline phosphatase sandwich fusion technique was utilized, in which alkaline phosphatase is inserted into an otherwise intact membrane protein. A cluster of alkaline phosphatase fusions to the carboxyl-terminal end of the Mtr permease exhibited high levels of alkaline phosphatase activity, giving support to the proposition of a periplasmically located carboxyl terminus. The majority of fusion proteins produced enzymatic activities which were in agreement with the positions of the fusion sites on the proposed topological model of the permease. The synthesis of a small cluster of hybrid proteins, whose enzymatic activity did not agree with the location of their fusion sites within putative transmembrane span VIII or the preceding periplasmic loop, was not detected by immunological techniques and did not necessitate modification of the proposed model in this region. Slight alterations may need to be made in the positioning of the carboxyl-terminal end of transmembrane span X.

Functional impact of HIV coreceptor-binding site mutations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Biscone, Mark J.; Miamidian, John L.; Muchiri, John M.

2006-07-20

The bridging sheet region of the gp120 subunit of the HIV-1 Env protein interacts with the major virus coreceptors, CCR5 and CXCR4. We examined the impact of mutations in and adjacent to the bridging sheet region of an X4 tropic HIV-1 on membrane fusion and entry inhibitor susceptibility. When the V3-loop of this Env was changed so that CCR5 was used, the effects of these same mutations on CCR5 use were assayed as well. We found that coreceptor-binding site mutations had greater effects on CXCR4-mediated fusion and infection than when CCR5 was used as a coreceptor, perhaps related to differencesmore » in coreceptor affinity. The mutations also reduced use of the alternative coreceptors CCR3 and CCR8 to varying degrees, indicating that the bridging sheet region is important for the efficient utilization of both major and minor HIV coreceptors. As seen before with a primary R5 virus strain, bridging sheet mutations increased susceptibility to the CCR5 inhibitor TAK-779, which correlated with CCR5 binding efficiency. Bridging sheet mutations also conferred increased susceptibility to the CXCR4 ligand AMD-3100 in the context of the X4 tropic Env. However, these mutations had little effect on the rate of membrane fusion and little effect on susceptibility to enfuvirtide, a membrane fusion inhibitor whose activity is dependent in part on the rate of Env-mediated membrane fusion. Thus, mutations that reduce coreceptor binding and enhance susceptibility to coreceptor inhibitors can affect fusion and enfuvirtide susceptibility in an Env context-dependent manner.« less

Optimal Recursive Digital Filters for Active Bending Stabilization

NASA Technical Reports Server (NTRS)

Orr, Jeb S.

2013-01-01

In the design of flight control systems for large flexible boosters, it is common practice to utilize active feedback control of the first lateral structural bending mode so as to suppress transients and reduce gust loading. Typically, active stabilization or phase stabilization is achieved by carefully shaping the loop transfer function in the frequency domain via the use of compensating filters combined with the frequency response characteristics of the nozzle/actuator system. In this paper we present a new approach for parameterizing and determining optimal low-order recursive linear digital filters so as to satisfy phase shaping constraints for bending and sloshing dynamics while simultaneously maximizing attenuation in other frequency bands of interest, e.g. near higher frequency parasitic structural modes. By parameterizing the filter directly in the z-plane with certain restrictions, the search space of candidate filter designs that satisfy the constraints is restricted to stable, minimum phase recursive low-pass filters with well-conditioned coefficients. Combined with optimal output feedback blending from multiple rate gyros, the present approach enables rapid and robust parametrization of autopilot bending filters to attain flight control performance objectives. Numerical results are presented that illustrate the application of the present technique to the development of rate gyro filters for an exploration-class multi-engined space launch vehicle.

Target Soil Impact Verification: Experimental Testing and Kayenta Constitutive Modeling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Broome, Scott Thomas; Flint, Gregory Mark; Dewers, Thomas

2015-11-01

This report details experimental testing and constitutive modeling of sandy soil deformation under quasi - static conditions. This is driven by the need to understand constitutive response of soil to target/component behavior upon impact . An experimental and constitutive modeling program was followed to determine elastic - plastic properties and a compressional failure envelope of dry soil . One hydrostatic, one unconfined compressive stress (UCS), nine axisymmetric compression (ACS) , and one uniaxial strain (US) test were conducted at room temperature . Elastic moduli, assuming isotropy, are determined from unload/reload loops and final unloading for all tests pre - failuremore » and increase monotonically with mean stress. Very little modulus degradation was discernable from elastic results even when exposed to mean stresses above 200 MPa . The failure envelope and initial yield surface were determined from peak stresses and observed onset of plastic yielding from all test results. Soil elasto - plastic behavior is described using the Brannon et al. (2009) Kayenta constitutive model. As a validation exercise, the ACS - parameterized Kayenta model is used to predict response of the soil material under uniaxial strain loading. The resulting parameterized and validated Kayenta model is of high quality and suitable for modeling sandy soil deformation under a range of conditions, including that for impact prediction.« less

A Polymorphism within the Internal Fusion Loop of the Ebola Virus Glycoprotein Modulates Host Cell Entry.

PubMed

Hoffmann, Markus; Crone, Lisa; Dietzel, Erik; Paijo, Jennifer; González-Hernández, Mariana; Nehlmeier, Inga; Kalinke, Ulrich; Becker, Stephan; Pöhlmann, Stefan

2017-05-01

The large scale of the Ebola virus disease (EVD) outbreak in West Africa in 2013-2016 raised the question whether the host cell interactions of the responsible Ebola virus (EBOV) strain differed from those of other ebolaviruses. We previously reported that the glycoprotein (GP) of the virus circulating in West Africa in 2014 (EBOV2014) exhibited reduced ability to mediate entry into two nonhuman primate (NHP)-derived cell lines relative to the GP of EBOV1976. Here, we investigated the molecular determinants underlying the differential entry efficiency. We found that EBOV2014-GP-driven entry into diverse NHP-derived cell lines, as well as human monocyte-derived macrophages and dendritic cells, was reduced compared to EBOV1976-GP, although entry into most human- and all bat-derived cell lines tested was comparable. Moreover, EBOV2014 replication in NHP but not human cells was diminished relative to EBOV1976, suggesting that reduced cell entry translated into reduced viral spread. Mutagenic analysis of EBOV2014-GP and EBOV1976-GP revealed that an amino acid polymorphism in the receptor-binding domain, A82V, modulated entry efficiency in a cell line-independent manner and did not account for the reduced EBOV2014-GP-driven entry into NHP cells. In contrast, polymorphism T544I, located in the internal fusion loop in the GP2 subunit, was found to be responsible for the entry phenotype. These results suggest that position 544 is an important determinant of EBOV infectivity for both NHP and certain human target cells. IMPORTANCE The Ebola virus disease outbreak in West Africa in 2013 entailed more than 10,000 deaths. The scale of the outbreak and its dramatic impact on human health raised the question whether the responsible virus was particularly adept at infecting human cells. Our study shows that an amino acid exchange, A82V, that was acquired during the epidemic and that was not observed in previously circulating viruses, increases viral entry into diverse target cells. In contrast, the epidemic virus showed a reduced ability to enter cells of nonhuman primates compared to the virus circulating in 1976, and a single amino acid exchange in the internal fusion loop of the viral glycoprotein was found to account for this phenotype. Copyright © 2017 American Society for Microbiology.

Efficient numerical evaluation of Feynman integrals

NASA Astrophysics Data System (ADS)

Li, Zhao; Wang, Jian; Yan, Qi-Shu; Zhao, Xiaoran

2016-03-01

Feynman loop integrals are a key ingredient for the calculation of higher order radiation effects, and are responsible for reliable and accurate theoretical prediction. We improve the efficiency of numerical integration in sector decomposition by implementing a quasi-Monte Carlo method associated with the CUDA/GPU technique. For demonstration we present the results of several Feynman integrals up to two loops in both Euclidean and physical kinematic regions in comparison with those obtained from FIESTA3. It is shown that both planar and non-planar two-loop master integrals in the physical kinematic region can be evaluated in less than half a minute with accuracy, which makes the direct numerical approach viable for precise investigation of higher order effects in multi-loop processes, e.g. the next-to-leading order QCD effect in Higgs pair production via gluon fusion with a finite top quark mass. Supported by the Natural Science Foundation of China (11305179 11475180), Youth Innovation Promotion Association, CAS, IHEP Innovation (Y4545170Y2), State Key Lab for Electronics and Particle Detectors, Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Y4KF061CJ1), Cluster of Excellence Precision Physics, Fundamental Interactions and Structure of Matter (PRISMA-EXC 1098)

Two loop correction to interference in $$gg \\to ZZ$$

DOE PAGES

Campbell, John M.; Ellis, R. Keith; Czakon, Michal; ...

2016-08-01

We present results for the production of a pair of on-shell Z bosons via gluon-gluon fusion. This process occurs both through the production and decay of the Higgs boson, and through continuum production where the Z boson couples to a loop of massless quarks or to a massive quark. We calculate the interference of the two processes and its contribution to the cross section up to and including order O(αmore » $$_{s}^{3}$$ ). The two-loop contributions to the amplitude are all known analytically, except for the continuum production through loops of top quarks of mass m. The latter contribution is important for the invariant mass of the two Z bosons, (as measured by the mass of their leptonic decay products, m$$_{4l}$$), in a regime where m$$_{4l}$$ ≥ 2m because of the contributions of longitudinal bosons. We examine all the contributions to the virtual amplitude involving top quarks, as expansions about the heavy top quark limit combined with a conformal mapping and Padé approximants. Comparison with the analytic results, where known, allows us to assess the validity of the heavy quark expansion, and it extensions. We give results for the NLO corrections to this interference, including both real and virtual radiation.« less

Improving nondestructive characterization of dual phase steels using data fusion

NASA Astrophysics Data System (ADS)

Kahrobaee, Saeed; Haghighi, Mehdi Salkhordeh; Akhlaghi, Iman Ahadi

2018-07-01

The aim of this paper is to introduce a novel methodology for nondestructive determination of microstructural and mechanical properties (due to the various heat treatments), as well as thickness variations (as a result of corrosion effect) of dual phase steels. The characterizations are based on the variations in the electromagnetic properties extracted from magnetic hysteresis loop and eddy current methods which are coupled with a data fusion system. This study was conducted on six groups of samples (with different thicknesses, from 1 mm to 4 mm) subjected to the various intercritical annealing processes to produce different fractions of martensite/ferrite phases and consequently, changes in hardness, yield strength and ultra tensile strength (UTS). This study proposes a novel soft computing technique to increase accuracy of nondestructive measurements and resolving overlapped NDE outputs related to the various samples. The empirical results indicate that applying the proposed data fusion technique on the two electromagnetic NDE data sets nondestructively, causes an increase in the accuracy and reliability of determining material features including ferrite fraction, hardness, yield strength, UTS, as well as thickness variations.

Process Model of A Fusion Fuel Recovery System for a Direct Drive IFE Power Reactor

NASA Astrophysics Data System (ADS)

Natta, Saswathi; Aristova, Maria; Gentile, Charles

2008-11-01

A task has been initiated to develop a detailed representative model for the fuel recovery system (FRS) in the prospective direct drive inertial fusion energy (IFE) reactor. As part of the conceptual design phase of the project, a chemical process model is developed in order to observe the interaction of system components. This process model is developed using FEMLAB Multiphysics software with the corresponding chemical engineering module (CEM). Initially, the reactants, system structure, and processes are defined using known chemical species of the target chamber exhaust. Each step within the Fuel recovery system is modeled compartmentally and then merged to form the closed loop fuel recovery system. The output, which includes physical properties and chemical content of the products, is analyzed after each step of the system to determine the most efficient and productive system parameters. This will serve to attenuate possible bottlenecks in the system. This modeling evaluation is instrumental in optimizing and closing the fusion fuel cycle in a direct drive IFE power reactor. The results of the modeling are presented in this paper.

Data fusion strategies for hazard detection and safe site selection for planetary and small body landings

NASA Astrophysics Data System (ADS)

Câmara, F.; Oliveira, J.; Hormigo, T.; Araújo, J.; Ribeiro, R.; Falcão, A.; Gomes, M.; Dubois-Matra, O.; Vijendran, S.

2015-06-01

This paper discusses the design and evaluation of data fusion strategies to perform tiered fusion of several heterogeneous sensors and a priori data. The aim is to increase robustness and performance of hazard detection and avoidance systems, while enabling safe planetary and small body landings anytime, anywhere. The focus is on Mars and asteroid landing mission scenarios and three distinct data fusion algorithms are introduced and compared. The first algorithm consists of a hybrid camera-LIDAR hazard detection and avoidance system, the H2DAS, in which data fusion is performed at both sensor-level data (reconstruction of the point cloud obtained with a scanning LIDAR using the navigation motion states and correcting the image for motion compensation using IMU data), feature-level data (concatenation of multiple digital elevation maps, obtained from consecutive LIDAR images, to achieve higher accuracy and resolution maps while enabling relative positioning) as well as decision-level data (fusing hazard maps from multiple sensors onto a single image space, with a single grid orientation and spacing). The second method presented is a hybrid reasoning fusion, the HRF, in which innovative algorithms replace the decision-level functions of the previous method, by combining three different reasoning engines—a fuzzy reasoning engine, a probabilistic reasoning engine and an evidential reasoning engine—to produce safety maps. Finally, the third method presented is called Intelligent Planetary Site Selection, the IPSIS, an innovative multi-criteria, dynamic decision-level data fusion algorithm that takes into account historical information for the selection of landing sites and a piloting function with a non-exhaustive landing site search capability, i.e., capable of finding local optima by searching a reduced set of global maps. All the discussed data fusion strategies and algorithms have been integrated, verified and validated in a closed-loop simulation environment. Monte Carlo simulation campaigns were performed for the algorithms performance assessment and benchmarking. The simulations results comprise the landing phases of Mars and Phobos landing mission scenarios.

Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.

PubMed

Xiao, Yibei; Luo, Min; Hayes, Robert P; Kim, Jonathan; Ng, Sherwin; Ding, Fang; Liao, Maofu; Ke, Ailong

2017-06-29

Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop. These structures provide the much-needed temporal and spatial resolution to resolve key mechanistic steps leading to Cas3 recruitment. In the early steps, PAM recognition causes severe DNA bending, leading to spontaneous DNA unwinding to form a seed-bubble. The full R-loop formation triggers conformational changes in Cascade, licensing Cas3 to bind. The same process also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage. The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Escherichia coli tatC mutations that suppress defective twin-arginine transporter signal peptides.

PubMed

Strauch, Eva-Maria; Georgiou, George

2007-11-23

In vitro studies have suggested that the TatBC complex serves as the receptor for signal peptides targeted for export via the twin-arginine translocation (Tat) pathway. Substitution of the hallmark twin-arginine dipeptide with two lysines abrogates export of physiological substrates in all organisms. We report the isolation and characterization of suppressor mutations that allow export of an ssTor(KK)-GFP-SsrA tripartite fusion. We identified two amino acid suppressor mutations in the first cytoplasmic loop of TatC. In addition, two other amino acids in the first cytoplasmic loop exhibit epistatic suppression. Surprisingly, we also identified a suppressor mutation predicted to lie within the second periplasmic loop of TatC, a region that is not expected to interact directly with the signal peptide. The suppressor mutations allowed export of the native Esherichia coli Tat substrate trimethylamine N-oxide reductase with a twin-lysine substitution in its signal sequence. The cytoplasmic suppressor mutations conferred SDS sensitivity and partial filamentation, indicating that Tat export of authentic substrates was impaired.

Advanced ECCD based NTM control in closed-loop operation at ASDEX Upgrade (AUG)

NASA Astrophysics Data System (ADS)

Reich, Matthias; Barrera-Orte, Laura; Behler, Karl; Bock, Alexander; Giannone, Louis; Maraschek, Marc; Poli, Emanuele; Rapson, Chris; Stober, Jörg; Treutterer, Wolfgang

2012-10-01

In high performance plasmas, Neoclassical Tearing Modes (NTMs) are regularly observed at reactor-grade beta-values. They limit the achievable normalized beta, which is undesirable because fusion performance scales as beta squared. The method of choice for controlling and avoiding NTMs at AUG is the deposition of ECCD inside the magnetic island for stabilization in real-time (rt). Our approach to tackling such complex control problems using real-time diagnostics allows rigorous optimization of all subsystems. Recent progress in rt-equilibrium reconstruction (< 3.5 ms), rt-localization of NTMs (< 8 ms) and rt beam tracing (< 25 ms) allows closed-loop feedback operation using multiple movable mirrors as the ECCD deposition actuator. The rt-equilibrium uses function parametrization or a fast Grad-Shafranov solver with an option to include rt-MSE measurements. The island localization is based on a correlation of ECE and filtered Mirnov signals. The rt beam-tracing module provides deposition locations and their derivative versus actuator position of multiple gyrotrons. The ``MHD controller'' finally drives the actuators. Results utilizing closed-loop operation with multiple gyrotrons and their effect on NTMs are shown.

Hydrogen retention in Li and Li-C-O films

NASA Astrophysics Data System (ADS)

Buzi, Luxherta; Nelson, Andrew O.; Yang, Yuxin; Kaita, Robert; Koel, Bruce E.

2017-10-01

The efficiency of Li in binding H isotopes has led to reduced recycling in magnetic fusion devices and improved plasma performance. Since elemental Li surfaces are challenging to maintain in fusion devices due to the presence of impurities, parameterizing and understanding the mechanisms for H retention in various Li compounds (Li-C-O), in addition to pure Li, is crucial for Li plasma-facing material applications. To determine H retention in Li and Li-C-O films, measurements were done under ultrahigh vacuum conditions using temperature programmed desorption (TPD). Thin Li films (20 monolayers) were deposited on a nickel single crystal substrate and irradiated with 500 eV H2+ions at surface temperatures from 90K to 520K. Initial measurements on Li and Li-O films showed that the retention was comparable and dropped exponentially with surface temperature, from 95% at 90 K to 35% at 520 K. Auger electron spectroscopy and TPD showed that H was retained as lithium hydride (LiH) in pure Li and as lithium hydroxide (LiOH) in Li2O, which decomposed to H2O and Li2O at temperatures higher than 470K. H retention in Li-C and Li-C-O films will be determined over a similar temperature range, and the sputtering rate of these layers with H ions will also be reported. This material is based upon work supported by the U.S. Department of Energy, Office of Science/Fusion Energy Sciences under Award Number DE-SC0012890.

Monitoring of "all-weather" evapotranspiration using optical and passive microwave remote sensing imagery over the River Source Region in Southwest China

NASA Astrophysics Data System (ADS)

Ma, Y.; Liu, S.

2017-12-01

Accurate estimation of surface evapotranspiration (ET) with high quality is one of the biggest obstacles for routine applications of remote sensing in eco-hydrological studies and water resource management at basin scale. However, many aspects urgently need to deeply research, such as the applicability of the ET models, the parameterization schemes optimization at the regional scale, the temporal upscaling, the selecting and developing of the spatiotemporal data fusion method and ground-based validation over heterogeneous land surfaces. This project is based on the theoretically robust surface energy balance system (SEBS) model, which the model mechanism need further investigation, including the applicability and the influencing factors, such as local environment, and heterogeneity of the landscape, for improving estimation accuracy. Due to technical and budget limitations, so far, optical remote sensing data is missing due to frequent cloud contamination and other poor atmospheric conditions in Southwest China. Here, a multi-source remote sensing data fusion method (ESTARFM: Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model) method will be proposed through blending multi-source remote sensing data acquired by optical, and passive microwave remote sensors on board polar satellite platforms. The accurate "all-weather" ET estimation will be carried out for daily ET of the River Source Region in Southwest China, and then the remotely sensed ET results are overlapped with the footprint-weighted images of EC (eddy correlation) for ground-based validation.

High-level Closed-loop Fusion and Decision Making with INFORM Lab

DTIC Science & Technology

2011-06-01

gling fr eighte r zodiac Toolbox / Library node. The output of the editor is an XML file that contains all the information needed to run the ...surveillance. It uses two land-based zodiacs to offload the illegal immigrants, by making multiple trips to/from the freighter to ferry persons to the ...mapped in Figure 9. Figure 9 Map of Non-Cooperative Search Vignette The freighter and zodiacs will attempt various elusive manoeuvres depending on

Common Evolutionary Origin for the Rotor Domain of Rotary Atpases and Flagellar Protein Export Apparatus

PubMed Central

Kishikawa, Jun-ichi; Ibuki, Tatsuya; Nakamura, Shuichi; Nakanishi, Astuko; Minamino, Tohru; Miyata, Tomoko; Namba, Keiichi; Konno, Hiroki; Ueno, Hiroshi; Imada, Katsumi; Yokoyama, Ken

2013-01-01

The V1- and F1- rotary ATPases contain a rotor that rotates against a catalytic A3B3 or α3β3 stator. The rotor F1-γ or V1-DF is composed of both anti-parallel coiled coil and globular-loop parts. The bacterial flagellar type III export apparatus contains a V1/F1-like ATPase ring structure composed of FliI6 homo-hexamer and FliJ which adopts an anti-parallel coiled coil structure without the globular-loop part. Here we report that FliJ of Salmonella enterica serovar Typhimurium shows a rotor like function in Thermus thermophilus A3B3 based on both biochemical and structural analysis. Single molecular analysis indicates that an anti-parallel coiled-coil structure protein (FliJ structure protein) functions as a rotor in A3B3. A rotary ATPase possessing an F1-γ-like protein generated by fusion of the D and F subunits of V1 rotates, suggesting F1-γ could be the result of a fusion of the genes encoding two separate rotor subunits. Together with sequence comparison among the globular part proteins, the data strongly suggest that the rotor domains of the rotary ATPases and the flagellar export apparatus share a common evolutionary origin. PMID:23724081

Incorporation of aptamers in the terminal loop of shRNAs yields an effective and novel combinatorial targeting strategy.

PubMed

Pang, Ka Ming; Castanotto, Daniela; Li, Haitang; Scherer, Lisa; Rossi, John J

2018-01-09

Gene therapy by engineering patient's own blood cells to confer HIV resistance can potentially lead to a functional cure for AIDS. Toward this goal, we have previously developed an anti-HIV lentivirus vector that deploys a combination of shRNA, ribozyme and RNA decoy. To further improve this therapeutic vector against viral escape, we sought an additional reagent to target HIV integrase. Here, we report the development of a new strategy for selection and expression of aptamer for gene therapy. We developed a SELEX protocol (multi-tag SELEX) for selecting RNA aptamers against proteins with low solubility or stability, such as integrase. More importantly, we expressed these aptamers in vivo by incorporating them in the terminal loop of shRNAs. This novel strategy allowed efficient expression of the shRNA-aptamer fusions that targeted RNAs and proteins simultaneously. Expressed shRNA-aptamer fusions targeting HIV integrase or reverse transcriptase inhibited HIV replication in cell cultures. Viral inhibition was further enhanced by combining an anti-integrase aptamer with an anti-HIV Tat-Rev shRNA. This construct exhibited efficacy comparable to that of integrase inhibitor Raltegravir. Our strategy for the selection and expression of RNA aptamers can potentially extend to other gene therapy applications. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Radio-frequency-assisted current startup in the fusion engineering device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borowski, S. K.; Peng, Yueng Kay Martin; Kammash, T.

1984-01-01

Auxiliary radio-frequency (RF) heating of electrons before and during the current rise phase of a large tokamak, such as the Fusion Engineering Device (FED) (R{sub 0} = 4.8 m, a = 1.3 m, sigma = 1.6, B(R{sub 0}) = 3.62 T), is examined as a means of reducing both the initiation loop voltage and resistive flux expenditure during startup. Prior to current initiation, 1 to 2 MW of electron cyclotron resonance heating power at about90 GHz is used to create a small volume of high conductivity plasma (T {sub e} approx. = 100 eV, n {sub e} approx. = 10{supmore » 19} m{sup -3}) near the upper hybrid resonance (UHR) region. This plasma conditioning, referred to as preheating, permits a small radius (a{sub 0} approx. = 0.2 to 0.4 m) current channel to be established with a relatively low initial loop voltage (less than or equal to 25 V as opposed to about 100 V without rf assist). During the subsequent plasma expansion and current rise phase, a combination of rf heating (up to 5 MW) and linear current ramping leads to a substantial savings in voltseconds by (a) minimizing the resistive flux consumption and (b) producing broad current density profiles. (With such broad profiles, the internal flux requirements are maintained at or near the flat profile limit.)« less

Radio-frequency-assisted current startup in the Fusion Engineering Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borowski, S.K.; Kammash, T.; Martin Peng, Y.K.

1984-07-01

Auxiliary radio-frequency (RF) heating of electrons before and during the current rise phase of a large tokamak, such as the Fusion Engineering Device (FED) (R/sub 0/ = 4.8 m, a = 1.3 m, sigma = 1.6, B(R/sub 0/) = 3.62 T), is examined as a means of reducing both the initiation loop voltage and resistive flux expenditure during startup. Prior to current initiation, 1 to 2 MW of electron cyclotron resonance heating power at about90 GHz is used to create a small volume of high conductivity plasma (T /sub e/ approx. = 100 eV, n /sub e/ approx. = 10/supmore » 19/ m/sup -3/) near the upper hybrid resonance (UHR) region. This plasma conditioning, referred to as preheating, permits a small radius (a/sub 0/ approx. = 0.2 to 0.4 m) current channel to be established with a relatively low initial loop voltage (less than or equal to 25 V as opposed to about 100 V without rf assist). During the subsequent plasma expansion and current rise phase, a combination of rf heating (up to 5 MW) and linear current ramping leads to a substantial savings in voltseconds by (a) minimizing the resistive flux consumption and (b) producing broad current density profiles. (With such broad profiles, the internal flux requirements are maintained at or near the flat profile limit.)« less

Collaborative autonomous sensing with Bayesians in the loop

NASA Astrophysics Data System (ADS)

Ahmed, Nisar

2016-10-01

There is a strong push to develop intelligent unmanned autonomy that complements human reasoning for applications as diverse as wilderness search and rescue, military surveillance, and robotic space exploration. More than just replacing humans for `dull, dirty and dangerous' work, autonomous agents are expected to cope with a whole host of uncertainties while working closely together with humans in new situations. The robotics revolution firmly established the primacy of Bayesian algorithms for tackling challenging perception, learning and decision-making problems. Since the next frontier of autonomy demands the ability to gather information across stretches of time and space that are beyond the reach of a single autonomous agent, the next generation of Bayesian algorithms must capitalize on opportunities to draw upon the sensing and perception abilities of humans-in/on-the-loop. This work summarizes our recent research toward harnessing `human sensors' for information gathering tasks. The basic idea behind is to allow human end users (i.e. non-experts in robotics, statistics, machine learning, etc.) to directly `talk to' the information fusion engine and perceptual processes aboard any autonomous agent. Our approach is grounded in rigorous Bayesian modeling and fusion of flexible semantic information derived from user-friendly interfaces, such as natural language chat and locative hand-drawn sketches. This naturally enables `plug and play' human sensing with existing probabilistic algorithms for planning and perception, and has been successfully demonstrated with human-robot teams in target localization applications.

Angiogram, fundus, and oxygen saturation optic nerve head image fusion

NASA Astrophysics Data System (ADS)

Cao, Hua; Khoobehi, Bahram

2009-02-01

A novel multi-modality optic nerve head image fusion approach has been successfully designed. The new approach has been applied on three ophthalmologic modalities: angiogram, fundus, and oxygen saturation retinal optic nerve head images. It has achieved an excellent result by giving the visualization of fundus or oxygen saturation images with a complete angiogram overlay. During this study, two contributions have been made in terms of novelty, efficiency, and accuracy. The first contribution is the automated control point detection algorithm for multi-sensor images. The new method employs retina vasculature and bifurcation features by identifying the initial good-guess of control points using the Adaptive Exploratory Algorithm. The second contribution is the heuristic optimization fusion algorithm. In order to maximize the objective function (Mutual-Pixel-Count), the iteration algorithm adjusts the initial guess of the control points at the sub-pixel level. A refinement of the parameter set is obtained at the end of each loop, and finally an optimal fused image is generated at the end of the iteration. It is the first time that Mutual-Pixel-Count concept has been introduced into biomedical image fusion area. By locking the images in one place, the fused image allows ophthalmologists to match the same eye over time and get a sense of disease progress and pinpoint surgical tools. The new algorithm can be easily expanded to human or animals' 3D eye, brain, or body image registration and fusion.

Pilot study of bipolar radiofrequency-induced anastomotic thermofusion-exploration of therapy parameters ex vivo.

PubMed

Winter, Hanno; Holmer, Christoph; Buhr, Heinz-Johannes; Lindner, Gerd; Lauster, Roland; Kraft, Marc; Ritz, Jörg-Peter

2010-01-01

Vessel sealing has been well-established in surgical practice in recent years. Bipolar radiofrequency-induced thermofusion (BIRTH) of intestinal tissue might replace traditionally used staples or sutures in the near future. In this experimental study, the influence of compressive pressure, fusion temperature, and duration of heating on the quality of intestinal anastomosis was investigated to obtain the relevant major parameters for the in vivo use of this system. An experimental setup for a closed-loop temperature-controlled bipolar radiofrequency-induced thermofusion of porcine intestinal tissue was developed. Twenty-four colon samples were harvested from nine different Saalower-Kräuter pigs and then anastomosed altering compressive pressure on five different levels to explore its influence on anastomotic bursting pressure. The anastomotic bursting strength depends on the compressive pressure applied to the colonic fusion site. An optimal interval of compressive pressure (CP = 1.125 N/mm(2)) in respect of a high amount of burst pressure was detected. A correlation (r = 0.54, p = 0.015) of burst pressure to delta compression indicated that increasing colonic wall thickness probably strengthens the anastomotic fusion. This study is a first step to enlighten the major parameters of tissue fusion, though effects and interactions of various main parameters of bipolar radiofrequency-induced thermofusion of colonic tissue remain unclear. Further studies exploring the main effects and interactions of tissue and process parameters to the quality of the fusion site have to follow.

A synthetic polymer system with repeatable chemical recyclability

NASA Astrophysics Data System (ADS)

Zhu, Jian-Bo; Watson, Eli M.; Tang, Jing; Chen, Eugene Y.-X.

2018-04-01

The development of chemically recyclable polymers offers a solution to the end-of-use issue of polymeric materials and provides a closed-loop approach toward a circular materials economy. However, polymers that can be easily and selectively depolymerized back to monomers typically require low-temperature polymerization methods and also lack physical properties and mechanical strengths required for practical uses. We introduce a polymer system based on γ-butyrolactone (GBL) with a trans-ring fusion at the α and β positions. Such trans-ring fusion renders the commonly considered as nonpolymerizable GBL ring readily polymerizable at room temperature under solvent-free conditions to yield a high–molecular weight polymer. The polymer has enhanced thermostability and can be repeatedly and quantitatively recycled back to its monomer by thermolysis or chemolysis. Mixing of the two enantiomers of the polymer generates a highly crystalline supramolecular stereocomplex.

Higgs Boson Pair Production in Gluon Fusion at Next-to-Leading Order with Full Top-Quark Mass Dependence.

PubMed

Borowka, S; Greiner, N; Heinrich, G; Jones, S P; Kerner, M; Schlenk, J; Schubert, U; Zirke, T

2016-07-01

We present the calculation of the cross section and invariant mass distribution for Higgs boson pair production in gluon fusion at next-to-leading order (NLO) in QCD. Top-quark masses are fully taken into account throughout the calculation. The virtual two-loop amplitude has been generated using an extension of the program GoSam supplemented with an interface to Reduze for the integral reduction. The occurring integrals have been calculated numerically using the program SecDec. Our results, including the full top-quark mass dependence for the first time, allow us to assess the validity of various approximations proposed in the literature, which we also recalculate. We find substantial deviations between the NLO result and the different approximations, which emphasizes the importance of including the full top-quark mass dependence at NLO.

Parton shower and NLO-matching uncertainties in Higgs boson pair production

NASA Astrophysics Data System (ADS)

Jones, Stephen; Kuttimalai, Silvan

2018-02-01

We perform a detailed study of NLO parton shower matching uncertainties in Higgs boson pair production through gluon fusion at the LHC based on a generic and process independent implementation of NLO subtraction and parton shower matching schemes for loop-induced processes in the Sherpa event generator. We take into account the full top-quark mass dependence in the two-loop virtual corrections and compare the results to an effective theory approximation. In the full calculation, our findings suggest large parton shower matching uncertainties that are absent in the effective theory approximation. We observe large uncertainties even in regions of phase space where fixed-order calculations are theoretically well motivated and parton shower effects expected to be small. We compare our results to NLO matched parton shower simulations and analytic resummation results that are available in the literature.

Robust curb detection with fusion of 3D-Lidar and camera data.

PubMed

Tan, Jun; Li, Jian; An, Xiangjing; He, Hangen

2014-05-21

Curb detection is an essential component of Autonomous Land Vehicles (ALV), especially important for safe driving in urban environments. In this paper, we propose a fusion-based curb detection method through exploiting 3D-Lidar and camera data. More specifically, we first fuse the sparse 3D-Lidar points and high-resolution camera images together to recover a dense depth image of the captured scene. Based on the recovered dense depth image, we propose a filter-based method to estimate the normal direction within the image. Then, by using the multi-scale normal patterns based on the curb's geometric property, curb point features fitting the patterns are detected in the normal image row by row. After that, we construct a Markov Chain to model the consistency of curb points which utilizes the continuous property of the curb, and thus the optimal curb path which links the curb points together can be efficiently estimated by dynamic programming. Finally, we perform post-processing operations to filter the outliers, parameterize the curbs and give the confidence scores on the detected curbs. Extensive evaluations clearly show that our proposed method can detect curbs with strong robustness at real-time speed for both static and dynamic scenes.

Analytical design of an industrial two-term controller for optimal regulatory control of open-loop unstable processes under operational constraints.

PubMed

Tchamna, Rodrigue; Lee, Moonyong

2018-01-01

This paper proposes a novel optimization-based approach for the design of an industrial two-term proportional-integral (PI) controller for the optimal regulatory control of unstable processes subjected to three common operational constraints related to the process variable, manipulated variable and its rate of change. To derive analytical design relations, the constrained optimal control problem in the time domain was transformed into an unconstrained optimization problem in a new parameter space via an effective parameterization. The resulting optimal PI controller has been verified to yield optimal performance and stability of an open-loop unstable first-order process under operational constraints. The proposed analytical design method explicitly takes into account the operational constraints in the controller design stage and also provides useful insights into the optimal controller design. Practical procedures for designing optimal PI parameters and a feasible constraint set exclusive of complex optimization steps are also proposed. The proposed controller was compared with several other PI controllers to illustrate its performance. The robustness of the proposed controller against plant-model mismatch has also been investigated. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Robustly stable adaptive control of a tandem of master-slave robotic manipulators with force reflection by using a multiestimation scheme.

PubMed

Ibeas, Asier; de la Sen, Manuel

2006-10-01

The problem of controlling a tandem of robotic manipulators composing a teleoperation system with force reflection is addressed in this paper. The final objective of this paper is twofold: 1) to design a robust control law capable of ensuring closed-loop stability for robots with uncertainties and 2) to use the so-obtained control law to improve the tracking of each robot to its corresponding reference model in comparison with previously existing controllers when the slave is interacting with the obstacle. In this way, a multiestimation-based adaptive controller is proposed. Thus, the master robot is able to follow more accurately the constrained motion defined by the slave when interacting with an obstacle than when a single-estimation-based controller is used, improving the transparency property of the teleoperation scheme. The closed-loop stability is guaranteed if a minimum residence time, which might be updated online when unknown, between different controller parameterizations is respected. Furthermore, the analysis of the teleoperation and stability capabilities of the overall scheme is carried out. Finally, some simulation examples showing the working of the multiestimation scheme complete this paper.

Comparison of the resulting error in data fusion techniques when used with remote sensing, earth observation, and in-situ data sets for water quality applications

NASA Astrophysics Data System (ADS)

Ziemba, Alexander; El Serafy, Ghada

2016-04-01

Ecological modeling and water quality investigations are complex processes which can require a high level of parameterization and a multitude of varying data sets in order to properly execute the model in question. Since models are generally complex, their calibration and validation can benefit from the application of data and information fusion techniques. The data applied to ecological models comes from a wide range of sources such as remote sensing, earth observation, and in-situ measurements, resulting in a high variability in the temporal and spatial resolution of the various data sets available to water quality investigators. It is proposed that effective fusion into a comprehensive singular set will provide a more complete and robust data resource with which models can be calibrated, validated, and driven by. Each individual product contains a unique valuation of error resulting from the method of measurement and application of pre-processing techniques. The uncertainty and error is further compounded when the data being fused is of varying temporal and spatial resolution. In order to have a reliable fusion based model and data set, the uncertainty of the results and confidence interval of the data being reported must be effectively communicated to those who would utilize the data product or model outputs in a decision making process[2]. Here we review an array of data fusion techniques applied to various remote sensing, earth observation, and in-situ data sets whose domains' are varied in spatial and temporal resolution. The data sets examined are combined in a manner so that the various classifications, complementary, redundant, and cooperative, of data are all assessed to determine classification's impact on the propagation and compounding of error. In order to assess the error of the fused data products, a comparison is conducted with data sets containing a known confidence interval and quality rating. We conclude with a quantification of the performance of the data fusion techniques and a recommendation on the feasibility of applying of the fused products in operating forecast systems and modeling scenarios. The error bands and confidence intervals derived can be used in order to clarify the error and confidence of water quality variables produced by prediction and forecasting models. References [1] F. Castanedo, "A Review of Data Fusion Techniques", The Scientific World Journal, vol. 2013, pp. 1-19, 2013. [2] T. Keenan, M. Carbone, M. Reichstein and A. Richardson, "The model-data fusion pitfall: assuming certainty in an uncertain world", Oecologia, vol. 167, no. 3, pp. 587-597, 2011.

The ancient claudin Dni2 facilitates yeast cell fusion by compartmentalizing Dni1 into a membrane subdomain.

PubMed

Curto, M-Ángeles; Moro, Sandra; Yanguas, Francisco; Gutiérrez-González, Carmen; Valdivieso, M-Henar

2018-05-01

Dni1 and Dni2 facilitate cell fusion during mating. Here, we show that these proteins are interdependent for their localization in a plasma membrane subdomain, which we have termed the mating fusion domain. Dni1 compartmentation in the domain is required for cell fusion. The contribution of actin, sterol-dependent membrane organization, and Dni2 to this compartmentation was analysed, and the results showed that Dni2 plays the most relevant role in the process. In turn, the Dni2 exit from the endoplasmic reticulum depends on Dni1. These proteins share the presence of a cysteine motif in their first extracellular loop related to the claudin GLWxxC(8-10 aa)C signature motif. Structure-function analyses show that mutating each Dni1 conserved cysteine has mild effects, and that only simultaneous elimination of several cysteines leads to a mating defect. On the contrary, eliminating each single cysteine and the C-terminal tail in Dni2 abrogates Dni1 compartmentation and cell fusion. Sequence alignments show that claudin trans-membrane helixes bear small-XXX-small motifs at conserved positions. The fourth Dni2 trans-membrane helix tends to form homo-oligomers in Escherichia plasma membrane, and two concatenated small-XXX-small motifs are required for efficient oligomerization and for Dni2 export from the yeast endoplasmic reticulum. Together, our results strongly suggest that Dni2 is an ancient claudin that blocks Dni1 diffusion from the intercellular region where two plasma membranes are in close proximity, and that this function is required for Dni1 to facilitate cell fusion.

Engineering Encodable Lanthanide-Binding Tags (LBTs) into Loop Regions of Proteins

PubMed Central

Barthelmes, Katja; Reynolds, Anne M.; Peisach, Ezra; Jonker, Hendrik R. A.; DeNunzio, Nicholas J.; Allen, Karen N.; Imperiali, Barbara; Schwalbe, Harald

2011-01-01

Lanthanide-binding-tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography and luminescence studies. We have inserted LBTs into three different loop positions (denoted L, R, and S) of the model protein interleukin-1β and varied the length of the spacer between the LBT and the protein (denoted 1-3). Luminescence studies demonstrate that all nine constructs bind Tb3+ tightly in the low nanomolar range. No significant change in the fusion protein occurs from insertion of the LBT, as shown by two X-ray crystallographic structures of the IL1β-S1 and IL1β-L3 constructs and for the remaining constructs by comparing 1H-15N-HSQC NMR spectra with wild-type IL1β. Additionally, binding of LBT-loop IL1β proteins to their native binding partner in vitro remains unaltered. X-ray crystallographic phasing was successful using only the signal from the bound lanthanide. Large residual dipolar couplings (RDCs) could be determined by NMR spectroscopy for all LBT-loop-constructs and revealed that the LBT-2 series were rigidly incorporated into the interleukin-1β structure. The paramagnetic NMR spectra of loop-LBT mutant IL1β-R2 were assigned and the Δχ tensor components were calculated based on RDCs and pseudocontact shifts (PCSs). A structural model of the IL1β-R2 construct was calculated using the paramagnetic restraints. The current data provide support that encodable LBTs serve as versatile biophysical tags when inserted into loop regions of proteins of known structure or predicted via homology modelling. PMID:21182275

Broad Neutralization of Ebolaviruses via a Fusion Loop Epitope Elicited by Immunization

DTIC Science & Technology

2017-03-31

overnight. After incubation with blocking buffer (BB, 2% non- fat milk , 5% FBS in PBS), the WT or mutant supernatant in five-fold serial dilution in BB was...replication competent rVSV pseudotyped with filovirus GP, which also expressed the reporter protein GFP (rVSV-GP-GFP) (Miller et al., 2012). CA45 potently...for proper protein folding and expression. The epitope mapping identified EBOV GP residues R64 within the N-terminus of GP1 in addition to Y517

A Guide to Using STITCHER for Overlapping Assembly PCR Applications.

PubMed

O'Halloran, Damien M

2017-01-01

Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping assembly PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online.

A Virtual Upgrade Validation Method for Software-Reliant Systems

DTIC Science & Technology

2012-06-01

3.4 Root Cause Areas of System-Level Faults 11 3.4.1 End-to-End Flow of Data Streams 11 3.4.2 Distributed Communicating State Machines 13 3.4.3...FlyByWire/FlyByWire_english.pdf (Accessed on November 11 , 2011.) [Apple 2005] Apple Support Communities , jazzman40. iTunes Crashes When Ripping...Strategies 39 7.1 Application Pattern Modeling Strategies 39 7.1.1 Control Loops 39 7.1.2 State Transition Communication 42 7.1.3 Sensor/Signal Fusion

Development of Lead Compounds as Fusion Inhibitors for Dengue Virus

DTIC Science & Technology

2009-08-01

19a. NAME OF RESPONSIBLE PERSON USAMRMC a. REPORT U b . ABSTRACT U c. THIS PAGE U UU 61 19b. TELEPHONE NUMBER (include area code...and III (blue). B ) Structural alignment of E2 protein monomer in the absence and presence of βOG (pdbIDs 1OAN and 1OKE respectively), with the kl-β...hairpin loop colored as follows: prefusion state (yellow), intermediate βOG-E2 complex (blue), secondary structure colored by B -factor from blue

Molecular basis of endosomal-membrane association for the dengue virus envelope protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rogers, David M.; Kent, Michael S.; Rempe, Susan B.

Dengue virus is coated by an icosahedral shell of 90 envelope protein dimers that convert to trimers at low pH and promote fusion of its membrane with the membrane of the host endosome. We provide the first estimates for the free energy barrier and minimum for two key steps in this process: host membrane bending and protein–membrane binding. Both are studied using complementary membrane elastic, continuum electrostatics and all-atom molecular dynamics simulations. The predicted host membrane bending required to form an initial fusion stalk presents a 22–30 kcal/mol free energy barrier according to a constrained membrane elastic model. Combined continuummore » and molecular dynamics results predict a 15 kcal/mol free energy decrease on binding of each trimer of dengue envelope protein to a membrane with 30% anionic phosphatidylglycerol lipid. The bending cost depends on the preferred curvature of the lipids composing the host membrane leaflets, while the free energy gained for protein binding depends on the surface charge density of the host membrane. The fusion loop of the envelope protein inserts exactly at the level of the interface between the membrane's hydrophobic and head-group regions. As a result, the methods used in this work provide a means for further characterization of the structures and free energies of protein-assisted membrane fusion.« less

Molecular basis of endosomal-membrane association for the dengue virus envelope protein

DOE PAGES

Rogers, David M.; Kent, Michael S.; Rempe, Susan B.

2015-01-02

Dengue virus is coated by an icosahedral shell of 90 envelope protein dimers that convert to trimers at low pH and promote fusion of its membrane with the membrane of the host endosome. We provide the first estimates for the free energy barrier and minimum for two key steps in this process: host membrane bending and protein–membrane binding. Both are studied using complementary membrane elastic, continuum electrostatics and all-atom molecular dynamics simulations. The predicted host membrane bending required to form an initial fusion stalk presents a 22–30 kcal/mol free energy barrier according to a constrained membrane elastic model. Combined continuummore » and molecular dynamics results predict a 15 kcal/mol free energy decrease on binding of each trimer of dengue envelope protein to a membrane with 30% anionic phosphatidylglycerol lipid. The bending cost depends on the preferred curvature of the lipids composing the host membrane leaflets, while the free energy gained for protein binding depends on the surface charge density of the host membrane. The fusion loop of the envelope protein inserts exactly at the level of the interface between the membrane's hydrophobic and head-group regions. As a result, the methods used in this work provide a means for further characterization of the structures and free energies of protein-assisted membrane fusion.« less

Layer-Based Approach for Image Pair Fusion.

PubMed

Son, Chang-Hwan; Zhang, Xiao-Ping

2016-04-20

Recently, image pairs, such as noisy and blurred images or infrared and noisy images, have been considered as a solution to provide high-quality photographs under low lighting conditions. In this paper, a new method for decomposing the image pairs into two layers, i.e., the base layer and the detail layer, is proposed for image pair fusion. In the case of infrared and noisy images, simple naive fusion leads to unsatisfactory results due to the discrepancies in brightness and image structures between the image pair. To address this problem, a local contrast-preserving conversion method is first proposed to create a new base layer of the infrared image, which can have visual appearance similar to another base layer such as the denoised noisy image. Then, a new way of designing three types of detail layers from the given noisy and infrared images is presented. To estimate the noise-free and unknown detail layer from the three designed detail layers, the optimization framework is modeled with residual-based sparsity and patch redundancy priors. To better suppress the noise, an iterative approach that updates the detail layer of the noisy image is adopted via a feedback loop. This proposed layer-based method can also be applied to fuse another noisy and blurred image pair. The experimental results show that the proposed method is effective for solving the image pair fusion problem.

From pure fusion to fusion-fission Demo tokamaks

NASA Astrophysics Data System (ADS)

Mirnov, S. V.

2013-04-01

The major requirements for pure fusion tokamak reactors and tokamak-based fusion neutron sources (FNS) are analyzed together with possible paths from the present-day tokamak towards the FNS tokamak. The FNS are of interest for traditional fission reactors as a method of waste management by burning of long-lived transuranic radionuclides (minorities) and fission fuel breeding. The Russian fission community places several hard requirements on the quality of FNS suitable for the first step of the investigation program of minority burning and breeding. They are (a) a steady-state regime of neutron production (more than 80% of the operational time), (b) a neutron power flux density greater than >0.2 MW m-2, (c) a total surface integrated neutron power >10 MW. Among the different FNS projects, based on magnetically confined plasmas, only ‘classical tokamak’ is most likely to fulfill these requirements in the nearest future. Some of the most important improvements of the ‘classical tokamak’ needed for successful realization of the FNS are (1) decrease in Zeff (probably, by making use of lithium as a part of plasma-facing components), (2) He removal and closed loop DT fuel circulation, (3) increase in the energy of stationary injected neutral tritium beams up to 150-170 keV and (4) control of impurity contamination at the plasma center (probably, by local RF heating). These key issues are discussed.

Safety and environmental aspects of organic coolants for fusion facilities

NASA Astrophysics Data System (ADS)

Natalizio, A.; Hollies, R. E.; Gierszewski, P.

1993-06-01

Organic coolants, such as OS-84, offer unique advantages for fusion reactor applications. These advantages are with respect to both reactor operation and safety. The key operational advantage is a coolant that can provide high temperature (350-400°C) at modest pressure (2-4 MPa). These temperatures are needed for conditioning the plasma-facing components and, in reactors, for achieving high thermodynamic conversion efficiencies (>40%). The key safety advantage of organic coolants is the low vapor pressure, which significantly reduces the containment pressurization transient (relative to water) following a loss of coolant event. Also, from an occupational dose viewpoint, organic coolants significantly reduce corrosion and erosion inside the cooling system and consequently reduce the quantity of activation products deposited in cooling system equipment. On the negative side, organic coolants undergo both pyrolytic and radiolytic decomposition, and are flammable. While the decomposition rate can be minimized by coolant system design (by reducing coolant inventories exposed to neutron flux and to high temperatures), decomposition products are formed and these degrade the coolant properties. Both heavy compounds and light gases are produced from the decomposition process, and both must be removed to maintain adequate coolant properties. As these hydrocarbons may become tritiated by permeation, or activated through impurities, their disposal could create an environmental concern. Because of this potential waste disposal problem, consideration has been given to the recycling of both the light and heavy products, thereby reducing the quantity of waste to be disposed. Preliminary assessments made for various fusion reactor designs, including ITER, suggest that it is feasible to use organic coolants for several applications. These applications range from first wall and blanket coolant (the most demanding with respect to decomposition), to shield and vacuum vessel cooling, to an intermediate cooling loop removing heat from a liquid metal loop and transferring it to a steam generator or heat exchanger.

A vanadium alloy for the application in a liquid metal blanket of a fusion reactor

NASA Astrophysics Data System (ADS)

Borgstedt, H. U.; Grundmann, M.; Konys, J.; Perić, Z.

1988-07-01

The vanadium alloy V3Ti1Si has been corrosion tested in liquid lithium and the eutectic alloy Pb-17Li at 550°C. This alloy has a comparable corrosion resistance to the alloy V15Cr5Ti in lithium. In this molten metal it is superior to stainless steel AISI 316. In the Pb-17Li melt it is even superior to martensitic steels. The alloy has only a weak tendency to be dissolved. It is sensitive to an exchange of non-metallic elements, which causes the formation of a hardened surface layer. These chemical effects are influenced by the mass and surface ratios of the vanadium alloy to the molten metals and other structural materials. These ratios are unfavorable in the two test loops. The effects might be less pronounced in a vanadium alloy/liquid metal fusion reactor blanket.

The Flavivirus Precursor Membrane-Envelope Protein Complex: Structure and Maturation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Long; Lok, Shee-Mei; Yu, I-Mei

2008-09-17

Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of the precursor membrane protein (prM), turning inert virus into infectious particles. We have determined the 2.2 angstrom resolution crystal structure of a recombinant protein in which the dengue virus prM is linked to the envelope glycoprotein E. The structure represents the prM-E heterodimer and fits well into the cryo-electron microscopy density of immature virus at neutral pH. The pr peptide {beta}-barrel structure covers the fusion loop in E, preventingmore » fusion with host cell membranes. The structure provides a basis for identifying the stages of its pH-directed conformational metamorphosis during maturation, ending with release of pr when budding from the host.« less

Potent peptidic fusion inhibitors of influenza virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kadam, Rameshwar U.; Juraszek, Jarek; Brandenburg, Boerries

Influenza therapeutics with new targets and mechanisms of action are urgently needed to combat potential pandemics, emerging viruses, and constantly mutating strains in circulation. We report here on the design and structural characterization of potent peptidic inhibitors of influenza hemagglutinin. The peptide design was based on complementarity-determining region loops of human broadly neutralizing antibodies against the hemagglutinin (FI6v3 and CR9114). The optimized peptides exhibit nanomolar affinity and neutralization against influenza A group 1 viruses, including the 2009 H1N1 pandemic and avian H5N1 strains. The peptide inhibitors bind to the highly conserved stem epitope and block the low pH–induced conformational rearrangementsmore » associated with membrane fusion. These peptidic compounds and their advantageous biological properties should accelerate the development of new small molecule– and peptide-based therapeutics against influenza virus.« less

Lipid raft-like liposomes used for targeted delivery of a chimeric entry-inhibitor peptide with anti-HIV-1 activity.

PubMed

Gómara, María José; Pérez-Pomeda, Ignacio; Gatell, José María; Sánchez-Merino, Victor; Yuste, Eloisa; Haro, Isabel

2017-02-01

The work reports the design and synthesis of a chimeric peptide that is composed of the peptide sequences of two entry inhibitors which target different sites of HIV-1 gp41. The chimeric peptide offers the advantage of targeting two gp41 regions simultaneously: the fusion peptide and the loop both of which are membrane active and participate in the membrane fusion process. We therefore use lipid raft-like liposomes as a tool to specifically direct the chimeric inhibitor peptide to the membrane domains where the HIV-1 envelope protein is located. Moreover, the liposomes that mimic the viral membrane composition protect the chimeric peptide against proteolytic digestion thereby increasing the stability of the peptide. The described liposome preparations are suitable nanosystems for managing hydrophobic entry-inhibitor peptides as putative therapeutics. Copyright © 2016 Elsevier Inc. All rights reserved.

Parton shower and NLO-matching uncertainties in Higgs boson pair production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Stephen; Kuttimalai, Silvan

We perform a detailed study of NLO parton shower matching uncertainties in Higgs boson pair production through gluon fusion at the LHC based on a generic and process independent implementation of NLO subtraction and parton shower matching schemes for loop-induced processes in the Sherpa event generator. We take into account the full top-quark mass dependence in the two-loop virtual corrections and compare the results to an effective theory approximation. In the full calculation, our findings suggest large parton shower matching uncertainties that are absent in the effective theory approximation. Here, we observe large uncertainties even in regions of phase spacemore » where fixed-order calculations are theoretically well motivated and parton shower effects expected to be small. We compare our results to NLO matched parton shower simulations and analytic resummation results that are available in the literature.« less

Parton shower and NLO-matching uncertainties in Higgs boson pair production

DOE PAGES

Jones, Stephen; Kuttimalai, Silvan

2018-02-28

We perform a detailed study of NLO parton shower matching uncertainties in Higgs boson pair production through gluon fusion at the LHC based on a generic and process independent implementation of NLO subtraction and parton shower matching schemes for loop-induced processes in the Sherpa event generator. We take into account the full top-quark mass dependence in the two-loop virtual corrections and compare the results to an effective theory approximation. In the full calculation, our findings suggest large parton shower matching uncertainties that are absent in the effective theory approximation. Here, we observe large uncertainties even in regions of phase spacemore » where fixed-order calculations are theoretically well motivated and parton shower effects expected to be small. We compare our results to NLO matched parton shower simulations and analytic resummation results that are available in the literature.« less

Markov logic network based complex event detection under uncertainty

NASA Astrophysics Data System (ADS)

Lu, Jingyang; Jia, Bin; Chen, Genshe; Chen, Hua-mei; Sullivan, Nichole; Pham, Khanh; Blasch, Erik

2018-05-01

In a cognitive reasoning system, the four-stage Observe-Orient-Decision-Act (OODA) reasoning loop is of interest. The OODA loop is essential for the situational awareness especially in heterogeneous data fusion. Cognitive reasoning for making decisions can take advantage of different formats of information such as symbolic observations, various real-world sensor readings, or the relationship between intelligent modalities. Markov Logic Network (MLN) provides mathematically sound technique in presenting and fusing data at multiple levels of abstraction, and across multiple intelligent sensors to conduct complex decision-making tasks. In this paper, a scenario about vehicle interaction is investigated, in which uncertainty is taken into consideration as no systematic approaches can perfectly characterize the complex event scenario. MLNs are applied to the terrestrial domain where the dynamic features and relationships among vehicles are captured through multiple sensors and information sources regarding the data uncertainty.

Non-rigid Reconstruction of Casting Process with Temperature Feature

NASA Astrophysics Data System (ADS)

Lin, Jinhua; Wang, Yanjie; Li, Xin; Wang, Ying; Wang, Lu

2017-09-01

Off-line reconstruction of rigid scene has made a great progress in the past decade. However, the on-line reconstruction of non-rigid scene is still a very challenging task. The casting process is a non-rigid reconstruction problem, it is a high-dynamic molding process lacking of geometric features. In order to reconstruct the casting process robustly, an on-line fusion strategy is proposed for dynamic reconstruction of casting process. Firstly, the geometric and flowing feature of casting are parameterized in manner of TSDF (truncated signed distance field) which is a volumetric block, parameterized casting guarantees real-time tracking and optimal deformation of casting process. Secondly, data structure of the volume grid is extended to have temperature value, the temperature interpolation function is build to generate the temperature of each voxel. This data structure allows for dynamic tracking of temperature of casting during deformation stages. Then, the sparse RGB features is extracted from casting scene to search correspondence between geometric representation and depth constraint. The extracted color data guarantees robust tracking of flowing motion of casting. Finally, the optimal deformation of the target space is transformed into a nonlinear regular variational optimization problem. This optimization step achieves smooth and optimal deformation of casting process. The experimental results show that the proposed method can reconstruct the casting process robustly and reduce drift in the process of non-rigid reconstruction of casting.

Performance evaluation of dispersion parameterization schemes in the plume simulation of FFT-07 diffusion experiment

NASA Astrophysics Data System (ADS)

Pandey, Gavendra; Sharan, Maithili

2018-01-01

Application of atmospheric dispersion models in air quality analysis requires a proper representation of the vertical and horizontal growth of the plume. For this purpose, various schemes for the parameterization of dispersion parameters σ‧s are described in both stable and unstable conditions. These schemes differ on the use of (i) extent of availability of on-site measurements (ii) formulations developed for other sites and (iii) empirical relations. The performance of these schemes is evaluated in an earlier developed IIT (Indian Institute of Technology) dispersion model with the data set in single and multiple releases conducted at Fusion Field Trials, Dugway Proving Ground, Utah 2007. Qualitative and quantitative evaluation of the relative performance of all the schemes is carried out in both stable and unstable conditions in the light of (i) peak/maximum concentrations, and (ii) overall concentration distribution. The blocked bootstrap resampling technique is adopted to investigate the statistical significance of the differences in performances of each of the schemes by computing 95% confidence limits on the parameters FB and NMSE. The various analysis based on some selected statistical measures indicated consistency in the qualitative and quantitative performances of σ schemes. The scheme which is based on standard deviation of wind velocity fluctuations and Lagrangian time scales exhibits a relatively better performance in predicting the peak as well as the lateral spread.

ARC: A compact, high-field, disassemblable fusion nuclear science facility and demonstration power plant

NASA Astrophysics Data System (ADS)

Sorbom, Brandon; Ball, Justin; Palmer, Timothy; Mangiarotti, Franco; Sierchio, Jennifer; Bonoli, Paul; Kasten, Cale; Sutherland, Derek; Barnard, Harold; Haakonsen, Christian; Goh, Jon; Sung, Choongki; Whyte, Dennis

2014-10-01

The Affordable, Robust, Compact (ARC) reactor conceptual design aims to reduce the size, cost, and complexity of a combined Fusion Nuclear Science Facility (FNSF) and demonstration fusion pilot power plant. ARC is a 270 MWe tokamak reactor with a major radius of 3.3 m, a minor radius of 1.1 m, and an on-axis magnetic field of 9.2 T. ARC has Rare Earth Barium Copper Oxide (REBCO) superconducting toroidal field coils with joints to allow disassembly, allowing for removal and replacement of the vacuum vessel as a single component. Inboard-launched current drive of 25 MW LHRF power and 13.6 MW ICRF power is used to provide a robust, steady state core plasma far from disruptive limits. ARC uses an all-liquid blanket, consisting of low pressure, slowly flowing Fluorine Lithium Beryllium (FLiBe) molten salt. The liquid blanket acts as a working fluid, coolant, and tritium breeder, and minimizes the solid material that can become activated. The large temperature range over which FLiBe is liquid permits blanket operation at 800-900 K with single phase fluid cooling and allows use of a high-efficiency Brayton cycle for electricity production in the secondary coolant loop.

Gyro Drift Correction for An Indirect Kalman Filter Based Sensor Fusion Driver.

PubMed

Lee, Chan-Gun; Dao, Nhu-Ngoc; Jang, Seonmin; Kim, Deokhwan; Kim, Yonghun; Cho, Sungrae

2016-06-11

Sensor fusion techniques have made a significant contribution to the success of the recently emerging mobile applications era because a variety of mobile applications operate based on multi-sensing information from the surrounding environment, such as navigation systems, fitness trackers, interactive virtual reality games, etc. For these applications, the accuracy of sensing information plays an important role to improve the user experience (UX) quality, especially with gyroscopes and accelerometers. Therefore, in this paper, we proposed a novel mechanism to resolve the gyro drift problem, which negatively affects the accuracy of orientation computations in the indirect Kalman filter based sensor fusion. Our mechanism focuses on addressing the issues of external feedback loops and non-gyro error elements contained in the state vectors of an indirect Kalman filter. Moreover, the mechanism is implemented in the device-driver layer, providing lower process latency and transparency capabilities for the upper applications. These advances are relevant to millions of legacy applications since utilizing our mechanism does not require the existing applications to be re-programmed. The experimental results show that the root mean square errors (RMSE) before and after applying our mechanism are significantly reduced from 6.3 × 10(-1) to 5.3 × 10(-7), respectively.

Autoinhibition of Munc18-1 modulates synaptobrevin binding and helps to enable Munc13-dependent regulation of membrane fusion.

PubMed

Sitarska, Ewa; Xu, Junjie; Park, Seungmee; Liu, Xiaoxia; Quade, Bradley; Stepien, Karolina; Sugita, Kyoko; Brautigam, Chad A; Sugita, Shuzo; Rizo, Josep

2017-05-06

Munc18-1 orchestrates SNARE complex assembly together with Munc13-1 to mediate neurotransmitter release. Munc18-1 binds to synaptobrevin, but the relevance of this interaction and its relation to Munc13 function are unclear. NMR experiments now show that Munc18-1 binds specifically and non-specifically to synaptobrevin. Specific binding is inhibited by a L348R mutation in Munc18-1 and enhanced by a D326K mutation designed to disrupt the 'furled conformation' of a Munc18-1 loop. Correspondingly, the activity of Munc18-1 in reconstitution assays that require Munc18-1 and Munc13-1 for membrane fusion is stimulated by the D326K mutation and inhibited by the L348R mutation. Moreover, the D326K mutation allows Munc13-1-independent fusion and leads to a gain-of-function in rescue experiments in Caenorhabditis elegans unc-18 nulls. Together with previous studies, our data support a model whereby Munc18-1 acts as a template for SNARE complex assembly, and autoinhibition of synaptobrevin binding contributes to enabling regulation of neurotransmitter release by Munc13-1.

Rf-assisted current startup in the Fusion Engineering Device (FED)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borowski, S.K.; Peng, Y.K.M.; Kammash, T.

1982-08-01

Auxiliary rf heating of electrons before and during the current rise phase in the Fusion Engineering Device is examined as a means of reducing both the initiation loop voltage and resistive flux expenditure during startup. Prior to current initiation 1 to 2 MW of electron cyclotron resonance heating (ECRH) power at approx. 90 GHz is used to create a small volume of high conductivity plasma (T/sub e/ approx. = 100 eV, n/sub e/ approx. = 10/sup 13/ cm/sup -3/) near the upper hybrid resonance (UHR) region. This plasma conditioning permits a small radius (a/sub o/ approx. = 0.2 to 0.4more » m) current channel to be established with a relatively low initial loop voltage (less than or equal to 25 V). During the subsequent plasma expansion and current ramp phase, additional rf power is introduced to reduce volt-second consumption due to plasma resistance. A near classical particle and energy transport model has been developed to estimate the efficiency of electron heating in a currentless toroidal plasma. The model assumes that preferential electron heating at the UHR leads to the formation of an ambipolar sheath potential between the neutral plasma and the conducting vacuum vessel and limiter. The ambipolar electric field (E/sub AMB/) enables the plasma to neutralize itself via poloidal E vector/sub AMB/ x B vector drift. This form of effective rotational transform short-circuits the vertical charge separation and improves particle confinement.« less

Continuous processing of recombinant proteins: Integration of inclusion body solubilization and refolding using simulated moving bed size exclusion chromatography with buffer recycling.

PubMed

Wellhoefer, Martin; Sprinzl, Wolfgang; Hahn, Rainer; Jungbauer, Alois

2013-12-06

An integrated process which combines continuous inclusion body dissolution with NaOH and continuous matrix-assisted refolding based on closed-loop simulated moving bed size exclusion chromatography was designed and experimentally evaluated at laboratory scale. Inclusion bodies from N(pro) fusion pep6His and N(pro) fusion MCP1 from high cell density fermentation were continuously dissolved with NaOH, filtered and mixed with concentrated refolding buffer prior to refolding by size exclusion chromatography (SEC). This process enabled an isocratic operation of the simulated moving bed (SMB) system with a closed-loop set-up with refolding buffer as the desorbent buffer and buffer recycling by concentrating the raffinate using tangential flow filtration. With this continuous refolding process, we increased the refolding and cleavage yield of both model proteins by 10% compared to batch dilution refolding. Furthermore, more than 99% of the refolding buffer of the raffinate could be recycled which reduced the buffer consumption significantly. Based on the actual refolding data, we compared throughput, productivity, and buffer consumption between two batch dilution refolding processes - one using urea for IB dissolution, the other one using NaOH for IB dissolution - and our continuous refolding process. The higher complexity of the continuous refolding process was rewarded with higher throughput and productivity as well as significantly lower buffer consumption compared to the batch dilution refolding processes. Copyright © 2013 Elsevier B.V. All rights reserved.

Human-centric predictive model of task difficulty for human-in-the-loop control tasks

PubMed Central

Majewicz Fey, Ann

2018-01-01

Quantitatively measuring the difficulty of a manipulation task in human-in-the-loop control systems is ill-defined. Currently, systems are typically evaluated through task-specific performance measures and post-experiment user surveys; however, these methods do not capture the real-time experience of human users. In this study, we propose to analyze and predict the difficulty of a bivariate pointing task, with a haptic device interface, using human-centric measurement data in terms of cognition, physical effort, and motion kinematics. Noninvasive sensors were used to record the multimodal response of human user for 14 subjects performing the task. A data-driven approach for predicting task difficulty was implemented based on several task-independent metrics. We compare four possible models for predicting task difficulty to evaluated the roles of the various types of metrics, including: (I) a movement time model, (II) a fusion model using both physiological and kinematic metrics, (III) a model only with kinematic metrics, and (IV) a model only with physiological metrics. The results show significant correlation between task difficulty and the user sensorimotor response. The fusion model, integrating user physiology and motion kinematics, provided the best estimate of task difficulty (R2 = 0.927), followed by a model using only kinematic metrics (R2 = 0.921). Both models were better predictors of task difficulty than the movement time model (R2 = 0.847), derived from Fitt’s law, a well studied difficulty model for human psychomotor control. PMID:29621301

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, John M.; Ellis, R. Keith; Czakon, Michal

We present results for the production of a pair of on-shell Z bosons via gluon-gluon fusion. This process occurs both through the production and decay of the Higgs boson, and through continuum production where the Z boson couples to a loop of massless quarks or to a massive quark. We calculate the interference of the two processes and its contribution to the cross section up to and including order O(αmore » $$_{s}^{3}$$ ). The two-loop contributions to the amplitude are all known analytically, except for the continuum production through loops of top quarks of mass m. The latter contribution is important for the invariant mass of the two Z bosons, (as measured by the mass of their leptonic decay products, m$$_{4l}$$), in a regime where m$$_{4l}$$ ≥ 2m because of the contributions of longitudinal bosons. We examine all the contributions to the virtual amplitude involving top quarks, as expansions about the heavy top quark limit combined with a conformal mapping and Padé approximants. Comparison with the analytic results, where known, allows us to assess the validity of the heavy quark expansion, and it extensions. We give results for the NLO corrections to this interference, including both real and virtual radiation.« less

Toroidal midplane neutral beam armor and plasma limiter

DOEpatents

Kugel, H.W.; Hand, S.W. Jr.; Ksayian, H.

1985-05-31

This invention contemplates an armor shield/plasma limiter positioned upon the inner wall of a toroidal vacuum chamber within which is magnetically confined an energetic plasma in a tokamak nuclear fusion reactor. The armor shield/plasma limiter is thus of a general semi-toroidal shape and is comprised of a plurality of adjacent graphite plates positioned immediately adjacent to each other so as to form a continuous ring upon and around the toroidal chamber's inner wall and the reactor's midplane coil. Each plate has a generally semi-circular outer circumference and a recessed inner portion and is comprised of upper and lower half sections positioned immediately adjacent to one another along the midplane of the plate. With the upper and lower half sections thus joined, a channel or duct is provided within the midplane of the plate in which a magnetic flux loop is positioned. The magnetic flux loop is thus positioned immediately adjacent to the fusing toroidal plasma and serves as a diagnostic sensor with the armor shield/plasma limiter minimizing the amount of power from the energetic plasma as well as from the neutral particle beams heating the plasma incident upon the flux loop.

Image fusion of contrast enhanced ultrasound (CEUS) with computed tomography (CT) or magnetic resonance imaging (MRI) using volume navigation for detection, characterization and planning of therapeutic interventions of liver tumors.

PubMed

Rennert, J; Georgieva, M; Schreyer, A G; Jung, W; Ross, C; Stroszczynski, C; Jung, E M

2011-01-01

To evaluate, whether image fusion of contrast enhanced ultrasound (CEUS) with CT or MRI affects the diagnosis and characterization of liver lesions or the therapeutic strategy of surgical or interventional procedures compared to the preliminary diagnosis. In a retrospective study the image fusion scans of CEUS with contrast enhanced CT or MRI of 100 patients (71 male, mean age 59 years, 0.3-85 years) with benign or malignant liver lesions were evaluated. Fundamental B-scan, color Doppler imaging and CEUS were performed in all patients by an experienced examiner using a multifrequency convex transducer (1-5 MHz, LOGIQ 9/GE) and volume navigation (Vnav). After a bolus injections of up to 2.4 ml SonoVue® (BRACCO, Italy) digital raw data was stored as cine-loops up to 5 min. In 74 patients, CEUS was fused with a pre-existing ceCT, in 26 patients a ceMRI was used. In all 100 patients (100%) the image quality in all modalities (ceCT, ceMRI and CEUS) was excellent or with only minor diagnostic limitations. Regarding the number of lesions revealed in image fusion of CEUS/ceCT/ceMRI and the preceding diagnostic method, concordant results were found in 84 patients. In 12 patients, additional lesions were found using fusion imaging causing subsequently a change of the therapeutical strategy. In 15 out of 21 patients with either concordant or discordant results regarding the number of lesions, image fusion allowed a definite diagnosis due to a continuous documentation of the microcirculation of the tumor and its contrast enhancement. A significant coherency (p < 0.05) among image fusion with either ceCT or ceMRI and CEUS and a subsequent change of therapeutic strategy was found. Image fusion with volume navigation (VNav) of CEUS with ceCT or ceMRI frequently allows a definite localization and diagnosis of hepatic lesions in patients with primary hepatic carcinoma or metastatic diseases. This might cause a change of the therapeutic strategy in many patients with hepatic lesions.

Robust Curb Detection with Fusion of 3D-Lidar and Camera Data

PubMed Central

Tan, Jun; Li, Jian; An, Xiangjing; He, Hangen

2014-01-01

Curb detection is an essential component of Autonomous Land Vehicles (ALV), especially important for safe driving in urban environments. In this paper, we propose a fusion-based curb detection method through exploiting 3D-Lidar and camera data. More specifically, we first fuse the sparse 3D-Lidar points and high-resolution camera images together to recover a dense depth image of the captured scene. Based on the recovered dense depth image, we propose a filter-based method to estimate the normal direction within the image. Then, by using the multi-scale normal patterns based on the curb's geometric property, curb point features fitting the patterns are detected in the normal image row by row. After that, we construct a Markov Chain to model the consistency of curb points which utilizes the continuous property of the curb, and thus the optimal curb path which links the curb points together can be efficiently estimated by dynamic programming. Finally, we perform post-processing operations to filter the outliers, parameterize the curbs and give the confidence scores on the detected curbs. Extensive evaluations clearly show that our proposed method can detect curbs with strong robustness at real-time speed for both static and dynamic scenes. PMID:24854364

Validation of snow characteristics and snow albedo feedback in the Canadian Regional Climate Model simulations over North America

NASA Astrophysics Data System (ADS)

Fang, B.; Sushama, L.; Diro, G. T.

2015-12-01

Snow characteristics and snow albedo feedback (SAF) over North America, as simulated by the fifth-generation Canadian Regional Climate Model (CRCM5), when driven by ERA-40/ERA-Interim, CanESM2 and MPI-ESM-LR at the lateral boundaries, are analyzed in this study. Validation of snow characteristics is performed by comparing simulations against available observations from MODIS, ISCCP and CMC. Results show that the model is able to represent the main spatial distribution of snow characteristics with some overestimation in snow mass and snow depth over the Canadian high Arctic. Some overestimation in surface albedo is also noted for the boreal region which is believed to be related to the snow unloading parameterization, as well as the overestimation of snow albedo. SAF is assessed both in seasonal and climate change contexts when possible. The strength of SAF is quantified as the amount of additional net shortwave radiation at the top of the atmosphere as surface albedo decreases in association with a 1°C increase in surface temperature. Following Qu and Hall (2007), this is expressed as the product of the variation in planetary albedo with surface albedo and the change in surface albedo for 1°C change in surface air temperature during the season, which in turn is determined by the strength of the snow cover and snowpack metamorphosis feedback loops. Analysis of the latter term in the seasonal cycle suggests that for CRCM5 simulations, the snow cover feedback loop is more dominant compared to the snowpack metamorphosis feedback loop, whereas for MODIS, the two feedback loops have more or less similar strength. Moreover, the SAF strength in the climate change context appears to be weaker than in the seasonal cycle and is sensitive to the driving GCM and the RCP scenario.

Experimental investigation of the deformable mirror with bidirectional thermal actuators.

PubMed

Huang, Lei; Ma, Xingkun; Gong, Mali; Bian, Qi

2015-06-29

A deformable mirror with actuators of thermoelectric coolers (TECs) is introduced in this paper. Due to the bidirectional thermal actuation property of the TEC, both upward and downward surface control is available for the DM. The response functions of the actuators are investigated. A close-loop wavefront control experiment is performed too, where the defocus and the astigmatism were corrected. The results reveal that there is a promising prospect for the novel design to be used in corrections of static aberrations, such as in the Inertial Confinement Fusion (ICF).

Structured Uncertainty Bound Determination From Data for Control and Performance Validation

NASA Technical Reports Server (NTRS)

Lim, Kyong B.

2003-01-01

This report attempts to document the broad scope of issues that must be satisfactorily resolved before one can expect to methodically obtain, with a reasonable confidence, a near-optimal robust closed loop performance in physical applications. These include elements of signal processing, noise identification, system identification, model validation, and uncertainty modeling. Based on a recently developed methodology involving a parameterization of all model validating uncertainty sets for a given linear fractional transformation (LFT) structure and noise allowance, a new software, Uncertainty Bound Identification (UBID) toolbox, which conveniently executes model validation tests and determine uncertainty bounds from data, has been designed and is currently available. This toolbox also serves to benchmark the current state-of-the-art in uncertainty bound determination and in turn facilitate benchmarking of robust control technology. To help clarify the methodology and use of the new software, two tutorial examples are provided. The first involves the uncertainty characterization of a flexible structure dynamics, and the second example involves a closed loop performance validation of a ducted fan based on an uncertainty bound from data. These examples, along with other simulation and experimental results, also help describe the many factors and assumptions that determine the degree of success in applying robust control theory to practical problems.

Hydrogen retention in lithium and lithium oxide films

NASA Astrophysics Data System (ADS)

Buzi, L.; Yang, Y.; Domínguez-Gutiérrez, F. J.; Nelson, A. O.; Hofman, M.; Krstić, P. S.; Kaita, R.; Koel, B. E.

2018-04-01

Pure lithium (Li) surfaces are difficult to maintain in fusion devices due to rapid oxide formation, therefore, parameterizing and understanding the mechanisms of hydrogen (H, D) retention in lithium oxide (Li2O) in addition to pure Li is crucial for Li plasma-facing material applications. To compare H retention in Li and Li2O films, measurements were made as a function of surface temperature (90-520 K) under ultrahigh vacuum (UHV) conditions using temperature programmed desorption (TPD). In both cases, the total retention dropped with surface temperature, from 95% at 90 K to 35% at 520 K Li2O films retained H in similar amounts as pure Li. Molecular Dynamics (MD) modeling was used to elucidate the mechanisms of H retention, and results were consistent with experiments in terms of both retention fraction and the drop of retention with temperature.

Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin.

PubMed

Zhou, Yu; Wu, Chao; Zhao, Lifeng; Huang, Niu

2014-10-01

Hemagglutinin (HA) mediates the membrane fusion process of influenza virus through its pH-induced conformational change. However, it remains challenging to study its structure reorganization pathways in atomic details. Here, we first applied continuous constant pH molecular dynamics approach to predict the pK(a) values of titratable residues in H2 subtype HA. The calculated net-charges in HA1 globular heads increase from 0e (pH 7.5) to +14e (pH 4.5), indicating that the charge repulsion drives the detrimerization of HA globular domains. In HA2 stem regions, critical pH sensors, such as Glu103(2), His18(1), and Glu89(1), are identified to facilitate the essential structural reorganizations in the fusing pathways, including fusion peptide release and interhelical loop transition. To probe the contribution of identified pH sensors and unveil the early steps of pH-induced conformational change, we carried out conventional molecular dynamics simulations in explicit water with determined protonation state for each titratable residue in different environmental pH conditions. Particularly, energy barriers involving previously uncharacterized hydrogen bonds and hydrophobic interactions are identified in the fusion peptide release pathway. Nevertheless, comprehensive comparisons across HA family members indicate that different HA subtypes might employ diverse pH sensor groups along with different fusion pathways. Finally, we explored the fusion inhibition mechanism of antibody CR6261 and small molecular inhibitor TBHQ, and discovered a novel druggable pocket in H2 and H5 subtypes. Our results provide the underlying mechanism for the pH-driven conformational changes and also novel insight for anti-flu drug development. © 2014 Wiley Periodicals, Inc.

Advances in data representation for hard/soft information fusion

NASA Astrophysics Data System (ADS)

Rimland, Jeffrey C.; Coughlin, Dan; Hall, David L.; Graham, Jacob L.

2012-06-01

Information fusion is becoming increasingly human-centric. While past systems typically relegated humans to the role of analyzing a finished fusion product, current systems are exploring the role of humans as integral elements in a modular and extensible distributed framework where many tasks can be accomplished by either human or machine performers. For example, "participatory sensing" campaigns give humans the role of "soft sensors" by uploading their direct observations or as "soft sensor platforms" by using mobile devices to record human-annotated, GPS-encoded high quality photographs, video, or audio. Additionally, the role of "human-in-the-loop", in which individuals or teams using advanced human computer interface (HCI) tools such as stereoscopic 3D visualization, haptic interfaces, or aural "sonification" interfaces can help to effectively engage the innate human capability to perform pattern matching, anomaly identification, and semantic-based contextual reasoning to interpret an evolving situation. The Pennsylvania State University is participating in a Multi-disciplinary University Research Initiative (MURI) program funded by the U.S. Army Research Office to investigate fusion of hard and soft data in counterinsurgency (COIN) situations. In addition to the importance of this research for Intelligence Preparation of the Battlefield (IPB), many of the same challenges and techniques apply to health and medical informatics, crisis management, crowd-sourced "citizen science", and monitoring environmental concerns. One of the key challenges that we have encountered is the development of data formats, protocols, and methodologies to establish an information architecture and framework for the effective capture, representation, transmission, and storage of the vastly heterogeneous data and accompanying metadata -- including capabilities and characteristics of human observers, uncertainty of human observations, "soft" contextual data, and information pedigree. This paper describes our findings and offers insights into the role of data representation in hard/soft fusion.

Adaptive Neural Output Feedback Control for Nonstrict-Feedback Stochastic Nonlinear Systems With Unknown Backlash-Like Hysteresis and Unknown Control Directions.

PubMed

Yu, Zhaoxu; Li, Shugang; Yu, Zhaosheng; Li, Fangfei

2018-04-01

This paper investigates the problem of output feedback adaptive stabilization for a class of nonstrict-feedback stochastic nonlinear systems with both unknown backlashlike hysteresis and unknown control directions. A new linear state transformation is applied to the original system, and then, control design for the new system becomes feasible. By combining the neural network's (NN's) parameterization, variable separation technique, and Nussbaum gain function method, an input-driven observer-based adaptive NN control scheme, which involves only one parameter to be updated, is developed for such systems. All closed-loop signals are bounded in probability and the error signals remain semiglobally bounded in the fourth moment (or mean square). Finally, the effectiveness and the applicability of the proposed control design are verified by two simulation examples.

Structural analysis of the intracellular domain of (pro)renin receptor fused to maltose-binding protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yanfeng; Gao, Xiaoli; Michael Garavito, R., E-mail: garavito@msu.edu

2011-04-22

Highlights: {yields} Crystal structure of the intracellular domain of (pro)renin receptor (PRR-IC) as MBP fusion protein at 2.0 A (maltose-free) and 2.15 A (maltose-bound). {yields} MBP fusion protein is a dimer in crystals in the presence and absence of maltose. {yields} PRR-IC domain is responsible for the dimerization of the fusion protein. {yields} Residues in the PRR-IC domain, particularly two tyrosines, dominate the intermolecular interactions, suggesting a role for the PRR-IC domain in PRR dimerization. -- Abstract: The (pro)renin receptor (PRR) is an important component of the renin-angiotensin system (RAS), which regulates blood pressure and cardiovascular function. The integral membranemore » protein PRR contains a large extracellular domain ({approx}310 amino acids), a single transmembrane domain ({approx}20 amino acids) and an intracellular domain ({approx}19 amino acids). Although short, the intracellular (IC) domain of the PRR has functionally important roles in a number of signal transduction pathways activated by (pro)renin binding. Meanwhile, together with the transmembrane domain and a small portion of the extracellular domain ({approx}30 amino acids), the IC domain is also involved in assembly of V{sub 0} portion of the vacuolar proton-translocating ATPase (V-ATPase). To better understand structural and multifunctional roles of the PRR-IC, we report the crystal structure of the PRR-IC domain as maltose-binding protein (MBP) fusion proteins at 2.0 A (maltose-free) and 2.15 A (maltose-bound). In the two separate crystal forms having significantly different unit-cell dimensions and molecular packing, MBP-PRR-IC fusion protein was found to be a dimer, which is different with the natural monomer of native MBP. The PRR-IC domain appears as a relatively flexible loop and is responsible for the dimerization of MBP fusion protein. Residues in the PRR-IC domain, particularly two tyrosines, dominate the intermonomer interactions, suggesting a role for the PRR-IC domain in protein oligomerization.« less

A monolithic 3D-0D coupled closed-loop model of the heart and the vascular system: Experiment-based parameter estimation for patient-specific cardiac mechanics.

PubMed

Hirschvogel, Marc; Bassilious, Marina; Jagschies, Lasse; Wildhirt, Stephen M; Gee, Michael W

2016-10-15

A model for patient-specific cardiac mechanics simulation is introduced, incorporating a 3-dimensional finite element model of the ventricular part of the heart, which is coupled to a reduced-order 0-dimensional closed-loop vascular system, heart valve, and atrial chamber model. The ventricles are modeled by a nonlinear orthotropic passive material law. The electrical activation is mimicked by a prescribed parameterized active stress acting along a generic muscle fiber orientation. Our activation function is constructed such that the start of ventricular contraction and relaxation as well as the active stress curve's slope are parameterized. The imaging-based patient-specific ventricular model is prestressed to low end-diastolic pressure to account for the imaged, stressed configuration. Visco-elastic Robin boundary conditions are applied to the heart base and the epicardium to account for the embedding surrounding. We treat the 3D solid-0D fluid interaction as a strongly coupled monolithic problem, which is consistently linearized with respect to 3D solid and 0D fluid model variables to allow for a Newton-type solution procedure. The resulting coupled linear system of equations is solved iteratively in every Newton step using 2  ×  2 physics-based block preconditioning. Furthermore, we present novel efficient strategies for calibrating active contractile and vascular resistance parameters to experimental left ventricular pressure and stroke volume data gained in porcine experiments. Two exemplary states of cardiovascular condition are considered, namely, after application of vasodilatory beta blockers (BETA) and after injection of vasoconstrictive phenylephrine (PHEN). The parameter calibration to the specific individual and cardiovascular state at hand is performed using a 2-stage nonlinear multilevel method that uses a low-fidelity heart model to compute a parameter correction for the high-fidelity model optimization problem. We discuss 2 different low-fidelity model choices with respect to their ability to augment the parameter optimization. Because the periodic state conditions on the model (active stress, vascular pressures, and fluxes) are a priori unknown and also dependent on the parameters to be calibrated (and vice versa), we perform parameter calibration and periodic state condition estimation simultaneously. After a couple of heart beats, the calibration algorithm converges to a settled, periodic state because of conservation of blood volume within the closed-loop circulatory system. The proposed model and multilevel calibration method are cost-efficient and allow for an efficient determination of a patient-specific in silico heart model that reproduces physiological observations very well. Such an individual and state accurate model is an important predictive tool in intervention planning, assist device engineering and other medical applications. Copyright © 2016 John Wiley & Sons, Ltd.

Radiation damage studies of ion-irradiated low-activation developmental martensitic steel alloys for fusion applications

NASA Astrophysics Data System (ADS)

Mazey, D. J.; Hanks, W.; Lurcook, O. K.

1990-09-01

Five martensitic, nominally 9 and 11% Cr-W-V-Mn-Ta stainless steels which have been developed as low-activation alloys for fusion-reactor structural applications have been irradiated with 52 MeV Cr 6+ ions to 20 dpa at 475°C in the Harwell Variable Energy Cyclotron (VEC). Four of the alloys contained additions of 0.1 wt% Ta and these had been shown in prior tests to have mechanical properties comparable with the conventional FV 448 alloy. Examinations by TEM showed that irradiation-induced precipitates were present on a fine-scale in all of the alloys. These comprised Cr-rich lath-like defects in the 9Cr, Ta-free alloy; small Cr-rich particles in the 9Cr-3W-0.1Ta alloy and Cr-rich planar precipitates in the remaining alloys. Little or no irradiation-induced cavitation was observed. The other important irradiation-induced response was in the dislocation structure in the Ta-containing alloys which comprised an extensive rafted array of elongated a <100> type dislocation loops having major axes aligned in <100> directions. A significant fraction of the presumed a <100> loops contained stacking-fault fringes and analysis suggested that these were Cr 2N or Fe 4N nitride phase which it is known can form on {001} habit planes. Such nitrides are observed frequently under thermal-annealing conditions in ferritic steels, but less frequently under irradiation. Their formation in relation to the void swelling resistance of ferritic-martensitic alloys is discussed.

Functional and real-time requirements of a multisensor data fusion (MSDF) situation and threat assessment (STA) resource management (RM) system

NASA Astrophysics Data System (ADS)

Duquet, Jean Remi; Bergeron, Pierre; Blodgett, Dale E.; Couture, Jean; Macieszczak, Maciej; Mayrand, Michel; Chalmers, Bruce A.; Paradis, Stephane

1998-03-01

The Research and Development group at Lockheed Martin Canada, in collaboration with the Defence Research Establishment Valcartier, has undertaken a research project in order to capture and analyze the real-time and functional requirements of a next generation Command and Control System (CCS) for the Canadian Patrol Frigates, integrating Multi- Sensor Data Fusion (MSDF), Situation and Threat Assessment (STA) and Resource Management (RM). One important aspect of the project is to define how the use of Artificial Intelligence may optimize the performance of an integrated, real-time MSDF/STA/RM system. A closed-loop simulation environment is being developed to facilitate the evaluation of MSDF/STA/RM concepts, algorithms and architectures. This environment comprises (1) a scenario generator, (2) complex sensor, hardkill and softkill weapon models, (3) a real-time monitoring tool, (4) a distributed Knowledge-Base System (KBS) shell. The latter is being completely redesigned and implemented in-house since no commercial KBS shell could adequately satisfy all the project requirements. The closed- loop capability of the simulation environment, together with its `simulated real-time' capability, allows the interaction between the MSDF/STA/RM system and the environment targets during the execution of a scenario. This capability is essential to measure the performance of many STA and RM functionalities. Some benchmark scenarios have been selected to demonstrate quantitatively the capabilities of the selected MSDF/STA/RM algorithms. The paper describes the simulation environment and discusses the MSDF/STA/RM functionalities currently implemented and their performance as an automatic CCS.

CORSICA modelling of ITER hybrid operation scenarios

NASA Astrophysics Data System (ADS)

Kim, S. H.; Bulmer, R. H.; Campbell, D. J.; Casper, T. A.; LoDestro, L. L.; Meyer, W. H.; Pearlstein, L. D.; Snipes, J. A.

2016-12-01

The hybrid operating mode observed in several tokamaks is characterized by further enhancement over the high plasma confinement (H-mode) associated with reduced magneto-hydro-dynamic (MHD) instabilities linked to a stationary flat safety factor (q ) profile in the core region. The proposed ITER hybrid operation is currently aiming at operating for a long burn duration (>1000 s) with a moderate fusion power multiplication factor, Q , of at least 5. This paper presents candidate ITER hybrid operation scenarios developed using a free-boundary transport modelling code, CORSICA, taking all relevant physics and engineering constraints into account. The ITER hybrid operation scenarios have been developed by tailoring the 15 MA baseline ITER inductive H-mode scenario. Accessible operation conditions for ITER hybrid operation and achievable range of plasma parameters have been investigated considering uncertainties on the plasma confinement and transport. ITER operation capability for avoiding the poloidal field coil current, field and force limits has been examined by applying different current ramp rates, flat-top plasma currents and densities, and pre-magnetization of the poloidal field coils. Various combinations of heating and current drive (H&CD) schemes have been applied to study several physics issues, such as the plasma current density profile tailoring, enhancement of the plasma energy confinement and fusion power generation. A parameterized edge pedestal model based on EPED1 added to the CORSICA code has been applied to hybrid operation scenarios. Finally, fully self-consistent free-boundary transport simulations have been performed to provide information on the poloidal field coil voltage demands and to study the controllability with the ITER controllers. Extended from Proc. 24th Int. Conf. on Fusion Energy (San Diego, 2012) IT/P1-13.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Feng; Fong, Rachel H.; Austin, Stephen K.

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. In this paper, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain’s β-ribbon connector of the viral glycoprotein E2. The footprints ofmore » these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. Finally, this finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes.« less

Inhibition of Influenza H7 Hemagglutinin-Mediated Entry

PubMed Central

Antanasijevic, Aleksandar; Cheng, Han; Wardrop, Duncan J.; Rong, Lijun; Caffrey, Michael

2013-01-01

The recent outbreak of H7N9 influenza in China is of high concern to public health. H7 hemagglutinin (HA) plays a critical role in influenza entry and thus HA presents an attractive target for antivirals. Previous studies have suggested that the small molecule tert-butyl hydroquinone (TBHQ) inhibits the entry of influenza H3 HA by binding to the stem loop of HA and stabilizing the neutral pH conformation of HA, thereby disrupting the membrane fusion step. Based on amino acid sequence, structure and immunogenicity, H7 is a related Group 2 HA. In this work we show, using a pseudovirus entry assay, that TBHQ inhibits H7 HA-mediated entry, as well as H3 HA-mediated entry, with an IC50∼6 µM. Using NMR, we show that TBHQ binds to the H7 stem loop region. STD NMR experiments indicate that the aromatic ring of TBHQ makes extensive contact with the H7 HA surface. Limited proteolysis experiments indicate that TBHQ inhibits influenza entry by stabilizing the H7 HA neutral pH conformation. Together, this work suggests that the stem loop region of H7 HA is an attractive target for therapeutic intervention and that TBHQ, which is a widely used food preservative, is a promising lead compound. PMID:24194835

Program user's manual: cryogen system for the analysis for the Mirror Fusion Test Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1979-04-01

The Mirror Fusion Test Facility being designed and constructed at the Lawrence Livermore Laboratory requires a liquid helium liquefaction, storage, distribution, and recovery system and a liquid nitrogen storage and distribution system. To provide a powerful analytical tool to aid in the design evolution of this system through hardware, a thermodynamic fluid flow model was developed. This model allows the Lawrence Livermore Laboratory to verify that the design meets desired goals and to play what if games during the design evolution. For example, what if the helium flow rate is changed in the magnet liquid helium flow loop; how doesmore » this affect the temperature, fluid quality, and pressure. This manual provides all the information required to run all or portions of this program as desired. In addition, the program is constructed in a modular fashion so changes or modifications can be made easily to keep up with the evolving design.« less

Protection of tokamak plasma facing components by a capillary porous system with lithium

NASA Astrophysics Data System (ADS)

Lyublinski, I.; Vertkov, A.; Mirnov, S.; Lazarev, V.

2015-08-01

Development of plasma facing material (PFM) based on the Capillary-Porous System (CPS) with lithium and activity on realization of lithium application strategy are addressed to meet the challenges under the creation of steady-state tokamak fusion reactor and fusion neutron source. Presented overview of experimental study of lithium CPS in plasma devices demonstrates the progress in protection of tokamak plasma facing components (PFC) from damage, stabilization and self-renewal of liquid lithium surface, elimination of plasma pollution and lithium accumulation in tokamak chamber. The possibility of PFC protection from the high power load related to cooling of the tokamak boundary plasma by radiation of non-fully stripped lithium ions supported by experimental results. This approach demonstrated in scheme of closed loops of Li circulation in the tokamak vacuum chamber and realized in a series of design of tokamak in-vessel elements.

Sensor fusion of cameras and a laser for city-scale 3D reconstruction.

PubMed

Bok, Yunsu; Choi, Dong-Geol; Kweon, In So

2014-11-04

This paper presents a sensor fusion system of cameras and a 2D laser sensorfor large-scale 3D reconstruction. The proposed system is designed to capture data on afast-moving ground vehicle. The system consists of six cameras and one 2D laser sensor,and they are synchronized by a hardware trigger. Reconstruction of 3D structures is doneby estimating frame-by-frame motion and accumulating vertical laser scans, as in previousworks. However, our approach does not assume near 2D motion, but estimates free motion(including absolute scale) in 3D space using both laser data and image features. In orderto avoid the degeneration associated with typical three-point algorithms, we present a newalgorithm that selects 3D points from two frames captured by multiple cameras. The problemof error accumulation is solved by loop closing, not by GPS. The experimental resultsshow that the estimated path is successfully overlaid on the satellite images, such that thereconstruction result is very accurate.

Experimental measurement of oil-water two-phase flow by data fusion of electrical tomography sensors and venturi tube

NASA Astrophysics Data System (ADS)

Liu, Yinyan; Deng, Yuchi; Zhang, Maomao; Yu, Peining; Li, Yi

2017-09-01

Oil-water two-phase flows are commonly found in the production processes of the petroleum industry. Accurate online measurement of flow rates is crucial to ensure the safety and efficiency of oil exploration and production. A research team from Tsinghua University has developed an experimental apparatus for multiphase flow measurement based on an electrical capacitance tomography (ECT) sensor, an electrical resistance tomography (ERT) sensor, and a venturi tube. This work presents the phase fraction and flow rate measurements of oil-water two-phase flows based on the developed apparatus. Full-range phase fraction can be obtained by the combination of the ECT sensor and the ERT sensor. By data fusion of differential pressures measured by venturi tube and the phase fraction, the total flow rate and single-phase flow rate can be calculated. Dynamic experiments were conducted on the multiphase flow loop in horizontal and vertical pipelines and at various flow rates.

Practical Considerations for Optic Nerve Estimation in Telemedicine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karnowski, Thomas Paul; Aykac, Deniz; Chaum, Edward

The projected increase in diabetes in the United States and worldwide has created a need for broad-based, inexpensive screening for diabetic retinopathy (DR), an eye disease which can lead to vision impairment. A telemedicine network with retina cameras and automated quality control, physiological feature location, and lesion / anomaly detection is a low-cost way of achieving broad-based screening. In this work we report on the effect of quality estimation on an optic nerve (ON) detection method with a confidence metric. We report on an improvement of the fusion technique using a data set from an ophthalmologists practice then show themore » results of the method as a function of image quality on a set of images from an on-line telemedicine network collected in Spring 2009 and another broad-based screening program. We show that the fusion method, combined with quality estimation processing, can improve detection performance and also provide a method for utilizing a physician-in-the-loop for images that may exceed the capabilities of automated processing.« less

Residues in the membrane-spanning domain core modulate conformation and fusogenicity of the HIV-1 envelope glycoprotein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shang Liang; Hunter, Eric, E-mail: eric.hunter2@emory.ed

2010-09-01

The membrane-spanning domain (MSD) of human immunodeficiency virus type I (HIV-1) envelope glycoprotein (Env) is critical for its biological activity. Initial studies have defined an almost invariant 'core' structure in the MSD and demonstrated that it is crucial for anchoring Env in the membrane and virus entry. We show here that amino acid substitutions in the MSD 'core' do not influence specific virus-cell attachment, nor CD4 receptor and CXCR4 coreceptor recognition by Env. However, substitutions within the MSD 'core' delayed the kinetics and reduced the efficiency of cell-cell fusion mediated by Env. Although we observed no evidence that membrane fusionmore » mediated by the MSD core mutants was arrested at a hemifusion stage, impaired Env fusogenicity was correlated with minor conformational changes in the V2, C1, and C5 regions in gp120 and the immunodominant loop in gp41. These changes could delay initiation of the conformational changes required in the fusion process.« less

Present status of the liquid lithium target facility in the international fusion materials irradiation facility (IFMIF)

NASA Astrophysics Data System (ADS)

Nakamura, Hiroo; Riccardi, B.; Loginov, N.; Ara, K.; Burgazzi, L.; Cevolani, S.; Dell'Orco, G.; Fazio, C.; Giusti, D.; Horiike, H.; Ida, M.; Ise, H.; Kakui, H.; Matsui, H.; Micciche, G.; Muroga, T.; Nakamura, Hideo; Shimizu, K.; Sugimoto, M.; Suzuki, A.; Takeuchi, H.; Tanaka, S.; Yoneoka, T.

2004-08-01

During the three year key element technology phase of the International Fusion Materials Irradiation Facility (IFMIF) project, completed at the end of 2002, key technologies have been validated. In this paper, these results are summarized. A water jet experiment simulating Li flow validated stable flow up to 20 m/s with a double reducer nozzle. In addition, a small Li loop experiment validated stable Li flow up to 14 m/s. To control the nitrogen content in Li below 10 wppm will require surface area of a V-Ti alloy getter of 135 m 2. Conceptual designs of diagnostics have been carried out. Moreover, the concept of a remote handling system to replace the back wall based on `cut and reweld' and `bayonet' options has been established. Analysis by FMEA showed safe operation of the target system. Recent activities in the transition phase, started in 2003, and plan for the next phase are also described.

Biophysical characterization of V3-lipopeptide liposomes influencing HIV-1 infectivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rizos, Apostolos K.; Baritaki, Stavroula; Department of Virology, Medical School, University of Crete, Heraklion, Crete

2007-04-20

The V3-loop of the HIV-1 gp120 alters host cell immune function and modulates infectivity. We investigated biophysical parameters of liposome constructs with embedded lipopeptides from the principle neutralizing domain of the V3-loop and their influence on viral infectivity. Dynamic light scattering measurements showed liposome supramolecular structures with hydrodynamic radius of the order of 900 and 1300 nm for plain and V3-lipopeptide liposomes. Electron paramagnetic resonance measurements showed almost identical local microenvironment. The difference in liposome hydrodynamic radius was attributed to the fluctuating ionic environment of the V3-lipopeptide liposomes. In vitro HIV-1 infectivity assays showed that plain liposomes reduced virus productionmore » in all cell cultures, probably due to the hydrophobic nature of the aggregates. Liposomes carrying V3-lipopeptides with different cationic potentials restored and even enhanced infectivity (p < 0.05). These results highlight the need for elucidation of the involvement of lipid bilayers as dynamic components in supramolecular structures and in HIV-1 fusion mechanisms.« less

QCD corrections to ZZ production in gluon fusion at the LHC

DOE PAGES

Caola, Fabrizio; Melnikov, Kirill; Rontsch, Raoul; ...

2015-11-23

We compute the next-to-leading-order QCD corrections to the production of two Z-bosons in the annihilation of two gluons at the LHC. Being enhanced by a large gluon flux, these corrections provide a distinct and, potentially, the dominant part of the N 3LO QCD contributions to Z-pair production in proton collisions. The gg → ZZ annihilation is a loop-induced process that receives the dominant contribution from loops of five light quarks, that are included in our computation in the massless approximation. We find that QCD corrections increase the gg → ZZ production cross section by O(50%–100%) depending on the values ofmore » the renormalization and factorization scales used in the leading-order computation and the collider energy. Furthermore, the large corrections to the gg → ZZ channel increase the pp → ZZ cross section by about 6% to 8%, exceeding the estimated theoretical uncertainty of the recent next-to-next-to-leading-order QCD calculation.« less

Vaporization of liquid Pb-Li eutectic alloy from 1000K to 1200K - A high temperature mass spectrometric study

NASA Astrophysics Data System (ADS)

Jain, U.; Mukherjee, A.; Dey, G. K.

2017-09-01

Liquid lead-lithium eutectic will be used as a coolant in fusion reactor blanket loop. Vapor pressure of the eutectic is an important parameter to accurately predict its in-loop behavior. Past measurements of vapor pressure of the eutectic relied on indirect methods. In this paper, we report for the first time the in-situ vaporization behavior of the liquid alloy between 1042 and 1176 K by Knudsen effusion mass spectrometry (KEMS). It was seen that the vaporization occurred by independent evaporation of lead and lithium. No complex intermetallic vapor was seen in the mass spectra. The partial pressures and enthalpy of vaporization of Pb and Li were evaluated directly from the measured ion intensities formed from the equilibrium vapor over the alloy. The activity of Li over a temperature range of 1042-1176 K was found to be 4.8 × 10-5 to that of pure Li, indicating its very low activity in the alloy.

Split green fluorescent protein as a modular binding partner for protein crystallization.

PubMed

Nguyen, Hau B; Hung, Li-Wei; Yeates, Todd O; Terwilliger, Thomas C; Waldo, Geoffrey S

2013-12-01

A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was tested by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10-11) hairpin in complex with GFP(1-9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10-11) hairpin with a variety of GFP(1-9) mutants engineered for favorable crystallization.

An experimental and theoretical investigation of the liquefaction dynamics of a phase change material in a normal gravity environment

NASA Technical Reports Server (NTRS)

Bain, R. L.; Stermole, F. J.; Golden, J. O.

1972-01-01

Experimental and theoretical investigations were undertaken to determine the role of gravity-induced free convection upon the liquefaction dynamics of a cylindrical paraffin slab under normal gravity conditions. The experimental equipment consisted of a test cell, a fluid-loop heating system, and a multipoint recorder. The test chamber was annular in shape with an effective radius of 1.585 cm and a length of 5.08 cm. The heating chamber was a 1.906 cm diameter tube going through the center of the test chamber, and connected to the fluid loop heating system. All experimental runs were made with the longitudinal axis of the test cell in the vertical direction to insure that convection was not a function of the angular axis of the cell. Ten melting runs were made at various hot wall temperatures. Also, two pure conduction solidification runs were made to determine an experimental latent heat of fusion.

Hydrogen retention in lithium and lithium oxide films

DOE PAGES

Buzi, L.; Yang, Y.; Dominguez-Gutierrez, F. J.; ...

2018-02-09

Pure lithium (Li) surfaces are difficult to maintain in fusion devices due to rapid oxide formation, therefore, parameterizing and understanding the mechanisms of hydrogen (H, D) retention in lithium oxide (Li 2O) in addition to pure Li is crucial for Li plasma-facing material applications. To compare H retention in Li and Li 2O films, measurements were made as a function of surface temperature (90–520 K) under ultrahigh vacuum (UHV) conditions using temperature programmed desorption (TPD). In both cases, the total retention dropped with surface temperature, from 95% at 90 K to 35% at 520 K Li 2O films retained Hmore » in similar amounts as pure Li. Finally, Molecular Dynamics (MD) modeling was used to elucidate the mechanisms of H retention, and results were consistent with experiments in terms of both retention fraction and the drop of retention with temperature.« less

Hydrogen retention in lithium and lithium oxide films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buzi, L.; Yang, Y.; Dominguez-Gutierrez, F. J.

Pure lithium (Li) surfaces are difficult to maintain in fusion devices due to rapid oxide formation, therefore, parameterizing and understanding the mechanisms of hydrogen (H, D) retention in lithium oxide (Li 2O) in addition to pure Li is crucial for Li plasma-facing material applications. To compare H retention in Li and Li 2O films, measurements were made as a function of surface temperature (90–520 K) under ultrahigh vacuum (UHV) conditions using temperature programmed desorption (TPD). In both cases, the total retention dropped with surface temperature, from 95% at 90 K to 35% at 520 K Li 2O films retained Hmore » in similar amounts as pure Li. Finally, Molecular Dynamics (MD) modeling was used to elucidate the mechanisms of H retention, and results were consistent with experiments in terms of both retention fraction and the drop of retention with temperature.« less

Study of SOL in DIII-D tokamak with SOLPS suite of codes.

NASA Astrophysics Data System (ADS)

Pankin, Alexei; Bateman, Glenn; Brennan, Dylan; Coster, David; Hogan, John; Kritz, Arnold; Kukushkin, Andrey; Schnack, Dalton; Snyder, Phil

2005-10-01

The scrape-of-layer (SOL) region in DIII-D tokamak is studied with the SOLPS integrated suite of codes. The SOLPS package includes the 3D multi-species Monte-Carlo neutral code EIRINE and 2D multi-fluid code B2. The EIRINE and B2 codes are cross-coupled through B2-EIRINE interface. The results of SOLPS simulations are used in the integrated modeling of the plasma edge in DIII-D tokamak with the ASTRA transport code. Parameterized dependences for neutral particle fluxes that are computed with the SOLPS code are implemented in a model for the H-mode pedestal and ELMs [1] in the ASTRA code. The effects of neutrals on the H-mode pedestal and ELMs are studied in this report. [1] A. Y. Pankin, I. Voitsekhovitch, G. Bateman, et al., Plasma Phys. Control. Fusion 47, 483 (2005).

Next-to-leading order γ γ + 2 - jet production at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bern, Z.; Dixon, L. J.; Febres Cordero, F.

We present next-to-leading-order QCD predictions for cross sections and for a comprehensive set of distributions in γγ+2-jet production at the Large Hadron Collider. We consider the contributions from loop amplitudes for two photons and four gluons, but we neglect top quarks. We use BlackHat together with SHERPA to carry out the computation. We use a Frixione cone isolation for the photons. We study standard sets of cuts on the jets and the photons and also sets of cuts appropriate for studying backgrounds to Higgs-boson production via vector-boson fusion.

Alteration of a Second Putative Fusion Peptide of Structural Glycoprotein E2 of Classical Swine Fever Virus Alters Virus Replication and Virulence in Swine

PubMed Central

Holinka, L. G.; Largo, E.; Gladue, D. P.; O'Donnell, V.; Risatti, G. R.; Nieva, J. L.

2016-01-01

ABSTRACT E2, the major envelope glycoprotein of classical swine fever virus (CSFV), is involved in several critical virus functions, including cell attachment, host range susceptibility, and virulence in natural hosts. Functional structural analysis of E2 based on a Wimley-White interfacial hydrophobicity distribution predicted the involvement of a loop (residues 864 to 881) stabilized by a disulfide bond (869CKWGGNWTCV878, named FPII) in establishing interactions with the host cell membrane. This loop further contains an 872GG873 dipeptide, as well as two aromatic residues (871W and 875W) accessible to solvent. Reverse genetics utilizing a full-length infectious clone of the highly virulent CSFV strain Brescia (BICv) was used to evaluate how amino acid substitutions within FPII may affect replication of BICv in vitro and virus virulence in swine. Recombinant CSFVs containing mutations in different residues of FPII were constructed. A particular construct, harboring amino acid substitutions W871T, W875D, and V878T (FPII.2), demonstrated a significantly decreased ability to replicate in a swine cell line (SK6) and swine macrophage primary cell cultures. Interestingly, mutated virus FPII.2 was completely attenuated in pigs. Also, animals infected with FPII.2 virus were protected against virulent challenge with Brescia virus at 21 days postvaccination. Supporting a role for the E2 the loop from residues 864 to 881 in membrane fusion, only synthetic peptides that were based on the native E2 functional sequence were competent for insertion into model membranes and perturbation of their integrity, and this functionality was lost in synthetic peptides harboring amino acid substitutions W871T, W875D, and V878T in FPII.2. IMPORTANCE This report describes the identification and characterization of a putative fusion peptide (FP) in the major structural protein E2 of classical swine fever virus (CSFV). The FP identification was performed by functional structural analysis of E2. We characterized the functional significance of this FP by using artificial membranes. Replacement of critical amino acid residues within the FP radically alters how it interacts with the artificial membranes. When we introduced the same mutations into the viral sequence, there was a reduction in replication in cell cultures, and when we infected domestic swine, the natural host of CSFV host, we observed that the virus was now completely attenuated in swine. In addition, the virus mutant that was attenuated in vivo efficiently protected pigs against wild-type virus. These results provide the proof of principle to support as a strategy for vaccine development the discovery and manipulation of FPs. PMID:27605674

Exploring new technologies to facilitate laparoscopic surgery: creating intestinal anastomoses without sutures or staples, using a radio-frequency-energy-driven bipolar fusion device.

PubMed

Smulders, J F; de Hingh, I H J T; Stavast, J; Jackimowicz, J J

2007-11-01

Intestinal anastomotic healing requires apposition of the collagen containing submucosal layers of the opposing intestinal walls, which is traditionally achieved by staples or sutures. Recently, a feedback-controlled bipolar sealing system (LigaSure) has been successfully introduced to seal and transect vessels. Since this technology depends on fusion of collagen fibres which are abundantly present in the intestinal wall, the possibility to create intestinal anastomoses using this technology was investigated in the present study. For this purpose a new-generation radiofrequency (RF) generator and a prototype of the Ligasure Anastomotic Device (LAD) have been developed. The generator incorporates a closed loop control system which monitors tissue fusion, compares it with a mathematical model of ideal fusion based on the density and compliance of intestinal tissue and adjusts energy output accordingly. In total 8 anastomoses were created in a porcine model (4 pigs, 2 anastomoses each) and healing was assessed by macroscopic and histological examination. All seals were macroscopic intact both immediate after creation and at sacrifice at the 7th postoperative day. Between operations, pigs appeared healthy and had normal intestinal passage. Histological examination of the anastomoses revealed undisturbed healing with granulation tissue, newly synthesised collagen in the submucosa and re-epithelialization at the borders of the seals. These results confirm the feasibility to create experimental intestinal anastomoses using LigaSure technology. This may be an important step towards the development of new laparoscopic equipment combining dissecting and reconstructive properties within one single instrument.

Dressing the Coronal Magnetic Extrapolations of Active Regions with a Parameterized Thermal Structure

NASA Astrophysics Data System (ADS)

Nita, Gelu M.; Viall, Nicholeen M.; Klimchuk, James A.; Loukitcheva, Maria A.; Gary, Dale E.; Kuznetsov, Alexey A.; Fleishman, Gregory D.

2018-01-01

The study of time-dependent solar active region (AR) morphology and its relation to eruptive events requires analysis of imaging data obtained in multiple wavelength domains with differing spatial and time resolution, ideally in combination with 3D physical models. To facilitate this goal, we have undertaken a major enhancement of our IDL-based simulation tool, GX_Simulator, previously developed for modeling microwave and X-ray emission from flaring loops, to allow it to simulate quiescent emission from solar ARs. The framework includes new tools for building the atmospheric model and enhanced routines for calculating emission that include new wavelengths. In this paper, we use our upgraded tool to model and analyze an AR and compare the synthetic emission maps with observations. We conclude that the modeled magneto-thermal structure is a reasonably good approximation of the real one.

Compensation in the presence of deep turbulence using tiled-aperture architectures

NASA Astrophysics Data System (ADS)

Spencer, Mark F.; Brennan, Terry J.

2017-05-01

The presence of distributed-volume atmospheric aberrations or "deep turbulence" presents unique challenges for beam-control applications which look to sense and correct for disturbances found along the laser-propagation path. This paper explores the potential for branch-point-tolerant reconstruction algorithms and tiled-aperture architectures to correct for the branch cuts contained in the phase function due to deep-turbulence conditions. Using wave-optics simulations, the analysis aims to parameterize the fitting-error performance of tiled-aperture architectures operating in a null-seeking control loop with piston, tip, and tilt compensation of the individual optical beamlet trains. To evaluate fitting-error performance, the analysis plots normalized power in the bucket as a function of the Fried coherence diameter, the log-amplitude variance, and the number of subapertures for comparison purposes. Initial results show that tiled-aperture architectures with a large number of subapertures outperform filled-aperture architectures with continuous-face-sheet deformable mirrors.

Transient cage formation around hot gold colloids dispersed in polymer solutions.

PubMed

Schwaiger, F; Zimmermann, W; Köhler, W

2011-12-14

Gold colloids dispersed in dilute to concentrated polymer solutions can efficiently be heated by laser irradiation and act as almost pointlike heat sources. In systems with positive Soret coefficients S(T) of the polymer, such as solutions of polystyrene in toluene, the polymer can almost entirely be removed from the particle surface. The colloid attracts the solvent and a transient cage of low viscosity and dramatically enhanced mobility is formed, which follows the motion of the particle with a certain retardation. Based on a complete parameterization of S(T)(M, c, T), we analyze in detail the stationary temperature, concentration, and viscosity profiles. Depending on the polymer molar mass and concentration on the distance to the glass transition temperature, the negative or positive feedback-loops are established that lead to either attenuation or self-amplification of the polymer depletion. © 2011 American Institute of Physics

Functional and structural analysis of the sialic acid-binding domain of rotaviruses.

PubMed Central

Isa, P; López, S; Segovia, L; Arias, C F

1997-01-01

The infectivity of most animal rotaviruses is dependent on the interaction of the virus spike protein VP4 with a sialic acid (SA)-containing cell receptor, and the SA-binding domain of this protein has been mapped between amino acids 93 and 208 of its trypsin cleavage fragment VP8. To identify which residues in this region are essential for the SA-binding activity, we performed alanine mutagenesis of the rotavirus RRV VP8 expressed in bacteria as a fusion polypeptide with glutathione S-transferase. Tyrosines were primarily targeted since tyrosine has been involved in the interaction of other viral hemagglutinins with SA. Of the 15 substitutions carried out, 10 abolished the SA-dependent hemagglutination activity of the protein, as well as its ability to bind to glycophorin A in a solid-phase assay. However, only alanine substitutions for tyrosines 155 and 188 and for serine 190 did not affect the overall conformation of the protein, as judged by their interaction with a panel of conformationally sensitive neutralizing VP8 monoclonal antibodies (MAbs). These findings suggest that these three amino acids play an essential role in the SA-binding activity of the protein, presumably by interacting directly with the SA molecule. The predicted secondary structure of VP8 suggests that it is organized as 11 beta-strands separated by loops; in this model, Tyr-155 maps to loop 7 while Tyr-188 and Ser-190 map to loop 9. The close proximity of these two loops is also supported by previous results from competition experiments with neutralizing MAbs directed at RRV VP8. PMID:9261399

Synthesis of single- and double-chain fluorocarbon and hydrocarbon galactosyl amphiphiles and their anti-HIV-1 activity.

PubMed

Faroux-Corlay, B; Clary, L; Gadras, C; Hammache, D; Greiner, J; Santaella, C; Aubertin, A M; Vierling, P; Fantini, J

2000-07-24

Galactosylceramide (GalCer) is an alternative receptor allowing HIV-1 entry into CD4(-)/GalCer(+) cells. This glycosphingolipid recognizes the V3 loop of HIV gp120, which plays a key role in the fusion of the HIV envelope and cellular membrane. To inhibit HIV uptake and infection, we designed and synthesized analogs of GalCer. These amphiphiles and bolaamphiphiles consist of single and double hydrocarbon and/or fluorocarbon chain beta-linked to galactose and galactosamine. They derive from serine (GalSer), cysteine (GalCys), and ethanolamine (GalAE). The anti-HIV activity and cytotoxicity of these galactolipids were evaluated in vitro on CEM-SS (a CD4(+) cell line), HT-29, a CD4(-) cell line expressing high levels of GalCer receptor, and/or HT29 genetically modified to express CD4. GalSer and GalAE derivatives, tested in aqueous medium or as part of liposome preparation, showed moderate anti-HIV-1 activities (IC50 in the 20-220 microM range), whereas none of the GalCys derivatives was found to be active. Moreover, only some of these anti-HIV active analogs inhibited the binding of [3H]suramin (a polysulfonyl compound which displays a high affinity for the V3 loop) to SPC3, a synthetic peptide which contains the conserved GPGRAF region of the V3 loop. Our results most likely indicate that the neutralization of the virion through masking of this conserved V3 loop region is not the only mechanism involved in the HIV-1 antiviral activity of our GalCer analogs.

Space-Time Data Fusion

NASA Technical Reports Server (NTRS)

Braverman, Amy; Nguyen, Hai; Olsen, Edward; Cressie, Noel

2011-01-01

Space-time Data Fusion (STDF) is a methodology for combing heterogeneous remote sensing data to optimally estimate the true values of a geophysical field of interest, and obtain uncertainties for those estimates. The input data sets may have different observing characteristics including different footprints, spatial resolutions and fields of view, orbit cycles, biases, and noise characteristics. Despite these differences all observed data can be linked to the underlying field, and therefore the each other, by a statistical model. Differences in footprints and other geometric characteristics are accounted for by parameterizing pixel-level remote sensing observations as spatial integrals of true field values lying within pixel boundaries, plus measurement error. Both spatial and temporal correlations in the true field and in the observations are estimated and incorporated through the use of a space-time random effects (STRE) model. Once the models parameters are estimated, we use it to derive expressions for optimal (minimum mean squared error and unbiased) estimates of the true field at any arbitrary location of interest, computed from the observations. Standard errors of these estimates are also produced, allowing confidence intervals to be constructed. The procedure is carried out on a fine spatial grid to approximate a continuous field. We demonstrate STDF by applying it to the problem of estimating CO2 concentration in the lower-atmosphere using data from the Atmospheric Infrared Sounder (AIRS) and the Japanese Greenhouse Gasses Observing Satellite (GOSAT) over one year for the continental US.

A polycrystal plasticity model of strain localization in irradiated iron

NASA Astrophysics Data System (ADS)

Barton, Nathan R.; Arsenlis, Athanasios; Marian, Jaime

2013-02-01

At low to intermediate homologous temperatures, the degradation of structural materials performance in nuclear environments is associated with high number densities of nanometric defects produced in irradiation cascades. In polycrystalline ferritic materials, self-interstitial dislocations loops are a principal signature of irradiation damage, leading to a mechanical response characterized by increased yield strengths, decreased total strain to failure, and decreased work hardening as compared to the unirradiated behavior. Above a critical defect concentration, the material deforms by plastic flow localization, giving rise to strain softening in terms of the engineering stress-strain response. Flow localization manifests itself in the form of defect-depleted crystallographic channels, through which all dislocation activity is concentrated. In this paper, we describe the formulation of a crystal plasticity model for pure Fe embedded in a finite element polycrystal simulator and present results of uniaxial tensile deformation tests up to 10% strain. We use a tensorial damage descriptor variable to capture the evolution of the irradiation damage loop subpopulation during deformation. The model is parameterized with detailed dislocation dynamics simulations of tensile tests up to 1.5% deformation of systems containing various initial densities of irradiation defects. The coarse-grained simulations are shown to capture the essential details of the experimental stress response observed in ferritic alloys and steels. Our methodology provides an effective linkage between the defect scale, of the order of one nanometer, and the continuum scale involving multiple grain orientations.

Pion, Kaon, Proton and Antiproton Production in Proton-Proton Collisions

NASA Technical Reports Server (NTRS)

Norbury, John W.; Blattnig, Steve R.

2008-01-01

Inclusive pion, kaon, proton, and antiproton production from proton-proton collisions is studied at a variety of proton energies. Various available parameterizations of Lorentz-invariant differential cross sections as a function of transverse momentum and rapidity are compared with experimental data. The Badhwar and Alper parameterizations are moderately satisfactory for charged pion production. The Badhwar parameterization provides the best fit for charged kaon production. For proton production, the Alper parameterization is best, and for antiproton production the Carey parameterization works best. However, no parameterization is able to fully account for all the data.

Hydraulic Conductivity Estimation using Bayesian Model Averaging and Generalized Parameterization

NASA Astrophysics Data System (ADS)

Tsai, F. T.; Li, X.

2006-12-01

Non-uniqueness in parameterization scheme is an inherent problem in groundwater inverse modeling due to limited data. To cope with the non-uniqueness problem of parameterization, we introduce a Bayesian Model Averaging (BMA) method to integrate a set of selected parameterization methods. The estimation uncertainty in BMA includes the uncertainty in individual parameterization methods as the within-parameterization variance and the uncertainty from using different parameterization methods as the between-parameterization variance. Moreover, the generalized parameterization (GP) method is considered in the geostatistical framework in this study. The GP method aims at increasing the flexibility of parameterization through the combination of a zonation structure and an interpolation method. The use of BMP with GP avoids over-confidence in a single parameterization method. A normalized least-squares estimation (NLSE) is adopted to calculate the posterior probability for each GP. We employee the adjoint state method for the sensitivity analysis on the weighting coefficients in the GP method. The adjoint state method is also applied to the NLSE problem. The proposed methodology is implemented to the Alamitos Barrier Project (ABP) in California, where the spatially distributed hydraulic conductivity is estimated. The optimal weighting coefficients embedded in GP are identified through the maximum likelihood estimation (MLE) where the misfits between the observed and calculated groundwater heads are minimized. The conditional mean and conditional variance of the estimated hydraulic conductivity distribution using BMA are obtained to assess the estimation uncertainty.

Sequence-Specific Interaction between the Disintegrin Domain of Mouse ADAM 3 and Murine Eggs: Role of β1 Integrin-associated Proteins CD9, CD81, and CD98

PubMed Central

Takahashi, Yuji; Bigler, Dora; Ito, Yasuhiko; White, Judith M.

2001-01-01

ADAM 3 is a sperm surface glycoprotein that has been implicated in sperm-egg adhesion. Because little is known about the adhesive activity of ADAMs, we investigated the interaction of ADAM 3 disintegrin domains, made in bacteria and in insect cells, with murine eggs. Both recombinant proteins inhibited sperm-egg binding and fusion with potencies similar to that which we recently reported for the ADAM 2 disintegrin domain. Alanine scanning mutagenesis revealed a critical importance for the glutamine at position 7 of the disintegrin loop. Fluorescent beads coated with the ADAM 3 disintegrin domain bound to the egg surface. Bead binding was inhibited by an authentic, but not by a scrambled, peptide analog of the disintegrin loop. Bead binding was also inhibited by the function-blocking anti-α6 monoclonal antibody (mAb) GoH3, but not by a nonfunction blocking anti-α6 mAb, or by mAbs against either the αv or β3 integrin subunits. We also present evidence that in addition to the tetraspanin CD9, two other β1-integrin-associated proteins, the tetraspanin CD81 as well as the single pass transmembrane protein CD98 are expressed on murine eggs. Antibodies to CD9 and CD98 inhibited in vitro fertilization and binding of the ADAM 3 disintegrin domain. Our findings are discussed in terms of the involvement of multiple sperm ADAMs and multiple egg β1 integrin-associated proteins in sperm-egg binding and fusion. We propose that an egg surface “tetraspan web” facilitates fertilization and that it may do so by fostering ADAM–integrin interactions. PMID:11294888

Sequence-specific interaction between the disintegrin domain of mouse ADAM 3 and murine eggs: role of beta1 integrin-associated proteins CD9, CD81, and CD98.

PubMed

Takahashi, Y; Bigler, D; Ito, Y; White, J M

2001-04-01

ADAM 3 is a sperm surface glycoprotein that has been implicated in sperm-egg adhesion. Because little is known about the adhesive activity of ADAMs, we investigated the interaction of ADAM 3 disintegrin domains, made in bacteria and in insect cells, with murine eggs. Both recombinant proteins inhibited sperm-egg binding and fusion with potencies similar to that which we recently reported for the ADAM 2 disintegrin domain. Alanine scanning mutagenesis revealed a critical importance for the glutamine at position 7 of the disintegrin loop. Fluorescent beads coated with the ADAM 3 disintegrin domain bound to the egg surface. Bead binding was inhibited by an authentic, but not by a scrambled, peptide analog of the disintegrin loop. Bead binding was also inhibited by the function-blocking anti-alpha6 monoclonal antibody (mAb) GoH3, but not by a nonfunction blocking anti-alpha6 mAb, or by mAbs against either the alphav or beta3 integrin subunits. We also present evidence that in addition to the tetraspanin CD9, two other beta1-integrin-associated proteins, the tetraspanin CD81 as well as the single pass transmembrane protein CD98 are expressed on murine eggs. Antibodies to CD9 and CD98 inhibited in vitro fertilization and binding of the ADAM 3 disintegrin domain. Our findings are discussed in terms of the involvement of multiple sperm ADAMs and multiple egg beta1 integrin-associated proteins in sperm-egg binding and fusion. We propose that an egg surface "tetraspan web" facilitates fertilization and that it may do so by fostering ADAM-integrin interactions.

A Positive Feedback Loop between Glial Cells Missing 1 and Human Chorionic Gonadotropin (hCG) Regulates Placental hCGβ Expression and Cell Differentiation

PubMed Central

Cheong, Mei-Leng; Wang, Liang-Jie; Chuang, Pei-Yun; Chang, Ching-Wen; Lee, Yun-Shien; Lo, Hsiao-Fan; Tsai, Ming-Song

2015-01-01

Human chorionic gonadotropin (hCG) is composed of a common α subunit and a placenta-specific β subunit. Importantly, hCG is highly expressed in the differentiated and multinucleated syncytiotrophoblast, which is formed via trophoblast cell fusion and stimulated by cyclic AMP (cAMP). Although the ubiquitous activating protein 2 (AP2) transcription factors TFAP2A and TFAP2C may regulate hCGβ expression, it remains unclear how cAMP stimulates placenta-specific hCGβ gene expression and trophoblastic differentiation. Here we demonstrated that the placental transcription factor glial cells missing 1 (GCM1) binds to a highly conserved promoter region in all six hCGβ paralogues by chromatin immunoprecipitation-on-chip (ChIP-chip) analyses. We further showed that cAMP stimulates GCM1 and the CBP coactivator to activate the hCGβ promoter through a GCM1-binding site (GBS1), which also constitutes a previously identified AP2 site. Given that TFAP2C may compete with GCM1 for GBS1, cAMP enhances the association between the hCGβ promoter and GCM1 but not TFAP2C. Indeed, the hCG-cAMP-protein kinase A (PKA) signaling pathway also stimulates Ser269 and Ser275 phosphorylation of GCM1, which recruits CBP to mediate GCM1 acetylation and stabilization. Consequently, hCG stimulates the expression of GCM1 target genes, including the fusogenic protein syncytin-1, to promote placental cell fusion. Our study reveals a positive feedback loop between GCM1 and hCG regulating placental hCGβ expression and cell differentiation. PMID:26503785

Conceptualizing the dynamics of workplace stress: a systems-based study of nursing aides.

PubMed

Jetha, Arif; Kernan, Laura; Kurowski, Alicia

2017-01-05

Workplace stress is a complex phenomenon that may often be dynamic and evolving over time. Traditional linear modeling does not allow representation of recursive feedback loops among the implicated factors. The objective of this study was to develop a multidimensional system dynamics model (SDM) of workplace stress among nursing aides and conduct simulations to illustrate how changes in psychosocial perceptions and workplace factors might influence workplace stress over time. Eight key informants with prior experience in a large study of US nursing home workers participated in model building. Participants brainstormed the range of components related to workplace stress. Components were grouped together based on common themes and translated into feedback loops. The SDM was parameterized through key informant insight on the shape and magnitude of the relationship between model components. Model construction was also supported utilizing survey data collected as part of the larger study. All data was entered into the software program, Vensim. Simulations were conducted to examine how adaptations to model components would influence workplace stress. The SDM included perceptions of organizational conditions (e.g., job demands and job control), workplace social support (i.e., managerial and coworker social support), workplace safety, and demands outside of work (i.e. work-family conflict). Each component was part of a reinforcing feedback loop. Simulations exhibited that scenarios with increasing job control and decreasing job demands led to a decline in workplace stress. Within the context of the system, the effects of workplace social support, workplace safety, and work-family conflict were relatively minor. SDM methodology offers a unique perspective for researchers and practitioners to view workplace stress as a dynamic process. The portrayal of multiple recursive feedback loops can guide the development of policies and programs within complex organizational contexts with attention both to interactions among causes and avoidance of adverse unintended consequences. While additional research is needed to further test the modeling approach, findings might underscore the need to direct workplace interventions towards changing organizational conditions for nursing aides.

Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity

DOE PAGES

Long, Feng; Fong, Rachel H.; Austin, Stephen K.; ...

2015-10-26

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. In this paper, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain’s β-ribbon connector of the viral glycoprotein E2. The footprints ofmore » these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. Finally, this finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes.« less

Assessing the performance of wave breaking parameterizations in shallow waters in spectral wave models

NASA Astrophysics Data System (ADS)

Lin, Shangfei; Sheng, Jinyu

2017-12-01

Depth-induced wave breaking is the primary dissipation mechanism for ocean surface waves in shallow waters. Different parametrizations were developed for parameterizing depth-induced wave breaking process in ocean surface wave models. The performance of six commonly-used parameterizations in simulating significant wave heights (SWHs) is assessed in this study. The main differences between these six parameterizations are representations of the breaker index and the fraction of breaking waves. Laboratory and field observations consisting of 882 cases from 14 sources of published observational data are used in the assessment. We demonstrate that the six parameterizations have reasonable performance in parameterizing depth-induced wave breaking in shallow waters, but with their own limitations and drawbacks. The widely-used parameterization suggested by Battjes and Janssen (1978, BJ78) has a drawback of underpredicting the SWHs in the locally-generated wave conditions and overpredicting in the remotely-generated wave conditions over flat bottoms. The drawback of BJ78 was addressed by a parameterization suggested by Salmon et al. (2015, SA15). But SA15 had relatively larger errors in SWHs over sloping bottoms than BJ78. We follow SA15 and propose a new parameterization with a dependence of the breaker index on the normalized water depth in deep waters similar to SA15. In shallow waters, the breaker index of the new parameterization has a nonlinear dependence on the local bottom slope rather than the linear dependence used in SA15. Overall, this new parameterization has the best performance with an average scatter index of ∼8.2% in comparison with the three best performing existing parameterizations with the average scatter index between 9.2% and 13.6%.

Overview of the IFMIF/EVEDA project

NASA Astrophysics Data System (ADS)

Knaster, J.; Garin, P.; Matsumoto, H.; Okumura, Y.; Sugimoto, M.; Arbeiter, F.; Cara, P.; Chel, S.; Facco, A.; Favuzza, P.; Furukawa, T.; Heidinger, R.; Ibarra, A.; Kanemura, T.; Kasugai, A.; Kondo, H.; Massaut, V.; Molla, J.; Micciche, G.; O'hira, S.; Sakamoto, K.; Yokomine, T.; Wakai, E.; the IFMIF/EVEDA Integrated Project Team

2017-10-01

IFMIF, the International Fusion Materials Irradiation Facility, is presently in its engineering validation and engineering design activities (EVEDA) phase under the Broader Approach Agreement. The engineering design activity (EDA) phase was successfully accomplished within the allocated time. The engineering validation activity (EVA) phase has focused on validating the Accelerator Facility (AF), the Target Facility and the Test Facility (TF) by constructing prototypes. The ELTL at JAEAc, Oarai successfully demonstrated the long-term stability of a Li flow under the IFMIF’s nominal operational conditions keeping the specified free-surface fluctuations below  ±1 mm in a continuous manner for 25 d. A full-scale prototype of the high flux test module (HFTM) was successfully tested in the HELOKA loop (KIT, Karlsruhe), where it was demonstrated that the irradiation temperature can be set individually and kept uniform. LIPAc, designed and constructed in European labs under the coordination of F4E, presently under installation and commissioning in the Rokkasho Fusion Institute, aims at validating the concept of IFMIF accelerators with a D+ beam of 125 mA continuous wave (CW) and 9 MeV. The commissioning phases of the H+/D+ beams at 100 keV are progressing and should be concluded in 2017; in turn, the commissioning of the 5 MeV beam is due to start during 2017. The D+ beam through the superconducting cavities is expected to be achieved within the Broader Approach Agreement time frame with the superconducting cryomodule being assembled in Rokkasho. The realisation of a fusion-relevant neutron source is a necessary step for the successful development of fusion. The ongoing success of the IFMIF/EVEDA involves ruling out concerns about potential technical showstoppers which were raised in the past. Thus, a situation has emerged where soon steps towards constructing a Li(d,xn) fusion-relevant neutron source could be taken, which is also justified in the light of costs which are marginal to those of a fusion plant. In Memoriam Yoshikazu Okumura who passed away on 6 March 2017.

Site-directed mutagenesis of the hinge peptide from the hemagglutinin protein: enhancement of the pH-responsive conformational change.

PubMed

Casali, Monica; Banta, Scott; Zambonelli, Carlo; Megeed, Zaki; Yarmush, Martin L

2008-06-01

Environmentally responsive proteins and peptides are increasingly finding utility in various engineered systems due to their ability to respond to the presentation of external stimuli. A classic example of this behavior is the influenza hemagglutinin (HA) fusion protein. At neutral pH, HA exists in a non-fusogenic state, but upon exposure to low pH, the conformation of the structure changes to expose a fusogenic peptide. During this structural change, massive rearrangements occur in a subunit of HA (HA2). Crystallography data has shown that a loop of 28 amino acids (residues 54-81) undergoes a dramatic transition from a random coil to an alpha-helix. This segment connects to two flanking helical regions (short and long) to form a long, continuous helix. Here, we report the results of site-directed mutagenesis study on LOOP-36 to further understand the mechanism of this important stimulus-responsive peptide. The conformational transition of a bacterially expressed LOOP-36 was found to be less dramatic than has been previously reported. The systematic mutation of glutamate and histidine residues in the peptide to glutamines (glutamine scanning) did not impact the conformational behavior of the peptide, but the substitution of the glycine residue at position 22 with alanine resulted in significant pH-responsive behavior. Therefore this mutant stimulus-responsive peptide may be more valuable for future protein engineering and bionanotechnology efforts.

HCV RNA traffic and association with NS5A in living cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fiches, Guillaume N.; Eyre, Nicholas S.; Aloia, Amanda L.

The spatiotemporal dynamics of Hepatitis C Virus (HCV) RNA localisation are poorly understood. To address this we engineered HCV genomes harbouring MS2 bacteriophage RNA stem-loops within the 3′-untranslated region to allow tracking of HCV RNA via specific interaction with a MS2-Coat-mCherry fusion protein. Despite the impact of these insertions on viral fitness, live imaging revealed that replication of tagged-HCV genomes induced specific redistribution of the mCherry-tagged-MS2-Coat protein to motile and static foci. Further analysis showed that HCV RNA was associated with NS5A in both static and motile structures while a subset of motile NS5A structures was devoid of HCV RNA.more » Further investigation of viral RNA traffic with respect to lipid droplets (LDs) revealed HCV RNA-positive structures in close association with LDs. These studies provide new insights into the dynamics of HCV RNA traffic with NS5A and LDs and provide a platform for future investigations of HCV replication and assembly. - Highlights: • HCV can tolerate can bacteriophage MS2 stem-loop insertions within the 3′ UTR. • MS2 stem-loop containing HCV genomes allow for real-time imaging of HCV RNA. • HCV RNA is both static and motile and associates with NS5A and lipid droplets.« less

Assessment of groundwater quality: a fusion of geochemical and geophysical information via Bayesian neural networks.

PubMed

Maiti, Saumen; Erram, V C; Gupta, Gautam; Tiwari, Ram Krishna; Kulkarni, U D; Sangpal, R R

2013-04-01

Deplorable quality of groundwater arising from saltwater intrusion, natural leaching and anthropogenic activities is one of the major concerns for the society. Assessment of groundwater quality is, therefore, a primary objective of scientific research. Here, we propose an artificial neural network-based method set in a Bayesian neural network (BNN) framework and employ it to assess groundwater quality. The approach is based on analyzing 36 water samples and inverting up to 85 Schlumberger vertical electrical sounding data. We constructed a priori model by suitably parameterizing geochemical and geophysical data collected from the western part of India. The posterior model (post-inversion) was estimated using the BNN learning procedure and global hybrid Monte Carlo/Markov Chain Monte Carlo optimization scheme. By suitable parameterization of geochemical and geophysical parameters, we simulated 1,500 training samples, out of which 50 % samples were used for training and remaining 50 % were used for validation and testing. We show that the trained model is able to classify validation and test samples with 85 % and 80 % accuracy respectively. Based on cross-correlation analysis and Gibb's diagram of geochemical attributes, the groundwater qualities of the study area were classified into following three categories: "Very good", "Good", and "Unsuitable". The BNN model-based results suggest that groundwater quality falls mostly in the range of "Good" to "Very good" except for some places near the Arabian Sea. The new modeling results powered by uncertainty and statistical analyses would provide useful constrain, which could be utilized in monitoring and assessment of the groundwater quality.

The response of the SSM/I to the marine environment. Part 2: A parameterization of the effect of the sea surface slope distribution on emission and reflection

NASA Technical Reports Server (NTRS)

Petty, Grant W.; Katsaros, Kristina B.

1994-01-01

Based on a geometric optics model and the assumption of an isotropic Gaussian surface slope distribution, the component of ocean surface microwave emissivity variation due to large-scale surface roughness is parameterized for the frequencies and approximate viewing angle of the Special Sensor Microwave/Imager. Independent geophysical variables in the parameterization are the effective (microwave frequency dependent) slope variance and the sea surface temperature. Using the same physical model, the change in the effective zenith angle of reflected sky radiation arising from large-scale roughness is also parameterized. Independent geophysical variables in this parameterization are the effective slope variance and the atmospheric optical depth at the frequency in question. Both of the above model-based parameterizations are intended for use in conjunction with empirical parameterizations relating effective slope variance and foam coverage to near-surface wind speed. These empirical parameterizations are the subject of a separate paper.

Automatic PID Control Loops Design for Performance Improvement of Cryogenic Turboexpander

NASA Astrophysics Data System (ADS)

Joshi, D. M.; Patel, H. K.; Shah, D. K.

2015-04-01

Cryogenics field involves temperature below 123 K which is much less than ambient temperature. In addition, many industrially important physical processes—from fulfilling the needs of National Thermonuclear Fusion programs, superconducting magnets to treatment of cutting tools and preservation of blood cells, require extreme low temperature. The low temperature required for liquefaction of common gases can be obtained by several processes. Liquefaction is the process of cooling or refrigerating a gas to a temperature below its critical temperature so that liquid can be formed at some suitable pressure which is below the critical pressure. Helium liquefier is used for the liquefaction process of helium gas. In general, the Helium Refrigerator/Liquefier (HRL) needs turboexpander as expansion machine to produce cooling effect which is further used for the production of liquid helium. Turboexpanders, a high speed device that is supported on gas bearings, are the most critical component in many helium refrigeration systems. A very minor fault in the operation and manufacturing or impurities in the helium gas can destroy the turboexpander. However, since the performance of expanders is dependent on a number of operating parameters and the relations between them are quite complex, the instrumentation and control system design for turboexpander needs special attention. The inefficiency of manual control leads to the need of designing automatic control loops for turboexpander. Proper design and implementation of the control loops plays an important role in the successful operation of the cryogenic turboexpander. The PID control loops has to be implemented with accurate interlocks and logic to enhance the performance of the cryogenic turboexpander. For different normal and off-normal operations, speeds will be different and hence a proper control method for critical rotational speed avoidance is must. This paper presents the design of PID control loops needed for the efficient performance of cryogenic turboexpander (Radial Inflow type) to ensure that the control systems meet the technical conditions and constraints more accurately and ensure the equipment safety.

Continuous processing of recombinant proteins: integration of refolding and purification using simulated moving bed size-exclusion chromatography with buffer recycling.

PubMed

Wellhoefer, Martin; Sprinzl, Wolfgang; Hahn, Rainer; Jungbauer, Alois

2014-04-11

Continuous processing of recombinant proteins was accomplished by combining continuous matrix-assisted refolding and purification by tandem simulated moving bed (SMB) size-exclusion chromatography (SEC). Recombinant proteins, N(pro) fusion proteins from inclusion bodies were dissolved with NaOH and refolded in the SMB system with a closed-loop set-up with refolding buffer as the desorbent buffer and buffer recycling of the refolding buffer of the raffinate by tangential flow filtration. For further purification of the refolded proteins, a second SMB operation also based on SEC was added. The whole system could be operated isocratically with refolding buffer as the desorbent buffer, and buffer recycling could also be applied in the purification step. Thus, a significant reduction in buffer consumption was achieved. The system was evaluated with two proteins, the N(pro) fusion pep6His and N(pro) fusion MCP-1. Refolding solution, which contained residual N(pro) fusion peptide, the cleaved autoprotease N(pro), and the cleaved target peptide was used as feed solution. Full separation of the cleaved target peptide from residual proteins was achieved at a purity and recovery in the raffinate and extract, respectively, of approximately 100%. In addition, more than 99% of the refolding buffer of the raffinate was recycled. A comparison of throughput, productivity, and buffer consumption of the integrated continuous process with two batch processes demonstrated that up to 60-fold higher throughput, up to 180-fold higher productivity, and at least 28-fold lower buffer consumption can be obtained by the integrated continuous process, which compensates for the higher complexity. Copyright © 2014 Elsevier B.V. All rights reserved.

Clustering of low-valence particles: structure and kinetics.

PubMed

Markova, Olga; Alberts, Jonathan; Munro, Edwin; Lenne, Pierre-François

2014-08-01

We compute the structure and kinetics of two systems of low-valence particles with three or six freely oriented bonds in two dimensions. The structure of clusters formed by trivalent particles is complex with loops and holes, while hexavalent particles self-organize into regular and compact structures. We identify the elementary structures which compose the clusters of trivalent particles. At initial stages of clustering, the clusters of trivalent particles grow with a power-law time dependence. Yet at longer times fusion and fission of clusters equilibrates and clusters form a heterogeneous phase with polydispersed sizes. These results emphasize the role of valence in the kinetics and stability of finite-size clusters.

The shaped pulses control and operation on the SG-III prototype facility

NASA Astrophysics Data System (ADS)

Ping, Li; Wei, Wang; Sai, Jin; Wanqing, Huang; Wenyi, Wang; Jingqin, Su; Runchang, Zhao

2018-04-01

The laser driven inertial confined fusion experiments require careful temporal shape control of the laser pulse. Two approaches are introduced to improve the accuracy and efficiency of the close loop feedback system for long term operation in TIL; the first one is a statistical model to analyze the variation of the parameters obtained from previous shots, the other is a matrix algorithm proposed to relate the electrical signal and the impulse amplitudes. With the model and algorithm applied in the pulse shaping in TIL, a variety of shaped pulses were produced with a 10% precision in half an hour for almost three years under different circumstance.

Structure of Epstein-Barr Virus Glycoprotein 42 Suggests a Mechanism for Triggering Receptor-Activated Virus Entry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirschner, Austin N.; Sorem, Jessica; Longnecker, Richard

Epstein-Barr virus requires glycoproteins gH/gL, gB, and gp42 to fuse its lipid envelope with B cells. Gp42 is a type II membrane protein consisting of a flexible N-terminal region, which binds gH/gL, and a C-terminal lectin-like domain that binds to the B-cell entry receptor human leukocyte antigen (HLA) class II. Gp42 triggers membrane fusion after HLA binding, a process that requires simultaneous binding to gH/gL and a functional hydrophobic pocket in the lectin domain adjacent to the HLA binding site. Here we present the structure of gp42 in its unbound form. Comparisons to the previously determined structure of a gp42:HLAmore » complex reveals additional N-terminal residues forming part of the gH/gL binding site and structural changes in the receptor binding domain. Although the core of the lectin domain remains similar, significant shifts in two loops and an {alpha} helix bordering the essential hydrophobic pocket suggest a structural mechanism for triggering fusion.« less

Crystal Structure of Dengue Virus Type 1 Envelope Protein in the Postfusion Conformation and Its Implications for Membrane Fusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nayak, Vinod; Dessau, Moshe; Kucera, Kaury

Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flavivirusesmore » and are part of the 'pH sensor' that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.« less

Crystal Structure of Dengue Type 1 Envelope Protein in the Postfusion Conformation and its Implication for Receptor Binding, Membrane Fusion and Antibody Recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nayak, V.; Dessau, M; Kucera, K

Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flavivirusesmore » and are part of the pH sensor that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.« less

Anaplastic lymphoma kinase: role in cancer pathogenesis and small-molecule inhibitor development for therapy

PubMed Central

Webb, Thomas R; Slavish, Jake; George, Rani E; Look, A Thomas; Xue, Liquan; Jiang, Qin; Cui, Xiaoli; Rentrop, Walter B; Morris, Stephan W

2009-01-01

Anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase in the insulin receptor superfamily, was initially identified in constitutively activated oncogenic fusion forms – the most common being nucleophosmin-ALK – in anaplastic large-cell lymphomas, and subsequent studies have identified ALK fusions in diffuse large B-cell lymphomas, systemic histiocytosis, inflammatory myofibroblastic tumors, esophageal squamous cell carcinomas and non-small-cell lung carcinomas. More recently, genomic DNA amplification and protein overexpression, as well as activating point mutations, of ALK have been described in neuroblastomas. In addition to those cancers for which a causative role for aberrant ALK activity is well validated, more circumstantial links implicate the full-length, normal ALK receptor in the genesis of other malignancies – including glioblastoma and breast cancer – via a mechanism of receptor activation involving autocrine and/or paracrine growth loops with the reported ALK ligands, pleiotrophin and midkine. This review summarizes normal ALK biology, the confirmed and putative roles of ALK in the development of human cancers and efforts to target ALK using small-molecule kinase inhibitors. PMID:19275511

RAD51 and RTEL1 compensate telomere loss in the absence of telomerase.

PubMed

Olivier, Margaux; Charbonnel, Cyril; Amiard, Simon; White, Charles I; Gallego, Maria E

2018-03-16

Replicative erosion of telomeres is naturally compensated by telomerase and studies in yeast and vertebrates show that homologous recombination can compensate for the absence of telomerase. We show that RAD51 protein, which catalyzes the key strand-invasion step of homologous recombination, is localized at Arabidopsis telomeres in absence of telomerase. Blocking the strand-transfer activity of the RAD51 in telomerase mutant plants results in a strikingly earlier onset of developmental defects, accompanied by increased numbers of end-to-end chromosome fusions. Imposing replication stress through knockout of RNaseH2 increases numbers of chromosome fusions and reduces the survival of these plants deficient for telomerase and homologous recombination. This finding suggests that RAD51-dependent homologous recombination acts as an essential backup to the telomerase for compensation of replicative telomere loss to ensure genome stability. Furthermore, we show that this positive role of RAD51 in telomere stability is dependent on the RTEL1 helicase. We propose that a RAD51 dependent break-induced replication process is activated in cells lacking telomerase activity, with RTEL1 responsible for D-loop dissolution after telomere replication.

Natural circulation in a liquid metal one-dimensional loop

NASA Astrophysics Data System (ADS)

Tarantino, M.; De Grandis, S.; Benamati, G.; Oriolo, F.

2008-06-01

A wide use of pure lead, as well as its alloys (such as lead-bismuth, lead-lithium), is foreseen in several nuclear-related fields: it is studied as coolant in critical and sub-critical nuclear reactors, as spallation target for neutron generation in several applications and for tritium generation in fusion systems. In this framework, a new facility named NAtural CIrculation Experiment (NACIE), has been designed at ENEA-Brasimone Research Centre. NACIE is a rectangular loop, made by stainless steel pipes. It consists mainly of a cold and hot leg and an expansion tank installed on the top of the loop. A fuel bundle simulator, made by three electrical heaters placed in a triangular lattice, is located in the lower part of the cold leg, while a tube in tube heat exchanger is installed in the upper part of the hot leg. The adopted secondary fluid is THT oil, while the foreseen primary fluid for the tests is lead-bismuth in eutectic composition (LBE). The aim of the facility is to carry out experimental tests of natural circulation and collect data on the heat transfer coefficient (HTC) for heavy liquid metal flowing through rod bundles. The paper is focused on the preliminary estimation of the LBE flow rate along the loop. An analytical methodology has been applied, solving the continuity, momentum and energy transport equations under appropriate hypothesis. Moreover numerical simulations have been performed. The FLUENT 6.2 CFD code has been utilized for the numerical simulations. The main results carried out from the pre-tests simulations are illustrated in the paper, and a comparison with the theoretical estimations is done.

Neutron Tomography Using Mobile Neutron Generators for Assessment of Void Distributions in Thermal Hydraulic Test Loops

NASA Astrophysics Data System (ADS)

Andersson, P.; Bjelkenstedt, T.; Sundén, E. Andersson; Sjöstrand, H.; Jacobsson-Svärd, S.

Detailed knowledge of the lateral distribution of steam (void) and water in a nuclear fuel assembly is of great value for nuclear reactor operators and fuel manufacturers, with consequences for both reactor safety and economy of operation. Therefore, nuclear relevant two-phase flows are being studied at dedicated thermal-hydraulic test loop, using two-phase flow systems ranging from simplified geometries such as heated circular pipes to full scale mock-ups of nuclear fuel assemblies. Neutron tomography (NT) has been suggested for assessment of the lateral distribution of steam and water in such test loops, motivated by a good ability of neutrons to penetrate the metallic structures of metal pipes and nuclear fuel rod mock-ups, as compared to e.g. conventional X-rays, while the liquid water simultaneously gives comparatively good contrast. However, these stationary test loops require the measurement setup to be mobile, which is often not the case for NT setups. Here, it is acknowledged that fast neutrons of 14 MeV from mobile neutron generators constitute a viable option for a mobile NT system. We present details of the development of neutron tomography for this purpose at the division of Applied Nuclear Physics at Uppsala University. Our concept contains a portable neutron generator, exploiting the fusion reaction of deuterium and tritium, and a detector with plastic scintillator elements designed to achieveadequate spatial and energy resolution, all mounted in a light-weight frame without collimators or bulky moderation to allow for a mobile instrument that can be moved about the stationary thermal hydraulic test sections. The detector system stores event-to-event pulse-height information to allow for discrimination based on the energy deposition in the scintillator elements.

Sensory integration of a light touch reference in human standing balance.

PubMed

Assländer, Lorenz; Smith, Craig P; Reynolds, Raymond F

2018-01-01

In upright stance, light touch of a space-stationary touch reference reduces spontaneous sway. Moving the reference evokes sway responses which exhibit non-linear behavior that has been attributed to sensory reweighting. Reweighting refers to a change in the relative contribution of sensory cues signaling body sway in space and light touch cues signaling finger position with respect to the body. Here we test the hypothesis that the sensory fusion process involves a transformation of light touch signals into the same reference frame as other sensory inputs encoding body sway in space, or vice versa. Eight subjects lightly gripped a robotic manipulandum which moved in a circular arc around the ankle joint. A pseudo-randomized motion sequence with broad spectral characteristics was applied at three amplitudes. The stimulus was presented at two different heights and therefore different radial distances, which were matched in terms of angular motion. However, the higher stimulus evoked a significantly larger sway response, indicating that the response was not matched to stimulus angular motion. Instead, the body sway response was strongly related to the horizontal translation of the manipulandum. The results suggest that light touch is integrated as the horizontal distance between body COM and the finger. The data were well explained by a model with one feedback loop minimizing changes in horizontal COM-finger distance. The model further includes a second feedback loop estimating the horizontal finger motion and correcting the first loop when the touch reference is moving. The second loop includes the predicted transformation of sensory signals into the same reference frame and a non-linear threshold element that reproduces the non-linear sway responses, thus providing a mechanism that can explain reweighting.

Sensory integration of a light touch reference in human standing balance

PubMed Central

Smith, Craig P.; Reynolds, Raymond F.

2018-01-01

In upright stance, light touch of a space-stationary touch reference reduces spontaneous sway. Moving the reference evokes sway responses which exhibit non-linear behavior that has been attributed to sensory reweighting. Reweighting refers to a change in the relative contribution of sensory cues signaling body sway in space and light touch cues signaling finger position with respect to the body. Here we test the hypothesis that the sensory fusion process involves a transformation of light touch signals into the same reference frame as other sensory inputs encoding body sway in space, or vice versa. Eight subjects lightly gripped a robotic manipulandum which moved in a circular arc around the ankle joint. A pseudo-randomized motion sequence with broad spectral characteristics was applied at three amplitudes. The stimulus was presented at two different heights and therefore different radial distances, which were matched in terms of angular motion. However, the higher stimulus evoked a significantly larger sway response, indicating that the response was not matched to stimulus angular motion. Instead, the body sway response was strongly related to the horizontal translation of the manipulandum. The results suggest that light touch is integrated as the horizontal distance between body COM and the finger. The data were well explained by a model with one feedback loop minimizing changes in horizontal COM-finger distance. The model further includes a second feedback loop estimating the horizontal finger motion and correcting the first loop when the touch reference is moving. The second loop includes the predicted transformation of sensory signals into the same reference frame and a non-linear threshold element that reproduces the non-linear sway responses, thus providing a mechanism that can explain reweighting. PMID:29874252

First Plasma Results from the HIT-SI Spheromak

NASA Astrophysics Data System (ADS)

Sieck, P. E.; Hamp, W. T.; Izzo, V. A.; Jarboe, T. R.; Nelson, B. A.; O'Neill, R. G.; Redd, A. J.; Smith, R. J.

2003-10-01

HIT-SI is the newest device in the Helicity Injected Torus (HIT) program. HIT-SI is a ``bow tie'' spheromak formed and sustained by Steady Inductive Helicity Injection (SIHI) current drive. SIHI injects helicity at a nearly constant rate with no open field lines intersecting the boundary. (T. R. Jarboe, Fusion Technology 36) (1), p. 85, 1999 HIT-SI has been designed with a bow tie geometry to achieve stable high-β (>10%) spheromak equilibria. (U. Shumlak and T. R. Jarboe, Phys. Plasmas 7) (7), p. 2959, 2000 Diagnostics currently include surface magnetic probes and flux loops, visible light imaging, H-alpha line radiation monitors, voltage measurements across insulating breaks, injector current Rogowski coils, and injector flux loops. HIT-SI is currently operating in parallel with experiments on HIT-II. At the conclusion of HIT-II operations, HIT-SI will inherit a multi-point Thomson Scattering system, a scanning two-chord FIR interferometer, and other advanced diagnostics, as well as more power supplies to extend the discharge duration. Results are presented which characterize injector operation and possible evidence for spheromak formation.

Parameterizing deep convection using the assumed probability density function method

DOE PAGES

Storer, R. L.; Griffin, B. M.; Höft, J.; ...

2014-06-11

Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method. The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and mid-latitude deep convection. These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing ismore » weak. The same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less

Parameterizing deep convection using the assumed probability density function method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Storer, R. L.; Griffin, B. M.; Höft, J.

2015-01-06

Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method.The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and midlatitude deep convection. These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing is weak.more » The same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less

Parameterizing deep convection using the assumed probability density function method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Storer, R. L.; Griffin, B. M.; Hoft, Jan

2015-01-06

Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method.The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and mid-latitude deep convection.These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing is weak. Themore » same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less

Enlarged symmetry algebras of spin chains, loop models, and S-matrices

NASA Astrophysics Data System (ADS)

Read, N.; Saleur, H.

2007-08-01

The symmetry algebras of certain families of quantum spin chains are considered in detail. The simplest examples possess m states per site ( m⩾2), with nearest-neighbor interactions with U(m) symmetry, under which the sites transform alternately along the chain in the fundamental m and its conjugate representation m¯. We find that these spin chains, even with arbitrary coefficients of these interactions, have a symmetry algebra A much larger than U(m), which implies that the energy eigenstates fall into sectors that for open chains (i.e., free boundary conditions) can be labeled by j=0,1,…,L, for the 2 L-site chain such that the degeneracies of all eigenvalues in the jth sector are generically the same and increase rapidly with j. For large j, these degeneracies are much larger than those that would be expected from the U(m) symmetry alone. The enlarged symmetry algebra A(2L) consists of operators that commute in this space of states with the Temperley-Lieb algebra that is generated by the set of nearest-neighbor interaction terms; A(2L) is not a Yangian. There are similar results for supersymmetric chains with gl(m+n|n) symmetry of nearest-neighbor interactions, and a richer representation structure for closed chains (i.e., periodic boundary conditions). The symmetries also apply to the loop models that can be obtained from the spin chains in a spacetime or transfer matrix picture. In the loop language, the symmetries arise because the loops cannot cross. We further define tensor products of representations (for the open chains) by joining chains end to end. The fusion rules for decomposing the tensor product of representations labeled j and j take the same form as the Clebsch-Gordan series for SU(2). This and other structures turn the symmetry algebra A into a ribbon Hopf algebra, and we show that this is "Morita equivalent" to the quantum group U(sl) for m=q+q. The open-chain results are extended to the cases |m|<2 for which the algebras are no longer semisimple; these possess continuum limits that are critical (conformal) field theories, or massive perturbations thereof. Such models, for open and closed boundary conditions, arise in connection with disordered fermions, percolation, and polymers (self-avoiding walks), and certain non-linear sigma models, all in two dimensions. A product operation is defined in a related way for the Temperley-Lieb representations also, and the fusion rules for this are related to those for A or U(sl) representations; this is useful for the continuum limits also, as we discuss in a companion paper.

Global model comparison of heterogeneous ice nucleation parameterizations in mixed phase clouds

NASA Astrophysics Data System (ADS)

Yun, Yuxing; Penner, Joyce E.

2012-04-01

A new aerosol-dependent mixed phase cloud parameterization for deposition/condensation/immersion (DCI) ice nucleation and one for contact freezing are compared to the original formulations in a coupled general circulation model and aerosol transport model. The present-day cloud liquid and ice water fields and cloud radiative forcing are analyzed and compared to observations. The new DCI freezing parameterization changes the spatial distribution of the cloud water field. Significant changes are found in the cloud ice water fraction and in the middle cloud fractions. The new DCI freezing parameterization predicts less ice water path (IWP) than the original formulation, especially in the Southern Hemisphere. The smaller IWP leads to a less efficient Bergeron-Findeisen process resulting in a larger liquid water path, shortwave cloud forcing, and longwave cloud forcing. It is found that contact freezing parameterizations have a greater impact on the cloud water field and radiative forcing than the two DCI freezing parameterizations that we compared. The net solar flux at top of atmosphere and net longwave flux at the top of the atmosphere change by up to 8.73 and 3.52 W m-2, respectively, due to the use of different DCI and contact freezing parameterizations in mixed phase clouds. The total climate forcing from anthropogenic black carbon/organic matter in mixed phase clouds is estimated to be 0.16-0.93 W m-2using the aerosol-dependent parameterizations. A sensitivity test with contact ice nuclei concentration in the original parameterization fit to that recommended by Young (1974) gives results that are closer to the new contact freezing parameterization.

Ion channeling study of defects in compound crystals using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Turos, A.; Jozwik, P.; Nowicki, L.; Sathish, N.

2014-08-01

Ion channeling is a well-established technique for determination of structural properties of crystalline materials. Defect depth profiles have been usually determined basing on the two-beam model developed by Bøgh (1968) [1]. As long as the main research interest was focused on single element crystals it was considered as sufficiently accurate. New challenge emerged with growing technological importance of compound single crystals and epitaxial heterostructures. Overlap of partial spectra due to different sublattices and formation of complicated defect structures makes the two beam method hardly applicable. The solution is provided by Monte Carlo computer simulations. Our paper reviews principal aspects of this approach and the recent developments in the McChasy simulation code. The latter made it possible to distinguish between randomly displaced atoms (RDA) and extended defects (dislocations, loops, etc.). Hence, complex defect structures can be characterized by the relative content of these two components. The next refinement of the code consists of detailed parameterization of dislocations and dislocation loops. Defect profiles for variety of compound crystals (GaN, ZnO, SrTiO3) have been measured and evaluated using the McChasy code. Damage accumulation curves for RDA and extended defects revealed non monotonous defect buildup with some characteristic steps. Transition to each stage is governed by the different driving force. As shown by the complementary high resolution XRD measurements lattice strain plays here the crucial role and can be correlated with the concentration of extended defects.

DART system analysis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boggs, Paul T.; Althsuler, Alan; Larzelere, Alex R.

2005-08-01

The Design-through-Analysis Realization Team (DART) is chartered with reducing the time Sandia analysts require to complete the engineering analysis process. The DART system analysis team studied the engineering analysis processes employed by analysts in Centers 9100 and 8700 at Sandia to identify opportunities for reducing overall design-through-analysis process time. The team created and implemented a rigorous analysis methodology based on a generic process flow model parameterized by information obtained from analysts. They also collected data from analysis department managers to quantify the problem type and complexity distribution throughout Sandia's analyst community. They then used this information to develop a communitymore » model, which enables a simple characterization of processes that span the analyst community. The results indicate that equal opportunity for reducing analysis process time is available both by reducing the ''once-through'' time required to complete a process step and by reducing the probability of backward iteration. In addition, reducing the rework fraction (i.e., improving the engineering efficiency of subsequent iterations) offers approximately 40% to 80% of the benefit of reducing the ''once-through'' time or iteration probability, depending upon the process step being considered. Further, the results indicate that geometry manipulation and meshing is the largest portion of an analyst's effort, especially for structural problems, and offers significant opportunity for overall time reduction. Iteration loops initiated late in the process are more costly than others because they increase ''inner loop'' iterations. Identifying and correcting problems as early as possible in the process offers significant opportunity for time savings.« less

Non-singular black holes and the limiting curvature mechanism: a Hamiltonian perspective

NASA Astrophysics Data System (ADS)

Ben Achour, J.; Lamy, F.; Liu, H.; Noui, K.

2018-05-01

We revisit the non-singular black hole solution in (extended) mimetic gravity with a limiting curvature from a Hamiltonian point of view. We introduce a parameterization of the phase space which allows us to describe fully the Hamiltonian structure of the theory. We write down the equations of motion that we solve in the regime deep inside the black hole, and we recover that the black hole has no singularity, due to the limiting curvature mechanism. Then, we study the relation between such black holes and effective polymer black holes which have been introduced in the context of loop quantum gravity. As expected, contrary to what happens in the cosmological sector, mimetic gravity with a limiting curvature fails to reproduce the usual effective dynamics of spherically symmetric loop quantum gravity which are generically not covariant. Nonetheless, we exhibit a theory in the class of extended mimetic gravity whose dynamics reproduces the general shape of the effective corrections of spherically symmetric polymer models, but in an undeformed covariant manner. These covariant effective corrections are found to be always metric dependent, i.e. within the bar mu-scheme, underlying the importance of this ingredient for inhomogeneous polymer models. In that respect, extended mimetic gravity can be viewed as an effective covariant theory which naturally implements a covariant notion of point wise holonomy-like corrections. The difference between the mimetic and polymer Hamiltonian formulations provides us with a guide to understand the deformation of covariance in inhomogeneous polymer models.

Scaling magnetized liner inertial fusion on Z and future pulsed-power accelerators

DOE PAGES

Slutz, Stephen A.; Stygar, William A.; Gomez, Matthew R.; ...

2016-02-04

In this study, the MagLIF (Magnetized Liner Inertial Fusion) concept [S. A. Slutz et al., Phys. Plasmas 17, 056303 (2010)] has demonstrated fusion–relevant plasma conditions [M. R. Gomez et al., Phys. Rev. Lett. 113, 155003 (2014)] on the Z accelerator with a peak drive current of about 18 MA. We present 2D numerical simulations of the scaling of MagLIF on Z as a function of drive current, preheat energy, and applied magnetic field. The results indicate that deuterium-tritium (DT) fusion yields greater than 100 kJ could be possible on Z when all of these parameters are at the optimum values:more » i.e., peak current = 25 MA, deposited preheat energy = 5 kJ, and B z = 30 T. Much higher yields have been predicted [S. A. Slutz and R. A. Vesey, Phys. Rev. Lett. 108, 025003 (2012)] for MagLIF driven with larger peak currents. Two high performance pulsed-power accelerators (Z300 and Z800) based on linear-transformer-driver technology have been designed [W. A. Stygar et al., Phys. Rev. ST Accel. Beams 18, 110401 (2015)]. The Z300 design would provide 48 MA to a MagLIF load, while Z800 would provide 65 MA. Parameterized Thevenin-equivalent circuits were used to drive a series of 1D and 2D numerical MagLIF simulations with currents ranging from what Z can deliver now to what could be achieved by these conceptual future pulsed-power accelerators. 2D simulations of simple MagLIF targets containing just gaseous DT have yields of 18 MJ for Z300 and 440 MJ for Z800. The 2D simulated yield for Z800 is increased to 7 GJ by adding a layer of frozen DT ice to the inside of the liner.« less

Scaling magnetized liner inertial fusion on Z and future pulsed-power accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slutz, Stephen A.; Stygar, William A.; Gomez, Matthew R.

In this study, the MagLIF (Magnetized Liner Inertial Fusion) concept [S. A. Slutz et al., Phys. Plasmas 17, 056303 (2010)] has demonstrated fusion–relevant plasma conditions [M. R. Gomez et al., Phys. Rev. Lett. 113, 155003 (2014)] on the Z accelerator with a peak drive current of about 18 MA. We present 2D numerical simulations of the scaling of MagLIF on Z as a function of drive current, preheat energy, and applied magnetic field. The results indicate that deuterium-tritium (DT) fusion yields greater than 100 kJ could be possible on Z when all of these parameters are at the optimum values:more » i.e., peak current = 25 MA, deposited preheat energy = 5 kJ, and B z = 30 T. Much higher yields have been predicted [S. A. Slutz and R. A. Vesey, Phys. Rev. Lett. 108, 025003 (2012)] for MagLIF driven with larger peak currents. Two high performance pulsed-power accelerators (Z300 and Z800) based on linear-transformer-driver technology have been designed [W. A. Stygar et al., Phys. Rev. ST Accel. Beams 18, 110401 (2015)]. The Z300 design would provide 48 MA to a MagLIF load, while Z800 would provide 65 MA. Parameterized Thevenin-equivalent circuits were used to drive a series of 1D and 2D numerical MagLIF simulations with currents ranging from what Z can deliver now to what could be achieved by these conceptual future pulsed-power accelerators. 2D simulations of simple MagLIF targets containing just gaseous DT have yields of 18 MJ for Z300 and 440 MJ for Z800. The 2D simulated yield for Z800 is increased to 7 GJ by adding a layer of frozen DT ice to the inside of the liner.« less

Scaling magnetized liner inertial fusion on Z and future pulsed-power accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slutz, S. A.; Stygar, W. A.; Gomez, M. R.

The MagLIF (Magnetized Liner Inertial Fusion) concept [S. A. Slutz et al., Phys. Plasmas 17, 056303 (2010)] has demonstrated fusion–relevant plasma conditions [M. R. Gomez et al., Phys. Rev. Lett. 113, 155003 (2014)] on the Z accelerator with a peak drive current of about 18 MA. We present 2D numerical simulations of the scaling of MagLIF on Z as a function of drive current, preheat energy, and applied magnetic field. The results indicate that deuterium-tritium (DT) fusion yields greater than 100 kJ could be possible on Z when all of these parameters are at the optimum values: i.e., peak current = 25 MA, deposited preheatmore » energy = 5 kJ, and B{sub z} = 30 T. Much higher yields have been predicted [S. A. Slutz and R. A. Vesey, Phys. Rev. Lett. 108, 025003 (2012)] for MagLIF driven with larger peak currents. Two high performance pulsed-power accelerators (Z300 and Z800) based on linear-transformer-driver technology have been designed [W. A. Stygar et al., Phys. Rev. ST Accel. Beams 18, 110401 (2015)]. The Z300 design would provide 48 MA to a MagLIF load, while Z800 would provide 65 MA. Parameterized Thevenin-equivalent circuits were used to drive a series of 1D and 2D numerical MagLIF simulations with currents ranging from what Z can deliver now to what could be achieved by these conceptual future pulsed-power accelerators. 2D simulations of simple MagLIF targets containing just gaseous DT have yields of 18 MJ for Z300 and 440 MJ for Z800. The 2D simulated yield for Z800 is increased to 7 GJ by adding a layer of frozen DT ice to the inside of the liner.« less

Evaluation of Warm-Rain Microphysical Parameterizations in Cloudy Boundary Layer Transitions

NASA Astrophysics Data System (ADS)

Nelson, K.; Mechem, D. B.

2014-12-01

Common warm-rain microphysical parameterizations used for marine boundary layer (MBL) clouds are either tuned for specific cloud types (e.g., the Khairoutdinov and Kogan 2000 parameterization, "KK2000") or are altogether ill-posed (Kessler 1969). An ideal microphysical parameterization should be "unified" in the sense of being suitable across MBL cloud regimes that include stratocumulus, cumulus rising into stratocumulus, and shallow trade cumulus. The recent parameterization of Kogan (2013, "K2013") was formulated for shallow cumulus but has been shown in a large-eddy simulation environment to work quite well for stratocumulus as well. We report on our efforts to implement and test this parameterization into a regional forecast model (NRL COAMPS). Results from K2013 and KK2000 are compared with the operational Kessler parameterization for a 5-day period of the VOCALS-REx field campaign, which took place over the southeast Pacific. We focus on both the relative performance of the three parameterizations and also on how they compare to the VOCALS-REx observations from the NOAA R/V Ronald H. Brown, in particular estimates of boundary-layer depth, liquid water path (LWP), cloud base, and area-mean precipitation rate obtained from C-band radar.

A unified parameterization of clouds and turbulence using CLUBB and subcolumns in the Community Atmosphere Model

DOE PAGES

Thayer-Calder, K.; Gettelman, A.; Craig, C.; ...

2015-06-30

Most global climate models parameterize separate cloud types using separate parameterizations. This approach has several disadvantages, including obscure interactions between parameterizations and inaccurate triggering of cumulus parameterizations. Alternatively, a unified cloud parameterization uses one equation set to represent all cloud types. Such cloud types include stratiform liquid and ice cloud, shallow convective cloud, and deep convective cloud. Vital to the success of a unified parameterization is a general interface between clouds and microphysics. One such interface involves drawing Monte Carlo samples of subgrid variability of temperature, water vapor, cloud liquid, and cloud ice, and feeding the sample points into amore » microphysics scheme.This study evaluates a unified cloud parameterization and a Monte Carlo microphysics interface that has been implemented in the Community Atmosphere Model (CAM) version 5.3. Results describing the mean climate and tropical variability from global simulations are presented. The new model shows a degradation in precipitation skill but improvements in short-wave cloud forcing, liquid water path, long-wave cloud forcing, precipitable water, and tropical wave simulation. Also presented are estimations of computational expense and investigation of sensitivity to number of subcolumns.« less

A unified parameterization of clouds and turbulence using CLUBB and subcolumns in the Community Atmosphere Model

DOE PAGES

Thayer-Calder, Katherine; Gettelman, A.; Craig, Cheryl; ...

2015-12-01

Most global climate models parameterize separate cloud types using separate parameterizations.This approach has several disadvantages, including obscure interactions between parameterizations and inaccurate triggering of cumulus parameterizations. Alternatively, a unified cloud parameterization uses one equation set to represent all cloud types. Such cloud types include stratiform liquid and ice cloud, shallow convective cloud, and deep convective cloud. Vital to the success of a unified parameterization is a general interface between clouds and microphysics. One such interface involves drawing Monte Carlo samples of subgrid variability of temperature, water vapor, cloud liquid, and cloud ice, and feeding the sample points into a microphysicsmore » scheme. This study evaluates a unified cloud parameterization and a Monte Carlo microphysics interface that has been implemented in the Community Atmosphere Model (CAM) version 5.3. Results describing the mean climate and tropical variability from global simulations are presented. In conclusion, the new model shows a degradation in precipitation skill but improvements in short-wave cloud forcing, liquid water path, long-wave cloud forcing, perceptible water, and tropical wave simulation. Also presented are estimations of computational expense and investigation of sensitivity to number of subcolumns.« less

The temperature and ion energy dependence of deuterium retention in lithium films

NASA Astrophysics Data System (ADS)

Buzi, Luxherta; Koel, Bruce E.; Skinner, Charles H.

2016-10-01

Lithium conditioning of plasma facing components in magnetic fusion devices has improved plasma performance and lowered hydrogen recycling. For applications of lithium in future high heat flux and long pulse duration machines it is important to understand and parameterize deuterium retention in lithium. This work presents surface science studies of deuterium retention in lithium films as a function of surface temperature, incident deuterium ion energy and flux. Initial experiments are performed on thin (3-30 ML) lithium films deposited on a single crystal molybdenum substrate to avoid effects due to grain boundaries, intrinsic defects and impurities. A monoenergetic and mass-filtered deuterium ion beam was generated in a differentially pumped Colutron ion gun. Auger electron spectroscopy and X-ray photoelectron spectroscopy were used to identify the elemental composition and temperature programmed desorption was used to measure the deuterium retention under the different conditions. Support was provided through DOE Contract Number DE-AC02-09CH11466.

The Berkeley Out-of-Order Machine (BOOM): An Industry-Competitive, Synthesizable, Parameterized RISC-V Processor

DTIC Science & Technology

2015-06-13

The Berkeley Out-of-Order Machine (BOOM): An Industry- Competitive, Synthesizable, Parameterized RISC-V Processor Christopher Celio David A...Synthesizable, Parameterized RISC-V Processor Christopher Celio, David Patterson, and Krste Asanović University of California, Berkeley, California 94720...Order Machine BOOM is a synthesizable, parameterized, superscalar out- of-order RISC-V core designed to serve as the prototypical baseline processor

Deletion modification enhances anthrax specific immunity and protective efficacy of a hepatitis B core particle-based anthrax epitope vaccine.

PubMed

Yin, Ying; Zhang, Sheng; Cai, Chenguang; Zhang, Jun; Dong, Dayong; Guo, Qiang; Fu, Ling; Xu, Junjie; Chen, Wei

2014-02-01

Protective antigen (PA) is one of the major virulence factors of anthrax and is also the major constituent of the current anthrax vaccine. Previously, we found that the 2β2-2β3 loop of PA contains a dominant neutralizing epitope, the SFFD. We successfully inserted the 2β2-2β3 loop of PA into the major immunodominant region (MIR) of hepatitis B virus core (HBc) protein. The resulting fusion protein, termed HBc-N144-PA-loop2 (HBcL2), can effectively produce anthrax specific protective antibodies in an animal model. However, the protective immunity caused by HBcL2 could still be improved. In this research, we removed amino acids 79-81 from the HBc MIR of the HBcL2. This region was previously reported to be the major B cell epitope of HBc, and in keeping with this finding, we observed that the short deletion in the MIR not only diminished the intrinsic immunogenicity of HBc but also stimulated a higher titer of anthrax specific immunity. Most importantly, this deletion led to the full protection of the immunized mice against a lethal dose anthrax toxin challenge. We supposed that the conformational changes which occurred after the short deletion and foreign insertion in the MIR of HBc were the most likely reasons for the improvement in the immunogenicity of the HBc-based anthrax epitope vaccine. Copyright © 2013 Elsevier GmbH. All rights reserved.

The MYB23 Gene Provides a Positive Feedback Loop for Cell Fate Specification in the Arabidopsis Root Epidermis[C][W

PubMed Central

Kang, Yeon Hee; Kirik, Victor; Hulskamp, Martin; Nam, Kyoung Hee; Hagely, Katherine; Lee, Myeong Min; Schiefelbein, John

2009-01-01

The specification of cell fates during development requires precise regulatory mechanisms to ensure robust cell type patterns. Theoretical models of pattern formation suggest that a combination of negative and positive feedback mechanisms are necessary for efficient specification of distinct fates in a field of differentiating cells. Here, we examine the role of the R2R3-MYB transcription factor gene, AtMYB23 (MYB23), in the establishment of the root epidermal cell type pattern in Arabidopsis thaliana. MYB23 is closely related to, and is positively regulated by, the WEREWOLF (WER) MYB gene during root epidermis development. Furthermore, MYB23 is able to substitute for the function of WER and to induce its own expression when controlled by WER regulatory sequences. We also show that the MYB23 protein binds to its own promoter, suggesting a MYB23 positive feedback loop. The localization of MYB23 transcripts and MYB23-green fluorescent protein (GFP) fusion protein, as well as the effect of a chimeric MYB23-SRDX repressor construct, links MYB23 function to the developing non-hair cell type. Using mutational analyses, we find that MYB23 is necessary for precise establishment of the root epidermal pattern, particularly under conditions that compromise the cell specification process. These results suggest that MYB23 participates in a positive feedback loop to reinforce cell fate decisions and ensure robust establishment of the cell type pattern in the Arabidopsis root epidermis. PMID:19395683

The MYB23 gene provides a positive feedback loop for cell fate specification in the Arabidopsis root epidermis.

PubMed

Kang, Yeon Hee; Kirik, Victor; Hulskamp, Martin; Nam, Kyoung Hee; Hagely, Katherine; Lee, Myeong Min; Schiefelbein, John

2009-04-01

The specification of cell fates during development requires precise regulatory mechanisms to ensure robust cell type patterns. Theoretical models of pattern formation suggest that a combination of negative and positive feedback mechanisms are necessary for efficient specification of distinct fates in a field of differentiating cells. Here, we examine the role of the R2R3-MYB transcription factor gene, AtMYB23 (MYB23), in the establishment of the root epidermal cell type pattern in Arabidopsis thaliana. MYB23 is closely related to, and is positively regulated by, the WEREWOLF (WER) MYB gene during root epidermis development. Furthermore, MYB23 is able to substitute for the function of WER and to induce its own expression when controlled by WER regulatory sequences. We also show that the MYB23 protein binds to its own promoter, suggesting a MYB23 positive feedback loop. The localization of MYB23 transcripts and MYB23-green fluorescent protein (GFP) fusion protein, as well as the effect of a chimeric MYB23-SRDX repressor construct, links MYB23 function to the developing non-hair cell type. Using mutational analyses, we find that MYB23 is necessary for precise establishment of the root epidermal pattern, particularly under conditions that compromise the cell specification process. These results suggest that MYB23 participates in a positive feedback loop to reinforce cell fate decisions and ensure robust establishment of the cell type pattern in the Arabidopsis root epidermis.

Dissecting binding of a β-barrel membrane protein by phage display.

PubMed

Meneghini, Luz M; Tripathi, Sarvind; Woodworth, Marcus A; Majumdar, Sudipta; Poulos, Thomas L; Weiss, Gregory A

2017-07-25

Membrane proteins (MPs) constitute a third of all proteomes, and contribute to a myriad of cellular functions including intercellular communication, nutrient transport and energy generation. For example, TonB-dependent transporters (TBDTs) in the outer membrane of Gram-negative bacteria play an essential role transporting iron and other nutrients into the bacterial cell. The inherently hydrophobic surfaces of MPs complicates protein expression, purification, and characterization. Thus, dissecting the functional contributions of individual amino acids or structural features through mutagenesis can be a challenging ordeal. Here, we apply a new approach for the expedited protein characterization of the TBDT ShuA from Shigella dysenteriae, and elucidate the protein's initial steps during heme-uptake. ShuA variants were displayed on the surface of an M13 bacteriophage as fusions to the P8 coat protein. Each ShuA variant was analyzed for its ability to display on the bacteriophage surface, and functionally bind to hemoglobin. This technique streamlines isolation of stable MP variants for rapid characterization of binding to various ligands. Site-directed mutagenesis studies targeting each extracellular loop region of ShuA demonstrate no specific extracellular loop is required for hemoglobin binding. Instead two residues, His420 and His86 mediate this interaction. The results identify a loop susceptible to antibody binding, and also a small molecule motif capable of disrupting ShuA from S. dysenteriae. The approach is generalizable to the dissection of other phage-displayed TBDTs and MPs.

Evaluation of different parameterizations of the spatial heterogeneity of subsurface storage capacity for hourly runoff simulation in boreal mountainous watershed

NASA Astrophysics Data System (ADS)

Hailegeorgis, Teklu T.; Alfredsen, Knut; Abdella, Yisak S.; Kolberg, Sjur

2015-03-01

Identification of proper parameterizations of spatial heterogeneity is required for precipitation-runoff models. However, relevant studies with a specific aim at hourly runoff simulation in boreal mountainous catchments are not common. We conducted calibration and evaluation of hourly runoff simulation in a boreal mountainous watershed based on six different parameterizations of the spatial heterogeneity of subsurface storage capacity for a semi-distributed (subcatchments hereafter called elements) and distributed (1 × 1 km2 grid) setup. We evaluated representation of element-to-element, grid-to-grid, and probabilistic subcatchment/subbasin, subelement and subgrid heterogeneities. The parameterization cases satisfactorily reproduced the streamflow hydrographs with Nash-Sutcliffe efficiency values for the calibration and validation periods up to 0.84 and 0.86 respectively, and similarly for the log-transformed streamflow up to 0.85 and 0.90. The parameterizations reproduced the flow duration curves, but predictive reliability in terms of quantile-quantile (Q-Q) plots indicated marked over and under predictions. The simple and parsimonious parameterizations with no subelement or no subgrid heterogeneities provided equivalent simulation performance compared to the more complex cases. The results indicated that (i) identification of parameterizations require measurements from denser precipitation stations than what is required for acceptable calibration of the precipitation-streamflow relationships, (ii) there is challenges in the identification of parameterizations based on only calibration to catchment integrated streamflow observations and (iii) a potential preference for the simple and parsimonious parameterizations for operational forecast contingent on their equivalent simulation performance for the available input data. In addition, the effects of non-identifiability of parameters (interactions and equifinality) can contribute to the non-identifiability of the parameterizations.

Comprehensive assessment of parameterization methods for estimating clear-sky surface downward longwave radiation

NASA Astrophysics Data System (ADS)

Guo, Yamin; Cheng, Jie; Liang, Shunlin

2018-02-01

Surface downward longwave radiation (SDLR) is a key variable for calculating the earth's surface radiation budget. In this study, we evaluated seven widely used clear-sky parameterization methods using ground measurements collected from 71 globally distributed fluxnet sites. The Bayesian model averaging (BMA) method was also introduced to obtain a multi-model ensemble estimate. As a whole, the parameterization method of Carmona et al. (2014) performs the best, with an average BIAS, RMSE, and R 2 of - 0.11 W/m2, 20.35 W/m2, and 0.92, respectively, followed by the parameterization methods of Idso (1981), Prata (Q J R Meteorol Soc 122:1127-1151, 1996), Brunt and Sc (Q J R Meteorol Soc 58:389-420, 1932), and Brutsaert (Water Resour Res 11:742-744, 1975). The accuracy of the BMA is close to that of the parameterization method of Carmona et al. (2014) and comparable to that of the parameterization method of Idso (1981). The advantage of the BMA is that it achieves balanced results compared to the integrated single parameterization methods. To fully assess the performance of the parameterization methods, the effects of climate type, land cover, and surface elevation were also investigated. The five parameterization methods and BMA all failed over land with the tropical climate type, with high water vapor, and had poor results over forest, wetland, and ice. These methods achieved better results over desert, bare land, cropland, and grass and had acceptable accuracies for sites at different elevations, except for the parameterization method of Carmona et al. (2014) over high elevation sites. Thus, a method that can be successfully applied everywhere does not exist.

Evaluation of wave runup predictions from numerical and parametric models

USGS Publications Warehouse

Stockdon, Hilary F.; Thompson, David M.; Plant, Nathaniel G.; Long, Joseph W.

2014-01-01

Wave runup during storms is a primary driver of coastal evolution, including shoreline and dune erosion and barrier island overwash. Runup and its components, setup and swash, can be predicted from a parameterized model that was developed by comparing runup observations to offshore wave height, wave period, and local beach slope. Because observations during extreme storms are often unavailable, a numerical model is used to simulate the storm-driven runup to compare to the parameterized model and then develop an approach to improve the accuracy of the parameterization. Numerically simulated and parameterized runup were compared to observations to evaluate model accuracies. The analysis demonstrated that setup was accurately predicted by both the parameterized model and numerical simulations. Infragravity swash heights were most accurately predicted by the parameterized model. The numerical model suffered from bias and gain errors that depended on whether a one-dimensional or two-dimensional spatial domain was used. Nonetheless, all of the predictions were significantly correlated to the observations, implying that the systematic errors can be corrected. The numerical simulations did not resolve the incident-band swash motions, as expected, and the parameterized model performed best at predicting incident-band swash heights. An assimilated prediction using a weighted average of the parameterized model and the numerical simulations resulted in a reduction in prediction error variance. Finally, the numerical simulations were extended to include storm conditions that have not been previously observed. These results indicated that the parameterized predictions of setup may need modification for extreme conditions; numerical simulations can be used to extend the validity of the parameterized predictions of infragravity swash; and numerical simulations systematically underpredict incident swash, which is relatively unimportant under extreme conditions.

MC3, Version 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cawkwell, Marc Jon

2016-09-09

The MC3 code is used to perform Monte Carlo simulations in the isothermal-isobaric ensemble (constant number of particles, temperature, and pressure) on molecular crystals. The molecules within the periodic simulation cell are treated as rigid bodies, alleviating the requirement for a complex interatomic potential. Intermolecular interactions are described using generic, atom-centered pair potentials whose parameterization is taken from the literature [D. E. Williams, J. Comput. Chem., 22, 1154 (2001)] and electrostatic interactions arising from atom-centered, fixed, point partial charges. The primary uses of the MC3 code are the computation of i) the temperature and pressure dependence of lattice parameters andmore » thermal expansion coefficients, ii) tensors of elastic constants and compliances via the Parrinello and Rahman’s fluctuation formula [M. Parrinello and A. Rahman, J. Chem. Phys., 76, 2662 (1982)], and iii) the investigation of polymorphic phase transformations. The MC3 code is written in Fortran90 and requires LAPACK and BLAS linear algebra libraries to be linked during compilation. Computationally expensive loops are accelerated using OpenMP.« less

Distributed adaptive asymptotically consensus tracking control of uncertain Euler-Lagrange systems under directed graph condition.

PubMed

Wang, Wei; Wen, Changyun; Huang, Jiangshuai; Fan, Huijin

2017-11-01

In this paper, a backstepping based distributed adaptive control scheme is proposed for multiple uncertain Euler-Lagrange systems under directed graph condition. The common desired trajectory is allowed totally unknown by part of the subsystems and the linearly parameterized trajectory model assumed in currently available results is no longer needed. To compensate the effects due to unknown trajectory information, a smooth function of consensus errors and certain positive integrable functions are introduced in designing virtual control inputs. Besides, to overcome the difficulty of completely counteracting the coupling terms of distributed consensus errors and parameter estimation errors in the presence of asymmetric Laplacian matrix, extra information transmission of local parameter estimates are introduced among linked subsystem and adaptive gain technique is adopted to generate distributed torque inputs. It is shown that with the proposed distributed adaptive control scheme, global uniform boundedness of all the closed-loop signals and asymptotically output consensus tracking can be achieved. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Adaptive Neural Tracking Control for Switched High-Order Stochastic Nonlinear Systems.

PubMed

Zhao, Xudong; Wang, Xinyong; Zong, Guangdeng; Zheng, Xiaolong

2017-10-01

This paper deals with adaptive neural tracking control design for a class of switched high-order stochastic nonlinear systems with unknown uncertainties and arbitrary deterministic switching. The considered issues are: 1) completely unknown uncertainties; 2) stochastic disturbances; and 3) high-order nonstrict-feedback system structure. The considered mathematical models can represent many practical systems in the actual engineering. By adopting the approximation ability of neural networks, common stochastic Lyapunov function method together with adding an improved power integrator technique, an adaptive state feedback controller with multiple adaptive laws is systematically designed for the systems. Subsequently, a controller with only two adaptive laws is proposed to solve the problem of over parameterization. Under the designed controllers, all the signals in the closed-loop system are bounded-input bounded-output stable in probability, and the system output can almost surely track the target trajectory within a specified bounded error. Finally, simulation results are presented to show the effectiveness of the proposed approaches.

Methods used to parameterize the spatially-explicit components of a state-and-transition simulation model

USGS Publications Warehouse

Sleeter, Rachel; Acevedo, William; Soulard, Christopher E.; Sleeter, Benjamin M.

2015-01-01

Spatially-explicit state-and-transition simulation models of land use and land cover (LULC) increase our ability to assess regional landscape characteristics and associated carbon dynamics across multiple scenarios. By characterizing appropriate spatial attributes such as forest age and land-use distribution, a state-and-transition model can more effectively simulate the pattern and spread of LULC changes. This manuscript describes the methods and input parameters of the Land Use and Carbon Scenario Simulator (LUCAS), a customized state-and-transition simulation model utilized to assess the relative impacts of LULC on carbon stocks for the conterminous U.S. The methods and input parameters are spatially explicit and describe initial conditions (strata, state classes and forest age), spatial multipliers, and carbon stock density. Initial conditions were derived from harmonization of multi-temporal data characterizing changes in land use as well as land cover. Harmonization combines numerous national-level datasets through a cell-based data fusion process to generate maps of primary LULC categories. Forest age was parameterized using data from the North American Carbon Program and spatially-explicit maps showing the locations of past disturbances (i.e. wildfire and harvest). Spatial multipliers were developed to spatially constrain the location of future LULC transitions. Based on distance-decay theory, maps were generated to guide the placement of changes related to forest harvest, agricultural intensification/extensification, and urbanization. We analyze the spatially-explicit input parameters with a sensitivity analysis, by showing how LUCAS responds to variations in the model input. This manuscript uses Mediterranean California as a regional subset to highlight local to regional aspects of land change, which demonstrates the utility of LUCAS at many scales and applications.

Correction of Excessive Precipitation over Steep and High Mountains in a GCM: A Simple Method of Parameterizing the Thermal Effects of Subgrid Topographic Variation

NASA Technical Reports Server (NTRS)

Chao, Winston C.

2015-01-01

The excessive precipitation over steep and high mountains (EPSM) in GCMs and meso-scale models is due to a lack of parameterization of the thermal effects of the subgrid-scale topographic variation. These thermal effects drive subgrid-scale heated slope induced vertical circulations (SHVC). SHVC provide a ventilation effect of removing heat from the boundary layer of resolvable-scale mountain slopes and depositing it higher up. The lack of SHVC parameterization is the cause of EPSM. The author has previously proposed a method of parameterizing SHVC, here termed SHVC.1. Although this has been successful in avoiding EPSM, the drawback of SHVC.1 is that it suppresses convective type precipitation in the regions where it is applied. In this article we propose a new method of parameterizing SHVC, here termed SHVC.2. In SHVC.2 the potential temperature and mixing ratio of the boundary layer are changed when used as input to the cumulus parameterization scheme over mountainous regions. This allows the cumulus parameterization to assume the additional function of SHVC parameterization. SHVC.2 has been tested in NASA Goddard's GEOS-5 GCM. It achieves the primary goal of avoiding EPSM while also avoiding the suppression of convective-type precipitation in regions where it is applied.

Hardwired Control Changes For NSTX DC Power Feeds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramakrishnan, S.

The National Spherical Torus Experiment (NSTX) has been designed and installed in the existing facilities at Princeton Plasma Physics Laboratory (PPPL). Most of the hardware, plant facilities, auxiliary sub-systems, and power systems originally used for the Tokamak Fusion Test Reactor (TFTR) have been used with suitable modifications to reflect NSTX needs. The original TFTR Hardwired Control System (HCS) with electromechanical relays was used for NSTX DC Power loop control and protection during NSTX operations. As part of the NSTX Upgrade, the HCS is being changed to a PLC-based system with the same control logic. This paper gives a description ofmore » the changeover to the new PLC-based system __________________________________________________« less

ORNL-TNS/PEPR overall heating requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Y. K.M.; Rome, J. A.

1977-01-01

The ORNL TNS/PEPR studies have the objectives of (1) leading to a system that demonstrates the fusion reactor core in the mid-to-late 1980's and extrapolates to an economic tokamak power reactor, and (2) providing a near-term focus for the scientific and technological programs toward the power reactor. This discussion of the overall heating requirements for the ORNL TNS/PEPR is concerned with the neutral beams as the primary heating method, the electron-cyclotron resonance (ECR) heating at a lower power level for profile control, and the upper hybrid resonance (UHR) initiation and preheating of currentless plasmas to reduce current start-up loop voltagemore » (V/sub l/) requirements.« less

Designing Guiding Systems for Brain-Computer Interfaces

PubMed Central

Kosmyna, Nataliya; Lécuyer, Anatole

2017-01-01

Brain–Computer Interface (BCI) community has focused the majority of its research efforts on signal processing and machine learning, mostly neglecting the human in the loop. Guiding users on how to use a BCI is crucial in order to teach them to produce stable brain patterns. In this work, we explore the instructions and feedback for BCIs in order to provide a systematic taxonomy to describe the BCI guiding systems. The purpose of our work is to give necessary clues to the researchers and designers in Human–Computer Interaction (HCI) in making the fusion between BCIs and HCI more fruitful but also to better understand the possibilities BCIs can provide to them. PMID:28824400

Evaluation of scale-aware subgrid mesoscale eddy models in a global eddy-rich model

NASA Astrophysics Data System (ADS)

Pearson, Brodie; Fox-Kemper, Baylor; Bachman, Scott; Bryan, Frank

2017-07-01

Two parameterizations for horizontal mixing of momentum and tracers by subgrid mesoscale eddies are implemented in a high-resolution global ocean model. These parameterizations follow on the techniques of large eddy simulation (LES). The theory underlying one parameterization (2D Leith due to Leith, 1996) is that of enstrophy cascades in two-dimensional turbulence, while the other (QG Leith) is designed for potential enstrophy cascades in quasi-geostrophic turbulence. Simulations using each of these parameterizations are compared with a control simulation using standard biharmonic horizontal mixing.Simulations using the 2D Leith and QG Leith parameterizations are more realistic than those using biharmonic mixing. In particular, the 2D Leith and QG Leith simulations have more energy in resolved mesoscale eddies, have a spectral slope more consistent with turbulence theory (an inertial enstrophy or potential enstrophy cascade), have bottom drag and vertical viscosity as the primary sinks of energy instead of lateral friction, and have isoneutral parameterized mesoscale tracer transport. The parameterization choice also affects mass transports, but the impact varies regionally in magnitude and sign.

Evaluation of Surface Flux Parameterizations with Long-Term ARM Observations

DOE PAGES

Liu, Gang; Liu, Yangang; Endo, Satoshi

2013-02-01

Surface momentum, sensible heat, and latent heat fluxes are critical for atmospheric processes such as clouds and precipitation, and are parameterized in a variety of models ranging from cloud-resolving models to large-scale weather and climate models. However, direct evaluation of the parameterization schemes for these surface fluxes is rare due to limited observations. This study takes advantage of the long-term observations of surface fluxes collected at the Southern Great Plains site by the Department of Energy Atmospheric Radiation Measurement program to evaluate the six surface flux parameterization schemes commonly used in the Weather Research and Forecasting (WRF) model and threemore » U.S. general circulation models (GCMs). The unprecedented 7-yr-long measurements by the eddy correlation (EC) and energy balance Bowen ratio (EBBR) methods permit statistical evaluation of all six parameterizations under a variety of stability conditions, diurnal cycles, and seasonal variations. The statistical analyses show that the momentum flux parameterization agrees best with the EC observations, followed by latent heat flux, sensible heat flux, and evaporation ratio/Bowen ratio. The overall performance of the parameterizations depends on atmospheric stability, being best under neutral stratification and deteriorating toward both more stable and more unstable conditions. Further diagnostic analysis reveals that in addition to the parameterization schemes themselves, the discrepancies between observed and parameterized sensible and latent heat fluxes may stem from inadequate use of input variables such as surface temperature, moisture availability, and roughness length. The results demonstrate the need for improving the land surface models and measurements of surface properties, which would permit the evaluation of full land surface models.« less

Gene fusions AHRR-NCOA2, NCOA2-ETV4, ETV4-AHRR, P4HA2-TBCK, and TBCK-P4HA2 resulting from the translocations t(5;8;17)(p15;q13;q21) and t(4;5)(q24;q31) in a soft tissue angiofibroma

PubMed Central

Panagopoulos, Ioannis; Gorunova, Ludmila; Viset, Trond; Heim, Sverre

2016-01-01

We present an angiofibroma of soft tissue with the karyotype 46,XY,t(4;5)(q24;q31),t(5;8;17)(p15;q13;q21) [8]/46,XY,t(1;14)(p31;q32)[2]/46,XY[3]. RNA-sequencing showed that the t(4;5)(q24;q31) resulted in recombination of the genes TBCK on 4q24 and P4HA2 on 5q31.1 with generation of an in-frame TBCK-P4HA2 and the reciprocal but out-of-frame P4HA2-TBCK fusion transcripts. The putative TBCK-P4HA2 protein would contain the kinase, the rhodanese-like domain, and the Tre-2/Bub2/Cdc16 (TBC) domains of TBCK together with the P4HA2 protein which is a component of the prolyl 4-hydroxylase. The t(5;8;17)(p15;q13;q21) three-way chromosomal translocation targeted AHRR (on 5p15), NCOA2 (on 8q13), and ETV4 (on 17q21) generating the in-frame fusions AHRR-NCOA2 and NCOA2-ETV4 as well as an out-of-frame ETV4-AHRR transcript. In the AHRR-NCOA2 protein, the C-terminal part of AHRR is replaced by the C-terminal part of NCOA2 which contains two activation domains. The NCOA2-ETV4 protein would contain the helix-loop-helix, PAS_9 and PAS_11, CITED domains, the SRC-1 domain of NCOA2 and the ETS DNA-binding domain of ETV4. No fusion gene corresponding to t(1;14)(p31;q32) was found. Our findings indicate that, in spite of the recurrence of AHRR-NCOA2 in angiofibroma of soft tissue, additional genetic events (or fusion genes) might be required for the development of this tumor. PMID:27633981

Towards improved parameterization of a macroscale hydrologic model in a discontinuous permafrost boreal forest ecosystem

DOE PAGES

Endalamaw, Abraham; Bolton, W. Robert; Young-Robertson, Jessica M.; ...

2017-09-14

Modeling hydrological processes in the Alaskan sub-arctic is challenging because of the extreme spatial heterogeneity in soil properties and vegetation communities. Nevertheless, modeling and predicting hydrological processes is critical in this region due to its vulnerability to the effects of climate change. Coarse-spatial-resolution datasets used in land surface modeling pose a new challenge in simulating the spatially distributed and basin-integrated processes since these datasets do not adequately represent the small-scale hydrological, thermal, and ecological heterogeneity. The goal of this study is to improve the prediction capacity of mesoscale to large-scale hydrological models by introducing a small-scale parameterization scheme, which bettermore » represents the spatial heterogeneity of soil properties and vegetation cover in the Alaskan sub-arctic. The small-scale parameterization schemes are derived from observations and a sub-grid parameterization method in the two contrasting sub-basins of the Caribou Poker Creek Research Watershed (CPCRW) in Interior Alaska: one nearly permafrost-free (LowP) sub-basin and one permafrost-dominated (HighP) sub-basin. The sub-grid parameterization method used in the small-scale parameterization scheme is derived from the watershed topography. We found that observed soil thermal and hydraulic properties – including the distribution of permafrost and vegetation cover heterogeneity – are better represented in the sub-grid parameterization method than the coarse-resolution datasets. Parameters derived from the coarse-resolution datasets and from the sub-grid parameterization method are implemented into the variable infiltration capacity (VIC) mesoscale hydrological model to simulate runoff, evapotranspiration (ET), and soil moisture in the two sub-basins of the CPCRW. Simulated hydrographs based on the small-scale parameterization capture most of the peak and low flows, with similar accuracy in both sub-basins, compared to simulated hydrographs based on the coarse-resolution datasets. On average, the small-scale parameterization scheme improves the total runoff simulation by up to 50 % in the LowP sub-basin and by up to 10 % in the HighP sub-basin from the large-scale parameterization. This study shows that the proposed sub-grid parameterization method can be used to improve the performance of mesoscale hydrological models in the Alaskan sub-arctic watersheds.« less

Towards improved parameterization of a macroscale hydrologic model in a discontinuous permafrost boreal forest ecosystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Endalamaw, Abraham; Bolton, W. Robert; Young-Robertson, Jessica M.

Modeling hydrological processes in the Alaskan sub-arctic is challenging because of the extreme spatial heterogeneity in soil properties and vegetation communities. Nevertheless, modeling and predicting hydrological processes is critical in this region due to its vulnerability to the effects of climate change. Coarse-spatial-resolution datasets used in land surface modeling pose a new challenge in simulating the spatially distributed and basin-integrated processes since these datasets do not adequately represent the small-scale hydrological, thermal, and ecological heterogeneity. The goal of this study is to improve the prediction capacity of mesoscale to large-scale hydrological models by introducing a small-scale parameterization scheme, which bettermore » represents the spatial heterogeneity of soil properties and vegetation cover in the Alaskan sub-arctic. The small-scale parameterization schemes are derived from observations and a sub-grid parameterization method in the two contrasting sub-basins of the Caribou Poker Creek Research Watershed (CPCRW) in Interior Alaska: one nearly permafrost-free (LowP) sub-basin and one permafrost-dominated (HighP) sub-basin. The sub-grid parameterization method used in the small-scale parameterization scheme is derived from the watershed topography. We found that observed soil thermal and hydraulic properties – including the distribution of permafrost and vegetation cover heterogeneity – are better represented in the sub-grid parameterization method than the coarse-resolution datasets. Parameters derived from the coarse-resolution datasets and from the sub-grid parameterization method are implemented into the variable infiltration capacity (VIC) mesoscale hydrological model to simulate runoff, evapotranspiration (ET), and soil moisture in the two sub-basins of the CPCRW. Simulated hydrographs based on the small-scale parameterization capture most of the peak and low flows, with similar accuracy in both sub-basins, compared to simulated hydrographs based on the coarse-resolution datasets. On average, the small-scale parameterization scheme improves the total runoff simulation by up to 50 % in the LowP sub-basin and by up to 10 % in the HighP sub-basin from the large-scale parameterization. This study shows that the proposed sub-grid parameterization method can be used to improve the performance of mesoscale hydrological models in the Alaskan sub-arctic watersheds.« less

Extensions and applications of a second-order landsurface parameterization

NASA Technical Reports Server (NTRS)

Andreou, S. A.; Eagleson, P. S.

1983-01-01

Extensions and applications of a second order land surface parameterization, proposed by Andreou and Eagleson are developed. Procedures for evaluating the near surface storage depth used in one cell land surface parameterizations are suggested and tested by using the model. Sensitivity analysis to the key soil parameters is performed. A case study involving comparison with an "exact" numerical model and another simplified parameterization, under very dry climatic conditions and for two different soil types, is also incorporated.

Development and Testing of Coupled Land-surface, PBL and Shallow/Deep Convective Parameterizations within the MM5

NASA Technical Reports Server (NTRS)

Stauffer, David R.; Seaman, Nelson L.; Munoz, Ricardo C.

2000-01-01

The objective of this investigation was to study the role of shallow convection on the regional water cycle of the Mississippi and Little Washita Basins using a 3-D mesoscale model, the PSUINCAR MM5. The underlying premise of the project was that current modeling of regional-scale climate and moisture cycles over the continents is deficient without adequate treatment of shallow convection. It was hypothesized that an improved treatment of the regional water cycle can be achieved by using a 3-D mesoscale numerical model having a detailed land-surface parameterization, an advanced boundary-layer parameterization, and a more complete shallow convection parameterization than are available in most current models. The methodology was based on the application in the MM5 of new or recently improved parameterizations covering these three physical processes. Therefore, the work plan focused on integrating, improving, and testing these parameterizations in the MM5 and applying them to study water-cycle processes over the Southern Great Plains (SGP): (1) the Parameterization for Land-Atmosphere-Cloud Exchange (PLACE) described by Wetzel and Boone; (2) the 1.5-order turbulent kinetic energy (TKE)-predicting scheme of Shafran et al.; and (3) the hybrid-closure sub-grid shallow convection parameterization of Deng. Each of these schemes has been tested extensively through this study and the latter two have been improved significantly to extend their capabilities.

Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.

2012-03-13

Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-{angstrom} resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimermore » in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.« less

Advantages and Challenges of Radiative Liquid Lithium Divertor

NASA Astrophysics Data System (ADS)

Ono, Masayuki

2017-10-01

Steady-state fusion power plant designs present major divertor technology challenges, including high divertor heat flux both in steady-state and during transients. In addition to these concerns, there are the unresolved technology issues of long term dust accumulation and associated tritium inventory and safety issues. The application of lithium (Li) in NSTX resulted in improved H-mode confinement, H-mode power threshold reduction, and reduction in the divertor peak heat flux while maintaining essentially Li-free core plasma operation even during H-modes. These promising results in NSTX and related modeling calculations motivated the radiative liquid Li divertor (RLLD) concept and its variant, the active liquid Li divertor concept (ARLLD), taking advantage of the enhanced Li radiation in relatively poorly confined divertor plasmas. It has been suggested that radiation-based liquid lithium (LL) divertor concepts with a modest Li-loop could provide a possible solution for the outstanding fusion reactor technology issues such as divertor heat flux mitigation and real time dust removal, while potentially improving the reactor plasma performance. Laboratory tests are also planned to investigate the Li-T recover efficiency and other relevant research topics of the RLLD. This work supported by DoE Contract No. DE-AC02-09CH11466.

Improved efficacy of soluble human receptor activator of nuclear factor kappa B (RANK) fusion protein by site-directed mutagenesis.

PubMed

Son, Young Jun; Han, Jihye; Lee, Jae Yeon; Kim, HaHyung; Chun, Taehoon

2015-06-01

Soluble human receptor activator of nuclear factor kappa B fusion immunoglobulin (hRANK-Ig) has been considered as one of the therapeutic agents to treat osteoporosis or diseases associated with bone destruction by blocking the interaction between RANK and the receptor activator of nuclear factor kappa B ligand (RANKL). However, no scientific record showing critical amino acid residues within the structural interface between the human RANKL and RANK complex is yet available. In this study, we produced several mutants of hRANK-Ig by replacement of amino acid residue(s) and tested whether the mutants had increased binding affinity to human RANKL. Based on the results from flow cytometry and surface plasmon resonance analyses, the replacement of E(125) with D(125), or E(125) and C(127) with D(125) and F(127) within loop 3 of cysteine-rich domain 3 of hRANK-Ig increases binding affinity to human RANKL over the wild-type hRANK-Ig. This result may provide the first example of improvement in the efficacy of hRANK-Ig by protein engineering and may give additional information to understand a more defined structural interface between hRANK and RANKL.

Crystal structure of the Japanese encephalitis virus envelope protein.

PubMed

Luca, Vincent C; AbiMansour, Jad; Nelson, Christopher A; Fremont, Daved H

2012-02-01

Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-Å resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen

PubMed Central

Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S.; Wrapp, Daniel; Kirchdoerfer, Robert N.; Turner, Hannah L.; Cottrell, Christopher A.; Becker, Michelle M.; Wang, Lingshu; Shi, Wei; Kong, Wing-Pui; Andres, Erica L.; Kettenbach, Arminja N.; Denison, Mark R.; Chappell, James D.; Graham, Barney S.; Ward, Andrew B.

2017-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines. PMID:28807998

Crystal structure of the GTPase domain and the bundle signalling element of dynamin in the GDP state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anand, Roopsee; Eschenburg, Susanne; Reubold, Thomas F., E-mail: Reubold.Thomas@mh-hannover.de

Dynamin is the prototype of a family of large multi-domain GTPases. The 100 kDa protein is a key player in clathrin-mediated endocytosis, where it cleaves off vesicles from membranes using the energy from GTP hydrolysis. We have solved the high resolution crystal structure of a fusion protein of the GTPase domain and the bundle signalling element (BSE) of dynamin 1 liganded with GDP. The structure provides a hitherto missing snapshot of the GDP state of the hydrolytic cycle of dynamin and reveals how the switch I region moves away from the active site after GTP hydrolysis and release of inorganic phosphate.more » Comparing our structure of the GDP state with the known structures of the GTP state, the transition state and the nucleotide-free state of dynamin 1 we describe the structural changes through the hydrolytic cycle. - Highlights: • High resolution crystal structure of the GDP-state of a dynamin 1 GTPase-BSE fusion. • Visualizes one of the key states of the hydrolytic cycle of dynamin. • The dynamin-specific loop forms a helix as soon as a guanine base is present.« less

RAD51 and RTEL1 compensate telomere loss in the absence of telomerase

PubMed Central

Olivier, Margaux; Charbonnel, Cyril; Amiard, Simon

2018-01-01

Abstract Replicative erosion of telomeres is naturally compensated by telomerase and studies in yeast and vertebrates show that homologous recombination can compensate for the absence of telomerase. We show that RAD51 protein, which catalyzes the key strand-invasion step of homologous recombination, is localized at Arabidopsis telomeres in absence of telomerase. Blocking the strand-transfer activity of the RAD51 in telomerase mutant plants results in a strikingly earlier onset of developmental defects, accompanied by increased numbers of end-to-end chromosome fusions. Imposing replication stress through knockout of RNaseH2 increases numbers of chromosome fusions and reduces the survival of these plants deficient for telomerase and homologous recombination. This finding suggests that RAD51-dependent homologous recombination acts as an essential backup to the telomerase for compensation of replicative telomere loss to ensure genome stability. Furthermore, we show that this positive role of RAD51 in telomere stability is dependent on the RTEL1 helicase. We propose that a RAD51 dependent break-induced replication process is activated in cells lacking telomerase activity, with RTEL1 responsible for D-loop dissolution after telomere replication. PMID:29346668

Discovery of an antibody for pan-ebolavirus therapy.

PubMed

Furuyama, Wakako; Marzi, Andrea; Nanbo, Asuka; Haddock, Elaine; Maruyama, Junki; Miyamoto, Hiroko; Igarashi, Manabu; Yoshida, Reiko; Noyori, Osamu; Feldmann, Heinz; Takada, Ayato

2016-02-10

During the latest outbreak of Ebola virus disease in West Africa, monoclonal antibody therapy (e.g., ZMapp) was utilized to treat patients. However, due to the antigenic differences among the five ebolavirus species, the current therapeutic monoclonal antibodies are only effective against viruses of the species Zaire ebolavirus. Although this particular species has indeed caused the majority of human infections in Central and, recently, West Africa, other ebolavirus species (e.g., Sudan ebolavirus and Bundibugyo ebolavirus) have also repeatedly caused outbreaks in Central Africa and thus should not be neglected in the development of countermeasures against ebolaviruses. Here we report the generation of an ebolavirus glycoprotein-specific monoclonal antibody that effectively inhibits cellular entry of representative isolates of all known ebolavirus species in vitro and show its protective efficacy in mouse models of ebolavirus infections. This novel neutralizing monoclonal antibody targets a highly conserved internal fusion loop in the glycoprotein molecule and prevents membrane fusion of the viral envelope with cellular membranes. The discovery of this highly cross-neutralizing antibody provides a promising option for broad-acting ebolavirus antibody therapy and will accelerate the design of improved vaccines that can selectively elicit cross-neutralizing antibodies against multiple species of ebolaviruses.

A Simple Parameterization of 3 x 3 Magic Squares

ERIC Educational Resources Information Center

Trenkler, Gotz; Schmidt, Karsten; Trenkler, Dietrich

2012-01-01

In this article a new parameterization of magic squares of order three is presented. This parameterization permits an easy computation of their inverses, eigenvalues, eigenvectors and adjoints. Some attention is paid to the Luoshu, one of the oldest magic squares.

New Technique of AC drive in Tokamak using Permanent Magnets

NASA Astrophysics Data System (ADS)

Matteucci, Jackson; Zolfaghari, Ali

2013-10-01

This study investigates a new technique of capturing the rotational energy of alternating permanent magnets in order to inductively drive an alternating current in tokamak devices. The use of rotational motion bypasses many of the pitfalls seen in typical inductive and non-inductive current drives. Three specific designs are presented and assessed in the following criteria: the profile of the current generated, the RMS loop voltage generated as compared to the RMS power required to maintain it, the system's feasibility from an engineering perspective. All of the analysis has been done under ideal E&M conditions using the Maxwell 3D program. Preliminary results indicate that it is possible to produce an over 99% purely toroidal current with a RMS d Φ/dt of over 150 Tm2/s, driven by 20 MW or less of rotational power. The proposed mechanism demonstrates several key advantages including an efficient mechanical drive system, the generation of pure toroidal currents, and the potential for a quasi-steady state fusion reactor. The following quantities are presented for various driving frequencies and magnet strengths: plasma current generated, loop voltage, torque and power required. This project has been supported by DOE Funding under the SULI program.

Purification and characterization of the three Snf1-activating kinases of Saccharomyces cerevisiae.

PubMed

Elbing, Karin; McCartney, Rhonda R; Schmidt, Martin C

2006-02-01

Members of the Snf1/AMPK family of protein kinases are activated by distinct upstream kinases that phosphorylate a conserved threonine residue in the Snf1/AMPK activation loop. Recently, the identities of the Snf1- and AMPK-activating kinases have been determined. Here we describe the purification and characterization of the three Snf1-activating kinases of Saccharomyces cerevisiae. The identities of proteins associated with the Snf1-activating kinases were determined by peptide mass fingerprinting. These kinases, Sak1, Tos3 and Elm2 do not appear to require the presence of additional subunits for activity. Sak1 and Snf1 co-purify and co-elute in size exclusion chromatography, demonstrating that these two proteins form a stable complex. The Snf1-activating kinases phosphorylate the activation loop threonine of Snf1 in vitro with great specificity and are able to do so in the absence of beta and gamma subunits of the Snf1 heterotrimer. Finally, we showed that the Snf1 kinase domain isolated from bacteria as a GST fusion protein can be activated in vitro and shows substrate specificity in the absence of its beta and gamma subunits.

Purification and characterization of the three Snf1-activating kinases of Saccharomyces cerevisiae

PubMed Central

2005-01-01

Members of the Snf1/AMPK family of protein kinases are activated by distinct upstream kinases that phosphorylate a conserved threonine residue in the Snf1/AMPK activation loop. Recently, the identities of the Snf1- and AMPK-activating kinases have been determined. Here we describe the purification and characterization of the three Snf1-activating kinases of Saccharomyces cerevisiae. The identities of proteins associated with the Snf1-activating kinases were determined by peptide mass fingerprinting. These kinases, Sak1, Tos3 and Elm2 do not appear to require the presence of additional subunits for activity. Sak1 and Snf1 co-purify and co-elute in size exclusion chromatography, demonstrating that these two proteins form a stable complex. The Snf1-activating kinases phosphorylate the activation loop threonine of Snf1 in vitro with great specificity and are able to do so in the absence of β and γ subunits of the Snf1 heterotrimer. Finally, we showed that the Snf1 kinase domain isolated from bacteria as a GST fusion protein can be activated in vitro and shows substrate specificity in the absence of its β and γ subunits. PMID:16201971

Substrate specificity of human protein arginine methyltransferase 7 (PRMT7): the importance of acidic residues in the double E loop.

PubMed

Feng, You; Hadjikyriacou, Andrea; Clarke, Steven G

2014-11-21

Protein arginine methyltransferase 7 (PRMT7) methylates arginine residues on various protein substrates and is involved in DNA transcription, RNA splicing, DNA repair, cell differentiation, and metastasis. The substrate sequences it recognizes in vivo and the enzymatic mechanism behind it, however, remain to be explored. Here we characterize methylation catalyzed by a bacterially expressed GST-tagged human PRMT7 fusion protein with a broad range of peptide and protein substrates. After confirming its type III activity generating only ω-N(G)-monomethylarginine and its distinct substrate specificity for RXR motifs surrounded by basic residues, we performed site-directed mutagenesis studies on this enzyme, revealing that two acidic residues within the double E loop, Asp-147 and Glu-149, modulate the substrate preference. Furthermore, altering a single acidic residue, Glu-478, on the C-terminal domain to glutamine nearly abolished the activity of the enzyme. Additionally, we demonstrate that PRMT7 has unusual temperature dependence and salt tolerance. These results provide a biochemical foundation to understanding the broad biological functions of PRMT7 in health and disease. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Dynamically Consistent Parameterization of Mesoscale Eddies This work aims at parameterization of eddy effects for use in non-eddy-resolving ocean models and focuses on the effect of the stochastic part of the eddy forcing that backscatters and induces eastward jet extension of the western boundary currents and its adjacent recirculation zones.

NASA Astrophysics Data System (ADS)

Berloff, P. S.

2016-12-01

This work aims at developing a framework for dynamically consistent parameterization of mesoscale eddy effects for use in non-eddy-resolving ocean circulation models. The proposed eddy parameterization framework is successfully tested on the classical, wind-driven double-gyre model, which is solved both with explicitly resolved vigorous eddy field and in the non-eddy-resolving configuration with the eddy parameterization replacing the eddy effects. The parameterization focuses on the effect of the stochastic part of the eddy forcing that backscatters and induces eastward jet extension of the western boundary currents and its adjacent recirculation zones. The parameterization locally approximates transient eddy flux divergence by spatially localized and temporally periodic forcing, referred to as the plunger, and focuses on the linear-dynamics flow solution induced by it. The nonlinear self-interaction of this solution, referred to as the footprint, characterizes and quantifies the induced eddy forcing exerted on the large-scale flow. We find that spatial pattern and amplitude of each footprint strongly depend on the underlying large-scale flow, and the corresponding relationships provide the basis for the eddy parameterization and its closure on the large-scale flow properties. Dependencies of the footprints on other important parameters of the problem are also systematically analyzed. The parameterization utilizes the local large-scale flow information, constructs and scales the corresponding footprints, and then sums them up over the gyres to produce the resulting eddy forcing field, which is interactively added to the model as an extra forcing. Thus, the assumed ensemble of plunger solutions can be viewed as a simple model for the cumulative effect of the stochastic eddy forcing. The parameterization framework is implemented in the simplest way, but it provides a systematic strategy for improving the implementation algorithm.

Enabling co-simulation of tokamak plant models and plasma control systems

DOE PAGES

Walker, M. L.

2017-12-22

A system for connecting the Plasma Control System and a model of the tokamak Plant in closed loop co-simulation for plasma control development has been in routine use at DIII-D for more than 20 years and at other fusion labs that use variants of the DIII-D PCS for approximately the last decade. Here, co-simulation refers to the simultaneous execution of two independent codes with the exchange of data - Plant actuator commands and tokamak diagnostic data - between them during execution. Interest in this type of PCS-Plant simulation technology has also been growing recently at other fusion facilities. In fact,more » use of such closed loop control simulations is assumed to play an even larger role in the development of both the ITER Plasma Control System (PCS) and the experimental operation of the ITER device, where they will be used to support verification/validation of the PCS and also for ITER pulse schedule development and validation. We describe the key use cases that motivate the co-simulation capability and the features that must be provided by the Plasma Control System to support it. These features could be provided by the PCS itself or by a model of the PCS. If the PCS itself is chosen to provide them, there are requirements imposed on its architecture. If a PCS model is chosen, there are requirements imposed on the initial implementation of this simulation as well as long-term consequences for its continued development and maintenance. We describe these issues for each use case and discuss the relative merits of the two choices. Several examples are given illustrating uses of the co-simulation method to address problems of plasma control during the operation of DIII-D and of other devices that use the DIII-D PCS.« less

Enabling co-simulation of tokamak plant models and plasma control systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, M. L.

A system for connecting the Plasma Control System and a model of the tokamak Plant in closed loop co-simulation for plasma control development has been in routine use at DIII-D for more than 20 years and at other fusion labs that use variants of the DIII-D PCS for approximately the last decade. Here, co-simulation refers to the simultaneous execution of two independent codes with the exchange of data - Plant actuator commands and tokamak diagnostic data - between them during execution. Interest in this type of PCS-Plant simulation technology has also been growing recently at other fusion facilities. In fact,more » use of such closed loop control simulations is assumed to play an even larger role in the development of both the ITER Plasma Control System (PCS) and the experimental operation of the ITER device, where they will be used to support verification/validation of the PCS and also for ITER pulse schedule development and validation. We describe the key use cases that motivate the co-simulation capability and the features that must be provided by the Plasma Control System to support it. These features could be provided by the PCS itself or by a model of the PCS. If the PCS itself is chosen to provide them, there are requirements imposed on its architecture. If a PCS model is chosen, there are requirements imposed on the initial implementation of this simulation as well as long-term consequences for its continued development and maintenance. We describe these issues for each use case and discuss the relative merits of the two choices. Several examples are given illustrating uses of the co-simulation method to address problems of plasma control during the operation of DIII-D and of other devices that use the DIII-D PCS.« less

First Results of the Testing of the Liquid Gallium Jet Limiter Concept for ISTTOK

NASA Astrophysics Data System (ADS)

Gomes, R. B.; Fernandes, H.; Silva, C.; Borba, D.; Carvalho, B.; Varandas, C.; Lielausis, O.; Klyukin, A.; Platacis, E.; Mikelsons, A.; Platnieks, I.

2006-12-01

The use of liquid metals as plasma facing components in tokamaks has recently experienced a renewed interest stimulated by their advantages to the development of a fusion reactor. Liquid metals have been proposed to solve problems related to the erosion and neutronic activation of solid walls submitted to high power loads allowing an efficient heat exhaustion from fusion devices. Presently the most promising materials are Lithium and Gallium. ISTTOK, a small size tokamak, will be used to test the behavior of a liquid Gallium jet in the vacuum chamber and its influence on the plasma. This paper presents a description of the conceived setup as well as experimental results. The liquid Gallium jet is generated by hydrostatic pressure and injected in a radial position close to a moveable stainless steel limiter. Both the jet and the limiter positions are variable allowing for a controlled exposure of the liquid Gallium to the edge plasma. The main components of the Gallium loop are a MHD pump, the liquid metal injector and a filtering system. The MHD pump is of the induction type, based on rotating permanent magnets. The injector is build from a ¼″ stainless steel pipe ended by a shaping nozzle. A setup has been developed to introduce oxide-free Gallium inside the loop's main supply tank. Raw liquid metal is placed inside a chamber heated and degassed under high vacuum while clean Gallium is extracted from the main body of the liquefied metal. Prior to installation on the tokamak, the experimental rig has been implemented using a Pyrex tube as test chamber to investigate the stability of the Gallium jet and its break-up length for several nozzle sizes. Results are presented in this paper. This rig was also useful to assess the behavior of the overall implemented apparatus.

Development of a two-dimensional zonally averaged statistical-dynamical model. III - The parameterization of the eddy fluxes of heat and moisture

NASA Technical Reports Server (NTRS)

Stone, Peter H.; Yao, Mao-Sung

1990-01-01

A number of perpetual January simulations are carried out with a two-dimensional zonally averaged model employing various parameterizations of the eddy fluxes of heat (potential temperature) and moisture. The parameterizations are evaluated by comparing these results with the eddy fluxes calculated in a parallel simulation using a three-dimensional general circulation model with zonally symmetric forcing. The three-dimensional model's performance in turn is evaluated by comparing its results using realistic (nonsymmetric) boundary conditions with observations. Branscome's parameterization of the meridional eddy flux of heat and Leovy's parameterization of the meridional eddy flux of moisture simulate the seasonal and latitudinal variations of these fluxes reasonably well, while somewhat underestimating their magnitudes. New parameterizations of the vertical eddy fluxes are developed that take into account the enhancement of the eddy mixing slope in a growing baroclinic wave due to condensation, and also the effect of eddy fluctuations in relative humidity. The new parameterizations, when tested in the two-dimensional model, simulate the seasonal, latitudinal, and vertical variations of the vertical eddy fluxes quite well, when compared with the three-dimensional model, and only underestimate the magnitude of the fluxes by 10 to 20 percent.

Resolution-dependent behavior of subgrid-scale vertical transport in the Zhang-McFarlane convection parameterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Heng; Gustafson, Jr., William I.; Hagos, Samson M.

2015-04-18

With this study, to better understand the behavior of quasi-equilibrium-based convection parameterizations at higher resolution, we use a diagnostic framework to examine the resolution-dependence of subgrid-scale vertical transport of moist static energy as parameterized by the Zhang-McFarlane convection parameterization (ZM). Grid-scale input to ZM is supplied by coarsening output from cloud-resolving model (CRM) simulations onto subdomains ranging in size from 8 × 8 to 256 × 256 km 2s.

Parameterizing by the Number of Numbers

NASA Astrophysics Data System (ADS)

Fellows, Michael R.; Gaspers, Serge; Rosamond, Frances A.

The usefulness of parameterized algorithmics has often depended on what Niedermeier has called "the art of problem parameterization". In this paper we introduce and explore a novel but general form of parameterization: the number of numbers. Several classic numerical problems, such as Subset Sum, Partition, 3-Partition, Numerical 3-Dimensional Matching, and Numerical Matching with Target Sums, have multisets of integers as input. We initiate the study of parameterizing these problems by the number of distinct integers in the input. We rely on an FPT result for Integer Linear Programming Feasibility to show that all the above-mentioned problems are fixed-parameter tractable when parameterized in this way. In various applied settings, problem inputs often consist in part of multisets of integers or multisets of weighted objects (such as edges in a graph, or jobs to be scheduled). Such number-of-numbers parameterized problems often reduce to subproblems about transition systems of various kinds, parameterized by the size of the system description. We consider several core problems of this kind relevant to number-of-numbers parameterization. Our main hardness result considers the problem: given a non-deterministic Mealy machine M (a finite state automaton outputting a letter on each transition), an input word x, and a census requirement c for the output word specifying how many times each letter of the output alphabet should be written, decide whether there exists a computation of M reading x that outputs a word y that meets the requirement c. We show that this problem is hard for W[1]. If the question is whether there exists an input word x such that a computation of M on x outputs a word that meets c, the problem becomes fixed-parameter tractable.

Parameterized Cross Sections for Pion Production in Proton-Proton Collisions

NASA Technical Reports Server (NTRS)

Blattnig, Steve R.; Swaminathan, Sudha R.; Kruger, Adam T.; Ngom, Moussa; Norbury, John W.; Tripathi, R. K.

2000-01-01

An accurate knowledge of cross sections for pion production in proton-proton collisions finds wide application in particle physics, astrophysics, cosmic ray physics, and space radiation problems, especially in situations where an incident proton is transported through some medium and knowledge of the output particle spectrum is required when given the input spectrum. In these cases, accurate parameterizations of the cross sections are desired. In this paper much of the experimental data are reviewed and compared with a wide variety of different cross section parameterizations. Therefore, parameterizations of neutral and charged pion cross sections are provided that give a very accurate description of the experimental data. Lorentz invariant differential cross sections, spectral distributions, and total cross section parameterizations are presented.

Collaborative Research: Reducing tropical precipitation biases in CESM — Tests of unified parameterizations with ARM observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Vincent; Gettelman, Andrew; Morrison, Hugh

In state-of-the-art climate models, each cloud type is treated using its own separate cloud parameterization and its own separate microphysics parameterization. This use of separate schemes for separate cloud regimes is undesirable because it is theoretically unfounded, it hampers interpretation of results, and it leads to the temptation to overtune parameters. In this grant, we are creating a climate model that contains a unified cloud parameterization and a unified microphysics parameterization. This model will be used to address the problems of excessive frequency of drizzle in climate models and excessively early onset of deep convection in the Tropics over land.more » The resulting model will be compared with ARM observations.« less

Surface water areas significantly impacted 2014 dengue outbreaks in Guangzhou, China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Huaiyu; Huang, Shanqian

Dengue transmission in urban areas is strongly influenced by a range of biological and environmental factors, yet the key drivers still need further exploration. To better understand mechanisms of environment–mosquito–urban dengue transmission, we propose an empirical model parameterized and cross-validated from a unique dataset including viral gene sequences, vector dynamics and human dengue cases in Guangzhou, China, together with a 36-year urban environmental change maps investigated by spatiotemporal satellite image fusion. The dengue epidemics in Guangzhou are highly episodic and were not associated with annual rainfall over time. Our results indicate that urban environmental changes, especially variations in surface areamore » covered by water in urban areas, can substantially alter the virus population and dengue transmission. The recent severe dengue outbreaks in Guangzhou may be due to the surge in an artificial lake construction, which could increase infection force between vector (mainly Aedes albopictus) and host when urban water area significantly increased. Impacts of urban environmental change on dengue dynamics may not have been thoroughly investigated in the past studies and more work needs to be done to better understand the consequences of urbanization processes in our changing world. - Highlights: • Urban dengue outbreak is associated with water area in Guangzhou, 1978–2014. • Surface water area can alter population size of dengue virus in urban area. • Urban dengue outbreak is not associated with annual rainfall in Guangzhou. • Spatiotemporal satellite image fusion can investigate urban environmental change. • Urban environmental change could induce virus, vector, and dengue epidemic change.« less

Calibration of a Fusion Experiment to Investigate the Nuclear Caloric Curve

NASA Astrophysics Data System (ADS)

Keeler, Ashleigh

2017-09-01

In order to investigate the nuclear equation of state (EoS), the relation between two thermodynamic quantities can be examined. The correlation between the temperature and excitation energy of a nucleus, also known as the caloric curve, has been previously observed in peripheral heavy-ion collisions to exhibit a dependence on the neutron-proton asymmetry. To further investigate this result, fusion reactions (78Kr + 12C and 86Kr + 12C) were measured; the beam energy was varied in the range 15-35 MeV/u in order to vary the excitation energy. The light charged particles (LCPs) evaporated from the compound nucleus were measured in the Si-CsI(TI)/PD detector array FAUST (Forward Array Using Silicon Technology). The LCPs carry information about the temperature. The calibration of FAUST will be described in this presentation. The silicon detectors have resistive surfaces in perpendicular directions to allow position measurement of the LCP's to better than 200 um. The resistive nature requires a position-dependent correction to the energy calibration to take full advantage of the energy resolution. The momentum is calculated from the energy of these particles, and their position on the detectors. A parameterized formula based on the Bethe-Bloch equation was used to straighten the particle identification (PID) lines measured with the dE-E technique. The energy calibration of the CsI detectors is based on the silicon detector energy calibration and the PID. A precision slotted mask enables the relative positions of the detectors to be determined. DOE Grant: DE-FG02-93ER40773 and REU Grant: PHY - 1659847.

Ice-nucleating particle emissions from photochemically aged diesel and biodiesel exhaust

NASA Astrophysics Data System (ADS)

Schill, G. P.; Jathar, S. H.; Kodros, J. K.; Levin, E. J. T.; Galang, A. M.; Friedman, B.; Link, M. F.; Farmer, D. K.; Pierce, J. R.; Kreidenweis, S. M.; DeMott, P. J.

2016-05-01

Immersion-mode ice-nucleating particle (INP) concentrations from an off-road diesel engine were measured using a continuous-flow diffusion chamber at -30°C. Both petrodiesel and biodiesel were utilized, and the exhaust was aged up to 1.5 photochemically equivalent days using an oxidative flow reactor. We found that aged and unaged diesel exhaust of both fuels is not likely to contribute to atmospheric INP concentrations at mixed-phase cloud conditions. To explore this further, a new limit-of-detection parameterization for ice nucleation on diesel exhaust was developed. Using a global-chemical transport model, potential black carbon INP (INPBC) concentrations were determined using a current literature INPBC parameterization and the limit-of-detection parameterization. Model outputs indicate that the current literature parameterization likely overemphasizes INPBC concentrations, especially in the Northern Hemisphere. These results highlight the need to integrate new INPBC parameterizations into global climate models as generalized INPBC parameterizations are not valid for diesel exhaust.

Radiative flux and forcing parameterization error in aerosol-free clear skies

DOE PAGES

Pincus, Robert; Mlawer, Eli J.; Oreopoulos, Lazaros; ...

2015-07-03

This article reports on the accuracy in aerosol- and cloud-free conditions of the radiation parameterizations used in climate models. Accuracy is assessed relative to observationally validated reference models for fluxes under present-day conditions and forcing (flux changes) from quadrupled concentrations of carbon dioxide. Agreement among reference models is typically within 1 W/m 2, while parameterized calculations are roughly half as accurate in the longwave and even less accurate, and more variable, in the shortwave. Absorption of shortwave radiation is underestimated by most parameterizations in the present day and has relatively large errors in forcing. Error in present-day conditions is essentiallymore » unrelated to error in forcing calculations. Recent revisions to parameterizations have reduced error in most cases. As a result, a dependence on atmospheric conditions, including integrated water vapor, means that global estimates of parameterization error relevant for the radiative forcing of climate change will require much more ambitious calculations.« less

[Formula: see text] regularity properties of singular parameterizations in isogeometric analysis.

PubMed

Takacs, T; Jüttler, B

2012-11-01

Isogeometric analysis (IGA) is a numerical simulation method which is directly based on the NURBS-based representation of CAD models. It exploits the tensor-product structure of 2- or 3-dimensional NURBS objects to parameterize the physical domain. Hence the physical domain is parameterized with respect to a rectangle or to a cube. Consequently, singularly parameterized NURBS surfaces and NURBS volumes are needed in order to represent non-quadrangular or non-hexahedral domains without splitting, thereby producing a very compact and convenient representation. The Galerkin projection introduces finite-dimensional spaces of test functions in the weak formulation of partial differential equations. In particular, the test functions used in isogeometric analysis are obtained by composing the inverse of the domain parameterization with the NURBS basis functions. In the case of singular parameterizations, however, some of the resulting test functions do not necessarily fulfill the required regularity properties. Consequently, numerical methods for the solution of partial differential equations cannot be applied properly. We discuss the regularity properties of the test functions. For one- and two-dimensional domains we consider several important classes of singularities of NURBS parameterizations. For specific cases we derive additional conditions which guarantee the regularity of the test functions. In addition we present a modification scheme for the discretized function space in case of insufficient regularity. It is also shown how these results can be applied for computational domains in higher dimensions that can be parameterized via sweeping.

Parameterization Interactions in Global Aquaplanet Simulations

NASA Astrophysics Data System (ADS)

Bhattacharya, Ritthik; Bordoni, Simona; Suselj, Kay; Teixeira, João.

2018-02-01

Global climate simulations rely on parameterizations of physical processes that have scales smaller than the resolved ones. In the atmosphere, these parameterizations represent moist convection, boundary layer turbulence and convection, cloud microphysics, longwave and shortwave radiation, and the interaction with the land and ocean surface. These parameterizations can generate different climates involving a wide range of interactions among parameterizations and between the parameterizations and the resolved dynamics. To gain a simplified understanding of a subset of these interactions, we perform aquaplanet simulations with the global version of the Weather Research and Forecasting (WRF) model employing a range (in terms of properties) of moist convection and boundary layer (BL) parameterizations. Significant differences are noted in the simulated precipitation amounts, its partitioning between convective and large-scale precipitation, as well as in the radiative impacts. These differences arise from the way the subcloud physics interacts with convection, both directly and through various pathways involving the large-scale dynamics and the boundary layer, convection, and clouds. A detailed analysis of the profiles of the different tendencies (from the different physical processes) for both potential temperature and water vapor is performed. While different combinations of convection and boundary layer parameterizations can lead to different climates, a key conclusion of this study is that similar climates can be simulated with model versions that are different in terms of the partitioning of the tendencies: the vertically distributed energy and water balances in the tropics can be obtained with significantly different profiles of large-scale, convection, and cloud microphysics tendencies.

On testing two major cumulus parameterization schemes using the CSU Regional Atmospheric Modeling System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kao, C.Y.J.; Bossert, J.E.; Winterkamp, J.

1993-10-01

One of the objectives of the DOE ARM Program is to improve the parameterization of clouds in general circulation models (GCMs). The approach taken in this research is two fold. We first examine the behavior of cumulus parameterization schemes by comparing their performance against the results from explicit cloud simulations with state-of-the-art microphysics. This is conducted in a two-dimensional (2-D) configuration of an idealized convective system. We then apply the cumulus parameterization schemes to realistic three-dimensional (3-D) simulations over the western US for a case with an enormous amount of convection in an extended period of five days. In themore » 2-D idealized tests, cloud effects are parameterized in the ``parameterization cases`` with a coarse resolution, whereas each cloud is explicitly resolved by the ``microphysics cases`` with a much finer resolution. Thus, the capability of the parameterization schemes in reproducing the growth and life cycle of a convective system can then be evaluated. These 2-D tests will form the basis for further 3-D realistic simulations which have the model resolution equivalent to that of the next generation of GCMs. Two cumulus parameterizations are used in this research: the Arakawa-Schubert (A-S) scheme (Arakawa and Schubert, 1974) used in Kao and Ogura (1987) and the Kuo scheme (Kuo, 1974) used in Tremback (1990). The numerical model used in this research is the Regional Atmospheric Modeling System (RAMS) developed at Colorado State University (CSU).« less

Brain Surface Conformal Parameterization Using Riemann Surface Structure

PubMed Central

Wang, Yalin; Lui, Lok Ming; Gu, Xianfeng; Hayashi, Kiralee M.; Chan, Tony F.; Toga, Arthur W.; Thompson, Paul M.; Yau, Shing-Tung

2011-01-01

In medical imaging, parameterized 3-D surface models are useful for anatomical modeling and visualization, statistical comparisons of anatomy, and surface-based registration and signal processing. Here we introduce a parameterization method based on Riemann surface structure, which uses a special curvilinear net structure (conformal net) to partition the surface into a set of patches that can each be conformally mapped to a parallelogram. The resulting surface subdivision and the parameterizations of the components are intrinsic and stable (their solutions tend to be smooth functions and the boundary conditions of the Dirichlet problem can be enforced). Conformal parameterization also helps transform partial differential equations (PDEs) that may be defined on 3-D brain surface manifolds to modified PDEs on a two-dimensional parameter domain. Since the Jacobian matrix of a conformal parameterization is diagonal, the modified PDE on the parameter domain is readily solved. To illustrate our techniques, we computed parameterizations for several types of anatomical surfaces in 3-D magnetic resonance imaging scans of the brain, including the cerebral cortex, hippocampi, and lateral ventricles. For surfaces that are topologically homeomorphic to each other and have similar geometrical structures, we show that the parameterization results are consistent and the subdivided surfaces can be matched to each other. Finally, we present an automatic sulcal landmark location algorithm by solving PDEs on cortical surfaces. The landmark detection results are used as constraints for building conformal maps between surfaces that also match explicitly defined landmarks. PMID:17679336

Radiofrequency-induced small bowel thermofusion: an ex vivo study of intestinal seal adequacy using mechanical and imaging modalities.

PubMed

Arya, Shobhit; Hadjievangelou, Nancy; Lei, Su; Kudo, Hiromi; Goldin, Robert D; Darzi, Ara W; Elson, Daniel S; Hanna, George B

2013-09-01

Bipolar radiofrequency (RF) induced tissue fusion is believed to have the potential to seal and anastomose intestinal tissue thereby providing an alternative to current techniques which are associated with technical and functional complications. This study examines the mechanical and cellular effects of RF energy and varying compressive pressures when applied to create ex vivo intestinal seals. A total of 299 mucosa-to-mucosa fusions were formed on ex vivo porcine small bowel segments using a prototype bipolar RF device powered by a closed-loop, feedback-controlled RF generator. Compressive pressures were increased at 0.05 MPa intervals from 0.00 to 0.49 MPa and RF energy was applied for a set time period to achieve bowel tissue fusion. Seal strength was subsequently assessed using burst pressure and tensile strength testing, whilst morphological changes were determined through light microscopy. To further identify the subcellular tissue changes that occur as a result of RF energy application, the collagen matrix in the fused area of a single bowel segment sealed at an optimal pressure was examined using transmission electron microscopy (TEM). An optimal applied compressive pressure range was observed between 0.10 and 0.25 MPa. Light microscopy demonstrated a step change between fused and unfused tissues but was ineffective in distinguishing between pressure levels once tissues were sealed. Non uniform collagen damage was observed in the sealed tissue area using TEM, with some areas showing complete collagen denaturation and others showing none, despite the seal being complete. This finding has not been described previously in RF-fused tissue and may have implications for in vivo healing. This study shows that both bipolar RF energy and optimal compressive pressures are needed to create strong intestinal seals. This finding suggests that RF fusion technology can be effectively applied for bowel sealing and may lead to the development of novel anastomosis tools.

Experimental evidence for dynamic friction on rock fractures from frequency-dependent nonlinear hysteresis and harmonic generation

NASA Astrophysics Data System (ADS)

Saltiel, Seth; Bonner, Brian P.; Mittal, Tushar; Delbridge, Brent; Ajo-Franklin, Jonathan B.

2017-07-01

Frictional properties affect the propagation of high-amplitude seismic waves across rock fractures and faults. Laboratory evidence suggests that these properties can be measured in active seismic surveys, potentially offering a route to characterizing friction in situ. We present experimental results from a subresonance torsional modulus and attenuation apparatus that utilizes micron-scale sinusoidal oscillations to probe the nonlinear stress-strain relation at a range of strain amplitudes and rates. Nonlinear effects are further quantified using harmonic distortion; however, time series data best illuminate underlying physical processes. The low-frequency stress-strain hysteretic loops show stiffening at the sinusoid's static ends, but stiffening is reduced above a threshold frequency. This shape is determined by harmonic generation in the strain; the stress signal has no harmonics, confirming that the fractured sample is the source of the nonlinearity. These qualitative observations suggest the presence of rate-dependent friction and are consistent between fractures in three different rock types. We propose that static friction at the low strain rate part of the cycle, when given sufficient "healing" time at low oscillation frequencies, causes this stiffening cusp shape in the hysteresis loop. While rate-and-state friction is commonly used to represent dynamic friction, it cannot capture static friction or negative slip velocities. So we implement another dynamic friction model, based on the work of Dahl, which describes this process and produces similar results. Since the two models have a similar form, parameterizations of field data could constraint fault model inputs, such as specific location velocity strengthening or weakening properties.

Impact of Apex Model parameterization strategy on estimated benefit of conservation practices

USDA-ARS?s Scientific Manuscript database

Three parameterized Agriculture Policy Environmental eXtender (APEX) models for corn-soybean rotation on clay pan soils were developed with the objectives, 1. Evaluate model performance of three parameterization strategies on a validation watershed; and 2. Compare predictions of water quality benefi...

Single-Column Modeling, GCM Parameterizations and Atmospheric Radiation Measurement Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somerville, R.C.J.; Iacobellis, S.F.

2005-03-18

Our overall goal is identical to that of the Atmospheric Radiation Measurement (ARM) Program: the development of new and improved parameterizations of cloud-radiation effects and related processes, using ARM data at all three ARM sites, and the implementation and testing of these parameterizations in global and regional models. To test recently developed prognostic parameterizations based on detailed cloud microphysics, we have first compared single-column model (SCM) output with ARM observations at the Southern Great Plains (SGP), North Slope of Alaska (NSA) and Topical Western Pacific (TWP) sites. We focus on the predicted cloud amounts and on a suite of radiativemore » quantities strongly dependent on clouds, such as downwelling surface shortwave radiation. Our results demonstrate the superiority of parameterizations based on comprehensive treatments of cloud microphysics and cloud-radiative interactions. At the SGP and NSA sites, the SCM results simulate the ARM measurements well and are demonstrably more realistic than typical parameterizations found in conventional operational forecasting models. At the TWP site, the model performance depends strongly on details of the scheme, and the results of our diagnostic tests suggest ways to develop improved parameterizations better suited to simulating cloud-radiation interactions in the tropics generally. These advances have made it possible to take the next step and build on this progress, by incorporating our parameterization schemes in state-of-the-art 3D atmospheric models, and diagnosing and evaluating the results using independent data. Because the improved cloud-radiation results have been obtained largely via implementing detailed and physically comprehensive cloud microphysics, we anticipate that improved predictions of hydrologic cycle components, and hence of precipitation, may also be achievable. We are currently testing the performance of our ARM-based parameterizations in state-of-the--art global and regional models. One fruitful strategy for evaluating advances in parameterizations has turned out to be using short-range numerical weather prediction as a test-bed within which to implement and improve parameterizations for modeling and predicting climate variability. The global models we have used to date are the CAM atmospheric component of the National Center for Atmospheric Research (NCAR) CCSM climate model as well as the National Centers for Environmental Prediction (NCEP) numerical weather prediction model, thus allowing testing in both climate simulation and numerical weather prediction modes. We present detailed results of these tests, demonstrating the sensitivity of model performance to changes in parameterizations.« less

The role of multisensor data fusion in neuromuscular control of a sagittal arm with a pair of muscles using actor-critic reinforcement learning method.

PubMed

Golkhou, V; Parnianpour, M; Lucas, C

2004-01-01

In this study, we consider the role of multisensor data fusion in neuromuscular control using an actor-critic reinforcement learning method. The model we use is a single link system actuated by a pair of muscles that are excited with alpha and gamma signals. Various physiological sensor information such as proprioception, spindle sensors, and Golgi tendon organs have been integrated to achieve an oscillatory movement with variable amplitude and frequency, while achieving a stable movement with minimum metabolic cost and coactivation. The system is highly nonlinear in all its physical and physiological attributes. Transmission delays are included in the afferent and efferent neural paths to account for a more accurate representation of the reflex loops. This paper proposes a reinforcement learning method with an Actor-Critic architecture instead of middle and low level of central nervous system (CNS). The Actor in this structure is a two layer feedforward neural network and the Critic is a model of the cerebellum. The Critic is trained by the State-Action-Reward-State-Action (SARSA) method. The Critic will train the Actor by supervisory learning based on previous experiences. The reinforcement signal in SARSA is evaluated based on available alternatives concerning the concept of multisensor data fusion. The effectiveness and the biological plausibility of the present model are demonstrated by several simulations. The system showed excellent tracking capability when we integrated the available sensor information. Addition of a penalty for activation of muscles resulted in much lower muscle coactivation while keeping the movement stable.

A Compact Self-Driven Liquid Lithium Loop for Industrial Neutron Generation

NASA Astrophysics Data System (ADS)

Stemmley, Steven; Szott, Matt; Kalathiparambil, Kishor; Ahn, Chisung; Jurczyk, Brian; Ruzic, David

2017-10-01

A compact, closed liquid lithium loop has been developed at the University of Illinois to test and utilize the Li-7(d,n) reaction. The liquid metal loop is housed in a stainless steel trench module with embedded heating and cooling. The system was designed to handle large heat and particle fluxes for use in neutron generators as well as fusion devices, solely operating via thermo-electric MHD. The objectives of this project are two-fold, 1) produce a high energy, MeV-level, neutron source and 2) provide a self-healing, low Z, low recycling plasma facing component. The flowing volume will keep a fresh, clean, lithium surface allowing Li-7(d,n) reactions to occur as well as deuterium adsorption in the fluid, increasing the overall neutron output. Expected yields of this system are 107 n/s for 13.5 MeV neutrons and 108 n/s for 2.45 MeV neutrons. Previous work has shown that using a tapered trench design prevents dry out and allows for an increase in velocity of the fluid at the particle strike point. For heat fluxes on the order of 10's MW/m2, COMSOL models have shown that high enough velocities ( 70 cm/s) are attainable to prevent significant lithium evaporation. Future work will be aimed at addressing wettability issues of lithium in the trenches, experimentally determine the velocities required to prevent dry out, and determine the neutron output of the system. The preliminary results and discussion will be presented. DOE SBIR project DE-SC0013861.

Improved parameterization for the vertical flux of dust aerosols emitted by an eroding soil

USDA-ARS?s Scientific Manuscript database

The representation of the dust cycle in atmospheric circulation models hinges on an accurate parameterization of the vertical dust flux at emission. However, existing parameterizations of the vertical dust flux vary substantially in their scaling with wind friction velocity, require input parameters...

Climate and the equilibrium state of land surface hydrology parameterizations

NASA Technical Reports Server (NTRS)

Entekhabi, Dara; Eagleson, Peter S.

1991-01-01

For given climatic rates of precipitation and potential evaporation, the land surface hydrology parameterizations of atmospheric general circulation models will maintain soil-water storage conditions that balance the moisture input and output. The surface relative soil saturation for such climatic conditions serves as a measure of the land surface parameterization state under a given forcing. The equilibrium value of this variable for alternate parameterizations of land surface hydrology are determined as a function of climate and the sensitivity of the surface to shifts and changes in climatic forcing are estimated.

Cross-Section Parameterizations for Pion and Nucleon Production From Negative Pion-Proton Collisions

NASA Technical Reports Server (NTRS)

Norbury, John W.; Blattnig, Steve R.; Norman, Ryan; Tripathi, R. K.

2002-01-01

Ranft has provided parameterizations of Lorentz invariant differential cross sections for pion and nucleon production in pion-proton collisions that are compared to some recent data. The Ranft parameterizations are then numerically integrated to form spectral and total cross sections. These numerical integrations are further parameterized to provide formula for spectral and total cross sections suitable for use in radiation transport codes. The reactions analyzed are for charged pions in the initial state and both charged and neutral pions in the final state.

Anisotropic Shear Dispersion Parameterization for Mesoscale Eddy Transport

NASA Astrophysics Data System (ADS)

Reckinger, S. J.; Fox-Kemper, B.

2016-02-01

The effects of mesoscale eddies are universally treated isotropically in general circulation models. However, the processes that the parameterization approximates, such as shear dispersion, typically have strongly anisotropic characteristics. The Gent-McWilliams/Redi mesoscale eddy parameterization is extended for anisotropy and tested using 1-degree Community Earth System Model (CESM) simulations. The sensitivity of the model to anisotropy includes a reduction of temperature and salinity biases, a deepening of the southern ocean mixed-layer depth, and improved ventilation of biogeochemical tracers, particularly in oxygen minimum zones. The parameterization is further extended to include the effects of unresolved shear dispersion, which sets the strength and direction of anisotropy. The shear dispersion parameterization is similar to drifter observations in spatial distribution of diffusivity and high-resolution model diagnosis in the distribution of eddy flux orientation.

Controllers, observers, and applications thereof

NASA Technical Reports Server (NTRS)

Gao, Zhiqiang (Inventor); Zhou, Wankun (Inventor); Miklosovic, Robert (Inventor); Radke, Aaron (Inventor); Zheng, Qing (Inventor)

2011-01-01

Controller scaling and parameterization are described. Techniques that can be improved by employing the scaling and parameterization include, but are not limited to, controller design, tuning and optimization. The scaling and parameterization methods described here apply to transfer function based controllers, including PID controllers. The parameterization methods also apply to state feedback and state observer based controllers, as well as linear active disturbance rejection (ADRC) controllers. Parameterization simplifies the use of ADRC. A discrete extended state observer (DESO) and a generalized extended state observer (GESO) are described. They improve the performance of the ESO and therefore ADRC. A tracking control algorithm is also described that improves the performance of the ADRC controller. A general algorithm is described for applying ADRC to multi-input multi-output systems. Several specific applications of the control systems and processes are disclosed.

Balancing accuracy, efficiency, and flexibility in a radiative transfer parameterization for dynamical models

NASA Astrophysics Data System (ADS)

Pincus, R.; Mlawer, E. J.

2017-12-01

Radiation is key process in numerical models of the atmosphere. The problem is well-understood and the parameterization of radiation has seen relatively few conceptual advances in the past 15 years. It is nonthelss often the single most expensive component of all physical parameterizations despite being computed less frequently than other terms. This combination of cost and maturity suggests value in a single radiation parameterization that could be shared across models; devoting effort to a single parameterization might allow for fine tuning for efficiency. The challenge lies in the coupling of this parameterization to many disparate representations of clouds and aerosols. This talk will describe RRTMGP, a new radiation parameterization that seeks to balance efficiency and flexibility. This balance is struck by isolating computational tasks in "kernels" that expose as much fine-grained parallelism as possible. These have simple interfaces and are interoperable across programming languages so that they might be repalced by alternative implementations in domain-specific langauges. Coupling to the host model makes use of object-oriented features of Fortran 2003, minimizing branching within the kernels and the amount of data that must be transferred. We will show accuracy and efficiency results for a globally-representative set of atmospheric profiles using a relatively high-resolution spectral discretization.

Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule

PubMed Central

Vařeková, Radka Svobodová; Jiroušková, Zuzana; Vaněk, Jakub; Suchomel, Šimon; Koča, Jaroslav

2007-01-01

The Electronegativity Equalization Method (EEM) is a fast approach for charge calculation. A challenging part of the EEM is the parameterization, which is performed using ab initio charges obtained for a set of molecules. The goal of our work was to perform the EEM parameterization for selected sets of organic, organohalogen and organometal molecules. We have performed the most robust parameterization published so far. The EEM parameterization was based on 12 training sets selected from a database of predicted 3D structures (NCI DIS) and from a database of crystallographic structures (CSD). Each set contained from 2000 to 6000 molecules. We have shown that the number of molecules in the training set is very important for quality of the parameters. We have improved EEM parameters (STO-3G MPA charges) for elements that were already parameterized, specifically: C, O, N, H, S, F and Cl. The new parameters provide more accurate charges than those published previously. We have also developed new parameters for elements that were not parameterized yet, specifically for Br, I, Fe and Zn. We have also performed crossover validation of all obtained parameters using all training sets that included relevant elements and confirmed that calculated parameters provide accurate charges.

Spectral cumulus parameterization based on cloud-resolving model

NASA Astrophysics Data System (ADS)

Baba, Yuya

2018-02-01

We have developed a spectral cumulus parameterization using a cloud-resolving model. This includes a new parameterization of the entrainment rate which was derived from analysis of the cloud properties obtained from the cloud-resolving model simulation and was valid for both shallow and deep convection. The new scheme was examined in a single-column model experiment and compared with the existing parameterization of Gregory (2001, Q J R Meteorol Soc 127:53-72) (GR scheme). The results showed that the GR scheme simulated more shallow and diluted convection than the new scheme. To further validate the physical performance of the parameterizations, Atmospheric Model Intercomparison Project (AMIP) experiments were performed, and the results were compared with reanalysis data. The new scheme performed better than the GR scheme in terms of mean state and variability of atmospheric circulation, i.e., the new scheme improved positive bias of precipitation in western Pacific region, and improved positive bias of outgoing shortwave radiation over the ocean. The new scheme also simulated better features of convectively coupled equatorial waves and Madden-Julian oscillation. These improvements were found to be derived from the modification of parameterization for the entrainment rate, i.e., the proposed parameterization suppressed excessive increase of entrainment, thus suppressing excessive increase of low-level clouds.

TSTA Piping and Flame Arrestor Operating Experience Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cadwallader, Lee C.; Willms, R. Scott

The Tritium Systems Test Assembly (TSTA) was a facility dedicated to tritium handling technology and experiment research at the Los Alamos National Laboratory. The facility operated from 1984 to 2001, running a prototype fusion fuel processing loop with ~100 grams of tritium as well as small experiments. There have been several operating experience reports written on this facility’s operation and maintenance experience. This paper describes analysis of two additional components from TSTA, small diameter gas piping that handled small amounts of tritium in a nitrogen carrier gas, and the flame arrestor used in this piping system. The operating experiences andmore » the component failure rates for these components are discussed in this paper. Comparison data from other applications are also presented.« less

Design of an auto change mechanism and intelligent gripper for the space station

NASA Technical Reports Server (NTRS)

Dehoff, Paul H.; Naik, Dipak P.

1989-01-01

Robot gripping of objects in space is inherently demanding and dangerous and nowhere is this more clearly reflected than in the design of the robot gripper. An object which escapes the gripper in a micro g environment is launched not dropped. To prevent this, the gripper must have sensors and signal processing to determine that the object is properly grasped, e.g., grip points and gripping forces and, if not, to provide information to the robot to enable closed loop corrections to be made. The sensors and sensor strategies employed in the NASA/GSFC Split-Rail Parallel Gripper are described. Objectives and requirements are given followed by the design of the sensor suite, sensor fusion techniques and supporting algorithms.

Introduction of statistical information in a syntactic analyzer for document image recognition

NASA Astrophysics Data System (ADS)

Maroneze, André O.; Coüasnon, Bertrand; Lemaitre, Aurélie

2011-01-01

This paper presents an improvement to document layout analysis systems, offering a possible solution to Sayre's paradox (which states that an element "must be recognized before it can be segmented; and it must be segmented before it can be recognized"). This improvement, based on stochastic parsing, allows integration of statistical information, obtained from recognizers, during syntactic layout analysis. We present how this fusion of numeric and symbolic information in a feedback loop can be applied to syntactic methods to improve document description expressiveness. To limit combinatorial explosion during exploration of solutions, we devised an operator that allows optional activation of the stochastic parsing mechanism. Our evaluation on 1250 handwritten business letters shows this method allows the improvement of global recognition scores.

The importance of parameterization when simulating the hydrologic response of vegetative land-cover change

NASA Astrophysics Data System (ADS)

White, Jeremy; Stengel, Victoria; Rendon, Samuel; Banta, John

2017-08-01

Computer models of hydrologic systems are frequently used to investigate the hydrologic response of land-cover change. If the modeling results are used to inform resource-management decisions, then providing robust estimates of uncertainty in the simulated response is an important consideration. Here we examine the importance of parameterization, a necessarily subjective process, on uncertainty estimates of the simulated hydrologic response of land-cover change. Specifically, we applied the soil water assessment tool (SWAT) model to a 1.4 km2 watershed in southern Texas to investigate the simulated hydrologic response of brush management (the mechanical removal of woody plants), a discrete land-cover change. The watershed was instrumented before and after brush-management activities were undertaken, and estimates of precipitation, streamflow, and evapotranspiration (ET) are available; these data were used to condition and verify the model. The role of parameterization in brush-management simulation was evaluated by constructing two models, one with 12 adjustable parameters (reduced parameterization) and one with 1305 adjustable parameters (full parameterization). Both models were subjected to global sensitivity analysis as well as Monte Carlo and generalized likelihood uncertainty estimation (GLUE) conditioning to identify important model inputs and to estimate uncertainty in several quantities of interest related to brush management. Many realizations from both parameterizations were identified as behavioral in that they reproduce daily mean streamflow acceptably well according to Nash-Sutcliffe model efficiency coefficient, percent bias, and coefficient of determination. However, the total volumetric ET difference resulting from simulated brush management remains highly uncertain after conditioning to daily mean streamflow, indicating that streamflow data alone are not sufficient to inform the model inputs that influence the simulated outcomes of brush management the most. Additionally, the reduced-parameterization model grossly underestimates uncertainty in the total volumetric ET difference compared to the full-parameterization model; total volumetric ET difference is a primary metric for evaluating the outcomes of brush management. The failure of the reduced-parameterization model to provide robust uncertainty estimates demonstrates the importance of parameterization when attempting to quantify uncertainty in land-cover change simulations.

The importance of parameterization when simulating the hydrologic response of vegetative land-cover change

USGS Publications Warehouse

White, Jeremy; Stengel, Victoria G.; Rendon, Samuel H.; Banta, John

2017-01-01

Computer models of hydrologic systems are frequently used to investigate the hydrologic response of land-cover change. If the modeling results are used to inform resource-management decisions, then providing robust estimates of uncertainty in the simulated response is an important consideration. Here we examine the importance of parameterization, a necessarily subjective process, on uncertainty estimates of the simulated hydrologic response of land-cover change. Specifically, we applied the soil water assessment tool (SWAT) model to a 1.4 km2 watershed in southern Texas to investigate the simulated hydrologic response of brush management (the mechanical removal of woody plants), a discrete land-cover change. The watershed was instrumented before and after brush-management activities were undertaken, and estimates of precipitation, streamflow, and evapotranspiration (ET) are available; these data were used to condition and verify the model. The role of parameterization in brush-management simulation was evaluated by constructing two models, one with 12 adjustable parameters (reduced parameterization) and one with 1305 adjustable parameters (full parameterization). Both models were subjected to global sensitivity analysis as well as Monte Carlo and generalized likelihood uncertainty estimation (GLUE) conditioning to identify important model inputs and to estimate uncertainty in several quantities of interest related to brush management. Many realizations from both parameterizations were identified as behavioral in that they reproduce daily mean streamflow acceptably well according to Nash–Sutcliffe model efficiency coefficient, percent bias, and coefficient of determination. However, the total volumetric ET difference resulting from simulated brush management remains highly uncertain after conditioning to daily mean streamflow, indicating that streamflow data alone are not sufficient to inform the model inputs that influence the simulated outcomes of brush management the most. Additionally, the reduced-parameterization model grossly underestimates uncertainty in the total volumetric ET difference compared to the full-parameterization model; total volumetric ET difference is a primary metric for evaluating the outcomes of brush management. The failure of the reduced-parameterization model to provide robust uncertainty estimates demonstrates the importance of parameterization when attempting to quantify uncertainty in land-cover change simulations.

FINAL REPORT (DE-FG02-97ER62338): Single-column modeling, GCM parameterizations, and ARM data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richard C. J. Somerville

2009-02-27

Our overall goal is the development of new and improved parameterizations of cloud-radiation effects and related processes, using ARM data at all three ARM sites, and the implementation and testing of these parameterizations in global models. To test recently developed prognostic parameterizations based on detailed cloud microphysics, we have compared SCM (single-column model) output with ARM observations at the SGP, NSA and TWP sites. We focus on the predicted cloud amounts and on a suite of radiative quantities strongly dependent on clouds, such as downwelling surface shortwave radiation. Our results demonstrate the superiority of parameterizations based on comprehensive treatments ofmore » cloud microphysics and cloud-radiative interactions. At the SGP and NSA sites, the SCM results simulate the ARM measurements well and are demonstrably more realistic than typical parameterizations found in conventional operational forecasting models. At the TWP site, the model performance depends strongly on details of the scheme, and the results of our diagnostic tests suggest ways to develop improved parameterizations better suited to simulating cloud-radiation interactions in the tropics generally. These advances have made it possible to take the next step and build on this progress, by incorporating our parameterization schemes in state-of-the-art three-dimensional atmospheric models, and diagnosing and evaluating the results using independent data. Because the improved cloud-radiation results have been obtained largely via implementing detailed and physically comprehensive cloud microphysics, we anticipate that improved predictions of hydrologic cycle components, and hence of precipitation, may also be achievable.« less

Parametric soil water retention models: a critical evaluation of expressions for the full moisture range

NASA Astrophysics Data System (ADS)

Madi, Raneem; Huibert de Rooij, Gerrit; Mielenz, Henrike; Mai, Juliane

2018-02-01

Few parametric expressions for the soil water retention curve are suitable for dry conditions. Furthermore, expressions for the soil hydraulic conductivity curves associated with parametric retention functions can behave unrealistically near saturation. We developed a general criterion for water retention parameterizations that ensures physically plausible conductivity curves. Only 3 of the 18 tested parameterizations met this criterion without restrictions on the parameters of a popular conductivity curve parameterization. A fourth required one parameter to be fixed. We estimated parameters by shuffled complex evolution (SCE) with the objective function tailored to various observation methods used to obtain retention curve data. We fitted the four parameterizations with physically plausible conductivities as well as the most widely used parameterization. The performance of the resulting 12 combinations of retention and conductivity curves was assessed in a numerical study with 751 days of semiarid atmospheric forcing applied to unvegetated, uniform, 1 m freely draining columns for four textures. Choosing different parameterizations had a minor effect on evaporation, but cumulative bottom fluxes varied by up to an order of magnitude between them. This highlights the need for a careful selection of the soil hydraulic parameterization that ideally does not only rely on goodness of fit to static soil water retention data but also on hydraulic conductivity measurements. Parameter fits for 21 soils showed that extrapolations into the dry range of the retention curve often became physically more realistic when the parameterization had a logarithmic dry branch, particularly in fine-textured soils where high residual water contents would otherwise be fitted.

How certain are the process parameterizations in our models?

NASA Astrophysics Data System (ADS)

Gharari, Shervan; Hrachowitz, Markus; Fenicia, Fabrizio; Matgen, Patrick; Razavi, Saman; Savenije, Hubert; Gupta, Hoshin; Wheater, Howard

2016-04-01

Environmental models are abstract simplifications of real systems. As a result, the elements of these models, including system architecture (structure), process parameterization and parameters inherit a high level of approximation and simplification. In a conventional model building exercise the parameter values are the only elements of a model which can vary while the rest of the modeling elements are often fixed a priori and therefore not subjected to change. Once chosen the process parametrization and model structure usually remains the same throughout the modeling process. The only flexibility comes from the changing parameter values, thereby enabling these models to reproduce the desired observation. This part of modeling practice, parameter identification and uncertainty, has attracted a significant attention in the literature during the last years. However what remains unexplored in our point of view is to what extent the process parameterization and system architecture (model structure) can support each other. In other words "Does a specific form of process parameterization emerge for a specific model given its system architecture and data while no or little assumption has been made about the process parameterization itself? In this study we relax the assumption regarding a specific pre-determined form for the process parameterizations of a rainfall/runoff model and examine how varying the complexity of the system architecture can lead to different or possibly contradictory parameterization forms than what would have been decided otherwise. This comparison implicitly and explicitly provides us with an assessment of how uncertain is our perception of model process parameterization in respect to the extent the data can support.

Sensitivity of Pacific Cold Tongue and Double-ITCZ Bias to Convective Parameterization

NASA Astrophysics Data System (ADS)

Woelfle, M.; Bretherton, C. S.; Pritchard, M. S.; Yu, S.

2016-12-01

Many global climate models struggle to accurately simulate annual mean precipitation and sea surface temperature (SST) fields in the tropical Pacific basin. Precipitation biases are dominated by the double intertropical convergence zone (ITCZ) bias where models exhibit precipitation maxima straddling the equator while only a single Northern Hemispheric maximum exists in observations. The major SST bias is the enhancement of the equatorial cold tongue. A series of coupled model simulations are used to investigate the sensitivity of the bias development to convective parameterization. Model components are initialized independently prior to coupling to allow analysis of the transient response of the system directly following coupling. These experiments show precipitation and SST patterns to be highly sensitive to convective parameterization. Simulations in which the deep convective parameterization is disabled forcing all convection to be resolved by the shallow convection parameterization showed a degradation in both the cold tongue and double-ITCZ biases as precipitation becomes focused into off-equatorial regions of local SST maxima. Simulations using superparameterization in place of traditional cloud parameterizations showed a reduced cold tongue bias at the expense of additional precipitation biases. The equatorial SST responses to changes in convective parameterization are driven by changes in near equatorial zonal wind stress. The sensitivity of convection to SST is important in determining the precipitation and wind stress fields. However, differences in convective momentum transport also play a role. While no significant improvement is seen in these simulations of the double-ITCZ, the system's sensitivity to these changes reaffirm that improved convective parameterizations may provide an avenue for improving simulations of tropical Pacific precipitation and SST.

New Parameterizations for Neutral and Ion-Induced Sulfuric Acid-Water Particle Formation in Nucleation and Kinetic Regimes

NASA Astrophysics Data System (ADS)

Määttänen, Anni; Merikanto, Joonas; Henschel, Henning; Duplissy, Jonathan; Makkonen, Risto; Ortega, Ismael K.; Vehkamäki, Hanna

2018-01-01

We have developed new parameterizations of electrically neutral homogeneous and ion-induced sulfuric acid-water particle formation for large ranges of environmental conditions, based on an improved model that has been validated against a particle formation rate data set produced by Cosmics Leaving OUtdoor Droplets (CLOUD) experiments at European Organization for Nuclear Research (CERN). The model uses a thermodynamically consistent version of the Classical Nucleation Theory normalized using quantum chemical data. Unlike the earlier parameterizations for H2SO4-H2O nucleation, the model is applicable to extreme dry conditions where the one-component sulfuric acid limit is approached. Parameterizations are presented for the critical cluster sulfuric acid mole fraction, the critical cluster radius, the total number of molecules in the critical cluster, and the particle formation rate. If the critical cluster contains only one sulfuric acid molecule, a simple formula for kinetic particle formation can be used: this threshold has also been parameterized. The parameterization for electrically neutral particle formation is valid for the following ranges: temperatures 165-400 K, sulfuric acid concentrations 104-1013 cm-3, and relative humidities 0.001-100%. The ion-induced particle formation parameterization is valid for temperatures 195-400 K, sulfuric acid concentrations 104-1016 cm-3, and relative humidities 10-5-100%. The new parameterizations are thus applicable for the full range of conditions in the Earth's atmosphere relevant for binary sulfuric acid-water particle formation, including both tropospheric and stratospheric conditions. They are also suitable for describing particle formation in the atmosphere of Venus.

Parameterization of ALMANAC crop simulation model for non-irrigated dry bean in semi-arid temperate areas in Mexico

USDA-ARS?s Scientific Manuscript database

Simulation models can be used to make management decisions when properly parameterized. This study aimed to parameterize the ALMANAC (Agricultural Land Management Alternatives with Numerical Assessment Criteria) crop simulation model for dry bean in the semi-arid temperate areas of Mexico. The par...

A parameterization scheme for the x-ray linear attenuation coefficient and energy absorption coefficient.

PubMed

Midgley, S M

2004-01-21

A novel parameterization of x-ray interaction cross-sections is developed, and employed to describe the x-ray linear attenuation coefficient and mass energy absorption coefficient for both elements and mixtures. The new parameterization scheme addresses the Z-dependence of elemental cross-sections (per electron) using a simple function of atomic number, Z. This obviates the need for a complicated mathematical formalism. Energy dependent coefficients describe the Z-direction curvature of the cross-sections. The composition dependent quantities are the electron density and statistical moments describing the elemental distribution. We show that it is possible to describe elemental cross-sections for the entire periodic table and at energies above the K-edge (from 6 keV to 125 MeV), with an accuracy of better than 2% using a parameterization containing not more than five coefficients. For the biologically important elements 1 < or = Z < or = 20, and the energy range 30-150 keV, the parameterization utilizes four coefficients. At higher energies, the parameterization uses fewer coefficients with only two coefficients needed at megavoltage energies.

A unified spectral,parameterization for wave breaking: from the deep ocean to the surf zone

NASA Astrophysics Data System (ADS)

Filipot, J.

2010-12-01

A new wave-breaking dissipation parameterization designed for spectral wave models is presented. It combines wave breaking basic physical quantities, namely, the breaking probability and the dissipation rate per unit area. The energy lost by waves is fi[|#12#|]rst calculated in the physical space before being distributed over the relevant spectral components. This parameterization allows a seamless numerical model from the deep ocean into the surf zone. This transition from deep to shallow water is made possible by a dissipation rate per unit area of breaking waves that varies with the wave height, wavelength and water depth.The parameterization is further tested in the WAVEWATCH III TM code, from the global ocean to the beach scale. Model errors are smaller than with most specialized deep or shallow water parameterizations.

Methods of testing parameterizations: Vertical ocean mixing

NASA Technical Reports Server (NTRS)

Tziperman, Eli

1992-01-01

The ocean's velocity field is characterized by an exceptional variety of scales. While the small-scale oceanic turbulence responsible for the vertical mixing in the ocean is of scales a few centimeters and smaller, the oceanic general circulation is characterized by horizontal scales of thousands of kilometers. In oceanic general circulation models that are typically run today, the vertical structure of the ocean is represented by a few tens of discrete grid points. Such models cannot explicitly model the small-scale mixing processes, and must, therefore, find ways to parameterize them in terms of the larger-scale fields. Finding a parameterization that is both reliable and plausible to use in ocean models is not a simple task. Vertical mixing in the ocean is the combined result of many complex processes, and, in fact, mixing is one of the less known and less understood aspects of the oceanic circulation. In present models of the oceanic circulation, the many complex processes responsible for vertical mixing are often parameterized in an oversimplified manner. Yet, finding an adequate parameterization of vertical ocean mixing is crucial to the successful application of ocean models to climate studies. The results of general circulation models for quantities that are of particular interest to climate studies, such as the meridional heat flux carried by the ocean, are quite sensitive to the strength of the vertical mixing. We try to examine the difficulties in choosing an appropriate vertical mixing parameterization, and the methods that are available for validating different parameterizations by comparing model results to oceanographic data. First, some of the physical processes responsible for vertically mixing the ocean are briefly mentioned, and some possible approaches to the parameterization of these processes in oceanographic general circulation models are described in the following section. We then discuss the role of the vertical mixing in the physics of the large-scale ocean circulation, and examine methods of validating mixing parameterizations using large-scale ocean models.

Comparison of Gravity Wave Temperature Variances from Ray-Based Spectral Parameterization of Convective Gravity Wave Drag with AIRS Observations

NASA Technical Reports Server (NTRS)

Choi, Hyun-Joo; Chun, Hye-Yeong; Gong, Jie; Wu, Dong L.

2012-01-01

The realism of ray-based spectral parameterization of convective gravity wave drag, which considers the updated moving speed of the convective source and multiple wave propagation directions, is tested against the Atmospheric Infrared Sounder (AIRS) onboard the Aqua satellite. Offline parameterization calculations are performed using the global reanalysis data for January and July 2005, and gravity wave temperature variances (GWTVs) are calculated at z = 2.5 hPa (unfiltered GWTV). AIRS-filtered GWTV, which is directly compared with AIRS, is calculated by applying the AIRS visibility function to the unfiltered GWTV. A comparison between the parameterization calculations and AIRS observations shows that the spatial distribution of the AIRS-filtered GWTV agrees well with that of the AIRS GWTV. However, the magnitude of the AIRS-filtered GWTV is smaller than that of the AIRS GWTV. When an additional cloud top gravity wave momentum flux spectrum with longer horizontal wavelength components that were obtained from the mesoscale simulations is included in the parameterization, both the magnitude and spatial distribution of the AIRS-filtered GWTVs from the parameterization are in good agreement with those of the AIRS GWTVs. The AIRS GWTV can be reproduced reasonably well by the parameterization not only with multiple wave propagation directions but also with two wave propagation directions of 45 degrees (northeast-southwest) and 135 degrees (northwest-southeast), which are optimally chosen for computational efficiency.

The Influence of Microphysical Cloud Parameterization on Microwave Brightness Temperatures

NASA Technical Reports Server (NTRS)

Skofronick-Jackson, Gail M.; Gasiewski, Albin J.; Wang, James R.; Zukor, Dorothy J. (Technical Monitor)

2000-01-01

The microphysical parameterization of clouds and rain-cells plays a central role in atmospheric forward radiative transfer models used in calculating passive microwave brightness temperatures. The absorption and scattering properties of a hydrometeor-laden atmosphere are governed by particle phase, size distribution, aggregate density., shape, and dielectric constant. This study identifies the sensitivity of brightness temperatures with respect to the microphysical cloud parameterization. Cloud parameterizations for wideband (6-410 GHz observations of baseline brightness temperatures were studied for four evolutionary stages of an oceanic convective storm using a five-phase hydrometeor model in a planar-stratified scattering-based radiative transfer model. Five other microphysical cloud parameterizations were compared to the baseline calculations to evaluate brightness temperature sensitivity to gross changes in the hydrometeor size distributions and the ice-air-water ratios in the frozen or partly frozen phase. The comparison shows that, enlarging the rain drop size or adding water to the partly Frozen hydrometeor mix warms brightness temperatures by up to .55 K at 6 GHz. The cooling signature caused by ice scattering intensifies with increasing ice concentrations and at higher frequencies. An additional comparison to measured Convection and Moisture LA Experiment (CAMEX 3) brightness temperatures shows that in general all but, two parameterizations produce calculated T(sub B)'s that fall within the observed clear-air minima and maxima. The exceptions are for parameterizations that, enhance the scattering characteristics of frozen hydrometeors.

The application of depletion curves for parameterization of subgrid variability of snow

Treesearch

C. H. Luce; D. G. Tarboton

2004-01-01

Parameterization of subgrid-scale variability in snow accumulation and melt is important for improvements in distributed snowmelt modelling. We have taken the approach of using depletion curves that relate fractional snowcovered area to element-average snow water equivalent to parameterize the effect of snowpack heterogeneity within a physically based mass and energy...

Method of Moments Applied to the Analysis of Precision Spectra from the Neutron Time-of- flight Diagnostics at the National Ignition Facility

NASA Astrophysics Data System (ADS)

Hatarik, Robert; Caggiano, J. A.; Callahan, D.; Casey, D.; Clark, D.; Doeppner, T.; Eckart, M.; Field, J.; Frenje, J.; Gatu Johnson, M.; Grim, G.; Hartouni, E.; Hurricane, O.; Kilkenny, J.; Knauer, J.; Ma, T.; Mannion, O.; Munro, D.; Sayre, D.; Spears, B.

2015-11-01

The method of moments was introduced by Pearson as a process for estimating the population distributions from which a set of ``random variables'' are measured. These moments are compared with a parameterization of the distributions, or of the same quantities generated by simulations of the process. Most diagnostics processes extract scalar parameters depending on the moments of spectra derived from analytic solutions to the fusion rate, necessarily based on simplifying assumptions of the confined plasma. The precision of the TOF spectra, and the nature of the implosions at the NIF require the inclusion of factors beyond the traditional analysis and require the addition of higher order moments to describe the data. This talk will present a diagnostic process for extracting the moments of the neutron energy spectrum for a comparison with theoretical considerations as well as simulations of the implosions. Work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344.

A Flexible Parameterization for Shortwave Optical Properties of Ice Crystals

NASA Technical Reports Server (NTRS)

VanDiedenhoven, Bastiaan; Ackerman, Andrew S.; Cairns, Brian; Fridlind, Ann M.

2014-01-01

A parameterization is presented that provides extinction cross section sigma (sub e), single-scattering albedo omega, and asymmetry parameter (g) of ice crystals for any combination of volume, projected area, aspect ratio, and crystal distortion at any wavelength in the shortwave. Similar to previous parameterizations, the scheme makes use of geometric optics approximations and the observation that optical properties of complex, aggregated ice crystals can be well approximated by those of single hexagonal crystals with varying size, aspect ratio, and distortion levels. In the standard geometric optics implementation used here, sigma (sub e) is always twice the particle projected area. It is shown that omega is largely determined by the newly defined absorption size parameter and the particle aspect ratio. These dependences are parameterized using a combination of exponential, lognormal, and polynomial functions. The variation of (g) with aspect ratio and crystal distortion is parameterized for one reference wavelength using a combination of several polynomials. The dependences of g on refractive index and omega are investigated and factors are determined to scale the parameterized (g) to provide values appropriate for other wavelengths. The parameterization scheme consists of only 88 coefficients. The scheme is tested for a large variety of hexagonal crystals in several wavelength bands from 0.2 to 4 micron, revealing absolute differences with reference calculations of omega and (g) that are both generally below 0.015. Over a large variety of cloud conditions, the resulting root-mean-squared differences with reference calculations of cloud reflectance, transmittance, and absorptance are 1.4%, 1.1%, and 3.4%, respectively. Some practical applications of the parameterization in atmospheric models are highlighted.

Domain-averaged snow depth over complex terrain from flat field measurements

NASA Astrophysics Data System (ADS)

Helbig, Nora; van Herwijnen, Alec

2017-04-01

Snow depth is an important parameter for a variety of coarse-scale models and applications, such as hydrological forecasting. Since high-resolution snow cover models are computational expensive, simplified snow models are often used. Ground measured snow depth at single stations provide a chance for snow depth data assimilation to improve coarse-scale model forecasts. Snow depth is however commonly recorded at so-called flat fields, often in large measurement networks. While these ground measurement networks provide a wealth of information, various studies questioned the representativity of such flat field snow depth measurements for the surrounding topography. We developed two parameterizations to compute domain-averaged snow depth for coarse model grid cells over complex topography using easy to derive topographic parameters. To derive the two parameterizations we performed a scale dependent analysis for domain sizes ranging from 50m to 3km using highly-resolved snow depth maps at the peak of winter from two distinct climatic regions in Switzerland and in the Spanish Pyrenees. The first, simpler parameterization uses a commonly applied linear lapse rate. For the second parameterization, we first removed the obvious elevation gradient in mean snow depth, which revealed an additional correlation with the subgrid sky view factor. We evaluated domain-averaged snow depth derived with both parameterizations using flat field measurements nearby with the domain-averaged highly-resolved snow depth. This revealed an overall improved performance for the parameterization combining a power law elevation trend scaled with the subgrid parameterized sky view factor. We therefore suggest the parameterization could be used to assimilate flat field snow depth into coarse-scale snow model frameworks in order to improve coarse-scale snow depth estimates over complex topography.

Parameterization of eddy sensible heat transports in a zonally averaged dynamic model of the atmosphere

NASA Technical Reports Server (NTRS)

Genthon, Christophe; Le Treut, Herve; Sadourny, Robert; Jouzel, Jean

1990-01-01

A Charney-Branscome based parameterization has been tested as a way of representing the eddy sensible heat transports missing in a zonally averaged dynamic model (ZADM) of the atmosphere. The ZADM used is a zonally averaged version of a general circulation model (GCM). The parameterized transports in the ZADM are gaged against the corresponding fluxes explicitly simulated in the GCM, using the same zonally averaged boundary conditions in both models. The Charney-Branscome approach neglects stationary eddies and transient barotropic disturbances and relies on a set of simplifying assumptions, including the linear appoximation, to describe growing transient baroclinic eddies. Nevertheless, fairly satisfactory results are obtained when the parameterization is performed interactively with the model. Compared with noninteractive tests, a very efficient restoring feedback effect between the modeled zonal-mean climate and the parameterized meridional eddy transport is identified.

Predictive Compensator Optimization for Head Tracking Lag in Virtual Environments

NASA Technical Reports Server (NTRS)

Adelstein, Barnard D.; Jung, Jae Y.; Ellis, Stephen R.

2001-01-01

We examined the perceptual impact of plant noise parameterization for Kalman Filter predictive compensation of time delays intrinsic to head tracked virtual environments (VEs). Subjects were tested in their ability to discriminate between the VE system's minimum latency and conditions in which artificially added latency was then predictively compensated back to the system minimum. Two head tracking predictors were parameterized off-line according to cost functions that minimized prediction errors in (1) rotation, and (2) rotation projected into translational displacement with emphasis on higher frequency human operator noise. These predictors were compared with a parameterization obtained from the VE literature for cost function (1). Results from 12 subjects showed that both parameterization type and amount of compensated latency affected discrimination. Analysis of the head motion used in the parameterizations and the subsequent discriminability results suggest that higher frequency predictor artifacts are contributory cues for discriminating the presence of predictive compensation.

New insights in the electroweak phase transition in the NMSSM

NASA Astrophysics Data System (ADS)

Huang, Weicong; Kang, Zhaofeng; Shu, Jing; Wu, Peiwen; Yang, Jin Min

2015-01-01

We perform a detailed semianalytical analysis of the electroweak phase transition (EWPT) property in the Next-to-Minimal Supersymmetric standard model, which serves as a good benchmark model in which the 126 GeV Higgs mixes with a singlet. In this case, a strongly first-order electroweak phase transition (SFOEWPT) is achieved by the tree-level effects, and the phase transition strength γc is determined by the vacua energy gap at T =0 . We make an anatomy of the energy gap at both tree level and loop level and extract out a dimensionless phase transition parameter Rκ≡4 κ vs/Aκ, which can replace Aκ in the parameterization and affect the light CP-odd/even Higgs spectra. We find that SFOEWPT only occurs in Rκ˜-1 and positive Rκ≲O (10 ), which in the non-PQ limit case would prefer either a relatively light CP-odd or CP-even Higgs boson ˜(60 ,100 ) GeV , and therefore serves as a smoking gun signal and requires new search strategies at the LHC.

Simple robust control laws for robot manipulators. Part 2: Adaptive case

NASA Technical Reports Server (NTRS)

Bayard, D. S.; Wen, J. T.

1987-01-01

A new class of asymptotically stable adaptive control laws is introduced for application to the robotic manipulator. Unlike most applications of adaptive control theory to robotic manipulators, this analysis addresses the nonlinear dynamics directly without approximation, linearization, or ad hoc assumptions, and utilizes a parameterization based on physical (time-invariant) quantities. This approach is made possible by using energy-like Lyapunov functions which retain the nonlinear character and structure of the dynamics, rather than simple quadratic forms which are ubiquitous to the adaptive control literature, and which have bound the theory tightly to linear systems with unknown parameters. It is a unique feature of these results that the adaptive forms arise by straightforward certainty equivalence adaptation of their nonadaptive counterparts found in the companion to this paper (i.e., by replacing unknown quantities by their estimates) and that this simple approach leads to asymptotically stable closed-loop adaptive systems. Furthermore, it is emphasized that this approach does not require convergence of the parameter estimates (i.e., via persistent excitation), invertibility of the mass matrix estimate, or measurement of the joint accelerations.

Near minimum-time maneuvers of the advanced space structures technology research experiment (ASTREX) test article: Theory and experiments

NASA Technical Reports Server (NTRS)

Vadali, Srinivas R.; Carter, Michael T.

1994-01-01

The Phillips Laboratory at the Edwards Air Force Base has developed the Advanced Space Structures Technology Research Experiment (ASTREX) facility to serve as a testbed for demonstrating the applicability of proven theories to the challenges of spacecraft maneuvers and structural control. This report describes the work performed on the ASTREX test article by Texas A&M University under contract NAS119373 as a part of the Control-Structure Interaction (CSI) Guest Investigator Program. The focus of this work is on maneuvering the ASTREX test article with compressed air thrusters that can be throttled, while attenuating structural excitation. The theoretical foundation for designing the near minimum-time thrust commands is based on the generation of smooth, parameterized optimal open-loop control profiles, and the determination of control laws for final position regulation and tracking using Lyapunov stability theory. Details of the theory, mathematical modeling, model updating, and compensation for the presence of 'real world' effects are described and the experimental results are presented. The results show an excellent match between theory and experiments.

Multiphase magnetic systems: Measurement and simulation

NASA Astrophysics Data System (ADS)

Cao, Yue; Ahmadzadeh, Mostafa; Xu, Ke; Dodrill, Brad; McCloy, John S.

2018-01-01

Multiphase magnetic systems are common in nature and are increasingly being recognized in technical applications. One characterization method which has shown great promise for determining separate and collective effects of multiphase magnetic systems is first order reversal curves (FORCs). Several examples are given of FORC patterns which provide distinguishing evidence of multiple phases. In parallel, a visualization method for understanding multiphase magnetic interaction is given, which allocates Preisach magnetic elements as an input "Preisach hysteron distribution pattern" to enable simulation of different "wasp-waisted" magnetic behaviors. These simulated systems allow reproduction of different major hysteresis loops and FORC patterns of real systems and parameterized theoretical systems. The experimental FORC measurements and FORC diagrams of four commercially obtained magnetic materials, particularly those sold as nanopowders, show that these materials are often not phase pure. They exhibit complex hysteresis behaviors that are not predictable based on relative phase fraction obtained by characterization methods such as diffraction. These multiphase materials, consisting of various fractions of BaFe12O19, ɛ-Fe2O3, and γ-Fe2O3, are discussed.

Cross section parameterizations for cosmic ray nuclei. 1: Single nucleon removal

NASA Technical Reports Server (NTRS)

Norbury, John W.; Townsend, Lawrence W.

1992-01-01

Parameterizations of single nucleon removal from electromagnetic and strong interactions of cosmic rays with nuclei are presented. These parameterizations are based upon the most accurate theoretical calculations available to date. They should be very suitable for use in cosmic ray propagation through interstellar space, the Earth's atmosphere, lunar samples, meteorites, spacecraft walls and lunar and martian habitats.

Improvement of the GEOS-5 AGCM upon Updating the Air-Sea Roughness Parameterization

NASA Technical Reports Server (NTRS)

Garfinkel, C. I.; Molod, A.; Oman, L. D.; Song, I.-S.

2011-01-01

The impact of an air-sea roughness parameterization over the ocean that more closely matches recent observations of air-sea exchange is examined in the NASA Goddard Earth Observing System, version 5 (GEOS-5) atmospheric general circulation model. Surface wind biases in the GEOS-5 AGCM are decreased by up to 1.2m/s. The new parameterization also has implications aloft as improvements extend into the stratosphere. Many other GCMs (both for operational weather forecasting and climate) use a similar class of parameterization for their air-sea roughness scheme. We therefore expect that results from GEOS-5 are relevant to other models as well.

Observational and Modeling Studies of Clouds and the Hydrological Cycle

NASA Technical Reports Server (NTRS)

Somerville, Richard C. J.

1997-01-01

Our approach involved validating parameterizations directly against measurements from field programs, and using this validation to tune existing parameterizations and to guide the development of new ones. We have used a single-column model (SCM) to make the link between observations and parameterizations of clouds, including explicit cloud microphysics (e.g., prognostic cloud liquid water used to determine cloud radiative properties). Surface and satellite radiation measurements were used to provide an initial evaluation of the performance of the different parameterizations. The results of this evaluation will then used to develop improved cloud and cloud-radiation schemes, which were tested in GCM experiments.

Structural and parameteric uncertainty quantification in cloud microphysics parameterization schemes

NASA Astrophysics Data System (ADS)

van Lier-Walqui, M.; Morrison, H.; Kumjian, M. R.; Prat, O. P.; Martinkus, C.

2017-12-01

Atmospheric model parameterization schemes employ approximations to represent the effects of unresolved processes. These approximations are a source of error in forecasts, caused in part by considerable uncertainty about the optimal value of parameters within each scheme -- parameteric uncertainty. Furthermore, there is uncertainty regarding the best choice of the overarching structure of the parameterization scheme -- structrual uncertainty. Parameter estimation can constrain the first, but may struggle with the second because structural choices are typically discrete. We address this problem in the context of cloud microphysics parameterization schemes by creating a flexible framework wherein structural and parametric uncertainties can be simultaneously constrained. Our scheme makes no assuptions about drop size distribution shape or the functional form of parametrized process rate terms. Instead, these uncertainties are constrained by observations using a Markov Chain Monte Carlo sampler within a Bayesian inference framework. Our scheme, the Bayesian Observationally-constrained Statistical-physical Scheme (BOSS), has flexibility to predict various sets of prognostic drop size distribution moments as well as varying complexity of process rate formulations. We compare idealized probabilistic forecasts from versions of BOSS with varying levels of structural complexity. This work has applications in ensemble forecasts with model physics uncertainty, data assimilation, and cloud microphysics process studies.

Evaluating and Improving Wind Forecasts over South China: The Role of Orographic Parameterization in the GRAPES Model

NASA Astrophysics Data System (ADS)

Zhong, Shuixin; Chen, Zitong; Xu, Daosheng; Zhang, Yanxia

2018-06-01

Unresolved small-scale orographic (SSO) drags are parameterized in a regional model based on the Global/Regional Assimilation and Prediction System for the Tropical Mesoscale Model (GRAPES TMM). The SSO drags are represented by adding a sink term in the momentum equations. The maximum height of the mountain within the grid box is adopted in the SSO parameterization (SSOP) scheme as compensation for the drag. The effects of the unresolved topography are parameterized as the feedbacks to the momentum tendencies on the first model level in planetary boundary layer (PBL) parameterization. The SSOP scheme has been implemented and coupled with the PBL parameterization scheme within the model physics package. A monthly simulation is designed to examine the performance of the SSOP scheme over the complex terrain areas located in the southwest of Guangdong. The verification results show that the surface wind speed bias has been much alleviated by adopting the SSOP scheme, in addition to reduction of the wind bias in the lower troposphere. The target verification over Xinyi shows that the simulations with the SSOP scheme provide improved wind estimation over the complex regions in the southwest of Guangdong.

The zonally averaged transport characteristics of the atmosphere as determined by a general circulation model

NASA Technical Reports Server (NTRS)

Plumb, R. A.

1985-01-01

Two dimensional modeling has become an established technique for the simulation of the global structure of trace constituents. Such models are simpler to formulate and cheaper to operate than three dimensional general circulation models, while avoiding some of the gross simplifications of one dimensional models. Nevertheless, the parameterization of eddy fluxes required in a 2-D model is not a trivial problem. This fact has apparently led some to interpret the shortcomings of existing 2-D models as indicating that the parameterization procedure is wrong in principle. There are grounds to believe that these shortcomings result primarily from incorrect implementations of the predictions of eddy transport theory and that a properly based parameterization may provide a good basis for atmospheric modeling. The existence of these GCM-derived coefficients affords an unprecedented opportunity to test the validity of the flux-gradient parameterization. To this end, a zonally averaged (2-D) model was developed, using these coefficients in the transport parameterization. Results from this model for a number of contrived tracer experiments were compared with the parent GCM. The generally good agreement substantially validates the flus-gradient parameterization, and thus the basic principle of 2-D modeling.

A statistical comparison of cirrus particle size distributions measured using the 2-D stereo probe during the TC4, SPARTICUS, and MACPEX flight campaigns with historical cirrus datasets

NASA Astrophysics Data System (ADS)

Schwartz, M. Christian

2017-08-01

This paper addresses two straightforward questions. First, how similar are the statistics of cirrus particle size distribution (PSD) datasets collected using the Two-Dimensional Stereo (2D-S) probe to cirrus PSD datasets collected using older Particle Measuring Systems (PMS) 2-D Cloud (2DC) and 2-D Precipitation (2DP) probes? Second, how similar are the datasets when shatter-correcting post-processing is applied to the 2DC datasets? To answer these questions, a database of measured and parameterized cirrus PSDs - constructed from measurements taken during the Small Particles in Cirrus (SPARTICUS); Mid-latitude Airborne Cirrus Properties Experiment (MACPEX); and Tropical Composition, Cloud, and Climate Coupling (TC4) flight campaigns - is used.Bulk cloud quantities are computed from the 2D-S database in three ways: first, directly from the 2D-S data; second, by applying the 2D-S data to ice PSD parameterizations developed using sets of cirrus measurements collected using the older PMS probes; and third, by applying the 2D-S data to a similar parameterization developed using the 2D-S data themselves. This is done so that measurements of the same cloud volumes by parameterized versions of the 2DC and 2D-S can be compared with one another. It is thereby seen - given the same cloud field and given the same assumptions concerning ice crystal cross-sectional area, density, and radar cross section - that the parameterized 2D-S and the parameterized 2DC predict similar distributions of inferred shortwave extinction coefficient, ice water content, and 94 GHz radar reflectivity. However, the parameterization of the 2DC based on uncorrected data predicts a statistically significantly higher number of total ice crystals and a larger ratio of small ice crystals to large ice crystals than does the parameterized 2D-S. The 2DC parameterization based on shatter-corrected data also predicts statistically different numbers of ice crystals than does the parameterized 2D-S, but the comparison between the two is nevertheless more favorable. It is concluded that the older datasets continue to be useful for scientific purposes, with certain caveats, and that continuing field investigations of cirrus with more modern probes is desirable.

Evaluation of five dry particle deposition parameterizations for incorporation into atmospheric transport models

NASA Astrophysics Data System (ADS)

Khan, Tanvir R.; Perlinger, Judith A.

2017-10-01

Despite considerable effort to develop mechanistic dry particle deposition parameterizations for atmospheric transport models, current knowledge has been inadequate to propose quantitative measures of the relative performance of available parameterizations. In this study, we evaluated the performance of five dry particle deposition parameterizations developed by Zhang et al. (2001) (Z01), Petroff and Zhang (2010) (PZ10), Kouznetsov and Sofiev (2012) (KS12), Zhang and He (2014) (ZH14), and Zhang and Shao (2014) (ZS14), respectively. The evaluation was performed in three dimensions: model ability to reproduce observed deposition velocities, Vd (accuracy); the influence of imprecision in input parameter values on the modeled Vd (uncertainty); and identification of the most influential parameter(s) (sensitivity). The accuracy of the modeled Vd was evaluated using observations obtained from five land use categories (LUCs): grass, coniferous and deciduous forests, natural water, and ice/snow. To ascertain the uncertainty in modeled Vd, and quantify the influence of imprecision in key model input parameters, a Monte Carlo uncertainty analysis was performed. The Sobol' sensitivity analysis was conducted with the objective to determine the parameter ranking from the most to the least influential. Comparing the normalized mean bias factors (indicators of accuracy), we find that the ZH14 parameterization is the most accurate for all LUCs except for coniferous forest, for which it is second most accurate. From Monte Carlo simulations, the estimated mean normalized uncertainties in the modeled Vd obtained for seven particle sizes (ranging from 0.005 to 2.5 µm) for the five LUCs are 17, 12, 13, 16, and 27 % for the Z01, PZ10, KS12, ZH14, and ZS14 parameterizations, respectively. From the Sobol' sensitivity results, we suggest that the parameter rankings vary by particle size and LUC for a given parameterization. Overall, for dp = 0.001 to 1.0 µm, friction velocity was one of the three most influential parameters in all parameterizations. For giant particles (dp = 10 µm), relative humidity was the most influential parameter. Because it is the least complex of the five parameterizations, and it has the greatest accuracy and least uncertainty, we propose that the ZH14 parameterization is currently superior for incorporation into atmospheric transport models.

Robust tracking of dexterous continuum robots: Fusing FBG shape sensing and stereo vision.

PubMed

Rumei Zhang; Hao Liu; Jianda Han

2017-07-01

Robust and efficient tracking of continuum robots is important for improving patient safety during space-confined minimally invasive surgery, however, it has been a particularly challenging task for researchers. In this paper, we present a novel tracking scheme by fusing fiber Bragg grating (FBG) shape sensing and stereo vision to estimate the position of continuum robots. Previous visual tracking easily suffers from the lack of robustness and leads to failure, while the FBG shape sensor can only reconstruct the local shape with integral cumulative error. The proposed fusion is anticipated to compensate for their shortcomings and improve the tracking accuracy. To verify its effectiveness, the robots' centerline is recognized by morphology operation and reconstructed by stereo matching algorithm. The shape obtained by FBG sensor is transformed into distal tip position with respect to the camera coordinate system through previously calibrated registration matrices. An experimental platform was set up and repeated tracking experiments were carried out. The accuracy estimated by averaging the absolute positioning errors between shape sensing and stereo vision is 0.67±0.65 mm, 0.41±0.25 mm, 0.72±0.43 mm for x, y and z, respectively. Results indicate that the proposed fusion is feasible and can be used for closed-loop control of continuum robots.

Online energy management strategy of fuel cell hybrid electric vehicles based on data fusion approach

NASA Astrophysics Data System (ADS)

Zhou, Daming; Al-Durra, Ahmed; Gao, Fei; Ravey, Alexandre; Matraji, Imad; Godoy Simões, Marcelo

2017-10-01

Energy management strategy plays a key role for Fuel Cell Hybrid Electric Vehicles (FCHEVs), it directly affects the efficiency and performance of energy storages in FCHEVs. For example, by using a suitable energy distribution controller, the fuel cell system can be maintained in a high efficiency region and thus saving hydrogen consumption. In this paper, an energy management strategy for online driving cycles is proposed based on a combination of the parameters from three offline optimized fuzzy logic controllers using data fusion approach. The fuzzy logic controllers are respectively optimized for three typical driving scenarios: highway, suburban and city in offline. To classify patterns of online driving cycles, a Probabilistic Support Vector Machine (PSVM) is used to provide probabilistic classification results. Based on the classification results of the online driving cycle, the parameters of each offline optimized fuzzy logic controllers are then fused using Dempster-Shafer (DS) evidence theory, in order to calculate the final parameters for the online fuzzy logic controller. Three experimental validations using Hardware-In-the-Loop (HIL) platform with different-sized FCHEVs have been performed. Experimental comparison results show that, the proposed PSVM-DS based online controller can achieve a relatively stable operation and a higher efficiency of fuel cell system in real driving cycles.

Characterization of secretory phospholipase A₂ with phospholipase A₁ activity in tobacco, Nicotiana tabacum (L.).

PubMed

Fujikawa, Yukichi; Fujikawa, Ritsuko; Iijima, Noriaki; Esaka, Muneharu

2012-03-01

A cDNA encoding protein with homology to plant secretory phospholipase A₂ (sPLA₂), denoted as Nt1 PLA₂, was isolated from tobacco (Nicotiana tabacum). The cDNA encodes a mature protein of 118 amino acid residues with a putative signal peptide of 29 residues. The mature form of Nt1 PLA₂ has 12 cysteines, Ca²⁺ binding loop and catalytic site domain that are commonly conserved in plant sPLA₂s. The recombinant Nt1 PLA₂ was expressed as a fusion protein with thioredoxin in E. coli BL21 cells and was purified by an ion exchange chromatography after digestion of the fusion proteins by Factor Xa protease to obtain the mature form. Interestingly, Nt1 PLA₂ could hydrolyze the ester bond at the sn-1 position of glycerophospholipids as well as at the sn-2 position, when the activities were determined using mixed-micellar phospholipids with sodium cholate. Both activities for the sn-1 and -2 positions of glycerophospholipids required Ca²⁺ essentially, and maximal activities were found in an alkaline region when phosphatidylcholine, phosphatidylglycerol or phosphatidylethanolamine was used as a substrate. The level of Nt1 PLA₂ mRNA was detected at a higher level in tobacco flowers than stem, leaves and roots, and was induced by salicylic acid.

The accomplishments of lithium target and test facility validation activities in the IFMIF/EVEDA phase

NASA Astrophysics Data System (ADS)

Arbeiter, Frederik; Baluc, Nadine; Favuzza, Paolo; Gröschel, Friedrich; Heidinger, Roland; Ibarra, Angel; Knaster, Juan; Kanemura, Takuji; Kondo, Hiroo; Massaut, Vincent; Saverio Nitti, Francesco; Miccichè, Gioacchino; O'hira, Shigeru; Rapisarda, David; Sugimoto, Masayoshi; Wakai, Eiichi; Yokomine, Takehiko

2018-01-01

As part of the engineering validation and engineering design activities (EVEDA) phase for the international fusion materials irradiation facility IFMIF, major elements of a lithium target facility and the test facility were designed, prototyped and validated. For the lithium target facility, the EVEDA lithium test loop was built at JAEA and used to test the stability (waves and long term) of the lithium flow in the target, work out the startup procedures, and test lithium purification and analysis. It was confirmed by experiments in the Lifus 6 plant at ENEA that lithium corrosion on ferritic martensitic steels is acceptably low. Furthermore, complex remote handling procedures for the remote maintenance of the target in the test cell environment were successfully practiced. For the test facility, two variants of a high flux test module were prototyped and tested in helium loops, demonstrating their good capabilities of maintaining the material specimens at the desired temperature with a low temperature spread. Irradiation tests were performed for heated specimen capsules and irradiation instrumentation in the BR2 reactor at SCK-CEN. The small specimen test technique, essential for obtaining material test results with limited irradiation volume, was advanced by evaluating specimen shape and test technique influences.

EMG and EPP-integrated human-machine interface between the paralyzed and rehabilitation exoskeleton.

PubMed

Yin, Yue H; Fan, Yuan J; Xu, Li D

2012-07-01

Although a lower extremity exoskeleton shows great prospect in the rehabilitation of the lower limb, it has not yet been widely applied to the clinical rehabilitation of the paralyzed. This is partly caused by insufficient information interactions between the paralyzed and existing exoskeleton that cannot meet the requirements of harmonious control. In this research, a bidirectional human-machine interface including a neurofuzzy controller and an extended physiological proprioception (EPP) feedback system is developed by imitating the biological closed-loop control system of human body. The neurofuzzy controller is built to decode human motion in advance by the fusion of the fuzzy electromyographic signals reflecting human motion intention and the precise proprioception providing joint angular feedback information. It transmits control information from human to exoskeleton, while the EPP feedback system based on haptic stimuli transmits motion information of the exoskeleton back to the human. Joint angle and torque information are transmitted in the form of air pressure to the human body. The real-time bidirectional human-machine interface can help a patient with lower limb paralysis to control the exoskeleton with his/her healthy side and simultaneously perceive motion on the paralyzed side by EPP. The interface rebuilds a closed-loop motion control system for paralyzed patients and realizes harmonious control of the human-machine system.

High-performance fractional order terminal sliding mode control strategy for DC-DC Buck converter

PubMed Central

Xu, Dan; Zhou, Huan; Bai, Anning; Lu, Wei

2017-01-01

This paper presents an adaption of the fractional order terminal sliding mode control (AFTSMC) strategy for DC-DC Buck converter. The following strategy aims to design a novel nonlinear sliding surface function, with a double closed-loop structure of voltage and current. This strategy is a fusion of two characteristics: terminal sliding mode control (TSMC) and fractional order calculation (FOC). In addition, the influence of “the controller parameters” on the “performance of double closed-loop system” is investigated. It is observed that the value of terminal power has to be chosen to make a compromise between start-up and transient response of the converter. Therefore the AFTSMC strategy chooses the value of the terminal power adaptively, and this strategy can lead to the appropriate number of fractional order as well. Furthermore, through the fractional order analysis, the system can reach the sliding mode surface in a finite time. And the theoretical considerations are verified by numerical simulation. The performance of the AFTSMC and TSMC strategies is tested by computer simulations. And the comparison simulation results show that the AFTSMC exhibits a considerable improvement in terms of a faster output voltage response during load changes. Moreover, AFTSMC obtains a faster dynamical response, smaller steady-state error rate and lower overshoot. PMID:29084255

Complex cardiac defects after ethanol exposure during discrete cardiogenic events in zebrafish: Prevention with folic acid

PubMed Central

Sarmah, Swapnalee; Marrs, James A.

2014-01-01

BACKGROUND Fetal alcohol spectrum disorder (FASD) describes a range of birth defects including various congenital heart defects (CHDs). Mechanisms of FASD-associated CHDs are not understood. Whether alcohol interferes with a single critical event or with multiple events in heart formation is not known. RESULTS Our zebrafish embryo experiments showed that ethanol interrupts different cardiac regulatory networks and perturbed multiple steps of cardiogenesis (specification, myocardial migration, looping, chamber morphogenesis and endocardial cushion formation). Ethanol exposure during gastrulation until cardiac specification or during myocardial midline migration did not produce severe or persistent heart development defects. However, exposure comprising gastrulation until myocardial precursor midline fusion or during heart patterning stages produced aberrant heart looping and defective endocardial cushions. Continuous exposure during entire cardiogenesis produced complex cardiac defects leading to severely defective myocardium, endocardium, and endocardial cushions. Supplementation of retinoic acid with ethanol partially rescued early heart developmental defects, but the endocardial cushions did not form correctly. In contrast, supplementation of folic acid rescued normal heart development, including the endocardial cushions. CONCLUSIONS Our results indicate that ethanol exposure interrupted divergent cardiac morphogenesis events causing heart defects. Folic acid supplementation was effective in preventing a wide spectrum of ethanol-induced heart developmental defects. PMID:23832875

Inductive current startup in large tokamaks with expanding minor radius and rf assist

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borowski, S.K.

1984-02-01

Auxiliary rf heating of electrons before and during the current-rise phase of a large tokamak, such as the Fusion Engineering Device (R = 4.8 m, a = 1.3 m, sigma = 1.6, B/sub T/ = 3.62 T), is examined as a means of reducing both the initiation loop voltage and resistive flux expenditure during startup. Prior to current initiation, 1 to 2 MW of electron cyclotron resonance heating power at approx. 90 GHz is used to create a small volume of high conductivity plasma (T/sub e/ approx. = 100 eV, n/sub e/ approx. = 10/sup 19/ m/sup -3/) near themore » upper hybrid resonance (UHR) region. This plasma conditioning permits a small radius (a/sub 0/ approx. = 0.2 to 0.4 m) current channel to be established with a relatively low initial loop voltage (less than or equal to 25 V as opposed to approx. 100 V without rf assist). During the subsequent plasma expansion and current ramp phase, a combination of rf heating (up to 5 MW) and current profile control leads to a substantial savings in volt-seconds by: (1) minimizing the resistive flux consumption; and (2) maintaining the internal flux at or near the flat profile limit.« less

Inductive current startup in large tokamaks with expanding minor radius and RF assist

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borowski, S.K.

1983-01-01

Auxiliary RF heating of electrons before and during the current rise phase of a large tokamak, such as the Fusion Engineering Device, is examined as a means of reducing both the initiation loop voltage and resistive flux expenditure during startup. Prior to current initiation, 1 to 2 MW of electron cyclotron resonance heating power at approx.90 GHz is used to create a small volume of high conductivity plasma (T/sub e/ approx. = 100 eV, n/sub e/ approx. = 10/sup 19/m/sup -3/) near the upper hybrid resonance (UHR) region. This plasma conditioning permits a small radius (a/sup 0/ approx.< 0.4 m)more » current channel to be established with a relatively low initial loop voltage (approx.< 25 V as opposed to approx.100 V without RF assist). During the subsequent plasma expansion and current ramp phase, additional RF power is introduced to reduce volt-second consumption due to plasma resistance. To study the preheating phase, a near classical particle and energy transport model is developed to estimate the electron heating efficiency in a currentless toroidal plasma. The model assumes that preferential electron heating at the UHR leads to the formation of an ambipolar sheath potential between the neutral plasma and the conducting vacuum vessel and limiter.« less

Split green fluorescent protein as a modular binding partner for protein crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Hau B.; Hung, Li-Wei; Yeates, Todd O.

2013-12-01

A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was testedmore » by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization.« less

High-performance fractional order terminal sliding mode control strategy for DC-DC Buck converter.

PubMed

Wang, Jianlin; Xu, Dan; Zhou, Huan; Bai, Anning; Lu, Wei

2017-01-01

This paper presents an adaption of the fractional order terminal sliding mode control (AFTSMC) strategy for DC-DC Buck converter. The following strategy aims to design a novel nonlinear sliding surface function, with a double closed-loop structure of voltage and current. This strategy is a fusion of two characteristics: terminal sliding mode control (TSMC) and fractional order calculation (FOC). In addition, the influence of "the controller parameters" on the "performance of double closed-loop system" is investigated. It is observed that the value of terminal power has to be chosen to make a compromise between start-up and transient response of the converter. Therefore the AFTSMC strategy chooses the value of the terminal power adaptively, and this strategy can lead to the appropriate number of fractional order as well. Furthermore, through the fractional order analysis, the system can reach the sliding mode surface in a finite time. And the theoretical considerations are verified by numerical simulation. The performance of the AFTSMC and TSMC strategies is tested by computer simulations. And the comparison simulation results show that the AFTSMC exhibits a considerable improvement in terms of a faster output voltage response during load changes. Moreover, AFTSMC obtains a faster dynamical response, smaller steady-state error rate and lower overshoot.

Organization of tcp, acf, and toxT genes within a ToxT-dependent operon.

PubMed

Brown, R C; Taylor, R K

1995-05-01

The toxin coregulated pilus (TCP) is required for Vibrio cholerae to colonize the human intestine. The expression of the pilin gene, tcpA, is dependent upon ToxR and upon ToxT. The toxT gene was recently mapped within the TCP biogenesis gene cluster and shown to be capable of activating a tcpA::TnphoA fusion when cloned in Escherichia coli. In this study, we determined that ToxR/ToxT activation occurs at the level of tcpA transcription. ToxT expressed in E. coli could activate a tcp operon fusion, while ToxR, ToxR with ToxS, or a ToxR-PhoA fusion failed to activate the tcp operon fusion and we could not demonstrate binding of a ToxR extract to the tcpA promoter region in DNA mobility-shift assays. The start site for the regulated promoter was shown by primer extension to lie 75 bp upstream of the first codon of tcpA. An 800-base tcpA message was identified, by Northern analysis, that correlates by size to the distance between the transcriptional start and a hairpin-loop sequence between tcpA and tcpB. The more-sensitive assay of RNase protection analysis demonstrated that a regulated transcript probably extends through the rest of the downstream tcp genes, including toxT and the adjacent accessory colonization factor (acf) genes. An in-frame tcpA deletion, but not a polar tcpA::TnphoA fusion, could be complemented for pilus surface expression by providing tcpA in trans. This evidence suggests that the tcp genes, including toxT, are organized in an operon directly activated by ToxT in a ToxR-dependent manner. Most of the toxT expression under induced conditions requires transcription of the tcpA promoter. Further investigation of how tcp::TnphoA insertions that are polar on toxT expression retain regulation showed that a low basal level of toxT expression is present in toxR and tcp::TnphoA strains. Overall, these observations support the ToxR/ToxT cascade of regulation for tcp. Once induced, toxT expression becomes autoregulatory via the tcp promoter, linking tcp expression to that of additional colonization factors, exotoxin production, and genes of unknown function in cholera pathogenesis.

Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections.

PubMed

Xiong, Xiaoli; Tortorici, M Alejandra; Snijder, Joost; Yoshioka, Craig; Walls, Alexandra C; Li, Wentao; McGuire, Andrew T; Rey, Félix A; Bosch, Berend-Jan; Veesler, David

2017-11-01

Coronaviruses recently emerged as major human pathogens causing outbreaks of severe acute respiratory syndrome and Middle-East respiratory syndrome. They utilize the spike (S) glycoprotein anchored in the viral envelope to mediate host attachment and fusion of the viral and cellular membranes to initiate infection. The S protein is a major determinant of the zoonotic potential of coronaviruses and is also the main target of the host humoral immune response. We report here the 3.5 Å resolution cryo-electron microscopy structure of the S glycoprotein trimer from the pathogenic porcine deltacoronavirus (PDCoV), which belongs to the recently identified delta genus. Structural and glycoproteomics data indicate that the glycans of PDCoV S are topologically conserved when compared with the human respiratory coronavirus HCoV-NL63 S, resulting in similar surface areas being shielded from neutralizing antibodies and implying that both viruses are under comparable immune pressure in their respective hosts. The structure further reveals a shortened S 2 ' activation loop, containing a reduced number of basic amino acids, which participates to rendering the spike largely protease-resistant. This property distinguishes PDCoV S from recently characterized betacoronavirus S proteins and suggests that the S protein of enterotropic PDCoV has evolved to tolerate the protease-rich environment of the small intestine and to fine-tune its fusion activation to avoid premature triggering and reduction of infectivity. IMPORTANCE Coronaviruses use transmembrane spike (S) glycoprotein trimers to promote host attachment and fusion of the viral and cellular membranes. We determined a near-atomic resolution cryo-electron microscopy structure of the S ectodomain trimer from the pathogenic porcine deltacoronavirus (PDCoV), which is responsible for diarrhea in piglets and has had devastating consequences for the swine industry worldwide. Structural and glycoproteomics data reveal that PDCoV S is decorated with 78 N-linked glycans obstructing the protein surface to limit accessibility to neutralizing antibodies in a way reminiscent of what has recently been described for a human respiratory coronavirus. PDCoV S is largely protease-resistant which distinguishes it from most other characterized coronavirus S glycoproteins and suggests that enteric coronaviruses have evolved to fine-tune fusion activation in the protease-rich environment of the small intestine of infected hosts. Copyright © 2017 American Society for Microbiology.

Shortwave radiation parameterization scheme for subgrid topography

NASA Astrophysics Data System (ADS)

Helbig, N.; LöWe, H.

2012-02-01

Topography is well known to alter the shortwave radiation balance at the surface. A detailed radiation balance is therefore required in mountainous terrain. In order to maintain the computational performance of large-scale models while at the same time increasing grid resolutions, subgrid parameterizations are gaining more importance. A complete radiation parameterization scheme for subgrid topography accounting for shading, limited sky view, and terrain reflections is presented. Each radiative flux is parameterized individually as a function of sky view factor, slope and sun elevation angle, and albedo. We validated the parameterization with domain-averaged values computed from a distributed radiation model which includes a detailed shortwave radiation balance. Furthermore, we quantify the individual topographic impacts on the shortwave radiation balance. Rather than using a limited set of real topographies we used a large ensemble of simulated topographies with a wide range of typical terrain characteristics to study all topographic influences on the radiation balance. To this end slopes and partial derivatives of seven real topographies from Switzerland and the United States were analyzed and Gaussian statistics were found to best approximate real topographies. Parameterized direct beam radiation presented previously compared well with modeled values over the entire range of slope angles. The approximation of multiple, anisotropic terrain reflections with single, isotropic terrain reflections was confirmed as long as domain-averaged values are considered. The validation of all parameterized radiative fluxes showed that it is indeed not necessary to compute subgrid fluxes in order to account for all topographic influences in large grid sizes.

Analysis of sensitivity to different parameterization schemes for a subtropical cyclone

NASA Astrophysics Data System (ADS)

Quitián-Hernández, L.; Fernández-González, S.; González-Alemán, J. J.; Valero, F.; Martín, M. L.

2018-05-01

A sensitivity analysis to diverse WRF model physical parameterization schemes is carried out during the lifecycle of a Subtropical cyclone (STC). STCs are low-pressure systems that share tropical and extratropical characteristics, with hybrid thermal structures. In October 2014, a STC made landfall in the Canary Islands, causing widespread damage from strong winds and precipitation there. The system began to develop on October 18 and its effects lasted until October 21. Accurate simulation of this type of cyclone continues to be a major challenge because of its rapid intensification and unique characteristics. In the present study, several numerical simulations were performed using the WRF model to do a sensitivity analysis of its various parameterization schemes for the development and intensification of the STC. The combination of parameterization schemes that best simulated this type of phenomenon was thereby determined. In particular, the parameterization combinations that included the Tiedtke cumulus schemes had the most positive effects on model results. Moreover, concerning STC track validation, optimal results were attained when the STC was fully formed and all convective processes stabilized. Furthermore, to obtain the parameterization schemes that optimally categorize STC structure, a verification using Cyclone Phase Space is assessed. Consequently, the combination of parameterizations including the Tiedtke cumulus schemes were again the best in categorizing the cyclone's subtropical structure. For strength validation, related atmospheric variables such as wind speed and precipitable water were analyzed. Finally, the effects of using a deterministic or probabilistic approach in simulating intense convective phenomena were evaluated.

Correlations with operative anatomy of real time three-dimensional echocardiographic imaging of congenital aortic valvar stenosis.

PubMed

Sadagopan, Shankar N; Veldtman, Gruschen R; Sivaprakasam, Muthukumaran C; Keeton, Barry R; Gnanapragasam, James P; Salmon, Anthony P; Haw, Marcus P; Vettukattil, Joseph J

2006-10-01

To define the anatomic characteristics of the congenitally malformed and severely stenotic aortic valve using trans-thoracic real time three-dimensional echocardiography, and to compare and contrast this with the valvar morphology as seen at surgery. Prospective cross-sectional observational study. Tertiary centre for paediatric cardiology. All patients requiring aortic valvotomy between December 2003 and July 2004 were evaluated prior to surgery with three-dimensional echocardiography. Full volume loop images were acquired using the Phillips Sonos 7500 system. A single observer analysed the images using "Q lab 4.1" software. The details were then compared with operative findings. We identified 8 consecutive patients, with a median age of 16 weeks, ranging from 1 day to 11 years, with median weight of 7.22 kilograms, ranging from 2.78 to 22 kilograms. The measured diameter of the valvar orifice, and the number of leaflets identified, corresponded closely with surgical assessment. The sites of fusion of the leaflets were correctly identified by the echocardiographic imaging in all cases. Fusion between the right and non-coronary leaflets was identified in half the patients. Dysplasia was observed in 3 patients, with 1 patient having nodules and 2 shown to have excrescences. At surgery, nodules were excised, and excrescences were trimmed. The dysplastic changes correlated well with operative findings, though statistically not significant. We recommend trans-thoracic real time three-dimensional echocardiography for the assessment of the congenitally malformed aortic valve, particularly to identify sites of fusion between leaflets and to measure the orificial diameter. The definition of nodularity, and the prognosis of nodules based on the mode of intervention, will need a comparative study of patients submitted to balloon dilation as well as those undergoing surgical valvotomy.

Signaling of the ITK (interleukin 2-inducible T cell kinase)-SYK (spleen tyrosine kinase) fusion kinase is dependent on adapter SLP-76 and on the adapter function of the kinases SYK and ZAP70.

PubMed

Hussain, Alamdar; Mohammad, Dara K; Gustafsson, Manuela O; Uslu, Merve; Hamasy, Abdulrahman; Nore, Beston F; Mohamed, Abdalla J; Smith, C I Edvard

2013-03-08

The inducible T cell kinase-spleen tyrosine kinase (ITK-SYK) oncogene consists of the Tec homology-pleckstrin homology domain of ITK and the kinase domain of SYK, and it is believed to be the cause of peripheral T cell lymphoma. We and others have recently demonstrated that this fusion protein is constitutively tyrosine-phosphorylated and is transforming both in vitro and in vivo. To gain a deeper insight into the molecular mechanism(s) underlying its activation and signaling, we mutated a total of eight tyrosines located in the SYK portion of the chimera into either phenylalanine or to the negatively charged glutamic acid. Although mutations in the interdomain-B region affected ITK-SYK kinase activity, they only modestly altered downstream signaling events. In contrast, mutations that were introduced in the kinase domain triggered severe impairment of downstream signaling. Moreover, we show here that SLP-76 is critical for ITK-SYK activation and is particularly required for the ITK-SYK-dependent phosphorylation of SYK activation loop tyrosines. In Jurkat cell lines, we demonstrate that expression of ITK-SYK fusion requires an intact SLP-76 function and significantly induces IL-2 secretion and CD69 expression. Furthermore, the SLP-76-mediated induction of IL-2 and CD69 could be further enhanced by SYK or ZAP-70, but it was independent of their kinase activity. Notably, ITK-SYK expression in SYF cells phosphorylates SLP-76 in the absence of SRC family kinases. Altogether, our data suggest that ITK-SYK exists in the active conformation state and is therefore capable of signaling without SRC family kinases or stimulation of the T cell receptor.

Signaling of the ITK (Interleukin 2-inducible T Cell Kinase)-SYK (Spleen Tyrosine Kinase) Fusion Kinase Is Dependent on Adapter SLP-76 and on the Adapter Function of the Kinases SYK and ZAP70*

PubMed Central

Hussain, Alamdar; Mohammad, Dara K.; Gustafsson, Manuela O.; Uslu, Merve; Hamasy, Abdulrahman; Nore, Beston F.; Mohamed, Abdalla J.; Smith, C. I. Edvard

2013-01-01

The inducible T cell kinase-spleen tyrosine kinase (ITK-SYK) oncogene consists of the Tec homology-pleckstrin homology domain of ITK and the kinase domain of SYK, and it is believed to be the cause of peripheral T cell lymphoma. We and others have recently demonstrated that this fusion protein is constitutively tyrosine-phosphorylated and is transforming both in vitro and in vivo. To gain a deeper insight into the molecular mechanism(s) underlying its activation and signaling, we mutated a total of eight tyrosines located in the SYK portion of the chimera into either phenylalanine or to the negatively charged glutamic acid. Although mutations in the interdomain-B region affected ITK-SYK kinase activity, they only modestly altered downstream signaling events. In contrast, mutations that were introduced in the kinase domain triggered severe impairment of downstream signaling. Moreover, we show here that SLP-76 is critical for ITK-SYK activation and is particularly required for the ITK-SYK-dependent phosphorylation of SYK activation loop tyrosines. In Jurkat cell lines, we demonstrate that expression of ITK-SYK fusion requires an intact SLP-76 function and significantly induces IL-2 secretion and CD69 expression. Furthermore, the SLP-76-mediated induction of IL-2 and CD69 could be further enhanced by SYK or ZAP-70, but it was independent of their kinase activity. Notably, ITK-SYK expression in SYF cells phosphorylates SLP-76 in the absence of SRC family kinases. Altogether, our data suggest that ITK-SYK exists in the active conformation state and is therefore capable of signaling without SRC family kinases or stimulation of the T cell receptor. PMID:23293025

Selection of a rigid internal fixation construct for stabilization at the craniovertebral junction in pediatric patients.

PubMed

Anderson, Richard C E; Ragel, Brian T; Mocco, J; Bohman, Leif-Erik; Brockmeyer, Douglas L

2007-07-01

Atlantoaxial and occipitocervical instability in children have traditionally been treated with posterior bone and wire fusion and external halo orthoses. Recently, successful outcomes have been achieved using rigid internal fixation, particularly C1-2 transarticular screws. The authors describe flow diagrams created to help clinicians determine which method of internal fixation to use in complex anatomical circumstances when bilateral transarticular screw placement is not possible. The records of children who underwent either atlantoaxial or occipitocervical fixation with rigid internal fixation over an 11-year period were retrospectively reviewed to define flow diagrams used to determine treatment protocols. Among the 95 patients identified who underwent atlantoaxial or occipitocervical fixation, the craniocervical anatomy in 25 patients (six atlantoaxial and 19 occipitocervical fixations [26%]) required alternative methods of internal fixation. Types of screw fixation included loop or rod constructs anchored by combinations of C1-2 transarticular screws (15 constructs), C-1 lateral mass screws (11), C-2 pars screws (24), C-2 translaminar screws (one), and subaxial lateral mass screws (six). The mean age of the patients (15 boys and 10 girls) was 9.8 years (range 1.3-17 years). All 22 patients with greater than 3-month follow-up duration achieved solid bone fusion and maintained stable constructs on radiographic studies. Clinical improvement was seen in all patients who had preoperative symptoms. Novel flow diagrams are suggested to help guide selection of rigid internal fixation constructs when performing pediatric C1-2 and occipitocervical stabilizations. Use of these flow diagrams has led to successful fusion in 25 pediatric patients with difficult anatomy requiring less common constructs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Arunava; Prevelige, Peter E

The primary goal of the project was to develop protein-templated approaches for the synthesis and directed assembly of semiconductor nanomaterials that are efficient for visible light absorption and hydrogen production. In general, visible-light-driven photocatalysis reactions exhibit low quantum efficiency for solar energy conversion primarily because of materials-related issues and limitations, such as the control of the band gap, band structure, photochemical stability, and available reactive surface area of the photocatalyst. Synthesis of multicomponent hierarchical nano-architectures, consisting of semiconductor nanoparticles (NPs) with desired optical properties fabricated to maximize spatial proximity for optimum electron and energy transfer represents an attractive route formore » addressing the problem. Virus capsids are highly symmetrical, self-assembling protein cage nanoparticles that exist in a range of sizes and symmetries. Selective deposition of inorganic, by design, at specific locations on virus capsids affords precise control over the size, spacing, and assembly of nanomaterials, resulting in uniform and reproducible nano-architectures. We utilized the self-assembling capabilities of the 420 subunit, 60 nm icosahedral, P22 virus capsid to direct the nucleation, growth, and proximity of a range of component materials. Controlled fabrication on the exterior of the temperature stable shell was achieved by genetically encoding specific binding peptides into an externally exposed loop which is displayed on each of the 420 coat protein subunits. Localization of complimentary materials to the interior of the particle was achieved through the use “scaffolding-fusion proteins. The scaffolding domain drives coat protein polymerization resulting in a coat protein shell surrounding a core of approximately 300 scaffolding/fusion molecules. The fusion domain comprises a peptide which specifically binds the semiconductor material of interest.« less

Evaluation of a hierarchy of models reveals importance of substrate limitation for predicting carbon dioxide and methane exchange in restored wetlands

NASA Astrophysics Data System (ADS)

Oikawa, P. Y.; Jenerette, G. D.; Knox, S. H.; Sturtevant, C.; Verfaillie, J.; Dronova, I.; Poindexter, C. M.; Eichelmann, E.; Baldocchi, D. D.

2017-01-01

Wetlands and flooded peatlands can sequester large amounts of carbon (C) and have high greenhouse gas mitigation potential. There is growing interest in financing wetland restoration using C markets; however, this requires careful accounting of both CO2 and CH4 exchange at the ecosystem scale. Here we present a new model, the PEPRMT model (Peatland Ecosystem Photosynthesis Respiration and Methane Transport), which consists of a hierarchy of biogeochemical models designed to estimate CO2 and CH4 exchange in restored managed wetlands. Empirical models using temperature and/or photosynthesis to predict respiration and CH4 production were contrasted with a more process-based model that simulated substrate-limited respiration and CH4 production using multiple carbon pools. Models were parameterized by using a model-data fusion approach with multiple years of eddy covariance data collected in a recently restored wetland and a mature restored wetland. A third recently restored wetland site was used for model validation. During model validation, the process-based model explained 70% of the variance in net ecosystem exchange of CO2 (NEE) and 50% of the variance in CH4 exchange. Not accounting for high respiration following restoration led to empirical models overestimating annual NEE by 33-51%. By employing a model-data fusion approach we provide rigorous estimates of uncertainty in model predictions, accounting for uncertainty in data, model parameters, and model structure. The PEPRMT model is a valuable tool for understanding carbon cycling in restored wetlands and for application in carbon market-funded wetland restoration, thereby advancing opportunity to counteract the vast degradation of wetlands and flooded peatlands.

Using Additive Manufacturing to Optimize FLiBe Coolant Blanket in Fusion Reactors

NASA Astrophysics Data System (ADS)

Fry, Vincent Michael

Fusion reactors have often been hailed as the holy grail of clean energy generation, though a power-generating reactor has never been built due to a multitude of limiting factors. One such factor is the immense 12-15 MW/m2 heat fluxes experienced by the inner wall of the reactor. Multiple groups have proposed the use of tungsten swirl tubes to withstand the heat generated within the reactor core. The primary focus of this investigation is to parameterize this 'first wall' interior structure to determine the highest achievable heat transfer coefficient given the many tungsten configurations enabled via additive manufacturing. Two general tube structures were considered: an orthogonal three-dimensional mesh of various diameters and spacings, as well as a swirl tube geometry with varying 'tape' thicknesses. The coolant liquid proposed is FLiBe (2LiF-BeF2) due to its high specific heat capacity as well as its ability to breed tritium, the fuel for the reactor. This was accomplished using theoretical calculations; computational fluid dynamics and conjugate heat transfer simulations in ANSYS Workbench; as well as an experimental setup to confirm tube pressure drop along the pipe. It was determined that heat transfer coefficients between upwards of 60,000 W/m 2K were readily achievable, keeping the first wall temperature around 1300 K. A multitude of designs proved to be feasible given the pumping power restrictions, though the suggested design going forward is a swirl tube with 2 mm 'tape' thickness and 3 m/s inlet velocity. Simulated pressure drop with water was accurate to within 30% of experimentally measured values, giving confidence in the credibility of the results.

HIV-1 Clinical Isolates Resistant to CCR5 Antagonists Exhibit Delayed Entry Kinetics That Are Corrected in the Presence of Drug

PubMed Central

Putcharoen, Opass; Lee, Sun Hee; Henrich, Timothy J.; Hu, Zixin; Vanichanan, Jakapat; Coakley, Eoin; Greaves, Wayne; Gulick, Roy M.; Kuritzkes, Daniel R.

2012-01-01

HIV CCR5 antagonists select for env gene mutations that enable virus entry via drug-bound coreceptor. To investigate the mechanisms responsible for viral adaptation to drug-bound coreceptor-mediated entry, we studied viral isolates from three participants who developed CCR5 antagonist resistance during treatment with vicriviroc (VCV), an investigational small-molecule CCR5 antagonist. VCV-sensitive and -resistant viruses were isolated from one HIV subtype C- and two subtype B-infected participants; VCV-resistant isolates had mutations in the V3 loop of gp120 and were cross-resistant to TAK-779, an investigational antagonist, and maraviroc (MVC). All three resistant isolates contained a 306P mutation but had variable mutations elsewhere in the V3 stem. We used a virus-cell β-lactamase (BlaM) fusion assay to determine the entry kinetics of recombinant viruses that incorporated full-length VCV-sensitive and -resistant envelopes. VCV-resistant isolates exhibited delayed entry rates in the absence of drug, relative to pretherapy VCV-sensitive isolates. The addition of drug corrected these delays. These findings were generalizable across target cell types with a range of CD4 and CCR5 surface densities and were observed when either population-derived or clonal envelopes were used to construct recombinant viruses. V3 loop mutations alone were sufficient to restore virus entry in the presence of drug, and the accumulation of V3 mutations during VCV therapy led to progressively higher rates of viral entry. We propose that the restoration of pre-CCR5 antagonist therapy HIV entry kinetics drives the selection of V3 loop mutations and may represent a common mechanism that underlies the emergence of CCR5 antagonist resistance. PMID:22090117

Gene conversion as a mechanism for divergence of a chloroplast tRNA gene inserted in the mitochondrial genome of Brassica oleracea.

PubMed Central

Dron, M; Hartmann, C; Rode, A; Sevignac, M

1985-01-01

We have characterized a 1.7 kb sequence, containing a tRNA Leu2 gene shared by the ct and mt genomes of Brassica oleracea. The two sequences are completely homologous except in two short regions where two distinct gene conversion events have occurred between two sets of direct repeats leading to the insertion of 5 bp in the T loop of the mt copy of the ct gene. This is the first evidence that gene conversion represents the initial evolutionary step in inactivation of transferred ct genes in the mt genome. We also indicate that organelle DNA transfer by organelle fusion is an ongoing process which could be useful in genetic engineering. PMID:4080548

Digitally controlled twelve-pulse firing generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berde, D.; Ferrara, A.A.

1981-01-01

Control System Studies for the Tokamak Fusion Test Reactor (TFTR) indicate that accurate thyristor firing in the AC-to-DC conversion system is required in order to achieve good regulation of the various field currents. Rapid update and exact firing angle control are required to avoid instabilities, large eddy currents, or parasitic oscillations. The Prototype Firing Generator was designed to satisfy these requirements. To achieve the required /plus or minus/0.77/degree/firing accuracy, a three-phase-locked loop reference was designed; otherwise, the Firing Generator employs digital circuitry. The unit, housed in a standard CAMAC crate, operates under microcomputer control. Functions are performed under program control,more » which resides in nonvolatile read-only memory. Communication with CICADA control system is provided via an 11-bit parallel interface.« less

Higgs boson gluon-fusion production in QCD at three loops.

PubMed

Anastasiou, Charalampos; Duhr, Claude; Dulat, Falko; Herzog, Franz; Mistlberger, Bernhard

2015-05-29

We present the cross section for the production of a Higgs boson at hadron colliders at next-to-next-to-next-to-leading order (N^{3}LO) in perturbative QCD. The calculation is based on a method to perform a series expansion of the partonic cross section around the threshold limit to an arbitrary order. We perform this expansion to sufficiently high order to obtain the value of the hadronic cross at N^{3}LO in the large top-mass limit. For renormalization and factorization scales equal to half the Higgs boson mass, the N^{3}LO corrections are of the order of +2.2%. The total scale variation at N^{3}LO is 3%, reducing the uncertainty due to missing higher order QCD corrections by a factor of 3.

Experiments on Condensed Matter Nuclear Events in Kobe University

NASA Astrophysics Data System (ADS)

Minari, T.; Nishio, R.; Taniike, A.; Furuyama, Y.; Kitamura, A.

2006-02-01

We review three kinds of experimental works underway in our laboratory to investigate nuclear events in solid or liquid materials. The largest effort has been given to experiments to confirm the 7Li(d, n2α) reaction rate enhancement reaching 1015 in liquid lithium which was reported by H. Ikegami and R. Pettersson, Evidence of Enhanced Nonthermal Nuclear Fusion (Bulletin of Institute of Chemistry, BENF No. 3, Uppsala University, Sweden, September 2002). Li liquid droplets are formed as targets, and to keep them as pure as possible, we built a liquid Li loop. Thus far, in all cases of irradiation at the temperature from 520 to 570 K with 10-24 keV deuterons, we have not been able to reproduce the Ikegami enhancement for the 7Li(d, n2α) reaction.

Sensitivity of Glacier Mass Balance Estimates to the Selection of WRF Cloud Microphysics Parameterization in the Indus River Watershed

NASA Astrophysics Data System (ADS)

Johnson, E. S.; Rupper, S.; Steenburgh, W. J.; Strong, C.; Kochanski, A.

2017-12-01

Climate model outputs are often used as inputs to glacier energy and mass balance models, which are essential glaciological tools for testing glacier sensitivity, providing mass balance estimates in regions with little glaciological data, and providing a means to model future changes. Climate model outputs, however, are sensitive to the choice of physical parameterizations, such as those for cloud microphysics, land-surface schemes, surface layer options, etc. Furthermore, glacier mass balance (MB) estimates that use these climate model outputs as inputs are likely sensitive to the specific parameterization schemes, but this sensitivity has not been carefully assessed. Here we evaluate the sensitivity of glacier MB estimates across the Indus Basin to the selection of cloud microphysics parameterizations in the Weather Research and Forecasting Model (WRF). Cloud microphysics parameterizations differ in how they specify the size distributions of hydrometeors, the rate of graupel and snow production, their fall speed assumptions, the rates at which they convert from one hydrometeor type to the other, etc. While glacier MB estimates are likely sensitive to other parameterizations in WRF, our preliminary results suggest that glacier MB is highly sensitive to the timing, frequency, and amount of snowfall, which is influenced by the cloud microphysics parameterization. To this end, the Indus Basin is an ideal study site, as it has both westerly (winter) and monsoonal (summer) precipitation influences, is a data-sparse region (so models are critical), and still has lingering questions as to glacier importance for local and regional resources. WRF is run at a 4 km grid scale using two commonly used parameterizations: the Thompson scheme and the Goddard scheme. On average, these parameterizations result in minimal differences in annual precipitation. However, localized regions exhibit differences in precipitation of up to 3 m w.e. a-1. The different schemes also impact the radiative budgets over the glacierized areas. Our results show that glacier MB estimates can differ by up to 45% depending on the chosen cloud microphysics scheme. These findings highlight the need to better account for uncertainties in meteorological inputs into glacier energy and mass balance models.

Integrability in AdS/CFT correspondence: quasi-classical analysis

NASA Astrophysics Data System (ADS)

Gromov, Nikolay

2009-06-01

In this review, we consider a quasi-classical method applicable to integrable field theories which is based on a classical integrable structure—the algebraic curve. We apply it to the Green-Schwarz superstring on the AdS5 × S5 space. We show that the proposed method reproduces perfectly the earlier results obtained by expanding the string action for some simple classical solutions. The construction is explicitly covariant and is not based on a particular parameterization of the fields and as a result is free from ambiguities. On the other hand, the finite size corrections in some particularly important scaling limit are studied in this paper for a system of Bethe equations. For the general superalgebra \\su(N|K) , the result for the 1/L corrections is obtained. We find an integral equation which describes these corrections in a closed form. As an application, we consider the conjectured Beisert-Staudacher (BS) equations with the Hernandez-Lopez dressing factor where the finite size corrections should reproduce quasi-classical results around a general classical solution. Indeed, we show that our integral equation can be interpreted as a sum of all physical fluctuations and thus prove the complete one-loop consistency of the BS equations. We demonstrate that any local conserved charge (including the AdS energy) computed from the BS equations is indeed given at one loop by the sum of the charges of fluctuations with an exponential precision for large S5 angular momentum of the string. As an independent result, the BS equations in an \\su(2) sub-sector were derived from Zamolodchikovs's S-matrix. The paper is based on the author's PhD thesis.

New experimental approaches to the biology of flight control systems.

PubMed

Taylor, Graham K; Bacic, Marko; Bomphrey, Richard J; Carruthers, Anna C; Gillies, James; Walker, Simon M; Thomas, Adrian L R

2008-01-01

Here we consider how new experimental approaches in biomechanics can be used to attain a systems-level understanding of the dynamics of animal flight control. Our aim in this paper is not to provide detailed results and analysis, but rather to tackle several conceptual and methodological issues that have stood in the way of experimentalists in achieving this goal, and to offer tools for overcoming these. We begin by discussing the interplay between analytical and empirical methods, emphasizing that the structure of the models we use to analyse flight control dictates the empirical measurements we must make in order to parameterize them. We then provide a conceptual overview of tethered-flight paradigms, comparing classical ;open-loop' and ;closed-loop' setups, and describe a flight simulator that we have recently developed for making flight dynamics measurements on tethered insects. Next, we provide a conceptual overview of free-flight paradigms, focusing on the need to use system identification techniques in order to analyse the data they provide, and describe two new techniques that we have developed for making flight dynamics measurements on freely flying birds. First, we describe a technique for obtaining inertial measurements of the orientation, angular velocity and acceleration of a steppe eagle Aquila nipalensis in wide-ranging free flight, together with synchronized measurements of wing and tail kinematics using onboard instrumentation and video cameras. Second, we describe a photogrammetric method to measure the 3D wing kinematics of the eagle during take-off and landing. In each case, we provide demonstration data to illustrate the kinds of information available from each method. We conclude by discussing the prospects for systems-level analyses of flight control using these techniques and others like them.

Testing a common ice-ocean parameterization with laboratory experiments

NASA Astrophysics Data System (ADS)

McConnochie, C. D.; Kerr, R. C.

2017-07-01

Numerical models of ice-ocean interactions typically rely upon a parameterization for the transport of heat and salt to the ice face that has not been satisfactorily validated by observational or experimental data. We compare laboratory experiments of ice-saltwater interactions to a common numerical parameterization and find a significant disagreement in the dependence of the melt rate on the fluid velocity. We suggest a resolution to this disagreement based on a theoretical analysis of the boundary layer next to a vertical heated plate, which results in a threshold fluid velocity of approximately 4 cm/s at driving temperatures between 0.5 and 4°C, above which the form of the parameterization should be valid.

Parameterization of light absorption by components of seawater in optically complex coastal waters of the Crimea Peninsula (Black Sea).

PubMed

Dmitriev, Egor V; Khomenko, Georges; Chami, Malik; Sokolov, Anton A; Churilova, Tatyana Y; Korotaev, Gennady K

2009-03-01

The absorption of sunlight by oceanic constituents significantly contributes to the spectral distribution of the water-leaving radiance. Here it is shown that current parameterizations of absorption coefficients do not apply to the optically complex waters of the Crimea Peninsula. Based on in situ measurements, parameterizations of phytoplankton, nonalgal, and total particulate absorption coefficients are proposed. Their performance is evaluated using a log-log regression combined with a low-pass filter and the nonlinear least-square method. Statistical significance of the estimated parameters is verified using the bootstrap method. The parameterizations are relevant for chlorophyll a concentrations ranging from 0.45 up to 2 mg/m(3).

A second-order Budkyo-type parameterization of landsurface hydrology

NASA Technical Reports Server (NTRS)

Andreou, S. A.; Eagleson, P. S.

1982-01-01

A simple, second order parameterization of the water fluxes at a land surface for use as the appropriate boundary condition in general circulation models of the global atmosphere was developed. The derived parameterization incorporates the high nonlinearities in the relationship between the near surface soil moisture and the evaporation, runoff and percolation fluxes. Based on the one dimensional statistical dynamic derivation of the annual water balance, it makes the transition to short term prediction of the moisture fluxes, through a Taylor expansion around the average annual soil moisture. A comparison of the suggested parameterization is made with other existing techniques and available measurements. A thermodynamic coupling is applied in order to obtain estimations of the surface ground temperature.

Electron Impact Ionization: A New Parameterization for 100 eV to 1 MeV Electrons

NASA Technical Reports Server (NTRS)

Fang, Xiaohua; Randall, Cora E.; Lummerzheim, Dirk; Solomon, Stanley C.; Mills, Michael J.; Marsh, Daniel; Jackman, Charles H.; Wang, Wenbin; Lu, Gang

2008-01-01

Low, medium and high energy electrons can penetrate to the thermosphere (90-400 km; 55-240 miles) and mesosphere (50-90 km; 30-55 miles). These precipitating electrons ionize that region of the atmosphere, creating positively charged atoms and molecules and knocking off other negatively charged electrons. The precipitating electrons also create nitrogen-containing compounds along with other constituents. Since the electron precipitation amounts change within minutes, it is necessary to have a rapid method of computing the ionization and production of nitrogen-containing compounds for inclusion in computationally-demanding global models. A new methodology has been developed, which has parameterized a more detailed model computation of the ionizing impact of precipitating electrons over the very large range of 100 eV up to 1,000,000 eV. This new parameterization method is more accurate than a previous parameterization scheme, when compared with the more detailed model computation. Global models at the National Center for Atmospheric Research will use this new parameterization method in the near future.

Parameterization of Shortwave Cloud Optical Properties for a Mixture of Ice Particle Habits for use in Atmospheric Models

NASA Technical Reports Server (NTRS)

Chou, Ming-Dah; Lee, Kyu-Tae; Yang, Ping; Lau, William K. M. (Technical Monitor)

2002-01-01

Based on the single-scattering optical properties pre-computed with an improved geometric optics method, the bulk absorption coefficient, single-scattering albedo, and asymmetry factor of ice particles have been parameterized as a function of the effective particle size of a mixture of ice habits, the ice water amount, and spectral band. The parameterization has been applied to computing fluxes for sample clouds with various particle size distributions and assumed mixtures of particle habits. It is found that flux calculations are not overly sensitive to the assumed particle habits if the definition of the effective particle size is consistent with the particle habits that the parameterization is based. Otherwise, the error in the flux calculations could reach a magnitude unacceptable for climate studies. Different from many previous studies, the parameterization requires only an effective particle size representing all ice habits in a cloud layer, but not the effective size of individual ice habits.

Anisotropic shear dispersion parameterization for ocean eddy transport

NASA Astrophysics Data System (ADS)

Reckinger, Scott; Fox-Kemper, Baylor

2015-11-01

The effects of mesoscale eddies are universally treated isotropically in global ocean general circulation models. However, observations and simulations demonstrate that the mesoscale processes that the parameterization is intended to represent, such as shear dispersion, are typified by strong anisotropy. We extend the Gent-McWilliams/Redi mesoscale eddy parameterization to include anisotropy and test the effects of varying levels of anisotropy in 1-degree Community Earth System Model (CESM) simulations. Anisotropy has many effects on the simulated climate, including a reduction of temperature and salinity biases, a deepening of the southern ocean mixed-layer depth, impacts on the meridional overturning circulation and ocean energy and tracer uptake, and improved ventilation of biogeochemical tracers, particularly in oxygen minimum zones. A process-based parameterization to approximate the effects of unresolved shear dispersion is also used to set the strength and direction of anisotropy. The shear dispersion parameterization is similar to drifter observations in spatial distribution of diffusivity and high-resolution model diagnosis in the distribution of eddy flux orientation.

A unified spectral parameterization for wave breaking: From the deep ocean to the surf zone

NASA Astrophysics Data System (ADS)

Filipot, J.-F.; Ardhuin, F.

2012-11-01

A new wave-breaking dissipation parameterization designed for phase-averaged spectral wave models is presented. It combines wave breaking basic physical quantities, namely, the breaking probability and the dissipation rate per unit area. The energy lost by waves is first explicitly calculated in physical space before being distributed over the relevant spectral components. The transition from deep to shallow water is made possible by using a dissipation rate per unit area of breaking waves that varies with the wave height, wavelength and water depth. This parameterization is implemented in the WAVEWATCH III modeling framework, which is applied to a wide range of conditions and scales, from the global ocean to the beach scale. Wave height, peak and mean periods, and spectral data are validated using in situ and remote sensing data. Model errors are comparable to those of other specialized deep or shallow water parameterizations. This work shows that it is possible to have a seamless parameterization from the deep ocean to the surf zone.

Parameterized spectral distributions for meson production in proton-proton collisions

NASA Technical Reports Server (NTRS)

Schneider, John P.; Norbury, John W.; Cucinotta, Francis A.

1995-01-01

Accurate semiempirical parameterizations of the energy-differential cross sections for charged pion and kaon production from proton-proton collisions are presented at energies relevant to cosmic rays. The parameterizations, which depend on both the outgoing meson parallel momentum and the incident proton kinetic energy, are able to be reduced to very simple analytical formulas suitable for cosmic ray transport through spacecraft walls, interstellar space, the atmosphere, and meteorites.

Implementation of a Parameterization Framework for Cybersecurity Laboratories

DTIC Science & Technology

2017-03-01

designer of laboratory exercises with tools to parameterize labs for each student , and automate some aspects of the grading of laboratory exercises. A...is to provide the designer of laboratory exercises with tools to parameterize labs for each student , and automate some aspects of the grading of...support might assist the designer of laboratory exercises to achieve the following? 1. Verify that students performed lab exercises, with some

Relativistic three-dimensional Lippmann-Schwinger cross sections for space radiation applications

NASA Astrophysics Data System (ADS)

Werneth, C. M.; Xu, X.; Norman, R. B.; Maung, K. M.

2017-12-01

Radiation transport codes require accurate nuclear cross sections to compute particle fluences inside shielding materials. The Tripathi semi-empirical reaction cross section, which includes over 60 parameters tuned to nucleon-nucleus (NA) and nucleus-nucleus (AA) data, has been used in many of the world's best-known transport codes. Although this parameterization fits well to reaction cross section data, the predictive capability of any parameterization is questionable when it is used beyond the range of the data to which it was tuned. Using uncertainty analysis, it is shown that a relativistic three-dimensional Lippmann-Schwinger (LS3D) equation model based on Multiple Scattering Theory (MST) that uses 5 parameterizations-3 fundamental parameterizations to nucleon-nucleon (NN) data and 2 nuclear charge density parameterizations-predicts NA and AA reaction cross sections as well as the Tripathi cross section parameterization for reactions in which the kinetic energy of the projectile in the laboratory frame (TLab) is greater than 220 MeV/n. The relativistic LS3D model has the additional advantage of being able to predict highly accurate total and elastic cross sections. Consequently, it is recommended that the relativistic LS3D model be used for space radiation applications in which TLab > 220MeV /n .

How to assess the impact of a physical parameterization in simulations of moist convection?

NASA Astrophysics Data System (ADS)

Grabowski, Wojciech

2017-04-01

A numerical model capable in simulating moist convection (e.g., cloud-resolving model or large-eddy simulation model) consists of a fluid flow solver combined with required representations (i.e., parameterizations) of physical processes. The later typically include cloud microphysics, radiative transfer, and unresolved turbulent transport. Traditional approaches to investigate impacts of such parameterizations on convective dynamics involve parallel simulations with different parameterization schemes or with different scheme parameters. Such methodologies are not reliable because of the natural variability of a cloud field that is affected by the feedback between the physics and dynamics. For instance, changing the cloud microphysics typically leads to a different realization of the cloud-scale flow, and separating dynamical and microphysical impacts is difficult. This presentation will present a novel modeling methodology, the piggybacking, that allows studying the impact of a physical parameterization on cloud dynamics with confidence. The focus will be on the impact of cloud microphysics parameterization. Specific examples of the piggybacking approach will include simulations concerning the hypothesized deep convection invigoration in polluted environments, the validity of the saturation adjustment in modeling condensation in moist convection, and separation of physical impacts from statistical uncertainty in simulations applying particle-based Lagrangian microphysics, the super-droplet method.

Sensitivity of Cirrus and Mixed-phase Clouds to the Ice Nuclei Spectra in McRAS-AC: Single Column Model Simulations

NASA Technical Reports Server (NTRS)

Betancourt, R. Morales; Lee, D.; Oreopoulos, L.; Sud, Y. C.; Barahona, D.; Nenes, A.

2012-01-01

The salient features of mixed-phase and ice clouds in a GCM cloud scheme are examined using the ice formation parameterizations of Liu and Penner (LP) and Barahona and Nenes (BN). The performance of LP and BN ice nucleation parameterizations were assessed in the GEOS-5 AGCM using the McRAS-AC cloud microphysics framework in single column mode. Four dimensional assimilated data from the intensive observation period of ARM TWP-ICE campaign was used to drive the fluxes and lateral forcing. Simulation experiments where established to test the impact of each parameterization in the resulting cloud fields. Three commonly used IN spectra were utilized in the BN parameterization to described the availability of IN for heterogeneous ice nucleation. The results show large similarities in the cirrus cloud regime between all the schemes tested, in which ice crystal concentrations were within a factor of 10 regardless of the parameterization used. In mixed-phase clouds there are some persistent differences in cloud particle number concentration and size, as well as in cloud fraction, ice water mixing ratio, and ice water path. Contact freezing in the simulated mixed-phase clouds contributed to transfer liquid to ice efficiently, so that on average, the clouds were fully glaciated at T approximately 260K, irrespective of the ice nucleation parameterization used. Comparison of simulated ice water path to available satellite derived observations were also performed, finding that all the schemes tested with the BN parameterization predicted 20 average values of IWP within plus or minus 15% of the observations.

Impacts of subgrid-scale orography parameterization on simulated atmospheric fields over Korea using a high-resolution atmospheric forecast model

NASA Astrophysics Data System (ADS)

Lim, Kyo-Sun Sunny; Lim, Jong-Myoung; Shin, Hyeyum Hailey; Hong, Jinkyu; Ji, Young-Yong; Lee, Wanno

2018-06-01

A substantial over-prediction bias at low-to-moderate wind speeds in the Weather Research and Forecasting (WRF) model has been reported in the previous studies. Low-level wind fields play an important role in dispersion of air pollutants, including radionuclides, in a high-resolution WRF framework. By implementing two subgrid-scale orography parameterizations (Jimenez and Dudhia in J Appl Meteorol Climatol 51:300-316, 2012; Mass and Ovens in WRF model physics: problems, solutions and a new paradigm for progress. Preprints, 2010 WRF Users' Workshop, NCAR, Boulder, Colo. http://www.mmm.ucar.edu/wrf/users/workshops/WS2010/presentations/session%204/4-1_WRFworkshop2010Final.pdf, 2010), we tried to compare the performance of parameterizations and to enhance the forecast skill of low-level wind fields over the central western part of South Korea. Even though both subgrid-scale orography parameterizations significantly alleviated the positive bias at 10-m wind speed, the parameterization by Jimenez and Dudhia revealed a better forecast skill in wind speed under our modeling configuration. Implementation of the subgrid-scale orography parameterizations in the model did not affect the forecast skills in other meteorological fields including 10-m wind direction. Our study also brought up the problem of discrepancy in the definition of "10-m" wind between model physics parameterizations and observations, which can cause overestimated winds in model simulations. The overestimation was larger in stable conditions than in unstable conditions, indicating that the weak diurnal cycle in the model could be attributed to the representation error.

Finescale parameterizations of energy dissipation in a region of strong internal tides and sheared flow, the Lucky-Strike segment of the Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

Pasquet, Simon; Bouruet-Aubertot, Pascale; Reverdin, Gilles; Turnherr, Andreas; Laurent, Lou St.

2016-06-01

The relevance of finescale parameterizations of dissipation rate of turbulent kinetic energy is addressed using finescale and microstructure measurements collected in the Lucky Strike segment of the Mid-Atlantic Ridge (MAR). There, high amplitude internal tides and a strongly sheared mean flow sustain a high level of dissipation rate and turbulent mixing. Two sets of parameterizations are considered: the first ones (Gregg, 1989; Kunze et al., 2006) were derived to estimate dissipation rate of turbulent kinetic energy induced by internal wave breaking, while the second one aimed to estimate dissipation induced by shear instability of a strongly sheared mean flow and is a function of the Richardson number (Kunze et al., 1990; Polzin, 1996). The latter parameterization has low skill in reproducing the observed dissipation rate when shear unstable events are resolved presumably because there is no scale separation between the duration of unstable events and the inverse growth rate of unstable billows. Instead GM based parameterizations were found to be relevant although slight biases were observed. Part of these biases result from the small value of the upper vertical wavenumber integration limit in the computation of shear variance in Kunze et al. (2006) parameterization that does not take into account internal wave signal of high vertical wavenumbers. We showed that significant improvement is obtained when the upper integration limit is set using a signal to noise ratio criterion and that the spatial structure of dissipation rates is reproduced with this parameterization.

Sensitivity of CONUS Summer Rainfall to the Selection of Cumulus Parameterization Schemes in NU-WRF Seasonal Simulations

NASA Technical Reports Server (NTRS)

Iguchi, Takamichi; Tao, Wei-Kuo; Wu, Di; Peters-Lidard, Christa; Santanello, Joseph A.; Kemp, Eric; Tian, Yudong; Case, Jonathan; Wang, Weile; Ferraro, Robert;

A chimera encoding the fusion of an acetylcholine-binding protein to an ion channel is stabilized in a state close to the desensitized form of ligand-gated ion channels.

PubMed

Grutter, Thomas; Prado de Carvalho, Lia; Virginie, Dufresne; Taly, Antoine; Fischer, Markus; Changeux, Jean-Pierre

2005-03-01

To understand the mechanism of allosteric coupling between the ligand-binding domain and the ion channel of the Cys-loop ligand-gated ion channels (LGICs), we fused the soluble acetylcholine-binding protein (AChBP), which lacks an ion channel, to either the cationic serotonin type-3A ion channel (5HT(3A)) or the anionic glycine ion channel. Both linear chimeras expressed in HEK-293 cells display high affinity for the nicotinic agonist epibatidine (K(D) = 0.2-0.5 nM), but are not targeted to the cell surface. Only after substituting a ring of three loops located at the putative membrane side of the AChBP three-dimensional structure by the homologous residues of 5HT(3A), the resulting chimera AChBP(ring)/5HT(3A) (i) still displayed on intact cells an apparent high affinity for epibatidine, yet with a fourfold decrease (K(D) = 2.1 nM), (ii) displayed a high proportion of low affinity sites (11 +/- 7 microM) for the resting state stabilizing competitive antagonist alpha-bungarotoxin and (iii) was successfully targeted to the cell surface, as seen by immunofluorescence labelling. The AChBP(ring)/5HT(3A) chimera forms a pentameric structure, as revealed by sucrose gradient sedimentation. However, no whole-cell patch-clamp currents were detectable. Interestingly, binding assays with membrane fragments prepared from cells expressing AChBP(ring)/5HT(3A) showed a decrease in the apparent affinity for the agonists nicotine and epibatidine (5-fold), concomitant with an increase in the proportion of high-affinity sites (48 +/- 1 nM) for alpha-bungarotoxin. These results indicate that fusion of AChBP to an ion channel forms a pentameric receptor exposed to the cell surface and able to convert between discrete allosteric states, but stabilized in a high affinity state for epibatidine that likely corresponds to a desensitized form of LGICs. These artificial chimeras might offer a useful system to investigate signal transduction in LGICs.

Surface expression of an immunodominant malaria protein B cell epitope by yellow fever virus.

PubMed

Bonaldo, Myrna C; Garratt, Richard C; Caufour, Philippe S; Freire, Marcos S; Rodrigues, Mauricio M; Nussenzweig, Ruth S; Galler, Ricardo

2002-01-25

The yellow fever 17D virus (YF17D) has several characteristics that are desirable for the development of new, live attenuated vaccines. We approached its development as a vector for heterologous antigens by studying the expression of a humoral epitope at the surface of the E protein based on the results of modelling its three-dimensional structure. This model indicated that the most promising insertion site is between beta-strands f and g, a site that is exposed at the external surface of the virus. The large deletion of six residues from the fg loop of the E protein from yellow fever virus, compared to tick-born encephalitis virus, leaves space at the dimer interface for a large insertion without creating steric hindrance. We have tested this hypothesis by inserting a model humoral epitope from the circumsporozoite protein of Plasmodium falciparum consisting of triple NANP repeats. Recombinant virus (17D/8) expressing this insertion flanked by two glycine residues at each end, is specifically neutralized by a monoclonal antibody to the model epitope. Furthermore, mouse antibodies raised to the recombinant virus recognize the parasite protein in an ELISA assay. Serial passage analysis confirmed the genetic stability of the insertion made in the viral genome and the resulting 17D/8 virus is significantly more attenuated in mouse neurovirulence tests than the 17DD vaccine. The fg loop belongs to the dimerization domain of the E protein and lies at the interface between monomers. This domain undergoes a low pH transition, which is related to the fusion of the viral envelope to the endosome membrane. It is conceivable that a slower rate of fusion, resulting from the insertion close to the dimer interface, may delay the onset of virus production and thereby lead to a milder infection of the host. This would account for the more attenuated phenotype of the recombinant virus in the mouse model and lower extent of replication in cultured cells. The vectorial capacity of the yellow fever virus is being further explored for the expression and presentation of other epitopes, including those mediating T-cell responses. Copyright 2002 Academic Press.

The Grell-Freitas Convection Parameterization: Recent Developments and Applications Within the NASA GEOS Global Model

NASA Technical Reports Server (NTRS)

Freitas, Saulo R.; Grell, Georg; Molod, Andrea; Thompson, Matthew A.

2017-01-01

We implemented and began to evaluate an alternative convection parameterization for the NASA Goddard Earth Observing System (GEOS) global model. The parameterization is based on the mass flux approach with several closures, for equilibrium and non-equilibrium convection, and includes scale and aerosol awareness functionalities. Recently, the scheme has been extended to a tri-modal spectral size approach to simulate the transition from shallow, mid, and deep convection regimes. In addition, the inclusion of a new closure for non-equilibrium convection resulted in a substantial gain of realism in model simulation of the diurnal cycle of convection over the land. Here, we briefly introduce the recent developments, implementation, and preliminary results of this parameterization in the NASA GEOS modeling system.

Parameterized LMI Based Diagonal Dominance Compensator Study for Polynomial Linear Parameter Varying System

NASA Astrophysics Data System (ADS)

Han, Xiaobao; Li, Huacong; Jia, Qiusheng

2017-12-01

For dynamic decoupling of polynomial linear parameter varying(PLPV) system, a robust dominance pre-compensator design method is given. The parameterized precompensator design problem is converted into an optimal problem constrained with parameterized linear matrix inequalities(PLMI) by using the conception of parameterized Lyapunov function(PLF). To solve the PLMI constrained optimal problem, the precompensator design problem is reduced into a normal convex optimization problem with normal linear matrix inequalities (LMI) constraints on a new constructed convex polyhedron. Moreover, a parameter scheduling pre-compensator is achieved, which satisfies robust performance and decoupling performances. Finally, the feasibility and validity of the robust diagonal dominance pre-compensator design method are verified by the numerical simulation on a turbofan engine PLPV model.

Development of a Scanning Microscale Fast Neutron Irradiation Platform for Examining the Correlation Between Local Neutron Damage and Graphite Microstructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinhero, Patrick; Windes, William

2015-03-10

The fast particle radiation damage effect of graphite, a main material in current and future nuclear reactors, has significant influence on the utilization of this material in fission and fusion plants. Atoms on graphite crystals can be easily replaced or dislocated by fast protons and result in interstitials and vacancies. The currently accepted model indicates that after most of the interstitials recombine with vacancies, surviving interstitials form clusters and furthermore gather to create loops with each other between layers. Meanwhile, surviving vacancies and interstitials form dislocation loops on the layers. The growth of these inserted layers cause the dimensional increase,more » i.e. swelling, of graphite. Interstitial and vacancy dislocation loops have been reported and they can easily been observed by electron microscope. However, observation of the intermediate atom clusters becomes is paramount in helping prove this model. We utilize fast protons generated from the University of Missouri Research Reactor (MURR) cyclotron to irradiate highly- oriented pyrolytic graphite (HOPG) as target for this research. Post-irradiation examination (PIE) of dosed targets with high-resolution transmission electron microscopy (HRTEM) has permit observation and analysis of clusters and dislocation loops to support the proposed theory. Another part of the research is to validate M.I. Heggie’s Ruck and Tuck model, which introduced graphite layers may fold under fast particle irradiation. Again, we employed microscopy to image irradiated specimens to determine how the extent of Ruck and Tuck by calculating the number of folds as a function of dose. Our most significant accomplishment is the invention of a novel class of high-intensity pure beta-emitters for long-term lightweight batteries. We have filed four invention disclosure records based on the research conducted in this project. These batteries are lightweight because they consist of carbon and tritium and can be fabricated to conform to many geometric shapes. In addition, we have published eight peer-reviewed American Nuclear Society (ANS) transactions, and presented our findings at ANS National Meetings, and several universities.« less

Modeling particle nucleation and growth over northern California during the 2010 CARES campaign

NASA Astrophysics Data System (ADS)

Lupascu, A.; Easter, R.; Zaveri, R.; Shrivastava, M.; Pekour, M.; Tomlinson, J.; Yang, Q.; Matsui, H.; Hodzic, A.; Zhang, Q.; Fast, J. D.

2015-11-01

Accurate representation of the aerosol lifecycle requires adequate modeling of the particle number concentration and size distribution in addition to their mass, which is often the focus of aerosol modeling studies. This paper compares particle number concentrations and size distributions as predicted by three empirical nucleation parameterizations in the Weather Research and Forecast coupled with chemistry (WRF-Chem) regional model using 20 discrete size bins ranging from 1 nm to 10 μm. Two of the parameterizations are based on H2SO4, while one is based on both H2SO4 and organic vapors. Budget diagnostic terms for transport, dry deposition, emissions, condensational growth, nucleation, and coagulation of aerosol particles have been added to the model and are used to analyze the differences in how the new particle formation parameterizations influence the evolving aerosol size distribution. The simulations are evaluated using measurements collected at surface sites and from a research aircraft during the Carbonaceous Aerosol and Radiative Effects Study (CARES) conducted in the vicinity of Sacramento, California. While all three parameterizations captured the temporal variation of the size distribution during observed nucleation events as well as the spatial variability in aerosol number, all overestimated by up to a factor of 2.5 the total particle number concentration for particle diameters greater than 10 nm. Using the budget diagnostic terms, we demonstrate that the combined H2SO4 and low-volatility organic vapor parameterization leads to a different diurnal variability of new particle formation and growth to larger sizes compared to the parameterizations based on only H2SO4. At the CARES urban ground site, peak nucleation rates are predicted to occur around 12:00 Pacific (local) standard time (PST) for the H2SO4 parameterizations, whereas the highest rates were predicted at 08:00 and 16:00 PST when low-volatility organic gases are included in the parameterization. This can be explained by higher anthropogenic emissions of organic vapors at these times as well as lower boundary-layer heights that reduce vertical mixing. The higher nucleation rates in the H2SO4-organic parameterization at these times were largely offset by losses due to coagulation. Despite the different budget terms for ultrafine particles, the 10-40 nm diameter particle number concentrations from all three parameterizations increased from 10:00 to 14:00 PST and then decreased later in the afternoon, consistent with changes in the observed size and number distribution. We found that newly formed particles could explain up to 20-30 % of predicted cloud condensation nuclei at 0.5 % supersaturation, depending on location and the specific nucleation parameterization. A sensitivity simulation using 12 discrete size bins ranging from 1 nm to 10 μm diameter gave a reasonable estimate of particle number and size distribution compared to the 20 size bin simulation, while reducing the associated computational cost by ~ 36 %.

Application of new parameterizations of gas transfer velocity and their impact on regional and global marine CO 2 budgets

NASA Astrophysics Data System (ADS)

Fangohr, Susanne; Woolf, David K.

2007-06-01

One of the dominant sources of uncertainty in the calculation of air-sea flux of carbon dioxide on a global scale originates from the various parameterizations of the gas transfer velocity, k, that are in use. Whilst it is undisputed that most of these parameterizations have shortcomings and neglect processes which influence air-sea gas exchange and do not scale with wind speed alone, there is no general agreement about their relative accuracy. The most widely used parameterizations are based on non-linear functions of wind speed and, to a lesser extent, on sea surface temperature and salinity. Processes such as surface film damping and whitecapping are known to have an effect on air-sea exchange. More recently published parameterizations use friction velocity, sea surface roughness, and significant wave height. These new parameters can account to some extent for processes such as film damping and whitecapping and could potentially explain the spread of wind-speed based transfer velocities published in the literature. We combine some of the principles of two recently published k parameterizations [Glover, D.M., Frew, N.M., McCue, S.J. and Bock, E.J., 2002. A multiyear time series of global gas transfer velocity from the TOPEX dual frequency, normalized radar backscatter algorithm. In: Donelan, M.A., Drennan, W.M., Saltzman, E.S., and Wanninkhof, R. (Eds.), Gas Transfer at Water Surfaces, Geophys. Monograph 127. AGU,Washington, DC, 325-331; Woolf, D.K., 2005. Parameterization of gas transfer velocities and sea-state dependent wave breaking. Tellus, 57B: 87-94] to calculate k as the sum of a linear function of total mean square slope of the sea surface and a wave breaking parameter. This separates contributions from direct and bubble-mediated gas transfer as suggested by Woolf [Woolf, D.K., 2005. Parameterization of gas transfer velocities and sea-state dependent wave breaking. Tellus, 57B: 87-94] and allows us to quantify contributions from these two processes independently. We then apply our parameterization to a monthly TOPEX altimeter gridded 1.5° × 1.5° data set and compare our results to transfer velocities calculated using the popular wind-based k parameterizations by Wanninkhof [Wanninkhof, R., 1992. Relationship between wind speed and gas exchange over the ocean. J. Geophys. Res., 97: 7373-7382.] and Wanninkhof and McGillis [Wanninkhof, R. and McGillis, W., 1999. A cubic relationship between air-sea CO2 exchange and wind speed. Geophys. Res. Lett., 26(13): 1889-1892]. We show that despite good agreement of the globally averaged transfer velocities, global and regional fluxes differ by up to 100%. These discrepancies are a result of different spatio-temporal distributions of the processes involved in the parameterizations of k, indicating the importance of wave field parameters and a need for further validation.

Mixing parametrizations for ocean climate modelling

NASA Astrophysics Data System (ADS)

Gusev, Anatoly; Moshonkin, Sergey; Diansky, Nikolay; Zalesny, Vladimir

2016-04-01

The algorithm is presented of splitting the total evolutionary equations for the turbulence kinetic energy (TKE) and turbulence dissipation frequency (TDF), which is used to parameterize the viscosity and diffusion coefficients in ocean circulation models. The turbulence model equations are split into the stages of transport-diffusion and generation-dissipation. For the generation-dissipation stage, the following schemes are implemented: the explicit-implicit numerical scheme, analytical solution and the asymptotic behavior of the analytical solutions. The experiments were performed with different mixing parameterizations for the modelling of Arctic and the Atlantic climate decadal variability with the eddy-permitting circulation model INMOM (Institute of Numerical Mathematics Ocean Model) using vertical grid refinement in the zone of fully developed turbulence. The proposed model with the split equations for turbulence characteristics is similar to the contemporary differential turbulence models, concerning the physical formulations. At the same time, its algorithm has high enough computational efficiency. Parameterizations with using the split turbulence model make it possible to obtain more adequate structure of temperature and salinity at decadal timescales, compared to the simpler Pacanowski-Philander (PP) turbulence parameterization. Parameterizations with using analytical solution or numerical scheme at the generation-dissipation step of the turbulence model leads to better representation of ocean climate than the faster parameterization using the asymptotic behavior of the analytical solution. At the same time, the computational efficiency left almost unchanged relative to the simple PP parameterization. Usage of PP parametrization in the circulation model leads to realistic simulation of density and circulation with violation of T,S-relationships. This error is majorly avoided with using the proposed parameterizations containing the split turbulence model. The high sensitivity of the eddy-permitting circulation model to the definition of mixing is revealed, which is associated with significant changes of density fields in the upper baroclinic ocean layer over the total considered area. For instance, usage of the turbulence parameterization instead of PP algorithm leads to increasing circulation velocity in the Gulf Stream and North Atlantic Current, as well as the subpolar cyclonic gyre in the North Atlantic and Beaufort Gyre in the Arctic basin are reproduced more realistically. Consideration of the Prandtl number as a function of the Richardson number significantly increases the modelling quality. The research was supported by the Russian Foundation for Basic Research (grant № 16-05-00534) and the Council on the Russian Federation President Grants (grant № MK-3241.2015.5)

Subgrid-scale parameterization and low-frequency variability: a response theory approach

NASA Astrophysics Data System (ADS)

Demaeyer, Jonathan; Vannitsem, Stéphane

2016-04-01

Weather and climate models are limited in the possible range of resolved spatial and temporal scales. However, due to the huge space- and time-scale ranges involved in the Earth System dynamics, the effects of many sub-grid processes should be parameterized. These parameterizations have an impact on the forecasts or projections. It could also affect the low-frequency variability present in the system (such as the one associated to ENSO or NAO). An important question is therefore to know what is the impact of stochastic parameterizations on the Low-Frequency Variability generated by the system and its model representation. In this context, we consider a stochastic subgrid-scale parameterization based on the Ruelle's response theory and proposed in Wouters and Lucarini (2012). We test this approach in the context of a low-order coupled ocean-atmosphere model, detailed in Vannitsem et al. (2015), for which a part of the atmospheric modes is considered as unresolved. A natural separation of the phase-space into a slow invariant set and its fast complement allows for an analytical derivation of the different terms involved in the parameterization, namely the average, the fluctuation and the long memory terms. Its application to the low-order system reveals that a considerable correction of the low-frequency variability along the invariant subset can be obtained. This new approach of scale separation opens new avenues of subgrid-scale parameterizations in multiscale systems used for climate forecasts. References: Vannitsem S, Demaeyer J, De Cruz L, Ghil M. 2015. Low-frequency variability and heat transport in a low-order nonlinear coupled ocean-atmosphere model. Physica D: Nonlinear Phenomena 309: 71-85. Wouters J, Lucarini V. 2012. Disentangling multi-level systems: averaging, correlations and memory. Journal of Statistical Mechanics: Theory and Experiment 2012(03): P03 003.

Engelmann Spruce Site Index Models: A Comparison of Model Functions and Parameterizations

PubMed Central

Nigh, Gordon

2015-01-01

Engelmann spruce (Picea engelmannii Parry ex Engelm.) is a high-elevation species found in western Canada and western USA. As this species becomes increasingly targeted for harvesting, better height growth information is required for good management of this species. This project was initiated to fill this need. The objective of the project was threefold: develop a site index model for Engelmann spruce; compare the fits and modelling and application issues between three model formulations and four parameterizations; and more closely examine the grounded-Generalized Algebraic Difference Approach (g-GADA) model parameterization. The model fitting data consisted of 84 stem analyzed Engelmann spruce site trees sampled across the Engelmann Spruce – Subalpine Fir biogeoclimatic zone. The fitted models were based on the Chapman-Richards function, a modified Hossfeld IV function, and the Schumacher function. The model parameterizations that were tested are indicator variables, mixed-effects, GADA, and g-GADA. Model evaluation was based on the finite-sample corrected version of Akaike’s Information Criteria and the estimated variance. Model parameterization had more of an influence on the fit than did model formulation, with the indicator variable method providing the best fit, followed by the mixed-effects modelling (9% increase in the variance for the Chapman-Richards and Schumacher formulations over the indicator variable parameterization), g-GADA (optimal approach) (335% increase in the variance), and the GADA/g-GADA (with the GADA parameterization) (346% increase in the variance). Factors related to the application of the model must be considered when selecting the model for use as the best fitting methods have the most barriers in their application in terms of data and software requirements. PMID:25853472

Constraints to Dark Energy Using PADE Parameterizations

NASA Astrophysics Data System (ADS)

Rezaei, M.; Malekjani, M.; Basilakos, S.; Mehrabi, A.; Mota, D. F.

2017-07-01

We put constraints on dark energy (DE) properties using PADE parameterization, and compare it to the same constraints using Chevalier-Polarski-Linder (CPL) and ΛCDM, at both the background and the perturbation levels. The DE equation of the state parameter of the models is derived following the mathematical treatment of PADE expansion. Unlike CPL parameterization, PADE approximation provides different forms of the equation of state parameter that avoid the divergence in the far future. Initially we perform a likelihood analysis in order to put constraints on the model parameters using solely background expansion data, and we find that all parameterizations are consistent with each other. Then, combining the expansion and the growth rate data, we test the viability of PADE parameterizations and compare them with CPL and ΛCDM models, respectively. Specifically, we find that the growth rate of the current PADE parameterizations is lower than ΛCDM model at low redshifts, while the differences among the models are negligible at high redshifts. In this context, we provide for the first time a growth index of linear matter perturbations in PADE cosmologies. Considering that DE is homogeneous, we recover the well-known asymptotic value of the growth index (namely {γ }∞ =\\tfrac{3({w}∞ -1)}{6{w}∞ -5}), while in the case of clustered DE, we obtain {γ }∞ ≃ \\tfrac{3{w}∞ (3{w}∞ -5)}{(6{w}∞ -5)(3{w}∞ -1)}. Finally, we generalize the growth index analysis in the case where γ is allowed to vary with redshift, and we find that the form of γ (z) in PADE parameterization extends that of the CPL and ΛCDM cosmologies, respectively.

Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme.

PubMed

Jirousková, Zuzana; Vareková, Radka Svobodová; Vanek, Jakub; Koca, Jaroslav

2009-05-01

The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, this approach can be used for calculation of average electronegativity and charge distribution in a molecule. The aim of this work is to perform the EEM parameterization using the Merz-Kollman-Singh (MK) charge distribution scheme obtained from B3LYP/6-31G* and HF/6-31G* calculations. To achieve this goal, we selected a set of 380 organic molecules from the Cambridge Structural Database (CSD) and used the methodology, which was recently successfully applied to EEM parameterization to calculate the HF/STO-3G Mulliken charges on large sets of molecules. In the case of B3LYP/6-31G* MK charges, we have improved the EEM parameters for already parameterized elements, specifically C, H, N, O, and F. Moreover, EEM parameters for S, Br, Cl, and Zn, which have not as yet been parameterized for this level of theory and basis set, we also developed. In the case of HF/6-31G* MK charges, we have developed the EEM parameters for C, H, N, O, S, Br, Cl, F, and Zn that have not been parameterized for this level of theory and basis set so far. The obtained EEM parameters were verified by a previously developed validation procedure and used for the charge calculation on a different set of 116 organic molecules from the CSD. The calculated EEM charges are in a very good agreement with the quantum mechanically obtained ab initio charges. 2008 Wiley Periodicals, Inc.

Comments on “A Unified Representation of Deep Moist Convection in Numerical Modeling of the Atmosphere. Part I”

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Guang; Fan, Jiwen; Xu, Kuan-Man

2015-06-01

Arakawa and Wu (2013, hereafter referred to as AW13) recently developed a formal approach to a unified parameterization of atmospheric convection for high-resolution numerical models. The work is based on ideas formulated by Arakawa et al. (2011). It lays the foundation for a new parameterization pathway in the era of high-resolution numerical modeling of the atmosphere. The key parameter in this approach is convective cloud fraction. In conventional parameterization, it is assumed that <<1. This assumption is no longer valid when horizontal resolution of numerical models approaches a few to a few tens kilometers, since in such situations convective cloudmore » fraction can be comparable to unity. Therefore, they argue that the conventional approach to parameterizing convective transport must include a factor 1 - in order to unify the parameterization for the full range of model resolutions so that it is scale-aware and valid for large convective cloud fractions. While AW13’s approach provides important guidance for future convective parameterization development, in this note we intend to show that the conventional approach already has this scale awareness factor 1 - built in, although not recognized for the last forty years. Therefore, it should work well even in situations of large convective cloud fractions in high-resolution numerical models.« less

Cloud Simulations in Response to Turbulence Parameterizations in the GISS Model E GCM

NASA Technical Reports Server (NTRS)

Yao, Mao-Sung; Cheng, Ye

2013-01-01

The response of cloud simulations to turbulence parameterizations is studied systematically using the GISS general circulation model (GCM) E2 employed in the Intergovernmental Panel on Climate Change's (IPCC) Fifth Assessment Report (AR5).Without the turbulence parameterization, the relative humidity (RH) and the low cloud cover peak unrealistically close to the surface; with the dry convection or with only the local turbulence parameterization, these two quantities improve their vertical structures, but the vertical transport of water vapor is still weak in the planetary boundary layers (PBLs); with both local and nonlocal turbulence parameterizations, the RH and low cloud cover have better vertical structures in all latitudes due to more significant vertical transport of water vapor in the PBL. The study also compares the cloud and radiation climatologies obtained from an experiment using a newer version of turbulence parameterization being developed at GISS with those obtained from the AR5 version. This newer scheme differs from the AR5 version in computing nonlocal transports, turbulent length scale, and PBL height and shows significant improvements in cloud and radiation simulations, especially over the subtropical eastern oceans and the southern oceans. The diagnosed PBL heights appear to correlate well with the low cloud distribution over oceans. This suggests that a cloud-producing scheme needs to be constructed in a framework that also takes the turbulence into consideration.

Modelling heterogeneous ice nucleation on mineral dust and soot with parameterizations based on laboratory experiments

NASA Astrophysics Data System (ADS)

Hoose, C.; Hande, L. B.; Mohler, O.; Niemand, M.; Paukert, M.; Reichardt, I.; Ullrich, R.

2016-12-01

Between 0 and -37°C, ice formation in clouds is triggered by aerosol particles acting as heterogeneous ice nuclei. At lower temperatures, heterogeneous ice nucleation on aerosols can occur at lower supersaturations than homogeneous freezing of solutes. In laboratory experiments, the ability of different aerosol species (e.g. desert dusts, soot, biological particles) has been studied in detail and quantified via various theoretical or empirical parameterization approaches. For experiments in the AIDA cloud chamber, we have quantified the ice nucleation efficiency via a temperature- and supersaturation dependent ice nucleation active site density. Here we present a new empirical parameterization scheme for immersion and deposition ice nucleation on desert dust and soot based on these experimental data. The application of this parameterization to the simulation of cirrus clouds, deep convective clouds and orographic clouds will be shown, including the extension of the scheme to the treatment of freezing of rain drops. The results are compared to other heterogeneous ice nucleation schemes. Furthermore, an aerosol-dependent parameterization of contact ice nucleation is presented.

Evaluation of Aerosol-cloud Interaction in the GISS Model E Using ARM Observations

NASA Technical Reports Server (NTRS)

DeBoer, G.; Bauer, S. E.; Toto, T.; Menon, Surabi; Vogelmann, A. M.

2013-01-01

Observations from the US Department of Energy's Atmospheric Radiation Measurement (ARM) program are used to evaluate the ability of the NASA GISS ModelE global climate model in reproducing observed interactions between aerosols and clouds. Included in the evaluation are comparisons of basic meteorology and aerosol properties, droplet activation, effective radius parameterizations, and surface-based evaluations of aerosol-cloud interactions (ACI). Differences between the simulated and observed ACI are generally large, but these differences may result partially from vertical distribution of aerosol in the model, rather than the representation of physical processes governing the interactions between aerosols and clouds. Compared to the current observations, the ModelE often features elevated droplet concentrations for a given aerosol concentration, indicating that the activation parameterizations used may be too aggressive. Additionally, parameterizations for effective radius commonly used in models were tested using ARM observations, and there was no clear superior parameterization for the cases reviewed here. This lack of consensus is demonstrated to result in potentially large, statistically significant differences to surface radiative budgets, should one parameterization be chosen over another.

Multi-Scale Modeling and the Eddy-Diffusivity/Mass-Flux (EDMF) Parameterization

NASA Astrophysics Data System (ADS)

Teixeira, J.

2015-12-01

Turbulence and convection play a fundamental role in many key weather and climate science topics. Unfortunately, current atmospheric models cannot explicitly resolve most turbulent and convective flow. Because of this fact, turbulence and convection in the atmosphere has to be parameterized - i.e. equations describing the dynamical evolution of the statistical properties of turbulence and convection motions have to be devised. Recently a variety of different models have been developed that attempt at simulating the atmosphere using variable resolution. A key problem however is that parameterizations are in general not explicitly aware of the resolution - the scale awareness problem. In this context, we will present and discuss a specific approach, the Eddy-Diffusivity/Mass-Flux (EDMF) parameterization, that not only is in itself a multi-scale parameterization but it is also particularly well suited to deal with the scale-awareness problems that plague current variable-resolution models. It does so by representing small-scale turbulence using a classic Eddy-Diffusivity (ED) method, and the larger-scale (boundary layer and tropospheric-scale) eddies as a variety of plumes using the Mass-Flux (MF) concept.

A Testbed for Model Development

NASA Astrophysics Data System (ADS)

Berry, J. A.; Van der Tol, C.; Kornfeld, A.

2014-12-01

Carbon cycle and land-surface models used in global simulations need to be computationally efficient and have a high standard of software engineering. These models also make a number of scaling assumptions to simplify the representation of complex biochemical and structural properties of ecosystems. This makes it difficult to use these models to test new ideas for parameterizations or to evaluate scaling assumptions. The stripped down nature of these models also makes it difficult to "connect" with current disciplinary research which tends to be focused on much more nuanced topics than can be included in the models. In our opinion/experience this indicates the need for another type of model that can more faithfully represent the complexity ecosystems and which has the flexibility to change or interchange parameterizations and to run optimization codes for calibration. We have used the SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes) model in this way to develop, calibrate, and test parameterizations for solar induced chlorophyll fluorescence, OCS exchange and stomatal parameterizations at the canopy scale. Examples of the data sets and procedures used to develop and test new parameterizations are presented.

Approaches for Subgrid Parameterization: Does Scaling Help?

NASA Astrophysics Data System (ADS)

Yano, Jun-Ichi

2016-04-01

Arguably the scaling behavior is a well-established fact in many geophysical systems. There are already many theoretical studies elucidating this issue. However, the scaling law is slow to be introduced in "operational" geophysical modelling, notably for weather forecast as well as climate projection models. The main purpose of this presentation is to ask why, and try to answer this question. As a reference point, the presentation reviews the three major approaches for traditional subgrid parameterization: moment, PDF (probability density function), and mode decomposition. The moment expansion is a standard method for describing the subgrid-scale turbulent flows both in the atmosphere and the oceans. The PDF approach is intuitively appealing as it directly deals with a distribution of variables in subgrid scale in a more direct manner. The third category, originally proposed by Aubry et al (1988) in context of the wall boundary-layer turbulence, is specifically designed to represent coherencies in compact manner by a low--dimensional dynamical system. Their original proposal adopts the proper orthogonal decomposition (POD, or empirical orthogonal functions, EOF) as their mode-decomposition basis. However, the methodology can easily be generalized into any decomposition basis. The mass-flux formulation that is currently adopted in majority of atmospheric models for parameterizing convection can also be considered a special case of the mode decomposition, adopting the segmentally-constant modes for the expansion basis. The mode decomposition can, furthermore, be re-interpreted as a type of Galarkin approach for numerically modelling the subgrid-scale processes. Simple extrapolation of this re-interpretation further suggests us that the subgrid parameterization problem may be re-interpreted as a type of mesh-refinement problem in numerical modelling. We furthermore see a link between the subgrid parameterization and downscaling problems along this line. The mode decomposition approach would also be the best framework for linking between the traditional parameterizations and the scaling perspectives. However, by seeing the link more clearly, we also see strength and weakness of introducing the scaling perspectives into parameterizations. Any diagnosis under a mode decomposition would immediately reveal a power-law nature of the spectrum. However, exploiting this knowledge in operational parameterization would be a different story. It is symbolic to realize that POD studies have been focusing on representing the largest-scale coherency within a grid box under a high truncation. This problem is already hard enough. Looking at differently, the scaling law is a very concise manner for characterizing many subgrid-scale variabilities in systems. We may even argue that the scaling law can provide almost complete subgrid-scale information in order to construct a parameterization, but with a major missing link: its amplitude must be specified by an additional condition. The condition called "closure" in the parameterization problem, and known to be a tough problem. We should also realize that the studies of the scaling behavior tend to be statistical in the sense that it hardly provides complete information for constructing a parameterization: can we specify the coefficients of all the decomposition modes by a scaling law perfectly when the first few leading modes are specified? Arguably, the renormalization group (RNG) is a very powerful tool for reducing a system with a scaling behavior into a low dimension, say, under an appropriate mode decomposition procedure. However, RNG is analytical tool: it is extremely hard to apply it to real complex geophysical systems. It appears that it is still a long way to go for us before we can begin to exploit the scaling law in order to construct operational subgrid parameterizations in effective manner.

Preparation of oligoribonucleotides containing 4-thiouridine using Fpmp chemistry. Photo-crosslinking to RNA binding proteins using 350 nm irradiation.

PubMed Central

McGregor, A; Rao, M V; Duckworth, G; Stockley, P G; Connolly, B A

1996-01-01

The preparation of a 4-thiouridine phosphoramidite suitable for RNA synthesis and its subsequent incorporation into oligoribonucleotides is described. The thiol group is protected with a 2-cyanoethyl group and the 2'-OH with a 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl function. Thiouridine-containing oligoribonucleotides were used as 350 nm UV crosslinking probes for the photoaffinity labelling of RNA binding proteins. Specific crosslinking was demonstrated between the Rev protein of HIV-1 (as a glutathione S-transferase fusion protein) and its RNA target, the Rev-responsive element. It was not possible to generate crosslinks between the RNA bacteriophage MS2 coat protein and the initiator stem-loop of the replicase gene, to which it binds. These results are consistent with the structural data available on both systems. PMID:8774897

Translational control of ribosomal protein S15.

PubMed

Portier, C; Philippe, C; Dondon, L; Grunberg-Manago, M; Ebel, J P; Ehresmann, B; Ehresmann, C

1990-08-27

The expression of ribosomal protein S15 is shown to be translationally and negatively autocontrolled using a fusion within a reporter gene. Isolation and characterization of several deregulated mutants indicate that the regulatory site (the translational operator site) overlaps the ribosome loading site of the S15 messenger. In this region, three domains, each exhibiting a stem-loop structure, were determined using chemical and enzymatic probes. The most downstream hairpin carries the Shine-Dalgarno sequence and the initiation codon. Genetic and structural data derived from mutants constructed by site-directed mutagenesis show that the operator is a dynamic structure, two domains of which can form a pseudoknot. Binding of S15 to these two domains suggests that the pseudoknot could be stabilized by S15. A model is presented in which two alternative structures would explain the molecular basis of the S15 autocontrol.

Data error and highly parameterized groundwater models

USGS Publications Warehouse

Hill, M.C.

2008-01-01

Strengths and weaknesses of highly parameterized models, in which the number of parameters exceeds the number of observations, are demonstrated using a synthetic test case. Results suggest that the approach can yield close matches to observations but also serious errors in system representation. It is proposed that avoiding the difficulties of highly parameterized models requires close evaluation of: (1) model fit, (2) performance of the regression, and (3) estimated parameter distributions. Comparisons to hydrogeologic information are expected to be critical to obtaining credible models. Copyright ?? 2008 IAHS Press.

A scheme for parameterizing ice cloud water content in general circulation models

NASA Technical Reports Server (NTRS)

Heymsfield, Andrew J.; Donner, Leo J.

1989-01-01

A method for specifying ice water content in GCMs is developed, based on theory and in-cloud measurements. A theoretical development of the conceptual precipitation model is given and the aircraft flights used to characterize the ice mass distribution in deep ice clouds is discussed. Ice water content values derived from the theoretical parameterization are compared with the measured values. The results demonstrate that a simple parameterization for atmospheric ice content can account for ice contents observed in several synoptic contexts.

Automated trajectory planning for multiple-flyby interplanetary missions

NASA Astrophysics Data System (ADS)

Englander, Jacob

Many space mission planning problems may be formulated as hybrid optimal control problems (HOCP), i.e. problems that include both real-valued variables and categorical variables. In interplanetary trajectory design problems the categorical variables will typically specify the sequence of planets at which to perform flybys, and the real-valued variables will represent the launch date, ight times between planets, magnitudes and directions of thrust, flyby altitudes, etc. The contribution of this work is a framework for the autonomous optimization of multiple-flyby interplanetary trajectories. The trajectory design problem is converted into a HOCP with two nested loops: an "outer-loop" that finds the sequence of flybys and an "inner-loop" that optimizes the trajectory for each candidate yby sequence. The problem of choosing a sequence of flybys is posed as an integer programming problem and solved using a genetic algorithm (GA). This is an especially difficult problem to solve because GAs normally operate on a fixed-length set of decision variables. Since in interplanetary trajectory design the number of flyby maneuvers is not known a priori, it was necessary to devise a method of parameterizing the problem such that the GA can evolve a variable-length sequence of flybys. A novel "null gene" transcription was developed to meet this need. Then, for each candidate sequence of flybys, a trajectory must be found that visits each of the flyby targets and arrives at the final destination while optimizing some cost metric, such as minimizing ▵v or maximizing the final mass of the spacecraft. Three different classes of trajectory are described in this work, each of which requireda different physical model and optimization method. The choice of a trajectory model and optimization method is especially challenging because of the nature of the hybrid optimal control problem. Because the trajectory optimization problem is generated in real time by the outer-loop, the inner-loop optimization algorithm cannot require any a priori information and must always return a solution. In addition, the upper and lower bounds on each decision variable cannot be chosen a priori by the user because the user has no way to know what problem will be solved. Instead a method of choosing upper and lower bounds via a set of simple rules was developed and used for all three types of trajectory optimization problem. Many optimization algorithms were tested and discarded until suitable algorithms were found for each type of trajectory. The first class of trajectories use chemical propulsion and may only apply a ▵v at the periapse of each flyby. These Multiple Gravity Assist (MGA) trajectories are optimized using a cooperative algorithm of Differential Evolution (DE) and Particle Swarm Optimization (PSO). The second class of trajectories, known as Multiple Gravity Assist with one Deep Space Maneuver (MGA-DSM), also use chemical propulsion but instead of maneuvering at the periapse of each flyby as in the MGA case a maneuver is applied at a free point along each planet-to-planet arc, i.e. there is one maneuver for each pair of flybys. MGA-DSM trajectories are parameterized by more variables than MGA trajectories, and so the cooperative algorithm of DE and PSO that was used to optimize MGA trajectories was found to be less effective when applied to MGA-DSM. Instead, either PSO or DE alone were found to be more effective. The third class of trajectories addressed in this work are those using continuousthrust propulsion. Continuous-thrust trajectory optimization problems are more challenging than impulsive-thrust problems because the control variables are a continuous time series rather than a small set of parameters and because the spacecraft does not follow a conic section trajectory, leading to a large number of nonlinear constraints that must be satisfied to ensure that the spacecraft obeys the equations of motion. Many models and optimization algorithms were applied including direct transcription with nonlinear programming (DTNLP), the inverse-polynomial shapebased method, and feasible region analysis. However the only physical model and optimization method that proved reliable enough were the Sims-Flanagan transcription coupled with a nonlinear programming solver and the monotonic basin hopping (MBH) global search heuristic. The methods developed here are demonstrated to optimize a set of example trajectories, including a recreation of the Cassini mission, a Galileo-like mission, and conceptual continuous-thrust missions to Jupiter, Mercury, and Uranus.

Dual-Spectroscopy Platform for the Surveillance of Mars Mineralogy Using a Decisions Fusion Architecture on Simultaneous LIBS-Raman Data.

PubMed

Moros, Javier; ElFaham, Mohamed Mostafa; Laserna, J Javier

2018-02-06

A single platform, integrated by a laser-induced breakdown spectroscopy detector and a Raman spectroscopy sensor, has been designed to remotely (5 m) and simultaneously register the elemental and molecular signatures of rocks under Martian surface conditions. From this information, new data fusion architecture at decisions level is proposed for the correct categorization of the rocks. The approach is based on a decision-making process from the sequential checking of the spectral features representing the cationic and anionic counterparts of the specimen. The scrutiny of the LIBS response by using a moving-window algorithm informs on the diversity of the elemental constituents. The output rate of emission lines allows projecting in a loop the elements as the cationic counterpart of the rock. In parallel, the Raman response of the unknown is compared with all the molecular counterparts of the hypothesized cation that are stored in a spectral library. The largest similarity rate unveils the final identity of the unknown. The identification capabilities of the architecture have been underscored through blind tests of 10 natural rocks with different origins. The great majority of forecasts have matched with the real identities of the inspected targets. The strength of this platform to simultaneously acquire the multielemental and the molecular information from a specimen by using the same laser events greatly enhances the "on-surface" missions for the surveillance of mineralogy.

Topology mapping to characterize cyanobacterial bicarbonate transporters: BicA (SulP/SLC26 family) and SbtA.

PubMed

Price, G Dean; Howitt, Susan M

2014-09-01

This mini-review addresses advances in understanding the transmembrane topologies of two unrelated, single-subunit bicarbonate transporters from cyanobacteria, namely BicA and SbtA. BicA is a Na(+)-dependent bicarbonate transporter that belongs to the SulP/SLC26 family that is widespread in both eukaryotes and prokaryotes. Topology mapping of BicA via the phoA/lacZ fusion reporter method identified 12 transmembrane helices with an unresolved hydrophobic region just beyond helix 8. Re-interpreting this data in the light of a recent topology study on rat prestin leads to a consensus topology of 14 transmembrane domains with a 7+7 inverted repeat structure. SbtA is also a Na(+)-dependent bicarbonate transporter, but of considerably higher affinity (Km 2-5 μM versus >100 μM for BicA). Whilst SbtA is widespread in cyanobacteria and a few bacteria, it appears to be absent from eukaryotes. Topology mapping of SbtA via the phoA/lacZ fusion reporter method identified 10 transmembrane helices. The topology consists of a 5+5 inverted repeat, with the two repeats separated by a large intracellular loop. The unusual location of the N and C-termini outside the cell raises the possibility that SbtA forms a novel fold, not so far identified by structural and topological studies on transport proteins.

Fusion of Haptic and Gesture Sensors for Rehabilitation of Bimanual Coordination and Dexterous Manipulation.

PubMed

Yu, Ningbo; Xu, Chang; Li, Huanshuai; Wang, Kui; Wang, Liancheng; Liu, Jingtai

2016-03-18

Disabilities after neural injury, such as stroke, bring tremendous burden to patients, families and society. Besides the conventional constrained-induced training with a paretic arm, bilateral rehabilitation training involves both the ipsilateral and contralateral sides of the neural injury, fitting well with the fact that both arms are needed in common activities of daily living (ADLs), and can promote good functional recovery. In this work, the fusion of a gesture sensor and a haptic sensor with force feedback capabilities has enabled a bilateral rehabilitation training therapy. The Leap Motion gesture sensor detects the motion of the healthy hand, and the omega.7 device can detect and assist the paretic hand, according to the designed cooperative task paradigm, as much as needed, with active force feedback to accomplish the manipulation task. A virtual scenario has been built up, and the motion and force data facilitate instantaneous visual and audio feedback, as well as further analysis of the functional capabilities of the patient. This task-oriented bimanual training paradigm recruits the sensory, motor and cognitive aspects of the patient into one loop, encourages the active involvement of the patients into rehabilitation training, strengthens the cooperation of both the healthy and impaired hands, challenges the dexterous manipulation capability of the paretic hand, suits easy of use at home or centralized institutions and, thus, promises effective potentials for rehabilitation training.

Fusion of Haptic and Gesture Sensors for Rehabilitation of Bimanual Coordination and Dexterous Manipulation

PubMed Central

Yu, Ningbo; Xu, Chang; Li, Huanshuai; Wang, Kui; Wang, Liancheng; Liu, Jingtai

2016-01-01

Disabilities after neural injury, such as stroke, bring tremendous burden to patients, families and society. Besides the conventional constrained-induced training with a paretic arm, bilateral rehabilitation training involves both the ipsilateral and contralateral sides of the neural injury, fitting well with the fact that both arms are needed in common activities of daily living (ADLs), and can promote good functional recovery. In this work, the fusion of a gesture sensor and a haptic sensor with force feedback capabilities has enabled a bilateral rehabilitation training therapy. The Leap Motion gesture sensor detects the motion of the healthy hand, and the omega.7 device can detect and assist the paretic hand, according to the designed cooperative task paradigm, as much as needed, with active force feedback to accomplish the manipulation task. A virtual scenario has been built up, and the motion and force data facilitate instantaneous visual and audio feedback, as well as further analysis of the functional capabilities of the patient. This task-oriented bimanual training paradigm recruits the sensory, motor and cognitive aspects of the patient into one loop, encourages the active involvement of the patients into rehabilitation training, strengthens the cooperation of both the healthy and impaired hands, challenges the dexterous manipulation capability of the paretic hand, suits easy of use at home or centralized institutions and, thus, promises effective potentials for rehabilitation training. PMID:26999149

Elastic full-waveform inversion and parameterization analysis applied to walk-away vertical seismic profile data for unconventional (heavy oil) reservoir characterization

NASA Astrophysics Data System (ADS)

Pan, Wenyong; Innanen, Kristopher A.; Geng, Yu

2018-03-01

Seismic full-waveform inversion (FWI) methods hold strong potential to recover multiple subsurface elastic properties for hydrocarbon reservoir characterization. Simultaneously updating multiple physical parameters introduces the problem of interparameter tradeoff, arising from the covariance between different physical parameters, which increases nonlinearity and uncertainty of multiparameter FWI. The coupling effects of different physical parameters are significantly influenced by model parameterization and acquisition arrangement. An appropriate choice of model parameterization is critical to successful field data applications of multiparameter FWI. The objective of this paper is to examine the performance of various model parameterizations in isotropic-elastic FWI with walk-away vertical seismic profile (W-VSP) dataset for unconventional heavy oil reservoir characterization. Six model parameterizations are considered: velocity-density (α, β and ρ΄), modulus-density (κ, μ and ρ), Lamé-density (λ, μ΄ and ρ‴), impedance-density (IP, IS and ρ″), velocity-impedance-I (α΄, β΄ and I_P^'), and velocity-impedance-II (α″, β″ and I_S^'). We begin analyzing the interparameter tradeoff by making use of scattering radiation patterns, which is a common strategy for qualitative parameter resolution analysis. In this paper, we discuss the advantages and limitations of the scattering radiation patterns and recommend that interparameter tradeoffs be evaluated using interparameter contamination kernels, which provide quantitative, second-order measurements of the interparameter contaminations and can be constructed efficiently with an adjoint-state approach. Synthetic W-VSP isotropic-elastic FWI experiments in the time domain verify our conclusions about interparameter tradeoffs for various model parameterizations. Density profiles are most strongly influenced by the interparameter contaminations; depending on model parameterization, the inverted density profile can be over-estimated, under-estimated or spatially distorted. Among the six cases, only the velocity-density parameterization provides stable and informative density features not included in the starting model. Field data applications of multicomponent W-VSP isotropic-elastic FWI in the time domain were also carried out. The heavy oil reservoir target zone, characterized by low α-to-β ratios and low Poisson's ratios, can be identified clearly with the inverted isotropic-elastic parameters.

Elastic full-waveform inversion and parameterization analysis applied to walk-away vertical seismic profile data for unconventional (heavy oil) reservoir characterization

DOE PAGES

Pan, Wenyong; Innanen, Kristopher A.; Geng, Yu

2018-03-06

We report seismic full-waveform inversion (FWI) methods hold strong potential to recover multiple subsurface elastic properties for hydrocarbon reservoir characterization. Simultaneously updating multiple physical parameters introduces the problem of interparameter tradeoff, arising from the covariance between different physical parameters, which increases nonlinearity and uncertainty of multiparameter FWI. The coupling effects of different physical parameters are significantly influenced by model parameterization and acquisition arrangement. An appropriate choice of model parameterization is critical to successful field data applications of multiparameter FWI. The objective of this paper is to examine the performance of various model parameterizations in isotropic-elastic FWI with walk-away vertical seismicmore » profile (W-VSP) dataset for unconventional heavy oil reservoir characterization. Six model parameterizations are considered: velocity-density (α, β and ρ'), modulus-density (κ, μ and ρ), Lamé-density (λ, μ' and ρ'''), impedance-density (IP, IS and ρ''), velocity-impedance-I (α', β' and I' P), and velocity-impedance-II (α'', β'' and I'S). We begin analyzing the interparameter tradeoff by making use of scattering radiation patterns, which is a common strategy for qualitative parameter resolution analysis. In this paper, we discuss the advantages and limitations of the scattering radiation patterns and recommend that interparameter tradeoffs be evaluated using interparameter contamination kernels, which provide quantitative, second-order measurements of the interparameter contaminations and can be constructed efficiently with an adjoint-state approach. Synthetic W-VSP isotropic-elastic FWI experiments in the time domain verify our conclusions about interparameter tradeoffs for various model parameterizations. Density profiles are most strongly influenced by the interparameter contaminations; depending on model parameterization, the inverted density profile can be over-estimated, under-estimated or spatially distorted. Among the six cases, only the velocity-density parameterization provides stable and informative density features not included in the starting model. Field data applications of multicomponent W-VSP isotropic-elastic FWI in the time domain were also carried out. Finally, the heavy oil reservoir target zone, characterized by low α-to-β ratios and low Poisson’s ratios, can be identified clearly with the inverted isotropic-elastic parameters.« less

Elastic full-waveform inversion and parameterization analysis applied to walk-away vertical seismic profile data for unconventional (heavy oil) reservoir characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Wenyong; Innanen, Kristopher A.; Geng, Yu

We report seismic full-waveform inversion (FWI) methods hold strong potential to recover multiple subsurface elastic properties for hydrocarbon reservoir characterization. Simultaneously updating multiple physical parameters introduces the problem of interparameter tradeoff, arising from the covariance between different physical parameters, which increases nonlinearity and uncertainty of multiparameter FWI. The coupling effects of different physical parameters are significantly influenced by model parameterization and acquisition arrangement. An appropriate choice of model parameterization is critical to successful field data applications of multiparameter FWI. The objective of this paper is to examine the performance of various model parameterizations in isotropic-elastic FWI with walk-away vertical seismicmore » profile (W-VSP) dataset for unconventional heavy oil reservoir characterization. Six model parameterizations are considered: velocity-density (α, β and ρ'), modulus-density (κ, μ and ρ), Lamé-density (λ, μ' and ρ'''), impedance-density (IP, IS and ρ''), velocity-impedance-I (α', β' and I' P), and velocity-impedance-II (α'', β'' and I'S). We begin analyzing the interparameter tradeoff by making use of scattering radiation patterns, which is a common strategy for qualitative parameter resolution analysis. In this paper, we discuss the advantages and limitations of the scattering radiation patterns and recommend that interparameter tradeoffs be evaluated using interparameter contamination kernels, which provide quantitative, second-order measurements of the interparameter contaminations and can be constructed efficiently with an adjoint-state approach. Synthetic W-VSP isotropic-elastic FWI experiments in the time domain verify our conclusions about interparameter tradeoffs for various model parameterizations. Density profiles are most strongly influenced by the interparameter contaminations; depending on model parameterization, the inverted density profile can be over-estimated, under-estimated or spatially distorted. Among the six cases, only the velocity-density parameterization provides stable and informative density features not included in the starting model. Field data applications of multicomponent W-VSP isotropic-elastic FWI in the time domain were also carried out. Finally, the heavy oil reservoir target zone, characterized by low α-to-β ratios and low Poisson’s ratios, can be identified clearly with the inverted isotropic-elastic parameters.« less

Improving and Understanding Climate Models: Scale-Aware Parameterization of Cloud Water Inhomogeneity and Sensitivity of MJO Simulation to Physical Parameters in a Convection Scheme

NASA Astrophysics Data System (ADS)

Xie, Xin

Microphysics and convection parameterizations are two key components in a climate model to simulate realistic climatology and variability of cloud distribution and the cycles of energy and water. When a model has varying grid size or simulations have to be run with different resolutions, scale-aware parameterization is desirable so that we do not have to tune model parameters tailored to a particular grid size. The subgrid variability of cloud hydrometers is known to impact microphysics processes in climate models and is found to highly depend on spatial scale. A scale- aware liquid cloud subgrid variability parameterization is derived and implemented in the Community Earth System Model (CESM) in this study using long-term radar-based ground measurements from the Atmospheric Radiation Measurement (ARM) program. When used in the default CESM1 with the finite-volume dynamic core where a constant liquid inhomogeneity parameter was assumed, the newly developed parameterization reduces the cloud inhomogeneity in high latitudes and increases it in low latitudes. This is due to both the smaller grid size in high latitudes, and larger grid size in low latitudes in the longitude-latitude grid setting of CESM as well as the variation of the stability of the atmosphere. The single column model and general circulation model (GCM) sensitivity experiments show that the new parameterization increases the cloud liquid water path in polar regions and decreases it in low latitudes. Current CESM1 simulation suffers from the bias of both the pacific double ITCZ precipitation and weak Madden-Julian oscillation (MJO). Previous studies show that convective parameterization with multiple plumes may have the capability to alleviate such biases in a more uniform and physical way. A multiple-plume mass flux convective parameterization is used in Community Atmospheric Model (CAM) to investigate the sensitivity of MJO simulations. We show that MJO simulation is sensitive to entrainment rate specification. We found that shallow plumes can generate and sustain the MJO propagation in the model.

Parameterization of plume chemistry into large-scale atmospheric models: Application to aircraft NOx emissions

NASA Astrophysics Data System (ADS)

Cariolle, D.; Caro, D.; Paoli, R.; Hauglustaine, D. A.; CuéNot, B.; Cozic, A.; Paugam, R.

2009-10-01

A method is presented to parameterize the impact of the nonlinear chemical reactions occurring in the plume generated by concentrated NOx sources into large-scale models. The resulting plume parameterization is implemented into global models and used to evaluate the impact of aircraft emissions on the atmospheric chemistry. Compared to previous approaches that rely on corrected emissions or corrective factors to account for the nonlinear chemical effects, the present parameterization is based on the representation of the plume effects via a fuel tracer and a characteristic lifetime during which the nonlinear interactions between species are important and operate via rates of conversion for the NOx species and an effective reaction rates for O3. The implementation of this parameterization insures mass conservation and allows the transport of emissions at high concentrations in plume form by the model dynamics. Results from the model simulations of the impact on atmospheric ozone of aircraft NOx emissions are in rather good agreement with previous work. It is found that ozone production is decreased by 10 to 25% in the Northern Hemisphere with the largest effects in the north Atlantic flight corridor when the plume effects on the global-scale chemistry are taken into account. These figures are consistent with evaluations made with corrected emissions, but regional differences are noticeable owing to the possibility offered by this parameterization to transport emitted species in plume form prior to their dilution at large scale. This method could be further improved to make the parameters used by the parameterization function of the local temperature, humidity and turbulence properties diagnosed by the large-scale model. Further extensions of the method can also be considered to account for multistep dilution regimes during the plume dissipation. Furthermore, the present parameterization can be adapted to other types of point-source NOx emissions that have to be introduced in large-scale models, such as ship exhausts, provided that the plume life cycle, the type of emissions, and the major reactions involved in the nonlinear chemical systems can be determined with sufficient accuracy.

An Evaluation of Lightning Flash Rate Parameterizations Based on Observations of Colorado Storms during DC3

NASA Astrophysics Data System (ADS)

Basarab, B.; Fuchs, B.; Rutledge, S. A.

2013-12-01

Predicting lightning activity in thunderstorms is important in order to accurately quantify the production of nitrogen oxides (NOx = NO + NO2) by lightning (LNOx). Lightning is an important global source of NOx, and since NOx is a chemical precursor to ozone, the climatological impacts of LNOx could be significant. Many cloud-resolving models rely on parameterizations to predict lightning and LNOx since the processes leading to charge separation and lightning discharge are not yet fully understood. This study evaluates predicted flash rates based on existing lightning parameterizations against flash rates observed for Colorado storms during the Deep Convective Clouds and Chemistry Experiment (DC3). Evaluating lightning parameterizations against storm observations is a useful way to possibly improve the prediction of flash rates and LNOx in models. Additionally, since convective storms that form in the eastern plains of Colorado can be different thermodynamically and electrically from storms in other regions, it is useful to test existing parameterizations against observations from these storms. We present an analysis of the dynamics, microphysics, and lightning characteristics of two case studies, severe storms that developed on 6 and 7 June 2012. This analysis includes dual-Doppler derived horizontal and vertical velocities, a hydrometeor identification based on polarimetric radar variables using the CSU-CHILL radar, and insight into the charge structure using observations from the northern Colorado Lightning Mapping Array (LMA). Flash rates were inferred from the LMA data using a flash counting algorithm. We have calculated various microphysical and dynamical parameters for these storms that have been used in empirical flash rate parameterizations. In particular, maximum vertical velocity has been used to predict flash rates in some cloud-resolving chemistry simulations. We diagnose flash rates for the 6 and 7 June storms using this parameterization and compare to observed flash rates. For the 6 June storm, a preliminary analysis of aircraft observations of storm inflow and outflow is presented in order to place flash rates (and other lightning statistics) in the context of storm chemistry. An approach to a possibly improved LNOx parameterization scheme using different lightning metrics such as flash area will be discussed.

A new fractional snow-covered area parameterization for the Community Land Model and its effect on the surface energy balance

NASA Astrophysics Data System (ADS)

Swenson, S. C.; Lawrence, D. M.

2011-11-01

One function of the Community Land Model (CLM4) is the determination of surface albedo in the Community Earth System Model (CESM1). Because the typical spatial scales of CESM1 simulations are large compared to the scales of variability of surface properties such as snow cover and vegetation, unresolved surface heterogeneity is parameterized. Fractional snow-covered area, or snow-covered fraction (SCF), within a CLM4 grid cell is parameterized as a function of grid cell mean snow depth and snow density. This parameterization is based on an analysis of monthly averaged SCF and snow depth that showed a seasonal shift in the snow depth-SCF relationship. In this paper, we show that this shift is an artifact of the monthly sampling and that the current parameterization does not reflect the relationship observed between snow depth and SCF at the daily time scale. We demonstrate that the snow depth analysis used in the original study exhibits a bias toward early melt when compared to satellite-observed SCF. This bias results in a tendency to overestimate SCF as a function of snow depth. Using a more consistent, higher spatial and temporal resolution snow depth analysis reveals a clear hysteresis between snow accumulation and melt seasons. Here, a new SCF parameterization based on snow water equivalent is developed to capture the observed seasonal snow depth-SCF evolution. The effects of the new SCF parameterization on the surface energy budget are described. In CLM4, surface energy fluxes are calculated assuming a uniform snow cover. To more realistically simulate environments having patchy snow cover, we modify the model by computing the surface fluxes separately for snow-free and snow-covered fractions of a grid cell. In this configuration, the form of the parameterized snow depth-SCF relationship is shown to greatly affect the surface energy budget. The direct exposure of the snow-free surfaces to the atmosphere leads to greater heat loss from the ground during autumn and greater heat gain during spring. The net effect is to reduce annual mean soil temperatures by up to 3°C in snow-affected regions.

A new fractional snow-covered area parameterization for the Community Land Model and its effect on the surface energy balance

NASA Astrophysics Data System (ADS)

Swenson, S. C.; Lawrence, D. M.

2012-11-01

One function of the Community Land Model (CLM4) is the determination of surface albedo in the Community Earth System Model (CESM1). Because the typical spatial scales of CESM1 simulations are large compared to the scales of variability of surface properties such as snow cover and vegetation, unresolved surface heterogeneity is parameterized. Fractional snow-covered area, or snow-covered fraction (SCF), within a CLM4 grid cell is parameterized as a function of grid cell mean snow depth and snow density. This parameterization is based on an analysis of monthly averaged SCF and snow depth that showed a seasonal shift in the snow depth-SCF relationship. In this paper, we show that this shift is an artifact of the monthly sampling and that the current parameterization does not reflect the relationship observed between snow depth and SCF at the daily time scale. We demonstrate that the snow depth analysis used in the original study exhibits a bias toward early melt when compared to satellite-observed SCF. This bias results in a tendency to overestimate SCF as a function of snow depth. Using a more consistent, higher spatial and temporal resolution snow depth analysis reveals a clear hysteresis between snow accumulation and melt seasons. Here, a new SCF parameterization based on snow water equivalent is developed to capture the observed seasonal snow depth-SCF evolution. The effects of the new SCF parameterization on the surface energy budget are described. In CLM4, surface energy fluxes are calculated assuming a uniform snow cover. To more realistically simulate environments having patchy snow cover, we modify the model by computing the surface fluxes separately for snow-free and snow-covered fractions of a grid cell. In this configuration, the form of the parameterized snow depth-SCF relationship is shown to greatly affect the surface energy budget. The direct exposure of the snow-free surfaces to the atmosphere leads to greater heat loss from the ground during autumn and greater heat gain during spring. The net effect is to reduce annual mean soil temperatures by up to 3°C in snow-affected regions.

Dynamically consistent parameterization of mesoscale eddies. Part III: Deterministic approach

NASA Astrophysics Data System (ADS)

Berloff, Pavel

2018-07-01

This work continues development of dynamically consistent parameterizations for representing mesoscale eddy effects in non-eddy-resolving and eddy-permitting ocean circulation models and focuses on the classical double-gyre problem, in which the main dynamic eddy effects maintain eastward jet extension of the western boundary currents and its adjacent recirculation zones via eddy backscatter mechanism. Despite its fundamental importance, this mechanism remains poorly understood, and in this paper we, first, study it and, then, propose and test its novel parameterization. We start by decomposing the reference eddy-resolving flow solution into the large-scale and eddy components defined by spatial filtering, rather than by the Reynolds decomposition. Next, we find that the eastward jet and its recirculations are robustly present not only in the large-scale flow itself, but also in the rectified time-mean eddies, and in the transient rectified eddy component, which consists of highly anisotropic ribbons of the opposite-sign potential vorticity anomalies straddling the instantaneous eastward jet core and being responsible for its continuous amplification. The transient rectified component is separated from the flow by a novel remapping method. We hypothesize that the above three components of the eastward jet are ultimately driven by the small-scale transient eddy forcing via the eddy backscatter mechanism, rather than by the mean eddy forcing and large-scale nonlinearities. We verify this hypothesis by progressively turning down the backscatter and observing the induced flow anomalies. The backscatter analysis leads us to formulating the key eddy parameterization hypothesis: in an eddy-permitting model at least partially resolved eddy backscatter can be significantly amplified to improve the flow solution. Such amplification is a simple and novel eddy parameterization framework implemented here in terms of local, deterministic flow roughening controlled by single parameter. We test the parameterization skills in an hierarchy of non-eddy-resolving and eddy-permitting modifications of the original model and demonstrate, that indeed it can be highly efficient for restoring the eastward jet extension and its adjacent recirculation zones. The new deterministic parameterization framework not only combines remarkable simplicity with good performance but also is dynamically transparent, therefore, it provides a powerful alternative to the common eddy diffusion and emerging stochastic parameterizations.

Effects of pre-existing ice crystals on cirrus clouds and comparison between different ice nucleation parameterizations with the Community Atmosphere Model (CAM5)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Xiangjun; Liu, Xiaohong; Zhang, Kai

In order to improve the treatment of ice nucleation in a more realistic manner in the Community Atmosphere Model version 5.3 (CAM5.3), the effects of pre-existing ice crystals on ice nucleation in cirrus clouds are considered. In addition, by considering the in-cloud variability in ice saturation ratio, homogeneous nucleation takes place spatially only in a portion of the cirrus cloud rather than in the whole area of the cirrus cloud. Compared to observations, the ice number concentrations and the probability distributions of ice number concentration are both improved with the updated treatment. The pre-existing ice crystals significantly reduce ice numbermore » concentrations in cirrus clouds, especially at mid- to high latitudes in the upper troposphere (by a factor of ~10). Furthermore, the contribution of heterogeneous ice nucleation to cirrus ice crystal number increases considerably. Besides the default ice nucleation parameterization of Liu and Penner (2005, hereafter LP) in CAM5.3, two other ice nucleation parameterizations of Barahona and Nenes (2009, hereafter BN) and Kärcher et al. (2006, hereafter KL) are implemented in CAM5.3 for the comparison. In-cloud ice crystal number concentration, percentage contribution from heterogeneous ice nucleation to total ice crystal number, and pre-existing ice effects simulated by the three ice nucleation parameterizations have similar patterns in the simulations with present-day aerosol emissions. However, the change (present-day minus pre-industrial times) in global annual mean column ice number concentration from the KL parameterization (3.24 × 10 6 m -2) is less than that from the LP (8.46 × 10 6 m -2) and BN (5.62 × 10 6 m -2) parameterizations. As a result, the experiment using the KL parameterization predicts a much smaller anthropogenic aerosol long-wave indirect forcing (0.24 W m -2) than that using the LP (0.46 W m −2) and BN (0.39 W m -2) parameterizations.« less

Effects of pre-existing ice crystals on cirrus clouds and comparison between different ice nucleation parameterizations with the Community Atmosphere Model (CAM5)

DOE PAGES

Shi, Xiangjun; Liu, Xiaohong; Zhang, Kai

2015-02-11

In order to improve the treatment of ice nucleation in a more realistic manner in the Community Atmosphere Model version 5.3 (CAM5.3), the effects of pre-existing ice crystals on ice nucleation in cirrus clouds are considered. In addition, by considering the in-cloud variability in ice saturation ratio, homogeneous nucleation takes place spatially only in a portion of the cirrus cloud rather than in the whole area of the cirrus cloud. Compared to observations, the ice number concentrations and the probability distributions of ice number concentration are both improved with the updated treatment. The pre-existing ice crystals significantly reduce ice numbermore » concentrations in cirrus clouds, especially at mid- to high latitudes in the upper troposphere (by a factor of ~10). Furthermore, the contribution of heterogeneous ice nucleation to cirrus ice crystal number increases considerably. Besides the default ice nucleation parameterization of Liu and Penner (2005, hereafter LP) in CAM5.3, two other ice nucleation parameterizations of Barahona and Nenes (2009, hereafter BN) and Kärcher et al. (2006, hereafter KL) are implemented in CAM5.3 for the comparison. In-cloud ice crystal number concentration, percentage contribution from heterogeneous ice nucleation to total ice crystal number, and pre-existing ice effects simulated by the three ice nucleation parameterizations have similar patterns in the simulations with present-day aerosol emissions. However, the change (present-day minus pre-industrial times) in global annual mean column ice number concentration from the KL parameterization (3.24 × 10 6 m -2) is less than that from the LP (8.46 × 10 6 m -2) and BN (5.62 × 10 6 m -2) parameterizations. As a result, the experiment using the KL parameterization predicts a much smaller anthropogenic aerosol long-wave indirect forcing (0.24 W m -2) than that using the LP (0.46 W m −2) and BN (0.39 W m -2) parameterizations.« less

Role of ATP binding and hydrolysis in assembly of MacAB-TolC macrolide transporter

PubMed Central

Lu, Shuo; Zgurskaya, Helen I.

2012-01-01

Summary MacB is a founding member of the Macrolide Exporter family of transporters belonging to the ATP-Binding Cassette superfamily. These proteins are broadly represented in genomes of both gram-positive and gram-negative bacteria and are implicated in virulence and protection against antibiotics and peptide toxins. MacB transporter functions together with MacA, a periplasmic membrane fusion protein, which stimulates MacB ATPase. In gram-negative bacteria, MacA is believed to couple ATP hydrolysis to transport of substrates across the outer membrane through a TolC-like channel. In this study, we report a real-time analysis of concurrent ATP hydrolysis and assembly of MacAB-TolC complex. MacB binds nucleotides with a low millimolar affinity and fast on- and off-rates. In contrast, MacA-MacB complex is formed with a nanomolar affinity, which further increases in the presence of ATP. Our results strongly suggest that association between MacA and MacB is stimulated by ATP binding to MacB but remains unchanged during ATP hydrolysis cycle. We also found that the large periplasmic loop of MacB plays the major role in coupling reactions separated in two different membranes. This loop is required for MacA-dependent stimulation of MacB ATPase and at the same time, contributes to recruitment of TolC into a trans-envelope complex. PMID:23057817

Water Phase Change Heat Exchanger System Level Analysis for Low Lunar Orbit

NASA Technical Reports Server (NTRS)

Navarro, Moses; Ungar, Eugene; Sheth, Rubik; Hansen, Scott

2016-01-01

In low Lunar orbit (LLO) the thermal environment is cyclic - extremely cold in the eclipse and as warm as room temperature near the subsolar point. Phase change material heat exchangers (PCHXs) are the best option for long term missions in these environments. The Orion spacecraft will use a n-pentadecane wax PCHX for its envisioned mission to LLO. Using water as a PCM material is attractive because its higher heat of fusion and greater density result in a lighter, more compact PCHX. To assess the use of a water PCHX for a human spacecraft in a circular LLO, a system level analysis was performed for the Orion spacecraft. Three cases were evaluated: 1) A one-to-one replacement of the wax PCHX on the internal thermal control loop with a water PCHX (including the appropriate control modifications), 2) reducing the radiator return setpoint temperature below Orion's value to enhance PCHX freezing, and 3) placing the water PCM on the external loop. The model showed that the water PCHX could not be used as a drop-in replacement for the wax PCHX. It did not freeze fully during the eclipse owing to its low freezing point. To obtain equivalent performance, 40% more radiator area than the Orion baseline was required. The study shows that, although water PCHXs are attractive at a component level, system level effects mean that they are not the best choice for LLO.

High-flux neutron source based on a liquid-lithium target

NASA Astrophysics Data System (ADS)

Halfon, S.; Feinberg, G.; Paul, M.; Arenshtam, A.; Berkovits, D.; Kijel, D.; Nagler, A.; Eliyahu, I.; Silverman, I.

2013-04-01

A prototype compact Liquid Lithium Target (LiLiT), able to constitute an accelerator-based intense neutron source, was built. The neutron source is intended for nuclear astrophysical research, boron neutron capture therapy (BNCT) in hospitals and material studies for fusion reactors. The LiLiT setup is presently being commissioned at Soreq Nuclear research Center (SNRC). The lithium target will produce neutrons through the 7Li(p,n)7Be reaction and it will overcome the major problem of removing the thermal power generated by a high-intensity proton beam, necessary for intense neutron flux for the above applications. The liquid-lithium loop of LiLiT is designed to generate a stable lithium jet at high velocity on a concave supporting wall with free surface toward the incident proton beam (up to 10 kW). During off-line tests, liquid lithium was flown through the loop and generated a stable jet at velocity higher than 5 m/s on the concave supporting wall. The target is now under extensive test program using a high-power electron-gun. Up to 2 kW electron beam was applied on the lithium flow at velocity of 4 m/s without any flow instabilities or excessive evaporation. High-intensity proton beam irradiation will take place at SARAF (Soreq Applied Research Accelerator Facility) superconducting linear accelerator currently in commissioning at SNRC.

Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tong, Junsen; Yang, Huiseon; Eom, Soo Hyun

2014-09-12

Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domainmore » of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering.« less

Modeling and Simulation of the ITER First Wall/Blanket Primary Heat Transfer System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ying, Alice; Popov, Emilian L

2011-01-01

ITER inductive power operation is modeled and simulated using a thermal-hydraulics system code (RELAP5) integrated with a 3-D CFD (SC-Tetra) code. The Primary Heat Transfer System (PHTS) functions are predicted together with the main parameters operational ranges. The control algorithm strategy and derivation are summarized as well. The First Wall and Blanket modules are the primary components of PHTS, used to remove the major part of the thermal heat from the plasma. The modules represent a set of flow channels in solid metal structure that serve to absorb the radiation heat and nuclear heating from the fusion reactions and tomore » provide shield for the vacuum vessel. The blanket modules are water cooled. The cooling is forced convective with constant blanket inlet temperature and mass flow rate. Three independent water loops supply coolant to the three blanket sectors. The main equipment of each loop consists of a pump, a steam pressurizer and a heat exchanger. A major feature of ITER is the pulsed operation. The plasma does not burn continuously, but on intervals with large periods of no power between them. This specific feature causes design challenges to accommodate the thermal expansion of the coolant during the pulse period and requires active temperature control to maintain a constant blanket inlet temperature.« less

Sclerotiorin inhibits protein kinase G from Mycobacterium tuberculosis and impairs mycobacterial growth in macrophages.

PubMed

Chen, Dongni; Ma, Shuangshuang; He, Lei; Yuan, Peibo; She, Zhigang; Lu, Yongjun

2017-03-01

As a eukaryotic-like Ser/Thr protein kinase, Mycobacterium tuberculosis virulent effector protein kinase G (PknG) mediates mycobacterial survival by regulating bacterial cell metabolic processes and preventing phagosome-lysosome fusion in host macrophages. Targeting PknG is an effective strategy for development of anti-tuberculosis (TB) drugs. In the study, we found that sclerotiorin, derived from marine fungi from the South China Sea, exhibited moderately strong inhibitory effects on recombinant PknG, with an IC 50 value of 76.5 μM, and acted as a non-competitive inhibitor. The dissociation constant (K D ) of sclerotiorin determined by MST was 11.4 μM, demonstrating a moderate binding strength between them. Sclerotiorin could substantially impair the mycobacterial survival in infected macrophages while the macrophage viability remained unaffected, though it did not inhibit the mycobacterial growth in culture. When sclerotiorin was used in combination with rifampicin, intracellular mycobacterial growth decreased as sclerotiorin concentration increased. Docking analysis suggested a binding mechanism of inhibition with performing interactions with the P-loop and catalytic loop of PknG. In summary, we reported that sclerotiorin had moderately strong PknG inhibitory activity, but no cytotoxicity, and it could substantially decrease the mycobacterial growth inside macrophages, suggesting that sclerotiorin has potential to supplement antibiotic therapy for TB. Copyright © 2017 Elsevier Ltd. All rights reserved.

Small bowel entrapment and ureteropelvic junction disruption associated with L3 Chance fracture-dislocation.

PubMed

Pesenti, Sebastien; Blondel, Benjamin; Faure, Alice; Peltier, Emilie; Launay, Franck; Jouve, Jean-Luc

2016-09-16

Paediatric Chance fracture are rare lesions but often associated with abdominal injuries. We herein present the case of a seven years old patient who sustained an entrapment of small bowel and an ureteropelvic disruption associated with a Chance fracture and spine dislocation following a traffic accident. Initial X-rays and computed tomographic (CT) scan showed a Chance fracture with dislocation of L3 vertebra, with an incarceration of a small bowel loop in the spinal canal and a complete section of the left lumbar ureter. Paraplegia was noticed on the initial neurological examination. A posterior L2-L4 osteosynthesis was performed firstly. In a second time she underwent a sus umbilical laparotomy to release the incarcerated jejunum loop in the spinal canal. An end-to-end anastomosis was performed on a JJ probe to suture the left injured ureter. One month after the traumatism, she started to complain of severe headaches related to a leakage of cerebrospinalis fluid. Three months after the traumatism there was a clear regression of the leakage. One year after the trauma, an anterior intervertebral fusion was done. At final follow-up, no neurologic recovery was noticed. In case of Chance fracture, all physicians should think about abdominal injuries even if the patient is asymptomatic. Initial abdominal CT scan and magnetic resonance imaging provide in such case crucial info for management of the spine and the associated lesions.

The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism

PubMed Central

Reilman, Ewoud; Mars, Ruben A. T.; van Dijl, Jan Maarten; Denham, Emma L.

2014-01-01

Expression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health. To obtain a better understanding of underlying regulatory mechanisms, we have dissected the transcriptional activation of the ATP-binding cassette (ABC) transporter BmrC/BmrD of the Gram-positive model bacterium Bacillus subtilis. By using promoter-GFP fusions and live cell array technology, we demonstrate a temporally controlled transcriptional activation of the bmrCD genes in response to antibiotics that target protein synthesis. Intriguingly, bmrCD expression only occurs during the late-exponential and stationary growth stages, irrespective of the timing of the antibiotic challenge. We show that this is due to tight transcriptional control by the transition state regulator AbrB. Moreover, our results show that the bmrCD genes are co-transcribed with bmrB (yheJ), a small open reading frame immediately upstream of bmrC that harbors three alternative stem-loop structures. These stem-loops are apparently crucial for antibiotic-induced bmrCD transcription. Importantly, the antibiotic-induced bmrCD expression requires translation of bmrB, which implies that BmrB serves as a regulatory leader peptide. Altogether, we demonstrate for the first time that a ribosome-mediated transcriptional attenuation mechanism can control the expression of a multidrug ABC transporter. PMID:25217586

The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy.

PubMed

Zhang, Libo; Zhu, Junjie; Ren, Hao; Liu, Dongdong; Meng, Dan; Wu, Yanjun; Luo, Tiejian

2017-10-14

Intelligent robots are part of a new generation of robots that are able to sense the surrounding environment, plan their own actions and eventually reach their targets. In recent years, reliance upon robots in both daily life and industry has increased. The protocol proposed in this paper describes the design and production of a handling robot with an intelligent search algorithm and an autonomous identification function. First, the various working modules are mechanically assembled to complete the construction of the work platform and the installation of the robotic manipulator. Then, we design a closed-loop control system and a four-quadrant motor control strategy, with the aid of debugging software, as well as set steering gear identity (ID), baud rate and other working parameters to ensure that the robot achieves the desired dynamic performance and low energy consumption. Next, we debug the sensor to achieve multi-sensor fusion to accurately acquire environmental information. Finally, we implement the relevant algorithm, which can recognize the success of the robot's function for a given application. The advantage of this approach is its reliability and flexibility, as the users can develop a variety of hardware construction programs and utilize the comprehensive debugger to implement an intelligent control strategy. This allows users to set personalized requirements based on their needs with high efficiency and robustness.

Toroidal midplane neutral beam armor and plasma limiter

DOEpatents

Kugel, Henry W.; Hand Jr, Samuel W.; Ksayian, Haig

1986-02-04

For use in a tokamak fusion reactor having a midplane magnetic coil on the inner wall of an evacuated toriodal chamber within which a neutral beam heated, fusing plasma is magnetically confined, a neutral beam armor shield and plasma limiter is provided on the inner wall of the toroidal chamber to shield the midplane coil from neutral beam shine-thru and plasma deposition. The armor shield/plasma limiter forms a semicircular enclosure around the midplane coil with the outer surface of the armor shield/plasma limiter shaped to match, as closely as practical, the inner limiting magnetic flux surface of the toroidally confined, indented, bean-shaped plasma. The armor shield/plasma limiter includes a plurality of semicircular graphite plates each having a pair of coupled upper and lower sections with each plate positioned in intimate contact with an adjacent plate on each side thereof so as to form a closed, planar structure around the entire outer periphery of the circular midplane coil. The upper and lower plate sections are adapted for coupling to heat sensing thermocouples and to a circulating water conduit system for cooling the armor shield/plasma limiter.The inner center portion of each graphite plate is adapted to receive and enclose a section of a circular diagnostic magnetic flux loop so as to minimize the power from the plasma confinement chamber incident upon the flux loop.

Toroidal midplane neutral beam armor and plasma limiter

DOEpatents

Kugel, Henry W.; Hand, Jr, Samuel W.; Ksayian, Haig

1986-01-01

For use in a tokamak fusion reactor having a midplane magnetic coil on the inner wall of an evacuated toriodal chamber within which a neutral beam heated, fusing plasma is magnetically confined, a neutral beam armor shield and plasma limiter is provided on the inner wall of the toroidal chamber to shield the midplane coil from neutral beam shine-thru and plasma deposition. The armor shield/plasma limiter forms a semicircular enclosure around the midplane coil with the outer surface of the armor shield/plasma limiter shaped to match, as closely as practical, the inner limiting magnetic flux surface of the toroidally confined, indented, bean-shaped plasma. The armor shield/plasma limiter includes a plurality of semicircular graphite plates each having a pair of coupled upper and lower sections with each plate positioned in intimate contact with an adjacent plate on each side thereof so as to form a closed, planar structure around the entire outer periphery of the circular midplane coil. The upper and lower plate sections are adapted for coupling to heat sensing thermocouples and to a circulating water conduit system for cooling the armor shield/plasma limiter.The inner center portion of each graphite plate is adapted to receive and enclose a section of a circular diagnostic magnetic flux loop so as to minimize the power from the plasma confinement chamber incident upon the flux loop.

High-flux neutron source based on a liquid-lithium target

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halfon, S.; Feinberg, G.; Paul, M.

2013-04-19

A prototype compact Liquid Lithium Target (LiLiT), able to constitute an accelerator-based intense neutron source, was built. The neutron source is intended for nuclear astrophysical research, boron neutron capture therapy (BNCT) in hospitals and material studies for fusion reactors. The LiLiT setup is presently being commissioned at Soreq Nuclear research Center (SNRC). The lithium target will produce neutrons through the {sup 7}Li(p,n){sup 7}Be reaction and it will overcome the major problem of removing the thermal power generated by a high-intensity proton beam, necessary for intense neutron flux for the above applications. The liquid-lithium loop of LiLiT is designed to generatemore » a stable lithium jet at high velocity on a concave supporting wall with free surface toward the incident proton beam (up to 10 kW). During off-line tests, liquid lithium was flown through the loop and generated a stable jet at velocity higher than 5 m/s on the concave supporting wall. The target is now under extensive test program using a high-power electron-gun. Up to 2 kW electron beam was applied on the lithium flow at velocity of 4 m/s without any flow instabilities or excessive evaporation. High-intensity proton beam irradiation will take place at SARAF (Soreq Applied Research Accelerator Facility) superconducting linear accelerator currently in commissioning at SNRC.« less

Modeling particle nucleation and growth over northern California during the 2010 CARES campaign

NASA Astrophysics Data System (ADS)

Lupascu, A.; Easter, R.; Zaveri, R.; Shrivastava, M.; Pekour, M.; Tomlinson, J.; Yang, Q.; Matsui, H.; Hodzic, A.; Zhang, Q.; Fast, J. D.

2015-07-01

Accurate representation of the aerosol lifecycle requires adequate modeling of the particle number concentration and size distribution in addition to their mass, which is often the focus of aerosol modeling studies. This paper compares particle number concentrations and size distributions as predicted by three empirical nucleation parameterizations in the Weather Research and Forecast coupled with chemistry (WRF-Chem) regional model using 20 discrete size bins ranging from 1 nm to 10 μm. Two of the parameterizations are based on H2SO4 while one is based on both H2SO4 and organic vapors. Budget diagnostic terms for transport, dry deposition, emissions, condensational growth, nucleation, and coagulation of aerosol particles have been added to the model and are used to analyze the differences in how the new particle formation parameterizations influence the evolving aerosol size distribution. The simulations are evaluated using measurements collected at surface sites and from a research aircraft during the Carbonaceous Aerosol and Radiative Effects Study (CARES) conducted in the vicinity of Sacramento, California. While all three parameterizations captured the temporal variation of the size distribution during observed nucleation events as well as the spatial variability in aerosol number, all overestimated by up to a factor of 2.5 the total particle number concentration for particle diameters greater than 10 nm. Using the budget diagnostic terms, we demonstrate that the combined H2SO4 and low-volatility organic vapors parameterization leads to a different diurnal variability of new particle formation and growth to larger sizes compared to the parameterizations based on only H2SO4. At the CARES urban ground site, peak nucleation rates were predicted to occur around 12:00 Pacific (local) standard time (PST) for the H2SO4 parameterizations, whereas the highest rates were predicted at 08:00 and 16:00 PST when low-volatility organic gases are included in the parameterization. This can be explained by higher anthropogenic emissions of organic vapors at these times as well as lower boundary layer heights that reduce vertical mixing. The higher nucleation rates in the H2SO4-organic parameterization at these times were largely offset by losses due to coagulation. Despite the different budget terms for ultrafine particles, the 10-40 nm diameter particle number concentrations from all three parameterizations increased from 10:00 to 14:00 PST and then decreased later in the afternoon, consistent with changes in the observed size and number distribution. Differences among the three simulations for the 40-100 nm particle diameter range are mostly associated with the timing of the peak total tendencies that shift the morning increase and afternoon decrease in particle number concentration by up to two hours. We found that newly formed particles could explain up to 20-30 % of predicted cloud condensation nuclei at 0.5 % supersaturation, depending on location and the specific nucleation parameterization. A sensitivity simulation using 12 discrete size bins ranging from 1 nm to 10 μm diameter gave a reasonable estimate of particle number and size distribution compared to the 20 size bin simulation, while reducing the associated computational cost by ∼ 36 %.

PyDBS: an automated image processing workflow for deep brain stimulation surgery.

PubMed

D'Albis, Tiziano; Haegelen, Claire; Essert, Caroline; Fernández-Vidal, Sara; Lalys, Florent; Jannin, Pierre

2015-02-01

Deep brain stimulation (DBS) is a surgical procedure for treating motor-related neurological disorders. DBS clinical efficacy hinges on precise surgical planning and accurate electrode placement, which in turn call upon several image processing and visualization tasks, such as image registration, image segmentation, image fusion, and 3D visualization. These tasks are often performed by a heterogeneous set of software tools, which adopt differing formats and geometrical conventions and require patient-specific parameterization or interactive tuning. To overcome these issues, we introduce in this article PyDBS, a fully integrated and automated image processing workflow for DBS surgery. PyDBS consists of three image processing pipelines and three visualization modules assisting clinicians through the entire DBS surgical workflow, from the preoperative planning of electrode trajectories to the postoperative assessment of electrode placement. The system's robustness, speed, and accuracy were assessed by means of a retrospective validation, based on 92 clinical cases. The complete PyDBS workflow achieved satisfactory results in 92 % of tested cases, with a median processing time of 28 min per patient. The results obtained are compatible with the adoption of PyDBS in clinical practice.