SDO/AIA AND HINODE/EIS OBSERVATIONS OF INTERACTION BETWEEN AN EUV WAVE AND ACTIVE REGION LOOPS

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

Yang, Liheng; Zhang, Jun; Li, Ting

2013-09-20

We present detailed analysis of an extreme-ultraviolet (EUV) wave and its interaction with active region (AR) loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly and the Hinode EUV Imaging Spectrometer (EIS). This wave was initiated from AR 11261 on 2011 August 4 and propagated at velocities of 430-910 km s{sup –1}. It was observed to traverse another AR and cross over a filament channel on its path. The EUV wave perturbed neighboring AR loops and excited a disturbance that propagated toward the footpoints of these loops. EIS observations of AR loops revealed that at the time of the wavemore » transit, the original redshift increased by about 3 km s{sup –1}, while the original blueshift decreased slightly. After the wave transit, these changes were reversed. When the EUV wave arrived at the boundary of a polar coronal hole, two reflected waves were successively produced and part of them propagated above the solar limb. The first reflected wave above the solar limb encountered a large-scale loop system on its path, and a secondary wave rapidly emerged 144 Mm ahead of it at a higher speed. These findings can be explained in the framework of a fast-mode magnetosonic wave interpretation for EUV waves, in which observed EUV waves are generated by expanding coronal mass ejections.« less

Finite-temperature phase transitions of third and higher order in gauge theories at large N

DOE PAGES

Nishimura, Hiromichi; Pisarski, Robert D.; Skokov, Vladimir V.

2018-02-15

We study phase transitions in SU(∞) gauge theories at nonzero temperature using matrix models. Our basic assumption is that the effective potential is dominated by double trace terms for the Polyakov loops. As a function of the various parameters, related to terms linear, quadratic, and quartic in the Polyakov loop, the phase diagram exhibits a universal structure. In a large region of this parameter space, there is a continuous phase transition whose order is larger than second. This is a generalization of the phase transition of Gross, Witten, and Wadia (GWW). Depending upon the detailed form of the matrix model,more » the eigenvalue density and the behavior of the specific heat near the transition differ drastically. Here, we speculate that in the pure gauge theory, that although the deconfining transition is thermodynamically of first order, it can be nevertheless conformally symmetric at infnite N.« less

Finite-temperature phase transitions of third and higher order in gauge theories at large N

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

Nishimura, Hiromichi; Pisarski, Robert D.; Skokov, Vladimir V.

We study phase transitions in SU(∞) gauge theories at nonzero temperature using matrix models. Our basic assumption is that the effective potential is dominated by double trace terms for the Polyakov loops. As a function of the various parameters, related to terms linear, quadratic, and quartic in the Polyakov loop, the phase diagram exhibits a universal structure. In a large region of this parameter space, there is a continuous phase transition whose order is larger than second. This is a generalization of the phase transition of Gross, Witten, and Wadia (GWW). Depending upon the detailed form of the matrix model,more » the eigenvalue density and the behavior of the specific heat near the transition differ drastically. Here, we speculate that in the pure gauge theory, that although the deconfining transition is thermodynamically of first order, it can be nevertheless conformally symmetric at infnite N.« less

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

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

Structure and Dynamics of Cool Flare Loops Observed by the Interface Region Imaging Spectrograph

NASA Astrophysics Data System (ADS)

Mikuła, K.; Heinzel, P.; Liu, W.; Berlicki, A.

2017-08-01

Flare loops were well observed with the Interface Region Imaging Spectrograph (IRIS) during the gradual phase of two solar flares on 2014 March 29 and 2015 June 22. Cool flare loops are visible in various spectral lines formed at chromospheric and transition-region temperatures and exhibit large downflows which correspond to the standard scenario. The principal aim of this work is to analyze the structure and dynamics of cool flare loops observed in Mg II lines. Synthetic profiles of the Mg II h line are computed using the classical cloud model and assuming a uniform background intensity. In this paper, we study novel IRIS NUV observations of such loops in Mg II h and k lines and also show the behavior of hotter lines detected in the FUV channel. We obtained the spatial evolution of the velocities: near the loop top, the flow velocities are small and they are increasing toward the loop legs. Moreover, from slit-jaw image (SJI) movies, we observe some plasma upflows into the loops, which are also detectable in Mg II spectra. The brightness of the loops systematically decreases with increasing flow velocity, and we ascribe this to the effect of Doppler dimming, which works for Mg II lines. Emission profiles of Mg II were found to be extremely broad, and we explain this through the large unresolved non-thermal motions.

Structure and Dynamics of Cool Flare Loops Observed by the Interface Region Imaging Spectrograph

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

Mikuła, K.; Berlicki, A.; Heinzel, P.

Flare loops were well observed with the Interface Region Imaging Spectrograph ( IRIS ) during the gradual phase of two solar flares on 2014 March 29 and 2015 June 22. Cool flare loops are visible in various spectral lines formed at chromospheric and transition-region temperatures and exhibit large downflows which correspond to the standard scenario. The principal aim of this work is to analyze the structure and dynamics of cool flare loops observed in Mg ii lines. Synthetic profiles of the Mg ii h line are computed using the classical cloud model and assuming a uniform background intensity. In thismore » paper, we study novel IRIS NUV observations of such loops in Mg ii h and k lines and also show the behavior of hotter lines detected in the FUV channel. We obtained the spatial evolution of the velocities: near the loop top, the flow velocities are small and they are increasing toward the loop legs. Moreover, from slit-jaw image (SJI) movies, we observe some plasma upflows into the loops, which are also detectable in Mg ii spectra. The brightness of the loops systematically decreases with increasing flow velocity, and we ascribe this to the effect of Doppler dimming, which works for Mg ii lines. Emission profiles of Mg ii were found to be extremely broad, and we explain this through the large unresolved non-thermal motions.« less

Enthalpy-Based Thermal Evolution of Loops: II. Improvements to the Model

NASA Technical Reports Server (NTRS)

Cargill, P. J.; Bradshaw, S. J.; Klimchuk, J. A.

2011-01-01

This paper further develops the zero-dimensional (0D) hydrodynamic coronal loop model "Enthalpy-based Thermal Evolution of Loops" (EBTEL) originally proposed by Klimchuk et al (2008), which studies the plasma response to evolving coronal heating. It has typically been applied to impulsive heating events. The basis of EBTEL is the modelling of mass exchange between the corona and transition region and chromosphere in response to heating variations, with the key parameter being the ratio of transition region to coronal radiation. We develop new models for this parameter that now include gravitational stratification and a physically motivated approach to radiative cooling. A number of examples are presented, including nanoflares in short and long loops, and a small flare. It is found that while the evolution of the loop temperature is rather insensitive to the details of the model, accurate tracking of the density requires the inclusion of our new features. In particular, we are able to now obtain highly over-dense loops in the late cooling phase and decreases to the coronal density arising due to stratification. The 0D results are compared to a 1D hydro code (Hydrad). The agreement is acceptable, with the exception of the flare case where some versions of Hydrad can give significantly lower densities. This is attributed to the method used to model the chromosphere in a flare. EBTEL is suitable for general use as a tool for (a) quick-look results of loop evolution in response to a given heating function and (b) situations where the modelling of hundreds or thousands of elemental loops is needed. A single run takes a few seconds on a contemporary laptop.

Simulations of flow induced structural transition of the β-switch region of glycoprotein Ibα.

PubMed

Han, Mengzhi; Xu, Ji; Ren, Ying; Li, Jinghai

2016-02-01

Binding of glycoprotein Ibα to von Willebrand factor induces platelet adhesion to injured vessel walls and initiates a multistep hemostatic process. It has been hypothesized that the flow condition could induce a loop to β-sheet conformational change in the β-switch region of glycoprotein Ibα, which regulates it binding to the von Willebrand factor and facilitates the blood clot formation and wound healing. In this work, direct molecular dynamics (MD), flow MD and metadynamics, were employed to investigate the mechanisms of this flow induced conformational transition process. Specifically, the free energy landscape of the whole transition process was drawn by metadynamics with the path collective variable approach. The results reveal that without flow, the free energy landscape has two main basins, including a random loop basin stabilized by large conformational entropy and a partially folded β-sheet basin. The free energy barrier separating these two basins is relatively high and the β-switch could not fold from loop to β-sheet state spontaneously. The fully β-sheet conformations located in high free energy regions, which are also unstable and gradually unfold into partially folded β-sheet state with flow. Relatively weak flow could trigger some folding of the β-switch but could not fold it into fully β-sheet state. Under strong flow conditions, the β-switch could readily overcome the high free energy barrier and fold into fully β-sheet state. Copyright © 2015 Elsevier B.V. All rights reserved.

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

NASA Astrophysics Data System (ADS)

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; Omand, Conor; Nishino, Masamichi

2016-02-01

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean-field method for a simplified model of a spin-crossover material with a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S =1 /2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley (equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shaped regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. We believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.

Loop-driven conformational transition between the alternative and collapsed form of prethrombin-2: targeted molecular dynamics study.

PubMed

Wu, Sangwook

2017-01-01

Two distinct crystal structures of prethrombin-2, the alternative and collapsed forms, are elucidated by X-ray crystallogrphy. We analyzed the conformational transition from the alternative to the collapsed form employing targeted molecular dynamics (TMD) simulation. Despite small RMSD difference in the two X-ray crystal structures, some hydrophobic residues (W60d, W148, W215, and F227) show a significant difference between the two conformations. TMD simulation shows that the four hydrophobic residues undergo concerted movement from dimer to trimer transition via tetramer state in the conformational change from the alternative to the collapsed form. We reveal that the concerted movement of the four hydrophobic residues is controlled by movement of specific loop regions behind. In this paper, we propose a sequential scenario for the conformational transition from the alternative form to the collapsed form, which is partially supported by the mutant W148A simulation.

Formation of Cool and Warm Jets by Magnetic Flux Emerging from the Solar Chromosphere to Transition Region

NASA Astrophysics Data System (ADS)

Yang, Liping; Peter, Hardi; He, Jiansen; Tu, Chuanyi; Wang, Linghua; Zhang, Lei; Yan, Limei

2018-01-01

In the solar atmosphere, jets are ubiquitous at various spatial-temporal scales. They are important for understanding the energy and mass transports in the solar atmosphere. According to recent observational studies, the high-speed network jets are likely to be intermittent but continual sources of mass and energy for the solar wind. Here, we conduct a 2D magnetohydrodynamics simulation to investigate the mechanism of these network jets. A combination of magnetic flux emergence and horizontal advection is used to drive the magnetic reconnection in the transition region between a strong magnetic loop and a background open flux. The simulation results show that not only a fast warm jet, much similar to the network jets, is found, but also an adjacent slow cool jet, mostly like classical spicules, is launched. Differing from the fast warm jet driven by magnetic reconnection, the slow cool jet is mainly accelerated by gradients of both thermal pressure and magnetic pressure near the outer border of the mass-concentrated region compressed by the emerging loop. These results provide a different perspective on our understanding of the formation of both the slow cool jets from the solar chromosphere and the fast warm jets from the solar transition region.

Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure.

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-12-01

DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆V tr , of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75.5cm 3 mol -1 , which was larger than that of TBA (54.6cm 3 mol -1 ). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆V tr of 41.1cm 3 mol -1 . In the presence of poly(ethylene)glycol 200 (PEG200), ∆V tr values were 14.7cm 3 mol -1 for TBA T3A and 13.2cm 3 mol -1 for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures. Copyright © 2017 Elsevier B.V. All rights reserved.

Mass and energy supply of a cool coronal loop near its apex

NASA Astrophysics Data System (ADS)

Yan, Limei; Peter, Hardi; He, Jiansen; Xia, Lidong; Wang, Linghua

2018-03-01

Context. Different models for the heating of solar corona assume or predict different locations of the energy input: concentrated at the footpoints, at the apex, or uniformly distributed. The brightening of a loop could be due to the increase in electron density ne, the temperature T, or a mixture of both. Aim. We investigate possible reasons for the brightening of a cool loop at transition region temperatures through imaging and spectral observation. Methods: We observed a loop with the Interface Region Imaging Spectrograph (IRIS) and used the slit-jaw images together with spectra taken at a fixed slit position to study the evolution of plasma properties in and below the loop. We used spectra of Si IV, which forms at around 80 000 K in equilibrium, to identify plasma motions and derive electron densities from the ratio of inter-combination lines of O IV. Additional observations from the Solar Dynamics Observatory (SDO) were employed to study the response at coronal temperatures (Atmospheric Imaging Assembly, AIA) and to investigate the surface magnetic field below the loop (Helioseismic and Magnetic Imager, HMI). Results: The loop first appears at transition region temperatures and later also at coronal temperatures, indicating a heating of the plasma in the loop. The appearance of hot plasma in the loop coincides with a possible accelerating upflow seen in Si IV, with the Doppler velocity shifting continuously from -70 km s-1 to -265 km s-1. The 3D magnetic field lines extrapolated from the HMI magnetogram indicate possible magnetic reconnection between small-scale magnetic flux tubes below or near the loop apex. At the same time, an additional intensity enhancement near the loop apex is visible in the IRIS slit-jaw images at 1400 Å. These observations suggest that the loop is probably heated by the interaction between the loop and the upflows, which are accelerated by the magnetic reconnection between small-scale magnetic flux tubes at lower altitudes. Before and after the possible heating phase, the intensity changes in the optically thin (Si IV) and optical thick line (C II) are mainly contributed by the density variation without significant heating. Conclusions: We therefore provide evidence for the heating of an envelope loop that is affected by accelerating upflows, which are probably launched by magnetic reconnection between small-scale magnetic flux tubes underneath the envelope loop. This study emphasizes that in the complex upper atmosphere of the Sun, the dynamics of the 3D coupled magnetic field and flow field plays a key role in thermalizing 1D structures such as coronal loops. An animation associated to Fig. 1 is available at http://https://www.aanda.org

A second-order all-digital phase-locked loop

NASA Technical Reports Server (NTRS)

Holmes, J. K.; Tegnelia, C. R.

1974-01-01

A simple second-order digital phase-locked loop has been designed to synchronize itself to a square-wave subcarrier. Analysis and experimental performance are given for both acquisition behavior and steady-state phase error performance. In addition, the damping factor and the noise bandwidth are derived analytically. Although all the data are given for the square-wave subcarrier case, the results are applicable to arbitrary subcarriers that are odd symmetric about their transition region.

On the thermal stability of coronal loop plasma

NASA Technical Reports Server (NTRS)

Antiochos, S. K.; Emslie, A. G.; Shoub, E. C.; An, C. H.

1982-01-01

The stability to thermal perturbation of static models of coronal loops is considered including the effects of cool, radiatively stable material at the loop base. The linear stability turns out to be sensitive only to the boundary conditions assumed on the velocity at the loop base. The question of the appropriate boundary conditions is discussed, and it is concluded that the free surface condition (the pressure perturbation vanishes), rather than the rigid wall (the velocity vanishes), is relevant to the solar case. The static models are found to be thermally unstable, with a growth time of the order of the coronal cooking time. The physical implications of these results for the solar corona and transition region are examined.

Sunspot Oscillations From The Chromosphere To The Corona

NASA Astrophysics Data System (ADS)

Brynildsen, N.; Maltby, P.; Fredvik, T.; Kjeldseth-Moe, O.

The behavior of the 3 minute sunspot oscillations is studied as a function of temper- ature through the transition region using observations with CDS/SOHO and TRACE. The oscillations occur above the umbra, with amplitudes increasing to a maximum near 200 000 K, then decreasing towards higher temperatures. Deviations from pure linear oscillations are present in several cases. Power spectra of the oscillations are remarkably similar in the chromosphere and through the transition region in contra- diction to the predictions of the sunspot filter theory. The 3 minute oscillations pene- trate to the low temperature end of the corona, where they are channeled into smaller areas coinciding with the endpoints of sunspot coronal loops. This differs from the transition zone where the oscillating region covers the umbra.

CLASP/SJ Observations of Rapid Time Variations in the Ly α Emission in a Solar Active Region

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

Ishikawa, Shin-nosuke; Kubo, Masahito; Katsukawa, Yukio

The Chromospheric Ly α SpectroPolarimeter (CLASP) is a sounding rocket experiment launched on 2015 September 3 to investigate the solar chromosphere and transition region. The slit-jaw (SJ) optical system captured Ly α images with a high time cadence of 0.6 s. From the CLASP/SJ observations, many variations in the solar chromosphere and transition region emission with a timescale of <1 minute were discovered. In this paper, we focus on the active region within the SJ field of view and investigate the relationship between short (<30 s) temporal variations in the Ly α emission and the coronal structures observed by Solarmore » Dynamics Observatory/Atmospheric Imaging Assembly (AIA). We compare the Ly α temporal variations at the coronal loop footpoints observed in the AIA 211 Å (≈2 MK) and AIA 171 Å (≈0.6 MK) channels with those in the regions with bright Ly α features without a clear association with the coronal loop footpoints. We find more short (<30 s) temporal variations in the Ly α intensity in the footpoint regions. Those variations did not depend on the temperature of the coronal loops. Therefore, the temporal variations in the Ly α intensity at this timescale range could be related to the heating of the coronal structures up to temperatures around the sensitivity peak of 171 Å. No signature was found to support the scenario that these Ly α intensity variations were related to the nanoflares. Waves or jets from the lower layers (lower chromosphere or photosphere) are possible causes for this phenomenon.« less

Skylab

NASA Image and Video Library

1973-01-01

Breaking the grip of the closed magnetic loops that constrain other gases around it, a spray of chromospheric material surges upward, free of the Sun. Views 1 through 5 were recorded about 5 minutes apart by Skylab and comprise a composite of separate images made in chromospheric (red), transition region (green), and coronal (blue) temperatures of an ultraviolet sequence that depicts a solar eruption. Eruption begins (view 2) as material in or near a small, compact loop develops enough energy to overcome the Sun's magnetic bonds.

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

DOE PAGES

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; ...

2016-02-16

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains

NASA Astrophysics Data System (ADS)

Zhang, Shuangshuang; Qi, Shuanhu; Klushin, Leonid I.; Skvortsov, Alexander M.; Yan, Dadong; Schmid, Friederike

2018-01-01

We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter ɛ and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force F applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i.e., the mean number of surface contacts in the case of the adsorption transition and the mean position of the chain end in the case of the loop-stretch transition. Close to the transition points, both the static behavior and the dynamic behavior of chains with different length N are very well described by a scaling ansatz with the scaling parameters (ɛ - ɛ*)Nϕ (adsorption transition) and (F - F*)Nν (loop-stretch transition), respectively, where ϕ is the crossover exponent of the adsorption transition and ν is the Flory exponent. We show that both the loop-stretch and the loop adsorption transitions provide an exceptional opportunity to construct explicit analytical expressions for the crossover functions which perfectly describe all simulation results on static properties in the finite-size scaling regime. Explicit crossover functions are based on the ansatz for the analytical form of the order parameter distributions at the respective transition points. In contrast to the close similarity in equilibrium static behavior, the dynamic relaxation at the two transitions shows qualitative differences, especially in the strongly ordered regimes. This is attributed to the fact that the surface contact dynamics in a strongly adsorbed chain is governed by local processes, whereas the end height relaxation of a strongly stretched chain involves the full spectrum of Rouse modes.

Wilson loop's phase transition probed by non-local observable

NASA Astrophysics Data System (ADS)

Li, Hui-Ling; Feng, Zhong-Wen; Yang, Shu-Zheng; Zu, Xiao-Tao

2018-04-01

In order to give further insights into the holographic Van der Waals phase transition, it would be of great interest to investigate the behavior of Wilson loop across the holographic phase transition for a higher dimensional hairy black hole. We offer a possibility to proceed with a numerical calculation in order to discussion on the hairy black hole's phase transition, and show that Wilson loop can serve as a probe to detect a phase structure of the black hole. Furthermore, for a first order phase transition, we calculate numerically the Maxwell's equal area construction; and for a second order phase transition, we also study the critical exponent in order to characterize the Wilson loop's phase transition.

Spectroscopic Study of a Dark Lane and a Cool Loop in a Solar Limb Active Region by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, Kyoung-Sun; Imada, S.; Moon, Y.-J.; Lee, Jin-Yi

2014-01-01

We investigated a cool loop and a dark lane over a limb active region on 2007 March 14 using the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in the coronal spectral lines and is rooted on a bright point. We examined their electron densities, Doppler velocities, and nonthermal velocities as a function of distance from the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII, and Fe XIV spectra. We also compared the observed density scale heights with the calculated scale heights from each peak formation temperatures of the spectral lines under the hydrostatic equilibrium. We noted that the observed density scale heights of the cool loop are consistent with the calculated heights, with the exception of one observed cooler temperature; we also found that the observed scale heights of the dark lane are much lower than their calculated scale heights. The nonthermal velocity in the cool loop slightly decreases along the loop, while nonthermal velocity in the dark lane sharply falls off with height. Such a decrease in the nonthermal velocity may be explained by wave damping near the solar surface or by turbulence due to magnetic reconnection near the bright point.

Observations and Modeling of Transition Region and Coronal Heating Associated with Spicules

NASA Astrophysics Data System (ADS)

De Pontieu, B.; Martinez-Sykora, J.; De Moortel, I.; Chintzoglou, G.; McIntosh, S. W.

2017-12-01

Spicules have been proposed as significant contributorsto the coronal energy and mass balance. While previous observationshave provided a glimpse of short-lived transient brightenings in thecorona that are associated with spicules, these observations have beencontested and are the subject of a vigorous debate both on the modelingand the observational side so that it remains unclear whether plasmais heated to coronal temperatures in association with spicules. We use high-resolution observations of the chromosphere and transition region with the Interface Region Imaging Spectrograph (IRIS) and ofthe corona with the Atmospheric Imaging Assembly (AIA) onboard theSolar Dynamics Observatory (SDO) to show evidence of the formation of coronal structures as a result of spicular mass ejections andheating of plasma to transition region and coronaltemperatures. Our observations suggest that a significant fraction of the highly dynamic loop fan environment associated with plage regions may be the result of the formation of such new coronal strands, a process that previously had been interpreted as the propagation of transient propagating coronal disturbances (PCD)s. Our observationsare supported by 2.5D radiative MHD simulations that show heating tocoronal temperatures in association with spicules. Our results suggest that heating and strong flows play an important role in maintaining the substructure of loop fans, in addition to the waves that permeate this low coronal environment. Our models also matches observations ofTR counterparts of spicules and provides an elegant explanation forthe high apparent speeds of these "network jets".

Relating Alfvén Wave Heating Model to Observations of a Solar Active Region

NASA Astrophysics Data System (ADS)

Yoritomo, J. Y.; Van Ballegooijen, A. A.

2012-12-01

We compared images from the Solar Dynamics Observatory's (SDO) Atmospheric Imaging Assembly (AIA) with simulations of propagating and dissipating Alfvén waves from a three-dimensional magnetohydrodynamic (MHD) model (van Ballegooijen et. al 2011; Asgari-Targhi & van Ballegooijen 2012). The goal was to search for observational evidence of Alfvén waves in the solar corona and understand their role in coronal heating. We looked at one particular active region on the 5th of May 2012. Certain distinct loops in the SDO/AIA observations were selected and expanded. Movies were created from these selections in an attempt to discover transverse motions that may be Alfvén waves. Using a magnetogram of that day and the corresponding synoptic map, a potential field model was created for the active region. Three-dimensional MHD models for several loops in different locations in the active region were created. Each model specifies the temperature, pressure, magnetic field strength, average heating rate, and other parameters along the loop. We find that the heating is intermittent in the loops and reflection occurs at the transition region. For loops at larger and larger height, a point is reached where thermal non-equilibrium occurs. In the center this critical height is much higher than in the periphery of the active region. Lastly, we find that the average heating rate and coronal pressure decrease with increasing height in the corona. This research was supported by an NSF grant for the Smithsonian Astrophysical Observatory (SAO) Solar REU program and a SDO/AIA grant for the Smithsonian Astrophysical Observatory.

Prediction of beta-turns in proteins using the first-order Markov models.

PubMed

Lin, Thy-Hou; Wang, Ging-Ming; Wang, Yen-Tseng

2002-01-01

We present a method based on the first-order Markov models for predicting simple beta-turns and loops containing multiple turns in proteins. Sequences of 338 proteins in a database are divided using the published turn criteria into the following three regions, namely, the turn, the boundary, and the nonturn ones. A transition probability matrix is constructed for either the turn or the nonturn region using the weighted transition probabilities computed for dipeptides identified from each region. There are two such matrices constructed for the boundary region since the transition probabilities for dipeptides immediately preceding or following a turn are different. The window used for scanning a protein sequence from amino (N-) to carboxyl (C-) terminal is a hexapeptide since the transition probability computed for a turn tetrapeptide is capped at both the N- and C- termini with a boundary transition probability indexed respectively from the two boundary transition matrices. A sum of the averaged product of the transition probabilities of all the hexapeptides involving each residue is computed. This is then weighted with a probability computed from assuming that all the hexapeptides are from the nonturn region to give the final prediction quantity. Both simple beta-turns and loops containing multiple turns in a protein are then identified by the rising of the prediction quantity computed. The performance of the prediction scheme or the percentage (%) of correct prediction is evaluated through computation of Matthews correlation coefficients for each protein predicted. It is found that the prediction method is capable of giving prediction results with better correlation between the percent of correct prediction and the Matthews correlation coefficients for a group of test proteins as compared with those predicted using some secondary structural prediction methods. The prediction accuracy for about 40% of proteins in the database or 50% of proteins in the test set is better than 70%. Such a percentage for the test set is reduced to 30 if the structures of all the proteins in the set are treated as unknown.

Simulations of Solar Jets Confined by Coronal Loops

NASA Technical Reports Server (NTRS)

Wyper, P. F.; De Vore, C. R.

2016-01-01

Coronal jets are collimated, dynamic events that occur over a broad range of spatial scales in the solar corona. In the open magnetic field of coronal holes, jets form quasi-radial spires that can extend far out into the heliosphere, while in closed-field regions the jet outflows are confined to the corona. We explore the application of the embedded-bipole model to jets occurring in closed coronal loops. In this model, magnetic free energy is injected slowly by footpoint motions that introduce twist within the closed dome of the jet source region, and is released rapidly by the onset of an ideal kink-like instability. Two length scales characterize the system: the width (N) of the jet source region and the footpoint separation (L) of the coronal loop that envelops the jet source. We find that both the conditions for initiation and the subsequent dynamics are highly sensitive to the ratio L/N. The longest-lasting and most energetic jets occur along long coronal loops with large L/N ratios, and share many of the features of open-field jets, while smaller L/N ratios produce shorter-duration, less energetic jets that are affected by reflections from the far-loop footpoint. We quantify the transition between these behaviors and show that our model replicates key qualitative and quantitative aspects of both quiet Sun and active-region loop jets. We also find that there connection between the closed dome and surrounding coronal loop is very extensive: the cumulative reconnected flux at least matches the total flux beneath the dome for small L/N, and is more than double that value for large L/N.

SIMULATIONS OF SOLAR JETS CONFINED BY CORONAL LOOPS

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

Wyper, P. F.; DeVore, C. R., E-mail: peter.f.wyper@nasa.gov, E-mail: c.richard.devore@nasa.gov

Coronal jets are collimated, dynamic events that occur over a broad range of spatial scales in the solar corona. In the open magnetic field of coronal holes, jets form quasi-radial spires that can extend far out into the heliosphere, while in closed-field regions the jet outflows are confined to the corona. We explore the application of the embedded-bipole model to jets occurring in closed coronal loops. In this model, magnetic free energy is injected slowly by footpoint motions that introduce twist within the closed dome of the jet source region, and is released rapidly by the onset of an idealmore » kink-like instability. Two length scales characterize the system: the width (N) of the jet source region and the footpoint separation (L) of the coronal loop that envelops the jet source. We find that both the conditions for initiation and the subsequent dynamics are highly sensitive to the ratio L/N. The longest-lasting and most energetic jets occur along long coronal loops with large L/N ratios, and share many of the features of open-field jets, while smaller L/N ratios produce shorter-duration, less energetic jets that are affected by reflections from the far-loop footpoint. We quantify the transition between these behaviors and show that our model replicates key qualitative and quantitative aspects of both quiet Sun and active-region loop jets. We also find that the reconnection between the closed dome and surrounding coronal loop is very extensive: the cumulative reconnected flux at least matches the total flux beneath the dome for small L/N, and is more than double that value for large L/N.« less

3D MHD MODELING OF TWISTED CORONAL LOOPS

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

Reale, F.; Peres, G.; Orlando, S.

We perform MHD modeling of a single bright coronal loop to include the interaction with a non-uniform magnetic field. The field is stressed by random footpoint rotation in the central region and its energy is dissipated into heating by growing currents through anomalous magnetic diffusivity that switches on in the corona above a current density threshold. We model an entire single magnetic flux tube in the solar atmosphere extending from the high- β chromosphere to the low- β corona through the steep transition region. The magnetic field expands from the chromosphere to the corona. The maximum resolution is ∼30 km.more » We obtain an overall evolution typical of loop models and realistic loop emission in the EUV and X-ray bands. The plasma confined in the flux tube is heated to active region temperatures (∼3 MK) after ∼2/3 hr. Upflows from the chromosphere up to ∼100 km s{sup −1} fill the core of the flux tube to densities above 10{sup 9} cm{sup −3}. More heating is released in the low corona than the high corona and is finely structured both in space and time.« less

Numerical simulations of loops heated to solar flare temperatures. III - Asymmetrical heating

NASA Technical Reports Server (NTRS)

Cheng, C.-C.; Doschek, G. A.; Karpen, J. T.

1984-01-01

A numerical model is defined for asymmetric full solar flare loop heating and comparisons are made with observational data. The Dynamic Flux Tube Model is used to describe the heating process in terms of one-dimensional, two fluid conservation equations of mass, energy and momentum. An adaptive grid allows for the downward movement of the transition region caused by an advancing conduction front. A loop 20,000 km long is considered, along with a flare heating system and the hydrodynamic evolution of the loop. The model was applied to generating line profiles and spatial X-ray and UV line distributions, which were compared with SMM, P78-1 and Hintori data for Fe, Ca and Mg spectra. Little agreement was obtained, and it is suggested that flares be treated as multi-loop phenomena. Finally, it is concluded that chromospheric evaporation is not an effective mechanism for generating the soft X-ray bursts associated with flares.

Atomistic Simulations of the pH Induced Functional Rearrangement of Influenza Hemagglutinin

NASA Astrophysics Data System (ADS)

Lin, Xingcheng; Noel, Jeffrey; Wang, Qinghua; Ma, Jianpeng; Onuchic, Jose

Influenza hemagglutinin (HA), a surface glycoprotein responsible for the entry and replication of flu viruses in their host cells, functions by starting a dramatic conformational rearrangement, which leads to a fusion of the viral and endosomal membranes. It has been claimed that a loop-to-coiled-coil transition of the B-loop domain of HA drives the HA-induced membrane fusion. On the lack of dynamical details, however, the microscopic picture for this proposed ``spring-loaded'' movement is missing. To elaborate on the transition of the B-loop, we performed a set of unbiased all-atom molecular dynamics simulations of the full B-loop structure with the CHARMM36 force field. The complete free-energy profile constructed from our simulations reveals a slow transition rate for the B-loop that is incompatible with a downhill process. Additionally, our simulations indicate two potential sources of kinetic traps in the structural switch of the B-loop: Desolvation barriers and non-native secondary structure formation. The slow timescale of the B-loop transition also confirms our previous discovery from simulations using a coarse-grained structure-based model, which identified two competitive pathways both with a slow B-loop transition for HA to guide the membrane fusion.

Spectroscopic study of a dark lane and a cool loop in a solar limb active region by Hinode/EIS

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

Lee, Kyoung-Sun; Imada, S.; Moon, Y.-J.

2014-01-10

We investigated a cool loop and a dark lane over a limb active region on 2007 March 14 using the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in the coronal spectral lines and is rooted on a bright point. We examined their electron densities, Doppler velocities, and nonthermal velocities as a function of distance from the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII, and Femore » XIV spectra. We also compared the observed density scale heights with the calculated scale heights from each peak formation temperatures of the spectral lines under the hydrostatic equilibrium. We noted that the observed density scale heights of the cool loop are consistent with the calculated heights, with the exception of one observed cooler temperature; we also found that the observed scale heights of the dark lane are much lower than their calculated scale heights. The nonthermal velocity in the cool loop slightly decreases along the loop, while nonthermal velocity in the dark lane sharply falls off with height. Such a decrease in the nonthermal velocity may be explained by wave damping near the solar surface or by turbulence due to magnetic reconnection near the bright point.« less

Enthalpy-Based Thermal Evolution of Loops: III. Comparison of Zero-Dimensional Models

NASA Technical Reports Server (NTRS)

Cargill, P. J.; Bradshaw, Stephen J.; Klimchuk, James A.

2012-01-01

Zero dimensional (0D) hydrodynamic models, provide a simple and quick way to study the thermal evolution of coronal loops subjected to time-dependent heating. This paper presents a comparison of a number of 0D models that have been published in the past and is intended to provide a guide for those interested in either using the old models or developing new ones. The principal difference between the models is the way the exchange of mass and energy between corona, transition region and chromosphere is treated, as plasma cycles into and out of a loop during a heating-cooling cycle. It is shown that models based on the principles of mass and energy conservation can give satisfactory results at some, or, in the case of the Enthalpy Based Thermal Evolution of Loops (EBTEL) model, all stages of the loop evolution. Empirical models can lead to low coronal densities, spurious delays between the peak density and temperature, and, for short heating pulses, overly short loop lifetimes.

Simultaneous Solar Maximum Mission and Very Large Array (VLA) observations of solar active regions

NASA Technical Reports Server (NTRS)

Lang, K. R.

1985-01-01

Simultaneous observations of solar active regions with the Solar Maximum Mission (SMM) Satellite and the Very Large Array (VLA) have been obtained and analyzed. Combined results enhance the scientific return for beyond that expeted from using either SMM or VLA alone. A total of two weeks of simultaneous SMM/VLA data were obtained. The multiple wavelength VLA observations were used to determine the temperature and magnetic structure at different heights within coronal loops. These data are compared with simultaneous SMM observations. Several papers on the subject are in progress. They include VLA observations of compact, transient sources in the transition region; simultaneous SMM/VLA observations of the coronal loops in one active region and the evolution of another one; and sampling of the coronal plasma using thermal cyclotron lines (magnetic field - VLA) and soft X ray spectral lines (electron density and electron temperaure-SMM).

PROPERTIES AND MODELING OF UNRESOLVED FINE STRUCTURE LOOPS OBSERVED IN THE SOLAR TRANSITION REGION BY IRIS

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

Brooks, David H.; Reep, Jeffrey W.; Warren, Harry P.

Recent observations from the Interface Region Imaging Spectrograph ( IRIS ) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads.more » We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.« less

Formation of prismatic loops from C15 Laves phase interstitial clusters in body-centered cubic iron

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

Zhang, Yongfeng; Bai, Xian-Ming; Tonks, Michael R.

2015-03-01

This Letter reports the transition of C15 phase self-interstitial clusters to loops in body-centered-cubic Iron. Molecular dynamics simulations are performed to evaluate the relative stabilities of difference interstitial cluster configurations including C15 phase structure and <100> and <111>/2 loops. Within a certain size range, C15 cluster are found more stable than loops, and the relative stabilities are reversed beyond that range. In accordance to the crossover in relative stabilities, C15 clusters may grow by absorbing individual interstitials at small sizes and transitions into loops eventually. The transition takes place by nucleation and reaction of <111>/2 loop segments. These observations explainmore » the absence of C15 phase interstitial clusters predicted by density-functional-theory calculations in previous experimental observations. More importantly, the current results provide a new formation mechanism of <100> loops which requires no interaction of loops.« less

Energy balance and stability. [in stellar coronae

NASA Technical Reports Server (NTRS)

Hammer, R.

1982-01-01

The energy balance of the outer atmospheres of solarlike stars is discussed. The energy balance of open coronal regions is considered, discussing the construction and characteristics of models of such regions in some detail. In particular, the temperature as a function of height is considered, as are the damping length dependence of the global energy balance in the region between the base of the transition region and the critical point, and the effects of changing the amount of coronal heating, the stellar mass, and the stellar radius. Models of coronal loops are more briefly discussed. The chromosphere is then included in the discussion of the energy balance, and the connection between global energy balance and global thermal stability is addressed. The observed positive correlations between the chromospheric and coronal energy losses and the pressure of the transition region is qualitatively explained.

Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.

PubMed

Banerjee, Rahul; Yan, Honggao; Cukier, Robert I

2015-06-04

Signal transduction is of vital importance to the growth and adaptation of living organisms. The key to understand mechanisms of biological signal transduction is elucidation of the conformational dynamics of its signaling proteins, as the activation of a signaling protein is fundamentally a process of conformational transition from an inactive to an active state. A predominant form of signal transduction for bacterial sensing of environmental changes in the wild or inside their hosts is a variety of two-component systems, in which the conformational transition of a response regulator (RR) from an inactive to an active state initiates responses to the environmental changes. Here, RR activation has been investigated using RR468 as a model system by extensive unbiased all-atom molecular dynamics (MD) simulations in explicit solvent, starting from snapshots along a targeted MD trajectory that covers the conformational transition. Markov state modeling, transition path theory, and geometric analyses of the wealth of the MD data have provided a comprehensive description of the RR activation. It involves a network of metastable states, with one metastable state essentially the same as the inactive state and another very similar to the active state that are connected via a small set of intermediates. Five major pathways account for >75% of the fluxes of the conformational transition from the inactive to the active-like state. The thermodynamic stability of the states and the activation barriers between states are found, to identify rate-limiting steps. The conformal transition is initiated predominantly by movements of the β3α3 loop, followed by movements of the β4α4-loop and neighboring α4 helix region, and capped by additional movements of the β3α3 loop. A number of transient hydrophobic and hydrogen bond interactions are revealed, and they may be important for the conformational transition.

Height Dependence of Plasma Properties of a Dark Lane and a Cool Loop in a Solar Limb Active Region Observed by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, K.; Imada, S.; Moon, Y.; Lee, J.

2013-12-01

We investigate spectral properties of a cool loop and a dark lane over a limb active region on 2007 March 14 by the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in coronal spectral lines and rooted on a bright point. We determine their electron densities, Doppler velocities, and non-thermal velocities with height over the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII and Fe XIV spectra. Under the hydrostatic equilibrium and isothermal assumption, we determine their temperatures from the density scale height. Comparing the scale height temperatures to the peak formation temperatures of the spectral lines, we note that the scale height temperature of the cool loop is consistent with a peak formation temperature of the Fe XII and the scale height temperatures of the dark lane from each spectral lines are much lower than their peak formation temperatures. The non-thermal velocity in the cool loop slightly decreases along the loop while that in the dark lane sharply falls off with height. The variation of non-thermal velocity with height in the cool loop and the dark lane is contrast to that in off-limb polar coronal holes which are considered as source of the solar wind. Such a decrease in the non-thermal velocity may be explained by wave damping near the solar surface or turbulence due to magnetic reconnection near the bright point.

20-Hydroxyecdysone (20E) Primary Response Gene E75 Isoforms Mediate Steroidogenesis Autoregulation and Regulate Developmental Timing in Bombyx*

PubMed Central

Li, Kang; Tian, Ling; Guo, Zhongjian; Guo, Sanyou; Zhang, Jianzhen; Gu, Shi-Hong; Palli, Subba R.; Cao, Yang; Li, Sheng

2016-01-01

The temporal control mechanisms that precisely control animal development remain largely elusive. The timing of major developmental transitions in insects, including molting and metamorphosis, is coordinated by the steroid hormone 20-hydroxyecdysone (20E). 20E involves feedback loops to maintain pulses of ecdysteroid biosynthesis leading to its upsurge, whereas the underpinning molecular mechanisms are not well understood. Using the silkworm Bombyx mori as a model, we demonstrated that E75, the 20E primary response gene, mediates a regulatory loop between ecdysteroid biosynthesis and 20E signaling. E75 isoforms A and C directly bind to retinoic acid receptor-related response elements in Halloween gene promoter regions to induce gene expression thus promoting ecdysteroid biosynthesis and developmental transition, whereas isoform B antagonizes the transcriptional activity of isoform A/C through physical interaction. As the expression of E75 isoforms is differentially induced by 20E, the E75-mediated regulatory loop represents a fine autoregulation of steroidogenesis, which contributes to the precise control of developmental timing. PMID:27365399

Transition probability spaces in loop quantum gravity

NASA Astrophysics Data System (ADS)

Guo, Xiao-Kan

2018-03-01

We study the (generalized) transition probability spaces, in the sense of Mielnik and Cantoni, for spacetime quantum states in loop quantum gravity. First, we show that loop quantum gravity admits the structures of transition probability spaces. This is exemplified by first checking such structures in covariant quantum mechanics and then identifying the transition probability spaces in spin foam models via a simplified version of general boundary formulation. The transition probability space thus defined gives a simple way to reconstruct the discrete analog of the Hilbert space of the canonical theory and the relevant quantum logical structures. Second, we show that the transition probability space and in particular the spin foam model are 2-categories. Then we discuss how to realize in spin foam models two proposals by Crane about the mathematical structures of quantum gravity, namely, the quantum topos and causal sites. We conclude that transition probability spaces provide us with an alternative framework to understand various foundational questions of loop quantum gravity.

Alfven-wave dissipation: A support mechanism for quiescent prominences

NASA Technical Reports Server (NTRS)

Jensen, Eberhart

1986-01-01

High resolution filtergrams or spectrograms of the main body of quiescent prominences often show a very vivid dynamical picture that cannot be reconciled with static models. Even if large differences exist between individual prominences in this respect, at least parts of the prominence are usually found to be in a 'choppy', turbulent state. Evidence for systematic flows are found in local regions in the prominence and also in the transition zone in the surroundings. These two regions are probably decoupled magnetically. Alfven waves are generally believed to be responsible for the heating in the upper chromosphere and corona (Hollweg 1986). Since evidence for the presence of Alfven-waves has also been found in the solar wind field, it is highly probable that such waves are generated in the convection zone of the sun and propagated outwards in the solar atmosphere wherever a proper magnetic field is present to carry the waves. The most basic magnetic formations in the solar atmosphere are simple loops. They occur all over the solar surface and cover a large range of magnetic field strengths. Loops with the strongest magnetic fields are found in active regions. It is to be expected that the Alfven-wave flux which is channelled into the loops from below, could show considerable variation both with heliocentric latitude, with time and locally between neighbouring loops. What happens when a magnetic loop is exposed to the appropriate Alfven-wave flux required to heat the upper solar atmosphere is examined.

Coronal loop hydrodynamics. The solar flare observed on November 12, 1980 revisited: The UV line emission

NASA Astrophysics Data System (ADS)

Betta, R. M.; Peres, G.; Reale, F.; Serio, S.

2001-12-01

We revisit a well-studied solar flare whose X-ray emission originating from a simple loop structure was observed by most of the instruments on board SMM on November 12, 1980. The X-ray emission of this flare, as observed with the XRP, was successfully modeled previously. Here we include a detailed modeling of the transition region and we compare the hydrodynamic results with the UVSP observations in two EUV lines, measured in areas smaller than the XRP rasters, covering only some portions of the flaring loop (the top and the foot-points). The single loop hydrodynamic model, which fits well the evolution of coronal lines (those observed with the XRP and the Fe XXI 1354.1 Å line observed with the UVSP) fails to model the flux level and evolution of the O V 1371.3 Åline.

The effect of nonequilibrium ionization on ultraviolet line shifts in the solar transition region

NASA Technical Reports Server (NTRS)

Spadaro, D.; Noci, G.; Zappala, R. A.; Antiochos, S. K.

1990-01-01

The line profiles and wavelength positions of all the important emission lines due to carbon were computed for a variety of steady state siphon flow loop models. For the lines from the lower ionization states (C II-C IV) a preponderance of blueshifts was found, contrary to the observations. The lines from the higher ionization states can show either a net red- or blueshift, depending on the position of the loop on the solar disk. Similar results are expected for oxygen. It is concluded that the observed redshifts cannot be explained by the models proposed here.

Intensity of emission lines of the quiescent solar corona: comparison between calculated and observed values

NASA Astrophysics Data System (ADS)

Krissinel, Boris

2018-03-01

The paper reports the results of calculations of the center-to-limb intensity of optically thin line emission in EUV and FUV wavelength ranges. The calculations employ a multicomponent model for the quiescent solar corona. The model includes a collection of loops of various sizes, spicules, and free (inter-loop) matter. Theoretical intensity values are found from probabilities of encountering parts of loops in the line of sight with respect to the probability of absence of other coronal components. The model uses 12 loops with sizes from 3200 to 210000 km with different values of rarefaction index and pressure at the loop base and apex. The temperature at loop apices is 1 400 000 K. The calculations utilize the CHIANTI database. The comparison between theoretical and observed emission intensity values for coronal and transition region lines obtained by the SUMER, CDS, and EIS telescopes shows quite satisfactory agreement between them, particularly for the solar disk center. For the data acquired above the limb, the enhanced discrepancies after the analysis refer to errors in EIS measurements.

Effects of Composite Pions on the Chiral Condensate within the PNJL Model at Finite Temperature

NASA Astrophysics Data System (ADS)

Blaschke, D.; Dubinin, A.; Ebert, D.; Friesen, A. V.

2018-05-01

We investigate the effect of composite pions on the behaviour of the chiral condensate at finite temperature within the Polyakov-loop improved NJL model. To this end we treat quark-antiquark correlations in the pion channel (bound states and scattering continuum) within a Beth-Uhlenbeck approach that uses medium-dependent phase shifts. A striking medium effect is the Mott transition which occurs when the binding energy vanishes and the discrete pion bound state merges the continuum. This transition is triggered by the lowering of the continuum edge due to the chiral restoration transition. This in turn also entails a modification of the Polyakov-loop so that the SU(3) center symmetry gets broken at finite temperature and dynamical quarks (and gluons) appear in the system, taking over the role of the dominant degrees of freedom from the pions. At low temperatures our model reproduces the chiral perturbation theory result for the chiral condensate while at high temperatures the PNJL model result is recovered. The new aspect of the current work is a consistent treatment of the chiral restoration transition region within the Beth-Uhlenbeck approach on the basis of mesonic phase shifts for the treatment of the correlations.

Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II.

PubMed

Bairagya, Hridoy R; Mukhopadhyay, Bishnu P; Bera, Asim K

2011-01-01

Inosine monophosphate dehydrogenase (IMPDH) of human is involved in GMP biosynthesis pathway, increased level of IMPDH-II (an isoform of enzyme) activity have found in leukemic and sarcoma cells. Modeling and extensive molecular dynamics simulation (15 ns) studies of IMPDH-II (1B3O PDB structure) have indicated the intricate involvement of four conserved water molecules (W 1, W 2, W 3, and W 4) in the conformational transition or the mobilities of "flap" (residues 400-450) and "loop" (residues 325-342) regions in enzyme. The stabilization of active site residues Asn 303, Gly 324, Ser 329, Cys 331, Asp 364, and Tyr 411 through variable H-bonding coordination from the conserved water molecular center seems interesting in the uninhibited hydrated form of human IMPDH-II structures. This conformational transition or the flexibility of mobile regions, water molecular recognition to active site residues Cys 331 and Tyr 411, and the presence of a hydrophilic cavity approximately 540 Å(3) (enclaved by the loop and flap region) near the C-terminal surface of this enzyme may explore a rational hope toward the water mimic inhibitor or anticancer agent design for human. 2010 John Wiley & Sons, Ltd.

Physiological control of a rotary blood pump with selectable therapeutic options: control of pulsatility gradient.

PubMed

Arndt, Andreas; Nüsser, Peter; Graichen, Kurt; Müller, Johannes; Lampe, Bernhard

2008-10-01

A control strategy for rotary blood pumps meeting different user-selectable control objectives is proposed: maximum support with the highest feasible flow rate versus medium support with maximum ventricular washout and controlled opening of the aortic valve (AoV). A pulsatility index (PI) is calculated from the pressure difference, which is deduced from the axial thrust measured by the magnetic bearing of the pump. The gradient of PI with respect to pump speed (GPI) is estimated via online system identification. The outer loop of a cascaded controller regulates GPI to a reference value satisfying the selected control objective. The inner loop controls the PI to a reference value set by the outer loop. Adverse pumping states such as suction and regurgitation can be detected on the basis of the GPI estimates and corrected by the controller. A lumped-parameter computer model of the assisted circulation was used to simulate variations of ventricular contractility, pulmonary venous pressure, and aortic pressure. The performance of the outer control loop was demonstrated by transitions between the two control modes. Fast reaction of the inner loop was tested by stepwise reduction of venous return. For maximum support, a low PI was maintained without inducing ventricular collapse. For maximum washout, the pump worked at a high PI in the transition region between the opening and the permanently closed AoV. The cascaded control of GPI and PI is able to meet different control objectives and is worth testing in vitro and in vivo.

OBSERVING CORONAL NANOFLARES IN ACTIVE REGION MOSS

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

Testa, Paola; DeLuca, Ed; Golub, Leon

2013-06-10

The High-resolution Coronal Imager (Hi-C) has provided Fe XII 193A images of the upper transition region moss at an unprecedented spatial ({approx}0.''3-0.''4) and temporal (5.5 s) resolution. The Hi-C observations show in some moss regions variability on timescales down to {approx}15 s, significantly shorter than the minute-scale variability typically found in previous observations of moss, therefore challenging the conclusion of moss being heated in a mostly steady manner. These rapid variability moss regions are located at the footpoints of bright hot coronal loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly in the 94 A channel, and by the Hinode/X-Raymore » Telescope. The configuration of these loops is highly dynamic, and suggestive of slipping reconnection. We interpret these events as signatures of heating events associated with reconnection occurring in the overlying hot coronal loops, i.e., coronal nanoflares. We estimate the order of magnitude of the energy in these events to be of at least a few 10{sup 23} erg, also supporting the nanoflare scenario. These Hi-C observations suggest that future observations at comparable high spatial and temporal resolution, with more extensive temperature coverage, are required to determine the exact characteristics of the heating mechanism(s).« less

Analysis of Inter-Moss Loops in the Solar Region with IRIS and SDO AIA: Automatic Event Detection and Characterization

NASA Technical Reports Server (NTRS)

Fayock, Brian; Winebarger, Amy; De Pontieu, Bart; Alexander, Caroline

2016-01-01

The Interface Region Imaging Spectrograph (IRIS), launched in the summer of 2013, is designed specifically to observe and investigate the transition region and adjacent layers of the solar atmosphere, obtaining images in high spatial, temporal, and spectral resolution. Our particular work is focused on the evolution of inter-moss loops, which have been detected in the lower corona by the Atmospheric Imaging Assembly (AIA) and the High-Resolution Coronal Imager (Hi- C), but are known to have foot points below the transition region. With the high-resolution capabilities of IRIS and its Si IV pass band, which measures activity in the upper chromosphere, we can study these magnetic loops in detail and compare their characteristic length and time scales to those obtained from several AIA image sets, particularly the 171, 193, and 211 pass bands. By comparing the results between these four data sets, one can potentially establish a measure of the ionization equilibrium for the location in question. To explore this idea, we found a large, sit-and-stare observation within the IRIS database that fit our specifications. This data set contained a number of well-defined inter-moss loops (by visual inspection) with a cadence less than or equal to that of AIA (approximately 12 seconds). This particular data set was recorded on October 23, 2013 at 07:09:30, lasting for 3219 seconds with a field of view of 120.6 by 128.1 arcseconds, centered on -53.9 by 59.1 arcseconds from disk center. For ease of comparison, the AIA data has been interpolated to match the IRIS cadence and resolution. In the main portion of the poster, we demonstrate the detection of events, the information collected, and the immediate results to the right, showing the progress of an event with green as the start, blue as the peak, and red as the end. Below here, we demonstrate how pixels are combined to form groups. The 3D results are shown to the right

Analysis of Inter-Moss Loops in the Solar Region with IRIS and SDO AIA: Automatic Event Detection and Characterization

NASA Technical Reports Server (NTRS)

Fayock, Brian; Winebarger, Amy; De Pontieu, Bart

2014-01-01

The Interface Region Imaging Spectrograph (IRIS), launched in the summer of 2013, is designed specifically to observe and investigate the transition region and adjacent layers of the solar atmosphere, obtaining images in high spatial, temporal, and spectral resolution. Our particular work is focused on the evolution of inter-moss loops, which have been detected in the lower corona by the Atmospheric Imaging Assembly (AIA) and the High-Resolution Coronal Imager (Hi- C), but are known to have foot points below the transition region. With the high-resolution capabilities of IRIS and its Si IV pass band, which measures activity in the upper chromosphere, we can study these magnetic loops in detail and compare their characteristic length and time scales to those obtained from several AIA image sets, particularly the 171, 193, and 211 pass bands. By comparing the results between these four data sets, one can potentially establish a measure of the ionization equilibrium for the location in question. To explore this idea, we found a large, sit-and-stare observation within the IRIS database that fit our specifications. This data set contained a number of well-defined inter-moss loops (by visual inspection) with a cadence less than or equal to that of AIA (approximately 12 seconds). This particular data set was recorded on October 23, 2013 at 07:09:30, lasting for 3219 seconds with a field of view of 120.6 by 128.1 arcseconds, centered on -53.9 by 59.1 arcseconds from disk center. For ease of comparison, the AIA data has been interpolated to match the IRIS cadence and resolution. In the main portion of the poster, we demonstrate the detection of events, the information collected, and the immediate results to the right, showing the progress of an event with green as the start, blue as the peak, and red as the end. Below here, we demonstrate how pixels are combined to form groups. The 3D results are shown to the right.

Generalized ensemble method applied to study systems with strong first order transitions

DOE PAGES

Malolepsza, E.; Kim, J.; Keyes, T.

2015-09-28

At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub, where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM).more » This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. Lastly, the method is illustrated in a study of the very strong solid/liquid transition in water.« less

Generalized ensemble method applied to study systems with strong first order transitions

NASA Astrophysics Data System (ADS)

Małolepsza, E.; Kim, J.; Keyes, T.

2015-09-01

At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub [1], where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM). This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. The method is illustrated in a study of the very strong solid/liquid transition in water.

Spectroscopic Study of a Dark Lane and a Cool Loop in a Solar Limb Active Region by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, K.; Imada, S.; Moon, Y.; Lee, J.

2012-12-01

We investigate a cool loop and a dark lane over a limb active region on 2007 March 14 by the Hinode/EUV Imaging Spectrometer (EIS). The cool loop is clearly seen in the EIS spectral lines formed at the transition region temperature (log T = 5.8). The dark lane is characterized by an elongated faint structure in coronal spectral lines (log T = 5.8 - 6.1) and rooted on a bright point. We examine their electron densities, Doppler velocities, and non-thermal velocities as a function of distance from the limb using the spectral lines formed at different temperatures (log T = 5.4 - 6.4). The electron densities of the cool loop and the dark lane are derived from the density sensitive line pairs of Mg VII, Fe XII, and Fe XIV spectra. Under the hydrostatic equilibrium and isothermal assumption, we determine their temperatures from the density scale height. Comparing the scale height temperatures to the peak formation temperatures of the spectral lines, we note that the scale height temperature of the cool loop is consistent with a peak formation temperature of the Mg VII (log T = 5.8) and the scale height temperature of the dark lane is close to a peak formation temperature of the Fe XII and Fe XIII (log T = 6.1 - 6.2). It is interesting to note that the structures of the cool loop and the dark lane are most visible in these temperature lines. While the non-thermal velocity in the cool loop slightly decreases (less than 7 km {s-1}) along the loop, that in the dark lane sharply falls off with height. The variation of non-thermal velocity with height in the cool loop and the dark lane is contrast to that in off-limb polar coronal holes which are considered as source of the fast solar wind. Such a decrease in the non-thermal velocity may be explained by wave damping near the solar surface or turbulence due to magnetic reconnection near the bright point.

The temperature dependence of heavy-ion damage in iron: A microstructural transition at elevated temperatures

NASA Astrophysics Data System (ADS)

Yao, Z.; Jenkins, M. L.; Hernández-Mayoral, M.; Kirk, M. A.

2010-12-01

A transition is reported in the dislocation microstructure of pure Fe produced by heavy-ion irradiation of thin foils, which took place between irradiation temperatures (T irr) of 300°C and 500°C. At T irr ≤ 400°C, the microstructure was dominated by round or irregular non-edge dislocation loops of interstitial nature and with Burgers vectors b = ½ ⟨111⟩, although interstitial ⟨100⟩ loops were also present; at 500°C only rectilinear pure-edge ⟨100⟩ loops occurred. At intermediate temperatures there was a gradual transition between the two types of microstructure. At temperatures just below 500°C, mobile ½⟨111⟩ loops were seen to be subsumed by sessile ⟨100⟩ loops. A possible explanation of these observations is given.

Multiprotein DNA Looping

NASA Astrophysics Data System (ADS)

Vilar, Jose M. G.; Saiz, Leonor

2006-06-01

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

Bayesian, maximum parsimony and UPGMA models for inferring the phylogenies of antelopes using mitochondrial markers.

PubMed

Khan, Haseeb A; Arif, Ibrahim A; Bahkali, Ali H; Al Farhan, Ahmad H; Al Homaidan, Ali A

2008-10-06

This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers.

Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers

PubMed Central

Khan, Haseeb A.; Arif, Ibrahim A.; Bahkali, Ali H.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.

2008-01-01

This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers. PMID:19204824

Thermal stability of static coronal loops: Part 1: Effects of boundary conditions

NASA Technical Reports Server (NTRS)

Antiochos, S. K.; Shoub, E. C.; An, C. H.; Emslie, A. G.

1985-01-01

The linear stability of static coronal-loop models undergoing thermal perturbations was investigated. The effect of conditions at the loop base on the stability properties of the models was considered in detail. The question of appropriate boundary conditions at the loop base was considered and it was concluded that the most physical assumptions are that the temperature and density (or pressure) perturbations vanish there. However, if the base is taken to be sufficiently deep in the chromosphere, either several chromospheric scale heights or several coronal loop lengths in depth, then the effect of the boundary conditions on loop stability becomes negligible so that all physically acceptable conditions are equally appropriate. For example, one could as well assume that the velocity vanishes at the base. The growth rates and eigenmodes of static models in which gravity is neglected and in which the coronal heating is a relatively simple function, either constant per-unit mass or per-unit volume were calculated. It was found that all such models are unstable with a growth rate of the order of the coronal cooling time. The physical implications of these results for the solar corona and transition region are discussed.

Probing the Quiet Solar Atmosphere from the Photosphere to the Corona

NASA Astrophysics Data System (ADS)

Kontogiannis, Ioannis; Gontikakis, Costis; Tsiropoula, Georgia; Tziotziou, Kostas

2018-04-01

We investigate the morphology and temporal variability of a quiet-Sun network region in different solar layers. The emission in several extreme ultraviolet (EUV) spectral lines through both raster and slot time-series, recorded by the EUV Imaging Spectrometer (EIS) on board the Hinode spacecraft is studied along with Hα observations and high-resolution spectropolarimetric observations of the photospheric magnetic field. The photospheric magnetic field is extrapolated up to the corona, showing a multitude of large- and small-scale structures. We show for the first time that the smallest magnetic structures at both the network and internetwork contribute significantly to the emission in EUV lines, with temperatures ranging from 8× 104 K to 6× 105 K. Two components of transition region emission are present, one associated with small-scale loops that do not reach coronal temperatures, and another component that acts as an interface between coronal and chromospheric plasma. Both components are associated with persistent chromospheric structures. The temporal variability of the EUV intensity at the network region is also associated with chromospheric motions, pointing to a connection between transition region and chromospheric features. Intensity enhancements in the EUV transition region lines are preferentially produced by Hα upflows. Examination of two individual chromospheric jets shows that their evolution is associated with intensity variations in transition region and coronal temperatures.

Shear-induced structural transitions in Newtonian non-Newtonian two-phase flow

NASA Astrophysics Data System (ADS)

Cristobal, G.; Rouch, J.; Colin, A.; Panizza, P.

2000-09-01

We show the existence under shear flow of steady states in a two-phase region of a brine-surfactant system in which lyotropic dilute lamellar (non-Newtonian) and sponge (Newtonian) phases are coexisting. At high shear rates and low sponge phase-volume fractions, we report on the existence of a dynamic transition corresponding to the formation of a colloidal crystal of multilamellar vesicles (or ``onions'') immersed in the sponge matrix. As the sponge phase-volume fraction increases, this transition exhibits a hysteresis loop leading to a structural bistability of the two-phase flow. Contrary to single phase lamellar systems where it is always 100%, the onion volume fraction can be monitored continuously from 0 to 100 %.

Transition scenario and transition control of the flow over a semi-infinite square leading-edge plate

NASA Astrophysics Data System (ADS)

Huang, Yadong; Zhou, Benmou; Tang, Zhaolie; Zhang, Fei

2017-07-01

In recent investigations of the flow over a square leading-edge flat plate, elliptic instability and transient growth of perturbations are proposed to explain the turbulent transition mechanism of the separating and reattaching flow reported in early experimental visualizations. An original transition scenario as well as a transition control method is presented by a detailed numerical study in this paper. The transient growth of perturbations in the separation bubble induces the primary instability that causes the 2D unsteady flow consisting of Kelvin-Helmholtz (KH) vortices. The pairing instability of the KH vortices induces the subharmonic secondary instability, and then resonance transition occurs. The streamwise Lorentz force as the control input is applied in the recirculation region where the separation bubble generates. The maximum energy amplification magnitude of perturbations takes a linear attenuation with the interaction number; thus, the primary instability is reduced under control. The interaction number represents the strength of the streamwise Lorentz force relative to the inertial force of the fluid. The reduced primary instability is not strong enough to induce the secondary instability, so the flow is globally stable under control. Three-dimensional direct numerical simulation confirms the results of the linear stability analysis. Although the growth rate of the convectively unstable secondary instability is limited by the flow field scale, the feedback loop of the energy transfer promotes the resonance transition. However, as the separation bubble scale is reduced and the feedback loop is broken by the streamwise Lorentz force, the three-dimensional transition is suppressed and a skin-friction drag reduction is achieved.

Multiple states and hysteresis in a two-layer loop current type system

NASA Astrophysics Data System (ADS)

Kuehl, J.; Sheremet, V.

2017-12-01

Rotating table experiments are considered of a two-layer loop current type or gap-leaping system. Such experiments are representative of oceanic regions including the Kuroshio current crossing the Luzon Strait, the Gulf of Mexico Loop Current, the Northeast Chanel of the Gulf of Maine where Scotian shelf water leaps directly from Browns bank to Georges Bank and more. Systems such as these are known to admit two dominant states: leaping across the gap or penetrating into the gap forming a loop current. Which state the system will assume and when transitions between states will occur are open problems. We show that such systems admit multiple steady states with hysteresis when the strength of the current is varied. When the state of the system is viewed in a parameter space representing inertia and vorticity constraint, the system is found to be characterized by a cusp topology of solutions. The existence of such dynamics in two-layer quasi-geostrophic systems has significant implications for oceanographic predictability.

The Coronal Monsoon: Thermal Nonequilibrium Revealed by Periodic Coronal Rain

NASA Astrophysics Data System (ADS)

Auchère, Frédéric; Froment, Clara; Soubrié, Elie; Antolin, Patrick; Oliver, Ramon; Pelouze, Gabriel

2018-02-01

We report on the discovery of periodic coronal rain in an off-limb sequence of Solar Dynamics Observatory/Atmospheric Imaging Assembly images. The showers are co-spatial and in phase with periodic (6.6 hr) intensity pulsations of coronal loops of the sort described by Auchère et al. and Froment et al. These new observations make possible a unified description of both phenomena. Coronal rain and periodic intensity pulsations of loops are two manifestations of the same physical process: evaporation/condensation cycles resulting from a state of thermal nonequilibrium. The fluctuations around coronal temperatures produce the intensity pulsations of loops, and rain falls along their legs if thermal runaway cools the periodic condensations down and below transition-region temperatures. This scenario is in line with the predictions of numerical models of quasi-steadily and footpoint heated loops. The presence of coronal rain—albeit non-periodic—in several other structures within the studied field of view implies that this type of heating is at play on a large scale.

Does TRACE Resolve Isothermal Coronal Loops?

NASA Astrophysics Data System (ADS)

Weber, Mark A.; Schmelz, J.; Kashyap, V.; Roames, J.

2006-06-01

Historically, increasing resolution of solar data has revealed ever smaller length scales for both the thermodynamics and the magnetic structure of the corona. Furthermore, the dynamics there are governed by magnetohydrodynamic processes which are difficult to observe or model. Recent results in the literature suggest that some coronal loops with cross-sections near the resolution limits of the Transition Region and Coronal Explorer (pixel size = 0.5 arc-seconds, or approx. 360 km) are, in fact, isothermally homogeneous and thus may be identified as elementary loop strands. This poster presents some ongoing work that applies state-of-the-art estimation of differential emission measures in order to evaluate these claims for a sample of loops. We find that the data give no evidence to prefer the "isothermal" hypothesis over the "multithermal" hypothesis. The authors are supported by the following funds: contract SP02H820IR to the Lockheed-Martin Corp.; NSF grant ATM-0402729; NASA grant NNG05GE68G; and NASA contracts NAS8-39073 and NAS8-03060.

A Hot Downflowing Model Atmosphere for Umbral Flashes and the Physical Properties of Their Dark Fibrils

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

Henriques, V. M. J.; Mathioudakis, M.; Socas-Navarro, H.

We perform non-LTE inversions in a large set of umbral flashes, including the dark fibrils visible within them, and in the quiescent umbra by using the inversion code NICOLE on a set of full Stokes high-resolution Ca ii λ 8542 observations of a sunspot at disk center. We find that the dark structures have Stokes profiles that are distinct from those of the quiescent and flashed regions. They are best reproduced by atmospheres that are more similar to the flashed atmosphere in terms of velocities, even if with reduced amplitudes. We also find two sets of solutions that finely fitmore » the flashed profiles: a set that is upflowing, featuring a transition region that is deeper than in the quiescent case and preceded by a slight dip in temperature, and a second solution with a hotter atmosphere in the chromosphere but featuring downflows close to the speed of sound at such heights. Such downflows may be related, or even dependent, on the presence of coronal loops, rooted in the umbra of sunspots, as is the case in the region analyzed. Similar loops have been recently observed to have supersonic downflows in the transition region and are consistent with the earlier “sunspot plumes,” which were invariably found to display strong downflows in sunspots. Finally, we find, on average, a magnetic field reduction in the flashed areas, suggesting that the shock pressure is moving field lines in the upper layers.« less

Free energy and phase transition of the matrix model on a plane wave

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

Hadizadeh, Shirin; Ramadanovic, Bojan; Semenoff, Gordon W.

2005-03-15

It has recently been observed that the weakly coupled plane-wave matrix model has a density of states which grows exponentially at high energy. This implies that the model has a phase transition. The transition appears to be of first order. However, its exact nature is sensitive to interactions. In this paper, we analyze the effect of interactions by computing the relevant parts of the effective potential for the Polyakov loop operator in the finite temperature plane-wave matrix model to three-loop order. We show that the phase transition is indeed of first order. We also compute the correction to the Hagedornmore » temperature to order two loops.« less

MULTI-STRAND CORONAL LOOP MODEL AND FILTER-RATIO ANALYSIS

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

Bourouaine, Sofiane; Marsch, Eckart, E-mail: bourouaine@mps.mpg.d

2010-01-10

We model a coronal loop as a bundle of seven separate strands or filaments. Each of the loop strands used in this model can independently be heated (near their left footpoints) by Alfven/ion-cyclotron waves via wave-particle interactions. The Alfven waves are assumed to penetrate the strands from their footpoints, at which we consider different wave energy inputs. As a result, the loop strands can have different heating profiles, and the differential heating can lead to a varying cross-field temperature in the total coronal loop. The simulation of Transition Region and Coronal Explorer (TRACE) observations by means of this loop modelmore » implies two uniform temperatures along the loop length, one inferred from the 171:195 filter ratio and the other from the 171:284 ratio. The reproduced flat temperature profiles are consistent with those inferred from the observed extreme-ultraviolet coronal loops. According to our model, the flat temperature profile is a consequence of the coronal loop consisting of filaments, which have different temperatures but almost similar emission measures in the cross-field direction. Furthermore, when we assume certain errors in the simulated loop emissions (e.g., due to photometric uncertainties in the TRACE filters) and use the triple-filter analysis, our simulated loop conditions become consistent with those of an isothermal plasma. This implies that the use of TRACE or EUV Imaging Telescope triple filters for observation of a warm coronal loop may not help in determining whether the cross-field isothermal assumption is satisfied or not.« less

High-resolution observations of active region moss and its dynamics

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

Morton, R. J.; McLaughlin, J. A., E-mail: richard.morton@northumbria.ac.uk

2014-07-10

The High Resolution Coronal Imager has provided the sharpest view of the EUV corona to date. In this paper, we exploit its impressive resolving power to provide the first analysis of the fine-scale structure of moss in an active region. The data reveal that the moss is made up of a collection of fine threads that have widths with a mean and standard deviation of 440 ± 190 km (FWHM). The brightest moss emission is located at the visible head of the fine-scale structure and the fine structure appears to extend into the lower solar atmosphere. The emission decreases alongmore » the features, implying that the lower sections are most likely dominated by cooler transition region plasma. These threads appear to be the cool, lower legs of the hot loops. In addition, the increased resolution allows for the first direct observation of physical displacements of the moss fine structure in a direction transverse to its central axis. Some of these transverse displacements demonstrate periodic behavior, which we interpret as a signature of kink (Alfvénic) waves. Measurements of the properties of the transverse motions are made and the wave motions have means and standard deviations of 55 ± 37 km for the transverse displacement amplitude, 77 ± 33 s for the period, and 4.7 ± 2.5 km s{sup –1} for the velocity amplitude. The presence of waves in the transition region of hot loops could have important implications for the heating of active regions.« less

ANALYSIS OF CORONAL RAIN OBSERVED BY IRIS , HINODE /SOT, AND SDO /AIA: TRANSVERSE OSCILLATIONS, KINEMATICS, AND THERMAL EVOLUTION

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

Kohutova, P.; Verwichte, E., E-mail: p.kohutova@warwick.ac.uk

Coronal rain composed of cool plasma condensations falling from coronal heights along magnetic field lines is a phenomenon occurring mainly in active region coronal loops. Recent high-resolution observations have shown that coronal rain is much more common than previously thought, suggesting its important role in the chromosphere-corona mass cycle. We present the analysis of MHD oscillations and kinematics of the coronal rain observed in chromospheric and transition region lines by the Interface Region Imaging Spectrograph (IRIS) , the Hinode Solar Optical Telescope (SOT), and the Solar Dynamics Observatory ( SDO) Atmospheric Imaging Assembly (AIA). Two different regimes of transverse oscillationsmore » traced by the rain are detected: small-scale persistent oscillations driven by a continuously operating process and localized large-scale oscillations excited by a transient mechanism. The plasma condensations are found to move with speeds ranging from few km s{sup −1} up to 180 km s{sup −1} and with accelerations largely below the free-fall rate, likely explained by pressure effects and the ponderomotive force resulting from the loop oscillations. The observed evolution of the emission in individual SDO /AIA bandpasses is found to exhibit clear signatures of a gradual cooling of the plasma at the loop top. We determine the temperature evolution of the coronal loop plasma using regularized inversion to recover the differential emission measure (DEM) and by forward modeling the emission intensities in the SDO /AIA bandpasses using a two-component synthetic DEM model. The inferred evolution of the temperature and density of the plasma near the apex is consistent with the limit cycle model and suggests the loop is going through a sequence of periodically repeating heating-condensation cycles.« less

Is the kinetoplast DNA a percolating network of linked rings at its critical point?

NASA Astrophysics Data System (ADS)

Michieletto, Davide; Marenduzzo, Davide; Orlandini, Enzo

2015-05-01

In this work we present a computational study of the kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation transition between a gas of unlinked rings and a network of linked loops which spans the whole system. Close to the percolation transition, we find that the mean valency of the network, i.e. the average number of loops which are linked to any one loop, is around three, as found experimentally for the kinetoplast DNA (kDNA). Even more importantly, by simulating the digestion of the network by a restriction enzyme, we show that the distribution of oligomers, i.e. structures formed by a few loops which remain linked after digestion, quantitatively matches experimental data obtained from gel electrophoresis, provided that the density is, once again, close to the percolation transition. With respect to previous work, our analysis builds on a reduced number of assumptions, yet can still fully explain the experimental data. Our findings suggest that the kDNA can be viewed as a network of linked loops positioned very close to the percolation transition, and we discuss the possible biological implications of this remarkable fact.

Thermodynamics of single polyethylene and polybutylene glycols with hydrogen-bonding ends: A transition from looped to open conformations

NASA Astrophysics Data System (ADS)

Lee, Eunsang; Paul, Wolfgang

2018-02-01

A variety of linear polymer precursors with hydrogen bonding motifs at both ends enable us to design supramolecular polymer systems with tailored macroscopic properties including self-healing. In this study, we investigate thermodynamic properties of single polyethylene and polybutylene glycols with hydrogen bonding motifs. In this context, we first build a coarse-grained model of building blocks of the supramolecular polymer system based on all-atom molecular structures. The density of states of the single precursor is obtained using the stochastic approximation Monte Carlo method. Constructing canonical partition functions from the density of states, we find the transition from looped to open conformations at transition temperatures which are non-monotonously changing with an increasing degree of polymerization due to the competition between chain stiffness and loop-forming entropy penalty. In the complete range of chain length under investigation, a coexistence of the looped and open morphologies at the transition temperature is shown regardless of whether the transition is first-order-like or continuous. Polyethylene and polybutylene glycols show similar behavior in all the thermodynamic properties but the transition temperature of the more flexible polybutylene glycol is shown to change more gradually.

Thermal instability in post-flare plasmas

NASA Technical Reports Server (NTRS)

Antiochos, S. K.

1976-01-01

The cooling of post-flare plasmas is discussed and the formation of loop prominences is explained as due to a thermal instability. A one-dimensional model was developed for active loop prominences. Only the motion and heat fluxes parallel to the existing magnetic fields are considered. The relevant size scales and time scales are such that single-fluid MHD equations are valid. The effects of gravity, the geometry of the field and conduction losses to the chromosphere are included. A computer code was constructed to solve the model equations. Basically, the system is treated as an initial value problem (with certain boundary conditions at the chromosphere-corona transition region), and a two-step time differencing scheme is used.

The pressure and energy balance of the cool corona over sunspots

NASA Technical Reports Server (NTRS)

Foukal, P. V.

1976-01-01

The 22 largest sunspots observed with the Skylab SO55 spectrometer are studied for a relation between their EUV radiation and their umbral size or magnetic classification. The ultimate goal is to determine why the coronal plasma is so cool over a sunspot and how this cool plasma manages to support itself against gravity. Based on the time behavior of the EUV emission, a steady-state model is developed for the pressure and energy balance of the cool coronal-plasma loops over the spots. Analysis of the temperature structure in a typical loop indicates that the loop is exceedingly well insulated from the outside corona, that its energy balance is determined purely by internal heating and cooling processes, and that a heat input of about 0.0001 erg/cu cm per sec is required along the full length of the loop. It is proposed that: (1) coronal material flows steadily across the field lines at the tops of the loops and falls downward along both sides under gravity; (2) the corona is heated by mechanical-energy transport across the very thin transition region immediately over network-cell interiors; and (3) strong magnetic fields tend to inhibit mechanical-energy dissipation in the corona.

Explosive Chromospheric Evaporation Driven by Nonthermal Electrons around One Footpoint of a Solar Flare Loop

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

Li, D.; Ning, Z. J.; Huang, Y.

We explore the temporal relationship between microwave/hard X-ray (HXR) emission and Doppler velocity during the impulsive phase of a solar flare on 2014 October 27 (SOL2014-10-27) that displays a pulse on the light curves in the microwave (34 GHz) and HXR (25–50 keV) bands before the flare maximum. Imaging observation shows that this pulse mainly comes from one footpoint of a solar flare loop. The slit of the Interface Region Imaging Spectrograph ( IRIS ) stays at this footpoint during this solar flare. The Doppler velocities of Fe xxi 1354.09 Å and Si iv 1402.77 Å are extracted from themore » Gaussian fitting method. We find that the hot line of Fe xxi 1354.09 Å (log T ∼ 7.05) in the corona exhibits blueshift, while the cool line of Si iv 1402.77 Å (log T ∼ 4.8) in the transition region exhibits redshift, indicating explosive chromospheric evaporation. Evaporative upflows along the flare loop are also observed in the AIA 131 Å image. To our knowledge, this is the first report of chromospheric evaporation evidence from both spectral and imaging observations in the same flare. Both microwave and HXR pulses are well correlated with the Doppler velocities, suggesting that the chromospheric evaporation is driven by nonthermal electrons around this footpoint of a solar flare loop.« less

Abundance Variations and Flows in Plage Regions Observed with CDS/SOHO

NASA Astrophysics Data System (ADS)

Rank, G.; Bagalá, L. G.; Czaykowska, A.; Haerendel, G.

1999-10-01

We present results from CDS/SOHO observations of the spotless active region NOAA-8208, obtained on 28th April 1998 near disk center. MDI images show a bipolar magnetic configuration. The regions of enhanced He I emission correspond to the areas with strong magnetic flux and also with bright plage areas seen in Ca II and H-alpha images. A high correlation is found between intensity maps of the transition region lines He I (logTmax = 4.3), O III (logTmax = 5.0), and O V (logTmax = 5.4). The line-of-sight velocities of He I reveal a strong downflow in the plage areas. Further, the line-of-sight velocities of He I, O III, and O V are well correlated, showing that the downflow pattern exists up to temperatures of about 0.25 MK. At higher temperatures (Mg VIII at logTmax = 5.8) this flow is not detected, suggesting that material streams into the plage region from sideways in the high transition region. Maps of the electron density in the transition region have been constructed from several line ratios yielding densities of about 9.0 cm-3 in the plage regions, about dex 0.5 cm-3 higher compared to the surrounding. To study the spatial variation of the first ionization potential (FIP) effect, the abundance ratio has been mapped for the ion ratio MgVI/NeVI. The ratio is highly variable on spatial scales down to a few arcsec from photospheric values to enhancements of a factor of 10. The strongest FIP enhancements are not correlated with transition region line emission, but are found outside of the plage regions. Some areas of strong FIP enhancement appear stretched and elongated, suggesting that the material is confined in loop-like structures.

Transequatorial loops interconnecting McMath regions 12472 and 12474

NASA Technical Reports Server (NTRS)

Svestka, Z.; Krieger, A. S.; Chase, R. C.; Howard, R.

1977-01-01

The paper reviews the life history of one transequatorial loop in a system observed in soft X-rays for at least 1.5 days and which interconnected a newly born active region with an old region. The birth of the selected loop is discussed along with properties of the interconnected active regions, sharpening and brightening of the loop, decay of the loop system, and physical relations between the interconnected regions. It is concluded that: (1) the loop was most probably born via reconnection of magnetic-field lines extending from the two active regions toward the equator, which occurred later than 33 hr after the younger region was born; (2) the fully developed interconnection was composed of several loops, all of which appeared to be rooted in a spotless magnetic hill of preceding northern polarity but were spread over two separate spotty regions of southern polarity in the magnetically complex new region; (3) the loop electron temperature increased from 2.1 million to 3.1 million K in one to three hours when the loop system brightened; and (4) the loops became twisted during the brightening, possibly due to their rise in the corona while remaining rooted in moving magnetic features in the younger region.

Pre-T Cell Receptors (Pre-TCRs) Leverage Vβ Complementarity Determining Regions (CDRs) and Hydrophobic Patch in Mechanosensing Thymic Self-ligands.

PubMed

Das, Dibyendu Kumar; Mallis, Robert J; Duke-Cohan, Jonathan S; Hussey, Rebecca E; Tetteh, Paul W; Hilton, Mark; Wagner, Gerhard; Lang, Matthew J; Reinherz, Ellis L

2016-12-02

The pre-T cell receptor (pre-TCR) is a pTα-β heterodimer functioning in early αβ T cell development. Although once thought to be ligand-autonomous, recent studies show that pre-TCRs participate in thymic repertoire formation through recognition of peptides bound to major histocompatibility molecules (pMHC). Using optical tweezers, we probe pre-TCR bonding with pMHC at the single molecule level. Like the αβTCR, the pre-TCR is a mechanosensor undergoing force-based structural transitions that dynamically enhance bond lifetimes and exploiting allosteric control regulated via the Cβ FG loop region. The pre-TCR structural transitions exhibit greater reversibility than TCRαβ and ordered force-bond lifetime curves. Higher piconewton force requires binding through both complementarity determining region loops and hydrophobic Vβ patch apposition. This patch functions in the pre-TCR as a surrogate Vα domain, fostering ligand promiscuity to favor development of β chains with self-reactivity but is occluded by α subunit replacement of pTα upon αβTCR formation. At the double negative 3 thymocyte stage where the pre-TCR is first expressed, pre-TCR interaction with self-pMHC ligands imparts growth and survival advantages as revealed in thymic stromal cultures, imprinting fundamental self-reactivity in the T cell repertoire. Collectively, our data imply the existence of sequential mechanosensor αβTCR repertoire tuning via the pre-TCR. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Pre-T Cell Receptors (Pre-TCRs) Leverage Vβ Complementarity Determining Regions (CDRs) and Hydrophobic Patch in Mechanosensing Thymic Self-ligands*♦

PubMed Central

Das, Dibyendu Kumar; Mallis, Robert J.; Duke-Cohan, Jonathan S.; Hussey, Rebecca E.; Tetteh, Paul W.; Hilton, Mark; Wagner, Gerhard; Lang, Matthew J.; Reinherz, Ellis L.

2016-01-01

The pre-T cell receptor (pre-TCR) is a pTα-β heterodimer functioning in early αβ T cell development. Although once thought to be ligand-autonomous, recent studies show that pre-TCRs participate in thymic repertoire formation through recognition of peptides bound to major histocompatibility molecules (pMHC). Using optical tweezers, we probe pre-TCR bonding with pMHC at the single molecule level. Like the αβTCR, the pre-TCR is a mechanosensor undergoing force-based structural transitions that dynamically enhance bond lifetimes and exploiting allosteric control regulated via the Cβ FG loop region. The pre-TCR structural transitions exhibit greater reversibility than TCRαβ and ordered force-bond lifetime curves. Higher piconewton force requires binding through both complementarity determining region loops and hydrophobic Vβ patch apposition. This patch functions in the pre-TCR as a surrogate Vα domain, fostering ligand promiscuity to favor development of β chains with self-reactivity but is occluded by α subunit replacement of pTα upon αβTCR formation. At the double negative 3 thymocyte stage where the pre-TCR is first expressed, pre-TCR interaction with self-pMHC ligands imparts growth and survival advantages as revealed in thymic stromal cultures, imprinting fundamental self-reactivity in the T cell repertoire. Collectively, our data imply the existence of sequential mechanosensor αβTCR repertoire tuning via the pre-TCR. PMID:27707880

Coronal O VI emission observed with UVCS/SOHO during solar flares: Comparison with soft X-ray observations

NASA Astrophysics Data System (ADS)

Mancuso, S.; Giordano, S.; Raymond, J. C.

2016-06-01

In this work, we derive the O VI 1032 Å luminosity profiles of 58 flares, during their impulsive phase, based on off-limb measurements by the Ultraviolet Coronagraph Spectrometer (UVCS) aboard the SOlar and Heliospheric Observatory (SOHO). The O VI luminosities from the transition region plasma (here defined as the region with temperatures 5.0 ≤ log T (K) ≤ 6.0) were inferred from the analysis of the resonantly scattered radiation of the O VI coronal ions. The temperature of maximum ionization for O VI is log Tmax (K) = 5.47. By comparison with simultaneous soft X-ray measurements, we investigate the likely source (chromospheric evaporation, footpoint emission, or heated prominence ejecta) for the transition region emission observed during the impulsive phase. In our study, we find evidence of the main characteristics predicted by the evaporation scenario. Specifically, most O VI flares precede the X-ray peaks typically by several minutes with a mean of 3.2 ± 0.1 min, and clear correlations are found between the soft X-ray and transition region luminosities following power laws with indices ~ 0.7 ± 0.3. Overall, the results are consistent with transition region emission originating from chromospheric evaporation; the thermal X-ray emission peaks after the emission from the evaporation flow as the loops fill with hot plasma. Finally, we were able to infer flow speeds in the range ~20-100 km s-1 for one-third of the events, 14 of which showed speeds between 60 and 80 km s-1. These values are compatible with those found through direct spectroscopic observations at transition region temperatures by the EUV Imaging Spectrometer (EIS) on board Hinode.

Diffusional encounter of barnase and barstar.

PubMed

Spaar, Alexander; Dammer, Christian; Gabdoulline, Razif R; Wade, Rebecca C; Helms, Volkhard

2006-03-15

We present an analysis of trajectories from Brownian dynamics simulations of diffusional protein-protein encounter for the well-studied system of barnase and barstar. This analysis reveals details about the optimal association pathways, the regions of the encounter complex, possible differences of the pathways for dissociation and association, the coupling of translational and rotation motion, and the effect of mutations on the trajectories. We found that a small free-energy barrier divides the energetically most favorable region into a region of the encounter complex above the barnase binding interface and a region around a second energy minimum near the RNA binding loop. When entering the region of the encounter complex from the region near the RNA binding loop, barstar has to change its orientation to increase the electrostatic attraction between the proteins. By concentrating the analysis on the successful binding trajectories, we found that the region of the second minimum is not essential for the binding of barstar to barnase. Nevertheless, this region may be helpful to steer barstar into the region of the encounter complex. When applying the same analysis to several barnase mutants, we found that single mutations may drastically change the free-energy landscape and may significantly alter the population of the two minima. Therefore, certain protein-protein pairs may require careful adaptation of the positions of encounter and transition states when interpreting mutation effects on kinetic rates of association and/or dissociation.

Brightness and magnetic evolution of solar coronal bright points

NASA Astrophysics Data System (ADS)

Ugarte Urra, Ignacio

This thesis presents a study of the brightness and magnetic evolution of several Extreme ultraviolet (EUV) coronal bright points (hereafter BPs). The study was carried out using several instruments on board the Solar and Heliospheric Observatory, supported by the high resolution imaging from the Transition Region And Coronal Explorer. The results confirm that, down to 1" resolution, BPs are made of small loops with lengths of [approximate]6 Mm and cross-sections of ≈2 Mm. The loops are very dynamic, evolving in time scales as short as 1 - 2 minutes. This is reflected in a highly variable EUV response with fluctuations highly correlated in spectral lines at transition region temperatures, but not always at coronal temperatures. A wavelet analysis of the intensity variations reveals the existence of quasi-periodic oscillations with periods ranging 400--1000s, in the range of periods characteristic of the chromospheric network. The link between BPs and network bright points is discussed, as well as the interpretation of the oscillations in terms of global acoustic modes of closed magnetic structures. A comparison of the magnetic flux evolution of the magnetic polarities to the EUV flux changes is also presented. Throughout their lifetime, the intrinsic EUV emission of BPs is found to be dependent on the total magnetic flux of the polarities. In short time scales, co-spatial and co-temporal coronal images and magnetograms, reveal the signature of heating events that produce sudden EUV brightenings simultaneous to magnetic flux cancellations. This is interpreted in terms of magnetic reconnection events. Finally, a electron density study of six coronal bright points produces values of ≈1.6×10 9 cm -3 , closer to active region plasma than to quiet Sun. The analysis of a large coronal loop (half length of 72 Mm) introduces the discussion on the prospects of future plasma diagnostics of BPs with forthcoming solar missions.

Topology-driven phase transitions in the classical monomer-dimer-loop model.

PubMed

Li, Sazi; Li, Wei; Chen, Ziyu

2015-06-01

In this work, we investigate the classical loop models doped with monomers and dimers on a square lattice, whose partition function can be expressed as a tensor network (TN). In the thermodynamic limit, we use the boundary matrix product state technique to contract the partition function TN, and determine the thermodynamic properties with high accuracy. In this monomer-dimer-loop model, we find a second-order phase transition between a trivial monomer-condensation and a loop-condensation (LC) phase, which cannot be distinguished by any local order parameter, while nevertheless the two phases have distinct topological properties. In the LC phase, we find two degenerate dominating eigenvalues in the transfer-matrix spectrum, as well as a nonvanishing (nonlocal) string order parameter, both of which identify the topological ergodicity breaking in the LC phase and can serve as the order parameter for detecting the phase transitions.

Loop corrections to primordial fluctuations from inflationary phase transitions

NASA Astrophysics Data System (ADS)

Wu, Yi-Peng; Yokoyama, Jun'ichi

2018-05-01

We investigate loop corrections to the primordial fluctuations in the single-field inflationary paradigm from spectator fields that experience a smooth transition of their vacuum expectation values. We show that when the phase transition involves a classical evolution effectively driven by a negative mass term from the potential, important corrections to the curvature perturbation can be generated by field perturbations that are frozen outside the horizon by the time of the phase transition, yet the correction to tensor perturbation is naturally suppressed by the spatial derivative couplings between spectator fields and graviton. At one-loop level, the dominant channel for the production of primordial fluctuations comes from a pair-scattering of free spectator fields that decay into the curvature perturbations, and this decay process is only sensitive to field masses comparable to the Hubble scale of inflation.

Thermal phase transition with full 2-loop effective potential

NASA Astrophysics Data System (ADS)

Laine, M.; Meyer, M.; Nardini, G.

2017-07-01

Theories with extended Higgs sectors constructed in view of cosmological ramifications (gravitational wave signal, baryogenesis, dark matter) are often faced with conflicting requirements for their couplings; in particular those influencing the strength of a phase transition may be large. Large couplings compromise perturbative studies, as well as the high-temperature expansion that is invoked in dimensionally reduced lattice investigations. With the example of the inert doublet extension of the Standard Model (IDM), we show how a resummed 2-loop effective potential can be computed without a high-T expansion, and use the result to scrutinize its accuracy. With the exception of Tc, which is sensitive to contributions from heavy modes, the high-T expansion is found to perform well. 2-loop corrections weaken the transition in IDM, but they are moderate, whereby a strong transition remains an option.

Characterizing Peptide β-HAIRPIN Loops via Cold Ion Spectroscopy of Model Compounds

NASA Astrophysics Data System (ADS)

Lawler, John T.; DeBlase, Andrew F.; Harrilal, Christopher P.; Fischer, Joshua L.; McLuckey, Scott A.; Zwier, Timothy S.

2017-06-01

The introduction of non-native D-amino acids into peptides is known to reduce conformational entropy in peptides. D-proline has been shown to promote the formation of β-hairpin loops when paired with Gly, providing a framework for building these loops with different lengths of anti-parallel beta-sheet. This study seeks to characterize and compare the conformational preferences of a model protonated pentapeptide containing DPG, [YAP^{D}GA+H]^{+}, with its L-Pro counterpart via conformation specific cold ion spectroscopy as a foundation for future consideration of larger beta-hairpin models. The UV spectrum of YAP^{D}GA of the Tyr chromophore is beautifully sharp, but contains a complicated set of transitions that could arise from the presence of more than one conformer. To assess this possibility, we recorded non-conformation specific IR "gain" spectra in the hydride stretch region. The IR spectrum so obtained displays a set of five strong IR transitions that bear a close resemblance to those found in one of the conformers of its close analog, [YAP^{D}AA+H]^{+}, signaling that a single conformer dominates the population. Two transitions at 3392 and 3464 cm-1 are slightly shifted versions of the C10 and C14 hydrogen bonds found in one of the conformers of [YAP^{D}AA+H]^{+}, and are characteristic of formation of a β-hairpin loop. Notably, in [YAP^{D}GA+H]^{+}, there is at most a minor second conformer with a free carboxylic acid OH, appearing weakly in the IR "gain" spectrum. As expected, the UV spectrum of YAP^{L}GA is more congested, which suggests the presence of multiple conformers. Further investigation into this peptide will reveal the conformational preferences of the L-pro containing molecule. Preliminary data affirms that D-proline containing peptides show reduced conformational states when compared to their natural counterparts.

A comparison of Manchester symbol tracking loops for block 5 applications

NASA Technical Reports Server (NTRS)

Holmes, J. K.

1991-01-01

The linearized tracking errors of three Manchester (biphase coded) symbol tracking loops are compared to determine which is appropriate for Block 5 receiver applications. The first is a nonreturn to zero (NRZ) symbol synchronizer loop operating at twice the symbol rate (NRZ x 2) so that it operates on half symbols. The second near optimally processes the mid-symbol transitions and ignores the between symbol transitions. In the third configuration, the first two approaches are combined as a hybrid to produce the best performance. Although this hybrid loop is the best at low symbol signal to noise ratios (SNRs), it has about the same performance as the NRZ x 2 loop at higher SNRs (greater than 0-dB E sub s/N sub 0). Based on this analysis, it is tentatively recommended that the hybrid loop be implemented for Manchester data in the Block 5 receiver. However, the high data rate case and the hardware implications of each implementation must be understood and analyzed before the hybrid loop is recommended unconditionally.

Effective model approach to the dense state of QCD matter

NASA Astrophysics Data System (ADS)

Fukushima, Kenji

2011-12-01

The first-principle approach to the dense state of QCD matter, i.e. the lattice-QCD simulation at finite baryon density, is not under theoretical control for the moment. The effective model study based on QCD symmetries is a practical alternative. However the model parameters that are fixed by hadronic properties in the vacuum may have unknown dependence on the baryon chemical potential. We propose a new prescription to constrain the effective model parameters by the matching condition with the thermal Statistical Model. In the transitional region where thermal quantities blow up in the Statistical Model, deconfined quarks and gluons should smoothly take over the relevant degrees of freedom from hadrons and resonances. We use the Polyakov-loop coupled Nambu-Jona-Lasinio (PNJL) model as an effective description in the quark side and show how the matching condition is satisfied by a simple ansäatz on the Polyakov loop potential. Our results favor a phase diagram with the chiral phase transition located at slightly higher temperature than deconfinement which stays close to the chemical freeze-out points.

Transition to Quantum Turbulence and the Propagation of Vortex Loops at Finite Temperatures

NASA Astrophysics Data System (ADS)

Yamamoto, Shinji; Adachi, Hiroyuki; Tsubota, Makoto

2011-02-01

We performed numerical simulation of the transition to quantum turbulence and the propagation of vortex loops at finite temperatures in order to understand the experiments using vibrating wires in superfluid 4He by Yano et al. We injected vortex rings to a finite volume in order to simulate emission of vortices from the wire. When the injected vortices are dilute, they should decay by mutual friction. When they are dense, however, vortex tangle are generated through vortex reconnections and emit large vortex loops. The large vortex loops can travel a long distance before disappearing, which is much different from the dilute case. The numerical results are consistent with the experimental results.

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.

Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate.

PubMed Central

Zhang, K. Y.; Cascio, D.; Eisenberg, D.

1994-01-01

The crystal structure of unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate, was determined to 2.7 A resolution by X-ray crystallography. The transition state analog binds at the active site in an extended conformation. As compared to the binding of the same analog in the activated enzyme, the analog binds in a reverse orientation. The active site Lys 201 is within hydrogen bonding distance of the carboxyl oxygen of the analog. Loop 6 (residues 330-339) remains open and flexible upon binding of the analog in the unactivated enzyme, in contrast to the closed and ordered loop 6 in the activated enzyme complex. The transition state analog is exposed to solvent due to the open conformation of loop 6. PMID:8142899

Coronal temperatures of selected active cool stars as derived from low resolution Einstein observations

NASA Technical Reports Server (NTRS)

Vilhu, Osmi; Linsky, Jeffrey L.

1990-01-01

Mean coronal temperatures of some active G-K stars were derived from Rev1-processed Einstein-observatory's IPC-spectra. The combined X-ray and transition region emission line data are in rough agreement with static coronal loop models. Although the sample is too small to derive any statistically significant conclusions, it suggests that the mean coronal temperature depends linearly on the inverse Rossby-number, with saturation at short rotation periods.

Brightness and magnetic evolution of solar coronal bright points

NASA Astrophysics Data System (ADS)

Ugarte-Urra, I.

2004-12-01

This thesis presents a study of the brightness and magnetic evolution of several Extreme ultraviolet (EUV) coronal bright points (hereafter BPs). BPs are loop-like features of enhanced emission in the coronal EUV and X-ray images of the Sun, that are associated to the interaction of opposite photospheric magnetic polarities with magnetic fluxes of ≈1018 - 1019 Mx. The study was carried out using several instruments on board the Solar and Heliospheric Observatory (SOHO): the Extreme Ultraviolet Imager (EIT), the Coronal Diagnostic Spectrometer (CDS) and the Michelson Doppler Imager (MDI), supported by the high resolution imaging from the Transition Region And Coronal Explorer (TRACE). The results confirm that, down to 1'' (i.e. ~715 km) resolution, BPs are made of small loops with lengths of ~6 Mm and cross-sections of ~2 Mm. The loops are very dynamic, evolving in time scales as short as 1 - 2 minutes. This is reflected in a highly variable EUV response with fluctuations highly correlated in spectral lines at transition region temperatures (in the range 3.2x10^4 - 3.5x10^5 K), but not always at coronal temperatures. A wavelet analysis of the intensity variations reveals, for the first time, the existence of quasi-periodic oscillations with periods ranging 400 -- 1000 s, in the range of periods characteristic of the chromospheric network. The link between BPs and network bright points is discussed, as well as the interpretation of the oscillations in terms of global acoustic modes of closed magnetic structures. A comparison of the magnetic flux evolution of the magnetic polarities to the EUV flux changes is also presented. Throughout their lifetime, the intrinsic EUV emission of BPs is found to be dependent on the total magnetic flux of the polarities. In short time scales, co-spatial and co-temporal TRACE and MDI images, reveal the signature of heating events that produce sudden EUV brightenings simultaneous to magnetic flux cancellations. This is interpreted in terms of magnetic reconnection events. Finally, a electron density study of six coronal bright points produces values of ~1.6x109 cm-3, closer to active region plasma than to quiet Sun. The analysis of a large coronal loop (half length of 72 Mm) introduces the discussion on the prospects of future plasma diagnostics of BPs with forthcoming solar missions like Solar-B.

3D MHD Models of Active Region Loops

NASA Technical Reports Server (NTRS)

Ofman, Leon

2004-01-01

Present imaging and spectroscopic observations of active region loops allow to determine many physical parameters of the coronal loops, such as the density, temperature, velocity of flows in loops, and the magnetic field. However, due to projection effects many of these parameters remain ambiguous. Three dimensional imaging in EUV by the STEREO spacecraft will help to resolve the projection ambiguities, and the observations could be used to setup 3D MHD models of active region loops to study the dynamics and stability of active regions. Here the results of 3D MHD models of active region loops are presented, and the progress towards more realistic 3D MHD models of active regions. In particular the effects of impulsive events on the excitation of active region loop oscillations, and the generation, propagations and reflection of EIT waves are shown. It is shown how 3D MHD models together with 3D EUV observations can be used as a diagnostic tool for active region loop physical parameters, and to advance the science of the sources of solar coronal activity.

Investigating the Response of Loop Plasma to Nanoflare Heating Using RADYN Simulations

NASA Astrophysics Data System (ADS)

Polito, V.; Testa, P.; Allred, J.; De Pontieu, B.; Carlsson, M.; Pereira, T. M. D.; Gošić, Milan; Reale, Fabio

2018-04-01

We present the results of 1D hydrodynamic simulations of coronal loops that are subject to nanoflares, caused by either in situ thermal heating or nonthermal electron (NTE) beams. The synthesized intensity and Doppler shifts can be directly compared with Interface Region Imaging Spectrograph (IRIS) and Atmospheric Imaging Assembly (AIA) observations of rapid variability in the transition region (TR) of coronal loops, associated with transient coronal heating. We find that NTEs with high enough low-energy cutoff ({E}{{C}}) deposit energy in the lower TR and chromosphere, causing blueshifts (up to ∼20 km s‑1) in the IRIS Si IV lines, which thermal conduction cannot reproduce. The {E}{{C}} threshold value for the blueshifts depends on the total energy of the events (≈5 keV for 1024 erg, up to 15 keV for 1025 erg). The observed footpoint emission intensity and flows, combined with the simulations, can provide constraints on both the energy of the heating event and {E}{{C}}. The response of the loop plasma to nanoflares depends crucially on the electron density: significant Si IV intensity enhancements and flows are observed only for initially low-density loops (<109 cm‑3). This provides a possible explanation of the relative scarcity of observations of significant moss variability. While the TR response to single heating episodes can be clearly observed, the predicted coronal emission (AIA 94 Å) for single strands is below current detectability and can only be observed when several strands are heated closely in time. Finally, we show that the analysis of the IRIS Mg II chromospheric lines can help further constrain the properties of the heating mechanisms.

Runtime Assurance Framework Development for Highly Adaptive Flight Control Systems

DTIC Science & Technology

2015-12-01

performing a surveillance mission. The demonstration platform consisted of RTA systems for the inner- loop control, outer- loop guidance, ownship flight...For the inner- loop , the concept of employing multiple transition controllers in the reversionary control system was studied. For all feedback levels...5 RTA Protection Applied to Inner- Loop Control Systems .................................................61 5.1 General Description of Morphing Wing

Mass motions in impulsive flarelike brightenings as observed by OSO 8. [mechanism response for solar flares

NASA Technical Reports Server (NTRS)

Bruner, E. C., Jr.; Lites, B. W.

1979-01-01

C IV 1548-A line profiles obtained with the University of Colorado spectrometer aboard OSO 8 reveal transient, redshifted brightenings in the chromosphere-corona transition region above active regions and sunspots. In these events the intensity rises by factors of up to 5 in less than the profile sampling interval of 27 sec. These events indicate that the emitting material is moving downward at velocities of up to 30 km/sec. The increase in line intensity and the amount of motion are consistent with the interpretation of these events as pressure waves propagating down magnetic flux loops.

Ferroelectric properties and polarization dynamics in Ba{sub 4}Sm{sub 2}Ti{sub 4}Ta{sub 6}O{sub 30} tungsten bronze ceramics

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

Zhu, Xiao Li, E-mail: xiaolizi0618@zju.edu.cn; Chen, Xiang Ming

2016-04-11

Ferroelectricity and polarization reversal dynamics in Ba{sub 4}Sm{sub 2}Ti{sub 4}Ta{sub 6}O{sub 30} tungsten bronze ceramics were investigated by measuring dielectric spectra and the evolution of hysteresis loops over a wide temperature range. With decreasing temperature, the dielectric properties and differential scanning calorimetry results showed diffuse peaks at ∼280 K with large thermal hysteresis, suggesting a first order ferroelectric transition. A dielectric relaxation was observed at low temperature that followed the Vogel–Fulcher relationship. The saturation and remanent polarizations of the Ba{sub 4}Sm{sub 2}Ti{sub 4}Ta{sub 6}O{sub 30} ceramics showed remarkable dependence on the applied field and temperature. The temperature dependence of the coercivemore » field was divided into three linear regions and fitted to the Vopsaroiu model. Activation energies for polarization reversal of 0.73, 0.79, and 0.65 eV were determined for the following three regions: (I) the diffuse ferroelectric transition region (323.15–293.15 K), (II) the region just below the ferroelectric transition temperature (293.15–233.15 K), and (III) the low temperature relaxation region (233.15–173.15 K), respectively. The decrease of the activation energy in region III was attributed to the low temperature relaxation of Ba{sub 4}Sm{sub 2}Ti{sub 4}Ta{sub 6}O{sub 30}.« less

Vortex Loops at the Superfluid Lambda Transition: An Exact Theory?

NASA Technical Reports Server (NTRS)

Williams, Gary A.

2003-01-01

A vortex-loop theory of the superfluid lambda transition has been developed over the last decade, with many results in agreement with experiments. It is a very simple theory, consisting of just three basic equations. When it was first proposed the main uncertainty in the theory was the use Flory scaling to find the fractal dimension of the random-walking vortex loops. Recent developments in high-resolution Monte Carlo simulations have now made it possible to verify the accuracy of this Flory-scaling assumption. Although the loop theory is not yet rigorously proven to be exact, the Monte Carlo results show at the least that it is an extremely good approximation. Recent loop calculations of the critical Casimir effect in helium films in the superfluid phase T < Tc will be compared with similar perturbative RG calculations in the normal phase T > Tc; the two calculations are found to match very nicely right at Tc.

Radio physics of the sun; Proceedings of the Symposium, University of Maryland, College Park, Md., August 7-10, 1979

NASA Technical Reports Server (NTRS)

Kundu, M. R. (Editor); Gergely, T. E.

1980-01-01

Papers are presented in the areas of the radio characteristics of the quiet sun and active regions, the centimeter, meter and decameter wavelength characteristics of solar bursts, space observations of low-frequency bursts, theoretical interpretations of solar active regions and bursts, joint radio, visual and X-ray observations of active regions and bursts, and the similarities of stellar radio characteristics to solar radio phenomena. Specific topics include the centimeter and millimeter wave characteristics of the quiet sun, radio fluctuations arising upon the transit of shock waves through the transition region, microwave, EUV and X-ray observations of active region loops and filaments, interferometric observations of 35-GHz radio bursts, emission mechanisms for radio bursts, the spatial structure of microwave bursts, observations of type III bursts, the statistics of type I bursts, and the numerical simulation of type III bursts. Attention is also given to the theory of type IV decimeter bursts, Voyager observations of type II and III bursts at kilometric wavelengths, radio and whitelight observations of coronal transients, and the possibility of obtaining radio observations of current sheets on the sun.

Analysis of the Functions of Recombination-Related Genes in the Generation of Large Chromosomal Deletions by Loop-Out Recombination in Aspergillus oryzae

PubMed Central

Ogawa, Masahiro; Koyama, Yasuji

2012-01-01

Loop-out-type recombination is a type of intrachromosomal recombination followed by the excision of a chromosomal region. The detailed mechanism underlying this recombination and the genes involved in loop-out recombination remain unknown. In the present study, we investigated the functions of ku70, ligD, rad52, rad54, and rdh54 in the construction of large chromosomal deletions via loop-out recombination and the effect of the position of the targeted chromosomal region on the efficiency of loop-out recombination in Aspergillus oryzae. The efficiency of generation of large chromosomal deletions in the near-telomeric region of chromosome 3, including the aflatoxin gene cluster, was compared with that in the near-centromeric region of chromosome 8, including the tannase gene. In the Δku70 and Δku70-rdh54 strains, only precise loop-out recombination occurred in the near-telomeric region. In contrast, in the ΔligD, Δku70-rad52, and Δku70-rad54 strains, unintended chromosomal deletions by illegitimate loop-out recombination occurred in the near-telomeric region. In addition, large chromosomal deletions via loop-out recombination were efficiently achieved in the near-telomeric region, but barely achieved in the near-centromeric region, in the Δku70 strain. Induction of DNA double-strand breaks by I-SceI endonuclease facilitated large chromosomal deletions in the near-centromeric region. These results indicate that ligD, rad52, and rad54 play a role in the generation of large chromosomal deletions via precise loop-out-type recombination in the near-telomeric region and that loop-out recombination between distant sites is restricted in the near-centromeric region by chromosomal structure. PMID:22286092

Pairing transition, coherence transition, and the irreversibility line in granular GdBa2Cu3O7-δ

NASA Astrophysics Data System (ADS)

Roa-Rojas, J.; Menegotto Costa, R.; Pureur, P.; Prieto, P.

2000-05-01

We report on electrical magnetoconductivity experiments near the superconducting transition of a granular sample of GdBa2Cu3O7-δ. The measurements were performed in magnetic fields ranging from 0 to 500 Oe applied parallel to the current orientation. The results show that the transition proceeds in two steps. When the temperature is decreased we first observe the pairing transition, which stabilizes superconductivity within the grains at a temperature practically coincident with the bulk critical temperature Tc. Analysis of the fluctuation contributions to the conductivity shows that the universality class for this transition is that of the three dimensional (3D)-XY model in the ordered case, with dynamic critical exponent z=3/2. Close to the zero-resistance state, the measurements reveal the occurrence of a coherence transition, where the phases of the order parameter in individual grains become long-range ordered. The critical temperature Tco for this transition is close to the point where the resistivity vanishes. A strong enlargement of the fluctuation interval preceding the coherence transition is caused by the applied magnetic field. In this region, a 3D-Gaussian regime and an asymptotic critical regime were clearly identified. The critical conductivity behavior for the coherence transition is interpreted within a 3D-XY model where disorder and frustration are relevant. The irreversibility line is determined from magnetoconductivity measurements performed according to the zero-field-cooled (ZFC) and field-cooled data collected on cooling (FCC) recipes. The locus of this line coincides with the upper temperature limit for the fluctuation region above the coherence transition. The irreversibility line is interpreted as an effect of the formation of small clusters with closed loops of Josephson-coupled grains.

System Control for the Transitional DCS.

DTIC Science & Technology

1978-12-01

hour. The equipment destroyed includes the TTC-39 switch, all RF and multiplex equipment, emergency power equipment, distribution frames, antennal and...switch executes loop test to Rhein Main ULS, activating a local alarm at Donnersberg. Since restoral activity has not already been completed, alarm is...ITEM COMMENTS (BYTES) Loop ID Switch number and physical loop number 6 (BCD). Loop circuit CCSD 8 Telephone number 3 Location Physical location of

A quality assurance device for measuring afterloader performance and transit dose for nasobiliary high-dose-rate brachytherapy.

PubMed

Deufel, Christopher L; Mullins, John P; Zakhary, Mark J

2018-05-17

Nasobiliary high-dose-rate (HDR) brachytherapy has emerged as an effective tool to boost the radiation dose for patients with unresectable perihilar cholangiocarcinoma. This work describes a quality assurance (QA) tool for measuring the HDR afterloader's performance, including the transit dose, when the source wire travels through a tortuous nasobiliary catheter path. The nasobiliary QA device was designed to mimic the anatomical path of a nasobiliary catheter, including the nasal, stomach, duodenum, and bile duct loops. Two of these loops, the duodenum and bile duct loops, have adjustable radii of curvature, resulting in the ability to maximize stress on the source wire in transit. The device was used to measure the performance over time for the HDR afterloader and the differences between intraluminal catheter lots. An upper limit on the transit dose was also measured using radiochromic film and compared with a simple theoretical model. The QA device was capable of detecting performance variations among nasobiliary catheter lots and following radioactive source replacement. The transit dose from a nasobiliary treatment increased by up to one order of magnitude when the source wire encountered higher than normal friction. Three distinct travel speeds of the source wire were observed: 5.2, 17.4, and 54.7 cm/s. The maximum transit dose was 0.3 Gy at a radial distance of 5 mm from a 40.3 kU 192 Ir source. The source wire encounters substantially greater friction when it navigates through the nasobiliary brachytherapy catheter. A QA tool that mimics the nasal, stomach, duodenum, and bile duct loops may be used to evaluate transit dose and the afterloader's performance over time. Copyright © 2018 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

A steady-state supersonic downflow in the transition region above a sunspot umbra

NASA Astrophysics Data System (ADS)

Straus, Thomas; Fleck, Bernhard; Andretta, Vincenzo

2015-10-01

We investigate a small-scale (~1.5 Mm along the slit), supersonic downflow of about 90 km s-1 in the transition region above the lightbridged sunspot umbra in AR 11836. The observations were obtained with the Interface Region Spectrograph (IRIS) on 2013 September 2 from 16:40 to 17:59 UT. The downflow shows up as redshifted "satellite" lines of the Si iv and O iv transition region lines and is remarkably steady over the observing period of nearly 80 min. The downflow is not visible in the chromospheric lines, which only show an intensity enhancement at the location of the downflow. The density inferred from the line ratio of the redshifted satellites of the O iv lines (Ne = 1010.6 ± 0.25 cm-3) is only a factor 2 smaller than the one inferred from the main components (Ne = 1010.95 ± 0.20 cm-3). Consequently, this implies a substantial mass flux (~5 × 10-7 g cm-2 s-1), which would evacuate the overlying corona on timescales close to 10 s. We interpret these findings as evidence of a stationary termination shock of a supersonic siphon flow in a cool loop that is rooted in the central umbra of the spot. The movie is available in electronic form at http://www.aanda.org

Determination of the V- I characteristic of NbTi wires in a wide resistivity range

NASA Astrophysics Data System (ADS)

Musenich, R.; Fabbricatore, P.; Farinon, S.; Greco, M.

2004-01-01

The voltage-current curve of superconducting wires and cables is generally directly measured within the resistivity range 10 -15-10 -12 Ω m being limited by the sensitivity and the Joule dissipation. Indirect measurements, based on the current decay in a superconducting loop, allow the determination of the curve in lower resistivity regions. Using a loop made with a Cu-NbTi wire we performed indirect V- I measurements in the range 10 -19-10 -16 Ω m. The comparison of the curves obtained by the direct and indirect method allows the experimental verification of the power law describing the transition of the superconducting wire to the normal state in a wide resistivity range. The law is discussed and justified on the basis of the superconductor behaviour in the flux creep dynamic regime.

Chiral phase transition of three flavor QCD with nonzero magnetic field using standard staggered fermions

NASA Astrophysics Data System (ADS)

Tomiya, Akio; Ding, Heng-Tong; Mukherjee, Swagato; Schmidt, Christian; Wang, Xiao-Dan

2018-03-01

Lattice simulations for (2+1)-flavor QCD with external magnetic field demon-strated that the quark mass is one of the important parameters responsible for the (inverse) magnetic catalysis. We discuss the dependences of chiral condensates and susceptibilities, the Polyakov loop on the magnetic field and quark mass in three degenerate flavor QCD. The lattice simulations are performed using standard staggered fermions and the plaquette action with spatial sizes Nσ = 16 and 24 and a fixed temporal size Nτ = 4. The value of the quark masses are chosen such that the system undergoes a first order chiral phase transition and crossover with zero magnetic field. We find that in light mass regime, the quark chiral condensate undergoes magnetic catalysis in the whole temperature region and the phase transition tend to become stronger as the magnetic field increases. In crossover regime, deconfinement transition temperature is shifted by the magnetic field when quark mass ma is less than 0:4. The lattice cutoff effects are also discussed.

Multiple tipping points and optimal repairing in interacting networks

PubMed Central

Majdandzic, Antonio; Braunstein, Lidia A.; Curme, Chester; Vodenska, Irena; Levy-Carciente, Sary; Eugene Stanley, H.; Havlin, Shlomo

2016-01-01

Systems composed of many interacting dynamical networks—such as the human body with its biological networks or the global economic network consisting of regional clusters—often exhibit complicated collective dynamics. Three fundamental processes that are typically present are failure, damage spread and recovery. Here we develop a model for such systems and find a very rich phase diagram that becomes increasingly more complex as the number of interacting networks increases. In the simplest example of two interacting networks we find two critical points, four triple points, ten allowed transitions and two ‘forbidden' transitions, as well as complex hysteresis loops. Remarkably, we find that triple points play the dominant role in constructing the optimal repairing strategy in damaged interacting systems. To test our model, we analyse an example of real interacting financial networks and find evidence of rapid dynamical transitions between well-defined states, in agreement with the predictions of our model. PMID:26926803

Performance of the all-digital data-transition tracking loop in the advanced receiver

NASA Astrophysics Data System (ADS)

Cheng, U.; Hinedi, S.

1989-11-01

The performance of the all-digital data-transition tracking loop (DTTL) with coherent or noncoherent sampling is described. The effects of few samples per symbol and of noncommensurate sampling rates and symbol rates are addressed and analyzed. Their impacts on the loop phase-error variance and the mean time to lose lock (MTLL) are quantified through computer simulations. The analysis and preliminary simulations indicate that with three to four samples per symbol, the DTTL can track with negligible jitter because of the presence of earth Doppler rate. Furthermore, the MTLL is also expected to be large engough to maintain lock over a Deep Space Network track.

The Ndc80 internal loop is required for recruitment of the Ska complex to establish end-on microtubule attachment to kinetochores.

PubMed

Zhang, Gang; Kelstrup, Christian D; Hu, Xiao-Wen; Kaas Hansen, Mathilde J; Singleton, Martin R; Olsen, Jesper V; Nilsson, Jakob

2012-07-01

The Ndc80 complex establishes end-on attachment of kinetochores to microtubules, which is essential for chromosome segregation. The Ndc80 subunit is characterized by an N-terminal region that binds directly to microtubules, and a long coiled-coil region that interacts with Nuf2. A loop region in Ndc80 that generates a kink in the structure disrupts the long coiled-coil region but the exact function of this loop, has until now, not been clear. Here we show that this loop region is essential for end-on attachment of kinetochores to microtubules in human cells. Cells expressing loop mutants of Ndc80 are unable to align the chromosomes, and stable kinetochore fibers are absent. Through quantitative mass spectrometry and immunofluorescence we found that the binding of the spindle and kinetochore associated (Ska) complex depends on the loop region, explaining why end-on attachment is defective. This underscores the importance of the Ndc80 loop region in coordinating chromosome segregation through the recruitment of specific proteins to the kinetochore.

Viscoplasticity based on overstress with a differential growth law for the equilibrium stress

NASA Technical Reports Server (NTRS)

Krempl, E.; Mcmahon, J. J.; Yao, D.

1985-01-01

Two coupled, nonlinear differential equations are proposed for the modeling of the elastic and rate (time) dependent inelastic behavior of structural metals in the absence of recovery and aging. The structure of the model is close to the unified theories but contains essential differences. It is shown that the model reproduces almost elastic regions upon initial loading and in the unloading regions of the hysteresis loop. Under loading, unloading and reloading in strain control the model simulated the experimentally observed sharp transition from nearly elastic to inelastic behavior. When a formulation akin to existing unified theories is adopted the almost elastic regions reduce the points and the transition upon reloading is very gradual. For different formulations the behavior under sudden in(de)creases of the strain rate by two orders of magnitude is simulated by numerical experiments and differences are noted. The model represents cyclically neutral behavior and contains three constants and two positive, decreasing functions. The determination of constants and functions from monotonic loading with strain rate changes and relaxation periods is described.

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

Li, Cui-Ping; Nie, Li; College of Materials Science and Engineering, Nanjing Tech University, Nanjing 210009

A new salt [H{sub 2}DABCO][Pt(mnt){sub 2}]{sub 2} (1) (mnt{sup 2-}=maleonitriledithiolate and H{sub 2}DABCO{sup 2+} is diprotonated 1,4-diazabicyclo[2.2.2]octane) has been synthesized; its crystal structure, magnetic and near-IR absorption properties have been investigated. Two different [Pt(mnt){sub 2}]{sup -} anions form the strong π-dimers, labeled as Pt(1)-dimer and Pt(2)-dimer, with quite shorter Pt…Pt and S…S distances and molecular plane-to-plane distance (<3.5 Å) within a dimer. The [Pt(mnt){sub 2}]{sub 2}{sup 2-} π-dimers are connected through the cations in the strong H-bond manner to form three-dimensional H-bond supramolecular crystal. The salt shows weak paramagnetism in 1.99–300 K and this is due to the existence ofmore » strong antiferromagnetic coupling within a π-dimer. In addition, a small thermal hysteresis loop is observed at ca. 120 K, indicating that a phase transition probably occurs that is further confirmed by variable-temperature IR spectra. Another fascinating functionality of 1 is the intense near-IR absorption in the region of 750–2500 nm, and this near-IR absorption feature makes it to be a promising optical material. - Graphical abstract: A H-bond supramolecular crystal of [H{sub 2}DABCO][Pt(mnt){sub 2}]{sub 2} shows a magnetic phase transition at ca. 120 K with sizable thermal hysteresis loop and intense near-IR absorption in the region of 750–2500 nm.« less

Coronal loops and active region structure

NASA Technical Reports Server (NTRS)

Webb, D. F.; Zirin, H.

1981-01-01

Synoptic H-alpha Ca K, magnetograph and Skylab soft X-ray and EUV data were compared for the purpose of identifying the basic coronal magnetic structure of loops in a 'typical' active region and studying its evolution. A complex of activity in July 1973, especially McMath 12417, was emphasized. The principal results are: (1) most of the brightest loops connected the bright f plage to either the sunspot penumbra or to p satellite spots; no non-flaring X-ray loops end in umbrae; (2) short, bright loops had one or both ends in regions of emergent flux, strong field or high field gradients; (3) stable, strongly sheared loop arcades formed over filaments; (4) EFRs were always associated with compact X-ray arcades; and (5) loops connecting to other active regions had their bases in outlying plage of weak field strength in McM 417 where H-alpha fibrils marked the direction of the loops

All-digital phase-lock loops for noise-free signals

NASA Technical Reports Server (NTRS)

Anderson, T. O.

1973-01-01

Bit-synchronizers utilize all-digital phase-lock loops that are referenced to a high frequency digital clock. Phase-lock loop of first design acquires frequency within nominal range and tracks phase; second design is modified for random binary data by addition of simple transition detector; and third design acquires frequency over wide dynamic range.

Skylab observations of X-ray loops connecting separate active regions. [solar activity

NASA Technical Reports Server (NTRS)

Chase, R. C.; Krieger, A. S.; Svestka, Z.; Vaiana, G. S.

1976-01-01

One hundred loops interconnecting 94 separate active solar regions detectable in soft X-rays were identified during the Skylab mission. While close active regions are commonly interconnected with loops, the number of such interconnections decreases steeply for longer distances; the longest interconnecting loop observed in the Skylab data connected regions separated by 37 deg. Several arguments are presented which support the point of view that this is the actual limit of the size of magnetic interconnections between active regions. No sympathetic flares could be found in the interconnected regions. These results cast doubt on the hypothesis that accelerated particles can be guided in interconnecting loops from one active region to another over distances of 100 deg or more and eventually produce sympathetic flares in them.

A new insight into the phase transition in the early Universe with two Higgs doublets

NASA Astrophysics Data System (ADS)

Bernon, Jérémy; Bian, Ligong; Jiang, Yun

2018-05-01

We study the electroweak phase transition in the alignment limit of the CP-conserving two-Higgs-doublet model (2HDM) of Type I and Type II. The effective potential is evaluated at one-loop, where the thermal potential includes Daisy corrections and is reliably approximated by means of a sum of Bessel functions. Both 1-stage and 2-stage electroweak phase transitions are shown to be possible, depending on the pattern of the vacuum development as the Universe cools down. For the 1-stage case focused on in this paper, we analyze the properties of phase transition and discover that the field value of the electroweak symmetry breaking vacuum at the critical temperature at which the first order phase transition occurs is largely correlated with the vacuum depth of the 1-loop potential at zero temperature. We demonstrate that a strong first order electroweak phase transition (SFOEWPT) in the 2HDM is achievable and establish benchmark scenarios leading to different testable signatures at colliders. In addition, we verify that an enhanced triple Higgs coupling (including loop corrections) is a typical feature of the SFOPT driven by the additional doublet. As a result, SFOEWPT might be able to be probed at the LHC and future lepton colliders through Higgs pair production.

Compact solar UV burst triggered in a magnetic field with a fan-spine topology

NASA Astrophysics Data System (ADS)

Chitta, L. P.; Peter, H.; Young, P. R.; Huang, Y.-M.

2017-09-01

Context. Solar ultraviolet (UV) bursts are small-scale features that exhibit intermittent brightenings that are thought to be due to magnetic reconnection. They are observed abundantly in the chromosphere and transition region, in particular in active regions. Aims: We investigate in detail a UV burst related to a magnetic feature that is advected by the moat flow from a sunspot towards a pore. The moving feature is parasitic in that its magnetic polarity is opposite to that of the spot and the pore. This comparably simple photospheric magnetic field distribution allows for an unambiguous interpretation of the magnetic geometry leading to the onset of the observed UV burst. Methods: We used UV spectroscopic and slit-jaw observations from the Interface Region Imaging Spectrograph (IRIS) to identify and study chromospheric and transition region spectral signatures of said UV burst. To investigate the magnetic topology surrounding the UV burst, we used a two-hour-long time sequence of simultaneous line-of-sight magnetograms from the Helioseismic and Magnetic Imager (HMI) and performed data-driven 3D magnetic field extrapolations by means of a magnetofrictional relaxation technique. We can connect UV burst signatures to the overlying extreme UV (EUV) coronal loops observed by the Atmospheric Imaging Assembly (AIA). Results: The UV burst shows a variety of extremely broad line profiles indicating plasma flows in excess of ±200 km s-1 at times. The whole structure is divided into two spatially distinct zones of predominantly up- and downflows. The magnetic field extrapolations show a persistent fan-spine magnetic topology at the UV burst. The associated 3D magnetic null point exists at a height of about 500 km above the photosphere and evolves co-spatially with the observed UV burst. The EUV emission at the footpoints of coronal loops is correlated with the evolution of the underlying UV burst. Conclusions: The magnetic field around the null point is sheared by photospheric motions, triggering magnetic reconnection that ultimately powers the observed UV burst and energises the overlying coronal loops. The location of the null point suggests that the burst is triggered low in the solar chromosphere. Movies associated to Figs. 2 and 4 are available at http://www.aanda.org

The structural coupling between ATPase activation and recovery stroke in the myosin II motor.

PubMed

Koppole, Sampath; Smith, Jeremy C; Fischer, Stefan

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates approximately 65 degrees . Simultaneous with this "recovery stroke," myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 A-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transition at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

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

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

Compensation effects and relation between the activation energy of spin transition and the hysteresis loop width for an iron(ii) complex.

PubMed

Bushuev, Mark B; Pishchur, Denis P; Nikolaenkova, Elena B; Krivopalov, Viktor P

2016-06-22

The enthalpy-entropy compensation was observed for the cooperative → spin transition (the phase is a mononuclear complex [FeL2](BF4)2, L is 4-(3,5-dimethyl-1H-pyrazol-1-yl)-2-(pyridin-2-yl)-6-methylpyrimidine). The physical origin of this effect is the fact that the → spin transition is the first order phase transition accompanied by noticeable variations in the Tonset↑, ΔH and ΔS values. Higher ΔH and ΔS values are correlated with higher Tonset↑ values. The higher the enthalpy and entropy of the spin transition, the wider the hysteresis loop. The kinetic compensation effect, i.e. a linear relationship between ln A and Ea, was observed for the → spin transition. Moreover, an isokinetic relationship was detected in this system: the Arrhenius lines (ln k vs. 1/T) obtained from magnetochemical data for different samples of the phase undergoing the → transition show a common point of intersection (Tiso = 490 ± 2 K, ln kiso = -6.0 ± 0.2). The validity of this conclusion was confirmed by the Exner-Linert statistical method. This means that the isokinetic relationship and the kinetic compensation effect (ln A vs. Ea) in this system are true ones. The existence of a true kinetic compensation effect is supported independently by the fact that the hysteresis loop width for the cooperative spin transition ↔ increases with increasing activation barrier height. Estimating the energy of excitations for the phase with Tiso ∼ 490 K yields wavenumbers of ca. 340 cm(-1) corresponding to the frequencies of the stretching vibrations of the Fe(LS)-N bonds, i.e. the bonds directly involved in the mechanism of the spin transition. This is the first observation of the kinetic compensation effect (ln A vs. Ea) and the isokinetic relationship for a cooperative spin crossover system showing thermal hysteresis. Our results provide the first experimental evidence that the higher the activation barrier for the spin transition, the wider the hysteresis loop for a series of related spin crossover systems.

Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions.

PubMed

Charbonneau, Patrick; Yaida, Sho

2017-05-26

The transformation of the free-energy landscape from smooth to hierarchical is one of the richest features of mean-field disordered systems. A well-studied example is the de Almeida-Thouless transition for spin glasses in a magnetic field, and a similar phenomenon-the Gardner transition-has recently been predicted for structural glasses. The existence of these replica-symmetry-breaking phase transitions has, however, long been questioned below their upper critical dimension, d_{u}=6. Here, we obtain evidence for the existence of these transitions in d

Slipping magnetic reconnection during an X-class solar flare observed by SDO/AIA

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

Dudík, J.; Del Zanna, G.; Mason, H. E.

2014-04-01

We present SDO/AIA observations of an eruptive X-class flare of 2012 July 12, and compare its evolution with the predictions of a three-dimensional (3D) numerical simulation. We focus on the dynamics of flare loops that are seen to undergo slipping reconnection during the flare. In the Atmospheric Imaging Assembly (AIA) 131 Å observations, lower parts of 10 MK flare loops exhibit an apparent motion with velocities of several tens of km s{sup –1} along the developing flare ribbons. In the early stages of the flare, flare ribbons consist of compact, localized bright transition-region emission from the footpoints of the flaremore » loops. A differential emission measure analysis shows that the flare loops have temperatures up to the formation of Fe XXIV. A series of very long, S-shaped loops erupt, leading to a coronal mass ejection observed by STEREO. The observed dynamics are compared with the evolution of magnetic structures in the 'standard solar flare model in 3D.' This model matches the observations well, reproducing the apparently slipping flare loops, S-shaped erupting loops, and the evolution of flare ribbons. All of these processes are explained via 3D reconnection mechanisms resulting from the expansion of a torus-unstable flux rope. The AIA observations and the numerical model are complemented by radio observations showing a noise storm in the metric range. Dm-drifting pulsation structures occurring during the eruption indicate plasmoid ejection and enhancement of the reconnection rate. The bursty nature of radio emission shows that the slipping reconnection is still intermittent, although it is observed to persist for more than an hour.« less

Computational Model of a Positive BDNF Feedback Loop in Hippocampal Neurons Following Inhibitory Avoidance Training

ERIC Educational Resources Information Center

Zhang, Yili; Smolen, Paul; Alberini, Cristina M.; Baxter, Douglas A.; Byrne, John H.

2016-01-01

Inhibitory avoidance (IA) training in rodents initiates a molecular cascade within hippocampal neurons. This cascade contributes to the transition of short- to long-term memory (i.e., consolidation). Here, a differential equation-based model was developed to describe a positive feedback loop within this molecular cascade. The feedback loop begins…

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

PubMed Central

Vacic, Vladimir; Markwick, Phineus R. L.; Oldfield, Christopher J.; Zhao, Xiaoyue; Haynes, Chad; Uversky, Vladimir N.; Iakoucheva, Lilia M.

2012-01-01

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7–2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs) more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q) collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study offer a new perspective on the role of mutations in disease, with implications for improving predictors of the functional impact of missense mutations. PMID:23055912

Alterations in aerobic energy expenditure and neuromuscular function during a simulated cross-country skiathlon with the skating technique.

PubMed

Fabre, Nicolas; Mourot, Laurent; Zoppirolli, Chiara; Andersson, Erik; Willis, Sarah J; Holmberg, Hans-Christer

2015-04-01

Here, we tested the hypothesis that aerobic energy expenditure (AEE) is higher during a simulated 6-km (2 loops of 3-km each) "skiathlon" than during skating only on a treadmill and attempted to link any such increase to biomechanical and neuromuscular responses. Six elite male cross-country skiers performed two pre-testing time-trials (TT) to determine their best performances and to choose an appropriate submaximal speed for collection of physiological, biomechanical and neuromuscular data during two experimental sessions (exp). Each skier used, in randomized order, either the classical (CL) or skating technique (SK) for the first 3-km loop, followed by transition to the skating technique for the second 3-km loop. Respiratory parameters were recorded continuously. The EMG activity of the triceps brachii (TBr) and vastus lateralis (VLa) muscles during isometric contractions performed when the skiers were stationary (i.e., just before the first loop, during the transition, and after the second loop); their corresponding activity during dynamic contractions; and pole and plantar forces during the second loop were recorded. During the second 3-km of the TT, skating speed was significantly higher for the SK-SK than CL-SK. During this second loop, AEE was also higher (+1.5%) for CL-SKexp than SK-SKexp, in association with higher VLa EMG activity during both isometric and dynamic contractions, despite no differences in plantar or pole forces, poling times or cycle rates. Although the underlying mechanism remains unclear, during a skiathlon, the transition between the sections of classical skiing and skating alters skating performance (i.e., skiing speed), AEE and neuromuscular function. Copyright © 2015 Elsevier B.V. All rights reserved.

Preparation and investigation of sputtered vanadium dioxide films with large phase-transition hysteresis loops

NASA Astrophysics Data System (ADS)

Zhang, Huafu; Wu, Zhiming; He, Qiong; Jiang, Yadong

2013-07-01

Vanadium dioxide (VO2) films with large phase-transition hysteresis loops were fabricated on glass substrates by reactive direct current (DC) magnetron sputtering in Ar/O2 atmosphere and subsequent in situ annealing process in pure oxygen. The crystal structure, chemical composition, morphology and metal-insulator transition (MIT) properties of the deposited films were investigated. The results reveal that the films show a polycrystalline nature with a (0 1 1) preferred orientation and consist of small spheroidal nanoparticles. All the deposited VO2 films show large hysteresis loops due to the small density of nucleating defects and the large interfacial energies, which are determined by the characteristics of the particles in the films, namely the small transversal grain size and the spheroidal shape. The film comprising the smallest spheroidal nanoparticles not only shows a large hysteresis width of 36.3 °C but also shows a low transition temperature of 32.2 °C upon cooling. This experiment facilitates the civilian applications of the VO2 films on glass substrates in optical storage-type devices.

Trajectory Design Enhancements to Mitigate Risk for the Transiting Exoplanet Survey Satellite (TESS)

NASA Technical Reports Server (NTRS)

Dichmann, Donald; Parker, Joel; Nickel, Craig; Lutz, Stephen

2016-01-01

The Transiting Exoplanet Survey Satellite (TESS) will employ a highly eccentric Earth orbit, in 2:1 lunar resonance, which will be reached with a lunar flyby preceded by 3.5 phasing loops. The TESS mission has limited propellant and several constraints on the science orbit and on the phasing loops. Based on analysis and simulation, we have designed the phasing loops to reduce delta-V (DV) and to mitigate risk due to maneuver execution errors. We have automated the trajectory design process and use distributed processing to generate and optimal nominal trajectories; to check constraint satisfaction; and finally to model the effects of maneuver errors to identify trajectories that best meet the mission requirements.

Strongly first-order electroweak phase transition and classical scale invariance

NASA Astrophysics Data System (ADS)

Farzinnia, Arsham; Ren, Jing

2014-10-01

In this work, we examine the possibility of realizing a strongly first-order electroweak phase transition within the minimal classically scale-invariant extension of the standard model (SM), previously proposed and analyzed as a potential solution to the hierarchy problem. By introducing one complex gauge-singlet scalar and three (weak scale) right-handed Majorana neutrinos, the scenario was successfully rendered capable of achieving a radiative breaking of the electroweak symmetry (by means of the Coleman-Weinberg mechanism), inducing nonzero masses for the SM neutrinos (via the seesaw mechanism), presenting a pseudoscalar dark matter candidate (protected by the CP symmetry of the potential), and predicting the existence of a second CP-even boson (with suppressed couplings to the SM content) in addition to the 125 GeV scalar. In the present treatment, we construct the full finite-temperature one-loop effective potential of the model, including the resummed thermal daisy loops, and demonstrate that finite-temperature effects induce a first-order electroweak phase transition. Requiring the thermally driven first-order phase transition to be sufficiently strong at the onset of the bubble nucleation (corresponding to nucleation temperatures TN˜100-200 GeV) further constrains the model's parameter space; in particular, an O(0.01) fraction of the dark matter in the Universe may be simultaneously accommodated with a strongly first-order electroweak phase transition. Moreover, such a phase transition disfavors right-handed Majorana neutrino masses above several hundreds of GeV, confines the pseudoscalar dark matter masses to ˜1-2 TeV, predicts the mass of the second CP-even scalar to be ˜100-300 GeV, and requires the mixing angle between the CP-even components of the SM doublet and the complex singlet to lie within the range 0.2≲sinω ≲0.4. The obtained results are displayed in comprehensive exclusion plots, identifying the viable regions of the parameter space. Many of these predictions lie within the reach of the next LHC run.

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2017-06-02

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.

Solar Radio Burst Associated with the Falling Bright EUV Blob

NASA Astrophysics Data System (ADS)

Karlický, Marian; Zemanová, Alena; Dudík, Jaroslav; Radziszewski, Krzysztof

2018-02-01

At the beginning of the 2015 November 4 flare, in the 1300–2000 MHz frequency range, we observed a very rare slow positively drifting burst. We searched for associated phenomena in simultaneous EUV observations made by IRIS, SDO/AIA, and Hinode/XRT, as well as in H α observations. We found that this radio burst was accompanied with the bright blob, visible at transition region, coronal, and flare temperatures, falling down to the chromosphere along the dark loop with a velocity of about 280 km s‑1. The dark loop was visible in H α but disappeared afterward. Furthermore, we found that the falling blob interacted with the chromosphere as expressed by a sudden change of the H α spectra at the location of this interaction. Considering different possibilities, we propose that the observed slow positively drifting burst is generated by the thermal conduction front formed in front of the falling hot EUV blob.

Possible higher order phase transition in large-N gauge theory at finite temperature

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

Nishimura, Hiromichi

2017-08-07

We analyze the phase structure of SU(¥) gauge theory at finite temperature using matrix models. Our basic assumption is that the effective potential is dominated by double-trace terms for the Polyakov loops. As a function of the temperature, a background field for the Polyakov loop, and a quartic coupling, it exhibits a universal structure: in the large portion of the parameter space, there is a continuous phase transition analogous to the third-order phase transition of Gross,Witten and Wadia, but the order of phase transition can be higher than third. We show that different confining potentials give rise to drastically differentmore » behavior of the eigenvalue density and the free energy. Therefore lattice simulations at large N could probe the order of phase transition and test our results. Critical« less

End-to-end crosstalk within the hepatitis C virus genome mediates the conformational switch of the 3′X-tail region

PubMed Central

Romero-López, Cristina; Barroso-delJesus, Alicia; García-Sacristán, Ana; Briones, Carlos; Berzal-Herranz, Alfredo

2014-01-01

The hepatitis C virus (HCV) RNA genome contains multiple structurally conserved domains that make long-distance RNA–RNA contacts important in the establishment of viral infection. Microarray antisense oligonucelotide assays, improved dimethyl sulfate probing methods and 2′ acylation chemistry (selective 2’-hydroxyl acylation and primer extension, SHAPE) showed the folding of the genomic RNA 3′ end to be regulated by the internal ribosome entry site (IRES) element via direct RNA–RNA interactions. The essential cis-acting replicating element (CRE) and the 3′X-tail region adopted different 3D conformations in the presence and absence of the genomic RNA 5′ terminus. Further, the structural transition in the 3′X-tail from the replication-competent conformer (consisting of three stem-loops) to the dimerizable form (with two stem-loops), was found to depend on the presence of both the IRES and the CRE elements. Complex interplay between the IRES, the CRE and the 3′X-tail region would therefore appear to occur. The preservation of this RNA–RNA interacting network, and the maintenance of the proper balance between different contacts, may play a crucial role in the switch between different steps of the HCV cycle. PMID:24049069

LPV control for the full region operation of a wind turbine integrated with synchronous generator.

PubMed

Cao, Guoyan; Grigoriadis, Karolos M; Nyanteh, Yaw D

2015-01-01

Wind turbine conversion systems require feedback control to achieve reliable wind turbine operation and stable current supply. A robust linear parameter varying (LPV) controller is proposed to reduce the structural loads and improve the power extraction of a horizontal axis wind turbine operating in both the partial load and the full load regions. The LPV model is derived from the wind turbine state space models extracted by FAST (fatigue, aerodynamics, structural, and turbulence) code linearization at different operating points. In order to assure a smooth transition between the two regions, appropriate frequency-dependent varying scaling parametric weighting functions are designed in the LPV control structure. The solution of a set of linear matrix inequalities (LMIs) leads to the LPV controller. A synchronous generator model is connected with the closed LPV control loop for examining the electrical subsystem performance obtained by an inner speed control loop. Simulation results of a 1.5 MW horizontal axis wind turbine model on the FAST platform illustrates the benefit of the LPV control and demonstrates the advantages of this proposed LPV controller, when compared with a traditional gain scheduling PI control and prior LPV control configurations. Enhanced structural load mitigation, improved power extraction, and good current performance were obtained from the proposed LPV control.

LPV Control for the Full Region Operation of a Wind Turbine Integrated with Synchronous Generator

PubMed Central

Grigoriadis, Karolos M.; Nyanteh, Yaw D.

2015-01-01

Wind turbine conversion systems require feedback control to achieve reliable wind turbine operation and stable current supply. A robust linear parameter varying (LPV) controller is proposed to reduce the structural loads and improve the power extraction of a horizontal axis wind turbine operating in both the partial load and the full load regions. The LPV model is derived from the wind turbine state space models extracted by FAST (fatigue, aerodynamics, structural, and turbulence) code linearization at different operating points. In order to assure a smooth transition between the two regions, appropriate frequency-dependent varying scaling parametric weighting functions are designed in the LPV control structure. The solution of a set of linear matrix inequalities (LMIs) leads to the LPV controller. A synchronous generator model is connected with the closed LPV control loop for examining the electrical subsystem performance obtained by an inner speed control loop. Simulation results of a 1.5 MW horizontal axis wind turbine model on the FAST platform illustrates the benefit of the LPV control and demonstrates the advantages of this proposed LPV controller, when compared with a traditional gain scheduling PI control and prior LPV control configurations. Enhanced structural load mitigation, improved power extraction, and good current performance were obtained from the proposed LPV control. PMID:25884036

EXTREME-ULTRAVIOLET OBSERVATIONAL CONSEQUENCES OF THE SPATIAL LOCALIZATION OF NANOFLARE HEATING WITHIN A MULTISTRANDED ATMOSPHERIC LOOP

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

Sarkar, Aveek; Walsh, Robert W.

2009-07-10

Determining the preferred spatial location of the energy input to solar coronal loops would be an important step forward toward a more complete understanding of the coronal heating problem. Following from the 2008 paper of Sarkar and Walsh, this paper presents a short (10{sup 9} cm {identical_to}10 Mm) 'global loop' as 125 individual strands, where each strand is modeled independently by a one-dimensional hydrodynamic simulation. The strands undergo small-scale episodic heating and are coupled together through the frequency distribution of the total energy input to the loop which follows a power-law distribution with index {approx}2.29. The spatial preference of themore » swarm of heating events from apex to footpoint is investigated. From a theoretical perspective, the resulting emission-measure-weighted temperature profiles along these two extreme cases do demonstrate a possible observable difference. Subsequently, the simulated output is folded through the Transition Region and Coronal Explorer (TRACE) instrument response functions and a rederivation of the temperature using different filter ratio techniques is performed. Given the multithermal scenario created by this many-strand loop model, a broad differential emission measure results; the subsequent double and triple filter ratios are very similar to those obtained from observations. However, any potential observational signature to differentiate between apex and footpoint dominant heating is possibly below instrumental thresholds. The consequences of using a broadband instrument like TRACE and Hinode-XRT in this way are discussed.« less

Coherent random lasing controlled by Brownian motion of the active scatterer

NASA Astrophysics Data System (ADS)

Liang, Shuofeng; Yin, Leicheng; Zhang, ZhenZhen; Xia, Jiangying; Xie, Kang; Zou, Gang; Hu, Zhijia; Zhang, Qijin

2018-05-01

The stability of the scattering loop is fundamental for coherent random lasing in a dynamic scattering system. In this work, fluorescence of DPP (N, N-di [3-(isobutyl polyhedral oligomeric silsesquioxanes) propyl] perylene diimide) is scattered to produce RL and we realize the transition from incoherent RL to coherent RL by controlling the Brownian motion of the scatterers (dimer aggregates of DPP) and the stability of scattering loop. To produce coherent random lasers, the loop needs to maintain a stable state within the loop-stable time, which can be determined through controlled Brownian motion of scatterers in the scattering system. The result shows that the loop-stable time is within 5.83 × 10‑5 s to 1.61 × 10‑4 s based on the transition from coherent to incoherent random lasing. The time range could be tuned by finely controlling the viscosity of the solution. This work not only develops a method to predict the loop-stable time, but also develops the study between Brownian motion and random lasers, which opens the road to a variety of novel interdisciplinary investigations involving modern statistical mechanics and disordered photonics.

Different mutation patterns of mitochondrial DNA displacement-loop in hepatocellular carcinomas induced by N-nitrosodiethylamine and a choline-deficient l-amino acid-defined diet in rats.

PubMed

Onishi, Mariko; Sokuza, Yui; Nishikawa, Tomoki; Mori, Chiharu; Uwataki, Kimiko; Honoki, Kanya; Tsujiuchi, Toshifumi

2007-10-12

Mutations of the mitochondria DNA (mtDNA) displacement loop (D-loop) were investigated to clarify different changes of exogenous and endogenous liver carcinogenesis in rats. We induced hepatocellular carcinomas (HCCs) in rats with N-nitrosodiethylamine (DEN) and a choline-deficient l-amino acid-defined (CDAA) diet. DNAs were extracted from 10 HCCs induced by DEN and 10 HCCs induced by the CDAA diet. To identify mutations in mtDNA D-loop, polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) analysis, followed by nucleotide sequencing, was performed. Mutations were detected in 5 out of 10 HCCs (50%) induced by DEN. Four out of 5 mutations were G/C to A/T transitions at positions 15707, 15717, 15930, and 16087, and one T/A to C/G transition at position 15559. By contrast, no mutations were found in 10 HCCs induced by the CDAA diet. These results demonstrated that mutations in mtDNA D-loop occur in rat HCCs induced by DEN but not by the CDAA diet, suggesting that mtDNA D-loop is a target of exogenous liver carcinogenesis in rats.

Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.

PubMed

Jung, Young-Sang; Cai, Mengli; Clore, G Marius

2010-02-05

The solution structure of the IIA-IIB complex of the N,N'-diacetylchitobiose (Chb) transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state and the active site Cys-10 of IIB(Chb) was substituted by serine to prevent intermolecular disulfide bond formation. Binding is weak with a K(D) of approximately 1.3 mm. The two complementary interaction surfaces are largely hydrophobic, with the protruding active site loop (residues 9-16) of IIB(Chb) buried deep within the active site cleft formed at the interface of two adjacent subunits of the IIA(Chb) trimer. The central hydrophobic portion of the interface is surrounded by a ring of polar and charged residues that provide a relatively small number of electrostatic intermolecular interactions that serve to correctly align the two proteins. The conformation of the active site loop in unphosphorylated IIB(Chb) is inconsistent with the formation of a phosphoryl transition state intermediate because of steric hindrance, especially from the methyl group of Ala-12 of IIB(Chb). Phosphorylation of IIB(Chb) is accompanied by a conformational change within the active site loop such that its path from residues 11-13 follows a mirror-like image relative to that in the unphosphorylated state. This involves a transition of the phi/psi angles of Gly-13 from the right to left alpha-helical region, as well as smaller changes in the backbone torsion angles of Ala-12 and Met-14. The resulting active site conformation is fully compatible with the formation of the His-89-P-Cys-10 phosphoryl transition state without necessitating any change in relative translation or orientation of the two proteins within the complex.

Does High Plasma-β Dynamics ``Load'' Active Regions?

NASA Astrophysics Data System (ADS)

McIntosh, Scott W.

2007-03-01

Using long-duration observations in the He II 304 Å passband of SOHO EIT, we investigate the spatial and temporal appearance of impulsive intensity fluctuations in the pixel light curves. These passband intensity fluctuations come from plasma emitting in the chromosphere, in the transition region, and in the lowest portions of the corona. We see that they are spatially tied to the supergranular scale and that their rate of occurrence is tied to the unsigned imbalance of the magnetic field in which they are observed. The signature of the fluctuations (in space and time) is consistent with their creation by magnetoconvection-forced reconnection, which is driven by the flow field in the high-β plasma. The signature of the intensity fluctuations around an active region suggests that the bulk of the mass and energy going into the active region complex observed in the hotter coronal plasma is supplied by this process, dynamically forcing the looped structure from beneath.

Effects of low sampling rate in the digital data-transition tracking loop

NASA Technical Reports Server (NTRS)

Mileant, A.; Million, S.; Hinedi, S.

1994-01-01

This article describes the performance of the all-digital data-transition tracking loop (DTTL) with coherent and noncoherent sampling using nonlinear theory. The effects of few samples per symbol and of noncommensurate sampling and symbol rates are addressed and analyzed. Their impact on the probability density and variance of the phase error are quantified through computer simulations. It is shown that the performance of the all-digital DTTL approaches its analog counterpart when the sampling and symbol rates are noncommensurate (i.e., the number of samples per symbol is an irrational number). The loop signal-to-noise ratio (SNR) (inverse of phase error variance) degrades when the number of samples per symbol is an odd integer but degrades even further for even integers.

Varietal Loops

NASA Image and Video Library

2016-09-15

A series of active regions stretched along the right side of the sun exhibited a wide variety of loops cascading above them (Sept. 12-14, 2016). The active region near the center has tightly coiled loops, while the region rotating over the right edge has some elongated and some very stretched loops above it. The loops are actually charged particles spiraling along magnetic field lines, observed here in a wavelength of extreme ultraviolet light. Near the middle of the video the Earth quickly passes in front of a portion of the sun as viewed by SDO. http://photojournal.jpl.nasa.gov/catalog/PIA16997

Topological insulating phases from two-dimensional nodal loop semimetals

NASA Astrophysics Data System (ADS)

Li, Linhu; Araújo, Miguel A. N.

2016-10-01

Starting from a minimal model for a two-dimensional nodal loop semimetal, we study the effect of chiral mass gap terms. The resulting Dirac loop anomalous Hall insulator's Chern number is the phase-winding number of the mass gap terms on the loop. We provide simple lattice models, analyze the topological phases, and generalize a previous index characterizing topological transitions. The responses of the Dirac loop anomalous Hall and quantum spin Hall insulators to a magnetic field's vector potential are also studied both in weak- and strong-field regimes, as well as the edge states in a ribbon geometry.

Modal analysis of dislocation vibration and reaction attempt frequency

DOE PAGES

Sobie, Cameron; Capolungo, Laurent; McDowell, David L.; ...

2017-02-04

Transition state theory is a fundamental approach for temporal coarse-graining. It estimates the reaction rate for a transition processes by quantifying the activation free energy and attempt frequency for the unit process. To calculate the transition rate of a gliding dislocation, the attempt frequency is often obtained from line tension estimates of dislocation vibrations, a highly simplified model of dislocation behavior. This work revisits the calculation of attempt frequency for a dislocation bypassing an obstacle, in this case a self-interstitial atom (SIA) loop. First, a direct calculation of the vibrational characteristics of a finite pinned dislocation segment is compared tomore » line tension estimates before moving to the more complex case of dislocation-obstacle bypass. The entropic factor associated with the attempt frequency is calculated for a finite dislocation segment and for an infinite glide dislocation interacting with an SIA loop. Lastly, it is found to be dislocation length independent for three cases of dislocation-self interstitial atom (SIA) loop interactions.« less

MHD Modelling of Coronal Loops: Injection of High-Speed Chromospheric Flows

NASA Technical Reports Server (NTRS)

Petralia, A.; Reale, F.; Orlando, S.; Klimchuk, J. A.

2014-01-01

Context. Observations reveal a correspondence between chromospheric type II spicules and bright upward-moving fronts in the corona observed in the extreme-ultraviolet (EUV) band. However, theoretical considerations suggest that these flows are probably not the main source of heating in coronal magnetic loops. Aims. We investigate the propagation of high-speed chromospheric flows into coronal magnetic flux tubes and the possible production of emission in the EUV band. Methods. We simulated the propagation of a dense 104 K chromospheric jet upward along a coronal loop by means of a 2D cylindrical MHD model that includes gravity, radiative losses, thermal conduction, and magnetic induction. The jet propagates in a complete atmosphere including the chromosphere and a tenuous cool (approximately 0.8 MK) corona, linked through a steep transition region. In our reference model, the jet initial speed is 70 km per second, its initial density is 10(exp 11) per cubic centimeter, and the ambient uniform magnetic field is 10 G. We also explored other values of jet speed and density in 1D and different magnetic field values in 2D, as well as the jet propagation in a hotter (approximately 1.5 MK) background loop. Results. While the initial speed of the jet does not allow it to reach the loop apex, a hot shock-front develops ahead of it and travels to the other extreme of the loop. The shock front compresses the coronal plasma and heats it to about 10(exp 6) K. As a result, a bright moving front becomes visible in the 171 Angstrom channel of the SDO/AIA mission. This result generally applies to all the other explored cases, except for the propagation in the hotter loop. Conclusions. For a cool, low-density initial coronal loop, the post-shock plasma ahead of upward chromospheric flows might explain at least part of the observed correspondence between type II spicules and EUV emission excess.

Description and User Manual for a Web-Based Interface to a Transit-Loss Accounting Program for Monument and Fountain Creeks, El Paso and Pueblo Counties, Colorado

USGS Publications Warehouse

Kuhn, Gerhard; Krammes, Gary S.; Beal, Vivian J.

2007-01-01

The U.S. Geological Survey, in cooperation with Colorado Springs Utilities, the Colorado Water Conservation Board, and the El Paso County Water Authority, began a study in 2004 with the following objectives: (1) Apply a stream-aquifer model to Monument Creek, (2) use the results of the modeling to develop a transit-loss accounting program for Monument Creek, (3) revise an existing accounting program for Fountain Creek to easily incorporate ongoing and future changes in management of return flows of reusable water, and (4) integrate the two accounting programs into a single program and develop a Web-based interface to the integrated program that incorporates simple and reliable data entry that is automated to the fullest extent possible. This report describes the results of completing objectives (2), (3), and (4) of that study. The accounting program for Monument Creek was developed first by (1) using the existing accounting program for Fountain Creek as a prototype, (2) incorporating the transit-loss results from a stream-aquifer modeling analysis of Monument Creek, and (3) developing new output reports. The capabilities of the existing accounting program for Fountain Creek then were incorporated into the program for Monument Creek and the output reports were expanded to include Fountain Creek. A Web-based interface to the new transit-loss accounting program then was developed that provided automated data entry. An integrated system of 34 nodes and 33 subreaches was integrated by combining the independent node and subreach systems used in the previously completed stream-aquifer modeling studies for the Monument and Fountain Creek reaches. Important operational criteria that were implemented in the new transit-loss accounting program for Monument and Fountain Creeks included the following: (1) Retain all the reusable water-management capabilities incorporated into the existing accounting program for Fountain Creek; (2) enable daily accounting and transit-loss computations for a variable number of reusable return flows discharged into Monument Creek at selected locations; (3) enable diversion of all or a part of a reusable return flow at any selected node for purposes of storage in off-stream reservoirs or other similar types of reusable water management; (4) and provide flexibility in the accounting program to change the number of return-flow entities, the locations at which the return flows discharge into Monument or Fountain Creeks, or the locations to which the return flows are delivered. The primary component of the Web-based interface is a data-entry form that displays data stored in the accounting program input file; the data-entry form allows for entry and modification of new data, which then is rewritten to the input file. When the data-entry form is displayed, up-to-date discharge data for each station are automatically computed and entered on the data-entry form. Data for native return flows, reusable return flows, reusable return flow diversions, and native diversions also are entered automatically or manually, if needed. In computing the estimated quantities of reusable return flow and the associated transit losses, the accounting program uses two sets of computations. The first set of computations is made between any two adjacent streamflow-gaging stations (termed 'stream-segment loop'); the primary purpose of the stream-segment loop is to estimate the loss or gain in native discharge between the two adjacent streamflow-gaging stations. The second set of computations is made between any two adjacent nodes (termed 'subreach loop'); the actual transit-loss computations are made in the subreach loop, using the result from the stream-segment loop. The stream-segment loop is completed for a stream segment, and then the subreach loop is completed for each subreach within the segment. When the subreach loop is completed for all subreaches within a stream segment, the stream-segment loop is initiated for the ne

Study of structural morphologies of thermoresponsive diblock AB and triblock BAB copolymers (A = poly(N-isopropylacrylamide), B = polystyrene)

NASA Astrophysics Data System (ADS)

Rodríguez-Hidalgo, María del Rosario; Soto-Figueroa, César; Vicente, Luis

2018-03-01

Structural morphologies of diblock AB and triblock BAB copolymers (A = poly(N-isopropylacrylamide), B = polystyrene) in aqueous environment have been investigated by dissipative particle dynamics (DPD). In triblock copolymers insoluble PS blocks contract while soluble pNIPAM blocks stay at the periphery forming looped chains as corona. As the temperature is increased there is a continuous morphological transition and micelles form ellipsoidal structures with segregated polymer zones. The phase transition of looped pNIPAM chains occurs at lower temperature than for linear chains and within broader temperature range. It is discussed how the chain topology of pNIPAM affects the phase transition.

Nucleation and hysteresis of vapor-liquid phase transitions in confined spaces: effects of fluid-wall interaction.

PubMed

Men, Yumei; Yan, Qingzhao; Jiang, Guangfeng; Zhang, Xianren; Wang, Wenchuan

2009-05-01

In this work, we propose a method to stabilize a nucleus in the framework of lattice density-functional theory (LDFT) by imposing a suitable constraint. Using this method, the shape of critical nucleus and height of the nucleation barrier can be determined without using a predefined nucleus as input. As an application of this method, we study the nucleation behavior of vapor-liquid transition in nanosquare pores with infinite length and relate the observed hysteresis loop on an adsorption isotherm to the nucleation mechanism. According to the dependence of hysteresis and the nucleation mechanism on the fluid-wall interaction, w , in this work, we have classified w into three regions ( w>0.9 , 0.1< or =w< or =0.9 , and w<0.1 ), which are denoted as strongly, moderately, and weakly attractive fluid-wall interaction, respectively. The dependence of hysteresis on the fluid-wall interaction is interpreted by the different nucleation mechanisms. Our constrained LDFT calculations also show that the different transition paths may induce different nucleation behaviors. The transition path dependence should be considered if morphological transition of nuclei exists during a nucleation process.

Dynamics of protein-protein interactions at the MscL periplasmic-lipid interface.

PubMed

Zhong, Dalian; Yang, Li-Min; Blount, Paul

2014-01-21

MscL, the highly conserved bacterial mechanosensitive channel of large conductance, is one of the best studied mechanosensors. It is a homopentameric channel that serves as a biological emergency release valve that prevents cell lysis from acute osmotic stress. We previously showed that the periplasmic region of the protein, particularly a single residue located at the TM1/periplasmic loop interface, F47 of Staphylococcus aureus and I49 of Escherichia coli MscL, plays a major role in both the open dwell time and mechanosensitivity of the channel. Here, we introduced cysteine mutations at these sites and found they formed disulfide bridges that decreased the channel open dwell time. By scanning a likely interacting domain, we also found that these sites could be disulfide trapped by addition of cysteine mutations in other locations within the periplasmic loop of MscL, and this also led to rapid channel kinetics. Together, the data suggest structural rearrangements and protein-protein interactions that occur within this region upon normal gating, and further suggest that locking portions of the channel into a transition state decreases the stability of the open state. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The Strength of an Ig Switch Region is Determined by its Ability to Drive R-loop Formation and its Number of WGCW Sites

PubMed Central

Zhang, Zheng Z.; Pannunzio, Nicholas R.; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

2014-01-01

SUMMARY R-loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R-loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR, regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R-loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R-loop formation, and on the number of WGCW sites. PMID:25017067

Three flavor Nambu-Jona-Lasinio model with Polyakov loop and competition with nuclear matter

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

Ciminale, M.; Ippolito, N. D.; Nardulli, G.

2008-03-01

We study the phase diagram of the three flavor Polyakov-Nambu-Jona-Lasinio (PNJL) model and, in particular, the interplay between chiral symmetry restoration and deconfinement crossover. We compute chiral condensates, quark densities, and the Polyakov loop at several values of temperature and chemical potential. Moreover we investigate on the role of the Polyakov loop dynamics in the transition from nuclear matter to quark matter.

Molecular dynamics simulations on the conformational transitions from the GA 98 (GA 88) to GB 98 (GB 88) proteins.

PubMed

Song, Chunnian; Wang, Qing; Xue, Tuo; Wang, Yan; Chen, Guangju

2016-12-01

We performed conventional and targeted molecular dynamics simulations to address the dynamic transition mechanisms of the conformational transitions from the G A 98 protein with only 1 mutation of Leu45Tyr to G B 98 and from the G A 88 protein with 7 mutations of Gly24Ala, Ile25Thr, Ile30Phe, Ile33Tyr, Leu45Tyr, Ile49Thr, and Leu50Lys to G B 88. The results show that the conformational transition mechanism from the mutated 3α G A 98 (G A 88) state to the α+4β G B 98 (G B 88) state via several intermediate conformations involves the bending of loops at the N and C termini firstly, the unfolding of αA and αC, then the traversing of αB, and the formation of the 4β layer with the conversion of the hydrophobic core. The bending of loops at the N and C termini and the formation of the crucial transition conformation with the full unfolded structure are key factors in their transition processes. The communication of the interaction network, the bending directions of loops, and the traversing site of αB in the transition of G A 98 to G B 98 are markedly different from those in G A 88 to G B 88 because of the different mutated residues. The analysis of the correlations and the calculated mass center distances between some segments further supported their conformational transition mechanisms. These results could help people to better understand the Paracelsus challenge. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Thermal stability, structural features, and B-to-Z transition in DNA tetraloop hairpins as determined by optical spectroscopy in d(CG)(3)T(4)(CG)(3) and d(CG)(3)A(4)(CG)(3) oligodeoxynucleotides.

PubMed

Hernández, Belén; Baumruk, Vladimir; Gouyette, Catherine; Ghomi, Mahmoud

2005-05-01

NMR and CD data have previously shown the formation of the T(4) tetraloop hairpin in aqueous solutions, as well as the possibility of the B-to-Z transition in its stem in high salt concentration conditions. It has been shown that the stem B-to-Z transition in T(4) hairpins leads to S (south)- to N (north)-type conformational changes in the loop sugars, as well as anti to syn orientations in the loop bases. In this article, we have compared by means of UV absorption, CD, Raman, and Fourier transform infrared (FTIR), the thermodynamic and structural properties of the T(4) and A(4) tetraloop hairpins formed in 5'-d(CGCGCG-TTTT-CGCGCG)-3' and 5'-d(CGCGCG-AAAA-CGCGCG)-3', respectively. In presence of 5M NaClO(4), a complete B-to-Z transition of the stems is first proved by CD spectra. UV melting profiles are consistent with a higher thermal stability of the T(4) hairpin compared to the A(4) hairpin. Order-to-disorder transition of both hairpins has also been analyzed by means of Raman spectra recorded as a function of temperature. A clear Z-to-B transition of the stem has been confirmed in the T(4) hairpin, and not in the A(4) hairpin. With a right-handed stem, Raman and FTIR spectra have confirmed the C2'-endo/anti conformation for all the T(4) loop nucleosides. With a left-handed stem, a part of the T(4) loop sugars adopt a N-type (C3'-endo) conformation, and the C3'-endo/syn conformation seems to be the preferred one for the dA residues involved in the A(4) tetraloop.

DNA unzipping phase diagram calculated via replica theory.

PubMed

Roland, C Brian; Hatch, Kristi Adamson; Prentiss, Mara; Shakhnovich, Eugene I

2009-05-01

We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). Toward this end, we study a statistical-mechanics model for the fluctuating structure of a long molecule of dsDNA, and compute the equilibrium phase diagram for the experiment in which the molecule is unzipped under applied force. We consider a perfect-matching dsDNA model, in which the loops are volume-excluding chains with arbitrary loop exponent c . We include stacking interactions, hydrogen bonds, and main-chain entropy. We include sequence heterogeneity at the level of random sequences; in particular, there is no correlation in the base-pairing (bp) energy from one sequence position to the next. We present heuristic arguments to demonstrate that the low-temperature macrostate does not exhibit degenerate ergodicity breaking. We use this claim to understand the results of our replica-theoretic calculation of the equilibrium properties of the system. As a function of temperature, we obtain the minimal force at which the molecule separates completely. This critical-force curve is a line in the temperature-force phase diagram that marks the regions where the molecule exists primarily as a double helix versus the region where the molecule exists as two separate strands. We compare our random-sequence model to magnetic tweezer experiments performed on the 48 502 bp genome of bacteriophage lambda . We find good agreement with the experimental data, which is restricted to temperatures between 24 and 50 degrees C . At higher temperatures, the critical-force curve of our random-sequence model is very different for that of the homogeneous-sequence version of our model. For both sequence models, the critical force falls to zero at the melting temperature T_{c} like |T-T_{c}|;{alpha} . For the homogeneous-sequence model, alpha=1/2 almost exactly, while for the random-sequence model, alpha approximately 0.9 . Importantly, the shape of the critical-force curve is connected, via our theory, to the manner in which the helix fraction falls to zero at T_{c} . The helix fraction is the property that is used to classify the melting transition as a type of phase transition. In our calculation, the shape of the critical-force curve holds strong evidence that the zero-force melting transition of long natural dsDNA should be classified as a higher-order (continuous) phase transition. Specifically, the order is 3rd or greater.

Suppressing epidemic spreading in multiplex networks with social-support

NASA Astrophysics Data System (ADS)

Chen, Xiaolong; Wang, Ruijie; Tang, Ming; Cai, Shimin; Stanley, H. Eugene; Braunstein, Lidia A.

2018-01-01

Although suppressing the spread of a disease is usually achieved by investing in public resources, in the real world only a small percentage of the population have access to government assistance when there is an outbreak, and most must rely on resources from family or friends. We study the dynamics of disease spreading in social-contact multiplex networks when the recovery of infected nodes depends on resources from healthy neighbors in the social layer. We investigate how degree heterogeneity affects the spreading dynamics. Using theoretical analysis and simulations we find that degree heterogeneity promotes disease spreading. The phase transition of the infected density is hybrid and increases smoothly from zero to a finite small value at the first invasion threshold and then suddenly jumps at the second invasion threshold. We also find a hysteresis loop in the transition of the infected density. We further investigate how an overlap in the edges between two layers affects the spreading dynamics. We find that when the amount of overlap is smaller than a critical value the phase transition is hybrid and there is a hysteresis loop, otherwise the phase transition is continuous and the hysteresis loop vanishes. In addition, the edge overlap allows an epidemic outbreak when the transmission rate is below the first invasion threshold, but suppresses any explosive transition when the transmission rate is above the first invasion threshold.

Invisibility of Solar Active Region Umbra-to-Umbra Coronal Loops: New Evidence that Magnetoconvection Drives Solar-Stellar Coronal Heating

NASA Technical Reports Server (NTRS)

Tiwari, Sanjiv K.; Thalmann, Julia K.; Panesar, Navdeep K.; Moore, Ronald L.; Winebarger, Amy R.

2017-01-01

Coronal heating generally increases with increasing magnetic field strength: the EUV/X-ray corona in active regions is 10--100 times more luminous and 2--4 times hotter than that in quiet regions and coronal holes, which are heated to only about 1.5 MK, and have fields that are 10--100 times weaker than that in active regions. From a comparison of a nonlinear force-free model of the three-dimensional active region coronal field to observed extreme-ultraviolet loops, we find that (1) umbra-to-umbra coronal loops, despite being rooted in the strongest magnetic flux, are invisible, and (2) the brightest loops have one foot in an umbra or penumbra and the other foot in another sunspot's penumbra or in unipolar or mixed-polarity plage. The invisibility of umbra-to-umbra loops is new evidence that magnetoconvection drives solar-stellar coronal heating: evidently, the strong umbral field at both ends quenches the magnetoconvection and hence the heating. Our results from EUV observations and nonlinear force-free modeling of coronal magnetic field imply that, for any coronal loop on the Sun or on any other convective star, as long as the field can be braided by convection in at least one loop foot, the stronger the field in the loop, the stronger the coronal heating.

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

Cadavid, A. C.; Lawrence, J. K.; Christian, D. J.

We investigate the scaling properties of the long-range temporal evolution and intermittency of Atmospheric Imaging Assembly/ Solar Dynamics Observatory intensity observations in four solar environments: an active region core, a weak emission region, and two core loops. We use two approaches: the probability distribution function (PDF) of time series increments and multifractal detrended fluctuation analysis (MF-DFA). Noise taints the results, so we focus on the 171 Å waveband, which has the highest signal-to-noise ratio. The lags between pairs of wavebands distinguish between coronal versus transition region (TR) emission. In all physical regions studied, scaling in the range of 15–45 minutesmore » is multifractal, and the time series are anti-persistent on average. The degree of anti-correlation in the TR time series is greater than that for coronal emission. The multifractality stems from long-term correlations in the data rather than the wide distribution of intensities. Observations in the 335 Å waveband can be described in terms of a multifractal with added noise. The multiscaling of the extreme-ultraviolet data agrees qualitatively with the radiance from a phenomenological model of impulsive bursts plus noise, and also from ohmic dissipation in a reduced magnetohydrodynamic model for coronal loop heating. The parameter space must be further explored to seek quantitative agreement. Thus, the observational “signatures” obtained by the combined tests of the PDF of increments and the MF-DFA offer strong constraints that can systematically discriminate among models for coronal heating.« less

The Twist Limit for Bipolar Active Regions

NASA Technical Reports Server (NTRS)

Moore, Ron; Falconer, David; Gary, Allen

2008-01-01

We present new evidence that further supports the standard idea that active regions are emerged magnetic-flux-rope omega loops. When the axial magnetic twist of a cylindrical flux rope exceeds a critical amount, the flux rope becomes unstable to kinking, and the excess axial twist is converted into writhe twist by the kinking. This suggests that, if active regions are emerged omega loops, then (1) no active region should have magnetic twist much above the limit set by kinking, (2) active regions having twist near the limit should often arise from kinked omega loops, and (3) since active regions having large delta sunspots are outstandingly twisted, these arise from kinked omega loops and should have twist near the limit for kinking. From each of 36 vector magnetograms of bipolar active regions, we have measured (1) the total flux of the vertical field above 100 G, (2) the area covered by this flux, and (3) the net electric current that arches over the polarity inversion line. These three quantities yield an estimate of the axial magnetic twist in a simple model cylindrical flux rope that corresponds to the top of the active region s hypothetical omega loop prior to emergence. In all 36 cases, the estimated twist is below the critical limit for kinking. The 11 most twisted active regions (1) have estimated twist within a factor of approx.3 of the limit, and (2) include all of our 6 active regions having large delta sunspots. Thus, our observed twist limit for bipolar active regions is in good accord with active regions being emerged omega loops.

A Self-Organizing Incremental Spatiotemporal Associative Memory Networks Model for Problems with Hidden State

PubMed Central

2016-01-01

Identifying the hidden state is important for solving problems with hidden state. We prove any deterministic partially observable Markov decision processes (POMDP) can be represented by a minimal, looping hidden state transition model and propose a heuristic state transition model constructing algorithm. A new spatiotemporal associative memory network (STAMN) is proposed to realize the minimal, looping hidden state transition model. STAMN utilizes the neuroactivity decay to realize the short-term memory, connection weights between different nodes to represent long-term memory, presynaptic potentials, and synchronized activation mechanism to complete identifying and recalling simultaneously. Finally, we give the empirical illustrations of the STAMN and compare the performance of the STAMN model with that of other methods. PMID:27891146

Fundamental Physics and Practical Applications of Electromagnetic Local Flow Control in High Speed Flows (Rutgers)

DTIC Science & Technology

2010-02-16

field. Techniques utilizing this design use an open- loop control and no flow monitoring sensors are required. Conversely, reactive (or closed - loop ...and closed (dashed line) configuration. 38 closed configuration described above, the ambiguity in the critical limits of the transition...flow; a new vortex is then shed from the cavity leading edge, closing the feedback loop .[31] Open cavities with an L/D approximately greater than

Simulating nanostorm heating in coronal loops using hydrodynamics and non-thermal particle evolution

NASA Astrophysics Data System (ADS)

Migliore, Christina; Winter, Henry; Murphy, Nicholas

2018-01-01

The solar corona is filled with loop-like structures that appear bright against the background when observed in the extreme ultraviolet (EUV). These loops have several remarkable properties that are not yet well understood. Warm loops (∼ 1 MK) appear to be ∼ 2 ‑ 9 times as dense at their apex as the predictions of hydrostatic atmosphere models. These loops also appear to be of constant cross-section despite the fact that the field strength in a potential magnetic field should decrease in the corona, causing the loops to expand. It is not clear why many active region loops appear to be of constant cross-section. Theories range from an internal twist of the magnetic field to observational effects. In this work we simulate active region loops heated by nanoflare storms using a dipolar magnetic field. We calculate the hydrodynamic properties for each loop using advanced hydrodynamics codes to simulate the corona and chromospheric response and basic dipole models to represent the magnetic fields of the loops. We show that even modest variations of the magnetic field strength along the loop can lead to drastic changes in the density profiles of active region loops, and they can also explain the overpressure at the apex of these loops. Synthetic AIA images of each loop are made to show the observable consequences of varying magnetic field strengths along the loop’s axis of symmetry. We also show how this work can lead to improved modeling of larger solar and stellar flares.

Observations and Numerical Models of Solar Coronal Heating Associated with Spicules

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

Pontieu, B. De; Martinez-Sykora, J.; Moortel, I. De

Spicules have been proposed as significant contributors to the mass and energy balance of the corona. While previous observations have provided a glimpse of short-lived transient brightenings in the corona that are associated with spicules, these observations have been contested and are the subject of a vigorous debate both on the modeling and the observational side. Therefore, it remains unclear whether plasma is heated to coronal temperatures in association with spicules. We use high-resolution observations of the chromosphere and transition region (TR) with the Interface Region Imaging Spectrograph and of the corona with the Atmospheric Imaging Assembly on board themore » Solar Dynamics Observatory to show evidence of the formation of coronal structures associated with spicular mass ejections and heating of plasma to TR and coronal temperatures. Our observations suggest that a significant fraction of the highly dynamic loop fan environment associated with plage regions may be the result of the formation of such new coronal strands, a process that previously had been interpreted as the propagation of transient propagating coronal disturbances. Our observations are supported by 2.5D radiative MHD simulations that show heating to coronal temperatures in association with spicules. Our results suggest that heating and strong flows play an important role in maintaining the substructure of loop fans, in addition to the waves that permeate this low coronal environment.« less

Sweeping Arches and Loops [video

NASA Image and Video Library

2014-07-10

Two active regions with their intense magnetic fields produced towering arches and spiraling coils of solar loops above them (June 29 - July 1, 2014) as they rotated into view. When viewed in extreme ultraviolet light, magnetic field lines are revealed by charged particles that travel along them. These active regions appear as dark sunspots when viewed in filtered light. Note the small blast in the upper of the two major active regions, followed by more coils of loops as the region reorganizes itself. The still was taken on June 30 at 10:33 UT. Credit: NASA/Solar Dynamics Observatory Two active regions with their intense magnetic fields produced towering arches and spiraling coils of solar loops above them (June 29 - July 1, 2014) as they rotated into view. When viewed in extreme ultraviolet light, magnetic field lines are revealed by charged particles that travel along them. These active regions appear as dark sunspots when viewed in filtered light. Note the small blast in the upper of the two major active regions, followed by more coils of loops as the region reorganizes itself. The still was taken on June 30 at 10:33 UT. Credit: Solar Dynamics Observatory/NASA.

47 CFR 54.803 - Universal service zones.

Code of Federal Regulations, 2013 CFR

2013-10-01

... developing this transitional estimate, the loop and port costs estimated by the FCC cost model, or other... chapter. (b) In a price cap study area where the price cap local exchange carrier has not established state-approved prices for UNE loops by zone, the Administrator shall develop an estimate of the local...

47 CFR 54.803 - Universal service zones.

Code of Federal Regulations, 2011 CFR

2011-10-01

... developing this transitional estimate, the loop and port costs estimated by the FCC cost model, or other... chapter. (b) In a price cap study area where the price cap local exchange carrier has not established state-approved prices for UNE loops by zone, the Administrator shall develop an estimate of the local...

47 CFR 54.803 - Universal service zones.

Code of Federal Regulations, 2014 CFR

2014-10-01

... developing this transitional estimate, the loop and port costs estimated by the FCC cost model, or other... chapter. (b) In a price cap study area where the price cap local exchange carrier has not established state-approved prices for UNE loops by zone, the Administrator shall develop an estimate of the local...

47 CFR 54.803 - Universal service zones.

Code of Federal Regulations, 2012 CFR

2012-10-01

... developing this transitional estimate, the loop and port costs estimated by the FCC cost model, or other... chapter. (b) In a price cap study area where the price cap local exchange carrier has not established state-approved prices for UNE loops by zone, the Administrator shall develop an estimate of the local...

47 CFR 54.803 - Universal service zones.

Code of Federal Regulations, 2010 CFR

2010-10-01

... developing this transitional estimate, the loop and port costs estimated by the FCC cost model, or other... chapter. (b) In a price cap study area where the price cap local exchange carrier has not established state-approved prices for UNE loops by zone, the Administrator shall develop an estimate of the local...

Shock Position Control for Mode Transition in a Turbine Based Combined Cycle Engine Inlet Model

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Stueber, Thomas J.

2013-01-01

A dual flow-path inlet for a turbine based combined cycle (TBCC) propulsion system is to be tested in order to evaluate methodologies for performing a controlled inlet mode transition. Prior to experimental testing, simulation models are used to test, debug, and validate potential control algorithms which are designed to maintain shock position during inlet disturbances. One simulation package being used for testing is the High Mach Transient Engine Cycle Code simulation, known as HiTECC. This paper discusses the development of a mode transition schedule for the HiTECC simulation that is analogous to the development of inlet performance maps. Inlet performance maps, derived through experimental means, describe the performance and operability of the inlet as the splitter closes, switching power production from the turbine engine to the Dual Mode Scram Jet. With knowledge of the operability and performance tradeoffs, a closed loop system can be designed to optimize the performance of the inlet. This paper demonstrates the design of the closed loop control system and benefit with the implementation of a Proportional-Integral controller, an H-Infinity based controller, and a disturbance observer based controller; all of which avoid inlet unstart during a mode transition with a simulated disturbance that would lead to inlet unstart without closed loop control.

Preemptive vortex-loop proliferation in multicomponent interacting Bose-Einstein condensates

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

Dahl, E. K.; Kragset, S.; Sudboe, A.

2008-04-01

We use analytical arguments and large-scale Monte Carlo calculations to investigate the nature of the phase transitions between distinct complex superfluid phases in a two-component Bose-Einstein condensate when a nondissipative drag between the two components is being varied. We focus on understanding the role of topological defects in various phase transitions and develop vortex-matter arguments, allowing an analytical description of the phase diagram. We find the behavior of fluctuation induced vortex matter to be much more complex and substantially different from that of single-component superfluids. We propose and numerically investigate a drag-induced ''preemptive vortex loop proliferation'' scenario. Such a transitionmore » may be a quite generic feature in many multicomponent systems where symmetry is restored by a gas of several kinds of competing vortex loops.« less

Simulating Coronal Loop Implosion and Compressible Wave Modes in a Flare Hit Active Region

NASA Astrophysics Data System (ADS)

Sarkar, Aveek; Vaidya, Bhargav; Hazra, Soumitra; Bhattacharyya, Jishnu

2017-12-01

There is considerable observational evidence of implosion of magnetic loop systems inside solar coronal active regions following high-energy events like solar flares. In this work, we propose that such collapse can be modeled in three dimensions quite accurately within the framework of ideal magnetohydrodynamics. We furthermore argue that the dynamics of loop implosion is only sensitive to the transmitted disturbance of one or more of the system variables, e.g., velocity generated at the event site. This indicates that to understand loop implosion, it is sensible to leave the event site out of the simulated active region. Toward our goal, a velocity pulse is introduced to model the transmitted disturbance generated at the event site. Magnetic field lines inside our simulated active region are traced in real time, and it is demonstrated that the subsequent dynamics of the simulated loops closely resemble observed imploding loops. Our work highlights the role of plasma β in regards to the rigidity of the loop systems and how that might affect the imploding loops’ dynamics. Compressible magnetohydrodynamic modes such as kink and sausage are also shown to be generated during such processes, in accordance with observations.

An Assessment of Magnetic Conditions for Strong Coronal Heating in Solar Active Regions by Comparing Observed Loops with Computed Potential Field Lines

NASA Technical Reports Server (NTRS)

Gary, G. A.; Moore, R. L.; Porter, J. G.; Falconer, D. A.

1999-01-01

We report further results on the magnetic origins of coronal heating found from registering coronal images with photospheric vector magnetograms. For two complementary active regions, we use computed potential field lines to examine the global non-potentiality of bright extended coronal loops and the three-dimensional structure of the magnetic field at their feet, and assess the role of these magnetic conditions in the strong coronal heating in these loops. The two active regions are complementary, in that one is globally potential and the other is globally nonpotential, while each is predominantly bipolar, and each has an island of included polarity in its trailing polarity domain. We find the following: (1) The brightest main-arch loops of the globally potential active region are brighter than the brightest main- arch loops of the globally strongly nonpotential active region. (2) In each active region, only a few of the mainarch magnetic loops are strongly heated, and these are all rooted near the island. (3) The end of each main-arch bright loop apparently bifurcates above the island, so that it embraces the island and the magnetic null above the island. (4) At any one time, there are other main-arch magnetic loops that embrace the island in the same manner as do the bright loops but that are not selected for strong coronal heating. (5) There is continual microflaring in sheared core fields around the island, but the main-arch bright loops show little response to these microflares. From these observational and modeling results we draw the following conclusions: (1) The heating of the main-arch bright loops arises mainly from conditions at the island end of these loops and not from their global non-potentiality. (2) There is, at most, only a loose coupling between the coronal heating in the bright loops of the main arch and the coronal heating in the sheared core fields at their feet, although in both the heating is driven by conditions/events in and around the island. (3) The main-arch bright loops are likely to be heated via reconnection driven at the magnetic null over the island. The details of how and where (along the null line) the reconnection is driven determine which of the split-end loops are selected for strong heating. (4) The null does not appear to be directly involved in the heating of the sheared core fields or in the heating of an extended loop rooted in the island. Rather, these all appear to be heated by microflares in the sheared core field.

Probing the elastic limit of DNA bending

PubMed Central

Le, Tung T.; Kim, Harold D.

2014-01-01

Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA. PMID:25122748

LINE-OF-SIGHT SHELL STRUCTURE OF THE CYGNUS LOOP

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

Uchida, Hiroyuki; Tsunemi, Hiroshi; Katsuda, Satoru

We conducted a comprehensive study on the shell structure of the Cygnus Loop using 41 observation data obtained by the Suzaku and the XMM-Newton satellites. To investigate the detailed plasma structure of the Cygnus Loop, we divided our fields of view into 1042 box regions. From the spectral analysis, the spectra obtained from the limb of the Loop are well fitted by the single-component non-equilibrium ionization plasma model. On the other hand, the spectra obtained from the inner regions are well fitted by the two-component model. As a result, we confirmed that the low-temperature and high-temperature components originated from themore » surrounding interstellar matter (ISM) and the ejecta of the Loop, respectively. From the best-fit results, we showed a flux distribution of the ISM component. The distribution clearly shows the limb-brightening structure, and we found out some low-flux regions. Among them, the south blowout region has the lowest flux. We also found other large low-flux regions at slightly west and northeast from the center. We estimated the former thin shell region to be approx1.{sup 0}3 in diameter and concluded that there exists a blowout along the line of sight in addition to the south blowout. We also calculated the emission measure distribution of the ISM component and showed that the Cygnus Loop is far from the result obtained by a simple Sedov evolution model. From the results, we support that the Cygnus Loop originated from a cavity explosion. The emission measure distribution also suggests that the cavity-wall density is higher in the northeast than that in the southwest. These results suggest that the thickness of the cavity wall surrounding the Cygnus Loop is not uniform.« less

On the nature of fast sausage waves in coronal loops

NASA Astrophysics Data System (ADS)

Bahari, Karam

2018-05-01

The effect of the parameters of coronal loops on the nature of fast sausage waves are investigated. To do this three models of the coronal loop considered, a simple loop model, a current-carrying loop model and a model with radially structured density called "Inner μ" profile. For all the models the Magnetohydrodynamic (MHD) equations solved analytically in the linear approximation and the restoring forces of oscillations obtained. The ratio of the magnetic tension force to the pressure gradient force obtained as a function of the distance from the axis of the loop. In the simple loop model for all values of the loop parameters the fast sausages wave have a mixed nature of Alfvénic and fast MHD waves, in the current-carrying loop model with thick annulus and low density contrast the fast sausage waves can be considered as purely Alfvénic wave in the core region of the loop, and in the "Inner μ" profile for each set of the parameters of the loop the wave can be considered as a purely Alfvénic wave in some regions of the loop.

Propagating wave in active region-loops, located over the solar disk observed by the Interface Region Imaging Spectrograph

NASA Astrophysics Data System (ADS)

Zhang, B.; Hou, Y. J.; Zhang, J.

2018-03-01

Aims: We aim to ascertain the physical parameters of a propagating wave over the solar disk detected by the Interface Region Imaging Spectrograph (IRIS). Methods: Using imaging data from the IRIS and the Solar Dynamic Observatory (SDO), we tracked bright spots to determine the parameters of a propagating transverse wave in active region (AR) loops triggered by activation of a filament. Deriving the Doppler velocity of Si IV line from spectral observations of IRIS, we have determined the rotating directions of active region loops which are relevant to the wave. Results: On 2015 December 19, a filament was located on the polarity inversion line of the NOAA AR 12470. The filament was activated and then caused a C1.1 two-ribbon flare. Between the flare ribbons, two rotation motions of a set of bright loops were observed to appear in turn with opposite directions. Following the end of the second rotation, a propagating wave and an associated transverse oscillation were detected in these bright loops. In 1400 Å channel, there was bright material flowing along the loops in a wave-like manner, with a period of 128 s and a mean amplitude of 880 km. For the transverse oscillation, we tracked a given loop and determine the transverse positions of the tracking loop in a limited longitudinal range. In both of 1400 Å and 171 Å channels, approximately four periods are distinguished during the transverse oscillation. The mean period of the oscillation is estimated as 143 s and the displacement amplitude as between 1370 km and 690 km. We interpret these oscillations as a propagating kink wave and obtain its speed of 1400 km s-1. Conclusions: Our observations reveal that a flare associated with filament activation could trigger a kink propagating wave in active region loops over the solar disk. Movies associated to Figs. 1-4 are available at http://https://www.aanda.org

The Performance of A Sampled Data Delay Lock Loop Implemented with a Kalman Loop Filter.

DTIC Science & Technology

1980-01-01

que for analysis is computer simulation. Other techniques include state variable techniques and z-transform methods. Since the Kalman filter is linear...LOGIC NOT SHOWN Figure 2. Block diagram of the sampled data delay lock loop (SDDLL) Es A/ A 3/A/ Figure 3. Sampled error voltage ( Es ) as a function of...from a sum of two components. The first component is the previous filtered es - timate advanced one step forward by the state transition matrix. The 8

Submembranous recruitment of creatine kinase B supports formation of dynamic actin-based protrusions of macrophages and relies on its C-terminal flexible loop.

PubMed

Venter, Gerda; Polling, Saskia; Pluk, Helma; Venselaar, Hanka; Wijers, Mietske; Willemse, Marieke; Fransen, Jack A M; Wieringa, Bé

2015-02-01

Subcellular partitioning of creatine kinase contributes to the formation of patterns in intracellular ATP distribution and the fuelling of cellular processes with a high and sudden energy demand. We have previously shown that brain-type creatine kinase (CK-B) accumulates at the phagocytic cup in macrophages where it is involved in the compartmentalized generation of ATP for actin remodeling. Here, we report that CK-B catalytic activity also helps in the formation of protrusive ruffle structures which are actin-dependent and abundant on the surface of both unstimulated and LPS-activated macrophages. Recruitment of CK-B to these structures occurred transiently and inhibition of the enzyme's catalytic activity with cyclocreatine led to a general smoothening of surface morphology as visualized by scanning electron microscopy. Comparison of the dynamics of distribution of YFP-tagged CK-mutants and isoforms by live imaging revealed that amino acid residues in the C-terminal segment (aa positions 323-330) that forms one of the protein's two mobile loops are involved in partitioning over inner regions of the cytosol and nearby sites where membrane protrusions occur during induction of phagocytic cup formation. Although wt CK-B, muscle-type CK (CK-M), and a catalytically dead CK-B-E232Q mutant with intact loop region were normally recruited from the cytosolic pool, no dynamic transition to the phagocytic cup area was seen for the CK-homologue arginine kinase and a CK-B-D326A mutant protein. Bioinformatics analysis helped us to predict that conformational flexibility of the C-terminal loop, independent of conformational changes induced by substrate binding or catalytic activity, is likely involved in exposing the enzyme for binding at or near the sites of membrane protrusion formation. Copyright © 2014 Elsevier GmbH. All rights reserved.

Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design.

PubMed

Murray, Michael S; Holmes, Ross P; Lowther, W Todd

2008-02-26

Human glycolate oxidase (GO) catalyzes the FMN-dependent oxidation of glycolate to glyoxylate and glyoxylate to oxalate, a key metabolite in kidney stone formation. We report herein the structures of recombinant GO complexed with sulfate, glyoxylate, and an inhibitor, 4-carboxy-5-dodecylsulfanyl-1,2,3-triazole (CDST), determined by X-ray crystallography. In contrast to most alpha-hydroxy acid oxidases including spinach glycolate oxidase, a loop region, known as loop 4, is completely visible when the GO active site contains a small ligand. The lack of electron density for this loop in the GO-CDST complex, which mimics a large substrate, suggests that a disordered to ordered transition may occur with the binding of substrates. The conformational flexibility of Trp110 appears to be responsible for enabling GO to react with alpha-hydroxy acids of various chain lengths. Moreover, the movement of Trp110 disrupts a hydrogen-bonding network between Trp110, Leu191, Tyr134, and Tyr208. This loss of interactions is the first indication that active site movements are directly linked to changes in the conformation of loop 4. The kinetic parameters for the oxidation of glycolate, glyoxylate, and 2-hydroxy octanoate indicate that the oxidation of glycolate to glyoxylate is the primary reaction catalyzed by GO, while the oxidation of glyoxylate to oxalate is most likely not relevant under normal conditions. However, drugs that exploit the unique structural features of GO may ultimately prove to be useful for decreasing glycolate and glyoxylate levels in primary hyperoxaluria type 1 patients who have the inability to convert peroxisomal glyoxylate to glycine.

Observational Study of Particle Acceleration in the 2006 December 13 Flare

NASA Astrophysics Data System (ADS)

Minoshima, T.; Morimoto, T.; Kawate, T.; Imada, S.; Koshiishi, H.; Masuda, S.; Kubo, M.; Inoue, S.; Isobe, H.; Krucker, S.; Yokoyama, T.

2008-12-01

We study the particle acceleration in a flare on 2006 December 13, by using the Hinode, RHESSI, Nobeyama Radio Polarimeters (NoRP) and Nobeyama Radioheliograph (NoRH) observations. For technical reasons, both RHESSI and NoRH have a problem in imaging in this flare. Since we have succeeded in solving the problem, it is now possible to discuss the particle acceleration mechanism from an image analysis. This flare shows very long-lasting (1 hour) non-thermal emissions, consisting of many spikes. We focus on the second major spike at 02:29 UT, because the RHESSI image is available only in this period. The RHESSI 35-100 keV HXR image shows double sources located at the footpoints of the western soft X-ray (SXR) loop seen by the Hinode/XRT. The non-linear force-free (NLFF) modeling based on a magnetogram data by Inoue et al. shows the NLFF to potential magnetic transition of the loop, which would induce the electric field and then accelerate particles. Overlaying the HXR image on the photospheric three-dimensional magnetic field map taken by the Hinode Spectro-Polarimeter, we find that the HXR sources are located at the region where the horizontal magnetic fields invert. The NoRH 34 GHz microwave images show the loop structure connecting the HXR sources. The microwave peaks do not located at the top of the loop but between the loop top and the footpoints. The NoRP microwave spectrum shows the soft-hard-soft pattern in the period, same as the HXR spectrum (Ning 2008). From these observational results we suggest that the electrons were accelerated parallel to the magnetic field line near the magnetic separatrix.

ON THE CONNECTION BETWEEN PROPAGATING SOLAR CORONAL DISTURBANCES AND CHROMOSPHERIC FOOTPOINTS

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

Bryans, P.; McIntosh, S. W.; Moortel, I. De

2016-09-20

The Interface Region Imaging Spectrograph ( IRIS ) provides an unparalleled opportunity to explore the (thermal) interface between the chromosphere, transition region, and the coronal plasma observed by the Atmospheric Imaging Assembly (AIA) of the Solar Dynamics Observatory ( SDO ). The SDO /AIA observations of coronal loop footpoints show strong recurring upward propagating signals—“propagating coronal disturbances” (PCDs) with apparent speeds of the order of 100–120 km s{sup −1}. That signal has a clear signature in the slit-jaw images of IRIS in addition to identifiable spectral signatures and diagnostics in the Mg iih (2803 Å) line. In analyzing the Mgmore » iih line, we are able to observe the presence of magnetoacoustic shock waves that are also present in the vicinity of the coronal loop footpoints. We see there is enough of a correspondence between the shock propagation in Mg iih, the evolution of the Si iv line profiles, and the PCD evolution to indicate that these waves are an important ingredient for PCDs. In addition, the strong flows in the jet-like features in the IRIS Si iv slit-jaw images are also associated with PCDs, such that waves and flows both appear to be contributing to the signals observed at the footpoints of PCDs.« less

Critique of a Hughes shuttle Ku-band data sampler/bit synchronizer

NASA Technical Reports Server (NTRS)

Holmes, J. K.

1980-01-01

An alternative bit synchronizer proposed for shuttle was analyzed in a noise-free environment by considering the basic operation of the loop via timing diagrams and by linearizing the bit synchronizer as an equivalent, continuous, phased-lock loop (PLL). The loop is composed of a high-frequency phase-frequency detector which is capable of detecting both phase and frequency errors and is used to track the clock, and a bit transition detector which attempts to track the transitions of the data bits. It was determined that the basic approach was a good design which, with proper implementation of the accumulator, up/down counter and logic should provide accurate mid-bit sampling with symmetric bits. However, when bit asymmetry occurs, the bit synchronizer can lock up with a large timing error, yet be quasi-stable (timing will not change unless the clock and bit sequence drift). This will result in incorrectly detecting some bits.

Asymmetric processing of a substrate protein in sequential allosteric cycles of AAA+ nanomachines

NASA Astrophysics Data System (ADS)

Kravats, Andrea N.; Tonddast-Navaei, Sam; Bucher, Ryan J.; Stan, George

2013-09-01

Essential protein quality control includes mechanisms of substrate protein (SP) unfolding and translocation performed by powerful ring-shaped AAA+ (ATPases associated with various cellular activities) nanomachines. These SP remodeling actions are effected by mechanical forces imparted by AAA+ loops that protrude into the central channel. Sequential intra-ring allosteric motions, which underlie repetitive SP-loop interactions, have been proposed to comprise clockwise (CW), counterclockwise (CCW), or random (R) conformational transitions of individual AAA+ subunits. To probe the effect of these allosteric mechanisms on unfoldase and translocase functions, we perform Langevin dynamics simulations of a coarse-grained model of an all-alpha SP processed by the single-ring ClpY ATPase or by the double-ring p97 ATPase. We find that, in all three allosteric mechanisms, the SP undergoes conformational transitions along a common set of pathways, which reveals that the active work provided by the ClpY machine involves single loop-SP interactions. Nevertheless, the rates and yields of SP unfolding and translocation are controlled by mechanism-dependent loop-SP binding events, as illustrated by faster timescales of SP processing in CW allostery compared with CCW and R allostery. The distinct efficacy of allosteric mechanisms is due to the asymmetric collaboration of adjacent subunits, which involves CW-biased structural motions of AAA+ loops and results in CW-compatible torque applied onto the SP. Additional simulations of mutant ClpY rings, which render a subset of subunits catalytically-defective or reduce their SP binding affinity, reveal that subunit-based conformational transitions play the major role in SP remodeling. Based on these results we predict that the minimally functional AAA+ ring includes three active subunits, only two of which are adjacent.

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination.

PubMed

Ribeiro de Almeida, Claudia; Dhir, Somdutta; Dhir, Ashish; Moghaddam, Amin E; Sattentau, Quentin; Meinhart, Anton; Proudfoot, Nicholas J

2018-05-17

Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Stability of multiloop LQ regulators with nonlinearities. I - Regions of attraction. II - Regions of ultimate boundedness

NASA Technical Reports Server (NTRS)

Joshi, S. M.

1986-01-01

An investigation is conducted for the closed loop stability of linear time-invariant systems controlled by linear quadratic (LQ) regulators, in cases where nonlinearities exist in the control channels lying outside the stability sector in regions away from the origin. The estimate of the region of attraction thus obtained furnishes methods for the selection of performance function weights for more robust LQ designs. Attention is then given to the closed loop stability of linear time-invariant systems controlled by the LQ regulators when the nonlinearities in the loops escape the stability sector in a bounded region containing the origin.

Thermal, dielectric and barocaloric properties of NH4HSO4 crystallized from an aqueous solution and the melt

NASA Astrophysics Data System (ADS)

Mikhaleva, E. A.; Flerov, I. N.; Kartashev, A. V.; Gorev, M. V.; Bogdanov, E. V.; Bondarev, V. S.

2017-05-01

A study of heat capacity, thermal dilatation, permittivity, dielectric loops and susceptibility to hydrostatic pressure was carried out on quasi-ceramic samples of NH4HSO4 obtained from an aqueous solution as well as the melt. The main parameters of the successive P21/c (T1) ↔ Pc (T2) ↔ P1 phase transitions did not depend on the method of preparation of the samples, and were close to those determined in previous studies of single crystal and powder, except for the sign and magnitude of the baric coefficient for T2. Direct measurements of the pressure effect on the permittivity and thermal properties showed dT2/dp = -123 K·GPa-1, which is consistent in terms of magnitude and sign with the baric coefficient evaluated using dilatometric and calorimetric data in the framework of the Clausius-Clapeyron equation. Thus, the temperature region of the ferroelectric Pc phase existence is extended under pressure. A strong decrease in the entropy jump at the Pc ↔ P1 transformation with an increase in pressure, and the linear dependence of T2 on pressure, indicate that an increase in pressure shifts this phase transition towards the tricritical point on the T-p phase diagram. A significant barocaloric effect was found in the region of the Pc ↔ P1 phase transition.

Trajectory Design to Mitigate Risk on the Transiting Exoplanet Survey Satellite (TESS) Mission

NASA Technical Reports Server (NTRS)

Dichmann, Donald

2016-01-01

The Transiting Exoplanet Survey Satellite (TESS) will employ a highly eccentric Earth orbit, in 2:1 lunar resonance, reached with a lunar flyby preceded by 3.5 phasing loops. The TESS mission has limited propellant and several orbit constraints. Based on analysis and simulation, we have designed the phasing loops to reduce delta-V and to mitigate risk due to maneuver execution errors. We have automated the trajectory design process and use distributed processing to generate and to optimize nominal trajectories, check constraint satisfaction, and finally model the effects of maneuver errors to identify trajectories that best meet the mission requirements.

Phase control of squeezed state in double electromagnetically induced transparency system with a loop-transition structure

NASA Astrophysics Data System (ADS)

Li, Yuan; Zhou, Yusheng; Wang, Yong; Ling, Qiang; Chen, Bing; Dou, Yan; Zhang, Wei; Gao, Weiqing; Guo, Zhiqiang; Zhang, Junxiang

2018-03-01

We theoretically study the squeezed probe light passing through a double electromagnetically induced transparency (DEIT) system, in which a microwave field and two coupling lights drive a loop transition. It is shown that the output squeezing can be maintained in both two transparency windows of DEIT, and it can also be manipulated by the relative phase of the three driving fields. The influence of the intensity of applied fields and the optical depth of atoms on the squeezing is also investigated. This study offers possibilities to manipulate the squeezing propagation in atomic media by the phase of electromagnetic fields.

Transmutation of a trans-series: the Gross-Witten-Wadia phase transition

NASA Astrophysics Data System (ADS)

Ahmed, Anees; Dunne, Gerald V.

2017-11-01

We study the change in the resurgent asymptotic properties of a trans-series in two parameters, a coupling g 2 and a gauge index N, as a system passes through a large N phase transition, using the universal example of the Gross-Witten-Wadia third-order phase transition in the unitary matrix model. This transition is well-studied in the immediate vicinity of the transition point, where it is characterized by a double-scaling limit Painlevé II equation, and also away from the transition point using the pre-string difference equation. Here we present a complementary analysis of the transition at all coupling and all finite N, in terms of a differential equation, using the explicit Tracy-Widom mapping of the Gross-Witten-Wadia partition function to a solution of a Painlevé III equation. This mapping provides a simple method to generate trans-series expansions in all parameter regimes, and to study their transmutation as the parameters are varied. For example, at any finite N the weak coupling expansion is divergent, with a non-perturbative trans-series completion; on the other hand, the strong coupling expansion is convergent, and yet there is still a non-perturbative trans-series completion. We show how the different instanton terms `condense' at the transition point to match with the double-scaling limit trans-series. We also define a uniform large N strong-coupling expansion (a non-linear analogue of uniform WKB), which is much more precise than the conventional large N expansion through the transition region, and apply it to the evaluation of Wilson loops.

Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations

PubMed Central

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W.; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-01-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. PMID:24792385

Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

PubMed

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-09-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. Copyright © 2014. Published by Elsevier B.V.

Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions

PubMed Central

Dellisanti, Cosma D.; Ghosh, Borna; Hanson, Susan M.; Raspanti, James M.; Grant, Valerie A.; Diarra, Gaoussou M.; Schuh, Abby M.; Satyshur, Kenneth; Klug, Candice S.; Czajkowski, Cynthia

2013-01-01

Pentameric ligand-gated ion channels (pLGICs) are neurotransmitter-activated receptors that mediate fast synaptic transmission. In pLGICs, binding of agonist to the extracellular domain triggers a structural rearrangement that leads to the opening of an ion-conducting pore in the transmembrane domain and, in the continued presence of neurotransmitter, the channels desensitize (close). The flexible loops in each subunit that connect the extracellular binding domain (loops 2, 7, and 9) to the transmembrane channel domain (M2–M3 loop) are essential for coupling ligand binding to channel gating. Comparing the crystal structures of two bacterial pLGIC homologues, ELIC and the proton-activated GLIC, suggests channel gating is associated with rearrangements in these loops, but whether these motions accurately predict the motions in functional lipid-embedded pLGICs is unknown. Here, using site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and functional GLIC channels reconstituted into liposomes, we examined if, and how far, the loops at the ECD/TMD gating interface move during proton-dependent gating transitions from the resting to desensitized state. Loop 9 moves ∼9 Å inward toward the channel lumen in response to proton-induced desensitization. Loop 9 motions were not observed when GLIC was in detergent micelles, suggesting detergent solubilization traps the protein in a nonactivatable state and lipids are required for functional gating transitions. Proton-induced desensitization immobilizes loop 2 with little change in position. Proton-induced motion of the M2–M3 loop was not observed, suggesting its conformation is nearly identical in closed and desensitized states. Our experimentally derived distance measurements of spin-labeled GLIC suggest ELIC is not a good model for the functional resting state of GLIC, and that the crystal structure of GLIC does not correspond to a desensitized state. These findings advance our understanding of the molecular mechanisms underlying pLGIC gating. PMID:24260024

Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops.

PubMed

Olsen, Chris M; Lee, Hui-Ting; Marky, Luis A

2009-03-05

G-quadruplexes are a highly studied DNA motif with a potential role in a variety of cellular processes and more recently are considered novel targets for drug therapy in aging and anticancer research. In this work, we have investigated the thermodynamic contributions of the loops on the stable formation of G-quadruplexes. Specifically, we use a combination of UV, circular dichroism (CD) and fluorescence spectroscopies, and differential scanning calorimetry (DSC) to determine thermodynamic profiles, including the differential binding of ions and water, for the unfolding of the thrombin aptamer: d(GGT2GGTGTGGT2GG) that is referred to as G2. The sequences in italics, TGT and T2, are known to form loops. Other sequences examined contained base substitutions in the TGT loop (TAT, TCT, TTT, TAPT, and UUU), in the T2 loops (T4, U2), or in both loops (UGU and U2, UUU and U2). The CD spectra of all molecules show a positive band centered at 292 nm, which corresponds to the "chair" conformation. The UV and DSC melting curves of each G-quadruplex show monophasic transitions with transition temperatures (T(M)s) that remained constant with increasing strand concentration, confirming their intramolecular formation. These G-quadruplexes unfold with T(M)s in the range from 43.2 to 56.5 degrees C and endothermic enthalpies from 22.9 to 37.2 kcal/mol. Subtracting the contribution of a G-quartet stack from each experimental profile indicated that the presence of the loops stabilize each G-quadruplex by favorable enthalpy contributions, larger differential binding of K+ ions (0.1-0.6 mol K+/ mol), and a variable uptake/release of water molecules (-6 to 8 mol H2O/mol). The thermodynamic contributions for these specific base substitutions are discussed in terms of loop stacking (base-base stacking within the loops) and their hydration effects.

Effects of Zb states and bottom meson loops on ϒ (4 S )→ϒ (1 S ,2 S )π+π- transitions

NASA Astrophysics Data System (ADS)

Chen, Yun-Hua; Cleven, Martin; Daub, Johanna T.; Guo, Feng-Kun; Hanhart, Christoph; Kubis, Bastian; Meißner, Ulf-G.; Zou, Bing-Song

2017-02-01

We study the dipion transitions ϒ (4 S )→ϒ (n S )π+π- (n =1 ,2 ) . In particular, we consider the effects of the two intermediate bottomoniumlike exotic states Zb(10610 ) and Zb(10650 ) as well as bottom meson loops. The strong pion-pion final-state interactions, especially including channel coupling to K K ¯ in the S wave, are taken into account model independently by using dispersion theory. Based on a nonrelativistic effective field theory we find that the contribution from the bottom meson loops is comparable to those from the chiral contact terms and the Zb-exchange terms. For the ϒ (4 S )→ϒ (2 S )π+π- decay, the result shows that including the effects of the Zb exchange and the bottom meson loops can naturally reproduce the two-hump behavior of the π π mass spectra. Future angular distribution data are decisive for the identification of different production mechanisms. For the ϒ (4 S )→ϒ (1 S )π+π- decay, we show that there is a narrow dip around 1 GeV in the π π invariant mass distribution, caused by the final-state interactions. The distribution is clearly different from that in similar transitions from lower ϒ states, and needs to be verified by future data with high statistics. Also we predict the decay width and the dikaon mass distribution of the ϒ (4 S )→ϒ (1 S )K+K- process.

EMC MODEL FORECAST VERIFICATION STATS

Science.gov Websites

48-H FCST 54-H FCST 60-H FCST 72-H FCST 84-H FCST Loop 500 mb Height BIAS and RMSE CONUS VALID 00Z sub-regions) Surface Wind Vector BIAS and RMSE REGION VALID 00Z VALID 12Z VALID 00Z (loop) VALID 12Z (loop) GMC (Gulf of Mexico Coast) * * * * SEC (Southeast Coast) * * * * NEC (Northeast Coast

Hi-C Observations of an Active Region Corona, and Investigation of the Underlying Magnetic Structure

NASA Technical Reports Server (NTRS)

Tiwari, Sanjiv K.; Alexander, Caroline E.; Winebarger, Amy R.; Moore, Ronald L.

2014-01-01

Hi-C: first observational evidence of field line braiding in the AR corona; NLFFF extrapolations support. Flux emergence and/or cancellation in the coronal braided region generate large stresses and tension in the coronal field loops which is released as heat in the corona. The field in these sub-regions are highly sheared and have apparent high speed plasma flows, therefore, the contribution from shearing flows to power the coronal and transition region heating can not be ruled out! The spatial resolution of Hi-­C is five times better than AIA. The cadence of Hi-C is 2.5 - 6 times better than AIA. The 193 Å was selected because of the strong emission line of Fe XII (peak formation temperature of 1.5 MK). Hi-­C collected data for 345 s @ 5.4 s cadence. The Hi-C target region was NOAA AR 11520; 11 July 2012, 18:51-18:57 UT. NLFFF extrapolation confirms the braided structure, and free magnetic energy estimates in the given volume.

Feedback topology and XOR-dynamics in Boolean networks with varying input structure

NASA Astrophysics Data System (ADS)

Ciandrini, L.; Maffi, C.; Motta, A.; Bassetti, B.; Cosentino Lagomarsino, M.

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter γ . We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying γ , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Feedback topology and XOR-dynamics in Boolean networks with varying input structure.

PubMed

Ciandrini, L; Maffi, C; Motta, A; Bassetti, B; Cosentino Lagomarsino, M

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter gamma. We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying gamma , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Dynamic Response of a Magnetized Plasma to AN External Source: Application to Space and Solid State Plasmas

NASA Astrophysics Data System (ADS)

Zhou, Huai-Bei

This dissertation examines the dynamic response of a magnetoplasma to an external time-dependent current source. To achieve this goal a new method which combines analytic and numerical techniques to study the dynamic response of a 3-D magnetoplasma to a time-dependent current source imposed across the magnetic field was developed. The set of the cold electron and/or ion plasma equations and Maxwell's equations are first solved analytically in (k, omega)^ace; inverse Laplace and 3 -D complex Fast Fourier Transform (FFT) techniques are subsequently used to numerically transform the radiation fields and plasma currents from the (k, omega) ^ace to the (r, t) space. The dynamic responses of the electron plasma and of the compensated two-component plasma to external current sources are studied separately. The results show that the electron plasma responds to a time -varying current source imposed across the magnetic field by exciting whistler/helicon waves and forming of an expanding local current loop, induced by field aligned plasma currents. The current loop consists of two anti-parallel field-aligned current channels concentrated at the ends of the imposed current and a cross-field current region connecting these channels. The latter is driven by an electron Hall drift. A compensated two-component plasma responds to the same current source as following: (a) For slow time scales tau > Omega_sp{i}{-1} , it generates Alfven waves and forms a non-local current loop in which the ion polarization currents dominate the cross-field current; (b) For fast time scales tau < Omega_sp{i}{-1} , the dynamic response of the compensated two-component plasma is the same as that of the electron plasma. The characteristics of the current closure region are determined by the background plasma density, the magnetic field and the time scale of the current source. This study has applications to a diverse range of space and solid state plasma problems. These problems include current closure in emf inducing tethered satellite systems (TSS), generation of ELF/VLF waves by ionospheric heating, current closure and quasineutrality in thin magnetopause transitions, and short electromagnetic pulse generation in solid state plasmas. The cross-field current in TSS builds up on a time scale corresponding to the whistler waves and results in local current closure. Amplitude modulated HF ionospheric heating generates ELF/VLF waves by forming a horizontal magnetic dipole. The dipole is formed by the current closure in the modified region. For thin transition the time-dependent cross-field polarization field at the magnetopause could be neutralized by the formation of field aligned current loops that close by a cross-field electron Hall current. A moving current source in a solid state plasma results in microwave emission if the speed of the source exceeds the local phase velocity of the helicon or Alfven waves. Detailed analysis of the above problems is presented in the thesis.

THE COLD SHOULDER: EMISSION MEASURE DISTRIBUTIONS OF ACTIVE REGION CORES

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

Schmelz, J. T.; Pathak, S., E-mail: jschmelz@memphis.edu

2012-09-10

The coronal heating mechanism for active region core loops is difficult to determine because these loops are often not resolved and cannot be studied individually. Rather, we concentrate on the 'inter-moss' areas between loop footpoints. We use observations from the Hinode EUV Imaging Spectrometer and the X-Ray Telescope to calculate the emission measure distributions of eight inter-moss areas in five different active regions. The combined data sets provide both high- and low-temperature constraints and ensure complete coverage in the temperature range appropriate for active regions. For AR 11113, the emission can be modeled with heating events that occur on timescalesmore » less than the cooling time. The loops in the core regions appear to be close to equilibrium and are consistent with steady heating. The other regions studied, however, appear to be dominated by nanoflare heating. Our results are consistent with the idea that active region age is an important parameter in determining whether steady or nanoflare heating is primarily responsible for the core emission, that is, older regions are more likely to be dominated by steady heating, while younger regions show more evidence of nanoflares.« less

Phase structure of the Polyakov-quark-meson model

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

Schaefer, B.-J.; Pawlowski, J. M.; Wambach, J.

2007-10-01

The relation between the deconfinement and chiral phase transition is explored in the framework of a Polyakov-loop-extended two-flavor quark-meson (PQM) model. In this model the Polyakov loop dynamics is represented by a background temporal gauge field which also couples to the quarks. As a novelty an explicit quark chemical potential and N{sub f}-dependence in the Polyakov loop potential is proposed by using renormalization group arguments. The behavior of the Polyakov loop as well as the chiral condensate as function of temperature and quark chemical potential is obtained by minimizing the grand canonical thermodynamic potential of the system. The effect ofmore » the Polyakov loop dynamics on the chiral phase diagram and on several thermodynamic bulk quantities is presented.« less

Far-ultraviolet imagery of the Barnard Loop Nebula

NASA Technical Reports Server (NTRS)

Carruthers, G. R.; Opal, C. B.

1977-01-01

An electrographic Schmidt camera carried on a sounding rocket has yielded far-ultraviolet (1050-2000 A and 1230-2000 A) images of the Barnard Loop Nebula and of the general background in the Orion region due to scattering of ultraviolet starlight by interstellar dust particles. The total intensity in the Barnard Loop region agrees well with OAO-2 measurements, but the discrete Loop structure contributes only some 15% of the total. The measurements are consistent with a relatively high albedo for the dust grains in the far-ultraviolet.

On the performance of digital phase locked loops in the threshold region

NASA Technical Reports Server (NTRS)

Hurst, G. T.; Gupta, S. C.

1974-01-01

Extended Kalman filter algorithms are used to obtain a digital phase lock loop structure for demodulation of angle modulated signals. It is shown that the error variance equations obtained directly from this structure enable one to predict threshold if one retains higher frequency terms. This is in sharp contrast to the similar analysis of the analog phase lock loop, where the higher frequency terms are filtered out because of the low pass filter in the loop. Results are compared to actual simulation results and threshold region results obtained previously.

West Florida shelf circulation and temperature budget for the 1999 spring transition

USGS Publications Warehouse

He, Ruoying; Weisberg, Robert H.

2002-01-01

Mid-latitude continental shelves undergo a spring transition as the net surface heat flux changes from cooling to warming. Using in situ data and a numerical circulation model we investigate the circulation and temperature budget on the West Florida Continental Shelf (WFS) for the spring transition of 1999. The model is a regional adaptation of the primitive equation, Princeton Ocean Model forced by NCEP reanalysis wind and heat flux fields and by river inflows. Based on agreements between the modeled and observed fields we use the model to draw inferences on how the surface momentum and heat fluxes affect the seasonal and synoptic scale variability. We account for a strong southeastward current at mid-shelf by the baroclinic response to combined wind and buoyancy forcing, and we show how this local forcing leads to annually occurring cold and low salinity tongues. Through term-by-term analyses of the temperature budget we describe the WFS temperature evolution in spring. Heat flux largely controls the seasonal transition, whereas ocean circulation largely controls the synoptic scale variability. These two processes, however, are closely linked. Bottom topography and coastline geometry are important in generating regions of convergence and divergence. Rivers contribute to the local hydrography and are important ecologically. Along with upwelling, river inflows facilitate frontal aggregation of nutrients and the spring formation of a high concentration chlorophyll plume near the shelf break (the so-called ‘Green River’) coinciding with the cold, low salinity tongues. These features originate by local, shelf-wide forcing; the Loop Current is not an essential ingredient.

Analysis and design of a second-order digital phase-locked loop

NASA Technical Reports Server (NTRS)

Blasche, P. R.

1979-01-01

A specific second-order digital phase-locked loop (DPLL) was modeled as a first-order Markov chain with alternatives. From the matrix of transition probabilities of the Markov chain, the steady-state phase error of the DPLL was determined. In a similar manner the loop's response was calculated for a fading input. Additionally, a hardware DPLL was constructed and tested to provide a comparison to the results obtained from the Markov chain model. In all cases tested, good agreement was found between the theoretical predictions and the experimental data.

QUASI-PERIODIC SLIPPING MAGNETIC RECONNECTION DURING AN X-CLASS SOLAR FLARE OBSERVED BY THE SOLAR DYNAMICS OBSERVATORY AND INTERFACE REGION IMAGING SPECTROGRAPH

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

Li, Ting; Zhang, Jun, E-mail: liting@nao.cas.cn, E-mail: zjun@nao.cas.cn

2015-05-01

We first report the quasi-periodic slipping motion of flare loops during an eruptive X-class flare on 2014 September 10. The slipping motion was investigated at a specific location along one of the two ribbons and can be observed throughout the impulsive phase of the flare. The apparent slipping velocity was 20–110 km s{sup −1}, and the associated period was 3–6 minutes. The footpoints of flare loops appeared as small-scale bright knots observed in 1400 Å, corresponding to fine structures of the flare ribbon. These bright knots were observed to move along the southern part of the longer ribbon and alsomore » exhibited a quasi-periodic pattern. The Si iv 1402.77 Å line was redshifted by 30–50 km s{sup −1} at the locations of moving knots with a ∼40–60 km s{sup −1} line width, larger than other sites of the flare ribbon. We suggest that the quasi-periodic slipping reconnection is involved in this process and the redshift at the bright knots is probably indicative of reconnection downflow. The emission line of Si iv at the northern part of the longer ribbon also exhibited obvious redshifts of about 10–70 km s{sup −1} in the impulsive phase of the flare, with the redshifts at the outer edges of the ribbon larger than those in the middle. The redshift velocities at post-flare loops reached about 80–100 km s{sup −1} in the transition region.« less

The AdS/CFT Correspondence: Classical, Quantum, and Thermodynamical Aspects

NASA Astrophysics Data System (ADS)

Young, Donovan

2007-06-01

Certain aspects of the AdS/CFT correspondence are studied in detail. We investigate the one-loop mass shift to certain two-impurity string states in light-cone string field theory on a plane wave background. We find that there exist logarithmic divergences in the sums over intermediate mode numbers which cancel between the cubic Hamiltonian and quartic "contact term". We argue that generically, every order in intermediate state impurities contributes to the mass shift at leading perturbative order. The same mass shift is also computed using an improved 3-string vertex proposed by Dobashi and Yoneya. The result is found to agree with gauge theory at leading order and is close but not quite in agreement at subleading order. We extend the analysis to include discrete light-cone quantization, considering states with up to three units of p+. We study the (apparently) first-order phase transition in the weakly coupled plane-wave matrix model at finite temperature. We analyze the effect of interactions by computing the relevant parts of the effective potential for the Polyakov loop operator to three loop order. We show that the phase transition is indeed of first order. We also compute the 2-loop correction to the Hagedorn temperature. Finally, correlation functions of 1/4 BPS Wilson loops with the infinite family of 1/2 BPS chiral primary operators are computed in N=4 super Yang-Mills theory by summing planar ladder diagrams. The correlation functions are also computed in the strong-coupling limit using string theory; the result is found to agree with the extrapolation of the planar ladders. The result is related to similar correlators of 1/2 BPS loops by a simple re-scaling of the coupling constant, discovered by Drukker for the case of the 1/4 BPS loop VEV.

Comparison of Two Coronal Magnetic Field Models to Reconstruct a Sigmoidal Solar Active Region with Coronal Loops

NASA Astrophysics Data System (ADS)

Duan, Aiying; Jiang, Chaowei; Hu, Qiang; Zhang, Huai; Gary, G. Allen; Wu, S. T.; Cao, Jinbin

2017-06-01

Magnetic field extrapolation is an important tool to study the three-dimensional (3D) solar coronal magnetic field, which is difficult to directly measure. Various analytic models and numerical codes exist, but their results often drastically differ. Thus, a critical comparison of the modeled magnetic field lines with the observed coronal loops is strongly required to establish the credibility of the model. Here we compare two different non-potential extrapolation codes, a nonlinear force-free field code (CESE-MHD-NLFFF) and a non-force-free field (NFFF) code, in modeling a solar active region (AR) that has a sigmoidal configuration just before a major flare erupted from the region. A 2D coronal-loop tracing and fitting method is employed to study the 3D misalignment angles between the extrapolated magnetic field lines and the EUV loops as imaged by SDO/AIA. It is found that the CESE-MHD-NLFFF code with preprocessed magnetogram performs the best, outputting a field that matches the coronal loops in the AR core imaged in AIA 94 Å with a misalignment angle of ˜10°. This suggests that the CESE-MHD-NLFFF code, even without using the information of the coronal loops in constraining the magnetic field, performs as good as some coronal-loop forward-fitting models. For the loops as imaged by AIA 171 Å in the outskirts of the AR, all the codes including the potential field give comparable results of the mean misalignment angle (˜30°). Thus, further improvement of the codes is needed for a better reconstruction of the long loops enveloping the core region.

A dihydropyridine receptor alpha1s loop region critical for skeletal muscle contraction is intrinsically unstructured and binds to a SPRY domain of the type 1 ryanodine receptor.

PubMed

Cui, Yanfang; Tae, Han-Shen; Norris, Nicole C; Karunasekara, Yamuna; Pouliquin, Pierre; Board, Philip G; Dulhunty, Angela F; Casarotto, Marco G

2009-03-01

The II-III loop of the dihydropyridine receptor (DHPR) alpha(1s) subunit is a modulator of the ryanodine receptor (RyR1) Ca(2+) release channel in vitro and is essential for skeletal muscle contraction in vivo. Despite its importance, the structure of this loop has not been reported. We have investigated its structure using a suite of NMR techniques which revealed that the DHPR II-III loop is an intrinsically unstructured protein (IUP) and as such belongs to a burgeoning structural class of functionally important proteins. The loop does not possess a stable tertiary fold: it is highly flexible, with a strong N-terminal helix followed by nascent helical/turn elements and unstructured segments. Its residual structure is loosely globular with the N and C termini in close proximity. The unstructured nature of the II-III loop may allow it to easily modify its interaction with RyR1 following a surface action potential and thus initiate rapid Ca(2+) release and contraction. The in vitro binding partner for the II-III was investigated. The II-III loop interacts with the second of three structurally distinct SPRY domains in RyR1, whose function is unknown. This interaction occurs through two preformed N-terminal alpha-helical regions and a C-terminal hydrophobic element. The A peptide corresponding to the helical N-terminal region is a common probe of RyR function and binds to the same SPRY domain as the full II-III loop. Thus the second SPRY domain is an in vitro binding site for the II-III loop. The possible in vivo role of this region is discussed.

Comparison of Two Coronal Magnetic Field Models to Reconstruct a Sigmoidal Solar Active Region with Coronal Loops

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

Duan, Aiying; Zhang, Huai; Jiang, Chaowei

Magnetic field extrapolation is an important tool to study the three-dimensional (3D) solar coronal magnetic field, which is difficult to directly measure. Various analytic models and numerical codes exist, but their results often drastically differ. Thus, a critical comparison of the modeled magnetic field lines with the observed coronal loops is strongly required to establish the credibility of the model. Here we compare two different non-potential extrapolation codes, a nonlinear force-free field code (CESE–MHD–NLFFF) and a non-force-free field (NFFF) code, in modeling a solar active region (AR) that has a sigmoidal configuration just before a major flare erupted from themore » region. A 2D coronal-loop tracing and fitting method is employed to study the 3D misalignment angles between the extrapolated magnetic field lines and the EUV loops as imaged by SDO /AIA. It is found that the CESE–MHD–NLFFF code with preprocessed magnetogram performs the best, outputting a field that matches the coronal loops in the AR core imaged in AIA 94 Å with a misalignment angle of ∼10°. This suggests that the CESE–MHD–NLFFF code, even without using the information of the coronal loops in constraining the magnetic field, performs as good as some coronal-loop forward-fitting models. For the loops as imaged by AIA 171 Å in the outskirts of the AR, all the codes including the potential field give comparable results of the mean misalignment angle (∼30°). Thus, further improvement of the codes is needed for a better reconstruction of the long loops enveloping the core region.« less

Low temperature magnetic properties of monoclinic pyrrhotite with particular relevance to the Besnus transition

NASA Astrophysics Data System (ADS)

Volk, M.; Gilder, S.; Feinberg, J. M.

2016-12-01

Monoclinic pyrrhotite (Fe7S8) is an important mineral on earth as well as in some meteorites. It owes its ferrimagnetism to an ordered array of Fe vacancies. Its magnetic properties change markedly around 30 K, in what is known as the Besnus transition. Plausible explanations for the Besnus transition are either due to changes in crystalline anisotropy from a transformation in crystal symmetry or from the establishment of a two-phase system with magnetic interaction between the two phases. To help resolve this discrepancy, we measured hysteresis loops every 5° and back field curves every 10° in the basal plane of an oriented single crystal of monoclinic pyrrhotite at 300 K and at 21 temperature steps from 50 K through the Besnus transition until 20 K. Between 50 and 30 K, hysteresis loops possess double inflections between crystallographic a-axes and only a single inflection parallel to the a-axes. The second inflection phenomenon and relative differences of the loops show a six-fold symmetry in this temperature range. The Besnus transition is best characterized by changes in magnetic remanence and coercivity over a 6° temperature span with a maximum rate of change at 30 K. A surprising yet puzzling finding is that the coercivity ratio becomes less than unity below the transition when four-fold symmetry arises. The saturation magnetization of natural pyrrhotite cycled from room temperature to successively lower temperatures through the Besnus transition decreases 2-4 times less than equivalent grain sizes of magnetite, with less than a 10% loss in remanence between 300 K and 150 K in pseudo-single domain pyrrhotite. As pseudo-single domain monoclinic pyrrhotite carries the magnetic remanence in some meteorites, it is likely that low temperature cycling in space to the Earth's surface will have only a minor influence on paleointensity values derived from those meteorites.

The orthorhombic to high-P monoclinic phase transition in Mg-Fe Pyroxenes: Can it produce a seismic discontinuity?

NASA Astrophysics Data System (ADS)

Woodland, Alan B.

The orthorhombic to high-P monoclinic phase transition in (Mg,Fe)SiO3 pyroxene with a mantle-relevant composition (XFs = 0.1) is expected to occur at ˜300 km depth [Woodland and Angel, 1997]. However, the divariant nature of the phase transition in the Mg-Fe system leaves the question open as to whether this transition occurs over a narrow enough pressure interval to cause a seismic discontinuity. New experimental results with binary Mg-Fe pyroxenes constrain the divariant loop to be 0.2 GPa wide at the composition of XFs = 0.4 and on the order of 0.15 GPa for a mantle-relevant composition. This implies that the phase transition will be complete over a depth interval of about 5-6 km in the mantle and it is concluded that the divariant loop of the orthorhombic to high-P monoclinic phase transition in (Mg,Fe)SiO3 pyroxene is indeed narrow enough to produce a “jump” in seismic velocities. The experimentally observed metastable behavior of orthopyroxene could further reduce the effective depth interval of this phase transition. The expected location of this phase transition coincides with a small magnitude seismic discontinuity, the “X-discontinuity”, occasionally observed in seismic profiles at ˜300 km depth, and thus provides a viable petrologic explanation for the origin of this discontinuity, if it truly exists.

Stretched Loops

NASA Image and Video Library

2017-03-16

When an active region rotated over to the edge of the sun, it presented us with a nice profile view of its elongated loops stretching and swaying above it (Mar. 8-9, 2017). These loops are actually charged particles (made visible in extreme ultraviolet light) swirling along the magnetic field lines of the active region. The video covers about 30 hours of activity. Also of note is a darker twisting mass of plasma to the left of the active region being pulled and spun about by magnetic forces. Video is available at http://photojournal.jpl.nasa.gov/catalog/PIA21562

An investigation of coronal active region loop structures using AS&E rocket X-ray images

NASA Technical Reports Server (NTRS)

Webb, D. F.

1983-01-01

Simultaneous high spatial resolution observations at 6 cm in soft X-rays, in photospheric magnetograms, and in optical filtergrams were used to compare the most intense sources of centimetric emission in two active regions to coronal loops, sunspots, chromospheric structures, and photospheric magnetic fields. Results show that the majority of the bright microwave components are not associated with sunspots or X-ray emission. A nonthermal mechanism appears necessary to explain the brightest microwave components, discrete regions of continuous particle acceleration may be common in active regions. Studies of the plasma parameters of selected loops imply that the radio emission is consistent with gyro-resonance absorption at the third and fourth harmonic, at least from part of each loop. Results are presented for: (1) X-ray and microwave observations of active regions; (2) comparison of coronal holes observed in soft X-rays and Hel 10830 A spectrosheliograms; and (3) the reappearance of polar coronal holes and the evolution of the solar magnetic field.

Backbone ¹H, ¹³C, ¹⁵N NMR assignments of yeast OMP synthase in unliganded form and in complex with orotidine 5'-monophosphate.

PubMed

Hansen, Michael Riis; Harris, Richard; Barr, Eric W; Cheng, Hong; Girvin, Mark E; Grubmeyer, Charles

2014-04-01

The type I phosphoribosyltransferase OMP synthase (EC 2.4.2.10) is involved in de novo synthesis of pyrimidine nucleotides forming the UMP precursor orotidine 5'-monophosphate (OMP). The homodimeric enzyme has a Rossman α/β core topped by a base-enclosing "hood" domain and a flexible domain-swapped catalytic loop. High-resolution X-ray structures of the homologous Salmonella typhimurium and yeast enzymes show that a general compacting of the core as well as movement of the hood and a major disorder-to-order transition of the loop occur upon binding of ligands MgPRPP and orotate. Here we present backbone NMR assignments for the unliganded yeast enzyme (49 kDa) and its complex with product OMP. We were able to assign 212-213 of the 225 non-proline backbone (15)N and amide proton resonances. Significant difference in chemical shifts of the amide cross peaks occur in regions of the structure that undergo movement upon ligand occupancy in the S. typhimurium enzyme.

Greenland meltwater experiments

NASA Astrophysics Data System (ADS)

Olsen, S. M.; Schmith, T.

2012-04-01

We explore the climatic response to additional Greenland Ice Sheet melting in the EC-EARTH coupled climate model. As reference runs, we use an ensemble of two simulations from 1850 to present with historic forcing. For each of these we pick the years 1935,1950 and 1965, respectively as initial conditions for perturbed experiments with an additional freshwater forcing of 0.1 Sv distributed uniformly around Greenland , a plausible value in the upper end of future Greenland ice sheet melt estimates. We find give no evidence for abrupt transitions associated with tipping points in the Atlantic overturning circulation and mid-latitude heat transport. In fact, modelled decline in overturning in response to the additional forcing does not project onto a comparable reduction in the mid latitude (36N) ocean heat transport. This result points to an ongoing watermass transformation in the subpolar region and Arctic Mediterranean as a whole and a continued thermal mode of operation of the overturning. At the northern boundary of the subpolar region (60N) the response in overturning shows a contrasting increase in intensity along with an increase in heat transport. Whereas the latter may be expected as a result of freshwater capping and subsurface warming in the subpolar region, the increased overturning at 60N is more difficult to explain. In order to assess this in more detail we have quantified the individual thermohaline exchange components of light and dense water masses across the Greenland-Scotland Ridge. We find that the intensified overturning at 60N is reflected in increased transports of light Atlantic Water to the Nordic Seas. However, the vertical, thermohalinie overturning loop is not equally strengthened. On the contrary, we model a decline in the denser parts of the outflow, the overflows in the Denmark Strait and Faroe Bank Channel and a strong increase in the polar outflow in the Denmark Strait. We observe a gradual transition from a vertical mode of operation with 70% of the Atlantic Inflow being transformed to dense overflow towards a state approaching an equal contribution of the vertical and horizontal thermohaline circulation loops after 20-30 years. Along with this transition we find an overall decline in the intensity of the barotropic gyre circulation of the Nordic Seas reflecting in part a reduced winter deepening of the mixed layer. Thus, we may seek to explain this transition as a result of more efficient lateral mixing of the Atlantic Inflow during its cyclonic circulation around the basin margins. Finally, we show that the associated atmospheric response is a standing Rossby wave train reflected in the mean tropospheric thickness anomaly field with a through over Labrador Sea, a ridge over Barents Sea and a minor through over eastern Europe. Corresponding anomalies are found in the surface temperature field.

Magnetization reversal in epitaxial exchange-biased IrMn/FeGa bilayers with anisotropy geometries controlled by oblique deposition

NASA Astrophysics Data System (ADS)

Zhang, Yao; Zhan, Qingfeng; Zuo, Zhenghu; Yang, Huali; Zhang, Xiaoshan; Dai, Guohong; Liu, Yiwei; Yu, Ying; Wang, Jun; Wang, Baomin; Li, Run-Wei

2015-05-01

We fabricated epitaxial exchange biased (EB) IrMn/FeGa bilayers by oblique deposition and systematically investigated their magnetization reversal. Two different configurations with the uniaxial magnetic anisotropy Ku parallel and perpendicular to the unidirectional anisotropy Ke b were obtained by controlling the orientation of the incident FeGa beam during deposition. A large ratio of Ku/Ke b was obtained by obliquely depositing the FeGa layer to achieve a large Ku while reducing the IrMn thickness to obtain a small Ke b. Besides the previously reported square loops, conventional asymmetrically shaped loops, and one-sided and two-sided two-step loops, unusual asymmetrically shaped loops with a three-step magnetic transition for the descending branch and a two-step transition for the ascending branch and biased three-step loops were observed at various field orientations in the films of both IrMn (tIrMn=1.5 to 20 nm)/FeGa (10 nm) with Ku⊥ Ke b and IrMn (tIrMn≤2 nm)/FeGa (10 nm) with Ku|| Ke b . Considering the geometries of anisotropies, a model based on domain wall nucleation and propagation was employed to quantitatively describe the angular dependent behaviors of IrMn/FeGa bilayers. The biased three-step magnetic switching was predicted to take place when | Ku|> ɛ90°+Ke b , where ɛ90° is the 90° domain wall nucleation energy, and the EB leads to the appearance of the unusual asymmetrically shaped hysteresis loops.

Better Bet-Hedging with coupled positive and negative feedback loops

NASA Astrophysics Data System (ADS)

Narula, Jatin; Igoshin, Oleg

2011-03-01

Bacteria use the phenotypic heterogeneity associated with bistable switches to distribute the risk of activating stress response strategies like sporulation and persistence. However bistable switches offer little control over the timing of phenotype switching and first passage times (FPT) for individual cells are found to be exponentially distributed. We show that a genetic circuit consisting of interlinked positive and negative feedback loops allows cells to control the timing of phenotypic switching. Using a mathematical model we find that in this system a stable high expression state and stable low expression limit cycle coexist and the FPT distribution for stochastic transitions between them shows multiple peaks at regular intervals. A multimodal FPT distribution allows cells to detect the persistence of stress and control the rate of phenotype transition of the population. We further show that extracellular signals from cell-cell communication that change the strength of the feedback loops can modulate the FPT distribution and allow cells even greater control in a bet-hedging strategy.

Tilting the balance between canonical and noncanonical conformations for the H1 hypervariable loop of a llama VHH through point mutations.

PubMed

Mahajan, Sai Pooja; Velez-Vega, Camilo; Escobedo, Fernando A

2013-01-10

Nanobodies are single-domain antibodies found in camelids. These are the smallest naturally occurring binding domains and derive functionality via three hypervariable loops (H1-H3) that form the binding surface. They are excellent candidates for antibody engineering because of their favorable characteristics like small size, high solubility, and stability. To rationally engineer antibodies with affinity for a specific target, the hypervariable loops can be tailored to obtain the desired binding surface. As a first step toward such a goal, we consider the design of loops with a desired conformation. In this study, we focus on the H1 loop of the anti-hCG llama nanobody that exhibits a noncanonical conformation. We aim to "tilt" the stability of the H1 loop structure from a noncanonical conformation to a (humanized) type 1 canonical conformation by studying the effect of selected mutations to the amino acid sequence of the H1, H2, and proximal residues. We use all-atomistic, explicit-solvent, biased molecular dynamic simulations to simulate the wild-type and mutant loops in a prefolded framework. We thus find mutants with increasing propensity to form a stable type 1 canonical conformation of the H1 loop. Free energy landscapes reveal the existence of conformational isomers of the canonical conformation that may play a role in binding different antigenic surfaces. We also elucidate the approximate mechanism and kinetics of transitions between such conformational isomers by using a Markovian model. We find that a particular three-point mutant has the strongest thermodynamic propensity to form the H1 type 1 canonical structure but also to exhibit transitions between conformational isomers, while a different, more rigid three-point mutant has the strongest propensity to be kinetically trapped in such a canonical structure.

Suppression of Heating of Coronal Loops Rooted in Opposite Polarity Sunspot Umbrae

NASA Technical Reports Server (NTRS)

Tiwari, Sanjiv K.; Thalmann, Julia K.; Moore, Ronald L.; Panesar, Navdeep K.; Winebarger, Amy R.

2016-01-01

EUV observations of active region (AR) coronae reveal the presence of loops at different temperatures. To understand the mechanisms that result in hotter or cooler loops, we study a typical bipolar AR, near solar disk center, which has moderate overall magnetic twist and at least one fully developed sunspot of each polarity. From AIA 193 and 94 Å images we identify many clearly discernible coronal loops that connect plage or a sunspot of one polarity to an opposite-­polarity plage region. The AIA 94 Å images show dim regions in the umbrae of the spots. To see which coronal loops are rooted in a dim umbral area, we performed a non-linear force-free field (NLFFF) modeling using photospheric vector magnetic field measurements obtained with the Heliosesmic Magnetic Imager (HMI) onboard SDO. The NLFFF model, validated by comparison of calculated model field lines with observed loops in AIA 193 and 94 Å, specifies the photospheric roots of the model field lines. Some model coronal magnetic field lines arch from the dim umbral area of the positive-polarity sunspot to the dim umbral area of a negative-polarity sunspot. Because these coronal loops are not visible in any of the coronal EUV and X-ray images of the AR, we conclude they are the coolest loops in the AR. This result suggests that the loops connecting opposite polarity umbrae are the least heated because the field in umbrae is so strong that the convective braiding of the field is strongly suppressed.

Space Science

NASA Image and Video Library

2003-01-01

These banana-shaped loops are part of a computer-generated snapshot of our sun's magnetic field. The solar magnetic-field lines loop through the sun's corona, break through the sun's surface, and cornect regions of magnetic activity, such as sunspots. This image --part of a magnetic-field study of the sun by NASA's Allen Gary -- shows the outer portion (skins) of interconnecting systems of hot (2 million degrees Kelvin) coronal loops within and between two active magnetic regions on opposite sides of the sun's equator. The diameter of these coronal loops at their foot points is approximately the same size as the Earth's radius (about 6,000 kilometers).

Mass and energy flow in prominences

NASA Technical Reports Server (NTRS)

Poland, Arthur I.

1990-01-01

Mass and energy flow in quiescent prominences is considered based on the hypothesis that active region prominences have a different structure and thus different mass and energy flow characteristics. Several important physical parameters have been plotted using the computational model, representing the evolutionary process after the prominence formation. The temperature, velocity, conductive flux, and enthalpy flux are plotted against distance from the highest point in the loop to the coolest part of the prominence. It is shown that the maximum velocity is only about 5 km/s. The model calculations indicate that the transition region of prominences is dominated by complex processes. It is necessary to take into account mass flow at temperatures below 200,000 K, and both mass flow and optical depth effects in hydrogen at temperatures below 30,000 K. Both of these effects lead to a less steep temperature gradient through the prominence corona interface than can be obtained from the conduction alone.

Molecular driving forces behind the tetrahydrofuran–water miscibility gap

DOE PAGES

Smith, Micholas Dean; Mostofian, Barmak; Petridis, Loukas; ...

2016-01-06

The tetrahydrofuran water binary system exhibits an unusual closed-loop miscibility gap (transitions from a miscible regime to an immiscible regime back to another miscible regime as the temperature increases). Here, using all-atom molecular dynamics simulations, we probe the structural and dynamical behavior of the binary system in the temperature regime of this gap at four different mass ratios, and we compare the behavior of bulk water and tetrahydrofuran. The changes in structure and dynamics observed in the simulations indicate that the temperature region associated with the miscibility gap is distinctive. Within the miscibility-gap temperature region, the self diffusion of watermore » is significantly altered and the second virial coefficients (pair interaction strengths) show parabolic-like behavior. Altogether, the results suggest that the gap is the result of differing trends with temperature of minor structural changes, which produces interaction virials with parabolic temperature dependence near the miscibility gap.« less

Identification of Human Papillomavirus Type 16 L1 Surface Loops Required for Neutralization by Human Sera†

PubMed Central

Carter, Joseph J.; Wipf, Greg C.; Madeleine, Margaret M.; Schwartz, Stephen M.; Koutsky, Laura A.; Galloway, Denise A.

2006-01-01

The variable surface loops on human papillomavirus (HPV) virions required for type-specific neutralization by human sera remain poorly defined. To determine which loops are required for neutralization, a series of hybrid virus-like particles (VLPs) were used to adsorb neutralizing activity from HPV type 16 (HPV16)-reactive human sera before being tested in an HPV16 pseudovirion neutralization assay. The hybrid VLPs used were composed of L1 sequences of either HPV16 or HPV31, on which one or two regions were replaced with homologous sequences from the other type. The regions chosen for substitution were the five known loops that form surface epitopes recognized by monoclonal antibodies and two additional variable regions between residues 400 and 450. Pretreatment of human sera, previously found to react to HPV16 VLPs in enzyme-linked immunosorbent assays, with wild-type HPV16 VLPs and hybrid VLPs that retained the neutralizing epitopes reduced or eliminated the ability of sera to inhibit pseudovirus infection in vitro. Surprisingly, substitution of a single loop often ablated the ability of VLPs to adsorb neutralizing antibodies from human sera. However, for all sera tested, multiple surface loops were found to be important for neutralizing activity. Three regions, defined by loops DE, FG, and HI, were most frequently identified as being essential for binding by neutralizing antibodies. These observations are consistent with the existence of multiple neutralizing epitopes on the HPV virion surface. PMID:16641259

Identification of human papillomavirus type 16 L1 surface loops required for neutralization by human sera.

PubMed

Carter, Joseph J; Wipf, Greg C; Madeleine, Margaret M; Schwartz, Stephen M; Koutsky, Laura A; Galloway, Denise A

2006-05-01

The variable surface loops on human papillomavirus (HPV) virions required for type-specific neutralization by human sera remain poorly defined. To determine which loops are required for neutralization, a series of hybrid virus-like particles (VLPs) were used to adsorb neutralizing activity from HPV type 16 (HPV16)-reactive human sera before being tested in an HPV16 pseudovirion neutralization assay. The hybrid VLPs used were composed of L1 sequences of either HPV16 or HPV31, on which one or two regions were replaced with homologous sequences from the other type. The regions chosen for substitution were the five known loops that form surface epitopes recognized by monoclonal antibodies and two additional variable regions between residues 400 and 450. Pretreatment of human sera, previously found to react to HPV16 VLPs in enzyme-linked immunosorbent assays, with wild-type HPV16 VLPs and hybrid VLPs that retained the neutralizing epitopes reduced or eliminated the ability of sera to inhibit pseudovirus infection in vitro. Surprisingly, substitution of a single loop often ablated the ability of VLPs to adsorb neutralizing antibodies from human sera. However, for all sera tested, multiple surface loops were found to be important for neutralizing activity. Three regions, defined by loops DE, FG, and HI, were most frequently identified as being essential for binding by neutralizing antibodies. These observations are consistent with the existence of multiple neutralizing epitopes on the HPV virion surface.

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

NASA Astrophysics Data System (ADS)

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng; Elmhamdi, Abouazza; Su, Jiangtao; Liu, Ying D.; Kordi, Ayman. S.

2017-08-01

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory. The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observed at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s-1. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.

Active Knits for Radical Change Air Force Structures

DTIC Science & Technology

2012-10-01

for self - healing structures, but the material distribution could be optimized to achieve desired mechanical properties or obtain a predetermined...causes the material to transition from the soft martensite phase to the stiff austenite phase. When heated the loops attempt to return to their...nominally straight, is bent into the loop shape when in the cold, relatively soft martensite state. When heated to the relatively stiff austenite

New understanding of nano-scale interstitial dislocation loops in BCC iron

NASA Astrophysics Data System (ADS)

Gao, N.; Chen, J.; Kurtz, R. J.; Wang, Z. G.; Zhang, R. F.; Gao, F.

2017-11-01

Complex states of nanoscale interstitial dislocation loop can be described by its habit plane and Burgers vector. Using atomistic simulations, we provide direct evidences on the change of the habit plane of a 1/2〈1 1 1〉 loop from {1 1 1} to {1 1 0} and {2 1 1}, in agreement with TEM observations. A new {1 0 0} habit plane of this loop is also predicted by simulations. The non-conservation of the Burgers vector is approved theoretically for: (1) dislocation reactions between loops with different Burgers vectors and (2) the transition between 〈1 0 0〉 loops and 1/2〈1 1 1〉 loops. The rotation from a 1/2〈1 1 1〉 to a 〈1 0 0〉 loop has also been explored, which occurs at 570 K for time on the order of 10 s. The dislocation-precipitate phase duality and change of habit plane are then proposed as new features for nano-scale dislocation loops.

Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops

PubMed Central

Paslawski, Wojciech; Lillelund, Ove K.; Kristensen, Julie Veje; Schafer, Nicholas P.; Baker, Rosanna P.; Urban, Sinisa; Otzen, Daniel E.

2015-01-01

Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2–3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3–6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state–level structure in the transition state. We propose that loops 1–3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated. PMID:26056273

Detection of somatic mutations in the mitochondrial DNA control region D-loop in brain tumors: The first report in Malaysian patients.

PubMed

Mohamed Yusoff, Abdul Aziz; Mohd Nasir, Khairol Naaim; Haris, Khalilah; Mohd Khair, Siti Zulaikha Nashwa; Abdul Ghani, Abdul Rahman Izaini; Idris, Zamzuri; Abdullah, Jafri Malin

2017-11-01

Although the role of nuclear-encoded gene alterations has been well documented in brain tumor development, the involvement of the mitochondrial genome in brain tumorigenesis has not yet been fully elucidated and remains controversial. The present study aimed to identify mutations in the mitochondrial DNA (mtDNA) control region D-loop in patients with brain tumors in Malaysia. A mutation analysis was performed in which DNA was extracted from paired tumor tissue and blood samples obtained from 49 patients with brain tumors. The D-loop region DNA was amplified using the PCR technique, and genetic data from DNA sequencing analyses were compared with the published revised Cambridge sequence to identify somatic mutations. Among the 49 brain tumor tissue samples evaluated, 25 cases (51%) had somatic mutations of the mtDNA D-loop, with a total of 48 mutations. Novel mutations that had not previously been identified in the D-loop region (176 A-deletion, 476 C>A, 566 C>A and 16405 A-deletion) were also classified. No significant associations between the D-loop mutation status and the clinicopathological parameters were observed. To the best of our knowledge, the current study presents the first evidence of alterations in the mtDNA D-loop regions in the brain tumors of Malaysian patients. These results may provide an overview and data regarding the incidence of mitochondrial genome alterations in Malaysian patients with brain tumors. In addition to nuclear genome aberrations, these specific mitochondrial genome alterations may also be considered as potential cancer biomarkers for the diagnosis and staging of brain cancers.

Molecular dynamics simulations of certain RGD-based peptides from Kistrin provide insight into the higher activity of REI-RGD34 protein at higher temperature.

PubMed

Upadhyay, Sanjay K

2014-05-01

To determine the bioactive conformation required to bind with receptor aIIbb3, the peptide sequence RIPRGDMP from Kistrin was inserted into CDR 1 loop region of REI protein, resulting in REI-RGD34. The activity of REI-RGD34 was observed to increase at higher temperature towards the receptor aIIbb3. It could be justified in either way: the modified complex forces the restricted peptide to adapt bioactive conformation or it unfolds the peptide in a way that opens its binding surface with high affinity for receptor. Here, we model the conformational preference of RGD sequence in RIPRGDMP at 25 and 42 °C using multiple MD simulations. Further, we model the peptide sequence RGD, PRGD and PRGDMP from kistrin to observe the effect of flanking residues on conformational sampling of RGD. The presence of flanking residues around RGD peptide greatly influenced the conformational sampling. A transition from bend to turn conformation was observed for RGD sequence at 42 °C. The turn conformation shows pharmacophoric parameters required to recognize the receptor aIIbb3. Thus, the temperaturedependent activity of RIPRGDMP when inserted into the loop region of REI can be explained by the presence of the turn conformation. This study will help in designing potential antagonist for the receptor aIIbb3.

Magnetic and Mössbauer characterization of the magnetic properties of single-crystalline sub-micron sized Bi₂Fe₄O₉ cubes

DOE PAGES

Papaefthymiou, Georgia C.; Wong, Stanislaus S.; Viescas, Arthur J.; ...

2014-11-25

Magnetic and Mössbauer characterization of single crystalline, sub-micron sized Bi₂Fe₄O₉ cubes has been performed using SQUID magnetometry and transmission Mössbauer spectroscopy in the temperature range of 4.2 K ≤ T ≤ 300 K. A broad magnetic phase transition from the paramagnetic to the anti-ferromagnetic state is observed below 250 K, with the Mössbauer spectra exhibiting a superposition of magnetic, collapsed and quadrupolar spectra in the transition region of 200 K < T < 245 K. Room temperature Mössbauer spectra obtained in transmission geometry are identical to those recorded in back-scattering geometry via conversion electron Mössbauer spectroscopy, indicating the absence ofmore » strain at the surface. A small hysteresis loop is observed in SQUID measurements at 5 K, attributable to the presence of weak-ferromagnetism arising from the canting of Fe³⁺ ion sublattices in the antiferromagnetic matrix.« less

The fusion loops and membrane proximal region of Epstein-Barr virus glycoprotein B (gB) can function in the context of herpes simplex virus 1 gB when substituted individually but not in combination.

PubMed

Zago, Anna; Connolly, Sarah A; Spear, Patricia G; Longnecker, Richard

2013-01-01

Among the herpesvirus glycoprotein B (gB) fusion proteins, the hydrophobic content of fusion loops and membrane proximal regions (MPRs) are inversely correlated with each other. We examined the functional importance of the hydrophobicity of these regions by replacing them in herpes simplex virus type 1 gB with corresponding regions from Epstein-Barr virus gB. We show that fusion activity is dependent on the structural context in which the specific loops and MPR sequences exist, rather than a simple hydrophobic relationship. Copyright © 2012 Elsevier B.V. All rights reserved.

Suppression of heating of coronal loops rooted in opposite polarity sunspot umbrae

NASA Astrophysics Data System (ADS)

Tiwari, Sanjiv K.; Thalmann, Julia K.; Moore, Ronald L.; Panesar, Navdeep; Winebarger, Amy R.

2016-05-01

EUV observations of active region (AR) coronae reveal the presence of loops at different temperatures. To understand the mechanisms that result in hotter or cooler loops, we study a typical bipolar AR, near solar disk center, which has moderate overall magnetic twist and at least one fully developed sunspot of each polarity. From AIA 193 and 94 A images we identify many clearly discernible coronal loops that connect plage or a sunspot of one polarity to an opposite-polarity plage region. The AIA 94 A images show dim regions in the umbrae of the spots. To see which coronal loops are rooted in a dim umbral area, we performed a non-linear force-free field (NLFFF) modeling using photospheric vector magnetic field measurements obtained with the HMI onboard SDO. After validation of the NLFFF model by comparison of calculated model field lines and observed loops in AIA 193 and 94, we specify the photospheric roots of the model field lines. The model field then shows the coronal magnetic loops that arch from the dim umbral areas of the opposite polarity sunspots. Because these coronal loops are not visible in any of the coronal EUV and X-ray images of the AR, we conclude they are the coolest loops in the AR. This result suggests that the loops connecting opposite polarity umbrae are the least heated because the field in umbrae is so strong that the convective braiding of the field is strongly suppressed.We hypothesize that the convective freedom at the feet of a coronal loop, together with the strength of the field in the body of the loop, determines the strength of the heating. In particular, we expect the hottest coronal loops to have one foot in an umbra and the other foot in opposite-polarity penumbra or plage (coronal moss), the areas of strong field in which convection is not as strongly suppressed as in umbra. Many transient, outstandingly bright, loops in the AIA 94 movie of the AR do have this expected rooting pattern. We will also present another example of AR in which we find a similar rooting pattern of coronal loops.

Feel the Burn: What accounts for spatial variations in coronal heating?

NASA Astrophysics Data System (ADS)

Atwood, Shane; Kankelborg, Charles C.

2016-05-01

The coronal volume is filled with magnetic field, yet only part of that volume has sufficient heating to exhibit hot x-ray loops. How does the Sun decide where the heat goes? Using XRT and AIA images and HMI magnetograms, we identify footpoints of hot coronal loops, and magnetically similar regions underlying relatively unheated corona. We then use IRIS rasters and sit-and-stare observations to compare the spatial, temporal, and spectral structure of these relatively ``heated’’ and ``unheated’’ regions. We seek a signature of upward propagating energy that could be associated with hot active region loops.

Deciphering the roles of outer membrane protein A extracellular loops in the pathogenesis of Escherichia coli K1 meningitis.

PubMed

Mittal, Rahul; Krishnan, Subramanian; Gonzalez-Gomez, Ignacio; Prasadarao, Nemani V

2011-01-21

Outer membrane protein A (OmpA) has been implicated as an important virulence factor in several gram-negative bacterial infections such as Escherichia coli K1, a leading cause of neonatal meningitis associated with significant mortality and morbidity. In this study, we generated E. coli K1 mutants that express OmpA in which three or four amino acids from various extracellular loops were changed to alanines, and we examined their ability to survive in several immune cells. We observed that loop regions 1 and 2 play an important role in the survival of E. coli K1 inside neutrophils and dendritic cells, and loop regions 1 and 3 are needed for survival in macrophages. Concomitantly, E. coli K1 mutants expressing loop 1 and 2 mutations were unable to cause meningitis in a newborn mouse model. Of note, mutations in loop 4 of OmpA enhance the severity of the pathogenesis by allowing the pathogen to survive better in circulation and to produce high bacteremia levels. These results demonstrate, for the first time, the roles played by different regions of extracellular loops of OmpA of E. coli K1 in the pathogenesis of meningitis and may help in designing effective preventive strategies against this deadly disease.

Human immunodeficiency virus type 1 LTR TATA and TAR region sequences required for transcriptional regulation.

PubMed Central

Garcia, J A; Harrich, D; Soultanakis, E; Wu, F; Mitsuyasu, R; Gaynor, R B

1989-01-01

The human immunodeficiency virus (HIV) type 1 LTR is regulated at the transcriptional level by both cellular and viral proteins. Using HeLa cell extracts, multiple regions of the HIV LTR were found to serve as binding sites for cellular proteins. An untranslated region binding protein UBP-1 has been purified and fractions containing this protein bind to both the TAR and TATA regions. To investigate the role of cellular proteins binding to both the TATA and TAR regions and their potential interaction with other HIV DNA binding proteins, oligonucleotide-directed mutagenesis of both these regions was performed followed by DNase I footprinting and transient expression assays. In the TATA region, two direct repeats TC/AAGC/AT/AGCTGC surround the TATA sequence. Mutagenesis of both of these direct repeats or of the TATA sequence interrupted binding over the TATA region on the coding strand, but only a mutation of the TATA sequence affected in vivo assays for tat-activation. In addition to TAR serving as the site of binding of cellular proteins, RNA transcribed from TAR is capable of forming a stable stem-loop structure. To determine the relative importance of DNA binding proteins as compared to secondary structure, oligonucleotide-directed mutations in the TAR region were studied. Local mutations that disrupted either the stem or loop structure were defective in gene expression. However, compensatory mutations which restored base pairing in the stem resulted in complete tat-activation. This indicated a significant role for the stem-loop structure in HIV gene expression. To determine the role of TAR binding proteins, mutations were constructed which extensively changed the primary structure of the TAR region, yet left stem base pairing, stem energy and the loop sequence intact. These mutations resulted in decreased protein binding to TAR DNA and defects in tat-activation, and revealed factor binding specifically to the loop DNA sequence. Further mutagenesis which inverted this stem and loop mutation relative to the HIV LTR mRNA start site resulted in even larger decreases in tat-activation. This suggests that multiple determinants, including protein binding, the loop sequence, and RNA or DNA secondary structure, are important in tat-activation and suggests that tat may interact with cellular proteins binding to DNA to increase HIV gene expression. Images PMID:2721501

Nonequilibrium phase transitions in isotropic Ashkin-Teller model

NASA Astrophysics Data System (ADS)

Akıncı, Ümit

2017-03-01

Dynamic behavior of an isotropic Ashkin-Teller model in the presence of a periodically oscillating magnetic field has been analyzed by means of the mean field approximation. The dynamic equation of motion has been constructed with the help of a Glauber type stochastic process and solved for a square lattice. After defining the possible dynamical phases of the system, phase diagrams have been given and the behavior of the hysteresis loops has been investigated in detail. The hysteresis loop for specific order parameter of isotropic Ashkin-Teller model has been defined and characteristics of this loop in different dynamical phases have been given.

Decay-less kink oscillations in coronal loops

NASA Astrophysics Data System (ADS)

Anfinogentov, S.; Nisticò, G.; Nakariakov, V. M.

2013-12-01

Context. Kink oscillations of coronal loops in an off-limb active region are detected with the Imaging Assembly Array (AIA) instruments of the Solar Dynamics Observatory (SDO) at 171 Å. Aims: We aim to measure periods and amplitudes of kink oscillations of different loops and to determinate the evolution of the oscillation phase along the oscillating loop. Methods: Oscillating coronal loops were visually identified in the field of view of SDO/AIA and STEREO/EUVI-A: the loop length was derived by three-dimensional analysis. Several slits were taken along the loops to assemble time-distance maps. We identified oscillatory patterns and retrieved periods and amplitudes of the oscillations. We applied the cross-correlation technique to estimate the phase shift between oscillations at different segments of oscillating loops. Results: We found that all analysed loops show low-amplitude undamped transverse oscillations. Oscillation periods of loops in the same active region range from 2.5 to 11 min, and are different for different loops. The displacement amplitude is lower than 1 Mm. The oscillation phase is constant along each analysed loop. The spatial structure of the phase of the oscillations corresponds to the fundamental standing kink mode. We conclude that the observed behaviour is consistent with the empirical model in terms of a damped harmonic resonator affected by a non-resonant continuously operating external force. A movie is available in electronic form at http://www.aanda.org

Hardware platforms for MEMS gyroscope tuning based on evolutionary computation using open-loop and closed -loop frequency response

NASA Technical Reports Server (NTRS)

Keymeulen, Didier; Ferguson, Michael I.; Fink, Wolfgang; Oks, Boris; Peay, Chris; Terrile, Richard; Cheng, Yen; Kim, Dennis; MacDonald, Eric; Foor, David

2005-01-01

We propose a tuning method for MEMS gyroscopes based on evolutionary computation to efficiently increase the sensitivity of MEMS gyroscopes through tuning. The tuning method was tested for the second generation JPL/Boeing Post-resonator MEMS gyroscope using the measurement of the frequency response of the MEMS device in open-loop operation. We also report on the development of a hardware platform for integrated tuning and closed loop operation of MEMS gyroscopes. The control of this device is implemented through a digital design on a Field Programmable Gate Array (FPGA). The hardware platform easily transitions to an embedded solution that allows for the miniaturization of the system to a single chip.

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

Galle, G.; Degert, J.; Freysz, E.

We have studied the low spin to high spin phase transition induced by nanosecond laser pulses outside and within the thermal hysteresis loop of the [Fe(Htrz){sub 2} trz](BF{sub 4}){sub 2}-H{sub 2}O spin crossover nanoparticles. We demonstrate that, whatever the temperature of the compound, the photo-switching is achieved in less than 12.5 ns. Outside the hysteresis loop, the photo-induced high spin state remains up to 100 {mu}s and then relaxes. Within the thermal hysteresis loop, the photo-induced high spin state remains as long as the temperature of the sample is kept within the thermal loop. A Raman study indicates that themore » photo-switching can be completed using single laser pulse excitation.« less

Liquid-Vapor Flow Regime Transitions for Spacecraft Heat Transfer Loops

DTIC Science & Technology

1988-12-01

effects of fluid properties on flow regime transitions. 5 A carnauba wax with no additives was used because it resists dissolution by oil. 19 4.2...importance of an annular flow entrance geometry and of waxing the tube wall to change its wetting properties (to prevent inverse annular flow) were

Facilitating Systemic Research and Learning and the Transition to Agricultural Sustainability

ERIC Educational Resources Information Center

Eksvard, Karin

2010-01-01

This article focuses on how a facilitated process of triple loop learning can enable transition toward more sustainable forms of farming. The article is a case-based study of Participatory Learning and Action Research with organic tomato growers in Malardalen, Sweden. The importance of negotiating learning and action, capacity building, and…

Open magnetic fields in active regions

NASA Technical Reports Server (NTRS)

Svestka, Z.; Solodyna, C. V.; Howard, R.; Levine, R. H.

1977-01-01

Soft X-ray images and magnetograms of several active regions and coronal holes are examined which support the interpretation that some of the dark X-ray gaps seen between interconnecting loops and inner cores of active regions are foot points of open field lines inside the active regions. Characteristics of the investigated dark gaps are summarized. All the active regions with dark X-ray gaps at the proper place and with the correct polarity predicted by global potential extrapolation of photospheric magnetic fields are shown to be old active regions, indicating that field opening is accomplished only in a late phase of active-region development. It is noted that some of the observed dark gaps probably have nothing in common with open fields, but are either due to the decreased temperature in low-lying portions of interconnecting loops or are the roots of higher and less dense or cooler loops.

Influence of Nb doping on the phase transition properties of VO2 thin films prepared by ion beam co-sputtering deposition

NASA Astrophysics Data System (ADS)

Zhu, Huiqun; Li, Pengfei; Zhao, Lite; Liu, Jiahuan

2016-03-01

The Nb-doped VO2 thin films were successfully prepared on the glass substrates by ion beam co-sputtering at room temperature and post annealing under the air condition. The effects of the preparation processing and Nb doping on the thermal hysteresis loop and phase transition temperature of the VO2 thin films were analyzed by resistancetemperature measurement. The results show that Nb doping significantly changes the surface morphologies of VO2 thin films, and Nb-doped VO2 thin films exhibit VO2(002) preferred orientation growth with greatly improved crystallinity and orientation. Compared with pure VO2, the phase transition temperature of Nb-doped VO2 thin films drops to 40 ºC, and the width of thermal hysteresis loop narrows to 8 ºC. It is demonstrated that Nb-doped VO2 thin films prepared by ion beam co-sputtered at room temperature have an obvious thermal sensitive effect, and keep a good characteristic from metal to semiconductor phase transition.

RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability.

PubMed

Chang, Emily Yun-Chia; Novoa, Carolina A; Aristizabal, Maria J; Coulombe, Yan; Segovia, Romulo; Chaturvedi, Richa; Shen, Yaoqing; Keong, Christelle; Tam, Annie S; Jones, Steven J M; Masson, Jean-Yves; Kobor, Michael S; Stirling, Peter C

2017-12-04

Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1 Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability. © 2017 Chang et al.

West Florida shelf circulation and temperature budget for the 1998 fall transition

NASA Astrophysics Data System (ADS)

He, Ruoying; Weisberg, Robert H.

2003-05-01

Mid-latitude continental shelves undergo a fall transition as the net heat flux changes from warming to cooling. Using in situ data and a numerical model we investigate the circulation on the west Florida shelf (WFS) for the fall transition of 1998. The model is a regional adaptation of the primitive equation, Princeton Ocean Model forced by NCEP reanalysis wind, air pressure, and heat flux fields, plus river inflows. After comparison with observations the model is used to draw inferences on the seasonal and synoptic scale features of the shelf circulation. By running twin experiments, one without and the other with an idealized Loop Current (LC), we explore the relative importance of local versus deep-ocean forcing. We find that local forcing largely controls the inner-shelf circulation, including changes from the Florida Panhandle in the north to regions farther south. The effects of the LC in fall 1998 are to reinforce the mid-shelf currents and to increase the across-shelf transports in the bottom Ekman layer, thereby accentuating the shoreward transport of cold, nutrient rich water of deep-ocean origin. A three-dimensional analysis of the temperature budget reveals that surface heat flux largely controls both the seasonal and synoptic scale temperature variations. Surface cooling leads to convective mixing that rapidly alters temperature gradients. One interesting consequence is that upwelling can result in near-shore warming as warmer offshore waters are advected landward. The temperature balances on the shelf are complex and fully three-dimensional.

Nonlinear dielectric properties of planar structures based on ferroelectric betaine phosphite films

NASA Astrophysics Data System (ADS)

Balashova, E. V.; Krichevtsov, B. B.; Svinarev, F. B.; Yurko, E. I.

2014-02-01

Ferroelectric films of partly deuterated betaine phosphite are grown on NdGaO3(001) substrates with an interdigitated system of electrodes on their surfaces by evaporation at room temperature. These films have a high capacitance in the ferroelectric phase transition range. The dielectric nonlinearity of the grown structures is studied in small-signal and strong-signal response modes and in the intermediate region between these two modes by measuring the capacitance in a dc bias field, dielectric hysteresis loops, and the Fourier spectra of an output signal in the Sawyer-Tower circuit. In the phase transition range, the capacitance control ratio at a bias voltage U bias = 40 V is K ≅ 7. The dielectric nonlinearity of the structures in the paraelectric phase is described by the Landau theory of second-order phase transitions. The additional contribution to the nonlinearity in the ferroelectric phase is related to the motion of domain walls and manifests itself when the input signal amplitude is higher than U st ˜ 0.7-1.0 V. The relaxation times of domain walls are determined from an analysis of the frequency dependences of the dielectric hysteresis.

Performance Analysis of Digital Tracking Loops for Telemetry Ranging Applications

NASA Astrophysics Data System (ADS)

Vilnrotter, V.; Hamkins, J.; Xie, H.; Ashrafi, S.

2015-08-01

In this article, we analyze mathematical models of digital loops used to track the phase and timing of communications and navigation signals. The limits on the accuracy of phase and timing estimates play a critical role in the accuracy achievable in telemetry ranging applications. We describe in detail a practical algorithm to compute the loop parameters for discrete update (DU) and continuous update (CU) loop formulations, and we show that a simple power-series approximation to the DU model is valid over a large range of time-bandwidth product . Several numerical examples compare the estimation error variance of the DU and CU models to each other and to Cramer-Rao lower bounds. Finally, the results are applied to the problem of ranging, by evaluating the performance of a phase-locked loop designed to track a typical ambiguity-resolving pseudonoise (PN) code received and demodulated at the spacecraft on the uplink part of the two-way ranging link, and a data transition tracking loop (DTTL) on the downlink part.

Computer Generated Snapshot of Our Sun's Magnetic Field

NASA Technical Reports Server (NTRS)

2003-01-01

These banana-shaped loops are part of a computer-generated snapshot of our sun's magnetic field. The solar magnetic-field lines loop through the sun's corona, break through the sun's surface, and cornect regions of magnetic activity, such as sunspots. This image --part of a magnetic-field study of the sun by NASA's Allen Gary -- shows the outer portion (skins) of interconnecting systems of hot (2 million degrees Kelvin) coronal loops within and between two active magnetic regions on opposite sides of the sun's equator. The diameter of these coronal loops at their foot points is approximately the same size as the Earth's radius (about 6,000 kilometers).

An interacting loop model of solar flare bursts

NASA Technical Reports Server (NTRS)

Emslie, A. G.

1981-01-01

As a result of the strong heating produced at chromospheric levels during a solar flare burst, the local gas pressure can transiently attain very large values in certain regions. The effectiveness of the surrounding magnetic field at confining this high pressure plasma is therefore reduced and the flaring loop becomes free to expand laterally. In so doing it may drive magnetic field lines into neighboring, nonflaring, loops in the same active region, causing magnetic reconnection to take place and triggering another flare burst. The features of this interacting loop model are found to be in good agreement with the energetics and time structure of flare associated solar hard X-ray bursts.

Xrt And Shinx Joint Flare Study: Ar 11024

NASA Astrophysics Data System (ADS)

Engell, Alexander; Sylwester, J.; Siarkowski, M.

2010-05-01

From 12:00 UT on July 3 through July 7, 2009 SphinX (Solar Photometer IN X-rays) observes 130 flares with active region (AR) 11024 being the only AR on disk. XRT (X-Ray Telescope) is able to observe 64 of these flare events. The combination of both instruments results in a flare study revealing (1) a relationship between flux emergence and flare rate, (2) that the presence of active region loops typically results in different flare morphologies (single and multiple loop flares) then when there is a lack of an active region loop environment where more cusp and point-like flares are observed, (3) cusp and point-like flares often originate from the same location, and (4) a distribution of flare temperatures corresponding to the different flare morphologies. The differences between the observed flare morphologies may occur as the result of the heated plasma through the flaring process being confined by the proximity of loop structures as for the single and multiple loop flares, while for cusp and point-like flares they occur in an early-phase environment that lack loop presence. The continuing flux emergence of AR 11024 likely provides different magnetic interactions and may be the source responsible for all of the flares.

Loop models of low coronal structures observed by the Normal Incidence X-Ray Telescope (NIXT)

NASA Technical Reports Server (NTRS)

Peres, G.; Reale, F.; Golub, L.

1994-01-01

The X-ray pictures obtained with the Normal Incidence X-Ray Telescope (NIXT), apart from the ubiquitous coronal loops well known from previous X-ray observations, show a new and peculiar morphology: in many active regions there are wide and apparently low-lying areas of intense emission which resemble H alpha plages. By means of hydrostatic models of coronal arches, we analyze the distribution of temperature, density, emission measure, and plasma emissivity in the spectral band to which NIXT is sensitive, and we show that the above morphology can be explained by the characteristics of high pressure loops having a thin region of high surface brightness at the base. We therefore propose that this finding might help to identify high-pressure X-ray emitting coronal regions in NIXT images, and it is in principle applicable to any imaging instrument which has high sensitivity to 10(exp 4) - 10(exp 6) K plasma within a narrow coronal-temperature passband. As a more general result of this study, we propose that the comparison of NIXT observations with models of stationary loops might provide a new diagnostic: the determination of the loop plasma pressure from measurements of brightness distribution along the loop.

Evidence of suppressed heating of coronal loops rooted in opposite polarity sunspot umbrae

NASA Astrophysics Data System (ADS)

Tiwari, Sanjiv K.; Thalmann, Julia K.; Winebarger, Amy R.; Panesar, Navdeep K.; Moore, Ronald

2015-04-01

Observations of active region (AR) coronae in different EUV wavelengths reveal the presence of various loops at different temperatures. To understand the mechanisms that result in hotter or cooler loops, we study a typical bipolar AR, near solar disk center, which has moderate overall magnetic twist and at least one fully developed sunspot of each polarity. From AIA 193 and 94 A images we identify many clearly discernible coronal loops that connect opposite-polarity plage or a sunspot to a opposite-polarity plage region. The AIA 94 A images show dim regions in the umbrae of the spots. To see which coronal loops are rooted in a dim umbral area, we performed a non-linear force-free field (NLFFF) modeling using photospheric vector magnetic field measurements obtained with the Heliosesmic Magnetic Imager (HMI) onboard SDO. After validation of the NLFFF model by comparison of calculated model field lines and observed loops in AIA 193 and 94 A, we specify the photospheric roots of the model field lines. The model field then shows the coronal magnetic loops that arch from the dim umbral area of the positive-polarity sunspot to the dim umbral area of a negative-polarity sunspot. Because these coronal loops are not visible in any of the coronal EUV and X-ray images of the AR, we conclude they are the coolest loops in the AR. This result suggests that the loops connecting opposite polarity umbrae are the least heated because the field in umbrae is so strong that the convective braiding of the field is strongly suppressed.From this result, we further hypothesize that the convective freedom at the feet of a coronal loop, together with the strength of the field in the body of the loop, determines the strength of the heating. In particular, we expect the hottest coronal loops to have one foot in an umbra and the other foot in opposite-polarity penumbra or plage (coronal moss), the areas of strong field in which convection is not as strongly suppressed as in umbrae. Many transient, outstandingly bright, loops in the AIA 94 A movie of the AR do have this expected rooting pattern.

The Foggy EUV Corona and Coronal Heating by MHD Waves from Explosive Reconnection Events

NASA Technical Reports Server (NTRS)

Moore, Ron L.; Cirtain, Jonathan W.; Falconer, David A.

2008-01-01

In 0.5 arcsec/pixel TRACE coronal EUV images, the corona rooted in active regions that are at the limb and are not flaring is seen to consist of (1) a complex array of discrete loops and plumes embedded in (2) a diffuse ambient component that shows no fine structure and gradually fades with height. For each of two not-flaring active regions, found that the diffuse component is (1) approximately isothermal and hydrostatic and (2) emits well over half of the total EUV luminosity of the active-region corona. Here, from a TRACE Fe XII coronal image of another not-flaring active region, the large sunspot active region AR 10652 when it was at the west limb on 30 July 2004, we separate the diffuse component from the discrete loop component by spatial filtering, and find that the diffuse component has about 60% of the total luminosity. If under much higher spatial resolution than that of TRACE (e. g., the 0.1 arcsec/pixel resolution of the Hi-C sounding-rocket experiment proposed by J. W. Cirtain et al), most of the diffuse component remains diffuse rather being resolved into very narrow loops and plumes, this will raise the possibility that the EUV corona in active regions consists of two basically different but comparably luminous components: one being the set of discrete bright loops and plumes and the other being a truly diffuse component filling the space between the discrete loops and plumes. This dichotomy would imply that there are two different but comparably powerful coronal heating mechanisms operating in active regions, one for the distinct loops and plumes and another for the diffuse component. We present a scenario in which (1) each discrete bright loop or plume is a flux tube that was recently reconnected in a burst of reconnection, and (2) the diffuse component is heated by MHD waves that are generated by these reconnection events and by other fine-scale explosive reconnection events, most of which occur in and below the base of the corona where they are seen as UV explosive events, EUV blinkers, and type II spicules. These MHD waves propagate across field lines and dissipate, heating the plasma in the field between the bright loops and plumes.

Study of the Z{sub 3} symmetry in QCD at finite temperature and chemical potential using a worm algorithm

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

Krein, Gastao; Leme, Rafael R.; Woitek, Marcio

Traditional Monte Carlo simulations of QCD in the presence of a baryon chemical potential are plagued by the complex phase problem and new numerical approaches are necessary for studying the phase diagram of the theory. In this work we consider a Z{sub 3} Polyakov loop model for the deconfining phase transition in QCD and discuss how a flux representation of the model in terms of dimer and monomer variable solves the complex action problem. We present results of numerical simulations using a worm algorithm for the specific heat and two-point correlation function of Polyakov loops. Evidences of a first ordermore » deconfinement phase transition are discussed.« less

Energy-Looping Nanoparticles: Harnessing Excited-State Absorption for Deep-Tissue Imaging.

PubMed

Levy, Elizabeth S; Tajon, Cheryl A; Bischof, Thomas S; Iafrati, Jillian; Fernandez-Bravo, Angel; Garfield, David J; Chamanzar, Maysamreza; Maharbiz, Michel M; Sohal, Vikaas S; Schuck, P James; Cohen, Bruce E; Chan, Emory M

2016-09-27

Near infrared (NIR) microscopy enables noninvasive imaging in tissue, particularly in the NIR-II spectral range (1000-1400 nm) where attenuation due to tissue scattering and absorption is minimized. Lanthanide-doped upconverting nanocrystals are promising deep-tissue imaging probes due to their photostable emission in the visible and NIR, but these materials are not efficiently excited at NIR-II wavelengths due to the dearth of lanthanide ground-state absorption transitions in this window. Here, we develop a class of lanthanide-doped imaging probes that harness an energy-looping mechanism that facilitates excitation at NIR-II wavelengths, such as 1064 nm, that are resonant with excited-state absorption transitions but not ground-state absorption. Using computational methods and combinatorial screening, we have identified Tm(3+)-doped NaYF4 nanoparticles as efficient looping systems that emit at 800 nm under continuous-wave excitation at 1064 nm. Using this benign excitation with standard confocal microscopy, energy-looping nanoparticles (ELNPs) are imaged in cultured mammalian cells and through brain tissue without autofluorescence. The 1 mm imaging depths and 2 μm feature sizes are comparable to those demonstrated by state-of-the-art multiphoton techniques, illustrating that ELNPs are a promising class of NIR probes for high-fidelity visualization in cells and tissue.

Interacting cytoplasmic loops of subunits a and c of Escherichia coli F1F0 ATP synthase gate H+ transport to the cytoplasm.

PubMed

Steed, P Ryan; Kraft, Kaitlin A; Fillingame, Robert H

2014-11-25

H(+)-transporting F1F0 ATP synthase catalyzes the synthesis of ATP via coupled rotary motors within F0 and F1. H(+) transport at the subunit a-c interface in transmembranous F0 drives rotation of a cylindrical c10 oligomer within the membrane, which is coupled to rotation of subunit γ within the α3β3 sector of F1 to mechanically drive ATP synthesis. F1F0 functions in a reversible manner, with ATP hydrolysis driving H(+) transport. ATP-driven H(+) transport in a select group of cysteine mutants in subunits a and c is inhibited after chelation of Ag(+) and/or Cd(+2) with the substituted sulfhydryl groups. The H(+) transport pathway mapped via these Ag(+)(Cd(+2))-sensitive Cys extends from the transmembrane helices (TMHs) of subunits a and c into cytoplasmic loops connecting the TMHs, suggesting these loop regions could be involved in gating H(+) release to the cytoplasm. Here, using select loop-region Cys from the single cytoplasmic loop of subunit c and multiple cytoplasmic loops of subunit a, we show that Cd(+2) directly inhibits passive H(+) transport mediated by F0 reconstituted in liposomes. Further, in extensions of previous studies, we show that the regions mediating passive H(+) transport can be cross-linked to each other. We conclude that the loop-regions in subunits a and c that are implicated in H(+) transport likely interact in a single structural domain, which then functions in gating H(+) release to the cytoplasm.

ABOVE-THE-LOOP-TOP OSCILLATION AND QUASI-PERIODIC CORONAL WAVE GENERATION IN SOLAR FLARES

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

Takasao, Shinsuke; Shibata, Kazunari, E-mail: takasao@kwasan.kyoto-u.ac.jp

Observations revealed that various kinds of oscillations are excited in solar flare regions. Quasi-periodic pulsations (QPPs) in flare emissions are commonly observed in a wide range of wavelengths. Recent observations have found that fast-mode magnetohydrodynamic (MHD) waves are quasi-periodically emitted from some flaring sites (quasi-periodic propagating fast-mode magnetoacoustic waves; QPFs). Both QPPs and QPFs imply a cyclic disturbance originating from the flaring sites. However, the physical mechanisms remain puzzling. By performing a set of two-dimensional MHD simulations of a solar flare, we discovered the local oscillation above the loops filled with evaporated plasma (above-the-loop-top region) and the generation of QPFsmore » from such oscillating regions. Unlike all previous models for QPFs, our model includes essential physics for solar flares such as magnetic reconnection, heat conduction, and chromospheric evaporation. We revealed that QPFs can be spontaneously excited by the above-the-loop-top oscillation. We found that this oscillation is controlled by the backflow of the reconnection outflow. The new model revealed that flare loops and the above-the-loop-top region are full of shocks and waves, which is different from the previous expectations based on a standard flare model and previous simulations. In this paper, we show the QPF generation process based on our new picture of flare loops and will briefly discuss a possible relationship between QPFs and QPPs. Our findings will change the current view of solar flares to a new view in which they are a very dynamic phenomenon full of shocks and waves.« less

Genetic distance of Malaysian mousedeer based on mitochondrial DNA cytochrome oxidase I (COI) and D-loop region sequences

NASA Astrophysics Data System (ADS)

Bakar, Mohamad-Azam Akmal Abu; Rovie-Ryan, Jeffrine Japning; Ampeng, Ahmad; Yaakop, Salmah; Nor, Shukor Md; Md-Zain, Badrul Munir

2018-04-01

Mousedeer is one of the primitive mammals that can be found mainly in Southeast-Asia region. There are two species of mousedeer in Malaysia which are Tragulus kanchil and Tragulus napu. Both species can be distinguish by size, coat coloration, and throat pattern but clear diagnosis still cannot be found. The objective of the study is to show the genetic distance relationship between T. kanchil and T. napu and their population based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and D-loop region. There are 42 sample of mousedeer were used in this study collected by PERHILITAN from different locality. Another 29 D-loop sequence were retrieved from Genbank for comparative analysis. All sample were amplified using universal primer and species-specific primer for COI and D-loop genes via PCR process. The amplified sequences were analyzed to determine genetic distance of T. kanchil and T. napu. From the analysis, the average genetic distance between T. kanchil and T. napu based on locus COI and D-loop were 0.145 and 0.128 respectively. The genetic distance between populations of T. kanchil based on locus COI was between 0.003-0.013. For locus D-loop, genetic distance analysis showed distance in relationship between west-coast populations to east-coast population of T. kanchil. COI and D-loop mtDNA region provided a clear picture on the relationship within the mousedeer species. Last but not least, conservation effort toward protecting this species can be done by study the molecular genetics and prevent the extinction of this species.

Imagery and spectroscopy of supernova remnants and H-2 regions

NASA Technical Reports Server (NTRS)

Dufour, R. J.

1984-01-01

Research activities relating to supernova remnants were summarized. The topics reviewed include: progenitor stars of supernova remnants, UV/optical/radio/X-ray imagery of selected regions in the Cygnus Loop, UV/optical spectroscopy of the Cygnus Loop spur, and extragalactic supernova remnant spectra.

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

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

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory . The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observedmore » at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s{sup −1}. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.« less

Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization.

PubMed

Li, L; Falzone, C J; Wright, P E; Benkovic, S J

1992-09-01

The function of a highly mobile loop in Escherichia coli dihydrofolate reductase was studied by constructing a mutant (DL1) using cassette mutagenesis that had four residues deleted in the middle section of the loop (Met16-Ala19) and a glycine inserted to seal the gap. This part of the loop involves residues 16-20 and is disordered in the X-ray crystal structures of the apoprotein and the NADP+ binary complex but forms a hairpin turn that folds over the nicotinamide moiety of NADP+ and the pteridine moiety of folate in the ternary complex [Bystroff, C., & Kraut, J. (1991) Biochemistry 30, 2227-2239]. The steady-state and pre-steady-state kinetics and two-dimensional 1H NMR spectra were analyzed and compared to the wild-type protein. The kinetics on the DL1 mutant enzyme show that the KM value for NADPH (5.3 microM), the KM for dihydrofolate (2 microM), the rate constant for the release of the product tetrahydrofolate (10.3 s-1), and the intrinsic pKa value (6.2) are similar to those exhibited by the wild-type enzyme. However, the hydride-transfer rate declines markedly from the wild-type value of 950 s-1 to 1.7 s-1 for the DL1 mutant and when taken with data for substrate binding indicates that the loop contributes to substrate flux by a factor of 3.5 x 10(4). Thus, the mobility of loop I may provide a mechanism of recruiting hydrophobic residues which can properly align the nicotinamide and pteridine rings for the hydride-transfer process (a form of transition-state stabilization).(ABSTRACT TRUNCATED AT 250 WORDS)

Behaviour of fractional loop delay zero crossing digital phase locked loop (FR-ZCDPLL)

NASA Astrophysics Data System (ADS)

Nasir, Qassim

2018-01-01

This article analyses the performance of the first-order zero crossing digital phase locked loops (FR-ZCDPLL) when fractional loop delay is added to loop. The non-linear dynamics of the loop is presented, analysed and examined through bifurcation behaviour. Numerical simulation of the loop is conducted to proof the mathematical analysis of the loop operation. The results of the loop simulation show that the proposed FR-ZCDPLL has enhanced the performance compared to the conventional zero crossing DPLL in terms of wider lock range, captured range and stable operation region. In addition, extensive experimental simulation was conducted to find the optimum loop parameters for different loop environmental conditions. The addition of the fractional loop delay network in the conventional loop also reduces the phase jitter and its variance especially when the signal-to-noise ratio is low.

Effects of V2O3 buffer layers on sputtered VO2 smart windows: Improved thermochromic properties, tunable width of hysteresis loops and enhanced durability

NASA Astrophysics Data System (ADS)

Long, Shiwei; Cao, Xun; Sun, Guangyao; Li, Ning; Chang, Tianci; Shao, Zewei; Jin, Ping

2018-05-01

Vanadium dioxide (VO2) is one of the most well-known thermochromic materials, which exhibits a notable optical change from transparent to reflecting in the infrared region upon a metal-insulator phase transition. For practical applications, VO2 thin films should be in high crystalline quality to obtain a strong solar modulation ability (ΔTsol). Meanwhile, narrow hysteresis loops and robust ambient durability are also indispensable for sensitivity and long-lived utilization, respectively. In this work, a series of high-quality V2O3/VO2 bilayer structures were grown on quartz glass substrates by reactive magnetron sputtering. Basically, the bottom V2O3 acts as the buffer layer to improve the crystallinity of the top VO2, while the VO2 serves as the thermochromic layer to guarantee the solar modulation ability for energy-saving. We observed an obvious increase in ΔTsol of 76% (from 7.5% to 13.2%) for VO2 films after introducing V2O3 buffer layers. Simultaneously, a remarkable reduction by 79% (from 21.9 °C to 4.7 °C) in width of hysteresis loop was obtained when embedding 60 nm V2O3 buffer for 60 nm VO2. In addition, VO2 with non-stoichiometry of V2O3±x buffer demonstrates a broadening hysteresis loops width, which is derived from the lattice distortion caused by lattice imperfection. Finally, durability of VO2 has been significantly improved due to positive effects of V2O3 buffer layer. Our results lead to a comprehensive enhancement in crystallinity of VO2 and shed new light on the promotion of thermochromic property by homologous oxides for VO2.

A Closed-Loop Model of Operator Visual Attention, Situation Awareness, and Performance Across Automation Mode Transitions.

PubMed

Johnson, Aaron W; Duda, Kevin R; Sheridan, Thomas B; Oman, Charles M

2017-03-01

This article describes a closed-loop, integrated human-vehicle model designed to help understand the underlying cognitive processes that influenced changes in subject visual attention, mental workload, and situation awareness across control mode transitions in a simulated human-in-the-loop lunar landing experiment. Control mode transitions from autopilot to manual flight may cause total attentional demands to exceed operator capacity. Attentional resources must be reallocated and reprioritized, which can increase the average uncertainty in the operator's estimates of low-priority system states. We define this increase in uncertainty as a reduction in situation awareness. We present a model built upon the optimal control model for state estimation, the crossover model for manual control, and the SEEV (salience, effort, expectancy, value) model for visual attention. We modify the SEEV attention executive to direct visual attention based, in part, on the uncertainty in the operator's estimates of system states. The model was validated using the simulated lunar landing experimental data, demonstrating an average difference in the percentage of attention ≤3.6% for all simulator instruments. The model's predictions of mental workload and situation awareness, measured by task performance and system state uncertainty, also mimicked the experimental data. Our model supports the hypothesis that visual attention is influenced by the uncertainty in system state estimates. Conceptualizing situation awareness around the metric of system state uncertainty is a valuable way for system designers to understand and predict how reallocations in the operator's visual attention during control mode transitions can produce reallocations in situation awareness of certain states.

A training rule which guarantees finite-region stability for a class of closed-loop neural-network control systems.

PubMed

Kuntanapreeda, S; Fullmer, R R

1996-01-01

A training method for a class of neural network controllers is presented which guarantees closed-loop system stability. The controllers are assumed to be nonlinear, feedforward, sampled-data, full-state regulators implemented as single hidden-layer neural networks. The controlled systems must be locally hermitian and observable. Stability of the closed-loop system is demonstrated by determining a Lyapunov function, which can be used to identify a finite stability region about the regulator point.

Study of the post-flare loops on 29 July 1973. I - Dynamics of the X-ray loops

NASA Technical Reports Server (NTRS)

Nolte, J. T.; Gerassimenko, M.; Krieger, A. S.; Petrasso, R. D.; Svestka, Z.

1979-01-01

We derive an empirical model of the X-ray emitting post-flare loops observed during the decay phase of the 29 July 1973 flare. We find that the loops are elliptical, with the brightest emitting region at the tops. We determine the height, velocity of growth, and ratio of height to width of the loops at times from 3 to 12 hr after the flare onset.

Ship Compliance in Emission Control Areas: Technology Costs and Policy Instruments.

PubMed

Carr, Edward W; Corbett, James J

2015-08-18

This paper explores whether a Panama Canal Authority pollution tax could be an effective economic instrument to achieve Emission Control Area (ECA)-like reductions in emissions from ships transiting the Panama Canal. This tariff-based policy action, whereby vessels in compliance with International Maritime Organisation (IMO) ECA standards pay a lower transit tariff than noncompliant vessels, could be a feasible alternative to petitioning for a Panamanian ECA through the IMO. A $4.06/container fuel tax could incentivize ECA-compliant emissions reductions for nearly two-thirds of Panama Canal container vessels, mainly through fuel switching; if the vessel(s) also operate in IMO-defined ECAs, exhaust-gas treatment technologies may be cost-effective. The RATES model presented here compares current abatement technologies based on hours of operation within an ECA, computing costs for a container vessel to comply with ECA standards in addition to computing the Canal tax that would reduce emissions in Panama. Retrofitted open-loop scrubbers are cost-effective only for vessels operating within an ECA for more than 4500 h annually. Fuel switching is the least-cost option to industry for vessels that operate mostly outside of ECA regions, whereas vessels operating entirely within an ECA region could reduce compliance cost with exhaust-gas treatment technology (scrubbers).

A fluorescent probe-labeled Escherichia coli aspartate transcarbamoylase that monitors the allosteric conformational state.

PubMed

West, Jay M; Tsuruta, Hiro; Kantrowitz, Evan R

2004-01-09

A new system has been developed capable of monitoring conformational changes of the 240s loop of aspartate transcarbamoylase, which are tightly correlated with the quaternary structural transition, with high sensitivity in solution. Pyrene, a fluorescent probe, was conjugated to residue 241 in the 240s loop of aspartate transcarbamoylase to monitor changes in conformation by fluorescence spectroscopy. Pyrene maleimide was conjugated to a cysteine residue on the 240s loop of a previously constructed double catalytic chain mutant version of the enzyme, C47A/A241C. The pyrene-labeled enzyme undergoes the normal T to R structural transition, as demonstrated by small-angle x-ray scattering. Like the wild-type enzyme, the pyrene-labeled enzyme exhibits cooperativity toward aspartate, and is activated by ATP and inhibited by CTP at subsaturating concentrations of aspartate. The binding of the bisubstrate analogue N-(phosphonoacetyl)-l-aspartate (PALA), or the aspartate analogue succinate, in the presence of saturating carbamoyl phosphate, to the pyrenelabeled enzyme caused a sigmoidal change in the fluorescence emission. Saturation with ATP and CTP (in the presence of either subsaturating amounts of PALA or succinate and carbamoyl phosphate) caused a hyperbolic increase and decrease, respectively, in the fluorescence emission. The half-saturation values from the fluorescence saturation curves and kinetic saturation curves were, within error, identical. Fluorescence and small-angle x-ray scattering stopped-flow experiments, using aspartate and carbamoyl phosphate, confirm that the change in excimer fluorescence and the quaternary structure change correlate. These results in conjunction with previous studies suggest that the allosteric transition involves both global and local conformational changes and that the heterotropic effect of the nucleotides may be exerted through local conformational changes in the active site by directly influencing the conformation of the 240s loop.

Functional Loop Dynamics of the Streptavidin-Biotin Complex

PubMed Central

Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

2015-01-01

Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer. PMID:25601277

Extended molecular dynamics of a c-kit promoter quadruplex

PubMed Central

Islam, Barira; Stadlbauer, Petr; Krepl, Miroslav; Koca, Jaroslav; Neidle, Stephen; Haider, Shozeb; Sponer, Jiri

2015-01-01

The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex. PMID:26245347

OUTFLOWS AND DARK BANDS AT ARCADE-LIKE ACTIVE REGION CORE BOUNDARIES

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

Scott, J. T.; Martens, P. C. H.; Tarr, L.

Observations from the EUV Imaging Spectrometer (EIS) on board Hinode have revealed outflows and non-thermal line broadening in low intensity regions at the edges of active regions (ARs). We use data from Hinode's EIS, Solar Dynamic Observatory's Atmospheric Imaging Assembly and Helioseismic and Magnetic Imager, and the Transition Region and Coronal Explorer instrument to investigate the boundaries of arcade-like AR cores for NOAA ARs 11112, 10978, and 9077. A narrow, low intensity region that is observed at the core's periphery as a dark band shows outflows and increased spectral line broadening. This dark band is found to exist for daysmore » and appears between the bright coronal loop structures of different coronal topologies. We find a case where the dark band region is formed between the magnetic field from emerging flux and the field of the pre-existing flux. A magnetic field extrapolation indicates that this dark band is coincident with the spine lines or magnetic separatrices in the extrapolated field. This occurs over unipolar regions where the brightened coronal field is separated in connectivity and topology. This separation does not appear to be infinitesimal and an initial estimate of the minimum distance of separation is found to be Almost-Equal-To 1.5-3.5 Mm.« less

Regionally strong feedbacks between the atmosphere and terrestrial biosphere

NASA Astrophysics Data System (ADS)

Green, Julia K.; Konings, Alexandra G.; Alemohammad, Seyed Hamed; Berry, Joseph; Entekhabi, Dara; Kolassa, Jana; Lee, Jung-Eun; Gentine, Pierre

2017-06-01

The terrestrial biosphere and atmosphere interact through a series of feedback loops. Variability in terrestrial vegetation growth and phenology can modulate fluxes of water and energy to the atmosphere, and thus affect the climatic conditions that in turn regulate vegetation dynamics. Here we analyse satellite observations of solar-induced fluorescence, precipitation, and radiation using a multivariate statistical technique. We find that biosphere-atmosphere feedbacks are globally widespread and regionally strong: they explain up to 30% of precipitation and surface radiation variance in regions where feedbacks occur. Substantial biosphere-precipitation feedbacks are often found in regions that are transitional between energy and water limitation, such as semi-arid or monsoonal regions. Substantial biosphere-radiation feedbacks are often present in several moderately wet regions and in the Mediterranean, where precipitation and radiation increase vegetation growth. Enhancement of latent and sensible heat transfer from vegetation accompanies this growth, which increases boundary layer height and convection, affecting cloudiness, and consequently incident surface radiation. Enhanced evapotranspiration can increase moist convection, leading to increased precipitation. Earth system models underestimate these precipitation and radiation feedbacks mainly because they underestimate the biosphere response to radiation and water availability. We conclude that biosphere-atmosphere feedbacks cluster in specific climatic regions that help determine the net CO2 balance of the biosphere.

Cosmological density fluctuations produced by vacuum strings

NASA Astrophysics Data System (ADS)

Vilenkin, A.

1981-04-01

Consideration is given to the possible role of vacuum domain strings produced in the grand unification phase transition in the early universe in the generation of the density fluctuations giving rise to galaxies. The cosmological evolution of the strings formed in the grand unification phase transition is analyzed, with attention given to possible mechanisms for the damping out of oscillations produced by tension in convoluted strings and closed loops. The cosmological density fluctuations introduced by infinite strings and closed loops smaller than the horizon are then shown to be capable of giving rise to mass condensations on a scale of approximately 10 to the 9th solar masses at the time of the decoupling of radiation from matter, around which the galaxies condense. Differences between the present theory and that suggested by Zel'dovich (1980) are pointed out, and it is noted that string formation at the grand unification phase transition is possible only if the manifold of the degenerate vacua of the gauge theory is not simply connected.

The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein

PubMed Central

Baumketner, Andrij

2012-01-01

Upon ATP binding, myosin motor protein is found in two alternative conformations, pre-recovery state M* and post-recovery state M**. The transition from one state to the other, known as the recovery stroke, plays a key role in the myosin functional cycle. Despite much recent research, the microscopic details of this transition remain elusive. A critical step in the recovery stroke is the rotation of the converter domain from “up” position in pre-recovery state to “down” position in post-recovery state that leads to the swing of the lever arm attached to it. In this work, we demonstrate that the two rotational states of the converter domain are determined by the interactions within a small structural motif in the force-generating region of the protein that can be accurately modeled on computers using atomic representation and explicit solvent. Our simulations show that the transition between the two states is controlled by a small helix (SH1) located next to the relay helix and relay loop. A small translation in the position of SH1 away from the relay helix is seen to trigger the transition from “up” state to “down” state. The transition is driven by a cluster of hydrophobic residues I687, F487 and F506 that make significant contributions to the stability of both states. The proposed mechanism agrees well with the available structural and mutational studies. PMID:22855405

Magnetic Braids in Eruptions of a Spiral Structure in the Solar Atmosphere

NASA Astrophysics Data System (ADS)

Huang, Zhenghua; Xia, Lidong; Nelson, Chris J.; Liu, Jiajia; Wiegelmann, Thomas; Tian, Hui; Klimchuk, James A.; Chen, Yao; Li, Bo

2018-02-01

We report on high-resolution imaging and spectral observations of eruptions of a spiral structure in the transition region, which were taken with the Interface Region Imaging Spectrograph, and the Atmospheric Imaging Assembly (AIA) and the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO). The eruption coincided with the appearance of two series of jets, with velocities comparable to the Alfvén speeds in their footpoints. Several pieces of evidence of magnetic braiding in the eruption are revealed, including localized bright knots, multiple well-separated jet threads, transition region explosive events, and the fact that all three of these are falling into the same locations within the eruptive structures. Through analysis of the extrapolated 3D magnetic field in the region, we found that the eruptive spiral structure corresponded well to locations of twisted magnetic flux tubes with varying curl values along their lengths. The eruption occurred where strong parallel currents, high squashing factors, and large twist numbers were obtained. The electron number density of the eruptive structure is found to be ∼3 × 1012 cm‑3, indicating that a significant amount of mass could be pumped into the corona by the jets. Following the eruption, the extrapolations revealed a set of seemingly relaxed loops, which were visible in the AIA 94 Å channel, indicating temperatures of around 6.3 MK. With these observations, we suggest that magnetic braiding could be part of the mechanisms explaining the formation of solar eruption and the mass and energy supplement to the corona.

Properties of a large-scale interplanetary loop structure as deduced from low-energy proton anisotropy and magnetic field measurements

NASA Technical Reports Server (NTRS)

Tranquille, C.; Sanderson, T. R.; Marsden, R. G.; Wenzel, K.-P.; Smith, E. J.

1987-01-01

Correlated particle and magnetic field measurements by the ISEE 3 spacecraft are presented for the loop structure behind the interplanetary traveling shock event of Nov. 12, 1978. Following the passage of the turbulent shock region, strong bidirectional streaming of low-energy protons is observed for approximately 6 hours, corresponding to a loop thickness of about 0.07 AU. This region is also characterized by a low relative variance of the magnetic field, a depressed proton intensity, and a reduction in the magnetic power spectral density. Using quasi-linear theory applied to a slab model, a value of 3 AU is derived for the mean free path during the passage of the closed loop. It is inferred from this observation that the proton regime associated with the loop structure is experiencing scatter-free transport and that either the length of the loop is approximately 3 AU between the sun and the earth or else the protons are being reflected at both ends of a smaller loop.

Autoinhibition and signaling by the switch II motif in the G-protein chaperone of a radical B12 enzyme.

PubMed

Lofgren, Michael; Koutmos, Markos; Banerjee, Ruma

2013-10-25

MeaB is an accessory GTPase protein involved in the assembly, protection, and reactivation of 5'-deoxyadenosyl cobalamin-dependent methylmalonyl-CoA mutase (MCM). Mutations in the human ortholog of MeaB result in methylmalonic aciduria, an inborn error of metabolism. G-proteins typically utilize conserved switch I and II motifs for signaling to effector proteins via conformational changes elicited by nucleotide binding and hydrolysis. Our recent discovery that MeaB utilizes an unusual switch III region for bidirectional signaling with MCM raised questions about the roles of the switch I and II motifs in MeaB. In this study, we addressed the functions of conserved switch II residues by performing alanine-scanning mutagenesis. Our results demonstrate that the GTPase activity of MeaB is autoinhibited by switch II and that this loop is important for coupling nucleotide-sensitive conformational changes in switch III to elicit the multiple chaperone functions of MeaB. Furthermore, we report the structure of MeaB·GDP crystallized in the presence of AlFx(-) to form the putative transition state analog, GDP·AlF4(-). The resulting crystal structure and its comparison with related G-proteins support the conclusion that the catalytic site of MeaB is incomplete in the absence of the GTPase-activating protein MCM and therefore unable to stabilize the transition state analog. Favoring an inactive conformation in the absence of the client MCM protein might represent a strategy for suppressing the intrinsic GTPase activity of MeaB in which the switch II loop plays an important role.

Multi-loop positivity of the planar $$ \\mathcal{N} $$ = 4 SYM six-point amplitude

DOE PAGES

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.; ...

2017-02-22

We study the six-point NMHV ratio function in planarmore » $$ \\mathcal{N} $$ = 4 SYM theory in the context of positive geometry. The Amplituhedron construction of the integrand for the amplitudes provides a kinematical region in which the integrand was observed to be positive. It is natural to conjecture that this property survives integration, i.e. that the final result for the ratio function is also positive in this region. Establishing such a result would imply that preserving positivity is a surprising property of the Minkowski contour of integration and it might indicate some deeper underlying structure. We find that the ratio function is positive everywhere we have tested it, including analytic results for special kinematical regions at one and two loops, as well as robust numerical evidence through five loops. There is also evidence for not just positivity, but monotonicity in a “radial” direction. We also investigate positivity of the MHV six-gluon amplitude. While the remainder function ceases to be positive at four loops, the BDS-like normalized MHV amplitude appears to be positive through five loops.« less

Spatiotemporal dynamics of the spin transition in [Fe (HB(tz)3) 2] single crystals

NASA Astrophysics Data System (ADS)

Ridier, Karl; Rat, Sylvain; Shepherd, Helena J.; Salmon, Lionel; Nicolazzi, William; Molnár, Gábor; Bousseksou, Azzedine

2017-10-01

The spatiotemporal dynamics of the spin transition have been thoroughly investigated in single crystals of the mononuclear spin-crossover (SCO) complex [Fe (HB (tz )3)2] (tz = 1 ,2 ,4-triazol-1-yl) by optical microscopy. This compound exhibits an abrupt spin transition centered at 334 K with a narrow thermal hysteresis loop of ˜1 K (first-order transition). Most single crystals of this compound reveal exceptional resilience upon repeated switching (several hundred cycles), which allowed repeatable and quantitative measurements of the spatiotemporal dynamics of the nucleation and growth processes to be carried out. These experiments revealed remarkable properties of the thermally induced spin transition: high stability of the thermal hysteresis loop, unprecedented large velocities of the macroscopic low-spin/high-spin phase boundaries up to 500 µm/s, and no visible dependency on the temperature scan rate. We have also studied the dynamics of the low-spin → high-spin transition induced by a local photothermal excitation generated by a spatially localized (Ø = 2 μ m ) continuous laser beam. Interesting phenomena have been evidenced both in quasistatic and dynamic conditions (e.g., threshold effects and long incubation periods, thermal activation of the phase boundary propagation, stabilization of the crystal in a stationary biphasic state, and thermal cutoff frequency). These measurements demonstrated the importance of thermal effects in the transition dynamics, and they enabled an accurate determination of the thermal properties of the SCO compound in the framework of a simple theoretical model.

Simulation of Z(3) walls and string production via bubble nucleation in a quark-hadron transition

NASA Astrophysics Data System (ADS)

Gupta, Uma Shankar; Mohapatra, Ranjita K.; Srivastava, Ajit M.; Tiwari, Vivek K.

2010-10-01

We study the dynamics of confinement-deconfinement phase transition in the context of relativistic heavy-ion collisions within the framework of effective models for the Polyakov loop order parameter. We study the formation of Z(3) walls and associated strings in the initial transition from the confining (hadronic) phase to the deconfining [quark-gluon plasma (QGP)] phase via the so-called Kibble mechanism. Essential physics of the Kibble mechanism is contained in a sort of domain structure arising after any phase transition which represents random variation of the order parameter at distances beyond the typical correlation length. We implement this domain structure by using the Polyakov loop effective model with a first order phase transition and confine ourselves with temperature/time ranges so that the first order confinement-deconfinement transition proceeds via bubble nucleation, leading to a well defined domain structure. The formation of Z(3) walls and associated strings results from the coalescence of QGP bubbles expanding in the confining background. We investigate the evolution of the Z(3) wall and string network. We also calculate the energy density fluctuations associated with Z(3) wall network and strings which decay away after the temperature drops below the quark-hadron transition temperature during the expansion of QGP. We discuss evolution of these quantities with changing temperature via Bjorken’s hydrodynamical model and discuss possible experimental signatures resulting from the presence of Z(3) wall network and associate strings.

Simulation of Z(3) walls and string production via bubble nucleation in a quark-hadron transition

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

Gupta, Uma Shankar; Tiwari, Vivek K.; Mohapatra, Ranjita K.

2010-10-01

We study the dynamics of confinement-deconfinement phase transition in the context of relativistic heavy-ion collisions within the framework of effective models for the Polyakov loop order parameter. We study the formation of Z(3) walls and associated strings in the initial transition from the confining (hadronic) phase to the deconfining [quark-gluon plasma (QGP)] phase via the so-called Kibble mechanism. Essential physics of the Kibble mechanism is contained in a sort of domain structure arising after any phase transition which represents random variation of the order parameter at distances beyond the typical correlation length. We implement this domain structure by using themore » Polyakov loop effective model with a first order phase transition and confine ourselves with temperature/time ranges so that the first order confinement-deconfinement transition proceeds via bubble nucleation, leading to a well defined domain structure. The formation of Z(3) walls and associated strings results from the coalescence of QGP bubbles expanding in the confining background. We investigate the evolution of the Z(3) wall and string network. We also calculate the energy density fluctuations associated with Z(3) wall network and strings which decay away after the temperature drops below the quark-hadron transition temperature during the expansion of QGP. We discuss evolution of these quantities with changing temperature via Bjorken's hydrodynamical model and discuss possible experimental signatures resulting from the presence of Z(3) wall network and associate strings.« less

Coverage criteria for test case generation using UML state chart diagram

NASA Astrophysics Data System (ADS)

Salman, Yasir Dawood; Hashim, Nor Laily; Rejab, Mawarny Md; Romli, Rohaida; Mohd, Haslina

2017-10-01

To improve the effectiveness of test data generation during the software test, many studies have focused on the automation of test data generation from UML diagrams. One of these diagrams is the UML state chart diagram. Test cases are generally evaluated according to coverage criteria. However, combinations of multiple criteria are required to achieve better coverage. Different studies used various number and types of coverage criteria in their methods and approaches. The objective of this paper to propose suitable coverage criteria for test case generation using UML state chart diagram especially in handling loops. In order to achieve this objective, this work reviewed previous studies to present the most practical coverage criteria combinations, including all-states, all-transitions, all-transition-pairs, and all-loop-free-paths coverage. Calculation to determine the coverage percentage of the proposed coverage criteria were presented together with an example has they are applied on a UML state chart diagram. This finding would be beneficial in the area of test case generating especially in handling loops in UML state chart diagram.

Electron acceleration in solar flares and the transition from nonthermal to thermal hard X-ray phases

NASA Technical Reports Server (NTRS)

Smith, D. F.

1985-01-01

Observations are reviewed which indicate that hard X-rays during the impulsive phase of a flare typically start with a primarily nonthermal phase which undergoes a transition to a primarily thermal phase as the flare progresses. Recent theoretical work on the modified two-stream instability as an efficient electron accelerator and modeling of thermal hard X-ray sources is considered. A scenario which is termed the dissipative thermal model is proposed to explain the observations. Fast tearing modes occurring in a loop give rise to cross-field ion motion. This in turn excites the modified two-stream instability which converts about 50 percent of the ion energy into accelerated electrons along the loop as long as the plasma beta is less than 0.3. These electrons impact the chromosphere and boil off a part of it which rises up the loop. This density increase coupled with the temperature increase due to tearing causes the beta to increase beyond 0.3 and efficient electron acceleration ceases. This leads to the primarily thermal phase.

Fast de novo discovery of low-energy protein loop conformations.

PubMed

Wong, Samuel W K; Liu, Jun S; Kou, S C

2017-08-01

In the prediction of protein structure from amino acid sequence, loops are challenging regions for computational methods. Since loops are often located on the protein surface, they can have significant roles in determining protein functions and binding properties. Loop prediction without the aid of a structural template requires extensive conformational sampling and energy minimization, which are computationally difficult. In this article we present a new de novo loop sampling method, the Parallely filtered Energy Targeted All-atom Loop Sampler (PETALS) to rapidly locate low energy conformations. PETALS explores both backbone and side-chain positions of the loop region simultaneously according to the energy function selected by the user, and constructs a nonredundant ensemble of low energy loop conformations using filtering criteria. The method is illustrated with the DFIRE potential and DiSGro energy function for loops, and shown to be highly effective at discovering conformations with near-native (or better) energy. Using the same energy function as the DiSGro algorithm, PETALS samples conformations with both lower RMSDs and lower energies. PETALS is also useful for assessing the accuracy of different energy functions. PETALS runs rapidly, requiring an average time cost of 10 minutes for a length 12 loop on a single 3.2 GHz processor core, comparable to the fastest existing de novo methods for generating an ensemble of conformations. Proteins 2017; 85:1402-1412. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Overview of the Martian nightside suprathermal electron depletions

NASA Astrophysics Data System (ADS)

Steckiewicz, Morgane; Garnier, Philippe; André, Nicolas; Mitchell, David; Andersson, Laila; Penou, Emmanuel; Beth, Arnaud; Fedorov, Andrei; Sauvaud, Jean-André; Mazelle, Christian; Lillis, Robert; Brain, David; Espley, Jared; McFadden, James; Halekas, Jasper; Luhmann, Janet; Soobiah, Yasir; Jakosky, Bruce

2017-04-01

Nightside suprathermal electron depletions have been observed at Mars by three spacecraft to date: Mars Global Surveyor (MGS), Mars EXpress (MEX) and the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission. The global coverage of Mars by MEX and MGS at high altitudes (above approximately 250 km) revealed that these structures were mostly observed above strong crustal magnetic field sources which exclude the electrons coming from the dayside or from the tail. The MAVEN orbit now offers the possibility to observe this phenomenon at low altitudes, down to 125 km. A transition region near 170 km has been detected separating the collisional region where electron depletions are mainly due to electron absorption by atmospheric CO2 and the collisionless region where they are mainly due to closed crustal magnetic field loops. MAVEN is now in its third year of data recording and has covered a large range of latitudes, local times and solar zenith angles at low altitudes (<900km) in the nightside. These observations enable us to estimate where the EUV terminator is located, based on the observation that no electron depletions are expected above its location. Through this study the location of the EUV terminator appears to be raised on average by 125 km above the location of the geometrical terminator. However, this location is likely to be different between the dawn and dusk terminator and to vary throughout the different Martian seasons. This coverage has also allowed the observation of regions with recurrent absence of electron depletions even below the transition region near 170 km altitude. These 'no-depletion' areas are localized above the least magnetized area of Mars both in the Northern and Southern hemispheres. A modification in the CO2 density, gravity waves, or the presence of current sheets are potential drivers for that phenomenon.

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.

PubMed

Jiang, Jun; Aduri, Raviprasad; Chow, Christine S; SantaLucia, John

2014-04-01

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson-Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity.

Complex band structures of transition metal dichalcogenide monolayers with spin-orbit coupling effects

NASA Astrophysics Data System (ADS)

Szczęśniak, Dominik; Ennaoui, Ahmed; Ahzi, Saïd

2016-09-01

Recently, the transition metal dichalcogenides have attracted renewed attention due to the potential use of their low-dimensional forms in both nano- and opto-electronics. In such applications, the electronic and transport properties of monolayer transition metal dichalcogenides play a pivotal role. The present paper provides a new insight into these essential properties by studying the complex band structures of popular transition metal dichalcogenide monolayers (MX 2, where M  =  Mo, W; X  =  S, Se, Te) while including spin-orbit coupling effects. The conducted symmetry-based tight-binding calculations show that the analytical continuation from the real band structures to the complex momentum space leads to nonlinear generalized eigenvalue problems. Herein an efficient method for solving such a class of nonlinear problems is presented and yields a complete set of physically relevant eigenvalues. Solutions obtained by this method are characterized and classified into propagating and evanescent states, where the latter states manifest not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gap of MX 2 monolayers, where electrons can directly tunnel between the band gap edges. To describe these tunneling currents, decay behavior of electronic states in the forbidden energy region is elucidated and their importance within the ballistic transport regime is briefly discussed.

Static and Impulsive Models of Solar Active Regions

NASA Technical Reports Server (NTRS)

Patsourakos, S.; Klimchuk, James A.

2008-01-01

The physical modeling of active regions (ARs) and of the global coronal is receiving increasing interest lately. Recent attempts to model ARs using static equilibrium models were quite successful in reproducing AR images of hot soft X-ray (SXR) loops. They however failed to predict the bright EUV warm loops permeating ARs: the synthetic images were dominated by intense footpoint emission. We demonstrate that this failure is due to the very weak dependence of loop temperature on loop length which cannot simultaneously account for both hot and warm loops in the same AR. We then consider time-dependent AR models based on nanoflare heating. We demonstrate that such models can simultaneously reproduce EUV and SXR loops in ARs. Moreover, they predict radial intensity variations consistent with the localized core and extended emissions in SXR and EUV AR observations respectively. We finally show how the AR morphology can be used as a gauge of the properties (duration, energy, spatial dependence, repetition time) of the impulsive heating.

Evaluation of T-111 forced-convection loop tested with lithium at 1370 C. [free convection

NASA Technical Reports Server (NTRS)

Devan, J. H.; Long, E. L., Jr.

1975-01-01

A T-111 alloy (Ta-8% W-2% Hf) forced-convection loop containing molten lithium was operated 3000 hr at a maximum temperature of 1370 C. Flow velocities up to 6.3 m/sec were used, and the results of this forced-convection loop are very similar to those observed in lower velocity thermal-convection loops of T-111 containing lithium. Weight changes were determined at 93 positions around the loop. The maximum dissolution rate occurred at the maximum wall temperature of the loop and was less than 1.3 microns/year. Mass transfer of hafnium, nitrogen, and, to a lesser extent, carbon occurred from the hotter to cooler regions. Exposed surfaces in the highest temperature region were found to be depleted in hafnium to a depth of 60 microns with no detectable change in tungsten content. There was some loss in room-temperature tensile strength for specimens exposed to lithium at 1370 C, attributable to depletion of hafnium and nitrogen and to attendant grain growth.

Synthesis and piezoelectric properties of (1 - x)Bi0.5(Na0.8K0.2)0.5TiO3-xSr2ZrTiO6 ceramics

NASA Astrophysics Data System (ADS)

Onishi, Ryo; Ogawa, Hirotaka; Iida, Daiki; Kan, Akinori

2017-10-01

The effects of Sr2ZrTiO6 (SZT) addition on the piezoelectric properties of (1 - x)Bi0.5(Na0.8K0.2)0.5TiO3 (BNKT)-xSZT ceramics were characterized in this study. The X-ray powder diffraction (XRPD) profiles and Raman spectra of the ceramics in the composition range of 0-0.02 implies the presence of morphotropic phase boundary (MPB) which consists of the rhombohedral and tetragonal phases. Moreover, the temperature dependence of dielectric loss indicated a presence of the ferroelectric-relaxor transition temperature (T F-R) of around 75 °C for x = 0.005 and the temperature dependence shifted to a lower temperature at x = 0.01. The temperature dependence of the P-E hysteresis loop of the ceramics at the compositions of x = 0.005-0.02 showed pinched hysteresis loops above T F-R. Regarding the piezoelectric constant (d 33), it was increased by SZT addition in the MPB region (x = 0-0.01) and the highest d 33 of 202 pC/N was obtained at the composition of x = 0.0025. The S-E unipolar loop was also evaluated, the strain of the ceramic increased up to x = 0.02; and the highest d33* = 436 pm/V was obtained at the composition of x = 0.02.

Comparative PIV and LDA studies of Newtonian and non-Newtonian flows in an agitated tank.

PubMed

Story, Anna; Jaworski, Zdzisław; Simmons, Mark J; Nowak, Emilia

2018-01-01

The paper presents results of an experimental study of the fluid velocity field in a stirred tank equipped with a Prochem Maxflo T (PMT) type impeller which was rotating at a constant frequency of N  = 4.1 or 8.2 s -1 inducing transitional ( Re  = 499 or 1307) or turbulent ( Re  = 2.43 × 10 4 ) flow of the fluid. The experiments were performed for a Newtonian fluid (water) and a non-Newtonian fluid (0.2 wt% aqueous solution of carboxymethyl cellulose, CMC) exhibiting mild viscoelastic properties. Measurements were carried out using laser light scattering on tracer particles which follow the flow (2-D PIV). For both the water and the CMC solution one primary and two secondary circulation loops were observed within the fluid volume; however, the secondary loops were characterized by much lower intensity. The applied PMT-type impeller produced in the Newtonian fluid an axial primary flow, whilst in the non-Newtonian fluid the flow was more radial. The results obtained in the form of the local mean velocity components were in satisfactory agreement with the literature data from LDA. Distribution of the shear rate in the studied system was also analyzed. For the non-Newtonian fluid an area was computed where the elastic force dominates over the viscous one. The area was nearly matching the region occupied by the primary circulation loop.

Monte Carlo Analysis as a Trajectory Design Driver for the Transiting Exoplanet Survey Satellite (TESS) Mission

NASA Technical Reports Server (NTRS)

Nickel, Craig; Parker, Joel; Dichmann, Don; Lebois, Ryan; Lutz, Stephen

2016-01-01

The Transiting Exoplanet Survey Satellite (TESS) will be injected into a highly eccentric Earth orbit and fly 3.5 phasing loops followed by a lunar flyby to enter a mission orbit with lunar 2:1 resonance. Through the phasing loops and mission orbit, the trajectory is significantly affected by lunar and solar gravity. We have developed a trajectory design to achieve the mission orbit and meet mission constraints, including eclipse avoidance and a 30-year geostationary orbit avoidance requirement. A parallelized Monte Carlo simulation was performed to validate the trajectory after injecting common perturbations, including launch dispersions, orbit determination errors, and maneuver execution errors. The Monte Carlo analysis helped identify mission risks and is used in the trajectory selection process.

Transition Region and Chromospheric Signatures of Impulsive Heating Events. I. Observations

NASA Astrophysics Data System (ADS)

Warren, Harry P.; Reep, Jeffrey W.; Crump, Nicholas A.; Simões, Paulo J. A.

2016-09-01

We exploit the high spatial resolution and high cadence of the Interface Region Imaging Spectrograph (IRIS) to investigate the response of the transition region and chromosphere to energy deposition during a small flare. Simultaneous observations from the Reuven Ramaty High Energy Solar Spectroscopic Imager provide constraints on the energetic electrons precipitating into the flare footpoints, while observations of the X-Ray Telescope, Atmospheric Imaging Assembly, and Extreme Ultraviolet Imaging Spectrometer (EIS) allow us to measure the temperatures and emission measures from the resulting flare loops. We find clear evidence for heating over an extended period on the spatial scale of a single IRIS pixel. During the impulsive phase of this event, the intensities in each pixel for the Si IV 1402.770 Å, C II 1334.535 Å, Mg II 2796.354 Å, and O I 1355.598 Å emission lines are characterized by numerous small-scale bursts typically lasting 60 s or less. Redshifts are observed in Si IV, C II, and Mg II during the impulsive phase. Mg II shows redshifts during the bursts and stationary emission at other times. The Si IV and C II profiles, in contrast, are observed to be redshifted at all times during the impulsive phase. These persistent redshifts are a challenge for one-dimensional hydrodynamic models, which predict only short-duration downflows in response to impulsive heating. We conjecture that energy is being released on many small-scale filaments with a power-law distribution of heating rates.

Evidence for Widespread Cooling in an Active Region Observed with the SDO Atmospheric Imaging Assembly

NASA Technical Reports Server (NTRS)

Viall, Nicholeen M.; Klimchuk, James A.

2012-01-01

A well known behavior of EUV light curves of discrete coronal loops is that the peak intensities of cooler channels or spectral lines are reached at progressively later times. This time lag is understood to be the result of hot coronal loop plasma cooling through these lower respective temperatures. However, loops typically comprise only a minority of the total emission in active regions. Is this cooling pattern a common property of active region coronal plasma, or does it only occur in unique circumstances, locations, and times? The new SDO/AIA data provide a wonderful opportunity to answer this question systematically for an entire active region. We measure the time lag between pairs of SDO/AIA EUV channels using 24 hours of images of AR 11082 observed on 19 June 2010. We find that there is a time-lag signal consistent with cooling plasma, just as is usually found for loops, throughout the active region including the diffuse emission between loops for the entire 24 hour duration. The pattern persists consistently for all channel pairs and choice of window length within the 24 hour time period, giving us confidence that the plasma is cooling from temperatures of greater than 3 MK, and sometimes exceeding 7 MK, down to temperatures lower than approx. 0.8 MK. This suggests that the bulk of the emitting coronal plasma in this active region is not steady; rather, it is dynamic and constantly evolving. These measurements provide crucial constraints on any model which seeks to describe coronal heating.

Gauge-invariant effective potential: Equilibrium and nonequilibrium aspects

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

Boyanovsky, D.; Brahm, D.; Holman, R.

1996-07-01

We propose a gauge-invariant formulation of the effective potential in terms of a gauge-invariant order parameter, for the Abelian Higgs model. The one-loop contribution at zero and finite temperature is computed explicitly, and the leading terms in the high temperature expansion are obtained. The result is contrasted with the effective potential obtained in several covariant gauge-fixing schemes, and the gauge-invariant quantities that can be reliably extracted from these are identified. It is pointed out that the gauge-invariant effective potential in the one-loop approximation is complex for {ital all} {ital values} of the order parameter between the maximum and the minimummore » of the tree level potential, both at zero and nonzero temperatures. The imaginary part is related to long-wavelength instabilities towards phase separation. We study the real-time dynamics of initial states in the spinodal region, and relate the imaginary part of the effective potential to the growth rate of equal-time gauge-invariant correlation functions in these states. We conjecture that the spinodal instabilities may play a role in nonequilibrium processes {ital inside} the nucleating bubbles if the transition is first order. {copyright} {ital 1996 The American Physical Society.}« less

Current systems of coronal loops in 3D MHD simulations

NASA Astrophysics Data System (ADS)

Warnecke, J.; Chen, F.; Bingert, S.; Peter, H.

2017-11-01

Aims: We study the magnetic field and current structure associated with a coronal loop. Through this we investigate to what extent the assumptions of a force-free magnetic field break down and where they might be justified. Methods: We analyze a three-dimensional (3D) magnetohydrodynamic (MHD) model of the solar corona in an emerging active region with the focus on the structure of the forming coronal loops. The lower boundary of this simulation is taken from a model of an emerging active region. As a consequence of the emerging magnetic flux and the horizontal motions at the surface a coronal loop forms self-consistently. We investigate the current density along magnetic field lines inside (and outside) this loop and study the magnetic and plasma properties in and around this loop. The loop is defined as the bundle of field lines that coincides with enhanced emission in extreme UV. Results: We find that the total current along the emerging loop changes its sign from being antiparallel to parallel to the magnetic field. This is caused by the inclination of the loop together with the footpoint motion. Around the loop, the currents form a complex non-force-free helical structure. This is directly related to a bipolar current structure at the loop footpoints at the base of the corona and a local reduction of the background magnetic field (I.e., outside the loop) caused by the plasma flow into and along the loop. Furthermore, the locally reduced magnetic pressure in the loop allows the loop to sustain a higher density, which is crucial for the emission in extreme UV. The action of the flow on the magnetic field hosting the loop turns out to also be responsible for the observed squashing of the loop. Conclusions: The complex magnetic field and current system surrounding it can only be modeled in 3D MHD models where the magnetic field has to balance the plasma pressure. A one-dimensional coronal loop model or a force-free extrapolation cannot capture the current system and the complex interaction of the plasma and the magnetic field in the coronal loop, despite the fact that the loop is under low-β conditions.

Regionally Strong Feedbacks Between the Atmosphere and Terrestrial Biosphere

NASA Technical Reports Server (NTRS)

Green, Julia K.; Konings, Alexandra G.; Alemohammad, Seyed Hamed; Lee, Jung-Eun; Berry, Joseph; Entekhabi, Dara; Kolassa, Jana; Gentine, Pierre

2017-01-01

The terrestrial biosphere and atmosphere interact through a series of feedback loops. Variability in terrestrial vegetation growth and phenology can modulate fluxes of water and energy to the atmosphere, and thus affect the climatic conditions that in turn regulate vegetation dynamics. Here we analyze satellite observations of solar-induced fluorescence, precipitation, and radiation using a multivariate statistical technique. We find that biosphere-atmosphere feedbacks are globally widespread and regionally strong: they explain up to 30 of precipitation and surface radiation variance. Substantial biosphere-precipitation feedbacks are often found in regions that are transitional between energy and water limitation, such as semi-arid or monsoonal regions. Substantial biosphere-radiation feedbacks are often present in several moderately wet regions and in the Mediterranean, where precipitation and radiation increase vegetation growth. Enhancement of latent and sensible heat transfer from vegetation accompanies this growth, which increases boundary layer height and convection, affecting cloudiness, and consequently incident surface radiation. Enhanced evapotranspiration can increase moist convection, leading to increased precipitation. Earth system models underestimate these precipitation and radiation feedbacks mainly because they underestimate the biosphere response to radiation and water availability. We conclude that biosphere-atmosphere feedbacks cluster in specific climatic regions that help determine the net CO2 balance of the biosphere.

Complexity in Matuyama-Brunhes polarity transitions from North Atlantic IODP/ODP deep-sea sites

NASA Astrophysics Data System (ADS)

Channell, J. E. T.

2017-06-01

Integrated Ocean Drilling Program (IODP) Expedition 303 to the North Atlantic provided 16 records of the Matuyama-Brunhes polarity transition (MBT), based on u-channel and discrete samples, from holes drilled at three sites (Sites U1304, U1305 and U1306) that have mean Brunhes sedimentation rates of 16-18 cm/kyr. The MBT occurs during the transition from marine isotope stage (MIS) 19c to MIS 18e, with mid-point at ∼773 ka, and a transition duration of ∼8 kyr. Combining the new MBT records, including one new record for the top Jaramillo, with previously published North Atlantic MBT records (ODP Sites 983, 984 and 1063) yields a total of more than 20 high-sedimentation-rate polarity transition records. The MBT yields a repetitive pattern of transitional field states as virtual geomagnetic poles (VGPs) move from high southern latitudes to loop over the Pacific, group in NE Asia, and transit into the mid-latitude South Atlantic before reaching high latitudes in the Northern Hemisphere. The VGPs for the top Jaramillo transition feature a loop over the Pacific, then a NE Asia group before transit over the Indian Ocean to high southerly latitudes. The North Atlantic MBT records described here contrast with longitudinally-constrained VGP paths for the MBT, indicating that relatively low sedimentation rate (∼4 cm/kyr) records of the MBT are heavily smoothed by the remanence acquisition process and do not adequately represent the MBT field. The VGPs at the MBT and top Jaramillo, as measured in the North Atlantic, have similarities with excursion (Iceland Basin) VGP paths, and were apparently guided by maxima in downward vertical flux similar to those seen in the modern non-dipole (ND) field, implying longevity in ND features through time.

Dynamics of the active site loops in catalyzing aminoacylation reaction in seryl and histidyl tRNA synthetases.

PubMed

Dutta, Saheb; Kundu, Soumya; Saha, Amrita; Nandi, Nilashis

2018-03-01

Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ( mk SerRS) and histidyl tRNA synthetases from Thermus thermophilus ( tt HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain. Catalytic residues of the loops form a network of interaction with the substrates to form a reactive state. The loops undergo transitions between closed state and open state and the relaxation of the constituent residues occurs in femtosecond to nanosecond time scale. Order parameters are higher for constituent catalytic residues which form a specific network of interaction with the substrates to form a reactive state compared to the Gly residues within the loop. The development of interaction is supported from mutation studies where the catalytic domain with mutated loop exhibits unfavorable binding energy with the substrates. During the open-close motion of the loops, the catalytic residues make relaxation by ultrafast librational motion as well as fast diffusive motion and subsequently relax rather slowly via slower diffusive motion. The Gly residues act as a hinge to facilitate the loop closing and opening by their faster relaxation behavior. The role of bound water is analyzed by comparing implicit solvent-based and explicit solvent-based simulations. Loops fail to form catalytically competent geometry in absence of water. The present result, for the first time reveals the nature of the active site loop dynamics in aaRS and their influence on catalysis.

Arsenic trioxide promotes mitochondrial DNA mutation and cell apoptosis in primary APL cells and NB4 cell line.

PubMed

Meng, Ran; Zhou, Jin; Sui, Meng; Li, ZhiYong; Feng, GuoSheng; Yang, BaoFeng

2010-01-01

This study aimed to investigate the effects of arsenic trioxide (As(2)O(3)) on the mitochondrial DNA (mtDNA) of acute promyelocytic leukemia (APL) cells. The NB4 cell line was treated with 2.0 micromol/L As(2)O(3) in vitro, and the primary APL cells were treated with 2.0 micromol/L As(2)O(3) in vitro and 0.16 mg kg(-1) d(-1) As(2)O(3) in vivo. The mitochondrial DNA of all the cells above was amplified by PCR, directly sequenced and analyzed by Sequence Navigatore and Factura software. The apoptosis rates were assayed by flow cytometry. Mitochondrial DNA mutation in the D-loop region was found in NB4 and APL cells before As(2)O(3) use, but the mutation spots were remarkably increased after As(2)O(3) treatment, which was positively correlated to the rates of cellular apoptosis, the correlation coefficient: r (NB4-As2O3)=0.973818, and r (APL-As2O3)=0.934703. The mutation types include transition, transversion, codon insertion or deletion, and the mutation spots in all samples were not constant and regular. It is revealed that As(2)O(3) aggravates mtDNA mutation in the D-loop region of acute promyelocytic leukemia cells both in vitro and in vivo. Mitochondrial DNA might be one of the targets of As(2)O(3) in APL treatment.

Solar burst precursors and energy build-up at microwave wavelengths

NASA Technical Reports Server (NTRS)

Lang, Kenneth R.; Wilson, Robert F.

1986-01-01

We summarize high-resolution microwave observations (VLA) of heating and magnetic triggering in coronal loops. Magnetic changes that precede solar eruptions on time scales of tens of minutes involve primarily emerging coronal loops and the interaction of two or more loops. Thermal cyclotron lines have been detected in coronal loops, suggesting the presence of hot current sheets that enhance emission from relatively thin layers of enhanced temperature and constant magnetic field. These current sheets may play a role in the excitation of solar bursts. A filament-associated source with a high brightness temperature and steep radiation spectrum occurs above a region of apparently weak photospheric field. This source might be attributed to currents that enhance coronal magnetic fields. Compact (phi=5 sec) transient sources with lifetimes of 30 to 60 minutes have also been detected in regions of apparently weak photospheric field. We conclude by comparing VLA observations of coronal loops with simultaneous SMM-XRP observations.

Solar burst precursors and energy build-up at microwave wavelengths

NASA Astrophysics Data System (ADS)

Lang, Kenneth R.; Wilson, Robert F.

We summarize high-resolution microwave observations (VLA) of heating and magnetic triggering in coronal loops. Magnetic changes that precede solar eruptions on time scales of tens of minutes involve primarily emerging coronal loops and the interaction of two or more loops. Thermal cyclotron lines have been detected in coronal loops, suggesting the presence of hot current sheets that enhance emission from relatively thin layers of enhanced temperature and constant magnetic field. These current sheets may play a role in the excitation of solar bursts. A filament-associated source with a high brightness temperature and steep radiation spectrum occurs above a region of apparently weak photospheric field. This source might be attributed to currents that enhance coronal magnetic fields. Compact (phi=5 sec) transient sources with lifetimes of 30 to 60 minutes have also been detected in regions of apparently weak photospheric field. We conclude by comparing VLA observations of coronal loops with simultaneous SMM-XRP observations.

Manipulations of extracellular Loop 2 in α1 GlyR ultra-sensitive ethanol receptors (USERs) enhance receptor sensitivity to isoflurane, ethanol, and lidocaine, but not propofol

PubMed Central

Naito, Anna; Muchhala, Karan H.; Trang, Janice; Asatryan, Liana; Trudell, James R.; Homanics, Gregg E.; Alkana, Ronald L.; Davies, Daryl L.

2015-01-01

We recently developed Ultra-Sensitive Ethanol Receptors (USERs) as a novel tool for investigation of single receptor subunit populations sensitized to extremely low ethanol concentrations that do not affect other receptors in the nervous system. To this end, we found that mutations within the extracellular Loop 2 region of glycine receptors (GlyRs) and γ-aminobutyric acid type A receptors (GABAARs) can significantly increase receptor sensitivity to micro-molar concentrations of ethanol resulting in up to a 100-fold increase in ethanol sensitivity relative to wild type (WT) receptors. The current study investigated: 1) Whether structural manipulations of Loop 2 in α1 GlyRs could similarly increase receptor sensitivity to other anesthetics; and 2) If mutations exclusive to the C-terminal end of Loop 2 are sufficient to impart these changes. We expressed α1 GlyR USERs in Xenopus oocytes and tested the effects of three classes of anesthetics, isoflurane (volatile), propofol (intravenous), and lidocaine (local), known to enhance glycine-induced chloride currents using two-electrode voltage clamp electrophysiology. Loop 2 mutations produced a significant 10-fold increase in isoflurane and lidocaine sensitivity, but no increase in propofol sensitivity compared to WT α1 GlyRs. Interestingly, we also found that structural manipulations in the C-terminal end of Loop 2 were sufficient and selective for α1 GlyR modulation by ethanol, isoflurane, and lidocaine. These studies are the first to report the extracellular region of α1 GlyRs as a site of lidocaine action. Overall, the findings suggest that Loop 2 of α1 GlyRs is a key region that mediates isoflurane and lidocaine modulation. Moreover, the results identify important amino acids in Loop 2 that regulate isoflurane, lidocaine, and ethanol action. Collectively, these data indicate the commonality of the sites for isoflurane, lidocaine, and ethanol action, and the structural requirements for allosteric modulation on α1 GlyRs within the extracellular Loop 2 region. PMID:25827497

Flight Testing of the Capillary Pumped Loop 3 Experiment

NASA Technical Reports Server (NTRS)

Ottenstein, Laura; Butler, Dan; Ku, Jentung; Cheung, Kwok; Baldauff, Robert; Hoang, Triem

2002-01-01

The Capillary Pumped Loop 3 (CAPL 3) experiment was a multiple evaporator capillary pumped loop experiment that flew in the Space Shuttle payload bay in December 2001 (STS-108). The main objective of CAPL 3 was to demonstrate in micro-gravity a multiple evaporator capillary pumped loop system, capable of reliable start-up, reliable continuous operation, and heat load sharing, with hardware for a deployable radiator. Tests performed on orbit included start-ups, power cycles, low power tests (100 W total), high power tests (up to 1447 W total), heat load sharing, variable/fixed conductance transition tests, and saturation temperature change tests. The majority of the tests were completed successfully, although the experiment did exhibit an unexpected sensitivity to shuttle maneuvers. This paper describes the experiment, the tests performed during the mission, and the test results.

Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation.

PubMed

Cressman, William J; Beckett, Dorothy

2016-01-19

Allosteric coupling in proteins is ubiquitous but incompletely understood, particularly in systems characterized by coupling over large distances. Binding of the allosteric effector, bio-5'-AMP, to the Escherichia coli biotin protein ligase, BirA, enhances the protein's dimerization free energy by -4 kcal/mol. Previous studies revealed that disorder-to-order transitions at the effector binding and dimerization sites, which are separated by 33 Å, are integral to functional coupling. Perturbations to the transition at the ligand binding site alter both ligand binding and coupled dimerization. Alanine substitutions in four loops on the dimerization surface yield a range of energetic effects on dimerization. A glycine to alanine substitution at position 142 in one of these loops results in a complete loss of allosteric coupling, disruption of the disorder-to-order transitions at both functional sites, and a decreased affinity for the effector. In this work, allosteric communication between the effector binding and dimerization surfaces in BirA was further investigated by performing isothermal titration calorimetry measurements on nine proteins with alanine substitutions in three dimerization surface loops. In contrast to BirAG142A, at 20 °C all variants bind to bio-5'-AMP with free energies indistinguishable from that measured for wild-type BirA. However, the majority of the variants exhibit altered heat capacity changes for effector binding. Moreover, the ΔCp values correlate with the dimerization free energies of the effector-bound proteins. These thermodynamic results, combined with structural information, indicate that allosteric activation of the BirA monomer involves formation of a network of intramolecular interactions on the dimerization surface in response to bio-5'-AMP binding at the distant effector binding site.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.

PubMed

Islam, Barira; Stadlbauer, Petr; Gil-Ley, Alejandro; Pérez-Hernández, Guillermo; Haider, Shozeb; Neidle, Stephen; Bussi, Giovanni; Banas, Pavel; Otyepka, Michal; Sponer, Jiri

2017-06-13

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

PubMed Central

2017-01-01

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

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

Koppole, Sampath; Smith, Jeremy C; Fischer, S.

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates {approx} 65{sup o}. Simultaneous with this 'recovery stroke', myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 {angstrom}-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transitionmore » at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.« less

Beam current sensor

DOEpatents

Kuchnir, M.; Mills, F.E.

1984-09-28

A current sensor for measuring the dc component of a beam of charged particles employs a superconducting pick-up loop probe, with twisted superconducting leads in combination with a Superconducting Quantum Interference Device (SQUID) detector. The pick-up probe is in the form of a single-turn loop, or a cylindrical toroid, through which the beam is directed and within which a first magnetic flux is excluded by the Meisner effect. The SQUID detector acts as a flux-to-voltage converter in providing a current to the pick-up loop so as to establish a second magnetic flux within the electrode which nulls out the first magnetic flux. A feedback voltage within the SQUID detector represents the beam current of the particles which transit the pick-up loop. Meisner effect currents prevent changes in the magnetic field within the toroidal pick-up loop and produce a current signal independent of the beam's cross-section and its position within the toroid, while the combination of superconducting elements provides current measurement sensitivities in the nano-ampere range.

Beam current sensor

DOEpatents

Kuchnir, Moyses; Mills, Frederick E.

1987-01-01

A current sensor for measuring the DC component of a beam of charged particles employs a superconducting pick-up loop probe, with twisted superconducting leads in combination with a Superconducting Quantum Interference Device (SQUID) detector. The pick-up probe is in the form of a single-turn loop, or a cylindrical toroid, through which the beam is directed and within which a first magnetic flux is excluded by the Meisner effect. The SQUID detector acts as a flux-to-voltage converter in providing a current to the pick-up loop so as to establish a second magnetic flux within the electrode which nulls out the first magnetic flux. A feedback voltage within the SQUID detector represents the beam current of the particles which transit the pick-up loop. Meisner effect currents prevent changes in the magnetic field within the toroidal pick-up loop and produce a current signal independent of the beam's cross-section and its position within the toroid, while the combination of superconducting elements provides current measurement sensitivites in the nano-ampere range.

EUV SPECTRAL LINE FORMATION AND THE TEMPERATURE STRUCTURE OF ACTIVE REGION FAN LOOPS: OBSERVATIONS WITH HINODE/EIS AND SDO/AIA

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

Brooks, David H.; Young, Peter R.; Warren, Harry P., E-mail: dhbrooks@ssd5.nrl.navy.mil

2011-04-01

With the aim of studying active region fan loops using observations from the Hinode EUV Imaging Spectrometer (EIS) and Solar Dynamics Observatory Atmospheric Imaging Assembly (AIA), we investigate a number of inconsistencies in modeling the absolute intensities of Fe VIII and Si VII lines, and address why spectroheliograms formed from these lines look very similar despite the fact that ionization equilibrium calculations suggest that they have significantly different formation temperatures: log(T{sub e} /K) = 5.6 and 5.8, respectively. It is important to resolve these issues because confidence has been undermined in their use for differential emission measure (DEM) analysis, andmore » Fe VIII is the main contributor to the AIA 131 A channel at low temperatures. Furthermore, the strong Fe VIII 185.213 A and Si VII 275.368 A lines are the best EIS lines to use for velocity studies in the transition region, and for assigning the correct temperature to velocity measurements in the fans. We find that the Fe VIII 185.213 A line is particularly sensitive to the slope of the DEM, leading to disproportionate changes in its effective formation temperature. If the DEM has a steep gradient in the log(T{sub e} /K) = 5.6-5.8 temperature range, or is strongly peaked, Fe VIII 185.213 A and Si VII 275.368 A will be formed at the same temperature. We show that this effect explains the similarity of these images in the fans. Furthermore, we show that the most recent ionization balance compilations resolve the discrepancies in absolute intensities. With these difficulties overcome, we combine EIS and AIA data to determine the temperature structure of a number of fan loops and find that they have peak temperatures of 0.8-1.2 MK. The EIS data indicate that the temperature distribution has a finite (but narrow) width < log ({sigma}{sub Te}/K) = 5.5 which, in one detailed case, is found to broaden substantially toward the loop base. AIA and EIS yield similar results on the temperature, emission measure magnitude, and thermal distribution in the fans, though sometimes the AIA data suggest a relatively larger thermal width. The result is that both the Fe VIII 185.213 A and Si VII 275.368 A lines are formed at log(T{sub e} /K){approx} 5.9 in the fans, and the AIA 131 A response also shifts to this temperature.« less

Upwelling and downwelling induced by mesoscale circulation in the DeSoto Canyon region

NASA Astrophysics Data System (ADS)

Nguyen, T. T.; Chassignet, E.; Morey, S. L.; Dukhovskoy, D. S.

2014-12-01

Ocean dynamics are complex over irregular topography areas, and the northeastern Gulf of Mexico, specifically the DeSoto Canyon region, is a challenge for modelers and oceanographers. Vertical movement of waters, especially upwelling, is observed to take place over the canyon's head and along the coast; however, it is not well understood. We focus on upwelling/downwelling processes induced by the Loop Current and its associated eddy field using multi-decadal Hybrid Coordinate Ocean Model simulations. The Loop Current, part of the Gulf Stream, can develop northward into the Gulf through the Yucatan Channel and exit through the Florida Straits. It can reach the continental slope of the study domain and directly depress the isopycnals. Cyclonic eddies in front of the Loop Current also induce upwelling underneath. On the other hand, the Loop Current sometimes impinges on the West Florida Shelf and generates a high pressure disturbance, which travels northward along the shelf into the study region. Consequently, large-scale downwelling occurs across the continental slopes. Our analysis of sea surface height shows that the Loop Current pressure disturbance tends to propagate along the shallow isobaths of 100 to 300 m in the topographic wave direction from south of the West Florida Shelf to the Mississippi Delta. In addition, after shedding a large anticyclonic eddy, the Loop Current retracts southward and can touch the southeastern corner of the West Florida Shelf. This can result in a higher pressure disturbance, and therefore stronger large-scale downwelling in the DeSoto Canyon region.

Opto-Electronic Oscillator Stabilized By A Hyperfine Atomic Transition

NASA Technical Reports Server (NTRS)

Strekalov, Dmitry; Aveline, David; Matsko, Andrey B.; Thompson, Robert; Yu, Nan

2004-01-01

Opto-electronic oscillator (OEO) is a closed-loop system with part of the loop is implemented by an optical beam, and the rest by RF circuitry. The technological advantage of this approach over traditional all-RF loops in the gigahertz range comes from the that frequency filtering can be done far more efficiently in the optical range with compact, low power, and have superior stability. In this work, we report our preliminary results on using the phenomenon of coherent population trapping in (87) Rb vapor as an optical filter. Such a filter allows us to stabilize the OEO at the hyperfine splitting frequency of rubidium, thus implementing a novel type of frequency standard.

3D-Stereoscopic Analysis of Solar Active Region Loops. 2; SoHo/EIT Observations at Temperatures of 1.5-2.5 MK

NASA Technical Reports Server (NTRS)

Aschwanden, Markus J.; Alexander, David; Hurlburt, Neal; Newmark, Jeffrey S.; Neupert, Werner M.; Klimchuk, J. A.; Gary, G. Allen

1999-01-01

In this paper we study the three-dimensional (3D) structure of hot (T(sub e) approximately equals 1.5 - 2.5 MK) loops in solar active region NOAA 7986, observed on 1996 August 30 with the Extreme-ultraviolet Imaging Telescope (EIT) onboard the Solar and Heliospheric Observatory (SoHO). This complements a first study on cooler (T(sub e) approximately equals 1.0 - 1.5 MK) loops of the same active region, using the same method of Dynamic Stereoscopy to reconstruct the 3D geometry. We reconstruct the 3D-coordinates x(s), y(s), z(s), the density n(sub e)(s), and temperature profile T(sub e)(s) of 35 individual loop segments (as function of the loop coordinate s) using EIT 195 A and 284 A images. The major findings are: (1) All loops are found to be in hydrostatic equilibrium, in the entire temperature regime of T(sub e) = 1.0 - 2.5 MK; (2) The analyzed loops have a height of 2-3 scale heights, and thus only segments extending over about one vertical scale height have sufficient emission measure contrast for detection; (3) The temperature gradient over the lowest scale height is of order dT/ds is approximately 1 - 4 K/km; (4) The radiative loss rate is found to exceed the conductive loss rate by about two orders or magnitude, making thermal conduction negligible to explain the temperature structure of the loops; (5) A steady-state can only be achieved when the heating rate E(sub H) matches the radiative loss rate in hydrostatic equilibrium, requiring a heat deposition length lambda(sub H) of the half density scale height lambda, predicting a scaling law with the loop base pressure, EH varies as p(sub 0 exp 2). This favors coronal heating mechanisms that operate near the loop footpoints; (6) We find a reciprocal correlation between the loop pressure p(sub 0) and loop length L, i.e. p(sub 0) varies as 1/L, implying a scaling law of the steady-state requirement with loop length, i.e. E(sub H ) varies as 1/L(exp 2). The heating rate shows no correlation with the loop-aligned magnetic field component B(sub z) at the footpoints, but is correlated with the azimuthal field B(sub phi) = Bz(RDelta Phi/L) of a twisted loop, and is thus consistent with heating mechanisms based on field-aligned currents.

Replication stress induces accumulation of FANCD2 at central region of large fragile genes

PubMed Central

Okamoto, Yusuke; Iwasaki, Watal M; Kugou, Kazuto; Takahashi, Kazuki K; Oda, Arisa; Sato, Koichi; Kobayashi, Wataru; Kawai, Hidehiko; Sakasai, Ryo; Takaori-Kondo, Akifumi; Yamamoto, Takashi; Kanemaki, Masato T; Taoka, Masato; Isobe, Toshiaki; Kurumizaka, Hitoshi; Innan, Hideki; Ohta, Kunihiro; Ishiai, Masamichi; Takata, Minoru

2018-01-01

Abstract During mild replication stress provoked by low dose aphidicolin (APH) treatment, the key Fanconi anemia protein FANCD2 accumulates on common fragile sites, observed as sister foci, and protects genome stability. To gain further insights into FANCD2 function and its regulatory mechanisms, we examined the genome-wide chromatin localization of FANCD2 in this setting by ChIP-seq analysis. We found that FANCD2 mostly accumulates in the central regions of a set of large transcribed genes that were extensively overlapped with known CFS. Consistent with previous studies, we found that this FANCD2 retention is R-loop-dependent. However, FANCD2 monoubiquitination and RPA foci formation were still induced in cells depleted of R-loops. Interestingly, we detected increased Proximal Ligation Assay dots between FANCD2 and R-loops following APH treatment, which was suppressed by transcriptional inhibition. Collectively, our data suggested that R-loops are required to retain FANCD2 in chromatin at the middle intronic region of large genes, while the replication stress-induced upstream events leading to the FA pathway activation are not triggered by R-loops. PMID:29394375

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations

PubMed Central

Jiang, Jun; Aduri, Raviprasad; Chow, Christine S.; SantaLucia, John

2014-01-01

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson–Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity. PMID:24371282

Allosteric Inhibition via R-state Destabilization in ATP Sulfurylase from Penicillium chrysogenum

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

MacRae, I. J.

2002-01-01

The structure of the cooperative hexameric enzyme ATP sulfurylase from Penicillium chrysogenum bound to its allosteric inhibitor, 3'-phosphoadenosine-5'-phosphosulfate (PAPS), was determined to 2.6 {angstrom} resolution. This structure represents the low substrate-affinity T-state conformation of the enzyme. Comparison with the high substrate-affinity R-state structure reveals that a large rotational rearrangement of domains occurs as a result of the R-to-T transition. The rearrangement is accompanied by the 17 {angstrom} movement of a 10-residue loop out of the active site region, resulting in an open, product release-like structure of the catalytic domain. Binding of PAPS is proposed to induce the allosteric transition bymore » destabilizing an R-state-specific salt linkage between Asp 111 in an N-terminal domain of one subunit and Arg 515 in the allosteric domain of a trans-triad subunit. Disrupting this salt linkage by site-directed mutagenesis induces cooperative inhibition behavior in the absence of an allosteric effector, confirming the role of these two residues.« less

Exclusive QCD processes, quark-hadron duality, and the transition to perturbative QCD

NASA Astrophysics Data System (ADS)

Corianò, Claudio; Li, Hsiang-nan; Savkli, Cetin

1998-07-01

Experiments at CEBAF will scan the intermediate-energy region of the QCD dynamics for the nucleon form factors and for Compton Scattering. These experiments will definitely clarify the role of resummed perturbation theory and of quark-hadron duality (QCD sum rules) in this regime. With this perspective in mind, we review the factorization theorem of perturbative QCD for exclusive processes at intermediate energy scales, which embodies the transverse degrees of freedom of a parton and the Sudakov resummation of the corresponding large logarithms. We concentrate on the pion and proton electromagnetic form factors and on pion Compton scattering. New ingredients, such as the evolution of the pion wave function and the complete two-loop expression of the Sudakov factor, are included. The sensitivity of our predictions to the infrared cutoff for the Sudakov evolution is discussed. We also elaborate on QCD sum rule methods for Compton Scattering, which provide an alternative description of this process. We show that, by comparing the local duality analysis to resummed perturbation theory, it is possible to describe the transition of exclusive processes to perturbative QCD.

On the Occurrence of Thermal Nonequilibrium in Coronal Loops

NASA Astrophysics Data System (ADS)

Froment, C.; Auchère, F.; Mikić, Z.; Aulanier, G.; Bocchialini, K.; Buchlin, E.; Solomon, J.; Soubrié, E.

2018-03-01

Long-period EUV pulsations, recently discovered to be common in active regions, are understood to be the coronal manifestation of thermal nonequilibrium (TNE). The active regions previously studied with EIT/Solar and Heliospheric Observatory and AIA/SDO indicated that long-period intensity pulsations are localized in only one or two loop bundles. The basic idea of this study is to understand why. For this purpose, we tested the response of different loop systems, using different magnetic configurations, to different stratifications and strengths of the heating. We present an extensive parameter-space study using 1D hydrodynamic simulations (1020 in total) and conclude that the occurrence of TNE requires specific combinations of parameters. Our study shows that the TNE cycles are confined to specific ranges in parameter space. This naturally explains why only some loops undergo constant periodic pulsations over several days: since the loop geometry and the heating properties generally vary from one loop to another in an active region, only the ones in which these parameters are compatible exhibit TNE cycles. Furthermore, these parameters (heating and geometry) are likely to vary significantly over the duration of a cycle, which potentially limits the possibilities of periodic behavior. This study also confirms that long-period intensity pulsations and coronal rain are two aspects of the same phenomenon: both phenomena can occur for similar heating conditions and can appear simultaneously in the simulations.

Cooperative Allosteric Ligand Binding in Calmodulin

NASA Astrophysics Data System (ADS)

Nandigrami, Prithviraj

Conformational dynamics is often essential for a protein's function. For example, proteins are able to communicate the effect of binding at one site to a distal region of the molecule through changes in its conformational dynamics. This so called allosteric coupling fine tunes the sensitivity of ligand binding to changes in concentration. A conformational change between a "closed" (apo) and an "open" (holo) conformation upon ligation often produces this coupling between binding sites. Enhanced sensitivity between the unbound and bound ensembles leads to a sharper binding curve. There are two basic conceptual frameworks that guide our visualization about ligand binding mechanisms. First, a ligand can stabilize the unstable "open" state from a dynamic ensemble of conformations within the unbound basin. This binding mechanism is called conformational selection. Second, a ligand can weakly bind to the low-affinity "closed" state followed by a conformational transition to the "open" state. In this dissertation, I focus on molecular dynamics simulations to understand microscopic origins of ligand binding cooperativity. A minimal model of allosteric binding transitions must include ligand binding/unbinding events, while capturing the transition mechanism between two distinct meta-stable free energy basins. Due in part to computational timescales limitations, work in this dissertation describes large-scale conformational transitions through a simplified, coarse-grained model based on the energy basins defined by the open and closed conformations of the protein Calmodulin (CaM). CaM is a ubiquitous calcium-binding protein consisting of two structurally similar globular domains connected by a flexible linker. The two domains of CaM, N-terminal domain (nCaM) and C-terminal domain (cCaM) consists of two helix-loop-helix motifs (the EF-hands) connected by a flexible linker. Each domain of CaM consists of two binding loops and binds 2 calcium ions each. The intact domain binds up to 4 calcium ions. The simulations use a coupled molecular dynamics/monte carlo scheme where the protein dynamics is simulated explicitly, while ligand binding/unbinding are treated implicitly. In the model, ligand binding/unbinding events coupled with a conformational change of the protein within the grand canonical ensemble. Here, ligand concentration is controlled through the chemical potential (micro). This allows us to use a simple thermodynamic model to analyze the simulated data and quantify binding cooperativity. Simulated binding titration curves are calculated through equilibrium simulations at different values of micro. First, I study domain opening transitions of isolated nCaM and cCaM in the absence of calcium. This work is motivated by results from a recent analytic variational model that predicts distinct domain opening transition mechanism for the domains of CaM. This is a surprising result because the domains have the same folded state topology. In the simulations, I find the two domains of CaM have distinct transition mechanism over a broad range of temperature, in harmony with the analytic predictions. In particular, the simulated transition mechanism of nCaM follows a two-state behavior, while domain opening in cCaM involves global unfolding and refolding of the tertiary structure. The unfolded intermediate also appears in the landscape of nCaM, but at a higher temperature than it appears in cCaM's energy landscape. This is consistent with nCaM's higher thermal stability. Under approximate physiological conditions, majority of the sampled transitions in cCaM involves unfolding and refolding during conformational change. Kinetically, the transient unfolding and refolding in cCaM significantly slows the domain opening and closing rates in cCaM. Second, I investigate the structural origins of binding affinity and allosteric cooperativity of binding 2 calcium-ions to each domain of CaM. In my work, I predict the order of binding strength of CaM's loops. I analyze simulated binding curves within the framework of the classic Monod-Wyman-Changeux (MWC) model of allostery to extract the binding free energies to the closed and open ensembles. The simulations predict that cCaM binds calcium with higher affinity and greater cooperativity than nCaM. Where it is possible to compare, these predictions are in good agreement with experimental results. The analysis of the simulations offers a rationale for why the two domains differ in cooperativity: the higher cooperativity of cCaM is due to larger difference in affinity of its binding loops. Third, I extend the work to investigate structural origins of binding cooperativity of 4 calcium-ions to intact CaM. I characterize the microscopic cooperativities of each ligation state and provide a kinetic description of the binding mechanism. Due to the heterogeneous nature of CaM's loops, as predicted in our simulations of isolated domains, I focus on investigating the influence of this heterogeneity on the kinetic flux of binding pathways as a function of concentration. The formalism developed for Network Models of protein folding kinetics, is used to evaluate the directed flux of all possible pathways between unligated and fully loaded CaM. (Abstract shortened by ProQuest.).

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

Ahuatzin, G.; Bautista, I.; Hernandez-Lopez, J. A.

A constant antisymmetric 2-tensor can arise in general relativity with spontaneous symmetry breaking or in field theories formulated in a noncommutative space-time. In this work, the one-loop contribution of a nonstandard WW{gamma} vertex on the flavor violating quark transition q{sub i}{yields}q{sub j}{gamma} is studied in the context of the electroweak Yang-Mills sector extended with a Lorentz-violating constant 2-tensor. An exact analytical expression for the on-shell case is presented. It is found that the loop amplitude is gauge independent, electromagnetic gauge invariant, and free of ultraviolet divergences. The dipolar contribution to the b{yields}s{gamma} transition together with the experimental data on themore » B{yields}X{sub s{gamma}} decay is used to derive the constraint {Lambda}{sub LV}>1.96 TeV on the Lorentz-violating scale.« less

Cooperative and noncooperative magnetization reversal in alnicos

DOE PAGES

Skomski, Ralph; Ke, Liqin; Kramer, Matthew J.; ...

2017-02-08

Here, we investigate how magnetostatic interactions affect the coercivity of alnico-type magnets. Starting from exact micromagnetic relations, we also analyze two limits, namely cooperative reversal processes operative on short lengths scales and noncooperative reversal processes on long length scales. Furthermore, in alnicos, intrawire interactions are predominantly cooperative, whereas interwire effects are typically noncooperative. However, the transition between the regimes depends on feature size and hysteresis-loop shape, and interwire cooperative effects are largest for nearly rectangular loops. Our analysis revises the common shape-anisotropy interpretation of alnicos.

A new insight into diffusional escape from a biased cylindrical trap

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Dagdug, Leonardo; Bezrukov, Sergey M.

2017-09-01

Recent experiments with single biological nanopores, as well as single-molecule fluorescence spectroscopy and pulling studies of protein and nucleic acid folding raised a number of questions that stimulated theoretical and computational investigations of barrier crossing dynamics. The present paper addresses a closely related problem focusing on trajectories of Brownian particles that escape from a cylindrical trap in the presence of a force F parallel to the cylinder axis. To gain new insights into the escape dynamics, we analyze the "fine structure" of these trajectories. Specifically, we divide trajectories into two segments: a looping segment, when a particle unsuccessfully tries to escape returning to the trap bottom again and again, and a direct-transit segment, when it finally escapes moving without touching the bottom. Analytical expressions are derived for the Laplace transforms of the probability densities of the durations of the two segments. These expressions are used to find the mean looping and direct-transit times as functions of the biasing force F. It turns out that the force-dependences of the two mean times are qualitatively different. The mean looping time monotonically increases as F decreases, approaching exponential F-dependence at large negative forces pushing the particle towards the trap bottom. In contrast to this intuitively appealing behavior, the mean direct-transit time shows rather counterintuitive behavior: it decreases as the force magnitude, |F|, increases independently of whether the force pushes the particles to the trap bottom or to the exit from the trap, having a maximum at F = 0.

Stabilization and analytical tuning rule of double-loop control scheme for unstable dead-time process

NASA Astrophysics Data System (ADS)

Ugon, B.; Nandong, J.; Zang, Z.

2017-06-01

The presence of unstable dead-time systems in process plants often leads to a daunting challenge in the design of standard PID controllers, which are not only intended to provide close-loop stability but also to give good performance-robustness overall. In this paper, we conduct stability analysis on a double-loop control scheme based on the Routh-Hurwitz stability criteria. We propose to use this unstable double-loop control scheme which employs two P/PID controllers to control first-order or second-order unstable dead-time processes typically found in process industries. Based on the Routh-Hurwitz stability necessary and sufficient criteria, we establish several stability regions which enclose within them the P/PID parameter values that guarantee close-loop stability of the double-loop control scheme. A systematic tuning rule is developed for the purpose of obtaining the optimal P/PID parameter values within the established regions. The effectiveness of the proposed tuning rule is demonstrated using several numerical examples and the result are compared with some well-established tuning methods reported in the literature.

Analysis of blinkers and EUV brightenings in the quiet Sun observed with CDS

NASA Astrophysics Data System (ADS)

Brković, A.; Solanki, S. K.; Rüedi, I.

2001-07-01

Movies of quiet Sun regions at disc centre obtained with the Coronal Diagnostic Spectrometer (CDS) onboard the SOHO spacecraft are used to study the properties of transient brightenings seen in the extreme ultraviolet (EUV), so-called blinkers, at three different temperatures sampled simultaneously in the chromospheric He I 584.3 Å (2 x 104 K), the transition region O V 629.7 Å (2.5 x 105 K) and coronal Mg IX 368.1 Å (106 K) lines. Blinkers, here defined somewhat differently than in previous studies, were clearly detected in the O V and He I lines. Brightenings of the Mg IX line were also seen. A thorough analysis of blinker properties is carried out and their detailed properties are determined. Blinkers are found to be present in both bright (network) and dark (intranetwork) regions, but their number density is larger in the brighter areas (in O V) although the rest of their properties appear to be unaffected. The average sizes of brightenings range from 2.8 Mm2 in Mg IX, 12.4 Mm2 in He I to 23.5 Mm2 in O V. The durations of blinkers are in the range 3-110 min, with the average durations being 23 min in He I, about 16 min in O V and 12 min in Mg IX. The frequency distributions of ratio of peak to background intensity, excess energy and size follow power laws with exponents <-5 for the intensity ratio, and between -1 and -3 for the other two parameters. The correlation coefficients between pairs of ratio, energy and size are at least 0.5, while other pairs of parameters describing the blinkers appear to be uncorrelated. The best correlation is between size and energy. The blinker durations exhibit a distribution whose form is compatible with a log-normal function. Finally, blinkers in the 3 lines (i.e. 3 temperature regimes) are poorly correlated; with the correlation coefficient being always less than 0.4. This suggests that to a large extent the transition region reacts independently of the corona and chromosphere to energy deposition, so that these parts of the atmosphere are at least partly decoupled from each other. This agrees with the expectations from models having separate transition-region loops, but contradicts the classical picture of the transition region, as being heated dominantly by energy conduction from the corona.

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

Pisarski, Robert D.; Skokov, Vladimir V.

Previously, a matrix model of the region near the transition temperature, in the “semi”quark gluon plasma, was developed for the theory of SU(3) gluons without quarks. In this paper we develop a chiral matrix model applicable to QCD by including dynamical quarks with 2+1 flavors. This requires adding a nonet of scalar fields, with both parities, and coupling these to quarks through a Yukawa coupling, y. Treating the scalar fields in mean field approximation, the effective Lagrangian is computed by integrating out quarks to one loop order. As is standard, the potential for the scalar fields is chosen to bemore » symmetric under the flavor symmetry of SU (3) L × SU(3) R × Z (3) A , except for a term linear in the current quark mass, m qk . In addition, at a nonzero temperature T it is necessary to add a new term, ~ m qk T 2 . The parameters of the gluon part of the matrix model are identical to those for the pure glue theory without quarks. The parameters in the chiral matrix model are fixed by the values, at zero temperature, of the pion decay constant and the masses of the pions, kaons, η , and η' . The temperature for the chiral crossover at T$χ$ = 155 MeV is determined by adjusting the Yukawa coupling y . We find reasonable agreement with the results of numerical simulations on the lattice for the pressure and related quantities. In the chiral limit, besides the divergence in the chiral susceptibility there is also a milder divergence in the susceptibility between the Polyakov loop and the chiral order parameter, with critical exponent β $-$ 1 . We compute derivatives with respect to a quark chemical potential to determine the susceptibilities for baryon number, the $χ$ 2n . Especially sensitive tests are provided by $χ$ 4 $-$ $χ$ 2 and by $χ$ 6 , which changes in sign about T$χ$ . In conclusion, the behavior of the susceptibilities in the chiral matrix model strongly suggests that as the temperature increases from T$χ$ , that the transition to deconfinement is significantly quicker than indicated by the measurements of the (renormalized) Polyakov loop on the lattice.« less

Chiral matrix model of the semi-QGP in QCD

DOE PAGES

Pisarski, Robert D.; Skokov, Vladimir V.

2016-08-08

Previously, a matrix model of the region near the transition temperature, in the “semi”quark gluon plasma, was developed for the theory of SU(3) gluons without quarks. In this paper we develop a chiral matrix model applicable to QCD by including dynamical quarks with 2+1 flavors. This requires adding a nonet of scalar fields, with both parities, and coupling these to quarks through a Yukawa coupling, y. Treating the scalar fields in mean field approximation, the effective Lagrangian is computed by integrating out quarks to one loop order. As is standard, the potential for the scalar fields is chosen to bemore » symmetric under the flavor symmetry of SU (3) L × SU(3) R × Z (3) A , except for a term linear in the current quark mass, m qk . In addition, at a nonzero temperature T it is necessary to add a new term, ~ m qk T 2 . The parameters of the gluon part of the matrix model are identical to those for the pure glue theory without quarks. The parameters in the chiral matrix model are fixed by the values, at zero temperature, of the pion decay constant and the masses of the pions, kaons, η , and η' . The temperature for the chiral crossover at T$χ$ = 155 MeV is determined by adjusting the Yukawa coupling y . We find reasonable agreement with the results of numerical simulations on the lattice for the pressure and related quantities. In the chiral limit, besides the divergence in the chiral susceptibility there is also a milder divergence in the susceptibility between the Polyakov loop and the chiral order parameter, with critical exponent β $-$ 1 . We compute derivatives with respect to a quark chemical potential to determine the susceptibilities for baryon number, the $χ$ 2n . Especially sensitive tests are provided by $χ$ 4 $-$ $χ$ 2 and by $χ$ 6 , which changes in sign about T$χ$ . In conclusion, the behavior of the susceptibilities in the chiral matrix model strongly suggests that as the temperature increases from T$χ$ , that the transition to deconfinement is significantly quicker than indicated by the measurements of the (renormalized) Polyakov loop on the lattice.« less

Spatial structure and temporal development of a solar X-ray flare observed from Skylab on June 15, 1973

NASA Technical Reports Server (NTRS)

Pallavicini, R.; Vaiana, G. S.; Kahler, S. W.; Krieger, A. S.

1975-01-01

Morphological and quantitative analyses are presented of a 1B solar flare that was observed with high spatial and temporal resolution by the S-054 grazing-incidence X-ray telescope aboard Skylab. It is found that the flare had the configuration of a compact region with a characteristic size of the order of 30 arcsec at the intensity peak, the interior of the region appeared to be highly structured and to consist of temporally changing complex loop systems, brightening over an extended part of the active region preceded the flare onset, and the impulsive phase was marked by rapid brightening in the loop structures. The X-ray photographs also indicate that the X-ray emission was centered over the neutral line of the longitudinal magnetic field, loop systems formed at successively increasing heights during the decay phase, and different regions of the flare had distinctly different light curves. The flux profiles for the different regions are shown to suggest continued heating during the decay phase. It is concluded that flare models should be based on a multiplicity of volumes ordered in loops of successively larger scale lengths and heights rather than on a single point of energy release and deposition.

Enzymatic properties of a GH19 chitinase isolated from rice lacking a major loop structure involved in chitin binding.

PubMed

Tanaka, Jun; Fukamizo, Tamo; Ohnuma, Takayuki

2017-05-01

The catalytic domains of family GH19 chitinases have been found to consist of a conserved, α-helical core-region and different numbers (1-6) of loop structures, located at both ends of the substrate-binding groove and which extend over the glycon- and aglycon-binding sites. We expressed, purified and enzymatically characterized a GH19 chitinase from rice, Oryza sativa L. cv. Nipponbare (OsChia2a), lacking a major loop structure (loop III) connected to the functionally important β-stranded region. The new enzyme thus contained the five remaining loop structures (loops I, II, IV, V and C-term). The OsChia2a recombinant protein catalyzed hydrolysis of chitin oligosaccharides, (GlcNAc)n (n = 3-6), with inversion of anomeric configuration, indicating that OsChia2a correctly folded without loop III. From thermal unfolding experiments and calorimetric titrations using the inactive OsChia2a mutant (OsChia2a-E68Q), in which the catalytic residue Glu68 was mutated to glutamine, we found that the binding affinities towards (GlcNAc)n (n = 2-6) were almost proportional to the degree of polymerization of (GlcNAc)n, but were much lower than those obtained for a moss GH19 chitinase having only loop III [Ohnuma T, Sørlie M, Fukuda T, Kawamoto N, Taira T, Fukamizo T. 2011. Chitin oligosaccharide binding to a family GH19 chitinase from the moss, Bryum coronatum. FEBS J. 278:3991-4001]. Nevertheless, OsChia2a exhibited significant antifungal activity. It appears that loop III connected to the β-stranded region is important for (GlcNAc)n binding, but is not essential for antifungal activity. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Heating mechanisms for intermittent loops in active region cores from AIA/SDO EUV observations

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

Cadavid, A. C.; Lawrence, J. K.; Christian, D. J.

2014-11-01

We investigate intensity variations and energy deposition in five coronal loops in active region cores. These were selected for their strong variability in the AIA/SDO 94 Å intensity channel. We isolate the hot Fe XVIII and Fe XXI components of the 94 Å and 131 Å by modeling and subtracting the 'warm' contributions to the emission. HMI/SDO data allow us to focus on 'inter-moss' regions in the loops. The detailed evolution of the inter-moss intensity time series reveals loops that are impulsively heated in a mode compatible with a nanoflare storm, with a spike in the hot 131 Å signalsmore » leading and the other five EUV emission channels following in progressive cooling order. A sharp increase in electron temperature tends to follow closely after the hot 131 Å signal confirming the impulsive nature of the process. A cooler process of growing emission measure follows more slowly. The Fourier power spectra of the hot 131 Å signals, when averaged over the five loops, present three scaling regimes with break frequencies near 0.1 min{sup –1} and 0.7 min{sup –1}. The low frequency regime corresponds to 1/f noise; the intermediate indicates a persistent scaling process and the high frequencies show white noise. Very similar results are found for the energy dissipation in a 2D 'hybrid' shell model of loop magneto-turbulence, based on reduced magnetohydrodynamics, that is compatible with nanoflare statistics. We suggest that such turbulent dissipation is the energy source for our loops.« less

A digital optical phase-locked loop for diode lasers based on field programmable gate array.

PubMed

Xu, Zhouxiang; Zhang, Xian; Huang, Kaikai; Lu, Xuanhui

2012-09-01

We have designed and implemented a highly digital optical phase-locked loop (OPLL) for diode lasers in atom interferometry. The three parts of controlling circuit in this OPLL, including phase and frequency detector (PFD), loop filter and proportional integral derivative (PID) controller, are implemented in a single field programmable gate array chip. A structure type compatible with the model MAX9382∕MCH12140 is chosen for PFD and pipeline and parallelism technology have been adapted in PID controller. Especially, high speed clock and twisted ring counter have been integrated in the most crucial part, the loop filter. This OPLL has the narrow beat note line width below 1 Hz, residual mean-square phase error of 0.14 rad(2) and transition time of 100 μs under 10 MHz frequency step. A main innovation of this design is the completely digitalization of the whole controlling circuit in OPLL for diode lasers.

A digital optical phase-locked loop for diode lasers based on field programmable gate array

NASA Astrophysics Data System (ADS)

Xu, Zhouxiang; Zhang, Xian; Huang, Kaikai; Lu, Xuanhui

2012-09-01

We have designed and implemented a highly digital optical phase-locked loop (OPLL) for diode lasers in atom interferometry. The three parts of controlling circuit in this OPLL, including phase and frequency detector (PFD), loop filter and proportional integral derivative (PID) controller, are implemented in a single field programmable gate array chip. A structure type compatible with the model MAX9382/MCH12140 is chosen for PFD and pipeline and parallelism technology have been adapted in PID controller. Especially, high speed clock and twisted ring counter have been integrated in the most crucial part, the loop filter. This OPLL has the narrow beat note line width below 1 Hz, residual mean-square phase error of 0.14 rad2 and transition time of 100 μs under 10 MHz frequency step. A main innovation of this design is the completely digitalization of the whole controlling circuit in OPLL for diode lasers.

Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter

NASA Astrophysics Data System (ADS)

Lee, Yongchan; Nishizawa, Tomohiro; Yamashita, Keitaro; Ishitani, Ryuichiro; Nureki, Osamu

2015-01-01

SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the ‘binder clip-like’ motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.

Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene.

PubMed

Tan-Wong, Sue Mei; French, Juliet D; Proudfoot, Nicholas J; Brown, Melissa A

2008-04-01

The 85-kb breast cancer-associated gene BRCA1 is an established tumor suppressor gene, but its regulation is poorly understood. We demonstrate by gene conformation analysis in both human cell lines and mouse mammary tissue that gene loops are imposed on BRCA1 between the promoter, introns, and terminator region. Significantly, association between the BRCA1 promoter and terminator regions change upon estrogen stimulation and during lactational development. Loop formation is transcription-dependent, suggesting that transcriptional elongation plays an active role in BRCA1 loop formation. We show that the BRCA1 terminator region can suppress estrogen-induced transcription and so may regulate BRCA1 expression. Significantly, BRCA1 promoter and terminator interactions vary in different breast cancer cell lines, indicating that defects in BRCA1 chromatin structure may contribute to dysregulated expression of BRCA1 seen in breast tumors.

Modulation of dynamic modes by interplay between positive and negative feedback loops in gene regulatory networks

NASA Astrophysics Data System (ADS)

Wang, Liu-Suo; Li, Ning-Xi; Chen, Jing-Jia; Zhang, Xiao-Peng; Liu, Feng; Wang, Wei

2018-04-01

A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops. We developed an abstract model of such systems, largely based on the core p53 pathway, to explore the mechanism for the transformation of dynamic behaviors. Our results show that enhancing the positive feedback may promote or suppress oscillations depending on the strength of both feedback loops. We found that the system oscillates with low amplitudes in response to a moderate stimulus and switches to the on state upon a strong stimulus. When the positive feedback is activated much later than the negative one in response to a strong stimulus, the system exhibits long-term oscillations before switching to the on state. We explain this intriguing phenomenon using quasistatic approximation. Moreover, early switching to the on state may occur when the system starts from a steady state in the absence of stimuli. The interplay between the positive and negative feedback plays a key role in the transitions between oscillation and bistability. Of note, our conclusions should be applicable only to some specific gene regulatory networks, especially the p53 network, in which both oscillation and bistability exist in response to a certain type of stimulus. Our work also underscores the significance of transient dynamics in determining cellular outcome.

Age and Structure of the Laschamp Geomagnetic Excursion

NASA Astrophysics Data System (ADS)

Scaillet, S.; Laj, C.; Kissel, C.; Guillou, H.; Singer, B. S.

2004-12-01

The age of the Laschamp geomagnetic excursion has been recently re-investigated using unspiked K/Ar and Ar/Ar techniques (Guillou et al., Session V01, this conference). The new age determination of 40.4 +/- 2.0 ka (2 sigma) is more precise than those previously reported in the literature and agrees precisely with that deduced from the GLOPIS-75 sedimentary paleointensity stack calibrated against the GISP2 ice core chronology. Two of the North Atlantic cores used in GLOPIS-75 (MD95-2034 and PS2644-5) yield rather detailed transitional VGP paths. In the two cases the paths show large similarities, with the VGP initially descending along mid-western Pacific, then returning to normal polarities with a large clockwise loop over Africa and Europe. Differences in the highest southern latitudes reached by the VGP can be explained assuming more different degrees of smearing of the paleomagnetic record due to differences in sedimentation rate in the two cores. In the most detailed record, MD95-2034 , two smaller loops are present preceding the main excursion. In the two cores, the excursion is characterized by a significant drop in intensity. The reversal paths observed for the Laschamp event are very close in position to those reported for the Icelandic Basin Event (IBE) from sites in the North Atlantic and the South China Sea (Laj et al., this conference) but differ in the sense of looping: while a clockwise loop is observed here, a counterclockwise loop is observed for the IBE. Despite this difference, the similarity of the transitional records tends to suggest that a similar, relatively simple, geometry has dominated the two excursions and therefore that similar dynamo mechanisms have prevailed during the reversal process.

Electric properties and phase transition behavior in lead lanthanum zirconate stannate titanate ceramics with low zirconate content

NASA Astrophysics Data System (ADS)

Zeng, Tao; Lou, Qi-Wei; Chen, Xue-Feng; Zhang, Hong-Ling; Dong, Xian-Lin; Wang, Gen-Shui

2015-11-01

The phase transitions, dielectric properties, and polarization versus electric field (P-E) hysteresis loops of Pb0.97La0.02(Zr0.42Sn0.58-xTix)O3 (0.13≤ x ≤0.18) (PLZST) bulk ceramics were systematically investigated. This study exhibited a sequence of phase transitions by analyzing the change of the P-E hysteresis loops with increasing temperature. The antiferroelectric (AFE) to ferroelectric (FE) phase boundary of PLZST with the Zr content of 0.42 was found to locate at the Ti content between 0.14 and 0.15. This work is aimed to improve the ternary phase diagram of lanthanum-doped PZST with the Zr content of 0.42 and will be a good reference for seeking high energy storage density in the PLZST system with low-Zr content. Project supported by the National Natural Science Foundation of China (Grant Nos. 51202273, 11204304, and 11304334) and the Science and Technology Commission of Shanghai Municipality, China (Grant No. 14DZ2261000).

Temperature dependences of the electromechanical and electrocaloric properties of Ba(Zr,Ti)O3 and (Ba,Sr)TiO3 ceramics

NASA Astrophysics Data System (ADS)

Maiwa, Hiroshi

2017-10-01

The electrocaloric properties of Ba(Zr,Ti)O3 and (Ba,Sr)TiO3 ceramics (BZT and BST, respectively) were investigated by the indirect estimation and direct measurement of temperature-electric field (T-E) hysteresis loops. The measured T-E loops had shapes similar to those of the strain-electric field (s-E) loops. The measured temperature changes (ΔTs) at around 30 °C of the BZT ceramics sintered at 1450 °C and BST ceramics sintered at 1600 °C upon the release of the electric field from 30 kV/cm to 0 were 0.34 and 0.57 K, respectively. The temperature dependences of the electromechanical and electrocaloric properties were investigated. The BZT ceramics sintered at 1450 °C exhibited the largest electromechanical and electrocaloric properties at around 30 °C, which corresponds to the phase transition temperature. BST is more temperature dependent than BZT. BST ceramics sintered at 1600 °C exhibited the largest electromechanical and electrocaloric properties at around 29 °C, which is about 10 °C higher than the phase transition temperature.

Two Topologically Distinct Dirac-Line Semimetal Phases and Topological Phase Transitions in Rhombohedrally Stacked Honeycomb Lattices

NASA Astrophysics Data System (ADS)

Hyart, T.; Ojajärvi, R.; Heikkilä, T. T.

2018-04-01

Three-dimensional topological semimetals can support band crossings along one-dimensional curves in the momentum space (nodal lines or Dirac lines) protected by structural symmetries and topology. We consider rhombohedrally (ABC) stacked honeycomb lattices supporting Dirac lines protected by time-reversal, inversion and spin rotation symmetries. For typical band structure parameters there exists a pair of nodal lines in the momentum space extending through the whole Brillouin zone in the stacking direction. We show that these Dirac lines are topologically distinct from the usual Dirac lines which form closed loops inside the Brillouin zone. In particular, an energy gap can be opened only by first merging the Dirac lines going through the Brillouin zone in a pairwise manner so that they turn into closed loops inside the Brillouin zone, and then by shrinking these loops into points. We show that this kind of topological phase transition can occur in rhombohedrally stacked honeycomb lattices by tuning the ratio of the tunneling amplitudes in the directions perpendicular and parallel to the layers. We also discuss the properties of the surface states in the different phases of the model.

Symmetry transition via tetravalent impurity and investigations on magnetic properties of Li0.5Fe2.5O4

NASA Astrophysics Data System (ADS)

Kounsalye, Jitendra S.; Kharat, Prashant B.; Chavan, Apparao R.; Humbe, Ashok V.; Borade, R. M.; Jadhav, K. M.

2018-04-01

The present study, deals with the phase symmetry transformation of lithium ferrite after introducing tetravalent (Ti4+) impurity. The sol-gel auto combustion technique was adopted for the synthesis of nanoparticle samples with generic chemical formula Li0.5Fe2.5O4 and Li0.55Ti0.10Fe2.35O4. The synthesized nanoparticles were characterized by X-ray diffraction (XRD) technique for structural analysis. The XRD patterns show the single phase cubic structure without any impurity phase but the P4332 to Fd-3m transformation was observed after introducing Ti4+ impurity. The Nano size of the synthesized particles was confirmed by crystallite size ( 20nm) calculated using Debye-Scherrer's formula. The Fourier transform infrared spectroscopy (FTIR) studies shows shifting of band frequencies which reflect the structural changes after tetravalent substitutional impurities. The magnetic properties were studied through pulse field hysteresis loop (M-H loop) technique at room temperature, the M-H loops showdecrease in magnetic properties afternonmagnetic Ti4+ ion substitution. This is attributed to transition of inverse spinel structure of lithium ferrite to random spinel structure.

HOMOLOGOUS JET-DRIVEN CORONAL MASS EJECTIONS FROM SOLAR ACTIVE REGION 12192

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

Panesar, Navdeep K.; Sterling, Alphonse C.; Moore, Ronald L., E-mail: navdeep.k.panesar@nasa.gov

We report observations of homologous coronal jets and their coronal mass ejections (CMEs) observed by instruments onboard the Solar Dynamics Observatory (SDO) and the Solar and Heliospheric Observatory (SOHO) spacecraft. The homologous jets originated from a location with emerging and canceling magnetic field at the southeastern edge of the giant active region (AR) of 2014 October, NOAA 12192. This AR produced in its interior many non-jet major flare eruptions (X- and M- class) that made no CME. During October 20 to 27, in contrast to the major flare eruptions in the interior, six of the homologous jets from the edgemore » resulted in CMEs. Each jet-driven CME (∼200–300 km s{sup −1}) was slower-moving than most CMEs, with angular widths (20°–50°) comparable to that of the base of a coronal streamer straddling the AR and were of the “streamer-puff” variety, whereby the preexisting streamer was transiently inflated but not destroyed by the passage of the CME. Much of the transition-region-temperature plasma in the CME-producing jets escaped from the Sun, whereas relatively more of the transition-region plasma in non-CME-producing jets fell back to the solar surface. Also, the CME-producing jets tended to be faster and longer-lasting than the non-CME-producing jets. Our observations imply that each jet and CME resulted from reconnection opening of twisted field that erupted from the jet base and that the erupting field did not become a plasmoid as previously envisioned for streamer-puff CMEs, but instead the jet-guiding streamer-base loop was blown out by the loop’s twist from the reconnection.« less

Structural asymmetry and intersubunit communication in muscle creatine kinase.

PubMed

Ohren, Jeffrey F; Kundracik, Melisa L; Borders, Charles L; Edmiston, Paul; Viola, Ronald E

2007-03-01

The structure of a transition-state analog complex of a highly soluble mutant (R134K) of rabbit muscle creatine kinase (rmCK) has been determined to 1.65 A resolution in order to elucidate the structural changes that are required to support and regulate catalysis. Significant structural asymmetry is seen within the functional homodimer of rmCK, with one monomer found in a closed conformation with the active site occupied by the transition-state analog components creatine, MgADP and nitrate. The other monomer has the two loops that control access to the active site in an open conformation and only MgADP is bound. The N-terminal region of each monomer makes a substantial contribution to the dimer interface; however, the conformation of this region is dramatically different in each subunit. Based on this structural evidence, two mutational modifications of rmCK were conducted in order to better understand the role of the amino-terminus in controlling creatine kinase activity. The deletion of the first 15 residues of rmCK and a single point mutant (P20G) both disrupt subunit cohesion, causing the dissociation of the functional homodimer into monomers with reduced catalytic activity. This study provides support for a structural role for the amino-terminus in subunit association and a mechanistic role in active-site communication and catalytic regulation.

Coalescence of two current loops with a kink instability simulated by a three-dimensional electromagnetic particle code

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Sakai, J.-I.; Zhao, Jie; Neubert, T.; Buneman, Oscar

1994-01-01

We have studied the dynamics of a coalescence of current loops using three-dimensional electromagnetic (EM) particle simulation code. Our focus is the investigation of such kinetic processes as energy trasnfer, heating particles, and electromagnetic emissions associated with a current loop coalescence which cannot be studied by MHD simulations. First, the two loops undergo a pinching oscillation due to a pressure imbalance between the inside and outside of the current loop. During the pinching oscillation, a kinetic kink instability is excited and electrons in the loops are heated perpendicularly to an ambient magnetic field. Next, the two current loops collide and coalesce, while at the same time a helical structure grows further. Subsequently, the perturbed current, which is due to these helically bunched electrons, can drive a whistler instability. It should be noted in this case that the whistler wave is excited by the kinetic kink instability and not a beam instability. After the coalescence of two helical loops, tilting motions can be observed in the direction of left-hand rotation, and the helical structure will relax resulting in strong plasma heating mostly in the direction perpendicular to the ambient magnetic field. It is also shown that high-frequency electromagnetic waves can be emitted from the region where the two loops coalesce and propagate strongly in the direction of the electron drift velocity. These processes may be important in understanding heating mechansims for coronal loops as well as radio wave emission mechanisms from active regions of solar plasmas.

The mitochondrial intermembrane loop region of rat carnitine palmitoyltransferase 1A is a major determinant of its malonyl-CoA sensitivity.

PubMed

Borthwick, Karen; Jackson, Vicky N; Price, Nigel T; Zammit, Victor A

2006-11-03

Carnitine palmitoyltransferase (CPT) 1A adopts a polytopic conformation within the mitochondrial outer membrane, having both the N- and C-terminal segments on the cytosolic aspect of the membrane and a loop region connecting the two transmembrane (TM) segments protruding into the inter membrane space. In this study we demonstrate that the loop exerts major effects on the sensitivity of the enzyme to its inhibitor, malonyl-CoA. Insertion of a 16-residue spacer between the C-terminal part of the loop sequence (i.e. between residues 100 and 101) and TM2 (which is predicted to start at residue 102) increased the sensitivity to malonyl-CoA inhibition of the resultant mutant protein by more than 10-fold. By contrast, the same insertion made between TM1 and the loop had no effects on the kinetic properties of the enzyme, indicating that effects on the catalytic C-terminal segment were specifically induced by loop-TM2 interactions. Enhanced sensitivity was also observed in all mutants in which the native TM2-loop pairing was disrupted either by making chimeras in which the loops and TM2 segments of CPT 1A and CPT 1B were exchanged or by deleting successive 9-residue segments from the loop sequence. The data suggest that the sequence spanning the loop-TM2 boundary determines the disposition of this TM in the membrane so as to alter the conformation of the C-terminal segment and thus affect its interaction with malonyl-CoA.

3D-Stereoscopic Analysis of Solar Active Region Loops: I: SoHo/EIT Observations at Temperatures of 1.0-1.5 MK

NASA Technical Reports Server (NTRS)

Aschwanden, Markus J.; Newmark, Jeff; Delaboudiniere, Jean-Pierre; Neupert, Werner M.; Portier-Fozzani, Fabrice; Gary, G. Allen; Zucker, Arik

1998-01-01

The three-dimensional (3D) structure of solar active region NOAA 7986 observed on 1996 August 30 with the Extrem-ultraviolet Imaging Telescope (EIT) onboard the Solar and Heliospheric Observatory (SoHO) is analyzed. We develop a new method of Dynamic Stereoscopy to reconstruct the 3D geometry of dynamically changing loops, which allows us to determine the orientation of the loop plane with respect to the line-of-sight, a prerequisite to correct properly for projection effects in 3D loop models. With this method and the filter-ratio technique applied to EIT 171 A and 195 A images we determine the 3D coordinates (x(s), y(s), z(s)), the loop width) w(s), the electron density n(sub e)(s), and the electron temperature T(sub e)(s) as function of the loop length s for 30 loop segments. Fitting the loop densities with an exponential density model n(sub e)(h) we find that the so inferred scale height temperatures, T(sub e)(sup lambda) = 1.22 +/- 0.23 MK, match closely the EIT filter-ratio temperatures, T(sub e)(sup FIT) = 1.21 +/- 0.06 MK. We conclude that these rather large-scale loops (with heights of h approx. equals 50 - 200 Mm) that dominate EIT 171 A images are close to thermal equilibrium. Most of the loops show no significant thickness variation w(s), but many exhibit a trend of increasing temperature (dT/ds greater than 0) above the footpoint.

A loop-based neural architecture for structured behavior encoding and decoding.

PubMed

Gisiger, Thomas; Boukadoum, Mounir

2018-02-01

We present a new type of artificial neural network that generalizes on anatomical and dynamical aspects of the mammal brain. Its main novelty lies in its topological structure which is built as an array of interacting elementary motifs shaped like loops. These loops come in various types and can implement functions such as gating, inhibitory or executive control, or encoding of task elements to name a few. Each loop features two sets of neurons and a control region, linked together by non-recurrent projections. The two neural sets do the bulk of the loop's computations while the control unit specifies the timing and the conditions under which the computations implemented by the loop are to be performed. By functionally linking many such loops together, a neural network is obtained that may perform complex cognitive computations. To demonstrate the potential offered by such a system, we present two neural network simulations. The first illustrates the structure and dynamics of a single loop implementing a simple gating mechanism. The second simulation shows how connecting four loops in series can produce neural activity patterns that are sufficient to pass a simplified delayed-response task. We also show that this network reproduces electrophysiological measurements gathered in various regions of the brain of monkeys performing similar tasks. We also demonstrate connections between this type of neural network and recurrent or long short-term memory network models, and suggest ways to generalize them for future artificial intelligence research. Copyright © 2017 Elsevier Ltd. All rights reserved.

Specificity Rendering ‘Hot-Spots’ for Aurora Kinase Inhibitor Design: The Role of Non-Covalent Interactions and Conformational Transitions

PubMed Central

Badrinarayan, Preethi; Sastry, G. Narahari

2014-01-01

The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors. PMID:25485544

Entanglement entropy and correlations in loop quantum gravity

NASA Astrophysics Data System (ADS)

Feller, Alexandre; Livine, Etera R.

2018-02-01

Black hole entropy is one of the few windows into the quantum aspects of gravitation, and its study over the years has highlighted the holographic nature of gravity. At the non-perturbative level in quantum gravity, promising explanations are being explored in terms of the entanglement entropy between regions of space. In the context of loop quantum gravity, this translates into an analysis of the correlations between the regions of the spin network states defining the quantum state of the geometry of space. In this paper, we explore a class of states, motivated by results in condensed matter physics, satisfying an area law for entanglement entropy and having non-trivial correlations. We highlight that entanglement comes from holonomy operators acting on loops crossing the boundary of the region.

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

NASA Astrophysics Data System (ADS)

Dodani, Sheel C.; Kiss, Gert; Cahn, Jackson K. B.; Su, Ye; Pande, Vijay S.; Arnold, Frances H.

2016-05-01

The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate.

Solar-burst precursors and energy buildup at microwave wavelengths

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

Lang, K.R.; Willson, R.F.

High-resolution microwave observations (VLA) of heating and magnetic triggering in coronal loops are summarized. Magnetic changes that precede solar eruptions on time scales of tens of minutes involve primarily emerging coronal loops and the interaction of two or more loops. Thermal cyclotron lines were detected in coronal loops, suggesting the presence of hot current sheets that enhance emission from relatively thin layers of enhanced temperature and constant magnetic field. These current sheets may play a role in the excitation of solar bursts. A filament-associated source with a high brightness temperature and steep radiation spectrum occurs above a region of apparentlymore » weak photospheric field. This source might be attributed to currents that enhance coronal magnetic fields. Compact (phi=5 sec) transient sources with lifetimes of 30 to 60 minutes were also detected in regions of apparently weak photospheric field. VLA observations of coronal loops are compared with simultaneous SMM-XRP observations in conclusion.« less

The origin of morphological asymmetries in bipolar active regions. [magnetic field in solar convective envelope

NASA Technical Reports Server (NTRS)

Fan, Y.; Fisher, G. H.; Deluca, E. E.

1993-01-01

A series of 3D numerical simulations was carried out to examine the dynamical evolution of emerging flux loops in the solar convective envelope. The innermost portions of the loops are anchored beneath the base of the convective zone by the subadiabatic temperature gradient of the underlying overshoot region. It is found that, as the emerging loops approach the photosphere, the magnetic field strength of the leading side of each rising loop is about twice as large as that of the following side at the same depth. The evacuation of plasma out of the leading side of the rising loop results in an enhanced magnetic field strength there compared with the following side. It is argued that this result provides a natural explanation for the fact that the preceding (leading) polarity tends to have a less organized and more fragmented appearance, and that the preceding spots tend to be larger in area and fewer in number, and have a longer lifetime than the following spots.

Explosive site percolation with a product rule.

PubMed

Choi, Woosik; Yook, Soon-Hyung; Kim, Yup

2011-08-01

We study the site percolation under Achlioptas process with a product rule in a two-dimensional square lattice. From the measurement of the cluster size distribution P(s), we find that P(s) has a very robust power-law regime followed by a stable hump near the transition threshold. Based on the careful analysis on the PP(s) distribution, we show that the transition should be discontinuous. The existence of the hysteresis loop in order parameter also verifies that the transition is discontinuous in two dimensions. Moreover, we also show that the transition nature from the product rule is not the same as that from a sum rule in two dimensions.

Phenomenological Considerations of the Electric Field Induced Transitions in Improper Ferroelectrics and Ferroelastics. III. Application to Gd2(MoO4)3

NASA Astrophysics Data System (ADS)

Suzuki, Ikuo; Ishibashi, Yoshihiro

1987-02-01

The electric field induced phase transitions are discussed in the improper ferroelectrics and ferroelastics, where the high symmetry phase is assumed to be piezoelectric as in the gadolinium molybdate (GMO). The dependence on the electric field of the polarization is discussed, and the D-E hysteresis loops are compared with the one experimentally observed in GMO.

Supporting graduate nurse transition to practice through a quality assurance feedback loop.

PubMed

Phillips, Craig; Kenny, Amanda; Esterman, Adrian

2017-11-01

This mixed-method study focused on new graduate nurses and their transition to practice. Transition to practice can be a time of heightened stress and anxiety, leaving many new graduates disillusioned and dissatisfied with their work. The study explored how satisfaction levels with transition may improve during their first year, using a unique approach of a continuous quality assurance feedback loop. This assurance framework is utilised in hospitality, automotive and supply chain logistics and in health, primarily to monitor patient outcomes. However, an association with graduate nurse satisfaction has not been previously reported. Graduate nurses from two health services completed a short survey questionnaire every four weeks for 12 months. De-identified aggregated data was sent to health service management, giving them an opportunity to integrate the findings with the objective of potentially increasing graduate satisfaction ratings. Quantitative findings showed no statistical significance of graduate nurse satisfaction scores between health services, however, one health service consistently outperformed the other. Qualitative findings drawn from a seminar and interviews confirmed that one health service took a more proactive stance with the monthly reports, communicating the results to ward managers. Outcomes reflected a greater commitment of support and an overall increase of satisfaction scores. Copyright © 2017 Elsevier Ltd. All rights reserved.

"Complexity" in Polarity Transitions at the Matuyama-Brunhes Boundary and top Jaramillo in North Atlantic Deep-sea Sediments

NASA Astrophysics Data System (ADS)

Channell, J. E. T.

2016-12-01

Integrated Ocean Drilling Program (IODP) Expedition 303 to the North Atlantic provided 16 records of the Matuyama-Brunhes polarity transition (MBT) and the top Jaramillo transition, based on u-channel and discrete samples, from holes drilled at three sites (Sites U1304, U1305 and U1306) that have mean Brunhes sedimentation rates of 16-18 cm/kyr. The MBT occurs during the transition from marine isotope stage (MIS) 19.3 to MIS 18.4, with mid-point at 773 ka, and a transition duration of 5-8 kyr. The top Jaramillo occurs during MIS 28 at 992 ka with a similar 5 kyr transition duration. Combining the new records with previously published North Atlantic records (ODP Sites 983, 984 and 1063) yields a total of 24 high sedimentation rate records. The MBT yields a repetitive pattern of transitional field states as virtual geomagnetic poles (VGPs) move from high southern latitudes to loop over the Pacific, cluster in NE Asia, and transit into the mid-latitude South Atlantic before reaching high latitudes in the Northern Hemisphere. The VGPs for the top Jaramillo transition feature a loop over the Pacific, then occupation of the NE Asia cluster before transit over the Indian Ocean to high southerly latitudes. The North Atlantic MBT records described here are very different to the longitudinally constrained North Atlantic VGP paths from MBT records that are the basis for a 2007 Bayesian inversion of the MBT field. We conclude that the relatively low sedimentation rate ( 4 cm/kyr) records utilized in the Bayesian inversion have been heavily smoothed by the remanence acquisition process, and do not adequately represent the MBT field. The VGPs at the MBT and top Jaramillo, as measured in the North Atlantic, have similarities with excursion (Iceland Basin) VGP paths, and are apparently guided by maxima in downward vertical flux in the modern non-dipole (ND) field, implying longevity in ND features through time.

High-resolution imaging spectroscopy of two micro-pores and an arch filament system in a small emerging-flux region

NASA Astrophysics Data System (ADS)

González Manrique, S. J.; Bello González, N.; Denker, C.

2017-04-01

Context. Emerging flux regions mark the first stage in the accumulation of magnetic flux eventually leading to pores, sunspots, and (complex) active regions. These flux regions are highly dynamic, show a variety of fine structure, and in many cases live only for a short time (less than a day) before dissolving quickly into the ubiquitous quiet-Sun magnetic field. Aims: The purpose of this investigation is to characterize the temporal evolution of a minute emerging flux region, the associated photospheric and chromospheric flow fields, and the properties of the accompanying arch filament system. We aim to explore flux emergence and decay processes and investigate if they scale with structure size and magnetic flux contents. Methods: This study is based on imaging spectroscopy with the Göttingen Fabry-Pérot Interferometer at the Vacuum Tower Telescope, Observatorio del Teide, Tenerife, Spain on 2008 August 7. Photospheric horizontal proper motions were measured with Local correlation tracking using broadband images restored with multi-object multi-frame blind deconvolution. Cloud model (CM) inversions of line scans in the strong chromospheric absorption Hαλ656.28 nm line yielded CM parameters (Doppler velocity, Doppler width, optical thickness, and source function), which describe the cool plasma contained in the arch filament system. Results: The high-resolution observations cover the decay and convergence of two micro-pores with diameters of less than one arcsecond and provide decay rates for intensity and area. The photospheric horizontal flow speed is suppressed near the two micro-pores indicating that the magnetic field is already sufficiently strong to affect the convective energy transport. The micro-pores are accompanied by a small arch filament system as seen in Hα, where small-scale loops connect two regions with Hα line-core brightenings containing an emerging flux region with opposite polarities. The Doppler width, optical thickness, and source function reach the largest values near the Hα line-core brightenings. The chromospheric velocity of the cloud material is predominantly directed downwards near the footpoints of the loops with velocities of up to 12 km s-1, whereas loop tops show upward motions of about 3 km s-1. Some of the loops exhibit signs of twisting motions along the loop axis. Conclusions: Micro-pores are the smallest magnetic field concentrations leaving a photometric signature in the photosphere. In the observed case, they are accompanied by a miniature arch filament system indicative of newly emerging flux in the form of Ω-loops. Flux emergence and decay take place on a time-scale of about two days, whereas the photometric decay of the micro-pores is much more rapid (a few hours), which is consistent with the incipient submergence of Ω-loops. Considering lifetime and evolution timescales, impact on the surrounding photospheric proper motions, and flow speed of the chromospheric plasma at the loop tops and footpoints, the results are representative for the smallest emerging flux regions still recognizable as such.

Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer

PubMed Central

2015-01-01

Plexin-B1 is a single-pass transmembrane receptor. Its Rho GTPase binding domain (RBD) can associate with small Rho GTPases and can also self-bind to form a dimer. In total, more than 400 ns of NAMD molecular dynamics simulations were performed on RBD monomer and dimer. Different analysis methods, such as root mean squared fluctuation (RMSF), order parameters (S2), dihedral angle correlation, transfer entropy, principal component analysis, and dynamical network analysis, were carried out to characterize the motions seen in the trajectories. RMSF results show that after binding, the L4 loop becomes more rigid, but the L2 loop and a number of residues in other regions become slightly more flexible. Calculating order parameters (S2) for CH, NH, and CO bonds on both backbone and side chain shows that the L4 loop becomes essentially rigid after binding, but part of the L1 loop becomes slightly more flexible. Backbone dihedral angle cross-correlation results show that loop regions such as the L1 loop including residues Q25 and G26, the L2 loop including residue R61, and the L4 loop including residues L89–R91, are highly correlated compared to other regions in the monomer form. Analysis of the correlated motions at these residues, such as Q25 and R61, indicate two signal pathways. Transfer entropy calculations on the RBD monomer and dimer forms suggest that the binding process should be driven by the L4 loop and C-terminal. However, after binding, the L4 loop functions as the motion responder. The signal pathways in RBD were predicted based on a dynamical network analysis method using the pathways predicted from the dihedral angle cross-correlation calculations as input. It is found that the shortest pathways predicted from both inputs can overlap, but signal pathway 2 (from F90 to R61) is more dominant and overlaps all of the routes of pathway 1 (from F90 to P111). This project confirms the allosteric mechanism in signal transmission inside the RBD network, which was in part proposed in the previous experimental study. PMID:24901636

Steady State Model for Solar Coronal Loops

NASA Astrophysics Data System (ADS)

Sugiyama, L.; Asgari-Targhi, M.

2017-12-01

Solar coronal loops on the surface of the sun provide background magnetic and plasma structures for the release of a significant amount of the sun's energy, through energetic solar flares and coronal mass ejections and more gradual processes. Understanding their steady states is the first step in understanding loop dynamics. A consistent MHD steady state model, for a curved magnetic flux rope that contains plasma, has been developed[1] for simple coronal loops with both ends anchored in the photosphere. Plasma pressure or current makes the loop unstable to expansion in major radius and must be balanced by external forces, such as the solar gravity. The MHD momentum equation has a well defined small parameter ordering in the loop inverse aspect ratio ɛ=a/Ro (minor/major radius). Different types of common coronal loops fall in different parameter regimes, determined by the relative values of the plasma beta β=po/(Bo2/2μo), the MHD gravity parameter Ĝ≡ga/vA2 (the gravitational acceleration g normalized to the minor radius a and shear Alfvén velocity vA), and ɛ. The largest possible gravity, Ĝ ɛ1β, corresponds to the largest loops because it reduces the plasma density at the top of the loop exponentially compared to its lower ends, reducing the downward gravitational force -ρĜ there. The thin loops that are ubiquitous in solar active regions have ``high'' beta, β ɛ1, for ɛ≃0.02, and fit the predicted model scalings. The thicker loops that can give rise to flares and CMEs have ``low'' beta, β ɛ2. Cool loops, such as solar filaments outside active regions, that have a central pressure lower than that of the surrounding corona would have the strongest stability against radial expansion. The model raises a number of questions about the connection of loops to the photosphere and the force-free nature of the magnetic field there. [1] L. Sugiyama, M. Asgari-Targhi, Phys. Plasmas 24, 022904 (2017).

Combined deficiency of MSH2 and Sμ region abolishes class switch recombination.

PubMed

Leduc, Claire; Haddad, Dania; Laviolette-Malirat, Nathalie; Nguyen Huu, Ngoc-Sa; Khamlichi, Ahmed Amine

2010-10-01

Class switch recombination (CSR) is mediated by G-rich tandem repeated sequences termed switch regions. Transcription of switch regions generates single-stranded R loops that provide substrates for activation-induced cytidine deaminase. Mice deficient in MSH2 have a mild defect in CSR and analysis of their switch junctions has led to a model in which MSH2 is more critical for switch recombination events outside than within the tandem repeats. It is also known that deletion of the whole Sμ region severely impairs but does not abrogate CSR despite the lack of detectable R loops. Here, we demonstrate that deficiency of both MSH2 and the Sμ region completely abolishes CSR and that the abrogation occurs at the genomic level. This finding further supports the crucial role of MSH2 outside the tandem repeats. It also indicates that during CSR, MSH2 has access to activation-induced cytidine deaminase targets in R-loop-deficient Iμ-Cμ sequences rarely used in CSR, suggesting an MSH2-dependent DNA processing activity at the Iμ exon that may decrease with transcription elongation across the Sμ region.

Quantum loop corrections of a charged de Sitter black hole

NASA Astrophysics Data System (ADS)

Naji, J.

2018-03-01

A charged black hole in de Sitter (dS) space is considered and logarithmic corrected entropy used to study its thermodynamics. Logarithmic corrections of entropy come from thermal fluctuations, which play a role of quantum loop correction. In that case we are able to study the effect of quantum loop on black hole thermodynamics and statistics. As a black hole is a gravitational object, it helps to obtain some information about the quantum gravity. The first and second laws of thermodynamics are investigated for the logarithmic corrected case and we find that it is only valid for the charged dS black hole. We show that the black hole phase transition disappears in the presence of logarithmic correction.

First Imaging Observation of Standing Slow Wave in Coronal Fan Loops

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

Pant, V.; Tiwari, A.; Banerjee, D.

2017-09-20

We observe intensity oscillations along coronal fan loops associated with the active region AR 11428. The intensity oscillations were triggered by blast waves that were generated due to X-class flares in the distant active region AR 11429. To characterize the nature of oscillations, we created time–distance maps along the fan loops and noted that the intensity oscillations at two ends of the loops were out of phase. As we move along the fan loop, the amplitude of the oscillations first decreased and then increased. The out-of-phase nature together with the amplitude variation along the loop implies that these oscillations aremore » very likely to be standing waves. The period of the oscillations is estimated to be ∼27 minutes, damping time to be ∼45 minutes, and phase velocity projected in the plane of sky to be ∼65–83 km s{sup −1}. The projected phase speeds were in the range of the acoustic speed of coronal plasma at about 0.6 MK, which further indicates that these are slow waves. To the best of our knowledge, this is the first report on the existence of the standing slow waves in non-flaring fan loops.« less

MULTI-WAVELENGTH STUDY OF TRANSITION REGION PENUMBRAL SUBARCSECOND BRIGHT DOTS USING IRIS AND NST

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

Deng, Na; Liu, Chang; Xu, Yan

Using high-resolution transition region (TR) observations taken by the Interface Region Imaging Spectrograph ( IRIS ) mission, Tian et al. revealed numerous short-lived subarcsecond bright dots (BDs) above sunspots (mostly located in the penumbrae), which indicate yet unexplained small-scale energy releases. Moreover, whether or not these subarcsecond TR brightenings have any signature in the lower atmosphere and how they are formed are still not fully resolved. This paper presents a multi-wavelength study of the TR penumbral BDs using a coordinated observation of a near disk center sunspot with IRIS and the 1.6 m New Solar Telescope (NST) at the Bigmore » Bear Solar Observatory. NST provides high-resolution chromospheric and photospheric observations with narrowband H α imaging spectroscopy and broadband TiO images, respectively, complementary to IRIS TR observations. A total of 2692 TR penumbral BDs are identified from a 37 minute time series of IRIS 1400 Å slit-jaw images. Their locations tend to be associated more with downflowing and darker fibrils in the chromosphere, and weakly associated with bright penumbral features in the photosphere. However, temporal evolution analyses of the BDs show that there is no consistent and convincing brightening response in the chromosphere. These results are compatible with a formation mechanism of the TR penumbral BDs by falling plasma from coronal heights along more vertical and dense magnetic loops. The BDs may also be produced by small-scale impulsive magnetic reconnection taking place sufficiently high in the atmosphere that has no energy release in the chromosphere.« less

Modification of "Pressed" Atmospheres in Active Regions of Ultracool Stars

NASA Astrophysics Data System (ADS)

Zaitsev, V. V.; Kronshtadtov, P. V.; Stepanov, A. V.

2017-12-01

Ultracool stars usually have active regions, which is confirmed by their high-power radiofrequency emission modulated by the star axial rotation. The interpretation of this emission is commonly based on the electron cyclotron maser mechanism realized in the active regions. A plasma mechanism of radiofrequency emission is not considered, because ultracool star atmospheres are tightly "pressed" against the star surface, and the plasma frequency is much lower than the electron gyrofrequency ( f L ≪ f B) at the coronal levels. This paper explores active regions of ultracool stars for the possible existence of a system of coronal magnetic loops carrying electric current generated by photospheric convection. It is shown that current dissipation induces a temperature increase inside the loops to about 107 K, which causes an increase in the scale of height of the inhomogeneous atmosphere and, at the coronal levels, effectuates condition f L ≫ f B, at which the plasma mechanism of radiofrequency emission prevails over the electron cyclotron maser mechanism. The magnetic loop parameters, intensity of electric currents generated by the photospheric convection, and efficiency of plasma heating inside the magnetic loops are evaluated on the example of the brown dwarf TVLM513-46546. The scale of the height of the modified atmosphere, which appears to be comparable to the star radius, is calculated; it is shown that the soft X-ray flow created by the hot modified atmosphere inside a coronal magnetic loop is about equal to that observed for brown dwarf TVLM513-46546.

The Heating of Solar Coronal Loops by Alfvén Wave Turbulence

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

Van Ballegooijen, A. A.; Asgari-Targhi, M.; Voss, A.

2017-11-01

In this paper we further develop a model for the heating of coronal loops by Alfvén wave turbulence (AWT). The Alfvén waves are assumed to be launched from a collection of kilogauss flux tubes in the photosphere at the two ends of the loop. Using a three-dimensional magnetohydrodynamic model for an active-region loop, we investigate how the waves from neighboring flux tubes interact in the chromosphere and corona. For a particular combination of model parameters we find that AWT can produce enough heat to maintain a peak temperature of about 2.5 MK, somewhat lower than the temperatures of 3–4 MKmore » observed in the cores of active regions. The heating rates vary strongly in space and time, but the simulated heating events have durations less than 1 minute and are unlikely to reproduce the observed broad differential emission measure distributions of active regions. The simulated spectral line nonthermal widths are predicted to be about 27 km s{sup −1}, which is high compared to the observed values. Therefore, the present AWT model does not satisfy the observational constraints. An alternative “magnetic braiding” model is considered in which the coronal field lines are subject to slow random footpoint motions, but we find that such long-period motions produce much less heating than the shorter-period waves launched within the flux tubes. We discuss several possibilities for resolving the problem of producing sufficiently hot loops in active regions.« less

Complex folding and misfolding effects of deer-specific amino acid substitutions in the β2-α2 loop of murine prion protein

NASA Astrophysics Data System (ADS)

Agarwal, Sonya; Döring, Kristina; Gierusz, Leszek A.; Iyer, Pooja; Lane, Fiona M.; Graham, James F.; Goldmann, Wilfred; Pinheiro, Teresa J. T.; Gill, Andrew C.

2015-10-01

The β2-α2 loop of PrPC is a key modulator of disease-associated prion protein misfolding. Amino acids that differentiate mouse (Ser169, Asn173) and deer (Asn169, Thr173) PrPC appear to confer dramatically different structural properties in this region and it has been suggested that amino acid sequences associated with structural rigidity of the loop also confer susceptibility to prion disease. Using mouse recombinant PrP, we show that mutating residue 173 from Asn to Thr alters protein stability and misfolding only subtly, whilst changing Ser to Asn at codon 169 causes instability in the protein, promotes oligomer formation and dramatically potentiates fibril formation. The doubly mutated protein exhibits more complex folding and misfolding behaviour than either single mutant, suggestive of differential effects of the β2-α2 loop sequence on both protein stability and on specific misfolding pathways. Molecular dynamics simulation of protein structure suggests a key role for the solvent accessibility of Tyr168 in promoting molecular interactions that may lead to prion protein misfolding. Thus, we conclude that ‘rigidity’ in the β2-α2 loop region of the normal conformer of PrP has less effect on misfolding than other sequence-related effects in this region.

Slow Magnetosonic Waves and Fast Flows in Active Region Loops

NASA Technical Reports Server (NTRS)

Ofman, L.; Wang, T. J.; Davila, J. M.

2012-01-01

Recent extreme ultraviolet spectroscopic observations indicate that slow magnetosonic waves are present in active region (AR) loops. Some of the spectral data were also interpreted as evidence of fast (approx 100-300 km/s) quasiperiodic flows. We have performed three-dimensional magnetohydrodynamic (3D MHD) modeling of a bipolar AR that contains impulsively generated waves and flows in coronal loops. The model AR is initiated with a dipole magnetic field and gravitationally stratified density, with an upflow-driven steadily or periodically in localized regions at the footpoints of magnetic loops. The resulting flows along the magnetic field lines of the AR produce higher density loops compared to the surrounding plasma by injection of material into the flux tubes and the establishment of siphon flow.We find that the impulsive onset of flows with subsonic speeds result in the excitation of damped slow magnetosonic waves that propagate along the loops and coupled nonlinearly driven fast-mode waves. The phase speed of the slow magnetosonic waves is close to the coronal sound speed. When the amplitude of the driving pulses is increased we find that slow shock-like wave trains are produced. When the upflows are driven periodically, undamped oscillations are produced with periods determined by the periodicity of the upflows. Based on the results of the 3D MHD model we suggest that the observed slow magnetosonic waves and persistent upflows may be produced by the same impulsive events at the bases of ARs.

Simultaneous Solar Maximum Mission (SMM) and Very Large Array (VLA) observations of solar active regions

NASA Technical Reports Server (NTRS)

Willson, Robert F.

1991-01-01

Very Large Array observations at 20 cm wavelength can detect the hot coronal plasma previously observed at soft x ray wavelengths. Thermal cyclotron line emission was detected at the apex of coronal loops where the magnetic field strength is relatively constant. Detailed comparison of simultaneous Solar Maximum Mission (SMM) Satellite and VLA data indicate that physical parameters such as electron temperature, electron density, and magnetic field strength can be obtained, but that some coronal loops remain invisible in either spectral domain. The unprecedent spatial resolution of the VLA at 20 cm wavelength showed that the precursor, impulsive, and post-flare components of solar bursts originate in nearby, but separate loops or systems of loops.. In some cases preburst heating and magnetic changes are observed from loops tens of minutes prior to the impulsive phase. Comparisons with soft x ray images and spectra and with hard x ray data specify the magnetic field strength and emission mechanism of flaring coronal loops. At the longer 91 cm wavelength, the VLA detected extensive emission interpreted as a hot 10(exp 5) K interface between cool, dense H alpha filaments and the surrounding hotter, rarefield corona. Observations at 91 cm also provide evidence for time-correlated bursts in active regions on opposite sides of the solar equator; they are attributed to flare triggering by relativistic particles that move along large-scale, otherwise-invisible, magnetic conduits that link active regions in opposite hemispheres of the Sun.

Dose response relationship in anti-stress gene regulatory networks.

PubMed

Zhang, Qiang; Andersen, Melvin E

2007-03-02

To maintain a stable intracellular environment, cells utilize complex and specialized defense systems against a variety of external perturbations, such as electrophilic stress, heat shock, and hypoxia, etc. Irrespective of the type of stress, many adaptive mechanisms contributing to cellular homeostasis appear to operate through gene regulatory networks that are organized into negative feedback loops. In general, the degree of deviation of the controlled variables, such as electrophiles, misfolded proteins, and O2, is first detected by specialized sensor molecules, then the signal is transduced to specific transcription factors. Transcription factors can regulate the expression of a suite of anti-stress genes, many of which encode enzymes functioning to counteract the perturbed variables. The objective of this study was to explore, using control theory and computational approaches, the theoretical basis that underlies the steady-state dose response relationship between cellular stressors and intracellular biochemical species (controlled variables, transcription factors, and gene products) in these gene regulatory networks. Our work indicated that the shape of dose response curves (linear, superlinear, or sublinear) depends on changes in the specific values of local response coefficients (gains) distributed in the feedback loop. Multimerization of anti-stress enzymes and transcription factors into homodimers, homotrimers, or even higher-order multimers, play a significant role in maintaining robust homeostasis. Moreover, our simulation noted that dose response curves for the controlled variables can transition sequentially through four distinct phases as stressor level increases: initial superlinear with lesser control, superlinear more highly controlled, linear uncontrolled, and sublinear catastrophic. Each phase relies on specific gain-changing events that come into play as stressor level increases. The low-dose region is intrinsically nonlinear, and depending on the level of local gains, presence of gain-changing events, and degree of feedforward gene activation, this region can appear as superlinear, sublinear, or even J-shaped. The general dose response transition proposed here was further examined in a complex anti-electrophilic stress pathway, which involves multiple genes, enzymes, and metabolic reactions. This work would help biologists and especially toxicologists to better assess and predict the cellular impact brought about by biological stressors.

THE LITTLEST HIGGS MODEL AND ONE-LOOP ELECTROWEAK PRECISION CONSTRAINTS.

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

CHEN, M.C.; DAWSON,S.

2004-06-16

We present in this talk the one-loop electroweak precision constraints in the Littlest Higgs model, including the logarithmically enhanced contributions from both fermion and scalar loops. We find the one-loop contributions are comparable to the tree level corrections in some regions of parameter space. A low cutoff scale is allowed for a non-zero triplet VEV. Constraints on various other parameters in the model are also discussed. The role of triplet scalars in constructing a consistent renormalization scheme is emphasized.

Complex astrophysical experiments relating to jets, solar loops, and water ice dusty plasma

NASA Astrophysics Data System (ADS)

Bellan, P. M.; Zhai, X.; Chai, K. B.; Ha, B. N.

2015-10-01

> Recent results of three astrophysically relevant experiments at Caltech are summarized. In the first experiment magnetohydrodynamically driven plasma jets simulate astrophysical jets that undergo a kink instability. Lateral acceleration of the kinking jet spawns a Rayleigh-Taylor instability, which in turn spawns a magnetic reconnection. Particle heating and a burst of waves are observed in association with the reconnection. The second experiment uses a slightly different setup to produce an expanding arched plasma loop which is similar to a solar corona loop. It is shown that the plasma in this loop results from jets originating from the electrodes. The possibility of a transition from slow to fast expansion as a result of the expanding loop breaking free of an externally imposed strapping magnetic field is investigated. The third and completely different experiment creates a weakly ionized plasma with liquid nitrogen cooled electrodes. Water vapour injected into this plasma forms water ice grains that in general are ellipsoidal and not spheroidal. The water ice grains can become quite long (up to several hundred microns) and self-organize so that they are evenly spaced and vertically aligned.

An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis.

PubMed Central

Szewczak, A A; Cech, T R

1997-01-01

RNA molecules commonly consist of helical regions separated by internal loops, and in many cases these internal loops have been found to assume stable structures. We have examined the function and dynamics of an internal loop, J5/5a, that joins the two halves of the P4-P6 domain of the Tetrahymena self-splicing group I intron. P4-P6 RNAs with mutations in the J5/5a region showed nondenaturing gel electrophoretic mobilities and levels of Fe(II)-EDTA cleavage protection intermediate between those of wild-type RNA and a mutant incapable of folding into the native P4-P6 tertiary structure. Mutants with the least structured J5/5a loops behaved the most like wild-type P4-P6, and required smaller amounts of Mg2+ to rescue folding. The activity of reconstituted introns containing mutant P4-P6 RNAs correlated similarly with the nature of the J5/5a mutation. Our results suggest that, in solution, the P4-P6 RNA is in a two-state equilibrium between folded and unfolded states. We conclude that this internal loop mainly acts as a flexible hinge, allowing the coaxially stacked helical regions on either side of it to interact via specific tertiary contacts. To a lesser extent, the specific bases within the loop contribute to folding. Furthermore, it is crucial that the junction remain unstructured in the unfolded state. These conclusions cannot be derived from a simple examination of the P4-P6 crystal structure (Cate JH et al., 1996, Science 273:1678-1685), showing once again that structure determination must be supplemented with mutational and thermodynamic analysis to provide a complete picture of a folded macromolecule. PMID:9257643

Magnetic Field Configuration of Active Region NOAA 6555 at the Time of a Long Duration Flare on 23 March 1991: An Exception to Standard Flare Reconnection Model

NASA Technical Reports Server (NTRS)

Choudhary, Debi Prasad; Gary, Allen G.

1998-01-01

The high-resolution H(sub alpha) images observed during the decay phase of a long duration flare on 23 March 1991 are used to study the three-dimensional magnetic field configuration of the active region NOAA 6555. Whereas, all the large flares in NOAA 6555 occurred at the location of high magnetic shear and flux emergence, this long duration flare was observed in the region of low magnetic shear at the photosphere. The H(sub alpha) loop activity started soon after the maximum phase of the flare. There were few long loop at the initial phase of the activity. Some of these were sheared in the chromosphere at an angle of about 45 deg with the east-west axis. Gradually, increasing number of shorter loops, oriented along the east-west axis, started appearing. The chromospheric Dopplergrams show blue-shifts at the end points of the loops. By using different magnetic field models, we have extrapolated the photospheric magnetograms to the chromospheric heights. The magnetic field lines computed by using the potential field model correspond to most of the observed H(sub alpha) loops. The height of the H(sub alpha) loops were derived by comparing them with the computed field lines. From the temporal evolution of the H(sub alpha) loop activity, we derive the negative rate of appearance of H(sub alpha) features as a function of height. It is found that the field lines oriented along one of the neutral lines was sheared and low lying. The higher field lines were mostly potential. The paper also outlines a possible scenario for describing the post-flare stage of the observed long duration flare.

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

PubMed Central

Bozek, Katarzyna; Lengauer, Thomas; Sierra, Saleta; Kaiser, Rolf; Domingues, Francisco S.

2013-01-01

The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%). We additionally assessed the predictive power of the new method on clinically derived ‘bulk’ sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/. PMID:23555214

Excitation of flare-induced waves in coronal loops and the effects of radiative cooling

NASA Astrophysics Data System (ADS)

Provornikova, Elena; Ofman, Leon; Wang, Tongjiang

2018-01-01

EUV imaging observations from several space missions (SOHO/EIT, TRACE, and SDO/AIA) have revealed a presence of propagating intensity disturbances in solar coronal loops. These disturbances are typically interpreted as slow magnetoacoustic waves. However, recent spectroscopic observations with Hinode/EIS of active region loops revealed that the propagating intensity disturbances are associated with intermittent plasma upflows (or jets) at the footpoints which are presumably generated by magnetic reconnection. For this reason, whether these disturbances are waves or periodic flows is still being studied. This study is aimed at understanding the physical properties of observed disturbances by investigating the excitation of waves by hot plasma injections from below and the evolution of flows and wave propagation along the loop. We expand our previous studies based on isothermal 3D MHD models of an active region to a more realistic model that includes full energy equation accounting for the effects of radiative losses. Computations are initialized with an equilibrium state of a model active region using potential (dipole) magnetic field, gravitationally stratified density and temperature obtained from the polytropic equation of state. We model an impulsive injection of hot plasma into the steady plasma outflow along the loops of different temperatures, warm (∼1 MK) and hot (∼6 MK). The simulations show that hot jets launched at the coronal base excite slow magnetoacoustic waves that propagate to high altitudes along the loops, while the injected hot flows decelerate rapidly with heights. Our results support that propagating disturbances observed in EUV are mainly the wave features. We also find that the effect of radiative cooling on the damping of slow-mode waves in 1-6 MK coronal loops is small, in agreement with the previous conclusion based on 1D MHD models.

Are Complex Magnetic Field Structures Responsible for the Confined X-class Flares in Super Active Region 12192?

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

Zhang, Jun; Li, Ting; Chen, Huadong, E-mail: zjun@nao.cas.cn, E-mail: hdchen@nao.cas.cn

From 2014 October 19 to 27, six X-class flares occurred in super active region (AR) 12192. They were all confined flares and were not followed by coronal mass ejections. To examine the structures of the four flares close to the solar disk center from October 22 to 26, we firstly employ composite triple-time images in each flare process to display the stratified structure of these flare loops. The loop structures of each flare in both the lower (171 Å) and higher (131 Å) temperature channels are complex, e.g., the flare loops rooting at flare ribbons are sheared or twisted (enwound)more » together, and the complex structures were not destroyed during the flares. For the first flare, although the flare loop system appears as a spindle shape, we can estimate its structures from observations, with lengths ranging from 130 to 300 Mm, heights from 65 to 150 Mm, widths at the middle part of the spindle from 40 to 100 Mm, and shear angles from 16° to 90°. Moreover, the flare ribbons display irregular movements, such as the left ribbon fragments of the flare on October 22 sweeping a small region repeatedly, and both ribbons of the flare on October 26 moved along the same direction instead of separating from each other. These irregular movements also imply that the corresponding flare loops are complex, e.g., several sets of flare loops are twisted together. Although previous studies have suggested that the background magnetic fields prevent confined flares from erupting,based on these observations, we suggest that complex flare loop structures may be responsible for these confined flares.« less

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

Noncoherent pseudonoise code tracking performance of spread spectrum receivers

NASA Technical Reports Server (NTRS)

Simon, M. K.

1977-01-01

The optimum design and performance of two noncoherent PN tracking loop configurations, namely, the delay-locked loop and tau-dither loop, are described. In particular, the bandlimiting effects of the bandpass arm filters are considered by demonstrating that for a fixed data rate and data signal-to-noise ratio, there exists an optimum filter bandwidth in the sense of minimizing the loop's tracking jitter. Both the linear and nonlinear loop analyses are presented, and the region of validity of the former relative to the latter is indicated. In addition, numerical results are given for several filter types. For example, assuming ideal bandpass arm filters, it is shown that the tau-dither loop requires approximately 1 dB more signal-to-noise ratio than the delay-locked loop for equal rms tracking jitters.

Phylogeography, genetic diversity and demographic history of the Iranian Kurdish groups based on mtDNA sequences.

PubMed

Zarei, Fatah; Rajabi-Maham, Hassan

2016-12-01

Throughout the history of modern humans, the current Kurdish-inhabited area has served as part of a tricontinental crossroad for major human migrations. Also, a significant body of archaeological evidence points to this area as the site of Neolithic transition. To investigate the phylogeography, origins and demographic history, mtDNA D-loop region of individuals representing four Kurdish groups from Iran were analysed. Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased drift due to small population size; while in the Kurmanji group it indicated a bias towards drift or mass migration events during the 5-18th century AD. The Mantel test showed strong isolation by distance, and AMOVA results for global and regional scales confirmed that the geography had acted as the main driving force in shaping the current pattern of mtDNA diversity, rather than linguistic similarity. The results of demographic analyses, in agreement with archaeological data, revealed a recent expansion of the Kurds (~9,500 years before present) related to the Neolithic transition from hunting and gathering, to farming and cattle breeding in the Near East. Further, the high frequencies of typical haplogroups for early farmers (H; 37.1%) and hunter-gatherers (U; 13.8%) in the Kurds may testify the earlier hunter-gatherers in the Kurdish-inhabited area that adopted and admixed the Kurds ancestors following the Neolithic transition.

DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner.

PubMed

Wiedemann, Eva-Maria; Peycheva, Mihaela; Pavri, Rushad

2016-12-13

Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Simulations of fully deformed oscillating flux tubes

NASA Astrophysics Data System (ADS)

Karampelas, K.; Van Doorsselaere, T.

2018-02-01

Context. In recent years, a number of numerical studies have been focusing on the significance of the Kelvin-Helmholtz instability in the dynamics of oscillating coronal loops. This process enhances the transfer of energy into smaller scales, and has been connected with heating of coronal loops, when dissipation mechanisms, such as resistivity, are considered. However, the turbulent layer is expected near the outer regions of the loops. Therefore, the effects of wave heating are expected to be confined to the loop's external layers, leaving their denser inner parts without a heating mechanism. Aim. In the current work we aim to study the spatial evolution of wave heating effects from a footpoint driven standing kink wave in a coronal loop. Methods: Using the MPI-AMRVAC code, we performed ideal, three dimensional magnetohydrodynamic simulations of footpoint driven transverse oscillations of a cold, straight coronal flux tube, embedded in a hotter environment. We have also constructed forward models for our simulation using the FoMo code. Results: The developed transverse wave induced Kelvin-Helmholtz (TWIKH) rolls expand throughout the tube cross-section, and cover it entirely. This turbulence significantly alters the initial density profile, leading to a fully deformed cross section. As a consequence, the resistive and viscous heating rate both increase over the entire loop cross section. The resistive heating rate takes its maximum values near the footpoints, while the viscous heating rate at the apex. Conclusions: We conclude that even a monoperiodic driver can spread wave heating over the whole loop cross section, potentially providing a heating source in the inner loop region. Despite the loop's fully deformed structure, forward modelling still shows the structure appearing as a loop. A movie attached to Fig. 1 is available at http://https://www.aanda.org

Conversion from mutual helicity to self-helicity observed with IRIS

NASA Astrophysics Data System (ADS)

Li, L. P.; Peter, H.; Chen, F.; Zhang, J.

2014-10-01

Context. In the upper atmosphere of the Sun observations show convincing evidence for crossing and twisted structures, which are interpreted as mutual helicity and self-helicity. Aims: We use observations with the new Interface Region Imaging Spectrograph (IRIS) to show the conversion of mutual helicity into self-helicity in coronal structures on the Sun. Methods: Using far UV spectra and slit-jaw images from IRIS and coronal images and magnetograms from SDO, we investigated the evolution of two crossing loops in an active region, in particular, the properties of the Si IV line profile in cool loops. Results: In the early stage two cool loops cross each other and accordingly have mutual helicity. The Doppler shifts in the loops indicate that they wind around each other. As a consequence, near the crossing point of the loops (interchange) reconnection sets in, which heats the plasma. This is consistent with the observed increase of the line width and of the appearance of the loops at higher temperatures. After this interaction, the two new loops run in parallel, and in one of them shows a clear spectral tilt of the Si IV line profile. This is indicative of a helical (twisting) motion, which is the same as to say that the loop has self-helicity. Conclusions: The high spatial and spectral resolution of IRIS allowed us to see the conversion of mutual helicity to self-helicity in the (interchange) reconnection of two loops. This is observational evidence for earlier theoretical speculations. Movie associated with Fig. 1 and Appendix A are available in electronic form at http://www.aanda.org

Computer simulation of magnetic resonance spectra employing homotopy.

PubMed

Gates, K E; Griffin, M; Hanson, G R; Burrage, K

1998-11-01

Multidimensional homotopy provides an efficient method for accurately tracing energy levels and hence transitions in the presence of energy level anticrossings and looping transitions. Herein we describe the application and implementation of homotopy to the analysis of continuous wave electron paramagnetic resonance spectra. The method can also be applied to electron nuclear double resonance, electron spin echo envelope modulation, solid-state nuclear magnetic resonance, and nuclear quadrupole resonance spectra. Copyright 1998 Academic Press.

Velocity Measurements for a Solar Active Region Fan Loop from Hinode/EIS Observations

NASA Astrophysics Data System (ADS)

Young, P. R.; O'Dwyer, B.; Mason, H. E.

2012-01-01

The velocity pattern of a fan loop structure within a solar active region over the temperature range 0.15-1.5 MK is derived using data from the EUV Imaging Spectrometer (EIS) on board the Hinode satellite. The loop is aligned toward the observer's line of sight and shows downflows (redshifts) of around 15 km s-1 up to a temperature of 0.8 MK, but for temperatures of 1.0 MK and above the measured velocity shifts are consistent with no net flow. This velocity result applies over a projected spatial distance of 9 Mm and demonstrates that the cooler, redshifted plasma is physically disconnected from the hotter, stationary plasma. A scenario in which the fan loops consist of at least two groups of "strands"—one cooler and downflowing, the other hotter and stationary—is suggested. The cooler strands may represent a later evolutionary stage of the hotter strands. A density diagnostic of Mg VII was used to show that the electron density at around 0.8 MK falls from 3.2 × 109 cm-3 at the loop base, to 5.0 × 108 cm-3 at a projected height of 15 Mm. A filling factor of 0.2 is found at temperatures close to the formation temperature of Mg VII (0.8 MK), confirming that the cooler, downflowing plasma occupies only a fraction of the apparent loop volume. The fan loop is rooted within a so-called outflow region that displays low intensity and blueshifts of up to 25 km s-1 in Fe XII λ195.12 (formed at 1.5 MK), in contrast to the loop's redshifts of 15 km s-1 at 0.8 MK. A new technique for obtaining an absolute wavelength calibration for the EIS instrument is presented and an instrumental effect, possibly related to a distorted point-spread function, that affects velocity measurements is identified.

VELOCITY MEASUREMENTS FOR A SOLAR ACTIVE REGION FAN LOOP FROM HINODE/EIS OBSERVATIONS

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

Young, P. R.; O'Dwyer, B.; Mason, H. E.

2012-01-01

The velocity pattern of a fan loop structure within a solar active region over the temperature range 0.15-1.5 MK is derived using data from the EUV Imaging Spectrometer (EIS) on board the Hinode satellite. The loop is aligned toward the observer's line of sight and shows downflows (redshifts) of around 15 km s{sup -1} up to a temperature of 0.8 MK, but for temperatures of 1.0 MK and above the measured velocity shifts are consistent with no net flow. This velocity result applies over a projected spatial distance of 9 Mm and demonstrates that the cooler, redshifted plasma is physicallymore » disconnected from the hotter, stationary plasma. A scenario in which the fan loops consist of at least two groups of 'strands'-one cooler and downflowing, the other hotter and stationary-is suggested. The cooler strands may represent a later evolutionary stage of the hotter strands. A density diagnostic of Mg VII was used to show that the electron density at around 0.8 MK falls from 3.2 Multiplication-Sign 10{sup 9} cm{sup -3} at the loop base, to 5.0 Multiplication-Sign 10{sup 8} cm{sup -3} at a projected height of 15 Mm. A filling factor of 0.2 is found at temperatures close to the formation temperature of Mg VII (0.8 MK), confirming that the cooler, downflowing plasma occupies only a fraction of the apparent loop volume. The fan loop is rooted within a so-called outflow region that displays low intensity and blueshifts of up to 25 km s{sup -1} in Fe XII {lambda}195.12 (formed at 1.5 MK), in contrast to the loop's redshifts of 15 km s{sup -1} at 0.8 MK. A new technique for obtaining an absolute wavelength calibration for the EIS instrument is presented and an instrumental effect, possibly related to a distorted point-spread function, that affects velocity measurements is identified.« less

Impact of a small ellipticity on the sustainability condition of developed turbulence in a precessing spheroid

NASA Astrophysics Data System (ADS)

Horimoto, Yasufumi; Simonet-Davin, Gabriel; Katayama, Atsushi; Goto, Susumu

2018-04-01

We experimentally investigate the flow transition to developed turbulence in a precessing spheroid with a small ellipticity. Fully developed turbulence appears through a subcritical transition when we fix the Reynolds number (the spin rate) and gradually increase the Poincaré number (the precession rate). In the transitional range of the Poincaré number, two qualitatively different turbulent states (i.e., fully developed turbulence and quiescent turbulence with a spin-driven global circulation) are stable and they are connected by a hysteresis loop. This discontinuous transition is in contrast to the continuous transition in a precessing sphere, for which neither bistable turbulent states nor hysteresis loops are observed. The small ellipticity of the container makes the global circulation of the confined fluid more stable, and it requires much stronger precession of the spheroid, than a sphere, for fully developed turbulence to be sustained. Nevertheless, once fully developed turbulence is sustained, its flow structures are almost identical in the spheroid and sphere. The argument [Lorenzani and Tilgner, J. Fluid Mech. 492, 363 (2003), 10.1017/S002211200300572X; Noir et al., Geophys. J. Int. 154, 407 (2003), 10.1046/j.1365-246X.2003.01934.x] on the basis of the analytical solution [Busse, J. Fluid Mech. 33, 739 (1968), 10.1017/S0022112068001655] of the steady global circulation in a weak precession range well describes the onset of the fully developed turbulence in the spheroid.

Strings with a confining core in a quark-gluon plasma

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

Layek, Biswanath; Mishra, Ananta P.; Srivastava, Ajit M.

2005-04-01

We consider the intersection of N different interfaces interpolating between different Z{sub N} vacua of an SU(N) gauge theory using the Polyakov loop order parameter. Topological arguments show that at such a stringlike junction, the order parameter should vanish, implying that the core of this string (i.e. the junction region of all the interfaces) is in the confining phase. Using the effective potential for the Polyakov loop proposed by Pisarski for QCD, we use numerical minimization technique and estimate the energy per unit length of the core of this string to be about 2.7 GeV/fm at a temperature about twicemore » the critical temperature. For the parameters used, the interface tension is obtained to be about 7 GeV/fm{sup 2}. Lattice simulation of pure gauge theories should be able to investigate properties of these strings. For QCD with quarks, it has been discussed in the literature that this Z{sub N} symmetry may still be meaningful, with quark contributions leading to explicit breaking of this Z{sub N} symmetry. With this interpretation, such quark-gluon plasma strings may play important role in the evolution of the quark-gluon plasma phase and in the dynamics of quark-hadron transition.« less

Origin of the High-speed Jets Fom Magnetic Flux Emergence in the Solar Transition Region as well as Their Mass and Energy Contribuctions to the Solar Wind

NASA Astrophysics Data System (ADS)

Liping, Y.; He, J.; Peter, H.; Tu, C. Y.; Feng, X. S.

2015-12-01

In the solar atmosphere, the jets are ubiquitous and found to be at various spatia-temporal scales. They are significant to understand energy and mass transport in the solar atmosphere. Recently, the high-speed transition region jets are reported from the observation. Here we conduct a numerical simulation to investigate the mechanism in their formation, as well as their mass and energy contributions to the solar wind. Driven by the supergranular convection motion, the magnetic reconnection between the magnetic loop and the background open flux occurring in the transition region is simulated with a two-dimensional MHD model. The simulation results show that not only a fast hot jet, much resemble the found transition region jets, but also a adjacent slow cool jet, mostly like classical spicules, is launched. The force analysis shows that the fast hot jet is continually driven by the Lorentz force around the reconnection region, while the slow cool jet is induced by an initial kick through the Lorentz force associated with the emerging magnetic flux. Also, the features of the driven jets change with the amount of the emerging magnetic flux, giving the varieties of both jets.With the developed one-dimensional hydrodynamic solar wind model, the time-dependent pulses are imposed at the bottom to simulate the jet behaviors. The simulation results show that without other energy source, the injected plasmas are accelerated effectively to be a transonic wind with a substantial mass flux. The rapid acceleration occurs close to the Sun, and the resulting asymptotic speeds, number density at 0.3 AU, as well as mass flux normalized to 1 AU are compatible with in site observations. As a result of the high speed, the imposed pulses lead to a train of shocks traveling upward. By tracing the motions of the injected plasma, it is found that these shocks heat and accelerate the injected plasma to make part of them propagate upward and eventually escape. The parametric study shows that as the speed and temperature of the imposed pulses increase, we get an increase of the speed and temperature of the driven solar wind, which do not be influenced by the increase of the number density of the imposed pulses. When the recurring period of the imposed pulses decreases, the obtained solar wind becomes slower and cooler.

Velocity vector imaging fails to quantify regional myocardial dysfunction in a mouse model of isoprenaline-induced cardiotoxicity.

PubMed

Täng, Margareta Scharin; Redfors, Bjorn; Shao, Yangzhen; Omerovic, Elmir

2012-08-01

Regional myocardial deformation patterns are important in a variety of cardiac diseases, including stress-induced cardiomyopathy. Velocity-vector-based imaging is a speckle-tracking echocardiography (STE)-based algorithm that has been shown to allow in-depth cardiac phenotyping in humans. Regional posterior wall myocardial dysfunction occurs during severe isoprenaline stress in mice. We have previously shown that regional posterior wall end-systolic transmural strain decreases after severe isoprenaline toxicity in mice. We hypothesize that STE can detect and further quantify these perturbations. Twenty-three mice underwent echocardiographic examination using the VEVO2100 system. Regional transmural radial strain and strain rate were calculated in both parasternal short-axis and parasternal long-axis cine loops using the VisualSonics VEVO 2100 velocity vector imaging (VVI) STE algorithm. Eight C57BL/6 mice underwent baseline echocardiographic examination using the VisualSonics VEVO 770 system, which can acquire >1,000 frames/s cine loops. In a parasternal short-axis cine loop, the heart was divided into six segments, and regional fractional wall thickening (FWT) was assessed manually. The same protocols were also performed 90 minutes post 400 mg/kg intraperitoneally isoprenaline. Regional myocardial FWT is uniform at baseline but increases significantly in anterolateral segments, whereas it decreases significantly in posterior segments (P < 0.05). A similar pattern is seen using the VVI algorithm although the variance is larger, and differences are smaller and fail to reach significance. VVI is less sensitive in detecting regional perturbations in myocardial function than manual tracing, possibly due to the low frame rate in the cine loops used. © 2012, Wiley Periodicals, Inc.

Coronal rain in magnetic bipolar weak fields

NASA Astrophysics Data System (ADS)

Xia, C.; Keppens, R.; Fang, X.

2017-07-01

Aims: We intend to investigate the underlying physics for the coronal rain phenomenon in a representative bipolar magnetic field, including the formation and the dynamics of coronal rain blobs. Methods: With the MPI-AMRVAC code, we performed three dimensional radiative magnetohydrodynamic (MHD) simulation with strong heating localized on footpoints of magnetic loops after a relaxation to quiet solar atmosphere. Results: Progressive cooling and in-situ condensation starts at the loop top due to radiative thermal instability. The first large-scale condensation on the loop top suffers Rayleigh-Taylor instability and becomes fragmented into smaller blobs. The blobs fall vertically dragging magnetic loops until they reach low-β regions and start to fall along the loops from loop top to loop footpoints. A statistic study of the coronal rain blobs finds that small blobs with masses of less than 1010 g dominate the population. When blobs fall to lower regions along the magnetic loops, they are stretched and develop a non-uniform velocity pattern with an anti-parallel shearing pattern seen to develop along the central axis of the blobs. Synthetic images of simulated coronal rain with Solar Dynamics Observatory Atmospheric Imaging Assembly well resemble real observations presenting dark falling clumps in hot channels and bright rain blobs in a cool channel. We also find density inhomogeneities during a coronal rain "shower", which reflects the observed multi-stranded nature of coronal rain. Movies associated to Figs. 3 and 7 are available at http://www.aanda.org

Chromium:forsterite laser frequency comb stabilization and development of portable frequency references inside a hollow optical fiber

NASA Astrophysics Data System (ADS)

Thapa, Rajesh

We have made significant accomplishments in the development of portable frequency standard inside hollow optical fibers. Such standards will improve portable optical frequency references available to the telecommunications industry. Our approach relies on the development of a stabilized Cr:forsterite laser to generate the frequency comb in the near-IR region. This laser is self referenced and locked to a CW laser which in turn is stabilized to a sub-Doppler feature of a molecular transition. The molecular transition is realized using a hollow core fiber filled with acetylene gas. We finally measured the absolute frequency of these molecular transitions to characterize the references. In this thesis, the major ideas, techniques and experimental results for the development and absolute frequency measurement of the portable frequency references are presented. A prism-based Cr:forsterite frequency comb is stabilized. We have effectively used the prism modulation along with power modulation inside the cavity in order to actively stabilize the frequency comb. We have also studied the carrier-envelope-offset frequency (f0) dynamics of the laser and its effect on laser stabilization. A reduction of f0 linewidth from ˜2 MHz to ˜20 kHz has also been observed. Both our in-loop and out-of-loop measurements of the comb stability showed that the comb is stable within a part in 1011 at 1-s gate time and is currently limited by our reference signal. In order to develop this portable frequency standard, saturated absorption spectroscopy is performed on the acetylene v1 + v3 band near 1532 nm inside different kinds of hollow optical fibers. The observed linewidths are a factor 2 narrower in the 20 mum fiber as compared to 10 mum fiber, and vary from 20-40 MHz depending on pressure and power. The 70 mum kagome fiber shows a further reduction in linewidth to less than 10 MHz. In order to seal the gas inside the hollow optical fiber, we have also developed a technique of splicing the hollow fiber to solid fiber in a standard commercial arc splicer, rather than the more expensive filament splicer, and achieved comparable splice loss. We locked a CW laser to the saturated absorption feature using a Frequency Modulation technique and then compared to an optical frequency comb. The stabilized frequency comb, providing a dense grid of reference frequencies in near-infrared region is used to characterize and measure the absolute frequency reference based on these hollow optical fibers.

Carnegie Mellon University Space Architecture

NASA Technical Reports Server (NTRS)

Kennedy, Kriss J.

2016-01-01

A traditional architecture studio focusing on a "post-pioneering" settlement (a first step research station with an emphasis on material, resources, closed-loop systems, as well as programmatic network and spatial considerations) for the surface of Mars or for Earth-Mars transit.

Interactive Model-Centric Systems Engineering (IMCSE) Phase Two

DTIC Science & Technology

2015-02-28

109 Backend Implementation...42 Figure 10. Interactive Epoch-Era Analysis leverages humans-in-the-loop analysis and supporting infrastructure ...preliminary supporting 10 infrastructure . This will inform the transition strategies, additional case application and prototype user testing. • The

Predicted stem-loop structures and variation in nucleotide sequence of 3' noncoding regions among animal calicivirus genomes.

PubMed

Seal, B S; Neill, J D; Ridpath, J F

1994-07-01

Caliciviruses are nonenveloped with a polyadenylated genome of approximately 7.6 kb and a single capsid protein. The "RNA Fold" computer program was used to analyze 3'-terminal noncoding sequences of five feline calicivirus (FCV), rabbit hemorrhagic disease virus (RHDV), and two San Miguel sea lion virus (SMSV) isolates. The FCV 3'-terminal sequences are 40-46 nucleotides in length and 72-91% similar. The FCV sequences were predicted to contain two possible duplex structures and one stem-loop structure with free energies of -2.1 to -18.2 kcal/mole. The RHDV genomic 3'-terminal RNA sequences are 54 nucleotides in length and share 49% sequence similarity to homologous regions of the FCV genome. The RHDV sequence was predicted to form two duplex structures in the 3'-terminal noncoding region with a single stem-loop structure, resembling that of FCV. In contrast, the SMSV 1 and 4 genomic 3'-terminal noncoding sequences were 185 and 182 nucleotides in length, respectively. Ten possible duplex structures were predicted with an average structural free energy of -35 kcal/mole. Sequence similarity between the two SMSV isolates was 75%. Furthermore, extensive cloverleaflike structures are predicted in the 3' noncoding region of the SMSV genome, in contrast to the predicted single stem-loop structures of FCV or RHDV.

Observations of loops and prominences

NASA Technical Reports Server (NTRS)

Strong, Keith T.

1994-01-01

We review recent observations by the Yohkoh-SXT (Soft X-ray Telescope) in collaboration with other spacecraft and ground-based observatories of coronal loops and prominences. These new results point to problems that SoHO will be able to address. With a unique combination of rapid-cadence digital imaging (greater than or equal to 32 s full-disk and greater than or equal to 2 s partial-frame images), high spatial resolution (greater than or equal to 2.5 arcsec pixels), high sensitivity (EM less than or equal to 10(exp 42) cm(exp -3)), a low-scatter mirror, and large dynamic range, SXT can observe a vast range of targets on the Sun. Over the first 21 months of Yohkoh operations SXT has taken over one million images of the corona and so is building up an invaluable long-term database on the large-scale corona and loop geometry. The most striking thing about the SXT images is the range of loop sizes and shapes. The active regions are a bright tangle of magnetic field lines, surrounded by a network of large-scale quiet-Sun loops stretching over distances in excess of 105 km. The cross-section of most loops seems to be constant. Loops displaying significant Gamma's are the exception, not the rule, implying the presence of widespread currents in the corona. All magnetic structures show changes. Time scales range from seconds to months. The question of how these structures are formed, become filled with hot plasma, and are maintained is still open. While we see the propagation of brightenings along the length of active-region loops and in X-ray jets with velocities of several hundred km/s, much higher velocities are seen in the quiet Sun. In XBP flares, for example, velocities of over 1000 km/s are common. Active-region loops seem to be in constant motion, moving slowly outward, carrying plasma with them. During flares, loops often produce localized brightenings at the base and later at the apex of the loop. Quiescent filaments and prominences have been observed regularly. Their coronal manifestation seems to be an extended arcade of loops overlying the filament. Reliable alignment of the ground-based data with the X-ray images make it possible to make a detailed intercomparison of the hot and cold plasma structures over extended periods. Hence we are able to follow the long-term evolution of these structures and see how they become destabilized and erupt.

Dynamical behaviour in coronal loops

NASA Technical Reports Server (NTRS)

Haisch, Bernhard M.

1986-01-01

Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

Dynamical behaviour in coronal loops

NASA Astrophysics Data System (ADS)

Haisch, Bernhard M.

Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

Multiple Scenarios of Transition to Chaos in the Alternative Splicing Model

NASA Astrophysics Data System (ADS)

Kogai, Vladislav V.; Likhoshvai, Vitaly A.; Fadeev, Stanislav I.; Khlebodarova, Tamara M.

We have investigated the scenarios of transition to chaos in the mathematical model of a genetic system constituted by a single transcription factor-encoding gene, the expression of which is self-regulated by a feedback loop that involves protein isoforms. Alternative splicing results in the synthesis of protein isoforms providing opposite regulatory outcomes — activation or repression. The model is represented by a differential equation with two delayed arguments. The possibility of transition to chaos dynamics via all classical scenarios: a cascade of period-doubling bifurcations, quasiperiodicity and type-I, type-II and type-III intermittencies, has been numerically demonstrated. The parametric features of each type of transition to chaos have been described.

Transverse Oscillations of Coronal Loops

NASA Astrophysics Data System (ADS)

Ruderman, Michael S.; Erdélyi, Robert

2009-12-01

On 14 July 1998 TRACE observed transverse oscillations of a coronal loop generated by an external disturbance most probably caused by a solar flare. These oscillations were interpreted as standing fast kink waves in a magnetic flux tube. Firstly, in this review we embark on the discussion of the theory of waves and oscillations in a homogeneous straight magnetic cylinder with the particular emphasis on fast kink waves. Next, we consider the effects of stratification, loop expansion, loop curvature, non-circular cross-section, loop shape and magnetic twist. An important property of observed transverse coronal loop oscillations is their fast damping. We briefly review the different mechanisms suggested for explaining the rapid damping phenomenon. After that we concentrate on damping due to resonant absorption. We describe the latest analytical results obtained with the use of thin transition layer approximation, and then compare these results with numerical findings obtained for arbitrary density variation inside the flux tube. Very often collective oscillations of an array of coronal magnetic loops are observed. It is natural to start studying this phenomenon from the system of two coronal loops. We describe very recent analytical and numerical results of studying collective oscillations of two parallel homogeneous coronal loops. The implication of the theoretical results for coronal seismology is briefly discussed. We describe the estimates of magnetic field magnitude obtained from the observed fundamental frequency of oscillations, and the estimates of the coronal scale height obtained using the simultaneous observations of the fundamental frequency and the frequency of the first overtone of kink oscillations. In the last part of the review we summarise the most outstanding and acute problems in the theory of the coronal loop transverse oscillations.

The early history of the closed loop fiber optic gyro and derivative sensors at McDonnell Douglas, Blue Road Research and Columbia Gorge Research

NASA Astrophysics Data System (ADS)

Udd, Eric

2016-05-01

On September 29, 1977 the first written disclosure of a closed loop fiber optic gyro was witnessed and signed off by four people at McDonnell Douglas Astronautics Company in Huntington Beach, California. Over the next ten years a breadboard demonstration unit, and several prototypes were built. In 1987 the fundamental patent for closed loop operation began a McDonnell Douglas worldwide licensing process. Internal fiber optic efforts were redirected to derivative sensors and inventions. This included development of acoustic, strain and distributed sensors as well as a Sagnac interferometer based secure fiber optic communication system and the new field of fiber optic smart structures. This paper provides an overview of these activities and transitions.

Evidence and age-related distribution of mtDNA D-loop point mutations in skeletal muscle from healthy subjects and mitochondrial patients.

PubMed

Del Bo, Roberto; Bordoni, Andreina; Martinelli Boneschi, Filippo; Crimi, Marco; Sciacco, Monica; Bresolin, Nereo; Scarlato, Guglielmo; Comi, Giacomo Pietri

2002-10-15

The progressive accumulation of mitochondrial DNA (mtDNA) alterations, ranging from single mutations to large-scale deletions, in both the normal ageing process and pathological conditions is a relevant phenomenon in terms of frequency and heteroplasmic degree. Recently, two point mutations (A189G and T408A) within the Displacement loop (D-loop) region, the control region for mtDNA replication, were shown to occur in skeletal muscles from aged individuals. We evaluated the presence and the heteroplasmy levels of these two mutations in muscle biopsies from 91 unrelated individuals of different ages (21 healthy subjects and 70 patients affected by mitochondrial encephalomyopathies). Overall, both mutations significantly accumulate with age. However, a different relationship was discovered among the different subgroups of patients: a higher number of A189G positive subjects younger than 53 years was detected in the subgroup of multiple-deleted patients; furthermore, a trend towards an increased risk for the mutations was evidenced among patients carrying multiple deletions when compared to healthy controls. These findings support the idea that a common biological mechanism determines the accumulation of somatic point mutations in the D-loop region, both in healthy subjects and in mitochondrial myopathy patients. At the same time, it appears that disorders caused by mutations of nuclear genes controlling mtDNA replication (the "mtDNA multiple deletions" syndromes) present a temporal advantage to mutate in the D-loop region. This observation may be relevant to the definition of the molecular pathogenesis of these latter syndromes. Copyright 2002 Elsevier Science B.V.

Dynamic transitions in a model of the hypothalamic-pituitary-adrenal axis

NASA Astrophysics Data System (ADS)

Čupić, Željko; Marković, Vladimir M.; Maćešić, Stevan; Stanojević, Ana; Damjanović, Svetozar; Vukojević, Vladana; Kolar-Anić, Ljiljana

2016-03-01

Dynamic properties of a nonlinear five-dimensional stoichiometric model of the hypothalamic-pituitary-adrenal (HPA) axis were systematically investigated. Conditions under which qualitative transitions between dynamic states occur are determined by independently varying the rate constants of all reactions that constitute the model. Bifurcation types were further characterized using continuation algorithms and scale factor methods. Regions of bistability and transitions through supercritical Andronov-Hopf and saddle loop bifurcations were identified. Dynamic state analysis predicts that the HPA axis operates under basal (healthy) physiological conditions close to an Andronov-Hopf bifurcation. Dynamic properties of the stress-control axis have not been characterized experimentally, but modelling suggests that the proximity to a supercritical Andronov-Hopf bifurcation can give the HPA axis both, flexibility to respond to external stimuli and adjust to new conditions and stability, i.e., the capacity to return to the original dynamic state afterwards, which is essential for maintaining homeostasis. The analysis presented here reflects the properties of a low-dimensional model that succinctly describes neurochemical transformations underlying the HPA axis. However, the model accounts correctly for a number of experimentally observed properties of the stress-response axis. We therefore regard that the presented analysis is meaningful, showing how in silico investigations can be used to guide the experimentalists in understanding how the HPA axis activity changes under chronic disease and/or specific pharmacological manipulations.

Observation of relaxor ferroelectricity and multiferroic behaviour in nanoparticles of the ferromagnetic semiconductor La2NiMnO6

NASA Astrophysics Data System (ADS)

Masud, Md G.; Ghosh, Arijit; Sannigrahi, J.; Chaudhuri, B. K.

2012-07-01

We report a diffuse phase transition (extending over a finite temperature range of ˜50 K) in sol-gel derived nanoparticles (˜25 nm) of the ferromagnetic double perovskite La2NiMnO6. The macroscopic polarization (P-E hysteresis loop), validity of the Vogel-Fulcher relation and high dielectric permittivity (˜9 × 102) confirm relaxor ferroelectric phenomena in these magnetic nanoparticles. Compared to the corresponding bulk sample, appreciably large enhancement of the magnetocapacitive effect (MC ˜ 30%) is observed even under low magnetic field (0.5 T) around the broad relaxor dielectric peak temperature (˜220 K), which is close to the ferromagnetic transition temperature (θf ˜ 196 K). All of these features establish the multiferroic character of the La2NiMnO6 nanoparticles. The inhomogeneities arising from chemical and valence mixing in the present La2NiMnO6 nanoparticles and the inter-site, Ni/Mn-site disorder along with surface disorder of the individual nanoparticles resulting in local polar regions are attributed to the observed dielectric behaviour of the nanoparticles. The wave vector dependent spin-pair correlation is considered to be the plausible cause of the colossal magnetocapacitive response near the transition temperature. High permittivity and large magnetocapacitive properties make these ferromagnetic La2NiMnO6 nanoparticles technologically important.

A stromal region of cytochrome b6f subunit IV is involved in the activation of the Stt7 kinase in Chlamydomonas

PubMed Central

Zito, Francesca; Blangy, Stéphanie; Auroy, Pascaline; Johnson, Xenie; Peltier, Gilles

2017-01-01

The cytochrome (cyt) b6f complex and Stt7 kinase regulate the antenna sizes of photosystems I and II through state transitions, which are mediated by a reversible phosphorylation of light harvesting complexes II, depending on the redox state of the plastoquinone pool. When the pool is reduced, the cyt b6f activates the Stt7 kinase through a mechanism that is still poorly understood. After random mutagenesis of the chloroplast petD gene, coding for subunit IV of the cyt b6f complex, and complementation of a ΔpetD host strain by chloroplast transformation, we screened for impaired state transitions in vivo by chlorophyll fluorescence imaging. We show that residues Asn122, Tyr124, and Arg125 in the stromal loop linking helices F and G of cyt b6f subunit IV are crucial for state transitions. In vitro reconstitution experiments with purified cyt b6f and recombinant Stt7 kinase domain show that cyt b6f enhances Stt7 autophosphorylation and that the Arg125 residue is directly involved in this process. The peripheral stromal structure of the cyt b6f complex had, until now, no reported function. Evidence is now provided of a direct interaction with Stt7 on the stromal side of the membrane. PMID:29078388

Gravitational waves and Higgs boson couplings for exploring first order phase transition in the model with a singlet scalar field

NASA Astrophysics Data System (ADS)

Hashino, Katsuya; Kakizaki, Mitsuru; Kanemura, Shinya; Ko, Pyungwon; Matsui, Toshinori

2017-03-01

We calculate the spectrum of gravitational waves originated from strongly first order electroweak phase transition in the extended Higgs model with a real singlet scalar field. In order to calculate the bubble nucleation rate, we perform a two-field analysis and evaluate bounce solutions connecting the true and the false vacua using the one-loop effective potential at finite temperatures. Imposing the Sakharov condition of the departure from thermal equilibrium for baryogenesis, we survey allowed regions of parameters of the model. We then investigate the gravitational waves produced at electroweak bubble collisions in the early Universe, such as the sound wave, the bubble wall collision and the plasma turbulence. We find that the strength at the peak frequency can be large enough to be detected at future space-based gravitational interferometers such as eLISA, DECIGO and BBO. Predicted deviations in the various Higgs boson couplings are also evaluated at the zero temperature, and are shown to be large enough too. Therefore, in this model strongly first order electroweak phase transition can be tested by the combination of the precision study of various Higgs boson couplings at the LHC, the measurement of the triple Higgs boson coupling at future lepton colliders and the shape of the spectrum of gravitational wave detectable at future gravitational interferometers.

Usage of mitochondrial D-loop variation to predict risk for Huntington disease.

PubMed

Mousavizadeh, Kazem; Rajabi, Peyman; Alaee, Mahsa; Dadgar, Sepideh; Houshmand, Massoud

2015-08-01

Huntington's disease (HD) is an inherited autosomal neurodegenerative disease caused by the abnormal expansion of the CAG repeats in the Huntingtin (Htt) gene. It has been proven that mitochondrial dysfunction is contributed to the pathogenesis of Huntington's disease. The mitochondrial displacement loop (D-loop) is proven to accumulate mutations at a higher rate than other regions of mtDNA. Thus, we hypothesized that specific SNPs in the D-loop may contribute to the pathogenesis of Huntington's disease. In the present study, 30 patients with Huntington's disease and 463 healthy controls were evaluated for mitochondrial mutation sites within the D-loop region using PCR-sequencing method. Sequence analysis revealed 35 variations in HD group from Cambridge Mitochondrial Sequences. A significant difference (p < 0.05) was seen between patients and control group in eight SNPs. Polymorphisms at C16069T, T16126C, T16189C, T16519C and C16223T were correlated with an increased risk of HD while SNPs at C16150T, T16086C and T16195C were associated with a decreased risk of Huntington's disease.

Limit cycles in piecewise-affine gene network models with multiple interaction loops

NASA Astrophysics Data System (ADS)

Farcot, Etienne; Gouzé, Jean-Luc

2010-01-01

In this article, we consider piecewise affine differential equations modelling gene networks. We work with arbitrary decay rates, and under a local hypothesis expressed as an alignment condition of successive focal points. The interaction graph of the system may be rather complex (multiple intricate loops of any sign, multiple thresholds, etc.). Our main result is an alternative theorem showing that if a sequence of region is periodically visited by trajectories, then under our hypotheses, there exists either a unique stable periodic solution, or the origin attracts all trajectories in this sequence of regions. This result extends greatly our previous work on a single negative feedback loop. We give several examples and simulations illustrating different cases.

Phase transitions between lower and higher level management learning in times of crisis: an experimental study based on synergetics.

PubMed

Liening, Andreas; Strunk, Guido; Mittelstadt, Ewald

2013-10-01

Much has been written about the differences between single- and double-loop learning, or more general between lower level and higher level learning. Especially in times of a fundamental crisis, a transition between lower and higher level learning would be an appropriate reaction to a challenge coming entirely out of the dark. However, so far there is no quantitative method to monitor such a transition. Therefore we introduce theory and methods of synergetics and present results from an experimental study based on the simulation of a crisis within a business simulation game. Hypothesized critical fluctuations - as a marker for so-called phase transitions - have been assessed with permutation entropy. Results show evidence for a phase transition during the crisis, which can be interpreted as a transition between lower and higher level learning.

Feed-Forward Reciprocal Activation of PAFR and STAT3 Regulates Epithelial-Mesenchymal Transition in Non-Small Cell Lung Cancer.

PubMed

Chen, Jie; Lan, Tian; Zhang, Weimin; Dong, Lijia; Kang, Nan; Zhang, Shumin; Fu, Ming; Liu, Bing; Liu, Kangtai; Zhan, Qimin

2015-10-01

Platelet-activating factor receptor (PAFR), a G-protein-coupled receptor, has been implicated in tumorigenesis, but its contributions to metastatic progression have not been investigated. Here, we show that PAFR is overexpressed in non-small cell lung cancer (NSCLC) as well as in breast, colorectal, and gastric carcinomas. Expression of PAFR correlates closely with clinical stages, survival time, and distant metastasis. In human NSCLC cells, activation of the PAF/PAFR signaling axis accentuated malignant character, including by stimulating epithelial-mesenchymal transition (EMT). In contrast, silencing PAFR in aggressive NSCLC cells inhibited these effects. Mechanistic investigations showed that PAFR stimulated EMT by activating STAT3 via upregulation of G-protein-dependent SRC or JAK2 kinase activity. Notably, STAT3 transcriptionally elevated PAFR expression. Thus, activation of PAFR in NSCLC cells initiated a forward feedback loop responsible for mediating the aggressive malignant character of NSCLC cells in vitro and in vivo. Reinforcing this reciprocal activation loop, PAF/PAFR signaling also upregulated IL6 expression and thereby STAT3 activation. Overall, our results elucidated an important role for PAFR dysregulation in the pathogenicity of NSCLC and unraveled a forward feedback loop between PAFR and STAT3 that acts to drive the malignant progression of NSCLC. ©2015 American Association for Cancer Research.

Second-order electron self-energy loop-after-loop correction for low- Z hydrogen-like ions

NASA Astrophysics Data System (ADS)

Goidenko, Igor; Labzowsky, Leonti; Plunien, Günter; Soff, Gerhard

2005-07-01

The second-order electron self-energy loop-after-loop correction is investigated for hydrogen-like ions in the region of low nuclear charge numbers Z. Both irreducible and reducible parts of this correction are evaluated for the 1s1/2-state within the Fried-Yennie gauge. We confirm the result obtained first by Mallampalli and Sapirstein. The reducible part of this correction is evaluated numerically for the first time and it is consistent with the corresponding analytical αZ-expansion.

Silent initial conditions for cosmological perturbations with a change of spacetime signature

NASA Astrophysics Data System (ADS)

Mielczarek, Jakub; Linsefors, Linda; Barrau, Aurelien

Recent calculations in loop quantum cosmology suggest that a transition from a Lorentzian to a Euclidean spacetime might take place in the very early universe. The transition point leads to a state of silence, characterized by a vanishing speed of light. This behavior can be interpreted as a decoupling of different space points, similar to the one characterizing the BKL phase. In this study, we address the issue of imposing initial conditions for the cosmological perturbations at the transition point between the Lorentzian and Euclidean phases. Motivated by the decoupling of space points, initial conditions characterized by a lack of correlations are investigated. We show that the “white noise” gains some support from analysis of the vacuum state in the deep Euclidean regime. Furthermore, the possibility of imposing the silent initial conditions at the trans-Planckian surface, characterized by a vanishing speed for the propagation of modes with wavelengths of the order of the Planck length, is studied. Such initial conditions might result from the loop deformations of the Poincaré algebra. The conversion of the silent initial power spectrum to a scale-invariant one is also examined.

A digital optical phase-locked loop for diode lasers based on field programmable gate array

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

Xu Zhouxiang; Zhang Xian; Huang Kaikai

2012-09-15

We have designed and implemented a highly digital optical phase-locked loop (OPLL) for diode lasers in atom interferometry. The three parts of controlling circuit in this OPLL, including phase and frequency detector (PFD), loop filter and proportional integral derivative (PID) controller, are implemented in a single field programmable gate array chip. A structure type compatible with the model MAX9382/MCH12140 is chosen for PFD and pipeline and parallelism technology have been adapted in PID controller. Especially, high speed clock and twisted ring counter have been integrated in the most crucial part, the loop filter. This OPLL has the narrow beat notemore » line width below 1 Hz, residual mean-square phase error of 0.14 rad{sup 2} and transition time of 100 {mu}s under 10 MHz frequency step. A main innovation of this design is the completely digitalization of the whole controlling circuit in OPLL for diode lasers.« less

Apparatus for and method of monitoring for breached fuel elements

DOEpatents

Gross, K.C.; Strain, R.V.

1981-04-28

This invention teaches improved apparatus for the method of detecting a breach in cladded fuel used in a nuclear reactor. The detector apparatus uses a separate bypass loop for conveying part of the reactor coolant away from the core, and at least three separate delayed-neutron detectors mounted proximate this detector loop. The detectors are spaced apart so that the coolant flow time from the core to each detector is different, and these differences are known. The delayed-neutron activity at the detectors is a function of the delay time after the reaction in the fuel until the coolant carrying the delayed-neutron emitter passes the respective detector. This time delay is broken down into separate components including an isotopic holdup time required for the emitter to move through the fuel from the reaction to the coolant at the breach, and two transit times required for the emitter now in the coolant to flow from the breach to the detector loop and then via the loop to the detector.

Modeling Cyclic Fatigue Hysteresis Loops of 2D Woven Ceramic Matrix Composites at Elevated Temperatures in Steam

PubMed Central

Li, Longbiao

2016-01-01

In this paper, the cyclic fatigue hysteresis loops of 2D woven SiC/SiC ceramic matrix composites (CMCs) at elevated temperatures in steam have been investigated. The interface slip between fibers and the matrix existing in matrix cracking modes 3 and 5, in which matrix cracking and interface debonding occurred in longitudinal yarns, is considered as the major reason for hysteresis loops of 2D woven CMCs. The hysteresis loops of 2D SiC/SiC composites corresponding to different peak stresses, test conditions, and loading frequencies have been predicted using the present analysis. The damage parameter, i.e., the proportion of matrix cracking mode 3 in the entire matrix cracking modes of the composite, and the hysteresis dissipated energy increase with increasing fatigue peak stress. With increasing cycle number, the interface shear stress in the longitudinal yarns decreases, leading to transition of interface slip types of matrix cracking modes 3 and 5. PMID:28773544

First Results from a Hardware-in-the-Loop Demonstration of Closed-Loop Autonomous Formation Flying

NASA Technical Reports Server (NTRS)

Gill, E.; Naasz, Bo; Ebinuma, T.

2003-01-01

A closed-loop system for the demonstration of formation flying technologies has been developed at NASA s Goddard Space Flight Center. Making use of a GPS signal simulator with a dual radio frequency outlet, the system includes two GPS space receivers as well as a powerful onboard navigation processor dedicated to the GPS-based guidance, navigation, and control of a satellite formation in real-time. The closed-loop system allows realistic simulations of autonomous formation flying scenarios, enabling research in the fields of tracking and orbit control strategies for a wide range of applications. A sample scenario has been set up where the autonomous transition of a satellite formation from an initial along-track separation of 800 m to a final distance of 100 m has been demonstrated. As a result, a typical control accuracy of about 5 m has been achieved which proves the applicability of autonomous formation flying techniques to formations of satellites as close as 50 m.

Disruption of a hydrogen bond network in human versus spider monkey cytochrome c affects heme crevice stability.

PubMed

Goldes, Matthew E; Jeakins-Cooley, Margaret E; McClelland, Levi J; Mou, Tung-Chung; Bowler, Bruce E

2016-05-01

The hypothesis that the recent rapid evolution of primate cytochromes c, which primarily involves residues in the least stable Ω-loop (Ω-loop C, residues 40-57), stabilizes the heme crevice of cytochrome c relative to other mammals, is tested. To accomplish this goal, we have compared the properties of human and spider monkey cytochrome c and a set of four variants produced in the process of converting human cytochrome c into spider monkey cytochrome c. The global stability of all variants has been measured by guanidine hydrochloride denaturation. The stability of the heme crevice has been assessed with the alkaline conformational transition. Structural insight into the effects of the five amino acid substitutions needed to convert human cytochrome c into spider monkey cytochrome c is provided by a 1.15Å resolution structure of spider monkey cytochrome c. The global stability for all variants is near 9.0kcal/mol at 25°C and pH7, which is higher than that observed for other mammalian cytochromes c. The heme crevice stability is more sensitive to the substitutions required to produce spider monkey cytochrome c with decreases of up to 0.5 units in the apparent pKa of the alkaline conformational transition relative to human cytochrome c. The structure of spider monkey cytochrome c indicates that the Y46F substitution destabilizes the heme crevice by disrupting an extensive hydrogen bond network that connects three surface loops including Ω-loop D (residues 70-85), which contains the Met80 heme ligand. Copyright © 2015 Elsevier Inc. All rights reserved.

Effect of T- and C-loop mutations on the Herbaspirillum seropedicae GlnB protein in nitrogen signalling.

PubMed

Bonatto, Ana C; Souza, Emanuel M; Pedrosa, Fábio O; Yates, M Geoffrey; Benelli, Elaine M

2005-01-01

Proteins of the PII family are found in species of all kingdoms. Although these proteins usually share high identity, their functions are specific to the different organisms. Comparison of structural data from Escherichia coli GlnB and GlnK and Herbaspirillum seropedicae GlnB showed that the T-loop and C-terminus were variable regions. To evaluate the role of these regions in signal transduction by the H. seropedicae GlnB protein, four mutants were constructed: Y51F, G108A/P109a, G108W and Q3R/T5A. The activities of the native and mutated proteins were assayed in an E. coli background constitutively expressing the Klebsiella pneumoniae nifLA operon. The results suggested that the T-loop and C-terminus regions of H. seropedicae GlnB are involved in nitrogen signal transduction.

Numerical study of air ingress transition to natural circulation in a high temperature helium loop

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

Franken, Daniel; Gould, Daniel; Jain, Prashant K.

Here, the generation-IV high temperature gas cooled reactors (HTGRs) are designed with many passive safety features, one of which is the ability to passively remove heat under a loss of coolant accident (LOCA). However, several common reactor designs do not prevent against a large break in the coolant system and may therefore experience a depressurized LOCA. This would lead to air entering into the reactor system via several potential modes of ingress: diffusion, gravity currents, and natural circulation. At the onset of a LOCA, the initial rate of air ingress is expected to be very slow because it is governedmore » by molecular diffusion. However, after several hours, natural circulation would commence, thus, bringing the air into the reactor system at a much higher rate. As a consequence, air ingress would cause the high temperature graphite matrix to oxidize, leading to its thermal degradation and decreased passive heat (decay) removal capability. Therefore, it is essential to understand the transition of air ingress from molecular diffusion to natural circulation in an HTGR system. This paper presents results from a computational fluid dynamics (CFD) model to study the air ingress transition behavior. These results are validated against an h-shaped high temperature helium loop experiment. Details are provided to quantitatively predict the transition time from molecular diffusion to natural circulation.« less

Numerical study of air ingress transition to natural circulation in a high temperature helium loop

DOE PAGES

Franken, Daniel; Gould, Daniel; Jain, Prashant K.; ...

2017-09-21

Here, the generation-IV high temperature gas cooled reactors (HTGRs) are designed with many passive safety features, one of which is the ability to passively remove heat under a loss of coolant accident (LOCA). However, several common reactor designs do not prevent against a large break in the coolant system and may therefore experience a depressurized LOCA. This would lead to air entering into the reactor system via several potential modes of ingress: diffusion, gravity currents, and natural circulation. At the onset of a LOCA, the initial rate of air ingress is expected to be very slow because it is governedmore » by molecular diffusion. However, after several hours, natural circulation would commence, thus, bringing the air into the reactor system at a much higher rate. As a consequence, air ingress would cause the high temperature graphite matrix to oxidize, leading to its thermal degradation and decreased passive heat (decay) removal capability. Therefore, it is essential to understand the transition of air ingress from molecular diffusion to natural circulation in an HTGR system. This paper presents results from a computational fluid dynamics (CFD) model to study the air ingress transition behavior. These results are validated against an h-shaped high temperature helium loop experiment. Details are provided to quantitatively predict the transition time from molecular diffusion to natural circulation.« less

DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures

PubMed Central

Barth, Anna; Kobbe, Daniela; Focke, Manfred

2016-01-01

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology. PMID:26773051

Magnetic Properties and Magnetic Phase Diagrams of Trigonal DyNi3Ga9

NASA Astrophysics Data System (ADS)

Ninomiya, Hiroki; Matsumoto, Yuji; Nakamura, Shota; Kono, Yohei; Kittaka, Shunichiro; Sakakibara, Toshiro; Inoue, Katsuya; Ohara, Shigeo

2017-12-01

We report the crystal structure, magnetic properties, and magnetic phase diagrams of single crystalline DyNi3Ga9 studied using X-ray diffraction, electrical resistivity, specific heat, and magnetization measurements. DyNi3Ga9 crystallizes in the chiral structure with space group R32. The dysprosium ions, which are responsible for the magnetism in this compound, form a two-dimensional honeycomb structure on a (0001) plane. We show that DyNi3Ga9 exhibits successive phase transitions at TN = 10 K and T'N = 9 K. The former suggests quadrupolar ordering, and the latter is attributed to the antiferromagnetic order. It is considered that DyNi3Ga9 forms the canted-antiferromagnetic structure below T'N owing to a small hysteresis loop of the low-field magnetization curve. We observe the strong easy-plane anisotropy, and the multiple-metamagnetic transitions with magnetization-plateaus under the field applied along the honeycomb plane. For Hallel [2\\bar{1}\\bar{1}0], the plateau-region arises every 1/6 for saturation magnetization. The magnetic phase diagrams of DyNi3Ga9 are determined for the fields along principal-crystal axes.

Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations

PubMed Central

Baumketner, Andrij; Nesmelov, Yuri

2011-01-01

The recovery stroke is a key step in the functional cycle of muscle motor protein myosin, during which pre-recovery conformation of the protein is changed into the active post-recovery conformation, ready to exersice force. We study the microscopic details of this transition using molecular dynamics simulations of atomistic models in implicit and explicit solvent. In more than 2 μs of aggregate simulation time, we uncover evidence that the recovery stroke is a two-step process consisting of two stages separated by a time delay. In our simulations, we directly observe the first stage at which switch II loop closes in the presence of adenosine triphosphate at the nucleotide binding site. The resulting configuration of the nucleotide binding site is identical to that detected experimentally. Distribution of inter-residue distances measured in the force generating region of myosin is in good agreement with the experimental data. The second stage of the recovery stroke structural transition, rotation of the converter domain, was not observed in our simulations. Apparently it occurs on a longer time scale. We suggest that the two parts of the recovery stroke need to be studied using separate computational models. PMID:21922589

Microwave Spectra and AB Initio Studies of the Ne-Acetone Complex

NASA Astrophysics Data System (ADS)

Gao, Jiao; Thomas, Javix; Xu, Yunjie; Jäger, Wolfgang

2015-06-01

Microwave spectra of the neon-acetone van der Waals complex were measured using a cavity-based molecular beam Fourier-transform microwave spectrometer in the region from 5 to 18 GHz. Both 20Ne and 22Ne containing isotopologues were studied and both c- and weaker a-type rotational transitions were observed. The transitions are split into multiplets due to the internal rotation of two methyl groups in acetone. Electronic structure calculations were done at the MP2 level of theory with the 6-311++g (2d, p) basis set for all atoms and the internal rotation barrier height of the methyl groups was determined to be about 2.8 kJ/mol. The ab initio rotational constants were the basis for our spectroscopic searches, but the multiplet structures and floppiness of the complex made the quantum number assignment very difficult. The assignment was finally achieved with the aid of constructing closed frequency loops and predicting internal rotation splittings using the XIAM code. Analyses of the spectra yielded rotational and centrifugal distortion constants, as well as internal rotation parameters, which were interpreted in terms of structure and internal dynamics of the complex. H. Hartwig and H. Dreizler, Z. Naturforsch. A 51, 923 (1996).

The elusive role of the SPRY2 domain in RyR1

PubMed Central

Willemse, Hermia; Mirza, Shamaruh; Gallant, Esther M; Board, Philip G

2011-01-01

The second of three SPRY domains (SPRY2, S1085-V1208) located in the skeletal muscle ryanodine receptor (RyR1) is contained within regions of RyR1 that influence EC coupling and bind to imperatoxin A, a toxin probe of RyR1 channel gating. We examined the binding of the F loop (P1107-A1121) in SPRY2 to the ASI/basic region in RyR1 (T3471-G3500, containing both alternatively spliced (ASI) residues and neighboring basic amino acids). We then investigated the possible influence of this interaction on excitation contraction (EC) coupling. A peptide with the F loop sequence and an antibody to the SPRY2 domain each enhanced RyR1 activity at low concentrations and inhibited at higher concentrations. A peptide containing the ASI/basic sequence bound to SPRY2 and binding decreased ∼10-fold following mutation or structural disruption of the basic residues. Binding was abolished by mutation of three critical acidic F loop residues. Together these results suggest that the ASI/basic and SPRY2 domains interact in an F loop regulatory module. Although a region that includes the SPRY2 domain influences EC coupling, as does the ASI/basic region, Ca2+ release during ligand- and depolarization-induced RyR1 activation were not altered by mutation of the three critical F loop residues following expression of mutant RyR1 in RyR1-null myotubes. Therefore the electrostatic regulatory interaction between the SPRY2 F loop residues (that bind to imperatoxin A) and the ASI/basic residues of RyR1 does not influence bi-directional DHPR-RyR1 signaling during skeletal EC coupling, possibly because the interaction is interrupted by the influence of factors present in intact muscle cells. PMID:21239886

FeynArts model file for MSSM transition counterterms from DREG to DRED

NASA Astrophysics Data System (ADS)

Stöckinger, Dominik; Varšo, Philipp

2012-02-01

The FeynArts model file MSSMdreg2dred implements MSSM transition counterterms which can convert one-loop Green functions from dimensional regularization to dimensional reduction. They correspond to a slight extension of the well-known Martin/Vaughn counterterms, specialized to the MSSM, and can serve also as supersymmetry-restoring counterterms. The paper provides full analytic results for the counterterms and gives one- and two-loop usage examples. The model file can simplify combining MS¯-parton distribution functions with supersymmetric renormalization or avoiding the renormalization of ɛ-scalars in dimensional reduction. Program summaryProgram title:MSSMdreg2dred.mod Catalogue identifier: AEKR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: LGPL-License [1] No. of lines in distributed program, including test data, etc.: 7600 No. of bytes in distributed program, including test data, etc.: 197 629 Distribution format: tar.gz Programming language: Mathematica, FeynArts Computer: Any, capable of running Mathematica and FeynArts Operating system: Any, with running Mathematica, FeynArts installation Classification: 4.4, 5, 11.1 Subprograms used: Cat Id Title Reference ADOW_v1_0 FeynArts CPC 140 (2001) 418 Nature of problem: The computation of one-loop Feynman diagrams in the minimal supersymmetric standard model (MSSM) requires regularization. Two schemes, dimensional regularization and dimensional reduction are both common but have different pros and cons. In order to combine the advantages of both schemes one would like to easily convert existing results from one scheme into the other. Solution method: Finite counterterms are constructed which correspond precisely to the one-loop scheme differences for the MSSM. They are provided as a FeynArts [2] model file. Using this model file together with FeynArts, the (ultra-violet) regularization of any MSSM one-loop Green function is switched automatically from dimensional regularization to dimensional reduction. In particular the counterterms serve as supersymmetry-restoring counterterms for dimensional regularization. Restrictions: The counterterms are restricted to the one-loop level and the MSSM. Running time: A few seconds to generate typical Feynman graphs with FeynArts.

Spatial-pattern-induced evolution of a self-replicating loop network.

PubMed

Suzuki, Keisuke; Ikegami, Takashi

2006-01-01

We study a system of self-replicating loops in which interaction rules between individuals allow competition that leads to the formation of a hypercycle-like network. The main feature of the model is the multiple layers of interaction between loops, which lead to both global spatial patterns and local replication. The network of loops manifests itself as a spiral structure from which new kinds of self-replicating loops emerge at the boundaries between different species. In these regions, larger and more complex self-replicating loops live for longer periods of time, managing to self-replicate in spite of their slower replication. Of particular interest is how micro-scale interactions between replicators lead to macro-scale spatial pattern formation, and how these macro-scale patterns in turn perturb the micro-scale replication dynamics.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

PubMed

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.

PubMed

Pereira, Jose H; Goh, Ee-Been; Keasling, Jay D; Beller, Harry R; Adams, Paul D

2012-10-01

Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition.

Portable concrete barrier condition and transition plan synthesis.

DOT National Transportation Integrated Search

2012-06-01

Precast (or portable) Concrete Barrier (PCB) is a guardrail system that is intended to contain and redirect a vehicle that has left the travel lane. Barrier connections are typically formed using steel wire or bar to form loops which are joined by a ...

UNSTEADY DISPERSION IN RANDOM INTERMITTENT FLOW

EPA Science Inventory

The longitudinal dispersion coefficient of a conservative tracer was calculated from flow tests in a dead-end pipe loop system. Flow conditions for these tests ranged from laminar to transitional flow, and from steady to intermittent and random. Two static mixers linked in series...

Geophysical delineation of the freshwater/saline-water transition zone in the Barton Springs segment of the Edwards Aquifer, Travis and Hays Counties, Texas, September 2006

USGS Publications Warehouse

Payne, J.D.; Kress, W.H.; Shah, S.D.; Stefanov, J.E.; Smith, B.A.; Hunt, B.B.

2007-01-01

During September 2006, the U.S. Geological Survey, in cooperation with the Barton Springs/Edwards Aquifer Conservation District, conducted a geophysical pilot study to determine whether time-domain electromagnetic (TDEM) sounding could be used to delineate the freshwater/saline-water transition zone in the Barton Springs segment of the Edwards aquifer in Travis and Hays Counties, Texas. There was uncertainty regarding the application of TDEM sounding for this purpose because of the depth of the aquifer (200-500 feet to the top of the aquifer) and the relatively low-resistivity clayey units in the upper confining unit. Twenty-five TDEM soundings were made along four 2-3-mile-long profiles in a study area overlying the transition zone near the Travis-Hays County boundary. The soundings yield measurements of subsurface electrical resistivity, the variations in which were correlated with hydrogeologic and stratigraphic units, and then with dissolved solids concentrations in the aquifer. Geonics Protem 47 and 57 systems with 492-foot and 328-foot transmitter-loop sizes were used to collect the TDEM soundings. A smooth model (vertical delineation of calculated apparent resistivity that represents an estimate [non-unique] of the true resistivity) for each sounding site was created using an iterative software program for inverse modeling. The effectiveness of using TDEM soundings to delineate the transition zone was indicated by comparing the distribution of resistivity in the aquifer with the distribution of dissolved solids concentrations in the aquifer along the profiles. TDEM sounding data show that, in general, the Edwards aquifer in the study area is characterized by a sharp change in resistivity from west to east. The western part of the Edwards aquifer in the study area shows higher resistivity than the eastern part. The higher resistivity regions correspond to lower dissolved solids concentrations (freshwater), and the lower resistivity regions correspond to higher dissolved solids concentrations (saline water). On the basis of reasonably close matches between the inferred locations of the freshwater/saline-water transition zone in the Edwards aquifer in the study area from resistivities and from dissolved solids concentrations in three of the four profiles, TDEM sounding appears to be a suitable tool for delineating the transition zone.

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

PubMed Central

Serra, Martin J; Baird, John D; Dale, Taraka; Fey, Bridget L; Retatagos, Kimberly; Westhof, Eric

2002-01-01

Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated. PMID:12003491

Genotype-phenotype aspects of type 2 long QT syndrome.

PubMed

Shimizu, Wataru; Moss, Arthur J; Wilde, Arthur A M; Towbin, Jeffrey A; Ackerman, Michael J; January, Craig T; Tester, David J; Zareba, Wojciech; Robinson, Jennifer L; Qi, Ming; Vincent, G Michael; Kaufman, Elizabeth S; Hofman, Nynke; Noda, Takashi; Kamakura, Shiro; Miyamoto, Yoshihiro; Shah, Samit; Amin, Vinit; Goldenberg, Ilan; Andrews, Mark L; McNitt, Scott

2009-11-24

The purpose of this study was to investigate the effect of location, coding type, and topology of KCNH2(hERG) mutations on clinical phenotype in type 2 long QT syndrome (LQTS). Previous studies were limited by population size in their ability to examine phenotypic effect of location, type, and topology. Study subjects included 858 type 2 LQTS patients with 162 different KCNH2 mutations in 213 proband-identified families. The Cox proportional-hazards survivorship model was used to evaluate independent contributions of clinical and genetic factors to the first cardiac events. For patients with missense mutations, the transmembrane pore (S5-loop-S6) and N-terminus regions were a significantly greater risk than the C-terminus region (hazard ratio [HR]: 2.87 and 1.86, respectively), but the transmembrane nonpore (S1-S4) region was not (HR: 1.19). Additionally, the transmembrane pore region was significantly riskier than the N-terminus or transmembrane nonpore regions (HR: 1.54 and 2.42, respectively). However, for nonmissense mutations, these other regions were no longer riskier than the C-terminus (HR: 1.13, 0.77, and 0.46, respectively). Likewise, subjects with nonmissense mutations were at significantly higher risk than were subjects with missense mutations in the C-terminus region (HR: 2.00), but that was not the case in other regions. This mutation location-type interaction was significant (p = 0.008). A significantly higher risk was found in subjects with mutations located in alpha-helical domains than in subjects with mutations in beta-sheet domains or other locations (HR: 1.74 and 1.33, respectively). Time-dependent beta-blocker use was associated with a significant 63% reduction in the risk of first cardiac events (p < 0.001). The KCNH2 missense mutations located in the transmembrane S5-loop-S6 region are associated with the greatest risk.

A Theoretical Investigation of Optical Emission in Solar Flares

NASA Astrophysics Data System (ADS)

Abbett, William Paul

A dynamic theoretical model of a flare loop from its footpoints in the photosphere to its apex in the corona is presented, and the effects of non-thermal heating of the lower atmosphere by accelerated electrons and soft X-ray irradiation from the flare heated transition region and corona are investigated. Important transitions of hydrogen, helium, and singly ionized calcium and magnesium are treated in non-LTE. Three main conclusions are drawn from the models. First, even the strongest of impulsive events can be described as having two phases: a gentle phase characterized by a state of near equilibrium, and an explosive phase characterized by large material flows, and strong hydrodynamic waves and shocks. During the gentle phase, one or possibly two temperature 'plateaus' form in the upper chromosphere. The line emission generated in these regions produces profiles that are generally symmetric and undistorted, in contrast to emission produced during the explosive phase, where large velocity gradients that occur in the upper atmosphere produce line profiles that are highly asymmetric and show large emission peaks and troughs. Second, a significant continuum (or 'white light') brightening results from increased hydrogen recombination radiation in the upper chromosphere at the point where the accelerated electrons deposit the bulk of their energy. Third, there exists a measurable time lag between the brightening of the near wings of Hα and the brightening of the Paschen continuum. This delay is controlled by the amount of time it takes for electron densities in the upper chromosphere to become high enough, and the densities of hydrogen atoms in high energy bound states to become low enough, to allow the number of recombinations to dominate the number of photoionizations in the region.

Feedback Interactions of Polymerized Actin with the Cell Membrane: Waves, Pulses, and Oscillations

NASA Astrophysics Data System (ADS)

Carlsson, Anders

Polymerized filaments of the protein actin have crucial functions in cell migration, and in bending the cell membrane to drive endocytosis or the formation of protrusions. The nucleation and polymerization of actin filaments are controlled by upstream agents in the cell membrane, including nucleation-promoting factors (NPFs) that activate the Arp2/3 complex to form new branches on pre-existing filaments. But polymerized actin (F-actin) also feeds back on the assembly of NPFs. We explore the effects of the resulting feedback loop of F-actin and NPFs on two phenomena: actin pulses that drive endocytosis in yeast, and actin waves traveling along the membrane of several cell types. In our model of endocytosis in yeast, the actin network is grown explicitly in three dimensions, exerts a negative feedback interaction on localized patch of NPFs in the membrane, and bends the membrane by exerting a distribution of forces. This model explains observed actin and NPF pulse dynamics, and the effects of several interventions including i) NPF mutations, ii) inhibition of actin polymerization, and iii) deletion of a protein that allows F-actin to bend the cell membrane. The model predicts that mutation of the active region of an NPF will enhance the accumulation of that NPF, and we confirm this prediction by quantitative fluorescence microscopy. For actin waves, we treat a similar model, with NPFs distributed over a larger region of the cell membrane. This model naturally generates actin waves, and predicts a transition from wave behavior to spatially localized oscillations when NPFs are confined to a small region. We also predict a transition from waves to static polarization as the negative-feedback coupling between F-actin and the NPFs is reduced. Supported by NIGMS Grant R01 GM107667.

Remarkable sequence conservation of the last intron in the PKD1 gene.

PubMed

Rodova, Marianna; Islam, M Rafiq; Peterson, Kenneth R; Calvet, James P

2003-10-01

The last intron of the PKD1 gene (intron 45) was found to have exceptionally high sequence conservation across four mammalian species: human, mouse, rat, and dog. This conservation did not extend to the comparable intron in pufferfish. Pairwise comparisons for intron 45 showed 91% identity (human vs. dog) to 100% identity (mouse vs. rat) for an average for all four species of 94% identity. In contrast, introns 43 and 44 of the PKD1 gene had average pairwise identities of 57% and 54%, and exons 43, 44, and 45 and the coding region of exon 46 had average pairwise identities of 80%, 84%, 82%, and 80%. Intron 45 is 90 to 95 bp in length, with the major region of sequence divergence being in a central 4-bp to 9-bp variable region. RNA secondary structure analysis of intron 45 predicts a branching stem-loop structure in which the central variable region lies in one loop and the putative branch point sequence lies in another loop, suggesting that the intron adopts a specific stem-loop structure that may be important for its removal. Although intron 45 appears to conform to the class of small, G-triplet-containing introns that are spliced by a mechanism utilizing intron definition, its high sequence conservation may be a reflection of constraints imposed by a unique mechanism that coordinates splicing of this last PKD1 intron with polyadenylation.

Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture

PubMed Central

Shiue, Chiou-Nan; Nematollahi-Mahani, Amir; Wright, Anthony P.H.

2014-01-01

Chromatin domain organization and the compartmentalized distribution of chromosomal regions are essential for packaging of deoxyribonucleic acid (DNA) in the eukaryotic nucleus as well as regulated gene expression. Nucleoli are the most prominent morphological structures of cell nuclei and nucleolar organization is coupled to cell growth. It has been shown that nuclear scaffold/matrix attachment regions often define the base of looped chromosomal domains in vivo and that they are thereby critical for correct chromosome architecture and gene expression. Here, we show regulated organization of mammalian ribosomal ribonucleic acid genes into distinct chromatin loops by tethering to nucleolar matrix via the non-transcribed inter-genic spacer region of the ribosomal DNA (rDNA). The rDNA gene loop structures are induced specifically upon growth stimulation and are dependent on the activity of the c-Myc protein. Matrix-attached rDNA genes are hypomethylated at the promoter and are thus available for transcriptional activation. rDNA genes silenced by methylation are not recruited to the matrix. c-Myc, which has been shown to induce rDNA transcription directly, is physically associated with rDNA gene looping structures and the intergenic spacer sequence in growing cells. Such a role of Myc proteins in gene activation has not been reported previously. PMID:24609384

Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture.

PubMed

Shiue, Chiou-Nan; Nematollahi-Mahani, Amir; Wright, Anthony P H

2014-05-01

Chromatin domain organization and the compartmentalized distribution of chromosomal regions are essential for packaging of deoxyribonucleic acid (DNA) in the eukaryotic nucleus as well as regulated gene expression. Nucleoli are the most prominent morphological structures of cell nuclei and nucleolar organization is coupled to cell growth. It has been shown that nuclear scaffold/matrix attachment regions often define the base of looped chromosomal domains in vivo and that they are thereby critical for correct chromosome architecture and gene expression. Here, we show regulated organization of mammalian ribosomal ribonucleic acid genes into distinct chromatin loops by tethering to nucleolar matrix via the non-transcribed inter-genic spacer region of the ribosomal DNA (rDNA). The rDNA gene loop structures are induced specifically upon growth stimulation and are dependent on the activity of the c-Myc protein. Matrix-attached rDNA genes are hypomethylated at the promoter and are thus available for transcriptional activation. rDNA genes silenced by methylation are not recruited to the matrix. c-Myc, which has been shown to induce rDNA transcription directly, is physically associated with rDNA gene looping structures and the intergenic spacer sequence in growing cells. Such a role of Myc proteins in gene activation has not been reported previously. © 2014 The Author(s). Published by Oxford University Press [on behalf of Nucleic Acids Research].

Method to suppress DDFS spurious signals in a frequency-hopping synthesizer with DDFS-driven PLL architecture.

PubMed

Kwon, Kun-Sup; Yoon, Won-Sang

2010-01-01

In this paper we propose a method of removing from synthesizer output spurious signals due to quasi-amplitude modulation and superposition effect in a frequency-hopping synthesizer with direct digital frequency synthesizer (DDFS)-driven phase-locked loop (PLL) architecture, which has the advantages of high frequency resolution, fast transition time, and small size. There are spurious signals that depend on normalized frequency of DDFS. They can be dominant if they occur within the PLL loop bandwidth. We suggest that such signals can be eliminated by purposefully creating frequency errors in the developed synthesizer.

The evolution of the simulation environment in the ALMA Observatory

NASA Astrophysics Data System (ADS)

Shen, Tzu-Chiang; Soto, Ruben; Saez, Norman; Velez, Gaston; Staig, Tomas; Sepulveda, Jorge; Saez, Alejandro; Ovando, Nicolas; Ibsen, Jorge

2016-07-01

The Atacama Large Millimeter /submillimeter Array (ALMA) has entered into operation phase since 2013. This transition changed the priorities within the observatory, in which, most of the available time will be dedicated to science observations at the expense of technical time. Therefore, it was planned to design and implement a new simulation environment, which must be comparable - or at least- be representative of the production environment. Concepts of model in the loop and hardware in the loop were explored. In this paper we review experiences gained and lessons learnt during the design and implementation of the new simulation environment.

A Hardware Platform for Tuning of MEMS Devices Using Closed-Loop Frequency Response

NASA Technical Reports Server (NTRS)

Ferguson, Michael I.; MacDonald, Eric; Foor, David

2005-01-01

We report on the development of a hardware platform for integrated tuning and closed-loop operation of MEMS gyroscopes. The platform was developed and tested for the second generation JPL/Boeing Post-Resonator MEMS gyroscope. The control of this device is implemented through a digital design on a Field Programmable Gate Array (FPGA). A software interface allows the user to configure, calibrate, and tune the bias voltages on the micro-gyro. The interface easily transitions to an embedded solution that allows for the miniaturization of the system to a single chip.

Oxygen vacancy effect on dielectric and hysteretic properties of zigzag ferroelectric iron dioxide nanoribbon

NASA Astrophysics Data System (ADS)

Zriouel, S.; Taychour, B.; Yahyaoui, F. El; Drissi, L. B.

2017-07-01

Zigzag FeO2 nanoribbon defected by the removal of oxygen atoms is simulated using Monte Carlo simulations. All possible arrangements of positions and number of oxygen vacancy are investigated. Temperature dependence of polarization, dielectric susceptibility, internal energy, specific heat and dielectric hysteresis loops are all studied. Results show the presence of second order phase transition and Q - type behavior. Dielectric properties dependence on ribbon's edge, positions and number of oxygen vacancy are discussed in detail. Moreover, single and square hysteresis loops are observed whatever the number of oxygen vacancy in the system.

Measurement of the Branching Fraction of the Exclusive Decay B0 --> K*0gamma

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

Barrera, Barbara

The b {yields} s{gamma} transition proceeds by a loop penguin diagram. It may be used to measure precisely the couplings of the top quark and to search for the effects of any new particles appearing in the loop. We present a preliminary measurement of the branching fraction of the exclusive decay, B{sup 0} {yields} K*{sup 0}{gamma}. They use 8.6 x 10{sup 6} B{bar B} decays to measure B(B{sup 0} {yields} K*{sup 0}{gamma}) = (5.4 {+-} 0.8 {+-} 0.5) x 10{sup -5}.

Data-derived symbol synchronization of MASK and QASK signals. [for multilevel digital communication systems

NASA Technical Reports Server (NTRS)

Simon, M. K.

1974-01-01

Multilevel amplitude-shift-keying (MASK) and quadrature amplitude-shift-keying (QASK) as signaling techniques for multilevel digital communications systems, and the problem of providing symbol synchronization in the receivers of such systems are discussed. A technique is presented for extracting symbol sync from an MASK or QASK signal. The scheme is a generalization of the data transition tracking loop used in PSK systems. The performance of the loop was analyzed in terms of its mean-squared jitter and its effects on the data detection process in MASK and QASK systems.

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

PubMed Central

Day, Ryan; Lennox, Kristin P.; Sukhanov, Paul; Dahl, David B.; Vannucci, Marina; Tsai, Jerry

2011-01-01

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD <2.0 Å), the DPM-HMM method performs as well or better than the best templates, demonstrating that our automated method recaptures these canonical loops without inclusion of any IgG specific terms or manual intervention. In cases with poor or few good templates (mean RMSD >7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/. PMID:22028638

Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

PubMed

Komatsu, Setsuko; Takasaki, Hironori

2009-07-01

Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

Chiral and deconfinement phase transition in the Hamiltonian approach to QCD in Coulomb gauge

NASA Astrophysics Data System (ADS)

Reinhardt, H.; Vastag, P.

2016-11-01

The chiral and deconfinement phase transitions are investigated within the variational Hamiltonian approach to QCD in Coulomb gauge. The temperature β-1 is introduced by compactifying a spatial dimension. Thereby the whole temperature dependence is encoded in the vacuum state on the spatial manifold R2×S1(β ) . The chiral quark condensate and the dual quark condensate (dressed Polyakov loop) are calculated as a function of the temperature. From their inflection points the pseudocritical temperatures for the chiral and deconfinement crossover transitions are determined. Using the zero-temperature quark and gluon propagators obtained within the variational approach as input, we find 170 and 198 MeV, respectively, for the chiral and deconfinement transition.

Fe-rich and Si-rich ejecta distribution in the Cygnus Loop

NASA Astrophysics Data System (ADS)

Nakajima, Hiroshi; Tsunemi, Hiroshi; Kimura, Masashi; Uchida, Hiroyuki; Katsuda, Satoru

2012-03-01

We report on the results of Suzaku observations of central region of the proto-typical middle-aged Supernova remnant (SNR) Cygnus Loop. The southeastern region of the SNR with the distance from the geometric center ranging from 10' to 55' is observed using XIS. Thanks to the low and stable background of Suzaku, the distribution maps of heavy species such as Fe, S, Si, Mg, Ne and O arereliably obtained. We found that the relatively heavier four species are confined to the small centermost region while the lighter species show uniform distribution or depressed center region. These results exhibit an onion-like metallicity structure in this SNR, which reflects the metal distribution of the progenitor.

LARGE-SCALE CONTRACTION AND SUBSEQUENT DISRUPTION OF CORONAL LOOPS DURING VARIOUS PHASES OF THE M6.2 FLARE ASSOCIATED WITH THE CONFINED FLUX ROPE ERUPTION

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

Kushwaha, Upendra; Joshi, Bhuwan; Moon, Yong-Jae

We investigate evolutionary phases of an M6.2 flare and the associated confined eruption of a prominence. The pre-flare phase exhibits spectacular large-scale contraction of overlying extreme ultraviolet (EUV) coronal loops during which the loop system was subjected to an altitude decrease of ∼20 Mm (40% of the initial height) for an extended span of ∼30 minutes. This contraction phase is accompanied by sequential EUV brightenings associated with hard X-ray (HXR; up to 25 keV) and microwave (MW) sources from low-lying loops in the core region which together with X-ray spectra indicate strong localized heating in the source region before themore » filament activation. With the onset of the flare’s impulsive phase, we detect HXR and MW sources that exhibit intricate temporal and spatial evolution in relation to the fast rise of the prominence. Following the flare maximum, the filament eruption slowed down and subsequently became confined within the large overlying active region loops. During the confinement process of the erupting prominence, we detect MW emission from the extended coronal region with multiple emission centroids, which likely represent emission from hot blobs of plasma formed after the collapse of the expanding flux rope and entailing prominence material. RHESSI spectroscopy reveals high plasma temperature (∼30 MK) and substantial non-thermal characteristics (δ ∼ 5) during the impulsive phase of the flare. The time evolution of thermal energy exhibits a good correspondence with the variations in cumulative non-thermal energy, which suggests that the energy of accelerated particles is efficiently converted to hot flare plasma, implying an effective validation of the Neupert effect.« less

Topological and trivial magnetic oscillations in nodal loop semimetals

NASA Astrophysics Data System (ADS)

Oroszlány, László; Dóra, Balázs; Cserti, József; Cortijo, Alberto

2018-05-01

Nodal loop semimetals are close descendants of Weyl semimetals and possess a topologically dressed band structure. We argue by combining the conventional theory of magnetic oscillation with topological arguments that nodal loop semimetals host coexisting topological and trivial magnetic oscillations. These originate from mapping the topological properties of the extremal Fermi surface cross sections onto the physics of two dimensional semi-Dirac systems, stemming from merging two massless Dirac cones. By tuning the chemical potential and the direction of magnetic field, a sharp transition is identified from purely trivial oscillations, arising from the Landau levels of a normal two dimensional (2D) electron gas, to a phase where oscillations of topological and trivial origin coexist, originating from 2D massless Dirac and semi-Dirac points, respectively. These could in principle be directly identified in current experiments.

Meta-stable magnetic transitions and its field dependence in Co2.75Fe0.25O4 ferrite

NASA Astrophysics Data System (ADS)

Aswathi M., C.; Bhowmik, R. N.

2018-04-01

The Co2.75Fe0.25O4 ferrite has been prepared by chemical co-precipitation route. The as-prepared sample has been annealed at 500° C. X-ray diffraction pattern indicated cubic spinel structure in the sample. The sample showed ferrimagnetic nature with magnetic irreversibility and hysteresis loop. Magnetization data revealed high anisotropic nature and at least two prominent meta-stable magnetic transitions below the highest measurement temperature 350 K.

The future of radiology augmented with Artificial Intelligence: A strategy for success.

PubMed

Liew, Charlene

2018-05-01

The rapid development of Artificial Intelligence/deep learning technology and its implementation into routine clinical imaging will cause a major transformation to the practice of radiology. Strategic positioning will ensure the successful transition of radiologists into their new roles as augmented clinicians. This paper describes an overall vision on how to achieve a smooth transition through the practice of augmented radiology where radiologists-in-the-loop ensure the safe implementation of Artificial Intelligence systems. Copyright © 2018 Elsevier B.V. All rights reserved.

Observation and Modeling of Chromospheric Evaporation in a Coronal Loop Related to Active Region Transient Brightening

NASA Astrophysics Data System (ADS)

Gupta, G. R.; Sarkar, Aveek; Tripathi, Durgesh

2018-04-01

Using the observations recorded by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory and the Interface Region Imaging Spectrograph (IRIS) and the Extreme-ultraviolet Imaging Spectrometer and X-Ray Telescope both on board Hinode, we present evidence of chromospheric evaporation in a coronal loop after the occurrence of two active region transient brightenings (ARTBs) at the two footpoints. The chromospheric evaporation started nearly simultaneously in all of the three hot channels of AIA 131, 94, and 335 Å and was observed to be temperature dependent, being fastest in the highest temperature channel. The whole loop became fully brightened following the ARTBs after ≈25 s in 131 Å, ≈40 s in 94 Å, and ≈6.5 minutes in 335 Å. The differential emission measurements at the two footpoints (i.e., of two ARTBs) and at the loop top suggest that the plasma attained a maximum temperature of ∼10 MK at all these locations. The spectroscopic observations from IRIS revealed the presence of redshifted emission of ∼20 km s‑1 in cooler lines like C II and Si IV during the ARTBs that was cotemporal with the evaporation flow at the footpoint of the loop. During the ARTBs, the line width of C II and Si IV increased nearly by a factor of two during the peak emission. Moreover, enhancement in the line width preceded that in the Doppler shift, which again preceded enhancement in the intensity. The observed results were qualitatively reproduced by 1D hydrodynamic simulations, where energy was deposited at both of the footpoints of a monolithic coronal loop that mimicked the ARTBs identified in the observations.

S-ovalbumin, an ovalbumin conformer with properties analogous to those of loop-inserted serpins.

PubMed Central

Huntington, J. A.; Patston, P. A.; Gettins, P. G.

1995-01-01

Most serpins are inhibitors of serine proteinases and are thought to undergo a conformational change upon complex formation with proteinase that involves partial insertion of the reactive center loop into a beta-sheet of the inhibitor. Ovalbumin, although a serpin, is not an inhibitor of serine proteinases. It has been proposed that this deficiency arises from the presence of a charged residue, arginine, at a critical point (P14) in the reactive center region, which prevents loop insertion into the beta-sheet and thereby precludes inhibitory properties. To test whether loop insertion is prevented in ovalbumin we have examined the properties of two forms of ovalbumin: the native protein and S-ovalbumin, a form that forms spontaneously from native ovalbumin and has increased stability. Calorimetric measurements showed that S-ovalbumin was more stable than ovalbumin by about 3 kcal mol-1. CD spectra, which indicated that S-ovalbumin had less alpha-helix than native ovalbumin, and 1H NMR spectra, which indicated very similar overall structures, suggest limited conformational differences between the two forms. From comparison of the susceptibility of the reactive center region of each protein to proteolysis by porcine pancreatic elastase and by subtilisin Carlsberg, we concluded that the limited native-to-S conformational change specifically affected the reactive center region. These data are consistent with a structure for S-ovalbumin in which part of the reactive center loop has inserted into beta-sheet A to give a more stable structure, analogously to other serpins. However, the rate of loop insertion appears to be very much lower than for inhibitory serpins.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7613461

The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5′-CC to 5′-TC by a Single Amino Acid Substitution

PubMed Central

Rathore, Anurag; Carpenter, Michael A; Demir, Özlem; Ikeda, Terumasa; Li, Ming; Shaban, Nadine; Law, Emily K.; Anokhin, Dmitry; Brown, William L.; Amaro, Rommie E.; Harris, Reuben S.

2013-01-01

APOBEC3A and APOBEC3G are DNA cytosine deaminases with biological functions in foreign DNA and retrovirus restriction, respectively. APOBEC3A has an intrinsic preference for cytosine preceded by thymine (5′-TC) in single-stranded DNA substrates, whereas APOBEC3G prefers the target cytosine to be preceded by another cytosine (5′-CC). To determine the amino acids responsible for these strong dinucleotide preferences, we analyzed a series of chimeras in which putative DNA binding loop regions of APOBEC3G were replaced with the corresponding regions from APOBEC3A. Loop 3 replacement enhanced APOBEC3G catalytic activity but did not alter its intrinsic 5′-CC dinucleotide substrate preference. Loop 7 replacement caused APOBEC3G to become APOBEC3A-like and strongly prefer 5′-TC substrates. Simultaneous loop 3/7 replacement resulted in a hyperactive APOBEC3G variant that also preferred 5′-TC dinucleotides. Single amino acid exchanges revealed D317 as a critical determinant of dinucleotide substrate specificity. Multi-copy explicitly solvated all-atom molecular dynamics simulations suggested a model in which D317 acts as a helix-capping residue by constraining the mobility of loop 7, forming a novel binding pocket that favorably accommodates cytosine. All catalytically active APOBEC3G variants, regardless of dinucleotide preference, retained HIV-1 restriction activity. These data support a model in which the loop 7 region governs the selection of local dinucleotide substrates for deamination but is unlikely to be part of the higher level targeting mechanisms that direct these enzymes to biological substrates such as HIV-1 cDNA. PMID:23938202

Crystal structure of the anti-(carcinoembryonic antigen) single-chain Fv antibody MFE-23 and a model for antigen binding based on intermolecular contacts.

PubMed

Boehm, M K; Corper, A L; Wan, T; Sohi, M K; Sutton, B J; Thornton, J D; Keep, P A; Chester, K A; Begent, R H; Perkins, S J

2000-03-01

MFE-23 is the first single-chain Fv antibody molecule to be used in patients and is used to target colorectal cancer through its high affinity for carcinoembryonic antigen (CEA), a cell-surface member of the immunoglobulin superfamily. MFE-23 contains an N-terminal variable heavy-chain domain joined by a (Gly(4)Ser)(3) linker to a variable light-chain (V(L)) domain (kappa chain) with an 11-residue C-terminal Myc-tag. Its crystal structure was determined at 2.4 A resolution by molecular replacement with an R(cryst) of 19.0%. Five of the six antigen-binding loops, L1, L2, L3, H1 and H2, conformed to known canonical structures. The sixth loop, H3, displayed a unique structure, with a beta-hairpin loop and a bifurcated apex characterized by a buried Thr residue. In the crystal lattice, two MFE-23 molecules were associated back-to-back in a manner not seen before. The antigen-binding site displayed a large acidic region located mainly within the H2 loop and a large hydrophobic region within the H3 loop. Even though this structure is unliganded within the crystal, there is an unusually large region of contact between the H1, H2 and H3 loops and the beta-sheet of the V(L) domain of an adjacent molecule (strands DEBA) as a result of intermolecular packing. These interactions exhibited remarkably high surface and electrostatic complementarity. Of seven MFE-23 residues predicted to make contact with antigen, five participated in these lattice contacts, and this model for antigen binding is consistent with previously reported site-specific mutagenesis of MFE-23 and its effect on CEA binding.

On Heating Large Bright Coronal Loops by Magnetic Microexplosions at their Feet

NASA Technical Reports Server (NTRS)

Moore, Ronald L; Falconer, D. A.; Porter, Jason G.

1999-01-01

In previous work, by registering Yohkoh SXT coronal X-ray images with MSFC vector magnetograms, we found that: (1) many of the larger bright coronal loops rooted at one or both ends in an active region are rooted around magnetic islands of included polarity, (2) the core field encasing the neutral line encircling the island is strongly sheared, and (3) this sheared core field is the seat of frequent microflares. This suggests that the coronal heating in these extended bright loops is driven by many small explosive releases of stored magnetic energy from the sheared core field at their feet, some of which magnetic microexplosions also produce the microflare heating in the core fields. In this paper, we show that this scenario is feasible in terms of the energy Abstract: required for the observed coronal heating and the magnetic energy available in the observed sheared core fields. In a representative active region, from the X-ray and vector field data, we estimate the coronal heating consumption by a selected typical large bright loop, the coronal heating consumption by a typical microflare at the foot of this loop, the frequency of microflares at the foot, and the available magnetic energy in the microflaring core field. We find that: (1) the rate of magnetic energy release to power the microflares at the foot (approx. 6 x 10(ext 25)erg/s) is enough to also power the coronal heating in the body of the extended loop (approx. 2 x l0(exp 25 erg/s), and (2) there is enough stored magnetic energy in the sheared core field to sustain the microflaring and extended loop heating for about a day, which is a typical time for buildup of neutral-line magnetic shear in an active region. This work was funded by the Solar Physics Branch of NASA's Office of Space Science through the SR&T Program and the SEC Guest Investigator Program.

Atomistic modeling of shock-induced void collapse in copper

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

Davila, L P; Erhart, P; Bringa, E M

2005-03-09

Nonequilibrium molecular dynamics (MD) simulations show that shock-induced void collapse in copper occurs by emission of shear loops. These loops carry away the vacancies which comprise the void. The growth of the loops continues even after they collide and form sessile junctions, creating a hardened region around the collapsing void. The scenario seen in our simulations differs from current models that assume that prismatic loop emission is responsible for void collapse. We propose a new dislocation-based model that gives excellent agreement with the stress threshold found in the MD simulations for void collapse as a function of void radius.

The plasma filling factor of coronal bright points. II. Combined EIS and TRACE results

NASA Astrophysics Data System (ADS)

Dere, K. P.

2009-04-01

Aims: In a previous paper, the volumetric plasma filling factor of coronal bright points was determined from spectra obtained with the Extreme ultraviolet Imaging Spectrometer (EIS). The analysis of these data showed that the median plasma filling factor was 0.015. One interpretation of this result was that the small filling factor was consistent with a single coronal loop with a width of 1-2´´, somewhat below the apparent width. In this paper, higher spatial resolution observations with the Transition Region and Corona Explorer (TRACE) are used to test this interpretation. Methods: Rastered spectra of regions of the quiet Sun were recorded by the EIS during operations with the Hinode satellite. Many of these regions were simultaneously observed with TRACE. Calibrated intensities of Fe xii lines were obtained and images of the quiet corona were constructed from the EIS measurements. Emission measures were determined from the EIS spectra and geometrical widths of coronal bright points were obtained from the TRACE images. Electron densities were determined from density-sensitive line ratios measured with EIS. A comparison of the emission measure and bright point widths with the electron densities yielded the plasma filling factor. Results: The median electron density of coronal bright points is 3 × 109 cm-3 at a temperature of 1.6 × 106 K. The volumetric plasma filling factor of coronal bright points was found to vary from 3 × 10-3 to 0.3 with a median value of 0.04. Conclusions: The current set of EIS and TRACE coronal bright-point observations indicate the median value of their plasma filling factor is 0.04. This can be interpreted as evidence of a considerable subresolution structure in coronal bright points or as the result of a single completely filled plasma loop with widths on the order of 0.2-1.5´´ that has not been spatially resolved in these measurements.

Lepton flavor violating B meson decays via a scalar leptoquark

NASA Astrophysics Data System (ADS)

Sahoo, Suchismita; Mohanta, Rukmani

2016-06-01

We study the effect of scalar leptoquarks in the lepton flavor violating B meson decays induced by the flavor-changing transitions b →q li+lj- with q =s , d . In the standard model, these transitions are extremely rare as they are either two-loop suppressed or proceed via box diagrams with tiny neutrino masses in the loop. However, in the leptoquark model, they can occur at tree level and are expected to have significantly large branching ratios. The leptoquark parameter space is constrained using the experimental limits on the branching ratios of Bq→l+l- processes. Using such constrained parameter space, we predict the branching ratios of LFV semileptonic B meson decays, such as B+→K+(π+)li+lj-, B+→(K*+,ρ+)li+lj-, and Bs→ϕ li+lj-, which are found to be within the experimental reach of LHCb and the upcoming Belle II experiments. We also investigate the rare leptonic KL ,S→μ+μ-(e+e-) and KL→μ∓e± decays in the leptoquark model.

Coronal Heating: Testing Models of Coronal Heating by Forward-Modeling the AIA Emission of the Ansample of Coronal Loops

NASA Astrophysics Data System (ADS)

Malanushenko, A. V.

2015-12-01

We present a systemic exploration of the properties of coronal heating, by forward-modeling the emission of the ensemble of 1D quasi-steady loops. This approximations were used in many theoretical models of the coronal heating. The latter is described in many such models in the form of power laws, relating heat flux through the photosphere or volumetric heating to the strength of the magnetic field and length of a given field line. We perform a large search in the parameter space of these power laws, amongst other variables, and compare the resulting emission of the active region to that observed by AIA. We use a recently developed magnetic field model which uses shapes of coronal loops to guide the magnetic model; the result closely resembles observed structures by design. We take advantage of this, by comparing, in individual sub-regions of the active region, the emission of the active region and its synthetic model. This study allows us to rule out many theoretical models and formulate predictions for the heating models to come.

Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus.

PubMed

Balmith, Marissa; Soliman, Mahmoud E S

2017-02-28

The first account of the dynamic features of the loop region of VP40 of the Ebola virus (EboV) using accelerated molecular dynamics (aMD) simulations is reported herein. Due to its major role in the Ebola life cycle, VP40 is considered a promising therapeutic target. The available experimental data on the N-terminal domain (NTD) loop indicates that mutations K127A, T129A and N130A demonstrate an unrecognized role for NTD-plasma membrane (PM) interaction for efficient VP40-PM localization, oligomerization, matrix assembly and egress. Despite experimental results, the molecular description of VP40 and the information it can provide still remain vague. Therefore, to gain further molecular insight into the effect of mutations on the loop region of VP40 and its effects on the overall protein conformation and VP40 dimerization, aMD simulations and post-dynamic analyses were employed for wildtype (WT) and mutant systems. The results showed significant variations in the presence of mutations as per RMSF, RMSD, R g , PCA and distance calculations in comparison to the WT. These results could provide researchers with insight with regards to the conformational aspects concerning VP40 and its close relation to the experimental data. We believe that the results presented in this study will ultimately provide a useful understanding of the structural landscape of the loop region of VP40, which would contribute towards the discovery of novel EboV inhibitors.

CHROMOSPHERIC EVAPORATION IN AN X1.0 FLARE ON 2014 MARCH 29 OBSERVED WITH IRIS AND EIS

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

Li, Y.; Ding, M. D.; Qiu, J.

Chromospheric evaporation refers to dynamic mass motions in flare loops as a result of rapid energy deposition in the chromosphere. These motions have been observed as blueshifts in X-ray and extreme-ultraviolet (EUV) spectral lines corresponding to upward motions at a few tens to a few hundreds of km s{sup −1}. Past spectroscopic observations have also revealed a dominant stationary component, in addition to the blueshifted component, in emission lines formed at high temperatures (∼10 MK). This is contradictory to evaporation models predicting predominant blueshifts in hot lines. The recently launched Interface Region Imaging Spectrograph (IRIS) provides high-resolution imaging and spectroscopicmore » observations that focus on the chromosphere and transition region in the UV passband. Using the new IRIS observations, combined with coordinated observations from the EUV Imaging Spectrometer, we study the chromospheric evaporation process from the upper chromosphere to the corona during an X1.0 flare on 2014 March 29. We find evident evaporation signatures, characterized by Doppler shifts and line broadening, at two flare ribbons that are separating from each other, suggesting that chromospheric evaporation takes place in successively formed flaring loops throughout the flare. More importantly, we detect dominant blueshifts in the high-temperature Fe xxi line (∼10 MK), in agreement with theoretical predictions. We also find that, in this flare, gentle evaporation occurs at some locations in the rise phase of the flare, while explosive evaporation is detected at some other locations near the peak of the flare. There is a conversion from gentle to explosive evaporation as the flare evolves.« less

Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop

PubMed Central

Bohon, Jen; Jennings, Laura D.; Phillips, Christine M.; Licht, Stuart; Chance, Mark R.

2010-01-01

SUMMARY Synchrotron x-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation. PMID:18682217

Higher-order looping and nuclear organization of antigen receptor loci facilitate targeted RAG cleavage and regulated rearrangement in recombination centers

PubMed Central

Chaumeil, Julie; Micsinai, Mariann; Ntziachristos, Panagiotis; Deriano, Ludovic; Wang, Joy M-H; Ji, Yanhong; Nora, Elphege P.; Rodesch, Matthew J.; Jeddeloh, Jeffrey A.; Aifantis, Iannis; Kluger, Yuval; Schatz, David G.; Skok, Jane A.

2013-01-01

SUMMARY V(D)J recombination is essential for generating a diverse array of B and T cell receptors that can recognize and combat foreign antigen. As with any recombination event, tight control is essential to prevent the occurrence of genetic anomalies that drive cellular transformation. One important aspect of regulation is directed targeting of the RAG recombinase. Indeed, RAG accumulates at the 3’ end of individual antigen receptor loci poised for rearrangement, however, it is not known whether focal binding is involved in regulating cleavage, and what mechanisms lead to enrichment of RAG in this region. Here we show that mono-allelic looping out of the 3’ end of Tcra, coupled with transcription and increased chromatin/nuclear accessibility, are linked to focal RAG binding and ATM-mediated regulated mono-allelic cleavage on looped out 3’ regions. Our data identify higher order loop formation as a key determinant of directed RAG targeting and the maintenance of genome stability. PMID:23416051

OT2_wlanger_7: Dynamics of Giant Magnetic Gas Loops and Their Connection to the CMZ in the Galactic Center

NASA Astrophysics Data System (ADS)

Langer, W.

2011-09-01

Understanding the mass transfer and dynamics among the Galactic Center, the disk, and the halo of the Milky Way is fundamental to the study of the evolution of galaxies and star formation. Recently several giant loops of molecular gas (GML) have been found in the Galactic Center from CO maps, which are likely the result of the magnetic Parker instability. There is new evidence of a possible connection between these loops and the Central Molecular Zone as shown in a sparse [CII] sampling made by the Herschel Key Project GOT C+. Here we propose to map various features of the GMLs and the interface region in [CII] with HIFI. We will also map the foot points of the loop, which are thought to be highly shocked regions, in the ortho 110-101 line of water, which is a known shock tracer. With this data we will characterize different ISM components and their flow among these Galactic Center features.

Interstitial loop transformations in FeCr

DOE PAGES

Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.; ...

2015-03-27

Here, we improve the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) algorithm by integrating the Activation Relaxation Technique nouveau (ARTn), a powerful open-ended saddle-point search method, into the algorithm. We use it to investigate the reaction of 37-interstitial 1/2[1 1 1] and 1/2[View the MathML source] loops in FeCr at 10 at.% Cr. They transform into 1/2[1 1 1], 1/2[View the MathML source], [1 0 0] and [0 1 0] 74-interstitial clusters with an overall barrier of 0.85 eV. We find that Cr decoration locally inhibits the rotation of crowdions, which dictates the final loop orientation. Moreover, the final loop orientationmore » depends on the details of the Cr decoration. Generally, a region of a given orientation is favored if Cr near its interface with a region of another orientation is able to inhibit reorientation at this interface more than the Cr present at the other interfaces. Also, we find that substitutional Cr atoms can diffuse from energetically unfavorable to energetically favorable sites within the interlocked 37-interstitial loops conformation with barriers of less than 0.35 eV.« less

Characterization of the Interaction of Sclerostin with the Low Density Lipoprotein Receptor-related Protein (LRP) Family of Wnt Co-receptors*

PubMed Central

Holdsworth, Gill; Slocombe, Patrick; Doyle, Carl; Sweeney, Bernadette; Veverka, Vaclav; Le Riche, Kelly; Franklin, Richard J.; Compson, Joanne; Brookings, Daniel; Turner, James; Kennedy, Jeffery; Garlish, Rachael; Shi, Jiye; Newnham, Laura; McMillan, David; Muzylak, Mariusz; Carr, Mark D.; Henry, Alistair J.; Ceska, Thomas; Robinson, Martyn K.

2012-01-01

LRP5 and LRP6 are proteins predicted to contain four six-bladed β-propeller domains and both bind the bone-specific Wnt signaling antagonist sclerostin. Here, we report the crystal structure of the amino-terminal region of LRP6 and using NMR show that the ability of sclerostin to bind to this molecule is mediated by the central core of sclerostin and does not involve the amino- and carboxyl-terminal flexible arm regions. We show that this structured core region interacts with LRP5 and LRP6 via an NXI motif (found in the sequence PNAIG) within a flexible loop region (loop 2) within the central core region. This sequence is related closely to a previously identified motif in laminin that mediates its interaction with the β-propeller domain of nidogen. However, the NXI motif is not involved in the interaction of sclerostin with LRP4 (another β-propeller containing protein in the LRP family). A peptide derived from the loop 2 region of sclerostin blocked the interaction of sclerostin with LRP5/6 and also inhibited Wnt1 but not Wnt3A or Wnt9B signaling. This suggests that these Wnts interact with LRP6 in different ways. PMID:22696217

Hexagonal convection patterns and their evolutionary scenarios in electroconvection induced by a strong unipolar injection

NASA Astrophysics Data System (ADS)

Luo, Kang; Wu, Jian; Yi, Hong-Liang; Liu, Lin-Hua; Tan, He-Ping

2018-05-01

A regular hexagonal pattern of three-dimensional electroconvective flow induced by unipolar injection in dielectric liquids is numerically observed by solving the fully coupled governing equations using the lattice Boltzmann method. A small-amplitude perturbation in the form of a spatially periodic pattern of hexagonal cells is introduced initially. The transient development of convective cells that undergo a sequence of transitions agrees with the idea of flow seeking an optimal scale. Stable hexagonal convective cells and their subcritical bifurcation together with a hysteresis loop are clearly observed. In addition, the stability of the hexagonal flow pattern is analyzed in a wide range of relevant parameters, including the electric Rayleigh number T , nondimensional mobility M , and wave number k . It is found that centrally downflowing hexagonal cells, which are characterized by the central region being empty of charge, are preferred in the system.

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.

Favorable 2'-substitution in the loop region of a thrombin-binding DNA aptamer.

PubMed

Awachat, Ragini; Wagh, Atish A; Aher, Manisha; Fernandes, Moneesha; Kumar, Vaijayanti A

2018-06-01

Simple 2'-OMe-chemical modification in the loop region of the 15mer G-rich DNA sequence GGTTGGTGTGGTTGG is reported. The G-quadruplex structure of this thrombin-binding aptamer (TBA), is stabilized by single modifications (T → 2'-OMe-U), depending on the position of the modification. The structural stability also renders significantly increased inhibition of thrombin-induced fibrin polymerization, a process closely associated with blood-clotting. Copyright © 2018 Elsevier Ltd. All rights reserved.

Assessing the effect of D59P mutation in the DE loop region in amyloid aggregation propensity of β2-microglobulin: A molecular dynamics simulation study.

PubMed

Narang, Simranjeet S; Shuaib, Suniba; Goyal, Deepti; Goyal, Bhupesh

2018-01-01

Dialysis-related amyloidosis (DRA) is a severe condition characterized by the accumulation of amyloidogenic β2-microglobulin (β2m) protein around skeletal joints and bones. The recent studies highlighted a critical role of the DE loop region for β2m stability and amyloid aggregation propensity. Despite significant efforts, the molecular mechanism of enhanced aggregation due to D59P mutation in the DE loop region remain elusive. In the present study, explicit-solvent molecular dynamics (MD) simulations were performed to examine the key changes in the structural and dynamic properties of wild type (wt) β2m upon D59P mutation. MD simulations reveal a decrease in the average number of hydrogen bonds in the loop regions on D59P mutation that enhances conformational flexibility, which lead to higher aggregation propensity of D59P as compare to wt β2m. The principal component analysis (PCA) highlight that D59P covers a larger region of phase space and display a higher trace value than wt β2m, which suggest an overall enhancement in the conformational flexibility. D59P display two minimum energy basins in the free energy landscape (FEL) that are associated with thermodynamically less stable conformational states as compare to single minimum energy basin in wt β2m. The present study provides theoretical insights into the molecular mechanism behind the higher aggregation propensity of D59P as compare to wt β2m. © 2017 Wiley Periodicals, Inc.

FAST CONTRACTION OF CORONAL LOOPS AT THE FLARE PEAK

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

Liu Rui; Wang Haimin

On 2005 September 8, a coronal loop overlying the active region NOAA 10808 was observed in TRACE 171 A to contract at {approx}100 km s{sup -1} at the peak of an X5.4-2B flare at 21:05 UT. Prior to the fast contraction, the loop underwent a much slower contraction at {approx}6 km s{sup -1} for about 8 minutes, initiating during the flare preheating phase. The sudden switch to fast contraction is presumably corresponding to the onset of the impulsive phase. The contraction resulted in the oscillation of a group of loops located below, with the period of about 10 minutes. Meanwhile,more » the contracting loop exhibited a similar oscillatory pattern superimposed on the dominant downward motion. We suggest that the fast contraction reflects a suddenly reduced magnetic pressure underneath due either to (1) the eruption of magnetic structures located at lower altitudes or to (2) the rapid conversion of magnetic free energy in the flare core region. Electrons accelerated in the shrinking trap formed by the contracting loop can theoretically contribute to a late-phase hard X-ray burst, which is associated with Type IV radio emission. To complement the X5.4 flare which was probably confined, a similar event observed in SOHO/EIT 195 A on 2004 July 20 in an eruptive, M8.6 flare is briefly described, in which the contraction was followed by the expansion of the same loop leading up to a halo coronal mass ejection. These observations further substantiate the conjecture of coronal implosion and suggest coronal implosion as a new exciter mechanism for coronal loop oscillations.« less

G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch.

PubMed

Yan, Yi-Yong; Tan, Jia-Heng; Lu, Yu-Jing; Yan, Siu-Cheong; Wong, Kwok-Yin; Li, Ding; Gu, Lian-Quan; Huang, Zhi-Shu

2013-10-01

G-Quadruplex is a highly polymorphic structure, and its behavior in acidic condition has not been well studied. Circular dichroism (CD) spectra were used to study the conformational change of G-quadruplex. The thermal stabilities of the G-quadruplex were measured with CD melting. Interconversion kinetics profiles were investigated by using CD kinetics. The fluorescence of the inserted 2-Aminopurine (Ap) was monitored during pH change and acrylamide quenching, indicating the status of the loop. Proton NMR was adopted to help illustrate the change of the conformation. G-Quadruplex of specific loop was found to be able to transform upon pH variation. The transformation was resulted from the loop rearrangement. After screening of a library of diverse G-quadruplex, a sequence exhibiting the best transformation property was found. A pH-driven nanoswitch with three gears was obtained based on this transition cycle. Certain G-quadruplex was found to go through conformational change at low pH. Loop was the decisive factor controlling the interconversion upon pH variation. G-Quadruplex with TT central loop could be converted in a much milder condition than the one with TTA loop. It can be used to design pH-driven nanodevices such as a nanoswitch. These results provide more insights into G-quadruplex polymorphism, and also contribute to the design of DNA-based nanomachines and logic gates. © 2013.

Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.

PubMed

Lai, Cheng-Tsung; Li, Huei-Jiun; Yu, Weixuan; Shah, Sonam; Bommineni, Gopal R; Perrone, Victoria; Garcia-Diaz, Miguel; Tonge, Peter J; Simmerling, Carlos

2015-08-04

Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). However, rational modulation of residence time presents significant challenges because it requires additional mechanistic insight, such as the nature of the transition state for postbinding isomerization. Our previous work, based on X-ray crystallography, enzyme kinetics, and molecular dynamics simulation, suggested that the slow step in inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA involves a change in the conformation of the substrate binding loop from an open state in the initial enzyme-inhibitor complex to a closed state in the final enzyme-inhibitor complex. Here, we use multidimensional free energy landscapes for loop isomerization to obtain a computational model for the transition state. The results suggest that slow-onset inhibitors crowd key side chains on helices that slide past each other during isomerization, resulting in a steric clash. The landscapes become significantly flatter when residues involved in the steric clash are replaced with alanine. Importantly, this lower barrier can be increased by rational inhibitor redesign to restore the steric clash. Crystallographic studies and enzyme kinetics confirm the predicted effects on loop structure and flexibility, as well as inhibitor residence time. These loss and regain of function studies validate our mechanistic hypothesis for interactions controlling substrate binding loop isomerization, providing a platform for the future design of inhibitors with longer residence times and better in vivo potency. Similar opportunities for slow-onset inhibition via the same mechanism are identified in other pathogens.

Predictable Patterns in Planetary Transit Timing Variations and Transit Duration Variations Due to Exomoons

NASA Technical Reports Server (NTRS)

Heller, Rene; Hippke, Michael; Placek, Ben; Angerhausen, Daniel; Agol, Eric

2016-01-01

We present new ways to identify single and multiple moons around extrasolar planets using planetary transit timing variations (TTVs) and transit duration variations (TDVs). For planets with one moon, measurements from successive transits exhibit a hitherto undescribed pattern in the TTV-TDV diagram, originating from the stroboscopic sampling of the planet's orbit around the planet-moon barycenter. This pattern is fully determined and analytically predictable after three consecutive transits. The more measurements become available, the more the TTV-TDV diagram approaches an ellipse. For planets with multiple moons in orbital mean motion resonance (MMR), like the Galilean moon system, the pattern is much more complex and addressed numerically in this report. Exomoons in MMR can also form closed, predictable TTV-TDV figures, as long as the drift of the moons' pericenters is suciently slow.We find that MMR exomoons produce loops in the TTV-TDV diagram and that the number of these loops is equal to the order of the MMR, or the largest integer in the MMR ratio.We use a Bayesian model and Monte Carlo simulations to test the discoverability of exomoons using TTV-TDV diagrams with current and near-future technology. In a blind test, two of us (BP, DA) successfully retrieved a large moon from simulated TTV-TDV by co-authors MH and RH, which resembled data from a known Kepler planet candidate. Single exomoons with a 10 percent moon-to-planet mass ratio, like to Pluto-Charon binary, can be detectable in the archival data of the Kepler primary mission. Multi-exomoon systems, however, require either larger telescopes or brighter target stars. Complementary detection methods invoking a moon's own photometric transit or its orbital sampling effect can be used for validation or falsification. A combination of TESS, CHEOPS, and PLATO data would offer a compelling opportunity for an exomoon discovery around a bright star.

QUASI-PERIODIC ACCELERATION OF ELECTRONS IN THE FLARE ON 2012 JULY 19

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

Huang, Jing; Kontar, Eduard P.; Nakariakov, Valery M.

Quasi-periodic pulsations (QPPs) of nonthermal emission in an M7.7 class flare on 2012 July 19 are investigated with spatially resolved observations at microwave and HXR bands and with spectral observations at decimetric, metric waves. Microwave emission at 17 GHz of two footpoints, HXR emission at 20–50 keV of the north footpoint and loop top, and type III bursts at 0.7–3 GHz show prominent in-phase oscillations at 270 s. The microwave emission of the loop leg has less pulsation but stronger emission. Through the estimation of plasma density around the loop top from EUV observations, we find that the local plasmamore » frequency would be 1.5 GHz or even higher. Thus, type III bursts at 700 MHz originate above the loop top. Quasi-periodic acceleration or injection of energetic electrons is proposed to dominate these in-phase QPPs of nonthermal emission from footpoints, loop top, and above. In the overlying region, drifting pulsations (DPS) at 200–600 MHz oscillate at a distinct period (200 s). Its global structure drifts toward lower frequency, which is closely related to upward plasmoids observed simultaneously from EUV emission. Hence, nonthermal emission from overlying plasmoids and underlying flaring loops show different oscillating periods. Two individual systems of quasi-periodic acceleration of electrons are proposed to coincide in the bi-direction outflows from the reconnection region.« less

GLOBAL SAUSAGE OSCILLATION OF SOLAR FLARE LOOPS DETECTED BY THE INTERFACE REGION IMAGING SPECTROGRAPH

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

Tian, Hui; He, Jiansen; Young, Peter R.

An observation from the Interface Region Imaging Spectrograph reveals coherent oscillations in the loops of an M1.6 flare on 2015 March 12. Both the intensity and Doppler shift of Fe xxi 1354.08 Å show clear oscillations with a period of ∼25 s. Remarkably similar oscillations were also detected in the soft X-ray flux recorded by the Geostationary Operational Environmental Satellites ( GOES ). With an estimated phase speed of ∼2420 km s{sup −1} and a derived electron density of at least 5.4 × 10{sup 10} cm{sup −3}, the observed short-period oscillation is most likely the global fast sausage mode ofmore » a hot flare loop. We find a phase shift of ∼ π /2 (1/4 period) between the Doppler shift oscillation and the intensity/ GOES oscillations, which is consistent with a recent forward modeling study of the sausage mode. The observed oscillation requires a density contrast between the flare loop and coronal background of a factor ≥42. The estimated phase speed of the global mode provides a lower limit of the Alfvén speed outside the flare loop. We also find an increase of the oscillation period, which might be caused by the separation of the loop footpoints with time.« less

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

THE CORONAL LOOP INVENTORY PROJECT: EXPANDED ANALYSIS AND RESULTS

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

Schmelz, J. T.; Christian, G. M.; Chastain, R. A., E-mail: jschmelz@usra.edu

We have expanded upon earlier work that investigates the relative importance of coronal loops with isothermal versus multithermal cross-field temperature distributions. These results are important for determining if loops have substructure in the form of unresolved magnetic strands. We have increased the number of loops targeted for temperature analysis from 19 to 207 with the addition of 188 new loops from multiple regions. We selected all loop segments visible in the 171 Å images of the Atmospheric Imaging Assembly (AIA) that had a clean background. Eighty-six of the new loops were rejected because they could not be reliably separated frommore » the background in other AIA filters. Sixty-one loops required multithermal models to reproduce the observations. Twenty-eight loops were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within uncertainties. Ten loops were isothermal. Also, part of our inventory was one small flaring loop, one very cool loop whose temperature distribution could not be constrained by the AIA data, and one loop with inconclusive results. Our survey can confirm an unexpected result from the pilot study: we found no isothermal loop segments where we could properly use the 171-to-193 ratio method, which would be similar to the analysis done for many loops observed with TRACE and EIT. We recommend caution to observers who assume the loop plasma is isothermal, and hope that these results will influence the direction of coronal heating models and the effort modelers spend on various heating scenarios.« less