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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Filaments of the Slime Mold Cosmic Web and How They Affect Galaxy Evolution

Abstract We present a novel approach for identifying cosmic web filaments within theDisPerSEstructure identification framework, using cosmic density field estimates from the Monte Carlo Physarum Machine (MCPM), inspired by the slime mold organism. We apply our method to the IllustrisTNG (TNG100) cosmological simulations and investigate the impact of filaments on galaxies. The MCPM density field is superior to the Delaunay tessellation field estimator in tracing the true underlying matter distribution and allows filaments to be identified with higher fidelity, finding more low-prominence/diffuse filaments. Using our new filament catalogs, we find that ≳90% of galaxies are located within ∼1.5 Mpc of a filamentary spine, with little change in the median star formation activity with distance to the nearest filament. Instead, we uncover a differential effect of the local filament line density, Σ fil (MCPM)—the total MCPM overdensity per unit length along a filament segment—on galaxy formation: most galaxies are quenched and gas-poor near high-line density filaments atz≤ 1. At earlier times, the filamentary environment appears to have no effect on galactic gas supply and quenching. Atz= 0, quenching in log ( M * / M ⊙ ) ≳ 10.5 galaxies is mainly driven by mass, while lower-mass galaxies are significantly affected by the filament line density. Satellites are far more susceptible to filaments than centrals. The local environments of massive halos are not sufficient to account for the effect of filament line density on gas removal and quenching. Our new approach holds great promise for observationally identifying filaments from galaxy surveys such as SDSS and DESI.

Astronomy & Astrophysics↗
DOE OSTI2021

Interaction of radio frequency waves with cylindrical density filaments: scattering and radiation pressure

The propagation of radio-frequency (RF) waves in tokamaks can be affected by filamentary structures, or blobs, that are present in the edge plasma and the scrape-off layer. The difference in the permittivity between the surrounding plasma and interior of a filament leads to reflection, refraction and diffraction of the waves. This, in turn, can affect the power flow into the core of the plasma and reduce the efficiency of heating and/or current generation. The scattering of RF waves, lower hybrid, helicon and ion cyclotron waves, by a single cylindrical filament, embedded in a background plasma, is studied using a full-wave analytical theory developed previously (Ram & Hizanidis, Phys. Plasmas , vol. 23, 2016, 022504). The theory assumes that the plasma in and around a filament is homogeneous and cold. A detailed scattering analysis reveals a variety of common features that exist among the three distinctly different RF waves. These common attributes can be inferred intuitively based on an examination of the cold plasma dispersion relation. The physical intuition is a useful step to understanding experimental observations on scattering, as well as results from simulations that include general forms of edge plasma turbulence. While a filament can affect the propagation of RF waves, the radiation force exerted by the waves can influence the filament. The force on a filament is determined using the Maxwell stress tensor. In 1905, Poynting was the first to evaluate and measure the radiation force on an interface separating two different dielectric media (Poynting, London Edinburgh Dublin Philos. Mag. J. Sci. , vol. 9, 1905, pp. 393–406). For ordinary light propagating in vacuum and incident on a glass surface, Poynting noted that the surface is ‘pulled’ towards the vacuum. In a magnetized cold plasma, there are two independent wave modes. Even if only one of these modes is excited by an RF antenna, a filament will couple power to the other mode: a consequence of electromagnetic boundary conditions. This facet of scattering has consequences on the radiation force that go beyond Poynting's seminal contribution. The direction of the force depends on the polarization of the incident wave and on the mode structure of the waves inside and in the vicinity of a filament. It can either pull the filament toward the RF source or push it away. For slow lower hybrid waves, filaments with densities greater than the ambient density are pulled in, while filaments with lower densities are pushed out, thereby enhancing the density in front of the antenna. In the case of fast helicon and ion cyclotron waves, the direction of the force depends on the plasma and wave parameters; in particular, on the ambient density. The radiation force, in all three frequency ranges, is large enough to affect the motion of a filament and could be measured experimentally. This also suggests the possibility of modifying the edge turbulence using RF waves.

Physics↗
DOE OSTI2016

Scattering of radio frequency waves by cylindrical density filaments in tokamak plasmas

In tokamak fusion plasmas, coherent fluctuations in the form of blobs or filaments are routinely observed in the scrape-off layer. Radio frequency (RF) electromagnetic waves, excited by antenna structures placed near the wall of a tokamak, have to propagate through the scrape-off layer before reaching the core of the plasma. While the effect of fluctuations on the properties of RF waves has not been quantified experimentally, it is of interest to carry out a theoretical study to determine if fluctuations can affect the propagation characteristics of RF waves. Usually, the difference between the plasma density inside the filament and the background plasma density is sizable, the ratio of the density difference to the background density being of order one. Generally, this precludes the use of geometrical optics in determining the effect of fluctuations, since the relevant ratio has to be much less than one, typically, of the order of 10% or less. In this study, a full-wave, analytical model is developed for the scattering of a RF plane wave by a cylindrical plasma filament. It is assumed that the plasma inside and outside the filament is cold and uniform and that the major axis of the filament is aligned along the toroidal magnetic field. The ratio of the density inside the filament to the density of the background plasma is not restricted. The theoretical framework applies to the scattering of any cold plasma wave. In order to satisfy the boundary conditions at the interface between the filament and the background plasma, the electromagnetic fields inside and outside the filament need to have the same k ∥ , the wave vector parallel to the ambient magnetic field, as the incident plane wave. Consequently, in contrast to the scattering of a RF wave by a spherical blob [Ram et al., Phys. Plasmas 20, 056110-1–056110-10 (2013)], the scattering by a field-aligned filament does not broaden the k ∥ spectrum. However, the filament induces side-scattering leading to surface waves and can also couple some power to the cold plasma wave different from the incident wave. The changes induced by a filament in the propagation of electron cyclotron waves and lower hybrid waves are illustrated by numerical results displaying the properties of the Poynting vector. The Poynting flux in the wake of the filament, and directed towards the core of the plasma, develops a spatial structure due to diffraction and shadowing. Finally and thus, the fluctuations affect the uniformity of power flow into the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

OBSERVATIONS OF THE GROWTH OF AN ACTIVE REGION FILAMENT

We present observations of the growth of an active region filament caused by magnetic interactions among the filament and its adjacent superpenumbral filament (SF) and dark thread-like structures (T). Multistep reconnections are identified during the whole growing process. Magnetic flux convergence and cancellation occurring at the positive footpoint region of the filament is the first step reconnection, which resulted in the filament bifurcating into two sets of intertwined threads. One set anchored in situ, while the other set moved toward and interacted with the SF and part of T. This indicates the second step reconnection, which gave rise to the disappearance of the SF and the formation of a long thread-like structure that connects the far ends of the filament and T. The long thread-like structure further interacted with the T and then separated into two parts, representing the third step reconnection. Finally, another similar long thread-like structure, which intertwined with the fixed filament threads, appeared. H {sub α} observations show that this twisted structure is a longer sinistral filament. Based on the observed photospheric vector magnetograms, we performed a non-linear force-free field extrapolation to reconstruct the magnetic fields above the photosphere and found that the coronal magnetic field lines associated with the filament consists of two twisted flux ropes winding around each other. These results suggest that magnetic interactions among filaments and their adjacent SFs and T could lead to the growth of the filaments, and the filament is probably supported in a flux rope.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Interaction of radio frequency waves with cylindrical density filaments -- scattering and radiation pressure

The propagation of radio-frequency (RF) waves in tokamaks can be affected by filamentary structures, or blobs, that are present in the edge plasma and the scrape-off layer. The difference in the permittivity between the surrounding plasma and interior of a filament leads to reflection, refraction and diffraction of the waves. This, in turn, can affect the power flow into the core of the plasma and reduce the efficiency of heating and/or current generation. The scattering of RF waves, lower hybrid, helicon and ion cyclotron waves, by a single cylindrical filament, embedded in a background plasma, is studied using a full-wave analytical theory developed previously (Ram & Hizanidis, Phys. Plasmas, vol. 23, 2016, 022504). The theory assumes that the plasma in and around a filament is homogeneous and cold. A detailed scattering analysis reveals a variety of common features that exist among the three distinctly different RF waves. These common attributes can be inferred intuitively based on an examination of the cold plasma dispersion relation. The physical intuition is a useful step to understanding experimental observations on scattering, as well as results from simulations that include general forms of edge plasma turbulence. While a filament can affect the propagation of RF waves, the radiation force exerted by the waves can influence the filament. The force on a filament is determined using the Maxwell stress tensor. In 1905, Poynting was the first to evaluate and measure the radiation force on an interface separating two different dielectric media (Poynting, London Edinburgh Dublin Philos. Mag. J. Sci., vol. 9, 1905, pp. 393–406). For ordinary light propagating in vacuum and incident on a glass surface, Poynting noted that the surface is ‘pulled’ towards the vacuum. In a magnetized cold plasma, there are two independent wave modes. Even if only one of these modes is excited by an RF antenna, a filament will couple power to the other mode: a consequence of electromagnetic boundary conditions. This facet of scattering has consequences on the radiation force that go beyond Poynting's seminal contribution. The direction of the force depends on the polarization of the incident wave and on the mode structure of the waves inside and in the vicinity of a filament. It can either pull the filament toward the RF source or push it away. For slow lower hybrid waves, filaments with densities greater than the ambient density are pulled in, while filaments with lower densities are pushed out, thereby enhancing the density in front of the antenna. In the case of fast helicon and ion cyclotron waves, the direction of the force depends on the plasma and wave parameters; in particular, on the ambient density. The radiation force, in all three frequency ranges, is large enough to affect the motion of a filament and could be measured experimentally. This also suggests the possibility of modifying the edge turbulence using RF waves.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI

Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein–DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.

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

X-point and divertor filament dynamics from gas puff imaging on TCV

Abstract A new gas puff imaging diagnostic has been installed on the TCV tokamak, providing two-dimensional insights into scrape-off-layer (SOL) turbulence dynamics above, at and below the magnetic X-point. A detailed study in L-mode, attached, lower single-null discharges shows that statistical properties have little poloidal variations, while vast differences are present in the 2D behaviour of intermittent filaments. Strongly elongated filaments, just above the X-point and in the divertor far-SOL, show a good consistency in shape and dynamics with field-line tracing from filaments at the outboard midplane, highlighting their connection. In the near-SOL of the outer divertor leg, short-lived, high frequency and more circular (diameter ∼15 sound Larmor radii) filaments are observed. These divertor-localised filaments appear born radially at the position of maximum density and display a radially outward motion with velocity ≈400 m s −1 that is comparable to radial velocities of upstream-connected filaments. Conversely, in these discharges ( B → × ∇ B pointing away from the divertor), these divertor filaments’ poloidal velocities differ strongly from those of upstream-connected filaments. The importance of divertor-localised filaments upon radial transport and profile broadening is explored using filament statistics and in situ kinetic profile measurements along the divertor leg. This suggests that these filaments contribute significantly to electron density profile broadening in the divertor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Frontogenesis and frontal arrest of a dense filament in the oceanic surface boundary layer

The evolution of upper ocean currents involves a set of complex, poorly understood interactions between submesoscale turbulence (e.g. density fronts and filaments and coherent vortices) and smaller-scale boundary-layer turbulence. Here we simulate the lifecycle of a cold (dense) filament undergoing frontogenesis in the presence of turbulence generated by surface stress and/or buoyancy loss. This phenomenon is examined in large-eddy simulations with resolved turbulent motions in large horizontal domains using ${\sim}10^{10}$ grid points. Steady winds are oriented in directions perpendicular or parallel to the filament axis. Due to turbulent vertical momentum mixing, cold filaments generate a potent two-celled secondary circulation in the cross-filament plane that is frontogenetic, sharpens the cross-filament buoyancy and horizontal velocity gradients and blocks Ekman buoyancy flux across the cold filament core towards the warm filament edge. Within less than a day, the frontogenesis is arrested at a small width, ${\approx}100~\text{m}$ , primarily by an enhancement of the turbulence through a small submesoscale, horizontal shear instability of the sharpened filament, followed by a subsequent slow decay of the filament by further turbulent mixing. The boundary-layer turbulence is inhomogeneous and non-stationary in relation to the evolving submesoscale currents and density stratification. The occurrence of frontogenesis and arrest are qualitatively similar with varying stress direction or with convective cooling, but the detailed evolution and flow structure differ among the cases. Thus submesoscale filament frontogenesis caused by boundary-layer turbulence, frontal arrest by frontal instability and frontal decay by forward energy cascade, and turbulent mixing are generic processes in the upper ocean.

Mechanics↗
DOE OSTI2017

Computational studies on scattering of radio frequency waves by density filaments in fusion plasmas

In modern magnetic fusion devices, such as tokamaks and stellarators, radio frequency (RF) waves are commonly used for plasma heating and current profile control, as well as for certain diagnostics. The frequencies of the RF waves range from ion cyclotron frequency to the electron cyclotron frequency. The RF waves are launched from structures, like waveguides and current straps, placed near the wall in a very low density, tenuous plasma region of a fusion device. The RF electromagnetic fields have to propagate through this scrape-off layer before coupling power to the core of the plasma. The scrape-off layer is characterized by turbulent plasmas fluctuations and by blobs and filaments. The variations in the edge density due to these fluctuations and filaments can affect the propagation characteristics of the RF waves—changes in density leading to regions with differing plasma permittivity. Analytical full-wave theories have shown that scattering by blobs and filaments can alter the RF power flow into the core of the plasma in a variety of ways, such as through reflection, refraction, diffraction, and shadowing [see, for example, Ram and Hizanidis, Phys. Plasmas 23, 022504 (2016), and references therein]. There are changes in the wave vectors and the distribution of power–scattering leading to coupling of the incident RF wave to other plasma waves, side-scattering, surface waves, and fragmentation of the Poynting flux in the direction towards the core. However, these theoretical models are somewhat idealized. In particular, it is assumed that there is step-function discontinuity in the density between the plasma inside the filament and the background plasma. In this paper, results from numerical simulations of RF scattering by filaments using a commercial full-wave code are described. The filaments are taken to be cylindrical with the axis of the cylinder aligned along the direction of the ambient magnetic field. The plasma inside and outside the filament is assumed to be cold. There are three primary objectives of these studies. The first objective is to validate the numerical simulations by comparing with the analytical results for the same plasma description—a step-function discontinuity in density. A detailed comparison of the Poynting flux shows that numerical simulations lead to the same results as those from the theoretical model. The second objective is to extend the simulations to take into account a smooth transition in density from the background plasma to the interior of the filament. The ensuing comparison shows that the deviations from the results of the theoretical model are quite small. The third objective is to consider the scattering process for situations well beyond a reasonable theoretical analysis. This includes scattering off multiple filaments with different densities and sizes. In conclusion, simulations for these complex arrangements of filaments show that, in spite of the obvious limitations, the essential physics of RF scattering is captured by the analytical theory for a single filament

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Nearby galaxy filaments and the Lyα forest: Confronting simulations and the UV background with observations

Simulations of the formation of large-scale structures predict that dark matter, low density highly ionized gas, and galaxies form 10 to 40 Mpc scale filaments. These structures are easily recognized in the distribution of galaxies. Here we use Lyα absorption lines to study the gas in 30 × 6 Mpc filament at cz ∼ 3500 km s{sup −1}, defined using a new catalog of nearby (cz < 10,000 km s{sup −1}) galaxies, which is complete down to a luminosity of about 0.05 L{sub *} for the region of space analyzed here. Using Hubble Space Telescope spectra of 24 active galactic nuclei, we sample the gas in this filament. All of our sightlines pass outside the virial radius of any known filament galaxy. Within 500 kpc of the filament axis the detection rate is ∼80%, but no detections are seen more than 2.1 Mpc from the filament axis. The width of the Lyα lines correlates with filament impact parameter and the four BLAs in our sample occur within 400 kpc of the filament axis, indicating increased temperature and/or turbulence. Comparing to simulations, we find that the recent Haardt and Madau extragalactic ionizing background predicts a factor of 3–5 too few ionizing photons. Using a more intense radiation field matches the hydrogen density profile within 2.1 Mpc of the filament axis, but the simulations still overpredict the detection rate between 2.1 and 5 Mpc from the axis. The baryonic mass inside filament galaxies is 1.4 × 10{sup 13} M{sub ⊙}, while the mass of filament gas outside galaxy halos is found to be 5.2 × 10{sup 13} M{sub ⊙}.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2000

Freely Suspended Smectic Filaments and the Structure of the B7 Phase of MHOBOW

Our recent discovery of the spontaneous formation of chiral domains in fluid smectic phases of achiral bow-shaped molecules opens up a wide variety of possibilities for new liquid crystal phases and phenomena. The basic, spontaneously chiral layer structure of the highest temperature fluid smectic phases, the B2 and B7, are shown. One of the most intriguing aspects of this structure is the plethora of possible phases coming from different stacking sequences of the polar ordering and tilt directions. The four possibilities of next-nearest neighbor alternation are shown. In the original material studied, NOBOW, the ground states found are antiferroelectric, either the racemic SmC(sub S)P(sub A) or the chiral SmC(sub A)P(sub A). We are currently studying MHOBOW, synthesized by D. Walba which, by virtue of its methyl hexyloxy tail has a tendency to form anticlinic layer interfaces, in the hope of finding a phase with a ferroelectric ground state, either SmC(sub A)P(sub S) or SmC(sub S)P(sub A), which can be obtained in NOBOW only by applying a field. Preliminary observations of MHO-BOW have made its study, from the point of view of understanding novel LC structures, extremely high priority. The following truly remarkable characteristics have been revealed: (i) The smectic phase grows out of the isotropic in the form of helical ribbons. The resulting planar aligned textures of focal conics with layers normal to glass plates exhibit bizarre modulations, including stripes and checker-boards. These have also been seen in other materials suggesting that this is a new phase (tentatively called B7), which is a fluid smectic with some kind of in-layer structure. (ii) It is virtually impossible to make freely suspended films of MHOBOW. Rather it makes the freely suspended filaments which preliminary x-ray scattering experiments reveal to have the nested cylinder layer structure indicated; (iii) The powder x-ray diffraction exhibits four resolution-limited smectic layering peaks, very close in layer spacing, which vary continuously with T. This is further evidence for a more complex three dimensional structure than NOBOW, which has a typical single layering reflection. (iv) The x-ray structure factor of the layering peak of the filaments is extraordinarily complex and rich. Varying in qL (the scattering vector component along the filament axis) from a double slit-like pattern to modulated layer-like patterns, as qH (the scattering vector component normal to the filament axis) is varied over the range where the four powder peaks are located. These results suggest some kind of mosaic structure, perhaps with different layer spacings corresponding to the different stacking sequences. Recent x-ray diffraction experiments show that the peaks are modulated in intensity upon translation along a filament, in domains of several hundred microns dimension. These preliminary experiments suggest that the B7 is a fluid smectic with extremely unusual and fascinating structures. Of all of the many hundreds of fluid smectic materials we have attempted to study in the freely suspended film geometry over the years, only a few have failed to form films, and none showed any great tendency to form filaments, although this clearly should be a possible freely suspended smectic LC morphology. On several occasions in the past we have intentionally tried to make filaments from a variety of smectics without success. Thus the smectic filament formation property makes the B7 phase unique. It seems quite likely that the stability of filaments is related to the in-plane structure. The filaments exhibit other interesting structural and optical features. They are birefringent with a local optic axis which is oblique and which can vary continuously along filament and which can be manipulated with an electric field applied normal to the fiber, as if the field were causing a rotation of the optic axis about the fiber axis. Rapid displacement of the ends of the fiber toward one another causes a macroscopic helixing at low T and causes thick regions to transiently appear at high T, a 1D analog of island formation on a rapidly compressed film.

Clark, N.↗
DOE OSTI2017

Plasma Brightenings in a Failed Solar Filament Eruption

Failed filament eruptions are solar eruptions that are not associated with coronal mass ejections. In a failed filament eruption, the filament materials usually show some ascending and falling motions as well as generating bright EUV emissions. Here we report a failed filament eruption (SOL2016-07-22) that occurred in a quiet-Sun region observed by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory . In this event, the filament spreads out but gets confined by the surrounding magnetic field. When interacting with the ambient magnetic field, the filament material brightens up and flows along the magnetic field lines through the corona to the chromosphere. We find that some materials slide down along the lifting magnetic structure containing the filament and impact the chromosphere, and through kinetic energy dissipation, cause two ribbon-like brightenings in a wide temperature range. There is evidence suggesting that magnetic reconnection occurs between the filament magnetic structure and the surrounding magnetic fields where filament plasma is heated to coronal temperatures. In addition, thread-like brightenings show up on top of the erupting magnetic fields at low temperatures, which might be produced by an energy imbalance from a fast drop of radiative cooling due to plasma rarefaction. Thus, this single event of a failed filament eruption shows the existence of a variety of plasma brightenings that may be caused by completely different heating mechanisms.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

CHIRALITY AND MAGNETIC CONFIGURATIONS OF SOLAR FILAMENTS

It has been revealed that the magnetic topology in the solar atmosphere displays hemispheric preference, i.e., helicity is mainly negative/positive in the northern/southern hemispheres, respectively. However, the strength of the hemispheric rule and its cyclic variation are controversial. In this paper, we apply a new method based on the filament drainage to 571 erupting filaments from 2010 May to 2015 December in order to determine the filament chirality and its hemispheric preference. It is found that 91.6% of our sample of erupting filaments follows the hemispheric rule of helicity sign. It is also found that the strength of the hemispheric preference of the quiescent filaments decreases slightly from ∼97% in the rising phase to ∼85% in the declining phase of solar cycle 24, whereas the strength of the intermediate filaments keeps a high value around 96 ± 4% at all times. Only the active-region filaments show significant variations. Their strength of the hemispheric rule rises from ∼63% to ∼95% in the rising phase, and keeps a high value of 82% ± 5% during the declining phase. Furthermore, during a half-year period around the solar maximum, their hemispheric preference totally vanishes. Additionally, we also diagnose the magnetic configurations of the filaments based on our indirect method and find that in our sample of erupting events, 89% are inverse-polarity filaments with a flux rope magnetic configuration, whereas 11% are normal-polarity filaments with a sheared arcade configuration.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Measuring Filament Orientation: A New Quantitative, Local Approach

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitatively on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Ambient aging of rhenium filaments used in thermal ionization mass spectrometry: Growth of oxo-rhenium crystallites and anti-aging strategies

Degassing is a common preparation technique for rhenium filaments used for thermal ionization mass spectrometric analysis of actinides, including plutonium. Although optimization studies regarding degassing conditions have been reported, little work has been done to characterize filament aging after degassing. In this study, the effects of filament aging after degassing were explored to determine a “shelf-life” for degassed rhenium filaments, and methods to limit filament aging were investigated. Zone-refined rhenium filaments were degassed by resistance heating under high vacuum before exposure to ambient atmosphere for up to 2 months. After degassing the nucleation and preferential growth of oxo-rhenium crystallites on the surface of polycrystalline rhenium filaments was observed by atomic force microscopy and scanning electron microscopy (SEM). Compositional analysis of the crystallites was conducted using SEM-Raman spectroscopy and SEM energy dispersive X-ray spectroscopy, and grain orientation at the metal surface was investigated by electron back-scatter diffraction mapping. Spectra collected by SEM-Raman suggest crystallites are composed primarily of perrhenic acid. The relative extent of growth and crystallite morphology were found to be grain dependent and affected by the dissolution of carbon into filaments during annealing (often referred to as carbonization or carburization). Crystallites were observed to nucleate in region specific modes and grow over time through transfer of material from the surface. Factors most likely to affect the rates of crystallite growth include rhenium substrate properties such as grain size, orientation, levels of dissolved carbon, and relative abundance of defect sites; as well as environmental factors such as length of exposure to oxygen and relative humidity. Thin (~180 nm) hydrophobic films of poly(vinylbenzyl chloride) were found to slow the growth of oxo-rhenium crystallites on the filament surfaces and may serve as an alternative carbon source for filament carburization.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Experiments and gyrokinetic simulations of the nonlinear interaction between spinning magnetized plasma pressure filaments

A set of experiments using controlled, skin depth-sized plasma pressure filaments in close proximity have been carried out in a large linear magnetized plasma device. Two- and three-filament configurations have been used to determine the scale of cross field nonlinear interaction. When the filaments are separated by a distance of approximately five times the size of a single filament or less, a significant transfer of charge and energy occurs, leading to the generation of inter-filament electric fields. This has the effect of rotating the filaments and influencing the merging dynamics. Nonlinear gyrokinetic simulations using seeded filaments confirm the presence of unstable drift-Alfvén modes driven by the steep electron temperature gradient. When the filaments are within a few collisionless electron skin depths (separations twice the size of a single filament), the unstable perturbations drive the convective mixing of the density and temperature and rearrange the gradients such that they maximize in the region surrounding the filament bundle.

Sydora, R. D. (ORCID:0000000192543149)↗
DOE OSTI2018

Nebulin stiffens the thin filament and augments cross-bridge interaction in skeletal muscle

Nebulin is a giant sarcomeric protein that spans along the actin filament in skeletal muscle, from the Z-disk to near the thin filament pointed end. Mutations in nebulin cause muscle weakness in nemaline myopathy patients, suggesting that nebulin plays important roles in force generation, yet little is known about nebulin’s influence on thin filament structure and function. Here, we used small-angle X-ray diffraction and compared intact muscle deficient in nebulin (using a conditional nebulin-knockout, Neb cKO) with control (Ctrl) muscle. When muscles were activated, the spacing of the actin subunit repeat (27 Å) increased in both genotypes; when converted to thin filament stiffness, the obtained value was 30 pN/nm in Ctrl muscle and 10 pN/nm in Neb cKO muscle; that is, the thin filament was approximately threefold stiffer when nebulin was present. In contrast, the thick filament stiffness was not different between the genotypes. A significantly shorter left-handed (59 Å) thin filament helical pitch was found in passive and contracting Neb cKO muscles, as well as impaired tropomyosin and troponin movement. Additionally, a reduced myosin mass transfer toward the thin filament in contracting Neb cKO muscle was found, suggesting reduced cross-bridge interaction. Here, we conclude that nebulin is critically important for physiological force levels, as it greatly stiffens the skeletal muscle thin filament and contributes to thin filament activation and cross-bridge recruitment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Calcium has a direct effect on thick filament activation in porcine myocardium

Sarcomere activation in striated muscle requires both thin filament–based and thick filament–based activation mechanisms. Recent studies have shown that myosin heads on the thick filaments undergo OFF to ON structural transitions in response to calcium (Ca2+) in permeabilized porcine myocardium in the presence of a small molecule inhibitor that eliminated active force. The changes in X-ray diffraction signatures of OFF to ON transitions were interpreted as Ca2+ acting to activate the thick filaments. Alternatively, Ca2+ binding to troponin could initiate a Ca2+-dependent crosstalk from the thin filament to the thick filament via interfilament connections such as the myosin binding protein-C. Here, we exchanged native troponin in permeabilized porcine myocardium for troponin containing the cTnC D65A mutation, which disallows the activation of troponin through Ca2+ binding to determine if Ca2+-dependent thick filament activation persists in the absence of thin filament activation. After the exchange protocol, over 95% of the Ca2+-activated force was eliminated. Equatorial intensity ratio increased significantly in both WT and D65A exchanged myocardium with increasing Ca2+ concentration. The degree of helical ordering of the myosin heads decreased by the same amount in WT and D65A myocardium when Ca2+ concentration increased. These results are consistent with a direct effect of Ca2+ in activating the thick filament rather than an indirect effect due to Ca2+-mediated crosstalk between the thick and thin filaments.

Physiology↗