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At least 325 records · Page 18

Multi-omics Resources for Understanding Gene Regulation in Response to ER Stress in Plants

Proteotoxic stress of the endoplasmic reticulum (ER) is a potentially lethal condition that ensues when the biosynthetic capacity of the ER is overwhelmed. A sophisticated and largely conserved signaling, known as the unfolded protein response (UPR), is designed to monitor and alleviate ER stress. In plants, the emerging picture of gene regulation by the UPR now appears to be more complex than ever before, requiring multi-omics-enabled network-level approaches to be untangled. In the past decade, with an increasing access and decreasing costs of next-generation sequencing (NGS) and high-throughput protein–DNA interaction (PDI) screening technologies, multitudes of global molecular measurements, known as omics, have been generated and analyzed by the research community to investigate the complex gene regulation of plant UPR. In this chapter, we present a comprehensive catalog of omics resources at different molecular levels (transcriptomes, protein–DNA interactomes, and networks) along with the introduction of key concepts in experimental and computational tools in data generation and analyses. Finally, this chapter will serve as a starting point for both experimentalists and bioinformaticians to explore diverse omics datasets for their biological questions in the plant UPR, with likely applications also in other species for conserved mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

The role of orbital dynamics and cloud-cloud collisions in the formation of giant molecular clouds in global spiral structures

The role of orbit crowding and cloud-cloud collisions in the formation of GMCs and their organization in global spiral structure is investigated. Both N-body simulations of the cloud system and a detailed analysis of individual particle orbits are used to develop a conceptual understanding of how individual clouds participate in the collective density response. Detailed comparisons are made between a representative cloud-particle simulation in which the cloud particles collide inelastically with one another and give birth to and subsequently interact with young star associations and stripped down simulations in which the cloud particles are allowed to follow ballistic orbits in the absence of cloud-cloud collisions or any star formation processes. Orbit crowding is then related to the behavior of individual particle trajectories in the galactic potential field. The conceptual picture of how GMCs are formed in the clumpy ISMs of spiral galaxies is formulated, and the results are compared in detail with those published by other authors.

Roberts, William W., Jr.↗

Progress towards understanding and predicting convection heat transfer in the turbine gas path

A new era is drawing in the ability to predict convection heat transfer in the turbine gas path. We feel that the technical community now has the capability to mount a major assault on this problem, which has eluded significant progress for a long time. We hope to make a case for this bold statement by reviewing the state of the art in three major heat transfer, configuration-specific experiments, whose data have provided the big picture and guided both the fundamental modeling research and the code development. Following that, we review progress and directions in the development of computer codes to predict turbine gas path heat transfer. Finally, we cite examples and make observations on the more recent efforts to do all this work in a simultaneous, interactive, and more synergistic manner. We conclude with an assessment of progress, suggestions for how to use the current state of the art, and recommendations for the future.

Simoneau, Robert J.↗

NASA Earth Systems Digital Twins (ESDT)

"Similarly to artificial intelligence, which is now revolutionizing many aspects of our daily lives, Earth system digital twin technologies have the potential to revolutionize the way Earth Science research will be conducted in the future, and how results and knowledge from this research will provide information to support decision making and yield impactful societal benefits. An Earth System Digital Twin or ESDT is a dynamic and interactive information system that first provides a digital replica of the past and current states of the Earth or Earth system as accurately and timely as possible; second, allows for computing forecasts of future states under nominal assumptions and based on the current replica; and third, offers the capability to investigate many hypothetical scenarios under varying impact assumptions. In other words, an ESDT provides the integrated What-Now, What-Next, and What-If pictures of the Earth or Earth system, by continuously ingesting newly observed data and by leveraging multiple interconnected models, machine learning as well advanced computing and visualization capabilities. Digital twins have been developed in engineering since 2002, but the interest in digital twins for the Earth domain is more recent and stems from the convergence of several developments: - The huge amount of diverse data that has now been collected continuously for more than 50 years, and that is becoming more and more difficult to access, understand, and utilize. - At the same time, because of climate change and its impacts the information produced by all of this data is becoming of interest to many new non-traditional users for analyzing and predicting various phenomena. - Because of advances in computational and visualization capabilities and the parallel unprecedented development of machine learning (ML), extracting relevant information from these large amounts of data and running complex models faster has become possible. As a result, it is becoming necessary and possible to build intuitive and interactive frameworks that will enable users with various skill levels and/or organizational hierarchy levels to easily access large amounts of targeted information along with the relevant tools and models (Earth system and human activity models), to support them in analyzing and visualizing this information, to help them understand interactions among models, to visualize the potential outcomes of various impacts, and to support decision or policy making. The full power of digital twins is that, through an integrated representation and standardized tools and software technologies, the same digital replica can address the needs of multiple users at various resolutions (spatial and temporal) and for various applications (science, economic, policy, etc.) – “from farmer to scientist”. With all these interests at stake, the challenges of building optimal digital twins are many and complex. The first challenge is to determine if a Digital Twin should be global or local, and multi-domain or thematic. For example, some domains such as Climate or Weather will require a global Digital Twin or Digital Twin capabilities while science areas such as Biodiversity might be more local. We can also envision that multiple thematic ESDTs, e.g., Air Quality, Wildfires, Hydrology could be federated or provide input to other ESDTs, either on a regional level or to a more global ESDT. Overall, we can imagine a future “web” of Digital Twins co-existing in a hierarchy or in a network, and capable of being connected or federated depending on the needs. This last point brings up the very important challenge of interoperability, including standards and protocols that will need to be built into these systems from the beginning. Each individual digital twin would have full flexibility in internal construction but would need standards-based interfaces (input and output) or hooks to make it compatible with others. Another challenge when building digital twins will be to decide how to organize each digital replica. Based on the applications targeted by the DT under implementation, various amounts and types of raw data, Analysis Ready Data (ARD) and information will need to be incorporated. Depending on the required latencies and needs of the users, various solutions can be considered, including Data Cubes, Data Lakes, pointers, or computing information on demand. We envision that each ESDT will choose a solution adapted to its specific objectives. Another important challenge is the type(s) of visualization that will be used, as well as the level of interactivity and refresh rate that will be required. Again, this will depend on the objectives of the ESDT, but also on the various users’ needs. In most cases, several types of visualizations and human interfaces will need to be offered depending on the projected users of that system. In parallel to the challenges highlighted above, there are also many tools and technologies that will need to be developed or improved for all types of digital twins. Among those are improved machine learning technologies, for example providing explainability, but also ML techniques for causality and providing a better integration of physics models. Additionally, reliable uncertainty quantification methods will be needed for all ESDT components, from validating data fusion and assimilation to assessing the accuracy of ML models and weighing the values of decisions supported by those systems. This presentation introduces the ESDT concept, presents several ESDT use cases, and a proposed ESDT architecture framework, as well as various technologies being developed by the Advanced Information Systems Technology (AIST) Program."

Earth Science Remote Sensing; Information Systems↗

Flutter and Vibration Animation Program

Flutter and Vibration Animation (FLUVIAN) program produces animated picture of structure as it vibrates at constant amplitude. Permits visual observation of fluttering motion of components as they oscillate in combination of modes. Animated display provides insight into local deflection patterns induced in structure, overlooked if modal deflection patterns were separately examined and combined mentally. FLUVIAN program written in FORTRAN 77 for interactive execution.

Tischner, R. L.↗

The dust in the hydrogen-poor ejecta of Abell 30

We present new optical and near-infrared images of the hydrogen-poor planetary nebula Abell 30 and produce detailed models that account for the major observed morphological and IR properties. By imaging the nebula in the K band, we confirm the presence of hot dust in an expanding equatorial ring of H-poor gas. No emission was detected from the H-poor polar knots, suggesting a dust deficiency htere relative to the equatorial ring. The near-IR emission is attributed to small carbonaceous dust grains which are stochastically heated by stellar ultraviolet photons. Using an adaptive version of a matrix method devised by Guhathakurta & Draine (1989) to model stochastic heating, we find that the near-IR spectrum observed by Dinerstein & Lester (1984) requires the presence of dust grains down to approximately 0.0007 microns in radius. This minimum grain radius is in excellent agreement with our calculations of the grain destruction by energetic stellar UV photons: we find that carbon clusters with less than approximately 140 atoms (0.0007 microns in radius) are destroyed by stellar UV photons in approximately 1000 yr, the kinematic age of H-poor ejecta. Modeling of the far-IR dust emission implies that the bulk of the dust mass in A30 must reside at distances several times greater than the distance of the equatorial ring from the central star. This spatial dust distribution is attributed to the interaction of the stellar wind with the inhomogeneous H-poor ejecta. Most of the H-poor gas and dust has been apparently carried outward by the stellar wind, leaving behing dense, H-poor knots with prominent wind-blown tails in the equatorial ring and in the polar knots. This picture is supported by the presence of a stellar wind-blown bubble within the H-rich envelope in our optical images.

Borkowski, Kazimierz J.↗

Theory-guided design of high-entropy alloys with enhanced strength-ductility synergy

Abstract Metallic alloys have played essential roles in human civilization due to their balanced strength and ductility. Metastable phases and twins have been introduced to overcome the strength-ductility tradeoff in face-centered cubic (FCC) high-entropy alloys (HEAs). However, there is still a lack of quantifiable mechanisms to predict good combinations of the two mechanical properties. Here we propose a possible mechanism based on the parameter κ, the ratio of short-ranged interactions between closed-pack planes. It promotes the formation of various nanoscale stacking sequences and enhances the work-hardening ability of the alloys. Guided by the theory, we successfully designed HEAs with enhanced strength and ductility compared with other extensively studied CoCrNi-based systems. Our results not only offer a physical picture of the strengthening effects but can also be used as a practical design principle to enhance the strength-ductility synergy in HEAs.

36 MATERIALS SCIENCE↗

Linearly dispersive bands at the onset of correlations in K 𝑥 ⁢C 60 films

Molecular crystals are a flexible platform to induce novel electronic phases. Due to the weak forces between molecules, intermolecular distances can be varied over larger ranges than interatomic distances in atomic crystals. On the other hand, the hopping terms are generally small, which results in narrow bands, strong correlations, and heavy electrons. Here, by growing K x C 60 fullerides on hexagonal layered Bi 2 Se 3 , we show that upon doping the series undergoes a Mott transition from a molecular insulator to a correlated metal and an in-gap state evolves into highly dispersive Dirac-like fermions at half filling, where superconductivity occurs. This picture challenges the commonly accepted description of the low-energy quasiparticles as appearing from a gradual electron doping of the conduction states and suggests an intriguing parallel with the more famous family of the cuprate superconductors. More in general, it indicates that molecular crystals offer a viable route to engineer electron-electron interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Information-Theoretic Exploration of Multivariate Time-Varying Image Databases

Modern scientific simulations produce very large datasets, making interactive exploration of such data computationally prohibitive. An increasingly common data reduction technique is to store visualizations and other data extracts in a database. The Cinema project is one such approach, storing visualizations in an image database for post hoc exploration and interactive image-based analysis. This work focuses on developing efficient algorithms that can quantify various types of multivariate dependencies existing within multi-variable datasets. It applies specific mutual information measures for the quantification of salient regions from multivariate image data. Here, using such information measures, the opacity of the images is modulated so that the salient regions are automatically highlighted and the domain scientists can interactively explore the most relevant regions for scientific discovery.

97 MATHEMATICS AND COMPUTING↗

Neutrino oscillations

Neutrino oscillation measurements provide an important window on what lies beyond the Standard Model of particle physics. These measurements may unlock the mechanism by which the universe came to become matter-dominated, and may offer hints of another mechanism to generate particles with mass. Measurements of oscillations from muon neutrinos to electron neutrinos (and their antineutrino counterpart) as a function of time provide critical inputs to understanding both mechanisms. These are challenging measurements and a variety of techniques and strategies are required to get the complete picture. This article describes the current status of our understanding of neutrino masses and how neutrinos oscillate between one flavour and another as they propagate through space and time, and what remains to be understood. Taking the next steps in this field requires a variety of approaches and a better understanding of how neutrinos interact with nuclei. This article describes two of those next steps, highlighting where Canadian groups are active, and concludes with a discussion of the broad range of additional physics that becomes accessible by having two very different large sensitive neutrino detectors making these measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The UHECR dipole and quadrupole in the latest data from the original Auger and TA surface detectors

The sources of ultra-high-energy cosmic rays are still unknown, but assuming standard physics, they are expected to lie within a few hundred megaparsecs from us. Indeed, over cosmological distances cosmic rays lose energy to interactions with background photons, at a rate depending on their mass number and energy and properties of photonuclear interactions and photon backgrounds. The universe is not homogeneous at such scales, hence the distribution of the arrival directions of cosmic rays is expected to reflect the inhomogeneities in the distribution of galaxies; the shorter the energy loss lengths, the stronger the expected anisotropies. Galactic and intergalactic magnetic fields can blur and distort the picture, but the magnitudes of the largest-scale anisotropies, namely the dipole and quadrupole moments, are the most robust to their effects. Measuring them with no bias regardless of any higher-order multipoles is not possible except with full-sky coverage. In this work, we achieve this in three energy ranges (approximately $8$--$16~EeV$, $16$--$32~EeV$, and $32$--$\infty~EeV$) by combining surface-detector data collected at the Pierre Auger Observatory until 2020 and at the Telescope Array (TA) until 2019, before the completion of the upgrades of the arrays with new scintillator detectors. We find that the full-sky coverage achieved by combining Auger and TA data reduces the uncertainties on the north-south components of the dipole and quadrupole in half compared to Auger-only results.

79 ASTRONOMY AND ASTROPHYSICS↗

Metal/silicon interface formation - The Ni/Si and Pd/Si systems

The valence level spectra of the Ni/Si and Pd/Si systems have been investigated using high resolution X-ray photoelectron spectroscopy. Temperature dependence studies for Ni deposited on thin thermal SiO2 demonstrate the importance of metal aggregation effects in the interpretation of binding energies as chemical shifts. Temperature studies for the Ni/Si system indicate that substantial chemical interaction occurs at the interface at temperatures as low as 100 K. These studies also show the presence of Ni in interstitial voids in the Si near the interface. A comparative study of the core and valence band features for the Ni and Pd silicides provides many valuable insights and a self-consistent picture of the attendent valence charge redistribution and its influence on the observed chemical shifts.

Grunthaner, P. J.↗

Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state

The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown. Here, we report a 3.1 Å resolution crystal structure of Escherichia coli TPP riboswitch in the apo state, which exhibits an extended, Y-shaped conformation further supported by small-angle X-ray scattering data and driven molecular dynamics simulations. The loss of ligand interactions results in helical uncoiling of P5 and disruption of the key tertiary interaction between the sensory domains. Opening of the aptamer propagates to the gene-regulatory P1 helix and generates the key conformational flexibility needed for the switching behavior. Much of the ligand-binding site at the three-way junction is unaltered, thereby maintaining a partially preformed pocket. Together, these results paint a dynamic picture of the ligand-induced conformational changes in TPP riboswitches that confer conditional gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗

Spin-valley locking and bulk quantum Hall effect in a noncentrosymmetric Dirac semimetal BaMnSb 2

Spin-valley locking in monolayer transition metal dichalcogenides has attracted enormous interest, since it offers potential for valleytronic and optoelectronic applications. Such an exotic electronic state has sparsely been seen in bulk materials. Here, we report spin-valley locking in a Dirac semimetal BaMnSb 2 . This is revealed by comprehensive studies using first principles calculations, tight-binding and effective model analyses, angle-resolved photoemission spectroscopy measurements. Moreover, this material also exhibits a stacked quantum Hall effect (QHE). The spin-valley degeneracy extracted from the QHE is close to 2. This result, together with the Landau level spin splitting, further confirms the spin-valley locking picture. In the extreme quantum limit, we also observed a plateau in the z-axis resistance, suggestive of a two-dimensional chiral surface state present in the quantum Hall state. These findings establish BaMnSb 2 as a rare platform for exploring coupled spin and valley physics in bulk single crystals and accessing 3D interacting topological states.

36 MATERIALS SCIENCE↗

RCSB Protein Data Bank 1D tools and services

Abstract Motivation Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Results Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. Availabilityand implementation https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of plasma contactors for use with orbiting wires

The proposed Shuttle-based short tether experiments with hollow cathodes have the potential for providing important data that will not be obtained in long tether experiments. A critical property for hollow cathode effectiveness as a plasma contactor is the cross magnetic field conductivity of the emitted plasma. The different effects of hollow cathode cloud overlap in the cases of motion-driven and battery-driven operation are emphasized. The calculations presented on the size and shape of the hollow cathode cloud improve the qualitative picture of hollow cathodes in low Earth orbit and provide estimates of time constants for establishing the fully-expanded cloud. The magnetic boundary value problem calculations indicate the way in which the magnetic field will effect the shape of the cloud by resisting expansion in the direction perpendicular to the field. The large-scale interactions of the system were also considered. It was concluded that recent plasma chamber experiments by Stenzel and Urrutia do not model an electrodynamic tether well enough to apply the results to tethered system behavior. Orbiting short tether experiments on hollow cathodes will provide critical information on hollow cathode performance and the underlying physics that cannot be obtained any other way. Experiments should be conducted as soon as funding and a suitable space vehicle are available.

Estes, Robert D.↗

Tomographic optical emission spectroscopy of atmospheric pressure plasma interacting with complex surfaces

Plasma distribution in 3D space is heavily influenced by complex surfaces and the coupling interactions between plasma properties and interfacing material properties. For example, guided streamers that transition to surface ionization waves (SIWs) and propagate over structured dielectrics experience field enhancements that can lead to localized increases in ionization rates and complex 3D configurations that are difficult to analyze. Investigating these configurations requires techniques than can provide a more complete 3D picture. To help address this capability gap, a tomographic optical emission spectroscopy (tomo-OES) diagnostic system has been developed at Sandia National Laboratories that can resolve SIWs. The system includes four intensified cameras that measure the angular projections of the plasma light emission through bandpass filters. A dot calibration target co-registers each angular projection to the same voxel grid and an algebraic reconstruction technique (ART) recovers the light intensity at each voxel. An atmospheric pressure plasma jet (APPJ), provided by Peter Bruggeman, has been investigated and representative results are shown in Figure 1. Here, a bandpass filter was used to isolate emission from the N 2 second positive system (SPS) at 337.1 nm to capture the transition of the streamer to SIW on a planar dielectric surface (relative permittivity 3.3) located 3 mm below the APPJ [3]. The surface wave velocity was 3.5x10 4 (m/s), consistent with measurements made by Steven Shannon. Characterization of this APPJ will support the group effort of standing up a reproducible APPJ across institutions for applications such as liquid treatment, catalysis, and plasma aided combustion. Future work will investigate non-planar surfaces and eventually develop tomographic laser-induced fluorescence (tomo-LIF) approaches.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The electron temperature and optical emission structure of the central component of CTB 80

Optical spectra on the central component of the galactic supernova remnant CTB 80 are presented. Long slit CCD spectra reveal relative line-intensity variations among individual filaments, the presence of Balmer-dominated emission in the core's east and west optical lobes, and no radial velocities in excess of 300 km/s. Aperture spectrophotometry of the temperature-sensitive forbiddden O III lines suggests Te = 25,000 K, thus favoring a shock-heated interpretation for the remnant's optical core emission. These results indicate that fundamental differences exist betweem the optical emission of CTB 80's central core component and the Crab Nebula, despite similarities in these remnants' radio and X-ray properties. The optical emission from CTB 80's core is likely to be a direct result of the interaction of an active pulsar with its adjacent partially neutral interstellar medium. The size of CTB 80's outer structure and the absence of either high velocity or enhanced abundances in the region local to CTB 80's pulsar argue for a considerably larger age for CTB 80 than the Crab Nebula's 1000 yr. A qualitative picture for CTB 80 that can plausibly explain many of the core's properties is proposed.

Blair, William P.↗