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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 145 records · Page 8

Structural basis for SHOC2 modulation of RAS signalling

The RAS–RAF pathway is one of the most commonly dysregulated in human cancers. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation of the kinase RAF remains limited. Recent structures of inactive RAF monomer and active RAF dimer bound to 14-3-3 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS, but the structure of SHOC2 and the architecture of the presumptive SHOC2–PP1C–RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2–PP1C–MRAS complex to an overall resolution of 3Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.

59 BASIC BIOLOGICAL SCIENCES↗

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system—MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. The template-based modeling uses sequence alignment tools with deep multiple sequence alignments to search for structural templates, which are much faster and more accurate than MULTICOM1. The template-free (ab initio or de novo) modeling uses the inter-residue distances predicted by DeepDist to reconstruct tertiary structure models without using any known structure as template. In the blind CASP14 experiment, the average TM-score of the models predicted by our server predictor based on the MULTICOM2 system is 0.720 for 58 TBM (regular) domains and 0.514 for 38 FM and FM/TBM (hard) domains, indicating that MULTICOM2 is capable of predicting good tertiary structures across the board. It can predict the correct fold for 76 CASP14 domains (95% regular domains and 55% hard domains) if only one prediction is made for a domain. The success rate is increased to 3% for both regular and hard domains if five predictions are made per domain. Moreover, the prediction accuracy of the pure template-free structure modeling method on both TBM and FM targets is very close to the combination of template-based and template-free modeling methods. This demonstrates that the distance-based template-free modeling method powered by deep learning can largely replace the traditional template-based modeling method even on TBM targets that TBM methods used to dominate and therefore provides a uniform structure modeling approach to any protein. Finally, on the 38 CASP14 FM and FM/TBM hard domains, MULTICOM2 server predictors (MULTICOM-HYBRID, MULTICOM-DEEP, MULTICOM-DIST) were ranked among the top 20 automated server predictors in the CASP14 experiment. After combining multiple predictors from the same research group as one entry, MULTICOM-HYBRID was ranked no. 5. The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

97 MATHEMATICS AND COMPUTING↗

J-PLUS: Uncovering a large population of extreme [OIII] emitters in the local Universe

Over the past decades, several studies have discovered a population of galaxies that undergo very strong star formation events. They are called extreme emission line galaxies (EELGs). We exploit the capabilities of the Javalambre Photometric Local Universe Survey (J-PLUS), a wide-field multifilter survey, with which 2000 square degrees of the northern sky are already observed. We use it to identify EELGs at low redshift by their [OIII]5007 emission line. We intend to provide a more complete, deep, and less biased sample of local EELGs. We selected objects with an excess of flux in the J-PLUS medium-band J0515 filter, which covers the [OIII] line at z < 0.06. We removed contaminants (stars and higher-redshift systems) using J-PLUS and WISE infrared photometry, with SDSS spectra as a benchmark. We performed spectral energy distribution fitting to estimate the physical properties of the galaxies: line fluxes, equivalent widths (EWs), masses, stellar population ages, and so on. We identify 466 EELGs at z < 0.06 with [OIII] EW over 300 Å and an r-band magnitude below 20, of which 411 were previously unknown. Most show compact morphologies, low stellar masses (log(M • /M ⊙ ) ~ 8.13 –0.58 +0.61 ), low dust extinction (E( B–V ) ~ 0.1 –0.1 +0.2 ), and very young bursts of star formation (3.0 –2.0 +2.7 Myr). Our method is up to ~20 times more efficient in detecting EELGs per Mpc 3 than broadband surveys, and it is as complete as magnitude-limited spectroscopic surveys (but reaches fainter objects). The sample is not directly biased against strong Hα emitters, in contrast with works using broadband surveys. We demonstrate that J-PLUS can identify a large sample of previously unknown EELGs showing unique properties following a clear selection process. A fraction of the EELGs are probably similar to the first galaxies in the Universe, but they are at a much lower redshift, which makes them ideal targets for follow-up studies.

79 ASTRONOMY AND ASTROPHYSICS↗

Electron generation and multiplication at the initial stage of nanosecond breakdown in water

Electrical breakdown of liquid dielectrics under nanosecond pulsed high voltage has been investigated extensively in the last decade. Prior studies have focused on either experimental characterization of the breakdown process and discharge plasma or formulation/verification of the electrostrictive cavitation mechanism of the breakdown initiation. There remain knowledge gaps toward a clear physical picture of how the first plasma is generated in a region saturated by nanoscale cavities created by electrostrictive forces in inhomogeneous fields at the nanosecond timescale. Initial plasma results from the multiplication of primary electrons that gain energy collisionlessly in the cavities to cause collisional ionization of water molecules on the cavity walls. This paper quantitatively discusses the possible sources of primary electrons that seed the plasma discharge. Electron detachment from hydroxide is shown to be the most probable and sustainable electron source. Using numerical modeling, this study demonstrates the plausibility of an electron multiplication mechanism involving two neighboring cavities. The drift of hydrated electrons from one cavity to the next is the rate-limiting step and sets the minimum electric field requirement. Furthermore, this work will inform subsequent experimental studies and have implications in various applications such as plasma sources in biomedical applications, cavitation study, and insulation of pulsed power equipment.

42 ENGINEERING↗

Mono- and bilayer smectic liquid crystal ordering in dense solutions of “gapped” DNA duplexes

Significance Liquid crystalline behavior of DNA has been studied for decades, yet only recently has one of the most fundamental liquid crystal phases—the smectic phase in which rod-like objects assemble into stacks of fluid layers—been demonstrated in this system. Here, we describe distinct bilayer and monolayer smectic phases in solutions of “gapped” DNA (GDNA), consisting of two DNA duplexes connected by a single strand. The smectic order is amphotropic (sensitive to temperature as well as concentration), and the layer structure is stable against significant perturbations of the GDNA construct (e.g., “gap” length variation and asymmetry in duplex lengths). The temperature sensitivity may provide a means to compare end-to-end interaction strengths between DNA duplexes at biologically relevant concentrations.

36 MATERIALS SCIENCE↗

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.

59 BASIC BIOLOGICAL SCIENCES↗

Measurement of the dynamic charge susceptibility near the charge density wave transition in ErTe 3

A charge density wave (CDW) is a phase of matter characterized by a periodic modulation of valence electron density coupled with lattice distortion. Its formation is closely tied to the dynamical charge susceptibility, χ(q, ω) , which reflects the collective electron dynamics of the material. Despite decades of study, χ(q, ω) near a CDW transition has never been measured at nonzero momentum, q, with meV energy resolution. Here, we investigate the canonical CDW transition in ErTe 3 using momentum-resolved electron energy loss spectroscopy, a technique uniquely sensitive to valence band charge excitations. Unlike phonons, which soften via the Kohn anomaly, we find the electronic excitations exhibit purely relaxational dynamics well described by a diffusive model, with the diffusivity peaking just below the critical temperature, T C1 . Additionally, we report for the first time a divergence in the real part of χ(q, ω) in the static limit (ω → 0), a long-predicted hallmark of CDWs. Unexpectedly, this divergence occurs as T → 0, with only a weak thermodynamic signature at T = T C1 . Our study necessitates a reexamination of the traditional description of CDW formation in quantum materials.

M-EELS↗

Robust two-colour pyrometry uncertainty analysis to acquire spatially-resolved measurements

Two-colour pyrometry (2CP) has been used over several decades to study engine-relevant combustion processes, but results are generally regarded as qualitative or semi-quantitative. In many current 2CP systems, large measurement errors are introduced by parallax because the two measured wavelengths are not from the same line of sight. Here this work presents a spatially-resolved 2CP system with the objective of quantifying and reducing measurement uncertainty. An optical setup that eliminates parallax in 2CP is used together with pixel-by-pixel calibration of the camera sensor to increase measurement accuracy. Primary uncertainty terms are identified, and an error propagation analysis is performed to compute uncertainties in the final results of soot temperature, soot concentration parameter, KL, and soot mass. These methodologies are applied to investigate an auto-igniting fuel spray in a constant pressure flow rig at diesel-like conditions of high ambient pressure and temperature. Results show bias uncertainty of around 200 K (≈10%) for temperature and about 40%–60% for KL. High uncertainty was found to occur on the diffusion flame front where both optical thickness and soot concentrations are small. However, these uncertain measurement zones with relatively low soot concentrations contribute minimally to the total soot mass present in the reacting jet during the temporal evolution of the flame.

42 ENGINEERING↗

Quasioptical propagation and absorption of electron cyclotron waves: simulations and experiment

Electron-cyclotron resonance heating is an essential tool for manipulating fusion plasmas and has been diligently studied for decades through numerical simulations and experiments. Here, we report the first comparison of simulations using the quasioptical code PARADE (PAraxial RAy DEscription) with experiments using a target-plate system on the Large Helical Device. We find that the numerical and experimental results agree qualitatively, which makes PARADE a promising code for modeling of electron-cyclotron wave beams in future experiments. The signature advantage of PARADE is its ability to capture both mode conversion and inhomogeneity of the dissipation rate across the beam cross section. Accounting for these effects, which can noticeably affect the power deposition, significantly improves the agreement between numerical results and experimental data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The entropy of galaxy spectra: how much information is encoded?

Abstract The inverse problem of extracting the stellar population content of galaxy spectra is analysed here from a basic standpoint based on information theory. By interpreting spectra as probability distribution functions, we find that galaxy spectra have high entropy, thus leading to a rather low effective information content. The highest variation in entropy is unsurprisingly found in regions that have been well studied for decades with the conventional approach. We target a set of six spectral regions that show the highest variation in entropy – the 4000 Å break being the most informative one. As a test case with real data, we measure the entropy of a set of high-quality spectra from the Sloan Digital Sky Survey, and contrast entropy-based results with the traditional method based on line strengths. The data are classified into star-forming (SF), quiescent (Q), and active galactic nucleus (AGN) galaxies, and show – independently of any physical model – that AGN spectra can be interpreted as a transition between SF and Q galaxies, with SF galaxies featuring a more diverse variation in entropy. The high level of entanglement complicates the determination of population parameters in a robust, unbiased way, and affects traditional methods that compare models with observations, as well as machine learning (especially deep learning) algorithms that rely on the statistical properties of the data to assess the variations among spectra. Entropy provides a new avenue to improve population synthesis models so that they give a more faithful representation of real galaxy spectra.

Ferreras, Ignacio (ORCID:0000000345843127)↗

Graviton chirality and topological order in the half-filled Landau level

The fractional quantum Hall state at the Landau level filling factor 5/2 is extremely interesting because it is likely the first non-Abelian state, but its precise nature remains unclear after decades of study. Here we demonstrate this can be resolved by studying the chirality of its graviton excitations, using circularly polarized Raman scattering. We discuss the advantage of this bulk probe over the existing edge probes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Influence of the Turing instability on the motion of domain boundaries

Turing's theory of pattern formation has provided crucial insights into the behavior of various biological, geographical, and chemical systems over the last few decades. Existing studies have focused on moving-boundary Turing systems for which the motion of the boundary is prescribed by an external agent. In this paper, we present an extension of this theory to a class of systems in which the front motion is governed by the physical processes that occur within the domain. Biological systems exhibiting apically dominant growth and corrosion of metals and alloys highlight some of the noteworthy examples of such systems. In this study, we characterize the nature of interaction between the moving front and the Turing-instability for both an activator-inhibitor and an activator-substrate model. Behavioral regimes of periodic, as well as nonperiodic (nonconstant), growth rates are obtained. Furthermore, the trends in the first show striking similarities with the cyclic-boundary-kinetics observed in experimental systems. In general, a stationary, periodic structure is also left behind the moving front. If the periodicity of the boundary kinetics agrees with the allowed range of the stable-periodic solutions, the pattern formed tends to persist. Lastly, it evolves to a nearby energy-minimum either by peak-splitting, peak-decay, or by settling down to a spatially homogeneous state.

99 GENERAL AND MISCELLANEOUS↗

Simulations of multicomponent relativistic thermalization

Multicomponent relativistic fluids have been studied for decades. However, simulating the dynamics of the particles and fluids in such a mixture has been a challenge due to the fact that such simulations are computationally expensive in three spatial dimensions. Here, we report on the development and application of a multidimensional relativistic Monte Carlo code to explore the thermalization process in a relativistic multicomponent environment in a computationally inexpensive way. As an illustration we simulate the fully relativistic three-dimensional Brownian-motion-like solution to the thermalization of a high-mass particle (proton) in a bath of relativistic low-mass particles (electrons). Here, we follow the thermalization and ultimate equilibrium distribution of the Brownian-like particle as can happen in the cosmic plasma during big-bang nucleosynthesis. We also simulate the thermalization of energetic particles injected into the plasma as can occur, for example, by the decay of massive unstable particles during the big bang.

79 ASTRONOMY AND ASTROPHYSICS↗

Interaction-Induced Metallicity in a Two-Dimensional Disordered Non-Fermi Liquid

The interplay of interactions and disorder in two-dimensional (2D) electron systems has actively been studied for decades. The paradigmatic approach involves starting with a clean Fermi liquid and perturbing the system with both disorder and interactions. Here, we start instead with a clean non-Fermi liquid near a 2D ferromagnetic quantum critical point and consider the effects of disorder. In contrast with the disordered Fermi liquid, we find that our model does not suffer from runaway flows to strong coupling and the system has a marginally stable fixed point with perfect conduction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Convergence Rate of Model Reference Adaptive Control with Application to Building HVAC Systems

Model reference adaptive control (MRAC) has been studied for decades and successfully applied in multiple areas, including heating, ventilation, and air conditioning (HVAC) systems for buildings. MRAC is efficient in capturing the time-varying characteristics of buildings' indoor temperatures and outdoor weather environments. In this paper, the rate of convergence of MRAC is investigated, where a direct adaptive control with temperature set point reference tracking is used to regulate the indoor temperatures for buildings. Numerical results show that by controlling the HVAC systems of residential buildings using MRAC, the indoor temperatures converge Q-sublinearly to the desired temperature set points. In addition, the rate of convergence for MRAC is compared with a baseline adaptive model-free control method.

Wu, Tumin↗

Experimental Validation of a Command and Control Traffic Detection Model

Network intrusion detection systems (NIDS) are commonly used to detect malware communications, including command-and-control (C2) traffic from botnets. NIDS performance assessments have been studied for decades, but mathematical modeling has rarely been used to explore NIDS performance. This paper details a mathematical model that describes a NIDS performing packet inspection and its detection of malware's C2 traffic. Here, the paper further describes an emulation testbed and a set of cyber experiments that used the testbed to validate the model. These experiments included a commonly used NIDS (Snort) and traffic with contents from a pervasive malware (Emotet). Results are presented for two scenarios: a nominal scenario and a “stressed” scenario in which the NIDS cannot process all incoming packets. Model and experiment results match well, with model estimates mostly falling within 95 % confidence intervals on the experiment means. Model results were produced 70-3000 times faster than the experimental results. Consequently, the model's predictive capability could potentially be used to support decisions about NIDS configuration and effectiveness that require high confidence results, quantification of uncertainty, and exploration of large parameter spaces. Furthermore, the experiments provide an example for how emulation testbeds can be used to validate cyber models that include stochastic variability.

mathematical model↗

On the bulk compaction of brittle granular materials, part I: SeS analysis of axial compression to 4000 MPa

The bulk compaction of granular materials has been studied for decades to interpret and manage responses for soils and powder-based component fabrication, and geophysical, celestial, and ballistic impact. Their bulk or macroscopic compaction response is limited by what occurs at the granular or microstructural scale. Motivation existed to more closely examine that association specific to granular brittle materials (e.g., ceramics and glasses). That examination is offered in a series of three companion papers where Part I describes a new supplemental analysis adopted to bulk compaction response involving relatively high compaction stresses (4000 MPa). Bulk compactions of vitreous silicates and crystalline quartzes were interpreted in three ways, including that of a new analysis that considers the product of void ratio (e) and stress (S) as a function of S, hereafter referred to as “SeS analysis”. In conclusion, the SeS analysis was found to be an informative supplement to conventional bulk compaction analyses because it provides more consistent higher sensitivity for the identification of bulk density rate increase with increasing compaction (softening); a rate increase that arises from the cumulative effect of the onsets and progression of compaction-induced yielding, fracture or comminution, densification, phase change, or combinations thereof occurring at the granular or microstructural scale.

compaction↗

Addressing amorphization and transgranular fracture of B 4 C through Si doping and TiB 2 microparticle reinforcing

Over the last two decades, many studies have contributed to improving our understanding of the brittle failure mechanisms of boron carbide and provided a road map for inhibiting the underlying mechanisms and improving the mechanical response of boron carbide. This paper provides a review of the design and processing approaches utilized to address the amorphization and transgranular fracture of boron carbide, which are mainly based on what we have found through 9 years of work in the field of boron carbides as armor ceramics.

36 MATERIALS SCIENCE↗