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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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DOE OSTI2021

Phage display and other peptide display technologies

ABSTRACT Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 ‘for the phage display of peptides and antibodies’. In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.

Jaroszewicz, Weronika (ORCID:0000000302948682)↗
DOE OSTI2020

New H2O–H2O collisional rate coefficients for cometary applications

ABSTRACT We re-introduce a semiclassical methodology based on theories developed for the determination of broadening coefficients. We show that this simple and extremely fast methodology provides results that are in good agreement with results obtained using the more sophisticate MQCT approach. This semiclassical methodology could be an alternative approach which allows to provide large sets of collisional data for very complex molecular systems. It saves time both on the determination of potential energy surfaces and on the collisional dynamical calculations. In addition, this paper provides more complete sets of rotational de-excitation cross-sections and rate coefficients of H2O perturbed by a thermal average of water molecules. Those data can be used in the radiative transfer modelling of cometary atmospheres.

Boursier, C.↗
DOE OSTI2020

Physical effects on compact high-velocity clouds in the circumgalactic medium

ABSTRACT We numerically investigate the evolution of compact high-velocity clouds (CHVCs) passing through a hot, tenuous gas representing the highly ionized circumgalactic medium (CGM) by applying the adaptive-mesh refinement code flash. The model clouds start from both hydrostatic and thermal equilibrium and are in pressure balance with the CGM. Here, we present 14 models, divided into two mass categories and two metallicities each and different velocities. We allow for self-gravity and thermal conduction or not. All models experience mass diffusion, radiative cooling, and external heating leading to dissociation and ionization. Our main findings are (1) self-gravity stabilizes clouds against Rayleigh–Taylor instability, which is disrupted within 10 sound-crossing times without; (2) clouds can develop Jeans-instable regions internally even though they are initially below Jeans mass; (3) all clouds lose mass by ram pressure and Kelvin–Helmholtz instability; (4) thermal conduction substantially lowers mass-loss rates, by this, extending the clouds’ lifetimes, particularly, more than doubling the lifetime of low-mass clouds; (5) thermal conduction leads to continuous, filamentary stripping, while the removed gas is heated up quickly and mixes efficiently with the ambient CGM; (6) without thermal conduction the removed gas consists of dense, cool, clumpy fragments; (7) thermal conduction might prevent CHVCs from forming stars; and (8) clouds decelerated by means of drag from the ambient CGM form head-tail shapes and collapse after they reach velocities characteristic for intermediate-velocity clouds. Conclusively, only sophisticated modelling of CHVCs as non-homogeneous and non-isothermal clouds with thermal conduction and self-gravity explains observed morphologies and naturally leads to the suppression of star formation.

Sander, Bastian↗
DOE OSTI2022

Revision of Faraday rotation measure constraints on the primordial magnetic field using the IllustrisTNG simulation

ABSTRACT Previously derived Faraday rotation constraints on the volume-filling intergalactic magnetic field (IGMF) have used analytical models that made a range of simplifying assumptions about magnetic field evolution in the intergalactic medium and did not consider the effect of baryonic feedback on large-scale structures. In this work, we revise existing Faraday rotation constraints on the IGMF using a numerical model of the intergalactic medium from the IllustrisTNG cosmological simulation that includes a sophisticated model of the baryonic feedback. We use the IllustrisTNG model to calculate the rotation measure and compare the resulting mean and median of the absolute value of the rotation measure with data from the NRAO VLA Sky Survey (NVSS). The numerical model of the intergalactic medium includes a full magnetohydrodynamic model of the compressed primordial magnetic field as well as a model of the regions where the magnetic field is not primordial, but is rather produced by the process of baryonic feedback. Separating these two types of regions, we are able to assess the influence of the primordial magnetic field on the Faraday rotation signal. We find that by correcting for regions of compressed primordial field and accounting for the fact that part of the intergalactic medium is occupied by magnetic fields spread by baryonic feedback processes rather than by the primordial field relaxes the Faraday rotation bound by a factor of ≃3. This results in B0 < 1.8 × 10−9 G for large correlation length IGMFs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The Dark Energy Survey Year 3 and eBOSS: constraining galaxy intrinsic alignments across luminosity and colour space

ABSTRACT We present direct constraints on galaxy intrinsic alignments (IAs) using the Dark Energy Survey Year 3 (DES Y3), the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and its precursor, the Baryon Oscillation Spectroscopic Survey (BOSS). Our measurements incorporate photometric red sequence (redMaGiC) galaxies from DES with median redshift z ∼ 0.2–1.0, luminous red galaxies from eBOSS at z ∼ 0.8, and also an SDSS-III BOSS CMASS sample at z ∼ 0.5. We measure two-point IA correlations, which we fit using a model that includes lensing, magnification, and photometric redshift error. Fitting on scales 6 Mpc h−1 < rp < 70 Mpc h−1, we make a detection of IAs in each sample, at 5σ–22σ (assuming a simple one-parameter model for IAs). Using these red samples, we measure the IA–luminosity relation. Our results are statistically consistent with previous results, but offer a significant improvement in constraining power, particularly at low luminosity. With this improved precision, we see detectable dependence on colour between broadly defined red samples. It is likely that a more sophisticated approach than a binary red/blue split, which jointly considers colour and luminosity dependence in the IA signal, will be needed in future. We also compare the various signal components at the best-fitting point in parameter space for each sample, and find that magnification and lensing contribute $\sim 2\!-\!18~{{\ \rm per\ cent}}$ of the total signal. As precision continues to improve, it will certainly be necessary to account for these effects in future direct IA measurements. Finally, we make equivalent measurements on a sample of emission-line galaxies from eBOSS at z ∼ 0.8. We constrain the non-linear alignment amplitude to be $A_1=0.07^{+0.32}_{-0.42}$ (|A1| < 0.78 at 95 per cent CL).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Measuring the streaming motion in the Milky Way disc with Gaia EDR3+

We map the 3D kinematics of the Galactic disc out to 3.5 kpc from the Sun, and within 0.75 kpc from the mid-plane of the Galaxy. To this end, we combine high-quality astrometry from Gaia EDR3, with heliocentric line-of-sight velocities from Gaia DR2, and spectroscopic surveys including APOGEE, GALAH, and LAMOST. We construct an axisymmetric model for the mean velocity field, and subtract this on a star-by-star basis to obtain the residual velocity field in the Galactocentric components (V Φ , V R , V z ), and V los . The velocity residuals are quantified using the power spectrum, and we find that the peak power (A/[km s –1 ]) in the mid-plane (|z| < 0.25 kpc) is (A Φ , A R , A Z , A los ) = (4.2,8.5,2.6,4.6), at 0.25 < |z|/[kpc] < 0.5, is (A Φ , A R , A Z , A los ) = (4.0,7.9,3.6,5.3), and at 0.5 < |z|/[kpc] < 0.75, is (A Φ , A R , A Z , A los ) = (1.9,6.9,5.2,6.4). Our results provide a sophisticated measurement of the streaming motion in the disc and in the individual components. We find that streaming is most significant in VR, and at all heights (|Z|) probed, but is also non-negligible in other components. Additionally, we find that patterns in velocity field overlap spatially with models for spiral arms in the Galaxy. Our simulations show that phase-mixing of disrupting spiral arms can generate such residuals in the velocity field, where the radial component is dominant, just as in real data. Furthermore, we also find that with time evolution, both the amplitude and physical scale of the residual motion decrease.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Multiclustering needlet ILC for CMB B -mode component separation

ABSTRACT The Cosmic Microwave Background (CMB) primordial B-mode signal is predicted to be much lower than the polarized Galactic emission (foregrounds) in any region of the sky pointing to the need for sophisticated component separation methods. Among them, the blind Needlet Internal Linear Combination (NILC) has great relevance given our current poor knowledge of the B-mode foregrounds. However, the expected level of spatial variability of the foreground spectral properties complicates the NILC subtraction of the Galactic contamination. We therefore propose a novel extension of the NILC approach, the Multiclustering NILC (MC-NILC), which performs NILC variance minimization on separate regions of the sky (clusters) properly chosen to have similar spectral properties of the B-mode Galactic emission within them. Clusters are identified thresholding either the ratio of simulated foregrounds-only B modes (ideal case) or the one of cleaned templates of Galactic emission obtained from realistic simulations. In this work we present an application of MC-NILC to the future LiteBIRD satellite, which targets the observation of both reionization and recombination peaks of the primordial B-mode angular power spectrum with a total error on the tensor-to-scalar ratio δr < 0.001. We show that MC-NILC provides a CMB solution with residual foreground and noise contamination that is significantly lower than the NILC one and the primordial signal targeted by LiteBIRD at all angular scales for the ideal case and at the reionization peak for a realistic ratio. Thus, MC-NILC will represent a powerful method to mitigate B-mode foregrounds for future CMB polarization experiments.

Astronomy & Astrophysics↗
DOE OSTI2023

A semi-analytic study of self-interacting dark-matter haloes with baryons

ABSTRACT We combine the isothermal Jeans model and the model of adiabatic halo contraction into a semi-analytic procedure for computing the density profile of self-interacting dark-matter (SIDM) haloes with the gravitational influence from the inhabitant galaxies. The model agrees well with cosmological SIDM simulations over the entire core-forming stage up to the onset of gravothermal core-collapse. Using this model, we show that the halo response to baryons is more diverse in SIDM than in CDM and depends sensitively on galaxy size, a desirable feature in the context of the structural diversity of bright dwarfs. The fast speed of the method facilitates analyses that would be challenging for numerical simulations – notably, we quantify the SIDM halo response as functions of the baryonic properties, on a fine mesh grid spanned by the baryon-to-total-mass ratio, Mb/Mvir, and galaxy compactness, r1/2/Rvir; we show with high statistical precision that for typical Milky-Way-like systems, the SIDM profiles are similar to their CDM counterparts; and we delineate the regime of core-collapse in the Mb/Mvir − r1/2/Rvir space, for a given cross section and concentration. Finally, we compare the isothermal Jeans model with the more sophisticated gravothermal fluid model, and show that the former yields faster core formation and agrees better with cosmological simulations. We attribute the difference to whether the target CDM halo is used as a boundary condition or as the initial condition for the gravothermal evolution, and thus comment on possible improvements of the fluid model. We have made our model publicly available at https://github.com/JiangFangzhou/SIDM.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

GalaxyFlow: upsampling hydrodynamical simulations for realistic mock stellar catalogues

ABSTRACT Cosmological N-body simulations of galaxies operate at the level of ‘star particles’ with a mass resolution on the scale of thousands of solar masses. Turning these simulations into stellar mock catalogues requires ‘upsampling’ the star particles into individual stars following the same phase-space density. In this paper, we introduce two new upsampling methods. First, we describe GalaxyFlow, a sophisticated upsampling method that utilizes normalizing flows to both estimate the stellar phase-space density and sample from it. Secondly, we improve on existing upsamplers based on adaptive kernel density estimation (KDE), using maximum likelihood estimation to fine-tune the bandwidth for such algorithms in a way that improves both the density estimation accuracy and upsampling results. We demonstrate our upsampling techniques on a neighbourhood of the Solar location in two simulated galaxies: Auriga 6 and h277. Both yield smooth stellar distributions that closely resemble the stellar densities seen in the Gaia DR3 catalogue. Furthermore, we introduce a novel multimodel classifier test to compare the accuracy of different upsampling methods quantitatively. This test confirms that GalaxyFlow more accurately estimates the density of the underlying star particles than methods based on KDE, at the cost of being more computationally intensive.

Lim, Sung Hak (ORCID:0000000330981092)↗
DOE OSTI2022

BioTransformer 3.0 – A Web Server for Accurately Predicting Metabolic Transformation Products

BioTransformer 3.0 is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively viewable/sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes a few seconds. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0, uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human and/or environmental biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40-50% more accurate, much less prone to combinatorial “explosions” and far more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures

Abstract Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial chromosome has been extensively studied, the pathway targeting DNA replication structures remains poorly understood. We have used an integrative structural biology approach to elucidate how the Tn7-encoded protein TnsE recognizes replication sites. Using native mass spectrometry, we found that TnsE forms 1:1 and 2:1 (TnsE:DNA) complexes on 3′-recessed DNA, with gain-of-function TnsE variants favoring the formation of 2:1 complexes. Structural characterization confirms that two TnsE molecules bind to DNA with the C-terminal domain of the protein recognizing duplex DNA, leaving the N-terminal domain to impose DNA substrate specificity and recruit the core transposition machinery. Collectively, our work is consistent with a model where TnsE-mediated target-site selection relies on the formation of an asymmetric TnsE:DNA complex to recruit the Tn7 transposase to DNA replication structures.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Structural and chemical evolution in layered oxide cathodes of lithium-ion batteries revealed by synchrotron techniques

Abstract Rechargeable battery technologies have revolutionized electronics, transportation and grid energy storage. Many materials are being researched for battery applications, with layered transition metal oxides (LTMO) the dominating cathode candidate with remarkable electrochemical performance. Yet, daunting challenges persist in the quest for further battery developments targeting lower cost, longer lifespan, improved energy density and enhanced safety. This is, in part, because of the intrinsic complexity of real-world batteries, featuring sophisticated interplay among microstructural, compositional and chemical heterogeneities, which has motivated tremendous research efforts using state-of-the-art analytical techniques. In this research field, synchrotron techniques have been identified as a suite of effective methods for advanced battery characterization in a non-destructive manner with sensitivities to the lattice, electronic and morphological structures. This article provides a holistic overview of cutting-edge developments in synchrotron-based research on LTMO battery cathode materials. We discuss the complexity and evolution of LTMO’s material properties upon battery operation and review recent synchrotron-based research works that address the frontier challenges and provide novel insights in this field. Finally, we formulate a perspective on future directions of synchrotron-based battery research, involving next-generation X-ray facilities and advanced computational developments.

25 ENERGY STORAGE↗
DOE OSTI2021

Leading the way out: how a plant myosin facilitates vesicle tethering during exocytosis

Exocytosis is a process by which molecules, such as lipids, proteins, and polysaccharides, are delivered to the plasma membrane (PM) and the extracellular space via vesicular transport. Precise orchestration of this process ensures the spatiotemporal specificity of cargo delivery and therefore plays a vital role in cell growth, function, and response to environmental cues (reviewed in Wu and Guo, 2015; Ravikumar et al., 2017). Lastly, while sophisticated mechanisms for exocytosis have been described in animal and yeast cells, the extent of conservation of these mechanisms in plant systems is far less clear.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The small protein SbtC is a functional component of the CO 2 concentrating mechanism in Synechocystis sp. PCC 6803

Oxygenic phototrophs fix CO 2 via the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which shows relatively low CO 2 affinity and specificity. To circumvent low and fluctuating CO 2 concentrations in aquatic systems, cyanobacteria and algae have evolved sophisticated inorganic carbon (Ci) concentrating mechanisms (CCMs). Bicarbonate transporters such as SbtA play a crucial role in the cyanobacterial CCM and hence display multiple layers of tight regulation. Control of sbtA gene expression and corresponding transporter activity involves the PII-like protein SbtB, whose gene is frequently co-transcribed with sbtA. A previously non-annotated gene located upstream of the sbtAB operon in the model Synechocystis sp. PCC 6803 encodes the small protein SbtC, composed of 80 amino acids. Presence of SbtC was confirmed by immunoblotting of the sbtC-coding sequence fused to a Flag-tag. Similar to sbtAB , transcription of the sbtC locus is induced by low CO 2 availability; however, it is controlled independently. Mutation of the sbtC locus in a wild-type background produced only a mild phenotype, even under low CO 2 , but impaired diurnal growth resembled that of the mutant ΔsbtB . Biochemical analysis indicated a trimeric SbtABC complex in the membrane. Bicarbonate leakage from cells was strongly elevated when either sbtB or sbtC was deleted from recombinant Synechocystis strains harboring only SbtA as single Ci uptake system. Here, our results provide evidence that SbtC contributes to the formation of the SbtAB complex, thereby regulating bicarbonate exchange at the cytoplasmic membrane. Well-conserved SbtC-like proteins encoded in the neighborhood of sbtAB exist in many cyanobacterial genomes, pointing toward an important role in the cyanobacterial CCM.

Walke, Peter [Univ. of Rostock (Germany)] (ORCID:0↗
DOE OSTI2026

Inverse problem in the large momentum effective theory framework

One proposal to compute parton distributions from first principles is the large momentum effective theory (LaMET), which requires the Fourier transform of matrix elements computed nonperturbatively. Lattice quantum chromodynamics (QCD) provides calculations of these matrix elements over a finite range of Fourier harmonics that are often noisy or unreliable in the largest computed harmonics. It has been suggested that enforcing an exponential decay of the missing harmonics helps alleviate this issue. Using nonperturbative data, we show that the uncertainty introduced by this inverse problem in a realistic setup remains significant without very restrictive assumptions, and that the importance of the exact asymptotic behavior is minimal for values of 𝑥 where the framework is currently applicable. We show that the crux of the inverse problem lies in harmonics of the order of 𝜆 = 𝑧⁢𝑃 𝑧 ∼ 5–15, where the signal in the lattice data is often barely existent in current studies, and the asymptotic behavior is not firmly established. We stress the need for more sophisticated techniques to account for this inverse problem, whether in the LaMET or related frameworks like the short-distance factorization. We also address a misconception that, with available lattice methods, the LaMET framework allows a “direct” computation of the 𝑥-dependence, whereas the alternative short-distance factorization only gives access to moments or fits of the 𝑥-dependence.

Dutrieux, Hervé [Aix-Marseille Université, Marseil↗
DOE OSTI2021

Filtering states with total spin on a quantum computer

Starting from a general wave-function described on a set of spins or qubits, we propose several quantum algorithms to extract the components of this state on eigenstates of total spin S 2 and its z component S z . The method plays the role of total spin projection and gives access to the amplitudes of the initial state on a total spin basis. Here, the different algorithms have various degrees of sophistication depending on the requested tasks. They can either solely project onto the subspace with good total spin or completely uplift the degeneracy in this subspace. In the former case, when the projection on the total spin j is made, we show that the number of operations for the projection can be reduced from a quadratic to a linear dependence in j. After each measurement, the state collapses to one of the spin eigenstates that could be used for postprocessing. For this reason, we call the method total quantum spin filtering.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗