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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression and genomic aberrations, features that can be influenced by the 3D structure of chromosomes inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, from normal epithelium to bone metastasis. We describe spatial compartment identity (A-open versus B-closed) changes with progression in these cell lines and their relation to gene expression changes in both cell lines and patient samples. In particular, 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches are accompanied by changes in the structure, size, and boundaries of topologically associating domains (TADs). Further, compartment changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation. These results suggest that discrete 3D genome structure changes play a deleterious role in prostate cancer progression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The continued optical to mid-infrared evolution of V838 Monocerotis

The eruptive variable V838 Monocerotis (V838 Mon) gained notoriety in 2002 when it brightened nine magnitudes in a series of three outbursts and then rapidly evolved into an extremely cool supergiant. We present optical, near-infrared (near-IR), and mid-IR spectroscopic and photometric observations of V838 Mon obtained between 2008 and 2012 at the Apache Point Observatory 3.5 m, NASA IRTF 3 m, and Gemini South 8 m telescopes. We contemporaneously analyze the optical and IR spectroscopic properties of V838 Mon to arrive at a revised spectral type L3 supergiant and effective temperature T{sub eff}∼2000–2200 K. Because there are no existing optical observational data for L supergiants, we speculate that V838 Mon may represent the prototype for L supergiants in this wavelength regime. We find a low level of Hα emission present in the system, consistent with interaction between V838 Mon and its B3V binary; however, we cannot rule out a stellar collision as the genesis event, which could result in the observed Hα activity. Based upon a two-component blackbody fit to all wavelengths of our data, we conclude that, as of 2009, a shell of ejecta surrounded V838 Mon at a radius of R=263±10 AU with a temperature of T=285±2 K. This result is consistent with IR interferometric observations from the same era and predictions from the Lynch et al. model of the expanding system, which provides a simple framework for understanding this complicated system.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

HUBBLE SPACE TELESCOPE IMAGING OF THE BINARY NUCLEUS OF THE PLANETARY NEBULA EGB 6

EGB 6 is an ancient, low-surface-brightness planetary nebula. The central star, also cataloged as PG 0950+139, is a very hot DAOZ white dwarf (WD) with an apparent M dwarf companion, unresolved from the ground but detected initially through excesses in the JHK bands. Its kinematics indicates membership in the Galactic disk population. Inside of EGB 6 is an extremely dense emission knot-completely unexpected since significant mass loss from the WD should have ceased {approx}10{sup 5} yr ago. The electron density of the compact nebula is very high (2.2 Multiplication-Sign 10{sup 6} cm{sup -3}), as indicated by collisional de-excitation of forbidden emission lines. Hubble Space Telescope imaging and grism spectroscopy are reported here. These resolve the WD and apparent dM companion-at a separation of 0.''166, or a projected 96{sub -45}{sup +204} AU at the estimated distance of 576{sub -271}{sup +1224} pc (using the V magnitude). Much to our surprise, we found that the compact emission nebula is superposed on the dM companion, far from the photoionizing radiation of the WD. Moreover, a striking mid-infrared excess has recently been reported in the Spitzer/IRAC and MIPS bands, best fit with two dust shells. The derived ratio L{sub IR}/L{sub WD} = 2.7 Multiplication-Sign 10{sup -4} is the largest yet found for any WD or planetary nucleus. The compact nebula has maintained its high density for over three decades. We discuss two possible explanations for the origin and confinement of the compact nebula, neither of which is completely satisfactory. This leaves the genesis and confinement of the compact nebula an astrophysical puzzle, yet similar examples appear in the literature.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Imaging the supermassive black hole shadow and jet base of M87 with the event horizon telescope

The Event Horizon Telescope (EHT) is a project to assemble a Very Long Baseline Interferometry (VLBI) network of millimeter wavelength dishes that can resolve strong field general relativistic signatures near a supermassive black hole. As planned, the EHT will include enough dishes to enable imaging of the predicted black hole 'shadow', a feature caused by severe light bending at the black hole boundary. The center of M87, a giant elliptical galaxy, presents one of the most interesting EHT targets as it exhibits a relativistic jet, offering the additional possibility of studying jet genesis on Schwarzschild radius scales. Fully relativistic models of the M87 jet that fit all existing observational constraints now allow horizon-scale images to be generated. We perform realistic VLBI simulations of M87 model images to examine the detectability of the black shadow with the EHT, focusing on a sequence of model images with a changing jet mass load radius. When the jet is launched close to the black hole, the shadow is clearly visible both at 230 and 345 GHz. The EHT array with a resolution of 20-30 μas resolution (∼2-4 Schwarzschild radii) is able to image this feature independent of any theoretical models and we show that imaging methods used to process data from optical interferometers are applicable and effective for EHT data sets. We demonstrate that the EHT is also capable of tracing real-time structural changes on a few Schwarzschild radii scales, such as those implicated by very high-energy flaring activity of M87. While inclusion of ALMA in the EHT is critical for shadow imaging, the array is generally robust against loss of a station.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

When matter matters

We study a recently proposed scenario for the early universe:Subluminal Galilean Genesis. We prove that without any other matter present in the spatially flat Friedmann universe, the perturbations of the Galileon scalar field propagate with a speed at most equal to the speed of light. This proof applies to all cosmological solutions — to the whole phase space. However, in a more realistic situation, when one includes any matter which is not directly coupled to the Galileon, there always exists a region of phase space where these perturbations propagate superluminally, indeed with arbitrarily high speed. We illustrate our analytic proof with numerical computations. We discuss the implications of this result for the possible UV completion of the model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Freeze-in through portals

The popular freeze-out paradigm for Dark Matter (DM) production, relies on DM-baryon couplings of the order of the weak interactions. However, different search strategies for DM have failed to provide a conclusive evidence of such (non-gravitational) interactions, while greatly reducing the parameter space of many representative models. This motivates the study of alternative mechanisms for DM genesis. In the freeze-in framework, the DM is slowly populated from the thermal bath while never reaching equilibrium. In this work, we analyse in detail the possibility of producing a frozen-in DM via a mediator particle which acts as a portal. We give analytical estimates of different freeze-in regimes and support them with full numerical analyses, taking into account the proper distribution functions of bath particles. Finally, we constrain the parameter space of generic models by requiring agreement with DM relic abundance observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Magnification bias as a novel probe for primordial magnetic fields

In this paper we investigate magnetic fields generated in the early Universe. These fields are important candidates at explaining the origin of astrophysical magnetism observed in galaxies and galaxy clusters, whose genesis is still by and large unclear. Compared to the standard inflationary power spectrum, intermediate to small scales would experience further substantial matter clustering, were a cosmological magnetic field present prior to recombination. As a consequence, the bias and redshift distribution of galaxies would also be modified. Hitherto, primordial magnetic fields (PMFs) have been tested and constrained with a number of cosmological observables, e.g. the cosmic microwave background radiation, galaxy clustering and, more recently, weak gravitational lensing. Here, we explore the constraining potential of the density fluctuation bias induced by gravitational lensing magnification onto the galaxy-galaxy angular power spectrum. Such an effect is known as magnification bias. Compared to the usual galaxy clustering approach, magnification bias helps in lifting the pathological degeneracy present amongst power spectrum normalisation and galaxy bias. This is because magnification bias cross-correlates galaxy number density fluctuations of nearby objects with weak lensing distortions of high-redshift sources. Thus, it takes advantage of the gravitational deflection of light, which is insensitive to galaxy bias but powerful in constraining the density fluctuation amplitude. To scrutinise the potentiality of this method, we adopt a deep and wide-field spectroscopic galaxy survey. We show that magnification bias does contain important information on primordial magnetism, which will be useful in combination with galaxy clustering and shear. We find we shall be able to rule out at 95.4% CL amplitudes of PMFs larger than 5 × 10{sup −4} nG for values of the PMF power spectral index n{sub B} ∼ 0.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Melanopogenesis: dark matter of (almost) any mass and baryonic matter from the evaporation of primordial black holes weighing a ton (or less)

The evaporation of primordial black holes with a mass in the 1 gram≲ MPBH≲1000 kg range can lead to the production of dark matter particles of almost any mass in the range 0.1 MeV≲ m DM ≲ 10 18 GeV with the right relic density at very early times, τ≲ 10 -10 s. We calculate, as a function of the primordial black holes mass and initial abundance, the combination of dark matter particle masses and number of effective dark degrees of freedom leading to the right abundance of dark matter today, whether or not evaporation stops around the Planck scale. In addition, since black hole evaporation can also lead to the production of a baryon asymmetry, we calculate where dark matter production and baryogenesis can concurrently happen, under a variety of assumptions: baryogenesis via grand unification boson decay, via leptogenesis, or via asymmetric co-genesis of dark matter and ordinary matter. Finally, we comment on possible ways to test this scenario.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Understanding uncertainties in projections of western North Pacific tropical cyclogenesis

Reliable projections of tropical cyclone (TC) activities in the western North Pacific (WNP) are crucial for climate policy-making in densely-populated coastal Asia. Existing projections, however, exhibit considerable uncertainties with unclear sources. Here, based on future projections by the latest Coupled Model Intercomparison Project Phase 6 climate models, we identify a new and prevailing source of uncertainty arising from different TC identification schemes. Notable differences in projections of detected TCs and empirical genesis potential indices are found to be caused by inconsistent changes in dynamic and thermodynamic environmental factors affecting TC formations. While model uncertainty holds the secondary importance, we show large potential in reducing it through improved model simulations of present-day TC characteristics. Internal variability noticeably impacts near-term projections of the WNP tropical cyclogenesis, while the relative contribution of scenario uncertainty remains small. Our findings provide valuable insights into model development and TC projections, thereby aiding in adaptation decisions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

THE DOMINANT EPOCH OF STAR FORMATION IN THE MILKY WAY FORMED THE THICK DISK

We report the first robust measurement of the Milky Way star formation history using the imprint left on chemical abundances of long-lived stars. The formation of the Galactic thick disk occurs during an intense star formation phase between 9.0 (z ∼ 1.5) and 12.5 Gyr (z ∼ 4.5) ago and is followed by a dip (at z ∼ 1.1) lasting about 1 Gyr. Our results imply that the thick disk is as massive as the Milky Way's thin disk, suggesting a fundamental role of this component in the genesis of our Galaxy, something that had been largely unrecognized. This new picture implies that huge quantities of gas necessary to feed the building of the thick disk must have been present at these epochs, in contradiction with the long-term infall assumed by chemical evolution models in the last two decades. These results allow us to fit the Milky Way within the emerging features of the evolution of disk galaxies in the early universe.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank

Motivation: Glycans play a central role in many essential biological processes. Glycan Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection and annotation of sugars and glycosidic linkages between sugar units and to proteins, all based on atomic coordinates and connectivity information. Carbohydrates can have various chemical modifications at different positions, making their chemical space much diverse. Unfortunately, current PDB files do not provide exact annotations for most carbohydrate derivatives and more than 50% of PDB glycan chains have at least one carbohydrate derivative that could not be correctly recognized by the original Glycan Reader. Results: Glycan Reader has been improved and now identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported. CHARMM-GUI Glycan Reader is updated to generate the simulation system and input of various glycoconjugates with most sugar types and chemical modifications. It also offers a new functionality to edit the glycan structures through addition/deletion/modification of glycosylation types, sugar types, chemical modifications, glycosidic linkages, and anomeric states. The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Glycan Fragment Database in GlycanStructure. Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB.

Park, Sang-Jun↗
DOE OSTI2024

Toward distinguishing Dirac from Majorana neutrino mass with gravitational waves

We propose a new method toward distinguishing the Dirac versus Majorana nature of neutrino masses from the spectrum of gravitational waves (GWs) associated with neutrino mass genesis. Motivated by the principle of generating small neutrino masses without tiny Yukawa couplings, we assume generic seesaw mechanisms for both Majorana and Dirac neutrino masses. For Majorana neutrinos, we further assume a spontaneously broken gauged U ( 1 ) B − L symmetry, independently of the type of Majorana seesaw mechanism, which gives a cosmic string induced GW signal flat over a wide range of frequencies. For Dirac neutrinos, we assume the spontaneous breaking of a Z 2 symmetry, the minimal symmetry choice associated with all Dirac seesaw mechanisms, which is softly broken, generating a peaked GW spectrum from the annihilation of the resulting domain walls. In fact, the GW spectra for all types of Dirac seesaws with such a broken Z 2 symmetry are identical, subject to a mild caveat. As an illustrative example, we study the simplest respective type-I seesaw mechanisms, and show that the striking difference in the shapes of the GW spectra can help differentiate between these Dirac and Majorana seesaws, complementing results of neutrinoless double beta decay experiments. We also discuss detailed implications of the recent NANOGrav data for Majorana and Dirac seesaw models. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2017

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Standard Ruler at Cosmic Dawn

The matter in our Universe comes in two flavors: dark and baryonic. Of these, only the latter couples to photons, giving rise to the well-known baryon acoustic oscillations and, in the process, generating supersonic relative velocities between dark matter and baryons. These velocities—imprinted with the acoustic scale in their genesis—impede the formation of the first stars during cosmic dawn (z ~ 20), modulating the expected 21-cm signal from this era. In a companion paper we showed, combining numerical simulations and analytic models, that this modulation takes the form of robust velocity-induced acoustic oscillations (VAOs), with a well-understood shape that is frozen at recombination, and unaffected by the unknown astrophysics of star formation. Here we propose using these VAOs as a standard ruler at cosmic dawn. We find that three years of 21-cm power-spectrum data from the upcoming HERA interferometer should be able to measure the Hubble expansion rate H(z) at z = 15–20 to percent-level precision, ranging from 0.3% to 11% depending on the strength of astrophysical feedback processes and foregrounds. Furthermore, this would provide a new handle on the expansion rate of our Universe during an otherwise unprobed epoch, opening a window to the mysterious cosmic-dawn era.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Generation of Near-Equipartition Magnetic Fields in Turbulent Collisionless Plasmas

The mechanisms that generate “seed” magnetic fields in our Universe and that amplify them throughout cosmic time remain poorly understood. By means of fully kinetic particle-in-cell simulations of turbulent, initially unmagnetized plasmas, here we study the genesis of magnetic fields via the Weibel instability and follow their dynamo growth up to near-equipartition levels. In the kinematic stage of the dynamo, we find that the rms magnetic field strength grows exponentially with rate γ B ≃0.4⁢u rms /L, where L/2⁢π is the driving scale and u rms is the rms turbulent velocity. In the saturated stage, the magnetic field energy reaches about half of the turbulent kinetic energy. Here, magnetic field growth is balanced by dissipation via reconnection, as revealed by the appearance of plasmoid chains. At saturation, the integral-scale wave number of the magnetic spectrum approaches k int ≃12⁢π/L. Our results show that turbulence—induced by, e.g., the gravitational buildup of galaxies and galaxy clusters—can magnetize collisionless plasmas with large-scale near-equipartition fields.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Second harmonic Bessel-Gauss beam shaping with elliptic axicon aberrations

The second harmonic (SH) of an axicon generated Bessel-Gauss beam is created through the nonlinear interaction of photons with a crystal, resulting in the energy doubling of the output photons. In this work, we show experimentally that in addition to frequency doubling, the SH of Bessel-Gauss beams under asymmetric aberrations from an elliptic axicon exhibit intriguing beam formation. Particularly, the central region of the SH beam profile is composed of two central spots of various geometries surrounded by nested ellipses; one of which is the configuration of two central gamma dots with similar radius knotted by nested ellipses for a zeroth-order Bessel-Gauss pump. These SH beams consistently maintain their spatial profile throughout propagation, reminiscing the behavior of screw dislocations in wave patterns. Our numerical simulations produce beam dynamics consistent with that of experiments and further implicate the remarkable interweaving of bright spots with dark vortices. This is especially noticeable when the beams dynamically oscillate along the optical axis, resulting in the genesis of spatially polarized beams with a knotted framework. The insights gained from our study establish a novel paradigm for exploring interactions of Bessel-like beams with vortex dynamics. This, in turn, has the potential to spark innovations in optical applications, fostering new methodologies to harness and manipulate complex light structures. Our experimental findings could spur new methods of generating logical states of light and new opportunities for material processing control. Published by the American Physical Society 2025

Wang, Tianhong (ORCID:0000000169104201)↗
DOE OSTI2015

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH

Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca 2+ -triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca 2+ -bound holo s2b (1.4 Å resolution, R = 15.0%, R free = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, R free = 20.7%), as well as of Ca 2+ -free apo s2a (1.8 Å resolution, R = 20.7%, R free = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, R free = 21.2%; 1.6 Å resolution, R = 16.2%, R free = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca 2+ pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B -factor analyses suggest that in the presence of Ca 2+ the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca 2+ binding. Conserved residues not only interact with Ca 2+ , but also position the Ca 2+ -interacting water molecule. Ca 2+ aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca 2+ binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

Bauer, Ryan↗
DOE OSTI2022

The Ghost of Performance Reproducibility Past

The importance of ensemble computing is well established. However, executing ensembles at scale introduces interesting performance fluctuations that have not been well investigated. In this paper, we trace our experience uncovering performance fluctuations of ensemble applications (primarily constituting a workflow of GROMACS tasks), and unsuccessful attempts, so far, at trying to discern the underlying cause(s) of performance fluctuations. Is the failure to discern the causative or contributing factors a failure of capability? Or imagination? Do the fluctuations have their genesis in some inscrutable aspect of the system or software? Does it warrant a fundamental reassessment and rethinking of how we assume and conceptualize performance reproducibility? Answers to these questions are not straightforward, nor are they immediate or obvious. We conclude with a discussion about the performance of ensemble applications and ruminate over the implications for how we define and measure application performance.

97 MATHEMATICS AND COMPUTING↗