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At least 451 records · Page 25

Chimera D-Series Gravitational Wave Emission Sourced from Neutrino Anisotropy

Gravitational wave data sourced from the time-dependent anisotropic neutrino emission, as well as the time-dependent fluid quadrupole motion, in the Chimera D-Series three-dimensional core collapse supernova simulations. Data from three models initiated from three different progenitors are presented: D9.6-3D, D15-3D, and D25-3D. Please see the README for more information about the data structure and progenitors.

79 ASTRONOMY AND ASTROPHYSICS↗

DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.

Carra, Claudio↗

Using Molecular Structure to Tune Intrachain and Interchain Charge Transport in Indacenodithiophene-Based Copolymers

Here, in this work, we compare two structurally near-amorphous rigid-rod polymers-poly(indacenodithiophene-co-benzothiadiazole), p(IDT-BT), and poly(indacenodithiophene-co-benzopyrollodione), p(IDT-BPD)-with orders of magnitude different mobilities to understand the effect charge carrier intrachain delocalization has on electronic transport. Quantum chemical calculations show that p(IDT-BPD) has a barrier to torsion that is significantly lower than that of p(IDT-BT) and is thus more likely to have reduced conjugation lengths. We utilize absorption and photoluminescence spectroscopy to characterize energetic disorder and show that p(IDT-BPD) has higher energetic disorder. Charge modulation spectroscopy (CMS) and model calculations are used to show that charge carriers are substantially delocalized in p(IDT-BT) and occupy near-uniform energetic environments. We find that mobility activated hopping barriers are similar in these two materials. Electronic structure calculations show that both intrachain and interchain couplings of monomer units are poor enough in p(IDT-BPD) that charge carriers collapse to single IDT units and transport via a through-space tunneling mechanism. This work highlights the remarkable charge transport properties of p(IDT-BT) by showing that high mobilities are achievable on device-relevant length scales with only 1D carrier delocalization.

36 MATERIALS SCIENCE↗

Mott vs Kondo: Influence of various density functional based methods on the Ce isostructural phase transition mechanism

The cerium iso-structural phase transition (γ–α) is dominated by f-electron localization changes that results in a magnetic ordering change and a volume collapse. Generally, these physics are difficult to capture with ab initio and first principles methods. However, previous works have shown various methods to be successful in predicting at least some of the physics of the γ to α phase transition. Therefore, here, we perform a broad survey of density functional based methods across three levels of theory and types of functions [GGA (generalized gradient approximation), MetaGGA, and hybrid functionals] and compare the results, focusing on hydrostatic compression across the phase boundary at zero kelvin. For the methods that best reproduce experimental results, we directly probe the predicted mechanisms and frame the results in the Mott/Kondo debate, assessing how the underlying methods and assumptions of different functionals can assess the physical drivers in the phase transition, providing insight into the governing processes of this unique phase transition.

36 MATERIALS SCIENCE↗

Dissecting the Division of Labor in Microbial Consortia for the Production of Biofuels and Chemicals (Final Technical Report)

The overarching objective of this project is to elucidate the fundamental design rules for microbial division of labor (DOL), the core of ecosystem organization, in the context of artificial yeast—lactic acid bacteria consortia that produce advanced biofuel and chemical from cellulosic biomass. Over the course of four years, we have successfully achieved the objective through three lines of research that combines experiment with mathematical modeling. Specifically, we have shown that compositional and temporal DOL is effective in modulating mixed sugar fermentation by an engineered consortium and uncovered general quantitative criteria for conditions under which microbial DOL outperforms single superbugs for simultaneous utilization of mixed substrates. We also demonstrated, in synthetic consortia of yeast and lactic acid bacteria, that partitioning the labor for substrate breakdown and end-product synthesis can allow an efficient production of 2-butanol that is difficult otherwise for a single yeast strain. Additionally, by systematically probing the stability of an engineered cooperative consortium, we found that the stability of microbial symbiosis is governed by the topological structure of the underlying cellular interactions rather than specific microbial species and that rational modulation of the interactions may facilitate the restoration of collapsed consortia as well as the intervention of target communities. Together, this project has advanced the fundamental knowledge of microbial DOL in terms of its strength in mixed substrate fermentation, production of complex chemicals, and ecological system stability in the context of microbial consortia. It also provides valuable insights into the design, construction and optimization of artificial consortia for the utilization of cellulosic biomass and economic production of biofuel and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗

The Dynamics of Debris Disk Creation in Neutron Star Mergers

Abstract The detection of GW170817/AT2017gfo inaugurated an era of multimessenger astrophysics, in which gravitational-wave and multiwavelength photon observations complement one another to provide unique insight into astrophysical systems. A broad theoretical consensus exists, in which the photon phenomenology of neutron star mergers largely rests upon the evolution of the small amount of matter left on bound orbits around the black hole or massive neutron star remaining after the merger. Because this accretion disk is far from inflow equilibrium, its subsequent evolution depends very strongly on its initial state, yet very little is known about how this state is determined. Using both snapshot and tracer particle data from a numerical relativity/MHD simulation of an equal-mass neutron star merger that collapses to a black hole, we show how gravitational forces arising in a nonaxisymmetric, dynamical spacetime supplement hydrodynamical effects in shaping the initial structure of the bound debris disk. The work done by hydrodynamical forces is ∼10 times greater than that due to time-dependent gravity. Although gravitational torques prior to remnant relaxation are an order of magnitude larger than hydrodynamical torques, their intrinsic sign symmetry leads to strong cancellation; as a result, hydrodynamical and gravitational torques have a comparable effect. We also show that the debris disk’s initial specific angular momentum distribution is sharply peaked at roughly the specific angular momentum of the merged neutron star’s outer layers, a fewr g c, and identify the regulating mechanism.

Astronomy & Astrophysics↗

Strong temporal variation in treefall and branchfall rates in a tropical forest is related to extreme rainfall: results from 5 years of monthly drone data for a 50 ha plot

Abstract. A mechanistic understanding of how tropical-tree mortality responds to climate variation is urgently needed to predict how tropical-forest carbon pools will respond to anthropogenic global change, which is altering the frequency and intensity of storms, droughts, and other climate extremes in tropical forests. We used 5 years of approximately monthly drone-acquired RGB (red–green–blue) imagery for 50 ha of mature tropical forest on Barro Colorado Island, Panama, to quantify spatial structure; temporal variation; and climate correlates of canopy disturbances, i.e., sudden and major drops in canopy height due to treefalls, branchfalls, or the collapse of standing dead trees. Canopy disturbance rates varied strongly over time and were higher in the wet season, even though wind speeds were lower in the wet season. The strongest correlate of monthly variation in canopy disturbance rates was the frequency of extreme rainfall events. The size distribution of canopy disturbances was best fit by a Weibull function and was close to a power function for sizes above 25 m2. Treefalls accounted for 74 % of the total area and 52 % of the total number of canopy disturbances in treefalls and branchfalls combined. We hypothesize that extremely high rainfall is a good predictor because it is an indicator of storms having high wind speeds, as well as saturated soils that increase uprooting risk. These results demonstrate the utility of repeat drone-acquired data for quantifying forest canopy disturbance rates at fine temporal and spatial resolutions over large areas, thereby enabling robust tests of how temporal variation in disturbance relates to climate drivers. Further insights could be gained by integrating these canopy observations with high-frequency measurements of wind speed and soil moisture in mechanistic models to better evaluate proximate drivers and with focal tree observations to quantify the links to tree mortality and woody turnover.

54 ENVIRONMENTAL SCIENCES↗

HST observations of globular clusters in M 31. 1: Surface photometry of 13 objects

We present the initial results of a study of globular clusters in M 31, using the Faint Object Camera (FOC) on the Hubble Space Telescope (HST). The sample of objects consists of 13 clusters spanning a range of properties. Three independent image deconvolution techniques were used in order to compensate for the optical problems of the HST, leading to mutually fully consistent results. We present detailed tests and comparisons to determine the reliability and limits of these deconvolution methods, and conclude that high-quality surface photometry of M 31 globulars is possible with the HST data. Surface brightness profiles have been extracted, and core radii, half-light radii, and central surface brightness values have been measured for all of the clusters in the sample. Their comparison with the values from ground-based observations indicates the later to be systematically and strongly biased by the seeing effects, as it may be expected. A comparison of the structural parameters with those of the Galactic globulars shows that the structural properties of the M 31 globulars are very similar to those of their Galactic counterparts. A candidate for a post-core-collapse cluster, Bo 343 = G 105, has been already identified from these data; this is the first such detection in the M 31 globular cluster system.

Pecci, F. Fusi↗

Additional Observations of Actively Forming Lava Tubes and Associated Structures, Hawaii

Extensive changes occurred after the initial observations (Greeley, 1971) of lava tube and channel formation associated with the eruption of Mauna Ulu. Individual vents, which apparently acted somewhat independently, merged by collapse of intervening sections to form an elongate trench. Lava erupted from the summit vent flowed down the trench to the lower end and drained through lava tubes into Alae lava lake. Alae lava lake is in turn drained occasionally by other lava tubes and lava tube networks.

Greeley, Ronald↗

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↗

Structure and Kinematics of a Complex Crater: Upheaval Dome, Southeast, Utah

Two vastly different phenomena, extraterrestrial impact and salt diapirism, have been proposed for the origin of Upheaval Dome. Upheaval Dome is a about 2.5-km-diameter structural dome surrounded by a 5-km-diameter ring structural depression, which is in turn flanked by extensive, nearly flat-lying Colorado Plateau strata. Seismic refraction data and geologic mapping indicate that the dome originated by the collapse of a transient cavity formed by impact; data also show that rising salt has had a negligible influence on dome development. Evidence for this includes several factors: (1) a rare lag deposit of impactite is present; (2) fan-tailed fracture surfaces (shatter surfaces) and a few shattercones are present; (3) the top of the underlying salt horizon is at least 500 m below the center of the dome, with no exposures of salt in the dome to support the possibility that a salt diapir has ascended through it; (4) sedimentary strata in the center are significantly imbricated by top-to-the-center thrust faulting and are complexly folded; (5) top-to-the-center low-angle normal faults are found at the perimeter of the structure; and (6) clastic dikes are widespread. The scarcity of melt rocks and shock fabrics is attributed to approximately 0.5 km of erosion; the structures of the dome reflect processes of complex crater development at a depth of about 0.5 km below the crater floor. Based on mapping and kinematic analysis, we infer that the dome formed mainly by centerward motion of rock units along listric faults. Outcrop-scale folding and upturning of beds, especially common in the center, largely resulted from this motion. In addition, we have detected some centerward motion of fault-bounded wedges resulting from displacements on subhorizontal faults that conjoin and die out within horizontal bedding in the perimeter of the structure. Collectively, the observed deformation accounts for the creation of both the central uplift and the encircling ring syncline.

Kriens, B. J.↗

Pressure-induced spin crossover in a Fe 78 Si 9 B 13 metallic glass

The pressure effect on structures and properties of a Fe 78 Si 9 B 13 metallic glass was investigated by in situ high-pressure synchrotron Fe Kβ x-ray emission spectroscopy and x-ray diffraction, and electrical resistivity measurements up to ~51 GPa. The study reveals a reversible and continuous pressure-induced high- to low-spin crossover of Fe atoms in an amorphous structure. The changes of the local spin moment can be scaled to match its average atomic distance shrinkage very well during compression. The crossover of electronic spin states in the Fe 78 Si 9 B 13 metallic glass resembles that of typical crystalline Fe-bearing materials but without a sharp atomic volume collapse and an abrupt electrical resistivity jump. Furthermore, these findings could help guide applications of Fe-based metallic glasses as a soft ferromagnetic material at extreme conditions and also improve our understanding of magnetism and coupling of its changes with disordered atomic structures and other properties in metallic glasses.

36 MATERIALS SCIENCE↗

Large-scale structure of molecular gas in Heiles Cloud 2 - A remarkable rotating ring

The J = 1 - 0 transition of (C-13)O over a 3 sq deg region in Heiles Cloud 2 has been mapped using the Five College Radio Astronomy Observatory 14 m telescope. The complete map contains 3600 individual spectra of which 2400 were sampled with 1 arcmin spacing. The map suggests that the structure of Heiles Cloud 2 is dominated by a quasi-equilibrium rotating ring similar to those found in numerical calculations of the gravitational collapse of a rotating cloud. Within this ring, several dense condensations have been identified and partially mapped in C(O-18). These subcondensations, among which is the dense filament TMC-1, probably result from the instability of the ring to fragmentation and have masses on the order of the jeans mass. Thus, they are marginally unstable to further collapse and may be the precursors of fragments that will eventually form stars.

Schloerb, F. P.↗

The Fourier-Kelvin Stellar Interferometer Mission Concept

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging interferometer for the mid-infrared spectral region (5-30 microns). FKSI is conceived as a scientific and technological precursor to TPF as well as Space Infrared Interferometric Telescope (SPIRIT), Submillimeter Probe Evolution of Cosmic Structure (SPECS), and Single Aperture for Infrared Observatory (SAFIR). It will also be a high angular resolution system complementary to Next Generation Space Telescope (NGST). The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We are in the process of studying alternative interferometer architectures and beam combination techniques, and evaluating the relevant science and technology tradeoffs. Some of the technical challenges include the development of the cryocooler systems necessary for the telescopes and focal plane array, light and stiff but well-damped truss systems to support the telescopes, and lightweight and coolable optical telescopes. The goal of the design study is to determine if a mid-infrared interferometry mission can be performed within the cost and schedule requirements of a Discovery class mission. At the present time we envision the FKSI as comprised of five one meter diameter telescopes arranged along a truss structure in a linear non-redundant array, cooled to 35 K. A maximum baseline of 20 meters gives a nominal resolution of 26 mas at 5 microns. Using a Fizeau beam combination technique, a simple focal plane camera could be used to obtain both Fourier and spectral data simultaneously for a given orientation of the array. The spacecraft will be rotated to give sufficient Fourier data to reconstruct complex images of a broad range of astrophysical sources.

Danchi, W. C.↗

Predicting Rupture Pressure and Leak Rate of Alloy 600 U-bend Tubes with PWSCC and Comparing with Test Results (Technical Letter Report)

This report summarizes structural integrity work performed for the US NRC that predicts the structural integrity of steam generator (SG) tubes with flaws in the U-bend. The work covers model development and validation for U-bend tubes containing lab-induced primary water stress corrosion cracks (PWSCC). Limit load models for plastic collapse predicting ligament rupture pressure and leak rate of cracked U-bend tubes were developed and validated with pressure tests and finite element analyses (FEAs). Failure pressure and leak rate tests were conducted at room temperature on Alloy 600 U-bend tubes containing flaws located at various locations around the U-bend. Existing models for predicting structural integrity of straight tubes with well defined, rectangular, electro-discharge-machined (EDM) flaws were modified and used to predict the ligament rupture and unstable burst pressures as well as leak rates for the PWSCC flaws in the U-bend section.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Using DIC for Long Slender Structures

High-strain composite deployable structures have been developed for systems such as solar arrays, camera masts or solar sailing propulsion elements. Composite booms in such applications are often flattened and then rolled into a small footprint for low-packaged volume and are then deployed in space. There is a need to obtain deformation for long, slender composite booms on earth through gravity offloading by suspending them vertically and applying distal end (tip) loads. Three-dimensional digital image correlation (3D-DIC), along with other measurement techniques, were used to obtain strain and displacement along the length of a 7.5 m subscale composite Triangular, Rollable, and Collapsible (TRAC) boom in preparation for full scale testing of a 30 m boom. However, incorporating 3D-DIC as a primary measurement tool on long, slender, high-aspect-ratio boom structures presents significant challenges. Challenges include small correlated area due to high aspect ratio, limited standoff distance due to size of test area, coordinate system alignment of multiple camera systems along the length of the boom, nodal mesh extraction for adequate test/analysis correlation, as well as measurement comparison between DIC and other instrumentation used such as fiber optic strain sensing (FOSS) and laser displacement tracking. The contents of the proposed paper will focus on techniques and methods for overcoming the previously mentioned challenges associated with applying 3D-DIC to long, slender boom structures. Results from subscale test along with lessons learned will be discussed.

Deployable Boom↗

U-band CCD surface brightness profiles for candidate collapsed-core globular clusters

We have determined U-band CCD surface brightness profiles for 15 of the 21 globular clusters that have been characterized as having 'collapsed' cores by Djorgovski and King (1986). We have fitted these profiles with two types of seeing-convolved models: single-mass King models and power laws. We find that in many cases the characterization of a profile as being either 'King' or 'cusp' is somewhat subtle. Of the clusters in our sample, 10 appear to have central power-law cusps with either unresolved or marginally resolved cores, three appear to have resolved cores with surrounding power-law structure that is unlike a King model, and two are approximately described by King model fits. The observed power-law cusps are consistent with the predictions of Fokker-Planck models for core-collapse.

Lugger, Phyllis M.↗

A Variational Autoencoder Model Toward Molecular Structure Representation Learning of Fuels

Here, in this work, a Variational Autoencoder (VAE)-based data-driven modeling framework is developed with the overarching goal of enabling fuel design. The VAE model is trained on a large dataset with several chemical species to learn a compressed latent space molecular representation. Chemical structure in the form of Simplified Molecular Input Line Entry System (SMILES) string is fed as input, encoded into the VAE latent space, and decoded back to the SMILES string using Long Short-Term Memory (LSTM) networks. Complexities of the VAE training loss function are thoroughly examined by varying the weightage (beta (𝜷) parameter) of the latent space regularization term, thereby assessing the balance between reconstruction accuracy and validity, and focusing on both accurate molecular structure reconstruction and latent space consistency. Two different strategies for 𝜷 variation are evaluated: linear annealing and cyclic annealing. In addition, the impact of total correlation adjustment and hierarchical priors is also studied with regard to the balance between reconstruction fidelity and latent space regularization, and potential issues such as posterior collapse, over-regularization, and poor disentanglement of latent variables. Overall, the best performance of the model is achieved with hierarchical priors and incrementally increasing 𝜷 from 0 to a threshold value of 0.25 over 75 epochs. The generative VAE model can be readily coupled with Quantitative Structure–Property Relationship (QSPR) analysis to develop an integrated end-to-end framework for fuel-property prediction and molecular design of novel promising fuels.

fuel design↗