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At least 289 records · Page 16

Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg

The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the ‘Global Archaea Diversity’ (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.

59 BASIC BIOLOGICAL SCIENCES↗

An explicit solution to the optimal LQG problem for flexible structures with collocated rate sensors

We present a class of compensators in explicit form (not requiring numerical computer calculations) for stabilizing flexible structures with collocated rate sensors. They are based on the explicit solution, valid for both Continuum and FEM Models, of the LQG problem for minimizing mean square rate. They are robust with respect to system stability (will not destabilize modes even with mismatch of parameters), can be instrumented in state space form suitable for digital controllers, and can be specified directly from the structure modes and mode 'signature' (displacement vectors at sensor locations). Some simulation results are presented for the NASA LaRC Phase-Zero Evolutionary Model - a modal Trust model with 86 modes - showing damping ratios attainable as a function of compensator design parameters and complexity.

Balakrishnan, A. V.↗

PARAMESH: A Parallel Adaptive Mesh Refinement Community Toolkit

In this paper, we describe a community toolkit which is designed to provide parallel support with adaptive mesh capability for a large and important class of computational models, those using structured, logically cartesian meshes. The package of Fortran 90 subroutines, called PARAMESH, is designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement. Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package can provide them with an incremental evolutionary path for their code, converting it first to uniformly refined parallel code, and then later if they so desire, adding adaptivity.

MacNeice, Peter↗

Extrapolation methods for dynamic partial differential equations

Several extrapolation procedures are presented for increasing the order of accuracy in time for evolutionary partial differential equations. These formulas are based on finite difference schemes in both the spatial and temporal directions. On practical grounds the methods are restricted to schemes that are fourth order in time and either second, fourth or sixth order in space. For hyperbolic problems the second order in space methods are not useful while the fourth order methods offer no advantage over the Kreiss-Oliger method unless very fine meshes are used. Advantages are first achieved using sixth order methods in space coupled with fourth order accuracy in time. Computational results are presented confirming the analytic discussions.

Turkel, E.↗

Self-organization of the earth's biosphere-geochemical or geophysiological?

We explore the implications of indicating the biosphere's self-organization by the trend over time of the net entropic flow from the Earth's surface, the actual physical boundary of virtually all biotic mass. This flow, derived from the radiative surface entropy budget, is approximately inversely related to the surface temperature when the solar incident flux remains constant. In the geophysiological ('gaian') interpretation, biospheric self-organization has increased with the progressive colonization of the continents and evolutionary developments in the land biota, as a result of surface cooling arising from biotic enhancement of weathering. The key site for this self-organization is at the interface between land and atmosphere, the soil, where carbon is sequestered by its reaction (as carbonic and organic acids) with calcium magnesium silicates. Along with disequilibrium (steady-state) levels of carbon dioxide in the atmosphere, the occurrence of differentiated soil is the critical material evidence for biospheric self-organization, whether it be geophysiological or geochemical (ie., purely result of inorganic reactions). The computed equilibrium levels of carbon dioxide and corresponding equilibrium temperatures in the past are dramatically different from the steady-state levels. With future solar luminosity increase, the biospheric capacity for climatic regulation will decrease, leading to the ending of self-organization some two billion years from now. The Earth's surface will then approach chemical equilibrium with respect to the carbonate-silicate cycle.

Schwartzman, David W.↗

Evolution of the INMARSAT aeronautical system: Service, system, and business considerations

A market-driven approach was adopted to develop enhancements to the Inmarsat-Aeronautical system, to address the requirements of potential new market segments. An evolutionary approach and well differentiated product/service portfolio was required, to minimize system upgrade costs and market penetration, respectively. The evolved system definition serves to minimize equipment cost/size/mass for short/medium range aircraft, by reducing the antenna gain requirement and relaxing the performance requirements for non safety-related communications. A validation program involving simulation, laboratory tests, over-satellite tests and flight trials is being conducted to confirm the system definition. Extensive market research has been conducted to determine user requirements and to quantify market demand for future Inmarsat Aero-1 AES, using sophisticated computer assisted survey techniques.

Sengupta, Jay R.↗

Resource Allocation Planning Helper (RALPH): Lessons learned

The current task of Resource Allocation Process includes the planning and apportionment of JPL's Ground Data System composed of the Deep Space Network and Mission Control and Computing Center facilities. The addition of the data driven, rule based planning system, RALPH, has expanded the planning horizon from 8 weeks to 10 years and has resulted in large labor savings. Use of the system has also resulted in important improvements in science return through enhanced resource utilization. In addition, RALPH has been instrumental in supporting rapid turn around for an increased volume of special what if studies. The status of RALPH is briefly reviewed and important lessons learned from the creation of an highly functional design team are focused on through an evolutionary design and implementation period in which an AI shell was selected, prototyped, and ultimately abandoned, and through the fundamental changes to the very process that spawned the tool kit. Principal topics include proper integration of software tools within the planning environment, transition from prototype to delivered to delivered software, changes in the planning methodology as a result of evolving software capabilities and creation of the ability to develop and process generic requirements to allow planning flexibility.

Durham, Ralph↗

Kinematic misalignments in remnants of multiple mergers

Observations indicate that the rotation and minor axes in elliptical galaxies are usually well aligned. However, computer models of dissipationless mergers of pairs of disk galaxies have failed to establish such a correlation, implying that most ellipticals probably did not originate in this manner. Here we consider remnants produced from repeated merging in small groups of a half-dozen or so disk galaxies and find that the internal kinematics of such objects are more representative of actual elliptical galaxies. Although our coverage of parameter space is not complete, the remnants produced in our simulations invariably possess small kinematic misalignments. These results suggest that the majority of elliptical galaxies have had evolutionary histories more complex than those envisaged by simple merger hypotheses.

Weil, Melinda L.↗

VLTI-MATISSE L- and N-Band Aperture-Synthesis Imaging of the Unclassified B[e] star FS Canis Majoris

Context. FS Canis Majoris (FS CMa, HD 45677) is an unclassified B[e] star surrounded by an inclined dust disk. The evolutionary stage of FS CMa is still debated. Perpendicular to the circumstellar disk, a bipolar outflow was detected. Infrared aperture-synthesis imaging provides us with a unique opportunity to study the disk structure. Aims. Our aim is to study the intensity distribution of the disk of FS CMa in the mid-infrared L and N bands. Methods. We performed aperture-synthesis imaging of FS CMa with the MATISSE instrument (Multi AperTure mid-Infrared SpectroScopic Experiment) in the low spectral resolution mode to obtain images in the L and N bands. We computed radiative transfer models that reproduce the L- and N-band intensity distributions of the resolved disks. Results. We present L- and N-band aperture-synthesis images of FS CMa reconstructed in the wavelength bands of 3.4–3.8 and 8.6–9.0 μm. In the L-band image, the inner rim region of an inclined circumstellar disk and the central object can be seen with a spatial resolution of 2.7 milliarcsec (mas). An inner disk cavity with an angular diameter of ~6 × 12 mas is resolved. The L-band disk consists of a bright northwestern (NW) disk region and a much fainter southeastern (SE) region. The images suggest that we are looking at the bright inner wall of the NW disk rim, which is on the far side of the disk. In the N band, only the bright NW disk region is seen. In addition to deriving the inclination and the inner disk radius, fitting the reconstructed brightness distributions via radiative transfer modelling allows one to constrain the innermost disk structure, in particular the shape of the inner disk rim.

techniques↗

High Fidelity Modeling of Evolutionary Structures in IMOS

A methodology is proposed for testing, modal identification, and model correlation of structures which are assembled in an evolutionary manner. The methodology prescribes initial testing of a base structure without any attached components. The experimental modal properties are used to update the physical properties of the base structure finite element model using a Bayesian Estimation Technique (BET). The BET is implemented in METLAB using IMOS functions. As components are added to the base structure, additional tests are performed. Three testing options are proposed, all of which enable estimation of the physical parameters of the components alone. Furthermore, improvements to the original BET implementation have been made, which contribute to higher fidelity models and more efficient computational times.

structures testing assembling modeling BET Bayesia↗

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗

Turbomachinery Airfoil Design Optimization Using Differential Evolution

An aerodynamic design optimization procedure that is based on a evolutionary algorithm known at Differential Evolution is described. Differential Evolution is a simple, fast, and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems, including highly nonlinear systems with discontinuities and multiple local optima. The method is combined with a Navier-Stokes solver that evaluates the various intermediate designs and provides inputs to the optimization procedure. An efficient constraint handling mechanism is also incorporated. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated. Substantial reductions in the overall computing time requirements are achieved by using the algorithm in conjunction with neural networks.

Madavan, Nateri K.↗

Langley's CSI evolutionary model: Phase 2

Phase 2 testbed is part of a sequence of laboratory models, developed at NASA Langley Research Center, to enhance our understanding on how to model, control, and design structures for space applications. A key problem with structures that must perform in space is the appearance of unwanted vibrations during operations. Instruments, design independently by different scientists, must share the same vehicle causing them to interact with each other. Once in space, these problems are difficult to correct and therefore, prediction via analysis design, and experiments is very important. Phase 2 laboratory model and its predecessors are designed to fill a gap between theory and practice and to aid in understanding important aspects in modeling, sensor and actuator technology, ground testing techniques, and control design issues. This document provides detailed information on the truss structure and its main components, control computer architecture, and structural models generated along with corresponding experimental results.

Horta, Lucas G.↗

3D Simulations of Ion Thruster Accelerator Grid Erosion Accounting for Charge Exchange Ion Space Charge

Accelerator (accel) grid sputtering by ions formed through charge-exchange (CEX) reactions between beam ions and residual neutral gas is a critical life-limiting mechanism for gridded ion thrusters. The three-dimensional ion optics code CEX3D is designed to simulate this grid erosion for a single beamlet, with a particular emphasis on non-axisymmetric features such as the "pits and grooves" erosion commonly observed on the accel grid downstream face in two-grid thrusters. The treatment of CEX ions in the code was recently upgraded with a new particle-in-cell (PIC) module to account for the influence of these ions' space charge on the electrostatic potential downstream of the grids. In order to achieve reasonable computation times while resolving the Debye length near the grids and avoiding gross violations of the Courant-Friedrichs-Lewy (CFL) condition, macroparticle velocities in the PIC calculation are limited through a rescaling procedure that preserves ion trajectories and space charge density. The code accounts for beam divergence, finite momentum transfer in CEX collisions, and radial losses of CEX ions from the beam; these effects are important for determining the CEX ion flux to the accel grid because the calculated potential downstream of the grids can become very flat. The upgraded code has been used to simulate operation of NASA's Evolutionary Xenon Thruster (NEXT) during the 51 kHr Long Duration Test - a selection of results is presented and compared with experimental data.

Chaplin, Vernon H.↗

On the 2018 Outburst of the Accreting Millisecond X-Ray Pulsar Swift J1756.9-2508 As Seen with NICER

We report on the coherent timing analysis of the 182 Hz accreting millisecond X-ray pulsar SwiftJ1756.92508during its 2018 outburst as observed with the Neutron Star Interior Composition Explorer (NICER). Combiningour NICER observations with Rossi X-ray Timing Explorer observations of the 2007 and 2009 outbursts, we alsostudied the long-term spin and orbital evolution of this source. We find that the binary system is well describedby a constant orbital period model, with an upper limit on the orbital period derivative of Pb < 7.4 ´ 10-13 ss1.Additionally, we improve upon the source coordinates through astrometric analysis of the pulse arrival times,finding R.A.=17h56m57 18±0 08 and decl.=25°0627 8±3 5, while simultaneously measuring thelong-term spin frequency derivative as n = -7.3 ´ 10-16 Hzs1. We briefly discuss the implications of thesemeasurements in the context of the wider population of accreting millisecond pulsars. We reported on the coherent timing analysis of the 2018 outburst of Swift J1756 as observed with NICER. Consistent with analyses of the previous outbursts (Krimm et al. 2007b; Patruno et al. 2010), we find that the X-ray pulsations have energy dependent amplitudes; the fractional amplitude of the fundamental increases with energy, whereas the fractional amplitude of the harmonic shows a slight decline with energy. This energy dependent behavior is not unusual in AMXPs (Patruno & Watts 2012) and can be interpreted in terms of the thermal emission from the stellar hotspot and reprocessing in the accretion column (e.g., Gierliński et al. 2002; Ibragimov & Poutanen 2009). The pulse arrival times of the 2018 outburst are well described by a timing model consisting of a circular orbit with a constant spin frequency. The pulse phases with respect to this model do not show spurious residuals with time or orbital phase, and no evidence is found that the pulse arrival times exhibit an additional delay associated with passing through the gravitational well of the companion star (Shapiro delay). We note, however, that the expected Shapiro delay is given as (Shapiro et al. 1971) Equation (5) where Φ is the orbital phase, G is the gravitational constant, c is the speed of light, and i is the inclination. Even for the maximum allowed companion mass, ${M}_{C}=0.030\,{M}_{\odot }$ (Krimm et al. 2007b, but see Section 4.2 for more details) and an inclination of 90°, the largest delay we can expect is only 4 μs. As this time-delay is smaller than the uncertainty on our phase residuals by nearly two orders of magnitude (see Figure 1), we are not sensitive to Shapiro delays in Swift J1756. Comparing our measurements for the 2018 outburst with those of the 2007 and 2009 outbursts as observed with RXTE, we analyzed the long-term evolution of this source. We found that the binary system is consistent with having a constant orbital period and that the pulsar shows a spin frequency derivative of $\dot{\nu }=-7.3\times {10}^{-16}\,\mathrm{Hz}\,{{\rm{s}}}^{-1}$. 4.1. Spin-down Evolution The long-term spin frequency derivative measured in Swift J1756 is of the same order as the spin frequency derivatives measured in other AMXPs (Hartman et al. 2008; Patruno 2010; Riggio et al. 2011). This frequency change is most likely driven by the neutron star's loss of rotational energy. If so, then the spin-down luminosity is given as Equation (6) where I represents the neutron star moment of inertia. The long-term spin-down of a neutron star is usually assumed to be dominated by the braking torque associated with a spinning magnetic field. Assuming this mechanism is responsible for the observed spin-down in Swift J1756, we can compute the magnetic dipole moment as (Spitkovsky 2006) Equation (7) where α is the misalignment angle between the rotational and magnetic poles. Considering α = 0°–90°, we then find a magnetic field strength of $B\simeq (4\mbox{--}6)\times {10}^{8}$ G at the stellar magnetic poles. This magnetic field strength estimate is in line with those obtained for other accreting millisecond pulsars (see Mukherjee et al. 2015 and references therein). 4.2. Orbit Evolution The observed long-term binary evolution of Swift J1756 is consistent with this source having a constant orbital period and a lower limit on the evolutionary timescale of Equation (8) Binary evolution theory predicts that systems of this type evolve due to angular momentum loss through gravitational radiation (Kraft et al. 1962; Rappaport et al. 1982; Verbunt 1993). For conservative mass transfer, the binary period derivative is given by di Salvo et al. (2008), Equation (9) where MNS is the neutron star mass, $q={M}_{C}/{M}_{\mathrm{NS}}$ is the binary mass ratio, and −1/3 < n < 1 is the mass–radius index of the companion star. Depending on the source inclination, Krimm et al. (2007b) derived a companion mass of ${M}_{C}\,=0.007\mbox{--}0.022\,{M}_{\odot }$ for a neutron star mass of 1.4 ${M}_{\odot }$. For a neutron star mass of 2.2 ${M}_{\odot }$, the allowed range increased to ${M}_{C}=0.009\mbox{--}0.030\,{M}_{\odot }$. In both cases, they assumed an upper limit on the inclination of i < 85°, motivated by the fact that Swift J1756 does not show eclipses in its light curve. Accounting for the extreme cases of stellar masses and n, the binary may either be contracting or expanding. In either case, however, the rate of change is limited to $| {\dot{P}}_{b}| \lesssim 7\times {10}^{-14}$ s s−1, which is well below the upper limit obtained in this work. Although the binary evolution timescale we obtain for Swift J1756 is consistent with theory, it is worth noting that this is not generally true for low-mass X-ray binaries (see Patruno et al. 2017, for a comprehensive discussion). The AMXP SAX J1808.4–3658, in particular, has been found to evolve on a much shorter timescale, with a first derivative on the orbital period of $3.5\times {10}^{-12}$ s s−1 (Hartman et al. 2008; Patruno et al. 2012; Sanna et al. 2017a). Two models have been proposed to explain this discrepancy: highly nonconservative mass transfer due to irradiation of the companion star by the pulsar (di Salvo et al. 2008; Burderi et al. 2009), and spin–orbit coupling in the companion star (Hartman et al. 2008, 2009). While the latter depends on the companion star, and may vary from source to source, the former should operate in all AMXPs (see also Patruno 2017; Sanna et al. 2017c), including Swift J1756. The spin-down luminosity impinging on the companion star can be estimated as Equation (10) where ${\dot{E}}_{\mathrm{abl}}$ is the ablation luminosity, RL2 is the Roche lobe radius of the companion (Eggleton 1983), and a the binary separation. The irradiation fraction is $f={\dot{E}}_{\mathrm{abl}}/{\dot{E}}_{\mathrm{sd}}$, which, accounting for the range of allowed neutron star and companion masses, evaluates to f = 0.15%–0.35%. The associated mass loss for the companion is given by Equation (11) such that, assuming an efficiency of η = 100%, ${\dot{M}}_{C}\,\sim -3\times {10}^{-10}\,{M}_{\odot }$ yr−1. The effect of this mass loss on the orbital period follows through the relation (Frank et al. 2002) Equation (12) giving a period derivative due to mass loss of ${\dot{P}}_{b,\mathrm{ML}}\,=5\times {10}^{-12}$ s s−1. This value is well above our limit on the period derivative. Hence, in order for this mechanism to be consistent with our observations of Swift J1756, the efficiency at which the companion star converts the incident luminosity into mass loss must be η < 15%. This value is very different from the 40% required in SAX J1808.4–3658 (Patruno et al. 2016) and is instead in line with the <5% efficiency determined for IGR J00291+5934 (Patruno 2017). This work was supported by NASA through the NICER mission and the Astrophysics Explorers Program, and made use of data and software provided by the High Energy Astrophysics Science Archive Research Center (HEASARC). P.B. was supported by an NPP fellowship at NASA Goddard Space Flight Center. D.A. acknowledges support from the Royal Society.

Bult, Peter↗

CSI Flight Computer System and experimental test results

This paper describes the CSI Computer System (CCS) and the experimental tests performed to validate its functionality. This system is comprised of two major components: the space flight qualified Excitation and Damping Subsystem (EDS) which performs controls calculations; and the Remote Interface Unit (RIU) which is used for data acquisition, transmission, and filtering. The flight-like RIU is the interface between the EDS and the sensors and actuators positioned on the particular structure under control. The EDS and RIU communicate over the MIL-STD-1553B, a space flight qualified bus. To test the CCS under realistic conditions, it was connected to the Phase-0 CSI Evolutionary Model (CEM) at NASA Langley Research Center. The following schematic shows how the CCS is connected to the CEM. Various tests were performed which validated the ability of the system to perform control/structures experiments.

Sparks, Dean W., Jr.↗

Systems Engineering Metrics: Organizational Complexity and Product Quality Modeling

Innovative organizational complexity and product quality models applicable to performance metrics for NASA-MSFC's Systems Analysis and Integration Laboratory (SAIL) missions and objectives are presented. An intensive research effort focuses on the synergistic combination of stochastic process modeling, nodal and spatial decomposition techniques, organizational and computational complexity, systems science and metrics, chaos, and proprietary statistical tools for accelerated risk assessment. This is followed by the development of a preliminary model, which is uniquely applicable and robust for quantitative purposes. Exercise of the preliminary model using a generic system hierarchy and the AXAF-I architectural hierarchy is provided. The Kendall test for positive dependence provides an initial verification and validation of the model. Finally, the research and development of the innovation is revisited, prior to peer review. This research and development effort results in near-term, measurable SAIL organizational and product quality methodologies, enhanced organizational risk assessment and evolutionary modeling results, and 91 improved statistical quantification of SAIL productivity interests.

Mog, Robert A.↗

Turbomachinery Airfoil Design Optimization Using Differential Evolution

An aerodynamic design optimization procedure that is based on a evolutionary algorithm known at Differential Evolution is described. Differential Evolution is a simple, fast, and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems, including highly nonlinear systems with discontinuities and multiple local optima. The method is combined with a Navier-Stokes solver that evaluates the various intermediate designs and provides inputs to the optimization procedure. An efficient constraint handling mechanism is also incorporated. Results are presented for the inverse design of a turbine airfoil from a modern jet engine and compared to earlier methods. The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated. Substantial reductions in the overall computing time requirements are achieved by using the algorithm in conjunction with neural networks.

Madavan, Nateri K.↗