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Numerical simulation of conservation laws

A new numerical framework for solving conservation laws is being developed. This new approach differs substantially from the well established methods, i.e., finite difference, finite volume, finite element and spectral methods, in both concept and methodology. The key features of the current scheme include: (1) direct discretization of the integral forms of conservation laws, (2) treating space and time on the same footing, (3) flux conservation in space and time, and (4) unified treatment of the convection and diffusion fluxes. The model equation considered in the initial study is the standard one dimensional unsteady constant-coefficient convection-diffusion equation. In a stability study, it is shown that the principal and spurious amplification factors of the current scheme, respectively, are structurally similar to those of the leapfrog/DuFort-Frankel scheme. As a result, the current scheme has no numerical diffusion in the special case of pure convection and is unconditionally stable in the special case of pure diffusion. Assuming smooth initial data, it will be shown theoretically and numerically that, by using an easily determined optimal time step, the accuracy of the current scheme may reach a level which is several orders of magnitude higher than that of the MacCormack scheme, with virtually identical operation count.

Chang, Sin-Chung↗

Stakeholder Support for Wildlife Conservation Funding Policies

State wildlife management agencies in the United States have depended on a “user-pay” funding model for conservation efforts that relies on revenue from hunting license sales and a federal excise tax on firearms, ammunition, and archery equipment. Declines in hunting participation, however, jeopardize sustainability of the current funding model. Ensuring support among stakeholders for wildlife management and conservation may require expanding sources of funding and incorporating the perspectives and values of a diversifying constituency into decision making processes. We used a web-based survey of wildlife-associated recreationists in Michigan, USA to evaluate support for a range of conservation funding policies. Respondents self-identified primarily as hunters (n = 2,558) or wildlife watchers (n = 942). We used binary logistic regression to evaluate support for four conservation funding policy options: state sales tax, lottery proceeds, extractive industry revenue, and a user-based tax on outdoor gear (i.e., “backpack tax”). Determinants of support varied by type of policy and stakeholder characteristics. We found no statistically significant differences between hunters and wildlife watchers in their support for conservation funding policies when accounting for other variables such as wildlife value orientations, engagement in stewardship behaviors, age, and gender. The industry-based policy achieved the greatest level of approval, while the backpack tax had the lowest. Respondents were mixed in their support of the sales tax and lottery proceeds options. Cluster analysis revealed three homogenous groups related to conservation funding policies: “strong support,” “mixed/opposed,” and “anti-backpack tax.” Clusters differed in their support for conservation funding policies and on psychological and demographic variables. The “strong support” and “anti-backpack tax” groups differed in their levels of stewardship engagement, knowledge of conservation funding mechanisms, and support for the backpack tax option. The “mixed-opposed” group tended to be older, less educated, and less likely to be a member of a conservation organization. Results suggest support for conservation funding differs by policy type and social and psychological characteristics of stakeholders. Based on differences in policy support revealed in this study, we suggest a multi-tiered approach to funding conservation and building on support among wildlife stakeholders to mitigate the looming funding crisis for state wildlife agencies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant

Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.

(sub)stoichiometric shifting↗

A three-dimensional, time-dependent model of Mobile Bay

A three-dimensional, time-variant mathematical model for momentum and mass transport in estuaries was developed and its solution implemented on a digital computer. The mathematical model is based on state and conservation equations applied to turbulent flow of a two-component, incompressible fluid having a free surface. Thus, bouyancy effects caused by density differences between the fresh and salt water, inertia from thare river and tidal currents, and differences in hydrostatic head are taken into account. The conservation equations, which are partial differential equations, are solved numerically by an explicit, one-step finite difference scheme and the solutions displayed numerically and graphically. To test the validity of the model, a specific estuary for which scaled model and experimental field data are available, Mobile Bay, was simulated. Comparisons of velocity, salinity and water level data show that the model is valid and a viable means of simulating the hydrodynamics and mass transport in non-idealized estuaries.

Pitts, F. H.↗

"Hall" transport of liquid crystal solitons in Couette flow

Topology establishes a unifying framework for a diverse range of scientific areas including particle physics, cosmology, and condensed matter physics. One of the most fascinating manifestations of topology in the context of condensed matter is the topological Hall effect, and its relative: the Skyrmion Hall effect. Skyrmions are stable vortex-like spin configurations in certain chiral magnets, and when subject to external electric currents can drift in the transverse direction to the current. These quasi-particles are characterised by a conserved topological charge which in the Skyrmion Hall effect plays the role of electric charges in the ordinary Hall effect. Recently, it has been shown that liquid crystals endowed with chiral properties serve as an ideal testbed for the fundamental investigation of topological solitons, including their two- and three-dimensional realisations. Here, we show experimentally and numerically that three-dimensional solitons aka "torons" exhibit a Hall-like effect when driven by shear flows: the torons are deflected in the direction perpendicular to the shear plane. The experimental results are rationalised in terms of the dynamic Ericksen-Leslie equations, which predict the emergence of the transverse component of the net mass flow, the magnitude of which scales as the 3rd power of the shear rate. The perturbation analysis highlights an interplay of the viscous and chiral elastic torques as the mechanism for the emergence of net transverse currents. Numerical simulations demonstrate, however, that torons are not merely dragged by the flow but move with their own transverse speed, much larger than the average flow velocity in the transverse direction. Our findings may enable responsive microfluidic applications relying on soft topological solitons.

FOS: Physical sciences↗

Comprehensive Non-Destructive Conservation Documentation of Lunar Samples Using High-Resolution Image-Based 3D Reconstructions and X-Ray CT Data

Established contemporary conservation methods within the fields of Natural and Cultural Heritage encourage an interdisciplinary approach to preservation of heritage material (both tangible and intangible) that holds "Outstanding Universal Value" for our global community. NASA's lunar samples were acquired from the moon for the primary purpose of intensive scientific investigation. These samples, however, also invoke cultural significance, as evidenced by the millions of people per year that visit lunar displays in museums and heritage centers around the world. Being both scientifically and culturally significant, the lunar samples require a unique conservation approach. Government mandate dictates that NASA's Astromaterials Acquisition and Curation Office develop and maintain protocols for "documentation, preservation, preparation and distribution of samples for research, education and public outreach" for both current and future collections of astromaterials. Documentation, considered the first stage within the conservation methodology, has evolved many new techniques since curation protocols for the lunar samples were first implemented, and the development of new documentation strategies for current and future astromaterials is beneficial to keeping curation protocols up to date. We have developed and tested a comprehensive non-destructive documentation technique using high-resolution image-based 3D reconstruction and X-ray CT (XCT) data in order to create interactive 3D models of lunar samples that would ultimately be served to both researchers and the public. These data enhance preliminary scientific investigations including targeted sample requests, and also provide a new visual platform for the public to experience and interact with the lunar samples. We intend to serve these data as they are acquired on NASA's Astromaterials Acquisistion and Curation website at http://curator.jsc.nasa.gov/. Providing 3D interior and exterior documentation of astromaterial samples addresses the increasing demands for accessability to data and contemporary techniques for documentation, which can be realized for both current collections as well as future sample return missions.

Blumenfeld, E. H.↗

Wake Vortex Tracking Using a 35 GHz Pulsed Doppler Radar

A 35 GHz, pulsed-Doppler radar system has been designed and assembled for wake vortex detection and tracking in low visibility conditions. Aircraft wake vortices continue to be an important factor in determining safe following distances or spacings for aircraft in the terminal area. Currently, under instrument meteorological conditions (IMC), aircraft adhere to conservative, fixed following-distance guidelines based primarily on aircraft weight classifications. When ambient conditions are such that vortices will either drift or dissipate, leaving the flight corridor clear, the prescribed spacings are unnecessarily long and result in decreased airport throughput. There is a potential for significant airport efficiency improvement, if a system can be employed to aid regulators and pilots in setting safe and efficient following distances based on airport conditions. The National Aeronautics and Space Administration (NASA), the Federal Aviation Agency, and Volpe National Transportation Systems Center have promoted and worked to develop systems that would increase airport capacity and provide for safe reductions in aircraft separation. The NASA Aircraft Vortex Spacing System (AVOSS), a wake vortex spacing system that can provide dynamic adjustment of spacings based on real-time airport weather conditions, has demonstrated that Lidar systems can be successfully used to detect and track vortices in clear air conditions. To fill the need for detection capability in low-visibility conditions, a 35 GHz, pulsed-Doppler radar system is being investigated for use as a complimentary, low-visibility sensor for wake vortices. The radar sensor provides spatial and temporal information similar to that provided by Lidar, but under weather conditions that a Lidar cannot penetrate. Currently, we are analyzing the radar design based upon the data and experience gained during the wake vortex Lidar deployment with AVOSS at Dallas/Fort Worth International Airport. As part of this study, two numerical models were utilized in system simulations. The results of this study improve our understanding of the method of detection, resolution requirements for range and azimuth, pulse compression, and performance prediction. Simulations applying pulse compression techniques show that detection is good in heavy fog to greater than 2000 m. Both compressed and uncompressed short pulses show the vortex structure. To explore operational challenges, siting and scanning strategies were also analyzed. Simulation results indicate that excellent wake vortex detection, tracking and classification is possible in drizzle (+15 dBZ) and heavy fog (- 13 dBZ) using short pulse techniques (<99ns) at ranges on the order of 900 m, with a modest power of 500 W output. At 1600 m, detection can be expected at reflectivities as low as -13 dBZ (heavy fog). The radar system, as designed and built, has the potential to support field studies of a wake vortex spacing system in low-visibility conditions ranging from heavy fog to rain, when sited within 2000m of the flight path.

Neece, Robert T.↗

Helicity, spin, and infra-zilch of light: A Lorentz covariant formulation

Highlights: • Spin and orbital parts of angular momentum. • The helicity tensor contains the helicity, spin and infra-zilch currents. • The helicity tensor is a Noether current for a duality-symmetric action. • Symmetry generator for the helicity tensor. • The helicity tensor is conserved in Lorenz gauge. In this paper, a novel conserved Lorentz covariant tensor, termed the helicity tensor, is introduced in Maxwell theory. The conservation of the helicity tensor expresses the conservation laws contained in the helicity array, introduced by Cameron et al. (2012), including helicity, spin, as well as the spin-flux or infra-zilch. The Lorentz covariance of the helicity tensor is in contrast to previous formulations of the helicity hierarchy of conservation laws, which required the non-Lorentz covariant transverse gauge. The helicity tensor is shown to arise as a Noether current for a variational symmetry of a duality-symmetric Lagrangian for Maxwell theory. This symmetry transformation generalizes the duality symmetry and includes the symmetry underlying the conservation of the spin part of the angular momentum.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Conservation of angular momentum in ultrafast spin dynamics

The total angular momentum of a closed system is a conserved quantity, which should remain constant in time for any excitation experiment once the pumping signal has been extinguished. Such conservation, however, is never satisfied in practice in any real-time first-principles description of the demagnetization process. Furthermore, there is growing experimental evidence that the same takes place in experiments. The missing angular momentum is usually associated to lattice vibrations, which are not measured experimentally and are never considered in real-time simulations. Here, in this study, we critically analyze the issue and conclude that current state-of-the-art simulations violate angular momentum conservation already at the electronic level of description. This shortcoming originates from an oversimplified description of the spin-orbit coupling, which includes atomic contributions but neglects completely that of itinerant electrons. We corroborate our findings with time-dependent simulations using model tight-binding Hamiltonians, and show that indeed such conservation can be reintroduced by an appropriate choice of spin-orbit coupling. The consequences of our findings on recent experiments are also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Runaway electron deconfinement in SPARC and DIII-D by a passive 3D coil

The operation of a 3D coil—passively driven by the current quench (CQ) loop voltage—for the deconfinement of runaway electrons (REs) is modeled for disruption scenarios in the SPARC and DIII-D tokamaks. Nonlinear magnetohydrodynamic (MHD) modeling is carried out with the NIMROD code including time-dependent magnetic field boundary conditions to simulate the effect of the coil. Further modeling in some cases uses the ASCOT5 code to calculate advection and diffusion coefficients for REs based on the NIMROD-calculated fields, and the DREAM code to compute the runaway evolution in the presence of these transport coefficients. Compared with similar modeling in Tinguely et al (2021 Nucl. Fusion 61 124003), considerably more conservative assumptions are made with the ASCOT5 results, zeroing low levels of transport, particularly in regions in which closed flux surfaces have reformed. Of three coil geometries considered in SPARC, only the n = 1 coil is found to have sufficient resonant components to suppress the runaway current growth. Without the new conservative transport assumptions, full suppression of the RE current is maintained when the thermal quench MHD is included in the simulation or when the RE current is limited to 250kA, but when transport in closed flux regions is fully suppressed, these scenarios allow RE beams on the order of 1–2 MA to appear. Additional modeling is performed to consider the effects of the close ideal wall. In DIII-D, the CQ is modeled for both limited and diverted equilibrium shapes. In the limited shape, the onset of stochasticity is found to be insensitive to the coil current amplitude and governed largely by the evolution of the safety-factor profile. In both devices, prediction of the q-profile evolution is seen to be critical to predicting the later time effects of the coil.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fyn–Saracatinib Complex Structure Reveals an Active State-like Conformation

Fyn is a Src-family tyrosine kinase implicated in synaptic dysfunction and neuroinflammation across multiple neurodegenerative disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). Saracatinib (AZD0530) is a potent Src-family inhibitor that has been explored as a repurposed therapeutic; however, its clinical utility is limited by poor kinase selectivity caused by high sequence conservation within Src-family ATP-binding sites. Here, we combine surface plasmon resonance (SPR) and X-ray crystallography to define saracatinib recognition by the Fyn kinase domain (KD). SPR single-cycle kinetics shows that saracatinib binds the isolated Fyn KD and full-length Fyn with low-nanomolar affinity, whereas dasatinib binds with subnanomolar affinity and markedly slower dissociation. We determined the crystal structure of the Fyn KD-saracatinib complex at 2.22 Å resolution. The kinase adopts an active-like conformation with the DFG motif and αC-helix in the ‘in’ state and a conserved β3 αC Lys-Glu salt bridge. Saracatinib occupies the adenine and ribose pockets, and engages the hinge through direct and water-mediated hydrogen bonding while complementing a hydrophobic back pocket by van der Waals contacts. Comparison with reported saracatinib-bound structures of other kinases suggests that the active-state geometry observed for Fyn creates a pocket not observed in inactive-like complexes, providing a structural handle for designing Fyn-selective inhibitors. Comparison with all saracatinib-bound kinase co-structures currently available in the PDB (ALK2 and PKMYT1) indicates a conserved monodentate hinge binding mode but kinase-dependent αC-helix conformations, providing a structural rationale for designing Fyn-selective analogues.

AZD0530↗

Satellite remote sensing for environmental sustainable development goals: A review of applications for terrestrial and marine protected areas

With few years left to achieve the vital United Nations Sustainable Development Goals (SDGs), member nations must urgently leverage technological advancements in environmental monitoring to succeed. Remote sensing now provides decades of global observations at a variety of spatio-temporal scales and a litany of data products to guide comprehensive measures for climate action, and aquatic and terrestrial biota preservation. Protected areas, such as national parks and wildlife preserves, represent largely untapped resources for both applying robust conservation measures and testing ambitious new approaches to sustainable development that could jumpstart the much-needed adoption of strategies to efficiently pursue global sustainability. This review summarizes recent demonstrated utilities of remotely sensed data applied to protected areas for research related to SDG goals 13, 14, and 15: “Climate Action”, “Life below Water”, and “Life on Land”. We identify successful uses of such data for each SDG, identify areas for improvement, and provide recommendations from the literature on how to expand what others have done to achieve lofty goals with global impact. We demonstrate that remote sensing provides a valuable tool for achieving SDGs as it facilitates monitoring vegetation health, water quality and condition, and climate variables at large spatial and fine temporal scales, while also evaluating the effectiveness of management and conservation practices. Issues remain, however, in that there is currently no reference from which to relate goal progress to human livelihoods. Further, the current relationship between remotely sensed indices and ecological services that determine sustainable development omit steps that would establish this connection.

54 ENVIRONMENTAL SCIENCES↗

Deciphering coulombic loss in lithium-ion batteries and beyond

Lithium-ion batteries are pivotal for modern energy storage, yet accurately predicting their lifespan remains a critical challenge. While descriptors like coulombic efficiency are widely used to assess battery longevity, the unclear physical origins of coulombic losses cause semi-quantitative correlation with capacity, complicating battery development. Here, we combine high-precision leakage current and open-circuit-voltage measurements with charge conservation principles to explore microscopic charge consumptions at electrode-electrolyte interfaces across diverse chemistries. We demonstrate that coulombic loss arises from a synergy between local charge neutrality and global charge compensation, reconciling its quantitative correlation to capacity. Contrary to conventional assumptions equating coulombic loss with irreversible capacity loss, this framework resolves systematic overestimations and paradoxical phenomena in existing chemistries. Our findings establish physics-informed criteria for accelerated lifespan evaluation and guide rational design of long-life lithium-ion batteries and beyond.

Batteries↗

Composite Analysis for Low-Level Waste Disposal in the Hanford Site Central Plateau (FY 2020) (Rev. 2)

This document provides an updated Hanford Site composite analysis (CA). A Hanford Site CA was prepared and issued in 1998 (PNNL-11800) with an addendum provided in 2002 (PNNL-11800 Addendum 1). The CA was approved in 2002 (Frei, 2002) and has been maintained (DOE/RL-2000-29 and subsequent revisions) to support low-level waste disposal performance assessments (PAs) and disposal authorizations for facilities at the Hanford Site, including the following: Continued operation of the Environmental Restoration Disposal Facility (ERDF) and the 200 East and 200 West Low-Level Burial Grounds; Construction of the Integrated Disposal Facility (IDF); Forthcoming closure of tank residual waste systems such as Waste Management Area (WMA) C. The CA maintenance program resulted in a determination in 2015 (DOE/RL-2015-66) that the Hanford Site CA needed an update for the following reasons: While the initial Hanford Site CA has been maintained since 2001, the accumulation of basis changes reported in the annual summary reports over the succeeding 14 years merit evaluation in an updated analysis; The U.S. Department of Energy (DOE) Headquarters requested in a memorandum in 2015 (Gilbertson and Marcinowski, 2015) that “as soon as the relevant PAs are complete, the CA will be revised to account for all of the new information.” This updated Hanford Site CA accounts for the following new information: 1. Inclusion of a detailed Hanford Site baseline disposition that projects remedial activities through site closure. There have been significant changes through decision making in the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA) process that were not available when the original CA was produced; 2. Inclusion of an updated inventory basis, new modeling capabilities, and new decisions reached in the associated record of decision (ROD) that was provided by issuance of DOE/EIS-0391 in fiscal year (FY) 2013. Development of a Hanford Site groundwater model from the baseline provided in a technical transfer of models for the Final Tank Closure and Waste Management Environmental Impact Statement (DOE/EIS-0391) commenced in FY 2014 and resulted in the plateau-to-river (P2R) groundwater flow model that is used in this updated Hanford Site CA; 3. Accounting for pump and treat systems, which were not evaluated in the initial CA. Pump and treat systems have had significant impact on groundwater flow system behavior, contaminant transport, and contaminant removal from Hanford Site groundwater. This process is accounted for in the use of the P2R model for this updated Hanford Site CA; 4. Inclusion of water-level data collected since the initial CA was completed. Data collected as the unconfined aquifer water levels continue to recede since the cessation of large liquid discharges in the late 1990s have led to marked improvement in understanding of the flow system for future conditions, particularly regarding northward flow potential in the critical Gable Gap area. The calibration in the latest version of the P2R model accounts for this information; 5. Inclusion of results from the revised ERDF PA completed in 2013 (WCH-5209) that account for updated inventory and expansion of the ERDF facility to about twice the size that was evaluated in the original CA; 6. Use of updated geoframeworks to provide the structural basis for numerical fate and transport models in the groundwater pathway of this updated CA. The geologic basis for groundwater models has continued to improve with additional data collection and interpretation with the creation and maintenance of the Hanford South Geoframework and the Central Plateau Vadose Zone Geoframework tools; 7. Incorporation of updated tank residual inventory estimates. Tank residual inventory estimates have improved with the incorporation of tank retrieval inventory data for those tanks that have completed retrieval. The CA inventory data package includes this updated information; 8. Incorporation of WMA C PA results. Two additional PAs for tank farm closure decisions are in preparation during the period required to prepare an updated Hanford Site CA: WMA C (FY 2016) and WMA A-AX (in preparation). The WMA C PA results are incorporated into the updated Hanford Site CA, and its grouted residuals model is used as the basis for a release model to account for the other tank farm systems modeling in this updated CA; 9. An update to the IDF PA was submitted in FY 2017 and has been reviewed and approved. The results of the IDF PA are incorporated into this updated CA; 10. Updated risk assessment scenarios. The risk assessment scenarios currently in use for Hanford Site CERCLA and Resource Conservation and Recovery Act of 1976 (RCRA) analyses differ from those evaluated in the initial Hanford Site CA. The representative person exposure scenario evaluated in this updated Hanford Site CA is consistent with recent PAs and CERCLA and RCRA analyses as the Hanford Site. This updated Hanford Site CA provides the following: A comparison of the updated Hanford Site CA all-pathway dose results with the performance measures during the compliance period, which is assumed to begin with site closure in calendar 2070 with the last scheduled disposal action and continue for 1,000 years postclosure (to calendar year 3069); A comparison of Hanford Site CA all-pathway dose results with the performance measures during the postcompliance period to address potential peaks beyond the compliance period. This is accomplished by evaluating dose in the period for 9,000 years following the compliance period (i.e., from calendar year 3070 to 12070).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Use Case-Informed Framework for Utility Cloud Migration

This white paper presents a comprehensive methodology for assessing utilities’ cloud postures and frameworks. It aims to produce a roadmap and strategy for a cloud-enabled grid future, providing guidance for integrators, asset owners, and operators. Instead of offering a yes or no answer for cloud implementation, this framework offers strategic guidance on responsibly preparing for and deploying cloud solutions. This paper delves into cloud-service models pertinent to the electric sector, dissecting the shared responsibility model and elucidating what on-premise infrastructure as a service (IaaS), platform as a service (PaaS), and software as a service (SaaS) entail. A pivotal consideration within the context of the shared responsibility model is the allocation of responsibility for foundational security aspects—a decision that will be informed by a comprehensive risk assessment. The ensuing discussion will present a checklist of certifications necessary for a secure cloud transition, equipping utilities with the knowledge to navigate this digital transformation with confidence and with a strategic roadmap. Furthermore, the paper outlines gaps in understanding the U.S. government’s role in shaping technology development and responsible use. Its purpose is to aid decision-making by offering support for risk-informed solutions that benefit those managing assets and operating in the cloud environment. The primary objective is to enhance the resilience and future readiness of a decarbonized electric grid, with cloud solutions as one viable option. The paper synthesizes information on current and future grid architectures and applications, considering both conservative and progressive energy transitions, along with scalable and distributed computing considerations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Genomic Metrics Applied to Rhizobiales ( Hyphomicrobiales ): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

59 BASIC BIOLOGICAL SCIENCES↗

Spitzer Variability Properties of Low-gravity L Dwarfs

We present Spitzer Space Telescope variability monitoring observations of three low-gravity L dwarfs with previous detections of variability in the near-IR: 2MASS J0045+16, 2MASS J0501–00, and 2MASS J1425–36. We detect significant periodic variability in two of our targets, 2MASS J0045+16 and 2MASS J0501–00. We do not detect variability in 2MASS J1425–36. Combining our new rotation periods with rotational velocities, we calculate inclination angles of 22° ± 1°, 60{sub -8}{sup +13°}, and 52{sub -13}{sup +19°} for 2MASS J0045+16, 2MASS J0501–00, and 2MASS J1425–36, respectively. Our three new objects are consistent with the tentative relations between inclination, amplitude, and color anomaly previously reported. Objects with the highest variability amplitudes are inclined equator on, while the maximum observed amplitude decreases as the inclination angle decreases. We also find a correlation between the inclination angle and (J–K){sub 2MASS} color anomaly for the sample of objects with measured inclinations. Compiling the entire sample of brown dwarfs with Spitzer variability detections, we find no enhancement in amplitude for young, early-L dwarfs compared to the field dwarf population. We find a possible enhancement in amplitude of low-gravity late-L dwarfs at 4.5 μm. We do not find a correlation between amplitude ratio and spectral type for field dwarfs or for the young population. Finally, we compile the rotation periods of a large sample of brown dwarfs with ages 1 Myr–1 Gyr and compare the rotation rates predicted by evolutionary models assuming angular momentum conservation. We find that the rotation rates of the current sample of brown dwarfs fall within the expected range set by evolutionary models and breakup limits.

79 ASTRONOMY AND ASTROPHYSICS↗

A generalization of the method of harmonic balance

A procedure is provided for generalizing the method of harmonic balance to obtain higher-order approximations to the periodic solutions of differential equations for two systems, one a conservative system and the other nonconservative. The procedure is currently being applied to investigate the possible solution behaviors of singular, nonlinear oscillators, where the usual perturbation methods do not work.

Mickens, R. E.↗