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At least 145 records · Page 8

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.

59 BASIC BIOLOGICAL SCIENCES↗

A simple model linking galaxy and dark matter evolution

We construct a simple phenomenological model for the evolving galaxy population by incorporating predefined baryonic prescriptions into a dark matter hierarchical merger tree. The model is based on the simple gas-regulator model introduced by Lilly et al., coupled with the empirical quenching rules of Peng et al. The simplest model already does quite well in reproducing, without re-adjusting the input parameters, many observables, including the main sequence sSFR-mass relation, the faint end slope of the galaxy mass function, and the shape of the star forming and passive mass functions. Similar to observations and/or the recent phenomenological model of Behroozi et al., which was based on epoch-dependent abundance-matching, our model also qualitatively reproduces the evolution of the main sequence sSFR(z) and SFRD(z) star formation rate density relations, the M{sub s} – M{sub h} stellar-to-halo mass relation, and the SFR – M{sub h} relation. Quantitatively the evolution of sSFR(z) and SFRD(z) is not steep enough, the M{sub s} – M{sub h} relation is not quite peaked enough, and, surprisingly, the ratio of quenched to star forming galaxies around M* is not quite high enough. We show that these deficiencies can simultaneously be solved by ad hoc allowing galaxies to re-ingest some of the gas previously expelled in winds, provided that this is done in a mass-dependent and epoch-dependent way. These allow the model galaxies to reduce an inherent tendency to saturate their star formation efficiency, which emphasizes how efficient galaxies around M* are in converting baryons into stars and highlights the fact that quenching occurs at the point when galaxies are rapidly approaching the maximum possible efficiency of converting baryons into stars.

79 ASTRONOMY AND ASTROPHYSICS↗

Algorithmic Patterns for $$\mathcal {H}$$-Matrices on Many-Core Processors

In this work, we consider the reformulation of hierarchical ( \(\mathcal {H}\) ) matrix algorithms for many-core processors with a model implementation on graphics processing units (GPUs). \(\mathcal {H}\) matrices approximate specific dense matrices, e.g., from discretized integral equations or kernel ridge regression, leading to log-linear time complexity in dense matrix–vector products. The parallelization of \(\mathcal {H}\) matrix operations on many-core processors is difficult due to the complex nature of the underlying algorithms. While previous algorithmic advances for many-core hardware focused on accelerating existing \(\mathcal {H}\) matrix CPU implementations by many-core processors, we here aim at totally relying on that processor type. As main contribution, we introduce the necessary parallel algorithmic patterns allowing to map the full \(\mathcal {H}\) matrix construction and the fast matrix–vector product to many-core hardware. In this work, crucial ingredients are space filling curves, parallel tree traversal and batching of linear algebra operations. The resulting model GPU implementation hmglib is the, to the best of the authors knowledge, first entirely GPU-based Open Source \(\mathcal {H}\) matrix library of this kind. We investigate application examples as present in kernel ridge regression, Gaussian Process Regression and kernel-based interpolation. In this context, an in-depth performance analysis and a comparative performance study against a standard multi-core CPU \(\mathcal {H}\) matrix library highlights profound speedups of our many-core parallel approach.

97 MATHEMATICS AND COMPUTING↗

Learning the stable and metastable phase diagram to accelerate the discovery of metastable phases of boron

Boron, an element of captivating chemical intricacy, has been surrounded by controversies ever since its discovery in 1808. The complexities of boron stem from its unique position between metals and insulators in the Periodic Table. Recent computational studies have shed light on some of the stable boron allotropes. However, the demand for multifunctionality necessitates the need to go beyond the stable phases into the realm of metastability and explore the potentially vast but elusive metastable phases of boron. Traditional search for stable phases of materials has focused on identifying materials with the lowest enthalpy. Here, we introduce a workflow that uses reinforcement learning coupled with decision trees, such as Monte Carlo tree search, to search for stable and metastable boron phases, with enthalpy as the objective. We discover new boron metastable phases and construct a phase diagram that locates their phase space (T, P) at different levels of metastability (ΔG) from the ground state and provides useful information on the domains of relative stability of the various stable and metastable boron phases.

42 ENGINEERING↗

Contrasting responses to climate change at Himalayan treelines revealed by population demographics of two dominant species

Abstract Alpine treelines are expected to shift upward due to recent climate change. However, interpretation of changes in montane systems has been problematic because effects of climate change are frequently confounded with those of land use changes. The eastern Himalaya, particularly Langtang National Park, Central Nepal, has been relatively undisturbed for centuries and thus presents an opportunity for studying climate change impacts on alpine treeline uncontaminated by potential confounding factors. We studied two dominant species, Abies spectabilis (AS) and Rhododendron campanulatum (RC) , above and below the treeline on two mountains. We constructed 13 transects, each spanning up to 400 m in elevation, in which we recorded height and state (dead or alive) of all trees, as well as slope, aspect, canopy density, and measures of anthropogenic and animal disturbance. All size classes of RC plants had lower mortality above treeline than below it, and young RC plants (<2 m tall) were at higher density above treeline than below. AS shows little evidence of a position change from the historic treeline, with a sudden extreme drop in density above treeline compared to below. Recruitment, as measured by size–class distribution, was greater above treeline than below for both species but AS is confined to ~25 m above treeline whereas RC is luxuriantly growing up to 200 m above treeline. Synthesis . Evidence suggests that the elevational limits of RC have shifted upward both because (a) young plants above treeline benefited from facilitation of recruitment by surrounding vegetation, allowing upward expansion of recruitment, and (b) temperature amelioration to mature plants increased adult survival. We predict that the current pure stand of RC growing above treeline will be colonized by AS that will, in turn, outshade and eventually relegate RC to be a minor component of the community, as is the current situation below the treeline.

54 ENVIRONMENTAL SCIENCES↗

On the differential representation and color-kinematics duality of AdS boundary correlators

The AdS boundary correlators and their dual correlation functions of boundary operators have been the main dynamic observables of the holographic duality relating a bulk AdS theory and a boundary conformal field theory. We show that tree-level AdS boundary correlators for generic states can be expressed as nonlocal differential operators of a certain structure acting on contact Witten diagrams. We further write the boundary correlators in a form that is very similar to flat space amplitudes, with Mandelstam variables replaced by certain combinations of single-state conformal generators, prove that all tree-level AdS boundary correlators have a differential representation, and detail the conversion of such differential expressions to position space. We illustrate the construction through the computation of the boundary correlators of scalars coupled to gluons and gravitons; when converted to position space, they reproduce known results. Color-kinematics duality and BCJ relations can be defined in analogy with their flat space counterparts, and are respected by the scalar correlators with a gluon exchange. We also discuss potential approaches to the double copy and find that its direct generalization may require nontrivial extensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

One-loop corrections from higher dimensional tree amplitudes

We show how one-loop corrections to scattering amplitudes of scalars and gauge bosons can be obtained from tree amplitudes in one higher dimension. Starting with a complete tree-level scattering amplitude of n + 2 particles in five dimensions, one assumes that two of them cannot be “detected” and therefore an integration over their LIPS is carried out. The resulting object, function of the remaining n particles, is taken to be four-dimensional by restricting the corresponding momenta. We perform this procedure in the context of the tree-level CHY formulation of amplitudes. The scattering equations obtained in the procedure coincide with those derived by Geyer et al. from ambitwistor constructions and recently studied by two of the authors for bi-adjoint scalars. They have two sectors of solutions: regular and singular. We prove that the contribution from regular solutions generically gives rise to unphysical poles. However, using a BCFW argument we prove that the unphysical contributions are always homogeneous functions of the loop momentum and can be discarded. We also show that the contribution from singular solutions turns out to be homogeneous as well.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Machine Learning an Ab-Initio Based Bond-Order Potential for Bismuthene

Bismuthene is a heavy 2D material whose strong spin–orbit coupling and recently observed single-element ferroelectricity have intensified interest in its structural, vibrational, and transport properties. Accurate modeling of these behaviors requires a short-range interatomic potential that can reproduce the underlying bonding physics at a fraction of the computational cost of first-principles methods. However, such a potential is currently unavailable. Here, in this work, we construct a Tersoff bond-order potential for β-bismuthene using a reinforcement-learning framework that integrates a continuous Monte Carlo Tree Search with a simplex-based local optimizer. The optimized parameter sets reproduce first-principles lattice constants, cohesive energy, the equation of state, elastic constants, and phonon dispersion. We validate the models by performing thermal-conductivity calculations and uniaxial fracture simulations our findings confirm the reliability of the resulting models across multiple thermomechanical regimes. Comparison of the three best solutions reveals how differences in pairwise interactions, angular terms, and bond-order behavior govern phonon features and mechanical responses. We demonstrate an interpretable and computationally efficient potential for bismuthene and demonstrate a general reinforcement-learning strategy for developing bond-order models in emerging 2D materials.

deformation↗

Dynamics of fragments and associated phenomena in heavy-ion collisions using a modified secondary algorithm

We discuss the stability of fragments identified by secondary algorithms used to construct fragments within quantum molecular dynamics model. For this purpose we employ three different algorithms for fragment identification. 1) The conventional minimum spanning tree (MST) method based on the spatial correlations, 2) an improved version of MST with additional binding energy constraints of cold nuclear matter, 3) and that of hot matter. We find significant role of thermal binding energies over cold matter binding energies. Significant role is observed for fragment multiplicities and stopping of fragments. Whereas insignificant effect is observed on fragment’s flow.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

2022 Swainson Hawk Summary Report

This summary report, prepared by Condor Country Consulting Inc. (CCCI), covers all construction monitoring of the Swainson’s hawk (Buteo swainsoni, SWHA) nest that occurred from April 2022 to July 2022 at the Sandia National Laboratories, California (SNL/CA). SNL/CA personnel first observed the SWHA pair near the pine tree along East Avenue that contained last year’s nest on April 19th, 2022. SWHA are a threatened species in the state of California and require a quarter-mile non-disturbance buffer. SNL/CA received approval from the California Department of Fish and Wildlife (CDFW) to continue work within the buffer area with a biological monitor on site to observe the SWHA for construction related disturbances. Monitoring began on April 20th, 2022 and concluded on July 1st, 2022.

99 GENERAL AND MISCELLANEOUS↗

Strong CP and flavor in multi-Higgs theories

We introduce a class of multi-Higgs doublet extensions of the Standard Model that solve the strong problem with profound consequences for the flavor sector. The Yukawa matrices are constrained to have many zero entries by a “Higgs-flavor” symmetry, , that acts on Higgs and quark fields. The violation of both and occurs in the Higgs mass matrix so that, for certain choices of charges, the strong parameter is zero at tree level. Radiative corrections to are computed in this class of theories. They vanish in realistic two-Higgs doublet models with . We also construct realistic three-Higgs models with , where the one-loop results for are model-dependent. Requiring has important implications for the flavor problem by constraining the Yukawa coupling and Higgs mass matrices. Contributions to from higher-dimension operators are computed at one loop and can also be sufficiently small, although the hierarchy problem of this class of theories is worse than in the Standard Model.

Hall, Lawrence↗

Scattering equations in AdS: scalar correlators in arbitrary dimensions

We introduce a bosonic ambitwistor string theory in AdS space. Even though the theory is anomalous at the quantum level, one can nevertheless use it in the classical limit to derive a novel formula for correlation functions of boundary CFT operators in arbitrary space-time dimensions. The resulting construction can be treated as a natural extension of the CHY formalism for the flat-space S-matrix, as it similarly expresses tree-level amplitudes in AdS as integrals over the moduli space of Riemann spheres with punctures. These integrals localize on an operator-valued version of scattering equations, which we derive directly from the ambitwistor string action on a coset manifold. As a testing ground for this formalism we focus on the simplest case of ambitwistor string coupled to two cur- rent algebras, which gives bi-adjoint scalar correlators in AdS. In order to evaluate them directly, we make use of a series of contour deformations on the moduli space of punctured Riemann spheres and check that the result agrees with tree level Witten diagram computations to all multiplicity. We also initiate the study of eigenfunctions of scattering equations in AdS, which interpolate between conformal partial waves in different OPE channels, and point out a connection to an elliptic deformation of the Calogero-Sutherland model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The SAGEX review on scattering amplitudes Chapter 2: An invitation to color-kinematics duality and the double copy

Abstract Advances in scattering amplitudes have exposed previously-hidden color-kinematics and double-copy structures in theories ranging from gauge and gravity theories to effective field theories such as chiral perturbation theory and the Born–Infeld model. These novel structures both simplify higher-order calculations and pose tantalizing questions related to a unified framework underlying relativistic quantum theories. This introductory mini-review article invites further exploration of these topics. After a brief introduction to color-kinematics duality and the double copy as they emerge at tree and loop-level in gauge and gravity theories, we present two distinct examples: (1) an introduction to the web of double-copy-constructible theories, and (2) a discussion of the application of the double copy to calculation relevant to gravitational-wave physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A review for identification of initiating events in event tree development process on nuclear power plants

Initiating event is defined as any event either internal or external to the nuclear power plants (NPPs) that perturbs the steady state operation of the plant, if operating, thereby initiating an abnormal event such as transient or loss of coolant accident (LOCA) within the NPPs. These initiating events trigger sequences of events that challenge plant control and safety systems whose failure could potentially lead to core damage or large early release. Selection for initiating events consists of two steps i.e. first step, definition of possible events, such as by evaluating a comprehensive engineering, and by constructing a top level logic model. Then the second step, grouping of identified initiating event's by the safety function to be performed or combinations of systems responses. Therefore, the purpose of this paper is to discuss initiating events identification in event tree development process and to reviews other probabilistic safety assessments (PSA). The identification of initiating events also involves the past operating experience, review of other PSA, failure mode and effect analysis (FMEA), feedback from system modeling, and master logic diagram (special type of fault tree). By using the method of study for the condition of the traditional US PSA categorization in detail, could be obtained the important initiating events that are categorized into LOCA, transients and external events.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces—Recommendations for Two New Genera and One Species

National Aeronautics and Space Administration’s (NASA) spacecraft assembly facilities are monitored for the presence of any bacteria or fungi that might conceivably survive a transfer to an extraterrestrial environment. Fungi present a broad and diverse range of phenotypic and functional traits to adapt to extreme conditions, hence the detection of fungi and subsequent eradication of them are needed to prevent forward contamination for future NASA missions. During the construction and assembly for the Mars 2020 mission, three fungal strains with unique morphological and phylogenetic properties were isolated from spacecraft assembly facilities. The reconstruction of phylogenetic trees based on several gene loci (ITS, LSU, SSU, RPB, TUB, TEF1) using multi-locus sequence typing (MLST) and whole genome sequencing (WGS) analyses supported the hypothesis that these were novel species. Here we report the genus or species-level classification of these three novel strains via a polyphasic approach using phylogenetic analysis, colony and cell morphology, and comparative analysis of WGS. The strain FJI-L9-BK-P1 isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) exhibited a putative phylogenetic relationship with the strain Aaosphaeria arxii CBS175.79 but showed distinct morphology and microscopic features. Another JPL-SAF strain, FJII-L3-CM-DR1, was phylogenetically distinct from members of the family Trichomeriaceae and exhibited morphologically different features from the genera Lithohypha and Strelitziana. The strain FKI-L1-BK-DR1 isolated from the Kennedy Space Center facility was identified as a member of Dothideomycetes incertae sedis and is closely related to the family Kirschsteiniotheliaceae according to a phylogenetic analysis. The polyphasic taxonomic approach supported the recommendation for establishing two novel genera and one novel species. The names Aaosphaeria pasadenensis (FJI-L9-BK-P1 = NRRL 64424 = DSM 114621), Pasadenomyces melaninifex (FJII-L3-CM-DR1 = NRRL 64433 = DSM 114623), and Floridaphiala radiotolerans (FKI-L1-BK-DR1 = NRRL 64434 = DSM 114624) are proposed as type species. Furthermore, resistance to ultraviolet-C and presence of specific biosynthetic gene cluster(s) coding for metabolically active compounds are unique to these strains.

59 BASIC BIOLOGICAL SCIENCES↗

spot_bt v.0.1.1

SAND2024-08430O spot_bt allows users to easily construct complex, autonomous behaviors without having to overly rely on Boston Dynamic’s Spot robot software development kit. Using a form-of-state machine called a "behavior tree," the software develops and applies different "leaves" or actions to the robot. Attaching multiple actions in sequence creates a "branch," and a series of these make up the "tree." The software works on any x86 or aarch64 hardware but must run on a Linux OS. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525

Kakish, Zahi↗

The RISMC Approach to Perform Advanced PRA Analyses

The existing fleet of nuclear power plants is in the process of extending its lifetime and increasing the power generated from these plants via power uprates. In order to evaluate the impact of these two factors on the safety of the plant, the RISMC Pathway aims to develop simulation-based tools and methods to assess risks for existing nuclear power plants in order to optimize safety. This pathway, by developing new methods, is extending the state-of-the-practice methods that have been traditionally based on logic structures such as Event-Trees and Fault-Trees. These static types of models mimic system response in an inductive and deductive way respectively, yet are restrictive in the ways they can represent spatial and temporal constructs. RISMC analyses are performed by using a combination of thermal-hydraulic codes and a stochastic analysis tool currently under development at the Idaho National Laboratory, i.e. RAVEN. This paper presents a case study in order to show the capabilities of the RISMC methodology to assess impact of power uprate of a boiling water reactor system during a station blackout accident scenario. We employ the system simulator code, RELAP5-3D, coupled with RAVEN which perform the stochastic analysis. Our analysis is in fact performed by: 1) sampling values of a set of parameters from the uncertainty space of interest, 2) simulating the system behavior for that specific set of parameter values and 3) analyzing the set of simulation runs. Results obtained give a detailed investigation of the issues associated with a plant power uprate including the effects of station blackout accident scenarios. We are able to quantify how the timing of specific events was impacted by a higher nominal reactor core power. Such safety insights can provide useful information to the decision makers to perform risk informed margins management.

97 MATHEMATICS AND COMPUTING↗

Loop-level double-copy for massive fermions in the fundamental

We find that unitarity cuts and the duality between color and kinematics are sufficient constraints to bootstrap D-dimensional QCD scattering amplitudes starting from three-particle tree-level. Specifically, we calculate tree level amplitudes through six-points, as well as the four-point one-loop correction for massive fermions in the fundamental representation of the gauge group — constructing a color-dual representation of the latter for the first time. To do so we clarify a prescription for functional kinematic ansatze involving fermionic matter. The advantages of color-dual calculation, familiar from particles in the adjoint, also apply here: only a small number of basis topologies must be constrained via physical information of the theory, and algebraic relations propagate this to a full solution. As all the QCD amplitudes we construct here are color-dual, they trivially generate D-dimensional amplitudes in gravitational theories via double-copy construction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗