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Results for “Higher-Order Modifications”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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29 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Abstract Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

Higher-Order Finite Elements for Computing Thermal Radiation

Two variants of the finite-element method have been developed for use in computational simulations of radiative transfers of heat among diffuse gray surfaces. Both variants involve the use of higher-order finite elements, across which temperatures and radiative quantities are assumed to vary according to certain approximations. In this and other applications, higher-order finite elements are used to increase (relative to classical finite elements, which are assumed to be isothermal) the accuracies of final numerical results without having to refine computational meshes excessively and thereby incur excessive computation times. One of the variants is termed the radiation sub-element (RSE) method, which, itself, is subject to a number of variations. This is the simplest and most straightforward approach to representation of spatially variable surface radiation. Any computer code that, heretofore, could model surface-to-surface radiation can incorporate the RSE method without major modifications. In the basic form of the RSE method, each finite element selected for use in computing radiative heat transfer is considered to be a parent element and is divided into sub-elements for the purpose of solving the surface-to-surface radiation-exchange problem. The sub-elements are then treated as classical finite elements; that is, they are assumed to be isothermal, and their view factors and absorbed heat fluxes are calculated accordingly. The heat fluxes absorbed by the sub-elements are then transferred back to the parent element to obtain a radiative heat flux that varies spatially across the parent element. Variants of the RSE method involve the use of polynomials to interpolate and/or extrapolate to approximate spatial variations of physical quantities. The other variant of the finite-element method is termed the integration method (IM). Unlike in the RSE methods, the parent finite elements are not subdivided into smaller elements, and neither isothermality nor other unrealistic physical conditions are assumed. Instead, the equations of radiative heat transfer are integrated numerically over the parent finite elements by use of a computationally efficient Gaussian integration scheme.

Gould, Dana C.↗
DOE OSTI2023

Manipulating the 3D organization of the largest synthetic yeast chromosome

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Ephb2 Receptor Uses Homotypic, Head-to-Tail Interactions within Its Ectodomain as an Autoinhibitory Control Mechanism

The Eph receptor tyrosine kinases and their ephrin ligands direct axon pathfinding and neuronal cell migration, as well as mediate many other cell–cell communication events. Their dysfunctional signaling has been shown to lead to various diseases, including cancer. The Ephs and ephrins both localize to the plasma membrane and, upon cell–cell contact, form extensive signaling assemblies at the contact sites. The Ephs and the ephrins are divided into A and B subclasses based on their sequence conservation and affinities for each other. The molecular details of Eph–ephrin recognition have been previously revealed and it has been documented that ephrin binding induces higher-order Eph assemblies, which are essential for full biological activity, via multiple, distinct Eph–Eph interfaces. One Eph–Eph interface type is characterized by a homotypic, head-to-tail interaction between the ligand-binding and the fibronectin domains of two adjacent Eph molecules. While the previous Eph ectodomain structural studies were focused on A class receptors, we now report the crystal structure of the full ectodomain of EphB2, revealing distinct and unique head-to-tail receptor–receptor interactions. The EphB2 structure and structure-based mutagenesis document that EphB2 uses the head-to-tail interactions as a novel autoinhibitory control mechanism for regulating downstream signaling and that these interactions can be modulated by posttranslational modifications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Low and moderate x gluon contribution to exclusive Compton scattering processes

We revisit the high energy semi-classical description of the exclusive processes DVCS, TCS, and Double DVCS by explicitly keeping track of the Feynman x dependence in both the hard and the hadronic matrix elements. This is achieved by a modification of the standard shock wave approximation to derive the effective Feynman rules, which leads to a generic expression on which we then perform a partial twist expansion to get rid of quantities suppressed by the proper physical scales. We obtain a compact factorized master formula that can be used to investigate the Bjorken limit at leading twist. In particular, we recover the full one-loop result in the collinear limit for pure gluon exchange with the target. Finally, we discuss the subtleties in taking the simultaneous collinear and small x limit.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Flavor fragmentation function factorization

A definition of partonic jet flavor that is both theoretically well-defined and experimentally robust would have profound implications for measurements and predictions especially for heavy flavor applications. Recently, a definition of jet flavor was introduced as the net flavor flowing along the direction of the Winner-Take-All axis of a jet which is soft safe to all orders, but not collinear safe. Here, we exploit the lack of collinear safety and propose a factorization theorem of perturbative flavor fragmentation functions that resum collinear divergences and describe the evolution of flavor from the short distance of jet production to the long distance at which hadronization occurs. Collinear flavor evolution is governed by a small modification of the DGLAP equations. We present a detailed all-orders analysis and identify exact relations that must hold amongst the various anomalous dimensions by probability conservation and the existence of fixed points of the renormalization group flow. We explicitly validate the factorization theorem at one-loop order, and demonstrate its consistency at two loops in particular flavor channels. Starting at two-loops, constraints on phase space imposed by flavor measurements potentially allow for non-trivial soft contributions, but we demonstrate that they are scaleless and so explicitly vanish, ensuring that soft particles are summed inclusively and all divergences are exclusively collinear in nature. This factorization theorem opens the door to precision calculations with identified flavor in the infrared.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Refining the GENEVA method for Higgs boson production via gluon fusion

We describe a number of improvements to the Geneva method for matching NNLO calculations to parton shower programs. In particular, we detail changes to the resummed calculation used in the matching procedure, including disentangling the cross section dependence on factorisation and beam scales, and an improved treatment of timelike logarithms. We also discuss modifications in the implementation of the splitting functions which serve to make the resummed calculation differential in the higher multiplicity phase space. These changes improve the stability of the numerical cancellation of the nonsingular term at small values of the resolution parameter. As a case study, we consider the gluon-initiated Higgs boson production process gg → H. We validate the NNLO accuracy of our predictions against independent calculations, and compare our showered and hadronised results with recent data taken at the ATLAS and CMS experiments in the diphoton decay channel, finding good agreement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

PRISMS-PF: A general framework for phase-field modeling with a matrix-free finite element method

Abstract A new phase-field modeling framework with an emphasis on performance, flexibility, and ease of use is presented. Foremost among the strategies employed to fulfill these objectives are the use of a matrix-free finite element method and a modular, application-centric code structure. This approach is implemented in the new open-source PRISMS-PF framework. Its performance is enabled by the combination of a matrix-free variant of the finite element method with adaptive mesh refinement, explicit time integration, and multilevel parallelism. Benchmark testing with a particle growth problem shows PRISMS-PF with adaptive mesh refinement and higher-order elements to be up to 12 times faster than a finite difference code employing a second-order-accurate spatial discretization and first-order-accurate explicit time integration. Furthermore, for a two-dimensional solidification benchmark problem, the performance of PRISMS-PF meets or exceeds that of phase-field frameworks that focus on implicit/semi-implicit time stepping, even though the benchmark problem’s small computational size reduces the scalability advantage of explicit time-integration schemes. PRISMS-PF supports an arbitrary number of coupled governing equations. The code structure simplifies the modification of these governing equations by separating their definition from the implementation of the numerical methods used to solve them. As part of its modular design, the framework includes functionality for nucleation and polycrystalline systems available in any application to further broaden the phenomena that can be used to study. The versatility of this approach is demonstrated with examples from several common types of phase-field simulations, including coarsening subsequent to spinodal decomposition, solidification, precipitation, grain growth, and corrosion.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Computation of the Biot–Savart line integral with higher-order convergence using straight segments

One common approach to computing the magnetic field produced by a filamentary current-carrying coil is to approximate the coil as a series of straight segments. The Biot–Savart field from each straight segment is analytically known. However, if the endpoints of the straight segments are chosen to lie on the coil, then the accuracy of the Biot–Savart computation is generally only the second order in the number of endpoints. In this work, we propose a simple modification: shift each end point of the coil in the outward normal direction by an amount proportional to the local curvature. With this modification, the Biot–Savart accuracy increases to the fourth order and the numerical error is dramatically reduced for a given number of discretization points.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Flavor Fragmentation Function Factorization

A definition of partonic jet flavor that is both theoretically well-defined and experimentally robust would have profound implications for measurements and predictions especially for heavy flavor applications. Recently, a definition of jet flavor was introduced as the net flavor flowing along the direction of the Winner-Take-All axis of a jet which is soft safe to all orders, but not collinear safe. Here, we exploit the lack of collinear safety and propose a factorization theorem of perturbative flavor fragmentation functions that resum collinear divergences and describe the evolution of flavor from the short distance of jet production to the long distance at which hadronization occurs. Collinear flavor evolution is governed by a small modification of the DGLAP equations. We present a detailed all-orders analysis and identify exact relations that must hold amongst the various anomalous dimensions by probability conservation and the existence of fixed points of the renormalization group flow. We explicitly validate the factorization theorem at one-loop order, and demonstrate its consistency at two loops in particular flavor channels. Starting at two-loops, constraints on phase space imposed by flavor measurements potentially allow for non-trivial soft contributions, but we demonstrate that they are scaleless and so explicitly vanish, ensuring that soft particles are summed inclusively and all divergences are exclusively collinear in nature. This factorization theorem opens the door to precision calculations with identified flavor in the infrared.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS2019

An Initial Exploration of Improved Numerics within the Guidelines of the Negative Spalart-Allmaras Turbulence Model

A simple modification to the negative Spalart-Allmaras turbulence model is suggested so that when the turbulence working variable, ~v, is negative, diagonal dominance is increased, as is the tendency for the time-advancement scheme to push e toward positive values. Owing to the fact that the modification is only active when ~v is less than zero, the physical model is left unchanged. Using the proposed modification with a strong implicit solver based on Newton's method, convergence rates can be somewhat improved, with typical reductions in iterations and computer time on the order of 15-50%. The benefits are realized primarily when second- or higher-order accuracy is used for discretizing the convective terms in the turbulence model because of large overshoots that can occur with these schemes at the edges of boundary layers and wakes. For flowfields with few regions of negative ~v, or on very fine meshes where ~v is always greater than zero, little or no benefits should be expected.

Anderson, William K.↗