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At least 307 records · Page 17

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DOE OSTI2025

HOD-dependent systematics in Emission Line Galaxies for the DESI 2024 BAO analysis

The Dark Energy Spectroscopic Instrument (DESI) will provide precise measurements of Baryon Acoustic Oscillations (BAO) to constrain the expansion history of the Universe and set stringent constraints on dark energy. Therefore, precise control of the global error budget due to various systematic effects is required for the DESI 2024 BAO analysis. In this work, we estimate the level of systematics induced in the DESI BAO analysis due the assumed Halo Occupation Distribution (HOD) model for the Emission Line Galaxy (ELG) tracer. We make use of mock galaxy catalogs constructed by fitting various HOD models to early DESI data, namely the One-Percent survey data. Our analysis includes typical HOD models for the ELG tracer used in the literature as well as extensions to the baseline models. Among the extensions, we consider various recipes for galactic conformity and assembly bias. We use 25 AbacusSummit simulations under the ΛCDM cosmology for each HOD model and perform independent analyses in Fourier space and in configuration space. To recover the BAO signal from our mocks we perform BAO reconstruction and apply the control variates technique to reduce sample variance noise. Our BAO analyses can recover the isotropic BAO parameter α iso within 0.1% and the Alcock Paczynski parameter α AP within 0.3%. Overall, we find that the systematic error due to the HOD dependence is below 0.17%, with the Fourier space analysis being more robust against the HOD systematics. We conclude that our analysis pipeline is robust enough against the HOD systematics for the ELG tracer in the DESI 2024 BAO analysis, for the assumptions made.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Polyampholyte physics: Liquid–liquid phase separation and biological condensates

Here we review the current understanding of molecular interactions that govern liquid-liquid phase separation (LLPS) of biological condensates. The connection between sequence, chain conformation, and phase separation of intrinsically disordered proteins (IDPs) and their model polyampholytes is discussed. In particular, we highlight how the charge pattern influences the conformation and phase behavior of natural IDPs. We then describe recent results from theoretical treatments of polyampholytes implementing random phase approximation, field-theoretic simulations, and transfer matrix theory that show an increase in charge segregation results in an increased tendency to phase separate.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

Modern control concepts in hydrology

Two approaches to an identification problem in hydrology are presented based upon concepts from modern control and estimation theory. The first approach treats the identification of unknown parameters in a hydrologic system subject to noisy inputs as an adaptive linear stochastic control problem; the second approach alters the model equation to account for the random part in the inputs, and then uses a nonlinear estimation scheme to estimate the unknown parameters. Both approaches use state-space concepts. The identification schemes are sequential and adaptive and can handle either time invariant or time dependent parameters. They are used to identify parameters in the Prasad model of rainfall-runoff. The results obtained are encouraging and conform with results from two previous studies; the first using numerical integration of the model equation along with a trial-and-error procedure, and the second, by using a quasi-linearization technique. The proposed approaches offer a systematic way of analyzing the rainfall-runoff process when the input data are imbedded in noise.

Duong, N.↗

NASA NTRS1992

CAPTIONALS: A computer aided testing environment for the verification and validation of communication protocols

This paper covers the verification and protocol validation for distributed computer and communication systems using a computer aided testing approach. Validation and verification make up the so-called process of conformance testing. Protocol applications which pass conformance testing are then checked to see whether they can operate together. This is referred to as interoperability testing. A new comprehensive approach to protocol testing is presented which address: (1) modeling for inter-layer representation for compatibility between conformance and interoperability testing; (2) computational improvement to current testing methods by using the proposed model inclusive of formulation of new qualitative and quantitative measures and time-dependent behavior; (3) analysis and evaluation of protocol behavior for interactive testing without extensive simulation.

Feng, C.↗

DOE OSTI2023

Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology

Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme’s conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme’s conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Process-Oriented Diagnostics: Principles, Practice, Community Development, and Common Standards

Process-oriented diagnostics (PODs) aim to provide feedback for model developers through model analysis based on physical hypotheses. However, the step from a diagnostic based on relationships among variables, even when hypothesis driven, to specific guidance for revising model formulation or parameterizations can be substantial. The POD may provide more information than a purely performance-based metric, but a gap between POD principles and providing actionable information for specific model revisions can remain. Furthermore, in coordinating diagnostics development, there is a trade-off between freedom for the developer, aiming to capture innovation, and near-term utility to the modeling center. Best practices that allow for the former, while conforming to specifications that aid the latter, are important for community diagnostics development that leads to tangible model improvements. Promising directions to close the gap between principles and practice include the interaction of PODs with perturbed physics experiments and with more quantitative process models as well as the inclusion of personnel from modeling centers in diagnostics development groups for immediate feedback during climate model revisions. Examples are provided, along with best-practice recommendations, based on practical experience from the NOAA Model Diagnostics Task Force (MDTF). Common standards for metrics and diagnostics that have arisen from a collaboration between the MDTF and the Department of Energy’s Coordinated Model Evaluation Capability are advocated as a means of uniting community diagnostics efforts.

58 GEOSCIENCES↗

NASA NTRS1997

Validation of an Accurate Three-Dimensional Helical Slow-Wave Circuit Model

The helical slow-wave circuit embodies a helical coil of rectangular tape supported in a metal barrel by dielectric support rods. Although the helix slow-wave circuit remains the mainstay of the traveling-wave tube (TWT) industry because of its exceptionally wide bandwidth, a full helical circuit, without significant dimensional approximations, has not been successfully modeled until now. Numerous attempts have been made to analyze the helical slow-wave circuit so that the performance could be accurately predicted without actually building it, but because of its complex geometry, many geometrical approximations became necessary rendering the previous models inaccurate. In the course of this research it has been demonstrated that using the simulation code, MAFIA, the helical structure can be modeled with actual tape width and thickness, dielectric support rod geometry and materials. To demonstrate the accuracy of the MAFIA model, the cold-test parameters including dispersion, on-axis interaction impedance and attenuation have been calculated for several helical TWT slow-wave circuits with a variety of support rod geometries including rectangular and T-shaped rods, as well as various support rod materials including isotropic, anisotropic and partially metal coated dielectrics. Compared with experimentally measured results, the agreement is excellent. With the accuracy of the MAFIA helical model validated, the code was used to investigate several conventional geometric approximations in an attempt to obtain the most computationally efficient model. Several simplifications were made to a standard model including replacing the helical tape with filaments, and replacing rectangular support rods with shapes conforming to the cylindrical coordinate system with effective permittivity. The approximate models are compared with the standard model in terms of cold-test characteristics and computational time. The model was also used to determine the sensitivity of various circuit parameters including typical manufacturing dimensional tolerances and support rod permittivity. By varying the circuit parameters of an accurate model using MAFIA, these sensitivities can be computed for manufacturing concerns, and design optimization previous to fabrication, thus eliminating the need for costly experimental iterations. Several variations were made to a standard helical circuit using MAFIA to investigate the effect that variations on helical tape and support rod width, metallized loading height and support rod permittivity, have on TWT cold-test characteristics.

Kory, Carol L.↗

NASA NTRS1978

The moon - Composition determined by nebular processes

The Ganapathy-Anders seven-component model is used as the basis for an analysis of conditions in the early solar nebula as they pertain to the formation of the moon. Calculations incorporating improved geological data and petrological constraints are presented in terms of a model moon which meets trace element restrictions and conforms to known parameters of heat flow, density, and moment of inertia ratio, ie., 40 ppb U, and a core of 2% by weight. It is noted that a melt of the model composition approximates that of Apollo 15 green glass, together with a residuum of olivine, plus 3-4% spinel.

Morgan, J. W.↗

NASA NTRS1946

Flight Investigation at High Speeds of the Drag of Three Airfoils and a Circular Cylinder Representing Full-Scale Propeller Shanks

Tests have been made at high speeds to determine the drag of models, simulating propeller shanks, in the form of a circular cylinder and three airfoils, the NACA 16-025, the NACA 16-040, and the NACA 16-040 with the rear 25 percent chord cut off. All the models had a maximum thickness of 4 1/2 inches to conform with average propeller-shank dimensions and a span of 20 1/4 inches. For the tests the models were supported perpendicular to the lower surface of the wing of an XP-51 airplane. A wake-survey rake mounted below the wing directly behind the models was used to determine profile drag of Mach numbers of 0.3 to 0.8 over a small range of angle of attack. The drag of the cylinder was also determined from pressure-distribution and force measurements.

Barlow, William H↗

DOE OSTI2021

Magnetic structure, excitations and short-range order in honeycomb Na 2 Ni 2 TeO 6

Na 2 Ni 2 TeO 6 has a layered hexagonal structure with a honeycomb lattice constituted by Ni 2+ and a chiral charge distribution of Na + that resides between the Ni layers. In the present work, the antiferromagnetic transition temperature of Na 2 Ni 2 TeO 6 is confirmed at TN˜ 27 K, and further, it is found to be robust up to 8 T magnetic field and 1.2 GPa external pressure; and, without any frequency-dependence. Slight deviations from nominal Na-content (up to 5%) does not seem to influence the magnetic transition temperature, TN. Isothermal magnetization curves remain almost linear up to 13 T. Our analysis of neutron diffraction data shows that the magnetic structure of Na 2 Ni 2 TeO 6 is faithfully described by a model consisting of two phases described by the commensurate wave vectors vec kc, (0.5 0 0) and (0.5 0 0.5), with an additional short-range order component incorporated in to the latter phase. Consequently, a zig-zag long-range ordered magnetic phase of Ni 2+ results in the compound, mixed with a short-range ordered phase, which is supported by our specific heat data. Theoretical computations based on density functional theory (DFT) predict predominantly in-plane magnetic exchange interactions that conform to a J1-J2-J3 model with a strong J3 term. The computationally predicted parameters lead to a reliable estimate for TN and the experimentally observed zig-zag magnetic structure. A spin wave excitation in Na 2 Ni 2 TeO 6 at E ˜ 5 meV at T = 5 K is mapped out through inelastic neutron scattering experiments, which is reproduced by linear spin wave theory calculations using the J values from our computations. Our specific heat data and inelastic neutron scattering data strongly indicate the presence of short-range spin correlations, at T > TN, stemming from incipient antiferromagnetic clusters.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Multi-scale computer-aided design and photo-controlled macromolecular synthesis boosting uranium harvesting from seawater

By integrating multi-scale computational simulation with photo-regulated macromolecular synthesis, this study presents a new paradigm for smart design while customizing polymeric adsorbents for uranium harvesting from seawater. A dissipative particle dynamics (DPD) approach, combined with a molecular dynamics (MD) study, is performed to simulate the conformational dynamics and adsorption process of a model uranium grabber, i.e., PAO m -b-PPEGMA n , suggesting that the maximum adsorption capacity with atomic economy can be achieved with a preferred block ratio of 0.18. The designed polymers are synthesized using the PET-RAFT polymerization in a microfluidic platform, exhibiting a record high adsorption capacity of uranium (11.4 ± 1.2 mg/g) in real seawater within 28 days. This study offers an integrated perspective to quantitatively assess adsorption phenomena of polymers, bridging metal-ligand interactions at the molecular level with their spatial conformations at the mesoscopic level. The established protocol is generally adaptable for target-oriented development of more advanced polymers for broadened applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

On the parameter combinations that matter and on those that do not: data-driven studies of parameter (non)identifiability

Abstract We present a data-driven approach to characterizing nonidentifiability of a model’s parameters and illustrate it through dynamic as well as steady kinetic models. By employing Diffusion Maps and their extensions, we discover the minimal combinations of parameters required to characterize the output behavior of a chemical system: a set of effective parameters for the model. Furthermore, we introduce and use a Conformal Autoencoder Neural Network technique, as well as a kernel-based Jointly Smooth Function technique, to disentangle the redundant parameter combinations that do not affect the output behavior from the ones that do. We discuss the interpretability of our data-driven effective parameters, and demonstrate the utility of the approach both for behavior prediction and parameter estimation. In the latter task, it becomes important to describe level sets in parameter space that are consistent with a particular output behavior. We validate our approach on a model of multisite phosphorylation, where a reduced set of effective parameters (nonlinear combinations of the physical ones) has previously been established analytically.

Evangelou, Nikolaos↗

DOE OSTI2024

One- and two-dimensional higher-point conformal blocks as free-particle wavefunctions in $$ {\textrm{AdS}}_3^{\otimes m} $$

Abstract We establish that all of the one- and two-dimensional global conformal blocks are, up to some choice of prefactor, free-particle wavefunctions in tensor products of AdS 3 or limits thereof. Our first core observation is that the six-point comb-channel conformal blocks correspond to free-particle wavefunctions on an AdS 3 constructed directly in cross-ratio space. This construction generalizes to blocks for a special class of diagrams, which are determined as free-particle wavefunctions in tensor products of AdS 3 . Conformal blocks for all the remaining topologies are obtained as limits of the free wavefunctions mentioned above. Our results show directly that the integrable models associated with all one- and two-dimensional conformal blocks can be seen as limits of free theory, and manifest a relation between AdS and CFT kinematics that lies outside of the standard AdS/CFT dictionary. We complete the discussion by providing explicit Feynman-like rules that can be used to work out blocks for all topologies, as well as a Mathematica notebook that allows simple computation of Casimir equations and series expansions for blocks, by requiring just an OPE diagram as input.

Physics↗

DOE OSTI2023

Physics-Driven Convolutional Autoencoder Approach for CFD Data Compressions: Preprint

With the growing size and complexity of turbulent flow models, data compression approaches are of the utmost importance to analyze, visualize, or restart the simulations. Recently, in-situ autoencoder-based compression approaches have been proposed and shown to be effective at producing reduced representations of turbulent flow data. However, these approaches focus solely on training the model using point-wise sample reconstruction losses that do not take advantage of the physical properties of turbulent flows. In this paper, we show that training autoencoders with additional physics-informed regularizations, e.g., enforcing incompressibility and preserving enstrophy, improves the compression model in three ways: (i) the compressed data better conform to known physics for homogeneous isotropic turbulence without negatively impacting point-wise reconstruction quality, (ii) inspection of the gradients of the trained model uncovers changes to the learned compression mapping that can facilitate the use of explainability techniques, and (iii) as a performance byproduct, training losses are shown to converge up to 12x faster than the baseline model.

auto-encoders↗

DOE OSTI2020

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called “lag time”). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5–10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1986

Aeroelastic considerations for torsionally soft rotors

A research study was initiated to systematically determine the impact of selected blade tip geometric parameters on conformable rotor performance and loads characteristics. The model articulated rotors included baseline and torsionally soft blades with interchangeable tips. Seven blade tip designs were evaluated on the baseline rotor and six tip designs were tested on the torsionally soft blades. The designs incorporated a systemmatic variation in geometric parameters including sweep, taper, and anhedral. The rotors were evaluated in the NASA Langley Transonic Dynamics Tunnel at several advance ratios, lift and propulsive force values, and tip Mach numbers. A track sensitivity study was also conducted at several advance ratios for both rotors. Based on the test results, tip parameter variations generated significant rotor performance and loads differences for both baseline and torsionally soft blades. Azimuthal variation of elastic twist generated by variations in the tip parameters strongly correlated with rotor performance and loads, but the magnitude of advancing blade elastic twist did not. In addition, fixed system vibratory loads and rotor track for potential conformable rotor candidates appears very sensitive to parametric rotor changes.

Mantay, W. R.↗

NASA NTRS1984

Aeroelastic considerations for torsionally soft rotors

Mantay, W. R.↗

NASA NTRS2006

SmaggIce Version 1.8

SmaggIce version 1.8 is a set of software tools for geometrical modeling of, and generation of grids that conform to, both clean and iced airfoils. Ice shapes, especially those that include rough surfaces, pose difficulty in generating high-quality grids that are essential for predicting airflows by use of computational fluid dynamics. SmaggIce version 1.8 contains software tools needed to overcome this difficulty. For a given airfoil, it allows the user to define the flow domain, decompose the domain into blocks, generate grids, merge gridded blocks, and control the density and smoothness of each grid. Among the unique features of version 1.8 is a thin C-shaped block, called a "viscous sublayer block," which is wrapped around an iced airfoil and its wake line and serves as a means to generate highly controlled grids near the rough ice surface. Users can modify block boundary shapes using control points of non-uniform rational B-spline (NURBS) curves. Concave ice regions can be smoothed during geometrical modeling or creation of the viscous sublayer block.

Vickerman, Mary B.↗