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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Mass spectrometry-based proteomics for analysis of hydrophilic phosphopeptides

Protein phosphorylation is a critical post-translational modification (PTM), with cell signaling networks being tightly regulated by protein phosphorylation. Despite recent technological advances in reversed-phase liquid chromatography (RPLC)-mass spectrometry (MS)-based proteomics, comprehensive phosphoproteomic coverage in complex biological systems remains challenging, especially for hydrophilic phosphopeptides that often have multiple phosphorylation sites. Herein we describe an MS-based phosphoproteomics protocol for effective quantitative analysis of hydrophilic phosphopeptides. This protocol was built upon a simple tandem mass tag (TMT)-labeling method for significantly increasing peptide hydrophobicity, thus effectively enhancing RPLC-MS analysis of hydrophilic peptides. Through phosphoproteomic analyses of MCF7 cells, this method was demonstrated to greatly increase the number of identified hydrophilic phosphopeptides and improve MS signal detection. With the TMT labeling method, we were able to identify a previously unreported phosphopeptide from the G protein-coupled receptor (GPCR) CXCR3, QPpSSSR, which is thought to be important in regulating receptor signaling. This protocol is easy to adopt and implement, and thus should have broad utility for effective RPLC-MS analysis of the hydrophilic phosphoproteome as well as other highly hydrophilic analytes.

Hydrophilic phosphopeptide, Phosphoproteomics, TMT↗
DOE OSTI2021

Techniques in performance and efficiency improvements of processors in a cooling system

Embodiments of the present disclosure describe methods, apparatuses, storage media, and systems for Thermal Design Power (TDP) rebalancing among thermally-coupled processors and non-thermally-coupled processors, providing computing efficiency or homogeneity with respect to, including but not limited to, thermal requirements, power consumption, and processor operations. The TDP rebalancing may include implementing management circuitry and configuration control circuitry. Other embodiments may be described and claimed.

Keceli, Fuat↗
DOE OSTI2022

Application of Dynamical System Scaling for Accelerated Fuel Qualification Efforts

There are considerable ongoing research and testing campaigns to qualify new fuel designs such as metallic fuels for advanced reactor designs and the Accident Tolerant Fuel (ATF) campaign for light water reactors (LWR). The typical research and development lifecycle needed to qualify a nuclear fuel design, under ideal conditions, can take up to 20-25 years which limits the ability for new fuels to make fast deployments into commercial, test, and research reactors. While there are several efforts to accelerate nuclear fuel qualification through advanced modeling coupled with state-of-the-art experiments, there is not yet a framework to methodically quantify and rank distortions occurring in experimental test specimens needed to validate nuclear fuel performance codes. This study uses the Dynamical System Scaling (DSS) methodology to quantify transient scaling distortions that occur over experiment and simulated transients. DSS analysis metrics provide a researcher with several tools and information embedded within test data to identify dominant phenomena, associated timescales, and quantify a transient?s overall dynamic distortion. This is demonstrated with separate analyses of the SETH-C and CHF-SERTTA thermal-hydraulic experiments in the TREAT facility at Idaho National Laboratory. The outcome of this work is a scaling and data analysis approach to account for the influence a scaled fuel test specimen?s geometric and temporal distortions have on its ability to be representative of the full-scale design.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

An Efficient Three-Dimensional CFD-Based Numerical Wave Tank for a Wave Energy Converter in Extreme Irregular Waves: Preprint

A numerical wave tank approach for computational fluid dynamics (CFD) modelling of an extreme irregular seastate is presented. The technique couples a potential flow solution with a CFD solver for more efficient numerical predictions. This method has recently become attractive both for the research community and the industry working with offshore structures. The model is used to determine the response of a submerged pressure differential wave energy converter (WEC) in a fully nonlinear irregular wave condition using the high fidelity CFD code, STAR-CCM+. Potential flow based numerical models are commonly used to predict motions and performance of wave energy converters. Wave kinematics can deviate from potential flow predictions for extreme wave conditions; the excitation loads on an absorber can also be increasingly influenced by viscous effects, not captured in engineering level models. In these extreme conditions, a Reynolds-averaged Navier-Stokes CFD model can better predict motions and loads for a WEC. Long time series with varying random seed numbers can be used to identify singular extreme wave events from a stochastic irregular sea state. This approach simulates a more realistic wave series for a given sea state than a regular wave or a focused wave. However, it is computationally infeasible to run these long time series for three-dimensional (3D) CFD simulations. In this work, two-dimensional (2D) CFD simulations with a long domain allow the full development of an extreme nonlinear wave condition. The results are used to identify extreme events from a 50-year storm condition for the PacWave site off the coast of Oregon. A relatively short time window including this extreme event is then mapped to a 3D simulation using a user defined wave methodology. Convergence studies for domain length, wave forcing lengths, and time before the extreme event were conducted.

cfd↗
DOE OSTI2023

Simulating Catalysis with Realistic Pellet Geometries Using Mesoflow: A Case Study of Catalytic Propane Dehydrogenation

We present a case study of catalytic propane dehydrogenation with our open-source multiphysics solver, Mesoflow. The solver was developed to simulate reactive flow coupled to heterogeneous catalytic reactions and deactivation in the context of complex, mesoscale geometry. The method leverages cartesian block-structured adaptive mesh refinement to capture realistic catalyst microstructural features acquired directly from X-ray computed tomography data. A kinetic model for propane dehydrogenation and catalyst deactivation was developed based on temporal analysis of products (TAP) reactor experiments. The TAP reactor experiments allow for precise characterization of intrinsic kinetic reaction steps which are implemented into Mesoflow simulations to model the spatial and temporal evolution of reactants, products, and catalyst active sites. The short-term and long-term deactivation behavior is studied by using XCT data collected from fresh and aged catalyst pellets, which exhibit different microstructural features. This study employs time-splitting algorithms to connect disparate reaction and flow timescales, enabling the simulations to achieve realistic deactivation timescales on the order of minutes while the flow time-scales for small particles (100 microns) are several milliseconds. We also introduce a flexible automated python script that writes the necessary files to construct a Mesoflow simulation from user-created chemical mechanisms. We will also introduce a few new features that are added to Mesoflow such as higher order schemes, implicit chemistry integrators and the ability to run on AMD and NVIDIA graphics-processing-units.

AMReX↗
DOE OSTI2023

Coupled magnetostructural continuum model for multiferroic BiFeO 3

Here, a continuum approach to study magnetoelectric multiferroic BiFeO 3 (BFO) is proposed. Our modeling effort marries the ferroelectric (FE) phase field method and micromagnetic simulations to describe the entire multiferroic order parameter sector (polarization, oxygen antiphase tilts, strain, and magnetism) self-consistently on the same time- and length scale. In this paper, we discuss our choice of FE and magnetic energy terms and demonstrate benchmarks against known behavior. We parametrize the lowest order couplings of the structural distortions against previous predictions from density functional theory calculations giving access to simulations of the FE domain wall (DW) topology. This allows us to estimate the energetic hierarchy and thicknesses of the numerous structural DWs. We then extend the model to the canted antiferromagnetic order and demonstrate how the FE domain boundaries influence the resulting magnetic DWs. We also highlight some capabilities of this model by providing two examples relevant for applications. We demonstrate spin-wave transmission through the multiferroic domain boundaries which identify rectification in qualitative agreement with recent experimental observations. As a second example of application, we model fully dynamical magnetoelectric switching, where we find a sensitivity on the Gilbert damping with respect to switching pathways. We envision that this modeling effort will set the basis for further work on properties of arbitrary 3D nanostructures of BFO (and related multiferroics) at the mesoscale.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Iterative X-ray spectroscopic ptychography

Spectroscopic ptychography is a powerful technique to determine the chemical composition of a sample with high spatial resolution. In spectro-ptychography, a sample is rastered through a focused X-ray beam with varying photon energy so that a series of phaseless diffraction data are recorded. Each chemical component in the material under investigation has a characteristic absorption and phase contrast as a function of photon energy. Using a dictionary formed by the set of contrast functions of each energy for each chemical component, it is possible to obtain the chemical composition of the material from high-resolution multi-spectral images. This paper presents SPA (spectroscopic ptychography with alternating direction method of multipliers), a novel algorithm to iteratively solve the spectroscopic blind ptychography problem. First, a nonlinear spectro-ptychography model based on Poisson maximum likelihood is designed, and then the proposed method is constructed on the basis of fast iterative splitting operators. SPA can be used to retrieve spectral contrast when considering either a known or an incomplete (partially known) dictionary of reference spectra. By coupling the redundancy across different spectral measurements, the proposed algorithm can achieve higher reconstruction quality when compared with standard state-of-the-art two-step methods. It is demonstrated how SPA can recover accurate chemical maps from Poisson-noised measurements, and its enhanced robustness when reconstructing reduced-redundancy ptychography data using large scanning step sizes is shown.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Comparison of equilibrium climate sensitivity estimates from slab ocean, 150-year, and longer simulations

We compare equilibrium climate sensitivity (ECS) estimates from pairs of long (= 800-year) control and abruptly quadrupled CO2 simulations with shorter (150, 300 year) coupled atmosphere-ocean simulations and Slab Ocean Models (SOM). Consistent with previous work, ECS estimates from shorter coupled simulations based on annual averages for years 1-150 underestimate those from SOM (-8% ± 13%) and long (-14% ± 8%) simulations. Analysis of only years 21-150 improved agreement with SOM (-2% ± 14%) and long (-8% ± 10%) estimates. Use of pentadal averages for years 51-150 results in improved agreement with long simulations (-4% ± 11%). While ECS estimates from current generation US models based on SOM and coupled annual averages of years 1-150 range from 2.6°C to 5.3°C, estimates based longer simulations of the same models range from 3.2°C to 7.0°C. Such variations between methods argues for caution in comparison and interpretation of ECS estimates across models.

Dunne, John P.↗
DOE OSTI2020

Two-way coupled particle-turbulence interaction: Effect of numerics and resolution on fluid and particle statistics

Euler-Lagrange point-particle simulation has emerged as a premier methodology for studying dispersed particle-laden flows. This method's popularity stems from its ability to resolve fine-scale fluid structures while also tracking individual particles at reduced cost using an appropriate particle acceleration model. However, the point-particle model has known convergence issues in that refinement of the fluid grid can lead to changes in the predicted statistics. The reasons for non-convergence are twofold: the point-particle two-way coupling force in the Navier-Stokes equations requires a numerical regularization and, without careful implementation, yields a singular force on the fluid with grid refinement. The second factor that yields grid-dependent statistics is that the point-particle force model in general depends on the undisturbed fluid velocity. When the undisturbed fluid velocity is not robustly modeled in a grid-insensitive way, the calculated force for both particles and fluid will be grid-dependent, contaminating their respective statistics. While the first issue regarding regularizing the point-particle source term has received attention in the literature, the consequences of robustly modeling the undisturbed velocity in the context of grid refinement of turbulence has received little attention. Here, we consider decaying homogeneous isotropic turbulence laden with particles at different Stokes numbers. For a given Stokes number, we systematically refine the grid and demonstrate that explicitly modeling the undisturbed fluid velocity yields relative grid insensitivity for the energy of the particle and fluid phases, as well as acceleration of the particles. We also demonstrate that an appropriately defined dissipation rate is also grid-insensitive when an undisturbed fluid velocity correction is used. In contrast, when the undisturbed fluid velocity is modeled using the conventional approach of interpolating the local fluid velocity to the particle location, we show this procedure yields divergent statistics with grid refinement. In particular, we show that higher-order interpolation of the fluid velocity in two-way coupled problems is worse than lower-order interpolation, in the absence of a correction procedure to estimate the undisturbed fluid velocity. We also examine velocity derivative statistics of the fluid phase and demonstrate that these statistics are not in general convergent even when the undisturbed fluid velocity is explicitly modeled. Collectively, the observations in this paper are used to present a philosophy on the types of questions which are answerable with point-particle methods.

42 ENGINEERING↗
DOE OSTI2025

Directional finite difference method for directly solving 3D gyrokinetic field equations with enhanced accuracy

The gyrokinetic (GK) field equation is a three-dimensional (3D) elliptic equation, but it is often simplified to a set of two-dimensional (2D) equations by assuming that the field does not vary along a specific direction. However, this simplification can introduce inevitable 0th-order numerical errors, as nonlinear mode coupling in toroidal geometry can produce undesirable harmonic modes that violate the assumption. In this work, we propose a novel directional finite difference method (FDM) with a local coordinate transformation to better resolve the target field of interest. The directional FDM can accurately solve 3D GK field equations without simplifications, which can overcome the limitations of conventional methods. The accuracy and efficiency of different FDMs are analyzed in great detail for a variety of geometries, from simple 2D Cartesian coordinates to realistic 3D curvilinear coordinates. The 0th-order numerical errors of simplified 2D GK equations were found to be more problematic for low-harmonic modes and low aspect ratio geometries such as spherical tokamaks. On the other hand, the directional 3D FDM can accurately resolve a much wider range of harmonic modes aligned to the direction of interest, including the low-harmonic modes. In conclusion, we demonstrate that the directional 3D FDM is a highly effective algorithm for solving the 3D GK field equations, achieving accuracy improvements of 10 to 100 times or more, particularly for low-harmonic modes in spherical tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Implicit Multirate GARK Methods

This article considers multirate generalized-structure additively partitioned Runge–Kutta methods for solving stiff systems of ordinary differential equations with multiple time scales. These methods treat different partitions of the system with different timesteps for a more targeted and efficient solution compared to monolithic single rate approaches. With implicit methods used across all partitions, methods must find a balance between stability and the cost of solving nonlinear equations for the stages. In order to characterize this important trade-off, we explore multirate coupling strategies, problems for assessing linear stability, and techniques to efficiently implement Newton iterations for stage equations. Unlike much of the existing multirate stability analysis which is limited in scope to particular methods, we present general statements on stability and describe fundamental limitations for certain types of multirate schemes. New implicit multirate methods up to fourth order are derived, and their accuracy and efficiency properties are verified with numerical tests.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A self-consistent electrostatic electrified shallow water model for charged liquid surface dynamics

The dynamics of an electrified liquid surface are investigated using a shallow water model that is self-consistently coupled with an electrostatic solver. To account for the spatiotemporal variation of a curved liquid surface, the electric field on curved surfaces is calculated by solving a two-dimensional electrostatic equation using the weighted least squares (WLSQ) interpolation method. First, the WLSQ implementation is verified with analytical theory obtained from a Laplace solution assuming a half-cylinder liquid surface profile. Then, the coupled electrified shallow water model is used to study the instability of liquid surface perturbation as a function of the potential drop between an electrode and conducting liquid, surface tension, and gravity. We present a linear dispersion theory of liquid surface instability for long-wavelength perturbations, including the effects of liquid viscosity. Furthermore, the effects of multiple sinusoidal surface perturbations on the electrified liquid surface instability are investigated.

Capillary waves↗
DOE OSTI2023

DT-HYDRO

The software solves the time dependent, one dimensional (1D) coupled mass and momentum balance equations governing the elastic flow of water through the penstock, turbine and draft tube in a hydroelectric facility using a high order finite volume based method. The numerical method is based on the Kurganov-Tadmor central method paired with the Monotonic Upstream-centered Scheme for Conservation Laws (MUSCL). This solution method accurately resolves the fast transient behavior of the flow, including water hammer. Additionally, the software estimates the full 3D flow field within the turbine chamber in real time, a feat that is made possible by leveraging pre-computed CFD results by utilizing a reduced order modeling method based on an efficient randomized singular value decomposition (SVD) driven proper orthogonal decomposition (POD) with POD-mode weight regression. The reduced order model of the 3D flow is directly coupled to the 1D elastic flow model so the entire flow field through the penstock and turbine system is resolved quickly and with high fidelity.

Gurecky, William [Oak Ridge National Laboratory (O↗
DOE OSTI2026

A variational mimetic finite difference method for elliptic interface problems on non-matching polytopal meshes with geometric interface inconsistencies

A new variational mimetic finite difference method for elliptic interface problems with perfect and imperfect thermal contacts on non-matching polytopal meshes with geometric interface inconsistencies is developed and analyzed theoretically and numerically. The method is defined on multiple non-matching submeshes with gaps and overlaps along their interfaces. The discrete equations are derived from a minimization problem for the augmented Dirichlet functional. For a perfect thermal contact, the functional uses a modified mimetic gradient with extended stencil which couples unknowns from both sides of an interface, as well as penalty terms to enforce weak continuity of temperature across the interface. The method leads to a symmetric positive definite matrix for any scaling of the penalty terms. For an imperfect thermal contact, the Dirichlet functional is supplemented with a quadratic jump term along the interface related to the interface thermal resistance. We prove that the method conserves the total heat flux across each interface. In conclusion, the obtained results are verified with numerical experiments showing convergence in the discrete L 2 and L ∞ norms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Ultrafast Correlation Energy Estimator

A virtually no-cost method is proposed that can compute the correlation energies of general, covalently bonded, organic, and inorganic molecules (including conjugated π-electron systems) with a well-defined dominant Lewis structure at the accuracy of 99.5% of the near-exact values determined by the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] in the complete-basis-set (CBS) limit. This Correlation Energy Per Bond (CEPB) method assigns a partial correlation energy to each bond type (characterized by the identities of the two atoms forming the bond and its integer bond order) and to a lone pair, regardless of the bond length, bond angle, sp-hybridization, π-electron conjugation, ionicity, noncovalent interactions, etc. At its current stage, the method is mainly suitable for near-equilibrium geometries. The correlation energies per bond are determined by a fit to the CCSD(T)/CBS benchmarks. It can neither improve the equilibrium structures nor discern conformers or positional isomers, yet its accuracy for reaction energies rivals that of the second-order Møller–Plesset perturbation theory, which is far more expensive. Its promising performance underscores the possibility that surprisingly compact, chemically intuitive molecular fragments exist into which correlation energies can be partitioned, leading to various ultrafast correlation-energy estimators tailored to different purposes.

Binding energy↗
DOE OSTI2022

Coupled charge and energy transfer dynamics in light harvesting complexes from a hybrid hierarchical equations of motion approach

Here, we describe a method for simulating exciton dynamics in protein–pigment complexes, including effects from charge transfer as well as fluorescence. The method combines the hierarchical equations of motion, which are used to describe quantum dynamics of excitons, and the Nakajima–Zwanzig quantum master equation, which is used to describe slower charge transfer processes. We study the charge transfer quenching in light harvesting complex II, a protein postulated to control non-photochemical quenching in many plant species. Using our hybrid approach, we find good agreement between our calculation and experimental measurements of the excitation lifetime. Furthermore, our calculations reveal that the exciton energy funnel plays an important role in determining quenching efficiency, a conclusion we expect to extend to other proteins that perform protective excitation quenching. This also highlights the need for simulation methods that properly account for the interplay of exciton dynamics and charge transfer processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Comparison of continuum-continuum and Coulomb-laser-coupling delays from visible to midinfrared wavelengths

We compare the various proposed formulas for CLC and CC delays using analytical and numerical methods across a range of wavelengths spanning visible to midinfrared. We show that one of the CC definitions is nearly equal to the CLC delay over a range of photoelectron energies and wavelengths. We furthermore obtain alternate expressions for the CC delays. These expressions are simpler to use and show close correspondence to the CLC delays. Based on this correspondence, we suggest a correction to the CLC delay for low-energy electrons, where the currently used approximation breaks down. Our work provides guidance for when it is valid to treat CC and CLC delays as being equivalent.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Method and system for compact efficient laser architecture

A laser amplifier module having an enclosure includes an input window, a mirror optically coupled to the input window and disposed in a first plane, and a first amplifier head disposed along an optical amplification path adjacent a first end of the enclosure. The laser amplifier module also includes a second amplifier head disposed along the optical amplification path adjacent a second end of the enclosure and a cavity mirror disposed along the optical amplification path.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗