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At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Device and Method for Parallel Measurement of Phosphoproteome and Proteome from Single Cells

We present the development of an immobilized metal affinity chromatography (IMAC) chip designed to enable nanoscale phosphopeptide enrichment within microfabricated nanowells. This novel platform leverages surface chemistry to immobilize high-density Nickel-Nitrilotriacetic Acid (Ni-NTA) molecules on nanowells, followed by applying Fe 3+ . The nanowell surface serves as a capture media to enrich phosphopeptides based on IMAC. The system's efficiency was validated using ß-casein as a model protein, demonstrating the chip’s capability to significantly enrich phosphopeptides. Future applications of this technology are anticipated to enable the detection of over 100 phosphopeptides from individual cells and more than 500 phosphopeptides from pools of 100 cells, offering exciting potential for single-cell phosphoproteomics. We will next apply an integrated proteomics workflow to perform multi-omics measurements, including single-cell isolation, protein digestion, and phosphopeptide enrichment, followed by LC-MS analysis of both the global proteome and phosphoproteome. Future research will explore the use of this technology to study phosphorylation dynamics in cancer cells, enhancing our understanding of cellular signaling and disease mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Distributed-Memory Parallel Symmetric Nonnegative Matrix Factorization

We develop the first distributed-memory parallel implementation of Symmetric Nonnegative Matrix Factorization (SymNMF), a key data analytics kernel for clustering and dimensionality reduction. Our implementation includes two different algorithms for SymNMF, which give comparable results in terms of time and accuracy. The first algorithm is a parallelization of an existing sequential approach that uses solvers for non symmetric NMF. The second algorithm is a novel approach based on the Gauss-Newton method. It exploits second-order information without incurring large computational and memory costs. We evaluate the scalability of our algorithms on the Summit system at Oak Ridge National Laboratory, scaling up to 128 nodes (4,096 cores) with 70% efficiency. Additionally, we demonstrate our software on an image segmentation task.

Eswar, Srinivas↗
DOE OSTI2022

Clang UPC Compiler (Clang UPC) v3.9.1-1

Clang Unified Parallel C (Clang UPC) provides a compilation and execution environment for programs written in the UPC (Unified Parallel C) language. The Clang UPC compiler extends the capabilities of the Clang LLVM C compiler to comply with the UPC Language Specification version 1.3. It includes support for UPC collectives and a configurable pointer-to-shared representation. The compiler generates programs that run on a wide variety of systems ranging from workstations to leadership-class supercomputers, in conjunction with the Berkeley UPC runtime and GASNet communication system. This compiler generates assembly code / object code directly for Intel processors and IBM PowerPC.

Hargrove, Paul↗
DOE OSTI2024

Accelerating Thermochemical Equilibrium Calculations for Nuclear Reactor Applications

Thermochemical properties play a key role in modeling and simulation of several key phenomena in nuclear reactors. There has been an increasing interest in incorporating CALPHAD-based formulations in multiphysics simulations including for Molten Salt Reactors where knowledge of phase evolution of the salt and the chemical potentials of various elements are of utmost importance in source term analyses and redox control. However, the size of such simulations is often limited by the high computational cost of full thermodynamic equilibrium calculations. This work discusses the current efforts aimed at accelerating thermochemical equilibrium calculations for multiphysics simulations performed using the open-source finite element / finite volume code Multiphysics Object Oriented Simulation Environment (MOOSE) [1]. While several methods have been proposed for accelerating phase equilibrium calculations [2], most focus on relatively small systems and often rely on a- priori knowledge of the state-space of the system. Nuclear materials, however, are often multi-component systems owing to the evolution of composition under irradiation and an approach based on a-priori mapping of phase diagram is often not enough. This work is aimed at demonstrating an on-the-fly surrogate modeling framework that uses active learning to reduce the number of full equilibrium calculations that must be performed. By combining with efficient coupling approaches, the surrogate framework helps in reducing the computational cost of thermodynamic equilibrium informed multiphysics simulations of nuclear materials. The performance is benchmarked against full coupling with the thermochemistry library Thermochimica [3]. This work uses a machine learning based approach for constructing surrogate models to predict the stable phases in a multicomponent system. The surrogates were constructed using neural networks and Gaussian process classification. In this work, we compare the relative performance of the two methods. We also demonstrate the use of caching previous calculations by interpolating the values from nearest neighbors. References [1] Lindsay, A.D., et al. "2.0 – MOOSE: Enabling massively parallel multiphysics simulation", SoftwareX, 20 (2022): 101202. [2] Roos, W.A. and Zietsman J.H. "Accelerating complex chemical equilibrium calculations – A Review", Calphad, 77 (2022): 102380. [3] Piro, M.H.A., et al. "The thermochemistry library Thermochimica", Computational Materials Science, 67 (2013): 266-272.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Optimizing Grain Boundary Structures with LAMMPS Using Evolutionary Algorithms

Grain boundary structure optimization is an important part of materials modeling. Current methods for grain boundary structure optimization involve inefficient, time-consuming processes that do not fully explore the interface parameter space. Evolutionary algorithms have recently been demonstrated to be effective at determining both stable and metastable grain boundary interface structures. In this work, we demonstrate the use of GBOpt, a grain boundary structure optimization software designed to use the Large-scale Atomic/Molecular Massively Parallel Simulation (LAMMPS) software to efficiently determine grain boundary structures. We demonstrate that a only a few manipulations, namely atom insertion, atom removal, and relative grain displacement, are sufficient to explore much of the grain boundary structure parameter space. The efficacy of this approach is demonstrated on an FCC Ni system, and a BCC Fe system. The computational cost is compared against the gamma-surface sampling approach to demonstrate performance improvement.

Evolutionary algorithms↗
DOE OSTI2020

Pair plasma instability in homogeneous magnetic guide fields

Pair plasmas, collections of both matter and antimatter particles of equal mass, represent a paradigm for the study of basic plasma science, and many open questions exist regarding these unique systems. They are found in many astrophysical settings, such as gamma-ray bursts, and have recently also been produced in carefully designed laboratory experiments. A central research topic in plasma physics is instability; however, unlike their more common ion–electron siblings, pair plasmas are generally thought to be stable to cross field pressure gradients in homogeneous magnetic fields. It is shown here by means of kinetic full-f simulations that, when a pressure gradient is first established, the Gradient-driven Drift Coupling mode is destabilized and becomes turbulent. Force balance is eventually achieved by a combination of flattened pressure profiles due to turbulent transport and establishment of a magnetic field gradient, saturating the growth. During the unstable phase, key physics can be captured by a δf gyrokinetic description, where it is shown analytically and numerically that parallel particle motion results in a coupling of all electromagnetic field components. A fluid model derived therefrom accurately predicts linear eigenmodes and is used to resolve global profile effects. For laser-based electron–positron plasma experiments, prompt instability is predicted with growth times much shorter than plasma lifetimes. Similarly, growth rates are calculated for the planned APEX experiment as well as gamma-ray burst scenarios, suggesting that the instability may contribute to the early evolution of these systems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Validation of a Generalized Formulation for Load-Sharing Behavior in Epicyclic Gears for Wind Turbines: Preprint

In an ideal epicyclic gear set every parallel gear path transmits the same amount of torque. However, it is well known that certain manufacturing variations result in unequal load sharing between the parallel gear paths. Previous works have developed and validated a general closed-form analytical model of this phenomenon that describes the load sharing characteristics of epicyclic gear sets from three to six planets at any torque level. More recently, this analytical model has been reformulated to include the effects of gravity, carrier bearing clearance, and external applied moments, all of which are relevant to most gearboxes and their mounting configuration in horizontal-axis wind turbines. In this paper, the reformulated model is compared to load measurements collected from two similar wind turbine gearboxes with three-planet epicyclic gear sets. The resulting load sharing values are also compared to the mesh load factor requirements in the AGMA 6006 and IEC 61400-4 wind turbine gearbox design standards. Load sharing factors as high as 1.16 at extreme rotor moments and 1.08 with no moment were measured for the gearbox with cylindrical roller bearings, but the load sharing factor remained below 1.10 for the gearbox with tapered roller bearings The results show that in the wind turbine application, load sharing is not equal - even for three-planet systems with a floating central member because of the effects of gravity, rotor moments, and the resulting relative motions among the epicyclic gear components within the carrier bearing clearance.

closed-form analytical model↗
DOE OSTI2022

Impacts of Sub‐Grid Topographic Representations on Surface Energy Balance and Boundary Conditions in the E3SM Land Model: A Case Study in Sierra Nevada

Abstract Sub‐grid topographic heterogeneity has large impacts on surface energy balance and land‐atmosphere interactions. However, the impacts of representing sub‐grid topographic effects in land surface models (LSMs) on surface energy balance and boundary conditions remain unclear. This study analyzed and evaluated the impacts of sub‐grid topographic representations on surface energy balance, turbulent heat flux, and scalar (co‐)variances in the Energy Exascale Earth System Model (E3SM) land model (ELM). Three sub‐grid topographic representations in ELM were compared: (a) the default sub‐grid structure (D), (b) the recently developed sub‐grid topographic structure (T), and (c) high spatial resolution (1KM). Additionally, two different solar radiation schemes in ELM were compared: (a) the default plane‐parallel radiative transfer scheme (PP) and (b) the parameterization scheme (TOP) that accounts for sub‐grid topographic effects on solar radiation. A series of offline simulations with the three grid discretization structures (D, T, and 1KM) and two schemes of solar radiation (TOP and PP) were carried out using the Sierra Nevada, California. 1KM simulations with TOP well capture the spatial heterogeneity of surface fluxes compared to Moderate Resolution Imaging Spectroradiometer remote sensing data. There are significant differences between TOP and PP in the 1‐km simulated surface energy balance, but the differences in mean values and standard deviations become small when aggregated to the grid scale (i.e., 0.5°). The T configuration better mimics the 1KM simulations with TOP than the D configuration and better captures the sub‐grid topographic effects on surface energy balance and boundary conditions. These results underline the importance of representing sub‐grid topographic heterogeneities in LSMs and motivate future research to understand the sub‐grid topographic effects on land‐atmosphere interactions over mountainous areas.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Spinor $GW$ Bethe-Salpeter calculations in BerkeleyGW: Implementation, symmetries, benchmarking, and performance

Computing the GW quasiparticle band structure and Bethe-Salpeter equation (BSE) absorption spectra for materials with spin-orbit coupling have commonly been done by treating GW corrections and spin-orbit coupling (SOC) as separate perturbations to density-functional theory. However, accurate treatment of materials with strong spin-orbit coupling (such as many topological materials of recent interest, and thermoelectrics) often requires a nonperturbative approach using spinor wave functions in the Kohn-Sham equation and GW/BSE. Such calculations have only recently become available, in particular for the BSE. Here, we have implemented this approach in the plane-wave pseudopotential GW/BSE code BerkeleyGW, which is highly parallelized and widely used in the electronic-structure community. We present reference results for quasiparticle band structures and optical absorption spectra of solids with different strengths of spin-orbit coupling, including Si, Ge, GaAs, GaSb, CdSe, Au, and Bi 2 Se 3 . The calculated quasiparticle band gaps of these systems are found to agree with experiment to within a few tens of meV. SOC splittings are found to be generally in better agreement with experiment, including quasiparticle corrections to band energies. The absorption spectrum of GaAs is not significantly impacted by the inclusion of spin-orbit coupling due to its relatively small value (0.2 eV) in the Λ direction, while the absorption spectrum of GaSb calculated with the spinor GW/BSE captures the large spin-orbit splitting of peaks in the spectrum. For the prototypical topological insulator Bi 2 Se 3 , we find a drastic change in the low-energy band structure compared to that of DFT, with the spinorial treatment of the GW approximation correctly capturing the parabolic nature of the valence and conduction bands after including off-diagonal self-energy matrix elements. We present the detailed methodology, approach to spatial symmetries for spinors, comparison against other codes, and performance compared to spinless GW/BSE calculations and perturbative approaches to SOC. This work aims to spur further development of spinor GW/BSE methodology in excited-state research software and enables a more accurate and detailed exploration of electronic and optical properties of materials containing elements with large atomic numbers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

The Persistent Challenge of Data Locality in the Post-Exascale Era

The era of exascale computing, exemplified by systems like Frontier achieving exaflop-level performance, marks a milestone. However, the quest for sheer compute power leads to strong imbalance in system design. Hence, scaling advancements in memory, network bandwidth, and storage are also necessary and pose challenges, with a crucial need to address data locality issues. This article underscores the fundamental importance of data locality as a key abstraction for optimizing application performance. Despite notable software solutions, the growing complexity of parallelism and memory hierarchy demands performance-portable data locality solutions across diverse computing platforms. Additionally, the article revisits data locality aspects, covering hardware considerations, application perspectives, software stack abstractions, and tool support. It concludes with insights into data locality challenges and opportunities, emphasizing the ongoing significance of collaborative research for progress in this critical issue.

Unat, Didem [Koc University, Istanbul (Turkey)] (O↗
DOE OSTI2022

PETSc TSAdjoint: A Discrete Adjoint ODE Solver for First-Order and Second-Order Sensitivity Analysis

Here, we present a new software system PETSc TSAdjoint for first-order and second order adjoint sensitivity analysis of time-dependent nonlinear differential equations. The derivative calculation in PETSc TSAdjoint is essentially a high-level algorithmic differentiation process. The adjoint models are derived by differentiating the timestepping algorithms and implementing them based on the parallel infrastructure in PETSc. Full differentiation of the library code, including MPI routines, is avoided, and users do not need to derive their own adjoint models for their specific applications. PETSc TSAdjoint can compute the first-order derivative, that is, the gradient of a scalar functional, and the Hessian-vector product, which carries second-order derivative information, while requiring minimal input (a few callbacks) from the users. The adjoint model employs optimal checkpointing schemes in a manner that is transparent to users. Finally, usability, efficiency, and scalability are demonstrated through examples from a variety of applications.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Threat Agnostic Virulence Assessment of Pathogens

Virulence assessment of new, emerging, and engineered pathogens is critical to mounting an appropriate response to a biothreat agent. The capacity of the pathogen to colonize human and harm tissues must be characterized to understand pathogenicity pathways and optimize diagnosis and treatment of resulting disease. Respiratory pathogens are of interest because they can have high transmissibility rates, as observed with the SARS-CoV-2 virus, the causative agent of Covid-19. Current technologies are insufficient to assess threats due to their reliance on systems with only one cell type and on sequencing the pathogen. However, it is known that sequence is not an accurate predictor of function, and sequencing can be unreliable for newly emerged or engineered pathogens. An ideal system would consist of relevant epithelial cell types and an assay sensitive enough to detect changes in host responses that do not rely on DNA sequencing. We chose a system consisting of host lung epithelial cells that can be used to assess the virulence of unknown respiratory pathogens. We interrogated pathogens using this model and assess features of pathogenicity. Our objective is to leverage PNNLs strengths in tissue engineering and proteomics capabilities to build a multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) liquid chromatography-tandem mass spectrometry assay for human host cell proteins whose abundance is influenced by infection. These responses can were then assessed for relative virulence using pathogen agnostic signatures. When confronted with a pathogen, cells activate dedicated signaling pathways, typically through phosphorylation of regulatory proteins and downstream activation of host cell networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Enabling Floating Offshore VAWT Design by Coupling OWENS and OpenFAST

Vertical-axis wind turbines (VAWTs) have a long history, with a wide variety of turbine archetypes that have been designed and tested since the 1970s. While few utility-scale VAWTs currently exist, the placement of the generator near the turbine base could make VAWTs advantageous over tradition horizontal-axis wind turbines for floating offshore wind applications via reduced platform costs and improved scaling potential. However, there are currently few numerical design and analysis tools available for VAWTs. One existing engineering toolset for aero-hydro-servo-elastic simulation of VAWTs is the Offshore Wind ENergy Simulator (OWENS), but its current modeling capability for floating systems is non-standard and not ideal. This article describes how OWENS has been coupled to several OpenFAST modules to update and improve modeling of floating offshore VAWTs and discusses the verification of these new capabilities and features. The results of the coupled OWENS verification test agree well with a parallel OpenFAST simulation, validating the new modeling and simulation capabilities in OWENS for floating VAWT applications. These developments will enable the design and optimization of floating offshore VAWTs in the future.

17 WIND ENERGY↗
DOE OSTI2021

Restoration Strategy for Active Distribution Systems Considering Endogenous Uncertainty in Cold Load Pickup

Cold load pickup (CLPU) phenomenon is identified as the persistent power inrush upon a sudden load pickup after an outage. Under the active distribution system (ADS) paradigm, where distributed energy resources (DERs) are extensively installed, the decreased outage duration can induce a strong interdependence between CLPU pattern and load pickup decisions. In this paper, we propose a novel modelling technique to tractably capture the decision-dependent uncertainty (DDU) inherent in the CLPU process. Subsequently, a two-stage stochastic decision-dependent service restoration (SDDSR) model is constructed, where first stage searches for the optimal switching sequences to decide step-wise network topology, and the second stage optimizes the detailed generation schedule of DERs as well as the energization of switchable loads. Further, to tackle the computational burdens introduced by mixed-integer recourse, the progressive hedging algorithm (PHA) is utilized to decompose the original model into scenario-wise subproblems that can be solved in parallel. The numerical test on modified IEEE 123-node test feeders has verified the efficiency of our proposed SDDSR model and provided fresh insights into the monetary and secure values of DDU quantification.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Robust multi‐loop control of a floating wind turbine

Abstract A principal challenge facing the control of floating offshore wind turbines (FOWTs) is the problem of instability, or “negative damping,” when using blade pitch feedback to control generator speed. This closed‐loop instability can be attributed to non‐minimum phase zeros in the transfer function from blade pitch to generator speed. Standard approaches to improving stability and performance include robust tuning of control gains and introducing multiple feedback loops to respond to platform motion. Combining these approaches is nontrivial because multiple control loops complicate the impact of coupling in the system dynamics. The single‐loop approach to analyzing stability robustness neglects inter‐loop coupling, while a simplistic multi‐loop approach is highly sensitive to dimensional scaling and overestimates the robustness of the single‐loop controller. This work proposes a sensitivity representation that separates some of the natural FOWT dynamic coupling into a parallel feedback loop in the sensitivity function loop to address both of these concerns. The modified robustness measure is used with a simplified linear FOWT model to optimize scheduled multi‐loop control parameters in an automated tuning procedure. This controller is implemented for the 10‐MW Ultraflexible Smart FLoating Offshore Wind Turbine (USFLOWT) and compared against conventional single‐ and multi‐loop controllers tuned using frequency‐domain analysis and high‐fidelity OpenFAST simulations. The multi‐loop robust controller shows the highest overall performance in generator speed regulation and tower load reduction, though consideration of power quality, actuator usage, and other structural loading leads to additional trade‐offs.

Stockhouse, David↗
DOE OSTI2023

Multirate partitioned Runge–Kutta methods for coupled Navier–Stokes equations

Earth system models are complex integrated models of atmosphere, ocean, sea ice, and land surface. Coupling the components can be a significant challenge due to the difference in physics, temporal, and spatial scales. Further, this study explores multirate partitioned Runge-Kutta methods for the fluid-fluid interaction problem and demonstrates its parallel performance by using the PETSc library. We consider compressible Navier-Stokes equations with gravity coupled through a rigid-lid interface. Our large-scale numerical experiments reveal that multirate partitioned Runge-Kutta coupling schemes (1) can conserve total mass; (2) have second-order accuracy in time; and (3) provide favorable strong- and weak-scaling performance on modern computing architectures. We also show that the speedup factors of multirate partitioned Runge-Kutta methods match theoretical expectations over their base (single-rate) method.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Long-range current-induced spin accumulation in chiral crystals

Abstract Chiral materials, similarly to human hands, have distinguishable right-handed and left-handed enantiomers which may behave differently in response to external stimuli. Here, we use for the first time an approach based on the density functional theory (DFT)+PAOFLOW calculations to quantitatively estimate the so-called collinear Rashba–Edelstein effect (REE) that generates spin accumulation parallel to charge current and can manifest as chirality-dependent charge-to-spin conversion in chiral crystals. Importantly, we reveal that the spin accumulation induced in the bulk by an electric current is intrinsically protected by the quasi-persistent spin helix arising from the crystal symmetries present in chiral systems with the Weyl spin–orbit coupling. In contrast to conventional REE, spin transport can be preserved over large distances, in agreement with the recent observations for some chiral materials. This allows, for example, the generation of spin currents from spin accumulation, opening novel routes for the design of solid-state spintronics devices.

Roy, Arunesh↗