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At least 1,171 records · Page 65

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DOE OSTI2018

The Portals 4.2 Network Programming Interface

This report presents a specification for the Portals 4 network programming interface. Portals 4 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4 is well suited to massively parallel processing and embedded systems. Portals 4 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandia's Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4 is targeted to the next generation of machines employing advanced network interface architectures that support enhanced offload capabilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Computational design of metal oxides to enhance the wetting and adhesion of silver-based brazes on yttria-stabilized-zirconia

Not provided.

Materials Science↗

DOE OSTI2024

Foldy: An open-source web application for interactive protein structure analysis

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Collaborative Computing Support for Analysis Facilities Exploiting Software as Infrastructure Techniques

Prior to the public release of Kubernetes it was difficult to conduct joint development of elaborate analysis facilities due to the highly non-homogeneous nature of hardware and network topology across compute facilities. However, since the advent of systems like Kubernetes and OpenShift, which provide declarative interfaces for building fault-tolerant and self-healing deployments of networked software, it is possible for multiple institutes to collaborate more effectively since resource details are abstracted away through various forms of hardware and software virtualization. In this whitepaper we will outline the development of two analysis facilities: "Coffea-casa" at University of Nebraska Lincoln and the "Elastic Analysis Facility" at Fermilab, and how utilizing platform abstraction has improved the development of common software for each of these facilities, and future development plans made possible by this methodology.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

The Portals 4.0.2 Networking Programming Interface

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

The Portals 4.3 Network Programming Interface

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

CFD Evaluation of Pressure Change Along Coolant Passages in Sodium-Cooled Fast Reactor with Nek5000

To support the design efforts of advanced sodium-cooled fast reactors (SFRs), a series of computational fluid dynamics (CFD) simulations are performed to investigate the pressure change along various flow passages in the proposed SFR system. The simulations are carried out with the state-of-the-art spectral element flow solver, Nek5000. Two specific case studies are presented in this paper: the flow exiting the axial neutron reflector channels and the flow entering the fuel pin bundle. Due to the high Reynolds numbers expected, a Reynolds-averaged Navier-Stokes (RANS) approach is necessary to model the turbulence. A newly developed regularized k-omega RANS model is adopted in the related CFD calculations. The first case study explores the effect of Reynolds number on the pressure change when flow exits the reflector channels. The pressure change in this case has two major contributors: the change due to wall friction and the Bernoulli effect. It is noted that the nondimensional pressure loss follows a log-linear trend up to Re = 10 5 , and then the trend is flattened. In the second case study, the advanced NekNek coupling capability is tested where an integral domain can be divided into multiple subdomains with coupling interfaces, which would greatly ease the meshing process of complex engineering geometries and potentially save computational resources. The preliminary results obtained so far confirm the consistency between the NekNek results and those produced by regular Nek5000 simulation. The presented work demonstrates the readiness and flexibility of the related CFD techniques, which is part of the broader effort to leverage cutting-edge CFD to inform the advanced nuclear reactor designs.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

Flexible and Modular Simultaneous Modeling of Flow and Reactive Transport in Rivers and Hyporheic Zones

Investigations of coupled multiphysics processes in rivers and hyporheic zones have extensively used numerical models. Most existing models use a sequential, one-way coupling between the surface and subsurface domains. Such one-way coupling potentially introduces error. To overcome this, a fully coupled model, hyporheicFoam, was developed using the open-source computational platform OpenFOAM. It captures the coupled flow and multicomponent reactive transport processes within both surface and subsurface domains and across their interface. The coupling between two domains is implemented by mapping conservative flux boundary conditions at the interface through an iterative algorithm. Reactive transport is enabled by specifying a reaction network. To start, we have implemented reaction kinetics following the double Monod-type model with inhibition. The model capability is illustrated through modeling of both conservative and reactive hyporheic flow and transport through dune bedforms. With the novel coupled model, it is now possible to quantify reactions wherein the reactants and products are constantly exchanging between domains and have feedbacks. hyporheicFoam can simulate large, three-dimensional cases owing to the computational flexibility and power offered by the code structure and parallel design of OpenFOAM.

58 GEOSCIENCES↗

DOE OSTI2025

Intermetallic phase formation in Al-Si-Zr alloys during hot isostatic pressing revealed by experiments and molecular dynamics

Understanding phase transformations at alloy interfaces is critical for the design of advanced structural materials. Here, in this study, we investigate the formation mechanisms of the Al 2 SiZr intermetallic phase in the Al-Si-Zr system under hot isostatic pressing (HIP) using molecular dynamics (MD) simulations and thermodynamic analysis. A unique aspect of our approach in MD involves the replacement of a disordered Al 2 SiZr stoichiometry with an ordered phase at the Al-Zr interface once HIP results in the desired Al 2 SiZr stoichiometry, allowing us to compute the total energetic cost of transformation by accounting for both formation energies and diffusion barriers. Diffusion coefficients and activation energies, extracted across a range of temperatures, reveal that HIP substantially enhances atomic mobility, creating favorable stoichiometry for phase evolution. Our results show that Al 2 SiZr phase formation is kinetically unfavorable at lower temperatures but becomes feasible when the thermodynamic driving energy surpass a critical energy threshold.

Roy, Ankit [Pacific Northwest National Laboratory ↗

DOE OSTI2020

First-Principles Approach for Assessing Cold Electron Injection Efficiency of Dye-Sensitized Solar Cell: Elucidation of Mechanism of Charge Injection and Recombination

The adequacy of the inclusion of spacer units in the metal-free D-π–A organic dyes pertaining to the augmentation of dye-sensitized solar cell (DSSC) efficiency has been examined through the excited-state simulations of the charge injection and recombination processes at the dye–semiconductor interface. Within the framework of the time-dependent density functional theory, the proposed computational studies focus on the precise evaluation of pivotal factors controlling the rates of photoinduced charge-transfer and energy-transfer processes, including electronic coupling, reorganization energy, and threshold energy barrier in the semiclassical Marcus formalism. The estimation of the fluorescent state appears to be the crucial step while explaining the ultrafast electron injection process and the charge recombination at the Marcus inverted region, as revealed by the obtained results. The retardation of charge recombination is facilitated by the insertion of a thiophene moiety between the π-bridge and the acceptor units. The estimated cold electron injection efficiencies deploying the Onsager–Braun theory, that rely on the computations of cold electron injection lifetime and cold electron lifetime, show a linear correlation with the experimental photovoltaic parameters of the DSSC comprising short-circuit current density, open-circuit voltage, and power conversion efficiency. The outcomes of the present investigation establish a basis for unraveling the mechanism of intricate dynamical processes upon photoexcitation of the sensitizers, as well as devising plausible routes for functional DSSC materials.

14 SOLAR ENERGY↗

DOE OSTI2025

Curvature Memory in Electrically Stimulated Lipid Membranes

Here, we demonstrate, using non-equilibrium molecular dynamics simulations, that lipid membrane capacitance varies with surface charge accumulation linked to membrane shape and curvature changes. Specifically, we show that lipid membranes exhibit a hysteretic response when exposed to oscillatory electric fields. The electromechanical coupling in these membranes leads to hysteretic buckling, in which the membrane can spontaneously buckle in one of two distinct directions along the electric field, even for the same ionic charge accumulation at the water–membrane interface. In this regard, these binary buckled membrane states suggest potential applications in neuromorphic computing. Their bistable nature, characterized by two distinct and stable configurations, could serve as a foundation for implementing memory storage systems and logic operations. Furthermore, we introduce a circuit model that captures these dynamic effects, offering insights into emergent memory effects in electrically stimulated lipid membranes. Finally, this work presents lipid bilayers as dynamic, adaptable elements and suggests a new platform for exploring energy storage, information processing, and memory encoding at the lipid membrane level.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Postmortem analysis of sand grain crushing from pile interface using X-ray tomography

Pile foundations of offshore platforms, wind and water turbines are typically subjected to a variety of cyclic loading paths due to their complex environment. While many studies focus on global pile behaviour, the soil-pile interface is explored here by a micromechanical study of the soil layer in contact with the pile surface. This work is devoted to the analysis of frozen post-mortem silica sand samples recovered at the pile interface following installation and cyclic loading tests in a calibration chamber using x-ray tomography. An experimental procedure developed for three dimensional (3D) snow imaging was adapted for the recovery of the in-situ sand samples to preserve their structure during tomography scans. 3D images at a pixel size of 7 {mu}m were then obtained using a cryogenic cell. Results confirm the presence of a shear band at the pile surface as well as void ratios changes in the direction of the pile's radius.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Nanoscale thermal transport. II. 2003–2012

A diverse spectrum of technology drivers such as improved thermal barriers, higher efficiency thermoelectric energy conversion, phase-change memory, heat-assisted magnetic recording, thermal management of nanoscale electronics, and nanoparticles for thermal medical therapies are motivating studies of the applied physics of thermal transport at the nanoscale. This review emphasizes developments in experiment, theory, and computation in the past ten years and summarizes the present status of the field. Interfaces become increasingly important on small length scales. Research during the past decade has extended studies of interfaces between simple metals and inorganic crystals to interfaces with molecular materials and liquids with systematic control of interface chemistry and physics. At separations on the order of ∼1 nm, the science of radiative transport through nanoscale gaps overlaps with thermal conduction by the coupling of electronic and vibrational excitations across weakly bonded or rough interfaces between materials. Major advances in the physics of phonons include first principles calculation of the phonon lifetimes of simple crystals and application of the predicted scattering rates in parameter-free calculations of the thermal conductivity. Progress in the control of thermal transport at the nanoscale is critical to continued advances in the density of information that can be stored in phase change memory devices and new generations of magnetic storage that will use highly localized heat sources to reduce the coercivity of magnetic media. Ultralow thermal conductivity—thermal conductivity below the conventionally predicted minimum thermal conductivity—has been observed in nanolaminates and disordered crystals with strong anisotropy. Advances in metrology by time-domain thermoreflectance have made measurements of the thermal conductivity of a thin layer with micron-scale spatial resolution relatively routine. Scanning thermal microscopy and thermal analysis using proximal probes has achieved spatial resolution of 10 nm, temperature precision of 50 mK, sensitivity to heat flows of 10 pW, and the capability for thermal analysis of sub-femtogram samples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Continuum model for hydrogen pickup in zirconium alloys of LWR fuel cladding

A continuum model for calculating the time-dependent hydrogen pickup fractions in various Zirconium alloys under steam and pressured water oxidation has been developed in this paper. Using only one fitting parameter, the effective hydrogen gas partial pressure at the oxide surface, a qualitative agreement is obtained between the predicted and previously measured hydrogen pickup fractions. The calculation results therefore demonstrate that H diffusion through the dense oxide layer plays an important role in the hydrogen pickup process. Finally, the limitations and possible improvement of the model are also discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2020

An open source analysis framework for large-scale building energy modeling

Full integration of building energy modelling into the design and retrofit process has long been a goal of building scientists and practitioners. However, significant barriers still exist. Among them are the lack of available: (1) configurable technology stacks for performing both small- and large-scale analyses, (2) different classes of algorithms compatible with common design workflows, and (3) analysis tools for effectively visualizing large-scale simulation results. This article discusses the OpenStudio® Analysis Framework: a scalable analysis framework for building energy modelling that was developed to overcome the three barriers listed above. The framework is open-source and scalable to facilitate wider adoption and has a clearly defined application programming interface upon which other applications can be built. It runs on high-performance computing systems, within cloud infrastructure, and on laptops, and uses a common workflow to enable different classes of algorithms. Lessons learned from previous development efforts are also discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2014

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its proteinsolvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2014

SU-D-BRF-05: A Novel System to Provide Real-Time Image-Guidance for Intrauterine Tandem Insertion and Placement

Purpose: To develop a system that provides real-time image-guidance for intrauterine tandem insertion and placement for brachytherapy. Methods: The conceptualized system consists of an intrauterine tandem with a transparent, lensed tip, a flexible miniature fiber optic scope, light source and interface for CCD coupling. The tandem tip was designed to act as a lens providing a wide field-of-view (FOV) with minimal image distortion and focus length appropriate for the application. The system is designed so that once inserted, the image-guidance component of the system can be removed and brachytherapy can be administered without interfering with source transport or disturbing tandem placement. Proof-of-principle studies were conducted to assess the conceptualized system's (1) lens functionality (clarity, focus and FOV) (2) and ability to visualize the cervical os of a female placed in the lithotomy position. Results: A prototype of this device was constructed using a commercial tandem modified to incorporate a transparent tip that internally coupled with a 1.9mm diameter fiber optic cable. The 900mm-long cable terminated at an interface that provided illumination as well as facilitated visualization of patient anatomy on a computer. The system provided a 23mm FOV with a focal length of 1cm and provided clear visualization of the cervix, cervical fornix and cervical os. The optical components of the system are easily removed without perturbing the position of a tandem placed in a common fixation clamp. Conclusion: Clinicians frequently encounter difficulty inserting an intrauterine tandem through the cervical os, circumventing fibrotic tissue or masses within the uterus, and positioning the tandem without perforating the uterus. To mitigate these challenges, we have designed and conducted proof-of- principle studies to discern the utility of a prototype device that provides real-time image-guidance for intrauterine tandem placement using fiber optic components.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2025

Neutron-Friendly Li-Ion Battery Coin Cell for In Situ 3D Visualization of Li Plating

Advanced battery characterization using in situ/operando neutron imaging is critical for uncovering degradation modes such as lithium (Li) plating in Li-ion batteries (LIBs). However, conventional LIBs hinder operando neutron radiography (NR) and in situ neutron micro-computed tomography (N-μCT) for visualizing Li plating near the graphite-separator interface due to strong attenuation from hydrogen-rich components like PP–PE–PP separators, electrolyte, and Fe-based spacers. In this work, we designed and tested a neutron-friendly battery (NFB) optimized for in situ Li detection during extreme fast charging (XFC). Guided by neutron attenuation cross-sections and material transmission, the NFB enables clear visualization at the graphite–separator interface, which is typically opaque in standard LIBs. Electrochemical tests show the NFB exhibits voltage/current responses like standard cells for up to 50 XFC cycles. However, its lower reversibility and capacity are likely due to Cu-coated Al spacer degradation from delamination or corrosion. We propose titanium spacers as a more stable alternative, albeit requiring custom machining. Using this optimized cell, we achieved simultaneous neutron tomography of multiple cells, capturing in situ 3D images of dead Li accumulation, particularly near graphite edges. These heterogeneous deposits and disconnected Li clusters suggest localized current density hotspots during XFC.

25 ENERGY STORAGE↗