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DOE OSTI2024

OpenACC offloading of the MFC compressible multiphase flow solver on AMD and NVIDIA GPUs

GPUs are the heart of the latest generations of supercomputers. We efficiently accelerate a compressible multiphase flow solver via OpenACC on NVIDIA and AMD Instinct GPUs. Optimization is accomplished by specifying the directive clauses gang vector and collapse. Further speedups of six and ten times are achieved by packing user-defined types into coalesced multidimensional arrays and manual inlining via metaprogramming. Additional optimizations yield seven-times speedup of array packing and thirty-times speedup of select kernels on Frontier. Weak scaling efficiencies of 97% and 95% are observed when scaling to 50% of Summit and 87% of Frontier. Strong scaling efficiencies of 84% and 81% are observed when increasing the device count by a factor of 8 and 16 on V100 and MI250X hardware. The strong scaling efficiency of AMD’s MI250X increases to 92% when increasing the device count by a factor of 16 when GPU-aware MPI is used for communication.

Wilfong, Benjamin↗

DOE OSTI2024

Enhancing the Q-Factor of a Practical Qubit Niobium Three-Dimensional λ/4-Resonator Through Surface Treatment

Quantum computing stands as a revolutionary frontier in information technology, with the potential to solve complex problems far beyond the capacity of classical computers. At the heart of this disruptive innovation are qubits, forming the fundamental backbone of quantum computing. A leading-edge solution for constructing robust, enduring qubits involves embedding a Josephson junction within a high Q-factor, superconducting three-dimensional cavity. Further, our recent innovation lies in developing a uniquely optimized, quarter-wave resonator-based superconducting cavity, functioning at 6 GHz, specifically tailored for quantum computers. In this work, we elucidate our advancement towards elevating the Q-factor tenfold, an achievement made possible through the enhancement of machining precision, the application of rigorous postprocessing techniques—including mechanical, chemical, and surface treatments—as well as the refinement of our testing methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Cryogenic Design and Thermal Analysis of EIC Central Detector (ePIC) Solenoid Magnet (MARCO)

The Electron Ion Collider (EIC) physics program utilizes a 2.0 T superconducting magnet at the heart of its ePIC detector system. This approximately 3.5 m long and 2.84 m diameter warm bore magnet has a 20 tons cold mass which is conduction-cooled using liquid helium at 4.5 K. A closed loop active thermosiphon system is chosen to facilitate the cooling and to maintain a minimum of 2 K temperature margin on the peak operating temperature (4.7 K) of the superconductor. Here, this paper presents the cryogenic design of the cooling system and the thermal analysis of the solenoid. A Computational fluid dynamics (CFD) model was developed to quantify the performance of the two–phase closed thermosiphon system and predict the temperature gradient on the cold mass.

Gopinath, Sandesh [Thomas Jefferson National Accel↗

DOE OSTI2020

Design of a Continuous Pellet Fueling System for Wendelstein 7-X

A continuous pellet fueling system (CPFS) is currently being designed at the Oak Ridge National Laboratory (ORNL) for the long pulse operation of the Wendelstein 7-X (W7-X) stellarator. The purpose of the CPFS is to provide deep continuous fueling for feedback-controlled high-density operation and mitigation of predicted hollow density profiles. As described here, the system will provide the capability to inject cylindrical pellets of solid hydrogen or deuterium into the plasma core, with flexibility to vary the pellet size, velocity, and injection frequency. Pellets are nominally of 3 mm in diameter and have a length between 1 and 4 mm. The heart of the CPFS is a vertically oriented, twin-screw extruder, cooled by three Gifford-McMahon cryocoolers in parallel, designed to form a continuous filament of hydrogen or deuterium. The filament width, which determines the pellet length, can be adjusted by means of a variable nozzle driven by a linear actuator at the base of the extruder. Coupled to the nozzle is a solenoid-operated gas gun and cutter assembly. A pneumatic propellant valve pulses a burst of ~60 bar helium to accelerate the cut pellet into W7-X. Three gaps in the guide tubes provide pumping locations to remove the helium propellant before it reaches the plasma. The maximum velocity of the pellet is limited by its ability to survive navigating the guide tube trajectory intact. A microwave cavity located within the guide tube provides the capability to measure the pellet size and velocity. The mechanical and thermal designs of the W7-X extruder, adjustable nozzle, and gun and cutter assembly design are described. A guide tube design and experimental pellet survivability test results are presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Novel animal model of multiple sclerosis: The glial connexin gap junction as an environmental tuner for neuroinflammation

Abstract Connexins, which comprise gap junctions (GJs) via homotypic/heterotypic oligomerization, act as channels to connect opposing cells, mainly in solid organs such as the skin, liver, heart, and central/peripheral nervous system. Connexins are synthesized in the endoplasmic reticulum, assembled in the Golgi apparatus as hexamers, and inserted into the cell membrane as hemichannels. These hemichannels are closed under normal conditions until they combine to form clusters and connect to neighboring cells via GJs in a head‐to‐head configuration. Opening of hemichannels, which depends on the intra‐ or extracellular environment, allows various bioactive molecules to enter into or be released from the host cells. Recent pathological studies on human demyelinating diseases have revealed alterations of connexin expression patterns in demyelinating lesions. To elucidate the molecular mechanisms of connexins in the pathomechanisms of inflammatory demyelination, we induced experimental autoimmune encephalomyelitis (EAE) in connexin 30 (Cx30)‐deficient mice, oligodendroglia‐specific Cx47‐ablated mice, and astroglia‐specific Cx43‐ablated mice. We found that both astroglial‐Cx30‐deficient mice and Cx43‐ablated mice showed amelioration of the clinical course of EAE, while oligodendroglial‐Cx47‐ablated mice showed aggravation. These findings indicate the distinct role of connexins expressed in different cell types and the substantial contribution of connexin‐mediated pathology to demyelinating disorders. The imbalance in connexin expression, which is caused by the inflammatory environment, results in an increase in hemichannels in glial cells. The release of proinflammatory molecules induced by the increase in hemichannels on activated glial cells is a crucial mechanism of demyelinating disorders.

Yamasaki, Ryo↗

DOE OSTI2023

Identification of ancestral gnathostome Gli3 enhancers with activity in mammals

Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15–21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. In conclusion, these results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Multi‐hypothesis comparison of Farquhar and Collatz photosynthesis models reveals the unexpected influence of empirical assumptions at leaf and global scales

Abstract Mechanistic photosynthesis models are at the heart of terrestrial biosphere models (TBMs) simulating the daily, monthly, annual and decadal rhythms of carbon assimilation ( A ). These models are founded on robust mathematical hypotheses that describe how A responds to changes in light and atmospheric CO 2 concentration. Two predominant photosynthesis models are in common usage: Farquhar (FvCB) and Collatz (CBGB). However, a detailed quantitative comparison of these two models has never been undertaken. In this study, we unify the FvCB and CBGB models to a common parameter set and use novel multi‐hypothesis methods (that account for both hypothesis and parameter variability) for process‐level sensitivity analysis. These models represent three key biological processes: carboxylation, electron transport, triose phosphate use (TPU) and an additional model process: limiting‐rate selection. Each of the four processes comprises 1–3 alternative hypotheses giving 12 possible individual models with a total of 14 parameters. To broaden inference, TBM simulations were run and novel, high‐resolution photosynthesis measurements were made. We show that parameters associated with carboxylation are the most influential parameters but also reveal the surprising and marked dominance of the limiting‐rate selection process (accounting for 57% of the variation in A vs. 22% for carboxylation). The limiting‐rate selection assumption proposed by CBGB smooths the transition between limiting rates and always reduces A below the minimum of all potentially limiting rates, by up to 25%, effectively imposing a fourth limitation on A . Evaluation of the CBGB smoothing function in three TBMs demonstrated a reduction in global A by 4%–10%, equivalent to 50%–160% of current annual fossil fuel emissions. This analysis reveals a surprising and previously unquantified influence of a process that has been integral to many TBMs for decades, highlighting the value of multi‐hypothesis methods.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Collagen Fibril Orientation in Tissue Specimens From Atherosclerotic Plaque Explored Using Small Angle X-Ray Scattering

Atherosclerotic plaques can gradually develop in certain arteries. Disruption of fibrous tissue in plaques can result in plaque rupture and thromboembolism, leading to heart attacks and strokes. Collagen fibrils are important tissue building blocks and tissue strength depends on how fibrils are oriented. Fibril orientation in plaque tissue may potentially influence vulnerability to disruption. While X-ray scattering has previously been used to characterize fibril orientations in soft tissues and bones, it has never been used for characterization of human atherosclerotic plaque tissue. This study served to explore fibril orientation in specimens from human plaques using small angle X-ray scattering (SAXS). Additionally, plaque tissue was extracted from human femoral and carotid arteries, and each tissue specimen contained a region of calcified material. Three-dimensional (3D) collagen fibril orientation was determined along scan lines that started away from and then extended toward a given calcification. Fibrils were found to be oriented mainly in the circumferential direction of the plaque tissue at the majority of locations away from calcifications. However, in a number of cases, the dominant fibril direction differed near a calcification, changing from circumferential to longitudinal or thickness (radial) directions. Further study is needed to elucidate how these fibril orientations may influence plaque tissue stress–strain behavior and vulnerability to rupture.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

High phase resolution: Probing interactions in complex interfaces with sum frequency generation

An often-quoted statement attributed to Wolfgang Pauli is that God made the bulk, but the surface was invented by the devil. Although humorous, the statement really reflects frustration in developing a detailed picture of a surface. In the last several decades, that frustration has begun to abate with numerous techniques providing clues to interactions and reactions at surfaces. Often these techniques require considerable prior knowledge. Complex mixtures on irregular or soft surfaces—complex interfaces—thus represent the last frontier. Two optical techniques: sum frequency generation (SFG) and second harmonic generation (SHG) are beginning to lift the veil on complex interfaces. Of these techniques, SFG with one excitation in the infrared has the potential to provide exquisite molecular- and moiety-specific vibrational data. This Perspective is intended both to aid newcomers in gaining traction in this field and to demonstrate the impact of high-phase resolution. It starts with a basic description of light-induced surface polarization that is at the heart of SFG. The sum frequency is generated when the input fields are sufficiently intense that the interaction is nonlinear. This nonlinearity represents a challenge for disentangling data to reveal the molecular-level picture. Three, high-phase-resolution methods that reveal interactions at the surface are described.

Biophysics↗

DOE OSTI2020

Laser writing of nitrogen-doped silicon carbide for biological modulation

Conducting or semiconducting materials embedded in insulating polymeric substrates can be useful in biointerface applications; however, attainment of this composite configuration by direct chemical processes is challenging. Laser-assisted synthesis has evolved as a fast and inexpensive technique to prepare various materials, but its utility in the construction of biophysical tools or biomedical devices is less explored. Here, we use laser writing to convert portions of polydimethylsiloxane (PDMS) into nitrogen-doped cubic silicon carbide (3C-SiC). The dense 3C-SiC surface layer is connected to the PDMS matrix via a spongy graphite layer, facilitating electrochemical and photoelectrochemical activity. We demonstrate the fabrication of arbitrary two-dimensional (2D) SiC-based patterns in PDMS and freestanding 3D constructs. To establish the functionality of the laser-produced composite, we apply it as flexible electrodes for pacing isolated hearts and as photoelectrodes for local peroxide delivery to smooth muscle sheets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Deconstructing laws of accessibility and facility distribution in cities

The era of the automobile has seriously degraded the quality of urban life through costly travel and visible environmental effects. A new urban planning paradigm must be at the heart of our road map for the years to come, the one where, within minutes, inhabitants can access their basic living needs by bike or by foot. In this work, we present novel insights of the interplay between the distributions of facilities and population that maximize accessibility over the existing road networks. Results in six cities reveal that travel costs could be reduced in half through redistributing facilities. In the optimal scenario, the average travel distance can be modeled as a functional form of the number of facilities and the population density. As an application of this finding, it is possible to estimate the number of facilities needed for reaching a desired average travel distance given the population distribution in a city.

42 ENGINEERING↗

DOE OSTI2024

Trapped-ion quantum simulation of electron transfer models with tunable dissipation

Electron transfer is at the heart of many fundamental physical, chemical, and biochemical processes essential for life. The exact simulation of these reactions is often hindered by the large number of degrees of freedom and by the essential role of quantum effects. Here, we experimentally simulate a paradigmatic model of molecular electron transfer using a multispecies trapped-ion crystal, where the donor-acceptor gap, the electronic and vibronic couplings, and the bath relaxation dynamics can all be controlled independently. By manipulating both the ground-state and optical qubits, we observe the real-time dynamics of the spin excitation, measuring the transfer rate in several regimes of adiabaticity and relaxation dynamics. Our results provide a testing ground for increasingly rich models of molecular excitation transfer processes that are relevant for molecular electronics and light-harvesting systems.

Science & Technology - Other Topics↗

DOE OSTI2021

Spatiotemporal characterization of the field-induced insulator-to-metal transition

Watching a metal filament grow Resistive switching is a process in which the electrical resistance of a sample changes abruptly in response to a voltage pulse, often by orders of magnitude. This process is at the heart of many neuromorphic computing approaches but visualizing it in both space and time is tricky. del Valle et al . monitored the resistive switching in three different vanadium oxide compounds by measuring time- and space-resolved optical reflectivity (see the Perspective by Hilgenkamp and Gao). A characteristic conducting filament was quickly nucleated on the inhomogeneities in the sample and then propagated due to Joule heating. —JS

Science & Technology - Other Topics↗

DOE OSTI2021

Controlling quantum many-body dynamics in driven Rydberg atom arrays

Dynamic stabilization of an array Large-scale systems comprising one-dimensional chains and two-dimensional arrays of excited atoms held in a programmable optical lattice are a powerful platform with which to simulate emergent phenomena. Bluvstein et al. built an array of up to 200 Rydberg atoms and subjected the system to periodic excitation. Under such driven excitation, they found that the array of atoms stabilized, freezing periodically into what looked like time crystals. Understanding and controlling the dynamic interactions in quantum many-body systems lies at the heart of contemporary condensed matter physics and the exotic phenomena that can occur. Science , this issue p. 1355

Science & Technology - Other Topics↗

DOE OSTI2023

Bioadhesive polymer semiconductors and transistors for intimate biointerfaces

The use of bioelectronic devices relies on direct contact with soft biotissues. For transistor-type bioelectronic devices, the semiconductors that need to have direct interfacing with biotissues for effective signal transduction do not adhere well with wet tissues, thereby limiting the stability and conformability at the interface. Here we report a bioadhesive polymer semiconductor through a double-network structure formed by a bioadhesive brush polymer and a redox-active semiconducting polymer. The resulting semiconducting film can form rapid and strong adhesion with wet tissue surfaces together with high charge-carrier mobility of ~1 square centimeter per volt per second, high stretchability, and good biocompatibility. Further fabrication of a fully bioadhesive transistor sensor enabled us to produce high-quality and stable electrophysiological recordings on an isolated rat heart and in vivo rat muscles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein

Respiratory syncytial virus (RSV) causes severe disease in young infants, particularly those with heart or lung diseases or born prematurely. Because no vaccine is currently available, monoclonal antibodies are used to prevent severe RSV disease in high-risk infants. While it is known that RSV evolves to avoid recognition by antibodies, screening tools that can predict which changes to the virus may lead to antibody resistance are greatly needed.

molecular modeling↗

DOE OSTI2023

Impact of Polymicrobial Infection on Fitness of Streptococcus gordonii In Vivo

Pathogenic microbial ecosystems are often polymicrobial, and interbacterial interactions drive emergent properties of these communities. In the oral cavity, Streptococcus gordonii is a foundational species in the development of plaque biofilms, which can contribute to periodontal disease and, after gaining access to the bloodstream, target remote sites such as heart valves. Here, we used a transposon sequencing (Tn-Seq) library of S. gordonii to identify genes that influence fitness in a murine abscess model, both as a monoinfection and as a coinfection with an oral partner species, Porphyromonas gingivalis. In the context of a monoinfection, conditionally essential genes were widely distributed among functional pathways. Coinfection with P. gingivalis almost completely changed the nature of in vivo gene essentiality. Community-dependent essential (CoDE) genes under the coinfection condition were primarily related to DNA replication, transcription, and translation, indicating that robust growth and replication are required to survive with P. gingivalis in vivo. Interestingly, a group of genes in an operon encoding streptococcal receptor polysaccharide (RPS) were associated with decreased fitness of S. gordonii in a coinfection with P. gingivalis. Individual deletion of two of these genes (SGO_2020 and SGO_2024) resulted in the loss of RPS production by S. gordonii and increased susceptibility to killing by neutrophils. P. gingivalis protected the RPS mutants by inhibiting neutrophil recruitment, degranulation, and neutrophil extracellular trap (NET) formation. These results provide insight into genes and functions that are important for S. gordonii survival in vivo and the nature of polymicrobial synergy with P. gingivalis. Furthermore, we show that RPS-mediated immune protection in S. gordonii is dispensable and detrimental in the presence of a synergistic partner species that can interfere with neutrophil killing mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Targeted curation of the gut microbial gene content modulating human cardiovascular disease

Despite the promise of the gut microbiome to predict human health, few studies expose the molecular-scale processes underpinning such forecasts. We mined over 200,000 gut-derived genomes from cultivated and uncultivated microbial lineages to inventory the gut microorganisms and their gene content that control trimethylamine-induced cardiovascular disease. We assigned an atherosclerotic profile to the 6,341 microbial genomes that encoded metabolisms associated with heart disease, creating the Methylated Amine Gene Inventory of Catabolism database (MAGICdb). From microbiome gene expression data sets, we demonstrate that MAGICdb enhanced the recovery of disease-relevant genes and identified the most active microorganisms, unveiling future therapeutic targets. From the feces of healthy and diseased subjects, we show that MAGICdb predicted cardiovascular disease status as effectively as traditional lipid blood tests. This functional microbiome catalog is a public, exploitable resource, designed to enable a new era of microbiota-based therapeutics and diagnostics

metatranscriptomics↗