Guiding diamond spin qubit growth with computational methods
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Marcks, Jonathan C. (ORCID:0000000261628091)↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Magnon thermal conductivity in multiferroics with spin cycloids
Multiferroic materials, characterized by the occurrence of two or more ferroic properties, hold potential in future technological applications and also exhibit intriguing phenomena caused by the interplay of multiple orders. One such example is the formation of spin-cycloid structures within multiferroic materials, which we investigate in this work by focusing on their magnon excitations and transport based on a general multiferroic Hamiltonian with an antiferromagnetic order. More specifically, we identify the ground state and explore the dynamics of magnon modes, revealing distinct in-plane and out-of-plane modes with anisotropic dispersion relations. The magnon modes include a massless excitation, known as the Goldstone boson, originating from the spontaneous breaking of the translational symmetry by the formation of the cycloid structures. By employing the Boltzmann transport formalism, the magnonic thermal conductivity with spin cycloids and low-temperature anisotropic behaviors is discussed. This work provides pathways to envision the spin-textured multiferroics, which may serve as a fertile ground to look for novel thermal and spin transport with the rich interplay of quasiparticles such as magnons and phonons.
Park, Hyeon Woo↗
Community recommendations on cryoEM data archiving and validation
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
FPGA Computing
The articles in this special section focus on cutting-edge research on topics that relate to field programmable gate arrays (FPGA) in computing.
97 MATHEMATICS AND COMPUTING↗
Thermal Characterization of Tl 2 LiYCl 6 :Ce (TLYC)
Tl 2 LiYCl 6 :Ce (TLYC) is a new dual-detection elpasolite scintillator that can detect and distinguish between gamma rays and neutrons using pulse shape discrimination (PSD). It has a higher density and Z -number than the more mature and well-known elpasolite Cs 2 LiYCl 6 :Ce (CLYC), causing it to have a significantly better gamma-ray stopping power. These properties make TLYC an attractive alternative to CLYC for resource-constrained applications where size and weight are important, such as space or national security applications. Such applications may be subjected to a wide range of temperatures, and therefore, TLYC's performance was characterized for the first time over a temperature range of -20 °C to +50 °C in 10 °C increments. TLYC's thermal response effects on light-output linearity with energy, gamma-ray photopeak energy resolution, detected neutron energy, pulse shapes, and figure of merit (FOM) is analyzed and reported. The light output of TLYC was found to be linear with energy over the tested temperature range and was observed to decrease with increasing temperature. The decay time of the scintillation light output was observed to decrease with decreasing temperature at short times, leading to a decreasing PSD FOM. The gamma-ray photopeak energy resolution was also observed to degrade with decreasing temperature, due to an asymmetric broadening of the photopeak at low temperatures.
36 MATERIALS SCIENCE↗
Enabling Scalable and Extensible Memory-mapped Datastores in Userspace
Exascale workloads are expected to incorporate data-intensive processing in close coordination with traditional physics simulations. These emerging scientific, data-analytics and machine learning applications need to access a wide variety of datastores in flat files and structured databases. Programmer productivity is greatly enhanced by mapping datastores into the application process's virtual memory space to provide a unified “in-memory” interface. Currently, memory mapping is provided by system software primarily designed for generality and reliability. However, scalability at high concurrency is a formidable challenge on exascale systems. Also, there is a need for extensibility to support new datastores potentially requiring HPC data transfer services. In this article, we present UMap , a scalable and extensible userspace service for memory-mapping datastores. Furthermore, through decoupled queue management, concurrency aware adaptation, and dynamic load balancing, UMap enables application performance to scale even at high concurrency. We evaluate UMap in data-intensive applications, including sorting, graph traversal, database operations, and metagenomic analytics. Our results show that UMap as a userspace service outperforms an optimized kernel-based service across a wide range of intra-node concurrency by 1.22-1.9 × . We performed two case studies to demonstrate UMap 's extensibility. First, a new datastore residing in remote memory is incorporated into UMap as an application-specific plugin. Second, we present a persistent memory allocator Metall built atop UMap for unified storage/memory.
97 MATHEMATICS AND COMPUTING↗
Optimizing Management of Persistent Data Structures in High-Performance Analytics
Large-scale data analytics workflows ingest massive input data into various data structures, including graphs and key-value datastores. These data structures undergo multiple transformations and computations and are typically reused in incremental and iterative analytics workflows. Persisting in-memory views of these data structures enables reusing them beyond the scope of a single program run while avoiding repetitive raw data ingestion overheads. Memory-mapped I/O enables persisting in-memory data structures without data serialization and deserialization overheads. However, memory-mapped I/O lacks the key feature of persisting consistent snapshots of these data structures for incremental ingestion and processing. The obstacles to efficient virtual memory snapshots using memory-mapped I/O include background writebacks outside the application’s control, and the significantly high storage footprint of such snapshots. To address these limitations, we present Privateer, a memory and storage management tool that enables storage-efficient virtual memory snapshotting while also optimizing snapshot I/O performance. Here, we integrated Privateer into Metall, a state-of-the-art persistent memory allocator for C++, and the Lightning Memory-Mapped Database (LMDB), a widely-used key-value datastore in data analytics and machine learning. Privateer optimized application performance by 1.22× when storing data structure snapshots to node-local storage, and up to 16.7× when storing snapshots to a parallel file system. Privateer also optimizes storage efficiency of incremental data structure snapshots by up to 11× using data deduplication and compression.
Computer science↗
Mineralogy and petrology of fine‐grained samples recovered from the asteroid (162173) Ryugu
Abstract Samples returned from the carbonaceous asteroid (162173) Ryugu by the Hayabusa2 mission revealed that Ryugu is composed of materials consistent with CI chondrites and some types of space weathering. We report detailed mineralogy of the fine‐grained Ryugu samples allocated to our “Sand” team and report additional space weathering features found on the grains. The dominant mineralogy is composed of a fine‐grained mixture of Mg‐rich saponite and serpentine, magnetite, pyrrhotite, pentlandite, dolomite, and Fe‐bearing magnesite. These grains have mineralogy comparable to that of CI chondrites, showing severe aqueous alteration but lacking ferrihydrite and sulfate. These results are similar to previous works on large Ryugu grains. In addition to the major minerals, we also find many minerals that are rare or have not been reported among CI chondrites. Accessory minerals identified are hydroxyapatite, Mg‐Na phosphate, olivine, low‐Ca pyroxene, Mg‐Al spinel, chromite, manganochromite, eskolaite, ilmenite, cubanite, polydymite, transjordanite, schreibersite, calcite, moissanite, and poorly crystalline phyllosilicate. We also show scanning transmission electron microscope and scanning electron microscope compositional maps and images of some space‐weathered grains and severely heated and melted grains. Although our mineralogical results are consistent with that of millimeter‐sized grains, the fine‐grained fraction is best suited to investigate impact‐induced space weathering.
Geochemistry & Geophysics↗
Gating choreography and mechanism of the human proton-activated chloride channel $\mathrm{ASOR}$
The proton-activated chloride channel ASOR (TMEM206/PAC) permeates anions across cellular membranes in response to acidification, thereby enhancing acid-induced cell death and regulating endocytosis. The molecular mechanisms of pH-dependent control are not understood, in part because structural information for an activated conformation of ASOR is lacking. Here, we reconstitute function from purified protein and present a 3.1-Å-resolution cryo–electron microscopy structure of human ASOR at acidic pH in an activated conformation. The work contextualizes a previous acidic pH structure as a desensitized conformation. Combined with electrophysiological studies and high-resolution structures of resting and desensitized states, the work reveals mechanisms of proton sensing and ion pore gating. Clusters of extracellular acidic residues function as pH sensors and coalesce when protonated. Ensuing conformational changes induce metamorphosis of transmembrane helices to fashion an ion conduction pathway unique to the activated conformation. The studies identify a new paradigm of channel gating in this ubiquitous ion channel.
59 BASIC BIOLOGICAL SCIENCES↗
Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network
Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver. Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa. The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
59 BASIC BIOLOGICAL SCIENCES↗
Session Introduction: Graph Representations and Algorithms in Biomedicine
Connectivity is a fundamental property of biological systems: on the cellular level, proteins interact with each other to form protein-protein interaction networks (PPIs); on the organism level, neurons are arranged in a network; and on a community-level, species can have complex relationships with one another that drive the development and balance of an ecosystem. Graphs, representations of systems consisting of entities as vertices and their connections as edges, are a useful structure to characterize many such systems. Such models can be used to understand biological systems that naturally have a network structure, including PPIs, biological neurons, and ecosystems. In today’s information age, graph representations and algorithms (often in combination with machine learning techniques) are used to organize massive amounts of related data, much of which may be heterogeneous or unstructured, and identify patterns that represent novel biological insights. PSB’s 2023 session “Graph Representations and algorithms in Biomedicine,” encompasses modern developments in graph theory and its applications to various fields of biomedicine. This session includes a wide range of research - knowledge graphs built from text-mined health data, heterogeneous networks using multi-omic databases, and graphs refined to represent uncertainty or improve memory usage.
Chrisman, Brianna S.↗
Perspectives on AI Architectures and Codesign for Earth System Predictability
Abstract Recently, the U.S. Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER), and Advanced Scientific Computing Research (ASCR) programs organized and held the Artificial Intelligence for Earth System Predictability (AI4ESP) workshop series. From this workshop, a critical conclusion that the DOE BER and ASCR community came to is the requirement to develop a new paradigm for Earth system predictability focused on enabling artificial intelligence (AI) across the field, laboratory, modeling, and analysis activities, called model experimentation (ModEx). BER’s ModEx is an iterative approach that enables process models to generate hypotheses. The developed hypotheses inform field and laboratory efforts to collect measurement and observation data, which are subsequently used to parameterize, drive, and test model (e.g., process based) predictions. A total of 17 technical sessions were held in this AI4ESP workshop series. This paper discusses the topic of the AI Architectures and Codesign session and associated outcomes. The AI Architectures and Codesign session included two invited talks, two plenary discussion panels, and three breakout rooms that covered specific topics, including 1) DOE high-performance computing (HPC) systems, 2) cloud HPC systems, and 3) edge computing and Internet of Things (IoT). We also provide forward-looking ideas and perspectives on potential research in this codesign area that can be achieved by synergies with the other 16 session topics. These ideas include topics such as 1) reimagining codesign, 2) data acquisition to distribution, 3) heterogeneous HPC solutions for integration of AI/ML and other data analytics like uncertainty quantification with Earth system modeling and simulation, and 4) AI-enabled sensor integration into Earth system measurements and observations. Such perspectives are a distinguishing aspect of this paper. Significance Statement This study aims to provide perspectives on AI architectures and codesign approaches for Earth system predictability. Such visionary perspectives are essential because AI-enabled model-data integration has shown promise in improving predictions associated with climate change, perturbations, and extreme events. Our forward-looking ideas guide what is next in codesign to enhance Earth system models, observations, and theory using state-of-the-art and futuristic computational infrastructure.
54 ENVIRONMENTAL SCIENCES↗
The ECP SICM project: Managing complex memory hierarchies for exascale applications
The Exascale Computing Project (ECP)’s Simplified Interface to Complex Memories (SICM) effort focuses on developing universal interfaces for discovering, managing, and sharing data across complex memory hierarchies. These facilitate the exploitation of emerging memory technologies and support precise control over their various trade-offs such as high-bandwidth versus low-latency, persistent versus ephemeral, high-capacity versus low-capacity, and near-CPU versus near-GPU. SICM comprises three interrelated components: a low-level interface, a high-level interface, and a persistent-heap interface. The low-level SICM interface is intended for system and run-time developers as well as expert application developers who prefer full control of the memory objects used within their application. The high-level SICM interface builds upon the low-level interface, employing application-level profiling and analysis to optimize data management for complex memory hierarchies. The persistent-heap interface provides applications with a persistent memory allocator that can allocate custom C++ data structures in both block-storage and byte-addressable persistent memories.
97 MATHEMATICS AND COMPUTING↗
UMap: An application-oriented user level memory mapping library
Exploiting the prominent role of complex memories in exascale node architecture, the UMap page fault handler offers new capabilities to access large memory-mapped data sets directly. UMap provides flexible configuration options to customize page handling to each application, including analysis of massive observational and simulation data sets. The high-performance design features I/O decoupling, dynamic load balancing, and application-level controls. Page faults triggered by application threads and processes accessing data mapped to a UMapp’ed region are handled via the Linux userfaultfd protocol, an asynchronous message-oriented kernel-user communication mechanism that avoids the context switch penalty of traditional signal fault handlers. UMap is fully open source. In this paper, we give an overview of the UMap library architecture, its extensible plugin architecture, and the use/performance of UMap in emerging heterogeneous memory hierarchies such as near-node Non-volatile Memory (NVM) and network attached memories. We highlight new capabilities in two pagefault management plugins, the NetworkStore and SparseStore. We demonstrate the integration between UMap and multiple ECP products including Caliper, Metall, ZFP, Mochi, and Ripples.
97 MATHEMATICS AND COMPUTING↗
Expanded Validation of Uranium Systems with the KENO Monte Carlo Codes and SCALE 6.2.4
The development of accident-tolerant fuel and advanced reactors fueled with high-assay low-enriched uranium has created an increased focus on systems with uranium enrichments between 5 and 20 wt % 235 U. SCALE criticality safety validation reports generated at Oak Ridge National Laboratory contain very few benchmark experiments in this range. The work presented herein is an initial investigation of expanded validation of the entire range of enrichments for uranium-fueled systems, including consideration of over 300 newly developed KENO models. The vast majority of the new models are between 4.4 wt % and 37.5 wt % enrichment and include a variety of thermal, intermediate, and mixed neutron spectra. This work finds no strong evidence of an enrichment-dependent bias, but there are indications of a spectrum-dependent bias. There are, however, only a limited number of independent experiments included at this time to distinguish intermediate enrichment effects from intermediate spectrum effects. Further work in this area is ongoing for intermediate enrichment systems. In the long run, the addition of these models to the Verified, Archived Library and Inputs and Data is planned, as funding and staff availability allow.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Shock physics and shadowgraphic measurements of laser-produced cerium plasmas
Shadowgraphic measurements are combined with theory on gas-dynamics to investigate the shock physics associated with nanosecond laser ablation of cerium metal targets. Time-resolved shadowgraphic imaging is performed to measure the propagation and attenuation of the laser-induced shockwave through air and argon atmospheres at various background pressures, where stronger shockwaves characterized by higher propagation velocities are observed for higher ablation laser irradiances and lower pressures. The Rankine-Hugoniot relations are also employed to estimate the pressure, temperature, density, and flow velocity of the shock-heated gas located immediately behind the shock front, predicting larger pressure ratios and higher temperatures for stronger laser-induced shockwaves.
42 ENGINEERING↗
Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus
Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants’ experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.
59 BASIC BIOLOGICAL SCIENCES↗
Calibration verification for stochastic agent-based disease spread models
Accurate disease spread modeling is crucial for identifying the severity of outbreaks and planning effective mitigation efforts. To be reliable when applied to new outbreaks, model calibration techniques must be robust. However, current methods frequently forgo calibration verification (a stand-alone process evaluating the calibration procedure) and instead use overall model validation (a process comparing calibrated model results to data) to check calibration processes, which may conceal errors in calibration. In this work, we develop a stochastic agent-based disease spread model to act as a testing environment as we test two calibration methods using simulation-based calibration, which is a synthetic data calibration verification method. The first calibration method is a Bayesian inference approach using an empirically-constructed likelihood and Markov chain Monte Carlo (MCMC) sampling, while the second method is a likelihood-free approach using approximate Bayesian computation (ABC). Simulation-based calibration suggests that there are challenges with the empirical likelihood calculation used in the first calibration method in this context. These issues are alleviated in the ABC approach. Despite these challenges, we note that the first calibration method performs well in a synthetic data model validation test similar to those common in disease spread modeling literature. We conclude that stand-alone calibration verification using synthetic data may benefit epidemiological researchers in identifying model calibration challenges that may be difficult to identify with other commonly used model validation techniques.
60 APPLIED LIFE SCIENCES↗