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At least 973 records · Page 54

TU-F-BRD-01: Biomedical Informatics for Medical Physicists

Biomedical informatics encompasses a very large domain of knowledge and applications. This broad and loosely defined field can make it difficult to navigate. Physicists often are called upon to provide informatics services and/or to take part in projects involving principles of the field. The purpose of the presentations in this symposium is to help medical physicists gain some knowledge about the breadth of the field and how, in the current clinical and research environment, they can participate and contribute. Three talks have been designed to give an overview from the perspective of physicists and to provide a more in-depth discussion in two areas. One of the primary purposes, and the main subject of the first talk, is to help physicists achieve a perspective about the range of the topics and concepts that fall under the heading of 'informatics'. The approach is to de-mystify topics and jargon and to help physicists find resources in the field should they need them. The other talks explore two areas of biomedical informatics in more depth. The goal is to highlight two domains of intense current interest--databases and models--in enough depth into current approaches so that an adequate background for independent inquiry is achieved. These two areas will serve as good examples of how physicists, using informatics principles, can contribute to oncology practice and research. Learning Objectives: To understand how the principles of biomedical informatics are used by medical physicists. To put the relevant informatics concepts in perspective with regard to biomedicine in general. To use clinical database design as an example of biomedical informatics. To provide a solid background into the problems and issues of the design and use of data and databases in radiation oncology. To use modeling in the service of decision support systems as an example of modeling methods and data use. To provide a background into how uncertainty in our data and knowledge can be incorporated into modeling methods.

97 MATHEMATICS AND COMPUTING↗

Search for Low-Mass Dark Matter wtih SuperCDMS Soudan and Study of Shorted Electric Field Configurations in CDMS Detectors

The area of dark matter is one of the most interesting and exciting topics in physics today. Existing at the intersection of particle physics and astrophysics, the existence of a new dark matter particle can be used to explain many astrophysical and cosmological observations, as well as to reconcile outstanding issues in the standard model of particle physics. Experiments such as SuperCDMS are built to detect dark matter in the lab by looking for low-energy nuclear recoils produced by collisions between dark matter particles and atoms in terrestrial detectors. SuperCDMS Soudan is particularly well-suited to follow up on possible hints of low-mass dark matter seen by other recent experiments because of its low thresholds and excellent background discrimination. Analyzing SuperCDMS Soudan data to look for low-mass dark matter comes with particular challenges because of the low signal-to-noise very near threshold. However, with a detailed background model developed by scaling high-energy events down into the low-energy signal region, SuperCDMS Soudan produced worldleading limits on the existence of low-mass dark matter. In addition, a few SuperCDMS Soudan detectors experienced cold hardware problems that can affect the data collected. Of particular interest is one detector considered for the low-mass WIMP search that has one of its charge electrodes shorted to chassis ground. Three events were observed in this detector upon unblinding the SuperCDMS Soudan low-energy data, even though <1 event was expected based on pre-unblinding calulations. However, the data collected by the shorted detector may have been compromised since an electrode shorted to ground will modify the electric field in the detector. The SuperCDMS Detector Monte Carlo (DMC) provides an excellent way to model the effects of the modified electric field, so a new model of the expected backgrounds in the low-mass WIMP search is developed using the DMC to try to explain how the short may have affected the data collected. This thesis is organized as follows: Chapter 1 gives a broad introduction to dark matter, discussing the astrophysical and cosmological evidence for its existence, listing several possible particle physics candidates, and outlining several experimental strategies to look for dark matter. Chapter 2 is an overview of CDMS detector technology and the experimental setup at the Soudan Underground Laboratory, with a focus on how data coming out of Soudan is analyzed. Chapter 3 presents results from a search for low-mass dark matter at SuperCDMS Soudan and discusses the interpretation of the results. Chapter 4 contains follow-up work that uses the CDMS Detector Monte Carlo (DMC) to understand the possible systematics associated with a detector that had one of its charge electrodes shorted to ground. This chapter represents the first time the DMC has been used to inform ongoing CDMS analysis. Chapter 5 takes a brief detour into the world of effective field theory (EFT), examining the consequences of an expanded set of possible WIMP-nucleon interactions in the EFT framework. Finally, Chapter 6 wraps up the material of the previous chapters and discusses how the research presented in this thesis can be applied as CDMS moves toward SuperCDMS SNOLAB.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Editorial for Special Issue “Environmentally Sound In Situ Recovery Mining of Uranium”

This Special Issue features seven articles that cover a range of topics pertaining to the environmentally sound in situ recovery mining of uranium (U ISR). The topics include: (1) methods for assessing the potential environmental impacts of future U ISR operations using historical operational records and available geohydrologic, geochemical and climate data in a specific regional setting; (2) laboratory column studies to parameterize a uranium surface complexation model that can be used to predict uranium fate and transport in groundwater; and (3) a field evaluation of both a chemical reductant and a biostimulant to promote reducing geochemical conditions after oxidative mining at a U ISR facility.

54 ENVIRONMENTAL SCIENCES↗

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗

Large thermal hysteresis in a single-phase NiTiNb shape memory alloy

Large thermal hysteresis ($T$ hys ) is favorable in shape memory alloys (SMAs) because it renders wide service and storage temperature range of the SMA-made parts. In this letter, we show that large intrinsic $T$ hys up to 100 K is achieved in a low Nb content (2 at.%), β-Nb-free and single-phase NiTiNb SMA fabricated by casting, forging, wire-drawing and annealing. Such a large $T$ hys is comparable to that of the widely used dual-phase NiTiNb SMAs in which high Nb content and β-Nb are required. By exploiting the grain-size-dependence of $T$ hys in our single-phase NiTiNb SMA and that in an equiatomic NiTi SMA, we attribute the large $T$ hys to the enhanced kinetic resistance of transformation by the small grains. In conclusion, the connection between the $T$ hys and the kinetic resistance is demonstrated by a modified dislocation-based kinetic model.

36 MATERIALS SCIENCE↗

Phase transitions in few-monolayer spin ice films

Vertex models are an important class of statistical mechanical system that admit exact solutions and exotic physics. Applications include water ice, ferro- and antiferro-electrics, spin ice and artificial spin ice. Here we show that it is possible to engineer spin ice films with atomic-layer precision down to the monolayer limit. Specific heat measurements show that these films, which have a fundamentally different symmetry to bulk spin ice, realise systems close to the two-dimensional F-model, with exotic phase transitions on topologicallyconstrained configurational manifolds. Our results show how spin ice thin films can release the celebrated Pauling entropy of spin ice without an anomaly in the specific heat. They also significantly expand the class of vertex models available to experiment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

PAH101: A GW+BSE Dataset of 101 Polycyclic Aromatic Hydrocarbon (PAH) Molecular Crystals

Abstract The excited-state properties of molecular crystals are important for applications in organic electronic devices. TheGWapproximation and Bethe-Salpeter equation (GW+BSE) is the state-of-the-art method for calculating the excited-state properties of crystalline solids with periodic boundary conditions. We present the PAH101 dataset ofGW+BSE calculations for 101 molecular crystals of polycyclic aromatic hydrocarbons (PAHs) with up to ~500 atoms in the unit cell. To the best of our knowledge, this is the firstGW+BSE dataset for molecular crystals. The data records include theGWquasiparticle band structure, the fundamental band gap, the static dielectric constant, the first singlet exciton energy (optical gap), the first triplet exciton energy, the dielectric function, and optical absorption spectra for light polarized along the three lattice vectors. The dataset can be used to (i) discover materials with desired electronic/optical properties, (ii) identify correlations between DFT andGW+BSE quantities, and (iii) train machine learned models to help in materials discovery efforts.

Science & Technology - Other Topics↗

Uncertainty-aware mixed-variable machine learning for materials design

Abstract Data-driven design shows the promise of accelerating materials discovery but is challenging due to the prohibitive cost of searching the vast design space of chemistry, structure, and synthesis methods. Bayesian optimization (BO) employs uncertainty-aware machine learning models to select promising designs to evaluate, hence reducing the cost. However, BO with mixed numerical and categorical variables, which is of particular interest in materials design, has not been well studied. In this work, we survey frequentist and Bayesian approaches to uncertainty quantification of machine learning with mixed variables. We then conduct a systematic comparative study of their performances in BO using a popular representative model from each group, the random forest-based Lolo model (frequentist) and the latent variable Gaussian process model (Bayesian). We examine the efficacy of the two models in the optimization of mathematical functions, as well as properties of structural and functional materials, where we observe performance differences as related to problem dimensionality and complexity. By investigating the machine learning models’ predictive and uncertainty estimation capabilities, we provide interpretations of the observed performance differences. Our results provide practical guidance on choosing between frequentist and Bayesian uncertainty-aware machine learning models for mixed-variable BO in materials design.

36 MATERIALS SCIENCE↗

A new model for the effective thermal conductivity of polycrystalline solids

We introduce a novel model for the effective thermal conductivity of polycrystalline solids based on the thin-interface description of grain boundaries (GBs). In contrast to existing models, our new model treats a GB as an autonomous “phase” with its own thermal conductivity. The Kapitza resistance/conductance of a thin interface is then derived in terms of the interface thermal conductivity and width. In turn, the effective thermal conductivity of polycrystals is derived in terms of grain size, grain and GB conductivities, and GB width. This treatment allows the model to simulate the change of the Kapitza resistance/conductance with segregation/doping, GB structure/phase transition, or GB decohesion. Moreover, since the model assumes a finite width for GBs, it is expected to give better predictions than its sharp-interface-based counterparts for nanoscale grains. The predictions of the new model deviate from the corresponding ones from existing models by 1%–100% as the grain size approaches the GB width. High-fidelity finite-element simulations were conducted to validate the predictions of the new model. These simulations proved the higher accuracy of the new model. We also discuss how to generalize this treatment to other types of interfaces in heterogeneous materials. The advantages and limitations of the new model are summarized, and some future directions are highlighted.

36 MATERIALS SCIENCE↗

Human–Earth system interactions under climate change

This special issue, titled ‘Focus on human–Earth system interactions under climate change,’ compiles cutting-edge research that deepens our understanding of the complex feedback mechanisms between anthropogenic activities and Earth system processes in the context of a changing climate (figure 1). The featured articles employ a diverse array of methodologies—including field studies, remote sensing, modeling, and socio-ecological analyses—to explore these interconnections. A unifying theme across these contributions is the imperative to bridge disciplinary divides, integrating physical Earth sciences with social sciences to fully capture the spectrum of human-Earth system interactions. Key topics addressed the impacts of human activities on natural systems, encompassing land-use change and water resource management on biogeochemistry, climate dynamics, and feedback on the climate system and socioeconomics from local to global scales under a changing climate.

Li, Huidong [Vanderbilt Univ., Nashville, TN (Unit↗

Nuclear two point correlation functions on a quantum computer

The calculation of dynamic response functions is expected to be an early application benefiting from rapidly developing quantum hardware resources. The ability to calculate real-time quantities of strongly correlated quantum systems is one of the most exciting applications that can easily reach beyond the capabilities of traditional classical hardware. Response functions of fermionic systems at moderate momenta and energies corresponding roughly to the Fermi energy of the system are a potential early application because the relevant operators are nearly local, and the energies can be resolved in moderately short real time, reducing the spatial resolution and gate depth required. This is particularly the case in quasielastic electron and neutrino scattering from nuclei, a topic of great interest in the nuclear and particle physics communities and directly related to experiments designed to probe neutrino properties. In this paper we use current quantum hardware and error mitigation protocols to calculate response functions for a highly simplified nuclear model through calculations of a 2-point real time correlation function for a modified Fermi-Hubbard model in two dimensions with three distinguishable nucleons on four lattice sites.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Coupled Electro-Thermal Analysis of Permanent Magnet Synchronous Motor for Electric Vehicles

Permanent magnet synchronous motors (PMSM) are extensively used in electric vehicles. However, high internal heat generation and inefficient heat dissipation often limit the operational reliability, and longevity of the PMSM. Therefore, proper quantification of heat generation in electric motor and advanced embedded motor cooling techniques remain topics of immense interest. In order to accurately predict electro-magnetic performance, i.e., efficiency, component-wise heat losses and the corresponding temperature distribution of a jacket cooled machine, this paper presents a two-way iteratively coupled electro-thermal modeling framework. Finite element based software Motor-CAD has been utilized for electro-magnetic performance calculation of BMW i3 PMSM. Finite volume based computational fluid dynamics/heat transfer (CFD/HT) software ANSYS® FLUENT® has been employed to simulate the temperature distribution of the PMSM, using the electro-magnetic losses as heat input. Computed heat losses, stator, winding, rotor, and magnet temperatures are utilized as coupling parameters between the electro-magnetic and thermal models. A conventional one-way coupling algorithm has also been developed and compared to the newly proposed two-way coupling algorithm. Numerical results confirm that at high current density, one-way coupling algorithm significantly over-predicts the motor temperature compared to the two-way algorithm. A comprehensive analysis has been carried out to characterize the influences of current density, speed, and forced convection heat transfer coefficient on the heat losses, overall efficiency, and maximum temperature of the PMSM. Lastly, an efficiency map has been interpreted from the coupled electro-magnetic simulation.

42 ENGINEERING↗

Gold nanocrystal labels provide a sequence–to–3D structure map in SAXS reconstructions

Small-angle x-ray scattering (SAXS) is a powerful technique to probe the structure of biological macromolecules and their complexes under virtually arbitrary solution conditions, without the need for crystallization. While it is possible to reconstruct molecular shapes from SAXS data ab initio, the resulting electron density maps have a resolution of ~1 nm and are often insufficient to reliably assign secondary structure elements or domains. We show that SAXS data of gold-labeled samples significantly enhance the information content of SAXS measurements, allowing the unambiguous assignment of macromolecular sequence motifs to specific locations within a SAXS structure. We first demonstrate our approach for site-specifically internally and end-labeled DNA and an RNA motif. In addition, we present a protocol for highly uniform and site-specific labeling of proteins with small (~1.4 nm diameter) gold particles and apply our method to the signaling protein calmodulin. In all cases, the position of the small gold probes can be reliably identified in low-resolution electron density maps. Enhancing low-resolution measurements by site-selective gold labeling provides an attractive approach to aid modeling of a large range of macromolecular systems.

Science & Technology - Other Topics↗

Optical versus radiographic imaging and tomography: introduction to the ROADS feature issue

Optical imaging is an ancient branch of imaging dating back to thousands of years. Radiographic imaging and tomography (RadIT), including the first use of X-rays by Wilhelm Röntgen, and then, $γ$ -rays, energetic charged particles, neutrons, etc. are about 130 years young. The synergies between optical and radiographic imaging can be cast in the framework of these building blocks: Physics, Sources, Detectors, Methods, and Data Science, as described in Appl. Opt. 61, RDS1 (2022). Optical imaging has expanded to include three-dimensional (3D) tomography (including holography), due in to part the invention of optical (including infrared) lasers. RadIT are intrinsically 3D because of the penetrating power of ionizing radiation. Both optical imaging and tomography (OIT) and RadIT are evolving into even higher dimensional regimes, such as time-resolved tomography (4D) and temporarily and spectroscopically resolved tomography (4D + ). Further advances in OIT and RadIT will continue to be driven by desires for higher information yield, higher resolutions, and higher probability models with reduced uncertainties. Synergies in quantum physics, laser-driven sources, low-cost detectors, data-driven methods, automated processing of data, and artificially intelligent data acquisition protocols will be beneficial to both branches of imaging in many applications. These topics, along with an overview of the Radiography, Applied Optics, and Data Science virtual feature issue, are discussed here.

47 OTHER INSTRUMENTATION↗

Transient Studies of Nonequilibrium Transport in Two-Dimensional Semiconductors

The overarching objective of research under DOE support has been to investigate emergent carrier phenomena in different two-dimensional (2D) systems, under conditions where they are driven far from equilibrium. The description of nonequilibrium transport has long represented one of the most enduring challenges in condensed-matter physics, in large part due to the need to invoke the role of complex many-body phenomena (electron-phonon and electron-electron coupling) in this regime. In this project, we have explored aspects of this problem in a variety of different two-dimensional systems. These include the modulation-doped two-dimensional electrons gas, or 2DEG, in GaAs/AlGaAs heterostructures; the electron and hole systems in graphene and its related hetero-structures, and; the strongly-confined electron layers in transition-metal dichalcogenide (MoS 2 and WS 2 ) and trichalcogenide (TiS 3 ) materials. Significant understanding has been achieved in a number of different areas, as we elaborate upon in subsequent sections of this proposal: Nanoscale spectroscopy of defect-related barriers in MoS2 Negative differential conductance due to inter-valley scattering in WS 2 under high fields Incipient localization due to scattering from frozen-phonon disorder in quantum point contacts High-field transient transport in graphene/hexagonal BN heterostructures Universal voltage scaling of quantum corrections in graphene under nonequilibrium A defining feature of much of this research has been an approach to problem solving in which novel experimental techniques (such as transient electrical pulsing and scanning-probe microscopy) are combined with the development (in collaboration with colleagues from condensed-matter theory) of sophisticated models, a strategy that we propose to continue in our future research. In recent years, we have developed an increasing capacity for handling atomically-thin materials, and their van der Waals systems, a capacity that is reflected in the balance of topics listed above.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Fission In R-process Elements (FIRE)

The goal of the FIRE topical collaboration in nuclear theory was to determine the astrophysical conditions of the rapid neutron capture process (r-process), which is responsible for the formation of heavy elements. This was achieved by including in r-process simulations the most advanced models of fission (spontaneous, neutron-induced, β-delayed) that have been developed at LLNL and LANL. The collaboration was composed of LLNL (lead) and LANL for work on nuclear data (ground-state properties, fission, β-decay), BNL for nuclear data management, and the university of Notre Dame and North Carolina State University for r-process simulations. Under DOE/NNSA agreement, both universities received funds from the DOE Office of Science, while national laboratories received funds directly from NA221.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗