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At least 757 records · Page 42

WORKSHOP ON URBAN SCALE PROCESSES AND THEIR REPRESENTATION IN HIGH SPATIAL RESOLUTION EARTH SYSTEM MODELS

It is essential that numerical models used to study physics, chemistry, and biology affecting the Earth system at regional and global scales represent the effects of urban areas on climate and the effects of changing the climate on urban areas. At the same time, it is essential to develop state of the art, simple and accurate urban models to better understand the relevant processes and also toaddress issues related to urban security against the spectra of chemical, biological and radiological (CBR) hazards. Towards bringing these communities together, a 2.5-day international workshop was held at Argonne National Laboratory (ANL) in the Chicago area on May 22-24, 2019. This workshop brought together national and international experts to develop a roadmap for a better understanding of the issues associated with urban areas and at enhancing the capabilities of regional and global Earth System models (ESMs) in representing the atmospheric dynamics and chemistry, unique aspects of the biosphere and land use, and human dimensions of the urban environment. This workshop was especially important to those developing very high-resolution versions of regional and global models. The workshop also discussed existing datasets, including in situ and satellite observations, and the emerging smart city sensing technologies and their possible use in model development (e.g., the NSF-funded Array of Things network currently operating in Chicago and expanding to other cities).

54 ENVIRONMENTAL SCIENCES↗

Accelerating Adoption of Energy-Efficient Technology with the Thermalize Model

The accelerating impacts of climate change destabilize food systems and ecosystems alongside the communities that rely on them. Thus, climate resilience is a health equity issue at both a physical (relating to biological impacts of pollution and environmental degradation) and a cultural level (loss of subsistence lifestyles, languages, etc). With roughly 20% of US energy-related greenhouse gas emissions stemming from heating, cooling, and powering households, accessible energy-efficient home retrofits are a critical element of climate change mitigation strategies. For communities already producing electricity from renewable sources, like Juneau, incentivizing ductless heat pump upgrades and energy efficiency retrofits provides an accessible pathway to transition households away from oil heating and drastically reduce emissions. Thermalize Juneau is a pilot program that will explore a repeatable framework for accelerating the adoption of energy-efficient technology in Alaska communities. This poster will describe Thermalize Juneau's goals and framework, progress through spring 2021, and future plans.

ductless heat pumps↗

Cooperative effect of local active stresses on the macroscopic contractility of elastic fiber networks

The collective action of actively contractile units embedded in elastic biopolymer networks plays a crucial role in regulating the network's macroscopic mechanical response. Here, in this study, we investigate how the macroscopic boundary stress in model elastic fiber networks depends on the number and nature of embedded contractile units, each exerting an isotropic force dipole, as well as on the bending stiffness of fibers. We find that the macroscopic stress increases nonlinearly with the number of dipoles due to mutual stiffening of initially soft, bending-dominated networks. Using effective medium theory, we relate this enhanced contractility to an increase in the effective average network coordination number due to constraints imposed by the force dipoles. By comparing three distinct force dipole models that differ in their local structures, we demonstrate that the specific manner in which an active unit constrains the network strongly influences the onset and nature of the stiffening transition. Our results highlight that not only the quantity but also the local geometry of force-generating units critically determines the macroscopic mechanical behavior. This framework provides a physical basis for understanding how biological systems—such as molecular motors in the cytoskeleton, or adherent cells in the extracellular matrix—can modulate network-scale nonlinear elastic properties through local tuning of active force-generating units.

Biological and medical sciences↗

New Directions in NASA's Materials Science Program

Recently, NASA's Microgravity Research Division was re-aligned to match the Agency's increasing awareness of the importance of biological and nano-structural sciences. The Division has become the Physical Sciences Research section within the newly created Office of Biological and Physical Research. Within materials science and in the last few years, new programs aimed at biomaterials have been initiated. Results from these programs and also new research pertaining to materials for radiation protection will be discussed.

Gillies, Donald C.↗

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lunar Science Objectives and Opportunities

This presentation provides information on NASA strategic and top level Artemis lunar science objectives from publicly available documents. Also, it provides top level information on science, instruments, and hardware solicitation opportunities and institutes and analysis groups important to the space biology science, engineering, and technology communities

Space Biology↗

Ocean surface radiation measurement best practices

Ocean surface radiation measurement best practices have been developed as a first step to support the interoperability of radiation measurements across multiple ocean platforms and between land and ocean networks. This document describes the consensus by a working group of radiation measurement experts from land, ocean, and aircraft communities. The scope was limited to broadband shortwave (solar) and longwave (terrestrial infrared) surface irradiance measurements for quantification of the surface radiation budget. Best practices for spectral measurements for biological purposes like photosynthetically active radiation and ocean color are only mentioned briefly to motivate future interactions between the physical surface flux and biological radiation measurement communities. Topics discussed in these best practices include instrument selection, handling of sensors and installation, data quality monitoring, data processing, and calibration. It is recognized that platform and resource limitations may prohibit incorporating all best practices into all measurements and that spatial coverage is also an important motivator for expanding current networks. Thus, one of the key recommendations is to perform interoperability experiments that can help quantify the uncertainty of different practices and lay the groundwork for a multi-tiered global network with a mix of high-accuracy reference stations and lower-cost platforms and practices that can fill in spatial gaps.

54 ENVIRONMENTAL SCIENCES↗

Viking heat sterilization - Progress and problems

The Viking Mars landers to be launched in 1975 will carry experiments in biology, planetology, and atmospheric physics. A terminal dry-heat sterilization process using an inert gas was chosen to meet planetary quarantine requirements and preclude contamination of the biology experiment by terrestrial organisms. Deep sterilization is performed at the component level and terminal surface sterilization at the system level. Solutions to certain component problems relating to sterilization are discussed, involving the gyroscope, tape recorder, battery, electronic circuitry, and outgassing. Heat treatment placed special requirements on electronic packaging, including fastener preload monitoring and solder joints. Chemical and physical testing of nonmetallic materials was performed to establish data on their behavior in heat-treatment and vacuum environments. A Thermal Effects Test Model and a Proof Test Capsule were used. It is concluded that a space vehicle can be designed and fabricated to withstand heat sterilization requirements.

Daspit, L. P.↗

Physics and Chemistry of Te and HgTe-based Ternary Melts

Historically, the theoretical treatment of the liquid phases has always been more difficult and complicated than that for solid and gas phases. A liquid has no lattice structure as crystalline solids and the atoms/molecules in the liquid can migrate through it relatively rapidly. On the other hand, it is also interacting with many other atoms/molecules so that the simplifications of the kinetic theory of gases cannot be employed. For more complicated liquids, such as the liquids of high ionicity and those containing hydrogen bonds and electric dipoles, the understanding is far from complete. At the same time, accurate information on the physics and chemistry of semiconductor melts is needed for the quantitative descriptions of the process of crystal growth from melt. The pre-crystallization phenomena in the liquid phase are critical because the properties of the grown crystals depend on the state and structure of the melt as well as the thermal history of the melt during solidification process. However, the data on the liquid phase, such as thermophysical properties of semiconductor melts are scarce, especially for the HgTe-based II-VI ternary compound semiconductors because of their high vapor pressure and extreme toxicity. Analysis of the thermophysical properties of the melt can provide information about structural transitions of the melt during the solidification process. From a broader point of view, the structure of liquids is much more complicated than the crystalline solids, especially the relaxation behavior through different thermal histories. The theory of hetero-phase fluctuations of liquids is applicable to any many-body systems including condensed-matter physics, field theory, physics of nuclear-matter, cosmology, biology and even sociology. This book summarizes the physics and chemistry from the experimental measurements and theoretical analyses of phase diagram, thermodynamic properties, density, thermal conductivity, viscosity, and electrical conductivity on the binary, pseudo-binary and ternary melts of the most advanced IR-detector material systems of HgCdTe and HgZnTe as well as the analyses of these results. The main objectives of this study are: (1) to provide the phase diagrams and thermodynamic properties of Hg-Cd-Te and Hg-Zn-Te systems through quantitatively fitting the experimental data by assuming an associated solution model for the liquid phase, (2) to experimentally measure the thermophysical properties of the Hg-Cd-Te and Hg-Zn-Te melts, including density, viscosity, electrical conductivity and thermal conductivity as functions of temperature and composition and (3) to enhance the fundamental knowledge of hetero-phase fluctuations and relaxation phenomena in the melts and extend our understanding of the solidification process in order to interpret the experimental results of crystal growth so as to improve the melt growth processes of the compound semiconductor. The physics and chemistry of Te and HgTe-based ternary melts were explored through the studies of the structural transformation during melting, the supercooling during solidification, the relaxation phenomena after rapid cooling of the melts and the metal-semiconductor transition in the melts through the analyses of electrical conductivity and Lorenz number. An in-depth study on the thermophysical properties and their time-dependent structural dynamic processes taking place in the vicinity of the solid-liquid phase transition of the narrow homogeneity range HgTe-based ternary semiconductors as well as the analysis of the homogenization process in the melt will also be presented.

Thermophysical properties↗

Dose Summation Strategies for External Beam Radiation Therapy and Brachytherapy in Gynecologic Malignancy: A Review from the NRG Oncology and NCTN Medical Physics Subcommittees

Definitive, nonsurgical management of gynecologic malignancies involves external beam radiation therapy (EBRT) and/or brachytherapy (BT). Summation of the cumulative dose is critical to assess the total biologic effective dose to targets and organs at risk. Cumulative dose calculation from EBRT and BT can be performed with or without image registration (IR) and biologic dose summation. Among these dose summation strategies, linear addition of dose-volume histogram (DVH) parameters without IR is the global standard for composite dose reporting. This approach stems from an era without image guidance and simple external beam and brachytherapy treatment approaches. With technological advances, EBRT and high-dose-rate BT have evolved to allow for volume-based treatment planning and delivery. Modern conformal therapeutic radiation involves volumetric or intensity modulated EBRT, capable of simultaneously treating multiple targets at different specified dose levels. Therefore, given the complexity of modern radiation treatment, the linear addition of DVH parameters from EBRT and high-dose-rate BT is challenging to represent the combined dose distribution. Deformable image registration (DIR) between EBRT and image guided brachytherapy (IGBT) data sets may provide a more nuanced calculation of multimodal dose accumulation. However, DIR is still nascent in this regard, and needs further development for accuracy and efficiency for clinical use. Biologic dose summation can combine physical dose maps from EBRT and each IGBT fraction, thereby generating a composite DVH from the biologic effective dose. However, accurate radiobiologic parameters are tissue-dependent and not well characterized. A combination of voxel-based DIR and biologic weighted dose maps may be the best approximation of dose accumulation but remains invalidated. The purpose of this report is to review dose summation strategies for EBRT and BT, including conventional equivalent dose in 2-Gy fractions dose summation without image registration, physical dose summation using 3-dimensional rigid IR and DIR, and biologic dose summation. We also provide general clinical workflows for IGBT with a focus on cervical cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16

ABSTRACT In the CASP16 experiment, our team employed hybrid computational strategies to predict both protein–protein and protein–ligand complex structures. For protein–protein docking, we combined physics‐based sampling—using ClusPro FFT docking and molecular dynamics—with AlphaFold (AF)‐based sampling, followed by AF‐based refinement. Our method produced numerous high‐accuracy complex models, including cases where AF alone failed, underscoring the critical role of physics‐based sampling alongside deep learning‐based refinement. For protein–ligand docking, we integrated the ClusPro LigTBM template‐based approach with a machine learning‐based confidence model for rescoring. The method preserves conserved interaction fragments derived from homologous complexes, followed by local resampling using physics‐based sampling and a diffusion model. Our template‐based strategy achieved a mean lDDT‐PLI of 0.69 across 233 targets, which was highly competitive. These results demonstrate that combining physics‐based modeling with AI‐driven refinement can significantly enhance the accuracy of both protein–protein and protein–ligand structure predictions.

Ashizawa, Ryota [Department of Applied Mathematics↗

Quantum Annealing for Real-World Machine Learning Applications

Optimizing the training of a machine learning pipeline is important for reducing training costs and improving model performance. One such optimizing strategy is quantum annealing, which is an emerging computing paradigm that has shown potential in optimizing the training of a machine learning model. The implementation of a physical quantum annealer has been realized by D-Wave systems and is available to the research community for experiments. Recent experimental results on a variety of machine learning applications have shown interesting results especially under the conditions where the performance of classical machine learning techniques are limited such as limited training data and high dimensional features. This chapter explores the application of D-Wave’s quantum annealer for optimizing machine learning pipelines for real-world classification problems. We review the application domains on which a physical quantum annealer has been used to train machine learning classifiers. We discuss and analyze the experiments performed on the D-Wave quantum annealer for applications such as image recognition, remote sensing imagery, security, computational biology, biomedical sciences, and physics. We discuss the possible advantages and the problems for which quantum annealing is likely to be advantageous over classical computation.

Kumar nath, Rajdeep↗

Development of the Code RITRACKS

A document discusses the code RITRACKS (Relativistic Ion Tracks), which was developed to simulate heavy ion track structure at the microscopic and nanoscopic scales. It is a Monte-Carlo code that simulates the production of radiolytic species in water, event-by-event, and which may be used to simulate tracks and also to calculate dose in targets and voxels of different sizes. The dose deposited by the radiation can be calculated in nanovolumes (voxels). RITRACKS allows simulation of radiation tracks without the need of extensive knowledge of computer programming or Monte-Carlo simulations. It is installed as a regular application on Windows systems. The main input parameters entered by the user are the type and energy of the ion, the length and size of the irradiated volume, the number of ions impacting the volume, and the number of histories. The simulation can be started after the input parameters are entered in the GUI. The number of each kind of interactions for each track is shown in the result details window. The tracks can be visualized in 3D after the simulation is complete. It is also possible to see the time evolution of the tracks and zoom on specific parts of the tracks. The software RITRACKS can be very useful for radiation scientists to investigate various problems in the fields of radiation physics, radiation chemistry, and radiation biology. For example, it can be used to simulate electron ejection experiments (radiation physics).

Plante, Ianik↗

Biological Potential in Serpentinizing Systems

Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

the potential of serpentinizing systems to support↗

Marine biology and remote sensing

Remote sensing from manned orbital spacecraft for measuring characteristics of physical environment at sea surface - marine biology

SENSING↗