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At least 757 records · Page 42

Unified rational protein engineering with sequence-based deep representation learning

Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded. We show that the simplest models built on top of this unified representation (UniRep) are broadly applicable and generalize to unseen regions of sequence space. Our data-driven approach predicts the stability of natural and de novo designed proteins, and the quantitative function of molecularly diverse mutants, competitively with the state-of-the-art methods. UniRep further enables two orders of magnitude efficiency improvement in a protein engineering task. Lastly, UniRep is a versatile summary of fundamental protein features that can be applied across protein engineering informatics.

59 BASIC BIOLOGICAL SCIENCES↗

Quasi-bound states and continuum absorption background of polar Al{sub 0.5}Ga{sub 0.5}N/GaN quantum dots

A theoretical interpretation of the photoluminescence excitation spectra of self-organized polar GaN/(Al,Ga)N quantum dots is presented. A numerical method assuming a realistic shape of the dots and including the built-in electric field effects is developed to calculate their energy structure and hence their optical absorption. The electron and hole spectra show the existence of a set of quasi-bound states that does not originate from the wetting layer and plays a crucial role in the observed absorption spectrum of the GaN/(Al,Ga)N dots. Transitions involving these quasi-bound states and wetting layer states give a sufficient explanation for the observed continuum absorption background. The properties of this absorption band, especially its extension, depend strongly on the dot's size. Our simulation provides a natural explanation of the experimental luminescence excitation spectra of ensembles of dots of different heights. Our theoretical model can be convenient for future optical studies including systems with more complicated potentials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electronic and optical properties of pure and modified diamondoids studied by many-body perturbation theory and time-dependent density functional theory

Diamondoids are small diamond nanoparticles (NPs) that are built up from diamond cages. Unlike usual semiconductor NPs, their atomic structure is exactly known, thus they are ideal test-beds for benchmarking quantum chemical calculations. Their usage in spintronics and bioimaging applications requires a detailed knowledge of their electronic structure and optical properties. In this paper, we apply density functional theory (DFT) based methods to understand the electronic and optical properties of a few selected pure and modified diamondoids for which accurate experimental data exist. In particular, we use many-body perturbation theory methods, in the G{sub 0}W{sub 0} and G{sub 0}W{sub 0}+BSE approximations, and time-dependent DFT in the adiabatic local density approximation. We find large quasiparticle gap corrections that can exceed thrice the DFT gap. The electron-hole binding energy can be as large as 4 eV but it is considerably smaller than the GW corrections and thus G{sub 0}W{sub 0}+BSE optical gaps are about 50% larger than the Kohn-Sham (KS) DFT gaps. We find significant differences between KS time-dependent DFT and GW+BSE optical spectra on the selected diamondoids. The calculated G{sub 0}W{sub 0} quasiparticle levels agree well with the corresponding experimental vertical ionization energies. We show that nuclei dynamics in the ionization process can be significant and its contribution may reach about 0.5 eV in the adiabatic ionization energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evolution of microstructure and mechanical properties of selective laser melted Ti-5Al-5V-5Mo-3Cr after heat treatments

Titanium alloy Ti5553 (Ti-5Al-5Mo-5V-3Cr) is an excellent candidate for structural applications and additive manufacturing processes, since, unlike Ti6Al4 V, when built via selective laser melting and/or post additive manufactured welding, it maintains a near-beta microstructure that is both ductile and high strength. Another feature is that Ti5553 properties are adaptable through post build heat treatment. This study explores the heat treatability of selective laser melted Ti5553 up to temperatures approaching the β-transus. Here the results show strength increases while maintaining ductility at high temperatures (700–800°C), but embrittlement occurs at intermediate temperatures (400–600°C) likely due to changes in volume fraction and morphology of the α-phase and/or the presence of the ω-phase. Microstructure and X-ray diffraction are reported after heat-treating to better understand this mechanical response.

42 ENGINEERING↗

Response of a CMS HGCAL silicon-pad electromagnetic calorimeter prototype to 20–300 GeV positrons

The Compact Muon Solenoid collaboration is designing a new high-granularity endcap calorimeter, HGCAL, to be installed later this decade. As part of this development work, a prototype system was built, with an electromagnetic section consisting of 14 double-sided structures, providing 28 sampling layers. Each sampling layer has an hexagonal module, where a multipad large-area silicon sensor is glued between an electronics circuit board and a metal baseplate. The sensor pads of approximately 1.1 cm$^{2}$ are wire-bonded to the circuit board and are readout by custom integrated circuits. The prototype was extensively tested with beams at CERN's Super Proton Synchrotron in 2018. Based on the data collected with beams of positrons, with energies ranging from 20 to 300 GeV, measurements of the energy resolution and linearity, the position and angular resolutions, and the shower shapes are presented and compared to a detailed Geant4 simulation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

SU-F-T-351: Establishing a Workflow for IMRT Pre-Treatment Reviews for NRG-GY006 Clinical Trial

Purpose: To establish a workflow for NRG-GY006 IMRT pre-treatment reviews, incorporating advanced radiotherapy technologies being evaluated as part of the clinical trial. Methods: Pre-Treatment reviews are required for every IMRT case as part of NRG-GY006 (a randomized phase II trial of radiation therapy and cisplatin alone or in combination with intravenous triapine in women with newly diagnosed bulky stage I B2, stage II, IIIB, or IVA cancer of the uterine cervix or stage II-IVA vaginal cancer. The pretreatment review process includes structures review and generating an active bone marrow(ABM)- to be used as an avoidance structure during IMRT optimization- and evaluating initial IMRT plan quality using knowledgeengineering based planning (KBP). Institutions will initially submit their simulation CT scan, structures file and PET/CT to IROC QA center for generating ABM. The ABM will be returned to the institution for use in planning. Institutions will then submit an initial IMRT plan for review and will receive information back following implementation of a KBP algorithm, for use in re-optimization, before submitting the final IMRT used for treatment. Results: ABM structure is generated using MIM vista software (Version 6.5, MIM corporation, Inc.). Here, the planning CT and the diagnostic PET/CT are fused and a sub threshold structure is auto segmented above the mean value of the SUV of the bone marrow. The generated ABM were compared with those generated with other software system (e.g. Velocity, Varian) and Dice coefficient (reflects the overlap of structures) ranged between 80 – 90% was achieved. A KBP model was built in Varian Eclipse TPS using the RapidPlan KBP software to perform plan quality assurance. Conclusion: The workflow for IMRT pretreatment reviews has been established. It represents a major improvement of NRG Oncology clinical trial quality assurance and incorporates the latest radiotherapy technologies as part of NCI clinical trials. This project was supported by grants U24CA180803 (IROC), UG1CA189867 (NCORP), U10CA180868 (NRG Oncology Operations), U10CA180822 (NRG Oncology SDMC) from the National Cancer Institute (NCI) and PA CURE grant.

60 APPLIED LIFE SCIENCES↗

Structure of the saxiphilin:saxitoxin (STX) complex reveals a convergent molecular recognition strategy for paralytic toxins

Dinoflagelates and cyanobacteria produce saxitoxin (STX), a lethal bis-guanidinium neurotoxin causing paralytic shellfish poisoning. A number of metazoans have soluble STX-binding proteins that may prevent STX intoxication. However, their STX molecular recognition mechanisms remain unknown. Here, we present structures of saxiphilin (Sxph), a bullfrog high-affinity STX-binding protein, alone and bound to STX. The structures reveal a novel high-affinity STX-binding site built from a “proto-pocket” on a transferrin scaffold that also bears thyroglobulin domain protease inhibitor repeats. Comparison of Sxph and voltage-gated sodium channel STX-binding sites reveals a convergent toxin recognition strategy comprising a largely rigid binding site where acidic side chains and a cation-π interaction engage STX. These studies reveal molecular rules for STX recognition, outline how a toxin-binding site can be built on a naïve scaffold, and open a path to developing protein sensors for environmental STX monitoring and new biologics for STX intoxication mitigation.

60 APPLIED LIFE SCIENCES↗

ERF: Energy Research and Forecasting

The Energy Research and Forecasting (ERF) code is a new model that simulates the mesoscale and microscale dynamics of the atmosphere using the latest high-performance computing architectures. It employs hierarchical parallelism using an MPI+X model, where X may be OpenMP on multicore CPU-only systems, or CUDA, HIP, or SYCL on GPU-accelerated systems. ERF is built on AMReX (Zhang et al., 2019, 2021), a block-structured adaptive mesh refinement (AMR) software framework that provides the underlying performance-portable software infrastructure for block-structured mesh operations. The "energy" aspect of ERF indicates that the software has been developed with renewable energy applications in mind. In addition to being a numerical weather prediction model, ERF is designed to provide a flexible computational framework for the exploration and investigation of different physics parameterizations and numerical strategies, and to characterize the flow field that impacts the ability of wind turbines to extract wind energy. The ERF development is part of a broader effort led by the US Department of Energy's Wind Energy Technologies Office.

17 WIND ENERGY↗

Baseload Nitrate Salt Central Receiver Power Plant Design (Final Report)

The objectives of the work were to demonstrate that a 100 MWe central receiver plant, using nitrate salt as the receiver coolant, thermal storage medium, and heat transport fluid in the steam generator, can 1) operate, at full load, for 6,400 hours each year using only solar energy, and 2) satisfy the DOE levelized energy cost goal of $0.09/kWhe (real 2009 $). To achieve these objectives the work incorporated a large range of tasks relating to many different aspects of a molten salt tower plant. The first Phase of the project focused on developing a baseline design for a Molten Salt Tower and validating areas for improvement. Tasks included a market study, receiver design, heat exchanger design, preliminary heliostat design, solar field optimization, baseline system design including PFDs and P&IDs and detailed cost estimate. The baseline plant met the initial goal of less than $0.14/kWhe, and reinforced the need to reduce costs in several key areas to reach the overall $0.09/kWhe goal. The major improvements identified from Phase I were: 1) higher temperature salt to improve cycle efficiency and reduce storage requirements, 2) an improved receiver coating to increase the efficiency of the receiver, 3) a large receiver design to maximize storage and meet the baseload hours objective, and 4) lower cost heliostat field. The second Phase of the project looked at advancing the baseline tower with the identified improvements and included key prototypes. To validate increasing the standard solar salt temperature to 600 °C a dynamic test was conducted at Sandia. The results ultimately proved the hypothesis incorrect and showed high oxide production and corrosion rates. The results lead to further testing of systems to mitigate the oxide production to be able to increase the salt temperature for a commercial plant. Foster Wheeler worked on the receiver design in both Phase I and Phase II looking at both design and lowering costs utilizing commercial fossil boiler manufacturing. The cost and design goals for the project were met with this task, but the most interesting results had to do with defining the failure modes and looking at a “shakedown analysis” of the combined creep-fatigue failure. A separate task also looked at improving the absorber coatings on the receiver tubes that would improve the efficiency of the receiver. Significant progress was made on developing a novel paint with a high absorptivity that was on par with the current Pyromark, but shows additional potential to be optimized further. Although the coating did not meet the emissivity goals, preliminary testing the new paint shows potential to be much more durable, and potential to improve the receiver efficiency through a higher average absorptivity over the lifetime. Additional coatings were also designed and modeled results meet the project goals, but were not tested. Testing for low cycle fatigue of the full length receiver tubes was designed and constructed, but is still currently undergoing testing. A novel small heliostat was developed through an extensive brainstorming and down select. The concept was then detailed further with inputs from component testing and eventually a full prototype was built and tested. This task met or exceeded the accuracy and structure goals and also beat the cost goal. This provides a significant solar field costs savings for Abengoa that will be developed further to be used in future commercial plants. Ultimately the $0.09/kWhe (real 2009 $) and 6,400 hours goals of the project were met.

14 SOLAR ENERGY↗

Large Area Projection Microstereolithography: Characterization and Optimization of 3D Printing Parameters

Large Area Projection Microstereolithography (LAPμSL) is a new technology that allows the additive manufacture of parts that have feature sizes spanning from centimeters to tens of microns. Knowing the accuracy of builds from a system like this is a crucial step in development. This project explored the capabilities of the second and newest LAPμSL system that was built by comparing the features of actual builds to the desired structures. The system was then characterized in order to achieve the best results. The photo polymeric resins that were used were Autodesk PR48 and HDDA. Build parameters for Autodesk PR48 were found that allowed the prints to progress while using the full capacity of the system to print quality parts in a relatively short amount of time. One of the larger prints in particular had a print time that was nearly eighteen times faster than it would have been had printed in the first LAPμSL system. The characterization of HDDA resin helped the understanding that the flux of the light projected into the resin also affected the quality of the builds, rather than just the dose of light given. Future work for this project includes exploring the use of other resins in the LAPμSL systems, exploring the use of Raman Spectroscopy to analyze builds, and completing the characterization of the LAPμSL system.

36 MATERIALS SCIENCE↗

Methodology for system description using the software design & documentation language

The Software Design and Documentation Language (SDDL) can be loosely characterized as a text processor with built-in knowledge of, and methods for handling the concepts of structure and abstraction which are essential for developing software and other information intensive systems. Several aspects of system descriptions to which SDDL has been applied are presented and specific SDDL methodologies developed for these applications are discussed.

Kleine, H.↗

Very large Arecibo-type telescopes

The Arecibo-type radio telescope, based on a fixed spherical reflector, is a very effective design for a large radio telescope on the Moon. In such telescopes, major structural members are provided by the ground on which they are built, and thus are provided at no cost in materials or transportation. The strong compression members, the tall towers which support the suspended platform, are an expensive part of the Arecibo telescope. The need for such towers can be eliminated if a suitable valley or crater can be found wherein the rim of the depression can be used as the support point for the cables which support the suspended platform. With an Arecibo-type radio telescope on the Moon, there are no changing gravity loads because of the design and no changing wind loads because of the location; therefore, the only source of time variation in the telescope geometry is thermal changes. Calculations show that with conventional materials, such as steel, it should be possible to construct an Arecibo-type telescope with a reflector diameter of some 30 km on the Moon, and with a reflector diameter of some 60 to 90 km if materials of high specific strength are used.

Drake, Frank D.↗

Process and assembly plans for low cost commercial fuselage structure

Cost and weight reduction for a composite structure is a result of selecting design concepts that can be built using efficient low cost manufacturing and assembly processes. Since design and manufacturing are inherently cost dependent, concurrent engineering in the form of a Design-Build Team (DBT) is essential for low cost designs. Detailed cost analysis from DBT designs and hardware verification must be performed to identify the cost drivers and relationships between design and manufacturing processes. Results from the global evaluation are used to quantitatively rank design, identify cost centers for higher ranking design concepts, define and prioritize a list of technical/economic issues and barriers, and identify parameters that control concept response. These results are then used for final design optimization.

Willden, Kurtis↗

DTS: Building custom, intelligent schedulers

DTS is a decision-theoretic scheduler, built on top of a flexible toolkit -- this paper focuses on how the toolkit might be reused in future NASA mission schedulers. The toolkit includes a user-customizable scheduling interface, and a 'Just-For-You' optimization engine. The customizable interface is built on two metaphors: objects and dynamic graphs. Objects help to structure problem specifications and related data, while dynamic graphs simplify the specification of graphical schedule editors (such as Gantt charts). The interface can be used with any 'back-end' scheduler, through dynamically-loaded code, interprocess communication, or a shared database. The 'Just-For-You' optimization engine includes user-specific utility functions, automatically compiled heuristic evaluations, and a postprocessing facility for enforcing scheduling policies. The optimization engine is based on BPS, the Bayesian Problem-Solver (1,2), which introduced a similar approach to solving single-agent and adversarial graph search problems.

Hansson, Othar↗

Reduced Uncertainties in the Flutter Analysis of the Aerostructures Test Wing

Tuning the finite element model using measured data to minimize the model uncertainties is a challenging task in the area of structural dynamics. A test validated finite element model can provide a reliable flutter analysis to define the flutter placard speed to which the aircraft can be flown prior to flight flutter testing. Minimizing the difference between numerical and experimental results is a type of optimization problem. Through the use of the National Aeronautics and Space Administration Dryden Flight Research Center s (Edwards, California, USA) multidisciplinary design, analysis, and optimization tool to optimize the objective function and constraints; the mass properties, the natural frequencies, and the mode shapes are matched to the target data and the mass matrix orthogonality is retained. The approach in this study has been applied to minimize the model uncertainties for the structural dynamic model of the aerostructures test wing, which was designed, built, and tested at the National Aeronautics and Space Administration Dryden Flight Research Center. A 25-percent change in flutter speed has been shown after reducing the uncertainties

Pak, Chan-gi↗

COMPASS Final Report: Enceladus Solar Electric Propulsion Stage

The results of the NASA Glenn Research Center (GRC) COllaborative Modeling and Parametric Assessment of Space Systems (COMPASS) internal Solar Electric Propulsion (SEP) stage design are documented in this report (Figure 1.1). The SEP Stage was designed to deliver a science probe to Saturn (the probe design was performed separately by the NASA Goddard Space Flight Center s (GSFC) Integrated Mission Design Center (IMDC)). The SEP Stage delivers the 2444 kg probe on a Saturn trajectory with a hyperbolic arrival velocity of 5.4 km/s. The design carried 30 percent mass, 10 percent power, and 6 percent propellant margins. The SEP Stage relies on the probe for substantial guidance, navigation and control (GN&C), command and data handling (C&DH), and Communications functions. The stage is configured to carry the probe and to minimize the packaging interference between the probe and the stage. The propulsion system consisted of a 1+1 (one active, one spare) configuration of gimbaled 7 kW NASA Evolutionary Xenon Thruster (NEXT) ion propulsion thrusters with a throughput of 309 kg Xe propellant. Two 9350 W GaAs triple junction (at 1 Astronomical Unit (AU), includes 10 percent margin) ultra-flex solar arrays provided power to the stage, with Li-ion batteries for launch and contingency operations power. The base structure was an Al-Li hexagonal skin-stringer frame built to withstand launch loads. A passive thermal control system consisted of heat pipes to north and south radiator panels, multilayer insulation (MLI) and heaters for the Xe tank. All systems except tanks and solar arrays were designed to be single fault tolerant.

Oleson, Steven R.↗

Reduced Uncertainties in the Flutter Analysis of the Aerostructures Test Wing

Tuning the finite element model using measured data to minimize the model uncertainties is a challenging task in the area of structural dynamics. A test validated finite element model can provide a reliable flutter analysis to define the flutter placard speed to which the aircraft can be flown prior to flight flutter testing. Minimizing the difference between numerical and experimental results is a type of optimization problem. Through the use of the National Aeronautics and Space Administration Dryden Flight Research Center's (Edwards, California) multidisciplinary design, analysis, and optimization tool to optimize the objective function and constraints; the mass properties, the natural frequencies, and the mode shapes are matched to the target data, and the mass matrix orthogonality is retained. The approach in this study has been applied to minimize the model uncertainties for the structural dynamic model of the aerostructures test wing, which was designed, built, and tested at the National Aeronautics and Space Administration Dryden Flight Research Center. A 25 percent change in flutter speed has been shown after reducing the uncertainties.

Pak, Chan-Gi↗

In Situ Thermal Inspection of Automated Fiber Placement Operations for Tow and Ply Defect Detection

The advent of Automated Fiber Placement (AFP) systems have aided the rapid manufacturing of composite aerospace structures. One of the challenges that AFP systems pose is the uniformity of the deposited prepreg tape layers, which complicates detection of laps, gaps, overlaps and twists. The current detection method used in industry involves halting fabrication and performing a time consuming, visual inspection of each tape layer. Typical AFP systems use a quartz lamp to heat the base layer to make the surface tacky as it deposits another tape layer. The innovation proposed in this paper is to use the preheated base layer as a through-transmission heat source for inspecting the newly added tape layer in situ using a thermographic camera mounted on to the AFP hardware. Such a system would not only increase manufacturing throughput by reducing inspection times, but it would also aid in process development for new structural designs or material systems by providing data on as-built parts. To this end, a small thermal camera was mounted onto an AFP robotic research platform at NASA, and thermal data was collected during typical and experimental layup operations. The data was post processed to reveal defects such as tow overlap/gap, wrinkling, and peel-up. Defects that would have been impossible to detect visually were also discovered in the data, such as poor/loss of adhesion between plies and the effects of vacuum debulking. This paper will cover the results of our experiments, and the plans for future versions of this inspection system.

Juarez, Peter D.↗