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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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NASA NTRS1994

Direct simulation Monte Carlo and Navier-Stokes simulations of blunt body wake flows

Numerical results obtained with direct simulation Monte Carlo and Navier-Stokes methods are presented for a Mach-20 nitrogen flow about a 70-deg blunted cone. The flow conditions simuulated are those that can be obtained in existing low-density hypersonic wind tunnels. Three sets of flow conditions are considered with freestream Knudsen numbers ranging from 0.03 to 0.001. The focus is on the wake structure: how the wake structure changes as a function of rarefaction, what the afterbody levels of heating are, and to what limits the continuum models are realistic as rarefaction in the wake is progressively increased. Calculations are made with and without an afterbody sting. Results for the after body sting are emphasizes in anticipation of an experimental study for the current flow conditions and model configuration. The Navier-Stokes calculations were made with and without slip boundary conditions. Comparisons of the results obtained with the two simulation methodologies are made for both flowfield structure and surface quantities.

Moss, James N.↗
NASA NTRSDate not supplied

Governing Data Findability, Accessibility, Interoperability and Reusability (FAIR) Compliance

The most recent data strategy documents at both the federal and NASA levels stipulate that systems should strive for the data they manage to be Findable, Accessible, Interoperable, and Reusable (FAIR). The NASA Life Sciences Portal (NLSP) has already begun leading efforts in this area for HRP, initiating efforts to comply with the FAIR principles. The broad interpretation of the FAIR principles has led to a plethora of tools that use a splay of metrics specifically but variably developed to judge how compliant data and systems are with the principles. A recent review [3] identified and studied 1,180 metrics across 20 publicly available tools for checking FAIR compliance of data and systems. Because of their very recent development, many organizations and data systems managers and developers have not yet had adequate time or resources to understand these FAIR compliance tools and metrics, their variations in design, accuracy or ease of application to their specific data sets and systems. Thus, it would be best for larger organizations like NASA to approach formulating a strategy for governance of FAIR compliance that can be flexibly applied and is adaptable to an evolving awareness knowledge of FAIR compliance methods and tools. In September 2024, the NASA Science Mission Directorate(SMD) organized a workshop on NASA science data repositories, including the topics of implementing FAIR and governing FAIR compliance across SMD. The initial part of these FAIR discussions focused on developing consensus around required science metadata fields. This is challenging given the diverse nature of NASA’s scientific data portfolio, the variety of metadata models and vocabularies used, and variable level of resources available to curate these data. Later discussion focused on three possible approaches to governing FAIR compliance: distributed, in which various programs, projects or systems define their own methods for assessing FAIR compliance, reporting results up appropriate management lines; centralized, in which higher-level organization(s) specify compliance tools or methods for the various data systems; and multi-level, in which a group comprised of individuals with expertise from multiple levels with organizations is formed to provide guidance and/or specifications for governing FAIR compliance. We report on the recommendations this session yielded, and how these might be shaped specifically to help implement and govern the compliance with FAIR of Human Research Program data and systems.

governance↗
DOE OSTI2023

Acute stress reduces population-level metabolic and proteomic variation

Abstract Background Variation in omics data due to intrinsic biological stochasticity is often viewed as a challenging and undesirable feature of complex systems analyses. In fact, numerous statistical methods are utilized to minimize the variation among biological replicates. Results We demonstrate that the common statistics relative standard deviation (RSD) and coefficient of variation (CV), which are often used for quality control or part of a larger pipeline in omics analyses, can also be used as a metric of a physiological stress response. Using an approach we term Replicate Variation Analysis (RVA), we demonstrate that acute physiological stress leads to feature-wide canalization of CV profiles of metabolomes and proteomes across biological replicates. Canalization is the repression of variation between replicates, which increases phenotypic similarity. Multiple in-house mass spectrometry omics datasets in addition to publicly available data were analyzed to assess changes in CV profiles in plants, animals, and microorganisms. In addition, proteomics data sets were evaluated utilizing RVA to identify functionality of reduced CV proteins. Conclusions RVA provides a foundation for understanding omics level shifts that occur in response to cellular stress. This approach to data analysis helps characterize stress response and recovery, and could be deployed to detect populations under stress, monitor health status, and conduct environmental monitoring.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Topical Report – Findings on Subtask 2.7 – Wet ESP and Aerosol Testing at Coal Creek Station

Growing concerns over the impact of CO 2 emissions from combustion sources on global climate change have prompted numerous research and development projects aimed at developing cost-effective technologies for CO 2 capture. One family of technologies being demonstrated at pilot and full scale globally is postcombustion carbon capture (PCCC) systems that employ amine-based solvents. The captured CO 2 can be compressed and permanently stored underground or used for enhanced oil recovery. The proximity of North Dakota’s lignite-fired fleet of power plants to potential CO 2 storage options creates a unique atmosphere for PCCC within the state. However, the unique components present in lignite flue gas present a challenge for large-scale PCCC at North Dakota power plants by contributing to aerosol formation. Aerosols can negatively impact the long-term performance of amine-based solvents for CO 2 capture. Amine-based solvents are volatile, and flue gas particulate provides nucleation sites where amine vapors can condense as aerosols. Because aerosols cannot be easily captured at the column outlet using conventional technologies, the amine-laden aerosols escape the system and lead to accelerated solvent losses. Moreover, particulate components can chemically react with amines to form degradation products that can permanently deactivate the amine, cause fouling, and lead to hazardous emissions. Many of the elements that have been shown to catalyze solvent degradation are present in lignite coals and can exacerbate solvent replacement economics. Understanding this issue is critical to the implementation of solvent-based CO 2 capture systems as applied to lignite-fired generation systems. The Energy & Environmental Research Center (EERC) designed and carried out this project to fully characterize aerosol behavior with various control technologies installed to better optimize aerosol mitigation technology for CO 2 capture. To meet the goal of this project, the following objectives were identified: Determine the effectiveness of a wet electrostatic precipitator (WESP) on mitigating formation of problematic aerosols at Great River Energy’s Coal Creek Station, upstream of the PCCC system. Determine the effectiveness of the Mitsubishi Heavy Industries (MHI) proprietary amine emission reduction unit (AERU) as a postcapture solvent recovery system for reducing aerosol emissions and extending solvent life downstream of the PCCC system. Determine the impact of aerosols on the efficiency and degradation products of both commercial and advanced solvents within the PCCC system. Work was conducted at Coal Creek Station Unit 1 using a slipstream of flue gas from the outlet of the plant’s flue gas desulfurization (FGD) unit. Flue gas was routed through a pilot-scale FGD unit to remove SO 2 to very low levels (~1 ppm) and then through a direct contact cooler (DCC) to further cool the gas and to remove moisture. The gas exiting the DCC was then optionally routed through a WESP before passing to the CO 2 absorber columns. The MHI solvent was used to scrub CO 2 from the slipstream through a set of two absorber columns. The rich solvent was regenerated in a stripper column by heating to drive off captured CO 2 . Flue gas exiting the absorber column was routed to MHI’s proprietary AERU to recover entrained solvent. The system operated using a catch-and-release method where the CO 2 was separated to provide data on the process, but the captured CO 2 was released back into the host site stack. Particulate was measured, collected, and analyzed from multiple locations throughout the pilot-scale system. Unlike the performance observed in prior work, the inlet FGD and DCC did not remove significant particulate matter from the flue gas. This appears to be due to a difference in the nature of the particulate. The DCC seemed to increase particulate size and count, most likely owing to water condensing onto the surfaces of fly ash particles. When the WESP was operated, it achieved >95% particulate capture. Very little particulate matter or indications of solvent were detected at the AERU outlet. When operating with advanced KS 21 solvent, the particulate material at the AERU outlet was even further decreased. Solvent analysis showed that some species derived from flue gas and ash were slowly concentrating in the solvent over the duration of the test. The levels observed were reported to be within expected ranges and were not of concern to MHI. A high-level techno-economic assessment of installing CO 2 capture at Coal Creek Station suggested that, when using a standard monoethanolamine (MEA)-based solution with simple heat integration, the energy penalty to net generation would be 34%. The bulk of this was due to steam losses for regenerating solvent, followed by parasitic electrical demand for CO 2 compression and then by increased parasitic load for pushing flue gas through the absorber column. These demands could be decreased with a more advanced solvent that exhibits lower heat of regeneration and lower pressure drop than does a simple MEA solution. Further energy could be saved with more thorough heat integration to recover useful energy from the steam used for solvent regeneration. Installing a WESP was predicted to increase the cost of electricity by nearly $5/MWh. This would become cost-effective if solvent losses were roughly 10 times the baseline estimate when not using a WESP but could be returned to baseline by installing the WESP. Piping CO 2 for storage in more favorable geology could help with carbon capture and storage economics. Although storing off-site would necessitate construction of a CO 2 transport pipeline, the cost of this pipeline might be more than offset by reducing the number of wells required, the depths of the wells required, and the electrical demand for the CO 2 compressor. Additional factors that favor off-site storage costs include smaller expected CO 2 plume sizes, which translates to less monitoring and fewer landowner agreements. More detailed assessment of the specific geology in the region under and around Coal Creek Station would be needed to accurately assess the costs and benefits of different storage site options. This subtask was cofunded through the Energy & Environmental Research Center–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission.

Strege, Joshua↗
NASA NTRS1997

Efficient Gradient-Based Shape Optimization Methodology Using Inviscid/Viscous CFD

The formerly developed preconditioned-biconjugate-gradient (PBCG) solvers for the analysis and the sensitivity equations had resulted in very large error reductions per iteration; quadratic convergence was achieved whenever the solution entered the domain of attraction to the root. Its memory requirement was also lower as compared to a direct inversion solver. However, this memory requirement was high enough to preclude the realistic, high grid-density design of a practical 3D geometry. This limitation served as the impetus to the first-year activity (March 9, 1995 to March 8, 1996). Therefore, the major activity for this period was the development of the low-memory methodology for the discrete-sensitivity-based shape optimization. This was accomplished by solving all the resulting sets of equations using an alternating-direction-implicit (ADI) approach. The results indicated that shape optimization problems which required large numbers of grid points could be resolved with a gradient-based approach. Therefore, to better utilize the computational resources, it was recommended that a number of coarse grid cases, using the PBCG method, should initially be conducted to better define the optimization problem and the design space, and obtain an improved initial shape. Subsequently, a fine grid shape optimization, which necessitates using the ADI method, should be conducted to accurately obtain the final optimized shape. The other activity during this period was the interaction with the members of the Aerodynamic and Aeroacoustic Methods Branch of Langley Research Center during one stage of their investigation to develop an adjoint-variable sensitivity method using the viscous flow equations. This method had algorithmic similarities to the variational sensitivity methods and the control-theory approach. However, unlike the prior studies, it was considered for the three-dimensional, viscous flow equations. The major accomplishment in the second period of this project (March 9, 1996 to March 8, 1997) was the extension of the shape optimization methodology for the Thin-Layer Navier-Stokes equations. Both the Euler-based and the TLNS-based analyses compared with the analyses obtained using the CFL3D code. The sensitivities, again from both levels of the flow equations, also compared very well with the finite-differenced sensitivities. A fairly large set of shape optimization cases were conducted to study a number of issues previously not well understood. The testbed for these cases was the shaping of an arrow wing in Mach 2.4 flow. All the final shapes, obtained either from a coarse-grid-based or a fine-grid-based optimization, using either a Euler-based or a TLNS-based analysis, were all re-analyzed using a fine-grid, TLNS solution for their function evaluations. This allowed for a more fair comparison of their relative merits. From the aerodynamic performance standpoint, the fine-grid TLNS-based optimization produced the best shape, and the fine-grid Euler-based optimization produced the lowest cruise efficiency.

Baysal, Oktay↗
DOE OSTI2017

Groundwater recharge estimation in arid hardrock-alluvium aquifers using combined water-table fluctuation and groundwater balance approaches

This article proposes an approach to estimate groundwater recharge using an optimization-based water-table fluctuation method combined with a groundwater balance model in an arid hardrock-alluvium region, located at the Oman–United Arab Emirates border. Here, we introduce an “effective hardrock thickness” term to identify the percentage of the considered hardrock thickness in which effective groundwater flow takes place. The proposed method is based upon a Thiessen polygon zoning approach. The method includes subpolygons to represent specific geologic units and to enhance the confidence of the estimated groundwater recharge. Two linear and 1 nonlinear submodels were developed to evaluate the model components for the calibration (October 1996 to September 2008) and validation (October 2008 to September 2013) periods. Long-term annual groundwater recharge from rainfall and return flow over the model domain are estimated as 24.62 and 5.71 Mm 3 , respectively, while the effective groundwater flow circulation is found to occur in the upper 7% of the known hardrock thickness (42 m), confirming conclusions of previous field studies. Considering a total difference in groundwater levels between eastern and western points of the study area of the order of 220 m and a 12-year monthly calibration period, a weighted root mean squared error in predicted groundwater elevation of 2.75 m is considered quite reasonable for the study area characterized by remarkable geological and hydrogeological diversity. The proposed approach provides an efficient and robust method to estimate groundwater recharge in regions with a complex geological setting in which interaction between fractured and porous media cannot be easily assessed.

58 GEOSCIENCES↗
DOE OSTI2025

A fully ro-vibrationally resolved corona model for the molecular hydrogen Fulcher-𝛼 system

A ro-vibrationally resolved corona model for the molecular hydrogen Fulcher-𝛼 transition based on the Yacora solver is introduced. The model couples 1365 ro-vibrational levels of the 𝑋 1 ⁢𝛴$^+_𝑔$, 𝑑 3⁢ 𝛱 𝑢 and 𝑎 3 ⁢𝛴$^+_𝑔$ states via electron impact excitation from the ground state into the 𝑑 3⁢ 𝛱 𝑢 state and subsequent spontaneous emission into the 𝑎 3 ⁢𝛴$+_𝑔$ state. For the process of electron impact excitation a set of 45260 fully ro-vibrationally resolved cross sections calculated with the molecular convergent close-coupling (MCCC) method in the adiabatic-nuclei formulation is applied. The MCCC cross sections are compared with results of a scaling method used in other works, demonstrating the need for dedicated ro-vibrationally resolved cross sections. By post-processing the model output, entire Fulcher spectra can be simulated. These spectra are benchmarked with measurements from an inductively coupled plasma discharge at a pressure between 1.1–10 Pa and a RF power of 700 W. The model results agree very well with the experiment both in relative shape and in absolute value. A non-ro-vibrationally resolved, purely electronically resolved collisional radiative model for molecular hydrogen (including further states and reaction channels) is applied to investigate the validity of the corona approximation for the benchmark plasmas and the relevance of possible process extensions of the corona model. Furthermore, the influence of collisional quenching, autoionization and predissociation is discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Real-time coupled-cluster approach for the cumulant Green's function

Green’s function methods within many-body perturbation theory provide a general framework for treating electronic correlations in excited states. Here we investigate the cumulant form of the one-electron Green’s function based on the coupled-cluster equation of motion approach in an extension of our previous study. The approach yields a non-perturbative expression for the cumulant in terms of the solution to a set of coupled first order, non-linear differential equations. The method thereby adds non-linear corrections to traditional cumulant methods linear in the self energy. The approach is applied to the core-hole Green’s function and illustrated for a number of small molecular systems. For these systems we find that the non-linear contributions lead to significant improvements both for quasiparticle properties such as core-level binding energies, as well as the satellites corresponding to inelastic losses observed in photoemission spectra.

Vila, Fernando D.↗
DOE OSTI2024

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Coupled cluster evaluation of the frequency dispersion of the first and second hyperpolarizabilities of water, methanol, and dimethyl ether

The static and dynamic first (β{sub ‖}) and second (γ{sub ‖}) hyperpolarizabilities of water, methanol, and dimethyl ether have been evaluated within the response function approach using a hierarchy of coupled cluster levels of approximation and doubly augmented correlation consistent atomic basis sets. For the three compounds, the electronic β{sub ‖} and γ{sub ‖} values calculated at the CCSD and CC3 levels are in good agreement with gas phase electric field-induced second harmonic generation (EFISHG) measurements. In addition, for dimethyl ether, the frequency dispersion of both properties follows closely recent experimental values [V. W. Couling and D. P. Shelton, J. Chem. Phys. 143, 224307 (2015)] demonstrating the reliability of these methods and levels of approximation. This also suggests that the vibrational contributions to the EFISHG responses of these molecules are small.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Model Residuals as Shields: A Two-Level Formulation to Defend Smart Grids From Poisoning Attacks

The advancement of smart grids presents both vast opportunities and heightened cybersecurity risks. Data-driven defense mechanisms, though designed as a shield against these threats, can fall prey to poisoning attacks. We delve into regression settings, underscoring the imperative to fortify defenses against a spectrum of poison ratios, notably those above 0.5—an issue scarcely addressed in prior studies. Recognizing the susceptibilities of smart grids and their manipulable sensors, we exploit the very intent of poisoning attacks, compromising model accuracy, as our defense mechanism. Our proposed two-level optimization framework discerns between poisoned and authentic data based on model residuals, outperforming or matching existing methods in 72% to 77% of precision and 75% to 80% of recalls across various poisoning attacks, poison ratios, and datasets. Once the authentic data are identified, the trained model is adaptable for a variety of applications. Comprehensive evaluations on different smart grid datasets, pitted against myriad poisoning schemes, validate our methodology’s edge over existing methods. Here, we also shed light on the implications of model misspecification originating from temporal auto-correlation, a common feature in Internet of Things and smart grid data.

Adversarial machine learning (ML)↗
DOE OSTI2018

A Solar Time-based Analog Ensemble Method for Regional Solar Power Forecasting

This paper presents a new analog ensemble method for day-ahead regional photovoltaic (PV) power forecasting with hourly resolution. By utilizing open weather forecast and power measurement data, this prediction method is processed within a set of historical data with similar meteorological data (temperature and irradiance), and astronomical date (solar time and earth declination angle). Further, clustering and blending strategies are applied to improve its accuracy in regional PV forecasting. The robustness of the proposed method is demonstrated with three different numerical weather prediction models, the North American Mesoscale Forecast System, the Global Forecast System, and the Short-Range Ensemble Forecast, for both region level and single site level PV forecasts. Using real measured data, the new forecasting approach is applied to the load zone in Southeastern Massachusetts as a case study. In conclusion, the normalized root mean square error (NRMSE) has been reduced by 13.80%-61.21% when compared with three tested baselines.

14 SOLAR ENERGY↗
DOE OSTI2018

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Abstract Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.

09 BIOMASS FUELS↗
DOE OSTI2016

SU-G-JeP2-12: Quantification of 3D Geometric Distortion for 1.5T and 3T MRI Scanners Used for Radiation Therapy

Purpose: To quantify the magnitude of geometric distortion for MRI scanners and provide recommendations for MRI imaging for radiation therapy Methods: A novel phantom, QUASAR MRID3D [Modus Medical Devices Inc.], was scanned to evaluate the level of 3D geometric distortion present in five MRI scanners used for radiation therapy in our department. The phantom was scanned using the body coil with 1mm image slice thickness to acquire 3D images of the phantom body. The phantom was aligned to its geometric center for each scan, and the field of view was set to visualize the entire phantom. The dependence of distortion magnitude with distance from imaging isocenter and with magnetic field strength (1.5T and 3T) was investigated. Additionally, the characteristics of distortion for Siemens and GE machines were compared. The image distortion for each scanner was quantified in terms of mean, standard deviation (STD), maximum distortion, and skewness. Results: The 3T and 1.5T scans show a similar absolute distortion with a mean of 1.38mm (0.33mm STD) for 3T and 1.39mm (0.34mm STD) for 1.5T for a 100mm radius distance from isocenter. Some machines can have a distortion larger than 10mm at a distance of 200mm from the isocenter. The distortions are presented with plots of the x, y, and z directional components. Conclusion: The results indicate that quantification of MRI image distortion is crucial in radiation oncology for target and organ delineation and treatment planning. The magnitude of geometric distortion determines the margin needed for target contouring which is usually neglected in treatment planning process, especially for SRS/SBRT treatments. Understanding the 3D distribution of the MRI image distortion will improve the accuracy of target delineation and, hence, treatment efficacy. MRI imaging with proper patient alignment to the isocenter is vital to reducing the effects of MRI distortion in treatment planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

White Box Access to Quantum Testbeds for Co-Design

At Lawrence Livermore National Laboratory (LLNL), we operate and maintain the Quantum Device and Integration Testbed (QuDIT) facility, a small quantum testbed that supports about 10 active research teams (including our own) and over 50 internal and external collaborators. This testbed is designed to give remote white box access to users for research, training, and outreach. A guiding principle behind the development of our testbed infrastructure, software and user interfaces is to empower users to perform experiments at the cutting edge of quantum information science at any level of abstraction, from materials studies, device physics and control and characterization techniques to algorithm development and quantum operating system design. Our testbed targets a multilevel quantum system (qudit) to expand the accessible Hilbert space of a simple-to-manufacture quantum device and focuses on quantum simulation, typically implemented through custom gates designed with quantum optimal control methods, rather than on a universal computing framework with a fixed gate set. We leverage the Lab’s high-performance computing (HPC) program and related expertise to simulate quantum systems, develop hybrid algorithms, and generate gates optimized for given simulations. Additionally, we have adopted a co-design philosophy from the HPC community in designing new hardware, so that the systems we develop are optimized for the specific physics simulations we plan to use them for.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

A Two-Fold Structural Classification Method for Determining the Accurate Ensemble of Protein Structures

Atomic-level structural characterization of flexible proteins, such as intrinsically disordered proteins and multi-domain proteins connected by flexible linkers, is challenging as they possess distinct conformations in physiological conditions. Significant efforts have been made to develop integrated approaches by combining small angle neutron/X-ray scattering experiments with molecular simulations to reveal the distinct atomic structures and the corresponding populations for these flexible proteins. One widely used method, the basis-set supported ensemble method, classifies the simulation-generated protein conformations into a set of structural basis and then derives the corresponding populations by fitting to the experimental data. This method makes an implicit assumption that protein conformations of similar structures have similar small angle scattering profiles.The present work demonstrates that, for various protein systems ranging from compact globular proteins and flexible multidomain proteins through to intrinsically disordered proteins, this method provides inaccurate assessment of the structural ensemble of the protein molecules due to the breakdown of the assumption made. To alleviate this problem, a two-fold-clustering method is developed to cluster the simulation-generated protein structures using information on both 3D structure and scattering profiles. As benchmarked by both simulation and experimental results, this new method yields much more accurate populations of structural basis of protein molecules.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Hypersonic blunt body wake computations using DSMC and Navier-Stokes solvers

Numerical results obtained with direct simulation Monte Carlo (DSMC) and Navier-Stokes methods are presented for Mach 20 nitrogen flow about a 70-deg blunted cone. The flow conditions simulated are those that can be obtained in existing low-density hypersonic wind tunnels. Three sets of flow conditions are considered with freestream Knudsen numbers ranging from 0.03 to 0.001. The focus is on the wake structure: how does the wake structure change as a function of rarefaction, what are the afterbody levels of heating, and to what limits are continuum models realistic as rarefaction in the wake is progressively increased. Calculations are made with and without an afterbody sting. Results for the afterbody sting are emphasized in anticipation of an experimental study for the current flow conditions and model configuration. The Navier-Stokes calculations were made with and without slip boundary conditions. Comparisons of the results obtained with the two simulation methodologies are made for both flowfield structure and surface quantities.

Moss, James N.↗
NASA NTRS1994

Direct simulation Monte Carlo and Navier-Stokes simulations of blunt body wake flows

Numerical results obtained with direct simulation Monte Carlo and Navier-Stokes methods are presented for a Mach-20 nitrogen flow about a 70-deg blunted cone. The flow conditions simulated are those that can be obtained in existing low-density hypersonic wind tunnels. Three sets of flow conditions are considered with freestream Knudsen numbers ranging from 0.03 to 0.001. The focus is on the wake structure: how the wake structure changes as a function of rare faction, what the afterbody levels of heating are, and to what limits the continuum models are realistic as rarefunction in the wake is progressively increased. Calculations are made with and without an afterbody sting. Results for the afterbody sting are emphasized in anticipation of an experimental study for the current flow conditions and model configuration. The Navier-Stokes calculations were made with and without slip boundary conditions. Comparisons of the results obtained with the two simulation methodologies are made for both flowfield structure and surface quantities.

WAKE STRUCTURE↗