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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Potential underestimation of the internal target volume (ITV) from free-breathing CBCT

Purpose: Localization prior to delivery of SBRT to free-breathing patients is performed by aligning the planning internal target volume (ITV) from 4DCT with an on-board free-breathing cone-beam CT (FB-CBCT) image. The FB-CBCT image is assumed to also generate an ITV that captures the full range of motion, due to the acquisition spanning multiple respiratory cycles. However, the ITV could potentially be underestimated when the ratio of time spent in inspiration versus time spent in expiration (I/E ratio) deviates from unity. Therefore, the aim of this study was to investigate the effect of variable I/E ratios on the FB ITV generated from a FB-CBCT scan. Methods: This study employed both phantom and patient imaging data. For the phantom study, five periodic respiratory cycles were simulated with different I/E ratios. Six patient respiratory cycles with variable I/E ratios were also selected. All profiles were then programmed into a motion phantom for imaging and modified to exhibit three peak-to-peak motion amplitudes (0.5, 1.0, and 2.0 cm). Each profile was imaged using two spherical targets with 1.0 and 3.0 cm diameters. 2D projections were acquired with full gantry rotation of a kiloVoltage (kV) imager mounted onto the gantry of a modern linear accelerator. CBCT images were reconstructed from 2D projections using a standard filtered back-projection reconstruction algorithm. Quantitative analyses for the phantom study included computing the change in contrast along the direction of target motion as well as determining the area (which is proportional to the target volume) inside of the contour extracted using a Canny edge detector. For the patient study, projection data that were previously acquired under an investigational 4D CBCT slow-gantry imaging protocol were used to generate both FB-CBCT and 4D CBCT images. Volumes were then manually contoured from both datasets (using the same window and level) for quantitative comparison. Results: The phantom study indicated a reduction in contrast at the inferior edge of the ITV (corresponding to inspiration) as the ratio decreased, for both simulated and patient respiratory cycles. For the simulated phantom respiratory cycles, the contrast reduction of the smallest I/E ratio was 27.6% for the largest target with the smallest amplitude and 89.7% for the smallest target with the largest amplitude. For patient respiratory cycles, these numbers were 22.3% and 94.0%, respectively. The extracted area from inside of the target contours showed a decreasing trend as the I/E ratio decreased. In the patient study, the FB-CBCT ITVs of both lung tumors studied were underestimated when compared with their corresponding 4D CBCT ITV. The underestimations found were 40.1% for the smaller tumor and 24.2% for the larger tumor. Conclusions: The ITV may be underestimated in a FB-CBCT image when a patient's respiratory pattern is characterized by a disparate length of time spent in inspiration versus expiration. Missing the full target motion information during on-board verification imaging may result in localization errors.

61 RADIATION PROTECTION AND DOSIMETRY↗
NASA NTRS2004

Using a Low Cost Flight Simulation Environment for Interdisciplinary Education

A multi-disciplinary and inter-disciplinary education is increasingly being emphasized for engineering undergraduates. However, often the focus is on interaction between engineering disciplines. This paper discusses the experience at Tuskegee University in providing interdisciplinary research experiences for undergraduate students in both Aerospace Engineering and Psychology through the utilization of a low cost flight simulation environment. The environment, which is pc-based, runs a low-cost of-the-shelf software and is configured for multiple out-of-the-window views and a synthetic heads down display with joystick, rudder and throttle controls. While the environment is being utilized to investigate and evaluate various strategies for training novice pilots, students were involved to provide them with experience in conducting such interdisciplinary research. On the global inter-disciplinary level these experiences included developing experimental designs and research protocols, consideration of human participant ethical issues, and planning and executing the research studies. During the planning phase students were apprised of the limitations of the software in its basic form and the enhancements desired to investigate human factors issues. A number of enhancements to the flight environment were then undertaken, from creating Excel macros for determining the performance of the 'pilots', to interacting with the software to provide various audio/video cues based on the experimental protocol. These enhancements involved understanding the flight model and performance, stability & control issues. Throughout this process, discussions of data analysis included a focus from a human factors perspective as well as an engineering point of view.

Khan, M. Javed↗
DOE OSTI2019

Experimental Electron Density Distribution in Actinide Compounds – an Experimental Atoms in Molecules (AIM) Approach

Understanding the basic chemistry of the actinides, in particular of uranium, is essential to address issues related to nuclear fuels, nuclear waste and environmental concerns. Atoms in general are chemically bound to their neighbors via the distribution of electrons within the intervening space. However, this only represents a small proportion of the total electrons, the others are tightly bound to the atomic nuclei and do not participate in chemical bonding. The distribution of electrons in crystalline materials may be examined using the scattering of X-rays. As all electrons scatter X-rays, obtaining the information about the bonding electrons in the presence of a large excess of “irrelevant” electrons requires extremely accurate scattering measurements. Indeed, until recently this was considered impossible for elements as heavy as uranium. In our current project we have made significant improvements in the data quality obtainable for uranium containing compounds. In order to determine the electron density distribution we fit a mathematical model describing the scattering effect to the observed scattering data. This mathematical model has a number of variable parameters that describe the radial and angular distribution of electrons around an atomic center. We have developed such a model to be particularly useful for elements as heavy as uranium. Given the best fit parameters from this model, we are able to map the electron distribution around all atoms in a chemical compound. The topology of this distribution provides us with important characteristics with regard to the chemical bonds. We have now applied these methods to several uranium compounds. In particular we have studied the bonds made by uranium to oxygen, fluorine and chlorine in a number of different environments. The experimental protocols and data analysis protocols developed during this project will permit others in the field to explore the chemical bonding of other heavy element systems. From the few compounds studied to date, we are already discovering the parameters that are characteristic of bonding in such systems, and providing essential experimental benchmarks for theoreticians.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2012

Heat Melt Compaction as an Effective Treatment for Eliminating Microorganisms from Solid Waste

One of the technologies being tested at Ames Research Center as part of the logistics and repurposing project is heat melt compaction (HMC) of solid waste to reduce volume, remove water and render a biologically stable and safe product. Studies at Kennedy Space Center have focused on the efficacy of the heat melt compaction process for killing microorganisms in waste and specific compacter operation protocols, i.e., time and temperature, required to achieve a sterile, stable product. The work reported here includes a controlled study to examine the survival and potential re-growth of specific microorganisms over a 6-month period of storage after heating and compaction. Before heating and compaction, ersatz solid wastes were inoculated with Bacillus amyloliquefaciens and Rhodotorula mucilaginosa, previously isolated from recovered space shuttle mission food and packaging waste. Compacted HMC tiles were sampled for microbiological analysis at time points between 0 and 180 days of storage in a controlled environment chamber. In addition, biological indicator strips containing spores of Bacillus atrophaeus and Ceo bacillus stearothermophilus were imbedded in trash to assess the efficacy of the HMC process to achieve sterilization. Analysis of several tiles compacted at 180 C for times of 40 minutes to over 2 hours detected organisms in all tile samples with the exception of one exposed to 180 C for approximately 2 hours. Neither of the inoculated organisms was recovered, and the biological indicator strips were negative for growth in all tiles indicating at least local sterilization of tile areas. The findings suggest that minimum time/temperature combination is required for complete sterilization. Microbial analysis of tiles processed at lower temperatures from 130 C-150 C at varying times will be discussed, as well as analysis of the bacteria and fungi present on the compactor hardware as a result of exposure to the waste and the surrounding environment. The two organisms inoculated into the waste were among those isolated and identified from the HMC surfaces indicating the possibility of cross contamination.

Hummerick, Mary P.↗
NASA NTRS2013

Heat Melt Compaction as an Effective Treatment for Eliminating Microorganisms from Solid Waste

One of the technologies being tested at Ames Research Center as part of the logistics and repurposing project is heat melt compaction (HMC) of solid waste to reduce volume, remove water and render a biologically stable and safe product. Studies at Kennedy Space Center have focused on the efficacy of the heat melt compaction process for killing microorganisms in waste and specific compacter operation protocols, i.e., time and temperature required to achieve a sterile, stable product. The work. reported here includes a controlled study to examine the survival and potential re-growth of specific microorganisms over a 6-month period of storage after heating and compaction. Before heating and compaction, ersatz solid wastes were inoculated with Bacillus amyloliquefaciens and Rhodotorula mucilaginosa, previously isolated from recovered space shuttle mission food and packaging waste. Compacted HMC tiles were sampled for microbiological analysis at time points between 0 and 180 days of storage in a controlled environment chamber. In addition, biological indicator strips containing spores of Bacillus atrophaeus and Geobacillus stearothermophilus were imbedded in trash to assess the efficacy of the HMC process to achieve sterilization. Analysis of several tiles compacted at 180deg C for times of 40 minutes to over 2 hours detected organisms in all tile samples with the exception of one exposed to 180deg C for approximately 2 hours. Neither of the inoculated organisms was recovered, and the biological indicator strips were negative for growth in all tiles indicating at least local sterilization of tile areas. The findings suggest that minimum time/temperature combination is required for complete sterilization. Microbial analysis of tiles processed at lower temperatures from 130deg C-150deg C at varying times will be discussed, as well as analysis of the bacteria and fungi present on the compactor hardware as a result of exposure to the waste and the surrounding environment. The two organisms inoculated into the waste were among those isolated and identified from the HMC surfaces indicating the possibility of cross contamination.

Hummerick, Mary P.↗
DOE OSTI2014

MO-E-17A-10: Evaluation of Body and Head Dimensions of Pediatric Patients as a Function of Age

Purpose: Phantom development in medical physics plays an important role in radiation dose assessment and image quality evaluation, and this is especially true in the pediatric patient population. The purpose of this investigation was to establish the relationship between patient age and patient size, focusing on the abdomen-pelvis and head effective diameters, for patients ranging in age from newborn to 18 years. Methods: A dose reporting tool for computed tomography systems was installed at our institution to achieve compliance with state law commencing on July 1, 2012. The software records a number of patient-specific data, and also reports CT dose metrics (CTDIvol and DLP) into the patients interpretive report. The database generated by the software was mined to determine patient effective diameter as a function of age for pediatric patients aged 0–18 years. CT protocols including abdomen-pelvis and routine head were evaluated, and specific to this study the patients age, gender and equivalent diameter were recorded. Results: Six age ranges were evaluated: A(0–3), B(4–6), C(7–9), D(10–12),E(13–15),F(16–18). For the torso in these groups based upon 694 patients, median effective diameters were 147, 167, 184, 214, 231, 246 mm, respectively. For the head (N=1833), median diameters were 143, 157, 162, 168, 174, and 174, respectively. Conclusion: A solid understanding of the approximate dimensions of pediatric patients as a function of age is useful in the development of age-based imaging protocols and dose assessments. CT dose-reporting tools generate a great deal of data with respect to body dimensions automatically. In this study, median equivalent diameters for the abdomen-pelvis and head of pediatric patients were evaluated. These data may prove useful in the development of both mathematical and physical phantoms for dosimetry and image quality assessment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Developing Science-based fueling protocols for 250-bar hydrogen tanks onboard hydrogen ferries: Experiments and modeling

Combined modeling and experimental studies are reported of the fueling of a large (28 kg capacity) 250-bar Type IV hydrogen tank of the type being deployed on early hydrogen ferries, such as the MV Sea Change. The primary goal was to determine how such tanks can be successfully fueled with hydrogen (state of charge greater than 97%) within 45 minutes without exceeding the 82 °C temperature limit for such tanks. The modeling studies show that a gas injector is needed to avoid thermal stratification during hydrogen fueling which can result in potential hot spots. Empirically, precooling of the hydrogen to 0 °C was found to be needed in some of the cases examined, as ambient conditions greatly affected the need for a precooling to achieve the 45-minute fill time desired by end users. The experimental results afforded a calibration of the engineering model SOFIL for these large 250-bar tanks, which now enables using SOFIL to predict volume-averaged hydrogen fueling temperatures to an accuracy of ±2.7°C for these tanks. The model can therefore be used to evaluate potential scenarios for development of a standardized fueling methodology for ferries utilizing large Type-IV tanks.

08 HYDROGEN↗
DOE OSTI2013

A method to acquire CT organ dose map using OSL dosimeters and ATOM anthropomorphic phantoms

Purpose: To present the design and procedure of an experimental method for acquiring densely sampled organ dose map for CT applications, based on optically stimulated luminescence (OSL) dosimeters “nanoDots” and standard ATOM anthropomorphic phantoms; and to provide the results of applying the method—a dose data set with good statistics for the comparison with Monte Carlo simulation result in the future.Methods: A standard ATOM phantom has densely located holes (in 3 × 3 cm or 1.5 × 1.5 cm grids), which are too small (5 mm in diameter) to host many types of dosimeters, including the nanoDots. The authors modified the conventional way in which nanoDots are used, by removing the OSL disks from the holders before inserting them inside a standard ATOM phantom for dose measurements. The authors solved three technical difficulties introduced by this modification: (1) energy dependent dose calibration for raw OSL readings; (2) influence of the brief background exposure of OSL disks to dimmed room light; (3) correct pairing between the dose readings and measurement locations. The authors acquired 100 dose measurements at various positions in the phantom, which was scanned using a clinical chest protocol with both angular and z-axis tube current modulations.Results: Dose calibration was performed according to the beam qualities inside the phantom as determined from an established Monte Carlo model of the scanner. The influence of the brief exposure to dimmed room light was evaluated and deemed negligible. Pairing between the OSL readings and measurement locations was ensured by the experimental design. The organ doses measured for a routine adult chest scan protocol ranged from 9.4 to 18.8 mGy, depending on the composition, location, and surrounding anatomy of the organs. The dose distribution across different slices of the phantom strongly depended on the z-axis mA modulation. In the same slice, doses to the soft tissues other than the spinal cord demonstrated relatively small variations, with the maximum COV around 11.4%. This might be attributed to the angular mA modulation, the placement of the dosimeters, the chest cavity of the scanned region, and the size of the phantom. Doses to the spinal cord were consistently lower than those to other soft tissues.Conclusions: The method is suited for acquiring densely sampled organ dose maps, and can be used for studying dose distributions relevant to subject size, organ location, and clinical CT protocols.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2017

Impact of hydrogen SAE J2601 fueling methods on fueling time of light-duty fuel cell electric vehicles

Hydrogen fuel cell electric vehicles (HFCEVs) are zero-emission vehicles (ZEVs) that can provide drivers a similar experience to conventional internal combustion engine vehicles (ICEVs), in terms of fueling time and performance (i.e. power and driving range). The Society of Automotive Engineers (SAE) developed fueling protocol J2601 for light-duty HFCEVs to ensure safe vehicle fills while maximizing fueling performance. This study employs a physical model that simulates and compares the fueling performance of two fueling methods, known as the “lookup table” method and the “MC formula” method, within the SAE J2601 protocol. Both the fueling methods provide fast fueling of HFCEVs within minutes, but the MC formula method takes advantage of active measurement of precooling temperature to dynamically control the fueling process, and thereby provides faster vehicle fills. Here, the MC formula method greatly reduces fueling time compared to the lookup table method at higher ambient temperatures, as well as when the precooling temperature falls on the colder side of the expected temperature window for all station types. Although the SAE J2601 lookup table method is the currently implemented standard for refueling hydrogen fuel cell vehicles, the MC formula method provides significant fueling time advantages in certain conditions; these warrant its implementation in future hydrogen refueling stations for better customer satisfaction with fueling experience of HFCEVs.

13 HYDRO ENERGY↗
DOE OSTI2016

SU-F-T-196: Hypo-Fractionation with Intensity Modulated Proton Therapy for Unilateral Metallic Prosthesis Prostate Cancer Patients

Purpose: The purpose of this study is to investigate the dosimetric feasibility of hypo-fractionated intensity modulated proton therapy (IMPT) for unilateral metallic prosthesis prostate cancer patients based on proton collaborative group (PCG)-GU002-10 (NCT01230866) protocol criteria. Methods: A total of five unilateral metallic prosthesis prostate cancer cases were included in this retrospective study. For each case, IMPT plans were generated for treatment to be delivered with 7.6 Gy[RBE] per fraction in 5 fractions per week for a total dose of 38 Gy(RBE). Each plan was generated using two anterior-oblique beams and one lateral beam. Treatment plans were optimized with an objective meeting PCG-GU002-10 (NCT01230866) protocol criteria: (i) planning target volume (PTV): D99.5% > 36.1 Gy[RBE], (ii) rectum: V24 < 35%, V33.6 < 10%, (iii) bladder: V39 < 8 cc, and (iv) femoral head: V23 < 1cc. Results: All five cases satisfied PTV D99.5% (average=36.82 Gy[RBE]; range, 36.36–37.13 Gy[RBE]). PTV D95% ranged from 36.66 Gy[RBE] to 38.65 Gy[RBE] and PTV V100 ranged from 95.47% to 97.95%. For the rectum, V24 was less than 35% (average=14.07 Gy[RBE]; range, 6.22–18.42%, whereas V33.6 Gy[RBE] was less than 10% (average=6.83; range, 3.06 – 9.15%). Rectal mean dose ranged from 4.22 Gy[RBE] to 9.97 Gy[RBE]. For the bladder, V39 was found to be less than 8 cc (average=3.69 cc; range, 0.19–7.68 cc). Bladder mean dose ranged from 4.22 Gy[RBE] to 18.83 Gy[RBE]. For the femoral head, V23 was 0 in all five cases. Conclusion: All five unilateral metallic prosthesis prostate cancer IMPT plans generated with one lateral and two anterior-oblique beams satisfied the dosimetric criteria of PCG-GU002-10 (NCT01230866) protocol.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1997

[Ribosomal RNA Evolution]

It is generally believed that an RNA World existed at an early stage in the history of life. During this early period, RNA molecules are seen to be potentially involved in both catalysis and the storage of genetic information. Translation presents several interrelated themes of inquiry for exobiology. First, it is essential, for understanding the very origin of life, how peptides and eventually proteins might have come to be made on the early Earth in a template directed manner. Second, it is necessary to understand how a machinery of similar complexity to that found in the ribosomes of modern organisms came to exist by the time of the last common ancestor (as detected by 16S rRNA sequence studies). Third, the ribosomal RNAs themselves likely had a very early origin and studies of their history may be very informative about the nature of the RNA World. Moreover, studies of these RNAs will contribute to a better understanding of the potential roles of RNA in early evolution.During the past year we have ave conducted a comparative study of four completely sequenced bacterial genoames. We have focused initially on conservation of gene order. The second component of the project continues to build on the model system for studying the validity of variant 5S rRNA sequences in the vicinity of the modern Vibrio proteolyticus 5S rRNA that we established earlier. This system has made it possible to conduct a detailed and extensive analysis of a local portion of the sequence space. These core methods have been used to construct numerous mutants during the last several years. Although it has been a secondary focus, this work has continued over the last year such that we now have in excess of 125 V. proteolyticus derived constructs which have been made and characterized. We have also continued high resolution NMR work on RNA oligomers originally initiated by G. Kenneth Smith who was funded by a NASA Graduate Student Researcher's Fellowship Award until May of 1996. Mr. Smith developed synthesis & purification protocols in order to obtain large quantities of RNA oligomers for NMR studies. He succeeded in obtaining preliminary one dimensional spectra for an analog of the helix II/loop B/helix III domain of 5S rRNAs well as a 29mer which includes helix III and the highly characteristic 13 nucleotide loop C. Significant progress in laying the required groundwork for this work has been accomplished during the past year. A plasmid, pLeuS-1, carrying the E. coli leucine tRNA synthetase gene (LeuRS) has been obtained and used to overexpressed the leucine synthetase. A T7 runoff transcription has been established in our laboratory and successfully used to make both minihelix RNAs and tRNAs. In addition, encapsulation studies have been conducted and we have successfully encapsulated tRNA in lipid vesicles. Initial efforts to obtain peptide bond synthesis will be underway over the next several moths.

Source record↗
DOE OSTI2018

A Porphyrin Spin Qubit and Its 2D Framework Nanosheets

Abstract Molecular spin qubits have been shown to reach sufficiently long quantum coherence times to envision their use as hardware in quantum processors. These will however require their implementation in hybrid solid‐state devices for which the controlled localization and homogeneous orientation of the molecular qubits will be necessary. An alternative to isolated molecules that can ensure these key aspects is 2D framework in which the qubit would act as node. In this work, it is demonstrated that the isolated metalloporphyrin [Cu(H 4 TCPP)] molecule is a potential spin qubit, and maintains similar quantum coherence as node in a 2D [{CuTCPP}Zn 2 (H 2 O) 2 ] metal–organic framework. Mono‐ and multilayer deposits of nanosheets of a similar 2D framework are then successfully formed following a modular method based on Langmuir–Schaefer conditions. The orientation of the {CuTCPP} qubit nodes in these nanosheets is homogeneous parallel to the substrate. These nanosheets are also formed with a control over the qubit concentration, i.e., by dilution with the unmetallated porphyrin. Eventually, 2D nanosheets are formed in situ directly on a substrate, through a simple protocol devised to reproduce the Langmuir–Schaefer conditions locally. Altogether these studies show that 2D spin qubit frameworks are ideal components to develop a hybrid quantum computing architecture.

Urtizberea, Ainhoa↗
DOE OSTI2023

Elucidating the Effect of Ion Exchange Protocol on the Copper Exchange Efficacy, Copper Siting, and SCR activity in Cu-SSZ-13

The influence of the copper ion exchange protocol on SCR activity of SSZ-13 is quantified. Using the same parent SSZ-13 zeolite, four exchange protocols are used to assess how exchange protocol impacts metal uptake and SCR activity. Large differences in the SCR activity, nearly 30 percentage points at 160 °C at constant copper content, are observed for different exchange protocols implying that different exchange protocols lead to different copper species. Hydrogen temperature programmed reduction on selected samples and infrared spectroscopy of CO binding corroborates this conclusion as the reactivity at 160 °C correlates with the intensity of the IR band at 2162 cm -1 . DFT-based calculations show that such an IR assignment is consistent with CO adsorbed on a Cu(I) cation within an eight-membered ring. This work shows that SCR activity can be influenced by the ion exchange process even when different protocols lead to the same metal loading. Perhaps most interesting, a protocol used to generate Cu-MOR for methane to methanol studies led to the most active catalyst both on a unit mass or unit mole copper basis. This points to a yet not recognized means to tailor catalyst activity as the open literature is silent on this issue.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Agrobacterium ‐Mediated Transformation of Brachypodium distachyon

Abstract Brachypodium distachyon is an excellent model system for the grasses and has been adopted as a research organism by many laboratories around the world. It has all of the biological traits required for a model system, including small stature, short life cycle, small genome, simple growth requirements, and a close relationship to major crop plants (cereals). In addition, numerous resources have been developed for working with this species, including genome sequences for many lines, sequenced mutant collections, and a large, freely available germplasm collection. Fortunately, among grasses B. distachyon is one of the most easily transformed species, an absolute necessity for a model system. Agrobacterium ‐mediated transformation is the preferred method to transform plants because it usually results in simple insertions of target DNA. In this article, we describe a method for Agrobacterium ‐mediated transformation of the inbred B. distachyon lines Bd21 and Bd21‐3. Embryogenic callus induced from immature embryos is co‐cultivated with Agrobacterium tumefaciens strain AGL1 or Agrobacterium rhizogenes strain 18r12v. Hygromycin and paromomycin are used as selective agents, with comparable transformation efficiencies (defined as the percentage of co‐cultivated callus that produce transgenic plants) of 40% to 70%. It takes 20 to 30 weeks to obtain T 1 seeds starting from the initial step of dissecting out immature embryos. This protocol has been shown to be efficient and facile in several studies that resulted in the creation of over 22,000 T‐DNA mutants. © 2019 by John Wiley & Sons, Inc.

Chen, Fengjuan↗
DOE OSTI2017

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. As a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK —a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Development and application of a machine learning based multi-objective optimization workflow for CO 2 -EOR projects

Carbon dioxide-Enhanced Oil Recovery (CO 2 -EOR) is known as one of techniques for hydrocarbon production improvement as wells as an important candidate to reduce greenhouse gas emissions. Thus, an ideal development strategy for a CO 2 -EOR project would consider multiple objectives including to maximize oil recovery, CO 2 storage volume and project economic outcomes. This work proposes a robust computational framework that couples artificial neural network (ANN) and multi-objective optimizers to optimize the aforementioned objectives in CO 2 -EOR processes simultaneously. Expert ANN systems are trained and employed as surrogate models of the high-fidelity compositional simulator in the optimization workflow. The robustness of the development optimization protocol is confirmed via a synthetic injection-pattern-base case study. Afterward a field implementation to Morrow-B formation to optimize the tertiary recovery stage of the field development is discussed. This work compares the optimum solution found using an aggregate objective function and the solution repository (Pareto front) generated by the multi-objective optimization process. The comparison indicates the existence of potential multi-solutions satisfying certain criteria in a CO 2 -EOR project designing, which cannot be found using traditional weighted sum method. The optimization results provide significant insight into the decision-making process of CO 2 -EOR project when multiple objective functions are considered.

02 PETROLEUM↗
DOE OSTI2014

Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Toward the Minimal Floating Operation Count Cholesky Decomposition of Electron Repulsion Integrals

As quantum chemistry calculations deal with molecular systems of increasing size, the memory requirement to store electron-repulsion integrals (ERIs) greatly outpaces the physical memory available in computing hardware. Here, the Cholesky decomposition of ERIs provides a convenient yet accurate technique to reduce the storage requirement of integrals. Recent developments of a two-step algorithm have drastically reduced the memory operation (MOP) count, leaving the floating operation (FLOP) count as the last frontier of cost reduction in the Cholesky ERI algorithm. In this report, we introduce a dynamic integral tracking, reusing, and compression/elimination protocol embedded in the two-step Cholesky ERI method. Benchmark studies suggest that this technique becomes particularly advantageous when the basis set consists of many computationally expensive high-angular-momentum basis functions. With this dynamic ERI improvement, the Cholesky ERI approach proves to be a highly efficient algorithm with minimal FLOP and MOP count.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗