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At least 1,153 records · Page 64

Monte Carlo-based treatment planning system calculation engine for microbeam radiation therapy

Purpose: Microbeam radiation therapy (MRT) is a synchrotron radiotherapy technique that explores the limits of the dose-volume effect. Preclinical studies have shown that MRT irradiations (arrays of 25-75-{mu}m-wide microbeams spaced by 200-400 {mu}m) are able to eradicate highly aggressive animal tumor models while healthy tissue is preserved. These promising results have provided the basis for the forthcoming clinical trials at the ID17 Biomedical Beamline of the European Synchrotron Radiation Facility (ESRF). The first step includes irradiation of pets (cats and dogs) as a milestone before treatment of human patients. Within this context, accurate dose calculations are required. The distinct features of both beam generation and irradiation geometry in MRT with respect to conventional techniques require the development of a specific MRT treatment planning system (TPS). In particular, a Monte Carlo (MC)-based calculation engine for the MRT TPS has been developed in this work. Experimental verification in heterogeneous phantoms and optimization of the computation time have also been performed. Methods: The penelope/penEasy MC code was used to compute dose distributions from a realistic beam source model. Experimental verification was carried out by means of radiochromic films placed within heterogeneous slab-phantoms. Once validation was completed, dose computations in a virtual model of a patient, reconstructed from computed tomography (CT) images, were performed. To this end, decoupling of the CT image voxel grid (a few cubic millimeter volume) to the dose bin grid, which has micrometer dimensions in the transversal direction of the microbeams, was performed. Optimization of the simulation parameters, the use of variance-reduction (VR) techniques, and other methods, such as the parallelization of the simulations, were applied in order to speed up the dose computation. Results: Good agreement between MC simulations and experimental results was achieved, even at the interfaces between two different media. Optimization of the simulation parameters and the use of VR techniques saved a significant amount of computation time. Finally, parallelization of the simulations improved even further the calculation time, which reached 1 day for a typical irradiation case envisaged in the forthcoming clinical trials in MRT. An example of MRT treatment in a dog's head is presented, showing the performance of the calculation engine. Conclusions: The development of the first MC-based calculation engine for the future TPS devoted to MRT has been accomplished. This will constitute an essential tool for the future clinical trials on pets at the ESRF. The MC engine is able to calculate dose distributions in micrometer-sized bins in complex voxelized CT structures in a reasonable amount of time. Minimization of the computation time by using several approaches has led to timings that are adequate for pet radiotherapy at synchrotron facilities. The next step will consist in its integration into a user-friendly graphical front-end.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Wide-ranging predictions of new stable compounds powered by recommendation engines

The computational search for new stable inorganic compounds is faster than ever, thanks to high-throughput density functional theory (DFT). However, stable compound searches remain highly expensive because of the enormous search space and the cost of DFT calculations. To aid these searches, recommendation engines have been developed. We conduct a systematic comparison of the performance of previously developed recommendation engines, specifically ones based on elemental substitution, data mining, and neural network prediction of formation enthalpy. After identifying ways to improve the recommendation engines, we find the neural network to be superior at recommending stable Heusler compounds. Armed with improved recommendation engines, we identify tens of thousands of compounds that are stable at zero temperature and pressure, now available in the Open Quantum Materials Database. We summarize this diverse pool of compounds, including the elusive mixed anion compounds, and two of their many applications: thermoelectricity and solar thermochemical fuel production.

Science & Technology - Other Topics↗

Engineering the hyperthermophilic archaeon Pyrococcus furiosus for 1-propanol production

ABSTRACT Society relies heavily on chemicals traditionally produced through the refinement of fossil fuels. The conversion of renewable biomass to value-added chemicals by microbes, particularly hyperthermophiles (T opt ≥80°C), offers a renewable alternative to this traditional approach. Herein, we describe the engineering of the hyperthermophilic archaeon Pyrococcus furiosus , which grows optimally (T opt ) at 100°C, for the conversion of sugar to 1-propanol. This was accomplished by constructing a hybrid metabolic pathway consisting of two native and seven heterologously produced enzymes to convert acetyl-CoA from carbohydrate metabolism to 1-propanol. A total of eleven foreign genes from two other organisms were utilized, one from the thermophilic bacterium Thermoanaerobacter sp. strain X514 and 10 from the thermoacidophilic archaeon Metallosphaera sedula, both of which grow optimally near 70°C. The recombinant P. furiosus strain produced 1-propanol at similar concentrations (up to ~1 mM) when incubated at 75°C to activate the gene products of Thermoanaerobacter sp. strain X514 and M. sedula and by initially incubating at 95°C for P. furiosus growth and then subsequently returning to 75°C to promote 1-propanol formation. Note that 1-propanol was not produced if the culture was grown only at 95°C. This work has the potential for future optimization through harnessing the genome-scale metabolic model of P. furiosus that was used herein to identify engineering targets to increase 1-propanol titer. IMPORTANCE As petroleum reserves become increasingly strained, the development of renewable alternatives to traditional chemical synthesis becomes more important. In this work, a high-temperature biological system for sugar to 1-propanol conversion was demonstrated by metabolic engineering of the hyperthermophilic archaeon Pyrococcus furiosus (T opt 100°C). The engineered strain produced 1-propanol by temperature shifting from 75°C to 95°C and then back to 75°C to accommodate the temperature ranges for native and foreign proteins associated with 1-propanol biosynthesis. Genome-scale metabolic modeling informed the carbon and reductant flux in the system, identified potential factors limiting 1-propanol production, and revealed potential optimization targets.

O'Quinn, Hailey C. (ORCID:0009000274865755)↗

Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host

Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits—thermotolerance, lipid production, and facile transformation with exogenous DNA—into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.

59 BASIC BIOLOGICAL SCIENCES↗

DEFINING THE PLAYERS IN HIGHER-ORDER NETWORKS: PREDICTIVE MODELING FOR REVERSE ENGINEERING FUNCTIONAL INFLUENCE NETWORKS

A difficult problem that is currently growing rapidly due to the sharp increase in the amount of high-throughput data available for many systems is that of determining useful and informative causative influence networks. These networks can be used to predict behavior given observation of a small number of components, predict behavior at a future time point, or identify components that are critical to the functioning of the system under particular conditions. In these endeavors incorporating observations of systems from a wide variety of viewpoints can be particularly beneficial, but has often been undertaken with the objective of inferring networks that are generally applicable. The focus of the current work is to integrate both general observations and measurements taken for a particular pathology, that of ischemic stroke, to provide improved ability to produce useful predictions of systems behavior. A number of hybrid approaches have recently been proposed for network generation in which the Gene Ontology is used to filter or enrich network links inferred from gene expression data through reverse engineering methods. These approaches have been shown to improve the biological plausibility of the inferred relationships determined, but still treat knowledge-based and machine-learning inferences as incommensurable inputs. In this paper, we explore how further improvements may be achieved through a full integration of network inference insights achieved through application of the Gene Ontology and reverse engineering methods with specific reference to the construction of dynamic models of transcriptional regulatory networks. We show that integrating two approaches to network construction, one based on reverse-engineering from conditional transcriptional data, one based on reverse-engineering from in situ hybridization data, and another based on functional associations derived from Gene Ontology, using probabilities can improve results of clustering as evaluated by a predictive model of transcriptional expression levels.

59 BASIC BIOLOGICAL SCIENCES↗

Extending lean operating limit and reducing emissions of methane spark-ignited engines using a microwave-assisted spark plug

A microwave-assisted spark plug was used to extend the lean operating limit (lean limit) and reduce emissions of an engine burning methane-air. In-cylinder pressure data were collected at normalized air-fuel ratios of λ = 1.46, λ = 1.51, λ = 1.57, λ = 1.68, and λ = 1.75. For each λ , microwave energy (power supplied to the magnetron per engine cycle) was varied from 0 mJ (spark discharge alone) to 1600 mJ. At lean conditions, the results showed adding microwave energy to a standard spark plug discharge increased the number of complete combustion cycles, improving engine stability as compared to spark-only operation. Addition of microwave energy also increased the indicated thermal efficiency by 4% at λ = 1.68. At λ = 1.75, the spark discharge alone was unable to consistently ignite the air-fuel mixture, resulting in frequent misfires. Although microwave energy produced more consistent ignition than spark discharge alone at λ = 1.75, 59% of the cycles only partially burned. Overall, the microwave-assisted spark plug increased engine performance under lean operating conditions (λ = 1.68) but did not affect operation at conditions closer to stoichiometric.

Rapp, Vi H.↗

Multiplayer Engineering

INL engineers developed a special purpose software framework designed to establish real-time connections between multiple running Unity instances. The framework is developed in Unity, a game engine development platform. This framework programmatically attaches functions to engineering models, enabling users to interact with, observe, and make changes to virtual models. These interactions are broadcasted through websocket connections, and received by other engineers in real-time.

Woodruff, Nathan↗

Effect of engine conditions and injection timing on piston-top fuel films for stratified direct-injection spark-ignition operation using E30

Mid-level ethanol/gasoline blends can provide knock resistance benefits for stoichiometric spark-ignition engine operation, but previous studies have identified challenges associated with spray impingement and wall wetting, leading to excessive particulate matter emissions. At the same time, stratified-charge spark-ignition operation can provide increased thermal efficiency, but care has to be exercised to avoid excessive in-cylinder soot formation. In support of the use of mid-level ethanol/gasoline blends in advanced spark-ignition engines, this study presents spray and fuel-film measurements in a direct-injection spark-ignition engine operated with a 30 vol.%/70 vol.% ethanol/gasoline blend (E30). Crank-angle resolved fuel-film measurements at the piston surface are conducted using two different implementations of the refractive index matching technique. A small-angle refractive index matching implementation allows quantification of the wetted area, while a large-angle refractive index matching implementation enables semi-quantitative measurements of fuel-film thickness and volume, in addition to fuel-film area. The fuel-film measurements show that both the amount of fuel deposited on the piston and the shape of the fuel-film patterns are strongly influenced by the injection timing, duration, intake pressure, and coolant temperature. For combinations of high in-cylinder gas density and long injection duration, merging of the individual spray plumes, commonly referred to as spray collapse, can cause a dramatic change to the shape and thickness of the wall fuel films. Overall, the study provides guidance to engine designers aiming at minimizing wall wetting through tailored combinations of injection timings and durations.

Ding, Carl-Philipp↗

Investigation of the effects of passive pre-chamber nozzle pattern and ignition system on engine performance and emissions

The impact of passive pre-chamber (PC) internal volume, nozzle hole pattern (i.e. with and without a central axial nozzle), and PC igniter plug type on performance and emissions was investigated in an optically accessible, single-cylinder, gasoline research engine. The two PC igniter plugs investigated were a conventional inductive coil spark plug and a nanosecond repetitively pulsed (NRP) plasma discharge system previously demonstrated to accelerate early flame propagation. The baseline PC design featured a funnel shaped internal volume with a PC tip that contained six radial nozzles and a larger central axial nozzle. Two additional PC tip geometries were evaluated where either the baseline internal volume was increased or the axial nozzle was removed and the radial nozzle diameters were increased. A sweep of charge equivalence ratios ( ϕ) from nearly stoichiometric to the lean limit was performed for a fixed engine speed (1300 revolutions per minute), and engine load (3.5 bar gross indicated mean effective pressure). Time-resolved PC and main chamber (MC) pressure data as well as MC emissions data were collected to analyze engine performance and emissions characteristics. Combustion in the MC was further investigated using high-speed excited methylidyne radical (CH*) chemiluminescence imaging. Collected results highlighted that while all PC tips and ignition systems exhibited similar performance and emissions down to ϕ = 0.8, relevant differences in thermal efficiency and emissions for leaner charge mixtures were observed, with the results highly dependent on the nozzle pattern and ignition system. Major deviations were correlated to preferential de-pressurization of the PC through the axial nozzle for lean conditions that was not observed for mixture conditions closer to stoichiometric. Results show that a combination of radial and axial nozzle patterns in the PC extended lean-stability limits at the low-load condition evaluated. Further benefits were observed with the use of NRP ignition systems due to faster combustion within the PC volume provided that the volume was sufficiently large.

Di Sabatino, Francesco↗

Natural Gas Engine Performance Ignited by a Passively Q-Switched Microlaser

A robust end pumped, passively Q-switched, air-cooled, microlaser was designed and prototyped to yield a 1064 nm pulsed laser output of 21 mJ/P with a pulse width of 4.2 ns FWHM. This microlaser was coupled to a standard laser plug carrying a sapphire lens with 13 mm back focal length. This assembly was tested in a natural gas fueled single-cylinder engine, and in one cylinder of a turbocharged 6-cylinder engine. Single cylinder engine tests showed extension of the lean ignition limit which enabled an efficiency improvement of 0.2% while meeting emission regulations. The tests conducted in the 6-cylinder engine showed highly improved ignition stability.

Laser Ignition↗

ProtDataTherm: A database for thermostability analysis and engineering of proteins

Protein thermostability engineering is a powerful tool to improve resistance of proteins against high temperatures and thereafter broaden their applications. For efficient protein thermostability engineering, different thermostability-classified data sources including sequences and 3D structures are needed for different protein families. However, no data source is available providing such data easily. It is the first release of ProtDataTherm database for analysis and engineering of protein thermostability which contains more than 14 million protein sequences categorized based on their thermal stability and protein family. This database contains data needed for better understanding protein thermostability and stability engineering. Providing categorized protein sequences and structures as psychrophilic, mesophilic and thermophilic makes this database useful for the development of new tools in protein stability prediction. This database is available at http://profiles.bs.ipm.ir/ softwares/protdatatherm. As a proof of concept, the thermostability that improves mutations were suggested for one sample protein belonging to one of protein families with more than 20 mesophilic and thermophilic sequences and with known experimentally measured ΔT of mutations available within ProTherm database.

59 BASIC BIOLOGICAL SCIENCES↗

Foundations to the unified psycho-cognitive engine.

This document outlines the key features of the SNL psychological engine. The engine is designed to be a generic presentation of cognitive entities interacting among themselves and with the external world. The engine combines the most accepted theories of behavioral psychology with those of behavioral economics to produce a unified simulation of human response from stimuli through executed behavior. The engine explicitly recognizes emotive and reasoned contributions to behavior and simulates the dynamics associated with cue processing, learning, and choice selection. Most importantly, the model parameterization can come from available media or survey information, as well subject-matter-expert information. The framework design allows the use of uncertainty quantification and sensitivity analysis to manage confidence in using the analysis results for intervention decisions.

99 GENERAL AND MISCELLANEOUS↗

SLUDGE TREATMENT PROJECT ENGINEERED CONTAINER RETRIEVAL AND TRANSFER SYSTEM PRELMINARY DESIGN HAZARD AND OPERABILITY STUDY

This Hazard and Operability (HAZOP) study addresses the Sludge Treatment Project (STP) Engineered Container Retrieval and Transfer System (ECRTS) preliminary design for retrieving sludge from underwater engineered containers located in the 105-K West (KW) Basin, transferring the sludge as a sludge-water slurry (hereafter referred to as 'slurry') to a Sludge Transport and Storage Container (STSC) located in a Modified KW Basin Annex, and preparing the STSC for transport to T Plant using the Sludge Transport System (STS). There are six, underwater engineered containers located in the KW Basin that, at the time of sludge retrieval, will contain an estimated volume of 5.2 m{sup 3} of KW Basin floor and pit sludge, 18.4 m{sup 3} of 105-K East (KE) Basin floor, pit, and canister sludge, and 3.5 m{sup 3} of settler tank sludge. The KE and KW Basin sludge consists of fuel corrosion products (including metallic uranium, and fission and activation products), small fuel fragments, iron and aluminum oxide, sand, dirt, operational debris, and biological debris. The settler tank sludge consists of sludge generated by the washing of KE and KW Basin fuel in the Primary Clean Machine. A detailed description of the origin of sludge and its chemical and physical characteristics can be found in HNF-41051, Preliminary STP Container and Settler Sludge Process System Description and Material Balance. In summary, the ECRTS retrieves sludge from the engineered containers and hydraulically transfers it as a slurry into an STSC positioned within a trailer-mounted STS cask located in a Modified KW Basin Annex. The slurry is allowed to settle within the STSC to concentrate the solids and clarify the supernate. After a prescribed settling period the supernate is decanted. The decanted supernate is filtered through a sand filter and returned to the basin. Subsequent batches of slurry are added to the STSC, settled, and excess supernate removed until the prescribed quantity of sludge is collected. The sand filter is then backwashed into the STSC. The STSC and STS cask are then inerted and transported to T Plant.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

PBX 9502 Literature Review: An Engineering Perspective

Engineering analysis for the stockpile systems requires that materials used in the stockpile be characterized properly. One of these materials is PBX 9502, an insensitive high explosive (IHE). The Los Alamos National Laboratory (LANL) is working to improve its engineering material modeling capability for PBX 9502.This effort includes the development of requirements for an engineering material model (or models), review of material models currently used for engineering simulations, and review of currently available thermal-mechanical test data. The information obtained will either help to enhance the existing models or help the development and implementation of a new model or models. This document summarizes a review of literature on PBX 9502 that was performed over the past several months. The review was focused primarily on literature dealing with the characterization of PBX 9502 from a thermo-mechanical standpoint. Literature dealing with the formulation, explosive performance, and sensitivity was not included in this report. It should be noted that, like most research of this nature, this literature review is not intended to be all-inclusive. However, it provides a detailed baseline of the information that is available and will be very useful to those seeking to expand the PBX 9502 knowledge base.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

High Efficiency, Low Emissions Homogeneous Charge Compression Ignition (HCCI) Engines

This is the final report of the High Efficiency Clean Combustion (HECC) Research Program for the U.S. Department of Energy. Work under this co-funded program began in August 2005 and finished in July 2010. The objective of this program was to develop and demonstrate a low emission, high thermal efficiency engine system that met 2010 EPA heavy-duty on-highway truck emissions requirements (0.2g/bhp-hr NOx, 0.14g/bhp-hr HC and 0.01g/bhp-hr PM) with a thermal efficiency of 46%. To achieve this goal, development of diesel homogenous charge compression ignition (HCCI) combustion was the chosen approach. This report summarizes the development of diesel HCCI combustion and associated enabling technologies that occurred during the HECC program between August 2005 and July 2010. This program showed that although diesel HCCI with conventional US diesel fuel was not a feasible means to achieve the program objectives, the HCCI load range could be increased with a higher volatility, lower cetane number fuel, such as gasoline, if the combustion rate could be moderated to avoid excessive cylinder pressure rise rates. Given the potential efficiency and emissions benefits, continued research of combustion with low cetane number fuels and the effects of fuel distillation are recommended. The operation of diesel HCCI was only feasible at part-load due to a limited fuel injection window. A 4% fuel consumption benefit versus conventional, low-temperature combustion was realized over the achievable operating range. Several enabling technologies were developed under this program that also benefited non-HCCI combustion. The development of a 300MPa fuel injector enabled the development of extended lifted flame combustion. A design methodology for minimizing the heat transfer to jacket water, known as precision cooling, will benefit conventional combustion engines, as well as HCCI engines. An advanced combustion control system based on cylinder pressure measurements was developed. A Well-to-wheels analysis of the energy flows in a mobile vehicle system and a 2nd Law thermodynamic analysis of the engine system were also completed under this program.

33 ADVANCED PROPULSION SYSTEMS↗

PHEV Engine Control and Energy Management Strategy (FY12 Annual Report)

Our objective was to investigate novel engine control strategies targeted at rapid engine/catalyst warming for the purpose of mitigating tailpipe emissions from plug-in hybrid electric vehicles (PHEV) exposed to multiple engine cold start events, and to validate and optimize hybrid supervisory control techniques developed during previous and on-going research projects by integrating them into the vehicle level control system and complementing them with the modified engine control strategies in order to further reduce emissions during both cold start and engine re-starts.

Chambon, Paul H.↗

Genetic engineering of cyanobacteria as biodiesel feedstock.

Algal biofuels are a renewable energy source with the potential to replace conventional petroleum-based fuels, while simultaneously reducing greenhouse gas emissions. The economic feasibility of commercial algal fuel production, however, is limited by low productivity of the natural algal strains. The project described in this SAND report addresses this low algal productivity by genetically engineering cyanobacteria (i.e. blue-green algae) to produce free fatty acids as fuel precursors. The engineered strains were characterized using Sandia s unique imaging capabilities along with cutting-edge RNA-seq technology. These tools are applied to identify additional genetic targets for improving fuel production in cyanobacteria. This proof-of-concept study demonstrates successful fuel production from engineered cyanobacteria, identifies potential limitations, and investigates several strategies to overcome these limitations. This project was funded from FY10-FY13 through the President Harry S. Truman Fellowship in National Security Science and Engineering, a program sponsored by the LDRD office at Sandia National Laboratories.

Ruffing, Anne.↗

Quality Engineering as a Profession

Over the course of time, the profession of quality engineering has witnessed significant change, from its original emphasis on quality control and inspection to a more contemporary focus on upholding quality processes throughout the organization and its product realization activities. This paper describes the profession of quality engineering, exploring how today's quality engineers and quality professionals are certified individuals committed to upholding quality processes and principles while working with different dimensions of product development. It also discusses the future of the quality engineering profession and the future of the quality movement as a whole.

Kolb, Rachel R.↗