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Chapter 10: Advances in Protein Engineering and its Application in Synthetic Biology

Protein engineering has been used successfully in fields ranging from medicine to food science to biofuels. Applications of protein engineering include developing antiviral peptides or other protein therapeutics, antibody engineering, designing protein-based logic circuits, engineering enzymes to be more specific or to function under industrially relevant conditions such as at higher temperatures or high/low pH, modifying cell signaling or regulatory functions, and so on. Advances in recombinant DNA, "omics," and CRISPR-Cas (clustered regularly interspaced short palindromic repeats and its associated proteins) technologies, combined with high-throughput screening facilities, will lead to improved methods for protein engineering, enabling easy modification of more proteins/enzymes for new specific applications. New methods for rational design, directed evolution, and computer-aided protein design will further accelerate the speed of protein evolution and expand the scope for protein engineering. In this chapter we discuss general protein engineering strategies and advances in engineering proteins with desired functions, focusing on the "design" and "build" part of the design-build-test-learn cycle.

BIOMASS FUELS↗

Model predictive combustion control of a Gasoline Compression Ignition engine

Gasoline Compression Ignition is a novel combustion concept that derives its superiority from the high compression ratio of a compression ignition engine as well as the properties of gasoline fuel, such as longer ignition delay and higher volatility compared to diesel. Here, this combustion concept was experimentally tested on a 12.4L Class 8 truck engine. Based on these experimental data, prior efforts by the authors focused on the development of an engine model for a heavy-duty engine operating on a low-reactivity fuel. This engine model was leveraged within this study to investigate a combustion control strategy at different engine conditions and injection methods and was augmented to incorporate cycle-to-cycle combustion variations. State estimation is performed by means of a Kalman filter which feeds into a model predictive controller. The model predictive controller chooses control actions based on a predefined cost function under consideration of bounds reflecting physical constraints. The engine model was utilized to establish a state-space model that serves the Kalman filter and model predictive controller for estimation and prediction. A comparative study investigating control actions and engine behavior was performed with and without limiting in-cylinder peak pressure as well as combustion noise, which is of particular interest for early pilot injection strategies. In addition, the proposed control architecture was investigated at two different levels of cycle-to-cycle variations and compared to the performance of a control structure with input disturbance rejection. For increased cycle-to-cycle variations, disturbance estimation reduces state fluctuations and control effort. In general, this investigation highlights control aspects specific to a compression-ignited combustion regime with low-reactivity fuel. The control algorithm is able to maintain the desired references for brake mean effective pressure and combustion phasing while controlling peak in-cylinder pressure and combustion noise.

42 ENGINEERING↗

CFD modeling of near-wall combustion and unburned methane prediction in natural gas spark ignition engines

Natural gas-powered engines play a critical role in gas drilling, compression, and transmission sectors, but methane (CH 4 ) from engine combustion slip can be significant over their lifespan, contributing to atmospheric pollution and signaling reduced engine efficiency. Here, to address this challenge, computational fluid dynamics (CFD) simulations offer valuable insights into the in-cylinder combustion process, enabling the optimization of combustion strategies and engine designs to minimize unburned CH 4 slip. This study aims to evaluate and improve combustion models for simulating the combustion process and predicting unburned CH 4 concentrations in natural gas spark-ignition (SI) engines, including engines that are part of combined reformer-engine systems. Specifically, the performance of two flamelet-based combustion models—the Extended Coherent Flame Model (ECFM) and the G-equation model—was assessed using experimental engine data collected under varying excess-air ratio (λ) conditions and fuel compositions, including natural gas and syngas blends. In addition, to enhance the predictive capabilities of the G-equation model, a flame-wall interaction (FWI) sub-model was integrated into its framework. The effects of its model parameters, such as quenching and influence distance, on combustion behavior and unburned methane predictions were analyzed in detail. The ECFM tended to predict delayed combustion phasing under diluted mixture conditions, resulting in overprediction of unburned CH 4 concentrations. In contrast, the G-equation model provided reasonable predictions of combustion pressure, while representing higher the CH 4 reduction rate across the operating condition compared to experimental data. Incorporating the FWI sub-model—with the quenching distance calculated based on a pressure-dependent relation (P -0.48 ) and a fixed influence distance of 1.5 mm—further improved the G-equation model’s accuracy in predicting CH 4 reduction rates without compromising its ability to simulate the combustion process.

Combustion model↗

CONTROLLED END GAS AUTO IGNITION WITH EXHAUST GAS RECIRCULATION ON A STOICHIOMETRIC, SPARK IGNITED, NATURAL GAS ENGINE

The goal of this study is to address fundamental limitations to achieving diesel-like efficiencies in heavy duty on-highway natural gas (NG) engines. Engine knock and misfire are barriers to pathways leading to higher efficiency engines. This study explores enabling technologies for development of high efficiency stoichiometric, spark ignited, natural gas engines. These include design strategies for fast and stable combustion and higher dilution tolerance. Additionally, advanced control methodologies are implemented to maintain stable operation between knock and misfire limits. To implement controlled end- gas autoignition (C-EGAI) strategies a Combustion Intensity Metric (CIM) is used for ignition control with the use of a Woodward large engine control module (LECM). Tests were conducted using a single cylinder, variable compression ratio, cooperative fuel research (CFR) engine with baseline conditions of 900 RPM, engine load of 800 kPa indicated mean effective pressure (IMEP), and stoichiometric air/fuel ratio. Exhaust gas recirculation (EGR) tests were performed using a custom EGR system that simulates a high pressure EGR loop and can provide a range of EGR rates from 0 to 40%. The experimental measurements included the variance of EGR rate, compression ratio, engine speed, IMEP, and CIM. These five variables were optimized through a Modified Box- Benken design Surface Response Method (RSM), with brake efficiency as the merit function. A positive linear correlation between CIM and f-EGAI was identified. Consequently, CIM was used as the feedback control parameter for C-EGAI. As such, implementation of C-EGAI effectively allowed for the utilization of high EGR rates and CRs, controlling combustion between a narrower gap between knock and lean limits. The change from fixed to parametric ignition timing with CIM targeted select values of f-EGAI with an average coefficient of variance (COV) of peak pressure of 5.4. The RSM efficiency optimization concluded with operational conditions of 1080 RPM, 1150 kPa IMEP, 10.55:1 compression ratio, and 17.8% EGR rate with a brake efficiency of 21.3%. At this optimized point of peak performance, a f-EGAI for C-EGAI was observed at 34.1% heat release due to auto ignition, a knock onset crank angle value of 10.3° aTDC and ignition timing of - 24.7° aTDC. This work has demonstrated that combustion at a fixed f-EGAI can be maintained through advanced ignition control of CIM without experiencing heavy knocking events.

Cooperative Fuel Research Engine, Auto Ignition, E↗

Solid particulate mass and number from ducted fuel injection in an optically accessible diesel engine in skip-fired operation

Ducted fuel injection (DFI) is a new combustion strategy that has been shown to significantly attenuate soot formation in diesel engines. While previous studies have used optical diagnostics and optical filter smoke number methods to show that DFI reduces in-cylinder soot formation and engine-out soot emissions, respectively, this is the first study to measure solid particle number (PN) emissions in addition to particle mass (PM). Furthermore, this study quantitatively evaluates the use of transient particle instruments for measuring particles from skip-fired operation in an optical single cylinder research engine (SCRE). Engine-out PN was measured using an engine exhaust particle sizer following a catalytic stripper, and PM was measured using a photoacoustic analyzer. The study improves on earlier preliminary emissions studies by clearly showing that DFI reduces overall PM by 76%–79% and PN for particles larger than 23 nm by 77% relative to conventional diesel combustion at a 1200-rpm, 13.3-bar gross indicated mean effective pressure operating condition. The degree of engine-out PM reduction with DFI was similar across both particulate measurement instruments used in the work. Through the use of bimodal distribution fitting, DFI was also shown to reduce the geometric mean diameter of accumulation mode particles by 26%, similar to the effects of increased injection pressure in conventional diesel combustion systems. This work clearly shows the significant solid particulate matter reductions enabled by DFI while also demonstrating that engine-out PN can be accurately measured from an optical SCRE operating in a skip-fired mode. Based on these results, it is believed that DFI has the potential to enable fuel savings when implemented in multi-cylinder engines, both by lowering the required frequency of active diesel particulate filter regeneration, and by reducing the backpressure imposed by exhaust filtration systems.

33 ADVANCED PROPULSION SYSTEMS↗

Enabling off-highway diesel engine downsizing and performance improvement using electrically assisted turbocharging

Internal combustion engine (ICE) downsizing through various turbocharging configurations is generally known by the powertrain design community as an effective means to reduce frictional losses, increase waste heat recovery, and improve fuel efficiency while increasing engine power density. However, often is the case that turbocharging strategies, including variable geometry turbochargers, and regulated two-stage turbochargers, incur the performance tradeoff between transient response and fuel economy (pumping losses) at high engine speeds. For off-highway vehicles having particularly transient and high-powered duty cycles, efforts to improve this tradeoff and increase operational flexibility have turned to evaluating various electrified air system architectures. In this study, a 4.5 L diesel-ICE configured with an electrically driven compressor (eBooster ® ) is placed in series with a conventional turbocharger and integrated into a 48 V mild-hybrid powertrain architecture. The objective of this powertrain configuration is to enable engine downsizing by 34%, replacing the current 6.8 L ICE platform with the hybridized 4.5 L ICE concept. The commercial 1-D simulation software GT-SUITE is used for powertrain system development and system optimization. Development and validation of the GT-SUITE model and air system controls is concurrently supported through experimental data collection. The simulation model development includes using machine learning methods for optimizing exhaust gas dilution, injection timing, and eBooster ® power to improve steady-state and transient brake-specific fuel consumption while minimizing criteria pollutant emissions. It was found that total specific fluid consumption over the standardized non-road transient engine duty cycle could be reduced by 18% over the current 6.8 L engine by using an optimized eBoosted 4.5 L engine. The hybridized 4.5 L engine concept concurrently showed sufficient transient response capability and nearly an order of magnitude reduction in duty cycle total soot production.

25 ENERGY STORAGE↗

Hierarchical multi-time-scale predictive thermal management and fuel optimization for heavy-duty compression ignition engines

For heavy-duty diesel engines, NO X emissions reduction is strongly constrained by fuel efficiency. This paper presents a hierarchical model predictive controller (H-MPC) for coordinated control of tailpipe NO X emissions and fuel consumption. The H-MPC uses the separation of slow and fast dynamics that exist in the engine and its aftertreatment system. The controller is synthesized with an architecture in which a high-level MPC uses a longer prediction horizon compared to the low-level predictive controller which tracks the high-level controller command and manages the thermal dynamics of the aftertreatment system. Engine load preview enables the high-level controller to estimate the desired catalyst temperature ahead of time and addresses the selective catalytic reduction (SCR) slow thermal dynamics. Calculated by the high-level controller, the intake manifold pressure, and the start of injection (SOI) crank angle is used as reference trajectories in the low-level controller that regulates fast dynamical behaviors such as engine out NO X emissions. Hardware-in-the-loop (HIL) validation of this integrated H-MPC on a rapid prototype controller shows that when the SCR catalyst temperature is above light-off temperature (warmed-up condition), the engine operation is shifted to operate with the best fuel economy since the warmed-up SCR can efficiently reduce the engine-out NO X emissions. Results indicate that up to 0.8% benefit in cycle averaged BSFC along with a 13% reduction in tailpipe NO X compared to a stock engine calibration can be achieved with the coordinated engine and aftertreatment system through H-MPC.

Engineering↗

Development of a Physics-Based Combustion Model for Engine Knock Prediction

The objective of this project is to improve the prediction of engine knock by developing a new combustion modeling framework. Engine knock is a limiting factor to constrain the increase of fuel efficiency for spark ignition (SI) engines in most passenger cars. Efforts to increase fuel efficiency, increasing the compression ratio or downsizing, lead to the increase in the tendency of the knock occurrence. The knock is an undesired ignition of the end-gas, unburned fuel/air mixture ahead of the spark-ignited premixed flame, resulting in rapid in-cylinder pressure rises and engine damages. The combustion modeling framework developed in this project can consider turbulence-chemistry interactions during end-gas ignition, while using a reasonably detailed chemical mechanism developed for ignition and combustion reactions under engine relevant conditions, and the subtle characteristics of spark-ignited flame propagation. It is developed in the context of large eddy simulation (LES), which can capture stochastic in-cylinder processes. The developed model is incorporated into a commercial software for engine simulation, CONVERGE CFD, as a user defined function, and validated. Engine knock and knock-free experiments as well as direct numerical simulation (DNS) of end-gas ignition in homogeneous turbulence are performed to help model development and provide data sets for model validation. With further validation, the developed model is expected to advance the predictive capability for engine knock simulations and thus contribute to improving the fuel efficiency.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Optical Engine Lockout System Design and Operation

Engine run days in the Diesel Combustion and Fuel Effects Lab are hectic. The long mental lists that must be kept by engine operators, paired with the tight time constraints between experiments, can cause operational issues that may be dangerous to personnel and/or cause damage to test equipment. Until now, a paper sign has been used to warn operators not to motor the engine when a foreign object has been placed inside of it. Unfortunately, this simple administrative control has failed in the past, motivating this effort to develop an improved system. The lockout system described in this document introduces an engineering control that, when activated, actually prevents the engine from being motored. The new system consists of a primary and a secondary control panel. Prior to an operator placing a foreign object into the cylinder, they press a button on the secondary control panel near the engine. This breaks the interlock circuit for the engine dynamometer and activates LEDs on both control panels to notify operators that a foreign object is present within the engine cylinder. Once the work is done and all foreign objects have been removed from the combustion chamber, two operators must be present to disable the system by simultaneously pressing the buttons on the primary and secondary control panels. Requiring a second operator to disable the system increases accountability and reduces the likelihood of potentially costly mistakes.

42 ENGINEERING↗

Evaluation of Engineered Form MOFs CaSDB and HKUST-1

Idaho National Laboratory (INL) and Pacific Northwest National Laboratory (PNNL) have studied different sorbents for the purpose of separating krypton (Kr) and xenon (Xe). PNNL has researched various metal-organic frameworks (MOFs) that have characteristics theoretically suitable for the separation. Based on computational analysis, PNNL chose Calcium–4,4’–sulfonyl dibenzoate (CaSDB) and Hong Kong University of Science and Technology MOF1 (HKUST–1). The raw MOFs are supplied in a powder form and must be incorporated into a robust engineered form to be viable for gas separation. In 2016, PNNL produced an engineered form of CaSDB by compressing and grinding the raw MOF material. This form was sent to INL for adsorption testing. Gentle mechanical agitation of the compressed form produced a large amount of powder, resulting in the conclusion that the form was not viable for the application. In 2019, INL successfully produced two engineered forms, CaSDB–EF1 and HKUST–EF2, by incorporating the active MOF powders into a polyacrylonitrile (PAN) binder. PNNL also produced two engineered forms, CaSDB–10pmma and HKUST–10pmma, by using polymethyl methacrylate (PMMA) as a binder. Surface area analysis indicated that the forms could be viable for separations in which the CaSDB–EF1 retained 84% of the raw CaSDB surface area and CaSDB–10pmma retained 48%. HKUST–EF2 retained all the raw HKUST–1 surface area, whereas HKUST–10pmma retained only 28%. Mechanical stability testing demonstrated that the PMMA forms formed a fine powder whereas, the PAN forms did not. In general, adsorption testing showed that CaSDB–10pmma had a lower Xe breakthrough capacity than CaSDB–EF1, but a higher saturation capacity at both room temperature and at 253 K. The CaSDB MOF was intended to be used as a room temperature sorbent to capture Xe. However, both CaSDB engineered forms displayed relatively short initial break through times. Reduced temperature increased the Xe capacity of both engineered forms. HKUST–1 was expected to be effective only at sub-zero temperatures. At 195 K, HKUST–10pmma had an initial Xe breakthrough capacity of 119 mmol/ kg, compared to HKUST–EF2 at 339 mmol/ kg. The saturation capacities were 275 and 383 mmol/ kg, respectively. HKUST–10ppm also had a lower Kr capacity of 1.7 mmol/kg, whereas the HKUST–EF had a Kr capacity of 3 mmol/ kg. Test results indicate that the PAN engineered forms are a more suitable choice for the complete separation of Xe and Kr, due to the increase in initial breakthrough capacity. CaSDB allows rapid breakthrough of Kr and Xe regardless of the type of engineered form. At 253 K, it is more viable, but is still not the most effective sorbent. HKUST–EF2 demonstrated viability for Xe capture at 195 K, which may merit further study, however it may be cost prohibitive.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Development of a Physics-Based Combustion Model for Engine Knock Prediction

The objective of this project is to improve the prediction of engine knock by developing a new combustion modeling framework. Engine knock is a limiting factor to constrain the increase of fuel efficiency for spark ignition (SI) engines in most passenger cars. Efforts to increase fuel efficiency, increasing the compression ratio or downsizing, lead to the increase in the tendency of the knock occurrence. The knock is an undesired ignition of the end-gas, unburned fuel/air mixture ahead of the spark-ignited premixed flame, resulting in rapid in-cylinder pressure rises and engine damages. The combustion modeling framework developed in this project can consider turbulence-chemistry interactions during end-gas ignition, while using a reasonably detailed chemical mechanism developed for ignition and combustion reactions under engine relevant conditions, and the subtle characteristics of spark-ignited flame propagation. It is developed in the context of large eddy simulation (LES), which can capture stochastic in-cylinder processes. The developed model is incorporated into a commercial software for engine simulation, CONVERGE CFD, as a user defined function, and validated. Engine knock and knock-free experiments as well as direct numerical simulation (DNS) of end-gas ignition in homogeneous turbulence are performed to help model development and provide data sets for model validation. With further validation, the developed model is expected to advance the predictive capability for engine knock simulations and thus contribute to improving the fuel efficiency.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

New Directions for Chemical Engineering

Over the past century, the work of chemical engineers has helped transform societies and the lives of individuals, from the synthetic fertilizers that helped feed the world to the development of novel materials used in fuels, electronics, medical devices, and other products. Chemical engineers' ability to apply systems-level thinking from molecular to manufacturing scales uniquely positions them to address today’s most pressing problems, including climate change and the overuse of resources by a growing population. New Directions for Chemical Engineering details a vision to guide chemical engineering research, innovation, and education over the next few decades. This report calls for new investments in U.S. chemical engineering and the interdisciplinary, cross-sector collaborations necessary to advance the societal goals of transitioning to a low-carbon energy system, ensuring our production and use of food and water is sustainable, developing medical advances and engineering solutions to health equity, and manufacturing with less waste and pollution. The report also calls for changes in chemical engineering education to ensure the next generation of chemical engineers is more diverse and equipped with the skills necessary to address the challenges ahead.

National Academies of Sciences, Engineering, and M↗

SPC-70486 Rev 0 Stirling Engine Prototype Performance Specification

Idaho National Laboratory (INL) is developing a small microreactor to produce electrical power utilizing a small nuclear core and Stirling engines under the Microreactor Application Research Validation and Evaluation (MARVEL) program. The purpose of this performance specification is to define requirements to build and test the Stirling Engine prototype, including interfacing with Kinnetech in the development/test of the engines. This specification includes prototyping components only and are not for use in the reactor. Prototype testing is a preliminary test to be conducted with conceptual equipment from which a final design will be developed. The results of the testing defined herein will not be used as a qualification test. The Stirling Engines have an engine controller module (QEC). Currently, the QEC doesn’t have a means to stop the engine. An analog controlled engine braking system must be developed and tested with the engine prototype. Any conflict between this specification and any supplementary specifications in the procurement documents requires written clarification from the Contractor prior to proceeding with any work. Any deviation from the procurement documents requires approval by the Contractor with the change request process.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

Investigation of Cycle-to-Cycle Variations in Internal Combustion Engine Using Proper Orthogonal Decomposition

The understanding, modeling and control of the cycle-to-cycle variation (CCV) in the modern internal combustion engine (ICE) is a key scientific challenge to achieve stable engine operation. High CCV in the engine combustion chamber may contribute to partial burn, misfire and knock, which adversely affects the engine performance and may potentially damage the engine. The objective of the current study is to leverage high-fidelity numerical simulations to improve the understanding of the causes of CCV. Using the massively parallel code, Nek5000, multi-cycle, wall-resolved large-eddy simulations (LES) were performed for the General Motors (GM), Transparent Combustion Chamber (TCC-III) optical engine under motored operating conditions. Further, the large-scale structures of the in-cylinder flow were investigated using a triple proper orthogonal decomposition (POD) technique to explore the characteristics of different parts of the flow and their contributions to CCV. The kinetic energy of the subset of flow structures were determined and correlated between the intake and compression strokes. The insights from the analysis of the large-scale flow structures will be used to assist the development of improved engine designs with reduced CCV and enhance the engine performance.

33 ADVANCED PROPULSION SYSTEMS↗

Experimental validation of shock propagation through a foam with engineered macro-pores

The engineered macro-pore foam provides a new way to study thermonuclear burn physics by utilizing capsules containing deuterated (D) foam and filling tritium (T) gas in the engineered macro-pores. The implosion of a thermonuclear capsule filled with an engineered macro-pore foam will be complex due to the interaction of a shock wave with the engineered macro-pores. It is our goal to quantify how substantially complex foam structures affect the shape of shock and bulk shock speed. A cylinder-shape shock tube experiment has been designed and performed at the Omega Laser Facility. In order to examine how a foam structure will affect shock propagation, we performed several tests varying (1) engineered macro-pore size, (2) average foam density, and (3) with/without neopentane (C 5 H 12 ) gas. X-ray radiographic data indicate that shock speed through engineered macro-pore foams depends strongly on average foam density and less on pore size. In this work, experimental shock propagation data helped guide two numerical simulation approaches: (1) a 2D simulation with homogenizing foams rather than explicitly simulating engineered macro-pores and (2) a 2D toroidal-pore approximation adopting a toroidal-tube geometry to model engineered macro-pores.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Comparison of a Full-Scale and a 1:10 Scale Low-Speed Two-Stroke Marine Engine Using Computational Fluid Dynamics

International marine shipping is a growing component of international trade; a vast majority of all the world’s goods are being transported on large ocean-going vessels. The International Maritime Organization (IMO) introduced the Energy Efficiency Design Index in 2013, a regulatory framework of associated metrics for reducing emissions of CO 2 per tonne-mile from shipping by approximately 10% each decade. Therefore, decarbonizing the maritime sector requires the development of new fuel sources. Because of the extremely large physical size of the internal combustion engines present in shipping vessels, experimental iterative development of the engine and fuel system is cost-prohibitive. Thus, the ability to perform combustion system development in a scaled platform that can be more easily operated and modeled computationally is of interest. To that end, scaling relationships are needed to translate the results from a smaller engine to a larger counterpart. Scaling studies to date have been restricted to low scaling ratios, four-stroke light-duty engines, and under-resolved computational fluid dynamic simulations that likely do not accurately capture the physics of scaling. In this work, computational models of a 1:10 scale and a full-scale two-stroke crosshead low-speed marine engine were created and validated against experiments obtained in a real 1:10 scale engine installed at Oak Ridge National Laboratory. Further, due to the large size of the full-scale engine, the model required large high-performance computing resources to be evaluated. The availability of high-performance computing resources at the Department of Energy’s Leadership Computing Facilities is an enabler of the current work. The results of the small- and large-scale engine simulations were compared to analyze the effectiveness of the appropriate scaling laws under these extreme scaling ratio conditions.

33 ADVANCED PROPULSION SYSTEMS↗

Tools for genetic engineering and gene expression control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides

ABSTRACT Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts that have the potential to contribute to the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans , Rhodobacter sphaeroides , and Zymomonas mobilis show promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis , N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn 7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides . We screen a synthetic promoter library to identify isopropyl β-D-1-thiogalactopyranoside-inducible promoters with regulated activity in both organisms (up to ~15-fold induction in N. aromaticivorans and ~5-fold induction in R. sphaeroides ). Combining Tn 7 integration with promoters from our library, we establish CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) interference systems for N. aromaticivorans and R. sphaeroides (up to ~10-fold knockdown in N. aromaticivorans and R. sphaeroides ) that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these species and other Alphaproteobacteria. IMPORTANCE It is important to increase our understanding of the microbial world to improve health, agriculture, the environment, and biotechnology. For example, building a sustainable bioeconomy depends on the efficient conversion of plant material to valuable biofuels and bioproducts by microbes. One limitation in this conversion process is that microbes with otherwise promising properties for conversion are challenging to genetically engineer. Here we report genetic tools for Novosphingobium aromaticivorans and Rhodobacter sphaeroides that add to the burgeoning set of tools available for genome engineering and gene expression in Alphaproteobacteria. Our approaches allow straightforward insertion of engineered pathways into the N. aromaticivorans or R. sphaeroides genome and control of gene expression by inducing genes with synthetic promoters or repressing genes using CRISPR interference. These tools can be used in future work to gain additional insight into these and other Alphaproteobacteria and to aid in optimizing yield of biofuels and bioproducts.

Hall, Ashley N.↗

Development of prechamber enabled mixing-controlled combustion strategy for ultra-low methane emissions from lean burn natural gas engines

This numerical study explores the optimization of Prechamber Enabled Mixing-Controlled Combustion (PC-MCC) using natural gas in heavy-duty engines, aiming to enhance combustion efficiency to minimize methane slip and NOx emissions. The approach involves a prechamber ignition system, distinct from conventional spark ignition (SI) systems, to initiate combustion of direct injected natural gas. By leveraging the robust ignition characteristics of the prechamber, the PC-MCC method demonstrates significant potential in achieving efficient combustion akin to diesel engines but with lower greenhouse gas emissions. The research evaluates the effects of various geometric and operational parameters on the combustion process and emissions, including prechamber volume, nozzle diameter, direct injector (DI) geometry, and engine operating strategies. Computational Fluid Dynamics (CFD) simulations are utilized, focusing on a heavy-duty, single-cylinder engine modeled after the Caterpillar C9.3B engine. Key findings indicate that a prechamber volume of 3 cc, coupled with a nozzle diameter of 2.75 mm for two prechamber holes, strikes an optimal balance between combustion efficiency and emissions reduction. This configuration ensures robust combustion across a range of operating conditions while maintaining methane slip within targeted limits. Further investigation into DI geometry shows the significance of the injector umbrella angle and nozzle diameter in shaping the fuel-air mixing and combustion dynamics. An umbrella angle of 130° and a nozzle diameter of 300 microns are identified as optimal, promoting rapid and efficient combustion with minimized methane and NOx emissions. The study also investigates the impact of injection timing and pressure, highlighting their roles in controlling combustion timing and influencing emissions levels. Advanced injection timing is found to be crucial in achieving the desired low methane slip, whereas retarded injection timing assists to reduce NOx emissions while having a slight increase in methane emissions. Operating strategies incorporating various levels of Exhaust Gas Recirculation (EGR) are assessed for their effectiveness in further reducing emissions. The research demonstrates that a judicious combination of internal hot EGR and careful calibration of DI pressure and SOI timing can achieve significant reductions in NOx emissions while keeping methane slip under control. Specifically, an internal EGR level of 15%–25%, combined with DI pressures of 200–300 bar and injection timings at or after top dead center, is recommended. These findings contribute valuable insights into the development of advanced combustion techniques for natural gas engines, offering a viable pathway to reduce methane slip without compromising engine efficiency or performance. The PC-MCC system presents a promising solution for the future of heavy-duty natural gas engine technology to reduce methane emissions.

Nsaif, Osama↗