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At least 775 records · Page 43

A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering Escherichia coli for selective 1-decanol production using the reverse β-oxidation (rBOX) pathway

1-Decanol has great value in the pharmaceutical and fragrance industries and plays an important role in the chemical industry. Here, in this study, we engineered Escherichia coli to selectively synthesize 1-decanol by using enzymes of the core reverse β-oxidation (rBOX) pathway and termination module with overlapping chain-length specificity. Through screening for acyl-CoA reductase termination enzymes and proper regulation of rBOX pathway expression, a 1-decanol titer of 1.4 g/L was achieved. Further improvements were realized by engineering pyruvate dissimilation to ensure the generation of NADH through pyruvate dehydrogenase (PDH) and reducing byproduct synthesis via a tailored YigI thioesterase knockout, increasing 1-decanol titer to 1.9 g/L. The engineered strain produced about 4.4 g/L 1-decanol with a yield of 0.21 g/g in 36 hours in a bi-phasic fermentation that used a dodecane overlay to increase 1-decanol transport and reduce its toxicity. Adjustment of pathway expression (varying inducer concentration) and cell growth (oxygen availability) enabled 1-decanol production at 6.1 g/L (0.26 g/g yield) and 10.05 g/L (0.2 g/g yield) using rich in shake flasks and bioreactor, respectively. Remarkably, the use of minimal medium resulted in 1-decanol production at 100% specificity at 2.8 g/L (0.14 g/g yield) and a per cell mass yield higher than rich medium. These 1-decanol titers, yields and purity are at least 10-fold higher than others reported to date and the engineered strain shows great potential for industrial production. Taken together, our findings suggest that using rBOX pathway and termination enzymes of proper chain-length specificity in combination with optimal chassis engineering should be an effective approach for the selective production of alcohols.

1-decanol↗

Diagnostics of the Supernova Engine

The standard engine behind core-collapse supernovae is continuously evolving with increasingly detailed models. At this time, most simulations focus on an engine invoking turbulence above the proto-neutron star, sometimes termed the “convection-enhanced” engine. Finally, we review this engine and why it has become the standard for normal supernovae, focusing on a wide set of observations that provide insight into the supernova engine.

79 ASTRONOMY AND ASTROPHYSICS↗

Using phage display for rational engineering of a higher-affinity humanized 3’ phosphohistidine-specific antibody

Abstract Histidine phosphorylation is a non-canonical post-translational modification (PTM), with 1-phosphohistidine (1-pHis) and 3-phosphohistidine (3-pHis) isoforms, that is understudied due to a lack of robust reagents, including high-affinity pHis-specific antibodies. Engineering pHis antibodies is challenging due to the labile nature of its phosphoramidate (P-N) bond. We developed a strategy for in vitro engineering of antibodies for the detection of native 3-pHis targets, in which the rabbit SC44-8 anti-3-pTza mAb is humanized into a scaffold (hSC44) that is suitable for phage display. Six unique Fab phage-displayed hSC44 scaffold libraries were screened for antibodies that bound 3-pHis with higher affinity and had specificity for 3-pHis versus 3-pTza. hSC44.20N32F L , the best engineered antibody, has ~10-fold higher affinity for 3-pHis than parental hSC44. Eleven new Fab structures, including the first antibody-pHis peptide structures, together with structural and quantum mechanical calculations, provided molecular insights into 3-pHis and 3-pTza discrimination by hSC44.20N32F L and the increased affinity obtained through engineering. We demonstrated the utility of these high-affinity 3-pHis-specific antibodies for the recognition of pHis proteins in mammalian cells by immunoblotting and immunofluorescence staining. Our work describes a general method for engineering labile PTM-specific antibodies and provides novel antibodies for investigating the role of 3-pHis in cell biology.

Martyn, Gregory D.↗

Advanced fuel fusion, phase space engineering, and structure-preserving geometric algorithms

Non-thermal advanced fuel fusion trades the requirement of a large amount of recirculating tritium in the system for that of large recirculating power. Phase space engineering technologies utilizing externally injected electromagnetic fields can be applied to meet the challenge of maintaining non-thermal particle distributions at a reasonable cost. The physical processes of the phase space engineering are studied from a theoretical and algorithmic perspective. It is emphasized that the operational space of phase space engineering is limited by the underpinning symplectic dynamics of charged particles. The phase space incompressibility according to the Liouville theorem is just one of many constraints, and Gromov's non-squeezing theorem determines the minimum footprint of the charged particles on every conjugate phase space plane. In this sense and level of sophistication, the mathematical abstraction of phase space engineering is symplectic topology. To simulate the processes of phase space engineering, such as the Maxwell demon and electromagnetic energy extraction, and to accurately calculate the minimum footprints of charged particles, recently developed structure-preserving geometric algorithms can be used. The family of algorithms conserves exactly, on discretized spacetime, symplecticity and thus incompressibility, non-squeezability, and symplectic capacities. The algorithms apply to the dynamics of charged particles under the influence of external electromagnetic fields as well as the charged particle–electromagnetic field system governed by the Vlasov–Maxwell equations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Scaffoldless engineered enzyme assembly for enhanced methanol utilization

Methanol is an important feedstock derived from natural gas and can be chemically converted into commodity and specialty chemicals at high pressure and temperature. Although biological conversion of methanol can proceed at ambient conditions, there is a dearth of engineered microorganisms that use methanol to produce metabolites. In nature, methanol dehydrogenase (Mdh), which converts methanol to formaldehyde, highly favors the reverse reaction. Thus, efficient coupling with the irreversible sequestration of formaldehyde by 3-hexulose-6-phosphate synthase (Hps) and 6-phospho-3-hexuloseisomerase (Phi) serves as the key driving force to pull the pathway equilibrium toward central metabolism. An emerging strategy to promote efficient substrate channeling is to spatially organize pathway enzymes in an engineered assembly to provide kinetic driving forces that promote carbon flux in a desirable direction. Here, we report a scaffoldless, self-assembly strategy to organize Mdh, Hps, and Phi into an engineered supramolecular enzyme complex using an SH3–ligand interaction pair, which enhances methanol conversion to fructose-6-phosphate (F6P). To increase methanol consumption, an “NADH Sink” was created using Escherichia coli lactate dehydrogenase as an NADH scavenger, thereby preventing reversible formaldehyde reduction. Combination of the two strategies improved in vitro F6P production by 97-fold compared with unassembled enzymes. The beneficial effect of supramolecular enzyme assembly was also realized in vivo as the engineered enzyme assembly improved whole-cell methanol consumption rate by ninefold. This approach will ultimately allow direct coupling of enhanced F6P synthesis with other metabolic engineering strategies for the production of many desired metabolites from methanol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A NARROW SHORT-DURATION GRB JET FROM A WIDE CENTRAL ENGINE

We use two-dimensional relativistic hydrodynamic numerical calculations to show that highly collimated relativistic jets can be produced in neutron star merger models of short-duration gamma-ray bursts (GRBs) without the need for a highly directed engine or a large net magnetic flux. Even a hydrodynamic engine generating a very wide sustained outflow on small scales can, in principle, produce a highly collimated relativistic jet, facilitated by a dense surrounding medium that provides a cocoon surrounding the jet core. An oblate geometry to the surrounding gas significantly enhances the collimation process. Previous numerical simulations have shown that the merger of two neutron stars produces an oblate, expanding cloud of dynamical ejecta. We show that this gas can efficiently collimate the central engine power much like the surrounding star does in long-duration GRB models. For typical short-duration GRB central engine parameters, we find jets with opening angles of an order of 10° in which a large fraction of the total outflow power of the central engine resides in highly relativistic material. These results predict large differences in the opening angles of outflows from binary neutron star mergers versus neutron star–black hole mergers.

79 ASTRONOMY AND ASTROPHYSICS↗

Efficient Quantum Measurement Engines

We propose quantum engines powered entirely by a position-resolving measurement performed on a quantum particle. These engines produce work by moving the quantum particle against a force. Unlike classical information-driven engines (e.g., Maxwell’s demon), the energy is not extracted from a thermal hot source but directly from the observation process via a partial wave-function collapse of the particle. We present results for the work done and the efficiency for different values of the engine parameters. Feedback is required for optimal performance. We find that unit efficiency can be approached when one measurement outcome prepares the initial state of the next engine cycle, while the other outcomes leave the original state nearly unchanged.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Low Size, Weight, and Power Neuromorphic Computing to Improve Combustion Engine Efficiency

Neuromorphic computing offers one path forward for AI at the edge. However, accessing and effectively utilizing a neuromorphic hardware platform is non-trivial. In this work, we present a complete pipeline for neuromorphic computing at the edge, including a small, inexpensive, low-power, FPGA-based neuromorphic hardware platform, a training algorithm for designing spiking neural networks for neuromorphic hardware, and a software framework for connecting those components. We demonstrate this pipeline on a real-world application, engine control for a spark-ignition internal combustion engine. We illustrate how we connect engine simulations with neuromorphic hardware simulations and training software to produce hardware-compatible spiking neural networks that perform engine control to improve fuel efficiency. We present initial results on the performance of these spiking neural networks and illustrate that they outperform open-loop engine control. We also give size, weight, and power estimates for a deployed solution of this type.

Schuman, Catherine↗

Evaluation of Distributed Power Apportioning with Net Load Management Engine in Microgrids Using Power Hardware-in-the-Loop Simulation

This article presents the performance evaluation of ratio consensus-based distributed power apportioning engine along with centralized net load management (NLM) engine that ensures viable and stable operation of an islanded microgrid. Managing net load variability in a microgrid with high penetrations of uncertain renewable generation and ever-changing load demands is a crucial need in order to ensure viable and stable operation of the microgrid. Centralized “dispatch-rule”-based and/or multi-agent-based distributed control of distributed energy resources (DERs) in microgrid are well accepted for microgrid by adapting ANSI/ISA-95-based hierarchical control architecture. In the application where microgrid network has large geographical span with multiple DERs dispersed in the network, high penetration of uncertain renewable energy resources, and ever-changing load demands, a judicious selection of techniques/solutions for managing net-load resources for maintaining viability and stability is required. With this motivation, this article proposes a novel solution to mitigate the challenges by incorporating a mixed centralized NLM engine and distributed power apportioning control of DERs and loads. A power-hardware-in-the-loop (PHIL) -based experiment is conducted with the centralized NLM engine and the distributed power apportioning engine along with two commercial inverters. The experimental results validates the efficacy of the proposed method in ensuring viability and stability of a microgrid.

hardware-in-the-loop simulation↗

Bio-derived Fuel Blend Dilution of Marine Engine Oil and Imapct on Friction and Wear Behavior

To reduce the amount of petroleum-derived fuel used in vehicles and vessels powered by internal combustion engines, the addition of bio-derived fuel extenders is a common practice. Ethanol is perhaps the most common bio-derived fuel used for blending, and butanol is being evaluated as a promising alternative. The present study determined the fuel dilution rate of three lubricating oils (E0, E10, and i-B16) in a marine engine operating in on-water conditions with a start-and-stop cycle protocol. The level of fuel dilution increased with the number of cycles for all three fuels. The most dilution was observed with i-B16 fuel, and the least with E10 fuel. In all cases, fuel dilution substantially reduced the oil viscosity. The impacts of fuel dilution and the consequent viscosity reduction on the lubricating capability of the engine oil in terms of friction, wear, and scuffing prevention were evaluated by four different tests protocols. Although the fuel dilution of the engine oil had minimal effect on friction, because the test conditions were under the boundary lubrication regime, significant effects were observed on wear in many cases. Fuel dilution also was observed to reduce the load-carrying capacity of the engine oils in terms of scuffing load reduction.

Ajayi, Oyelayo O.↗

IMPLEMENTATION OF DETAILED CHEMISTRY MECHANISMS IN ENGINE SIMULATIONS

The stiffness of large chemistry mechanisms has been proved to be a major hurdle toward predictive engine simulations. As a result, detailed chemistry mechanisms with a few thousand species need to be reduced based on target conditions so that they can be accommodated within the available computational resources. The computational cost of simulations typically increases super-linearly with the number of species and reactions. This work aims to bring detailed chemistry mechanisms within the realm of engine simulations by coupling the framework of unsteady flamelets and fast chemistry solvers. A previously developed tabulated flamelet model (TFM) framework for nonpremixed combustion was used in this study. The flamelet solver consists of the traditional operator-splitting scheme with variable coefficient ordinary differential equation (ODE) solver (VODE) and a numerical Jacobian for solving the chemistry. In order to use detailed mechanisms with thousands of species, a new framework with the Livermore solver for ODEs in sparse form (LSODES) chemistry solver and an analytical Jacobian was implemented in this work. Results from 1D simulations show that with the new framework, the computational cost is linearly proportional to the number of species in a given chemistry mechanism. As a result, the new framework is 2-3 orders of magnitude faster than the conventional variable coefficient ODE (VODE) solver for large chemistry mechanisms. This new framework was used to generate unsteady flamelet libraries for ndodecane using a detailed chemistry mechanism with 2755 species and 11,173 reactions. The engine combustion network (ECN) spray A experiments, which consist of an igniting n-dodecane spray in turbulent, high-pressure engine conditions are simulated using large eddy simulations (LES) coupled with detailed mechanisms. A grid with 0.06 mm minimum cell size and 22 x 10(6) peak cell count was implemented. The framework is validated across a range of ambient temperatures against ignition delay and liftoff lengths (LOLs). Qualitative results from the simulations were compared against experimental OH and CH2O planar laser-induced fluorescence (PLIF) data. The models are able to capture the spatial and temporal trends in species compared to those observed in the experiments. Quantitative and qualitative comparisons between the predictions of the reduced and detailed mechanisms are presented in detail. The main goal of this study is to demonstrate that detailed reaction mechanisms (similar to 1000 species) can now be used in engine simulations with a linear increase in computation cost with number of species during the tabulation process and a small increase in the 3D simulation cost.

Kundu, Prithwish↗

Development of an Efficient Conjugate Heat Transfer Modeling Framework to Optimize Mixing-Limited Combustion of Ethanol in a Diesel Engine

Mixing controlled combustion of alcohol fuels has been identified as a promising technology based on their low propensity for particulate and NOx production, but the higher heats of vaporization and auto-ignition temperatures of these fuels make their direct use in diesel engine architectures a challenge. To realize the potential of alcohol-fueled combustion, a computational fluid dynamics (CFD) modeling framework is developed, validated, and exercised to identify designs that maximize engine thermal efficiency. To evaluate the use of thermal barrier coatings (TBCs), a simplified one-dimensional (1D) conjugate heat transfer (CHT) modeling framework is employed. The addition of the 1D CHT model only increases the computational expense by 15% relative to traditional approaches, yet offers more accurate heat transfer predictions over constant temperature boundary conditions. The validated model is then used to explore a range of injector orientations and piston bowl geometries. Using a design of experiments (DoE) approach, several designs were identified that improved fuel-air mixing, shortened the combustion duration, and increased thermal efficiency. The most promising design was fabricated and tested in a Caterpillar 1Y3700 single-cylinder oil test engine (SCOTE). Engine testing confirmed the findings from the CFD simulations and found that the co-optimized injector and piston bowl design yielded over 2-percentage point increase in thermal efficiency at the same equivalence ratio (0.96) and over 6-percentage point increase at the same engine load (10.1 bar indicated mean effective pressure (IMEP)), while satisfying design constraints for peak pressure and maximum pressure rise rate.

Magnotti, Gina M.↗

Initial Results on a New Light-Duty 2.7-L Opposed-Piston Gasoline Compression Ignition Multi-Cylinder Engine

Abstract Gasoline compression ignition (GCI) is a cost-effective approach to achieving diesel-like efficiencies with low emissions. The fundamental architecture of the two-stroke Achates Power Opposed-Piston (OP) Engine enables GCI by decoupling piston motion from cylinder scavenging, allowing for flexible and independent control of cylinder residual fraction and temperature leading to improved low-load combustion. In addition, the high peak cylinder pressure and noise challenges at high-load operation are mitigated by the lower brake mean effective pressure (BMEP) operation and faster heat release for the same pressure rise rate of the OP Engine. These advantages further solidify the performance benefits of the OP Engine and demonstrate the near-term feasibility of advanced combustion technologies, enabled by the opposed-piston architecture. This paper presents initial results from steady-state testing on a brand new 2.7-L OP GCI multi-cylinder engine (MCE) designed for light-duty truck applications. Successful GCI operation calls for a high compression ratio (CR), leading to higher combustion stability at low loads, higher efficiencies, and lower cycle HC + NOX emissions. Initial results show a cycle average brake thermal efficiency (BTE) of 31.7%, which is already greater than 11% conventional engines, after only ten weeks of testing. Emissions results suggest that Tier 3 Bin 160 levels can be achieved using a traditional diesel after-treatment system. Combustion noise was well controlled at or below the United States Council for Automotive Research limits. In addition, initial results on catalyst light-off mode with GCI are also presented.

Energy & Fuels↗

Gasoline Compression Ignition (GCI) on a Light-Duty Multi-Cylinder Engine Using a Wide Range of Fuel Reactivities and Heavy Fuel Stratification

Many research studies have focused on utilizing gasoline in modern compression ignition engines to reduce emissions and improve efficiency. Collectively, this combustion mode has become known as gasoline compression ignition (GCI). One of the biggest challenges with GCI operation is maintaining control over the combustion process through the fuel injection strategy, such that the engine can be controlled on a cycle-by-cycle basis. Research studies have investigated a wide variety of GCI injection strategies (i.e., fuel stratification levels) to maintain control over the heat release rate while achieving low temperature combustion (LTC). This work shows that at loads relevant to light-duty engines, partial fuel stratification (PFS) with gasoline provides very little controllability over the timing of combustion. On the contrary, heavy fuel stratification (HFS) provides very linear and pronounced control over the timing of combustion. However, the HFS strategy has challenges achieving LTC operation due to the air handling burdens associated with the high EGR rates that are required to reduce NOx emissions to near zero levels. In this work, a wide variety of gasoline fuel reactivities (octane numbers ranging from < 40 to 87) were investigated to understand the engine performance and emissions of HFS-GCI operation on a multi-cylinder light-duty engine. The results indicate that over an EGR sweep at 4 bar BMEP, the gasoline fuels can achieve LTC operation with ultra-low NOx and soot emissions, while conventional diesel combustion (CDC) is unable to simultaneously achieve low NOx and soot. At 10 bar BMEP, all the gasoline fuels were compared to diesel, but using mixing controlled combustion and not LTC.

Dempsey, Adam↗

Evaluation of the Performance and Exhaust Emissions of a 4 Cylinder CI Engine Operating With Dimethyl Ether (DME) and Propane Blends

In response to stringent emissions regulations and the need for higher efficiency engines, the utilization of DME and propane fuel blends in compression ignition (CI) engines has gained interest in the automotive industry. In this study, a range of DME-propane blends are explored in a CI combustion strategy at high injection pressures. A GT-Power model of a 2.2 L Hyundai CI engine was developed to facilitate evaluation of the impacts of variations of DME and propane blends at a light and medium engine speed-torque-load operating condition; specifically at 1500 rpm, 50 Nm and 2.84 bar brake mean effective pressure (BMEP); and 2000 rpm, 150 Nm, 8.53 bar BMEP speed-torque-load combination. Here, the GT-Power model was validated using Computational Fluid Dynamics (CFD) simulations. The results indicate that high diesel-like efficiencies can be achieved with a 100% DME mass substitution and up to 50% propane-DME blends could be implemented without a significant penalty on engine performance indicators. Significant brake specific nitrogen oxides (BSNOx) reductions were also observed along with reductions in carbon dioxide (CO2) and soot when leveraging these fuel blends.

computational fluid dynamics↗

Cyber-informed Engineering Microgrid Analysis Tool

The Cyber-Informed Engineering Microgrid Analysis Tool (CIEMAT) leverages the Department of Energy’s Cyber-Informed Engineering to prompt engineering designers and operators through an analysis of the critical functions to be supported by a microgrid installations, the criticality of those functions, the impacts of denial, disruption or misuse of those functions on the microgrid and dependent functions, and the mitigations which could best prevent impacts to those functions resulting from cyber attack. Through use of this tool, microgrid designers and operators can quickly identify appropriate engineering mitigations to limit impacts from cyber attack and functions where engineering and operational staff can prioritize and guide the application of cybersecurity protections to best support the resiliency of the system.

Wright, VirginiaL [Idaho National Laboratory (INL)↗

Cyber-informed Engineering Battery Analysis Tool

The Cyber-Informed Engineering Battery Analysis Tool (CIEBAT) leverages the Department of Energy’s Cyber-Informed Engineering to prompt engineering designers and operators through an analysis of the critical functions to be supported by a BESS installation, the criticality of those functions, the impacts of denial, disruption or misuse of those functions within the BESS system, and the mitigations which could best prevent impacts to those functions resulting from cyber attack. Through use of this tool, BESS designers and operators can quickly identify appropriate engineering mitigation opportunities to limit impacts from cyber attack and functions where engineering and operational staff can prioritize and guide the application of cybersecurity protections to best support the resiliency of the system.

Lampe, BenjaminR [Idaho National Laboratory (INL),↗