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At least 847 records · Page 47

Synthetic Biology: Molecular Tools for Engineering Organisms

Synthetic biology is a biological engineering discipline based on abstracting living systems through the lens of physical engineering concepts. In particular, synthetic biology places an emphasis on the characterisation of simple parts that can be modularly assembled into configurations that give rise to complex, higher-order behaviours. Within the past two decades, this approach has enabled the development number of new molecular biology tools for modifying living systems in order to investigate fundamental processes or imbuing functions into cells that do not exist in nature. While specific synthetic biology applications span a huge range of seemingly unrelated disciplines (from biofuel producing microbes, to malaria-resistant mosquitoes, to living medical therapies), these distinct examples derive from reuse and rearrangement of relatively limited set of cell engineering technologies. The continuing development of these core molecular biology tools for controlling gene expression, protein activity and signalling networks can promote evermore ambitious biological engineering projects.

gene expression↗

Cloning and characterization of a panel of mitochondrial targeting sequences for compartmentalization engineering in Saccharomyces cerevisiae

Mitochondrion is generally considered as the most promising subcellular organelle for compartmentalization engineering. Much progress has been made in reconstituting whole metabolic pathways in the mitochondria of yeast to harness the precursor pools (i.e., pyruvate and acetyl-CoA), bypass competing pathways, and minimize transportation limitations. However, only a few mitochondrial targeting sequences (MTSs) have been characterized (i.e., MTS of COX4), limiting the application of compartmentalization engineering for multigene biosynthetic pathways in the mitochondria of yeast. In the present study, based on the mitochondrial proteome, a total of 20 MTSs were cloned and the efficiency of these MTSs in targeting heterologous proteins, including the Escherichia coli FabI and enhanced green fluorescence protein (EGFP) into the mitochondria was evaluated by growth complementation and confocal microscopy. After systematic characterization, six of the well!performed MTSs were chosen for the colocalization of complete biosynthetic pathways into the mitochondria. As proof of concept, the full alpha-santalene biosynthetic pathway consisting of 10 expression cassettes capable of converting acety coA to alpha-santalene was compartmentalized into the mitochondria, leading to a 3.7 fold improvement in the production of alpha-santalene. Furthermore, the newly characterized MTSs should contribute to the expanded metabolic engineering and synthetic biology toolbox for yeast mitochondrial compartmentalization engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Application of machine learning to evaluating and remediating models for energy and environmental engineering

Machine learning (ML) algorithms have been increasingly successful in their applications to solve energy and environmental engineering problems. ML algorithms have the advantage of being able to solve highly nonlinear issues effectively. Furthermore, considering the limited sample size of data collected in energy and environmental engineering, obtaining a ML model with reasonable accuracy is simple. Unfortunately, the vast majority of the current applications of ML algorithms lack effective screening of dominant factors and comprehensive model validation, which weakens the predictive ability of the models. The present study takes the minimum miscible pressure (MMP) of CO 2 - oil systems as an example. It establishes a systematic and robust predictive model to address this issue. Based on 147 sets of slim tube tests, the predictive models of the MMPs are investigated by application of eight ML algorithms. The paper concludes that most of the published ML models in the field of energy and environmental engineering prediction are not reliable. Furthermore, it addresses the main reasons for the poor performance of some predictive models built by ML and provides guidelines on how to make such models robust. Further, to the best of our knowledge, this is the first study to point out the defects of current ML modeling methods and propose countermeasures for their application in energy and environmental engineering problems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Modeling of thermal and kinetic processes in non-equilibrium plasma ignition applied to a lean combustion engine

In recent years novel ignition systems have been developed to enable stable and efficient engine operations with lean mixtures. Among them, radio-frequency corona ignition systems create discharges that involve a much wider region compared to traditional spark, and produce non equilibrium plasma with high levels of active radicals and excited species. These devices considerably increase the early flame growth speed and extend stable operating limits. With the aim of expanding the knowledge on high efficiency lean-burn SI engines, this paper investigates and compares the combustion development generated by spark and corona ignitions through computational fluid dynamics, within the Reynolds-Averaged Navier-Stokes framework for turbulence modeling. In order to simultaneously take thermal and chemical effects into account, the Perfectly Stirred Reactor combustion model is used. Experimental data are also collected for validation in an optical access engine, for different mixture levels, from stoichiometric to very lean. Furthermore, the faster burn rate generated by the corona system in the initial stage of the combustion is well predicted by the simulations, in all the relative air-fuel ratio conditions. Remarkably, as the mixture becomes lean, simulations are able to capture the non-linear transition from fast to slow kernel growth, before a self-sustainable flame propagation is established. This correlates very well with the measured engine cyclic variability and the corresponding steep change in the duration of the flame kernel formation. Ultimately, this study highlights the important role of the atomic oxygen, as active radical, in promoting and enhancing the combustion initiated by a corona discharge, in addition to the volumetric ignition effect. By contrast, the validated simulations allow to explain that the high-temperature thermal plasma generated in a traditional spark discharge is insensitive to kinetic aspects.

42 ENGINEERING↗

Multigene engineering in plants: Technologies, applications, and future prospects

The emerging bioeconomy presents a promising solution to both economic and environmental challenges. Within the bioeconomy, plants serve as a renewable, sustainable, and cost-effective source of foods, fuels, chemicals, and materials. However, traditional breeding and single-gene engineering approaches fall short in addressing complex traits (e.g., drought tolerance, disease resistance, yield, nutrient use efficiency) which are controlled by multiple genes. The complexity of plant biology often necessitates the use of multigene engineering (MGE), which involves simultaneous ectopic expression, up/down-regulation, or editing of multiple genes, to enhance plant traits relevant to the bioeconomy. These genes may be associated with distinct traits or function as components of specific metabolic and regulatory pathways. This review summarizes current technologies for MGE within the synthetic biology-driven Design-Build-Test-Learn (DBTL) framework, detailing its four key stages: Design – gene construct development; Build – DNA assembly and plant transformation; Test – the molecular, biochemical, and physiological characterization of engineered plants; and Learn – computational modeling to refine, multiplex and iterate the process. Despite good progress in the applications of MGE in biofortification, metabolic engineering, and stress resilience, challenges remain in construct stability, coordinated gene expression, and regulatory predictability. We identified optimization paths and future directions to accelerate MGE deployment in sustainable agriculture, with possible societal benefits including reduced production costs, increased yield, and improved food and nutritional security.

AI-aided plant engineering↗

Role of fuel properties and piston shape in influencing soot oxidation in heavy-duty low swirl diesel engine combustion

The presented study evaluated effects on soot emissions of important diesel fuel properties (e.g. volatility T95, hydrogen to-carbon ratio H/C and oxygen content O/C) in a heavy-duty, low-swirl, direct injection diesel engine operated with cooled exhaust gas recirculation to control the emissions of nitrogen oxides. Variation of injection pressure was conducted in three representative operation points in the single-cylinder engine including conventional and wave piston bowl types. Additionally, detailed optical combustion studies were performed in a high pressure/high temperature combustion chamber with an engine-like flame-wall interaction geometry. The fuel properties mainly influenced parameters relating to events near the nozzle, such as the ignition delay, flame lift-off distance and spray air entrainment. Oxygenation of the fuel reduced soot formation (a known effect of spray-jet dilution), but the fuels’ H/C and T95 also influenced soot emissions. Viscosity, heating value and density, treated as secondary fuel parameters, affected the injected fuel’s kinetic energy, and hence mean flow field and local turbulent mixing late in the combustion cycle. The results suggested that fuel effects on soot oxidation during late phases of combustion are mainly governed by parameters related to the fuel injection profile under the specific cylinder gas conditions. With an oxygenated fuel, flow structures (local turbulent side vortices) which are typical for the investigated engine type were found to form in a similar way as with a reference fuel. Hence, improved internal flow using a wave piston in combination with a low-sooting oxygenated fuel gave additional reductions in net soot emissions.

42 ENGINEERING↗

Protein engineering of oxidoreductases utilizing nicotinamide-based coenzymes, with applications in synthetic biology

Two natural nicotinamide-based coenzymes (NAD and NADP) are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism, respectively. Most NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic roles. This coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology pathways. Changing the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering, which is closely related to product-oriented synthetic biology projects. This review focuses on the methodology of nicotinamide-based coenzyme engineering, with its application in improving product yields and decreasing production costs. Biomimetic nicotinamide-containing coenzymes have been proposed to replace natural coenzymes because they are more stable and less costly than natural coenzymes. Recent advances in the switching of coenzyme preference from natural to biomimetic coenzymes are also covered in this review. Engineering coenzyme preferences from natural to biomimetic coenzymes has become an important direction for coenzyme engineering, especially for in vitro synthetic pathways and in vivo bioorthogonal redox pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering Interlayer Electron–Phonon Coupling in WS 2 /BN Heterostructures

In van der Waals (vdW) heterostructures, the interlayer electron–phonon coupling (EPC) provides one unique channel to nonlocally engineer these elementary particles. However, limited by the stringent occurrence conditions, the efficient engineering of interlayer EPC remains elusive. Here we report a multitier engineering of interlayer EPC in WS2/boron nitride (BN) heterostructures, including isotope enrichments of BN substrates, temperature, and high-pressure tuning. The hyperfine isotope dependence of Raman intensities was unambiguously revealed. In combination with theoretical calculations, we anticipate that WS2/BN supercells could induce Brillouin-zone-folded phonons that contribute to the interlayer coupling, leading to a complex nature of broad Raman peaks. We further demonstrate the significance of a previously unexplored parameter, the interlayer spacing. By varying the temperature and high pressure, we effectively manipulated the strengths of EPC with on/off capabilities, indicating critical thresholds of the layer–layer spacing for activating and strengthening interlayer EPC. Our findings provide new opportunities to engineer vdW heterostructures with controlled interlayer coupling.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Systems engineering approach towards performance monitoring of emergency diesel generator

Systems engineering is an interdisciplinary approach and means to enable the realization of successful systems. In this study, systems engineering approach towards the performance monitoring of Emergency Diesel Generator (EDG) is presented. Performance monitoring is part and parcel of predictive maintenance where the systems and components conditions can be detected before they result into failures. In an effort to identify the proposal for addressing performance monitoring, the EDG boundary has been defined. Based on the Probabilistic Safety Analysis (PSA) results and industry operating experiences, the most critical component is identified. This paper proposed a systems engineering concept development framework towards EDG performance monitoring. The expected output of this study is that the EDG reliability can be improved by the performance monitoring alternatives through the systems engineering concept development effort.

42 ENGINEERING↗

A study experiment of auto idle application in the excavator engine performance

The purpose of this study was to analyze the effect of applying auto idle to excavator engine performance, such as machine unitization and fuel consumption in Excavator. Steps to be done are to modify the system JA 44 and 67 in Vehicle Electronic Control Unit (V-ECU). The modifications will be obtained from the pattern of the engine speed. If the excavator attachment is not operated, the engine speed will return to the idle speed automatically. From the experiment results the auto idle reduces fuel consumption in excavator engine.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Unsupervised Image-Based Classification of Corrosion Severity in Automobile Engine Connecting Rods

Corrosion in engine connecting rods is a critical issue in the automotive industry, potentially leading to catastrophic engine failure, monetary losses, and safety hazards. The labor shortage in the industry further emphasizes the need for fast, accurate, and automated corrosion detection methods to ensure appropriate surface treatments can be applied to restore component integrity. We present an unsupervised image-based framework for classifying corrosion severity in automobile engine connecting rods using short-wave infrared (SWIR) and telecentric grayscale imaging. We employ the structural similarity index measure (SSIM) as a dissimilarity metric and the k-medians clustering algorithm for classification. Our algorithm achieves an overall accuracy of 80.64% for SWIR images, with 100% accuracy in classifying highly corroded samples. For grayscale images, the method attains an overall accuracy of 77.42%, with 90.91% accuracy for highly corroded samples. The method’s ability to work with different imaging modalities and its high accuracy in identifying severe corrosion cases make it a promising tool for automated corrosion assessment in the automotive industry, potentially improving efficiency and safety in engine component maintenance.

42 ENGINEERING↗

Optogenetics Illuminates Applications in Microbial Engineering

Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe–host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Lastly, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering.

59 BASIC BIOLOGICAL SCIENCES↗

A perspective on the range of gasoline compression ignition combustion strategies for high engine efficiency and low NOx and soot emissions: Effects of in-cylinder fuel stratification

Many research studies have shown that low temperature combustion in compression ignition engines has the ability to yield ultra-low NOx and soot emissions while maintaining high thermal efficiency. To achieve low temperature combustion, sufficient mixing time between the fuel and air in a globally dilute environment is required, thereby avoiding fuel-rich regions and reducing peak combustion temperatures, which significantly reduces soot and NOx formation, respectively. It has been demonstrated that achieving low temperature combustion with diesel fuel over a wide range of conditions is difficult because of its properties, namely, low volatility and high chemical reactivity. On the contrary, gasoline has a high volatility and low chemical reactivity, meaning it is easier to achieve the amount of premixing time required prior to autoignition to achieve low temperature combustion. In order to achieve low temperature combustion while meeting other constraints, such as low pressure rise rates and maintaining control over the timing of combustion, in-cylinder fuel stratification has been widely investigated for gasoline low temperature combustion engines. The level of fuel stratification is, in reality, a continuum ranging from fully premixed (i.e. homogeneous charge of fuel and air) to heavily stratified, heterogeneous operation, such as diesel combustion. However, to illustrate the impact of fuel stratification on gasoline compression ignition, the authors have identified three representative operating strategies: partial, moderate, and heavy fuel stratification. Thus, this article provides an overview and perspective of the current research efforts to develop engine operating strategies for achieving gasoline low temperature combustion in a compression ignition engine via fuel stratification. In this paper, computational fluid dynamics modeling of the in-cylinder processes during the closed valve portion of the cycle was used to illustrate the opportunities and challenges associated with the various fuel stratification levels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhancing the efficiency benefit of thermal barrier coatings for homogeneous charge compression ignition engines through application of a low-k oxide

Prior experiments reported by the authors have proven the hypothesis that achieving a dynamic temperature swing on the combustion chamber surface will lead to improved thermal and combustion efficiencies of the homogeneous charge compression ignition engine. A thin layer of yttria-stabilized zirconia, roughly 150 μm, was plasma sprayed on the piston top. It led to markedly advanced ignition and heat release in the gasoline homogeneous charge compression ignition engine, accompanied with reduced unburnt hydrocarbon and carbon monoxide emissions, improved combustion efficiency, and a higher thermal efficiency. A related computational study highlighted the critical role of coating thermal conductivity in achieving a desired dynamic response; hence, the second phase of experimental investigations focused on introducing structured porosity in the yttria-stabilized zirconia coating, as a means of reducing effective conductivity. Indeed, additional incremental improvements were observed, as well as limitations related to adverse effects of the surface roughness and the fuel interactions with the surface roughness and open pores. Erosion can also be a problem in a direct injection engine. Therefore, the third round of investigations focused on a material with a natively low conductivity (low-k), sprayed on the top of an Al piston in a relatively dense form, and in a way that yields a smooth surface. The objective was to capitalize on the low conductivity, while avoiding the pitfalls accompanying high-porosity formulations. The heat-storage capacity was limited by keeping the thickness relatively low. The results verify the paramount importance of thermal conductivity in the context of high “temperature swing” behavior and indicate a potential to improve the homogeneous charge compression ignition engine’s combustion efficiency roughly 1.5%, with the overall indicated efficiency improvement on the order of 5%, on a relative basis. In addition, the low-k oxide thermal barrier applied to the piston extended significantly the low-load homogeneous charge compression ignition operability limit.

42 ENGINEERING↗

Laminar-to-turbulent flame transition and cycle-to-cycle variations in large eddy simulation of spark-ignition engines

This paper investigates the effect of laminar-to-turbulent flame transition modeling on the prediction of cycle-to-cycle variations (CCVs) in large eddy simulation (LES) of spark-ignition (SI) engines. A laminar-to-turbulent flame transition model that describes the non-equilibrium sub-filter flame speed evolution during an early stage of flame kernel growth is developed. In the present model, the flame transition is characterized by the flame kernel size at which the flame transition ends, defined here as the flame transition scale. The proposed model captures the effects that variations in a turbulent flow field have on the evolution of early-stage burning rates, through variations in the flame transition scale. The proposed flame transition model is combined with the front propagation formulation (FPF) method and a spark-ignition model to predict CCVs in a gasoline direct injection SI engine. It is found that multi-cycle LES with the proposed flame transition model reproduces experimentally-observed CCVs satisfactorily. When the transition model is not considered or when variations in the transition process are neglected, CCVs are significantly under-predicted for the case considered here. These results indicate the importance of modeling the laminar-to-turbulent flame transition and the effect of turbulence on the transition process, when predicting CCVs, under certain engine conditions. The LES results are also used to analyze sources for variations in the flame transition. It is found, for the present engine case, that the most important source is the cycle-to-cycle variation in the turbulence dissipation rate, which is used to measure the strength of turbulence in the proposed model, near a spark plug. The large-scale velocity field and the variations of the laminar flame speed due to the mixture composition and thermal stratification are also found to be important factors to contribute to the variations in the flame transition.

42 ENGINEERING↗

Sustainability Engineering: Challenges, Technologies, and Applications

Sustainability Engineering: Challenges, Technologies, and Applications focuses on emerging topics within sustainability science and engineering, including the circular economy, advanced recycling technologies, decarbonization, renewable energy, and waste valorization. Readers will learn the trends driving today's sustainability research and innovation as well as the latest in sustainable process technologies. This book: addresses emerging sustainability development challenges, progress, and disruptive technologies; discusses biological sustainability, recycling technologies, and sustainable process design and manufacture; and features a comprehensive view from renowned experts who are leaders in their respective research areas. This work is aimed at an interdisciplinary audience of engineers and scientists working on solutions to advance the development and application of sustainable technologies, including - but not limited to - chemical and environmental engineers.

advanced recycling technologies↗

Enhanced Genetic Tools for Engineering Multigene Traits into Green Algae

Transgenic microalgae have the potential to impact many diverse biotechnological industries including energy, human and animal nutrition, pharmaceuticals, health and beauty, and specialty chemicals. However, major obstacles to sophisticated genetic and metabolic engineering in algae have been the lack of well-characterized transformation vectors to direct engineered gene products to specific subcellular locations, and the inability to robustly express multiple nuclear-encoded transgenes within a single cell. Here we validate a set of genetic tools that enable protein targeting to distinct subcellular locations, and present two complementary methods for multigene engineering in the eukaryotic green microalga Chlamydomonas reinhardtii. The tools described here will enable advanced metabolic and genetic engineering to promote microalgae biotechnology and product commercialization.

59 BASIC BIOLOGICAL SCIENCES↗

System Design, Analysis, and Modeling Activities Supporting the DOE Hydrogen Storage Engineering Center of Excellence (HSECoE): Final Project Report

The objective of this project was to identify optimal pathways for successful hydrogen storage system technology through modeling, analysis, and testing support. The National Renewable Energy Laboratory (1) performed vehicle simulations of various system configurations to support the overall systems engineering, (2) led the storage system energy analysis and provided the Hydrogen Storage Engineering Center of Excellence (HSECoE) with results to help guide engineering design, and (3) compiled and obtained media engineering properties for the HSECoE.

30 DIRECT ENERGY CONVERSION↗