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Cyber Informed Engineering (CIE) Curriculum Guide

The Cyber-Informed Engineering (CIE) Curriculum Guide provides a framework, guidance, and resources for incorporating CIE into university-level engineering programs and related educational activities. A key goal of this guide is to help institutions deliver CIE focused education to produce future engineers and technicians who meet the nation’s infrastructure needs. To accommodate a broad range of educational goals and approaches, this guide outlines several practical integration strategies, links to resources that can accelerate CIE adoption, and offers perspectives from partner academic institutions on the various implementation strategies.

42 ENGINEERING↗

Permeability-Engineered Compartmentalization Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems

In nature, biological compartments such as cells rely on dynamically controlled permeability for matter exchange and complex cellular activities. Likewise, the ability to engineer compartment permeability is crucial for in vitro systems to gain sustainability, robustness, and complexity. However, rendering in vitro compartments such a capability is challenging. Here, a facile strategy is presented to build permeability-configurable compartments, and marked advantages of such compartmentalization are shown in reconstituting sustained synthetic biology systems in vitro. Through microfluidics, the strategy produces micrometer-sized layered microgels whose shell layer serves as a sieving structure for biomolecules and particles. In this configuration, the transport of DNAs, proteins, and bacteriophages across the compartments can be controlled an guided by a physical model. Through permeability engineering, a compartmentalized cell-free protein synthesis system sustains multicycle protein production; ≈100 000 compartments are repeatedly used in a five-cycle synthesis, featuring a yield of 2.2 mg mL -1 . Further, the engineered bacteria-enclosing compartments possess near-perfect phage resistance and enhanced environmental fitness. In a complex river silt environment, compartmentalized whole-cell biosensors show maintained activity throughout the 32 h pollutant monitoring. It is anticipated that permeability-engineered compartmentalization should pave the way for practical synthetic biology applications such as green bioproduction, environmental sensing, and bacteria-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering Clostridium cellulovorans for highly selective n ‐butanol production from cellulose in consolidated bioprocessing

Abstract Cellulosic n ‐butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans , a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adh E2 from C. acetobutylicum for n ‐butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl‐CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adh E2 would enhance n ‐butanol production. In this study, thiolase ( thl A CA ) from C. acetobutylicum and 3‐hydroxybutyryl‐CoA dehydrogenase ( hbd CT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adh E2 to increase the flux from acetyl‐CoA to butyryl‐CoA. In addition, ferredoxin‐NAD(P) + oxidoreductase ( fnr ), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl‐CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n ‐butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adh E2‐ fnr CA ‐ thl A CA ‐ hbd CT produced n ‐butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n ‐butanol production from cellulosic biomass in consolidated bioprocessing.

Bao, Teng↗

Engineered Sorghum Bagasse Enables a Sustainable Biorefinery with p-Hydroxybenzoic Acid-Based Deep Eutectic Solvent

Integrating multidisciplinary research in plant genetic engineering and renewable deep eutectic solvents (DESs) can facilitate a sustainable and economic biorefinery. In this work, we leveraged a plant genetic engineering approach to specifically incorporate C6C1 monomers into the lignin structure. By expressing the bacterial ubiC gene in sorghum, p-hydroxybenzoic acid (PB)-rich lignin was incorporated into the plant cell wall while this monomer was completely absent in the lignin of the wild-type (WT) biomass. A DES was synthesized with choline chloride (ChCl) and PB and applied to the pretreatment of the PB-rich mutant biomass for a sustainable biorefinery. The release of fermentable sugars was significantly enhanced (~190 % increase) compared to untreated biomass by the DES pretreatment. In particular, the glucose released from the pretreated mutant biomass was up to 12 % higher than that from the pretreated WT biomass. Lignin was effectively removed from the biomass with the preservation of more than half of the β-Ο-4 linkages without condensed aromatic structures. Hydrogenolysis of the fractionated lignin was conducted to demonstrate the potential of phenolic compound production. In addition, a simple hydrothermal treatment could selectively extract PB from the same engineered lignin, showing a possible circular biorefinery. These results suggest that the combination of PB-based DES and engineered PB-rich biomass is a promising strategy to achieve a sustainable closed-loop biorefinery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mono-/Bimetallic Doped and Heterostructure Engineering for Electrochemical Energy Applications

Designing efficient materials is crucial to meeting specific requirements in various electrochemical energy applications. Mono-/bimetallic doped and heterostructure engineering have attracted considerable research interest due to their unique functionalities and potential for electrochemical energy conversion and storage. However, addressing material imperfections such as low conductivity and poor active sites requires a strategic approach to design. This review explores the latest advancements in materials modified by mono-/bimetallic doped and heterojunction strategies for electrochemical energy applications. It can be subdivided into three key points: (i) the regulatory mechanisms of metal doping and heterostructure engineering for materials; (ii) the preparation methods of materials with various engineering strategies; and (iii) the synergistic effects of two engineering approaches, further highlighting their applications in supercapacitors, alkaline ion batteries, and electrocatalysis. Finally, the review concludes with perspectives and recommendations for further research to advance these technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Remarks on geometric engineering, symmetry TFTs and anomalies

Abstract Geometric engineering is a collection of tools developed to establish dictionaries between local singularities in string theory and (supersymmetric) quantum fields. Extended operators and defects, as well as their higher quantum numbers captured by topological symmetries, can be encoded within geometric engineering dictionaries. In this paper we revisit and clarify aspects of these techniques, with special emphasis on ’t Hooft anomalies, interpreted from the SymTFT perspective as obstructions to the existence of Neumann boundary conditions. These obstructions to gauging higher symmetries are captured via higher link correlators for the SymTFT on spheres. In this work, we give the geometric engineering counterpart of this construction in terms of higher links of topological membranes. We provide a consistency check in the context of 5D SCFTs with anomalous 1-form symmetries, where we give two independent derivations of the anomaly in terms of higher links, one purely field theoretical and the other purely geometrical. Along the way, we also recover the construction of non-invertible duality defects in 4D$$ \mathcal{N} $$ N = 4 SYM from a geometric engineering perspective.

Physics↗

Artificial-intelligence-based prediction and control of combustion instabilities in spark-ignition engines

In recent years, as engine control strategies have grown increasingly sophisticated in a continued drive for increasing efficiency and reducing emissions, engine operation has been pushed into regimes that are limited by combustion instabilities. These instabilities produce undesirable abnormal combustion events, which pose barriers to further improvement in engine efficiency. Many of the phenomena involved are difficult to model or control using traditional, purely physics-based models and reactive control approaches. Artificial intelligence (AI) techniques offer some promise for achieving more effective combustion stability control, especially when appropriately applied within a physics-informed framework. This chapter illustrates the current state-of-the-art in applying AI to combustion stability control and examines three case studies with application to the dilute stability limit in spark-ignition engines to illustrate the utility and limitations of AI in these applications.

Maldonado Puente, Bryan↗

Xylose metabolic engineering of Issatchenkia orientalis for 3-hydroxypropionic acid production from cellulosic hydrolysate without nutrient supplementation

Bioconversion of lignocellulosic biomass offers a promising alternative to petroleum-based chemical production. However, inefficient xylose utilization and toxic compounds in cellulosic hydrolysate limit microbial fermentation, as the hydrolysate contains substantial amounts of xylose in addition to glucose. To address these challenges, we engineered Issatchenkia orientalis to produce 3-hydroxypropionic acid (3-HP) directly from sorghum hydrolysate under low-pH conditions. A heterologous xylose utilization pathway consisting of XYL1, XYL2, and XYL3 from Scheffersomyces stipitis was introduced into an engineered 3-HP producing strain, enabling efficient conversion of xylose to 3-HP. The engineered strain produced 46.8 g/L 3-HP from sorghum hydrolysate without nutrient supplementation. To eliminate the lag phase under low-pH conditions, fermentation was conducted at pH 6.0 for the first three days, after which pH control was discontinued and in situ 3-HP accumulation buffered the culture. This partial pH control strategy increased 3-HP productivity by 55% from 0.20 to 0.31 g/L∙h, while maintaining low-pH conditions. Introducing an additional copy of XYL2 further increased 3-HP titer to 53.5 g/L and the yield by 33%, from 0.30 to 0.40 g/g sugars, with pH reaching 4.5 at the end of fermentation. This represents one of the highest reported 3-HP titers and yields from cellulosic hydrolysate without additional nutrient supplementation. This work demonstrates a nutrient-independent and low-pH bioprocess for upgrading lignocellulosic hydrolysate into 3-HP, highlighting the industrial potential of engineered xylose-utilizing I. orientalis for sustainable production of platform chemicals from renewable feedstocks.

3-Hydroxypropionic acid↗

Applications of targeted proteomics in metabolic engineering: advances and opportunities

Optimization of metabolically engineered organisms requires good understanding of producing balanced level of pathway proteins. Targeted proteomics via selected-reaction monitoring (SRM) has been increasingly used in metabolic engineering studies to detect and quantify sets of proteins with high selectivity, multiplexity, and reproducibility. In combination with metabolomics and other omics tools, targeted proteomics has helped optimize the production of many bio-based chemicals in various metabolic engineering cell factories. In this review, we present recent applications of targeted proteomics in metabolic engineering studies and highlight several successful cases of targeted proteomics in boosting production of commodity and high value chemicals. Additionally, we also discuss challenges and limitations of current targeted proteomics and map opportunities for future research.

59 BASIC BIOLOGICAL SCIENCES↗

Enhanced 2'-Fucosyllactose production by engineered Saccharomyces cerevisiae using xylose as a co-substrate

2'-Fucosyllactose (2'-FL), a human milk oligosaccharide with confirmed benefits for infant health, is a promising infant formula ingredient. Although Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Bacillus subtilis have been engineered to produce 2'-FL, their titers and productivities need be improved for economic production. Glucose along with lactose have been used as substrates for producing 2'-FL, but accu- mulation of by-products due to overflow metabolism of glucose hampered efficient production of 2' -FL regardless of a host strain. To circumvent this problem, we used xylose, which is the second most abundant sugar in plant cell wall hydrolysates and is metabolized through oxidative metabolism, for the production of 2'-FL by engi- neered yeast. Specifically, we modified an engineered S. cerevisiae strain capable of assimilating xylose to pro- duce 2' -FL from a mixture of xylose and lactose. First, a lactose transporter (Lac12) from Kluyveromyces lactis was introduced. Second, a heterologous 2'-FL biosynthetic pathway consisting of enzymes Gmd, WcaG, and WbgL from Escherichia coli was introduced. Third, we adjusted expression levels of the heterologous genes to maximize 2'-FL production. The resulting engineered yeast produced 25.5 g/L of 2'-FL with a volumetric productivity of 0.35 g/L∙h in a fed-batch fermentation with lactose and xylose feeding to mitigate the glucose repression. Interestingly, the major location of produced 2'-FL by the engineered yeast can be changed using different culture media. While 72% of the produced 2'-FL was secreted when a complex medium was used, 82% of the produced 2'-FL remained inside the cells when a minimal medium was used. In conclusion, as yeast extract is already used as food and animal feed ingredients, 2'-FL enriched yeast extract can be produced cost-effectively using the 2'-FL-accumu- lating yeast cells.

2′ -fucosyllactose↗

Embracing the Intersections of Environmental Science, Engineering, and Geosciences to Solve Grand Challenges of the 21st Century

The U.S. National Academies report on Environmental Engineering for the 21st Century identified five grand challenges of sustainably supplying food, water, and energy; curbing climate change and adapting to its impacts; designing a future without pollution and waste; creating efficient, healthy, resilient cities; and fostering informed decisions and actions. (1) Addressing many of the grand challenges will require embracing the intersections of environmental science, engineering, and geosciences. These three fields are inherently interdisciplinary, and they naturally intersect with each other (Figure 1). Geosciences, or Earth sciences, study the dynamics of different spheres of Earth. One of its missions is to detect the availability of mineral, water, and fuel resources, for sustainable development, and new research opportunities were identified in “coevolution of life, environment, and climate” and “biogeochemical and water cycles in terrestrial environments and impacts of global change” by the U.S. National Research Council. (2) Environmental science and engineering focus on the spheres that intersect with human activities. Environmental science puts an emphasis on understanding the migration of naturally occurring and anthropogenic contaminants in the environment and their impact on ecosystem and human health, and environmental engineering centers on developing technologies for water supply, mineral exploration, and environmental remediation to mitigate adverse impacts.

54 ENVIRONMENTAL SCIENCES↗

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Abstract Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

59 BASIC BIOLOGICAL SCIENCES↗

ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Abstract Machine learning has been increasingly used for protein engineering. However, because the general sequence contexts they capture are not specific to the protein being engineered, the accuracy of existing machine learning algorithms is rather limited. Here, we report ECNet (evolutionary context-integrated neural network), a deep-learning algorithm that exploits evolutionary contexts to predict functional fitness for protein engineering. This algorithm integrates local evolutionary context from homologous sequences that explicitly model residue-residue epistasis for the protein of interest with the global evolutionary context that encodes rich semantic and structural features from the enormous protein sequence universe. As such, it enables accurate mapping from sequence to function and provides generalization from low-order mutants to higher-order mutants. We show that ECNet predicts the sequence-function relationship more accurately as compared to existing machine learning algorithms by using ~50 deep mutational scanning and random mutagenesis datasets. Moreover, we used ECNet to guide the engineering of TEM-1 β-lactamase and identified variants with improved ampicillin resistance with high success rates.

59 BASIC BIOLOGICAL SCIENCES↗

A generalized platform for artificial intelligence-powered autonomous enzyme engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

59 BASIC BIOLOGICAL SCIENCES↗

Magnetic domain engineering in SrRuO3 thin films

Abstract Magnetic domain engineering in ferromagnetic thin films is a very important route toward the rational design of spintronics and memory devices. Although the magnetic domain formation has been extensively studied, artificial control of magnetic domain remains challenging. Here, we present the control of magnetic domain formation in paradigmatic SrRuO 3 /SrTiO 3 heterostructures via structural domain engineering. The formation of structural twin domains in SrRuO 3 films can be well controlled by breaking the SrTiO 3 substrate symmetry through engineering miscut direction. The combination of x-ray diffraction analysis of structural twin domains and magnetic imaging of reversal process demonstrates a one-to-one correspondence between structural domains and magnetic domains, which results in multi-step magnetization switching and anomalous Hall effect in films with twin domains. Our work sheds light on the control of the magnetic domain formation via structural domain engineering, which will pave a path toward desired properties and devices applications.

Materials Science↗

Enhanced microbial production of protocatechuate from engineered sorghum using an integrated feedstock-to-product conversion technology

Building a stronger bioeconomy requires production capabilities that are largely generated through microbial genetic engineering. Plant feedstocks can additionally be genetically engineered to generate desirable feedstock traits and provide precursors for direct microbial conversion into desired products. The oleaginous yeast Rhodosporidium toruloides is a promising organism for this type of conversion as it can grow on a wide range of deconstructed biomass and consume a variety of carbon sources. Here, we leveraged R. toruloides native p-coumaric acid consumption pathway to accumulate protocatechuate (PCA) from 4-hydroxybenzoate (4HBA) released from a sorghum feedstock line genetically engineered to overproduce 4HBA. We did so by generating and evaluating an R. toruloides strain that accumulates PCA, RSΔ12623. We then show that at two scales a cholinium lysinate pretreatment with enzymatic saccharification successfully extracts 95% of the 4HBA from the engineered sorghum biomass while producing deconstructed lignin that can be more efficiently depolymerized in a subsequent thermochemical reaction. We also demonstrate that strain RSΔ12623 can convert more than 95% of 4HBA to PCA while consuming >95% of the glucose and >80% of the xylose present in sorghum hydrolysates. Finally, to evaluate the scalability of such fermentations, we conducted the conversion of 4HBA to PCA in a 2 L bioreactor under controlled conditions. Importantly, this work demonstrates the potential of purposefully producing aromatic precursors in planta that can be liberated during biomass deconstruction for direct microbial conversion to desirable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Entanglement engineering of optomechanical systems by reinforcement learning

Entanglement is fundamental to quantum information science and technology, yet controlling and manipulating entanglement—so-called entanglement engineering—for arbitrary quantum systems remains a formidable challenge. There are two difficulties: the fragility of quantum entanglement and its experimental characterization. We develop a model-free deep reinforcement-learning (RL) approach to entanglement engineering, in which feedback control together with weak continuous measurement and partial state observation is exploited to generate and maintain desired entanglement. We employ quantum optomechanical systems with linear or nonlinear photon–phonon interactions to demonstrate the workings of our machine-learning-based entanglement engineering protocol. In particular, the RL agent sequentially interacts with one or multiple parallel quantum optomechanical environments, collects trajectories, and updates the policy to maximize the accumulated reward to create and stabilize quantum entanglement over an arbitrary amount of time. The machine-learning-based model-free control principle is applicable to the entanglement engineering of experimental quantum systems in general.

97 MATHEMATICS AND COMPUTING↗

Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels

Engineered antibody fragments (Fabs) have made major impacts on structural biology research, particularly to aid structural determination of membrane proteins. Nonetheless, Fabs generated by traditional monoclonal technology suffer from challenges of routine production and storage. Starting from the known IgG paratopes of an antibody that binds to the “turret loop” of the KcsA K+ channel, we engineered a synthetic Fab (sFab) based upon the highly stable Herceptin Fab scaffold, which can be recombinantly expressed in Escherichia coli and purified with single-step affinity chromatography. This synthetic Fab was used as a crystallization chaperone to obtain crystals of the KcsA channel that diffracted to a resolution comparable to that from the parent Fab. Furthermore, we show that the turret loop can be grafted into the unrelated voltage-gated Kv1.2–Kv2.1 channel and still strongly bind the engineered sFab, in support of the loop grafting strategy. Macroscopic electrophysiology recordings show that the sFab affects the activation and conductance of the chimeric voltage-gated channel. These results suggest that straightforward engineering of antibodies using recombinant formats can facilitate the rapid and scalable production of Fabs as structural biology tools and functional probes. The impact of this approach is expanded significantly based on the potential portability of the turret loop to a myriad of other K+ channels.

59 BASIC BIOLOGICAL SCIENCES↗