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At least 397 records · Page 22

Data analysis and modeling pipelines for controlled networked social science experiments

There is large interest in networked social science experiments for understanding human behavior at-scale. Significant effort is required to perform data analytics on experimental outputs and for computational modeling of custom experiments. Moreover, experiments and modeling are often performed in a cycle, enabling iterative experimental refinement and data modeling to uncover interesting insights and to generate/refute hypotheses about social behaviors. The current practice for social analysts is to develop tailor-made computer programs and analytical scripts for experiments and modeling. This often leads to inefficiencies and duplication of effort. In this work, we propose a pipeline framework to take a significant step towards overcoming these challenges. Our contribution is to describe the design and implementation of a software system to automate many of the steps involved in analyzing social science experimental data, building models to capture the behavior of human subjects, and providing data to test hypotheses. The proposed pipeline framework consists of formal models, formal algorithms, and theoretical models as the basis for the design and implementation. We propose a formal data model, such that if an experiment can be described in terms of this model, then our pipeline software can be used to analyze data efficiently. The merits of the proposed pipeline framework is elaborated by several case studies of networked social science experiments.

97 MATHEMATICS AND COMPUTING↗

Maximizing the Use of Ductless Mini-Splits in Homes with Existing Central or Zonal Heating and Cooling Equipment

In the residential retrofit application, ductless mini-split heat pumps (DHP) are often reported to hold high-energy savings potential, depending on the system they are supplementing or replacing. However, of late, there have been a number of studies and analyses indicating these energy savings are not being achieved. The primary goal of this project was to determine the most cost effective (lowest cost for the most energy saved) and persistent (e.g. automated, hard to change, etc.) solution for controlling a ductless heat pump in an existing home with central forced air furnace. Various control strategies were tested at the Pacific Northwest National Laboratory Lab Homes to compare the energy savings between the different energy efficient control strategies. A maximum of 40% energy savings was realized by using the ductless mini-split as the primary heat source with the central air conditioning unit as the secondary source.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Parameterization Study of Sew-EZ Materials: Types #6 and #8

Two material types identified by Sew-EZ were tested in various configurations, and under various conditions, by Sandia National Laboratories (SNL). The primary focus of this study was to assess the filtration performance of these two materials and identify if they perform similarly to certified N95 respirators. Testing was conducted on two systems which use distinctly different techniques to characterize the aerosol penetration characteristics of materials: a) R&D Filtration System: A large-scale R&D filtration system was used with testing parameters that mimicked NIOSH guidelines, where possible. Efficiency data as a function of particle size was attained using NaC1 as the test aerosol and a Scanning Mobility Particle Sizer (SMPS) for measurements. A more detailed system description can be found in Omana et al. 2020. b) Automated Tester: A commercial, automated filter tester (100Xs, Air Techniques International) was used to provide penetration/efficiency data for Sew EZ materials. The 100Xs aerosolizes a polydisperse NaC1 aerosol with a consistent concentration and size profile. The 100Xs manual (Air Techniques International 2018) states, "The aerosol particle size and distribution are designed to meet all requirements as defined in the relevant sections of NIOSH 42 CFR, Part 84 (pg. 32)."

36 MATERIALS SCIENCE↗

Development and Characterization of a Self-Tightening Tourniquet System

Uncontrolled hemorrhage remains a leading cause of death in both emergency and military medicine. Tourniquets are essential to stopping hemorrhage in these scenarios, but they suffer from subjective, inconsistent application. Here, we demonstrate how tourniquet application can be automated using sensors and computer algorithms. The auto-tourniquet self-tightens until blood pressure oscillations are no longer registered by the pressure sensor connected to the pneumatic pressure cuff. The auto-tourniquet’s performance in stopping the bleed was comparable to manual tourniquet application, but the time required to fully occlude the bleed was longer. Application of the tourniquet was significantly smoother, and less variable, for the automatic tourniquet compared to manual tourniquet application. This proof-of-concept study highlights how automated tourniquets can be integrated with sensors to provide a much more consistent application and use compared to manual application, even in controlled, low stress testing conditions. Future work will investigate different sensors and tourniquets to improve the application time and repeatability.

Vega, Saul J.↗

An objective inter-comparison of trash mark constellations generated by manual and automated detection methods

Trash marks are unintentional markings observed on printed, scanned, or photocopied documents that result from permanent defects or transient material in office machines and can be used for source attribution of questioned documents. Trash mark examinations have been in use in forensic laboratories for decades, yet the method remains relatively untested and relies on training, experience, and anecdotal information to support its validity. Herein this study generated and harnessed objective data to empirically test one of the foundational theories for assessing the origin of photocopied documents: provided trash marks are present in sufficient quantity and/or quality, no two machines will exhibit a constellation of trash marks that is indistinguishable from another. In this project, objective trash mark location and size data was generated for 50 known photocopiers using both a traditional and a novel, automated method. Inter-machine comparisons were conducted using a novel variant of the Hausdorff distance algorithm to generate a quantitative assessment of how similar or different the 2450 pairs of trash mark constellations were from one another. This study found that each of the machines bearing one or more trash marks exhibited objective differences in their trash mark constellations, ultimately providing support for the tested hypothesis

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying System Level Impact of Connected and Automated Vehicles in an Urban Corridor

Numerous studies have demonstrated significant energy reduction for an ego vehicle by up to 20% leveraging Vehicle-to-Everything (V2X) technologies [1-4]. Some studies have also analyzed the impact of such vehicles on the energy consumption of other vehicles in a suburban or a highway corridor [5, 6], but the impact in an urban setting has not been studied yet. Southwest Research Institute (SwRI), in collaboration with Continental and Hyundai, is currently working on a Department of Energy funded project that is focused on quantifying the impact of multiple ego vehicles (smart vehicles) on the total energy consumption of the corridor under various traffic conditions, vehicle electrification level, vehicle-to-vehicle (V2V) technology penetration, and the number of smart (ego) vehicles in an urban setting. A six-kilometer-long urban corridor from Columbus, Ohio was modeled and calibrated with real-world data in PTV Vissim traffic microsimulation software. Five forward-looking powertrain models, consisting of two battery electric vehicles (BEVs), a hybrid electric vehicle (HEV), and two internal combustion engine (ICE) powered vehicles, were developed to estimate the energy consumption of vehicles on the corridor. A comprehensive full factorial simulation study was performed. The simulation results indicate that for a traffic mix based on projected new vehicles sales in 2025, a 15% corridor-level energy consumption reduction can be achieved. The paper details the development and validation of the simulation framework, design of experiments conducted, a discussion of challenges faced, and results under various test conditions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format

Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes ( e . g ., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5–2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.

59 BASIC BIOLOGICAL SCIENCES↗

Building a Simplistic Automatic Extruder: Instrument Development Opportunities for the Laboratory

This work presents an automatic extruder as a research experience for undergraduate students. The system offers a user-friendly approach to preparing vesicles, such as liposomes or polymersomes, with a defined size and polydispersity properties crucial for research in biology and macromolecules. It comprises two syringe pumps connected by a membrane filter. The setup is controlled by software. Compared to manual extrusion, this automated system provides advantages, such as precisely controlled variables. The project describes a tool to enhance undergraduate learning in science and engineering laboratories. Building an automatic extruder serves as a simplified model of a complex industrial process. It offers a clear advantage: automating a well-understood manual extrusion process. To make this project accessible, it is broken down into three manageable tasks: software development, hardware assembly, and testing procedures. This breakdown describes the software created, the hardware components used, and the testing procedures conducted for this project. All project data, including software code, testing data, and procedures, are freely available online. This allows undergraduate students to not only begin their own projects but also contribute to this educational instrument’s ongoing development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiphysics Modeling of Microreactors with NEAMS codes, and Validation Based on KRUSTY Reactivity Insertion

The NEAMS Multiphysics Applications team continues to assess code usability and functionality for microreactor design and safety analyses, while demonstrating that NEAMS tools capture both steady-state and transient behavior across distinct microreactor concepts. In FY2025, the team advanced full-core, high-fidelity, multiphysics models that solve more complex problems and strengthen verification/validation for several microreactor systems: heat-pipe microreactor (HPMR), gas-cooled microreactor (GCMR), and the KRUSTY experiment. These models employ the MOOSE MultiApp/Transfers architecture with Griffin for neutronics, BISON for heat conduction/thermomechanics, Sockeye for heat pipes, SAM/THM for coolant channels and loops, and SWIFT for hydride behavior, with meshes generated via the MOOSE Reactor Module. The graphite models available in the Grizzly code were also investigated for future analyses. For the HPMR, a Na-HPMR variant was constructed to align with recently validated heat-pipe experiments and Sockeye’s LCVF capability, enabling mechanistic heat-pipe transients and startup modeling. The Na-HPMR will serve as the primary model for HPMR investigations in upcoming tasks. The load-following and single heat-pipe failure scenarios (Griffin/BISON/Sockeye), which were previously modeled for the K-HPMR, were replicated for the Na-HPMR, showing strong negative temperature feedback and highly localized thermal effects, respectively, while the startup case captured vapor-front progression and heat-removal activation. Solid mechanics was added to the previously built K-HPMR full-core model in BISON, showing minimal impact on steady-state reactivity yet enabling stress-field predictions that prepare the path for full-core TRISO performance analyses. For the GCMR, automated steady-state and four transient scenarios were executed using Griffin/BISON/SAM/SWIFT. Results confirm robust inherent safety: power collapses promptly in loss-of-cooling events, the inlet-temperature drop settles to a new equilibrium, and a single-channel blockage yields only a ~30 K local fuel-temperature rise with <0.4% power decrease. SWIFT-predicted hydrogen redistribution affects reactivity during both steady-state and transient conditions, underscoring its importance. A Brayton-cycle balance of plant (BOP) model in SAM/THM demonstrated stable startup behavior, and xenon-driven reactivity during load following was analyzed. To improve TRISO-compact temperature fidelity, a fast multiscale Heat Source Decomposition (HSD) treatment was implemented. Against heterogeneous benchmarks, HSD reduces underprediction of kernel temperatures and lowers predicted peak powers in reactivity-insertion transients compared to previous homogenized models. KRUSTY warm-critical validation progressed from FY2024 baselines: the 15Ȼ insertion shows excellent agreement in peak power (~2% high) and temperature trends, and the 30Ȼ case was automated via a feedback controller that maintained power near 3 kW for ~150 s with close agreement to data. The successful modeling of the warm critical tests has laid a strong foundation for simulating more complex nuclear system tests in the years ahead. Throughout FY2025, developer feedback was provided (e.g., MOOSE batch mesh generation, distributed pre-split meshes, Griffin sweeper on displaced meshes), several new models were contributed to the Virtual Test Bed, and an OECD-NEA WPRS multiphysics benchmark based on the HPMR was initiated to enable broader cross-comparison and best-practice development with the nuclear community at large.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A framework of computer vision-enhanced microfluidic approach for automated assessment of the transient sickling kinetics in sickle red blood cells

The occurrence of vaso-occlusive crisis greatly depends on the competition between the sickling delay time and the transit time of individual sickle cells, i.e., red blood cells from sickle cell disease (SCD) patients, while they are traversing the circulatory system. Many drugs for treating SCD work by inhibiting the polymerization of sickle hemoglobin (HbS), effectively delaying the sickling process in sickle cells (SS RBCs). Most previous studies on screening anti-sickling drugs, such as voxelotor, rely on in vitro testing of sickling characteristics, often conducted under prolonged deoxygenation for up to 1 hour. However, since the microcirculation of RBCs typically takes less than 1 minute, the results of these studies may be less accurate and less relevant for in vitro-in vivo correlation. In our current study, we introduce a computer vision-enhanced microfluidic framework designed to automatically capture the transient sickling kinetics of SS RBCs within a 1-min timeframe. Our study has successfully detected differences in the transient sickling kinetics between vehicle control and voxelotor-treated SS RBCs. This approach has the potential for broader applications in screening anti-sickling therapies.

59 BASIC BIOLOGICAL SCIENCES↗

Laboratory and field assessment of mid-infrared absorption (MIRA) instrument performance for methane and ethane dry mole fractions

Concurrent measurements of methane (CH 4 ) and ethane (C 2 H 6 ) can be used to identify and separate methane sources, as ethane is present in thermogenic sources (e.g., oil and natural gas) but not in biogenic sources (e.g., agriculture). In this study, we evaluated the performance of multiple Aeris MIRA Ultra instruments (Versions 1 and 2) through controlled laboratory tests and tower-based deployments under field conditions. The systems were modified with an external pump, flow control, a Nafion dryer, and a custom-built auxiliary box to automate the system and transmit near real-time data. We determined the best calibration approach for our application, given practical limitations, to be a full calibration cycle (with ambient and high calibration cylinders) about once per day and an ambient calibration cylinder sampled hourly. Measurement uncertainty was assessed, including the uncertainty due to instrument noise as a function of calibration frequency, uncertainty in the water vapor correction, and cylinder assignment uncertainty. Instrument noise was the dominant source of uncertainty for C 2 H 6 , while the water vapor correction dominated the CH 4 uncertainty. For Version 2 systems with hourly calibrations and a Nafion dryer with counterflow, the mean total uncertainty, including both systematic errors and noise, of hourly averages was 0.8–3.0 ppb CH 4 and 0.35–0.37 ppb C 2 H 6 . Laboratory intercomparisons showed network compatibility within 1.2 ppb CH 4 and 0.23 ppb C 2 H6, and a collocated deployment with a NOAA Picarro system agreed within 1.8 ppb CH 4 . Instrument noise varied substantially amongst the instruments, with errors reaching up to 11 ppb CH 4 and 2 ppb C 2 H 6 for hourly means, with similar variability indicated in a 50 h cylinder test. With appropriate engineering and calibration, the Aeris MIRA Ultra has the potential to distinguish regional methane emission sources in many field settings.

03 NATURAL GAS↗

Electron energy loss spectroscopy database synthesis and automation of core-loss edge recognition by deep-learning neural networks

Abstract The ionization edges encoded in the electron energy loss spectroscopy (EELS) spectra enable advanced material analysis including composition analyses and elemental quantifications. The development of the parallel EELS instrument and fast, sensitive detectors have greatly improved the acquisition speed of EELS spectra. However, the traditional way of core-loss edge recognition is experience based and human labor dependent, which limits the processing speed. So far, the low signal–noise ratio and the low jump ratio of the core-loss edges on the raw EELS spectra have been challenging for the automation of edge recognition. In this work, a convolutional-bidirectional long short-term memory neural network (CNN-BiLSTM) is proposed to automate the detection and elemental identification of core-loss edges from raw spectra. An EELS spectral database is synthesized by using our forward model to assist in the training and validation of the neural network. To make the synthesized spectra resemble the real spectra, we collected a large library of experimentally acquired EELS core edges. In synthesize the training library, the edges are modeled by fitting the multi-Gaussian model to the real edges from experiments, and the noise and instrumental imperfectness are simulated and added. The well-trained CNN-BiLSTM network is tested against both the simulated spectra and real spectra collected from experiments. The high accuracy of the network, 94.9%, proves that, without complicated preprocessing of the raw spectra, the proposed CNN-BiLSTM network achieves the automation of core-loss edge recognition for EELS spectra with high accuracy.

36 MATERIALS SCIENCE↗

Energy-Efficient Maneuvering of Connected and Automated Vehicles (CAVs) with Situational Awareness at Intersections (Final Progress Report)

The increased development of Connected and Automated Vehicle (CAV) systems, currently used for safety and driver convenience, presents new opportunities to improve the energy efficiency of vehicles. Southwest Research Institute (SwRI) achieved a 20% energy consumption reduction in a 2017 Toyota Prius Prime plug-in hybrid by using connectivity (V2V, V2I, V2X) as part of the Next Generation Energy Technologies for Connected and Automated on-Road Vehicles (NEXTCAR) program. The energy consumption gains were achieved by a combination of vehicle dynamics and powertrain control algorithms with a focus on SAE L1 and L2 automated vehicles where a human is still responsible for safe operation. SwRI is now involved in NEXTCAR-II, focusing on energy-efficient control tech for SAE Level 4/5 automated vehicles, aiming for a 30% energy reduction compared to stock hybrids. The rise of Mobility as a Service (MaaS) is driving investments in L4 and L5 automated vehicles. A study by the University of Michigan shows these vehicles might increase energy use and emissions by 3-20%. Technology similar to NEXTCAR can enhance energy efficiency in highly automated vehicles, leveraging improved sensing and actuation capabilities. While the NEXTCAR programs targeted energy efficiency improvements for a single vehicle, this program adopts a more expansive approach. It places its focus on understanding and testing the cumulative effects within a region or corridor, aiming to assess how a subset of vehicles equipped with NEXTCAR-style technologies influence the overall energy consumption of all vehicles traveling within that area. Additionally, the program explores infrastructure-based mobility solutions to optimize efficiency, and seeks to understand and quantify public perception and likelihood of technology adoption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Toward In Situ Synchrotron Mapping of Crystal Selection Processes during Crystal Growth

In this work, we present an automated and rapid method for non-destructive mapping of crystal grains in a rod-shaped sample. The approach was designed for application to in situ float-zone crystal growth experiments at an x-ray synchrotron source, but could be useful in other applications. The methods have been tested on a TiO 2 boule grown in an optical float zone furnace. The approach applies a statistical filter to polycrystalline diffraction patterns on 2D detectors to rapidly determine the degree of powder-quality 1of the signal. When larger crystals emerge in the growth, their position, size and shape can be tracked using an automated blob-tracking algorithm that follows individual Bragg peaks as a function of position in a grid-scan, even when multiple crystals are contributing spots to diffraction images. This method is found to be robust as the same crystal shape can be independently reconstructed using different sets of Bragg reflections. Image segmentation methods are then used to map out the polycrystalline grains. We also note that other information about crystal quality, such as mosaicity or strain state, may be inferred and mapped from the intensity variation of the Bragg peaks at different locations within the sample.

36 MATERIALS SCIENCE↗

Handheld Biosensor for COVID-19 Screening

We have made significant progress toward the development of an integrated nucleic acid amplification system for Autonomous Medical Devices Incorporated (AMDIs) Optikus handheld diagnostic device. In this effort, we developed a set of loop-mediated isothermal amplification (LAMP) primers for SARS-CoV-2 and then demonstrate amplification directly on a surface acoustic wave (SAW) sensor. We built associated hardware and developed a C-code to control the amplification process. The goal of this project was to develop a nucleic amplification assay that is compatible with SAW sensors to enable both nucleic and serological testing in a single handheld diagnostic device. Toward this goal, AMDI is collaborating Sandia National Laboratories to develop a rapid, portable diagnostic screening device that utilizes Sandias unique surface acoustic wave biosensor (SAW) for COVID-19 detection. Previously, the SANDIA- AMDI SAW sensor has successfully detected multiple high-profile bacteria viruses, including Ebola, HIV, Sin Nombre, and Anthrax. Over the last two years, AMDI and SANDIA have significantly improved the sensitivity and detection capability of the SAW biosensor and have also developed a modular hand-held, portable platform called the Optikus, which uses CD microfluidics and handheld instrumentation to automate all sample preparation, reagent introduction, sample delivery, and measurement for a number of different assay targets. We propose to use this platform for the development of a rapid (%3C30 minutes), point-of-care diagnostic test for detection of COVID-19 from nasal swab samples.

47 OTHER INSTRUMENTATION↗

Exploring Benchmarks for Self-Driving Labs using Color Matching

Self Driving Labs (SDLs) that combine automation of experimental procedures with autonomous decision making are gaining popularity as a means of increasing the throughput of scientific workflows. The task of identifying quantities of supplied colored pigments that match a target color, the color matching problem, provides a simple and flexible SDL test case, as it requires experiment proposal, sample creation, and sample analysis, three common components in autonomous discovery applications. We present a robotic solution to the color matching problem that allows for fully autonomous execution of a color matching protocol. Our solution leverages the WEI science factory platform to enable portability across different robotic hardware, the use of alternative optimization methods for continuous refinement, and automated publication of results for experiment tracking and post-hoc analysis.

Artificial intelligence↗

Salt Sampling FY21 Technical Report

The goal of the salt sampling program at Argonne is to develop and deploy automated molten salt sampling approaches to enable high-precision in-process salt sample analysis to improve the timeliness of sampling-based accountancy measurements. Tools currently under development in support of this goal include (1) a modular vacuum sampler with an accompanying sample handling method for coupling vacuum sampling with high-precision at-line sample analysis, (2) a pneumatic sample generator that enables high-throughput sample analysis to improve the precision of existing analytical techniques, and (3) a windowless flow cell to enable on-line optical analysis of molten salt in a sampling loop. Compared to point sampling approaches (i.e., dip probes), vacuum sampling systems and on-line sampling loops facilitate access to a larger cross-section of a process fluid. This is known to improve the characterization of the process fluid by producing more representative samples and by enabling the analysis of a larger cross section of the fluid. A vacuum sampling approach for molten salts eliminates the risk of dross contamination of samples and avoids the use of moving parts in the salt. In FY21, two methods for integrating a vacuum sampler with a pneumatic sample generator were tested. These included direct fluidic coupling and coupling using a solid salt transfer mechanism. Solid salt transfer was ultimately selected over fluidic coupling, primarily to enable the transport of samples over longer distances to support automated at-line integration with high-precision techniques (such as microcalorimetry) that cannot withstand the extreme conditions near an electrorefining process. To facilitate rapid solid salt coupling, new mechanisms were developed for rapidly charging and discharging salt sample tubes at the vacuum sampler and pneumatic sample generator, respectively. While the charging mechanism will be deployed in FY22, the tube transfer method and discharge mechanism were tested in FY21. These were deployed at one of Argonne’s engineering-scale electrorefiners to implement at-line high-throughput pneumatic micro-sample generation capabilities. The method was used to generate precise uranium- and lanthanide-bearing electrorefiner micro-samples with the specific dimensions requested by researchers at Los Alamos National Laboratory for use in testing their novel microcalorimeter x-ray techniques. The solid salt transfer mechanism proved not only to be an effective means of integrating the precision sample generator with vacuum sampling, but also improved the performance of the sampler generator. Because the modular sampling approach described here eliminates the need for new high-radiation sample handling capabilities, salt-wetted seals, salt-wetted moving parts, and heated transfer lines outside the electrorefiner, it will address most of the remaining technical challenges for the at-line deployment of high-precision analytical techniques. This will enable significant reductions in the time delay for sampling-based accountancy measurements by eliminating the need for manual off-line sample processing and analysis. On-line optical analysis of molten salt in a sampling loop would provide complementary information to at-line and in-situ techniques. In FY21, an open-aperture molten salt gravity flow cell with windowless optical access to flowing salt was successfully demonstrated. Future work should include the refinement and performance testing of the on-line and at-line sampling tools, integration of additional analysis techniques, stakeholder outreach and collaboration, evaluation of the integrated methods, and analyses to determine how the various tools might fit into an integrated safeguards monitoring system of unattended near real time monitoring tools.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Metabolic flux optimization of iterative pathways through orthogonal gene expression control: Application to the β-oxidation reversal

Balancing relative expression of pathway genes to minimize flux bottlenecks and metabolic burden is one of the key challenges in metabolic engineering. This is especially relevant for iterative pathways, such as reverse β-oxidation (rBOX) pathway, which require control of flux partition at multiple nodes to achieve efficient synthesis of target products. Here, we develop a plasmid-based inducible system for orthogonal control of gene expression (referred to as the TriO system) and demonstrate its utility in the rBOX pathway. Leveraging effortless construction of TriO vectors in a plug-and-play manner, we simultaneously explored the solution space for enzyme choice and relative expression levels. Remarkably, varying individual expression levels led to substantial change in product specificity ranging from no production to optimal performance of about 90% of the theoretical yield of the desired products. We obtained titers of 6.3 g/L butyrate, 2.2 g/L butanol and 4.0 g/L hexanoate from glycerol in E. coli, which exceed the best titers previously reported using equivalent enzyme combinations. Since a similar system behavior was observed with alternative termination routes and higher-order iterations, we envision our approach to be broadly applicable to other iterative pathways besides the rBOX. Here, considering that high throughput, automated strain construction using combinatorial promoter and RBS libraries remain out of reach for many researchers, especially in academia, tools like the TriO system could democratize the testing and evaluation of pathway designs by reducing cost, time and infrastructure requirements.

59 BASIC BIOLOGICAL SCIENCES↗