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At least 145 records · Page 8

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing

Next-Generation Energy Technologies for Connected and Automated On-Road Vehicles (NEXTCAR) - Predictive Data-Driven Vehicle Dynamics and Powertrain Control: from ECU to the Cloud (Final Scientific/Technical Report)

This project developed and demonstrated a predictive, data-driven vehicle control system designed to improve energy efficiency and driving performance. The team created intelligent self-driving car technology that optimizes fuel and electricity use by proactively planning vehicle actions. By combining Level 4 autonomous driving capabilities with vehicle-to-everything (V2X) connectivity, the system enables vehicles to adjust speed and change lanes in response to traffic signals, surrounding vehicles, and road conditions, reducing unnecessary stops and delays. In testing, the system improved vehicle fuel economy by more than 30% and reduced travel time by approximately 10%, compared to a conventional adaptive cruise control baseline. These results demonstrate the technical effectiveness of using predictive, V2X-enabled strategies, such as traffic light timing and surrounding traffic awareness, to inform real-time vehicle powertrain control and driving behavior. Additionally, a supporting cloud platform was developed to provide dispatch and route recommendations as well as to log vehicle data, demonstrating the economic feasibility of this approach at the fleet level. By optimizing dispatching and routing operations, this technology enables electric fleet operators to use their vehicles more efficiently and reduce reliance on diesel backups, lowering both operating costs and energy consumption. Overall, this project’s technology advances the future of clean, energy-efficient transportation, enabling vehicles and fleets to reduce energy waste, cut costs, and lower emissions through intelligent automation and connectivity.

33 ADVANCED PROPULSION SYSTEMS

Intelligent Experiments Through Real-time AI: Fast Data Processing and Autonomous Detector Control for sPHENIX and Future EIC Detectors (Final Report)

The overall vision of this project was to integrate real-time artificial intelligence (AI) directly into the data acquisition and detector-control systems of nuclear physics experiments, including both fast online event selection and an autonomous detector-control feedback loop. The work carried out under the award focused on the fast online event-selection half of that vision: the efficient recording of low-momentum heavy-flavor (HF) hadron decays in proton-proton collisions at the sPHENIX experiment at the Relativistic Heavy Ion Collider (RHIC)—an observable that requires fast tracking and topological trigger selection not previously demonstrated at RHIC, and that is essential for QCD studies at future facilities such as the Electron-Ion Collider (EIC). The autonomous detector-control (GPU-based feedback) component named in the project title remained a design concept and was not implemented under this award. The Massachusetts Institute of Technology (MIT) group led the offline simulation and data processing needed to train the machine-learning (ML) models, the translation of trained models to Field-Programmable Gate Array (FPGA) firmware using the hls4ml framework, and the physics validation of heavy-flavor reconstruction. Over the award period, the team developed and hardware-tested the principal components of an AI-based heavy-flavor trigger on simulated and recorded sPHENIX tracker data: a software Bipartite Graph Attention Network (BiGAT) trigger model reaching > 95% signal efficiency at 99% background rejection; an FPGA-native hit clusterizer matching the offline clustering; smaller networks synthesized to FPGA within the required sub-10 µs latency; and an assembled decoder–clusterizer–inference firmware chain exercised on the FELIX readout board. A complete, fully integrated hardware demonstrator was not finished within the award period. This report documents the project goals, the MIT group’s contributions, the technical accomplishments, and the outlook toward applications at the future EIC ePIC detector.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Human Supervision of Autonomous Vehicle Fleet Operations and Associated Passenger Communications: Preprint

Advances in automated vehicle (AV) technology and expanded operations are rapidly emerging with Automated Mobility District (AMD) deployments in global cities. NLR's AMD research addresses critical elements of human supervision of AV fleet operations and associated passenger communications for vehicles in which no driver or safety attendant is present. Although sufficiently advanced AVs no longer have direct oversight by a driver, fleet management remains staffed with operations personnel at the operations command and control (OCC) facility. This paper examines the functionality of the OCC, drawing comparisons of how automated train control and automated people mover OCCs operate. Within an AMD, the OCC manages various vehicle types, sizes, and operational modes, including on-demand and fixed route service, to facilitate a 'network of networks' for transport within a metropolitan area. The OCC serves as oversight for multiple AV fleets assisting AVs via remote operation of vehicles, communication, and dispatching personnel to resolve problems. The OCC also coordinates system operation, geographically staging vehicles, and managing weather, police, and emergency events. Informed by traffic management center (TMC) strategies using highly integrated software and communications, OCCs facilitate seamless information flows. OCC personnel remotely assist passengers and oversee multi-party operation to ensure safety and security. Although social norms mitigate large-capacity unattended vehicle operations, social interaction in multi-party automated small vehicles has little precedent. This poses a new frontier for society and requires research to effectively understand and manage. Future research will monitor OCC implementations, passenger interfaces, and deployment scaling of initial AMD systems.

33 ADVANCED PROPULSION SYSTEMS

An Approach to Realize Generalized Optimal Motion Primitives Using Physics Informed Neural Networks

Autonomous manipulation is a challenging problem in field robotics due to uncertainty in object properties, constraints, and coupling phenomenon with robot control systems. Humans learn motion primitives over time to effectively interact with the environment. We postulate that autonomous manipulation can be enabled by basic sets of motion primitives as well, but do not necessitate mimicking human motion primitives. Here, this work presents an approach to generalized optimal motion primitives using physics-informed neural networks. Our simulated and experimental results demonstrate that optimality is notionally maintained where the mean maximum observed final position percent error was 0.564% and the average mean error for all the trajectories was 1.53%. These results indicate that notional generalization is attained using a physics-informed neural network approach that enables near optimal real-time adaptation of primitive motion profiles.

97 MATHEMATICS AND COMPUTING

Data Driven Approach to Public Opinion Mining on Autonomous Vehicles: Sentiment Analysis of Social Media Comments Using Large Language Models

In the realm of online identity, social media has emerged as a rich and dynamic source of user-generated content, making it an invaluable resource for understanding public sentiment on a wide range of topics. Individuals often share their raw emotions and candid opinions on these platforms without fear of judgment or backlash. In this study, we conduct a sentiment analysis on user comments collected from various online platforms, with a specific focus on discussions surrounding autonomous vehicles. Leveraging the capabilities of large language models (LLMs), we classify each comment into one of five sentiment categories: Very Negative, Negative, Neutral, Positive, and Very Positive. Our approach demonstrates the effectiveness of LLMs in capturing nuanced contextual sentiment, offering a scalable and state-of-the-art alternative to traditional manual annotation methods. The results reveal key trends and insights into public perception, enabling a deeper understanding of how autonomous vehicle technologies are received by the online community. Our findings underscore the dynamic nature of public sentiment, which is shaped not only by advances in autonomous vehicle technology but also by contextual events such as regulatory developments, political adjustment and safety incidents.

24 POWER TRANSMISSION AND DISTRIBUTION

Human Factors Considerations for Anticipated Uses of Autonomy in Advanced Reactor Technologies

The objective of this report is examine anticipated advanced reactor designs that incorporate high levels of autonomy in operation of advanced reactor systems or facilities, and to begin identifying the human factors engineering (HFE) considerations relevant to those designs. The insights gained will help identify areas where U.S. Nuclear Regulatory Commission (NRC) may need to develop or update review guidance to adequately address HFE considerations essential for safe operation. The adequacy of existing guidance, along with recommendations for updates or new guidance, may be addressed in future reports. We use the term “landscape analysis” to describe the review, analysis, and characterization of publicly available information on the anticipated future state of the industry regarding particular technologies or operational concepts. This landscape analysis considers the potential range of advanced reactor automation concepts that may be used for monitoring and controlling nuclear systems and facilities, including the potential for highly automated, near autonomous, or fully autonomous operation of advanced nuclear reactors.

99 - GENERAL AND MISCELLANEOUS

Meeting the Challenges of Modern Transit through the Integration of Traditional Transit, On-Demand Micro-Transit Services and Vehicle Automation - A Case Study in Chandler, Arizona

Current technology trends of vehicle automation, electrification and on-demand transit are providing new tools to develop effective public mobility services, yet need to be balanced with traditional modes to serve the spectrum of demand effectively and efficiently. Automated vehicle transportation network company (TNC) services, better known as 'Robotaxis' are beginning to proliferate and scale across the US, with Waymo as the lead commercial entity. Chandler, AZ was the first fully automated deployment of Waymo technology. Chandler was also one of the first municipalities in Arizona to roll out micro-transit service to its citizens in 2022. At present the Chandler Flex micro-transit program is beginning to partner with Waymo to augment micro-transit services during peak demands, another first in the nation. However, the mix of services in Chandler relies not only on new technology, but also on traditional modes including fixed route transit and para-transit services. These are blended and balanced such that both old and new modes are applied within the context in which each excel. This presentation will provide background on the Chandler, AZ public mobility services, and the performance metrics that govern their use and selection within the spectrum of development and population density as well as socio-demographics within Chandler. Additionally, the behavioral response of the use of unmanned, automated vehicles employed to augment micro-transit is novel, the first in the nation - and initial feedback from public transit constituents in Chandler will be shared.

24 POWER TRANSMISSION AND DISTRIBUTION

Uncertainty quantification and sensitivity analysis of a nuclear thermal propulsion reactor startup sequence

The research presented in this article describes progress in applying stochastic methods, uncertainty quantification, parametric studies, and variance-based sensitivity analysis (also known as Sobol sensitivity analysis) to a full-core model of a nuclear thermal propulsion (NTP) system simulated via the radiation transport code Griffin to simulate neutronics. Our goal is to develop a reduced-order (surrogate) model that can be rapidly sampled with perturbations to multiple input parameters. In this NTP system, reactivity and power feedback affect the rotation of control drums (CDs), which is itself controlled by a hybrid proportional-integral-derivative (PID) controller actuated by the power demand and reactivity feedback from the numerical model. This model uses reactor kinetic feedback (mean generation time [Λ] and effective delayed neutron fraction [ β eff ] from a transient Griffin simulation executed via Griffin’s improved quasi-static solver to provide the kinetic parameters) as inputs to functions that control the CD rotation angle. By investigating numerous stochastic approaches, we developed a dual-purpose surrogate model of the NTP system, using polynomial regression in the Multiphysics Object-Oriented Simulation Environment (MOOSE) Stochastic Tools Module (STM). The trained model can be rapidly sampled while simultaneously perturbing various input parameters, such as coefficients on the PID control or temperature (directly affecting the neutron cross section). The surrogate model delivers accurate (within 5%) results at speeds orders of magnitude faster (minutes, not days of computational time) than the base model. Once the surrogate model has been trained, distributions of the uncertain parameters can be changed at will to investigate the effects of perturbing multiple inputs as well as the effects of these inputs on the model output. For example, coefficients used in the PID control system may vary due to some type of physical interference, or uncertainty may exist in the temperature of the neutron cross sections in various regions of the reactor. A distribution can be placed on these parameters, and operational boundaries can be determined. The goal of this work is to support development of an advanced control system for operating CDs in a functioning NTP system. This work is a scoping study of the MOOSE STM.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN

An Autonomous MCP Bridge to Rucio: Enhancing Data Management Accessibility for High Energy Physics

The Rucio Data Management System [1] is an important tool used by High Energy Physics experiments, including those at Fermi National Accelerator Laboratory, to store and manage exabyte-scale scientific datasets. Despite its central role in coordinating data across globally distributed storage sites, Rucio's command line interface (CLI) presents a steep learning curve, and makes it difficult for scientists to navigate through. To solve this issue, a containerized Model Context Protocol (MCP) [2] server was built that connects Large Language Models directly to Rucio, allowing AI agents to handle data tasks by using simple, natural language rather than memorized terminal commands. The core engineering focus of this project was moving the server away from slow terminal commands that require text parsing and replacing them with a native Python Client API toolset and a planned REST API framework. Moving to the Python API handles data operations directly in memory, which helps clear up formatting errors, provides the AI with clean, structured JSON data and speeds up tool execution. To prove that the system actually works, a benchmarking pipeline was also built with various questions to test the AI across four different model configurations. The questions included finding data scopes, tracking down specific datasets, and checking replication rules. Through benchmarking, early runs showed that with raw terminal text, the model would get confused and stuck, whereas switching to the Python API to feed the AI clean, structured data yielded massive improvement. By creating an intelligent and autonomous bridge to a storage network, this project shows how AI can be implemented in scientific data management, which ultimately helps scientists at Fermilab spend less time sorting through data and more time focusing on their experiments and analysis.

Akella, Kashyap [William Rainey Harper Coll.]

Infrastructure-Based Cooperative Perception at a Traffic Intersection: Overview and Challenges: Preprint

Recent advancement in autonomous driving vehicles and V2X communication has attracted increasing attention towards Intelligent Transportation Systems to build a safe and reliable traffic intersection. However, most of the systems are still at the initial stages and require significant progress to become a reality. This paper presents an overview of NREL Infrastructure Perception and Control (IPC) framework which is an open-source track-data fusion engine which takes input from infrastructure-based perception sensors and cooperatively shared messages from Connected Autonomous Vehicles (CAVs) and Connected Vehicle (CVs) and the challenges associated with deploying such cooperative perception framework at a four-way traffic intersection in the city of Colorado Springs, CO, USA. The sensor data is collected by deploying two radars and two LiDAR sensors on the IPC mobile lab and two radars on diagonally opposite traffic poles at the proposed intersection. The sensor output results imply the need for rapid sensor calibration to bring the collective perception to a common coordinate frame, the importance of time synchronization between the sensors in order to capture accurate spatial and temporal alignment of the objects, and the need for a health monitoring system with fail safe closed-loop detection model for real-time deployment.

camera

The future of subsurface monitoring: AEC’s breakthroughs in CCS technology

Carbon capture and storage (CCS) has emerged as a key solution in the fight against climate change. However, for CCS to succeed, it is crucial to ensure that the sequestered CO2 stays safely trapped underground. The U.S. Department of Energy (DOE) has emphasized the need for advancements in subsurface monitoring, measurement, reporting, and verification. Aside from caprock integrity failure, the other primary failure points usually involve defective cement in the casing annulus of wellbores or plugged and abandoned wells. In addition, many energy producers (e.g., oil and gas, geothermal) and storage and disposal operators (e.g., H2 and water) must deal with the same issue. Poorly placed or degraded cement can create pathways for gas or fluid to escape from casing annuli and in plugged and abandoned or orphan wells, posing environmental risks. Yet, a reliable and cost-effective way to monitor cement and well integrity over multiple decades is still unavailable. Traditional geophysical methods like 4D seismic imaging and surface-based electromagnetic monitoring lack the resolution and accuracy for detecting these types of failures (Vasco et al., 2022; Fawad and Mondol, 2021). Wireline logging is expensive to run continuously and is obtrusive to the operation. While fiber optics can potentially be a solution, its bulkiness can significantly compromise the cement's integrity. To address these challenges, the Advanced Energy Consortium (AEC) at The University of Texas at Austin’s Bureau of Economic Geology (the Bureau) has been pioneering research in subsurface monitoring using its portfolio of distributed autonomous microfabricated sensors for harsh subsurface environments since 2008. A class of these microsensors [System on a Chip (SoC)] can be mixed in cement and permanently placed without compromising the cement column; the sensors would then communicate with each other or a data acquisition (DAQ) master node. Another class of the AEC microsensors can be fully autonomous, with rechargeable micro-batteries capable of exceeding 100°C, flash memory, and, currently, a pressure and temperature sensor. They are designed to circulate in mud, geothermal fluids, U-loops, or pipelines. They can log data into memory and are unobtrusive to operations. Our team has been working on a multi-year DOE-funded project (DE-FE0031856)—supported by $2.95M in federal funding and $0.75M in cost-matching from the AEC—to demonstrate SoC sensor utility for CO2 leakage monitoring in CCS applications. This multi-institutional collaboration developed a novel sensing architecture utilizing radiofrequency (RF) microsensors embedded within the cement sheath. These sensors detect CO2 migration and are interrogated via a Smart Casing Collar (SCC).

58 GEOSCIENCES

Hardware-Based Demonstration of Temperature Control Functions for Reactor Systems

Establishing autonomy in reactor control systems has become essential for the expansion of nuclear technologies. Thermal regulation in particular remains crucial for maintaining stable operation and ensuring the integrity of fuel. To alleviate public skepticism of the safety of nuclear reactors, demonstrating control over this key factor is pivotal. Utilizing electric heat pads to simulate the heat released in a reactor core, thermocouples for temperature monitoring, and an Arduino micro programmable logic controller (PLC) for control, a hardware-based demonstration of a reactor heating system validates the efficacy of reactor control over this key parameter. To improve precision, a proportional-integral-derivative (PID) algorithm was implemented in the heating control loop to ensure meticulous control of reactor functions. In addition, the integration of this physical system with a digital simulator tool such as RELAP5-3D establishes a foundation for a comprehensive testing environment. This allows for a refinement of temperature control under various simulated reactor conditions, bringing another layer of reliability to the operation of the system. By facilitating a physical demonstration of reactor thermal management and control strategies, this project provides a foundation for expanded testing and educational outreach. Ultimately, this system advances the broader goal of demonstrating the safety and viability of autonomous reactor operations, contributing to public trust and future reactor deployment.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Beyond Optimization: Exploring Novelty Discovery in Autonomous Experiments

Autonomous experiments (AEs) are transforming how scientific research is conducted by integrating artificial intelligence with automated experimental platforms. Current AEs primarily focus on the optimization of a predefined target; while accelerating this goal, such an approach limits the discovery of unexpected or unknown physical phenomena. Here, we introduce a novel framework, INS 2 ANE (Integrated Novelty Score−Strategic Autonomous Non-Smooth Exploration), to enhance the discovery of novel phenomena in autonomous microscopy experimentation. Our method integrates two key components: (1) a novelty scoring system that evaluates the uniqueness of experimental results and (2) a strategic sampling mechanism that promotes exploration of under-sampled regions even if they appear less promising by conventional criteria. We validate this approach on a preacquired data set with a known ground truth comprising of image−spectral pairs. We further implement the process on autonomous scanning probe microscopy experiments. INS 2 ANE significantly increases the diversity of explored phenomena in comparison to conventional optimization routines, enhancing the likelihood of discovering previously unobserved phenomena. These results demonstrate the potential for autonomous microscopy experiments to enhance the scientific discovery by navigating complex experimental spaces to uncover novel phenomena.

Materials

Testing convolutional neural network based deep learning systems: a statistical metamorphic approach

Machine learning technology spans many areas and today plays a significant role in addressing a wide range of problems in critical domains,i.e., healthcare, autonomous driving, finance, manufacturing, cybersecurity,etc. Metamorphic testing (MT) is considered a simple but very powerful approach in testing such computationally complex systems for which either an oracle is not available or is available but difficult to apply. Conventional metamorphic testing techniques have certain limitations in verifying deep learning-based models (i.e., convolutional neural networks (CNNs)) that have a stochastic nature (because of randomly initializing the network weights) in their training. In this article, we attempt to address this problem by using a statistical metamorphic testing (SMT) technique that does not require software testers to worry about fixing the random seeds (to get deterministic results) to verify the metamorphic relations (MRs). We propose seven MRs combined with different statistical methods to statistically verify whether the program under test adheres to the relation(s) specified in the MR(s). We further use mutation testing techniques to show the usefulness of the proposed approach in the healthcare space and test two CNN-based deep learning models (used for pneumonia detection among patients). The empirical results show that our proposed approach uncovers 85.71% of the implementation faults in the classifiers under test (CUT). Furthermore, we also propose an MRs minimization algorithm for the CUT, thus saving computational costs and organizational testing resources.

Computer Science

Autonomous Electrochemistry Platform with Real-Time Normality Testing of Voltammetry Measurements Using ML

Electrochemistry workflows utilize various instruments and computing systems to execute workflows consisting of electrocatalyst synthesis, testing and evaluation tasks. The heterogeneity of the software and hardware of these ecosystems makes it challenging to orchestrate a complete workflow from production to characterization by automating its tasks. We propose an autonomous electrochemistry computing platform for a multi-site ecosystem that provides the services for remote experiment steering, real-time measurement transfer, and AI/ML-driven analytics. We describe the integration of a mobile robot and synthesis workstation into the ecosystem by developing custom hub-networks and software modules to support remote operations over the ecosystem’s wireless and wired networks. We describe a workflow task for generating I-V voltammetry measurements using a potentiostat, and a machine learning framework to ensure their normality by detecting abnormal conditions such as disconnected electrodes. We study a number of machine learning methods for the underlying detection problem, including smooth, non-smooth, structural and statistical methods, and their fusers. We present experimental results to illustrate the effectiveness of this platform, and also validate the proposed ML method by deriving its rigorous generalization equations.

Alnajjar, Anees