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DOE OSTI2024

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, in this paper, we describe and illustrate PeakQC’s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

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

Traffic intersections are crucial and challenging nodes in transportation networks where multiple lanes of vehicles and pedestrians converge. About one-quarter of traffic fatalities and about one-half of all traffic injuries in the United States happen at traffic intersections . Effective management of these intersections is important to ensure safety and efficiency of all users - vehicles, pedestrians, cyclists, and vulnerable road users (VRUs). With advancements in sensor perception technologies such as radar, light detection and ranging (lidar), and cameras, traffic intersections are developing into dynamic and data-rich environments. By using these data to create a real-time digital twin, we can enable real-time data-driven decision making and a range of applications such as sharing perception information to connected vehicles (CVs) and connected autonomous vehicles (CAVs), safety affirmative signaling, and curb optimizing to improve efficiency and enhance safety.This paper presents an overview of the concept and examines the challenges involved in implementing an infrastructure-based cooperative perception engine at a traffic intersection. In addition to outlining the physical components, this study also addresses important challenges involved in a multi-sensor system. We present results from deploying the National Renewable Energy Laboratory's (NREL's) Infrastructure Perception and Control (IPC) mobile trailer at a traffic intersection in the city of Colorado Springs, Colorado, USA that employed multiple radars and lidars to capture the data. This study provides necessary practical learning for the Cooperative Driving Automation (CDA) and traffic engineering communities for next-generation infrastructure-based cooperative perception that promises improvements in signal control for optimized traffic flow, among other applications, and documents findings for ongoing research and development efforts in other areas.

ADVANCED PROPULSION SYSTEMS,MATHEMATICS AND COMPUT↗

DOE OSTI2025

Multi-contrast machine learning improves schistosomiasis diagnostic performance

Schistosomiasis currently affects over 250 million people and remains a public health burden despite ongoing global control efforts. Conventional microscopy is a practical tool for diagnosis and screening ofSchistosoma haematobium, but identification of eggs requires a skilled microscopist. Here we present a machine learning (ML)-based strategy for automated detection ofS. haematobiumthat combines two imaging contrasts, brightfield (BF) and darkfield (DF), to improve diagnostic performance. We collected BF and DF images of urine samples, many of them containingS. haematobiumeggs, during two different field studies in Côte d’Ivoire using a mobile phone-based microscope, the SchistoScope. We then trained separate egg-detection ML models and compared the patient-level performance of BF and DF models alone to combinations of BF and DF models, using annotations from trained microscopists as the gold standard. We found that models trained on DF images, and almost all BF and DF combinations, performed significantly better than models trained on BF images only. When models were trained on images from the first field study (n = 349 patients, 748 images of each contrast), patient-level classification performance on patient images from the second study (n = 375 patients, 752 images of each contrast) met the WHO Diagnostic Target Product Profile (TPP) sensitivity and specificity for the monitoring and evaluation use case (sensitivity for all models and combinations was >75% when evaluated at a confidence score threshold that resulted in specificity >96.5%). When we used images from both field studies for the training set, performance of the models was improved. Overall, this work shows that the use of DF and BF increases the performance of ML models on images from devices with low-cost optics, while retaining the portability, power, and time-to-results of the WHO’s diagnostic TPP. DF requires no additional sample preparation and does not increase the complexity of the imaging system. It thus offers a practical means to improve performance of automated diagnostics forS. haematobiumas well as other microscopy-based diagnostics.

Infectious Diseases↗

DOE OSTI2024

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↗

DOE OSTI2025

Optimizing Traffic Signal Control to Enhance Transportation Efficiency and Maximize Pedestrian Benefits in the Road Network

Increasing urban mobility requirements demand efficient transportation system strategies for both vehicular and pedestrian movement. This study enhances the Decentralized Graph-based Multi-Agent Reinforcement Learning (DGMARL) approach, originally tailored for vehicular traffic signal timing, to incorporate pedestrian traffic dynamics. The improved algorithm considers crucial metrics such as Eco_PI, assesses vehicle fuel consumption by factoring in stops and delays, and addresses pedestrian waiting time, crucial for system efficiency while acknowledging driver waiting time impact. Utilizing Digital Twin simulation along the MLK Smart Corridor in Chattanooga, Tennessee, the algorithm's performance is compared for various pedestrian control scenarios. To evaluate the effectiveness of DGMARL, this study compared DGMARL-enabled signal management with automated pedestrian traffic detection and an actuated signal management system (real-word baseline) with pedestrian recall, which predetermingly enforces a pedestrian phase every cycle. Findings indicate substantial improvements with DGMARL, showing a 28.29% enhancement in vehicle Eco_PI, a 60.55 % reduction in pedestrian waiting time, and a 55.74% decrease in driver stop delay, on average, compared to the baseline actuated signal timing plan.

Kumarasamy, Vijayalakshmi K [The University of Ten↗

DOE OSTI2024

A Research Testbed for Experimental Connectivity and Automation in Cars

Cyber-physical systems (CPS) are engineered systems in which the computational components and physical components of the system are interdependent and deeply linked. Discovery and development of CPS technologies are changing the way people interact with engineered systems. To demonstrate this point, consider the Global Positioning System (GPS) which revolutionized personal mobility. Its research origins stem from the US Department of Defense in 1973 for military use. By 2000 limitations on civilian consumption of GPS service were lifted. Immediately, personal GPS products were shipped for in-car navigation systems. Soon after, GPS receivers were embedded into mobile phones with the introduction of the Nokia N95 and Apple iPhone for maps and turn-by-turn navigation. With the benefit of hindsight we can see that GPS has become a cornerstone technology of our daily life. Satellite-based navigation has gone from a radical space technology, to a matter of uninteresting availability; it is the typical way that people navigate through roadways now. The combination of the satellite infrastructure, the integration of receiver modules, and powerful maps applications has significantly changed mobility in the 21st century.

42 ENGINEERING↗

DOE OSTI2023

Mobile Hot Cell Digital Twin: End-of-life Management of Disused High Activity Radioactive Sources – 23598

Sealed radioactive sources are utilized for a wide range of applications across nuclear facilities, universities, hospitals, and industry. When these sources reach the end of serviceable life, they become waste. As waste, this radioactive material then goes through a process of recapture and then transfer to long term storage. With the advancement of technology in conjunction with better accessibility of technology, industries are exploring the use of digital automation to enhance productivity, efficiency, and safety while minimizing operation and maintenance costs, health and environmental risks, and uncertainty in the project life cycles. One area for exploration is the use of a digital twin to help design a robust, versatile, and safe solution for recapturing spent sources. We believe this avenue can also provide further advantages in the operations aspect of end-of-life management of spent radioactive sources by reducing the deployment time, increasing operator safety, and reducing operation & maintenance cost. We present a novel digital twin framework for end-of-life management of disused high activity radioactive sources. We have designed and developed a framework that houses a digital twin for visualizing and monitoring the recapture process to inform the engineering and design of a new Mobile Hot Cell. Furthermore, we demonstrate the feasibility of the proposed framework by providing a prototypical implementation, supporting the Mobile Hot Cell and human-machine interface's virtual replication.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2020

NLR OpenPATH™ (National Laboratory of the Rockie's Open Platform for Agile Trip Heuristics [SWR-20-73]

National Laboratory of the Rockies' Open Platform for Agile Trip Heuristics (NLR OpenPATH™) enables people to track their travel modes—by car, bus, bike, walking, etc.—and measure their associated energy use. Formerly known as e-mission, the NLR OpenPATH tool features continuous data collection and analysis via a smart phone app backed by a server and automated data processing. Its open nature enables transparent data collection and analysis while allowing for continuous improvement coupled with accessibility and adaptability by others. NLR OpenPATH empowers communities to collect and understand their own travel data while achieving place-based, locally relevant mobility goals.

Shankari, K.↗

DOE OSTI2021

Variable structure Human Intention Estimator with mobility and vision constraints as model selection criteria

Not provided.

Automation & Control Systems↗

DOE OSTI2023

Real-time control of connected vehicles in signalized corridors using pseudospectral convex optimization

Recent advances in Connected and Automated Vehicle (CAV) technologies have opened up new opportunities to enable safe, efficient, and sustainable transportation systems. However, developing reliable and rapid speed control algorithms in highly dynamic environments with complex inter-vehicle interactions and nonlinear vehicle dynamics is still a daunting task. In this paper, we develop a novel speed control method for CAVs to produce optimal speed profiles that minimize the fuel consumption and avoid idling at signalized intersections. To this end, an optimal control problem is formulated using the information of the upcoming traffic signal to adapt vehicles' speeds to avoid frequent stop-and-go driving patterns. Here, by applying the pseudospectral discretization method and the sequential convex programming method, the computational efficiency is greatly improved, enabling potential real-time on-vehicle applications. In addition, the algorithm is implemented under a model predictive control framework to ensure online control with instant response for collision avoidance and robust vehicle coordination. The proposed algorithm is verified through numerical simulations of three different traffic scenarios. The convergence and accuracy of the proposed approach are demonstrated by comparing with a popular nonlinear solver. Furthermore, the benefit of the proposed method in both traffic mobility and fuel efficiency is validated using the speed profile determined from a traffic following model in a simulation software as the baseline.

42 ENGINEERING↗

DOE OSTI2022

Automating Genetic Algorithm Mutations for Molecules Using a Masked Language Model

Inspired by the evolution of biological systems, genetic algorithms have been applied to generate solutions for optimization problems in a variety of scientific and engineering disciplines. For a given problem, a suitable genome representation must be defined along with a mutation operator to generate subsequent generations. Unlike natural systems which display a variety of complex rearrangements (e.g. mobile genetic elements), mutation for genetic algorithms commonly utilizes only random point-wise changes. Furthermore, generalizing beyond point-wise mutations poses a key difficulty as useful genome rearrangements depend on the representation and problem domain. To move beyond the limitations of manually defined point-wise changes, here we propose the use of techniques from masked language models to automatically generate mutations. As a first step, common subsequences within a given population are used to generate a vocabulary. The vocabulary is then used to tokenize each genome. A masked language model is trained on the tokenized data in order to generate possible rearrangements (i.e. mutations). In order to illustrate the proposed strategy, we use string representations of molecules and use a genetic algorithm to optimize for drug-likeness and synthesizability. Finally, our results show that moving beyond random point-wise mutations accelerates genetic algorithm optimization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Automated Transit Fleet Electrification Planning in Response to Route Dynamics, Vehicle Utilization, and Local Climate

Transit electrification is difficult, requiring the consideration of many factors including route dynamics, vehicle utilization, and local ambient temperatures. Incumbent planning tools typically rely upon static vehicle efficiency numbers which do not consider local factors specific to each fleet. This paper summarizes a collaboration between NREL and Microgrid Labs, which produced an automated sizing tool capable of producing vehicle battery and motor sizing for drop-in electrification. Furthermore, the workflow also exports the electric-vehicle supply equipment needed to support fleet electrification. The paper summarizes the model theory and includes a sample pilot study performed in support of the Via Mobility transit fleet.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2025

NEXT Generation Energy Technologies for Connected and Automated On-Road Vehicles (NEXTCAR Phase I & II)

The Ohio State University’s ARPA-E NEXTCAR project was a multi-phase, multi-year research, development, and demonstration program focused on improving the energy efficiency of connected and automated vehicles (CAVs). The team developed and validated advanced vehicle motion and powertrain control algorithms that coordinate propulsion and automation systems to optimize energy use. Key technologies included Dynamic Skip Fire engine control, predictive eco-driving functions such as Eco-Approach and Departure (Eco-AND) and Eco-Adaptive Cruise Control (Eco-ACC), and powertrain-agnostic optimization frameworks for hybrid, plug-in hybrid, and battery electric vehicles. The project successfully demonstrated up to 30% energy-efficiency improvement during real-world testing at the Transportation Research Center and the American Center for Mobility. The outcomes provide a foundation for scalable, cost-effective deployment of energy-optimized CAV technologies across the automotive industry.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Modifying Network Guided Vehicle for Repeatable EcoCAR ACC Energy Testing

The newest iteration of the Department of Energy (DOE) Advanced Vehicle Technology Competitions is the EcoCAR Mobility Challenge. In this paper, ANL and HORIBA MIRA collaborate to propose and pilot a test method that enables controlled, repeatable track-based energy consumption testing of semi-autonomous features. The testing was performed at MIRA’s proving ground facility in Nuneaton, UK, using their Network Guided Vehicle (NGV) connectivity and automation test platform. The NGV served as a repeatable lead vehicle following prescribed drive traces around two different track circuits while the host vehicle under test, a Honda Civic with full speed range Adaptive Cruise Control, followed behind. Over the course of a two day test, multiple iterations of certification and custom EPA drive traces were performed on track, demonstrating the viability of a two vehicle energy test. Results were analyzed to assess NGV lead vehicle performance in following the prescribed cycle using SAE J2951 standard calculations in an effort to quantify how repeatably and accurately the lead vehicle followed the trace. Host vehicle energy consumption was assessed using both vehicle CAN bus monitoring and an on-board fuel flow meter.

ACC↗

DOE OSTI2021

Mobile Hot Cell Digital Twin using Immersive Virtual Environment

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2021

The CanBikeCO Mini Pilot: Preliminary Results and Lessons Learned

In fall 2020, the Colorado Energy Office, as part of the State of Colorado’s “Can Do Colorado” initiative, initiated a project aimed at encouraging energy-efficient transportation during the COVID-19 pandemic. The initial mini-pilot provided e-bikes to 13 low-income households under an individual ownership model. This report assesses the impact of providing this additional mobility option on the travel behavior of participants. It also outlines the lessons learned from deploying a continuous monitoring platform to track the travel behavior. These lessons will influence the evaluation component for the full pilot, which will cover multiple geographic regions, starting in summer 2021, and run for 2 years. The continuous data collection was enabled by a customized version of the open-source e-mission platform, called CanBikeCO, configured with a behavioral gamification feature. The Colorado Energy Office used this system to collect a unique data set consisting of 3 months of partially automated travel diaries, combining sensed and surveyed data and linked with demographic information, from 12 participants. The data collection process worked well overall: users generally liked the app, appreciated the game, and did not complain about battery life. The long tracking period introduced behavioral challenges in user engagement, which we plan to address using repeated patterns and automated status checks for the full pilot. The analysis results, based on the subset of trips with user-reported labels (68%), indicate that the e-bike was the dominant commute mode share (31%), in sharp contrast to the census bicycle commute mode share (<1%). E-bike trips primarily replaced single-occupancy vehicle (SOV) trips (28%), followed closely by walking (24%) and regular bike (20%). The nonmotorized mode replacement corresponds to lower travel time and increased productivity enabled by the program. The emissions impact analysis of the program, computed using trip-level energy intensity factors, indicates savings of 1,367 lbs. of CO 2 . Although the results are strongly positive, the narrow demographic profile of study participants, their limited mobility alternatives, and nonuniform labeling indicate caution in broader interpretation. These preliminary results do suggest that such programs, supported by real-time education and support from program managers, can simultaneously meet equity and sustainability goals. The planned full pilot, addressing the data collection challenges and broadening the geographic scope, will provide additional insights into the generality of this approach.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

The CanBikeCO Mini Pilot: Procedure and Preliminary Results

In fall 2020, the Colorado Energy Office, as part of the State of Colorado's "Can Do Colorado" initiative, initiated a project aimed at encouraging energy-efficient transportation during the COVID-19 pandemic. The initial mini-pilot provided e-bikes to 13 low-income households under an individual ownership model. This report assesses the impact of providing this additional mobility option on the travel behavior of participants. It also outlines the lessons learned from deploying a continuous monitoring platform to track the travel behavior. These lessons will influence the evaluation component for the full pilot, which will cover multiple geographic regions, start in summer 2021, and run for 2 years. The continuous data collection was enabled by a customized version of the open-source e-mission platform, called CanBikeCO, configured with a behavioral gamification feature. The Colorado Energy Office used this system to collect a unique data set consisting of 3 months of partially automated travel diaries, combining sensed and surveyed data and linked with demographic information, from 12 participants. The data collection process worked well overall: users generally liked the app, appreciated the game, and did not complain about battery life. The long tracking period introduced behavioral challenges in user engagement, which we plan to address using repeated patterns and automated status checks for the full pilot. The analysis results, based on the subset of trips with user-reported labels (68%), indicate that the e-bike was the dominant commute mode share (31%), in sharp contrast to the census bicycle commute mode share (<1%). E-bike trips primarily replaced single-occupancy vehicle (SOV) trips (28%), followed closely by walking (24%) and regular bike (20%). The non-motorized mode replacement corresponds to lower travel time and increased productivity enabled by the program. The emissions impact analysis of the program, computed using trip-level energy intensity factors, indicates savings of 1,367 lbs. of CO2. Although the results are strongly positive, the narrow demographic profile of study participants, their limited mobility alternatives, and nonuniform labeling indicate caution in broader interpretation. These preliminary results do suggest that such programs, supported by real-time education and support from program managers, can simultaneously meet equity and sustainability goals. The planned full pilot, addressing the data collection challenges and broadening the geographic scope, will provide additional insights into the generality of this approach.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2025

Real-Twin

Real-Twin is a unified, model-agnostic scenario generation tool designed to streamline and standardize the evaluation of emerging mobility technologies. It provides an end-to-end framework that includes robust workflows, integrated tools, and comprehensive metrics to generate, calibrate, and benchmark microscopic traffic simulation scenarios across multiple platforms. Key Features of Real-Twin include: - Unified Scenario Generation: generate transferable, simulation-ready scenarios from heterogeneous data sources using a consistent workflow. - Automated Calibration Workflow: bridges simulation and real-world data, minimizing manual effort and making traffic simulation more accessible to researchers and engineers. - Model-Agnostic Compatibility: supports SUMO, VISSIM, and AIMSUN for cross-platform scenario generation and benchmarking. Enables reliable comparisons and reproducibility across different simulation tools. - Consistent Scenarios across Different Simulators: generate comparable simulation scenarios across different microscopic traffic simulators, providing users the ability to conduct benchmarking and cross-validation that are crucial for ensuring the reliability and reproducibility of simulation results. - Emerging Technology Support: includes a scenario database and pipeline for studying autonomous vehicles (AVs), with planned extensions to CAVs, EVs, and other advanced technologies.

Wang, Chieh (Ross) [Oak Ridge National Laboratory ↗