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At least 109 records · Page 6

Using Containers to Speed Up Development, to Run Integration Tests and to Teach About Distributed Systems

GlideinWMS is a workload manager provisioning resources for many experiments, including CMS and DUNE. The software is distributed both as native packages and specialized production containers. Following an approach used in other communities like web development, we built our workspaces, system-like containers to ease development and testing. Developers can change the source tree or check out a different branch and quickly reconfigure the services to see the effect of their changes. In this paper, we will talk about what differentiates workspaces from other containers. We will describe our base system, composed of three containers: a one-node cluster including a compute element and a batch system, a GlideinWMS Factory controlling pilot jobs, and a scheduler and Frontend to submit jobs and provision resources. Additional containers can be used for optional components. This system can easily run on a laptop, and we will share our evaluation of different container runtimes, with an eye for ease of use and performance. Finally, we will talk about our experience as developers and with students. The GlideinWMS workspaces are easily integrated with IDEs like VS Code, simplifying debugging and allowing development and testing of the system even when offline. They simplified the training and onboarding of new team members and summer interns. And they were useful in workshops where students could have first-hand experience with the mechanisms and components that, in production, run millions of jobs.

Mambelli, Marco [Fermilab] (ORCID:0000000294892681↗

Development of a second COMB dipole magnet with STAR wires

Rare-Earth Barium Copper Oxide (REBCO) coated conductors are an attractive option for application in high-field accelerator magnets due to their high critical field and the convenience of fabrication without heat treatment compared to some other superconductors. Fermilab plays a vital role in superconducting accelerator magnet R&D under the framework of the U.S. Magnet Development Program. An integral part of that program is the accelerator magnet development based on REBCO conductors to demonstrate self-fields of 5 T or greater compatible with operation in hybrid configurations to generate fields beyond 16 T for future High Energy Physics (HEP) applications. A small, two-layer REBCO dipole magnet based on the Conductor on Molded Barrel (COMB) magnet technology, developed at Fermilab with Symmetric Tape Round (STAR®) wires from AMPeers LLC was recently fabricated and tested in liquid helium, demonstrating the design feasibility. A second dipole magnet based on the same technology is currently under development at Fermilab. The coil has a 60-mm clear bore and a 120-mm OD and consists of six layers of STAR® conductor, which allows to significantly increase the magnetic field compared to the previous design, and potentially probe the 5 T self-field target. This presentation reports the progress in the magnet development.

Kashikhin, Vadim [Fermilab]↗

Hanford Tank Waste Technology Development Integration and Innovation Synergy

The Chief Technology Office (CTO) within Hanford Tank Waste Operations & Closure (H2C) identifies technology development needs and develops solutions for tank waste treatment. One key element of the technology development (TD) program is the annual Technology Development Integrated Coordination (TDIC) meeting series. The main goal of these meetings is to inform the National Laboratories and other entities of the needs identified by the end users of the technology. In turn, the meetings provide an opportunity for National Laboratories and others to provide insight into potential solutions. This dynamic facilitates dialogues that frequently identify not only new, innovative approaches, but also enhancements to ongoing technology development projects.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DEVELOPMENT AND DEMONSTRATION TESTBED FOR THE REMOTE OPERATIONS AND MONITORING OF MICROREACTORS

The nuclear industry is rapidly developing many advanced-reactor concepts for near-term deployment in both traditional and non-traditional nuclear-powered applications. One such category of advanced reactor is the microreactor, a class of reactor with less than 20MWth power output, intended for applications where the economics or logistics of traditional power sources are difficult. This includes applications such as remote communities, mining sites, defense installations, or humanitarian and disaster-relief missions. One key enabling feature for the successful deployment of microreactors is a remote operations capability. Remote operations provide monitoring and control capabilities which can significantly reduce staffing costs by eliminating the need for licensed operators at each reactor facility and improve the economic viability for microreactor deployment. A remote concept of operations is not currently an established capability in the nuclear industry. In addition, no demonstration microreactor is expected to complete construction or go critical until at least 2026. This leaves two major capability gaps: the successful demonstration of a remote concept of operations for microreactors and a test bed suitable for said demonstration. Both gaps must be addressed in order to advance the remote concepts of nuclear operation and, more broadly, microreactors themselves from paper to reality. This paper aims to fill these gaps and describes a test bed that would support development and deployment of a remote concept of nuclear operations, initial experimental results from that test bed, and the application of the test bed and experimental results for a digital-twin-based remote concept of operations underdevelopment at Idaho National Laboratory (INL). The platform chosen as a remote concept of nuclear operations test bed is the Single Primary Heat Extraction and Removal Emulator, known as SPHERE, located at INL. SPHERE is a small-scale non-nuclear test bed that emulates thermal behavior of a microreactor. The small-scale and non-nuclear nature of SHPERE limit safety concerns associated with remote operations while still providing the physical response representative of a microreactor. A network connection was added to SPHERE that enables remote-monitoring capability. This allows for real-time data streaming to networked workstations, data historians, and human-machine interfaces (HMIs). These are all critical components in a remote concept of operations, thus providing a robust development and demonstration platform. An initial experiment was performed using the SPHERE remote operations testbed. This included running a comprehensively instrumented SPHERE through a series of steady-state and transient operating scenarios in both normal and abnormal operating conditions, all while streaming live test data to a remote HMI and data warehouse. This initial experiment served three purposes: (1) characterizing the response of SPHERE, (2) demonstrating the remote connection to SPHERE, and (3) providing a baseline data set for development of a digital-twin-based remote concept of operations that is under development at INL.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DEVELOPMENT OF AN INTEGRATED SECURITY AND SAFETY MONITORING SYSTEM FOR SPENT NUCLEAR FUEL AND HIGH-LEVEL WASTE TRANSPORTATION

This paper provides an overview of the progress to date, and discussion of the path forward, related to designing, fabricating, and testing an integrated security and safety monitoring system (ISSMS) for railcars used to transport spent nuclear fuel (SNF) and high-level radioactive waste (HLW) in the United States. The system will comply with the US Department of Energy’s (DOE) Order 460.2B “Departmental Materials Transportation Management” and the Association of American Railroads’ (AAR) standard S-2043 “Performance Specification for Trains Used to Carry High-level Radioactive Material” [1] developed specifically for railcars used to transport high-level radioactive material (HLRM). DOE is in the process of developing and testing an ISSMS that will satisfy both DOE requirements and AAR standards. DOE has already developed railcar designs for transportation of HLRM. In 2024, DOE’s Atlas railcar project completed the design, fabrication and testing of three railcar types: transportation cask-carrying, buffer, and security escort, resulting in AAR conditional approval to operate on freight rail networks in North America. DOE decided to combine the required security and safety systems into one system, and this combined system is the subject of the current effort. DOE is developing and proposes to implement the ISSMS for these railcars as part of the build out of the railcar fleet. DOE began planning for development of the ISSMS in February 2020. The project is divided into seven phases starting with conceptual design and continuing through production design, as shown in Figure 1. An earlier version of the system was tested as part of the Atlas railcar consist demonstration test run in 2023. This paper describes the design features and system testing using the Atlas project railcars, and laboratory testing completed to date. The paper will also describe the activities planned to support the DOE project to ship the High Burn-Up Research Cask (HBRC) in 2027.

Schultze, Michael [ORNL] (ORCID:0000000283205671)↗

Small Signaling Peptides in Sorghum bicolor : Integrating Phylogeny and Gene Expression to Characterize Roles in Stem Development

Small signaling peptides (SSPs) are important regulators of plant growth, development, and responses to biotic and abiotic stress, yet their role in the C4 grass Sorghum bicolor is largely uncharacterized. To help fill this knowledge gap, 219 sorghum genes that encode SSPs were identified based on SSP sequences previously identified in Arabidopsis thaliana, Zea mays, Oryza sativa, Triticum aestivum , and Brachypodium distachyon . The 219 sorghum SSP-encoding genes were assigned to 19 gene families, analyzed for the presence of motifs, and aligned with genes that encode SSPs in other plants using phylogenetic analysis. Sorghum genes in 12 of the 19 SSP gene families had not been previously characterized. Expression of the 219 SSP-encoding genes in sorghum organs, during stem development, and in stem tissues and cell types revealed distinct spatial, temporal, and developmental patterns of expression. Genes associated with the SbCEP and SbRGF families were preferentially expressed in roots, whereas SbEPF genes were expressed in stem epidermal and pith parenchyma cells and panicles. The expression of genes during bioenergy sorghum stem growth and development was investigated because stems account for ~80% of harvested biomass and serve as conduits for water and nutrient transport between leaves and roots. During stem development, 28 SSP genes in several families ( CLE, EPF, CEP, GASS, PSY, ES, PSK, CAPE, POE ) were expressed at higher levels in zones of cell proliferation. For example, the TDIF homologs SbCLE41 and SbCLE42 were expressed at high levels in nascent stem nodes where they may regulate vascular bundle cambial activity and cell differentiation. A different set of 15 genes in the CIF, POE, CAPE, PSY, CEP, RALF , and CLE families were expressed at higher levels in zones of stem tissue differentiation highlighted by elevated expression of five SbRALFR s in the stem nodal plexus. Cell type–specific expression of many sorghum genes that encode SSPs was observed in fully elongated internodes indicating gene expression is regulated with high spatial resolution. Overall, the results provide a foundation of information for analysis of SSP function in sorghum that can be integrated with knowledge of sorghum gene regulatory networks to modulate traits important for production of sorghum crops.

bioenergy sorghum↗

Air quality impacts from the development of unconventional oil and gas well pads: Air toxics and other volatile organic compounds

Unconventional oil and natural gas development (UOGD) has expanded rapidly across the United States in recent decades and raised concerns about associated air quality impacts. While significant effort has been made to quantify methane emissions, relatively few observations have been made of Volatile Organic Compounds (VOCs), especially during drilling and completion of new wells. Extensive air monitoring during development of several large, multi-well pads in Broomfield, Colorado, in the Denver-Julesburg Basin, provides a novel opportunity to examine changes in local air toxics and other VOC concentrations during well drilling and completions and production. These operations offer an especially useful case to study as several management practices were implemented to reduce emissions (e.g., electrified, grid-powered drill rigs and closed loop fluid handling systems to reduce truck traffic and limit fluid handling on the pad). With simultaneous measurements of methane and 50 VOCs from October 2018 to December 2022 at as many as 19 sites near well pads, in adjacent neighborhoods, and at a more distant reference location, we identify impacts from each phase of well development and production. Use of weekly, time-integrated canisters, a Proton Transfer Reaction Mass Spectrometer (PTR-MS), continuous photoionization detectors (PID) to trigger canister collection upon detection of VOC-rich plumes, and an instrumented vehicle, provided a powerful suite of measurements to characterize both transient plumes and longer-term changes in air quality. Prior to the start of well development, VOC gradients were small across Broomfield. Once drilling commenced, concentrations of oil and gas (O&G) related VOCs, including alkanes and aromatics, increased around active well pads. Concentration increases were clearly apparent during certain operations, including drilling, coil tubing/millout operations, and production tubing installation. Emissions of C 8 –C 10 n-alkanes during drilling operations highlighted the importance of VOC emissions from synthetic drilling mud chosen to reduce odor impacts. More than 90 samples were collected of transient plumes. Using composition measurements, meteorological data, and information about well pad activities, these plumes were connected with specific UOGD operations including drilling, flowback, and production equipment maintenance. The chemical signatures of these plumes differed by operation type (e.g., C 8 –C 10 n-alkanes constituted a larger fraction of measured VOCs in drilling-related plumes). Concentrations of individual, oil and gas-related VOCs in these plumes were often several orders of magnitude higher than in background air, with maximum ethane and benzene concentrations of 79,600 and 819 ppbv, respectively. Because these plumes typically impact a monitoring site for just several minutes, they are easily missed by slower-responding instruments. Study measurements highlight future emission mitigation opportunities during UOGD operations, including better control of emissions from shakers that separate drill cuttings from drilling mud, production separator maintenance operations, and periodic emptying of sand cans during flowback operations.

54 ENVIRONMENTAL SCIENCES↗

Go slow to go fast? A review of the impacts of permitting on large-scale solar project development

State and local permitting challenges could impede the ability of large-scale solar (LSS) to meet growing electricity demand in the United States. Here, we review research that explores LSS permitting and its impacts on the pace and scale of LSS project development. Research on LSS permitting is relatively scarce, such that we support our review with research in the context of wind permitting, where appropriate. Further, few studies attempt to rigorously quantify the effects of permitting on the pace and scale of LSS project development. The available evidence allows us to identify various hypotheses and identify gaps for further research. Our review suggests that differences in permitting policies, regulations, and ordinances explain relatively little variation in LSS permitting and development outcomes across jurisdictions, except where jurisdictions implement rules designed to impede LSS. The evidence suggests LSS permitting challenges largely accrue during the implementation of permitting processes. Recent research suggests that community opposition to project development is a key driver of LSS permitting challenges, given that project opponents often use permitting processes to translate opposition into legal action. We call on future researchers to more concretely describe the LSS permitting challenge and to identify the specific actors responsible for implementing solutions.

Community opposition↗

Cell Population–resolved Multiomics Atlas of the Developing Lung

The lung is a vital organ that undergoes extensive morphological and functional changes during postnatal development. To disambiguate how different cell populations contribute to organ development, we performed proteomic and transcriptomic analyses of four sorted cell populations from the lung of human subjects aged 0 to 8 years-old with a focus on early life. The cell populations analyzed included epithelial, endothelial, mesenchymal, and immune cells. Our results revealed distinct molecular signatures for each of the sorted cell populations that enable the description of molecular shifts occurring in these populations during post-natal development. Here, we confirmed that the proteome of the different cell populations was distinct regardless of age and identified functions specific to each population. We identified a series of cell population protein markers, including those located at the cell surface, that show differential expression and distribution on RNA in situ hybridization and immunofluorescence imaging. We validated the spatial distribution of AT1 and endothelial cell surface markers. Temporal analyses of the proteome of each of the four populations revealed processes modulated during postnatal development and disambiguating results obtained on whole tissue proteome. Finally, the proteome was compared to a transcriptomics survey performed on the same lung samples to evaluate processes under post-transcriptional control.

59 BASIC BIOLOGICAL SCIENCES↗

Research and Development on Advanced Electrochemical Energy Storage Devices Enabling a Spectrum of Electrified Vehicles

The USABC Advanced Battery development plan had the following three focus areas: 1. Existing technology validation, implementation, and cost reduction 2. Identification of the next viable technology with emphasis on the potential to meet USABC cost and energy density goals. 3. Support high-risk, high-reward battery technology R&D The primary aim of this project was focused on the barriers that most impede wider public adoption of electrification in vehicles-cost, energy density, low-temp performance, calendar life, and improvements in abuse tolerance. The specific objectives are as follows: Cost Reduction: drive to significantly reduce battery cost to be in-line with the $\$$100/kWh or less (by the end of calendar year 2020) DOE cost goals. Additionally, goals of $\$$75/KWh were set for 2023 aligned with fast charge and some offset of energy density. Energy Density Increase: focus on improving the cell-level specific energy and energy densities to >350 watt hours per kilogram (Wh/kg) and >750Wh/L. Low Temperature Performance Increase: strive toward developments that improve the discharge power and eliminate or dramatically reduce the life limiting lithium plating associated with regenerative braking at low temperatures, during the program. Calendar Life Increase: drive to achieve a 15-year calendar life. Abuse Tolerance Improvement: strive to develop improvements in Li-ion abuse tolerance and/or development of electrochemical energy storage technologies with inherently better response to abuse circumstances. Emerging Areas: initiate new programs that address emerging technologies that arise during the contract period.

25 ENERGY STORAGE↗

Bench-Scale Development of Promoted High-Capacity Structured Sorbents (Final Technical Report)

The project objective was to develop high-capacity structured sorbent capable of achieving low CO 2 removal from air. The sorbent framework consists of an amine-functionalized onto hydrophobic polymer backbone with an added promoter. The functionalized amine provides high CO 2 capacity and adsorption rates and the polymer backbone to reduce water uptake. For the sorbent development, multiple functionalized amines and promoters were assessed to select a candidate that achieved high CO 2 capacity, high adsorption rate, and high stability. A sorbent-coated filter design was selected as the structured sorbent, which provides high sorbent loading capacity and contains an electrically conductive nonwoven filter substrate that can be Joule-heated to provide efficient utilization of available electricity for sorbent regeneration. A commercial partner operated a pilot filter manufacturing line to produce the filter panels coated with the developed sorbent. A 1 kg CO 2 /day bench unit was designed and fabricated to test the structured filter sorbent. The key achievements from the structured sorbent development activity were demonstrating that existing filter industrial-scale processes can be used for manufacturing Susteon’s structured sorbent and completing a proof-of-concept demonstration of the commercially manufactured structured sorbent filters for CO 2 capture from air with direct, Joule-heated regeneration. A techno-economic assessment with sensitivity analysis was conducted on a 100,000 TPY facility with 85% operating capacity. Through sorbent optimization and process design improvements, it is estimated that the cost of capture was reduced from $\$$349/tCO 2 to $\$$241/tCO 2 . The TEA projects further reductions to $165/tCO 2 through enhancements in CO 2 adsorption rate and sorbent capacity and reducing manufacturing and scale up risks. A life cycle analysis was conducted on the same 100,000 TPY facility and confirmed that the facility’s electricity demand drives its greenhouse gas impact. It was determined that electricity supplied through the current grid mix would result in net-positive CO 2 emissions and that achieving net-negative emissions is only possible by powering the system with renewable electricity or fossil fuel sources equipped with carbon capture and sequestration.

36 MATERIALS SCIENCE↗

SMR Accelerated Development Needs with Adequate Safety

The development of advanced Small Modular Reactors (SMRs) is ongoing. A customer-focused development approach requires accelerated design and analysis of the reactor system while minimizing engineering, regulatory, and economic challenges. SMRs, although not a new concept, are being considered for rapid deployment with optimized economic scalability, and several designs are currently seeking approval. Understanding the research and development needs, with adequate safety support, accelerates reactor development.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Accelerating technology development to monitor and minimize effects from land‐based wind energy on birds and bats

While wind energy is a key sector of domestic energy production for the United States, operation of wind turbines directly and indirectly adversely affects certain species of birds and bats. The cumulative effect of wind turbine strikes can have both biological and regulatory consequences, and, in some cases, delay permitting and construction or affect ongoing operations. Technology can help quantify and minimize these effects, but the pace of development, acceptance, and adoption of technological solutions is slow. Although adopting cost‐effective technologies may reduce negative effects on wildlife and help achieve both energy production and conservation goals, consensus is lacking among developers, regulators, and the conservation community regarding how to define technology effectiveness and acceptance and how to develop a standardized process for doing so. Removing barriers to technology advancement requires deviating from the status quo. Changes include 1) creating incentives to mitigate impacts, 2) establishing options for research as mitigation, 3) rethinking how research is funded, 4) increasing stakeholder coordination, and 5) increasing the efficiency of research and development. We recommend the creation of a national framework to establish clear criteria and protocols for technology evaluation and adoption.

17 WIND ENERGY↗

Lowering entry barriers to developing custom simulators of distributed applications and platforms with SimGrid

Researchers in parallel and distributed computing (PDC) often resort to simulation because experiments conducted using a simulator can be for arbitrary experimental scenarios, are less resource-, labor-, and time-consuming than their real-world counterparts, and are perfectly repeatable and observable. Many frameworks have been developed to ease the development of PDC simulators, and these frameworks provide different levels of accuracy, scalability, versatility, extensibility, and usability. Further, the SimGrid framework has been used by many PDC researchers to produce a wide range of simulators for over two decades. Its popularity is due to a large emphasis placed on accuracy, scalability, and versatility, and is in spite of shortcomings in terms of extensibility and usability. Although SimGrid provides sensible simulation models for the common case, it was difficult for users to extend these models to meet domain-specific needs. Furthermore, SimGrid only provided relatively low-level simulation abstractions, making the implementation of a simulator of a complex system a labor-intensive undertaking. In this work we describe developments in the last decade that have contributed to vastly improving extensibility and usability, thus lowering or removing entry barriers for users to develop custom SimGrid simulators.

97 MATHEMATICS AND COMPUTING↗

Automated Calibration for Rapid Optical Spectroscopy Sensor Development for Online Monitoring

An automated platform has been developed to assist researchers in the rapid development of optical spectroscopy sensors to quantify species from spectral data. This platform performs calibration and validation measurements simultaneously. Real-time, in situ monitoring of complex systems through optical spectroscopy has been shown to be a useful tool; however, building calibration models requires development time, which can be a limiting factor in the case of radiological or otherwise hazardous systems. While calibration time can be reduced through optimized design of experiments, this study approached the challenge differently through automation. The ATLAS (Automated Transient Learning for Applied Sensors) platform used pneumatic control of stock solutions to cycle flow profiles through desired calibration concentrations for multivariate model construction. Additionally, the transients between desired concentrations based on flow calculations were used as validation measurements to understand model predictive capabilities. This automated approach yielded an incredible 76% reduction in model development time and a 60% reduction in sample volume versus estimated manual sample preparation and static measurements. The ATLAS system was demonstrated on two systems: a three-lanthanide system with Pr/Nd/Ho representing a use case with significant overlap or interference between analyte signatures and an alternate system containing Pr/Nd/Ni to demonstrate a use case in which broad-band corrosion species signatures interfered with more distinct lanthanide absorbance profiles. Both systems resulted in strong model prediction performance (RMSEP < 9%). Lastly, ATLAS was demonstrated as a tool to simulate process monitoring scenarios (e.g., column separation) in which models can be further optimized to account for day-to-day changes as necessary (e.g., baseline correction). Ultimately, ATLAS offers a vital tool to rapidly screen monitoring methods, investigate sensor fusion, and explore more complex systems (i.e., larger numbers of species).

47 OTHER INSTRUMENTATION↗

Development of a micro-combined heat and power powered by an opposed-piston engine in building applications

Residential homes and light commercial buildings usually require substantial heat and electricity simultaneously. A combined heat and power system enables more efficient and environmentally friendly energy usage than that achieved when heat and electricity are produced in separate processes. However, due to financial and space constraints, residential and light commercial buildings often limit the use of traditional large-scale industrial equipment. Here we develop a micro–combined heat and power system powered by an opposed-piston engine to simultaneously generate electricity and provide heat to residential homes or light commercial buildings. The developed prototype attains the maximum AC electrical efficiency of 35.2%. The electrical efficiency breaks the typical upper boundary of 30% for micro–combined heat and power systems using small internal combustion engines (i.e., <10 kW). Moreover, the developed prototype enables maximum combined electrical and thermal efficiencies greater than 93%. The prototype is optimally designed for natural gas but can also run renewable biogas and hydrogen, supporting the transition from current conventional fossil fuels to zero carbon emissions in the future. The analysis of the unit’s decarbonization and cost-saving potential indicate that, except for specific locations, the developed prototype might excel in achieving decarbonization and cost savings primarily in US northern and middle climate zones.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Rising infrastructure inequalities accompany urbanization and economic development

Impending global urban population growth is expected to occur with considerable infrastructure expansion. However, our understanding of attendant infrastructure inequalities is limited, highlighting a critical knowledge gap in the sustainable development implications of urbanization. Using satellite data from 2000 to 2019, we examine country-level population-adjusted biases in infrastructure distribution within and between regions of varying urbanization levels and derive four key findings. First, we find long-run positive associations between infrastructure inequalities and both urbanization and economic development. Second, our estimates highlight increasing infrastructure inequalities across most of the countries examined. Third, we find greater future infrastructure inequality increases in the global south, where inequalities will rise more in countries with substantial urban primacy. Fourth, we find that infrastructure inequality may evolve differently than economic inequalities. Overall, advancing sustainable development vis-à-vis urbanization and economic development will require intentional infrastructure planning for spatial equity.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Multiomics and deep learning dissect regulatory syntax in human development

Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression1. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs or single modalities2. Here we present the Human Development Multiomic Atlas, a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and more than 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs that influence accessibility, including composite motifs exhibiting distinct syntactic constraints that are predicted to mediate transcription factor cooperativity. We identify ‘hard’ syntactic rules requiring precise motif spacing and orientation, ‘soft’ rules allowing flexible motif arrangements, and ubiquitous motifs inhibiting accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell-type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.

59 BASIC BIOLOGICAL SCIENCES↗