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DOE OSTI2025

Sequential Dosing Strategies for Controlling Selectivity and Plasma-Phase Contributions in Plasma Catalysis

Plasma-assisted catalysis has advanced in recent years, particularly for transforming stable reactants at atmospheric pressure and ambient temperature. However, achieving a deeper understanding of the many plasma and catalytic contributions remains a significant goal, as improving product yield and selectivity in plasma catalysis depends on proper catalyst selection, which is often challenging due to the complex interplay between plasma-phase and plasma-surface reactions. A sequential methodology has emerged as a means to decouple the catalyst activity from plasma-phase reactions. In this approach, nonthermal plasma is used in one step to activate and/or convert a gas phase or surface bound reactant, while in a second step, the catalyst directs product formation under steady-state or temperature-programmed conditions. This review examines studies using this technique for reactions involving N 2 , CO 2 , and SO 2 , offering insights into reaction mechanisms and catalyst behavior/selection for these transformations. These systematic studies provide a framework that can be applied to other plasma-assisted reactions. We also highlight remaining questions, propose directions for future studies, and discuss the potential of applying this methodology to other reaction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Opportunities for imaging light nuclei with a second interaction region at the Electron-Ion Collider

The upcoming Electron-Ion Collider (EIC) will address several outstanding puzzles in modern nuclear physics. Key questions—such as the partonic structure of nucleons and nuclei and the origin of their mass and spin—can be explored through high-energy electron-proton and electron-nucleus collisions. Here, to maximize its scientific reach, the EIC community has advocated for the addition of a second interaction region equipped with a detector complementary to the EIC general purpose collider detector, ePIC. The preconceptual design of this interaction region aims to provide a different configuration from the first interaction region, which enhances forward acceptance at very small scattering angles (𝜃 ∼0 mrad). This machine configuration would significantly benefit exclusive, tagging, and diffractive physics programs, complementing those of the ePIC experiment. In particular, accessing coherent diffractive processes on light nuclei by tagging of the full, intact nucleus is essential for mapping their spatial parton distributions. In this work, we present an exploratory study of the detection capabilities for light nuclei at a second EIC interaction region, with a detailed discussion of the accessible kinematic phase space and its implications for imaging.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

RxnRover/CyRxnOpt

CyRxnOpt aims to provide a single software interface to various optimization algorithms, mainly designed for chemical process optimization applications. CyRxnOpt generalizes the optimization process into four high-level “phases”: Installation, Configuration, Training, and Prediction. This allows developers to program to a general interface for each phase of the optimization, simplifying the development of user-friendly tools to lower the barrier of entry into chemical process optimization, especially for automated laboratory workflows which can greatly benefit from access to various optimization techniques. It is also designed so researchers can easily add new or existing algorithms into existing workflows in a user-friendly manner.

Kulathunga, Dulitha Prasanna [Iowa State Universit↗

DOE OSTI2025

A control-inspired approach for energy transition planning under uncertainty

As the global carbon footprint continues to grow, many countries are implementing carbon emission reduction policies which have incentivized the expansion of low-carbon and renewable technologies. However, the speed and scale of deployment falls short of that needed to meet climate goals. Energy system models serve as key tools for guiding investment decisions and helping policymakers evaluate the effects of various policies on the development of an energy system. This study focuses on the energy system of the United States and builds upon prior work by incorporating more geographic granularity to account for the trade of commodities and addresses transmission congestion through electricity price adjustments. Furthermore, real-world characteristics, such as delays in constructing new liquid fuel production and electricity generation facilities, are integrated using a sequential decision-making approach that better reflects how decisions can be updated as uncertainties unfold. Results demonstrate that stochastic programming combined with sequential decision-making produces energy transition pathways that are robust to multiple uncertain futures. Additionally, considering real-world characteristics significantly impacts the deployment of renewable technologies and the ability to meet carbon emission reduction goals while also reliably meeting demand. These findings highlight the importance of accounting for uncertainty and real-world characteristics to avoid overly optimistic projections in energy system planning.

energy systems↗

DOE OSTI2026

2026 Annual Molten Salt Reactor Campaign Review

This report documents the 2026 Annual Molten Salt Reactor (MSR) Campaign Review held in Albuquerque, New Mexico, from April 21–24, 2026. The review was organized by Dr. Patricia Paviet, National Technical Director of the Advanced Reactor Technology (ART) MSR program for the U.S. Department of Energy Office of Nuclear Energy (DOE-NE), and included participation from principal investigators, federal managers, developers, regulators, and members of the broader MSR community. The 2026 review expanded beyond the ART-MSR campaign to include related DOE-NE programs supporting molten salt reactor advancement, including the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the Advanced Materials and Manufacturing Technologies (AMMT) program, Advanced Reactor Safeguards and Security (ARSS), Material Protection, Accounting and Control Technologies (MPACT), and relevant advanced fuels activities. Three days were dedicated to technical presentations and panel discussions covering thermal properties, off-gas management, modeling and simulation, safety and licensing, safeguards and security, materials and corrosion, and irradiation activities. A fourth day was dedicated to technical tours of Sandia National Laboratories and Kairos Power facilities. Attendance was strong and comparable to the prior annual review, with approximately 75 in-person participants per day, 75–80 virtual attendees per day, and approximately 30 participants in the tour day. The review fostered significant technical exchange across national laboratories, universities, industry, regulators, and international participants. This report summarizes the review structure, technical themes, participation, tours, feedback, and conclusions relevant to future planning for the MSR campaign.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Programmed synthesis of mesoporous protein crystals in cellular reactors

Protein crystals are naturally derived mesoporous materials with versatile structures and physicochemical properties. Here we introduce an intracellular synthesis platform that enables controllable and programmable protein crystallization. In live cells, we show that, after initial nucleation, steady protein expression governs crystal growth, yielding predictable, tunable dynamics in live cells. Exploiting this feature, we combined HaloTag and click chemistries to achieve modular, programmable immobilization of diverse guest materials with spatial patterning down to ~100 nm resolution. We further demonstrated the sequential release of immobilized materials in physiologically relevant fluids. As a proof of concept, we programmed particles to carry human fibroblast growth factors in distinct layers, which elicited designed oscillatory Akt signalling patterns in cell culture. Finally, this work outlines a programmable method for producing mesoporous materials, with possible applications in catalysis and biomedicine.

Yang, Hongru [Johns Hopkins Univ., Baltimore, MD (↗

DOE OSTI2025

Optimizing Power Line Undergrounding Decisions under Varying Wildfire Risk and Weather Scenarios

Abstract—The threat of wildfire ignitions from electric power equipment has led utilities to increasingly turn to preemptive power shutoffs, which, while effective in reducing grid-induced wildfire risk, can cause significant load loss. Undergrounding power lines is an alternative strategy for preventing grid-induced wildfires. However, undergrounding lines is costly, so an efficient undergrounding plan must balance reductions in wildfire risk and load loss with the cost of undergrounding lines. We propose a robust optimization model to identify which power lines to underground to maximize load served while limiting wildfire risk across a range of wildfire risk and weather scenarios. Since solving this problem may be computationally heavy for large power grids and many operating scenarios, we present a delayed constraint generation algorithm to iteratively add scenarios until an optimal solution is found. We evaluate the performance of this framework on the RTS-GMLC with scenarios representing a year of operating conditions and compare it with a stochastic programming formulation. Our results indicate that our undergrounding model is successful in reducing load shed and risk compared to baseline cases in which no mitigation action is taken and only power shutoffs are implemented (no undergrounding). The robust formulation also reduces more load shed than the stochastic formulation in the most extreme scenarios. Index Terms—grid resilience, optimization, transmission systems, underground power lines, wildfire risk.

Taylor, S. [Department of Electrical and Computer ↗

DOE OSTI2025

Privacy-Protected Simultaneous Provision of Energy and Primary Frequency Control Reserve

This paper investigates a Mixed Integer Linear Programming (MILP) model for simultaneous scheduling of energy and primary frequency control reserve. Given the model’s unique structure and growing concerns about privacy, we adopt Dantzig-Wolfe Decomposition (DWD) algorithm to solve the problem in a decentralized fashion while obfuscating the privacy of the energy and reserve resources. Additionally, we present a novel criterion for checking the model’s feasibility. Finally, simulation results are given and discussed.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

3D modeling of the Staged Z-pinch with the FLASH code

The Staged Z-pinch (SZP) fusion concept is a magneto-inertial compression scheme developed by Magneto-Inertial Fusion Technologies, Inc. (MIFTI), in which small amounts of fusion fuel are brought to fusion-relevant conditions by passing multi-million amperes strong current through a cylindrical shell of high atomic number material. One- and two-dimensional modeling performed by MIFTI with the MACH2 code, suggests that net fusion energy gain can be achieved when currents in the 10 million amperes range compress a 50%-50% mixture of deuterium and tritium gas. In this project we enhance and use the FLASH code to execute high-fidelity, simulations of various SZP configurations, a collaboration between the Flash Center for Computational Science at the University of Rochester and the Laboratory for Laser Energetics, and MIFTI. FLASH is a high-performance computing, multi-physics, radiation magnetohydrodynamic (MHD) code with extended physics capabilities, which is developed at the Flash Center. The goal of this project is to assess the shell/fuel stability of the pinch to two- and three-dimensional MHD instabilities and to utilize FLASH’s extended physics capabilities to understand how extended-MHD effects impact implosion dynamics and plasma conditions at stagnation. The project is a natural extension of an ongoing collaborative effort between MIFTI and the Flash Center through the U.S. DOE Advanced Research Projects Agency-Energy (ARPA-E) BETHE program and can provide MIFTI with simulation capabilities that are currently beyond their reach with MACH2. Ultimately, MIFTI wants FLASH to become one of their simulation workhorses for reliable, high-fidelity SZP platform design. During the project, the Flash Center team developed a suite of in one- and two-dimensional FLASH simulations to model different variants of the SZP platform, performed code-to-code comparisons with MACH2, and used the FLASH code to design and model SZP experiments like the Double Eagle experiments that MIFTI recently performed. Also, the Flash Center team developed the capabilities of FLASH to be able to do three-dimensional simulations of pulsed-power experiments with the code for the first time. Two publications from this effort are currently under review and two more are in preparation. MIFTI has also committed to the use of FLASH for future SZP simulation efforts.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Phenomenological opportunities at the EIC

This review presents a comprehensive overview of key phenomenological opportunities at the future Electron–Ion Collider (EIC), synthesizing discussions and collaborative research efforts developed within the Korean EIC community and the EICφ collaboration. We explore a diverse range of physics topics central to the EIC scientific program, including the multidimensional tomography of nucleon and nuclear structure, precision Quantum Chromodynamics studies through jet physics and event-shape observables, heavy quarkonium production as a probe of partonic dynamics, and the spectroscopy of exotic hadrons. Furthermore, we discuss the transformative potential of emerging technologies—specifically Machine Learning and Quantum Computing—as essential tools for addressing the computational challenges and maximizing the scientific discovery potential of the EIC era.

Electron–Ion collider↗

DOE OSTI2026

Data for KETCHUP: Parameterizing of Large-Scale Kinetic Models Using Multiple Datasets with Different Reference States

Repository for Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP can use K-FIT [2] input files. Example K-FIT input files are located in the K-FIT repository at https://github.com/maranasgroup/K-FIT.

Metabolomics↗

DOE OSTI2024

Perform Design Support with MCNP for New Measurements

This report incorporates our work carried out during our 5-month internship at LANL under an internship agreement with EAMEA (École des Applications Militaires de l’Énergie Atomique). After outlining the context in which we worked, we present our work as aid to modeling and predicting the neutronic behavior of nuclear systems, with a view to carrying out criticality experiments qualifying the MCNP code as part of innovative projects. Fourth generation reactors will enable to tackle a lot of issues such as environmental crisis, affordable energy access, and nuclear waste management. They seem to be one of the keys for a sustainable future. Most of the projects that emerge nowadays include the use of HALEU (high assay low enriched uranium) or MOX recycled fuels. Our projects are part of this dynamic and addresses concrete scientific research issues in the nuclear field. Studies of HALEU package are essential to anticipate the need, therefore the Optimus L (OPTImal Modular Universal Shipping cask technology) designed by NAC (Nuclear Assurance Corporation) international but filled with 20 % enriched uranium dioxide (UO 2 ) will be studied to support safe transportation. However, it seems there is no benchmark with a high correlation with the combination of this fuel and this package to validate MCNP simulations. As such, the study will focus on the development of new criticality safety benchmarks for this case. On the other hand, there is a great need for critical benchmarks in the intermediate energy range with MOX fuel. An IER (Integral Experiment Request) has then be requested to answer it through a partnership between French institution IRSN and U.S. Department of Energy's Nuclear Criticality Safety Program (NCSP). This experience planned for 2025 requires to gather calculated data through a MCNP model to be realized safely. Finally, a presentation of our one-week experience at the DAF as part of our discovery of criticality experiments will be introduced in Appendix 1: Week at the DAF (Device Assembly Facility)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Molecular concentration field design using closed-form steady-state solutions

Control over spatial concentration fields represents a fundamental challenge in designing synthetic biological systems and programmable soft materials. While nature creates morphogen gradients that orchestrate complex developmental processes, synthetic approaches have largely relied on empirical optimization and computationally intensive simulations. Here, we present an analytical framework for steady-state concentration fields generated by finite-sized localized sources in diffusion–degradation systems and derive closed-form solutions for one-, two-, and three-dimensional geometries. By expressing these solutions in dimensionless form, we show that gradient steepness and spatial structure are organized by the Thiele modulus, which captures the competition between diffusion and degradation length scales. The analysis reveals distinct design regimes: in degradation-dominated systems, gradient shape is governed by exponential decay and becomes dimension-independent, whereas in diffusion-dominated systems, gradient magnitude and extent follow dimension-dependent power-law scaling. Building on these results, we introduce a quantitative design strategy that uses threshold-based criteria to program concentration ranges by tuning physically accessible parameters, most directly the production rate, while holding transport and degradation properties fixed. Comparisons with numerical solutions and reported experimental systems demonstrate consistency with the predicted scaling behavior. Together, this work provides a generalizable and physically transparent framework for designing steady-state concentration fields in synthetic biological and soft matter systems, enabling predictive control of gradient-mediated organization without reliance on extensive numerical optimization.

Kim, Dong Woo [Johns Hopkins University, Baltimore↗

DOE OSTI2026

Ornamental origins and genomic frontiers: a review of big-bracted dogwood research

The big-bracted (Benthamidia) dogwood clade consists of small- to medium-sized deciduous trees within the genus Cornus, known for their showy spring-time floral bract display. Cornus is within the family Cornaceae and order Cornales, and as Cornales is one of the earliest diverging asterids, these taxa have been important for phylogenetic research. Three species within the big-bracted clade, flowering (Cornus florida), kousa (C. kousa), and Pacific (C. nuttallii) dogwoods, are popular ornamental landscape plants in North America, with more than 130 cultivars released. Despite their commercial popularity, numerous research gaps have limited the expansion of fundamental research and dogwood breeding programs. In this present review, we aim to provide a thorough overview of our current understanding of 1) the phylogenetic and biogeographic context, 2) plant biology and major pests and pathogens impacting commercialization, 3) historical commercialization and propagation methods, and 4) genetic and genomic resources and how they have been implemented to understand these species. Research gaps and future directions to advance basic research and breeding of big-bracted ornamental dogwoods are discussed throughout.

Cornus florida↗

DOE OSTI2026

PACT Center: Perovskite PV Accelerator for Commercializing Technologies (Final Technical Report)

The Perovskite PV Accelerator for Commercializing Technologies (PACT) center was established in July 2021 as a national resource to accelerate the commercialization of perovskite photovoltaic (PV) technology in the United States. Since its inception, PACT has been led by Sandia National Laboratories (Sandia) in partnership with the National Laboratory of the Rockies (NLR), formerly known as NREL. From FY20-FY23, Los Alamos National Laboratory (LANL), CFV Labs, Black & Veatch (B&V), and the Electric Power Research Institute (EPRI) were part of the project team. LANL brought expertise in perovskite PV device designs and processing, CFV Labs (now GroundWork Renewables) provided initial indoor and outdoor measurement hardware technology, B&V led the initial effort on perovskite PV bankability, and EPRI worked on reviewing testing standards, identifying commercialization gaps, and helping to run PACT’s Industry Advisory Board, a group including representatives from commercial testing labs, independent engineering firms, insurance companies, state regulators, and electric utilities. To source perovskite PV module samples, PACT contracted with the University of North Carolina (UNC), the University of Toledo, the University of Washington, and SLAC/Stanford University to provide a steady stream of research-grade perovskite mini modules, enabling protocol development in advance of commercial module availability. The project period ran from July 1, 2021, through December 31, 2025, including a No Cost Extension. Starting in FY25, the project was continued as a Core Capability in the Lab Call portfolio and continues at a reduced budget with only Sandia and NLR as funded recipients. Notably, starting in FY25 PACT expanded its scope beyond MHP modules to accept all emerging PV mini module technologies for testing, including organic PV (OPV) and all-thin-film tandems, with the aim of supporting commercialization across the broader emerging PV ecosystem. With this change in scope the program was renamed the PV Accelerator for Commercializing Technologies, dropping perovskite from the name.

14 SOLAR ENERGY↗

DOE OSTI2026

UCB-GLOBES: An open-access mass spectral database of identified and unidentified atmospheric organic compounds

Chemical characterization of atmospheric organic aerosols using gas chromatography with 70 eV electron ionization mass spectrometry (GC/EI-MS) has been used for decades in advancing molecular marker detection and identification, though primarily through suspect screening and/or targeted analyses. To advance non-targeted analyses of environmental samples, we have catalogued approximately 27 000 mass spectra (MS) of the trimethylsilyl derivatives of semi-volatile organic aerosol (OA) analytes in the open-access University of California Berkeley Goldstein Library of Organic Biogenic Environmental Spectra (UCB-GLOBES). Analytes were observed in ambient samples from the U.S. and the Central Amazon and/or laboratory simulations of secondary OA (SOA) formation. These samples are representative of OA under urban and biomass burning influences as well as SOA derived from biogenic precursors (e.g., isoprene, monoterpenes, sesquiterpenes) and biomass burning intermediates. MS are documented in UCB-GLOBES without regard to known chemical identity, annotated with extensive metadata such as sample source/experimental conditions, any structural information gained from MS analyses, and predicted chemical properties such as average carbon oxidation state and carbon number. UCB-GLOBES MS are compatible for importing into the NIST MS Search program, and we have also provided a Jupyter Notebook for MS visualization and comparisons. We demonstrate the utility of UCB-GLOBES through MS reanalyses of prior analytes observed in ambient data, finding a 20 % reduction in the number of analytes assigned to OA source categories reliant solely on time series correlation and an overall 11 % increase in new MS-based OA source categorization for the Southeast U.S. For 1513 analytes observed previously in the Central Amazon, we found 375 MS matches using UCB-GLOBES vs. 136 MS matches during prior analyses, representing a 14 % gain in newly confirmed or newly categorized OA species. While OA from laboratory oxidation experiments in UCB-GLOBES are highly diverse chemically, on average only 29 % of UCB-GLOBES MS have a mass spectral match to another MS entry in UCB-GLOBES and/or in databases of known compounds (i.e. NIST MS Database, Adams Essential Oil, MANE Flavor and Fragrance Company). This indicates that roughly 70 % of UCB-GLOBES MS are unique thus far, not observed more than once among the laboratory oxidation samples and ambient data in UCB-GLOBES MS. Further, only 18 % can be positively identified using these databases or known authentic standards. This points to a large gap between these laboratory simulations and ambient OA. Overall, the UCB-GLOBES database can be utilized for improving confidence in OA source categorization and/or identification, novel chemical marker discovery, tracking chemical diversity, de novo structure and properties prediction, and improving MS search and matching algorithms. This can ultimately inform future research priorities for the chemical characterization of atmospheric organic samples.

Mass spectrometry↗

DOE OSTI2026

CHESS 2025: Spectrometer orthorectified at-sensor radiance from NEON AOP imaging spectroscopy surveys

This dataset provides Level 1 (L1) orthorectified at-sensor radiance derived from measurements collected by the Imaging Spectrometer-1 (NIS-1) onboard the NEON (National Ecological Observatory Network) Airborne Observation Platform (AOP) for the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS). NIS-1 captures light reflected from the Earth’s surface in 426 discrete wavelength bands as raw digital numbers (DNs; Level 0). These data are then calibrated to physical units (uW/cm²·sr·nm) following the processing steps described in the NEON Imaging Spectrometer Level 1B Calibrated Radiance Algorithm Theoretical Basis Document (ATBD; Gallery 2022). The data delivered here are the primary inputs for the surface reflectance product in “Custom surface reflectance, shade masks, and equivalent water thickness maps for the Colorado Headwaters Ecological Spectroscopy Study” (Carroll et al. 2026). For intertemporal comparison, the radiance data here are most directly relatable to the v2 radiance data in “NEON AOP Imaging Spectroscopy Survey of Upper East River Colorado Watersheds: Raw-Space Radiance and Observational Variable Dataset” (Goulden et al. 2018), to which the same processing methodology was applied. Together, the radiance and reflectance data enable users to exploit the unique reflection signatures of different surface objects for land cover classification, foliar trait mapping, plant vigor assessment, water content estimation, trace-element identification, and other scientific applications. The data were acquired over three study domains in the Upper Gunnison river basin: the upper East River watershed (CRBU); Almont Triangle and Taylor Canyon (ALMO); and Upper Taylor River watershed (UPTA) between 2025-06-13 and 2025-07-15. Within each domain, data are delivered by flightline as orthorectified and calibrated hyperspectral rasters in Hierarchical Data Format version 5 (HDF5) format, with radiance values provided in uW/cm²·sr·nm on a fixed, uniform Universal Transverse Mercator (UTM) grid at 1 meter spatial resolution. The radiance rasters include all 426 NIS-1 spectral bands, along with associated quality-assurance (QA) and diagnostic and ancillary layers needed for atmospheric correction workflows. Orthorectified radiance is produced from pushbroom spectrometer observations by applying NEON’s radiometric calibration (including bad pixel masking, dark subtract, dark pedestal shift correction, electronic panel ghost correction, grating ghost correction, deblur correction and flat-fielding) and spectral calibration (using spectral response function band centers and full-width at half-maximum intensity), followed by geolocation and regridding to the fixed grid. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

DOE OSTI2026

Navigating Large Chemical Spaces Using Graph Theory and Integer Programming

Navigating and analyzing large chemical spaces are necessary to accelerate the design and discovery of new molecules and chemical processes. In this work, we introduce a computational framework that integrates graph theory and integer programming to enable the efficient navigation of large chemical spaces. Our framework represents the chemical space as a graph, wherein nodes represent molecules and edges represent the degree of similarity or connectivity based on domain-specific information. Using the graph representation, we identify representative molecules by computing the so-called minimum dominating set (MDS), which in our context is the minimum set of molecules that is connected to all other molecules. We present a suite of solution strategies for the MDS problem including heuristic and rigorous integer programming (IP) approaches. We show that these approaches allow us to capture physicochemical properties and domain-specific logic and constraints, facilitating the identification of molecules with the target properties. We demonstrate the effectiveness of the proposed approach by navigating the chemical space of per- and polyfluoroalkyl substances (PFAS); this comprises approximately 15,000 molecular structures. We compare our framework against traditional dimensionality reduction and clustering methods such as t-SNE and K-means clustering.

Chemical structure↗