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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 163 records · Page 9

Restricted Partition Function Semiclassical Transition State Theory (RPF-SCTST): Applications to Reactions Involving Hydrogen Cyanide, Hydrogen Peroxide, and Formaldehyde Oxide

We demonstrate the efficiency of the numerical calculation of thermal semiclassical transition state theory (SCTST) rates across several representative chemical reactions using the restricted partition function (RPF)─viz a function that depends only on the imaginary action associated with a reaction. Here, we treat the potential energy surfaces (PESs) through fourth order expansions around the saddle point and integrate the Hamiltonian up to second order in employing vibrational perturbation theory. We apply this formalism to uni- and bimolecular reactions with different─though relatively high─barrier heights to uncover the influence of the barrier properties, minimal energies, and separability of the rotational motion on rate constants and tunneling corrections. Although all modes are coupled within the RPF, we found in our numerical examples that the rotational component in the absence of significant rotational distortions can be separated from the vibrational contributions. Moreover, a classical treatment of the rotational contribution is adequate over the temperature range from approximately 100 to 1000 K. We also found that the choice of DFT basis set can lead to variations in rate constants of up to an order of magnitude. Lastly, different schemes for counting eligible energy levels result in rate constants that differ by no more than a factor of 2, with the remaining discrepancies attributed to the treatment of near-convergent levels in perturbation theory.

74 ATOMIC AND MOLECULAR PHYSICS↗

Development of a Host-Based Intrusion Detection and Control Device for Industrial Field Control Devices

Industrial control systems contain a multitude of devices deployed into the field to observe and control a physical process. Currently, most of these devices lack common host-based cybersecurity features, which can lead them to be seen as vulnerable targets. The Cymbiote device was developed to address this problem by examining multiple streams of data to determine what might indicate a potential threat, and to evaluate and execute appropriate response actions. This paper discusses the evolution of the Cymbiote device in response to evaluation and testing done on real-world hardware. Experimental results are discussed, as are the new developments that have been made to the device in response to the findings. In addition, we describe future research directions for this approach along with the experimental setup changes in response to the requirements for statistical rigor.

Rice, Theora R.↗

Performance Assessment for the Disposal of Low Level Waste in the 200 East Area Burial Grounds (FY2019 Annual Status Report)

This annual review provides the projected dose estimates of radionuclide inventories disposed in the 200 East Area Low-Level Waste Burial Grounds (LLBGs) since September 26, 1988. These estimates are calculated using the original dose methodology developed in the performance assessment (PA) analysis (WHC-SD-WM-TI-730) and are compared with U.S. Department of Energy requirements (DOE O 435.1 and performance objectives defined in companion documents DOE M 435.1 and DOE-STD-5002-2017). All performance objectives are currently satisfied, and operational waste acceptance criteria (HNF-EP-0063) and waste acceptance practices continue to be sufficient to maintain compliance with performance objectives. Inventory estimates and associated dose estimates from future waste disposal actions are unchanged from previous years’ evaluations, indicating that potential impacts are well below performance objectives; therefore, future compliance with DOE O 435.1 is expected. A new PA study has been initiated in this fiscal year (FY) 2019 for evaluation of active disposal sites within the 200 West and East Areas (Trenches 31 and 34 in 200 West; Trench 94 in 200 East) because extended time has elapsed between the current annual status report and the original PA (WHC-SD-WM-TI-370) for the active disposal sites. The new PA for the active disposal sites is expected to be completed in FY 2021.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Performance Assessment for the Disposal of Low Level Waste in the 200 West Area Burial Grounds (FY2019 Annual Statius Report)

This annual review provides the projected dose estimates of radionuclide inventories disposed in the active 200 West Area Low-Level Waste Burial Grounds (LLBGs) since September 26, 1988. These estimates are calculated using the original dose methodology developed in the performance assessment (PA) analysis (WHC-EP-0645) and are compared with performance objectives defined in U.S. Department of Energy requirements (DOE O 435.1 and its companion documents DOE M 435.1-1 and DOE-STD-5002-2017). All performance objectives are currently satisfied, and operational waste acceptance criteria (HNF-EP-0063) and waste acceptance practices continue to be sufficient to maintain compliance with performance objectives. Inventory estimates and associated dose estimates from future waste disposal actions are unchanged from previous years’ evaluations, indicating that potential impacts are well below performance objectives; therefore, future compliance with DOE O 435.1 is expected.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Annual Status Report (FY 2020): Performance Assessment for the Disposal of Low Level Waste in the 200 East Area Burial Grounds

This annual review provides the projected dose estimates of radionuclide inventories disposed in the 200 East Area Low-Level Waste Burial Grounds (LLBGs) since September 26, 1988. These estimates are calculated using the original dose methodology developed in the performance assessment (PA) analysis (WHC-SD-WM-TI-730). The estimates are compared with requirements of DOE O 435.1 Chg 1 and performance objectives defined in companion documents DOE M 435.1-1 Chg 1and DOE-STD-5002-2017). All performance objectives are currently satisfied, and operational waste acceptance criteria (HNF-EP-0063) and waste acceptance practices continue to be sufficient to maintain compliance with performance objectives. Inventory estimates and associated dose estimates from future waste disposal actions are unchanged from previous years’ evaluations that indicate potential impacts well below performance objectives; therefore, future compliance with DOE O 435.1 Chg 1 is expected. A new PA study was initiated in fiscal year (FY) 2019 for evaluation of active disposal sites within the 200 East and 200 West Areas (Trench 94 in 200 East; Trenches 31 and 34 in 200 West) due to extended time elapsing between the current annual status report and the original PA for the active disposal sites. The new PA for the active disposal sites is expected to be completed in FY 2021. Within the active burial grounds in the 200 East Area, low-level waste and mixed low-level waste will continue to be disposed of in the dedicated U.S. Navy reactor compartment trench at the 218-E-12B Burial Ground (Trench 94). During this reporting period (FY 2020, from October 1, 2019, through September 30, 2020), two reactor compartments were disposed in Trench 94. Results from sorption experiments are summarized for this reporting period to quantify the efficacy of concrete waste forms in retaining key radionuclides (e.g., technetium-99 and iodine-129). The test durations ranged from 1 to 3 months. Continued groundwater monitoring of the 200 East Area LLBGs indicates no groundwater contamination due to LLBG waste. Current assumptions about future land use at the Hanford Site are consistent with PA analysis1 assumptions of a post-closure facility that will not be degraded by human activity. The LLBGs are located in an area identified for waste management and containment of residual contamination. This area will remain after final environmental remediation and the proposed shrinkage of Hanford Site boundaries to small sections within the 200 East and 200 West Areas in the Central Plateau (DOE/EIS-0391). The current closure plan for the LLBGs (DOE/RL-2000-707) estimates that the 200 East LLBGs will be closed in the 2050 timeframe. The Disposal Authorization Statement, other technical basis documents, and the radioactive waste management basis are of continued adequacy to meet the performance objectives of DOE O 435.1 Chg 1. Overall, there are no substantive changes to primary PA assumptions nor the PA analysis conclusion; therefore, compliance with DOE O 435.1 Chg 1 and the Disposal Authorization Statement is maintained.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Performance Assessment for the Disposal of Low-Level Waste in the 200 East Area Burial Grounds (Annual Status Report FY 2022)

This annual review provides the projected dose estimates of radionuclide inventories disposed in the 200 East Area Low-Level Waste Burial Grounds (LLBGs) since September 26, 1988. These estimates are calculated using the original dose methodology developed in the performance assessment (PA) analysis (WHC-SD-WM-TI-730). The estimates are compared with the performance objectives defined in U.S. Department of Energy requirements (DOE O 435.1 and its companion documents DOE M 435.1-1 and DOE-STD-5002-2017). All performance objectives are currently satisfied, and operational waste acceptance criteria (HNF-EP-0063) and waste acceptance practices continue to be sufficient to maintain compliance with performance objectives. Inventory estimates and associated dose estimates from future waste disposal actions are unchanged from previous years’ evaluations that indicate potential impacts well below performance objectives; therefore, future compliance with DOE O 435.1 is expected.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Performance Assessment for the Disposal of Low-Level Waste in the 200 West Area Burial Grounds (Annual Status Report FY 2021)

This annual review provides the projected dose estimates of radionuclide inventories disposed in the active 200 West Area Low-Level Waste Burial Grounds (LLBGs) since September 26, 1988. These estimates are calculated using the original dose methodology developed in the performance assessment (PA) analysis (WHC-EP-0645). The estimates are compared with the performance objectives defined in U.S. Department of Energy requirements (DOE O 435.1 and its companion documents DOE M 435.1-1 and DOE-STD-5002-2017). All performance objectives are currently satisfied, and operational waste acceptance criteria (HNF-EP-0063). and waste acceptance practices continue to be sufficient to maintain compliance with performance objectives. Inventory estimates and associated dose estimates from future waste disposal actions are unchanged from previous years’ evaluations that indicate potential impacts well below performance objectives; therefore, future compliance with DOE O 435.1 is expected.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Technical Specification Surveillance Interval Extension Using Self-Diagnostics

As part of the Light Water Reactor Sustainability program, an ongoing research effort is being conducted on technical specifications surveillance interval extension of digital equipment in nuclear power plants. The research team is led by Idaho National Laboratory and includes Pacific Northwest National Laboratory, Technology Resources, and Oak Ridge National Laboratory. This research focuses on developing methods for applying the U.S. Nuclear Regulatory Commission (NRC)–approved guidance to implement a licensee-controlled, risk-informed surveillance frequency change program in digital instrumentation and control (I&C) systems that include self-diagnostics and online monitoring (OLM) capabilities. Although approved methods exist for extending technical specifications (TS) surveillance test intervals (STIs) for general equipment, including analog I&C equipment, gaps remain in technology and guidance on crediting newer digital equipment’s internal self-diagnostics and OLM characteristics. Previous research described a general methodology for crediting internal self-diagnostics for extending surveillance test intervals. The methodology used self-diagnostics to detect—and credited recovery from—failure. Self-diagnostics were also applied for performance monitoring during the extended surveillance interval. This report discusses the status of recent activities to evaluate the previously developed methodology using a pilot study. Although both a utility partner for a pilot study and a specific digital asset were identified in FY2020, delays in obtaining proprietary information resulted in a limited ability to fully evaluate the methodology, and further interactions were complicated by the COVID pandemic. Therefore, at that time, the use of public-domain information—along with current processes for surveillance interval extension through a surveillance frequency control program—identified the need to fully assess diagnostic coverage as part of the pilot study. Furthermore, self-diagnostics were also identified as a potential option to replace the drift analyses conducted as part of current STI extension procedures. In FY2022, the project was reconstituted with the industry partner, and information and data were made available by the industry partner to the research team for review. The shared information included failure event descriptions and data for a digital I&C system since its implementation, as well as recent STI extension interval reports developed by the utility partner on that digital I&C system. This report presents an evaluation of this information and data and describes an application of the proposed methodology cited above. The methodology seeks to take advantage of the self-diagnostics and OLM capabilities to reduce risk or reduce the level of qualitative monitoring assessment needed to perform a risk-informed STI extension using existing NRC approved guidance or both. Addressing these issues of STI extension by crediting self-diagnostics is likely to result in benefits for current and future nuclear power plant (NPP) operations, including lowering the barriers to adoption of digital I&C systems and increasing cost savings by deferring or eliminating unneeded preventive maintenance (tasks or checks or activities). Specifically, self-diagnostic and OLM capabilities of newer digital equipment being installed in non-safety and safety applications are designed to detect failures, provide early warning of potential failures, and notify plant operators to take appropriate action to reduce out of service (OOS) time thus protecting safety margins. Moreover, the equipment is expected to provide information that time-related operational degradation is identified early to ensure timely and planned corrective actions instead of a reactive and unplanned approach ahead of an extended-surveillance interval.

42 ENGINEERING↗

Leadership and Community Engagement in Chile: Deploying Net-Zero Technologies and Solutions

The report presents the 2023 Net Zero World Chile program results from activities of the the four program workstreams: 1) energy-system wide modeling LEAP modeling and analysis results including accelerated Net Zero scenarios with aggressive energy efficiency improvements, fuel switching, and electrification across demand sector; 2) district energy chapter provides thermal district energy systems modeling results of the Recoleta-Independencia pilot project and comparative analysis of district energy systems' potential versus competing technologies in Chile; 3) just transition action steps for the creation of a sister city relationship between Tocopilla and a US counterpart city; and 4) power decarbonization capacity building activities focused on the selection and adoption of grid-enhancing technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A Simulation Modeling Approach to Optimizing Nuclear Waste Dispositioning

The dispositioning of nuclear waste generated at facilities across the country is an ongoing battle that affects us all. National laboratories and research centers dealing in medical research, clean energy, and other nuclear activities such as the Department of Energy (DOE) facilities face the need to properly manage and dispose of nuclear waste. A dynamic modeling solution would enable the DOE and others to make decisions on waste disposal and technological options. In doing so, this research explores modeling techniques using available data to address these situations. The focus being on developing an initial robust and adaptable discrete event model using the ExtendSim tool. This modeling effort will target the dispositioning of transuranic waste at the Savannah River National Laboratory (SRNL) which can be expanded to represent the current state of disposition process for waste generated at other DOE facilities. The model aims to assess resource allocation and waste processing options to stabilize productivity and cut the backlog of nuclear waste. By assessing the results of different scenarios, this research aims to provide actionable insights for the DOE. This approach has the potential to significantly improve the management of radioactive waste, offering the capability of evaluating options for optimizing the process for nuclear waste disposal. The findings of this study can serve as a valuable resource for decision-makers and other national laboratories, or research entities engaged in nuclear operations by enabling them to make more informed choices.

Andaverde, Alexis↗

Assessment of ROI for Workforce Development Efforts National & Homeland Security

The IDEAL Professional Engagement project at Idaho National Laboratory (INL) aims to enhance the laboratory's workforce diversity and inclusivity efforts, focusing on the U.S. National and Homeland Security mission areas. This project involves researching and evaluating opportunities for INL to engage in various professional events, particularly cyber conferences, to support recruitment and professional development. The project involved several key tasks: compiling comprehensive information on national laboratories and their mission statements, developing a deep understanding of INL’s role and efforts in national and homeland security, and identifying and engaging key stakeholders. Interviews were conducted with a set of targeted questions, and the findings were analyzed to identify common themes, insights, and actionable recommendations. Additionally, relevant upcoming cyber conferences were identified, various sponsorship levels and their associated benefits were evaluated, and the recruitment potential of these conferences was assessed. A detailed cost analysis was performed, including registration fees and travel expenses, and a cost-benefit analysis was conducted to evaluate the financial viability and potential return on investment (ROI) of conference participation and sponsorship. Based on the research and analysis, actionable recommendations for conference participation and sponsorship were formulated, ensuring alignment with INL’s mission and diversity goals. Preliminary results include a comprehensive list of relevant cyber conferences, a detailed cost analysis, and a set of actionable recommendations for future conference participation and sponsorship. The analysis highlights the financial requirements and geographical distribution of these conferences, providing valuable insights for INL's engagement strategies. This project underscores the importance of strategic engagement in professional events to attract and develop a diverse and skilled workforce, ultimately supporting INL’s mission areas in U.S. National and Homeland Security.

99 GENERAL AND MISCELLANEOUS↗

Charting the Path to Electrification: Analyzing the Economic and Technological Potential of Advanced Vehicle Powertrains

The U.S. Department of Energy’s Vehicle Technologies Office (DOE-VTO) is driving advancements in highway transportation by targeting energy efficiency, environmental sustainability, and cost reductions. This study investigates the fuel economy potential and cost implications of advanced powertrain technologies using comprehensive system simulations. Leveraging tools such as Autonomie and TechScape, developed by Argonne National Laboratory, this study evaluates multiple timeframes (2023–2050) and powertrain types, including conventional internal combustion engines, hybrid electric vehicles (HEVs), plug-in hybrid electric vehicles (PHEVs), and battery electric vehicles (BEVs). Simulations conducted across standard regulatory driving cycles provide detailed insights into fuel economy improvements, cost trajectories, and total cost of ownership. The findings highlight key innovations in battery energy density, lightweighting, and powertrain optimization, demonstrating the growing viability of BEVs and their projected economic competitiveness with conventional vehicles by 2050. This work delivers actionable insights for policymakers and industry stakeholders, underscoring the transformative potential of vehicle electrification in achieving sustainable transportation goals.

Islam, Ehsan Sabri (ORCID:0000000200220180)↗

Tool-Based Case Studies on Strategic Deployment of Untapped Micro-Pumped Hydro Storage in Michigan

With most classical hydropower sites already utilized and the global push for rapid integration of renewable energy sources accelerating, there is a critical need to identify alternative energy storage solutions. Pumped hydro energy storage, which accounts for the vast majority of global grid-scale storage, remains one of the most cost-effective and long-duration storage technologies available. Hence, this study presents a novel tool designed to assess the untapped potential of inland lakes and reservoirs for micro-PSH, using Michigan’s relatively flat landscape as a case study due to its extensive but underutilized water infrastructure. To ensure accuracy and reliability, the tool incorporates extensive data gathered from authorized sources, covering more than 420 water facilities and potential reservoirs in the state. The tool evaluates key parameters such as horizontal and vertical distances, volume, and the total storage capacity of each reservoir. Its robust assessment framework integrates these metrics to evaluate each site’s potential. The tool’s intuitive interface and geospatial visualizations support actionable insights for planners and scalable deployment of distributed storage infrastructure.

13 HYDRO ENERGY↗

Advanced Reactor Supply Chain Assessment (GAIN Report)

Several net-zero scenario evaluations predict a rapid ramp up of nuclear energy in the coming decades. If this materializes, it will most likely strain the supply chains associated with the potential advanced reactor concepts awaiting deployment. To help assess the current and potential capacities of the various advanced reactor supply chains, the Gateway for Accelerated Innovation in Nuclear (GAIN) conducted a survey of companies able to produce components for advanced reactors in the near future (namely for sodium, gas-cooled, and molten salt reactors). Using an aggressive nuclear deployment scenario, the objective was to assess the ability of the various supply chains to meet the considerable demand projections for certain key components (vessels, heat exchangers, pumps, graphite, and sensors) and identify potential challenges. While individual companies were unable to meet the most optimistic nuclear deployment rate projections, it was found that on aggregate, a United States-based supply chain projected that expansion could be ramped up to meet a larger future demand of these components. However, meeting projected demand for several more complex items (namely gas or salt heat exchangers) was found to be more challenging. Deploying new reactors at scale necessitates the production of more and more supply chain components, requiring a ramp up in production. Supply chain companies were surveyed, and respondents appeared less able to meet short term demand (next year) versus longer-term demand projections (5 and 10 years). This reflects the need to obtain orders with adequate lead times (can range from 3 to 30 months). Future demand will need to be met by expanding existing capacity. These expansions will require suppliers to raise capital or secure other types of support (federal loans or grants) to invest in facilities, equipment, and workforce. Individual suppliers indicated financial investments could be in the range of $\$ $100 million to $\$ $1 billion for their own facilities (depending on the type of facility). The biggest risk, according to respondents, related to general uncertainties surrounding the future nuclear industry and whether the potential demand projections will materialize into real demand that is actionable from a business perspective. Businesses do not seem willing to take investments risks without clear orders. If businesses are not able to invest to expand the supply, it will either delay the deployment of advanced nuclear technology, or the supply chain will be met by suppliers outside of the United States. This report only focuses on the domestic supply chain’s ability to meet the various projections stipulated here for the specific assessed components (vessels, heat exchangers, pumps, graphite, and sensors). The report does not cover all reactor designs or all components that may ultimately be needed for any one reactor design. It also does not address whether any specific aspect of the supply chain will be cost competitive in the global market, nor how potential state-backed entities could affect the expansion of a United States-based supply chain. The largest challenges in ramping up capacity among respondents appear to be workforce related. This includes workforce availability, experience, training, and turnover. In addition to facility investment, suppliers will also need to invest heavily in long-term workforce training to meet production goals. This issue is not nuclear-specific, and the expansion of any supply chain will likely face similar challenges. While suppliers evaluated expected normal business demand from other markets outside of nuclear, it is possible that other market segments could expand more than predicted and compete for the same suppliers. One potential market that may compete for the same supplier resources is the United States military, as many of these suppliers support both the commercial nuclear sector as well as the Navy with reactors and components. In summary, suppliers in the United States believe that there is a way to increase production in order to begin meeting the demand which will exist for advanced reactors—as long as appropriate investments can be made in the supply chain in an appropriate timeframe. Based on the capacity projections and lead times, investment will be needed to meet the 5-year and 10-year production targets. Therefore, if significant nuclear deployment is to occur in the 2030s, investment and ramp up of the advanced nuclear supply chain will need to begin in the near future for the United States to successfully deploy these advanced reactors with domestic supply chains.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A U.S.-China coal power transition and the global 1.5 °C pathway

As the world seeks to increase ambition rapidly to limit global warming to 1.5 °C, joint leadership from the world's largest greenhouse gas (GHG) emitters—the United States (U.S.) and China—will be critical to deliver significant emissions reductions from their own countries as well as to catalyze increased international action. After a period of uncertainty in international climate policy, these countries now both have current leadership that supports ambitious climate action. In this context, a feasible, high-impact, and potentially globally catalytic agreement by the U.S. and China to transition away from coal to clean energy would be a major contribution toward this global effort. We undertake a plant-by-plant assessment in the power sector to identify practical coal retirement pathways for each country that are in line with national priorities and the global 1.5 °C target. Our plant-by-plant analysis shows that the 1.5 °C-compatible pathways may result in an average retirement age of 47 years for the U.S. coal plants and 22 years for Chinese coal plants, raising important questions of how to compare broader economic, employment, and social impacts. We also demonstrate that such pathways would also lead to significant emissions reductions, lowering overall global energy-related CO 2 emissions by about 9% in 2030 relative to 2020. A catalytic effect from the possibility of other countries taking compatible actions is estimated to reduce global emissions by 5.1 Gt CO 2 in 2030 and by 10.1 Gt CO 2 in 2045.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Water–Hydrocarbon Interactions in Anionic Pyrene Monohydrate

Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the intermolecular potentials of the water-hydrocarbon interactions are underdeveloped compared to water-water potentials, and there are similarly few experimental probes that are sensitive to the details of the water-hydrocarbon potential. We present a combined experimental and computational study of anionic pyrene monohydrate, one of the simplest water/hydrocarbon clusters. The action spectrum in the OH region of the mass-selected cluster ion provides a rigorous benchmark for intermolecular potentials and computational methodologies. We identify missing intermolecular interactions and shortcomings in conventional dynamics calculations by comparing experimental data to density functional theory and classical molecular dynamics calculations. Kinetic trapping is prevalent, even for one water molecule and one pyrene molecule, leading to slow equilibration in conventional molecular dynamics calculations, even on nanosecond timescales and at low temperatures (50 K). At constant energy, temperature fluctuations for the pair of molecules are substantial. Immersing the system in a bath of soft spheres and employing parallel tempering alleviates kinetic trapping and dampens temperature fluctuations, bringing the system closer to the thermodynamic limit. With such augmented sampling, a simple, flexible water model reproduces the linewidth and the asymmetric broadening of the symmetric OH stretching mode, which we assign to spectral diffusion. In the OH stretching region, dynamics calculations predict a more intense antisymmetric peak than experiments observe but do not predict the bimodal split symmetric peak that the experiments show. Furthermore, our work suggests that electronic polarization, missing in the empirical force field, is responsible for the first discrepancy and that quantum nuclear effects, captured neither in density functional theory nor in classical dynamics, may be responsible for the second.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modification at the C2'-O-Position with 2-Methylbenzothiophene Induces Unique Structural Changes and Thermal Transitions on Duplexes of RNA and DNA

Oligonucleotides can be chemically modified for a variety of applications that include their use as biomaterials, in therapeutics, or as tools to understand biochemical processes, among others. This work focuses on the functionalization of oligonucleotides of RNA and DNA (12- or 14-nucleotides long) with methylbenzothiophene (BT), at the C2'-O-position, which led to unique structural features. Circular dichroism (CD) analyses showed that positioning the BT units on one strand led to significant thermal destabilization, while duplexes where each strand contained 4-BT rings formed a distinct arrangement with cooperativity/interactions among the modifications (evidenced from the appearance of a band with positive ellipticity at 235 nm). Interestingly, the structural arrays displayed increased duplex stabilization (>10 °C higher than the canonical analogue) as a function of [Na + ] with an unexpected structural rearrangement at temperatures above 50 °C. Density functional theory–polarizable continuum model (DFT-PCM) calculations were carried out, and the analyses were in agreement with induced structural changes as a function of salt content. A model was proposed where the hydrophobic surface allows for an internal nucleobase rearrangement into a more thermodynamically stable structure, before undergoing full denaturation, with increased heat. While this behavior is not common, B- to Z-form duplex transitions can occur and are dependent on parameters that were probed in this work, i.e., temperature, nature of modification, or ionic content. To take advantage of this phenomenon, we probed the ability of the modified duplexes to be recognized by Zα (an RNA binding protein that targets Z-form RNA) via electrophoretic analysis and CD. Interestingly, the protein did not bind to canonical duplexes of DNA or RNA; however, it recognized the modified duplexes, in a [monovalent/divalent salt] dependent manner. Overall, the findings describe methodology to attain unique structural motifs of modified duplexes of DNA or RNA, and control their behavior as a function of salt concentration. While their affinity to RNA binding proteins, and the corresponding mechanism of action, requires further exploration, the tunable properties can be of potential use to study this, and other, types of modifications. The novel arrays that formed, under the conditions described herein, provide a useful way to explore the structure and behavior of modified oligonucleotides, in general.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks

Motivation: Signaling pathways capable of switching between two states are ubiquitous within living organisms. They provide the cells with the means to produce reversible or irreversible decisions. Switchlike behavior of biological systems is realized through biochemical reaction networks capable of having two or more distinct steady states which are dependent on initial conditions. Investigation of whether a certain signaling pathway can confer bistability involves a substantial amount of hypothesis testing. The cost of direct experimental testing can be prohibitive. Therefore, constraining the hypothesis space is highly bene?cial. One such methodology is based on Chemical Reaction Network Theory which uses computational techniques to rule out pathways that are not capable of bistability regardless of kinetic constant values and molecule concentrations. Although useful, these methods are complicated from both pureandcomputationalmathematicsperspectives.Thus,theiradoptionisverylimitedamongstbiologists. Results: We brought Chemical Reaction Network Theory approaches closer to experimental biologists by automating all the necessary steps in CRNT4SMBL. The input is based on SBML format which is the community standard for biological pathway communication. The tool parses SBML and derives C-graph representations of the biological pathway with mass action kinetics. Next steps involve an ef?cient search for potential saddle-node bifurcation points using an optimization technique. This type of bifurcation is important as it has the potential of acting as a switching point between two steady states. Finally, if any bifurcation points are present, numerical continuation analysis extends the equilibria branches for generating the diagram. Presence of an S-shaped bifurcation diagram indicates that the pathway acts as a bistable switch for the given optimization parameters. Availability: CRNT4SBML is available via the Python Package Index. The documentation can be found at https://crnt4sbml.readthedocs.io. CRNT4SBML is licensed under the Apache Software License 2.0. Contact: vladislav.petyuk@pnnl.gov

Reyes, Brandon C.↗