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DOE OSTI2026

Beyond sequence similarity: toward function-based screening of nucleic acid synthesis

Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Processability and Material Behavior of NiTi Shape Memory Alloys Using Wire Laser-Directed Energy Deposition (WL-DED)

Utilizing additive manufacturing (AM) techniques with shape memory alloys (SMAs) like NiTi shows great promise for fabricating highly flexible and functionally superior 3D metallic structures. Compared to methods relying on powder feedstocks, wire-based additive manufacturing processes provide a viable alternative, addressing challenges such as chemical composition instability, material availability, higher feedstock costs, and limitations on part size while simplifying process development. This study presented a novel approach by thoroughly assessing the printability of Ni-rich Ni55.94Ti (Wt. %) SMA using the wire laser-directed energy deposition (WL-DED) technique, addressing the existing knowledge gap regarding the laser wire-feed metal additive manufacturing of NiTi alloys. For the first time, the impact of processing parameters—specifically laser power (400–1000 W) and transverse speed (300–900 mm/min)—on single-track fabrication using NiTi wires in the WL-DED process was examined. An optimal range of process parameters was determined to achieve high-quality prints with minimal defects, such as wire dripping, stubbing, and overfilling. Building upon these findings, we printed five distinct cubes, demonstrating the feasibility of producing nearly porosity-free specimens. Notably, this study investigated the effect of energy density on the printed part density, impurity pick-up, transformation temperature, and hardness of the manufactured NiTi cubes. The results from the cube study demonstrated that varying energy densities (46.66–70 J/mm3) significantly affected the quality of the deposits. Lower to intermediate energy densities achieved high relative densities (>99%) and favorable phase transformation temperatures. In contrast, higher energy densities led to instability in melt pool shape, increased porosity, and discrepancies in phase transformation temperatures. These findings highlighted the critical role of precise parameter control in achieving functional NiTi parts and offer valuable insights for advancing AM techniques in fabricating larger high-quality NiTi components. Additionally, our research highlighted important considerations for civil engineering applications, particularly in the development of seismic dampers for energy dissipation in structures, offering a promising solution for enhancing structural performance and energy management in critical infrastructure.

Dabbaghi, Hediyeh↗

DOE OSTI2020

Assessment of the Griffin Reactor Multiphysics Application Using the Empire Micro Reactor Design Concept

In late 2019, INL and ANL agreed to jointly develop the reactor physics code named Griffin based on the integration of the two code suites, MAMMOTH/Rattlesnake (INL) and MC2 - 3/PROTEUS (ANL). Griffin is being developed based on the MOOSE framework and MOOSE quality assurance procedures. This decision was made to be able to allow DOE-NE to efficiently invest funding to this area and to provide effective and timely support for existing and potential users; the latter includes industry and government organizations who are developing various types of advanced reactors in the near and long term. Since MAMMOTH/Rattlesnake has been developed based on the MOOSE framework, the INL/ANL Griffin development team agreed to build Griffin beginning with a merger of MAMMOTH and Rattlesnake into a single code and moving forward by implementing capabilities from the PROTEUS suite into Griffin. Moving forward, both ANL and INL efforts are equally invested in the Griffin project, with management support, to provide an advanced reactor multiphysics tool to assist in reactor design, optimization, and safety analysis. Much work remains in moving Griffin forward to migrate PROTEUS capabilities and to optimize performance to meet user needs. The main objective of this work is to assess the current status of Griffin capabilities in terms of performance and accuracy, to determine priorities for PROTEUS migration, and to identify capabilities and features to improve for supporting the code integration effort. For this assessment, the Empire micro reactor problem that was developed in the ARPA-E MEITNER program was selected as an advance reactor concept of interest to the technical community. The Empire reactor problem was expanded from its original incomplete specification to be a small heat-pipe-cooled micro reactor core with ~113 cm radius and 70 cm in height, composed of 18 fuel assemblies, 12 control drums, and beryllium radial and axial reflectors. In the current model, using 5 cm axial reflectors specified in the original Empire assembly model, more than 10% of neutrons leak axially and through the empty center safety hole, as well as through heat pipe channels in fuel assembly elements that extend through the top reflector region. Several calculation models of the core were defined for systematic assessment, including 2-D and 3-D fuel assemblies and whole cores with cylindrical boundaries. Cross sections were generated using Serpent 2, and meshes were produced using the Argonne mesh tool or the INL neutronics meshing tools combined with CUBIT. Cross sections and meshes were converted to the ISOXML and Exodus formats, respectively, so that Griffin and PROTEUS could use consistent data for solving the reactor problems. With the prepared cross sections and meshes, PROTEUS was run first to ensure that all input data were correctly generated and input options in terms of angle, mesh, and energy group were accurately determined. Comparisons against Serpent 2 solutions were made in terms of eigenvalue and pin power. The same calculations and comparisons were then conducted using Griffin. For the fuel assembly and whole core problems, the PROTEUS eigenvalues agreed well with reference Serpent 2 solutions within 100 and 30 pcm, respectively, and pin power differences relative to Serpent 2 were overall less than 2.2% and RMS 0.8% for the whole core models. This indicated that all input data were properly prepared. Using the same data, Griffin was run selecting the SAAF-CFEM SN solver with Legendre-Gaussian quadrature and NDA and DSA for acceleration. It was found that the SAAF-CFEM solver of Griffin required finer meshes to achieve eigenvalue and pin power solutions in good agreement with Serpent 2, consequently requiring more memory requirement and longer computation time. On the other hand, the SPH-Diffusion 2-D core calculations performed using Griffin were able to recover the exact eigenvalue from the reference Serpent 2 solutions, resulting in a pin-power distribution with an RMS of 0.6% and maximum absolute difference of less than 1.4%. The runtimes for SPH-Diffusion for the 2-D core were less than 3 minutes on 40 cores. During this evolution of this evaluation, many updates were made in Griffin by the Griffin development team of INL (focusing on software updates) and ANL (reviewing and supporting software updates) to complete this assessment. Observations from the code assessment are presented in the conclusion section of this report, followed by a discussion of recommendations for future work.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2026

Chemically Enabled CO 2 -Enhanced Oil Recovery in Multi-Porosity, Hydrothermally Altered Carbonates in the Southern Michigan Basin (Final Technical Report)

This is the Final Technical Report for the project "Chemically Enabled CO 2 -Enhanced Oil Recovery in Multi-Porosity, Hydrothermally Altered Carbonates in the Southern Michigan Basin." Over the course of six years of collaboration between Battelle and project partners, all stated objectives of the program have been completed, including full geological characterization of the TBR trend (See companion report for Task2), laboratory and modeling experiments to determine the optimum composition and design of CO 2 -EOR operations in the TBR trend, execution of a field test of chemically-enhanced CO 2 in a TBR well, and integration of the data and learnings gathered during these efforts into a full-trend development plan. Detailed reporting on these activities, their outcomes, and implications for trend-wide development is provided in the report. This report and encompassed data will provide TBR field operators with detailed information on what worked, what did not work, and how to proceed with production optimization of their TBR assets using chemically-enhanced CO 2 -EOR. CO 2 -EOR is a relatively well understood and broadly implemented strategy for increasing incremental production across the oil and gas industry, but its application has been primarily focused on reservoirs with limited heterogeneity. The intention of this project was show first that the same physical mechanisms that improve recovery factors in homogeneous reservoirs (namely wettability alteration, viscosity alteration, oil swelling, and mobility control) are at play in heterogeneous reservoirs. This was proven by the project’s laboratory studies and dynamic simulations, with the potential exception of mobility control, which needs further study. The second intention was to demonstrate via direct field testing that CO 2 -EOR can work in a strongly heterogeneous reservoir. While the field test strategy implemented during this project did not succeed in producing oil, data gathered during the test sheds light on what may work for field operators who try chemically-enhanced CO 2 -EOR within their own reservoirs, significantly reducing the level of uncertainty carried by first-of-a-kind commercial efforts that could (and should) follow this test. Simultaneously, the project has identified several large-volume ethanol plants and other sources of CO 2 emissions in the region and provided a handrail that CO 2 emitters and field operators can leverage to capture, transport, and inject that CO 2 into their fields. This project has also shown that, in many cases, the economics of CO 2 -EOR in the TBR are attractive. And finally, by completing a project of this scope in the southern Michigan Basin, the project has contributed to the knowledge base and operational experience of field operators, state regulatory agencies, local service companies, and state universities, with CO 2 -EOR projects which should allow follow-on projects to proceed safely and efficiently.

02 PETROLEUM↗

DOE OSTI2023

Error-Detectable Bosonic Entangling Gates with a Noisy Ancilla

Bosonic quantum error correction has proven to be a successful approach for extending the coherence of quantum memories, but to execute deep quantum circuits, high-fidelity gates between encoded qubits are needed. To that end, we present a family of error-detectable two-qubit gates for a variety of bosonic encodings. From a new geometric framework based on a “Bloch sphere” of bosonic operators, we construct ZZ L ⁡(θ) and exponential-swap(θ) gates for the binomial, four-legged cat, dual-rail, and several other bosonic codes. The gate Hamiltonian is simple to engineer, requiring only a programmable beam splitter between two bosonic qubits and an ancilla dispersively coupled to one qubit. This Hamiltonian can be realized in circuit QED hardware with ancilla transmons and microwave cavities. The proposed theoretical framework was developed for circuit QED but is generalizable to any platform that can effectively generate this Hamiltonian. Crucially, one can also detect first-order errors in the ancilla and the bosonic qubits during the gates. We show that this allows one to reach error-detected gate fidelities at the 0.01% level with today’s hardware, limited only by second-order hardware errors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Intranasal Nanoparticle Vaccination Elicits a Persistent, Polyfunctional CD4 T Cell Response in the Murine Lung Specific for a Highly Conserved Influenza Virus Antigen That Is Sufficient To Mediate Protection from Influenza Virus Challenge

We report lung-localized CD4 T cells play a critical role in the control of influenza virus infection and can provide broadly protective immunity. However, current influenza vaccination strategies primarily target influenza hemagglutinin (HA) and are administered peripherally to induce neutralizing antibodies. We have used an intranasal vaccination strategy targeting the highly conserved influenza nucleoprotein (NP) to elicit broadly protective lung-localized CD4 T cell responses. The vaccine platform consists of a self-assembling nanolipoprotein particle (NLP) linked to NP with an adjuvant. We have evaluated the functionality, in vivo localization, and persistence of the T cells elicited. Our study revealed that intranasal vaccination elicits a polyfunctional subset of lung-localized CD4 T cells that persist long term. A subset of these lung CD4 T cells localize to the airway, where they can act as early responders following encounter with cognate antigen. Polyfunctional CD4 T cells isolated from airway and lung tissue produce significantly more effector cytokines IFN-γ and TNF-α, as well as cytotoxic functionality. When adoptively transferred to naive recipients, CD4 T cells from NLP:NP-immunized lung were sufficient to mediate 100% survival from lethal challenge with H1N1 influenza virus.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide

Cytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

UNH TDP - Concurrent Measurements of Inflow, Power Performance, and Loads for a Grid-Synchronized Vertical Axis Cross-Flow Turbine Operating in a Tidal Estuary

This data was collected between October 12 and December 15 of 2021 at the University of New Hampshire (UNH) and Atlantic Marine Energy Center (AMEC) turbine deployment platform (TDP). This data set includes over 29 days of grid connected turbine operation during this 65 day time frame. The priority for this measurement campaign was to collect data while the turbine was electrically connected to the grid by means of a rectifier and inverter. The Fall_2021_UNH_Measurement_Timeline.png highlights when each instrument was functioning and the Fall_2021_UNH_Test_Log.jpg indicates the four main regions for analysis available from this measurement campaign. The TDP is a floating structure moored on the Portsmouth facing side of Memorial Bridge pier #2, which spans the Piscataqua River between Portsmouth, NH and Kittery, ME. The Piscataqua River connects the Great Bay Estuary to the Gulf of Maine and the river currents are dominated by tidal forcing with water velocities exceeding 2.5 m/s during spring ebb tides at this site which were previously characterized by Kaelin Chancey (Assessment Of The Localized Flow And Tidal Energy Conversion System At An Estuarine Bridge - UNH MS Thesis 2019). The turbine under test was a modified New Energy Corporation (Calgary, CA) model EVG-025 4-blade H-Darrius type vertical axis cross flow turbine that rotates in the clockwise direction with a rotor diameter of 3.2m and blade length of 1.7m. The hydro-foil profile was a NACA 0021 with a 10 inch chord length and a blade preset pitch angle of +4deg with a positive angle corresponding with the toe in direction. The standard EVG-025 has a rotor diameter of 3.4m and its rated power output is 25kW at 3 m/s. The rotor diameter was reduced to accommodate the size of the existing TDP moon-pool. This project was pursued to quantify device performance for cross flow turbines operating in a marine environment. Accurate physical models, to characterize cross flow turbine performance, require real operational data sets due to the complexity of blade fluid interactions. This data can help support model development which will help predict turbine performance when analyzing perspective project locations in the future. Instrumentation was deployed to measure; water speed/direction, electrical power output, turbine shaft speed, turbine thrust force, and platform motion. Concurrent measurements of these parameters allow for correlations (cause and affect) to be inferred, allowing for characterization of device performance over a range of operating conditions. Water currents were measured using Acoustic Doppler Current Profilers (ADCP's) and Acoustic Doppler Velocimeters (ADV's) directly upstream and downstream of the turbine for inflow, wake and turbulence measurements. Electrical power output was measured using the Voltsys rectifier and the Shark power meter. Shaft speed was calculated based on the Voltsys measurements of the permanent magnet three phase generator AC generation frequency, coupled directly to the cross flow turbine under test (i.e., no gear box). Platform motions were captured using a Yost IMU (inertial measurement unit). Turbine thrust loading was measured using a reaction arm about the turbine deployment platform spanning beam, where two bi-directional load cells were connected to the system via a pinned connection. This submission includes zipped folders for each instrument containing quality controlled (QC'd) data in daily .csv files for the relevant duration specific to each instrument, along with separate .csv file that contains the units for each variable. Some instrument daily files are quite large and can pose a challenge for a visual spreadsheet editor to open. A processing software like MATLAB or Python is recommended. Note the degree of QC varied between each instrument due to time constraints. Particular time and attention was given to perform quality control tests on the acoustic based instruments that are particularly suscep...

16 TIDAL AND WAVE POWER↗

DOE OSTI2021

Early detection of amyloid load using 18F-florbetaben PET

A low amount and extent of Aβ deposition at early stages of Alzheimer’s disease (AD) may limit the use of previously developed pathology-proven composite SUVR cutoffs. This study aims to characterize the population with earliest abnormal Aβ accumulation using 18F-florbetaben PET. Quantitative thresholds for the early (SUVR early ) and established (SUVR estab ) Aβ deposition were developed, and the topography of early Aβ deposition was assessed. Subsequently, Aβ accumulation over time, progression from mild cognitive impairment (MCI) to AD dementia, and tau deposition were assessed in subjects with early and established Aβ deposition. The study population consisted of 686 subjects (n = 287 (cognitively normal healthy controls), n = 166 (subjects with subjective cognitive decline (SCD)), n = 129 (subjects with MCI), and n = 101 (subjects with AD dementia)). Three categories in the Aβ-deposition continuum were defined based on the developed SUVR cutoffs: Aβ-negative subjects, subjects with early Aβ deposition (“gray zone”), and subjects with established Aβ pathology. SUVR using the whole cerebellum as the reference region and centiloid (CL) cutoffs for early and established amyloid pathology were 1.10 (13.5 CL) and 1.24 (35.7 CL), respectively. Cingulate cortices and precuneus, frontal, and inferior lateral temporal cortices were the regions showing the initial pathological tracer retention. Subjects in the “gray zone” or with established Aβ pathology accumulated more amyloid over time than Aβ-negative subjects. After a 4-year clinical follow-up, none of the Aβ-negative or the gray zone subjects progressed to AD dementia while 91% of the MCI subjects with established Aβ pathology progressed. Tau deposition was infrequent in those subjects without established Aβ pathology. This study supports the utility of using two cutoffs for amyloid PET abnormality defining a “gray zone”: a lower cutoff of 13.5 CL indicating emerging Aβ pathology and a higher cutoff of 35.7 CL where amyloid burden levels correspond to established neuropathology findings. These cutoffs define a subset of subjects characterized by pre-AD dementia levels of amyloid burden that precede other biomarkers such as tau deposition or clinical symptoms and accelerated amyloid accumulation. The determination of different amyloid loads, particularly low amyloid levels, is useful in determining who will eventually progress to dementia. Quantitation of amyloid provides a sensitive measure in these low-load cases and may help to identify a group of subjects most likely to benefit from intervention.

60 APPLIED LIFE SCIENCES↗