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DOE OSTI2025

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

New constraint on the Np 237 ( n , γ ) Np 238 integral cross section using the Godiva-IV critical assembly

Accurate knowledge of the 237 Np(n, γ) 238 Np cross section at fast neutron energies is important for applied nuclear science. The presently available experimental data has large disagreements in the fast neutron region. Perform a model-independent measurement of the 237 Np(n, γ) 238 Np integral cross section using a well characterized fast neutron source and compare the result with previous measurements and current nuclear data evaluations. Provide an integral measurement that can be used as a benchmark for current evaluations. Multiple samples of 237 Np were irradiated in the Godiva-IV critical assembly. Following the irradiation, the samples placed in a γ-ray counting setup and the γ-rays emitted from the decay of 238 Np were measured over a time period of approximately 7 days. Multiple γ-ray decay branches of 238 Np were observed. The observed activity of 238 Np was used to calculate the amount of 238 Np produced during the irradiation via the 237 Np(n, γ) 238 Np reaction and an integral cross section of 342(11) mb was measured for the Godiva-IV neutron spectrum. Further, the 238 Np half-life has been measured with a result of 50.31(5) hours. The 237 Np(n, γ) 238 Np integral cross section measured in this work is in agreement with overlapping 1σ error bands to ENDF/B-VIII.0. However, the measured value is 3σ away from the calculated integral cross section using JENDL-5. This measurement offers a reliable benchmark for future 237 Np(n, γ) 238 Np cross section evaluations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

Integral X-ray diffuse scattering for studying irradiation-induced dislocation loops in single crystals

Numerical diffuse scattering cross-section calculations are used to establish a rigorous basis for determining the concentration and size distribution of dislocation loops in irradiated single crystals from integral X-ray diffuse scattering (XRDS) measurements. Differential XRDS intensities for prismatic {111} type dislocation loops are numerically calculated as a function of loop radius R and wavevectors q relative to Bragg reflections in tungsten. The results show the well known 1/q 2 Huang scattering form at small q that transitions to a ∼1/q 4 dependence associated with the Stokes–Wilson approximation for q ≳ 1/R. More importantly, they show further that the 1/q 4 falloff is not the asymptotic large-q form of the diffuse scattering for small loops (R < 200 Å) as has often been assumed. Rather, for loop sizes as small as R ≃ 5 Å with strong curvature, the calculations show definitively that the scattering transitions to a robust 1/q 5 falloff at larger q that arises due to the local strains near the dislocation core defining the circumference of the dislocation loops. The presence of this 1/q 5 asymptotic form for both small and large loops is experimentally confirmed using an integral XRDS measurement around the 110 reflection on self-ion-irradiated tungsten combined with numerically calculated integral XRDS cross-sections. Accordingly, the historical two-region theoretical treatment of the cross-sections for integral XRDS is extended to a three-region model that has direct sensitivity to the (first-moment) dislocation line lengths of dislocation loops. In conclusion, these developments enable the use of both numerical and analytically modeled cross-sections to make accurate integral XRDS determinations of dislocation loop sizes and concentrations using modest-intensity laboratory X-ray sources.

42 ENGINEERING↗

DOE OSTI2025

A Polar Scaling Technique for the Regularization of Strongly Singular and Strongly Near-Singular Helmholtz Surface Integrals Evaluated Over 2-D Domains

The numerical integration of expressions containing strong singularities or strong near-singularities has long been a challenging problem in the electromagnetics community. Much attention has been paid to this problem, as strong $1/R^{{2}}$ singularities routinely appear when implementing electromagnetic simulation techniques like the method of moments (MoM). To date, several techniques, from singularity extraction to singularity cancellation (SC), have been employed to deal with problems that require the evaluation of 2-D strongly singular integrals. However, no single technique has been proposed that can deal with both strong singularities and strong near-singularities in a fully numerical manner for arbitrary 2-D domains. Moreover, it has been claimed that the Helmholtz-type strongly singular integral found in the MoM is convergent in a principal value sense, but this convergence value has yet to be proven mathematically. In this work, we will conduct the convergence proof and introduce a “polar scaling” change of variables method that may be used to evaluate Helmholtz integrals with both strong and weak singularities/near-singularities. The technique is fully numerical and can in principle be applied to any planar or curved polygon and any nonsingular basis function. We will also provide numerical results showing useful convergence behavior for integrals involving both exact and near-singularities.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

OpenFacadeControl: enabling integration of automated facades with other building systems

Automated facades are, for the most part, still considered as separate from other building systems throughout the design, installation, commissioning, operation, and maintenance cycle. This takes place despite the fact that their energy and comfort performance are deeply interlinked with the operation of lighting and HVAC systems. Over the last two decades, research has shown that there are significant advantages from operating facades as an integrated system with the rest of the building. Nevertheless, significant barriers prevent this type of integration becoming more common. One of them is the lack of a platform that is inexpensive to implement and that easily allows the practical implementation of integrated control algorithms across fenestration and other building systems, using a variety of communications protocols. This is particularly challenging when automated facades are installed in existing buildings, where interaction with legacy building systems that were installed over the past lifetime of the building can require a high degree of interoperability. OpenFacadeControl (OFC) is an open-source controls framework aimed at unified control of facades and other building systems, including the sharing of third-party sensor information. Through leveraging the Volttron controls platform, it allows the integration of systems and sensors that are manufactured by different companies and that use different communications protocols into an ensemble that functions as a single system. OFC is designed to enable integrated control algorithms of varying degrees of complexity, ranging from simple, heuristic controls to more sophisticated approaches like model-predictive control. Use of a research version to test advanced lighting and shading strategies in a full-scale experimental testbed has demonstrated the ease of deploying advanced control solutions using OpenFacadeControl. This paper presents the structure of OpenFacadeControl and a demonstration case showing the use of OFC in laboratory tests of advanced lighting and fenestration controls that coordinated motorized shades communicating via the BACnet building communications standard and lights communicating via internet-protocol-based application programming interface (API), based on the readings of a shared light level sensor communicating via a different API.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2026

Solar Heat for Industrial Processes: Integration with Chemical Reactors

The integration of solar thermal systems with chemical reactors has been proposed as part of a larger effort to develop and deploy solar heat for industrial processes (SHIP) technologies. A strong motivation for SHIP processes and technologies is the potential for high thermal efficiency coupled with low-cost thermal energy storage (TES) which can enable commercial deployment of such systems. While there are different ways to categorize SHIP technologies, one important such distinction is between directly irradiated systems and indirect off-sun process driven by a SHIP system. While directly irradiated systems can provide high thermal efficiencies and high fluxes, they usually require complex engineering solutions due to the need for redesigning the established processes and unit operations. In most cases, it is also more challenging to couple such a process to a TES system, losing some of the benefits of SHIP. On the other hand, using a SHIP system to drive an industrial process off-sun can allow better integration with existing process chains, easier TES capabilities, and potential for more applications fitting a specific SHIP technology. However, the integration of SHIP systems with the industrial processes is not fully explored in detail, especially in the case of high-temperature processes such as reforming, cracking, cement manufacturing, and iron/steelmaking. Many of these systems require heating fluxes of >50 kW/m^2, supplied via combustion of hydrocarbons in a fire box and benefitting from radiative heat transfer between the flue gases and the reaction zones. As such, using SHIP systems for such processes is more complex than providing the same thermal input in the form of a heat transfer medium (HTM) entering the reactor, kiln, or furnace. Moreover, in case convective heat transfer using SHIP is envisioned, for example using supercritical CO2 as the HTM from a particle receiver, the thermal integration might be more challenging than initially envisioned: lower heat transfer coefficients and limited approach temperature might require large flow rates, causing a mismatch between the process thermal requirements and the thermal capacity of the SHIP system. In addition, even if the heat exchange between SHIP and reactor is effective, there is still a cold leg HTM at the reaction temperature or slightly below it. Chemical plants usually include a set of heat exchangers, heat recovery steam generators, and even power generation units - in a tightly integrated design - to recover the flue gases which are eventually vented. With SHIP systems mostly operating on a closed HTM loop, bottoming the cold leg is crucial. In this talk, we will present different modeling results for a variety of syngas production reactions, using catalytic and chemical looping processes, and discuss some of the challenges and design considerations for off-sun chemical reactors using SHIP systems.

14 SOLAR ENERGY↗

DOE OSTI2024

Integrated Traction Drive Thermal Management: Keystone Project 3

The presentation represents a report of accomplishments during FY 2024 and is prepared for 2024 DOE VTO Annual Merit Review. The project goal is identifying pathways enabling high-performance, compact, and reliable integrated electric drives and facilitation of achieving DOE 2025 target of 33 kW/L system power density for an electric traction drive through support of other EDT consortium members in design and development of thermal management systems for their respective integrated drive concepts. Specific objectives are: 1) research and evaluation of motor-integrated power electronics packaging technologies and thermal management approaches; 2) explore novel materials and manufacturing options (3D printing with thermally enhanced polymers or ceramic materials) for key thermal management system components; 3) develop thermal management system and its sub-components to enable integrated electric drive DOE power density targets in collaboration with project partners; 4) support activities of DOE's Electric Drive Technologies (EDT) consortium members, Oak Ridge National Laboratory (ORNL), University of Wisconsin and Georgia Tech research teams in thermal management component design and thermal modeling of their integrated traction drives.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Two-loop master integrals for leading-color $$ pp\to t\overline{t}H $$ amplitudes with a light-quark loop

Abstract We compute the two-loop master integrals for leading-color QCD scattering amplitudes including a closed light-quark loop in$$ t\overline{t}H $$ t t ¯ H production at hadron colliders. Exploiting numerical evaluations in modular arithmetic, we construct a basis of master integrals satisfying a system of differential equations inϵ-factorized form. We present the analytic form of the differential equations in terms of a minimal set of differential one-forms. We explore properties of the function space of analytic solutions to the differential equations in terms of iterative integrals which can be exploited for studying the analytic form of related scattering amplitudes. Finally, we solve the differential equations using generalized series expansions to numerically evaluate the master integrals in physical phase space. As the first computation of a set of two-loop seven-scale master integrals, our results provide valuable input for analytic studies of scattering amplitudes in processes involving massive particles and a large number of kinematic scales.

Physics↗

DOE OSTI2025

Integration of renewable energy generation and storage systems for emissions reduction in an islanded campus microgrid

Microgrid connected building communities are projected to play an integral part in the clean energy transition. These types of systems, when integrated with distributed energy resources (DERs) such as combined heat and power (CHP), district heating and cooling, renewable generation, and energy storage, can provide clean, reliable power to critical facilities and vulnerable communities. The intermittent nature of renewable generation is a challenge when integrating renewables into any grid system, but particularly in islanded microgrids. The University of Texas at Austin (UT) operates an islanded microgrid powered by a CHP plant, while also utilizing district heating and cooling systems and thermal energy storage (TES). High fidelity operating data was used to develop a validated reduced order model of UT’s integrated campus energy systems to serve as a testbed for use in a case study. Hypothetical renewable energy installations on land owned by UT in west Texas were modeled and integrated into the validated campus models along with battery energy storage (BES). Simulations showed that a combination of renewable energy from wind, and optimally controlled 24-hour thermal and battery storage systems could reduce carbon dioxide emissions on campus by 45.4%. The additional retrofit of burner systems to utilize hydrogen natural gas blends resulted in an overall annual emissions reduction of 54.7%. Carbon capture and storage eliminated the majority of the remaining emissions with increased plant energy expenditure. The presented simulations display the practical limitations of a CHP system complemented by renewable generation and short-term storage in eliminating emissions. Furthermore, results highlight the need for further research and development in long duration storage technologies and hydrogen fueled turbines to increase penetration of renewable energy and reduce emissions.

CHP↗

DOE OSTI2026

Self-aligned heterogeneous quantum photonic integration

Integrated quantum photonics holds significant promise for scalable photonic quantum information processing, quantum repeaters, and quantum networks, but its development is hindered by the mismatch between materials hosting high-quality quantum emitters and those compatible with mature photonic technologies. Heterogeneous integration offers a potential solution to this challenge, yet practical implementations have been limited by inevitable insertion losses at material interfaces. Here, we present a self-aligned heterogeneous quantum photonic integration approach that enables near-unity coupling efficiency at the interface. To showcase our approach, we demonstrate Purcell enhancement of a silicon vacancy (SiV) center in diamond induced by a heterogeneous photonic crystal cavity defined by titanium dioxide (TiO 2 ), as well as optical spin control and readout via a TiO 2 photonic circuit. We further show that, when combined with inverse photonic design, our approach enables efficient and broadband collection of single photons from a color center into a heterogeneous waveguide. Our approach is not restricted to SiV centers or TiO 2 ; it has the potential to be broadly applied to integrate diverse solid-state quantum emitters with thin-film photonic devices where conformal deposition is possible. Together, these results establish a practical route to scalable quantum photonic integrated circuits that combine high-quality quantum emitters with technologically mature photonic platforms.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Productivity and cost of energy chipping with non-integrated harvesting systems in the Coastal Plain of the US south

Research from the 1980s–2010s suggested that integrated harvesting systems that harvest conventional products (e.g., sawtimber, pulpwood) and energy chips simultaneously were the most effective solution to produce energy chips in the US South. Alternatives, such as biomass-only systems, have important advantages in forest stands with low volumes of merchantable timber. The goal of this study was to estimate the productivity and cost of producing energy chips using non-integrated systems. Innovative chipping contractors using non-integrated systems were identified through contacts with procurement foresters responsible for purchasing energy chips. Elemental time-and-motion studies were conducted to estimate harvesting productivity on five operations, including one clearcut harvest and four first thinnings in overstocked stands. The hourly cost of equipment was estimated using the machine rate method. Cost per tonne was estimated by combining hourly productivity and hourly costs in a modified version of the Auburn Harvesting Analyzer. System productivity averaged 37 tonnes per scheduled machine hour (smh) and cut-and-haul costs averaged $33.86 t −1 (USD), which was comparable to previous estimates from integrated systems. In conclusion, this study suggests there are viable alternatives to integrated harvesting systems to produce energy chips, especially in stands with low volumes of merchantable timber.

09 BIOMASS FUELS↗

DOE OSTI2025

miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources

Abstract Motivation Precision medicine leverages patient-specific multimodal data to improve prevention, diagnosis, prognosis, and treatment of diseases. Advancing precision medicine requires the non-trivial integration of complex, heterogeneous, and potentially high-dimensional data sources, such as multi-omics and clinical data. In the literature, several approaches have been proposed to manage missing data, but are usually limited to the recovery of subsets of features for a subset of patients. A largely overlooked problem is the integration of multiple sources of data when one or more of them are completely missing for a subset of patients, a relatively common condition in clinical practice. Results We propose miss-Similarity Network Fusion (miss-SNF), a novel general-purpose data integration approach designed to manage completely missing data in the context of patient similarity networks. miss-SNF integrates incomplete unimodal patient similarity networks by leveraging a non-linear message-passing strategy borrowed from the SNF algorithm. miss-SNF is able to recover missing patient similarities and is “task agnostic”, in the sense that can integrate partial data for both unsupervised and supervised prediction tasks. Experimental analyses on nine cancer datasets from The Cancer Genome Atlas (TCGA) demonstrate that miss-SNF achieves state-of-the-art results in recovering similarities and in identifying patients subgroups enriched in clinically relevant variables and having differential survival. Moreover, amputation experiments show that miss-SNF supervised prediction of cancer clinical outcomes and Alzheimer’s disease diagnosis with completely missing data achieves results comparable to those obtained when all the data are available. Availability and implementation miss-SNF code, implemented in R, is available at https://github.com/AnacletoLAB/missSNF.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Quantum Hamilton-Jacobi theory, spectral path integrals, and exact WKB analysis

We propose a new way to perform path integrals in quantum mechanics by using a quantum version of Hamilton-Jacobi (HJ) theory. In classical mechanics, Hamilton-Jacobi theory is a powerful formalism, however, its utility is not explored in quantum theory beyond approximation schemes. The canonical transformation enables one to set the new Hamiltonian to constant or zero, but keeps the information about solution in Hamilton’s characteristic function. To benefit from this in quantum theory, one must work with a formulation in which classical Hamiltonian is used. This uniquely points to phase space path integral. However, the main variable in HJ formalism is energy, not time. Thus, we are led to consider the Fourier transform of the path integral, the spectral path integral Z ˜ ( E ) . The evaluation of path integrals reduces to determining the quantum Hamilton characteristic functions (which can be achieved via an asymptotic analysis) and a discrete sum over the quantum period lattice, generalizing Gutzwiller’s sum. Published by the American Physical Society 2025

Türe, Mustafa (ORCID:0009000975968618)↗

DOE OSTI2024

Strong Zero Modes in Integrable Quantum Circuits

It is a classic result that certain interacting integrable spin chains host robust edge modes known as strong zero modes (SZMs). In this Letter, we extend this result to the Floquet setting of local quantum circuits, focusing on a prototypical model providing an integrable Trotterization for the evolution of the XXZ Heisenberg spin chain. By exploiting the algebraic structures of integrability, we show that an exact SZM operator can be constructed for these integrable quantum circuits in certain regions of parameter space. Our construction, which recovers a well-known result by Paul Fendley in the continuous-time limit, relies on a set of commuting transfer matrices known from integrability, and allows us to easily prove important properties of the SZM, including normalizabilty. Our approach is different from previous methods and could be of independent interest even in the Hamiltonian setting. Furthermore, our predictions, which are corroborated by numerical simulations of infinite-temperature autocorrelation functions, are potentially interesting for implementations of the XXZ quantum circuit on available quantum platforms.

1-dimensional spin chains↗

DOE OSTI2025

Two transitions in complex eigenvalue statistics: Hermiticity and integrability breaking

Open quantum systems have complex energy eigenvalues which are expected to follow non-Hermitian random matrix statistics, when chaotic, or two-dimensional (2d) Poisson statistics, when integrable. We investigate the spectral properties of a many-body quantum spin chain, i.e., the Hermitian Heisenberg model with imaginary disorder. Its rich complex eigenvalue statistics is found to separately break both Hermiticity and integrability at different scales of the disorder strength. With no disorder, the system is integrable and Hermitian, with spectral statistics corresponding to the 1d Poisson point process. At very small disorder, we find a transition from 1d Poisson statistics to an effective D -dimensional Poisson point process, showing Hermiticity breaking. At intermediate disorder, we find integrability breaking, as inferred from the statistics matching that of non-Hermitian complex symmetric random matrices in class AI † . For large disorder, as the spins align, we recover the expected integrability (now in the non-Hermitian setup), indicated by 2d Poisson statistics. These conclusions are based on fitting the spin-chain data of numerically generated nearest- and next-to-nearest-neighbor spacing distributions to an effective 2d Coulomb gas description at inverse temperature β . We confirm that such an effective description of random matrices also applies in classes AI † and AII † up to next-to-nearest-neighbor spacings. Published by the American Physical Society 2025

Akemann, Gernot (ORCID:0000000217104258)↗

DOE OSTI2025

Integrated Multiport Conductive and Wireless Architecture for Electric Vehicle Charging

This paper explores the opportunity of integrating conductive and wireless electric vehicle charging architectures and presents an integrated multiport charging architecture suitable for simultaneous conductive and wireless charging of electric vehicles. The architecture successfully integrates the primary side power electronic high frequency inverter and the high frequency transformer with the wireless transmitter and receiver to achieve independent power flow at each port. Design of the integrated magnetics is discussed, and results are presented that demonstrate the decoupled power flow at each port. The proposed integrated architecture increases the utilization of the same charging infrastructure without a proportionate increase in the cost.

Mukherjee, Subho [ORNL] (ORCID:0009000672297925)↗

DOE OSTI2025

RE-INTEGRATE EMT Simulation Software: DAE Solvers and Automation

Existing electromagnetic transient (EMT) simulation tools face challenges in accelerating EMT simulations, especially for very large-scale power networks. To tackle this issue, next generation EMT simulation tools such as RE-INTEGRATE EMT are being researched upon. Such tools should be equipped with automation capabilities and advanced numerical differential-algebraic equation (DAE) solvers. In this paper, the DAE solvers incorporated within the RE-INTEGRATE EMT simulation tool are discussed. In particular, a modified ODEINT-based DAE solver and the ARKODE solver from SUN-DIALS are leveraged within RE-INTEGRATE EMT. In addition, the automation implemented within RE-INTEGRATE EMT to automate the DAE generation (replacing the need of manual discretization and assembling DAEs) is discussed. Different use cases were implemented using the RE-INTEGRATE EMT tool and were validated with respect to baseline simulations.

Marthi, Phani Ratna Vanamali [ORNL] (ORCID:0000000↗

DOE OSTI2024

Retrofittable Advanced Combined Cycle Integration for Flexible Decarbonized Generation

This is the final scientific / technical report for Front End Engineering Design (FEED) study “Retrofittable Advanced Combined Cycle Integration for Flexible Decarbonized Generation” funded by the US Department of Energy (DOE), Office of Fossil Energy and Carbon Management (FECM), Carbon Capture R&D Program under award DE-FE0032131. The prime recipient is General Electric Company working through its Gas Power division (GEGP) with subrecipients Southern Company and Linde Engineering plus subcontractor Kiewit. Southern Company’s Plant Barry, a 2x1 7F.04 CCGT, is the host site. GEGP led the overall integration of the carbon capture system (CCS) with the existing natural gas combined cycle (NGCC) facility. Linde provided the detailed process engineering and equipment costing for the carbon capture island. Kiewit focused on plant layout, constructability, and installation. With the FEED study finished, the engineering is approximately 50% complete towards the detailed design package needed to proceed to procure, install, build, commission, and operate the integrated NGCC+CCS facility. This FEED study focuses on retrofitting a 95% CO 2 capture system with attention on plant integration. The study was particularly challenging due to unique and substantial cost impacts related to global sourcing challenges associated with COVID. Additional incentives, regulatory support, and dispatch certainty are needed to move forward with implementing CCS at this or other sites in the US. This FEED study highlights the value of integrating NGCC+CCS and is a template for future CCS retrofit studies.

42 ENGINEERING↗