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DOE OSTI2025

A hybrid calorimetry-simulation model of mixing enthalpy for molten salt

Calorimetric determination of enthalpies of mixing (ΔH mix ) in multicomponent molten salts is often interpreted using empirical models that lack physically meaningful parameters. However, for improving pyrochemical separation of spent nuclear fuel, where lanthanides are major fission products and critical elements, a deeper thermodynamic understanding of the link between excess thermodynamic properties and solvation structure is critically needed. In this work, we implement a hybrid and physics-informed framework, MIVM+Calorimetry+AIMD, which integrates experimentally measured ΔH mix (via high temperature drop calorimetry) with solvation structures from ab initio molecular dynamics (AIMD). This approach is demonstrated using LaCl 3 mixed with eutectic LiCl-KCl (58 mol% – 42 mol%) at 873 K and 1133 K. MIVM-derived parameters enable extrapolation of excess Gibbs energy and La 3+ activity across compositions. In contrast, direct ΔH mix predictions from AIMD and polarizable ion model simulations deviate significantly. By incorporating experimentally benchmarked solvation structures into an interpretable thermodynamic model, the MIVM+Calorimetry+AIMD formalism achieves higher accuracy and generalizable method for studying molten salts, offering a robust path for understanding and optimizing molten salt chemistry relevant to nuclear fuel cycles and separation science.

Goncharov, Vitaliy G. [Washington State Univ., Pul↗

DOE OSTI2024

Spatially Local Surrogate Modeling of Subgrid-Scale Effects in Idealized Atmospheric Flows: A Deep Learned Approach Using High-Resolution Simulation Data

Abstract We introduce a machine learned surrogate model from high-resolution simulation data to capture the subgrid-scale effects in dry, stratified atmospheric flows. We use deep neural networks (NNs) to model the spatially local state differences between a coarse-resolution simulation and a high-resolution simulation. The setup enables the capture of both dissipative and antidissipative effects in the state differences. The NN model is able to accurately capture the state differences in offline tests outside the training regime. In online tests intended for production use, the NN-coupled coarse simulation has higher accuracy over a significant period of time compared to the coarse-resolution simulation without any correction. We provide evidence of the capability of the NN model to accurately capture high-gradient regions in the flow field. With the accumulation of the errors, the NN-coupled simulation becomes computationally unstable after approximately 90 coarse simulation time steps. Insights gained from these surrogate models further pave the way for formulating stable, complex, physics-based spatially local NN models which are driven by traditional subgrid-scale turbulence closure models. Significance Statement Flows in the atmosphere are highly chaotic and turbulent, comprising flow structures of broad scales. For effective computational modeling of atmospheric flows, the effects of the small- and large-scale structures need to be captured by the simulations. Capturing the small-scale structures requires fine-resolution simulations. Even with the current state-of-the-art supercomputers, it can be prohibitively expensive to simulate these flows when computed for the entire earth over climate time scales. Thus, it is necessary to focus on the larger-scale structures using a coarse-resolution simulation while capturing the effects of the smaller-scale structures using some parameterization (approximation) scheme and incorporating it into the coarse-resolution simulation. We use machine learning to model the effects of the small-scale structures (subgrid-scale effects) in atmospheric flows. Data from a fine-resolution simulation is used to compute the missing subgrid-scale effects in coarse-resolution simulations. We then use machine learning models to approximate these differences between the coarse- and fine-resolution simulations. We see improved accuracy for the coarse-resolution simulations when corrected using these machine learned models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Structural studies of the IFNλ4 receptor complex using cryoEM enabled by protein engineering

Abstract IFNλ4 has posed a conundrum in human immunology since its discovery in 2013, with its expression linked to complications with viral clearance. While genetic and cellular studies revealed the detrimental effects of IFNλ4 expression, extensive structural and functional characterization has been limited by the inability to express and purify the protein, complicating explanations of its paradoxical behavior. In this work, we report a method for robust production of IFNλ4. We then use yeast surface display to affinity-mature IL10Rβ and solve the 72 kilodalton structures of IFNλ4 (3.26 Å) and IFNλ3 (3.00 Å) in complex with their receptors IFNλR1 and IL10Rβ using cryogenic electron microscopy. Comparison of the structures highlights differences in receptor engagement and reveals a distinct 12-degree rotation in overall receptor geometry, providing a potential mechanistic explanation for differences in cell signaling, downstream gene induction, and antiviral activities. Further, we perform a structural analysis using molecular modeling and simulation to identify a unique region of IFNλ4 that, when replaced, enables secretion of the protein from cells. These findings provide a structural and functional understanding of the IFNλ4 protein and enable future comprehensive studies towards correcting IFNλ4 dysfunction in large populations of affected patients.

Science & Technology - Other Topics↗

DOE OSTI2025

Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures

It is essential that mesoscopic simulations of reactive systems reproduce the correct statistical distributions at thermodynamic equilibrium. By considering a compressible fluctuating hydrodynamics (FHD) simulation method of ideal gas mixtures undergoing reversible reactions described by the chemical Langevin equations, we show that thermodynamic consistency in reaction rates and the use of instantaneous temperatures for the evaluation of reaction rates is required for fluctuations for the overall system to be correct. We then formulate the required properties of a thermodynamically consistent reaction (TCR) model. As noted in the literature, while reactions are often discussed in terms of forward and reverse rates, these rates should not be modeled independently because they must be compatible with thermodynamic equilibrium for the system. Using a simple TCR model where each chemical species has constant heat capacity, we derive the explicit condition that the forward and reverse reaction rate constants must satisfy in order for the system to be thermodynamically consistent. We perform equilibrium and non-equilibrium simulations of ideal gas mixtures undergoing a reversible dimerization reaction to measure the fluctuational behavior of the system numerically. We confirm that FHD simulations with the TCR model give the correct static structure factor of equilibrium fluctuations. For the statistically steady simulation of a gas mixture between two isothermal walls with different temperatures, we show using the TCR model that the temperature variance agrees with the corresponding thermodynamic-equilibrium temperature variance in the interior of the system, whereas noticeable deviations are present in regions near walls, where chemistry is far from equilibrium.

Polimeno, Matteo [University of California, Merced↗

DOE OSTI2025

Interactive multiscale modeling to bridge atomic properties and electrochemical performance in Li-CO 2 battery design

Li-CO 2 batteries are promising energy storage systems due to their high theoretical energy density and CO 2 fixation capability, relying on reversible Li 2 CO 3 /C formation during discharge/charge cycles. Here, we present a multiscale modeling framework integrating Density Functional Theory (DFT), Ab-Initio Molecular Dynamics (AIMD), classical Molecular Dynamics (MD), and Finite Element Analysis (FEA) to investigate atomic and cell-level properties. The considered Li-CO 2 battery consists of a lithium metal anode, an ionic liquid electrolyte, and a carbon cloth cathode with Sb 0.67 Bi 1.33 Te 3 catalyst. DFT and AIMD determined the electrical conductivities of Sb 0.67 Bi 1.33 Te 3 and Li 2 CO 3 using the Kubo–Greenwood formalism and studied the CO 2 reduction mechanism on the cathode catalyst. MD simulations calculated the CO 2 diffusion coefficient, Li + transference number, ionic conductivity, and Li + solvation structure. The FEA model, parameterized with atomistic simulation data, reproduced the available experimental voltage–capacity profile at 1 mA/cm 2 and revealed spatio-temporal variations in Li 2 CO 3 /C deposition, porosity, and CO 2 concentration dependence on discharge rates in the cathode. Accordingly, Li 2 CO 3 can form large and thin film deposits, leading to dispersed and local porosity changes at 0.1 mA/cm 2 and 1 mA/cm 2 , respectively. The capacity decreases exponentially from 81,570 mAh/g at 0.1 mA/cm 2 to 6200 mAh/g at 1 mA/cm 2 , due to pore clogging from excessive discharge product deposition that limits CO 2 transport to the cathode interior. Therefore, the performance of Li-CO 2 batteries can be improved by enhancing CO 2 transport, regulating Li 2 CO 3 deposition, and optimizing cathode architecture.

Battery performance↗

DOE OSTI2026

Quantum fluctuations in dense plasma simulations

Molecular dynamics (MD) simulations are a powerful tool for modeling warm and hot dense matter. Density functional theory (DFT) MD simulations are often preferred in dense plasmas in order to accurately model quantum electronic structure. However, DFT-MD simulations neglect interaction effects due to fluctuations in excited states. In this work, we present an MD approach that uses excited state method pseudoatoms to run dense plasma simulations with many different core-electron configurations at classical MD speeds. We also allow for transitions between different configurations in our simulations and find that these fluctuations are especially important for highly excited states. Our results suggest that finite configuration lifetimes that are comparable to the inverse ion plasma frequency need to be accounted for in order to accurately model ion distributions in dense plasma simulations. We also demonstrate that excited state fluctuations have a direct impact on ion plasma microfields, generate different plasma microfields for different excitation levels, and thereby induce absorption–emission line shape asymmetries even in steady-state plasmas.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Advancing Multi-Hazard Risk and Safety Considerations for Aging Nuclear Facilities (Revision 1)

This project will demonstrate a multi-hazard time-dependent probabilistic risk assessment (PRA) approach for nuclear facilities considering aging-related deterioration of structures. A generic pressurized water reactor (PWR) reactor subjected to seismic mainshock-aftershock sequences considering the aging of the containment structure will be used as a case study to demonstrate the multi-hazard PRA approach. Using advanced modeling and simulation, seismic mainshock-aftershock fragility functions will be simulated for the containment structure considering aging effects. A multi-hazard PRA model for a generic PWR reactor will be built to quantify the multi-hazard core damage frequency (CDF) and large early release frequency (LERF) with explicit time-dependent modeling of event sequences. To date, the cascading impacts of multi-hazards are not adequately accounted for in the PRA models for nuclear facilities. In addition, for both initial and periodic evaluation of facilities to withstand natural phenomena hazards (NPH), deterioration of the SSCs due to aging and other effects is not adequately considered. By advancing multi-hazard considerations accounting for aging effects, this project will contribute to improved understanding of the safety of aging nuclear facilities. Project outcomes such as the multi-hazard CDF and LERF will also allow facility owners to optimize upgrade and retrofit protocols. This project is divided into two components: (1) advanced modeling and simulations; and (2) multi-hazard PRA. For the first component, Idaho National Laboratory’s (INL) Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON) and BlackBear codes will be used to simulate the seismic response and damage of a containment structure under cascading mainshock-aftershock sequences with aging effects. Uncertainties related to the seismic inputs, material parameters, and environmental factors such as temperature and humidity will be identified and propagated to the fragility functions. These fragility functions, which consider aging effects, will be time dependent. The second component will take the fragility information from the first component to build a multi-hazard time-dependent PRA model starting from a generic PWR model to evaluate the multi-hazard CDF and LERF and characterize the associated consequences. For this component, OpenPRA Web Application and SAPHIRE code will be used. Events such as the Fukushima Daiichi accident have highlighted the importance of considering the cascading impacts of multi-hazards for PRA. Moreover, many of the reactors in the current nuclear fleet in the United States (US) are already operating well beyond their initially planned design life, and applications for further extensions to operating licenses are being considered. Therefore, considering multi-hazard effects and aging deterioration in the NPH risk assessment process will contribute to the safety of both existing and future nuclear facilities. Outcomes of this project will thus directly benefit the standards DOE-STD-1020-16 and DOE-HDBK-1224-18.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Combining geometric-optical and spectral invariants theories for modeling canopy fluorescence anisotropy

The spectral invariants theory ( p -theory) has received much attention in the field of quantitative remote sensing over the past few decades and has been adopted for modeling of canopy solar-induced chlorophyll fluorescence (SIF). However, the spectral invariant properties (SIP) in simple analytical formulae have not been applied for modeling canopy fluorescence anisotropy primarily because they are parameterized in terms of leaf total scattering, which precludes the differentiation between forward and backward leaf SIF emissions. In this study, we have developed the canopy-SIP SIF model by combining geometric-optical (GO) theory to account for asymmetric leaf SIF forward and backward emissions at the first-order scattering and by modeling multiple scattering based on the p-theory, thus avoiding the dependence on radiative transfer models. The applicability of the model simulations especially over 3D heterogeneous canopies was improved by incorporating canopy structure through multi-angular clumping index, and by modeling single scattering from the four components of the scene in view according to the GO approach. The results show good consistency with both the state-of-the-art SIF models and multi-angular field SIF observations over grass and chickpea canopies. Further, the coefficient of determination (R²) between the simulated SIF and field measurements was 0.75 (red) and 0.74 (far-red) for chickpea, and 0.65 (both red and far-red) for grass. The average relative error was approximately 3% for 1D homogeneous scenes when comparing the canopy-SIP SIF model simulations to the SCOPE model simulations, and around 4% for the 3D heterogeneous scene when comparing to the LESS model simulations. The results indicate that the proposed approach for separating asymmetric leaf SIF emissions is a robust way to keep a balance between satisfactory simulation accuracy and efficiency. Model simulations suggest that neglecting the leaf SIF asymmetry can lead to an underestimation of canopy red SIF by 6.3% to 42.6% for various leaf biochemical and canopy structural parameters. This study presents a simple but efficient analytical approach for canopy fluorescence modeling, with potential for large-scale canopy fluorescence simulations.

3D heterogeneous structure↗

DOE OSTI2024

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d -Block

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper here we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Testing the thermal Sunyaev-Zel’dovich power spectrum of a halo model using hydrodynamical simulations

Statistical properties of large-scale cosmological structures serve as powerful tools for constraining the cosmological properties of our Universe. Tracing the gas pressure, the thermal Sunyaev-Zel’dovich (tSZ) effect is a biased probe of mass distribution and, hence, can be used to test the physics of feedback or cosmological models. Therefore, it is crucial to develop robust modelling of hot gas pressure for applications to tSZ surveys. Since gas collapses into bound structures, it is expected that most of the tSZ signal is within halos produced by cosmic accretion shocks. Hence, simple empirical halo models can be used to predict the tSZ power spectra. In this study, we employed the HMx halo model to compare the tSZ power spectra with those of several hydrodynamical simulations: the Horizon suite and the Magneticum simulation. We examine various contributions to the tSZ power spectrum across different redshifts, including the one- and two-halo term decomposition, the amount of bound gas, the importance of different masses, and the electron pressure profiles. Our comparison of the tSZ power spectrum reveals discrepancies between the halo model and cosmological simulations that increase with redshift. We find a 20% to 50% difference between the measured and predicted tSZ angular power spectrum over the multipole range ℓ = 10 3 − 10 4 . Our analysis reveals that these differences are driven by the excess of power in the predicted two-halo term at low k and in the one-halo term at high k . At higher redshifts ( z ∼ 3), simulations indicate that more power comes from outside the virial radius than from inside, suggesting a limitation in the applicability of the halo model. We also observe differences in the pressure profiles, despite the fair level of agreement on the tSZ power spectrum at low redshift with the default calibration of the halo model. In conclusion, our study suggests that the properties of the halo model need to be carefully controlled against real or mock data to be proven useful for cosmological purposes.

Ayçoberry, Emma (ORCID:0000000292351195)↗

DOE OSTI2025

Block-Structured Operator Inference for Coupled Multiphysics Model Reduction

This work presents a block-structured formulation of Operator Inference as a way to learn structured reduced-order models for multiphysics systems. The approach specifies the governing equation structure for each physics component and the structure of the coupling terms. Once the multiphysics structure is specified, the reduced-order model is learned from snapshot data following the nonintrusive Operator Inference methodology. In addition to preserving physical system structure, which in turn permits preservation of system properties such as stability and second-order structure, the block-structured approach has the advantages of reducing the overall dimensionality of the learning problem and admitting tailored regularization for each physics component. The numerical advantages of the block-structured formulation over a monolithic Operator Inference formulation are demonstrated for aeroelastic analysis, which couples aerodynamic and structural models. For the benchmark test case of the AGARD 445.6 wing, block-structured Operator Inference provides an average 20% online prediction speedup over monolithic Operator Inference across subsonic and supersonic flow conditions in both the stable and fluttering parameter regimes while preserving the accuracy achieved with monolithic Operator Inference.

42 ENGINEERING↗

DOE OSTI2025

A fully-integrated lattice Boltzmann method for fluid–structure interaction

Here we present a fully-integrated lattice Boltzmann (LB) method for fluid–structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples finite-strain solids to the LB fluid on the same fixed computational grid with the reference map technique (RMT). An integral part of the LBRMT is a new LB boundary condition for moving deformable interfaces across different densities. With this fully Eulerian solid–fluid coupling, the LBRMT is well-suited for parallelization and simulating multi-body contact without remeshing or extra meshes. We validate its accuracy via a benchmark of a deformable solid in a lid-driven cavity, then showcase its versatility through examples of soft solids rotating and settling. The LBRMT achieves a spatial convergence rate between first-order and second-order for FSI simulations and is designed for low to intermediate Reynolds number flows with finite inertia at small Mach numbers. With simulations of complex suspensions mixing, we highlight the potential of the LBRMT for studying collective behavior in soft matter and biofluid dynamics.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Multiple Pathways of Influence for Tightly and Loosely Structured Organizations: Implications for Systems Resilience

Organizations play a key role in supporting various societal functions, ranging from environmental governance to the manufacturing of goods. Here, the behaviors of organization are impacted by various influences, including information, technology, authority, economic leverage, historical experiences, and external factors, such as regulations. This paper introduces a generalized framework, focused on the relative structure of an organization (tight vs. loose), that can be used to understand how different influence pathways can impact decision-making within differently structured organizations. This generalized framework is then translated into a modeling and simulation platform to support and assess implications of these structural differences in resilience to disinformation (measured by organizational behaviors of timeliness and inclusion of quality information) using a systems dynamics approach Preliminary results indicate that a tightly structured organization may be less timely at processing information but could be more resilient against using poor quality information in organizational decisions compared to a loosely structured organization. Ongoing work is underway to understand the robustness of these findings and to validate current model design activities with empirical insights.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2025

Initial Engineering Framework for Species Tracking in MSRs Involving Fuel Salt and Structures

This report implements a high-fidelity multiphysics modeling framework using the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program tools to track leaching and plating of materials between the fuel salt and structures in Molten Salt Reactors (MSRs). Specifically, this framework is demonstrated in modeling various processes within MSRs including hot and cold leg corrosion, redox potential driven corrosion, colloid precipitation and deposition, and noble metal plating and decay heat modeling. The model integrates neutronics, thermal-hydraulics, depletion, and thermochemistry to simulate the evolving chemical behavior of the fuel salt in interactions with structural materials. Initial findings suggest that hot-cold leg corrosion in MSR systems may become significant if the redox potential of the fuel salt is not sufficiently controlled. Additionally, the impact of noble metal decay heat deposition in large power reactors is explored. The resulting engineering framework for species tracking will be applied in the future toward specific validation work with ongoing experimental efforts focusing on both chloride and fluoride salt loop experiments with in-situ corrosion and redox control instrumentation.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Cosmological Hydrodynamics at Exascale: A Trillion-Particle Leap in Capability

Resolving the most fundamental questions in cosmology requires simulations that match the scale, fidelity, and physical complexity demanded by next-generation sky surveys. To achieve the realism needed for this critical scientific partnership, detailed gas dynamics must be treated self-consistently with gravity for end-to-end modeling of structure formation. Exascale computing enables simulations that span survey-scale volumes while incorporating key astrophysical processes that shape complex cosmic structures. We present results from CRK-HACC, a cosmological hydrodynamics code built for extreme scalability. Using separation-of-scale techniques, GPU-resident tree solvers, in situ analysis pipelines, and multi-tiered I/O, CRK-HACCexecuted Frontier-E: a four trillion particle full-sky simulation, over an order of magnitude larger than previous efforts. The run achieved 513.1 PFLOPs peak performance, processing 46.6 billion particles per second and writing more than 100 PB of data in just over one week of runtime. Frontier-E marks a significant advance in predictive modeling for next-generation cosmological science.

Frontiere, Nicholas [Argonne National Laboratory (↗

DOE OSTI2024

How well are hazards associated with derechos reproduced in regional climate simulations?

Abstract. A 15-member ensemble of convection-permitting regional simulations of the fast-moving and destructive derecho of 29–30 June 2012 that impacted the northeastern urban corridor of the USA is presented. This event generated 1100 reports of damaging winds, generated significant wind gusts over an extensive area of up to 500 000 km2, caused several fatalities, and resulted in widespread loss of electrical power. Extreme events such as this are increasingly being used within pseudo-global-warming experiments to examine the sensitivity of historical, societally important events to global climate non-stationarity and how they may evolve as a result of changing thermodynamic and dynamic contexts. As such it is important to examine the fidelity with which such events are described in hindcast experiments. The regional simulations presented herein are performed using the Weather Research and Forecasting (WRF) model. The resulting ensemble is used to explore simulation fidelity relative to observations for wind gust magnitudes, spatial scales of convection (as is manifest in high composite reflectivity, cREF), and both rainfall and hail production as a function of model configuration (microphysics parameterization, lateral boundary conditions (LBCs), start date, use of nudging, compiler choice, damping, and number of vertical levels). We also examine the degree to which each ensemble member differs with respect to key mesoscale drivers of convective systems (e.g., convective available potential energy and vertical wind shear) and critical manifestations of deep convection, e.g., vertical velocities, cold-pool generation, and how those properties relate to the correct characterization of the associated atmospheric hazards (wind gusts and hail). Use of a double-moment, seven-class scheme with number concentrations for all species (including hail and graupel) results in the greatest fidelity of model-simulated wind gusts and convective structure to the observations of this event. All ensemble members, however, fail to capture the intensity of the event in terms of the spatial extent of convection and the production of high near-surface wind gusts. We further show very high sensitivity to the LBCs employed and specifically that simulation fidelity is higher for simulations nested within ERA-Interim compared to ERA5. Excess convective available potential energy (CAPE) in all ensemble members after the derecho passage leads to excess production of convective cells, wind gusts, cREF > 40 dBZ, and precipitation during a frontal passage on the subsequent day. This event proved very challenging to forecast in real time and to reproduce in the 15-member hindcast simulation ensemble presented here. Future work could examine if simulations with other initial and lateral boundary conditions can achieve greater fidelity.

Shepherd, Tristan (ORCID:0000000186276419)↗

DOE OSTI2025

Discrete-Event Model of WIPP Operations

The Waste Isolation Pilot Plant (WIPP) is the critical component of the Department of Energy's (DOE) Transuranic Radioactive Waste (TRU) disposition infrastructure. Quantifying the operations ofWIPP with a discrete-event model demonstrates the capability to assess efficiency, identity bottlenecks, and improve future operations. Such a model has been developed with the simulation software ExtendSim. This report outlines the structure of that model, summarizes the model's successful reproduction of the annual amount of emplaced waste, and demonstrates that WIPP is successfully receiving and emplacing waste at a rate consistent with the rate at which the waste arrives. The model serves as a first step toward future production enhancements at WIPP. Those enhancements will rely on close collaboration with the Carlsbad Field Office (CBFO), accurate interpretation and incorporation of the model results, and effective planning with other DOE Environmental Management (DOE-EM) entities.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Integrating chromosome conformation and DNA repair in a computational framework to assess cell radiosensitivity

Objective. The arrangement of chromosomes in the cell nucleus has implications for cell radiosensitivity. The development of new tools to utilize Hi-C chromosome conformation data in nanoscale radiation track structure simulations allows for in silico investigation of this phenomenon. We have developed a framework employing Hi-C-based cell nucleus models in Monte Carlo radiation simulations, in conjunction with mechanistic models of DNA repair, to predict not only the initial radiation-induced DNA damage, but also the repair outcomes resulting from this damage, allowing us to investigate the role chromosome conformation plays in the biological outcome of radiation exposure. Approach. In this study, we used this framework to generate cell nucleus models based on Hi-C data from fibroblast and lymphoblastoid cells and explore the effects of cell type-specific chromosome structure on radiation response. The models were used to simulate external beam irradiation including DNA damage and subsequent DNA repair. The kinetics of the simulated DNA repair were compared with previous results. Main results. We found that the fibroblast models resulted in a higher rate of inter-chromosome misrepair than the lymphoblastoid model, despite having similar amounts of initial DNA damage and total misrepairs for each irradiation scenario. Significance. This framework represents a step forward in radiobiological modeling and simulation allowing for more realistic investigation of radiosensitivity in different types of cells.

59 BASIC BIOLOGICAL SCIENCES↗