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DOE OSTI2025

Stochastic parametric skeletal dosimetry model for humans: Pediatric and adult computational skeleton phantoms for internal bone marrow dosimetry

Currently, computational phantoms that simulate skeletal tissues are used in active red bone marrow (AM) internal dosimetry. Up-to-date reference computational phantoms recommended by the ICRP are based on the analysis of CT-images of cadavers. Such phantoms have significant disadvantages. One disadvantage is that the assessment of uncertainty due to the population variability of skeleton dimensions and microstructure results from the limited availability of autopsy material. Another disadvantage is the simplified modelling of cortical layer and bone microarchitecture. A method of stochastic parametric skeletal dosimetry modelling of the bone structures – SPSD modelling – has been developed as an alternative to the ICRP reference phantoms. In the framework of this approach, skeletal phantom parameters are evaluated based on extensively reviewed results of published measurements of real bones. The SPSD approach allows for the assessment of both population-average values and their variability. SPSD-phantoms of the skeleton are modelled in voxel representation. They consist of smaller phantoms of the bone sites – segments – described by simple geometric shapes with uniform microarchitecture parameters. Such segmentation makes it possible to account for non-homogeneous skeletal microarchitecture and to model the bone structure with the required voxel resolution to elaborate suitable skeletal phantoms. The current study presents the parameters of the SPSD skeletal phantoms for the following age-groups: newborn, 1-year-old, 5-year-old, 10-year-old, 15-year-old (male and female), and adult (male and female). This skeletal phantom can be used for dosimetry as an alternative to available reference phantoms for bone-seeking radionuclides. The above-mentioned age- and sex-specific skeletal phantoms are comprised of 289 unique segments. The characteristics of the SPSD phantoms do not contradict published data and are in good agreement with the measurement results of real bones.

Science & Technology - Other Topics↗

DOE OSTI2026

CoLoRe-2LPT: Lyman-$α$ mock catalogues for the validation of DESI cosmological analyses

The Lyman-$α$ (Ly$α$) forest has become a crucial probe for studying the large-scale structure of the universe at high redshift ($z > 2$), providing powerful constraints on Baryon Acoustic Oscillations (BAO) and the full-shape (FS) clustering of matter. As a key ingredient for upcoming BAO and FS analyses, we present a new generation of fast cosmological Ly$α$ mocks based on second-order Lagrangian perturbation theory (2LPT). These new mocks significantly improve upon previous log-normal approaches, both at accurately capturing small scale clustering and at recovering the non-linear broadening of the BAO peak. They are able to reproduce Ly$α$ statistics within $10\%$ of the latest DESI measurement; including the Ly$α$ bias and the redshift-space distortion $β$ parameter, mean transmitted flux, and 1D power spectrum. The corresponding quasar (QSO) clustering is also improved with respect to previous approaches, calibrated against high-resolution Abacus simulations, recovering the observational QSO linear bias to less than $5\%$ and improving redshift-space distortions via 2LPT velocities and the addition of Fingers-of-God effects. Furthermore, these mocks incorporate high column density systems and metal lines, allowing us to explore the effects and systematics induced by these astrophysical contaminants. This new set of mocks has been key for enhancing the modeling and validation of the DESI DR2 Ly$α$ full shape cosmological analysis. This work provides a physically motivated and computationally efficient tool for simulating current and next-generation Ly$α$ surveys and validating FS and BAO analysis.

Bernal, M.F. Ruiz-Herrera [Madrid, CIEMAT] (ORCID:↗

DOE OSTI2024

End-Use Savings Shapes Upgrade Package Documentation: Wall and Roof Insulation, New Windows, LED Lighting, HP-RTU and ASHP-Boiler

Building on the successfully completed effort to calibrate and validate the U.S. Department of Energy’s ResStock™ and ComStock™ models over the past 3 years, the objective of this work is to produce national data sets that empower analysts working for federal, state, utility, city, and manufacturer stakeholders to answer a broad range of analysis questions. The goal of this work is to develop energy efficiency, electrification, and demand flexibility enduse load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) upgrade measures, or upgrades. “Measures” refers to energy efficiency variables that can be applied to buildings during modeling. An end-use savings shape is the difference in energy consumption between a baseline building and a building with an energy efficiency, electrification, or demand flexibility upgrade applied. It results in a time-series profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

A Framework for Identifying Building Energy Models of Localized Utility Service Areas Using Smart Meter Data

Bottom-up load modeling of buildings offers a versatile approach to simulating baseline demand and scenarios of future technology evolution and adoption at the individual building level. This capability is essential to understanding how future load shapes may change with the adoption of electric equipment and vehicles, particularly as it relates to grid planning and infrastructure investments. Traditionally, grid planning techniques have used historical load data to predict future load and infrastructure needs. However, with the anticipated rise in adoption of electrification technologies such as heat pumps and electric vehicles, historical data become less reliable predictors of the future. By employing ResStock, a high-fidelity building stock modeling tool, we can fine-tune electrification scenarios and aggregate models to represent varying geographic resolutions of the grid system, while considering the underlying features of homes. This may enable a more accurate and responsive approach to anticipate and plan for the evolving landscape of energy demands. We present a new framework that leverages building stock energy modeling to identify building models that align with the load shapes and housing attributes of buildings with AMI data. This approach applies two model layers: (1) a classification step that identifies the presence of air conditioning, electric heating, and electric water heating, and (2) an optimization routine that identifies building energy models aligning with load profile data from advanced metering infrastructure meters. This report demonstrates one approach to deploying this framework, and presents results for three test cases that use both modeled and AMI data to assess performance. For a test case using AMI data in Fort Collins, Colorado, we observed a median monthly electricity load CV-RMSE of 16.6%, and a top ten daily heating and cooling median absolute percent error of 7.7% and 8.3%, respectively. For each AMI meter, we identify a set of potential energy models so that downstream use-cases can account for uncertainty driven by variability of baseline technologies and occupant behavior, which impact the response to electrification and energy efficiency scenarios. Our results indicate that ResStock has potential as a scalable solution for modeling residential energy demand at local grid resolutions. Its performance depends on location-specific factors, underlying building characteristics, and the level of aggregation, offering a path towards more precise and adaptive distribution grid planning for the evolving energy landscape.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Study of impacts of two types of cellular aging on the yeast bud morphogenesis

Understanding the mechanisms of the cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short cell cycle, and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. By analyzing experimental data, this study shows that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional multiscale chemical-mechanical model was developed and used to suggest and test hypothesized impacts of aging on bud morphogenesis. Experimentally calibrated model simulations showed that during the early stage of budding, tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip, a process guided by the polarized Cdc42 signal. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage as observed in experiments in this work. The model simulation results suggest that the localization of new cell surface material insertion, regulated by chemical signal polarization, could be weakened due to cellular aging in yeast and other cell types, leading to the change and stabilization of the bud aspect ratio.

Tsai, Kevin↗

DOE OSTI2026

Design of monolithic piezoelectric bimorph mirrors made from lithium niobate

Recent advances in deformable mirrors based on monolithic piezoelectric substrates, such as lithium niobate, have the potential to improve the image quality of X-ray optical systems on synchrotron and free-electron laser beamlines and microscopes. However, the quantitative relationship between design parameters and the deformed shape has not been readily available in the literature. We present an analytical model, validated through finite element analysis, enabling calculation of tangential and sagittal curvatures based on mirror dimensions, crystallographic orientation, and applied voltage. We demonstrate that through the selection of material orientation, it is possible to achieve different deformed shapes (sphere, cylinder, or hyperbolic paraboloid). This methodology can be generalized to other piezoelectric materials and substrate-integrated actuator systems.

Marzari, Francesco [University of Trento (Italy); ↗

DOE OSTI2025

On the validity and limitations of 1D model for heat and mass transfer performance evaluation in a multilayer binder-free desiccant dehumidifier: isothermal dehumidification with internal cooling

Efficient humidity control is essential for maintaining indoor thermal comfort, yet conventional vapor-compression-based dehumidifiers are energy-intensive. Employing separate sensible and latent cooling through desiccant-coated heat exchangers (DCHEs) combined with evaporative coolers offers energy savings of up to 80 % compared to conventional systems. However, the dehumidification performance of DCHEs remains limited due to the use of polymer binders for coating desiccant materials onto heat exchange surfaces. In our previous study, we developed a multilayer fixed-bed binder-free desiccant dehumidifier (MFBDD) that demonstrated high dehumidification capacity and low pressure drop compared to rotary desiccant wheels. Nevertheless, its potential for further enhancement through internal cooling and the use of step-shaped adsorption isotherms has not been explored. In this study, a physics-based one-dimensional (1D) transient model is developed and validated to capture the coupled heat and mass transfer processes in the MFBDD and extended to simulate internal cooling using a high-capacity composite metal–organic framework, MIL-101/GO-6 (water uptake ≈1.6 g/g within 35–47 % RH). The model enables detailed analysis of local air and bed temperature dynamics and quantifies how internal cooling affects the dehumidification performance under a wide range of operating conditions. Results show that integrating internal cooling and using MIL-101/GO-6 enhance mass adsorbed, moisture removal capacity, and dehumidification effectiveness by 50 %–99 % compared with the M.S. Gel baseline. The study further reveals that achieving near-isothermal operation requires simultaneous enhancement of the convective heat transfer coefficient and heat exchange surface area. In conclusion, this work provides the first detailed physical insight into the interplay between internal cooling and step-shaped isotherms in a binder-free desiccant device and establishes a validated modeling framework for scaling up and system-level performance evaluation of next-generation energy-efficient dehumidification systems.

Heat and mass transfer↗

DOE OSTI2025

Gamma Decay of the 154 Sm Isovector Giant Dipole Resonance: Smekal-Raman Scattering as a Novel Probe of Nuclear Ground-State Deformation

𝛾 decays of the isovector giant dipole resonance (IVGDR) of the deformed nucleus 154 Sm were measured using 2$^{+}_{1}$-Smekal-Raman and elastic scattering of linearly polarized, quasimonochromatic photon beams. The two scattering processes were disentangled through their distinct angular distributions. Their branching ratio and cross sections were determined at six excitation energies covering the 154 Sm IVGDR. Both agree with the predictions of the geometrical model for the IVGDR and confirm 𝛾 decay as an observable sensitive to the structure of the resonance. Consequently, the data place strong constraints on the nuclear shape, including the degree of triaxiality. The derived 154 Sm shape parameters 𝛽 = 0.2925⁢(25) and 𝛾 = 5.0⁢(15)° agree well with other measurements and recent Monte Carlo shell-model calculations.

150 ≤ A ≤ 189↗

DOE OSTI2026

Galaxy Size and Rotation Curve Diversity in ΛCDM with Baryons

The observed rotation curves of dwarf galaxies exhibit significant diversity at fixed halo mass, challenging galaxy formation within the cold dark matter (CDM) model. Previous cosmological galaxy formation simulations with baryonic physics fail to reproduce the full diversity of rotation curves, suggesting that there is a flaw in baryonic feedback models, observational bias, or that an alternative to CDM must be invoked. In this work, we use the Marvelous Massive Dwarf zoom-in simulations, a suite of high-resolution dwarf simulations with M 200 ∼ 10 10 –10 11 M ⊙ and M * ∼ 10 7 –10 9 M ⊙ , designed to target the mass range where the galaxy rotation curve diversity is maximized, i.e., between and 100 km s −1 . We add to this a set of low-mass galaxies from the Marvel Dwarf Zoom Volumes to extend the galaxy mass range to lower values. Our fiducial star formation and feedback models produce simulated dwarfs with a broader range of rotation curve shapes, similar to observations. These simulations both create dark matter cores via baryonic feedback, reproducing the slower-rising rotation curves, while also allowing for compact galaxies and steeply rising rotation curves. Our simulated dwarfs also reproduce the observed size–M * relation, including scatter, producing both extended and compact dwarfs for the first time in simulated field dwarfs. However, the slowly rising and high baryon mass fraction, as well as the steeply rising and low baryon mass fraction, remain missing. We explore star formation and feedback models and conclude that previous simulations may have had feedback that was too strong to produce compact dwarfs.

Cruz, Akaxia [Flatiron Institute, New York, NY (Un↗

DOE OSTI2024

A three-dimensional model of terrain-induced updrafts for movement ecology studies

Abstract Background Spatially explicit simulation models of animal movements through the atmosphere necessarily require a representation of the spatial and temporal variation of atmospheric conditions. In particular, for movements of soaring birds that rely extensively on vertical updrafts to avoid flapping flight, accurate and reliable estimation of the vertical component of wind is critical. The interaction between wind and complex terrain shapes both the horizontal and vertical wind fields, highlighting the need to model the coupling between local terrain features and atmospheric conditions at scales relevant to animal movement. Methods In this work, we propose a new empirical model for estimating the orographic updraft field. The model is developed using computational fluid dynamics simulations of canonical atmospheric conditions over moderately complex terrain. To isolate buoyancy and thermal effects, and focus on terrain-induced effects, we use only simulations of a neutrally stratified atmosphere to develop the model. The model, which we name Engineering Vertical Velocity Estimator (EVVE), is simple to implement and is a function of the underlying terrain elevation map, the desired height above ground level (AGL), and wind conditions at a reference height (80 m). We validate the model with data from the Alaiz mountain (Spain) field campaign. Results Compared to observations, the proposed improved model estimates the updrafts at 120 m AGL with a mean error of 0.11 m/s ( $$\sigma =0.28$$ σ = 0.28 m/s), compared to 0.85 m/s ( $$\sigma =0.58$$ σ = 0.58 m/s) for its baseline. For typical land-based wind turbine hub heights of 80 m AGL, the proposed model has a mean error of 0.04 m/s ( $$\sigma =0.25$$ σ = 0.25 m/s), compared to baseline 0.54 m/s ( $$\sigma =0.45$$ σ = 0.45 m/s) estimations. We illustrate an application of the model in movement ecology by comparing simulated tracks and presence maps of golden eagles ( Aquila chrysaetos ) moving across two distinct landscapes. The tracks and presence maps are obtained using a simple heuristic-based movement model, with the updraft field given by the proposed model and a wind vector-based estimation approach that is currently in wide use in movement ecology studies of raptors and other soaring birds. Conclusions We highlight that movement model results can be sensitive to the underlying orographic updraft model, especially in studies of fine-scale movements in regions of complex topography. We suggest adopting the proposed model rather than the wind vector estimation method for studies of soaring bird movements.

17 WIND ENERGY↗

DOE OSTI2024

Results from a synthetic model of the ITER XRCS-Core diagnostic based on high-fidelity x-ray ray tracing

A high-fidelity synthetic diagnostic has been developed for the ITER core x-ray crystal spectrometer diagnostic based on x-ray ray tracing. This synthetic diagnostic has been used to model expected performance of the diagnostic, to aid in diagnostic design, and to develop engineering tolerances. The synthetic model is based on x-ray ray tracing using the recently developed xicsrt ray tracing code and includes a fully three-dimensional representation of the diagnostic based on the computer aided design. The modeled components are: plasma geometry and emission profiles, highly oriented pyrolytic graphite pre-reflectors, spherically bent crystals, and pixelated x-ray detectors. Plasma emission profiles have been calculated for Xe 44+ , Xe 47+ , and Xe 51+ , based on an ITER operational scenario available through the Integrated Modelling & Analysis Suite database, and modeled within the ray tracing code as a volumetric x-ray source; the shape of the plasma source is determined by equilibrium geometry and an appropriate wavelength distribution to match the expected ion temperature profile. All individual components of the x-ray optical system have been modeled with high-fidelity producing a synthetic detector image that is expected to closely match what will be seen in the final as-built system. Particular care is taken to maintain preservation of photon statistics throughout the ray tracing allowing for quantitative estimates of diagnostic performance.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Efficient general method for numerically modeling laser pulse propagation, overlap, and lifetime effects in amplifiers

An efficient numerical time-dependent general method is developed to address incoherent pulse overlap and lifetime effects in laser amplifiers. The alternating propagation-population laser energetics method (APPLE) has been validated against a semi-discrete coupled rate equation numerical method (SDRE) and analytic formalisms in bounding cases. APPLE is based on decoupled rates applied to a time-dependent framework where both space-time-dependent populations and pulse energetics are consistently updated in each time step. A significant advantage of APPLE lies in its conceptual simplicity, ease of implementation, and relatively small computational cost. SDRE tracks the populations through coupled rates and uses the method of lines to discretize the hyperbolic partial differential transport equations allowing for use of ordinary differential equation solvers. With reasonably sized mesh, we report both energetic and power pulse shape relative differences on the order of one percent between the models over a large range of initial conditions.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Triaxiality and shape dynamics in 70 Ge

The electromagnetic properties of low-lying states in 70 Ge were investigated via multi-step Coulomb excitation of a 70 Ge beam impinging on a 208 Pb target at the ATLAS facility of the Argonne National Laboratory. A total of 27 transitional elements and six diagonal matrix elements coupling 11 low-lying states, were extracted from the measured cross sections. These were used to calculate reduced transition probabilities, spectroscopic quadrupole moments, and rotational invariant shape parameters, providing enhanced precision and expanding on previous studies. The experimental data were compared within several theoretical frameworks, including the generalized triaxial rotor model, configuration interaction shell-model calculations, and computations within the combined frameworks of relativistic density functional theory and the five-dimensional collective Hamiltonian. The results demonstrate a good agreement with the experimental data and, in conjunction with calculations using a two-state mixing model, support significant triaxiality and strong mixing between the 0$^{+}_{1}$ and 0$^{+}_{2}$ states. This results in the magnitudes of their respective quadrupole deformations [β rms (0$^{+}_{1}$) = 0.228 (3), β rms (0$^{+}_{2}$) = 0.273 (1)] being more similar than previously observed. Furthermore, the implications of these results for understanding the complex shape coexistence phenomena, the role of triaxiality, and shape evolution along the Ge isotopic chain are discussed.

59 ≤ A ≤ 89↗

DOE OSTI2025

Multiplicity-dependent jet modification from di-hadron correlations in pp collisions at $ \sqrt{s} $ = 13 TeV

Short-range correlations between charged particles are studied via two-particle angular correlations in pp collisions at $\sqrt{s}$ = 13 TeV. The correlation functions are measured as a function of the relative azimuthal angle ∆φ and the pseudorapidity separation ∆η for pairs of primary charged particles within the pseudorapidity interval |η| < 0.9 and the transverse-momentum range 1 < p T < 8 GeV/c. Near-side (|∆φ| < 1.3) peak widths are extracted from a generalised Gaussian fitted over the correlations in full pseudorapidity separation (|∆η| < 1.8), while the per-trigger associated near-side yields are extracted for the short-range correlations (|∆η| < 1.3). Both are evaluated as a function of charged-particle multiplicity obtained by two different event activity estimators. The width of the near-side peak decreases with increasing multiplicity, and this trend is reproduced qualitatively by the Monte Carlo event generators PYTHIA 8, AMPT, and EPOS. However, the models overestimate the width in the low transverse-momentum region (p T < 3 GeV/c). The per-trigger associated near-side yield increases with increasing multiplicity. Although this trend is also captured qualitatively by the considered event generators, the yield is mostly overestimated by the models in the considered kinematic range. The measurement of the shape and yield of the short-range correlation peak can help us understand the interplay between jet fragmentation and event activity, quantify the narrowing trend of the near-side peak as a function of transverse momentum and multiplicity selections in pp collisions, and search for final-state jet modification in small collision systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Diagnosing hot-spot symmetry in surrogate ignition experiments via secondary DT-neutron spectroscopy at the NIF

The directional energy spectrum of neutrons generated from the in-flight fusion reaction of 1-MeV tritons contains information about the hot-spot symmetry. The National Ignition Facility (NIF) fields Symmetry Capsule (Symcap) implosions, which have historically measured the symmetry of the radiation, drive by measuring the hot-spot shape via x-ray self-emission. Symcaps are used to tune the hot-spot symmetry for ignition experiments at the NIF. This work shows the relationship between directional secondary DT-n spectra and x-ray imaging data for a large database of Symcap implosions. A correlation is observed between the relative widths of the DT-n spectra measured with nTOFs and the shape measured with x-ray imaging. A Monte Carlo model, which computes the directional secondary DT-n spectrum, is used to interpret the results. A comparison of the x-ray and secondary DT-n data with the Monte Carlo model indicates that 56% of the variance between the two datasets is explained by a P2 asymmetry. More advanced simulations using HYDRA suggest that the unaccounted variance is due to P1 and P4 asymmetries present in the hot spot. The comparison of secondary DT-n data and x-ray imaging data to the modeling shows the DT-n data contain important information that supplements current P2 measurements and contain new information about the P1 asymmetry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Diagnosing up-scattered deuterium–tritium fusion neutrons produced in burning plasmas at the National Ignition Facility (invited)

In the push to higher performance fusion plasmas, two critical quantities to diagnose are α-heat deposition that can improve and impurities mixed into the plasma that can limit performance. In high-density, highly collisional inertial confinement fusion burning plasmas, there is a significant probability that deuterium–tritium (DT) fusion products, 14.1 MeV neutrons and 3.5 MeV α-particles, will collide with and deposit energy onto (“up-scatter”) surrounding deuterium and tritium fuel ions. These up-scattered D and T ions can then undergo fusion while in-flight and produce an up-scattered neutron (15–30 MeV). These reaction-in-flight (RIF) neutrons can then be uniquely identified in the measured neutron energy spectrum. Further, the magnitude, shape, and relative size of this spectral feature can inform models of stopping-power in the DT plasma and hence is directly proportional to α-heat deposition. In addition, the RIF spectrum can be related to mix into the burning fuel, particularly relevant for high-Z shell and other emerging National Ignition Facility platforms. The neutron time-of-flight diagnostic upgrades needed to obtain this small signal, ~10 –5 times the primary DT neutron peak, will be discussed. Results from several gain > 1 implosions will be shown and compared to previous RIF spectra. Finally, comparisons of experimental data to a simplified computational model will be made.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Command of three-dimensional solitary waves via photopatterning

Multidimensional solitons are prevalent in numerous research fields. In orientationally ordered soft matter system, three-dimensional director solitons exemplify the localized distortion of molecular orientation. However, their precise manipulation remains challenging due to unpredictable and uncontrolled generation. Here, we utilize preimposed programmable photopatterning in nematics to control the kinetics of director solitons. This enables both unidirectional and bidirectional generation at specific locations and times, confinement within micron-scaled patterns of diverse shapes, and directed propagation along predefined trajectories. A focused dynamical model provides insight into the origins of these solitons and aligns closely with experimental observations, underscoring the pivotal role of anchoring conditions in soliton manipulation. Our findings pave the way for diverse fundamental research avenues and promising applications, including microcargo transportation and optical information processing.

Science & Technology - Other Topics↗

DOE OSTI2026

wavess 1.2: presenting an HLA-aware within-host virus sequence simulation framework

Motivation Understanding how virus sequences are shaped by selection can inform vaccine design and transmission inference. Modeling within-host evolution to interrogate these questions requires a detailed mechanistic framework that accurately captures sequence diversification. The CD8 + cytotoxic T-lymphocyte (CTL) response plays an important role in immune-mediated selection and can leave strong signatures in virus sequences; however, existing sequence-based within-host virus modeling frameworks do not explicitly include a human leukocyte antigen (HLA)-aware CTL response. Results We extended our previously published within-host sequence evolution simulator, wavess, to include an explicit CTL response, and share a method for identifying HLA-specific CTL epitopes given a founder virus sequence. We also updated the model to permit a variable recombination rate, which allows for modeling non-adjacent genes, segmented genomes, and recombination hotspots. These extensions to wavess allow for more accurate simulation of viruses and virus genes, particularly in regions of the genome where the immune response is dominated by CTLs (rather than antibodies). It also provides the foundation for investigations of how these newly-added biological mechanisms influence within-host evolution. Availability and implementation The core of wavess is written in Python 3, with helper functions written in R. It is available at https://github.com/MolEvolEpid/wavess.

60 APPLIED LIFE SCIENCES↗