SEARCH · Search NASA
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Explore the source record for details and available documents.
Advances in sequencing technologies have enhanced the understanding of gene regulation in cells. In particular, Perturb-seq has enabled high-resolution profiling of the transcriptomic response to genetic perturbations at the single-cell level. This understanding has implications in functional genomics and potentially for identifying therapeutic targets. Various computational models have been developed to predict perturbational effects. While deep learning models excel at interpolating observed perturbational data, they tend to overfit in the lack of enough data and may not generalize well to unseen perturbations. In contrast, mechanistic models, such as linear causal models based on gene regulatory networks, hold greater potential for extrapolation, as they encapsulate regulatory information that can predict responses to unseen perturbations. However, their application has been limited to small studies due to overly simplistic assumptions, making them less effective in handling noisy, large-scale single-cell data. We propose a hybrid approach that combines a mechanistic causal model with variational deep learning, termed Single Cell Causal Variational Autoencoder (SCCVAE). The mechanistic model employs a learned regulatory network to represent perturbational changes as shift interventions that propagate through the learned network. SCCVAE integrates this mechanistic causal model into a variational autoencoder, generating rich, comprehensive transcriptomic responses. Our results indicate that SCCVAE exhibits superior performance over current state-of-the-art baselines for extrapolating to predict unseen perturbational responses. Additionally, for the observed perturbations, the latent space learned by SCCVAE allows for the identification of functional perturbation modules and simulation of single-gene knockdown experiments of varying penetrance, presenting a robust tool for interpreting and interpolating perturbational responses at the single-cell level.
Superdiffusive transport with dynamical exponent z=3/2 has been firmly established at finite temperature for a class of integrable systems with a non-Abelian global symmetry G. On the inclusion of integrability-breaking perturbations, diffusive transport with z=2 is generically expected to hold in the limit of late time. Recent studies of the classical Haldane-Ishimori-Skylanin model have found that perturbations that preserve the global symmetry lead to a much slower time scale for the onset of diffusion, albeit with uncertainty over the exact scaling exponent. That is, for perturbations of strength λ, the characteristic timescale for diffusion goes as t*∼λ−α for some α. Using large-scale matrix product state simulations, we investigate this behavior for perturbations to the canonical quantum model showing superdiffusion: the S=1/2 quantum Heisenberg chain. We consider a ladder configuration and look at various perturbations that either break or preserve the SU(2) symmetry, leading to scaling exponents consistent with those observed in one classical study [McCarthy , Phys. Rev. B 110, L180301 (2024)2469-995010.1103/PhysRevB.110.L180301]: α=2 for symmetry-breaking terms and α=6 for symmetry-preserving terms. We also consider perturbations from another integrable point of the ladder model with G=SU(4) and find consistent results. Finally, we consider a generalization to an SU(3) ladder and find that the α=6 scaling appears to be universal across superdiffusive systems when the perturbations preserve the non-Abelian symmetry G.
Griffin is a Multiphysics Object-Oriented Simulation Environment (MOOSE) based reactor Multiphysics analysis application, jointly developed by Argonne and Idaho National Laboratories under the DOE-NE NEAMS program. This fiscal year, capabilities for reactivity and sensitivity evaluation using perturbation methods were implemented and verified. The First Order Perturbation Method (FOPT) was employed to compute reactivity worth resulting from small perturbations in input parameters, while the Generalized Perturbation Theory (GPT) was used to evaluate sensitivities of a range of response types, including reaction rate ratio, k-eigenvalue, neutron generation time, and effective delayed neutron fraction. These perturbation methods enable users to quantify how response quantities change due to a perturbation in a input parameter without explicitly performing an additional transport simulation for each perturbed state. In particular, the GPT formulation accounts for indirect effects arising from flux changes by solving generalized inhomogeneous equations, for which a Neumann series-based iterative solution method was developed and implemented in Griffin. The implemented reactivity and sensitivity evaluation capabilities were verified using two test problems: an infinite homogeneous system and a two-dimensional hexagonal core. The results showed excellent agreement with reference solutions obtained by a direct method based on finite difference approximation as well as GPT-based results from the PERSENT code, confirming the accuracy of both reactivity and sensitivity evaluations. Additionally, preliminary uncertainty quantification (UQ) results were obtained by combining the sensitivity values computed using GPT and external covariance data, demonstrating that the implemented sensitivity results can be reliably used for uncertainty calculations. To further demonstrate the generality and practical strength of the implementation, the sensitivity evaluation capability was successfully applied to the Empire microreactor with a geometrically complex design that poses significant modeling challenges. The results confirm that Griffin enables sensitivity evaluations even for irregular and highly heterogeneous reactor configurations, thereby establishing a foundation for UQ applications in advanced reactor designs and analyses.
Cosmological data provides us two key constraints on dark matter (DM): it must have a particular abundance, and it must have an adiabatic spectrum of density perturbations in the early universe. Many different cosmological scenarios have been proposed that establish the abundance of axion DM in qualitatively different ways. In this paper we emphasize that, despite this variety of backgrounds, the perturbations in axion DM can be understood from universal principles. How does a feebly interacting axion field acquire perturbations proportional to those of photons? How do the isocurvature power spectrum and non-Gaussianity depend on the background evolution of the universe? We answer these questions for a completely general choice of cosmological background and temperature-dependent axion potential. We show that the most general solution to the axion field equation on super-horizon scales is entirely determined by the family of background solutions for different initial field values . This holds for both the component in the field perturbation solution contributing to the DM isocurvature perturbation (enhanced at late times by the sensitivity of the DM abundance to the initial condition, , which can be large for initial conditions near the hilltop), and the other component that contributes to the DM curvature perturbation. In particular, we explain that an unperturbed axion field in the early universe evolving into one with nontrivial adiabatic perturbations is guaranteed by Weinberg's theorem on adiabatic modes. These results have been derived before with various assumptions, such as a radiation dominated background or a quadratic potential. Our aim is to give a clear, simple derivation that is manifestly independent of those assumptions, and thus can be applied to any cosmological axion scenario.
The nodal diffusion method is one of the most widely used approaches in modern reactor analysis. In the nodal diffusion method, a coarse multi-group set of “homogenized” parameters is constructed such that the complex geometry of a reactor core along with the energy dependence of neutron and gamma ray cross sections in a nuclear reactor are conserved in the simpler geometry. The homogenization is typically done on a fuel assembly level as is the case in the DIF3D code developed at Argonne National Laboratory. The nodal methodology is used primarily to predict fuel cycle behavior of nuclear systems of which there is a substantial amount of validation in the literature. Another use of the nodal method is to obtain reactivity coefficients and kinetics parameters for use in a safety analysis of a given nuclear reactor. While there are many ways to obtain reactivity worth and kinetics parameters, the work presented in this manuscript is unique as it provides the user with the ability to compute reactivity worths, kinetics parameters, and cross section sensitivities with a Cartesian and hexagonal geometry based transport code. This manuscript serves as a single manual for two separate codes: VARI3D and PERSENT. The VARI3D code (VARIational 3D) is based upon the classic finite difference diffusion theory solver available in DIF3D. The PERSENT code (PERturbation and SENitivity for Transport) is based upon the variational nodal method employed in DIF3D termed VARIANT. The VARIANT solver was added to DIF3D in 1995 and has seen continued development and use for the last 18 years. Because VARI3D primarily uses deprecated coding practices, rather than incorporating the perturbation and sensitivity treatments for transport within VARI3D, a new coding development was built using modern Fortran coding. The primary purpose of this manual is to describe the theory behind PERSENT (and by convenience, that of VARI3D) and discuss the input and output of PERSENT along with giving potential users an idea of how to use it. While this manuscript does describe the input and output of VARI3D, the PERSENT code is intended to be the replacement capability of VARI3D as PERSENT can generate nearly identical (if not superior) diffusion theory results. In this manuscript, the relevant aspects of generalized perturbation theory and exact perturbation theory that apply to both VARI3D and PERSENT are covered. The input and output of VARI3D is displayed by excerpting several of the example problems. Similarly, the input and output of PERSENT is displayed along with tips on how best to use the code. Note that the input and output of the inhomogeneous solver wrapped around DIF3D (DIF3D_IFS) is also discussed as it is needed to carry out some of the sensitivities in PERSENT such as reaction rate ratios. This manuscript describes several perturbation and sensitivity problems, and the results computed using PERSENT. From these sections, potential users should find that PERSENT provides not only the typical tables of numbers desired in perturbation and sensitivity analysis work, but also can visually plot the result for a more thorough understanding of the space and energy distribution (Section 5). Overall, PERSENT is observed to produce accurate reactivity worths and sensitivities for the displayed set of test problems and clearly demonstrates the need to have a transport-based sensitivity capability as evident from the thousands of percent errors observed in the 21-group hexagonal fast reactor problem (covered in Section 7). The uncertainty calculation capability is described in Section 3 and demonstrated in Section 7.
Fast ion (FI) loss properties in the presence of tearing mode and internal kink perturbations are numerically investigated for discharges in the MAST-U spherical tokamak, utilizing the MARS-F magnetohydrodynamic stability code and the REORBIT test particle guiding-center orbit-following module. Here, tracing about 100 000 particle markers sampled from the equilibrium distribution of the neutral-beam injection induced FIs, it is found that about 10% out of the total strike the limiting surface (including the divertor surface) in MAST-U discharge 46943, assuming a maximum perturbation of 100 G inside the plasma (corresponding to ~6 G at the Mirnov probe location at the outboard mid-plane). Detailed particle tracing, assuming a uniform initial distribution in the 2D phase space (at given radial locations), reveals that initially counter-current FIs launched near the plasma edge are subject to significant prompt losses, while almost all initially co-current ions remain well confined at the assumed perturbation level. Most lost FIs strike the lower-half of the limiting surface. Finite gyro-radius effects prevent lost ions from striking the top-outer corner of the super-X divertor chamber. A scan of the perturbation level (based on discharge 45163) reveals, not surprisingly, an approximately linear scaling of the particle loss fraction (for counter-current FIs) with respect to the perturbation amplitude.
The study of perturbations around black hole backgrounds in general relativity and Einstein-Maxwell theory has a long history, going back to the work of Regge and Wheeler in the 1950s. As part of a broader investigation of perturbations around black holes in supergravity, we describe here our results for the perturbations around the Gibbons-Maeda static charged black holes in a class of Einstein-Maxwell-Dilaton theories. Our analysis follows the general strategy developed by Chandrasekhar and Xanthopoulos for the perturbations of the Reissner-Nordström black hole. Here, the analysis is considerably more involved, because of the presence of the dilaton field, which couples to the other polar modes. We nonetheless find that the problem is completely solvable, in the sense that one can separate variables and eventually describe all the perturbations in terms of diagonalised second-order radial equations. We are able to prove the mode stability of all the Gibbons-Maeda black hole solutions. Published by the American Physical Society 2024
We investigate the production of dark matter from metric perturbations produced during inflation or in standard cosmology. Perturbations break Weyl flatness of the Friedmann-Lemaître-Robertson-Walker metric, allowing conformally coupled fields—in particular, fermions studied here—to be produced even when their mass is negligible. Particle production can be computed by studying the Bogoliubov transformation induced by the stochastic background. For perturbations generated during inflation, we present a closed formula for the resulting abundance of particles that depends solely on the power spectrum of curvature perturbations at the end of inflation. This production mechanism can be dominant especially if the amplitude of curvature perturbations is enhanced for modes that exit the horizon toward the end of inflation. In the simplest scenario, the critical dark matter abundance is reproduced for M ≳ 10 6 GeV . Published by the American Physical Society 2025
Subspace projection methods utilizing perturbative corrections have been proposed for computing the lowest few eigenvalues and corresponding eigenvectors of large Hamiltonian matrices. In this paper, we build upon these methods and introduce the term Subspace Projection with Perturbative Corrections (SPPC) method to refer to this approach. We tailor the SPPC for nuclear many-body Hamiltonians represented in a truncated configuration interaction subspace, i.e., the no-core shell model (NCSM). We use the hierarchical structure of the NCSM Hamiltonian to partition the Hamiltonian as the sum of two matrices. The first matrix corresponds to the Hamiltonian represented in a small configuration space, whereas the second is viewed as the perturbation to the first matrix. Eigenvalues and eigenvectors of the first matrix can be computed efficiently. Because of the split, perturbative corrections to the eigenvectors of the first matrix can be obtained efficiently from the solutions of a sequence of linear systems of equations defined in the small configuration space. These correction vectors can be combined with the approximate eigenvectors of the first matrix to construct a subspace from which more accurate approximations of the desired eigenpairs can be obtained. We show by numerical examples that the SPPC method can be more efficient than conventional iterative methods for solving large-scale eigenvalue problems such as the Lanczos, block Lanczos and the locally optimal block preconditioned conjugate gradient (LOBPCG) method. The method can also be combined with other methods to avoid convergence stagnation.
This paper presents perturbative experiments that enable the validation and development of control-oriented models for exhaust control. We identify the response of the divertor plasma and scrape-off layer in the DIII-D tokamak to deuterium and nitrogen multi-sine perturbations, in favorable and unfavorable field directions for H-mode access. We obtained good signal-to-noise ratios in the 1–10 Hz frequency range by measuring Balmer-alpha, Lyman-alpha, and N 4+ line emission, radiated power, and neutral pressure. We find a similar phase response across gas species and magnetic field directions, while the gain response is nonlinear. With these experiments, we identify a control-oriented model to design a divertor radiated power controller to track specified reference waveforms in conjunction with resonant magnetic perturbations. Although the physics basis for compatibility between detachment and resonant magnetic perturbation edge-localized mode suppression remains to be demonstrated, the present results provide a robust controller that represents a promising step toward future joint control strategies.
A careful theoretical analysis of the excitation of Alfvén eigenmodes (AEs), such as TAE (toroidicity-induced AE) and RSAE (reversed shear AE), by superalfvenic energetic particles is required for reliable predictions of energetic ion relaxation in present day fusion experiments. This includes the evaluation of different AE damping mechanisms including radiative and continuum dampings which are the focus of this study. A recent comprehensive benchmark of different eigenmode solvers including gyrokinetic, gyrofluid and hybrid magenetohydrodynamics (MHD) has shown that employed models may have deficiencies when addressing some of them (Taimourzadeh et al., Nucl. Fusion, vol. 59, 2019, 066006). Here, in this paper, we are studying the radiative and continuum dampings of RSAEs in details which were missing in hybrid NOVA/NOVA-C calculations to prepare a NOVA-C package with a substantial upgrade. Both dampings require the finite Larmor radius (FLR) corrections to AE mode structures to be accounted for. Accurately calculating different damping rates and understanding their parametric dependencies, we resolve the limitation coming out of the perturbative approach. In particular, here, the radiative damping is included perturbatively, whereas the continuum damping is computed non-perturbatively. Our comparison leads to the conclusion that the non-perturbative treatment of the unstable RSAE modes is needed to find the agreement with the gyrokinetic calculations. We expect that the RSAE mode structure modification plays a dominant role in determining the RSAE stability.
Quantum spin Hall insulators (QSHIs) leverage strong spin-orbit coupling (SOC) for efficient spin manipulation, making them promising for spintronics. Here, in this study, we investigate the noncollinear Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between two magnetic impurities in a perturbed Kane-Mele model with strong SOC, relevant to monolayer jacutingaite Pt 2 HgSe 3 as a prominent QSHI. Following the previous studies that mainly focused on the model and its general applications, we provide a systematic examination of the effects of various perturbations and strong spin-orbit hybridizations, which drive phase transitions that have not been extensively explored before. By incorporating these perturbations into the model and accurately accounting for spin-orbit hybridizations through spin-space Green's functions and the RKKY interactions, we uncover distinct, relative (rather than absolute) signatures of different phase transitions. These phase transitions are induced by both static and dynamic perturbations on the magnetic impurities. Notably, we identify additional phases emerging from the interplay with the magnetic substrate. All these influence the switching between ferromagnetic and antiferromagnetic, as well as clockwise and counterclockwise magnetic interactions. Our results provide a practical way to track topological phases through magnetic properties, offering new insights into phase control and spin manipulation in QSHIs.
In this study, we investigate the reliability of cluster perturbation (CP) theory applied to the calculation of electronically excited states through a comprehensive benchmark. In CP theory, perturbative corrections are added to the properties of a parent excitation space, which converge toward the properties of a target excitation space. For the CPS(D-n) model, perturbative corrections through order n are added to the coupled cluster singles (CCS) excitation energies to target the coupled cluster singles and doubles (CCSD) excitation energies. Through a comparative analysis of excitation energy calculations across a diverse set of molecules and wavefunction methods, we present a comprehensive evaluation of the accuracy of the third-order CPS(D) model, CPS(D-3), in calculating excitation energies. Further, our findings demonstrate that CPS(D-3) is a reliable alternative to established methods, particularly CCSD, while systematically overestimating the excitation energies compared to high-level coupled cluster methods such as CC3. These results highlight the strengths and limitations of CPS(D-3), as well as the promising directions for its future development.
We develop a framework for Large Scale Structure (LSS) perturbation theory, that solves the Vlasov-Poisson system of equations for the distribution function in full phase space. This approach relaxes the usual apriori assumption of negligible velocity dispersion underlying the Standard Perturbation Theory (SPT). We apply the new method to rederive the usual SPT kernels up to third order in the perturbative expansion. We also show that a counterterm, identical to the one introduced by standard Effective Field Theory (EFT) methods, naturally arises within our framework. We finish by making a precise connection to EFT techniques, which reveals the necessity of the EFTofLSS to self-consistently model the long-wavelength fluid, and illustrates the importance of having theoretical control over short distance fluctuations.
We show that multi-field inflationary models with negligible turning in field space during inflation can lead to an effective sourcing of adiabatic from entropic perturbations afterthe end of inflation. We illustrate this general phenomenon with a detailed analysis of an inflationary model whose scalar potential is determined by modular invariance. Its entropic perturbations are frozen during inflation, but instead, they are converted into adiabatic perturbations in the first post-inflationary e-folds. The curvature power spectrum, giving rise to CMB fluctuations, reaches a novel and enhanced plateau in this process; we address the implications for the inflationary observables As , n s and r.
Solenoid-free tokamak startup techniques are essential for spherical tokamaks and offer a pathway to cost reduction and design simplification in fusion energy systems. Local helicity injection (LHI) is one such approach, employing compact edge current sources to drive open field line current that initiates and sustains tokamak plasmas. The recently commissioned Pegasus-III Experiment provides a platform for advancing this and other solenoid-free startup methods. This study investigates the effect of LHI on magnetic topology in Pegasus-III plasmas. A helical filament model represents the injected current, and the linear plasma response to its three-dimensional field is calculated with M3D-C1. Poincaré mapping reveals substantial flux surface degradation in all modeled cases. The onset of overlapping magnetic structures and large-scale surface deformation begins near Ψ N ≈ 0.37, indicating a broad region of perturbed topology extending toward the edge. In rotating plasmas, both single-fluid and two-fluid models exhibit partial screening of the n = 1 perturbation, with two-fluid calculations showing stronger suppression near the edge. In contrast, the absence of rotation leads to strong resonant field amplification in the single-fluid case, while the two-fluid case with zero electron rotation mitigates this amplification and preserves edge screening. Magnetic probe measurements indicate that modeling the stream with spatial spreading—representing distributed current and/or oscillatory motion—better reproduces measured magnetic power profiles than a rigid filament model. The results underscore the role of rotation and two-fluid physics in screening stream perturbations and point to plasma flow measurements and refined stream models as key steps toward improving predictive fidelity.
We present an explicitly gauge-invariant observable of any general gravitational perturbation, ℎ 𝜇𝜈 [not necessarily due to gravitational waves (GWs)], in a laser interferometry-based GW detector, identifying the signature as the proper time elapsed of the beamsplitter observer, between two events: when a photon passes through the beamsplitter, and when the same photon returns to the beamsplitter after traveling through the interferometer arm and reflecting off the far mirror. Our formalism applies to simple Michelson interferometers and can be generalized to more advanced setups. We demonstrate that the proper time observable for a plane GW is equivalent to the detector strain commonly used by the GW community, though now the common framework can be easily generalized for other types of signals, such as dark matter clumps or spacetime fluctuations from quantum gravity. We provide a simple recipe for computing the proper time observable for a general metric perturbation in linearized gravity and explicitly show that it is invariant under diffeomorphisms of the perturbation, as any physical observable should be.