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Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 8046 CRISPRi perturbations targeting 1721 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual’s response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.
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.
Charged particles interacting with electromagnetic waves have a portion of their energy tied up in wave-driven oscillations. When these waves are localized to the exhaust of linear magnetic confinement systems, this ponderomotive effect can be utilized to enhance particle confinement. The same effect can be derived for particles moving via an E×B drift into a region of a static perturbation to the electromagnetic fields which has a large wave vector component in the direction of the motion. In this work, we use a simplified slab model to self-consistently solve for the electromagnetic fields within the fluid flowing plasma of a static flute-like (k∥=0) perturbation and evaluate the resulting ponderomotive potential. We find that two types of perturbations can exist within the flowing plasma, which are an O wave and an X wave in the frame moving with the fluid. In the case of tenuous plasma, these perturbations are magnetostatic or electrostatic multipole-analog perpendicular to the guiding magnetic field in the lab frame, respectfully. For denser plasmas, the O wave-like perturbation is screened at the electron skin depth scale, and the X wave-like perturbation is a combination of a similar perpendicular electric perturbation and parallel magnetic perturbation. The ponderomotive potential generated in the X wave-like case is gyrofrequency-dependent and can be used as either potential barriers or potential wells, depending on the direction of the flow velocity.
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.
Alfvén eigenmodes have been suppressed and excited in tokamak plasmas by (just) modifying the poloidal spectra of externally applied static magnetic perturbations. This effect is observed experimentally when toroidal spectra of n = 2, n = 4 as well as a mixed spectrum of n = 2 and n = 4 is applied. Under the n = 2 magnetic perturbations, the modes are excited or suppressed by modifying the coil phasing between the upper and the lower set of coils. Regardless of the absolute rotation, an even parity for the n = 4 perturbation is observed to reduce the amplitude of the Alfvénic instabilities, while an odd parity amplifies it. To combine the stabilizing (and destabilizing) effect of n = 2 and n = 4, a mixed spectrum is applied, finding similar reduction (and amplification) trends. However, the impact on the mode amplitude is more subtle, due to the reduced coil current required for a mixed spectrum. The signal level on the fast-ion loss detector is sensitive to the applied poloidal spectrum, which is consistent with Hamiltonian full-orbit modelling of an edge resonant transport layer activated by the 3D perturbative fields. An internal redistribution of the fast-ion population is induced, modifying the phase-space gradients driving the Alfvénic instabilities, and ultimately determining their existence. The calculated edge resonant layers for both n = 2 and n = 4 toroidal spectra are consistent with the observed suppressed and excited phases. Moreover, hybrid kinetic-magnetohydrodynamic (MHD) simulations reveal that this edge resonant transport layer overlaps in phase-space with the population responsible for the fast-ion drive. The results presented here may help to control fast-ion driven Alfvénic instabilities in future burning plasmas with a significant fusion born alpha particle population.
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.
This paper sets up a perturbative treatment of the evolving quantum state of a gravitational system, in a Schrödinger-like picture, working about a general background. This connects gauge symmetry, the constraints, gravitational dressing, and evolution. Starting with a general time slicing, we give a simple derivation of the relation between the constraints, the Hamiltonian, and its well-known boundary term. Among different approaches to quantization with constraints, we focus on a “gauge-invariant canonical quantization,” which is developed perturbatively in the gravitational coupling. The leading-order solution of the constraints (including the Wheeler-DeWitt equation) for perturbations about the background is given in terms of an explicit construction of gravitational dressings built using certain generalized Green’s functions; different such dressings corresponding to adding propagating gravitational waves to a particular solution of the constraints. Dressed operators commute with the constraints, expressing their gauge invariance, and have an algebraic structure differing significantly from the undressed operators of the underlying field theory. These operators can act on the vacuum to create dressed states, and evolution of general such states is then generated by the boundary Hamiltonian, and alternately may be characterized using other relational observables. This provides a concrete approach to studying perturbative time evolution, including the leading gravitational backreaction, of quantum states of black holes with flat or anti–de-Sitter asymptotics, for example on horizon-crossing slices. This description of evolution in turn provides a starting point for investigating possibly important corrections to quantum evolution, that go beyond quantized general relativity. Published by the American Physical Society 2024
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.