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At least 1,261 records · Page 70

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗

Effects of finite material size on axion-magnon conversion

Magnetic materials are particularly favorable targets for detecting axions interacting with electrons because the collective excitation of electron spins, the magnon, can be excited through the axion-magnon conversion process. It is often assumed that only the zero-momentum uniformly precessing magnetostatic (Kittel) mode of the magnon is excited. This is justified if the de Broglie wavelength of the axion is much longer than the size of the target magnetic material. However, if the de Broglie wavelength is shorter, finite-momentum magnon modes can also be excited. We systematically analyze the target material size dependence of the axion-magnon conversion rate. We discuss the importance of these effects in the detection of relativistic axions as well as in the detection of axion dark matter of relatively heavy mass with large material size.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Completely dark matter from rapid-turn multifield inflation

We study cosmological gravitational particle production as applied to “rapid-turn” models of inflation involving two scalar fields. We are interested in the production of massive spin-0 particles that only interact gravitationally and provide a candidate for the dark matter. Specifically, we study two models of rapid-turn multifield inflation, motivated in part by the de Sitter swampland conjecture, that are distinguished by the curvature of field space and the presence or absence of field space ‘angular momentum’ conservation. We find that one of these models leads to insufficient particle production and cannot explain the observed dark matter relic abundance. The second model is able to explain the origin of spin-0 dark matter via gravitational production, and we identify the relevant region of parameter space that is consistent with measurements of the dark-matter relic abundance, the dark-matter-photon isocurvature perturbations, and the spectrum of curvature perturbations that is probed by cosmological observations. Our work demonstrates the compatibility of the de Sitter swampland conjecture with completely dark matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Global aspects of conformal symmetry and the ANEC in dS and AdS

Starting from the averaged null energy condition (ANEC) in Minkowski we show that conformal symmetry implies the ANEC for a conformal field theory (CFT) in a de Sitter and anti-de Sitter background. A similar and novel bound is also obtained for a CFT in the Lorentzian cylinder. Using monotonicity of relative entropy, we rederive these results for dS and the cylinder. As a byproduct we obtain the vacuum modular Hamiltonian and entanglement entropy associated to null deformed regions of CFTs in (A)dS and the cylinder. A third derivation of the ANEC in dS is shown to follow from bulk causality in AdS/CFT. Finally, we use the Tomita-Takesaki theory to show that Rindler positivity of Minkowski correlators generalizes to conformal theories defined in dS and the cylinder.

79 ASTRONOMY AND ASTROPHYSICS↗

Compact scalars at the cosmological collider

Abstract We study the dynamics of scalar fields with compact field spaces, or axions, in de Sitter space. We argue that the field space topology can qualitatively affect the physics of these fields beyond just which terms are allowed in their actions. We argue that the sharpest difference is for massless fields — the free massless noncompact scalar field does not admit a two-point function that is both de Sitter-invariant and well-behaved at long distances, while the massless compact scalar does. As proof that this difference can be observable, we show that the long-distance behavior of a heavy scalar field, and thus its cosmological collider signal, can qualitatively change depending on whether it interacts with a light compact or noncompact scalar field. We find an interesting interplay between the circumference of the field space and the Hubble scale. When the field space is much larger than Hubble, the compact field behaves similarly to a light noncompact field and forces the heavy field to dilute much faster than any free field can. However, depending on how much smaller the field space is compared to Hubble, the compact field can cause the heavy scalar to decay either faster or slower than any free field and so we conclude that there can be qualitative and observable consequences of the field space’s topology in inflationary correlation functions.

Physics↗

The cosmological bootstrap: inflationary correlators from symmetries and singularities

Scattering amplitudes at weak coupling are highly constrained by Lorentz invariance, locality and unitarity, and depend on model details only through coupling constants and the particle content of the theory. For example, four-particle amplitudes are analytic for contact interactions and have simple poles with appropriately positive residues for tree-level exchange. In this paper, we develop an understanding of inflationary correlators which parallels that of flat-space scattering amplitudes. Specifically, we study slow-roll inflation with weak couplings to extra massive particles, for which all correlation functions are controlled by an approximate conformal symmetry on the boundary of the spacetime. After systematically classifying all possible contact terms in de Sitter space, we derive an analytic expression for the four-point function of conformally coupled scalars mediated by the tree-level exchange of massive scalars. Conformal symmetry implies that the correlator satisfies a pair of differential equations with respect to spatial momenta, encoding bulk time evolution in purely boundary terms. The absence of unphysical singularities (and the correct normalization of physical ones) completely fixes this correlator. Moreover, a “spin-raising” operator relates it to the correlators associated with the exchange of particles with spin, while “weight-shifting” operators map it to the four-point function of massless scalars. We explain how these de Sitter four-point functions can be perturbed to obtain inflationary three-point functions. Using our formalism, we reproduce many classic results in the literature, such as the three-point function of slow-roll inflation, and provide a complete classification of all inflationary three- and four-point functions arising from weakly broken conformal symmetry. Remarkably, the inflationary bispectrum associated with the exchange of particles with arbitrary spin is completely characterized by the soft limit of the simplest scalar-exchange four-point function of conformally coupled scalars and a series of contact terms. Finally, we demonstrate that the inflationary correlators contain flat-space scattering amplitudes via a suitable analytic continuation of the external momenta, which can also be directly connected with the signals for particle production seen in the squeezed limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Positivity from Cosmological Correlators

Abstract Effective field theories in flat space and in anti-de Sitter space are constrained by causality and unitarity, often in the form of positivity bounds. Similar bounds have been harder to demonstrate in cosmological backgrounds, where the roles of unitarity and causality are more obscure. Fortunately, the expansion of the universe ensures that late-time cosmological correlators are effectively classical and the role of unitarity is played by classical statistical inequalities. For multi-field inflation, the resulting positivity constraints have long been known in terms of the Suyama-Yamaguchi inequality. In this paper, we demonstrate that similar statistical bounds imply nontrivial constraints for massive fields in the early universe. We show that any real anomalous dimensions for principal series fields in de Sitter space must be positive. We also derive a limit on the amplitude of particular oscillatory signals from inflation, including those arising in cosmological collider physics. Finally, we demonstrate that these constraints manifest themselves directly in the two-point statistics of matter and galaxies that will be measured in upcoming surveys.

Physics↗

Cosmological decoherence from thermal gravitons

A bstract We study the effects of gravitationally-driven decoherence on tunneling processes associated with false vacuum decays, such as the Coleman-De Luccia instanton. We compute the thermal graviton-induced decoherence rate for a wave function describing a perfect fluid of nonzero energy density in a finite region. When the effective cosmological constant is positive, the thermal graviton background sourced by a de Sitter horizon provides an unavoidable decoherence effect, which may have important consequences for tunneling processes in cosmological history. We discuss generalizations and consequences of this effect and comment on its observability and applications to black hole physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Hyperbolic vacua in Minkowski space

Families of Lorentz, but not Poincare, invariant vacua are constructed for a massless scalar field in 4D Minkowski space. These are generalizations of the Rindler vacuum with a larger symmetry group. Explicit expressions are given as squeezed excitations of the Poincare vacuum. The effective reduced vacua on the 3D hyperbolic de Sitter slices are the well-known de Sitter α-vacua with antipodal singularities in the Wightman function. Several special interesting cases are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Geometries with mismatched branes

We study Randall-Sundrum two brane setups with mismatched brane tensions. For the vacuum solutions, boundary conditions demand that the induced metric on each of the branes is either de Sitter, Anti-de Sitter, or Minkowski. For incompatible boundary conditions, the bulk metric is necessarily time-dependent. This introduces a new class of time-dependent solutions with the potential to address cosmological issues and provide alternatives to conventional inflationary (or contracting) scenarios. We take a first step in this paper toward such solutions. One important finding is that the resulting solutions can be very succinctly described in terms of an effective action involving only the induced metric on either one of the branes and the radion field. But the full geometry cannot necessarily be simply described with a single coordinate patch. We concentrate here on the time- dependent solutions but argue that supplemented with a brane stabilization mechanism one can potentially construct interesting cosmological models this way. This is true both with and without a brane stabilization mechanism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Stochastic Inflation at NNLO

Stochastic Inflation is an important framework for understanding the physics of de Sitter space and the phenomenology of inflation. In the leading approximation, this approach results in a Fokker-Planck equation that calculates the probability distribution for a light scalar field as a function of time. Despite its successes, the quantum field theoretic origins and the range of validity for this equation have remained elusive, and establishing a formalism to systematically incorporate higher order effects has been an area of active study. In this paper, we calculate the next-to-next-to-leading order (NNLO) corrections to Stochastic Inflation using Soft de Sitter Effective Theory (SdSET). In this effective description, Stochastic Inflation manifests as the renormalization group evolution of composite operators. The leading impact of non-Gaussian quantum fluctuations appears at NNLO, which is presented here for the first time; we derive the coefficient of this term from a two-loop anomalous dimension calculation within SdSET. We solve the resulting equation to determine the NNLO equilibrium distribution and the low-lying relaxation eigenvalues. In the process, we must match the UV theory onto SdSET at one-loop order, which provides a non-trivial confirmation that the separation into Wilson-coefficient corrections and contributions to initial conditions persists beyond tree level. Furthermore, these results illustrate how the naive factorization of time and momentum integrals in SdSET no longer holds in the presence of logarithmic divergences. It is these effects that ultimately give rise to the renormalization group flow that yields Stochastic Inflation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Linking the singularities of cosmological correlators

Much of the structure of cosmological correlators is controlled by their singularities, which in turn are fixed in terms of flat-space scattering amplitudes. An important challenge is to interpolate between the singular limits to determine the full correlators at arbitrary kinematics. This is particularly relevant because the singularities of correlators are not directly observable, but can only be accessed by analytic continuation. In this paper, we study rational correlators — including those of gauge fields, gravitons, and the inflaton — whose only singularities at tree level are poles and whose behavior away from these poles is strongly constrained by unitarity and locality. We describe how unitarity translates into a set of cutting rules that consistent correlators must satisfy, and explain how this can be used to bootstrap correlators given information about their singularities. We also derive recursion relations that allow the iterative construction of more complicated correlators from simpler building blocks. In flat space, all energy singularities are simple poles, so that the combination of unitarity constraints and recursion relations provides an efficient way to bootstrap the full correlators. In many cases, these flat-space correlators can then be transformed into their more complex de Sitter counterparts. As an example of this procedure, we derive the correlator associated to graviton Compton scattering in de Sitter space, though the methods are much more widely applicable.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Asymptotic Behavior of Cosmologies with $$\Lambda >0$$ in $$2+1$$ Dimensions

We study, using mean curvature flow methods, 2+1 dimensional cosmologies with a positive cosmological constant and matter satisfying the dominant and the strong energy conditions. If the spatial slices are compact with non-positive Euler characteristic and are initially expanding everywhere, then we prove that the spatial slices reach infinite volume, asymptotically converge on average to de Sitter and they become, almost everywhere, physically indistinguishable from de Sitter. This holds true notwithstanding the presence of initial arbitrarily-large density fluctuations and the formation of black holes.

79 ASTRONOMY AND ASTROPHYSICS↗

Fundamental complement of a gravitating region

Any gravitating region a in any spacetime gives rise to a generalized entanglement wedge, the hologram e(a). Holograms exhibit properties expected of fundamental operator algebras, such as strong subadditivity, nesting, and no-cloning. But the entanglement wedge EW of an AdS boundary region B with commutant $\overline{B}$ satisfies an additional condition, complementarity: EW (B) is the spacelike complement of EW ($\overline{B}$) in the bulk. Here we identify an analogue of the boundary commutant $\overline{B}$ in general spacetimes: given a gravitating region a, its fundamental complement is the smallest wedge that contains all infinite world lines contained in the spacelike complement a' of a. We refine the definition of e(a) by requiring that it be spacelike to $\tilde{a}$. We prove that e(a) is the spacelike complement of e($\tilde{a}$) when the latter is computed in a'. We exhibit many examples of and of e(a) in de Sitter, flat, and cosmological spacetimes. Here, we find that a Big Bang cosmology (spatially closed or not) is trivially reconstructible: the whole universe is the entanglement wedge of any wedge inside it. But de Sitter space is not trivially reconstructible, despite being closed. We recover the AdS/CFT prescription by proving that EW (B) = e(causal wedge of B).

Bousso, Raphael [University of California, Berkele↗

Energy absorption of architectured PrintCast interpenetrating composites in tension

Additively manufactured (AM) metal-metal composites consisting of PrintCasted 316 L austenitic stainless-steel lattice structures infiltrated with A356 casting alloy, have recently been developed for use in high energy absorption systems with potential applications ranging from static load bearing to dynamic blast containment structures. This system has a unique mechanical behavior as the volume fraction of lattice increases showing a transition from localized to de-localized failure and dramatic increase in energy absorption capability. In this work, PrintCast A356/316 L composite tensile specimens were produced with lattice volume fractions ranging from 20 % to 50 % to capture the range of this behavior. Finite element simulations support neutron diffraction measurements of stress state. Results illustrate that in tension, the reinforcement material is in tension while the matrix support material is in compression, information offering significant insight into the transition to de-localized failure. Moreover, the simulation results provide further insight into how interfacial bonding (or lack of bonding) affects the energy absorption capabilities of the PrintCast composites.

36 MATERIALS SCIENCE↗

Corrigendum to “Cool Rooms for Indoor Heat Resilience: Evaluating Affordable Cooling Strategies in Heat-Stressed California Homes” [Building and Environment 287 (2026) 113877]

The authors regret an error in the acknowledgments section regarding the U.S. Department of Energy Solar Energy Technologies Office award number. The previously listed grant number, 2597–1625, was incorrect. The corrected acknowledgment should read: “This work was supported by the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Building Technologies of the United States Department of Energy (DOE), under Contract No. DE-AC02–05CH11231. This material is based upon work supported by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE) under the Solar Energy Technologies Office Award Number DE-EE00040384. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the Department of Energy.” The authors would like to apologise for any inconvenience caused.

Malik, Jeetika↗

Bayesian reduced-order deep learning surrogate model for dynamic systems described by partial differential equations

We propose a reduced-order deep-learning surrogate model for dynamic systems described by time-dependent partial differential equations. This method employs space–time Karhunen–Loève expansions (KLEs) of the state variables and space-dependent KLEs of space-varying parameters to identify the reduced (latent) dimensions. Subsequently, a deep neural network (DNN) is used to map the parameter latent space to the state variable latent space. An approximate Bayesian method is developed for uncertainty quantification (UQ) in the proposed KL-DNN surrogate model. The KL-DNN method is tested for the linear advection–diffusion and nonlinear diffusion equations, and the Bayesian approach for UQ is compared with the deep ensembling (DE) approach, commonly used for quantifying uncertainty in DNN models. It was found that the approximate Bayesian method provides a more informative distribution of the PDE solutions in terms of the coverage of the reference PDE solutions (the percentage of nodes where the reference solution is within the confidence interval predicted by the UQ methods) and log predictive probability. The DE method is found to underestimate uncertainty and introduce bias. For the nonlinear diffusion equation, we compare the KL-DNN method with the Fourier Neural Operator (FNO) method and find that KL-DNN is 10% more accurate and needs less training time than the FNO method.

97 MATHEMATICS AND COMPUTING↗

Graviton-photon oscillations in an expanding universe

Through the Gertsenshtein effect, the presence of a large external B-field may allow photons and gravitons to mix in a way that resembles neutrino oscillations and is even more similar to axion-photon mixing. Assuming a background B-field (or any field that behaves like one), we examine the Gertsenshtein mechanism in the context of FLRW expanding universe models, as well as de Sitter space. The conformal invariance of Maxwell’s equations and the conformal noninvariance of the Einstein equations preclude the operation of the Gertsenshtein effect at all scales. In general we find for the matter- and radiation-dominated cases, graviton-oscillations are possible only at late conformal times or when the wavelengths are much shorter than the horizon (kn $\gg$ 1), but that the time-dependent oscillations eventually damp out in any case. Further, the presence of charged particles additionally damps out the oscillations. For the de Sitter universe, we find that oscillations are possible only at early conformal times (n $\ll$ H -1 ) and for wavelengths short compared to the Hubble radius, but eventually freeze in when wavelengths become longer than the Hubble radius. In principle a Gertsenshtein-like mechanism might influence the balance of particle species in an inflationary phase before freezing in; however, we find that in all our models the mixing length is larger than the Hubble radius. We discuss several possible remedies to this situation.

79 ASTRONOMY AND ASTROPHYSICS↗