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DOE OSTI2023

A solvable model of a nonlinear extension of quantum mechanics

We introduce a particular nonlinear generalization of quantum mechanics which has the property that it is exactly solvable in terms of the eigenvalues and eigenfunctions of the Hamiltonian of the usual linear quantum mechanics problem. Here, we hope that this simple example will elucidate some of the issues of interpreting nonlinear generalization of quantum mechanics that have been put forth to resolve questions about quantum measurement theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Scalar-tensor extension of the ΛCDM model

We construct a cosmological scalar-tensor-theory model in which the Brans-Dicke type scalar Φ enters the effective (Jordan-frame) Hubble rate as a simple modification of the Hubble rate of the ΛCDM model. This allows us to quantify differences between the background dynamics of scalar-tensor theories and general relativity (GR) in a transparent and observationally testable manner in terms of one single parameter. Problems of the mapping of the scalar-field degrees of freedom on an effective fluid description in a GR context are discused. Data from supernovae, the differential age of old galaxies and baryon acoustic oscillations are shown to strongly limit potential deviations from the standard model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Scale genesis and gravitational wave in a classically scale invariant extension of the standard model

We assume that the origin of the electroweak (EW) scale is a gauge-invariant scalar-bilinear condensation in a strongly interacting non-abelian gauge sector, which is connected to the standard model via a Higgs portal coupling. The dynamical scale genesis appears as a phase transition at finite temperature, and it can produce a gravitational wave (GW) background in the early Universe. We find that the critical temperature of the scale phase transition lies above that of the EW phase transition and below few O(100) GeV and it is strongly first-order. We calculate the spectrum of the GW background and find the scale phase transition is strong enough that the GW background can be observed by DECIGO.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

CRPropa 3.1—a low energy extension based on stochastic differential equations

The propagation of charged cosmic rays through the Galactic environment influences all aspects of the observation at Earth. Energy spectrum, composition and arrival directions are changed due to deflections in magnetic fields and interactions with the interstellar medium. Today the transport is simulated with different simulation methods either based on the solution of a transport equation (multi-particle picture) or a solution of an equation of motion (single-particle picture). We developed a new module for the publicly available propagation software CRPropa 3.1, where we implemented an algorithm to solve the transport equation using stochastic differential equations. This technique allows us to use a diffusion tensor which is anisotropic with respect to an arbitrary magnetic background field. The source code of CRPropa is written in C++ with python steering via SWIG which makes it easy to use and computationally fast. In this paper, we present the new low-energy propagation code together with validation procedures that are developed to proof the accuracy of the new implementation. Furthermore, we show first examples of the cosmic ray density evolution, which depends strongly on the ratio of the parallel κ{sub ∥} and perpendicular κ{sub ⊥} diffusion coefficients. This dependency is systematically examined as well the influence of the particle rigidity on the diffusion process.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Multi-field effects in a simple extension of R {sup 2} inflation

We consider inflation in the system containing a Ricci scalar squared term and a canonical scalar field with quadratic mass term. In the Einstein frame this model takes the form of a two-field inflation model with a curved field space, and under the slow-roll approximation contains four free parameters corresponding to the masses of the two fields and their initial positions. We investigate how the inflationary dynamics and predictions for the primordial curvature perturbation depend on these four parameters. Our analysis is based on the δ N formalism, which allows us to determine predictions for the non-Gaussianity of the curvature perturbation as well as for quantities relating to its power spectrum. Depending on the choice of parameters, we find predictions that range from those of R {sup 2} inflation to those of quadratic chaotic inflation, with the non-Gaussianity of the curvature perturbation always remaining small. Using our results we are able to put constraints on the masses of the two fields.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Extensive analysis of reconstruction algorithms for DESI 2024 baryon acoustic oscillations

Reconstruction of the baryon acoustic oscillation (BAO) signal has been a standard procedure in BAO analyses over the past decade and has helped to improve the BAO parameter precision by a factor of ∼2 on average. The Dark Energy Spectroscopic Instrument (DESI) BAO analysis for the first year (DR1) data uses the “standard” reconstruction framework, in which the displacement field is estimated from the observed density field by solving the linearized continuity equation in redshift space, and galaxy and random positions are shifted in order to partially remove non-linearities. There are several approaches to solving for the displacement field in real survey data, including the multigrid (MG), iterative Fast Fourier Transform (iFFT), and iterative Fast Fourier Transform particle (iFFTP) algorithms. In this work, we analyze these algorithms and compare them with various metrics including two-point statistics and the displacement itself using realistic DESI mocks. We focus on three representative DESI samples, the emission line galaxies (ELG), quasars (QSO), and the bright galaxy sample (BGS), which cover the extreme redshifts and number densities, and potential wide-angle effects. We conclude that the MG and iFFT algorithms agree within 0.4% in post-reconstruction power spectrum on BAO scales with the RecSym convention, which does not remove large-scale redshift space distortions (RSDs), in all three tracers. The RecSym convention appears to be less sensitive to displacement errors than the RecIso convention, which attempts to remove large-scale RSDs. However, iFFTP deviates from the first two; thus, we recommend against using iFFTP without further development. In addition, we provide the optimal settings for reconstruction for five years of DESI observation. The analyses presented in this work pave the way for DESI DR1 analysis as well as future BAO analyses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

pKPDB: a protein data bank extension database of p Ka and pI theoretical values

Abstract Summary pKa values of ionizable residues and isoelectric points of proteins provide valuable local and global insights about their structure and function. These properties can be estimated with reasonably good accuracy using Poisson–Boltzmann and Monte Carlo calculations at a considerable computational cost (from some minutes to several hours). pKPDB is a database of over 12 M theoretical pKa values calculated over 120k protein structures deposited in the Protein Data Bank. By providing precomputed pKa and pI values, users can retrieve results instantaneously for their protein(s) of interest while also saving countless hours and resources that would be spent on repeated calculations. Furthermore, there is an ever-growing imbalance between experimental pKa and pI values and the number of resolved structures. This database will complement the experimental and computational data already available and can also provide crucial information regarding buried residues that are under-represented in experimental measurements. Availability and implementation Gzipped csv files containing p Ka and isoelectric point values can be downloaded from https://pypka.org/pKPDB. To query a single PDB code please use the PypKa free server at https://pypka.org. The pKPDB source code can be found at https://github.com/mms-fcul/pKPDB. Supplementary information Supplementary data are available at Bioinformatics online.

Reis, Pedro B. P. S. (ORCID:0000000335636239)↗
DOE OSTI2020

Extensions to models of the galaxy–halo connection

ABSTRACT We explore two widely used empirical models for the galaxy–halo connection, subhalo abundance matching (SHAM) and the halo occupation distribution (HOD), and compare them with the hydrodynamical simulation IllustrisTNG (TNG) for multiple statistics quantifying the galaxy distribution at $n_{\rm gal}\approx 1.3\times 10^{-3}\, ({\rm Mpc}\,h^{-1})^{-3}$. We observe that in their most straightforward implementations, both models fail to reproduce the two-point clustering measured in TNG. We find that SHAM models that use the relaxation velocity, Vrelax, and the peak velocity, Vpeak, perform best, and match the clustering reasonably well, although neither captures adequately the one-halo clustering. Splitting the total sample into sub-populations, we discover that SHAM overpredicts the clustering of high-mass, blue, star-forming, and late-forming galaxies and underpredicts that of low-mass, red, quiescent, and early-forming galaxies. We also study various baryonic effects, finding that subhaloes in the dark-matter-only simulation have consistently higher values of their SHAM-proxy properties than their full-physics counterparts. We then consider a 2D implementation of the HOD model augmented with a secondary parameter (environment, velocity anisotropy, σ2Rhalf-mass, and total potential) tuned so as to match the two-point clustering of the IllustrisTNG galaxies on large scales. We analyse these galaxy populations adopting alternative statistical tools such as galaxy–galaxy lensing, void–galaxy cross-correlations, and cumulants of the density field, finding that the hydrodynamical galaxy distribution disfavours σ2Rhalf-mass and the total potential as secondary parameters, while the environment and velocity anisotropy samples are consistent with full physics across all statistical probes examined. Our results demonstrate the power of examining multiple statistics for determining the secondary parameters that are vital for understanding the galaxy–halo connection.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Diffuse supernova neutrino background from extensive core-collapse simulations of 8–100 M ⊙ progenitors

Here we revisit the diffuse supernova neutrino background in light of recent systematic studies of stellar core collapse that reveal the quantitative impacts of the progenitor conditions on the collapse process. In general, the dependence of the core-collapse neutrino emission on the progenitor is not monotonic in progenitor initial mass, but we show that it can, at first order, be characterized by the core compactness. For the first time, we incorporate the detailed variations in the neutrino emission over the entire mass range 8–100 M ⊙ , based on (i) a long-term simulation of the core collapse of an 8.8 M ⊙ ONeMg core progenitor, (ii) over 100 simulations of iron core collapse to neutron stars, and (iii) half a dozen simulations of core collapse to black holes (the ‘failed channel’). The fraction of massive stars that undergo the failed channel remains uncertain, but in view of recent simulations which reveal high compactness to be conducive to collapse to black holes, we characterize the failed fraction by considering a threshold compactness above which massive stars collapse to black holes and below which the final remnant is a neutron star. We predict that future detections of the diffuse supernova neutrino background may have the power to reveal this threshold compactness, if its value is relatively small as suggested by interpretations of several recent astronomical observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

The spatial extension of extended narrow line regions in MaNGA AGN

ABSTRACT In this work, we revisit the size–luminosity relation of the extended narrow line regions (ENLRs) using a large sample of nearby active galactic nuclei (AGNs) from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey. The ENLRs ionized by the AGN are identified through the spatially resolved BPT diagram, which results in a sample of 152 AGN. By combining our AGN with the literature high-luminosity quasars, we found a tight log-linear relation between the size of the ENLR and the AGN $\rm [O\, III]$λ5007 Å luminosity over four orders of magnitude of the $\rm [O\, III]$ luminosity. The slope of this relation is 0.42 ± 0.02 which can be explained in terms of a distribution of clouds photoionized by the AGN. This relation also indicates that the AGNs have the potential to ionize and heat the gas clouds at a large distance from the nuclei without the aids of outflows and jets for the low-luminosity Seyferts.†

Chen, Jianhang↗
DOE OSTI2019

Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures

Abstract Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis

Abstract Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Nonparametric extensions of nuclear equations of state: Probing the breakdown scale of relativistic mean-field theory

Phenomenological calculations of the properties of dense matter, such as relativistic mean-field theories, represent a pathway to predicting the microscopic and macroscopic properties of neutron stars. However, such theories do not generically have well-controlled uncertainties and may break down within neutron stars. To faithfully represent the uncertainty in this breakdown scale, we develop a hybrid representation of the dense-matter equation of state, which assumes the form of a relativistic mean-field theory at low densities, while remaining agnostic to any nuclear theory at high densities. To achieve this, we use a nonparametric equation of state model to incorporate the correlations of the underlying relativistic mean-field theory equation of state at low pressures and transition to more flexible correlations above some chosen pressure scale. We perform astrophysical inference under various choices of the transition pressure between the theory-informed and theory-agnostic models. Here, we further study whether the chosen relativistic mean-field theory breaks down above some particular pressure and find no such evidence. Using simulated data for future astrophysical observations at about two-to-three times the precision of current constraints, we show that our method can identify the breakdown pressure associated with a potential strong phase transition.

Equations of state of nuclear matter↗