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DOE OSTI2014

Conservative GRMHD simulations of moderately thin, tilted accretion disks

This paper presents our latest numerical simulations of accretion disks that are misaligned with respect to the rotation axis of a Kerr black hole. In this work, we use a new, fully conservative version of the Cosmos++ general relativistic magnetohydrodynamics (GRMHD) code, coupled with an ad hoc cooling function designed to control the thickness of the disk. Together these allow us to simulate the thinnest tilted accretion disks ever using a GRMHD code. In this way, we are able to probe the regime where the dimensionless stress and scale height of the disk become comparable. We present results for both prograde and retrograde cases. The simulated prograde tilted disk shows no sign of Bardeen-Petterson alignment even in the innermost parts of the disk. The simulated retrograde tilted disk, however, does show modest alignment. The implication of these results is that the parameter space associated with Bardeen-Petterson alignment for prograde disks may be rather small, only including very thin disks. Unlike our previous work, we find no evidence for standing shocks in our simulated tilted disks. We ascribe this to the black hole spin, tilt angle, and disk scale height all being small in these simulations. We also add to the growing body of literature pointing out that the turbulence driven by the magnetorotational instability in global simulations of accretion disks is not isotropic. Finally, we provide a comparison between our moderately thin, untilted reference simulation and other numerical simulations of thin disks in the literature.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

ION KINETIC ENERGY CONSERVATION AND MAGNETIC FIELD STRENGTH CONSTANCY IN MULTI-FLUID SOLAR WIND ALFVÉNIC TURBULENCE

We investigate the properties of plasma fluid motion in the large-amplitude, low-frequency fluctuations of highly Alfvénic fast solar wind. We show that protons locally conserve total kinetic energy when observed from an effective frame of reference comoving with the fluctuations. For typical properties of the fast wind, this frame can be reasonably identified by alpha particles which, due to their drift with respect to protons at about the Alfvén speed along the magnetic field, do not partake in the fluid low-frequency fluctuations. Using their velocity to transform the proton velocity into the frame of Alfvénic turbulence, we demonstrate that the resulting plasma motion is characterized by a constant absolute value of the velocity, zero electric fields, and aligned velocity and magnetic field vectors as expected for unidirectional Alfvénic fluctuations in equilibrium. We propose that this constraint, via the correlation between velocity and magnetic field in Alfvénic turbulence, is the origin of the observed constancy of the magnetic field; while the constant velocity corresponding to constant energy can only be observed in the frame of the fluctuations, the corresponding constant total magnetic field, invariant for Galilean transformations, remains the observational signature in the spacecraft frame of the constant total energy in the Alfvén turbulence frame.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Consistency relations and conservation of ζ in holographic inflation

It is well known that, in single clock inflation, the curvature perturbation ζ is constant in time on superhorizon scales. In the standard bulk description this follows quite simply from the local conservation of the energy momentum tensor in the bulk. On the other hand, in a holographic description, the constancy of the curvature perturbation must be related to the properties of the RG flow in the boundary theory. Here, we show that, in single clock holographic inflation, the time independence of correlators of ζ follows from the absence of the anomolous dimension of the energy momentum tensor in the boundary theory, and from the so-called consistency relations for vertex functions with a soft leg.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Albedo-induced global warming impact of Conservation Reserve Program grasslands converted to annual and perennial bioenergy crops

Abstract Climate benefit assessments of bioenergy crops often focus on biogeochemical impacts, paying little if any attention to biogeophysical impacts. However, land conversions required for large-scale bioenergy crop production are substantial and may directly affect the climate by altering surface energy balance. In the US, such land conversions are likely to be met in part by converting Conservation Reserve Program (CRP) grassland to bioenergy crops. Here, we converted three 22 year old CRP smooth brome grass fields into no-till corn, switchgrass, or restored prairie bioenergy crops. We assessed the biogeophysical climate impact of the conversions using albedo changes relative to unconverted reference CRP grassland. The corn and perennial fields had higher annual albedo than the grassland they replaced—causing cooling of the local climate. The cooling of the corn field occurred solely during the non-growing season—especially when surfaces were snow-covered, whereas the cooling of the perennial fields was more prominent during the growing season. Compared to biogeochemical impacts with fossil fuel offsets for the same land conversions over eight years, the annual albedo-induced climate benefits add ∼35% and ∼78% to the annual biogeochemical benefits provided from the switchgrass and restored prairie fields, respectively, and offset ∼3.3% of the annual greenhouse gas (GHG) emissions from the corn field. We conclude that albedo-induced climate mitigation from conversion of CRP lands to perennial but not annual bioenergy crops can be substantial, and future climate impact assessments of bioenergy crops should include albedo changes in addition to GHG balances in order to better inform climate policies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution

Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

A conserved viral RNA fold enables nuclease resistance across kingdoms of life

Abstract Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence variability among xrRNAs from distantly related viruses raises questions about the shared molecular features that enable these RNAs to withstand the strong unwinding forces of exoribonucleases. Here, we present the first structure of a plant-virus xrRNA in its active conformation and uncover universal principles of xrRNA folding. Comparison with the structure of a human-pathogenic flavivirus xrRNA reveals that both share a core structural motif—a protective ring encircling the RNA’s 5′ end—despite lacking sequence similarity. Disrupting this core motif through targeted mutagenesis eliminates exoribonuclease-resistance and attenuates viral infection. We identify hundreds of related structures across multiple virus families, supporting the conservation of this mechanism. Our study demonstrates how distantly related RNA viruses have converged on a common structural strategy to inhibit cellular nucleases, with a universal ring topology as the defining feature of viral xrRNAs.

Biochemistry & Molecular Biology↗

DOE OSTI2023

The extracellular vesicle proteomes of Sorghum bicolor and Arabidopsis thaliana are partially conserved

Abstract Plant extracellular vesicles (EVs) are membrane-bound organelles involved mainly in intercellular communications and defense responses against pathogens. Recent studies have demonstrated the presence of proteins, nucleic acids including small RNAs, and lipids along with other metabolites in plant EVs. Here, we describe the isolation and characterization of EVs from sorghum (Sorghum bicolor). Nanoparticle tracking analysis, dynamic light scattering, and cryo-electron tomography showed the presence of a heterogeneous population of EVs isolated from the apoplastic wash of sorghum leaves. Cryo-electron microscopy revealed that EVs had a median size of 110 nm and distinct populations of vesicles with single or multiple lipid bilayers and low or high amounts of contents. The heterogeneity was further supported by data showing that only a subset of EVs that were stained with a membrane dye, Potomac Gold, were also stained with the membrane-permeant esterase-dependent dye, calcein acetoxymethyl ester. Proteomic analysis identified 437 proteins that were enriched in multiple EV isolations, with the majority of these also found in the EV proteome of Arabidopsis (Arabidopsis thaliana). These data suggest a partial conservation of EV contents and function between the monocot, sorghum, and a distantly related eudicot, Arabidopsis.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792

Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The goal of this study was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes were compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other V. harveyi strains (78 %) than to those of the other closely related species Vibrio owensii (67 %), Vibrio rotiferianus (63 %) and Vibrio campbellii (59 %). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA–DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. Laslty, the pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii may be divided into at least three subspecies, supported by intergenomic distance analysis. BLASTP atlases were created to identify unique regions among the genomes most related to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

From powerhouse to processing plant: conserved roles of mitochondrial outer membrane proteins in tRNA splicing

The mitochondrial cytoplasmic surface serves as a processing site for numerous RNAs from budding yeast to metazoans. We report that budding yeast mitochondrial outer membrane (MOM) proteins that are subunits of the translocase of the outer mitochondrial membrane (Tom70 and Tom 22) and sorting and assembly machinery (Sam37) are required for efficient pretransfer RNA (pre-tRNA) splicing. Defective pre-tRNA splicing in MOM mutants is due not to loss of respiratory metabolism but instead inefficient targeting/tethering of tRNA splicing endonuclease (SEN) subunits to mitochondria. Schizosaccharomyces pombe SEN subunits also localize to mitochondria, and Tom70 is required for this localization and pre-tRNA splicing. Thus, the role of MOM protein in targeting/tethering SEN subunits to mitochondria has been conserved for >500 million years.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Off forward non- s -channel helicity conserving contributions to exclusive vector quarkonium production from the spin dependent BFKL Pomeron

A novel contribution to off forward, exclusive vector quarkonium production, γ(*)+p → V+p, at high energy is derived which corresponds to a t-channel exchange of a Balitsky-Fadin-Kuraev-Lipatov (BFKL) hard Pomeron, with a helicity flip of the proton. This “spin-dependent BFKL Pomeron” is required in a consistent expansion in powers of the momentum transfer t ≈−Δ$^{2}_{⊥}$ beyond first order. The spin-dependent Pomeron violates s-channel helicity conservation at O(Δ$^{2}_{⊥}$), and beyond. Expanding to leading twist only, it corresponds to generalized parton distributions E g (x,t) for vanishing skewness. We derive explicit expressions for the eikonal BFKL amplitudes, to all orders in dipole size times momentum transfer, for all helicity configurations of the particles in the initial and final states. We also provide numerical estimates of the helicity flip two gluon exchange amplitude at moderate x from a light cone quark model of the proton. The spin dependent BFKL Pomeron could, in principle, be discovered via double spin asymmetries in e+p → e+p+J/ψ with a transversely polarized proton and longitudinally polarized electron in the initial state.

Deep inelastic scattering↗

DOE OSTI2020

Kinetically constrained freezing transition in a dipole-conserving system

Here, we study a stochastic lattice gas of particles in one dimension with strictly finite-range interactions that respect the fractonlike conservation laws of total charge and dipole moment. As the charge density is varied, the connectivity of the system's charge configurations under the dynamics changes qualitatively. We find two distinct phases: Near half filling the system thermalizes subdiffusively, with almost all configurations belonging to a single dynamically connected sector. As the charge density is tuned away from half filling there is a phase transition to a frozen phase, where locally active finite bubbles cannot exchange particles and the system fails to thermalize. The two phases exemplify what has recently been referred to as weak and strong Hilbert space fragmentation, respectively. We study the static and dynamic scaling properties of this weak-to-strong fragmentation phase transition in a kinetically constrained classical Markov circuit model, obtaining some conjectured exact critical exponents.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Energy and momentum conservation in spin transfer

We utilize simulations of spin-polarized electron scattering by a chain of localized quantum spins to show that energy and linear momentum conservation laws impose strong constraints on the properties of magnetic excitations induced by spin transfer. In turn, orbital and spin dynamics of conduction electrons depends on the dynamical characteristics of the local spins. Furthermore, our results suggest the possibility to achieve precise control of spin-transfer-driven magnetization dynamics by tailoring the spectral characteristics of the magnetic systems and of the driving electrons.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Reaction-diffusive dynamics of number-conserving dissipative quantum state preparation

The use of dissipation for the controlled creation of nontrivial quantum many-body correlated states is of much fundamental and practical interest. What is the result of imposing number conservation, which, in closed system, gives rise to diffusive spreading? For this work, we investigate this question for a paradigmatic model of a two-band system, with dissipative dynamics aiming to empty one band and to populate the other, which had been introduced before for the dissipative stabilization of topological states. Going beyond the mean-field treatment of the dissipative dynamics, we demonstrate the emergence of a diffusive regime for the particle and hole density modes at intermediate length- and timescales, which, interestingly, can only be excited in nonlinear response to external fields. We also identify processes that limit the diffusive behavior of this mode at the longest length- and timescales. Strikingly, we find that these processes lead to a reaction-diffusion dynamics governed by the Fisher-Kolmogorov-Petrovsky-Piskunov equation, making the designed dark state unstable towards a state with a finite particle and hole density.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Role of baryon number conservation in measurements of fluctuations

Here, I discuss the role and impact of net-baryon number conservation in measurements of net-proton fluctuations in heavy-ion collisions. I show that the magnitude of the fluctuations is entirely determined by the strength of two particle correlations. At LHC and top RHIC energy, this implies the fluctuations are proportional to the integral of the balance function (BF), B pp¯ of protons and antiprotons, while in the context of the RHIC beam energy scan (BES), one must also account for correlations of stopped protons. The integral of B pp¯ measured in a 4π detector depends on the relative cross sections of processes yielding pp¯ and those balancing the proton baryon number via the production of other antibaryons. The accepted integral of B pp¯ further depends on the shape and width of the BF relative to the width of the acceptance. The magnitude of the measured second-order cumulant of net-proton fluctuations thus has much less to do with QCD susceptibilities than with the creation/transport of baryons and antibaryons in heavy-ion collisions, and most particularly the impact of radial flow on the width of the BF. I thus advocate that net-proton fluctuations should be studied by means of differential BF measurements rather than with integral correlators. I also derive an expression of net-baryon fluctuations in terms of integrals of balance functions of identified baryon pairs and argue that measurements of such balance functions would enable a better understanding of the collision system expansion dynamics, the hadronization chemistry, and an experimental assessment of the strength of net-baryon fluctuations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Correlations of conserved quantities at finite baryon density

Correlations involving the seven conserved quantities, namely energy, baryon number, electric charge, strangeness, and the three components of momentum, give rise to correlations in heavy-ion collisions. Through the utilization of a simple one-dimensional hydrodynamic model, we calculate the evolution of the entire 7×7 matrix of correlations as a function of relative spatial rapidity. This comprehensive analysis accounts for finite baryon density, which results in off-diagonal correlations between the charge-related quantities and the energy-momentum quantities. These correlations in coordinate space are subsequently transformed into correlations in momentum space using statistical weighting. As a result, the entire matrix of correlations is revealed to be highly sensitive to the equation of state, viscosity, and diffusivity.

Equations of state of nuclear matter↗

DOE OSTI2021

Constraining the hadronic spectrum and repulsive interactions in a hadron resonance gas via fluctuations of conserved charges

We simultaneously incorporate two common extensions of the hadron resonance gas model, namely the addition of extra, unconfirmed resonances to the particle list and the excluded volume repulsive interactions. We emphasize the complementary nature of these two extensions and identify combinations of conserved charge susceptibilities that allow to constrain them separately. In particular, ratios of second-order susceptibilities like $\chi_{11}^{BQ}/\chi_2^B$ and $\chi_{11}^{BS}/\chi_2^B$ are sensitive only to the baryon spectrum, while fourth-to-second order ratios like $\chi_4^B/\chi_2^B$, $\chi_{31}^{BS}/\chi_{11}^{BS}$, or $\chi_{31}^{BQ}/\chi_{11}^{BQ}$ are mainly determined by repulsive interactions. Analysis of the available lattice results suggests the presence of both the extra states in the baryon-strangeness sector and the repulsive baryonic interaction, with indications that hyperons have a smaller repulsive core than non-strange baryons. Furthermore, the modified hadron resonance gas model presented here significantly improves the description of lattice QCD susceptibilities at chemical freeze-out and can be used for the analysis of event-by-event fluctuations in heavy-ion collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗