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DOE OSTI2024

Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast

Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, "universal" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Spectroscopic factors in dripline nuclei

Single-nucleon knockout reaction studies of the proton-dripline nuclei 9 C and 13 O suggest an appreciable suppression of spectroscopic factors. In this work, we calculate the one-neutron and one-proton spectroscopic factors for the mirror pair 9 C – 9 Li and 13 O using two variants of the continuum shell model: the complex-energy Gamow shell model and the real-energy shell model embedded in the continuum. Furthermore, our results indicate that the continuum effects strongly suppress the spectroscopic factors of well-bound orbits in the dripline systems but have less impact on the spectroscopic factors of weakly bound states.

6 ≤ A ≤ 19↗

DOE OSTI2023

Gravitational form factors of nuclei in the Skyrme model

Here, we compute the gravitational form factor D(t) of various nuclei in the generalized Skyrme model where nuclei are described as solitonic field configurations each with a definite baryon number B. We separately discuss the cases B = 1 (nucleons), B = 2 (deuteron), B = 3 (helium-3 and tritium), and extrapolate to larger B-values. Configurations with B > 1 are in general not spherically symmetric, and we demonstrate how group theory helps to extract the form factor. Numerical results are presented for the configurations with B = 1, 2, 3, 4, 5, 6, 7, 8, 32, 108. We find that the B-dependence is consistent with a power-law D(0) ∝ B β with β = 1.7–1.8. Other gravitational form factors can be calculated in the same framework, and we show the result for the J(t) form factor associated with the angular momentum for the B = 3 solution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

𝐵 → 𝜌⁢ℓ⁢$\bar{v}$ Resonance Form Factors from 𝐵→ 𝜋⁢𝜋⁢ℓ⁢$\bar{v}$ in Lattice QCD

The decay 𝐵 → 𝜌⁢ℓ⁢$\bar{v}$ is an attractive process for determining the magnitude of the smallest Cabibbo-Kobayashi-Maskawa matrix element, |𝑉 𝑢⁢𝑏 |, and can provide new insights into the origin of the long-standing exclusive-inclusive discrepancy in determinations of this standard-model parameter. This requires a nonperturbative QCD calculation of the 𝐵 → 𝜌 form factors 𝑉, 𝐴 0 , 𝐴 1 , and 𝐴 12 . The unstable nature of the 𝜌 resonance has prevented precise lattice QCD calculations of these form factors to date. Here, we present the first lattice QCD calculation of the 𝐵 → 𝜌 form factors in which the 𝜌 is treated properly as a resonance in 𝑃-wave 𝜋⁢𝜋 scattering. To this end, we use the Lellouch-Lüscher finite-volume formalism to compute the 𝐵 → 𝜋⁢𝜋 form factors as a function of both momentum transfer and 𝜋⁢𝜋 invariant mass, and then analytically continue to the 𝜌 resonance pole. This calculation is performed with 2 + 1 dynamical quark flavors at a pion mass of approximately 320 MeV, and demonstrates a clear path toward results at the physical point.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Estimation of Participation Factors Using the Synchrosqueezed Wavelet Transform

This paper proposes a data-driven approach for estimating participation factors for a power system using only simulation results on selected disturbances. The approach is purely response-based and does not need a linearized system model for eigen-analysis, which makes it applicable to systems whose detailed, complete mathematical models are not available. Considering the unavoidable nonlinearity as exhibited in the transient period of a system response, the Synchrosqueezed Wavelet Transform is applied to simulated responses for modal analysis to obtain participation factors. Based on simulations of Kundur's two-area system using both the electromagnetic transient model and phasor model, the participation factors estimated by the proposed approach are compared with two other signal processing tools, the Prony analysis and continuous wavelet transform, and are also benchmarked with conventional model-based participation factors.

participation factor↗

DOE OSTI2021

Butterfly Factorization Via Randomized Matrix-Vector Multiplications

This paper presents an adaptive randomized algorithm for computing the butterfly factorization of an m × n matrix with m ≈ n provided that both the matrix and its transpose can be rapidly applied to arbitrary vectors. The resulting factorization is composed of O(log n) sparse factors, each containing O(n) nonzero entries. The factorization can be attained using O(n 3/2 log n) computation and O(n log n) memory resources. Furthermore, the proposed algorithm can be implemented in parallel and can apply to matrices with strong or weak admissibility conditions arising from surface integral equation solvers as well as multi-frontal-based finite-difference, finite-element, or finite-volume solvers. A distributed-memory parallel implementation of the algorithm demonstrates excellent scaling behavior.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Charge radii of the nucleon from its flavor dependent Dirac form factors

In this report we have determined the proton and the neutron charge radii from a global analysis of the proton and the neutron elastic form factors, after first performing a flavor decomposition of these form factors under charge symmetry in the light cone frame formulation. We then extracted the transverse mean-square radii of the flavor dependent quark distributions. In turn, these are related in a model-independent way to the proton and neutron charge radii but allow us to take into account motion effects of the recoiling nucleon for data at finite but high momentum transfer. In the proton case we find $\langle r_p \rangle$ = 0.852±0.002 (stat.) ± 0.009 (syst.) (fm), consistent with the proton charge radius obtained from muonic hydrogen spectroscopy. The current method improves on the precision of the $\langle r_p \rangle$; extraction based on the form factor measurements. Furthermore, we find no discrepancy in the $\langle r_p \rangle$ determination among the different electron scattering measurements, all of which, utilizing the current method of extraction, result in a value that is consistent with the smallest $\langle r_p \rangle$ extraction from the electron scattering measurements. Concerning the neutron case, past results relied solely on the neutron-electron scattering length measurements, which suffer from an underestimation of underlying systematic uncertainties inherent to the extraction technique. Utilizing the present method we have performed the first extraction of the neutron charge radius based on nucleon form factor data, and we find $\langle r^2_n \rangle$ = -0.122±0.004 (stat.) ± 0.010 (syst.) (fm 2 ).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

CovS inactivation reduces CovR promoter binding at diverse virulence factor encoding genes in group A Streptococcus

The control of virulence gene regulator (CovR), also called caspsule synthesis regulator (CsrR), is critical to how the major human pathogen group A Streptococcus fine-tunes virulence factor production. CovR phosphorylation (CovR~P) levels are determined by its cognate sensor kinase CovS, and functional abrogating mutations in CovS can occur in invasive GAS isolates leading to hypervirulence. Presently, the mechanism of CovR-DNA binding specificity is unclear, and the impact of CovS inactivation on global CovR binding has not been assessed. Thus, we performed CovR chromatin immunoprecipitation sequencing (ChIP-seq) analysis in the emm1 strain MGAS2221 and its CovS kinase deficient derivative strain 2221-CovS-E281A. We identified that CovR bound in the promoter regions of nearly all virulence factor encoding genes in the CovR regulon. Additionally, direct CovR binding was observed for numerous genes encoding proteins involved in amino acid metabolism, but we found limited direct CovR binding to genes encoding other transcriptional regulators. The consensus sequence AATRANAAAARVABTAAA was present in the promoters of genes directly regulated by CovR, and mutations of highly conserved positions within this motif relieved CovR repression of the hasA and MGAS2221_0187 promoters. Analysis of strain 2221-CovS-E281A revealed that binding of CovR at repressed, but not activated, promoters is highly dependent on CovR~P state. CovR repressed virulence factor encoding genes could be grouped dependent on how CovR~P dependent variation in DNA binding correlated with gene transcript levels. Taken together, the data show that CovR repression of virulence factor encoding genes is primarily direct in nature, involves binding to a newly-identified DNA binding motif, and is relieved by CovS inactivation. These data provide new mechanistic insights into one of the most important bacterial virulence regulators and allow for subsequent focused investigations into how CovR-DNA interaction at directly controlled promoters impacts GAS pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Evolutionary Game Dynamics between Distributed Energy Resources and Microgrid Operator: Balancing Act for Power Factor Improvement

This article investigates the intricate dynamics between Distributed Energy Resources (DERs) and the Microgrid Operator (MGO) within a microgrid interconnected with the main grid. Employing an evolutionary game framework, the study scrutinizes the strategic evolution of DERs’ decision-making processes in their interactions with the MGO. Modeled as an evolutionary game, these interactions encapsulate the strategies adopted by DERs, resulting in stable equilibrium strategies over time. Motivated by direct benefits linked to increased active power production, DERs strive to sell all available power, while the MGO focuses on optimizing the microgrid’s overall performance. The study assesses the microgrid’s performance in terms of its power factor, emphasizing the strategic balance DERs must achieve in their active power generation to avoid penalization. This penalization results in decreased individual utility for DERs due to the overall power factor decrease resulting from their prioritization of active power generation. Additionally, the diminished overall power factor implies a decrease in MGO utility. The individual utility of each DER is further influenced by the strategies adopted by other DERs, impacting the penalization factor. Leveraging a modified IEEE 13-node distribution microgrid consisting of three DERs, the study presents case studies encompassing both cooperative and non-cooperative evolutionary game scenarios. These case studies illuminate the intricacies of interactions and the resulting equilibrium outcomes.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Biofuels Induced Land Use Change Emissions: The Role of Implemented Land Use Emission Factors

Biofuels’ induced land-use change (ILUC) emissions have been widely studied over the past 15 years. Many studies have addressed uncertainties associated with these estimates. These studies have broadly examined uncertainties associated with the choice of economic models, their assumptions and parameters, and a few bio-physical variables. However, uncertainties in land-use emission factors that represent the soil and vegetation carbon contents of various land types across the world and are used to estimate carbon fluxes due to land conversions are mostly overlooked. This paper calls attention to this important omission. It highlights some important sources of uncertainty in land-use emissions factors, explores the range in these factors from established data sources, and compares the influence of their variability on ILUC emissions for several sustainable aviation fuel (SAF) pathways. The estimated land-use changes for each pathway are taken from a well-known computable general equilibrium model, GTAP-BIO. Two well-known carbon calculator models (CCLUB and AEZ-EF) that represent two different sets of emissions factors are used to convert the GTAP-BIO estimated land-use changes to ILUC emissions. The results show that the calculated ILUC emissions obtained from these carbon calculators for each examined SAF pathway are largely different, even for the same amortization time horizon. For example, the ILUC emissions values obtained from the AEZ-EF and CCLUB models for producing jet fuel from corn ethanol for a 25-year amortization period are 24.9 gCO 2 e/MJ and 15.96 gCO 2 e/MJ, respectively. This represents a 60% difference between the results of these two carbon calculators for the same set of land-use changes. The results show larger differences for other pathways as well.

09 BIOMASS FUELS↗

DOE OSTI2026

Assessing Photovoltaic Capacity Factor Variability Using Long-Term Satellite Derived Solar Resource Data Under Brazilian Climate

Accurate estimation of photovoltaic (PV) energy yield and its variability is essential for reducing financial risk and supporting reliable system planning for rapidly expanding PV markets. In Brazil, high solar adoption and increasing levels of distributed energy resources are beginning to introduce operational challenges such as curtailment and evolving grid requirements. Understanding how natural variability in solar resource propagates into PV system performance is therefore increasingly important for both project design and grid integration. Modern PV yield assessments commonly rely on multi-year meteorological datasets and probabilistic exceedance metrics (e.g., P50/P90) to quantify energy yield uncertainty for project financing. However, the implications of long-term solar resource variability for PV system design choices and high-adoption grid conditions remain less well characterized for rapidly expanding markets such as Brazil. In particular, understanding how weather-driven variability propagates into PV production distributions and capacity factor expectations is important for evaluating curtailment exposure, deployment strategies, and storage requirements in regions experiencing rapid growth of distributed and utility-scale PV. Seasonal and interannual variability in atmospheric conditions can produce substantial fluctuations in monthly PV energy production, which propagate into uncertainty in annual energy yield and capacity factor expectations. Characterizing this variability using long-term meteorological datasets allows probabilistic estimation of PV system performance and provides improved insight into the range of expected PV energy outcomes. This study explores the use of long-term satellite-derived meteorological data from the National Solar Radiation Database (NSRDB) to evaluate the variability of photovoltaic system performance across multiple locations in Brazil. Using a 27-year dataset (1998-2024), PV system simulations are performed to characterize the distribution of annual and seasonal capacity factors and energy yield outcomes, while propagating key sources of meteorological variability and model uncertainty through the PV modeling chain. The analysis also investigates the sensitivity of PV performance outcomes to key system design assumptions within the PV modeling chain, including tracking configuration and system sizing parameters. The resulting probabilistic performance characterization provides insight into how weather-driven variability influences PV production expectations and capacity factor distributions. These results provide a foundation for evaluating how weather-driven variability interacts with high PV adoption and potential storage or curtailment mitigation strategies.

14 SOLAR ENERGY↗

DOE OSTI2024

Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum

Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Takayesu, Allen↗

DOE OSTI2023

Acceleration Factors for Combined‐Accelerated Stress Testing of Photovoltaic Modules

Combined‐accelerated stress testing (C‐AST) is developed to establish the durability of photovoltaic (PV) products, including for degradation modes that are not a priori known or examined in standardized tests. C‐AST aims to comprehensively represent the sample, stress factors, and their combinations using levels at the statistical tails of the natural environment. Acceleration factors for relevant climate sequences within the C‐AST cycle with respect to the Florida USA climate are estimated for selected degradation mechanisms. It is found that for degradation of the outer backsheet polymer layer, the acceleration factor of the tropical climate sequence (the longest of the climate sequences) is f ( T , G ) = 17.3 with ultraviolet photodegradation; for polyethylene terephthalate hydrolysis (backsheets), f ( T , RH ) = 426; for electrochemical corrosion (PV cell), f ( I ) = 14.1; and for PbSn solder fatigue f (Δ T , r ( T )) = 17.3. Here, T is the module temperature, G is the broadband spectrum irradiance on the plane of array of the module, RH is the relative humidity on the module surface, I is the leakage current through the module packaging, and r ( T ), the number of temperature reversals. The methods discussed herein are generally applicable for evaluating acceleration factors in other accelerated test methods.

14 SOLAR ENERGY↗

DOE OSTI2021

Factorization at subleading power and endpoint divergences in h → γγ decay. Part II. Renormalization and scale evolution

Building on the recent derivation of a bare factorization theorem for the b-quark induced contribution to the h → γγ decay amplitude based on soft-collinear effective theory, we derive the first renormalized factorization theorem for a process described at subleading power in scale ratios, where λ = m b /M h « 1 in our case. We prove two refactorization conditions for a matching coefficient and an operator matrix element in the endpoint region, where they exhibit singularities giving rise to divergent convolution integrals. The refactorization conditions ensure that the dependence of the decay amplitude on the rapidity regulator, which regularizes the endpoint singularities, cancels out to all orders of perturbation theory. We establish the renormalized form of the factorization formula, proving that extra contributions arising from the fact that “endpoint regularization” does not commute with renormalization can be absorbed, to all orders, by a redefinition of one of the matching coefficients. We derive the renormalization-group evolution equation satisfied by all quantities in the factorization formula and use them to predict the large logarithms of order $αα^2_sL^k$ in the three-loop decay amplitude, where $L=ln(-M^2_h/m^2_b)$ and k = 6, 5, 4, 3. We find perfect agreement with existing numerical results for the amplitude and analytical results for the three-loop contributions involving a massless quark loop. On the other hand, we disagree with the results of previous attempts to predict the series of subleading logarithms $~αα^n_sL^{2n+1}$

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Renormalization group improved photon impact factors and the high energy virtual photon scattering

We perform the renormalization group improved collinear resummation of the photon-gluon impact factors. We construct the resummed cross section for virtual photon-photon (γ ∗ γ ∗ ) scattering which incorporates the impact factors and BFKL gluon Green’s function up to the next-to-leading logarithmic accuracy in energy. The impact factors include important kinematical effects which are responsible for the most singular poles in Mellin space at next-to-leading order. Further conditions on the resummed cross section are obtained by requiring the consistency with the collinear limits. Our analysis is consistent with previous impact factor calculations at NLO, apart from a new term proportional to C F that we find for the longitudinal polarization. Finally, we use the resummed cross section to compare with the LEP data on the γ ∗ γ ∗ cross section and with previous calculations. The resummed result is lower than the leading logarithmic approximation but higher than the pure next-to-leading one, and is consistent with the experimental data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

A two-loop four-point form factor at function level

Recently, the maximally-helicity-violating four-point form factor for the chiral stress-energy tensor in planar $\mathcal{N}$ = 4 super Yang-Mills was computed to three loops at the level of the symbol associated with multiple polylogarithms. It exhibits antipodal self-duality, or invariance under the combined action of a kinematic map and reversing the ordering of letters in the symbol. Here we lift the two-loop form factor from symbol level to function level. We provide an iterated representation of the function’s derivatives (coproducts). In order to do so, we find a three-parameter limit of the five-parameter phase space where the symbol’s letters are all rational. We also use function-level information about dihedral symmetries and the soft, collinear, and factorization limits, as well as limits governed by the form-factor operator product expansion (FFOPE). We provide plots of the remainder function on several kinematic slices, and show that the result is compatible with the FFOPE data. We further verify that antipodal self-duality is valid at two loops beyond the level of the symbol.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Quarkonium semiclassical transport in quark-gluon plasma: factorization and quantum correction

We study quarkonium transport in the quark-gluon plasma by using the potential nonrelativistic QCD (pNRQCD) effective field theory and the framework of open quantum systems. We argue that the coupling between quarkonium and the thermal bath is weak using separation of scales, so the initial density matrix of the total system factorizes and the time evolution of the subsystem is Markovian. We derive the semiclassical Boltzmann equation for quarkonium by applying a Wigner transform to the Lindblad equation and carrying out a semiclassical expansion. We resum relevant interactions to all orders in the coupling constant at leading power of the nonrelativistic and multipole expansions. The derivation is valid for both weakly coupled and strongly coupled quark-gluon plasmas. We find reaction rates in the transport equation factorize into a quarkonium dipole transition function and a chromoelectric gluon distribution function. For the differential reaction rate, the definition of the momentum dependent chromoelectric gluon distribution function involves staple-shaped Wilson lines. For the inclusive reaction rate, the Wilson lines collapse into a straight line along the real time axis and the distribution becomes momentum independent. The relation between the two Wilson lines is analogous to the relation between the Wilson lines appearing in the gluon parton distribution function (PDF) and the gluon transverse momentum dependent parton distribution function (TMDPDF). The centrality dependence of the quarkonium nuclear modification factor measured by experiments probes the momentum independent distribution while the transverse momentum dependence and measurements of the azimuthal angular anisotropy may be able to probe the momentum dependent one. We discuss one way to indirectly constrain the quarkonium in-medium real potential by using the factorization formula and lattice calculations. The leading quantum correction to the semiclassical transport equation of quarkonium is also worked out. The study can be easily generalized to quarkonium transport in cold nuclear matter, which is relevant for quarkonium production in eA collisions in the future Electron-Ion Collider.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Rapidity-only TMD factorization at one loop

Typically, a production of a particle with a small transverse momentum in hadron-hadron collisions is described by CSS-based TMD factorization at moderate Bjorken x B ~ 1 and by k T -factorization at small x B . A uniform description valid for all x B is provided by rapidity-only TMD factorization developed in a series of recent papers at the tree level. In this paper the rapidity-only TMD factorization for particle production by gluon fusion is extended to the one-loop level.

deep inelastic scattering↗