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At least 739 records · Page 41

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DOE OSTI2024

Functional role of myosin-binding protein H in thick filaments of developing vertebrate fast-twitch skeletal muscle

Myosin-binding protein H (MyBP-H) is a component of the vertebrate skeletal muscle sarcomere with sequence and domain homology to myosin-binding protein C (MyBP-C). Whereas skeletal muscle isoforms of MyBP-C (fMyBP-C, sMyBP-C) modulate muscle contractility via interactions with actin thin filaments and myosin motors within the muscle sarcomere “C-zone,” MyBP-H has no known function. This is in part due to MyBP-H having limited expression in adult fast-twitch muscle and no known involvement in muscle disease. Quantitative proteomics reported here reveal that MyBP-H is highly expressed in prenatal rat fast-twitch muscles and larval zebrafish, suggesting a conserved role in muscle development and prompting studies to define its function. We take advantage of the genetic control of the zebrafish model and a combination of structural, functional, and biophysical techniques to interrogate the role of MyBP-H. Transgenic, FLAG-tagged MyBP-H or fMyBP-C both localize to the C-zones in larval myofibers, whereas genetic depletion of endogenous MyBP-H or fMyBP-C leads to increased accumulation of the other, suggesting competition for C-zone binding sites. Does MyBP-H modulate contractility in the C-zone? Globular domains critical to MyBP-C’s modulatory functions are absent from MyBP-H, suggesting that MyBP-H may be functionally silent. However, our results suggest an active role. In vitro motility experiments indicate MyBP-H shares MyBP-C’s capacity as a molecular “brake.” These results provide new insights and raise questions about the role of the C-zone during muscle development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

The Patterson function as auto-hologram and graph enables the direct solution to the phase problem for coherently illuminated atomistic structures

Abstract The coherent Patterson function, derived from the coherent scattering intensities from N atoms, can be described as an auto-holographic image, i.e., the superposition of N -holographic images in which each atom serves as the source of a different reference wave, and as a mathematical graph of the unknown structure. These insights indicate that the unknown structure is significantly over-determined by the inherent information content in a Patterson function by a factor of ( N − 1)/2 (for non-degenerate structures), independent of dimensionality. However, we also show that the ability to resolve the distinct features in the Patterson function depends strongly on details of the experimental design (data range, sampling frequency, and dimensionality). This re-interpretation suggests that the coherent Patterson function provides a natural context for describing the information content in coherent scattering, reveals that there is no inherent phase problem for coherently illuminated pointwise structures, and enables the design of an algorithm which retrieves the structure directly from the Patterson function, without using error metric minimization.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Isotropic N-point basis functions and their properties

Isotropic functions of positions r 1 , r 2 ,..., r N , i.e. functions invariant under simultaneous rotations of all the coordinates, are conveniently formed using spherical harmonics and Clebsch–Gordan coefficients. An orthonormal basis of such functions provides a formalism suitable for analyzing isotropic distributions such as those that arise in cosmology, for instance in the clustering of galaxies as revealed by large-scale structure surveys. The algebraic properties of the basis functions are conveniently expressed in terms of 6-j and 9-j symbols. Finally, the calculation of relations among the basis functions is facilitated by 'Yutsis' diagrams for the addition and recoupling of angular momenta.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Propagation of priors for more accurate and efficient spectroscopic functional fits and their application to ferroelectric hysteresis

Multi-dimensional spectral-imaging is a mainstay of the scanning probe and electron microscopies, micro-Raman, and various forms of chemical imaging. In many cases, individual spectra can be fit to a specific functional form, with the model parameter maps, providing direct insight into material properties. Since spectra are often acquired across a spatial grid of points, spatially adjacent spectra are likely to be similar to one another; yet, this fact is almost never used when considering parameter estimation for functional fits. On datasets tried here, we show that by utilizing proximal information, whether it be in the spatial or spectral domains, it is possible to improve the reliability and increase the speed of such functional fits by ~2-3x, as compared to random priors. We explore and compare three distinct new methods: (1) spatially averaging neighborhood spectra, and propagating priors based on functional fits to the averaged case, (2) hierarchical clustering-based methods where spectra are grouped hierarchically based on response, with the priors propagated progressively down the hierarchy, and (3) regular clustering without hierarchical methods with priors propagated from fits to cluster means. Our results highlight that utilizing spatial and spectral neighborhood information is often critical for accurate parameter estimation in noisy environments, which we show for ferroelectric hysteresis loops acquired on a prototypical PbTiO3 thin film with piezoresponse spectroscopy. This method is general and applicable to any spatially measured spectra where functional forms are available. Examples include exploring the superconducting gap with tunneling spectroscopy, using the Dynes formula, or current-voltage curve fits in conductive atomic force microscopy mapping. Here we explore the problem for ferroelectric hysteresis, which, given its large parameter space, constitutes a more difficult task than, for example, fitting current-voltage curves with a Schottky emission formula.

42 ENGINEERING↗

DOE OSTI2024

Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits

Abstract The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein–protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.

Genetics & Heredity↗

DOE OSTI2022

Impact of Surface Chemistry of Ultrasmall Superparamagnetic Iron Oxide Nanoparticles on Protein Corona Formation and Endothelial Cell Uptake, Toxicity, and Barrier Function

Ultrasmall superparamagnetic iron oxide nanoparticles (USPIONs) have been investigated for biomedical applications, including novel contrast agents, magnetic tracers for tumor imaging, targeted drug delivery vehicles, and magneto-mechanical actuators for hyperthermia and thrombolysis. Despite significant progress, recent clinical reports have raised concerns regarding USPION safety related to endothelial cell dysfunction; however, there is limited information on factors contributing to these clinical responses. The influence of USPION surface chemistry on nanoparticle interactions with proteins may impact endothelial cell function leading to adverse responses. Therefore, the goal of this study was to assess the effects of carboxyl-functionalized USPION (CU) or amine-functionalized USPION (AU) (approximately 30 nm diameter) on biological responses in human coronary artery endothelial cells. Increased protein adsorption was observed for AU compared with CU after exposure to serum proteins. Exposure to CU, but not AU, resulted in a concentration-dependent decrease in cell viability and perinuclear accumulation inside cytoplasmic vesicles. Internalization of CU was correlated with endothelial cell functional changes under non-cytotoxic conditions, as evidenced by a marked decreased expression of endothelial-specific adhesion proteins (eg, vascular endothelial-cadherin and platelet endothelial cell adhesion molecule-1) and increased endothelial permeability. Evaluation of downstream signaling indicated endothelial permeability is associated with actin cytoskeleton remodeling, possibly elicited by intracellular events involving reactive oxygen species, calcium ions, and the nanoparticle cellular uptake pathway. This study demonstrated that USPION surface chemistry significantly impacts protein adsorption and endothelial cell uptake, viability, and barrier function. This information will advance the current toxicological profile of USPION and improve development, safety assessment, and clinical outcomes of USPION-enabled medical products.

Toxicology↗

DOE OSTI2023

2022 Prentice Award Lecture: Advancing Retinal Imaging and Visual Function in Patient Management and Disease Mechanisms

Patient-based research plays a key role in probing basic visual mechanisms. Less-well recognized is the role of patient-based retinal imaging and visual function studies in elucidating disease mechanisms, which are accelerated by advances in imaging and function techniques and are most powerful when combined with the results from histology and animal models. A patient's visual complaints can be one key to patient management, but human data are also key to understanding disease mechanisms. Unfortunately, pathological changes can be difficult to detect. Before advanced retinal imaging, the measurement of visual function indicated the presence of pathological changes that were undetectable with existing clinical examination. Over the past few decades, advances in retinal imaging have increasingly revealed the unseen. This has led to great strides in the management of many diseases, particularly diabetic retinopathy and macular edema, and age-related macular degeneration. It is likely widely accepted that patient-based research, as in clinical trials, led to such positive outcomes. Both visual function measures and advanced retinal imaging have clearly demonstrated differences among retinal diseases. Contrary to initial thinking, sight-threatening damage in diabetes occurs to the outer retina and not only to the inner retina. This has been clearly indicated in patient results but has only gradually entered the clinical classifications and understanding of disease etiology. There is strikingly different pathophysiology for age-related macular degeneration compared with photoreceptor and retinal pigment epithelial genetic defects, yet research models and even some treatments confuse these. It is important to recognize the role that patient-based research plays in probing basic visual mechanisms and elucidating disease mechanisms, combining these findings with the concepts from histology and animal models. Thus, this article combines sample instrumentation from my laboratory and progress in the fields of retinal imaging and visual function.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Locally adaptive activation functions with slope recovery for deep and physics-informed neural networks

Here we propose two approaches of locally adaptive activation functions namely, layer-wise and neuron-wise locally adaptive activation functions, which improve the performance of deep and physics-informed neural networks. The local adaptation of activation function is achieved by introducing a scalable parameter in each layer (layer-wise) and for every neuron (neuron-wise) separately, and then optimizing it using a variant of stochastic gradient descent algorithm. In order to further increase the training speed, an activation slope-based slope recovery term is added in the loss function, which further accelerates convergence, thereby reducing the training cost. On the theoretical side, we prove that in the proposed method, the gradient descent algorithms are not attracted to sub-optimal critical points or local minima under practical conditions on the initialization and learning rate, and that the gradient dynamics of the proposed method is not achievable by base methods with any (adaptive) learning rates. We further show that the adaptive activation methods accelerate the convergence by implicitly multiplying conditioning matrices to the gradient of the base method without any explicit computation of the conditioning matrix and the matrix–vector product. The different adaptive activation functions are shown to induce different implicit conditioning matrices. Furthermore, the proposed methods with the slope recovery are shown to accelerate the training process.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Empirical investigation of nuclear correlation function distributions in lattice QCD

Two-point correlation functions of systems with baryon number 𝐵 ∈ {1,2,3,4} are investigated using lattice quantum chromodynamics (QCD). In particular, the empirical distributions of importance-sampling Monte-Carlo samples of these correlation functions are examined as a function of the spacetime separation between the two points and the baryon number. While the exact forms of these distributions are not known for QCD, recent work has determined asymptotic expressions for analogous correlation function distributions in simpler theories such as scalar field theory and the disordered phase of the 𝑂⁡(𝑁) model. The theoretical 𝑂⁡(𝑁) model distributions are found to provide an accurate description of the empirical QCD distributions at zero momentum over a wide range of temporal separations for each baryon number when assessed with a range of different statistical tests. In particular, the behavior of the baryon number 𝐵 QCD correlation function at large temporal separation is well reproduced by the 𝑂⁡(𝑁 ∼ 2/𝐵) model distribution.

Lattice field theory↗

DOE OSTI2021

Quantum Monte Carlo studies of a trimer scaling function with microscopic two- and three-body interactions

Here, we present an energy scaling function to predict, in a specific range, the energy of bosonic trimers with large scattering lengths and finite range interactions, which is validated by quantum Monte Carlo calculations using microscopic Hamiltonians with two- and three-body potentials. The proposed scaling function depends on the scattering length, effective range, and a reference energy, which we chose as the trimer energy at unitarity. We obtained the scaling function as a limit cycle from the solution of the renormalized zero-range model with effective range corrections. We proposed a simple parametrization of the energy scaling function. Besides the intrinsic interest in theoretical and experimental investigations, this scaling function allows one to probe Efimov physics with only the trimer ground states, which may open opportunities to identify Efimov trimers whenever access to excited states is limited.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Observation of a chiral wave function in the twofold-degenerate quadruple Weyl system BaPtGe

Topological states in quantum materials are defined by bulk wave functions that possess nontrivial topological invariants. While edge modes are widely presented as signatures of nontrivial topology, how bulk wave functions can manifest explicitly topological properties remains unresolved. Here, using high-resolution inelastic x-ray spectroscopy (IXS) combined with first principles calculations, we report experimental signatures of chiral wave functions in the bulk phonon spectrum of BaPtGe, which we show to host a previously undiscovered twofold-degenerate quadruple Weyl node. The chirality of the degenerate phononic wave function yields a nontrivial phonon dynamical structure factor, S(Q,ω), along high-symmetry directions, that is in excellent agreement with numerical and model calculations. Furthermore, our results establish IXS as a powerful tool to uncover topological wave functions, providing a key missing ingredient in the study of topological quantum matter.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Cumulants and correlation functions of net-proton, proton, and antiproton multiplicity distributions in Au+Au collisions at energies available at the BNL Relativistic Heavy Ion Collider

Here, we report a systematic measurement of cumulants, C n , for net-proton, proton, and antiproton multiplicity distributions, and correlation functions, κ n , for proton and antiproton multiplicity distributions up to the fourth order in Au+Au collisions at $\sqrt{s_{NN}}$ = 7.7, 11.5, 14.5, 19.6, 27, 39, 54.4, 62.4, and 200 GeV. The C n and κ n are presented as a function of collision energy, centrality and kinematic acceptance in rapidity, y, and transverse momentum, p T . The data were taken during the first phase of the Beam Energy Scan (BES) program (2010–2017) at the BNL Relativistic Heavy Ion Collider (RHIC) facility. The measurements are carried out at midrapidity (|y| < 0.5) and transverse momentum 0.4 < p T < 2.0 GeV/c, using the STAR detector at RHIC. We observe a nonmonotonic energy dependence ($\sqrt{s_{NN}}$ = 7.7–62.4 GeV) of the net-proton C 4 /C 2 with the significance of 3.1σ for the 0–5% central Au+Au collisions. This is consistent with the expectations of critical fluctuations in a QCD-inspired model. Thermal and transport model calculations show a monotonic variation with $\sqrt{s_{NN}}$. For the multiparticle correlation functions, we observe significant negative values for a two-particle correlation function, κ 2 , of protons and antiprotons, which are mainly due to the effects of baryon number conservation. Furthermore, it is found that the four-particle correlation function, κ 4 , of protons plays a role in determining the energy dependence of proton C 4 /C 1 below 19.6 GeV, which cannot be understood by the effect of baryon number conservation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Examination of the sensitivity of quasifree reactions to details of the bound-state overlap functions

It is often stated that heavy-ion nucleon knockout reactions are mostly sensitive to the tails of the bound-state wave functions. In contrast, (p,2p) and (p,pn) reactions are known to access information on the full overlap functions within the nucleus. We analyze the oxygen isotopic chain and explore the differences between single-particle wave functions generated with potential models, used in the experimental analysis of knockout reactions, and ab initio computations from self-consistent Green's function theory. Contrary to common belief, we find that not only the tail of the overlap functions, but also their internal part is assessed in both reaction mechanisms, which are crucial to yield accurately determined spectroscopic information.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Physical implications of the extrapolation and statistical bootstrap of nucleon structure function ratios F 2 n F 2 p for mirror nuclei He 3 and H 3

A nuclear physics example of statistical bootstrap is used on the MARATHON nucleon structure function ratio data in the quark momentum fraction regions x B → 0 and x B → 1. The extrapolated F 2 ratio as quark momentum fraction x B → 1 is $\frac{F^n_2}{F^p_2}$ → 0.4 ± 0.05 and this value is compared to theoretical predictions. The extrapolated ratio when x B → 0 favors the simple model of isospin symmetry with the complete dominance of sea quarks at low momentum fraction. At high- x B , the proton quark distribution function ratio d/u is derived from the F 2 ratio and found to be d/u → 1/6. Our extrapolated values for both the $\frac{F^n_2}{F^p_2}$ ratio and the d/u parton distribution function ratio are within uncertainties of perturbative QCD values from quark counting, helicity conservation arguments, and a Dyson-Schwinger equation with a contact interaction model. In addition, it is possible to match the statistical bootstrap value to theoretical predictions by allowing two compatible models to act simultaneously in the nucleon wave function. Finally, one such example is nucleon wave functions composed of a linear combination of a quark-diquark state and a three-valence quark correlated state with coefficients that combine to give the extrapolated F 2 ratio at x B = 1.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Universal function for heavy-ion fusion cross sections

A universal function for heavy-ion fusion cross sections, Y = $\sqrt{π}$ Xerfc (- X ) + exp(- X 2 ) is proposed. By scaling both the cross section σ(E) and the energy E, heavy-ion fusion cross section data are found to follow closely a universal function over the whole energy range. The scaling is developed from either a simple, empirical single-Gaussian barrier distribution model for the representation d 2 (σE)/dE 2 , or the modified Siwek-Wilczynski model. The cross section expressions of these models are analytical, and can be easily used for all heavy-ion fusion excitation functions. Thus a bench marking of heavy-ion fusion excitation functions has been achieved. Finally, a general discussion regarding the universal function is given.

low & intermediate energy heavy-ion reactions↗

DOE OSTI2024

Updated analyses of gluon distribution functions for the pion and kaon from the gauge-invariant nonlocal chiral quark model

In this work, we investigate the gluon distribution functions for the pion and kaon, in addition to the improved result of the valence-quark ones, in the gauge-invariant nonlocal chiral-quark model, in which the momentum dependence of the quark interactions is properly taken into account. We then analyze the gluon distribution functions, generated dynamically through the splitting functions in the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi QCD evolution. By comparing with the recent lattice QCD results and Jefferson Lab angular momentum global analyses, it is found that the present numerical results for the gluon parton distribution functions for the pion exhibit a good agreement and the valence up-quark distribution results for the pion by reproducing the reanalyzed experimental data with a remarkable agreement. Our prediction on the gluon distribution functions for the kaon is also consistent with the recent lattice data for the kaon within the errors. Published by the American Physical Society 2024

Hutauruk, Parada. T. P. (ORCID:0000000242257109)↗

DOE OSTI2024

Nonperturbative running of the tensor operator for N f = 3 QCD from the chirally rotated Schrödinger functional

We study the renormalization group (RG) running of the nonsinglet tensor operator, for N f = 3 QCD with Wilson fermions in a mixed action setup, with standard Schrödinger functional (SF) boundary conditions for sea quarks and chirally rotated Schrödinger functional ( χ SF ) boundary conditions for valence quarks. Based on a recursive finite-size scaling technique we compute nonperturbatively the tensor step-scaling function for an energy range between a hadronic scale and an electroweak scale, above which perturbation theory may be safely applied. Our result is expressed as the RG-running factor T RGI / [ T ( μ had ) ] R , where the numerator is the scale independent (renormalization group invariant—RGI) tensor operator and the denominator is its renormalized counterpart at a hadronic scale μ had = 233 ( 8 ) MeV in a given scheme. We determine the step-scaling function in four distinct renormalization schemes. We also compute the renormalization parameters of these schemes at μ had which, combined with the RG-running factor, gives the scheme-independent quantity Z T RGI ( g 0 2 ) in four schemes and for a range of bare gauge couplings in which large volume hadronic matrix element simulations are performed by the CLS consortium in N f = 2 + 1 QCD. All four results are compatible and also agree with a recent determination based on a unitary setup for Wilson quarks with Schrödinger functional boundary conditions [arXiv:2309.04314]. This provides a strong universality test. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

DOE OSTI2024

Electronic structure and optical properties of halide double perovskites from a Wannier-localized optimally-tuned screened range-separated hybrid functional

Halide double perovskites are a chemically diverse and growing class of compound semiconductors that are promising for optoelectronic applications. However, the prediction of their fundamental gaps and optical properties with density functional theory (DFT) and ab initio many-body perturbation theory has been a significant challenge. Recently, a nonempirical Wannier-localized optimally tuned screened range-separated hybrid (WOT-SRSH) functional has been shown to accurately produce the fundamental band gaps of a wide set of semiconductors and insulators, including lead halide perovskites. Here, in this study, we apply the WOT-SRSH functional to five halide double perovskites and compare the results with those obtained from other known functionals and previous GW calculations. We also use the approach as a starting point for GW calculations and we compute the band structures and optical absorption spectrum for Cs 2 AgBiBr 6 , using both time-dependent DFT and the GW-Bethe-Salpeter equation approach. We show that the WOT-SRSH functional leads to accurate fundamental and optical band gaps, as well as optical absorption spectra, consistent with spectroscopic measurements, thereby establishing WOT-SRSH as a viable method for the accurate prediction of optoelectronic properties of halide double perovskites.

36 MATERIALS SCIENCE↗