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DOE OSTI2018

Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation

hnRNPA2, a component of RNA-processing membraneless organelles, forms inclusions when mutatedin a syndrome characterized by the degeneration of neurons (bearing features of amyotrophic lateral sclerosis [ALS] and frontotemporal dementia), muscle,and bone. In this work we provide a unified structural view of hnRNPA2 self-assembly, aggregation, and interaction and the distinct effects of small chemical changes—disease mutations and arginine methylation—on these assemblies. The hnRNPA2 low-complexity (LC) domain is compact and intrinsically disordered as a monomer, retaining predominant disorder in a liquid-liquid phase-separated form. Disease mutations D290V and P298L induce aggregation by enhancing and extending, respectively, the aggregation-prone region. Co-aggregating in disease inclusions, hnRNPA2 LC directly interacts with and induces phase separation of TDP-43. Conversely, arginine methylation reduces hnRNPA2 phase separation, disrupting arginine-mediated contacts. These results highlight the mechanistic role of specific LC domain interactions and modifications conserved across many hnRNP family members but altered by aggregation-causing pathological mutations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Fluorescent Light‐up Probe for the Detection of Protein Aggregates

Abstract A fluorescent dye was decorated with water‐soluble pyridinium groups in order to be applied in the detection of cyclodextrins or DNA. The dye displays an enhancement of its emission intensity when the internal rotations are restricted due to the formation of an inclusion complex with cyclodextrins or upon interaction with DNA. In vivo , the fluorescent probe can stain protein aggregates with a selectivity comparable to the widely used Proteostat®.

Nunes da Silva, Raquel↗

DOE OSTI2019

A Review of Physical and Numerical Approaches for the Study of Gas Stirring in Ladle Metallurgy

This article presents a review of the research into gas stirring in ladle metallurgy carried out over the past few decades. Herein, the physical modeling experiments are divided into four major areas: (1) mixing and homogenization in the ladle; (2) gas bubble formation, transformation, and interactions in the plume zone; (3) inclusion behavior at the steel–slag interface and in the molten steel; and (4) open eye formation. Several industrial trials have also been carried out to optimize gas stirring and open eye formation. Approaches for selecting criteria for scaling to guarantee flow similarity between industrial trials and physical modeling experiments are discussed. To describe the bubble behavior and two-phase plume structure, four main mathematical models have been used in different research fields: (1) the quasi-single-phase model, (2) the volume of fluid (VOF) model, (3) the Eulerian multiphase (E–E) model, and (4) the Eulerian–Lagrangian (E–L) model. In recent years, the E–E model has been used to predict gas stirring conditions in the ladle, and specific models in commercial packages, as well as research codes, have been developed gradually to describe the complex physical and chemical phenomena. Furthermore, the coupling of turbulence models with multiphase models is also discussed. For physical modeling, some general empirical rules have not been analyzed sufficiently. Based on a comparison with the available experimental results, it is found that the mathematical models focusing on the mass transfer phenomenon and inclusion behaviors at the steel-slag interface, vacuum degassing at the gas–liquid interface, dissolution rate of the solid alloy at the liquid–solid interface, and the combination of fluid dynamics and thermodynamics need to be improved further. To describe industrial conditions using mathematical methods and improve numerical modeling, the results of physical modeling experiments and industrial trials must offer satisfactory validations for the improvement of numerical modeling.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Controlling the aqueous solubility of PNIPAM with hydrophobic molecular units

The effect of co-polymerization of thermo-sensitive polymers with hydrophilic or hydrophobic co-monomers on the LCST and the structure of proximal water remains a fundamental and challenging problem. Here, in this study, we employ all-atom molecular dynamics simulations to investigate the aqueous solubility of a thermo-sensitive polymer, poly(N-isopropylacrylamide) (PNIPAM), a hydrophobic polymer polystyrene (PS) and block co-polymers of PNIPAM-co-PS. The simulations of pure oligomers of PNIPAM and PS and their co-polymers are conducted below and above the LCST of PNIPAM to elucidate the effect of increase in number of PS units in PNIPAM-co-PS co-polymers on the coil-to-globule transition of PNIPAM and structure of proximal water. Our simulations suggest that while the LCST of pure PNIPAM oligomers is strongly associated with the structural changes in the proximal water molecules present near PNIPAM, inclusion of PS units disrupts the interactions between PNIPAM and water and promotes the faster dehydration of PNIPAM chains above its LCST. This phenomenon is manifested by a coil-to-globule transition in PNIPAM chains present in PNIPAM-co-PS co-polymers at much shorter times as compared to the pure PNIPAM oligomers. Our results also reveal that with increase in the number of PS units in PNIPAM-co-PS co-polymers the coil-to-globule transition is accelerated.

36 MATERIALS SCIENCE↗

DOE OSTI2017

A van der Waals Inclusive Density Functional Theory Study of the Nature of Bonding for Thiophene Adsorption on Ni(100) and Cu(100) Surfaces

We report the results of the first-principles density functional theory calculations for the adsorption of thiophene (C 4 H 4 S) on Cu(100) and Ni(100) surfaces. The adsorption properties on these surfaces are evaluated for several adsorption configurations, and the calculations are performed with the inclusion of van der Waals (vdW) interactions invoking the optimized vdW (optB86b-vdW, optB88-vdW, and optPBE-vdW) as well as revPBE-vdW and rPW86-vdW2 functionals. In agreement with the earlier reports, on both surfaces, the most stable adsorption configurations correspond to the hollow-45 at which the thiophene adsorbs parallel to the surface. For the adsorption on Ni(100), in agreement with the experimental observations, we confirm that thiophene spontaneously ruptures via breaking of a C–S bond when the center of the molecule is placed over a bridge site. On the basis of both the bond distribution and charge transfer analysis, we conclude that the rupturing of thiophene observed at the bridge-45 configuration on Ni(100) may result from large charge transfer from the surface. The analyses of the electronic and geometric structures and charge transfer reveal that the interaction of the thiophene molecule with Ni(100) is much stronger than that of the Cu(100) surface. Upon adsorption of the molecule, for the former surface, we observed much larger charge transfer, non-negligible changes in the positions of the surface atoms, and appreciable electronic structure changes (i.e., in the center and width of the d-band). The adsorption of thiophene on Ni(100) also leads to the decrease in the magnetic moment of the surface Ni atoms particularly those in the vicinity of the adsorbed molecule. All these observations considered, we conclude that the nature of bonding on Ni(100) can be classified as strong chemisorption, while on Cu(100) it can be classified between weak and strong physisorption depending on the vdW functional used.

36 MATERIALS SCIENCE↗

DOE OSTI2012

Excitonic energy transfer in light-harvesting complexes in purple bacteria

Two distinct approaches, the Frenkel-Dirac time-dependent variation and the Haken-Strobl model, are adopted to study energy transfer dynamics in single-ring and double-ring light-harvesting (LH) systems in purple bacteria. It is found that the inclusion of long-range dipolar interactions in the two methods results in significant increase in intra- or inter-ring exciton transfer efficiency. The dependence of exciton transfer efficiency on trapping positions on single rings of LH2 (B850) and LH1 is similar to that in toy models with nearest-neighbor coupling only. However, owing to the symmetry breaking caused by the dimerization of BChls and dipolar couplings, such dependence has been largely suppressed. In the studies of coupled-ring systems, both methods reveal an interesting role of dipolar interactions in increasing energy transfer efficiency by introducing multiple intra/inter-ring transfer paths. Importantly, the time scale (4 ps) of inter-ring exciton transfer obtained from polaron dynamics is in good agreement with previous studies. In a double-ring LH2 system, non-nearest neighbor interactions can induce symmetry breaking, which leads to global and local minima of the average trapping time in the presence of a non-zero dephasing rate, suggesting that environment dephasing helps preserve quantum coherent energy transfer when the perfect circular symmetry in the hypothetic system is broken. This study reveals that dipolar coupling between chromophores may play an important role in the high energy transfer efficiency in the LH systems of purple bacteria and many other natural photosynthetic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Probing the self-ionization of liquid water with ab initio deep potential molecular dynamics

The chemical equilibrium between self-ionized and molecular water dictates the acid–base chemistry in aqueous solutions, yet understanding the microscopic mechanisms of water self-ionization remains experimentally and computationally challenging. Herein, Density Functional Theory (DFT)–based deep neural network (DNN) potentials are combined with enhanced sampling techniques and a global acid–base collective variable to perform extensive atomistic simulations of water self-ionization for model systems of increasing size. The explicit inclusion of long-range electrostatic interactions in the DNN potential is found to be crucial to accurately reproduce the DFT free energy profile of solvated water ion pairs in small (64 and 128 H 2 O) cells. The reversible work to separate the hydroxide and hydronium to a distance S is found to converge for simulation cells containing more than 500 H 2 O, and a distance of ∼ 8 Å is the threshold beyond which the work to further separate the two ions becomes approximately zero. The slow convergence of the potential of mean force with system size is related to a restructuring of water and an increase of the local order around the water ions. Calculation of the dissociation equilibrium constant illustrates the key role of long-range electrostatics and entropic effects in the water autoionization process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Recent Neutrino Cross-section Results from MicroBooNE

MicroBooNE is a liquid argon time projection chamber that operates in the Booster Neutrino Beam at Fermilab. The detector provides high-resolution imaging of neutrino interactions with a low threshold and full angular coverage. Thanks to a high event rate and several years of continuous operation, the MicroBooNE collaboration has obtained the world’s largest dataset of neutrino-argon scattering events. A detailed understanding of these interactions, especially the impact of nuclear physics effects, will be critical to the success of future precision neutrino oscillation efforts, particularly the argon-based Deep Underground Neutrino Experiment (DUNE) and the Short-Baseline Neutrino (SBN) program. This talk presents an overview of the latest neutrino-argon cross section measurements in MicroBooNE, including measurements of protons produced in muon neutrino interactions, measurements of the electron neutrino inclusive cross section, and progress towards measurements of rare channels.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

First Simultaneous Measurement of Differential Muon-Neutrino Charged-Current Cross Sections on Argon for Final States with and without Protons Using MicroBooNE Data

We report the first double-differential neutrino-argon cross section measurement made simultaneously for final states with and without protons for the inclusive muon neutrino charged-current interaction channel. The proton kinematics of this channel are further explored with a differential cross section measurement as a function of the leading proton’s kinetic energy that extends across the detection threshold. These measurements use data collected with the MicroBooNE detector from 6.4 × 10 20 protons on target from the Fermilab booster neutrino beam with a mean neutrino energy of ∼ 0.8 GeV . Extensive data-driven model validation utilizing the conditional constraint formalism is employed. This motivates enlarging the uncertainties with an empirical reweighting approach to minimize the possibility of extracting biased cross section results. The extracted nominal flux-averaged cross sections are compared to widely used event generator predictions revealing severe mismodeling of final states without protons for muon neutrino charged-current interactions, possibly from insufficient treatment of final state interactions. These measurements provide a wealth of new information useful for improving event generators which will enhance the sensitivity of precision measurements in neutrino experiments. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1974

Penny-shaped crack in a fiber-reinforced matrix

Using a slender inclusion model developed earlier, the elastostatic interaction problem between a penny-shaped crack and elastic fibers in an elastic matrix is formulated. For a single set and for multiple sets of fibers oriented perpendicularly to the plane of the crack and distributed symmetrically on concentric circles, the problem was reduced to a system of singular integral equations. Techniques for the regularization and for the numerical solution of the system are outlined. For various fiber geometries numerical examples are given, and distribution of the stress intensity factor along the crack border was obtained. Sample results showing the distribution of the fiber stress and a measure of the fiber-matrix interface shear are also included.

Narayanan, T. V.↗

NASA NTRS1975

Penny-shaped crack in a fiber-reinforced matrix

Using the slender inclusion model developed earlier the elastostatic interaction problem between a penny-shaped crack and elastic fibers in an elastic matrix is formulated. For a single set and for multiple sets of fibers oriented perpendicularly to the plane of the crack and distributed symmetrically on concentric circles the problem is reduced to a system of singular integral equations. Techniques for the regularization and for the numerical solution of the system are outlined. For various fiber geometries numerical examples are given and distribution of the stress intensity factor along the crack border is obtained. Sample results showing the distribution of the fiber stress and a measure of the fiber-matrix interface shear are also included.

Narayanan, T. V.↗

NASA NTRS1985

Morphological stability and fluid dynamics of vapor crystal growth

Progress is reported in establishing the capabilities of thermal deflection spectroscopy for measurements of the concentration field around a growing crystal. Work was completed on the inclusion of the next nearest neighbor interaction into a surface roughness model and the resulting formalism was applied to copper, zinc, and lead. Other work in mass spectroscopy and vapor transport is discussed.

Rosenberger, F. E.↗

NASA NTRS1995

Fragmentation cross sections of O-16 between 0.9 and 200 GeV/nucleon

Inclusive cross sections for high energy interactions at 0.9, 2.3, 3.6, and 13.5 GeV/nucleon of O-16 with C, CR-39 (C12H18O7), CH2, Al, Cu, Ag, and Pb targets were measured. The total charge-changing cross sections and partial charge-changing cross sections for the production of fragments with charge Z = 6 and Z = 7 are compared to previous experiments at 60 and 200 GeV/nucleon. The contributions of Coulomb dissociation to the total cross sections are calculated. Using factorization rules the partial electromagnetic cross sections are separated from the nuclear components. Energy dependence of both components are investigated and discussed.

Hirzebruch, S. E.↗

NASA NTRS1992

Fragmentation cross sections of 16O between 0.9 and 200 GeV/nucleon

Inclusive cross sections for high energy interactions at 0.9, 2.3, 3.6, and 13.5 GeV/nucleon of 16O with C, CR-39 (C12H18O7), CH2, Al, Cu, Ag, and Pb targets were measured. The total charge-changing cross sections and partial charge-changing cross sections for the production of fragments with charge Z = 6 and Z = 7 are compared to previous experiments at 60 and 200 GeV/nucleon. The contributions of Coulomb dissociation to the total cross sections are calculated. Using factorization rules the partial electromagnetic cross sections are separated from the nuclear components. Energy dependence of both components are investigated and discussed.

NASA Program Radiation Health↗

NASA NTRS2010

Exploring a Physically Based Tool for Lightning Cessation: A Preliminary Study

The University of Alabama in Huntsville (UA Huntsville) and NASA's Marshall Space Flight Center are collaborating with the 45th Weather Squadron (45WS) at Cape Canaveral Air Force Station (CCAFS) to enable improved nowcasting of lightning cessation. The project centers on use of dual-polarimetric radar capabilities, and in particular, the new C-band dual-polarimetric weather radar acquired by the 45WS. Special emphasis is placed on the development of a physically based operational algorithm to predict lightning cessation. While previous studies have developed statistically based lightning cessation algorithms, we believe that dual-polarimetric radar variables offer the possibility to improve existing algorithms through the inclusion of physically meaningful trends reflecting interactions between in-cloud electric fields and microphysics. Specifically, decades of polarimetric radar research using propagation differential phase has demonstrated the presence of distinct phase and ice crystal alignment signatures in the presence of strong electric fields associated with lightning. One question yet to be addressed is: To what extent can these ice-crystal alignment signatures be used to nowcast the cessation of lightning activity in a given storm? Accordingly, data from the UA Huntsville Advanced Radar for Meteorological and Operational Research (ARMOR) along with the North Alabama Lightning Mapping Array are used in this study to investigate the radar signatures present before and after lightning cessation. A summary of preliminary results will be presented.

Schultz, Elise V.↗

NASA NTRS2010

Exploring a Physically Based Tool for Lightning Cessation: Preliminary Results

The University of Alabama in Huntsville (UAHuntsville) and NASA s Marshall Space Flight Center are collaborating with the 45th Weather Squadron (45WS) at Cape Canaveral Air Force Station (CCAFS) to enable improved nowcasting of lightning cessation. The project centers on use of dual-polarimetric radar capabilities, and in particular, the new C-band dual-polarimetric weather radar acquired by the 45WS. Special emphasis is placed on the development of a physically based operational algorithm to predict lightning cessation. While previous studies have developed statistically based lightning cessation algorithms, we believe that dual-polarimetric radar variables offer the possibility to improve existing algorithms through the inclusion of physically meaningful trends reflecting interactions between in-cloud electric fields and microphysics. Specifically, decades of polarimetric radar research using propagation differential phase has demonstrated the presence of distinct phase and ice crystal alignment signatures in the presence of strong electric fields associated with lightning. One question yet to be addressed is: To what extent can these ice-crystal alignment signatures be used to nowcast the cessation of lightning activity in a given storm? Accordingly, data from the UAHuntsville Advanced Radar for Meteorological and Operational Research (ARMOR) along with the North Alabama Lightning Mapping Array are used in this study to investigate the radar signatures present before and after lightning cessation. A summary of preliminary results will be presented.

Schultz, Elsie V.↗

NASA NTRS2011

Exploring the Use of Radar for Physically-Based Nowcasting of Lightning Cessation

NASA's Marshall Space Flight Center and the University of Alabama in Huntsville (UAHuntsville) are collaborating with the 45th Weather Squadron (45WS) at Cape Canaveral Air Force Station (CCAFS) to enable improved nowcasting of lightning cessation. This project centers on use of dual-polarimetric radar capabilities, and in particular, the new C-band dual polarimetric weather radar acquired by the 45WS. Special emphasis is placed on the development of a physically-based operational algorithm to predict lightning cessation. While previous studies have developed statistically based lightning cessation algorithms driven primarily by trending in the actual total lightning flash rate, we believe that dual polarimetric radar variables offer the possibility to improve existing algorithms through the inclusion of physically meaningful trends reflecting interactions between in-cloud electric fields and ice-microphysics. Specifically, decades of polarimetric radar research using propagation differential phase has demonstrated the presence of distinct phase and ice crystal alignment signatures in the presence of strong electric fields associated with lightning. One question yet to be addressed is: To what extent can propagation phase-based ice-crystal alignment signatures be used to nowcast the cessation of lightning activity in a given storm? Accordingly, data from the UAHuntsville Advanced Radar for Meteorological and Operational Research (ARMOR) along with the NASA-MSFC North Alabama Lightning Mapping Array are used in this study to investigate the radar signatures present before and after lightning cessation. Thus far our case study results suggest that the negative differential phase shift signature weakens and disappears after the analyzed storms ceased lightning production (i.e., after the last lightning flash occurred). This is a key observation because it suggests that while strong electric fields may still have been present, the lightning cessation signature was encompassed in the period of the polarimetric negative phase shift signature. To the extent this behavior is repeatable in other cases, even if only in a substantial fraction of those cases, the analysis suggests that differential propagation phase may prove to be a useful parameter for future lightning cessation algorithms. Indeed, a preliminary analysis of 15+ cases has shown additional indications of the weakening and disappearance of this ice alignment signature with lightning cessation. A summary of these case-study results is presented.

Schultz, Elise V.↗

NASA NTRS2011

Exploring the Use of Radar for a Physically Based Lightning Cessation Nowcasting Tool

NASA s Marshall Space Flight Center (MSFC) and the University of Alabama in Huntsville (UAHuntsville) are collaborating with the 45th Weather Squadron (45WS) at Cape Canaveral Air Force Station (CCAFS) to enable improved nowcasting of lightning cessation. This project centers on use of dual-polarimetric radar capabilities, and in particular, the new C-band dual-polarimetric weather radar acquired by the 45WS. Special emphasis is placed on the development of a physically based operational algorithm to predict lightning cessation. While previous studies have developed statistically based lightning cessation algorithms, we believe that dual-polarimetric radar variables offer the possibility to improve existing algorithms through the inclusion of physically meaningful trends reflecting interactions between in-cloud electric fields and hydrometeors. Specifically, decades of polarimetric radar research using propagation differential phase has demonstrated the presence of distinct phase and ice crystal alignment signatures in the presence of strong electric fields associated with lightning. One question yet to be addressed is: To what extent can these ice-crystal alignment signatures be used to nowcast the cessation of lightning activity in a given storm? Accordingly, data from the UAHuntsville Advanced Radar for Meteorological and Operational Research (ARMOR) along with the NASA-MSFC North Alabama Lightning Mapping Array are used in this study to investigate the radar signatures present before and after lightning cessation. Thus far, our case study results suggest that the negative differential phase shift signature weakens and disappears after the analyzed storms ceased lightning production (i.e., after the last lightning flash occurred). This is a key observation because it suggests that while strong electric fields may still have been present, the lightning cessation signature encompassed the period of the polarimetric negative phase shift signature. To the extent this behavior is repeatable in other cases, even if only in a substantial fraction of those cases, the case analyses suggests that differential propagation phase may prove to be a useful parameter for future lightning cessation algorithms. Indeed, analysis of 15+ cases has shown additional indications of the weakening and disappearance of this ice alignment signature with lightning cessation. A summary of results will be presented.

Schultz, Elise V.↗