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At least 703 records · Page 39

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

59 BASIC BIOLOGICAL SCIENCES↗

The Neurodata Without Borders ecosystem for neurophysiological data science

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB’s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

59 BASIC BIOLOGICAL SCIENCES↗

Nuclear Fuel and Pu Redox Studies from The Glenn T. Seaborg Institute at Idaho National Laboratory

The Glenn T. Seaborg Institute at Idaho National Laboratory (INL-GTSI) focuses on advancing fundamental research in the actinide sciences by providing unique opportunities to early career scientists and engineers to gain experience studying the actinide elements and their associated systems. The INL-GTSI is built from three focus areas that are based on the expertise and supporting infrastructure at INL and include solid state chemistry and physics, solution phase chemistry and physics, and forensic and isotope science. INL is the lead Laboratory for nuclear energy research and development in the U. S. and the research on nuclear fuels performed under the INL-GTSI gives good examples of solid state studies. Uranium-Molybdenum (U-Mo) alloys are leading fuel candidates for conversion of high performance research and test reactors to low-enriched fuels. During irradiation, generated fission gas accumulates into bubbles and self-organizes into a gas bubble superlattice (GBS) that effectively stores fission gases and inhibits fuel swelling. A study on the early self- organizing behavior of the GBS shows that not only grain boundaries but the interfaces between the U-Mo matrix and uranium carbide (UC) impurities are important to GBS formation.[1] In solution, understanding the complex redox behavior of plutonium in aqueous environments is critical for establishing optimized nuclear waste reprocessing solvent systems and storage tank environments. INL-GTSI researchers have produced an experimentally validated multi-scale model of the gamma radiation induced behavior of plutonium ions in concentrated aqueous HNO3 solutions.[2] Here, gamma radiation effected only minimal steady state changes in the redox distribution of the plutonium oxidation states. The redox cycling between Pu(IV) and Pu(III) is demonstrated to be mediated by the •OH/NO3• radical oxidation of Pu(III) and the H2O2/HNO3 driven reduction of Pu(IV). The INL-GTSI offers young researchers the unique chance to work directly with actinide bearing materials in a U. S. National Laboratory environment. Further topical areas of interest to the INL-GTSI include, but are not limited to, fundamental actinide properties, structure/property (electronic, magnetic, thermal) relations, actinide quantum criticality, f- electron interactions, electron correlations, computational studies, new phases, defect effects, interface interactions, isotope production and separation, forensic analytical chemistry, structure and dynamic properties of actinides in non-aqueous media, separations chemistry and kinetics for advanced nuclear fuel cycles, radiation effects, and innovative and advanced ligand design for complexation of the actinides.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

CFT and lattice correlators near an RG domain wall between minimal models

Conformal interfaces separating two conformal field theories (CFTs) provide maps between different CFTs, and naturally exist in nature as domain walls between different phases. One particularly interesting construction of a conformal interface is the renormalization group (RG) domain wall between CFTs. For a given Virasoro minimal model \mathcal{M}_{k+3,k+2} ℳ k + 3 , k + 2 , an RG domain wall can be generated by a specific deformation which triggers an RG flow towards its adjacent Virasoro minimal model \mathcal{M}_{k+2,k+1} ℳ k + 2 , k + 1 with the deformation turned on over part of the space. An algebraic construction of this domain wall was proposed by Gaiotto in [J. High Energy Phys. 12, 103 (2012)]. In this paper, we will provide a study of this RG domain wall for the minimal case k=2 k = 2 , which can be thought of as a nonperturbative check of the construction. In this case the wall is separating the Tricritical Ising Model (TIM) CFT and the Ising Model (IM) CFT. We will check the analytical results of correlation functions from the RG brane construction with the numerical density matrix renormalization group (DMRG) calculation using a lattice model proposed in [arXiv.1206.1332, Science 344, 280 (2014)], and find a perfect agreement. We comment on possible experimental realizations of this RG domain wall.

Cogburn, Cameron V.↗

TRACER-CAT-UCDAVIS Aerosol Optical Properties and Sizing - smps

Aerosol size distribution and optical properties collected in La Port TX, during TRACER-CAT-UCDavis, July 2022. Speciated particle composition measurements are reported separately. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by UC Davis (TRACER-CAT-UCDavis, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-UCDavis is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments include: UC Davis two-wavelength cavity ringdown-photoacoustic spectrometer (CRD-PAS); Brechtel scanning electrical mobility sizer (SEMS); modified humidified cavity attenuated phase shift spectrometer with single scatter albedo (H-CAPS-SSA)

54 ENVIRONMENTAL SCIENCES↗

TRACER-CAT-UCDAVIS Aerosol Optical Properties and Sizing - crdps

Aerosol size distribution and optical properties collected in La Port TX, during TRACER-CAT-UCDavis, July 2022. Speciated particle composition measurements are reported separately. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by UC Davis (TRACER-CAT-UCDavis, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-UCDavis is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments include: UC Davis two-wavelength cavity ringdown-photoacoustic spectrometer (CRD-PAS); Brechtel scanning electrical mobility sizer (SEMS); modified humidified cavity attenuated phase shift spectrometer with single scatter albedo (H-CAPS-SSA)

54 ENVIRONMENTAL SCIENCES↗

Stochastic Model for High Temperature Oxidation of Cr–Ni Austenitic Steels Assisted by Spallation

Abstract Cr–Ni austenitic steels offer significant high temperature corrosion protection by forming a surface oxide layer. However, above critical service conditions (temperature, atmosphere, thermal cycling), oxidized surface can experience intensive degradation because of scale spallation, which could be detrimental to the in-service life. To predict the effect of scale spallation on oxidation kinetics, a simulation was implemented using a stochastic model. The model considers topological parameters and intensity of spallation which can occur, while delivering a true oxidation constant. The experimental procedure identified the amount of formed spalled scale and topology of spallation based on the use of element mapping of the surface. This information was used to determine a true kinetic constant for a corresponding spallation intensity in oxidized Cr–Ni austenitic steel. To illustrate the capability of the stochastic model, a parametric analysis was performed. The model verified how the spallation parameters could change the oxidation processes from parabolic growth of an adhered oxide layer without spallation to a mixed linear-parabolic, or with a constant thickness of residual scale at high spallation intensity. The spallation model will be used in a separate article to characterize high temperature surface degradation of several Cr–Ni austenitic steels during harsh oxidation environments.

36 MATERIALS SCIENCE↗

A simple and practical process modeling methodology for pressure swing adsorption

Although many dynamic models exist for the design and simulation of pressure swing adsorption (PSA) processes, these models involve the solution of a complex system of coupled partial differential equations. Process engineers need a simple, practical, and yet robust short-cut model that helps decide whether to implement a PSA system in a process flowsheet. This work presents a “virtual” moving bed modeling methodology that considers only mass and energy balances and adsorption isotherms to describe the cyclic steady state behavior of PSA systems. Similar to tray efficiencies in distillation calculations, adsorption efficiencies are further introduced to account for system “non-ideality.” Finally, a lab-scale air separation system is used to illustrate the application of this modeling methodology.

42 ENGINEERING↗

Accumulation of Large Ion Populations with High Ion Densities and Effects Due to Space Charge in Traveling Wave-Based Structures for Lossless Ion Manipulations (SLIM) IMS-MS

The accumulation of very large ion populations in traveling wave (TW)-based Structures for Lossless ion Manipulations (SLIM) has been studied to better understand aspects of ‘in-SLIM’ ion accumulation, and particularly its use in conjunction with ion mobility spectrometry (IMS). A linear SLIM ion path was implemented that had a ‘gate’ for blocking and accumulating ions for arbitrary time periods. Removing the gate potential caused ions to exit and the spatial distributions of accumulated ions were examined. The ion populations for a set of peptides were observed to increase with increased accumulation times until space change effects became significant, after which the peptide precursor ion populations decreased due to growing space charge-related ion activation, reactions, and losses. Ions closest to the gate were preferentially activated, and increasingly so with added storage times, TW amplitude, and the size of the total ion population. For analytical applications, we found that relatively weak TWs in the accumulation/storage region should be utilized to prevent or minimize ion losses and/or ion heating effects that can also lead to fragmentation. Our results further indicate that an accumulation region close to the SLIM entrance is advantageous for both speeding accumulation, minimizing ion heating, and avoiding ion population profiles that result in IMS peak tailing. Importantly, space charge-driven separations were observed for large populations of accumulated species and attributed to the opposing effects of space charge and the TW. In these separations, ion species form distributions or peaks, sometimes moving against the TW, and ordered in the SLIM based on their mobilities. Such separations may offer utility for ion pre-fractionation of ions and increasing the dynamic range measurements, increasing the resolving power of IMS separations by decreasing peak widths for accumulated ion populations, and other purposes benefitting from separations of extremely large ion populations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Cloud Morphology Evolution in Arctic Cold‐Air Outbreak: Two Cases During COMBLE Period

Abstract Cloud feedbacks play an important role in Arctic warming. Cloud morphology, for example, cloud size and spatial distributions, is among key factors that directly impact their radiative effects. In this work, we use two cases observed during the Cold‐air Outbreak (CAO) in the Marine Boundary Layer Experiment (COMBLE) to study the evolution of cloud size distributions as an air mass is advected from the Arctic over a comparatively warm ocean and cloud mesoscale organization changes from rolls to cells. Cloud objects are identified from Moderate Resolution Imaging Spectroradiometer (MODIS) reflectance images through an object segmentation procedure and roll breakup is identified by homogeneities in cloud water path (CWP). Roll breakup is found to be accompanied by a local minimum in wind shear and local maxima in cloud size and marine cold air outbreak index. The mean cloud horizontal aspect ratio has weak fetch dependency and is around 2 in roll, transition, and cell regimes. Regardless of distance from the ice edge, smaller clouds (<10 km 2 ) dominate the population number but not cloud cover. Cloud size distributions show bimodality in transition and cell regimes. For clouds with comparable sizes, mean nearest neighbor distances normalized by equivalent cloud radius converge to a single value for all regimes and for all but the smallest clouds, suggesting that clouds of comparable sizes in CAOs are separated by distance proportional to their sizes. The presented statistical results pave the way to evaluating model simulated cloud organizations during CAO events.

54 ENVIRONMENTAL SCIENCES↗

Ferromagnetism and doublon localization in a Wannier-Hubbard chain

We derive a “Wannier-Hubbard” model consisting of an array of overlapping atomic orbitals interacting via a local Coulomb interaction. Transforming to an orthogonal Wannier basis set, the resulting Hamiltonian displays long-range hopping and interactions, with new terms such as correlated hopping and ferromagnetic direct exchange, among others. We numerically study the one-dimensional version of the model at half-filling using the density matrix renormalization group method, unveiling a rich phase diagram as a function of the interaction U and the overlap s with metallic and ferromagnetic phases separated by a ferrimagnetic region. Our results indicate a path toward understanding emergent phases under pressure and beyond standard model Hamiltonians.

36 MATERIALS SCIENCE↗

Walker Branch Watershed: Daily Stream Metabolism and Organic Carbon Spiraling Metrics in the West Fork of Walker Branch, Tennessee, USA, 2004-2010

This dataset contains daily metabolism estimates of gross primary production (GPP), ecosystem respiration (ER), and net ecosystem production (NEP), in addition to organic carbon spiraling length (SOC) and mineralization velocity (VfOC) estimates at the West Fork of Walker Branch, a small headwater stream, in the Walker Branch Watershed, Tennessee, USA. Observations were made from 2004-2010 (2004-01-01 to 2010-12-31). These data were generated to assess seasonal and interannual variability in metabolism and organic carbon spiraling and to explore potential driver variables, as analyses of intra- and interannual variability in metabolism and organic carbon spiraling are currently limited, leaving knowledge gaps in the driving mechanisms of and future changes to stream metabolism and carbon processing under climate change. Additionally, measurements of discharge (Q), stream width, stream- and canopy-level photosynthetically active radiation (PAR), water temperature, and precipitation from this time frame are included. This dataset contains one data file in comma separated (*.csv) format.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE S1 Bog and Bog Lake Fen Moss Decomposition and Litter Chemistry Data, 2014-2019

This dataset includes measurements of mass loss, decay rate, and litter chemistry of mosses decomposing in the S1 Bog and Bog Lake Fen located in the USDA Forest Service Marcell Experimental Forest (MEF) in northern Minnesota, 40 km north of Grand Rapids. A litterbag experiment was used to estimate decay rates of 3 different moss types (Sphagnum magellanicum, Sphagnum angustifolium/fallax, and Polytrichum sp.) from mass loss measurements after one and five years in hummock and hollow microtopographies in the bog and lawn microtopography in the poor fen. Carbon, nitrogen, and phosphorous contents of the mosses were measured initially, after 1 year, and after 5 years of decay. Sample collection and analyses started in 2014 and was completed in 2019 (2014-06-05 to 2019-06-05). These data are from outside the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental plots. Decomposition data (rates and chemistry changes) can be used to assess ecosystem carbon and nutrient cycles. These data were used in analyses reported in Shelley et al (2022). This dataset contains two data files in comma-separate values (*.csv) format. Additional metadata are provided: two data dictionaries and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE S1 Bog Production of Newly-Grown Fine Roots Assessed Using Root Ingrowth Cores in 2013

This dataset contains data from root ingrowth cores from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental site within the Marcell Experimental Forest in northern Minnesota, USA. Root ingrowth cores were used to capture newly-grown fine roots during the 2013 growing season (June - October) at 20 locations at the southern end of the S1-Bog. Rates of fine root production were measured with root ingrowth cores and fine root traits were measured on roots that grew into ingrowth cores. Traits are reported by plant species and root orders and include nitrogen (N) content, root tissue density, specific root length, average diameter. Ingrowth cores were used to compare species-specific depth distribution patterns with minirhizotron analyses and to obtain newly produced roots for chemical analysis and measurement of morphological traits prior to the construction of the SPRUCE experimental plots. This dataset contains two data files in comma-separate values (*.csv) format. Additional metadata are provided: two data dictionaries and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗