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DOE OSTI2018

Understanding the Structure, Multimerization, Subcellular Localization and mC Selectivity of a Genomic Mutator and Anti-HIV Factor APOBEC3H

APOBEC3H (A3H) is a member of the APOBEC3 subfamily of DNA cytosine deaminases that are important for innate immune defense and have been implicated in cancer biogenesis. To understand the structural basis for A3H biochemical function, we determined a high-resolution structure of human A3H and performed extensive biochemical analysis. The 2.49 Å crystal structure reveals a uniquely long C-terminal helix 6 (h6), a disrupted β5 strand of the canonical five-stranded β-sheet core, and a long loop 1 around the Zn-active center. Mutation of a loop 7 residue, W115, disrupted the RNA-mediated dimerization of A3H yielding an RNA-free monomeric form that still possessed nucleic acid binding and deaminase activity. A3H expressed in HEK293T cells showed RNA dependent HMW complex formation and RNase A-dependent deaminase activity. A3H has a highly positively charged surface surrounding the Zn-active center, and multiple positively charged residues within this charged surface play an important role in the RNA-mediated HMW formation and deaminase inhibition. Furthermore, these positively charged residues affect subcellular localization of A3H between the nucleus and cytosol. Finally, we have identified multiple residues of loop 1 and 7 that contribute to the overall deaminase activity and the methylcytosine selectivity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Theoretical studies of positron states and annihilation characteristics at the oxidized Cu(100) surface

In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. An ab-initio study of the electronic properties of the Cu(100) missing row reconstructed surface at various on surface and sub-surface oxygen coverages has been performed on the basis of the density functional theory (DFT) using the Dmol3 code and the generalized gradient approximation (GGA). Surface structures in calculations have been constructed by adding oxygen atoms to various surface hollow and sub-surface octahedral sites of the 0.5 monolayer (ML) missing row reconstructed phase of the Cu(100) surface with oxygen coverages ranging from 0.5 to 1.5 ML. The charge redistribution at the surface and variations in atomic structure and chemical composition of the topmost layers associated with oxidation and surface reconstruction have been found to affect the spatial extent and localization of the positron surface state wave function and annihilation probabilities of surface trapped positrons with relevant core electrons. Theoretical results are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES). It has been shown that positron annihilation probabilities with Cu 3s and 3p core electrons decrease when total (on-surface and sub-surface) oxygen coverage of the Cu(100) surface increases up to 1 ML. The calculations show that for high oxygen coverage when total oxygen coverage is 1. 5 ML the positron is not bound to the surface.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Design and development of a four-cell sorption compressor based J-T cooler using R134a as working fluid

The need of a cooler with no electromagnetic interference and practically zero vibration has led to sorption compressor based Joule-Thomson (J-T) coolers. These are useful for sophisticated electronic, ground based and space borne systems. In a Sorption compressor, adsorbed gases are desorbed into a confined volume by raising temperature of the sorption bed resulting in an increase in pressure of the liberated gas. In order to have the system (compressor) functioning on a continuous basis, with almost a constant gas flow rate, multiple cells are used with the adaptation of Temperature Swing Adsorption (TSA) process. As the mass of the desorbed gas dictates the compressor throughput, a combination of sorbent material with high adsorption capacity for a chosen gas or gas mixture has to be selected for efficient operation of the compressor. Commercially available (coconut-shell base) activated carbon has been selected for the present application. The characterization study for variation of discharge pressure is used to design the Four-cell sorption compressor based cryocooler with a desired output. Apart from compressor, the system includes a) After cooler b) Return gas heat exchanger c) capillary tube as the J-T expansion device and d) Evaporator.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2014

Interaction potentials and thermodynamic properties of two component semiclassical plasma

In this paper, the effective interaction potential in two component semiclassical plasma, taking into account the long-range screening and the quantum-mechanical diffraction effects at short distances, is obtained on the basis of dielectric response function method. The structural properties of the semiclassical plasma are considered. The thermodynamic characteristics (the internal energy and the equation of state) are calculated using two methods: the method of effective potentials and the method of micropotentials with screening effect taken into account by the Ornstein-Zernike equation in the HNC approximation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2014

Near-resonant rotational energy transfer in HCl–H{sub 2} inelastic collisions

We present a new four-dimensional (4D) potential energy surface for the HCl–H{sub 2} van der Waals system. Both molecules were treated as rigid rotors. Potential energy surface was obtained from electronic structure calculations using a coupled cluster with single, double, and perturbative triple excitations method. The four atoms were described using the augmented correlation-consistent quadruple zeta basis set and bond functions were placed at mid-distance between the HCl and H{sub 2} centers of mass for a better description of the van der Waals interaction. The global minimum is characterized by the well depth of 213.38 cm{sup −1} corresponding to the T-shape structure with H{sub 2} molecule on the H side of the HCl molecule. The dissociation energies D{sub 0} are 34.7 cm{sup −1} and 42.3 cm{sup −1} for the complex with para- and ortho-H{sub 2}, respectively. These theoretical results obtained using our new PES are in good agreement with experimental values [D. T. Anderson, M. Schuder, and D. J. Nesbitt, Chem. Phys. 239, 253 (1998)]. Close coupling calculations of the inelastic integral rotational cross sections of HCl in collisions with para-H{sub 2} and ortho-H{sub 2} were performed at low and intermediate collisional energies. Significant differences exist between para- and ortho-H{sub 2} results. The strongest collision-induced rotational HCl transitions are the transitions with Δj = 1 for collisions with both para-H{sub 2} and ortho-H{sub 2}. Rotational relaxation of HCl in collision with para-H{sub 2} in the rotationally excited states j = 2 is dominated by near-resonant energy transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Magnetic property and possible half-metal behavior in Co-doped graphene

The magnetic property and band structures of Co-monolayer doped graphene were examined on the basis of density-functional theory. The magnetic moment of the system is closely related to the interfacial spacing. Magnetic-nonmagnetic transition would be produced by decreasing the layer distance. Although the magnetic moment can also be reduced by increasing the lattice constant, the ground states are magnetic states under tension. Besides, the increase of lattice constant greatly enlarges the direct and indirect gaps of spin-down bands near the Fermi level. With a little increase of the Fermi level or the electron density, half-metal behavior would be expectable in the Co-doped graphene under tension.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Experimental analysis of conductive drying of paper and board

The primary heat transfer source in the conventional multi-cylinder drying of paper and board is conduction. Conduction is facilitated by high-tension contact with steam-heated cylinders, while convective drying, the main mass transfer source, operates as heated air flows over the paper web in the pockets. This conduction process occurs at elevated temperatures and contact pressures to ensure effective contact between the wet paper web and the heated cylinders. The contact pressures and temperatures of the hot surface significantly influence the conductive drying characteristics. This research paper presents an experimental study that involves designing a simple lab-scale setup with in-situ and continuous sensing capabilities for various commercially available grades of paper and board. Embedded thermocouples measure the temperatures of the heated platen and the sheet, allowing the collection of flux data to determine heat transfer characteristics. Here, the goal of this study is to ascertain the instantaneous contact coefficients for different basis weights as a function of moisture content. The acquired data will provide valuable insights and information towards process development, design and simulation of the paper drying process.

42 ENGINEERING↗

DOE OSTI2016

Testing chirality of primordial gravitational waves with Planck and future CMB data: no hope from angular power spectra

We use the 2015 Planck likelihood in combination with the Bicep2/Keck likelihood (BKP and BK14) to constrain the chirality, χ, of primordial gravitational waves in a scale-invariant scenario. In this framework, the parameter χ enters theory always coupled to the tensor-to-scalar ratio, r , e.g. in combination of the form χ ⋅ r . Thus, the capability to detect χ critically depends on the value of r . We find that with present data sets χ is de facto unconstrained. We also provide forecasts for χ from future CMB experiments, including COrE+, exploring several fiducial values of r . We find that the current limit on r is tight enough to disfavor a neat detection of χ. For example, in the unlikely case in which r ∼0.1(0.05), the maximal chirality case, i.e. χ = ±1, could be detected with a significance of ∼2.5(1.5)σ at best. We conclude that the two-point statistics at the basis of CMB likelihood functions is currently unable to constrain chirality and may only provide weak limits on χ in the most optimistic scenarios. Hence, it is crucial to investigate the use of other observables, e.g. provided by higher order statistics, to constrain these kinds of parity violating theories with the CMB.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Anisotropic excitonic magnetism from discrete C 4 symmetry in CeRhIn 5

Anisotropy in strongly correlated materials is a central parameter in determining the electronic ground state and is tuned through the local crystalline electric field. This is notably the case in the CeCo x Rh 1 − x In 5 system where the ground-state wave function can provide the basis for antiferromagnetism and/or unconventional superconductivity. We develop a methodology to understand the local magnetic anisotropy and experimentally investigate with neutron spectroscopy applied to antiferromagnetic ( T N = 3.8 K ) CeRhIn 5 , which is isostructural to d -wave superconducting ( T c = 2.3 K ) CeCoIn 5 . Through diagonalizing the local crystal field Hamiltonian with discrete tetragonal C 4 point group symmetry and coupling these states with the random phase approximation, we find two distinct modes polarized along the crystallographic c and a − b planes, agreeing with experiment. The anisotropy and bandwidth, underlying the energy scale of these modes, are tuneable with a magnetic field which we use experimentally to separate in energy single and multiparticle excitations thereby demonstrating the instability of excitations polarized within the crystallographic a − b plane in CeRhIn 5 . We compare this approach to a S eff = 1 2 parametrizations and argue for the need to extend conventional SU(2) theories of magnetic excitations to utilize the multilevel nature of the underlying crystal-field basis states constrained by the local point-group C 4 symmetry. Published by the American Physical Society 2024

Brener, D. J. (ORCID:0000000333400177)↗

DOE OSTI2017

Cusps enable line attractors for neural computation

Here, line attractors in neuronal networks have been suggested to be the basis of many brain functions, such as working memory, oculomotor control, head movement, locomotion, and sensory processing. In this paper, we make the connection between line attractors and pulse gating in feed-forward neuronal networks. In this context, because of their neutral stability along a one-dimensional manifold, line attractors are associated with a time-translational invariance that allows graded information to be propagated from one neuronal population to the next. To understand how pulse-gating manifests itself in a high-dimensional, nonlinear, feedforward integrate-and-fire network, we use a Fokker-Planck approach to analyze system dynamics. We make a connection between pulse-gated propagation in the Fokker-Planck and population-averaged mean-field (firing rate) models, and then identify an approximate line attractor in state space as the essential structure underlying graded information propagation. An analysis of the line attractor shows that it consists of three fixed points: a central saddle with an unstable manifold along the line and stable manifolds orthogonal to the line, which is surrounded on either side by stable fixed points. Along the manifold defined by the fixed points, slow dynamics give rise to a ghost. We show that this line attractor arises at a cusp catastrophe, where a fold bifurcation develops as a function of synaptic noise; and that the ghost dynamics near the fold of the cusp underly the robustness of the line attractor. Understanding the dynamical aspects of this cusp catastrophe allows us to show how line attractors can persist in biologically realistic neuronal networks and how the interplay of pulse gating, synaptic coupling, and neuronal stochasticity can be used to enable attracting one-dimensional manifolds and, thus, dynamically control the processing of graded information.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Structure of the virulence-associated protein VapD from the intracellular pathogen Rhodococcus equi

VapD is one of a set of highly homologous virulence-associated proteins from the multi-host pathogen Rhodococcus equi. The crystal structure reveals an eight-stranded β-barrel with a novel fold and a glycine rich ‘bald’ surface. Rhodococcus equi is a multi-host pathogen that infects a range of animals as well as immune-compromised humans. Equine and porcine isolates harbour a virulence plasmid encoding a homologous family of virulence-associated proteins associated with the capacity of R. equi to divert the normal processes of endosomal maturation, enabling bacterial survival and proliferation in alveolar macrophages. To provide a basis for probing the function of the Vap proteins in virulence, the crystal structure of VapD was determined. VapD is a monomer as determined by multi-angle laser light scattering. The structure reveals an elliptical, compact eight-stranded β-barrel with a novel strand topology and pseudo-twofold symmetry, suggesting evolution from an ancestral dimer. Surface-associated octyl-β-d-glucoside molecules may provide clues to function. Circular-dichroism spectroscopic analysis suggests that the β-barrel structure is preceded by a natively disordered region at the N-terminus. Sequence comparisons indicate that the core folds of the other plasmid-encoded virulence-associated proteins from R. equi strains are similar to that of VapD. It is further shown that sequences encoding putative R. equi Vap-like proteins occur in diverse bacterial species. Finally, the functional implications of the structure are discussed in the light of the unique structural features of VapD and its partial structural similarity to other β-barrel proteins.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

The Materials Plasma Exposure eXperiment: Status of the Physics Basis Together With the Conceptual Design and Plans Forward

The Materials Plasma Exposure eXperiment (MPEX) is a linear plasma device that will address the plasma–material interaction (PMI) science for future fusion reactors and will enable testing of plasma-facing components (PFCs). It is designed as a steady-state device eventually delivering an ion fluence of up to 10 31 m -2 to the target. The device will be designed to handle neutron-activated materials. These capabilities should push the technical readiness level of PFCs up to six for some end-of-life aspects. In order to achieve the relevant plasma conditions, as they are expected in future fusion reactor divertors, MPEX will utilize a novel plasma source concept. This plasma source concept uses a high-power helicon (200 kW, 13.56 MHz), an electron cyclotron heating (ECH) system, which will heat electrons via electron Bernstein wave (EBW) heating (about 400 kW, 70 GHz), and an ion cyclotron heating (ICH) system (400 kW, 6–9 MHz). The physics basis for this plasma source concept including the heating physics and transport is based on experiments on Proto-MPEX. An overview of the experimental results and the physics basis will be given. The physics basis directly translates into functional requirements of MPEX and the conceptual design. The status of the conceptual design of MPEX will be shown.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

A Double-Wiebe Function for Reactivity Controlled Compression Ignition Combustion Using Reformate Diesel

Abstract Reactivity controlled compression ignition (RCCI) combustion has previously been proposed as a method to achieve high fuel conversion efficiency and reduce engine emissions. A single-fuel RCCI combustion strategy can have decreased fuel system complexity by using a reformate fuel for port fuel injection and the parent fuel (diesel) for direct injection. This paper presents a one-dimensional computational model of a compression ignition engine with single-fuel RCCI. A Wiebe function is used to predict the combustion process by representing the mass fraction burned (MFB) on a crank angle resolved basis. One single-Wiebe function (SWF) and two double-Wiebe functions(DWFs) were fitted to experimentally derive MFB data using the least-square method. The fitted results were compared with MFBs calculated from experimental data to verify the accuracy. The SWF did not fully capture the MFB curve with high fidelity while the detailed DWF captured the MFB curve within a root mean square error of 1.4%. The reduced double-Wiebe function (RDWF) also resulted in a predicted combustion profile with similar accuracy. Hence, the RDWF was used in a GT-power thermodynamic study to understand the effects of the low-temperature heat release (LTHR) fraction and combustion phasing on combustion characteristics. At optimum phasing of 5–10 crank angle degree after the top dead center, increasing the LTHR fraction from 20% to 60% resulted in the fuel conversion efficiency increasing from 39.5% to 41.1%, thus suggesting that the reformate fuel-based RCCI strategy is viable to unlock improved combustion performance.

Energy & Fuels↗

DOE OSTI2019

Top Ten Blendstocks For Turbocharged Gasoline Engines: Bioblendstocks With Potential to Deliver the for Highest Engine Efficiency

More efficient engines enabled by better fuels derived from biomass could increase the fuel economy of the light duty (LD) fleet by 10% over current technology and planned developments. This report identifies top LD boosted spark ignition (BSI) biofuel candidates for further development and commercialization identified using a fuel property basis. The BSI merit function was used to evaluate the performance of candidate bio-blendstocks in improving engine efficiency. This report is aimed at biofuel researchers looking to better understand the efficiency implications of biofuels under development, as well as engine researchers who are interested in future biofuels with properties that enable more efficient engine design and operation.

09 BIOMASS FUELS↗

DOE OSTI2019

Top Ten Blendstocks Derived From Biomass For Turbocharged Spark Ignition Engines

09 BIOMASS FUELS↗

DOE OSTI2021

Nano-Engineered Catalyst Supported on Ceramic Hollow Fibers for the Utilization of CO 2 in Dry Reforming to Produce Syngas

The objective of this project was to develop a novel catalytic reactor containing nano-engineered catalysts for the utilization of CO 2 (captured from coal-fired power plants and other CO 2 emitting sources) in dry methane reforming (DMR) (CO 2 + CH 4 → 2 H 2 + 2 CO) to produce synthesis gas (syngas). The technology aims to reduce CO2 emissions by developing beneficial uses for CO 2 from coal-fired power plants. It also offers an alternative to mitigate CO 2 emissions in areas where geologic storage may not be an optimal solution and/or utilization could significantly offset the costs of carbon capture and sequestration. The nano-engineered Ni-based catalyst was prepared by atomic layer deposition (ALD). The Ni particles were as small as ~2-4 nm. The nano-engineered catalyst showed CH 4 conversion >95%, H 2 /CO ratio in the range of 0.7-1.0, and CH 4 reforming rate as high as 2,500 L/h/gNi at 850 ºC and pressure of 15-25 psia. The Ni-based ALD catalyst also showed good stability in DMR reaction during a 200-h continuous operation at 850 °C. This is due to strong bonding between the nanoparticles and substrates since the Ni nanoparticles were chemically bonded to the substrate during the ALD process. The high thermal stability maintains the high dispersion of Ni nanoparticles, which can inhibit coke formation because their step edges are small enough to limit carbon nucleation and growth. Technoeconomic analysis (TEA) indicates the levelized cost of syngas (LCOS) is $172/ton with our technology, which is lower than the equivalent (molar) cost of hydrogen produced by steam methane reforming (SMR) or autothermal reforming (ATR). The major operating cost is natural gas feed and fuel, and the levelized cost is highly sensitive to the price of natural gas and relatively insensitive to the CAPEX. Revenues from syngas could have a significant impact on the net cost of electricity (COE), depending on the cost of natural gas and the selling price of syngas, estimated at $36 per MWh if the syngas were sold at $195 per ton. Following DOE NETL’s guidance, a lifecycle analysis (LCA) was conducted to compare with SMR. The functional unit for the basis of comparison was defined as 1kg carbon monoxide in the product stream. The global warming potential (GWP) of our process was found to be 40% lower than the state-of-the-art SMR process. The sensitivity analysis confirms the emissions are most sensitive to the natural gas fuel requirements to deliver heat to the process.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2022

Elucidating the Determinants of Alkali Ionic Conductivity in Oxide and Sulfide Frameworks

The aim of this project is to elucidate the structural and chemical factors determining alkali conductivity in oxide and sulfide frameworks using large scale first principles calculations and topological analysis. The facile conduction of alkali ions in oxide and sulfide host structures is of critical importance in energy storage. Today, the dominant form of energy storage in portable electronics is the rechargeable alkali-ion battery, a device that functions entirely on the basis of the reversible transport of alkali ions. The Li+/Na+ conductivity of a cathode has a direct influence on the rate capability of a Li/Na-ion battery, i.e., the speed at which it can be charged and discharged. Alkali conductivity is arguably of even greater importance in the solid electrolytes currently being investigated for high safety, high energy all-solid-state batteries. The research performed in this project has provided critical new insights into the diffusion mechanisms in state-of-the-art alkali superionic conductors such as Li 7 P 3 S 11 , Li 3 OCl 1-x Br x anti-perovskite, argyrodite Li 6 PS 5 Cl. Two potential novel lithium superionic conductors (Li 3 Y(PS 4 ) 2 and Li 5 PS 4 Cl 2 ) with improved electrochemical stabilities were predicted. We have also conducted in-depth studies into alkali conduction in several important classes of electrodes, including the layered P2 NaMO 2 oxides and the highly promising novel disordered rock salt Li 3+x V 2 O 5 anode for high-rate applications. This project has resulted in more than 10 peer-reviewed articles in highly regarded journals as well as a new open-source software framework (pymatgen-analysis-diffusion) that is widely used by the materials research community for the study of diffusion in materials.

25 ENERGY STORAGE↗

DOE OSTI2025

Consideration of Decabromodiphenyl Ether Flame Retardant in Thermal and Radiation Aging of Crosslinked Polyethylene Cable Insulation

Decabromodiphenyl ether (decaBDE) has been used as a flame-retardant additive in nuclear-grade electrical cable insulation. However, decaBDE has been identified as a persistent, bioaccumulative and toxic (PBT) substance, leading to regulatory scrutiny. On January 6, 2021, the Environmental Protection Agency (EPA) published a final rule to phase out decaBDE. The 2021 rule set a two-year compliance deadline for “processing and distribution in commerce of decaBDE for use in wire and cable insulation in nuclear power generation facilities.” In recognition of industry concerns following a sudden discontinuation of decaBDE-containing Class 1E wire and cable essential for nuclear power operations and the time needed for qualifying the individual components using the alternative insulation technology, an extended compliance deadline was set in the finalized amendments to the 2021 rule as published by the Environmental Appeals Board on November 12, 2024. The 2024 rule set the compliance deadline for processing and distributing decaBDE-containing wire and cable insulation until the end of the service life of these materials. Since decaBDE has long been relied upon as the flame retardant in one of the most common cross-linked polyethylene (XLPE) nuclear cable insulation formulations, RSCC Firewall III insulation, questions have naturally arisen regarding whether changes in cable performance might be expected for XLPE containing a decaBDE alternative, especially for safety-related cables that must perform their safety function in a design basis event such as a loss of coolant accident.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗