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At least 415 records · Page 23

Nucleic acids encoding mosaic conserved region HIV immunogenic polypeptides

Disclosed herein are mosaic conserved region HIV polypeptides and immunogenic polypeptides including one or more of the mosaic conserved region polypeptides. In some embodiments, the immunogenic polypeptides are included in an immunogenic composition, such as a polyvalent immunogenic composition. Also disclosed herein are methods for treating or inhibiting HIV in a subject including administering one or more of the disclosed immunogenic polypeptides or compositions to a subject having or at risk of HIV infection. In some embodiments, the methods include inducing an immune response in a subject comprising administering to the subject at least one of the disclosed immunogenic polypeptides or a nucleic acid encoding at least one of the immunogenic polypeptides.

Korber, Bette T. M.↗

Conservation of Helium while Maintaining High System Purity

Recent helium shortages and helium price increases have lead to an increased emphasis being placed on conserving helium. The need to conserve helium must be balanced with need to maintain the high levels of purity necessary to prevent operational problems caused by contamination. Helium losses and contamination control are especially important for test stands that have cryogenic distribution systems operating continuously with frequent changeover of cryogenic temperature components that are being tested. This paper describes a mathematical model to estimate the quantity of helium lost and the purity of the helium after the pump and backfill procedure is complete. The process to determine the optimal time during pump down to cut off pumping and start backfilling is described. There is a tradeoff between trying to achieve the lowest possible pressure during pumping and the quantity of air leaking into the volume while pumping is occurring. An additional benefit of careful selection of pump and backfill parameters in conjunction with real-time pressure monitoring can reduce the labor and time required to complete a successful pump and backfill procedure. This paper is intended to be a tool for engineers to review their pump and backfill procedures and measured data to optimize helium losses, system purity, and labor required.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Harvest and nitrogen effects on bioenergy feedstock quality of grass-legume mixtures on Conservation Reserve Program grasslands

Perennial grass mixtures established on Conservation Reserve Program (CRP) lands can be an important source of feedstock for bioenergy production. This study aimed to evaluate management practices for optimizing the quality of bioenergy feedstock and stand persistence of grass-legume mixtures under diverse environments. A 5-year field study (2008–2012) was conducted to assess the effects of two harvest timings (at anthesis vs after complete senescence) and three nitrogen (N) rates (0, 56, 112 kg N ha -1 ) on biomass chemical compositions (i.e., cell wall components, ash, volatiles, total carbon, and N contents) and the feedstock energy potential, examined by the theoretical ethanol yield (TEY) and the total TEY (i.e., the product of biomass yield and TEY, L ha -1 ), of cool-season mixtures in Georgia and Missouri and a warm-season mixture in Kansas. The canonical correlation analysis (CCA) was used to investigate the effect of vegetative species transitions on feedstock quality. Although environmental variations (mainly precipitation) greatly influenced the management effect on chemical compositions, the delayed harvest after senescence generally improved feedstock quality. In particular, the overall cell wall concentrations and TEY of the warm-season mixtures increased by approximately 7%. Additional N supplies improved the total TEY of both mixtures by ~1.6–4.2 L ha -1 per 1.0 kg N ha -1 input but likely lowered the feedstock quality, particularly for the cool-season mixture. The cell wall concentrations of cool-season mixture reduced by approximately 3%–6%. The CCA results indicated that the increased legume compositions (under low N input) likely enhanced lignin but reduced ash concentrations. This field research demonstrated that with proper management, grass-legume mixtures on CRP lands can provide high-quality feedstock for bioenergy productions.

09 BIOMASS FUELS↗

An implicit, conservative and asymptotic-preserving electrostatic particle-in-cell algorithm for arbitrarily magnetized plasmas in uniform magnetic fields

Here, we introduce a new electrostatic particle-in-cell algorithm capable of using large timesteps compared to particle gyro-period under a uniform external magnetic field. The algorithm extends earlier electrostatic fully implicit PIC implementations with a new asymptotic-preserving particle-push scheme that allows timesteps much larger than particle gyroperiods. In the large-timestep limit, the integrator preserves all particle drifts, while recovering the full orbit for small timesteps. The scheme allows for a seamless, efficient treatment of particles with coexisting magnetized and unmagnetized species, and conserves energy and charge exactly without spoiling implicit solver performance. We demonstrate by numerical experiment with several problems of variable species magnetization (diocotron instability, modified two-stream instability, and drift instability) that orders of magnitude wall-clock-time speedups vs. the standard fully implicit electrostatic PIC algorithm are possible without sacrificing solution accuracy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Conservation of model degraded pine wood with selected organosilicons studied by XFM and nanoindentation

Previous research found that some organosilicon treatments proved effective in stabilizing waterlogged wood dimensions during drying. The present research aimed to determine the mechanism of wood stabilization by these chemicals to understand their mode of action. Here, the study used chemically (ChP) and biologically degraded (BP) model Scots pine wood treated with Methyltrimethoxysilane (MTMS), (3-Mercaptopropyl) trimethoxysilane (MPTMS), or 1,3-Bis(diethylamino)-3-propoxypropanol)-1,1,3,3-tetramethyldisiloxane (DEAPTMDS). Synchrotron-based X-ray fluorescence microscopy (XFM) was used to investigate the penetration of organosilicons into the wood cellular structure and cell walls, and nanoindentation was used to study the mechanical properties of the treated wood cell walls. All treatments resulted in high volumetric anti-shrink efficiency (ASE V ) values of 74-82%, except for MTMS-treated ChP with an ASE V of 52%. The multiscale XFM results revealed that all applied organosilicons penetrated throughout the whole wooden blocks and deposited in both cell lumina and cell walls. The retention of all applied organosilicons was highest in BP wood, and so was the dimensional stabilization effect. MTMS-treated ChP had the lowest measured cell wall infiltration, which likely contributed to its lower ASE v . DEAPTMDS treatments plasticized the cell walls and resulted in lowered nanoindentation elastic modulus (E s NI ) and hardness (H) for all types of wood. MTMS and MPTMS had modest effects on cell wall mechanical properties, and the effect depended on the type of wood. The final effect of organosilicon treatment on the dimensional wood stabilization and mechanical properties of wood cell walls depended not only on the type of the applied organosilicon but also the type of wood degradation. This means that the treatment cannot be considered universal, and specific approaches are needed for the conservation of individual wooden objects. Although some mechanisms are now better understood, such as the need for organosilicons to infiltrate the cell walls and the plasticizing effect of DEAPTMDS, other aspects will benefit from a more detailed analysis of the molecular interactions between organosilicons and wood polymers.

59 BASIC BIOLOGICAL SCIENCES↗

A fully implicit, scalable, conservative nonlinear relativistic Fokker–Planck 0D-2P solver for runaway electrons

Upon application of a sufficiently strong electric field, electrons break away from thermal equilibrium and approach relativistic speeds. These highly energetic ‘runaway’ electrons (~ MeV) play a significant role in tokamak disruption physics, and therefore their accurate understanding is essential to develop reliable mitigation strategies. As such, we have developed a fully implicit solver for the 0D-2P (i.e., including two momenta coordinates) relativistic nonlinear Fokker–Planck equation (rFP). As in earlier implicit rFP studies (NORSE, CQL3D), electron–ion interactions are modeled using the Lorentz operator, and synchrotron damping using the Abraham–Lorentz–Dirac reaction term. However, our implementation improves on these earlier studies by (1) ensuring exact conservation properties for electron collisions, (2) strictly preserving positivity, and (3) being scalable algorithmically and in parallel. Key to our proposed approach is an efficient multigrid preconditioner for the linearized rFP equation, a multigrid elliptic solver for the Braams–Karney potentials, and a novel adaptive technique to determine the associated boundary values. We verify the accuracy and efficiency of the proposed scheme with numerical results ranging from small electric-field electrical conductivity measurements to the accurate reproduction of runaway tail dynamics when strong electric fields are applied.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

An efficient, conservative, time-implicit solver for the fully kinetic arbitrary-species 1D-2V Vlasov-Ampère system

In this paper, we consider the solution of the fully kinetic (including electrons) Vlasov-Ampère system in a one-dimensional physical space and two-dimensional velocity space (1D-2V) for an arbitrary number of species with a time-implicit Eulerian algorithm. The problem of velocity-space meshing for disparate thermal and bulk velocities is dealt with by an adaptive coordinate transformation of the Vlasov equation for each species, which is then discretized, including the resulting inertial terms. Mass, momentum, and energy are conserved, and Gauss's law is enforced to within the nonlinear convergence tolerance of the iterative solver through a set of nonlinear constraint functions while permitting significant flexibility in choosing discretizations in time, configuration, and velocity space. We mitigate the temporal stiffness introduced by, e.g., the plasma frequency through the use of high-order/low-order (HOLO) acceleration of the iterative implicit solver. We present several numerical results for canonical problems of varying degrees of complexity, including the multiscale ion-acoustic shock wave problem, which demonstrate the efficacy, accuracy, and efficiency of the scheme.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Conservative DG method for the micro-macro decomposition of the Vlasov–Poisson–Lenard–Bernstein model

The micro-macro (mM) decomposition approach is considered for the numerical solution of the Vlasov– Poisson–Lenard–Bernstein (VPLB) system, which is relevant for plasma physics applications. In the mM approach, the kinetic distribution function is decomposed as $f$ = $\mathscr{E}$[$ρ_f$] + g , where $\mathscr{E}$ is a local equilibrium distribution, depending on the macroscopic moments $ρ_f$ = $∫_{\mathbb{R}}$ $efdv$ = $\langle$$ef$$\rangle$$_{\mathbb{R}}$, where e = (1, $v$, $\frac{1}{2}$ $v^2$) T , and $g$, the microscopic distribution, is defined such that $\langle$$eg$$\rangle$$_{\mathbb{R}}$ = 0. We aim to design numerical methods for the mM decomposition of the VPLB system, which consists of coupled equations for $ρ_f$ and $g$. To this end, we use the discontinuous Galerkin (DG) method for phase-space discretization, and implicit-explicit (IMEX) time integration, where the phase-space advection terms are integrated explicitly and the collision operator is integrated implicitly. We give special consideration to ensure that the resulting mM method maintains the $\langle$$eg$$\rangle$$_{\mathbb{R}}$ = 0 constraint, which may be necessary for obtaining (i) satisfactory results in the collision dominated regime with coarse velocity resolution, and (ii) unambiguous conservation properties. The constraint-preserving property is achieved through a consistent discretization of the equations governing the micro and macro components. Here, we present numerical results that demonstrate the performance of the mM method. The mM method is also compared against a corresponding DG-IMEX method solving directly for $f$.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Continuously bounds-preserving discontinuous Galerkin methods for hyperbolic conservation laws

For finite element approximations of transport phenomena, it is often necessary to apply a form of limiting to ensure that the discrete solution remains well-behaved and satisfies physical constraints. However, these limiting procedures are typically performed at discrete nodal locations, which is not sufficient to ensure the robustness of the scheme when the solution must be evaluated at arbitrary locations (e.g., for adaptive mesh refinement, remapping in arbitrary Lagrangian–Eulerian solvers, overset meshes, etc.). In this work, a novel limiting approach for discontinuous Galerkin methods is presented which ensures that the solution is continuously bounds-preserving (i.e., across the entire solution polynomial) for any arbitrary choice of basis, approximation order, and mesh element type. Through a modified formulation for the constraint functionals, the proposed approach requires only the solution of a single spatial scalar minimization problem per element for which a highly efficient numerical optimization procedure is presented. Here, the efficacy of this approach is shown in numerical experiments by enforcing continuous constraints in high-order unstructured discontinuous Galerkin discretizations of hyperbolic conservation laws, ranging from scalar transport with maximum principle preserving constraints to compressible gas dynamics with positivity-preserving constraints.

97 MATHEMATICS AND COMPUTING↗

SWAT model application for evaluating agricultural conservation practice effectiveness in reducing phosphorous loss from the Western Lake Erie Basin

Lake Erie is threatened by eutrophication and harmful algal blooms due to excess nutrient loading from agricultural sources. Agricultural conservation practices (ACPs) have been developed and implemented to reduce nutrient losses but estimating ACP effectiveness is challenging. The Soil and Water Assessment Tool (SWAT) has been used to investigate ACP effectiveness for water quality improvement. Many SWAT applications have been developed by different investigators to evaluate ACP effectiveness for reducing nutrient, particularly phosphorus (P), loading in the agriculturally-dominated Western Lake Erie Basin (WLEB). Our objective is to establish what has been achieved by past modeling research and make suggestions for future applications and improvements. We synthesized the findings of 28 SWAT modeling studies within the WLEB. Models generally performed satisfactorily against accepted criteria for streamflow and sediment, but performance for P loads, like soluble reactive P, was mostly “unsatisfactory”. The “unsatisfactory” performance maybe due to imperfections and idealizations in model formulations and/or parameterization. Thus, simulations of P transport and transformation processes need improvement. In addition, model parameter selection is the key part of model set-up. Most SWAT modeling studies used default values during initial set-up, then performed calibration and validation. It was found that the calibrated P related parameter values varied widely across different studies, even within the same watershed with some values unrealistic for the study areas. The phenomena of different combinations of model parameters producing similar outputs indicates equifinality. Equifinality in the baseline model may impact results when ACPs are incorporated. Furthermore, the unrealistic values used in ACP assessment undermine the credibility of ACP effectiveness. Future model applications should try to re-examine the calibrated P parameters and make sure they are realistic for the study area as well as reduce equifinality by constraining the model with characterization of watershed conditions, better understanding of hydrologic processes, and parameter values based on real-world observations. As a result, future model applications should focus on improving P transport and transformation processes, using measured watershed characteristics for parameterization, and improving reflections of climate change, which could result in more accurate assessments of ACP effectiveness to meet targeted goals.

54 ENVIRONMENTAL SCIENCES↗

Structural conserved moiety splitting of a stoichiometric matrix

Characterising biochemical reaction network structure in mathematical terms enables the inference of functional biochemical consequences from network structure with existing mathematical techniques and spurs the development of new mathematics that exploits the peculiarities of biochemical network structure. The structure of a biochemical network may be specified by reaction stoichiometry, that is, the relative quantities of each molecule produced and consumed in each reaction of the network. A biochemical network may also be specified at a higher level of resolution in terms of the internal structure of each molecule and how molecular structures are transformed by each reaction in a network. The stoichiometry for a set of reactions can be compiled into a stoichiometric matrix N ϵ Z mxn where each row corresponds to a molecule and each column corresponds to a reaction. We demonstrate that a stoichiometric matrix may be split into the sum of m - rank(N) moiety transition matrices, each of which corresponds to a subnetwork accessible to a structurally identifiable conserved moiety. The existence of this moiety matrix splitting is a property that distinguishes a stoichiometric matrix from an arbitrary rectangular matrix.

59 BASIC BIOLOGICAL SCIENCES↗

Reconciling and Improving Formulations for Thermodynamics and Conservation Principles in Earth System Models (ESMs)

Abstract This paper provides a comprehensive derivation of the total energy equations for the atmospheric components of Earth System Models (ESMs). The assumptions and approximations made in this derivation are motivated and discussed. In particular, it is emphasized that closing the energy budget is conceptually challenging and hard to achieve in practice without resorting to ad hoc fixers. As a concrete example, the energy budget terms are diagnosed in a realistic climate simulation using a global atmosphere model. The largest total energy errors in this example are spurious dynamical core energy dissipation, thermodynamic inconsistencies (e.g., coupling parameterizations with the host model) and missing processes/terms associated with falling precipitation and evaporation (e.g., enthalpy flux between components). The latter two errors are not, in general, reduced by increasing horizontal resolution. They are due to incomplete thermodynamic and dynamic formulations. Future research directions are proposed to reconcile and improve thermodynamics formulations and conservation principles.

54 ENVIRONMENTAL SCIENCES↗

Studies of the weak interaction in atomic systems: towards measurements of atomic parity non-conservation in francium

Abstract Tests of the standard model of particle physics should be carried out over the widest possible range of energies. Here we present our plans and progress for an atomic parity non-conservation experiment using the heaviest alkali, francium ( Z = 87), which has no stable isotope. Low-energy tests of this kind have sensitivity complementary to higher energy searches, e.g. at the large hadron collider.

74 ATOMIC AND MOLECULAR PHYSICS↗

Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen–fixing clade

Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen-fixing bacteria in the root nodule. This root–nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical, but undetermined, evolutionary event at the base of this clade. To identify putative regulatory sequences implicated in the evolution of RNS, we evaluated the genomes of 25 species capable of nodulation and identified 3091 conserved noncoding sequences (CNS) in the nitrogen-fixing clade (NFC). We show that the chromatin accessibility of 452 CNS correlates significantly with the regulation of genes responding to lipochitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of an Mtcre1 mutant showed a significant decrease of nodulation in the absence of the five CNS, when they are driving the expression of a functional copy of MtCRE1. CNS identified in the NFC may harbor elements required for the regulation of genes controlling RNS in M. truncatula.

59 BASIC BIOLOGICAL SCIENCES↗

Conservative High-Order Time Integration for Lagrangian Hydrodynamics

In tis study, we develop novel time integration methods for the compressible Euler equations in the Lagrangian frame that are of arbitrary high order and exactly preserve the mass, momentum, and total energy of the system. The equations are considered in nonconservative form, that is, common for staggered grid hydrodynamics (SGH) methods; namely, the evolved quantities are mass, momentum, and internal energy. A general family of time integration schemes is formulated, and practical pairs for orders three and four are derived. Numerical results on standard hydrodynamics benchmarks confirm the high-order convergence on smooth problems and the exact numerical preservation of all physically conserved quantities.

97 MATHEMATICS AND COMPUTING↗

Analysis of Conservation Voltage Reduction under Inverter-Based VAR-Support [Slides]

Conservation voltage reduction (CVR) is a common technique used by utilities to strategically reduce demand during peak periods. As penetration levels of distributed generation (DG) continue to rise and advanced inverter capabilities become more common, it is unclear how the effectiveness of CVR will be impacted and how CVR interacts with advanced inverter functions. In this work, we investigated the mutual impacts of CVR and DG from photovoltaic (PV) systems (with and without autonomous Volt-VAR enabled). The analysis was conducted on an actual utility dataset, including a feeder model, measurement data from smart meters and intelligent reclosers, and metadata for more than 30 CVR events triggered by the utility over the year. The installed capacity of the modeled PV systems represented 66% of peak load, but reached instantaneous penetrations reached up to 2.5x the load consumption over the year. While the objectives of CVR and autonomous Volt-VAR are opposed to one another, this study found that their interactions were mostly inconsequential since the CVR events occurred when total PV output was low.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Redox Biochemistry of Energy Conservation in Methanogens and their Syntrophic Partners

The primary objective of this project was to uncover previously unknown modes by which living organisms harvested energy. Specifically, it queried microbial systems, which were once thought to not be able to utilize oxygen. Through the use of cutting-edge approaches, we were able to identify novel mechanistic processes that allow organisms to thrive under varying environmental conditions. This constitutes a paradigm shift in the field. Our work has opened new vistas for expanding the horizons of energy conservation in biological systems, as well as shed light on green energy innovations.

59 BASIC BIOLOGICAL SCIENCES↗

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada, For Calendar Year 2019, Revision 0

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act Permit Number NEV HW0101 associated with the following closed corrective action units (CAUs): • CAU 90, Area 2 Bitcutter Containment • CAU 91, Area 3 U-3fi Injection Well • CAU 92, Area 6 Decon Pond Facility • CAU 110, Area 3 WMD U-3ax/bl Crater • CAU 111, Area 5 WMD Retired Mixed Waste Pits • CAU 112, Area 23 Hazardous Waste Trenches

54 ENVIRONMENTAL SCIENCES↗