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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Classical Swine Fever Virus Structural Glycoprotein E2 Interacts with Host Protein ACADM during the Virus Infectious Cycle

The E2 glycoprotein is one of the four structural proteins of the classical swine fever virus (CSFV) particle. E2 has been shown to be involved in many virus functions, including adsorption to host cells, virus virulence and interaction with several host proteins. Using a yeast two-hybrid screen, we have previously shown that the CSFV E2 specifically interacts with swine host protein medium-chain-specific acyl-Coenzyme A dehydrogenase (ACADM), an enzyme that catalyzes the initial step of the mitochondrial fatty acid beta-oxidation pathway. Here, we show that interaction between ACADM and E2 also happens in swine cells infected with CSFV using two different procedures: coimmunoprecipitation and a proximity ligation assay (PLA). In addition, the amino acid residues in E2 critically mediating the interaction with ACADM, M49 and P130 were identified via a reverse yeast two-hybrid screen using an expression library composed of randomly mutated versions of E2. A recombinant CSFV, E2ΔACADMv, harboring substitutions at residues M49I and P130Q in E2, was developed via reverse genomics from the highly virulent Brescia isolate. E2ΔACADMv was shown to have the same kinetics growth in swine primary macrophages and SK6 cell cultures as the parental Brescia strain. Similarly, E2ΔACADMv demonstrated a similar level of virulence when inoculated to domestic pigs as the parental Brescia. Animals intranasally inoculated with 10 5 TCID 50 developed a lethal form of clinical disease with virological and hematological kinetics changes undistinguishable from those produced by the parental strain. Therefore, interaction between CSFV E2 and host ACADM is not critically involved in the processes of virus replication and disease production.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The Interaction between the DOCK7 Protein and the E2 Protein of Classical Swine Fever Virus Is Not Involved with Viral Replication or Pathogenicity

The classical swine fever virus (CSFV) particle consists of three glycoproteins, all of which have been shown to be important proteins involved in many virus functions, including interaction with several host proteins. One of these proteins, E2, has been shown to be directly involved with adsorption to the host cell and important for virus virulence. Using the yeast two-hybrid system, we have previously shown that CSFV E2 specifically interacts with the (DOCK7) dedicator of cytokinesis, a scaffolding protein. In this report, the interaction between E2 and DOCK7 was evaluated. To confirm the yeast two-hybrid results and to determine that DOCK7 interacts in swine cells with E2, we performed co-immunoprecipitation and proximity ligation assay (PLA). After demonstrating the protein interaction in swine cells, E2 amino acid residues Y65, V283, and T149 were determined to be critical for interaction with Dock7 by using a random mutated library of E2 and a reverse yeast two-hybrid approach. That disruption of these three residues with mutations Y65F, V283D, and T149A abrogated the Dock7-E2 protein interaction. These mutations were then introduced into a recombinant CSFV, E2DOCK7v, by a reverse genomics approach using the highly virulent CSFV Brescia isolate as a backbone. E2DOCKv was shown to have similar growth kinetics in swine primary macrophages and SK6 cell cultures to the parental Brescia strain. Similarly, E2DOCK7v demonstrated a similar level of virulence to the parental Brescia when inoculated in domestic pigs. Animals intranasally inoculated with 10 5 TCID 50 developed a lethal form of clinical disease with virological and hematological kinetics changes indistinguishable from that produced by the parental strain. Therefore, interaction between CSFV E2 and host DOCK7 is not critically involved in the process of virus replication and disease production.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2003

Quantum and semi-classical transport in NEMO 1-D

The coupling of the fundamentally quantum mechanical nanoelectronic transport simulation through resonant tunneling diodes to semi-classical drift diffusion in the contacts is demonstrated.

quantum transport semi-classical transport tunneli↗
DOE OSTI2017

A Mesocrystal‐Like Morphology Formed by Classical Polymer‐Mediated Crystal Growth

Abstract Growth by oriented assembly of nanoparticles is a widely reported phenomenon for many crystal systems. While often deduced through morphological analyses, direct evidence for this assembly behavior is limited and, in the calcium carbonate (CaCO 3 ) system, has recently been disputed. However, in the absence of a particle‐based pathway, the mechanism responsible for the creation of the striking morphologies that appear to consist of subparticles is unclear. Therefore, in situ atomic force microscopy is used to investigate the growth of calcite crystals in solutions containing a polymer additive known for its ability to generate crystal morphologies associated with mesocrystal formation. It is shown that classical growth processes that begin with impurity pinning of atomic steps, leading to stabilization of new step directions, creation of pseudo‐facets, and extreme surface roughening, can produce a microscale morphology previously attributed to nonclassical processes of crystal growth by particle assembly.

Smeets, Paul J. M.↗
DOE OSTI2021

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Classical and quantum stability in putative landscapes

Landscape analyses often assume the existence of large numbers of fields, N, with all of the many couplings among these fields (subject to constraints such as local supersymmetry) selected independently and randomly from simple (say Gaussian) distributions. We point out that unitarity and perturbativity place significant constraints on behavior of couplings with N, eliminating otherwise puzzling results. In would-be flux compactifications of string theory, we point out that in order that there be large numbers of light fields, the compactification radii must scale as a positive power of N; scaling of couplings with N may also be necessary for perturbativity. We show that in some simple string theory settings with large numbers of fields, for fixed R and string coupling, one can bound certain sums of squares of couplings by order one numbers. This may argue for strong correlations, possibly calling into question the assumption of uncorrelated distributions. Finally, we consider implications of these considerations for classical and quantum stability of states without supersymmetry, with low energy supersymmetry arising from tuning of parameters, and with dynamical breaking of supersymmetry.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Emergent classical spacetime from microstates of an incipient black hole

Black holes have an enormous underlying space of microstates, but universal macroscopic physics characterized by mass, charge and angular momentum as well as a causally disconnected interior. This leads two related puzzles: (1) How does the effective factorization of interior and exterior degrees of freedom emerge in gravity?, and (2) How does the underlying degeneracy of states wind up having a geometric realization in the horizon area and in properties of the singularity? We explore these puzzles in the context of an incipient black hole in the AdS/CFT correspondence, the microstates of which are dual to half-BPS states of the $\mathcal{N}$ = 4 super-Yang-Mills theory. First, we construct a code subspace for this black hole and show how to organize it as a tensor product of a universal macroscopic piece (describing the exterior), and a factor corresponding to the microscopic degrees of freedom (describing the interior). We then study the classical phase space and symplectic form for low-energy excitations around the black hole. On the AdS side, we find that the symplectic form has a new physical degree of freedom at the stretched horizon of the black hole, reminiscent of soft hair, which is absent in the microstates. We explicitly show how such a soft mode emerges from the microscopic phase space in the dual CFT via a canonical transformation and how it encodes partial information about the microscopic degrees of freedom of the black hole.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Classical gluon production amplitude for nucleus-nucleus collisions: First saturation correction in the projectile

Here, we calculate the classical single-gluon production amplitude in nucleus-nucleus collisions including the first saturation correction in one of the nuclei (the projectile) while keeping multiple-rescattering (saturation) corrections to all orders in the other nucleus (the target). In our approximation only two nucleons interact in the projectile nucleus: the single-gluon production amplitude we calculate is order-g 3 and is leading-order in the atomic number of the projectile, while resumming all order-one saturation corrections in the target nucleus. Our result is the first step towards obtaining an analytic expression for the first projectile saturation correction to the gluon production cross section in nucleus-nucleus collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

The metamorphosis of semi-classical mechanisms of confinement: from monopoles on ℝ 3 × S 1 to center-vortices on ℝ 2 × T 2

There are two distinct regimes of Yang-Mills theory where we can demonstrate confinement, the existence of a mass gap, and the multi-branch structure of the effective potential as a function of the theta angle using a reliable semi-classical calculation. The two regimes are deformed Yang-Mills theory on ℝ 3 × S 1 , and Yang-Mills theory on ℝ 2 × T 2 where the torus is threaded by a ’t Hooft flux. The weak coupling regime is ensured by the small size of the circle or torus. In the first case the confinement mechanism is related to self-dual monopoles, whereas in the second case self-dual center-vortices play a crucial role. These two topological objects are distinct. In particular, they have different mutual statistics with Wilson loops. On the other hand, they carry the same topological charge and action. We consider the theory on ℝ × T 2 × S 1 and extrapolate both the monopole and vortex regimes to a quantum mechanical domain, where a cross-over takes place. Both sides of the cross-over are described by a deformed ℤ N TQFT. On ℝ 2 × S 1 × S 1 , we derive an effective field theory (EFT) of vortices from the EFT of monopoles in the presence of a ’t Hooft flux. This construction is based on a two-stage Higgs mechanism, reducing SU(N) to U(1) N−1 in 3d first, followed by reduction to a ℤ N EFT in 2d in the second step. This result shows how monopoles transmute into center-vortices, and suggests adiabatic continuity between the two confinement mechanisms. The basic mechanism is flux fractionalization: the magnetic flux of the monopoles splits up and is collimated in such a way that 2d Wilson loops detect it as a center vortex.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Classical Solvability of the Radial Viscous Fingering Problem in a Hele–Shaw Cell with Surface Tension

We consider the one-phase problem on radial viscous fingering structures in a Hele–Shaw cell with surface tension. This problem is a nonlinear free-boundary problem for elliptic equations. Unlike the Stefan problem for the heat equation, we deal with a problem of hydrodynamic type. We establish the classical solvability of the one-phase Hele–Shaw problem with radial geometry by using the same method as that used for the Stefan problem and justifying the vanishing coefficient of the time-derivative in the parabolic equation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Tasting nuclear pasta made with classical molecular dynamics simulations

Nuclear clusters or voids in the inner crust of neutron stars were predicted to have various shapes collectively nicknamed nuclear pasta. Furthermore, the recent review by López, Dorso and Frank summarized their systematic investigations into properties especially the morphological and thermodynamical phase transitions of the nuclear pasta within a Classical Molecular Dynamics model, providing further stimuli to find more observational evidences of the predicted nuclear pasta in neutron stars.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Tighter reformulations using classical Dawson and Sankoff bounds for approximating two-stage chance-constrained programs

We extend and improve recent results given by Singh and Watson on using classical bounds on the union of sets in a chance-constrained optimization problem. Specifically, we revisit the so-called Dawson and Sankoff bound that provided one of the best approximations of a chance constraint in the previous analysis. Next, we show that our work is a generalization of the previous work, and in fact the inequality employed previously is a very relaxed approximation with assumptions that do not generally hold. Computational results demonstrate on average over a 43% improvement in the bounds. As a byproduct, we provide an exact reformulation of the floor function in optimization models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Can classical DEM simultaneously capture compressibility and flowability of milled biomass?

Accurate prediction of the rheological behavior of biomass is essential for the design and operation of hoppers, feeders, and storage systems in biorefineries. This study examines whether the classical, coarse-grained discrete element method (DEM) formulation can simultaneously reproduce the compressibility and flowability of milled herbaceous biomass, using Miscanthus × giganteus as a representative material. The model represents particles as rigid spheres interacting through Hertz-Mindlin elastic-frictional contacts augmented with an area-dependent cohesion term. Laboratory cyclic compression and wedge-shaped hopper discharge experiments were used as calibration benchmarks. Although the model can independently reproduce each behavior by appropriately tuning particle Young's modulus E and cohesion energy density k, an extensive parametric investigation comprising more than 600 simulations reveals that the optimal parameter regions for compression and hopper flow are distinct and non-overlapping in (E, k) space. Surrogate surface analysis further shows that the corresponding objective-function valleys exhibit similar trends but are approximately parallel and spatially offset, precluding a unified calibration within the explored domain. Sensitivity analysis indicates that compressibility is governed predominantly by stiffness and cohesion, whereas the slope of the mass flow rate-opening relation in hopper discharge is primarily controlled by tangential friction. Extensions incorporating particle size distribution and clumped-sphere representations do not eliminate the incompatibility. These results systematically reveal, for the first time, the structural limitation of simplified DEM formulations in representing biomass rheological behavior, underscoring the necessity for models incorporating additional physical mechanisms, such as particle deformability or enhanced interlocking, to achieve unified predictive capability for biomass handling behavior.

09 BIOMASS FUELS↗
DOE OSTI2017

Beyond the classical kinetic model for chronic graphite oxidation by moisture in high temperature gas-cooled reactors

Four grades of nuclear graphite with various microstructures were subjected to accelerated oxidation tests in helium with traces of moisture and hydrogen in order to evaluate the effects of chronic oxidation on graphite components in high temperature gas cooled reactors. Kinetic analysis showed that the Langmuir-Hinshelwood (LH) model cannot consistently reproduce all results. In particular, at high temperatures and water partial pressures oxidation was always faster than the LH model predicts, with stronger deviations for superfine grain graphite than for medium grain grades. It was also found empirically that the apparent reaction order for water has a sigmoid-type variation with temperature which follows the integral Boltzmann distribution function. This suggests that the apparent activation with temperature of graphite reactive sites that causes deviations from the LH model is rooted in specific structural and electronic properties of surface sites on graphite. A semi-global kinetic model was proposed, whereby the classical LH model was modified with a temperature-dependent reaction order for water. The new Boltzmann-enhanced model (BLH) was shown to consistently predict experimental oxidation rates over large ranges of temperature (800-1100 oC) and partial pressures of water (3-1200 Pa) and hydrogen (0-300 Pa), not only for the four grades of graphite but also for the historic grade H-451. The BLH model offers as more reliable input for modeling the chemical environment effects during the life-time operation of new grades of graphite in advanced nuclear reactors operating at high and very high temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Accurate classical short-range forces for the study of collision cascades in Fe–Ni–Cr

The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded-atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed. The pairwise terms and the embedding terms of the potential are modi ed in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni 50 Fe 50 , Ni 80 Cr 20 and Ni 33 Fe 33 Cr 33 . The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.

36 MATERIALS SCIENCE↗