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At least 235 records · Page 13

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗

Operando Microscopy Characterization of Perovskite Solar Cells

In this work, we developed operando Kelvin probe force microscopy (KPFM) to study the electrostatic potential distribution across perovskite cells under light and forward bias to gain a deeper understanding of device operation physics. As a case study, we selected perovskite cells with a SnO 2 -based electron-selective layer (ESL), which showed great potential for fabricating high-efficiency, hysteresis-free devices due to the deeper conduction band and higher electron mobility of SnO 2 . The as-made device showed a main junction at the perovskite/spiro interface. After light soaking and applying forward bias, the junction quality improved, possibly explained by filling trap states at the interfaces and by the perovskite absorber perhaps having a self-poling effect; the main junction is observed at the ESL/perovskite interface. The results are consistent with current-voltage measurements, device performance improves mainly with fill factor enhancement. The operando KPFM results should more closely reflect the real case during current density-voltage measurements or solar cell operation. The operando KPFM technique that we have developed can be a powerful tool to provide a deeper understanding of the device operation mechanism and to further optimize the device.

14 SOLAR ENERGY↗

Advanced modeling of field enhanced thermionic emission

Shaped emitters are of interest to a broad range of applications in vacuum electronic devices. In particular, thermionic energy converters (TECs) take advantage of shaped emitters to increase the local surface field, thereby extracting more current for a given cathode temperature and applied voltage. However, modeling these devices is challenging; Warp [J.-L. Vay, D. P. Grote, R. H. Cohen, and A. Friedman, Comput. Sci. Discov. 5, 014019 (2012)] is a fully 3D particle-in-cell code capable of handling a wide range of physics problems and is well suited to modeling TECs. Additionally, recent improvements to Warp have enabled the accurate modeling of emitters with arbitrary curved surfaces. Specifically, the inclusion of subgrid resolution for computing the electrostatic potential and the ability to apply mesh refinement for specific areas of interest allow for a more accurate solution to the fields on these surfaces. These improvements coupled with Warp’s ability to handle variable particle weights make it an ideal candidate for simulating these complex devices. In this paper, the authors study the applicability of different subgrid configurations for simulating shaped emission surfaces and field convergence for different mesh-refinement techniques. They then implement a custom weighting algorithm that allows for uniform sampling of emission surfaces with a large variation in the surface electric field. They then use this algorithm to study emission for curved emitters in both the field-enhancement regime and the space-charge regime.

Edelen, Jonathan P. (ORCID:0000000215180652)↗

Strain-dependent luminescence and piezoelectricity in monolayer transition metal dichalcogenides

The modification of optical and electronic properties of transition metal dichalcogenides via mechanical deformation has been widely studied. Their ability to withstand large deformations before rupture has enabled large tunability of the bandgap, and further, the spatially varying strain has been shown to control the spatial distribution of the bandgap and lead to effects such as carrier funneling. Monolayer transition metal dichalcogenides exhibit a significant piezoelectric effect that could couple to a spatially inhomogeneous strain distribution to influence electronic and optical behavior. We investigate both experimentally and theoretically an example case of photoluminescence in structures with a strain distribution similar to that employed in single-photon emitters but generated here via nanoindentation. Using a mechanical model for strain induced by nanoindentation, we show that piezoelectricity can result in charge densities reaching 10 12 e/cm 2 and can generate electrostatic potential variations on the order of ±0.1 V across the suspended monolayer. We analyze the implications of these results for luminescence and exciton transport in monolayer transition metal dichalcogenides with spatially varying strain.

42 ENGINEERING↗

Determining valence band offsets in heterojunctions using a single core-level x-ray photoelectron spectrum

The behavior and functionality of semiconductor heterojunctions depend critically on the alignments of the valence and conduction bands at the various interfaces. Traditionally band alignment has been measured by x-ray photoelectron spectroscopy using pairs of distinct core levels, one from each side of the interface, to track the valence band maxima in the two materials. Here, we demonstrate that it is possible to determine band alignment using a single core-level photoelectron spectrum for an element that is common to both materials. The energy splitting between the photoemission features originating in the two materials is shown to be dominated by the difference in electrostatic potential across the interface, leading to a reliable determination of the band alignment.

Wang, Le↗

Gyrokinetic simulations of momentum flux parasitic to free-energy transfer

Ion Landau damping interacts with a portion of the E×B drift to cause a non-diffusive outward flux of co-current toroidal angular momentum. Quantitative evaluation of this momentum flux requires nonlinear simulations to determine fL, the fraction of fluctuation free energy that passes through ion Landau damping, in fully developed turbulence. Nonlinear gyrokinetic simulations with the GKW code confirm the presence of the systematic symmetry-breaking momentum flux. For simulations with adiabatic electrons, fL scales inversely with the ion temperature gradient, because only the ion curvature drift can transfer free energy to the electrostatic potential. Although kinetic electrons should in principle relax this restriction, the ion Landau damping measured in collisionless kinetic-electron simulations remained at low levels comparable with ion-curvature-drift transfer, except when magnetic shear was strong. A set of simulations scanning the electron pitch-angle scattering rate showed only a weak variation of fL with the electron collisionality. However, collisional-electron simulations with electron temperature greater than ion temperature unambiguously showed electron-curvature-drift transfer supporting ion Landau damping, leading to a corresponding enhancement of the symmetry-breaking momentum flux.

intrinsic rotation↗

Kinetic Plasma Simulation in the MOOSE Framework: Verification of Electrostatic Particle In Cell Capabilities

In magnetic confinement nuclear fusion reactors, the interaction between the plasma edge and plasma facing components is extremely important. At the plasma edge, a kinetic representation such as particle-in-cell (rather than a fluid representation) is required to accurately capture the plasma behavior. General purpose particle-in-cell plasma simulation capabilities have been developed in the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. This new capability is a part of the development of a new MOOSE-based framework for modeling plasma facing components, the Fusion ENergy Integrated multiphys-X (FENIX) framework. In this work, the verification of foundational particle-in-cell capabilities in FENIX is presented. This new plasma simulation capability has three main components: moving particles in discrete steps on the finite element mesh, mapping charge density from the particle's location to the finite element mesh, and solving for the electrostatic potential based on the charge density mapped from particles to the mesh. In this paper, simple verification problems demonstrating each of these new capabilities are presented, and future work includes electromagnetic capabilities and Monte Carlo collisions with neutral gas particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Close-Out Project Description for Koepke's Dept of Energy grant DE-SC0021405

Objectives: To establish, for lab & space conditions, EM-IEDDI’s (electromagnetic shear-driven instability's) dispersion relation, unstable range, instability threshold, and mode characteristics, we need LAPD’s Alfven-wave-favorable electromagnetic-style conditions, including higher "beta" (0.001 < beta ≤ 0.3) and low-collisionality. Also, we attempted to intentionally launch or spontaneously destabilize compressional and shear Alfven waves in the strong, localized, perpendicular-velocity-shear region at the interface between coaxial plasmas (one plasma cylinder inside an outer, otherwise hollow, tube, each having a different, controllable, value of plasma electrostatic potential, i.e., “space” potential (not to be confused with the temperature-dependent “floating” potential of an object immersed in the plasma). Nonlinear wave-wave interactions between same-family (EM-IEDD or Alfven) and cross-family (EM-IEDD-with-Alfven) fluctuations were targeted for documentation over a range of spectral overlap. Although laboratory experiments were conducted, the following theoretical work was left unfinished: Analytical non-modal prediction Computational non-modal prediction Check to see if Mikhailenko’s theory formulation leads to his published graphs

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Acid-Base Equilibrium and Dielectric Environment Regulate Charge in Supramolecular Nanofibers

Peptide amphiphiles are a class of molecules that can self-assemble into a variety of supramolecular structures, including high-aspect-ratio nanofibers. It is challenging to model and predict the charges in these supramolecular nanofibers because the ionization state of the peptides are not fixed but liable to change due to the acid-base equilibrium that is coupled to the structural organization of the peptide amphiphile molecules. Here, we have developed a theoretical model to describe and predict the amount of charge found on self-assembled peptide amphiphiles as a function of pH and ion concentration. In particular, we computed the amount of charge of peptide amphiphiles nanofibers with the sequence C 16 − V 2 A 2 E 2 . In our theoretical formulation, we consider charge regulation of the carboxylic acid groups, which involves the acid-base chemical equilibrium of the glutamic acid residues and the possibility of ion condensation. The charge regulation is coupled with the local dielectric environment by allowing for a varying dielectric constant that also includes a position-dependent electrostatic solvation energy for the charged species. We find that the charges on the glutamic acid residues of the peptide amphiphile nanofiber are much lower than the same functional group in aqueous solution. There is a strong coupling between the charging via the acid-base equilibrium and the local dielectric environment. Our model predicts a much lower degree of deprotonation for a position-dependent relative dielectric constant compared to a constant dielectric background. Furthermore, the shape and size of the electrostatic potential as well as the counterion distribution are quantitatively and qualitatively different. These results indicate that an accurate model of peptide amphiphile self-assembly must take into account charge regulation of acidic groups through acid–base equilibria and ion condensation, as well as coupling to the local dielectric environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visualization techniques for the gyrokinetic tokamak simulation code

Gyrokinetic simulations of plasma microturbulence in tokamaks are challenging to visualize because the compute grid follows the magnetic field lines that spiral around the torus. We have overcome this challenge by developing three new approaches that improve visualization of gyrokinetics. Our techniques work directly with the topology of magnetic flux surfaces where the simulation stores variables in concentric rings on poloidal planes (vertical cross sections of the torus). Our visualization preview step triangulates each consecutive pair of rings to display the data on a poloidal plane. The second visualization technique follows spiral field lines around the torus and constructs polygons to visualize a flux surface. Third, the poloidal triangles are connected between planes to form prisms that compose a 3-D model of the entire torus. The visualization workflow produces detailed geometry that matches the high resolution, irregular compute grid for every time step. The surface and solid models are displayed in scientific visualization programs to effectively explore and communicate the results, including fluctuation of electron density, ion temperature, and electrostatic potential. Highly detailed renderings verify plasma behavior along magnetic field lines over time.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Structural and Mechanistic Basis for the Inactivation of Human Ornithine Aminotransferase by (3 S ,4 S )-3-Amino-4-fluorocyclopentenecarboxylic Acid

Ornithine aminotransferase (OAT) is overexpressed in hepatocellular carcinoma (HCC), and we previously showed that inactivation of OAT inhibits the growth of HCC. Recently, we found that (3S,4S)-3-amino-4-fluorocyclopentenecarboxylic acid (5) was a potent inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), proceeding by an enamine mechanism. Here we describe our investigations into the activity and mechanism of 5 as an inactivator of human OAT. We have found that 5 exhibits 10-fold less inactivation efficiency (k inact /K I ) against hOAT than GABA-AT. A comprehensive mechanistic study was carried out to understand its inactivation mechanism with hOAT. pK a and electrostatic potential calculations were performed to further support the notion that the α,β-unsaturated alkene of 5 is critical for enhancing acidity and nucleophilicity of the corresponding intermediates and ultimately responsible for the improved inactivation efficiency of 5 over the corresponding saturated analogue (4). Intact protein mass spectrometry and the crystal structure complex with hOAT provide evidence to conclude that 5 mainly inactivates hOAT through noncovalent interactions, and that, unlike with GABA-AT, covalent binding with hOAT is a minor component of the total inhibition which is unique relative to other monofluoro-substituted derivatives. Furthermore, based on the results of transient-state measurements and free energy calculations, it is suggested that the α,β-unsaturated carboxylate group of PLP-bound 5 may be directly involved in the inactivation cascade by forming an enolate intermediate. Overall, compound 5 exhibits unusual structural conversions which are catalyzed by specific residues within hOAT, ultimately leading to an enamine mechanism-based inactivation of hOAT through noncovalent interactions and covalent modification.

59 BASIC BIOLOGICAL SCIENCES↗

Metal Oxide Silicon /MOS/ transistors protected from destructive damage by wire

Loop of flexible, small diameter, nickel wire protects metal oxide silicon /MOS/ transistors from a damaging electrostatic potential. The wire is attached to a music-wire spring, slipped over the MOS transistor case, and released so the spring tensions the wire loop around all the transistor leads, shorting them together. This allows handling without danger of damage.

Deboo, G. J.↗

Inhomogeneous two-stream instability.

Two oppositely charged particle beams interaction instability in cold plasma, discussing stabilization by periodic electrostatic potential

Knorr, G.↗

Kinetic theory of a two-dimensional magnetized plasma.

Several features of the equilibrium and nonequilibrium statistical mechanics of a two-dimensional plasma in a uniform dc magnetic field are investigated. The charges are assumed to interact only through electrostatic potentials. The problem is considered both with and without the guiding-center approximation. With the guiding-center approximation, an appropriate Liouville equation and BBGKY hierarchy predict no approach to thermal equilibrium for the spatially uniform case. For the spatially nonuniform situation, a guiding-center Vlasov equation is discussed and solved in special cases. For the nonequilibrium, nonguiding-center case, a Boltzmann equation, and a Fokker-Planck equation are derived in the appropriate limits. The latter is more tractable than the former, and can be shown to obey conservation laws and an H-theorem, but contains a divergent integral which must be cut off on physical grounds. Several unsolved problems are posed.

Vahala, G.↗

Conductivity of a two-dimensional guiding center plasma.

The Kubo method is used to calculate the electrical conductivity of a two-dimensional, strongly magnetized plasma. The particles interact through (logarithmic) electrostatic potentials and move with their guiding center drift velocities (Taylor-McNamara model). The thermal equilibrium dc conductivity can be evaluated analytically, but the ac conductivity involves numerical solution of a differential equation. Both conductivities fall off as the inverse first power of the magnetic field strength.

Montgomery, D.↗