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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 1,639 records · Page 91
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DOE OSTI2015

Noise analysis of genome-scale protein synthesis using a discrete computational model of translation

Noise in genetic networks has been the subject of extensive experimental and computational studies. However, very few of these studies have considered noise properties using mechanistic models that account for the discrete movement of ribosomes and RNA polymerases along their corresponding templates (messenger RNA (mRNA) and DNA). The large size of these systems, which scales with the number of genes, mRNA copies, codons per mRNA, and ribosomes, is responsible for some of the challenges. Additionally, one should be able to describe the dynamics of ribosome exchange between the free ribosome pool and those bound to mRNAs, as well as how mRNA species compete for ribosomes. We developed an efficient algorithm for stochastic simulations that addresses these issues and used it to study the contribution and trade-offs of noise to translation properties (rates, time delays, and rate-limiting steps). The algorithm scales linearly with the number of mRNA copies, which allowed us to study the importance of genome-scale competition between mRNAs for the same ribosomes. We determined that noise is minimized under conditions maximizing the specific synthesis rate. Moreover, sensitivity analysis of the stochastic system revealed the importance of the elongation rate in the resultant noise, whereas the translation initiation rate constant was more closely related to the average protein synthesis rate. We observed significant differences between our results and the noise properties of the most commonly used translation models. Overall, our studies demonstrate that the use of full mechanistic models is essential for the study of noise in translation and transcription.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Electronic structure and photovoltaic application of BiI{sub 3}

Rapid recent improvement in photovoltaic efficiency in hybrid lead halide perovskite materials has provided the impetus for understanding other, related main-group halide systems. Here, we show that the closely related but less toxic bismuth iodide BiI{sub 3} can show promising optoelectronic properties. Layered binary BiI{sub 3} is used here as the active layer in planar solar cell architectures (efficiency approximately 0.3%). Experimental and computational studies of absolute band positions of BiI{sub 3} are also presented, to help in the rational design of device architectures that would allow efficient charge transfer at the interfaces.

14 SOLAR ENERGY↗
DOE OSTI2016

A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Role of weakly bound complexes in temperature-dependence and relative rates of M x O y – + H 2 O ( M = Mo, W) reactions

Results of a systematic comparison of the Mo x O y – + H 2 O and W x O y – + H 2 O reaction rate coefficients are reported and compared to previous experimental and computational studies on these reactions. W x O y – clusters undergo more direct oxidation by water to yield W x O y+1 – + H 2 , while for Mo x O y – clusters, production of Mo x O y H 2 – (trapped intermediates in the oxidation reaction) is comparatively more prevalent. However, Mo x O y – clusters generally have higher rate coefficients than analogous W x O y – clusters if Mo x O y+1 H 2 – formation is included. Results of calculations on the M 2 O y – + H 2 O (M = Mo, W; y = 4, 5) reaction entrance channel are reported. They include charge-dipole complexes formed from long-range interactions, and the requisite conversion to a Lewis acid-base complex that leads to M x O y+1 H 2 – formation. The results predict that the Lewis acid-base complex is more strongly bound for Mo x O y – clusters than for W x O y – clusters. The calculated free energies along this portion of the reaction path are also consistent with the modest anti-Arrhenius temperature dependence measured for most Mo x O y – + H 2 O reactions, and the W x O y – + H 2 O reaction rate coefficients generally being constant over the temperature range sampled in this study. For clusters that exhibit evidence of both water addition and oxidation reactions, increasing the temperature increases the branching ratio toward oxidation for both species. In conclusion, a more direct reaction path to H 2 production may therefore become accessible at modest temperatures for certain cluster stoichiometries and structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Strain-engineering the anisotropic electrical conductance in ReS{sub 2} monolayer

Rhenium disulfide (ReS{sub 2}) is a semiconducting layered transition metal dichalcogenide that exhibits a stable distorted 1 T (Re in octahedral coordination) phase. The reduced symmetry in ReS{sub 2} leads to in-plane anisotropy in various material properties. In this work, we performed a comprehensive first-principle computational study of strain effect on the anisotropic mechanical and electronic properties of ReS{sub 2} monolayers. We found that the anisotropic ratio in electron mobility along two principle axes is 2.36 while the ratio in hole mobility reaches 7.76. The study of strain applied along different directions shows that the elastic modulus is largest for out-of-plane direction, and the strain along a-direction induces indirect bandgap while strain along b- or c-direction does not. In addition, the carrier mobility can be significantly improved by the c-direction tensile strain. This study indicates that the ReS{sub 2} monolayer has promising applications in nanoscale strain sensor and conductance-switch FETs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Active species delivered by dielectric barrier discharge filaments to bacteria biofilms on the surface of apple

The atmospheric pressure non-equilibrium plasma has shown a significant potential as a novel food decontamination technology. In this paper, we report a computational study of the intersection of negative streamer produced by air dielectric barrier discharge with bacteria biofilm on an apple surface. The structure, conductivities, and permittivities of bacteria biofilm have been considered in the Poisson's equations and transportation equations of charge and neutral species to realize self-consistent transportation of plasma between electrode and charging surfaces of apple. We find that the ionization near the biofilm facilitates the propagation of negative streamer when the streamer head is 1 mm from the biofilm. The structure of the biofilm results in the non-uniform distribution of ROS and RNS captured by flux and time fluence of these reactive species. The mean free path of charged species in μm scale permitted the plasma penetrate into the cavity of the biofilm, therefore, although the density of ROS and RNS decrease by 6–7 order of magnitude, the diffusion results in the uniform distribution of ROS and RNS inside the cavity during the pulse off period.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Surface nanopattern formation due to current-induced homoepitaxial nanowire edge instability

Physical nanopatterning based on a precise control of macroscopic forcing is an essential tool of nanoscale science and technology. Using an externally applied electric field as the macroscopic force, we report here a computational study on the formation of surface nanopatterns consisting of single-layer homoepitaxial islands as a result of a morphological instability that can occur under edge electromigration conditions on the straight edge of a single-layer nanowire grown epitaxially on a crystalline substrate. Direct dynamical simulations based on a model that has been validated experimentally for the Ag/Ag system show that the current-induced nanowire edge instability causes the breakup of the nanowire and leads to the formation of uniformly distributed islands, arranged in linear or V-shaped arrays, which are uniformly sized with nanoscale dimensions. The simulation results are supported by linear stability theory and demonstrate that the geometrical features of the island patterns and the island sizes can be controlled precisely by controlling the electric field direction with respect to the nanowire axis and the electric field strength. Our findings have important implications for developing physical nanopatterning approaches toward enabling future nanofabrication technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Simulation of a non-equilibrium helium plasma bullet emerging into oxygen at high pressure (250–760 Torr) and interacting with a substrate

A two-dimensional computational study of a plasma bullet emanating from a helium gas jet in oxygen ambient at high pressure (250–760 Torr) was performed, with emphasis on the bullet interaction with a substrate. Power was applied in the form of a trapezoidal +5 kV pulse lasting 150 ns. A neutral gas transport model was employed to predict the concentration distributions of helium and oxygen in the system. These were then used in a plasma dynamics model to investigate the characteristics of the plasma bullet during its propagation and interaction with a substrate. Upon ignition, the discharge first propagated as a surface wave along the inner wall of the containing tube, and then exited the tube with a well-defined ionization front (streamer or plasma bullet). The plasma bullet evolved from a hollow (donut-shaped) feature to one where the maximum of ionization was on axis. The bullet propagated in the gap between the tube exit and the substrate with an average speed of ~2 × 10 5 m/s. Upon encountering a metal substrate, the bullet formed a conductive channel to the substrate. Upon encountering a dielectric substrate, the bullet turned into an ionization wave propagating radially along the substrate surface. For a conductive substrate, the radial species fluxes to the surface peaked on the symmetry axis. For a dielectric substrate, a ring-shaped flux distribution was observed. The “footprint” of plasma-surface interaction increased either by decreasing the gap between tube exit and substrate, decreasing the relative permittivity of an insulating substrate, or decreasing pressure. As the system pressure was lowered from 760 to 250 Torr, the discharge was initiated earlier, and the plasma bullet propagation speed increased. A reverse electric field developed during the late stages of the ramp-down of the pulse, which accelerated electrons forming a brief backward discharge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Attainment of a stable, fully detached plasma state in innovative divertor configurations

A computational study of long-legged tokamak divertor configurations is performed with the edge transport code UEDGE. Several divertor configurations are considered, with radially or vertically extended, tightly baffled, outer divertor legs and with or without a secondary X-point in the divertor leg volume. For otherwise identical conditions, a scan of the input power from the core plasma is performed. As the power is reduced to a threshold value, the plasma in the outer leg transitions to a fully detached state, which defines the upper limit on the power for detached divertor operation. Reducing the power further results in the detachment front shifting upstream but remains stable. At low power, the detachment front eventually moves all the way to the primary X-point, which is usually associated with degradation of the core plasma, and this defines the lower limit on the power for the detached divertor operation. For the studied parameters, for long-legged divertors, the detached operation window is quite large, in particular, for the X-point target configuration using a secondary X-point in the divertor leg volume, allowing a factor of 5–10 variations in the input power. For the same parameters, for the standard divertor configuration, the detached operation window is very small or even non-existent. In conclusion, the present modeling results suggest the possibility of stable fully detached divertor operation for a tokamak with tightly baffled extended divertor legs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Orbital orientation mapping of V 2 O 5 thin films

We report the effects of growth methods on the orbital orientation in vanadium pentoxide (V 2 O 5 ) thin films, an important factor to consider when selecting growth techniques for highly selective catalysts and devices. Thermal evaporation and sol-gel methods were used to synthesize the V 2 O 5 films. The surface morphology, roughness, and orientation of the films were characterized by atomic force microscopy and x-ray diffraction. Surface electronic properties and oxidation states were assessed by x-ray photoemission spectroscopy. Polarized x-ray absorption spectroscopy demonstrated that the thermally evaporated film [which was in the (001) orientation] exhibited greater anisotropy than the (100) oriented sol-gel film. The observed increase in anisotropy agrees well with computational findings which revealed that more vanadyl bonds are present at the surface of the thermally evaporated film than at the surface of the sol-gel film. The same computational study also found that the orientation of these bonds is more parallel to the film surface in the thermally evaporated film than in the sol-gel film. Finally, the data suggest that the method of growth may be used as a controlled variable to select key film characteristics for potential applications.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Tunable bandgap in halogen doped 2D nitrogenated microporous materials

The quest for new materials with extraordinary electronic, magnetic, and optical properties leads to the synthesis of 2D nitrogenated microporous materials with the hole diameter of 1.16 nm. We computationally study the evolution of the energy bandgaps, optical, and transport properties with the following substituents: hydrogen, fluorine, chlorine, and iodine. We find that such a small perturbation by these atoms has a tremendous impact on the electronic properties of these materials. Indeed, the direct energy bandgaps can be tuned from 1.64 to 0.96 eV by the substituents from hydrogen to iodine. The optical gaps demonstrate similar dependence. From the transport properties, we calculate the effective masses of π-conjugated microporous polymers and find that the conduction electron effective masses are insensitive to halogen substituents while for some low-lying energy valence bands the effective masses can be drastically increased from 0.71 to 2.98 m e and 0.28 to 0.58 m e for the heavy and light holes, respectively. The application of the nitrogenated microporous materials is very broad. They can be useful as sensitizers in solar cells, for water splitting catalysis, in biomedicine, and for gas and energy storage.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Multiple branches of resistive wall mode instability in a resistive plasma

We observe that the resistive wall mode (RWM) instability is numerically investigated for a toroidal resistive plasma, with results compared to those of an analytic cylindrical model. The full toroidal code MARS-F [Liu et al. , Phys. Plasmas 7, 3681 (2000)] is applied for a computational study. The results indicate that there are two branches of unstable RWMs, when the toroidal favorable average curvature effect (the GGJ effect) is taken into account in the resistive layer. In addition, the GGJ physics not only directly affects the mode growth rate, but also indirectly modifies the mode stability by changing the continuum damping through modifying the mode frequency in the plasma frame. Furthermore, the plasma resistivity can either stabilize or destabilize the RWM, depending on the regime of key plasma parameters (e.g., the plasma rotation). Similarly, the plasma rotation can stabilize or destabilize the RWM, depending on the plasma resistivity. These numerical results from MARS-F are qualitatively confirmed by an analytic theory model which includes the GGJ effect.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Role of Translational Entropy in Spatially Inhomogeneous, Coarse-Grained Models

Coarse-grained models of polymer and biomolecular systems have enabled the computational study of cooperative phenomena, e.g., self-assembly, by lumping multiple atomistic degrees of freedom along the backbone of a polymer, lipid, or DNA molecule into one effective coarse-grained interaction center. Such a coarse-graining strategy leaves the number of molecules unaltered. In order to treat the surrounding solvent or counterions on the same coarse-grained level of description, one can also stochastically group several of those small molecules into an effective, coarse-grained solvent bead or "fluid element." Such a procedure reduces the number of molecules, and we discuss how to compensate the concomitant loss of translational entropy by density-dependent interactions in spatially inhomogeneous systems.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Effect of wetting on nucleation and growth of D 2 in confinement

We have performed a computational study to determine how the wetting of liquid deuterium to the walls of the material influences nucleation. We present the development of a pair-wise interatomic potential that includes zero-point motion of molecular deuterium. Deuterium is used in this study because of its importance to inertial confinement fusion and the potential to generate a superfluid state if the solidification can be suppressed. Our simulations show that wetting dominates undercooling compared to the pore geometries. We observe a transition from heterogeneous nucleation at the confining wall to homogeneous nucleation at the bulk of the liquid (and intermediate cases) as the interaction with the confining wall changes from perfect wetting to non-wetting. When nucleation is heterogeneous, the temperature needed for solidification changes by 4 K with decreasing deuterium-wall interaction, but it remains independent (and equal to the one from bulk samples) when homogeneous nucleation dominates. We find that growth and quality of the resulting microstructure also depends on the magnitude of liquid deuterium–wall interaction strength.

36 MATERIALS SCIENCE↗
DOE OSTI2018

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was explored using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ x HAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ x HAc ), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental findings. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations suggest that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Design of semiconductor surface pits for fabrication of regular arrays of quantum dots and nanorings

We report a systematic computational study on the formation of complex nanostructures consisting of quantum dots and nanorings on surfaces of coherently strained thin films grown epitaxially on pit-patterned substrates. The analysis is based on self-consistent dynamical simulations according to a film surface evolution model that has been validated experimentally by comparison of its predictions with experimental observations on Ge films grown on Si pit-patterned substrates and is supported by linear stability theory that explains the film surface nanopattern formation as the outcome of a Stranski-Krastanow instability. Emphasis is placed on the design of conical pit patterns and the effects on the resulting film surface nanopattern of varying geometrical design parameters including film thickness, pit-pattern period, pit depth, pit opening diameter, and pit wall inclination. We demonstrate that varying the pit opening diameter and the pit wall slope leads to formation of complex nanostructures inside the pits of a regular pit pattern on the film surface, which include quantum dots, as well as single nanorings and multiple concentric nanorings that may or may not surround a central quantum dot inside each pit. Our simulation predictions demonstrate that the ordered nanostructure patterns forming on the film surface can be controlled precisely by tuning the geometrical parameters of the pits on the pit-patterned substrate. Our findings have important implications for designing optimal semiconductor surface patterns toward enabling future nanofabrication technologies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Effect of target material on relativistic electron beam transport

A computational study using the hybrid-PIC code ZUMA investigated the transport of a fast electron beam (55 J, 10 13 A/cm 2 ) produced at Titan laser conditions (λ=1 µm, 0.7 ps, 10 20 W/cm 2 ) in materials ranging from low to high atomic number, specifically fast electron stopping and the evolution of resistive magnetic fields. Fast electron energy loss due to stopping was similar in Al, Cu, and Ag (21 - 27 %) and much higher in Au (54 %). Ohmic stopping was found to dominate over collisional stopping in all materials except Au. Resistive magnetic field growth was shown to depend on the dynamic competition between the resistivity and resistivity gradient source terms in Faraday’s Law. Moreover, the dependence of these terms on the background material ionization state and temperature evolution is presented. The advantages of mid-Z materials for collimation are discussed, as well as the implications for collimation at fast ignition conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Accuracy of tip-sample interaction measurements using dynamic atomic force microscopy techniques: Dependence on oscillation amplitude, interaction strength, and tip-sample distance

Atomic force microscopy (AFM) is a versatile surface characterization method that can map a sample’s topography with high spatial resolution while simultaneously interrogating its surface chemistry through the site-specific high-resolution quantification of the forces acting between the sample and the probe tip. Thanks to considerable advances in AFM measurement technology, such local measurements of chemical properties have gained much popularity in recent years. To this end, dynamic AFM methodologies are implemented where either the oscillation frequency or the oscillation amplitude and phase of the vibrating cantilever are recorded as a function of tip-sample distance and subsequently converted to reflect tip-sample forces or interaction potentials. Such conversion has, however, been shown to produce non-negligible errors when applying the most commonly used mathematical conversion procedures if oscillation amplitudes are of the order of the decay length of the interaction. Extending on these earlier findings, the computational study presented in this paper reveals that the degree of divergence from actual values may also critically depend on both the overall strength of tip-sample interaction and the distance at which the interaction is obtained. These systematic errors can, however, be effectively eliminated by using oscillation amplitudes that are sufficiently larger than the decay length of the interaction potential.

Electrical properties and parameters↗