Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “ATOMIC MODELS”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16

Elongation affinity, activation barrier, and stability of Aβ42 oligomers/fibrils in physiological saline

Amyloid-beta (Aβ) peptides, Aβ40 and the more neurotoxic Aβ42, have been the subject of many research efforts for Alzheimer's disease. In two recent independent investigations, the atomistic structure of Aβ42 fibril has been clearly established in the S-shaped conformation consisting of three β-sheets stabilized by salt bridges formed between the Lys28 sidechain and the C-terminus of Ala42. This structure distinctively differs from the long-known structure of Aβ40 in the β-hairpin shaped conformation consisting of two β-sheets. Recent in silico investigations based on all-atom models have reached closer agreement with the in vitro measurements of Aβ40 thermodynamics. In this study, we present an in silico investigation of Aβ42 thermodynamics. Using the established force field parameters in seven sets of all-atom simulations, we examined the stability of small Aβ42 oligomers in physiological saline. We computed the elongation affinity of the S-shaped Aβ42 fibril, reaching agreement with the experimental data. We also estimated the Arrhenius activation barrier along the elongation pathway (from the disordered conformation of a free Aβ42 peptide to its S-shaped conformation on a fibril) that amounts to about 16 kcal/mol, which is consistent with the experimental data. Based on these quantitative agreements, we conclude that aggregation of Aβ42 peptides into fibrils is thermodynamically slow without precipitation by extrinsic factors such as heparan sulfate proteoglycan and highlight the possibility to prevent Aβ42 aggregation by eliminating some precipitation factors or by increasing competitive agents to capture and transport free Aβ42 peptides from the cerebrospinal fluid. - Highlights: • Aβ42 fibril elongation affinity was computed with chemical accuracy, in agreement with in vitro data. • Small Aβ42 oligomers were found to be stable in physiological saline. • A long Aβ42 fibril-filament was shown to stabilize an Aβ dimer in its proximity.

60 APPLIED LIFE SCIENCES↗

Transport properties and equation of state for HCNO mixtures in and beyond the warm dense matter regime

We present simulations of a four component mixture of HCNO with orbital free molecular dynamics (OFMD). These simulations were conducted for 5–200 eV with densities ranging between 0.184 and 36.8 g/cm 3 . We extract the equation of state from the simulations and compare to average atom models. We found that we only need to add a cold curve model to find excellent agreement. In addition, we studied mass transport properties. We present fits to the self-diffusion and shear viscosity that are able to reproduce the transport properties over the parameter range studied. We compare these OFMD results to models based on the Coulomb coupling parameter and one-component plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Atomic resolution coherent x-ray imaging with physics-based phase retrieval

Coherent x-ray imaging and scattering from accelerator based sources such as synchrotrons continue to impact biology, medicine, technology, and materials science. Many synchrotrons around the world are currently undergoing major upgrades to increase their available coherent x-ray flux by approximately two orders of magnitude. The improvement of synchrotrons may enable imaging of materials in operando at the atomic scale which may revolutionize battery and catalysis technologies. Current algorithms used for phase retrieval in coherent x-ray imaging are based on the projection onto sets method. These traditional iterative phase retrieval methods will become more computationally expensive as they push towards atomic resolution and may struggle to converge. Additionally, these methods do not incorporate physical information that may additionally constrain the solution. In this work, we present an algorithm which incorporates molecular dynamics into Bragg coherent diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical techniques with molecular dynamics to solve the phase retrieval problem. We present several examples where our algorithm is applied to simulated coherent diffraction from 3D crystals and show convergence to the correct solution at the atomic scale.

47 OTHER INSTRUMENTATION↗

Average-atom calculations of bound-free and free-free cross sections in dense plasmas

Cross sections for photo-induced bound-free and free-free transitions in plasmas are evaluated in the average-atom approximation and applied to determine opacities of dense plasmas of light elements. Parameters characterizing the plasmas (chemical potential, average ionic charge, free electron density, bound and continuum wave functions, and occupation numbers) are obtained from the average-atom model. Lowest-order calculations of the free-free cross sections, which diverge in the low-frequency limit, are regularized by accounting for the finite electron-ion relaxation time. The resulting analysis provides the basis for average-atom studies of plasma opacities. Such studies are presented for dense lithium, beryllium, boron, and carbon. Applications are given to Rosseland mean opacities of dense hydrogen and deuterium plasmas and to comparisons of free-free to bound-free opacities in shock-compressed plasmas. Average-atom cross section and opacity calculations are extended to plasmas consisting of more than one ionic species, boron nitride, polystyrene, and a composite H, He, C plasma.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry

The type III CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated genes) systems are bacterially encoded adaptive immune systems for defense against invading nucleic acids. They accomplish this task through the coordinated cleavage of invading substrates of single-stranded RNA and DNA (ssDNA and ssRNA) by the Csm (type III-A) or Cmr (type III-B) effector complexes. The ssRNA is complementarily bound to the CRISPR RNA (crRNA). However, the structural basis for the DNase and RNase activation of the Csm nucleoprotein complex is largely unknown. Here we report cryo-EM structures of the Csm-crRNA complex, with or without target ssRNA, at near-atomic resolution. Our cryo-EM maps allow us to build atomic models of the key macromolecular components, including Cas10, Csm2, Csm3, Csm4, crRNA and the invading ssRNA. Our structure resolves unambiguously the stoichiometry and tertiary structures of the Csm protein complex and the interactions between protein components and the crRNA/ssRNA. Interestingly, the new atomic structures of the Csm proteins presented here are similar to those of previously known Csm proteins in other species despite their low sequence similarity. Our combined structural and biochemical data suggest that ssRNA cleavage is preferentially carried out near its 5’-end, that the extent of interactions among the ssRNA, crRNA and the protein components regulates the DNase activity of the Csm complex, and that the 3’ flanking sequence of ssRNA activates the Cas10 DNase activity allosterically.

59 BASIC BIOLOGICAL SCIENCES↗

On extreme-ultraviolet helium line intensity enhancement factors on the sun

Helium lines in the solar EUV spectrum provide useful diagnostics of the solar atmosphere plasma. Helium is one of the few elements that exhibits strong emission lines formed in the lower transition region, and it is the second most abundant element in the Sun. However, the analysis of helium lines is complicated by their optical thickness and the unusual behavior of their intensities, with enhancements by a factor of up to 15 reported in the literature. Detailed study requires spatially and spectrally resolved observations in the EUV range, as well as sophisticated atomic modeling. The present work focuses on the application of the differential emission measure distribution to reproduce the observed fluxes of the He i and He ii lines observed by the Solar and Heliospheric Observatory (SOHO)/Coronal Diagnostic Spectrometer and Hinode/EIS spectrometers, using the latest atomic data. It is found that the comparison between observed and reconstructed intensities for He i resonance lines λλ537.03, 522.21, and 515.62 and the intercombination line λ591.41 does not show a real enhancement. By contrast, He i λ584.33, the first line of the 1s{sup 2} {sup 1}S−1s np {sup 1}P resonance series, shows a depletion of a factor ∼2, due to the opacity effect, as supported by non-LTE radiative transfer calculations. For single ionized helium lines 303.78 and 256.32 Å, the enhancement factors obtained are higher and agree with those of previous work. The different behavior of He i and He ii lines suggests a mechanism that affects ionized helium only.

79 ASTRONOMY AND ASTROPHYSICS↗

Epitaxial columnar growth of strain-free antiferromagnetic Weyl semimetal Mn 3 Sn on wurtzite c -plane GaN/Al 2 O 3 (0001)

Weyl semimetal thin films with excellent crystalline quality are of great interest for antiferromagnetic spintronics. Mn 3 Sn is one Weyl semimetal with great properties and promise for exciting science and applications. It has proven very challenging, however, to grow Mn 3 Sn thin films with smooth surfaces, negligible strain, and excellent crystallinity. In this work, we discuss the successful preparation of epitaxial Mn 3 Sn (0001)-oriented thin films via molecular beam epitaxial growth on c -plane wurtzite GaN which was grown by MBE on Al 2 O 3 (0001). We present the reflection high energy electron diffraction analysis along with x-ray diffraction in order to demonstrate the crystalline quality of the film, and we give atomic models to explain the epitaxial orientation relationships between the crystal lattices of the substrate, GaN layer, and Mn 3 Sn layer. Importantly, we discuss the film lattice parameters as compared to expected values, demonstrating negligible strain both in-plane and out-of-plane . Atomic force microscopy reveals an epitaxial columnar growth mode characterized by flat-top-mesa islands, while scanning tunneling microscopy shows the atomically smooth surfaces of the mesa-top structures. Finally, Rutherford backscattering informs the stoichiometry of the film as well as the layer thicknesses.

Chiral antiferromagnetic material↗

Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT{sup OPLS}). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT{sup OPLS} PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT{sup CHARMM}) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT{sup OPLS} PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA){sub 3} peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret CG and AT simulation results on membrane proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Opacity of shock-heated boron plasmas

Standard measures of opacity, the imaginary part of the atomic scattering factor f 2 and the x-ray mass attenuation coefficient μ/ρ, are assessed in shock-heated boron, boron carbide and boron nitride plasmas. The Hugoniot equation, relating the temperature T behind a shock wave to the compression ratio ρ/ρ 0 across the shock front, is used in connection with the plasma equation of state to determine the pressure p, effective plasma charge Z* and the K-shell occupation in terms of ρ/ρ 0 . Solutions of the Hugoniot equation (determined within the framework of the generalized Thomas–Fermi theory) show that the K-shell occupation in low-Z ions decreases rapidly from 2 to 0.1 as the temperature increases from 20 eV to 500 eV; a temperature range in which the shock compression ratio is near 4. The average-atom model (a quantum mechanical version of the generalized Thomas–Fermi theory) is used to determine K-shell and continuum wave functions and the photoionization cross section for x-rays in the energy range ω = 1 eV to 10 keV, where the opacity is dominated by the atomic photoionization process. For an uncompressed boron plasma at T = 10 eV, where the K-shell is filled, the average-atom cross section, the atomic scattering factor and the mass attenuation coefficient are all shown to agree closely with previous (cold matter) tabulations [1, 2, 3]. For shock-compressed plasmas, the dependence of μ/ρ on temperature can be approximated by scaling previously tabulated cold-matter values by the relative K-shell occupation; yet, there is a relatively small residual dependence arising from the photoionization cross section. Attenuation coefficients μ for a 9 keV x-ray are given as functions of T along the Hugoniot for B, C, B 4 C and BN plasmas.

52.25.Os: Emission↗

Multiscale Modeling of Vinyl-Addition Polynorbornenes: The Effect of Stereochemistry

Vinyl-addition polynorbornenes are candidates for designing high-performance polymers due to unique characteristics, which include a high glass transition temperature associated with a rigid backbone. Recent studies have established that the processability and properties of these polymers can be fine-tuned by using targeted substitutions. However, synthesis with different catalysts results in materials with distinct properties, potentially due to the presence of various stereoisomers that are difficult to quantify experimentally. Herein, we develop all-atom models of polynorbornene oligomers based on classical force fields and density functional theory. To establish the relationship between chemical architecture, chain conformations, and melt structure, we perform detailed molecular dynamics simulations with the fine-tuned atomistic force field and propose simpler coarse-grained descriptions to address the high molecular weight limit. All-atom simulations of oligomers suggest high glass transition temperatures in the range of 550–600 K. In the melt state (800 K), meso chains form highly rigid extended coils (C∞≈11) with amorphous structural characteristics similar to the X-ray diffraction data observed in the literature. In contrast, simulations with racemo chains predict highly helical tubular chain conformations that could promote assembly into crystalline structures.

Polymer Science↗

Low-energy positron scattering by pyrimidine

This work reports elastic integral and differential cross sections for positron collisions with pyrimidine, for energies up to 20 eV. The cross sections were computed with the Schwinger multichannel method in the static plus polarization approximation. We also employed the Born closure procedure to account for the long range potential due to the permanent dipole moment of the molecule. Our results are compared with the experimental total cross section of Zecca et al. [J. Phys. B 43, 215204 (2010)], the experimental grand-total, quasi-elastic integral and differential cross section of Palihawadana et al. [Phys. Rev. A 88, 12717 (2013)]. We also compare our results with theoretical integral and differential cross sections obtained by Sanz et al. [Phys. Rev. A 88, 62704 (2013)] with the R-matrix and the independent atom model with screening-corrected additivity rule methods, and with the results computed by Franz and Gianturco [Phys. Rev. A 88, 042711 (2013)] using model correlation-polarization potentials. The agreement between the theory and the experiment is encouraging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of a three-phrase combustion code for modeling liquid rocket engines

A two-dimensional/axisymmetric program for the simulation of three-phase reactive flows is presented. The three phases are: a multiple-species gaseous phase, a single-species liquid phase, and a particulate droplet phase. The liquid and gaseous phases are described with continuous Eulerian equations, while the droplets are described in a discrete Lagrangian fashion. The three phases are fully coupled together. An atomization model, a multireaction chemical kinetics model, and a subgrid scale turbulence model completes the description of a general liquid/gas bipropellant combustion process. The code development criteria and qualitative features are highlighted.

Liang, P. Y.↗

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations of the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm{sup 3} and T = 15 625 to 500 000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a “Saha-type” model as a function of the CH plasma density and temperature, which gives an increasing ionization as the CH density increases even at low temperatures (T < 50 eV). The orbital-free molecular dynamics method is only used to gauge the average ionization behavior of CH under the average-atom model in conjunction with the pressure-matching mixing rule. The thermal conductivities (κ{sub QMD}) of CH, derived directly from the Kohn–Sham molecular-dynamics calculations, are then analytically fitted with a generalized Coulomb logarithm [(lnΛ){sub QMD}] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation–hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Hydrodynamic simulations of cryogenic deuterium–tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted ∼20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Rescattering photoelectron spectroscopy of the CO 2 molecule: Progress towards experimental discrimination between theoretical target-structure models

Photoelectron momentum distributions (PEMDs) generated in strong-field ionization of randomly oriented CO 2 molecules by intense infrared laser pulses at 1300-, 1450-, and 1650-nm wavelengths are measured experimentally and analyzed theoretically. Here, the experimental PEMDs extracted along the outermost backward rescattering caustic are well reproduced by theoretical calculations based on the recently derived factorization formula with an analytical returning photoelectron wave packet (RWP). The sensitivity of the theoretical results to the target structure models used in the calculations is investigated. It is shown that RWPs obtained in the single-active-electron (SAE) approximation and by the Hartree-Fock method have only minor differences. On the other hand, differential cross sections (DCSs) for elastic scattering of a photoelectron on the parent molecular ion calculated by ab initio , SAE, and independent-atom model methods are considerably different. This difference almost disappears after averaging over molecular orientations, so the present experiment does not enable us to discriminate between the different target structure models. However, we show that such a discrimination should become possible by measuring PEMD with aligned molecules. This will provide an access to the rich target structure information contained in the DCS.

74 ATOMIC AND MOLECULAR PHYSICS↗

Polarized Line Formation in Arbitrary Strength Magnetic Fields Angle-averaged and Angle-dependent Partial Frequency Redistribution

Magnetic fields in the solar atmosphere leave their fingerprints in the polarized spectrum of the Sun via the Hanle and Zeeman effects. While the Hanle and Zeeman effects dominate, respectively, in the weak and strong field regimes, both these effects jointly operate in the intermediate field strength regime. Therefore, it is necessary to solve the polarized line transfer equation, including the combined influence of Hanle and Zeeman effects. Furthermore, it is required to take into account the effects of partial frequency redistribution (PRD) in scattering when dealing with strong chromospheric lines with broad damping wings. In this paper, we present a numerical method to solve the problem of polarized PRD line formation in magnetic fields of arbitrary strength and orientation. This numerical method is based on the concept of operator perturbation. For our studies, we consider a two-level atom model without hyperfine structure and lower-level polarization. We compare the PRD idealization of angle-averaged Hanle–Zeeman redistribution matrices with the full treatment of angle-dependent PRD, to indicate when the idealized treatment is inadequate and what kind of polarization effects are specific to angle-dependent PRD. Because the angle-dependent treatment is presently computationally prohibitive when applied to realistic model atmospheres, we present the computed emergent Stokes profiles for a range of magnetic fields, with the assumption of an isothermal one-dimensional medium.

79 ASTRONOMY AND ASTROPHYSICS↗

Probability of Electron Capture by {sup 3}He{sup 2+} Ions from Argon Atoms at Different Impact Parameters

We have measured the absolute values of total cross sections of capture of one and two electrons by He{sup 2+} ions from argon atoms. The differential scattering cross sections have been determined for fast atoms and singly charged helium ions formed in each of these processes (without and with additional ionization of the formed slow argon ion). Measurements have been taken for He{sup 2+} ions with kinetic energy of 6 keV in scattering angle range 0–2.5°. Based on the measured differential cross sections using different model atomic particle interaction potentials, we have calculated the cross sections of these processes as functions of the impact parameter. The probabilities of realization of these processes with electron density distribution in different shells in the target atom have been compared. The applicability of the expressions for the screened Coulomb interaction potentials in the description of scattering of particles that have captured electrons has been demonstrated.

74 ATOMIC AND MOLECULAR PHYSICS↗

NASA Numerical and Experimental Evaluation of UTRC Low Emissions Injector

Computational and experimental analyses of a PICS-Pilot-In-Can-Swirler technology injector, developed by United Technologies Research Center (UTRC) are presented. NASA has defined technology targets for near term (called "N+1", circa 2015), midterm ("N+2", circa 2020) and far term ("N+3", circa 2030) that specify realistic emissions and fuel efficiency goals for commercial aircraft. This injector has potential for application in an engine to meet the Pratt & Whitney N+3 supersonic cycle goals, or the subsonic N+2 engine cycle goals. Experimental methods were employed to investigate supersonic cruise points as well as select points of the subsonic cycle engine; cruise, approach, and idle with a slightly elevated inlet pressure. Experiments at NASA employed gas analysis and a suite of laser-based measurement techniques to characterize the combustor flow downstream from the PICS dump plane. Optical diagnostics employed for this work included Planar Laser-Induced Fluorescence of fuel for injector spray pattern and Spontaneous Raman Spectroscopy for relative species concentration of fuel and CO2. The work reported here used unheated (liquid) Jet-A fuel for all fuel circuits and cycle conditions. The initial tests performed by UTRC used vaporized Jet-A to simulate the expected supersonic cruise condition, which anticipated using fuel as a heat sink. Using the National Combustion Code a PICS-based combustor was modeled with liquid fuel at the supersonic cruise condition. All CFD models used a cubic non-linear k-epsilon turbulence wall functions model, and a semi-detailed Jet-A kinetic mechanism based on a surrogate fuel mixture. Two initial spray droplet size distribution and spray cone conditions were used: (1) an initial condition (Lefebvre) with an assumed Rosin-Rammler distribution, and 7 degree Solid Spray Cone; and (2) the Boundary Layer Stripping (BLS) primary atomization model giving the spray size distribution and directional properties. Contour and line plots are shown in comparison with experimental data (where this data is available) for flow velocities, fuel, and temperature distribution. The CFD results are consistent with experimental observations for fuel distribution and vaporization. Analysis of gas sample results, using a previously-developed NASA NOx correlation, indicates that for sea-level takeoff, the PICS configuration is predicted to deliver an EINOx value of about three for the targeted supersonic aircraft. Emissions results at supersonic cruise conditions show potential for meeting the NASA goals with liquid fuel.

Hicks, Yolanda R.↗