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At least 919 records · Page 51

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.

59 BASIC BIOLOGICAL SCIENCES↗

Numerical solution of the compressible Navier-Stokes equations using density gradients as additional dependent variables

Numerical solution of two dimensional, time dependent, compressible viscous Navier-Stokes equations about arbitrary bodies was treated using density gradients as additional dependent variables. Thus, six dependent variables were computed with the SOR iteration method. Besides formulation for pressure gradient terms, a formulation for computing the body density was presented. To approximate the governing equations, an implicit finite difference method was employed. In computing the solution for the flow about a circular cylinder, a problem arose near the wall at both stagnation points. Thus, computations with various conditions were tried to examine the problem. Also, computations with and without formulations are compared. The flow variables were computed on 37 by 40 field first, then on an 81 by 40 field.

Kwon, J. H.↗

Prediction of the aerodynamic environment and heat transfer for rotor-stator configurations

A numerical study of the aerodynamic and thermal environment associated with axial turbine stages is presented. Computations were performed using a modification of the unsteady viscous code, ROTORI, and an improved version of the steady inviscid cascade system, MERIDL-TSONIC, coupled with boundary layer codes, BLAYER and STAN5. Two different turbine stages were analyzed: the first stage of the United Technologies Research Center Large Scale Rotating Rig (LSRR) and the first stage of the Space Shuttle Main Engine (SSME) high pressure fuel turbopump turbine. The time-averaged airfoil midspan pressure and heat transfer profiles were predicted for numerous thermal boundary conditions including adiabatic wall, prescribed surface temperature, and prescribed heat flux. Computed solutions are compared with each other and with experimental data in the case of the LSRR calculations. Modified ROTORI predictions of unsteady pressure envelopes and instantaneous contour plots are also presented. Relative merits of the two computational approaches are discussed.

Griffin, L. W.↗

Turbine stage aerodynamics and heat transfer prediction

A numerical study of the aerodynamic and thermal environment associated with axial turbine stages is presented. Computations were performed using a modification of the unsteady NASA Ames viscous code, ROTOR1, and an improved version of the NASA Lewis steady inviscid cascade system MERIDL-TSONIC coupled with boundary layer codes BLAYER and STAN5. Two different turbine stages were analyzed: the first stage of the United Technologies Research Center Large Scale Rotating Rig (LSRR) and the first stage of the Space Shuttle Main Engine (SSME) high pressure fuel turbopump turbine. The time-averaged airfoil midspan pressure and heat transfer profiles were predicted for numerous thermal boundary conditions including adiabatic wall, prescribed surface temperature, and prescribed heat flux. Computed solutions are compared with each other and with experimental data in the case of the LSRR calculations. Modified ROTOR1 predictions of unsteady pressure envelopes and instantaneous contour plots are also presented for the SSME geometry. Relative merits of the two computational approaches are discussed.

Griffin, Lisa W.↗

Rotating reactor studies

Undesired gravitational effects such as convection or sedimentation in a fluid can sometimes be avoided or decreased by the use of a closed chamber uniformly rotated about a horizontal axis. In a previous study, the spiral orbits of a heavy or buoyant particle in a uniformly rotating fluid were determined. The particles move in circles, and spiral in or out under the combined effects of the centrifugal force and centrifugal buoyancy. A optimization problem for the rotation rate of a cylindrical reactor rotated about its axis and containing distributed particles was formulated and solved. Related studies in several areas are addressed. A computer program based on the analysis was upgraded by correcting some minor errors, adding a sophisticated screen-and-printer graphics capability and other output options, and by improving the automation. The design, performance, and analysis of a series of experiments with monodisperse polystyrene latex microspheres in water were supported to test the theory and its limitations. The theory was amply confirmed at high rotation rates. However, at low rotation rates (1 rpm or less) the assumption of uniform solid-body rotation of the fluid became invalid, and there were increasingly strong secondary motions driven by variations in the mean fluid density due to variations in the particle concentration. In these tests the increase in the mean fluid density due to the particles was of order 0.015 percent. To a first approximation, these flows are driven by the buoyancy in a thin crescent-shaped depleted layer on the descending side of the rotating reactor. This buoyancy distribution is balanced by viscosity near the walls, and by the Coriolis force in the interior. A full analysis is beyond the scope of this study. Secondary flows are likely to be stronger for buoyant particles, which spiral in towards the neutral point near the rotation axis under the influence of their centrifugal buoyancy. This is because the depleted layer is thicker and extends all the way around the reactor.

Roberts, Glyn O.↗

Second mode interactions in supersonic boundary layers

The nonlinear evolution of a two-dimensional second mode unstable wave in a Mach 4.5 wall-bounded flow is computed by solving the full time-dependent compressible Navier-Stokes equations. A highly accurate solution is obtained using spectral collocation methods. It is shown that departure from linearity first occurs in the critical layer due to the cubic nonlinearities in the momentum equation. This is a direct result of the large density perturbations in this regime. Time evolution studies of the growth rate as a function of normal distance from the plate suggests that the mode is evolving toward a nonlinear saturated state, and that this problem is possibly amenable to standard weakly nonlinear perturbation methods.

Erlebacher, Gordon↗

Damping characteristics of dashpots

An investigation of the damping characteristics of dashpots was carried out combining theory and experiment. Laminar flow was assumed and three equations for the steady velocity of a piston moving in a cylinder filled with liquid were derived. In the first equation, the piston was assumed coaxial in the cylinder and, in the second equation, the piston was assumed eccentric in the cylinder with an element of the piston in contact with the cylinder wall. The third equation is for a piston of circular cross section in an elliptical cylinder. Experiments showed that the piston is normally eccentric in the cylinder. The pistons tested were 1.25 and 2 inches in diameter 0.062 to 1.00 inch long, and the clearances varied from 1.36 to 5.16 x 10 to the 3rd power inch. The difference in pressure on the two sides of the piston varied from about 2 to 55 pounds per square inch. The piston velocities for each assembly were measured with damping liquids of three different viscosities. At high piston velocities, when turbulent flow exists, the observed velocities were much lower than the velocities calculated on the basis of laminar flow. Results for a wide range of Reynolds numbers are presented in graphical form.

INSTRUMENTS-MICROMETERS↗

Recent Results of Turbulence Research

The first sections of this report deal with two prominent questions, namely the origin of turbulence and the characteristics of turbulent currents. In the third section conclusions are drawn for the flow along a rough wall, whereby an important relation for the velocity distribution is revealed. The principles are also applied to straight rough and smooth tubes.

Prandtl, L↗

Ifluence of crystallization and entrainment of cooler material on the emplacement of basaltic aa lava flows

A theoretical model is used to describe and investigate the effects of simultaneous crystallization, radiation loss, and entrainment of cooler material on the temperature of a well-mixed core of an active aa lava flow. Entrainment of crust, levee debris, and base material into the interior of active flows has been observed, but the degree of assimilation and the thermal consequences are difficult to quantify. The rate of entrainment can be constrained by supplementing the theoretical model with information on the crystallization along the path of the flow and estimation of the radiative loss from the flow interior. Application of the model is demonstrated with the 1984 Mauna Loa flow, which was erupted about 30 C undercooled. Without any entrainment of cooler material, the high crystallization rates would have driven temperatures in the core wall above temperatures measured by thermocouple and estimated from glass geothermometry. One plausible scenario for this flow, which agrees with available temperature and crystallinity measurements, has a high initial rate of entrainment during the first 8 hours of travel (a mass ratio of entrained material to fluid core of about 15% if the average temperature of the entrained material was 600 C), which counterbalances the latent heat from approximately 40% crystallization. In this scenario, the model suggests an additional 5% crystallization and a 5% entrainment mass ratio over the subsequent 16-hour period. Measurements of crystallization, radiative losses, and entrainment factors are necessary for understanding the detailed thermal histories of active lava flows.

Crisp, Joy↗

A Model for Rate-Dependent Hysteresis in Piezoceramic Materials Operating at Low Frequencies

This paper addresses the modeling of certain rate-dependent mechanisms which contribute to hysteresis inherent to piezoelectric materials operating at low frequencies. While quasistatic models are suitable for initial material characterization in some applications, the reduction in coercive field and polarization values which occur as frequencies increase must be accommodated to achieve the full capabilities of the materials. The model employed here quantifies the hysteresis in two steps. In the first, anhysteretic polarization switching is modeled through the application of Boltzmann principles to balance the electrostatic and thermal energy. Hysteresis is then incorporated through the quantification of energy required to translate and bend domain walls pinned at inclusions inherent to the materials. The performance of the model is illustrated through a fit to low frequency data (0.1 Hz - 1 Hz) from a PZT5A wafer.

Smith, Ralph C.↗

Microgravity-Enhanced Stem Cell Selection

Stem cells, both embryonic and adult, promise to revolutionize the practice of medicine in the future. In order to realize this potential, a number of hurdles must be overcome. Most importantly, the signaling mechanisms necessary to control the differentiation of stem cells into tissues of interest remain to be elucidated, and much of the present research on stem cells is focused on this goal. Nevertheless, it will also be essential to achieve large-scale expansion and, in many cases, assemble cells in 3D as transplantable tissues. To this end, microgravity analog bioreactors can play a significant role. Microgravity bioreactors were originally conceived as a tool to study the cellular responses to microgravity. However, the technology can address some of the shortcomings of conventional cell culture systems; namely, the deficiency of mass transport in static culture and high mechanical shear forces in stirred systems. Unexpectedly, the conditions created in the vessel were ideal for 3D cell culture. Recently, investigators have demonstrated the capability of the microgravity bioreactors to expand hematopoietic stem cells compared to static culture, and facilitate the differentiation of umbilical cord stem cells into 3D liver aggregates. Stem cells are capable of differentiating into functional cells. However, there are no reliable methods to induce the stem cells to form specific cells or to gain enough cells for transplantation, which limits their application in clinical therapy. The aim of this study is to select the best experimental setup to reach high proliferation levels by culturing these cells in a microgravity-based bioreactor. In typical cell culture, the cells sediment to the bottom surface of their container and propagate as a one-cell-layer sheet. Prevention of such sedimentation affords the freedom for self-assembly and the propagation of 3D tissue arrays. Suspension of cells is easily achievable using stirred technologies. Unfortunately, in conventional bioreactors, stirring invokes deleterious forces that disrupt cell aggregation and results in cell death. First-generation rotating bioreactors provided rotation on the horizontal axis, which resulted in the suspension of cells without stirring, thus providing a suitable environment to propagate cells without sedimentation to a surface. The rotating wall bioreactors did not provide a way to remove air bubbles that were causing shear and disrupting 3D cultures. Johnson Space Center successfully engineered the hydrofocusing bioreactor (HFB) that resolved the problem of removing the air bubbles from the fluid medium of NASA's rotating-wall space bioreactors. The HFB uses the principle of hydrodynamic focusing that simultaneously produces a low-shear fluid culture environment and a variable hydrofocusing force that can control the movement, location, and removal of suspended cells, tissues, and air bubbles from the bioreactor. The HFB is a rotating, domeshaped cell culture vessel with a centrally located sampling port and an internal viscous spinner. The vessel and spinner can rotate at different speeds either in the same or opposite directions. Rotation of the vessel and viscous interaction at the spinner generate a hydrofocusing force. Adjusting the differential rotation rate between vessel and spinner controls the magnitude of the force.

Claudio, Pier Paolo↗

Theoretical Limits of Vapor Cooling Large Cylindrical Structures Using Boil-Off

The Structural Heat Intercept, Insulation, and Vibration Evaluation Rig (SHIIVER) is planning to demonstrate the performance benefits of using boil-off to reduce the heat load on various upper stage structural members by using the boil-off vapor to intercept some of the heat load on the structures. A first order simplified analytical model was constructed in order to understand sensitivity of various parameters to performance as well as to understand the theoretical maximum performance of the vapor cooling of a thin-walled cylindrical structure. Constant fluid properties and a temperature dependent thermal conductivity of the structure material were assumed. The model showed that vapor cooling of an aluminum cylindrical structure with hydrogen can reduce the heat load along the cylinder by as much as 70%. Also, cooling a portion of the cylinder is quite effective in comparison with cooling it entirely.

R. Balasubramaniam↗

Computer program to calculate three-dimensional boundary layer flows over wings with wall mass transfer

A system of computer programs for calculating three dimensional transonic flow over wings, including details of the three dimensional viscous boundary layer flow, was developed. The flow is calculated in two overlapping regions: an outer potential flow region, and a boundary layer region in which the first order, three dimensional boundary layer equations are numerically solved. A consistent matching of the two solutions is achieved iteratively, thus taking into account viscous-inviscid interaction. For the inviscid outer flow calculations, the Jameson-Caughey transonic wing program FLO 27 is used, and the boundary layer calculations are performed by a finite difference boundary layer prediction program. Interface programs provide communication between the two basic flow analysis programs. Computed results are presented for the NASA F8 research wing, both with and without distributed surface suction.

Mclean, J. D.↗

Dangling bonds, the charge neutrality level, and band alignment in semiconductors

We present a systematic study of the electronic properties of dangling bonds (DBs) in a variety of semiconductors and examine the relationship between DBs and the charge neutrality level (CNL) in the context of band alignments of semiconductors. We use first-principles calculations based on density functional theory to assess the energetics of DBs in a set of diamond-structure group-IV and III–V or II–VI zinc-blende-structure semiconductors, considering both cation and anion-derived states. We examine the charge-state transition levels of DBs to assess whether they can serve as a CNL to align band structures, by comparing with offsets calculated from interface calculations. Our results show that this approach for evaluating the CNL yields quantitative results for band offsets and provides useful insights. We discuss the relation with alternative approaches for determination of CNLs based on branch-point energies or transition levels of interstitial hydrogen.

36 MATERIALS SCIENCE↗

Comparison of Integrated Radiation Transport Models with TEPC Measurements for the Average Quality Factors in Spaceflights

The purpose of this work is to test our theoretical model for the interpretation of radiation data measured in space. During the space missions astronauts are exposed to the complex field of radiation type and kinetic energies from galactic cosmic rays (GCR), trapped protons, and sometimes solar particle events (SPEs). The tissue equivalent proportional counter (TEPC) is a simple time-dependent approach for radiation monitoring for astronauts on board the International Space Station. Another and a newer approach to Microdosimetry is the use of silicon-on-insulator (SOI) technology launched on the MidSTAR-1 mission in low Earth orbit (LEO). In the radiation protection practice, the average quality factor of a radiation field is defined as a function of linear energy transfer (LET), Q(sub ave)(LET). However, TEPC measures the average quality factor as a function of the lineal energy y, Q(sub ave)(y), defined as the average energy deposition in a volume divided by the average chord length of the volume. Lineal energy, y, deviates from LET due to energy straggling, delta-ray escape or entry, and nuclear fragments produced in the detector volume. Monte Carlo track structure simulation was employed to obtain the response of a TEPC irradiated with charged particle for an equivalent site diameter of 1 micron of wall-less counter. The calculated data of the energy absorption in the wall-less counter were compiled for various y values for several ion types at various discrete projectile energy levels. For the simulation of TEPC response from the mixed radiation environments inside a spacecraft, such as, Space Shuttle and International Space Station, the complete microdosimetric TEPC response, f( y, E, Z), were calculated with the Monte Carlo theoretical results by using the first order Lagrangian interpolation for a monovariate function at a given y value (y = 0.1 keV/micron 5000 keV/micron) at any projectile energy level (E = 0.01 MeV/u to 50,000 MeV/u) of each specific radiation type (Z = 1 to 28). Because the anomalous response has been observed at large event sizes in the experiment due to the escape of energy out of sensitive volume by delta-rays and the entry of delta-rays from the high-density wall into the low-density gas-volume cavity, Monte Carlo simulation was also made for the response of a walled-TEPC with wall thickness 2 mm and density 1 g/cm(exp 3). The radius of cavity was set to 6.35 mm and a gas density 7.874 x 10(exp -5) g/cm(exp 3). The response of the walled- and the wall-less counters were compared. The average quality factor Q(sub ave)(y) for trapped protons on STS-89 demonstrated the good agreement between the model calculations and flight TEPC data as shown. Using an integrated space radiation model (this includes the transport codes HZETRN and BRYNTRN, the quantum nuclear interaction model QMSFRG) and the resultant response distribution functions of walled-TEPC from Monte-Carlo track simulations, we compared model calculations with walled-TEPC measurements from NASA missions in LEO and made predictions for the lunar and the Mars missions. The Q(sub ave)(y) values for the trapped or the solar protons ranged from 1.9-2.5. This over-estimates the Qave(LET) values which ranged from 1.4-1.6. Both quantities increase with shield thickness due to nuclear fragmentation. The Q(sub ave)(LET) for the complete GCR spectra was found to be 3.5-4.5, while flight TEPCs measured 2.9-3.4 for Q(sub ave)(y). The GCR values are decreasing with the shield thickness. Our analysis for a proper interpretation of data supports the use of TEPCs for monitoring space radiation environment.

Kim, Myung-Hee Y.↗

Carrier confinement and alloy disorder exacerbate Auger–Meitner recombination in AlGaN ultraviolet light-emitting diodes

The quantum efficiency of AlGaN ultraviolet light-emitting diodes declines (droops) at increasing operating powers due to Auger–Meitner recombination (AMR). Using first-principles density-functional theory, we show that indirect AMR mediated by electron–phonon coupling and alloy disorder can induce bulk C coefficients as large as ~10 –31 cm 6 /s. Furthermore, we find that the confinement of carriers by polarization fields within quantum wells severely relaxes crystal-momentum conservation, which exacerbates the rate of AMR over radiative recombination by an order of magnitude relative to the bulk. Furthermore, this results in a striking decrease in quantum efficiency at high power. Suppressing polarization fields and jointly increasing the well width would greatly mitigate AMR and efficiency droop.

36 MATERIALS SCIENCE↗

Velocity Measurements in Channel Gas Flows in the Slip Regime by means of Molecular Tagging Velocimetry

Direct measurements of the slip velocity in rarefied gas flows produced by local thermodynamic non-equilibrium at the wall represent crucial information for the validation of existing theoretical and numerical models. In this work, molecular tagging velocimetry (MTV) by direct phosphorescence is applied to argon and helium flows at low pressures in a 1-mm deep channel. MTV has provided accurate measurements of the molecular displacement of the gas at average pressures of the order of 1 kPa. To the best of our knowledge, this work reports the very first flow visualizations of a gas in a confined domain and in the slip flow regime, with Knudsen numbers up to 0.014. MTV is cross-validated with mass flowrate measurements by the constant volume technique. The two diagnostic methods are applied simultaneously, and the measurements in terms of average velocity at the test section are in good agreement. Moreover, preliminary results of the slip velocity at the wall are computed from the MTV data by means of a reconstruction method

74 ATOMIC AND MOLECULAR PHYSICS↗