Improved sampling techniques for the direct simulation Monte Carlo method

The direct simulation Monte Carlo (DSMC) method is a widely used approach for flow simulations having rarefied or nonequilibrium effects. It involves heavily to sample instantaneous values from prescribed distributions using random numbers. In this note, we briefly review the sampling techniques typically employed in the DSMC method and present two techniques to speedup related sampling processes. One technique is very efficient for sampling geometric locations of new particles and the other is useful for the Larsen-Borgnakke energy distribution.

Direct numerical simulation of hypersonic boundary layer transition over a blunt cone with a small angle of attack

The direct numerical simulation of boundary layer transition over a 5° half-cone-angle blunt cone is performed. The free-stream Mach number is 6 and the angle of attack is 1°. Random wall blow-and-suction perturbations are used to trigger the transition. Different from the authors’ previous work [Li et al., AIAA J. 46, 2899(2008)], the whole boundary layer flow over the cone is simulated (while in the author’s previous work, only two 45° regions around the leeward and the windward sections are simulated). The transition location on the cone surface is determined through the rapid increase in skin fraction coefficient (Cf). The transition line on the cone surface shows a nonmonotonic curve and the transition is delayed in the range of 0° ≤ θ ≤ 30° (θ = 0° is the leeward section). The mechanism of the delayed transition is studied by using joint frequency spectrum analysis and linear stability theory (LST). It is shown that the growth rates of unstable waves of the second mode are suppressed in the range of 20° ≤ θ ≤ 30°, which leads to the delayed transition location. Very low frequency waves VLFWs� are found in the time series recorded just before the transition location, and the periodic times of VLFWs are about one order larger than those of ordinary Mack second mode waves. Band-pass filter is used to analyze the low frequency waves, and they are deemed as the effect of large scale nonlinear perturbations triggered by LST waves when they are strong enough.The direct numerical simulation of boundary layer transition over a 5° half-cone-angle blunt cone is performed. The free-stream Mach number is 6 and the angle of attack is 1°. Random wall blow-and-suction perturbations are used to trigger the transition. Different from the authors’ previous work [ Li et al., AIAA J. 46, 2899 (2008) ], the whole boundary layer flow over the cone is simulated (while in the author’s previous work, only two 45° regions around the leeward and the windward sections are simulated). The transition location on the cone surface is determined through the rapid increase in skin fraction coefficient (Cf). The transition line on the cone surface shows a nonmonotonic curve and the transition is delayed in the range of 20° ≤ θ ≤ 30° (θ = 0° is the leeward section). The mechanism of the delayed transition is studied by using joint frequency spectrum analysis and linear stability theory (LST). It is shown that the growth rates of unstable waves of the second mode are suppressed in the range of 20° ≤ θ ≤ 30°, which leads to the delayed transition location. Very low frequency waves (VLFWs) are found in the time series recorded just before the transition location, and the periodic times of VLFWs are about one order larger than those of ordinary Mack second mode waves. Band-pass filter is used to analyze the low frequency waves, and they are deemed as the effect of large scale nonlinear perturbations triggered by LST waves when they are strong enough.

Two-Phase Flow In Anode Flow Field Of A Small Direct Methanol Fuel Cell In Different Gravities

An in-situ visualization of two-phase flow inside anode flow bed of a small liquid fed direct methanol fuel cells in normal and reduced gravity has been conducted in a drop tower. The anode flow bed consists of 11 parallel straight channels. The length, width and depth of single channel, which had rectangular cross section, are 48.0, 2.5 and 2.0 mm, respectively. The rib width was 2.0 mm. The experimental results indicated that when the fuel cell orientation is vertical, two-phase flow pattern in anode channels can evolve from bubbly flow in normal gravity into slug flow in microgravity. The size of bubbles in the reduced gravity is also bigger. In microgravity, the bubbles rising speed in vertical channels is obviously slower than that in normal gravity. When the fuel cell orientation is horizontal, the slug flow in the reduced gravity has almost the same characteristic with that in normal gravity. It implies that the effect of gravity on two-phase flow is small and the bubbles removal is governed by viscous drag. When the gas slugs or gas columns occupy channels, the performance of liquid fed direct methanol fuel cells is failing rapidly. It infers that in long-term microgravity, flow bed and operating condition should be optimized to avoid concentration polarization of fuel cells.

Direct observation of adsorption sites of protein impurities and their effects on step advancement of protein crystals

We measured noninvasively step velocities of elementary two-dimensional (2D) islands on {110} faces of tetragonal lysozyme crystals, under various supersaturations, by laser confocal microscopy combined with differential interference contrast microscopy. We studied the correlation between the effects of protein impurities on the growth of elementary steps and their adsorption sites on a crystal surface, using three kinds of proteins: fluorescent-labeled lysozyme (F-lysozyme), covalently bonded dimers of lysozyme (dimer), and a 18 kDa polypeptide (18 kDa). These three protein impurities suppressed the advancement of the steps. However, they exhibited different supersaturation dependencies of the suppression of the step velocities. To clarify the cause of this difference, we observed in situ the adsorption sites of individual molecules of F-lysozyme and fluorescent-labeled dimer (F-dimer) on the crystal surface by single-molecule visualization. We found that F-lysozyme adsorbed preferentially on steps (i.e., kinks), whereas F-dimer adsorbed randomly on terraces. Taking into account the different adsorption sites of F-lysozyme and F-dimer, we could successfully explain the different effects of the impurities on the step velocities. These observations strongly suggest that 18 kDa also adsorbs randomly on terraces. Seikagaku lysozyme exhibited a complex effect that could not alone be explained by the two major impurities (dimer and 18 kDa) present in Seikagaku lysozyme, indicating that trace amounts of other impurities significantly affect the step advancement.

Molecular Modeling and Affinity Determination of scFv Antibody: Proper Linker Peptide Enhances Its Activity

One of existing strategies to engineer active antibody is to link VH and VL domains via a linker peptide. How the composition, length, and conformation of the linker affect antibody activity, however, remains poorly understood. In this study, a dual approach that coordinates molecule modeling, biological measurements, and affinity evaluation was developed to quantify the binding activity of a novel stable miniaturized anti-CD20 antibody or singlechain fragment variable (scFv) with a linker peptide. Upon computer-guided homology modeling, distance geometry analysis, and molecular superimposition and optimization, three new linker peptides PT1, PT2, and PT3 with respective 7, 10, and 15 residues were proposed and three engineered antibodies were then constructed by linking the cloned VH and VL domains and fusing to a derivative of human IgG1. The binding stability and activity of scFv-Fc chimera to CD20 antigen was quantified using a micropipette adhesion frequency assay and a Scatchard analysis. Our data indicated that the binding affinity was similar for the chimera with PT2 or PT3 and ~24-fold higher than that for the chimera with PT1, supporting theoretical predictions in molecular modeling. These results further the understanding in the impact of linker peptide on antibody structure and activity.

WEFTA interlaboratory comparison on nitrogen determination by Kjeldahl digestion in fishery products and standard substances

14 Laboratorien aus 12 europäischen Ländern nahmen an einer Laborvergleichsuntersuchung zur Stickstoffbestimmung in Fischerzeugnissen und Standardsubstanzen nach Kjeldahl teil. 13 Laboratorien erzielten dabei Ergebnisse, die alle in engen Grenzen um die gefundenen Mittelwerte streuten. Der von den einzelnen Teilnehmern erzielte Variationskoeffizient war mit etwa 0,5 % gering. Auch die Standardsubstanzen mit bekanntem Stickstoffgehalt konnten überwiegend mit hinreichender Genauigkeit (98 % der vom Hertsteller angegebenen Gehalte) analysiert werden. Der ideale Kjeldahlaufschluß ist durch kurze Aufschlußzeiten (ca. 120 min), eine Aufschlußtemperatur bei 430° C und durch die Wahl des für die jeweilige Matrix geeigneten Katalysators gekennzeichnet.

2,4-dimethylene-1,3-cyclobutanediyl and 2,4-dimethylenebicyclobutane. Synthesis, spectroscopy, and reactivity of a triplet biradical and its covalent isomer

The preparation and direct observation of triplet 2,4-dimethylene-1,3- cyclobutanediyl (1), the non-Kekule isomer of benzene, is described. The biradical was generated by photolysis of 5,6-dimethylene-2,3- diazabicyclo[2.1.1]hex-2-ene (2) (which was synthesized in several steps from benzvalene) under cryogenic, matrix-isolation conditions. Biradical 1 was characterized by EPR spectroscopy (‌‌‌‌‌│D/hc│ =0.0204 cm^(-1), │E/hc│ =0.0028 cm^(-1)) and found to have a triplet ground state. The Δm_s= 2 transition displays hyperfine splitting attributed to a 7.3-G coupling to the ring methine and a 5.9-G coupling to the exocyclic methylene protons. Several experiments, including application of the magnetophotoselection (mps) technique in the generation of biradical 1, have allowed a determination of the zero-field triplet sublevels as x = -0.0040, y = +0.0136, and z = -0.0096 cm^(-1), where x and y are respectively the long and short in-plane axes and z the out-of-plane axis of 1.

Triplet 1 is yellow-orange and displays highly structured absorption (λ_(max)= 506 nm) and fluorescence (λ_(max) = 510 nm) spectra, with vibronic spacings of 1520 and 620 cm^(-1) for absorption and 1570 and 620 cm^(-1) for emission. The spectra were unequivocally assigned to triplet 1 by the use of a novel technique that takes advantage of the biradical's photolability. The absorption є = 7200 M^(-1) cm^(-1) and f = 0.022, establishing that the transition is spin-allowed. Further use of the mps technique has demonstrated that the transition is x-polarized, and the excited state 1s therefore of B_(1g) symmetry, in accord with theoretical predictions.

Thermolysis or direct photolysis of diazene 2 in fluid solution produces 2,4- dimethylenebicyclo[l.l.0]butane (3), whose ^(l)H NMR spectrum (-80°C, CD_(2)Cl_(2)) consists of singlets at δ 4.22 and 3.18 in a 2:1 ratio. Compound 3 is thermally unstable and dimerizes with second-order kinetics between -80 and -25°C (∆H^(‡) = 6.8 kcal mol^(-1), (∆s^(‡) = -28 eu) by a mechanism involving direct combination of two molecules of 3 in the rate-determining step. This singlet-manifold reaction ultimately produces a mixture of two dimers, 3,8,9- trimethylenetricyclo[5.1.1.0^(2,5)]non-4-ene (75) and trans-3,10-dimethylenetricyclo[6.2.0.0^(2,5)]deca-4,8-diene (76t), with the former predominating. In contrast, triplet-sensitized photolysis of 2, which leads to triplet 1, provides, in addition to 75 and 76t, a substantial amount of trans-5,10- dimethylenetricyclo[6.2.0.0^(3,6)]deca-3,8-diene (77t) and small amounts of two unidentified dimers.

In addition, triplet biradical 1 ring-closes to 3 in rigid media both thermally (77-140 K) and photochemically. In solution 3 forms triplet 1 upon energy transfer from sensitizers having relatively low triplet energies. The implications of the thermal chemistry for the energy surfaces of the system are discussed.

Determination of source finiteness and depth of large earthquakes

In this thesis, a method to retrieve the source finiteness, depth of faulting, and the mechanisms of large earthquakes from long-period surface waves is developed and applied to several recent large events.

In Chapter 1, source finiteness parameters of eleven large earthquakes were determined from long-period Rayleigh waves recorded at IDA and GDSN stations. The basic data set is the seismic spectra of periods from 150 to 300 sec. Two simple models of source finiteness are studied. The first model is a point source with finite duration. In the determination of the duration or source-process times, we used Furumoto's phase method and a linear inversion method, in which we simultaneously inverted the spectra and determined the source-process time that minimizes the error in the inversion. These two methods yielded consistent results. The second model is the finite fault model. Source finiteness of large shallow earthquakes with rupture on a fault plane with a large aspect ratio was modeled with the source-finiteness function introduced by Ben-Menahem. The spectra were inverted to find the extent and direction of the rupture of the earthquake that minimize the error in the inversion. This method is applied to the 1977 Sumbawa, Indonesia, 1979 Colombia-Ecuador, 1983 Akita-Oki, Japan, 1985 Valparaiso, Chile, and 1985 Michoacan, Mexico earthquakes. The method yielded results consistent with the rupture extent inferred from the aftershock area of these earthquakes.

In Chapter 2, the depths and source mechanisms of nine large shallow earthquakes were determined. We inverted the data set of complex source spectra for a moment tensor (linear) or a double couple (nonlinear). By solving a least-squares problem, we obtained the centroid depth or the extent of the distributed source for each earthquake. The depths and source mechanisms of large shallow earthquakes determined from long-period Rayleigh waves depend on the models of source finiteness, wave propagation, and the excitation. We tested various models of the source finiteness, Q, the group velocity, and the excitation in the determination of earthquake depths.

The depth estimates obtained using the Q model of Dziewonski and Steim (1982) and the excitation functions computed for the average ocean model of Regan and Anderson (1984) are considered most reasonable. Dziewonski and Steim's Q model represents a good global average of Q determined over a period range of the Rayleigh waves used in this study. Since most of the earthquakes studied here occurred in subduction zones Regan and Anderson's average ocean model is considered most appropriate.

Our depth estimates are in general consistent with the Harvard CMT solutions. The centroid depths and their 90 % confidence intervals (numbers in the parentheses) determined by the Student's t test are: Colombia-Ecuador earthquake (12 December 1979), d = 11 km, (9, 24) km; Santa Cruz Is. earthquake (17 July 1980), d = 36 km, (18, 46) km; Samoa earthquake (1 September 1981), d = 15 km, (9, 26) km; Playa Azul, Mexico earthquake (25 October 1981), d = 41 km, (28, 49) km; El Salvador earthquake (19 June 1982), d = 49 km, (41, 55) km; New Ireland earthquake (18 March 1983), d = 75 km, (72, 79) km; Chagos Bank earthquake (30 November 1983), d = 31 km, (16, 41) km; Valparaiso, Chile earthquake (3 March 1985), d = 44 km, (15, 54) km; Michoacan, Mexico earthquake (19 September 1985), d = 24 km, (12, 34) km.

In Chapter 3, the vertical extent of faulting of the 1983 Akita-Oki, and 1977 Sumbawa, Indonesia earthquakes are determined from fundamental and overtone Rayleigh waves. Using fundamental Rayleigh waves, the depths are determined from the moment tensor inversion and fault inversion. The observed overtone Rayleigh waves are compared to the synthetic overtone seismograms to estimate the depth of faulting of these earthquakes. The depths obtained from overtone Rayleigh waves are consistent with the depths determined from fundamental Rayleigh waves for the two earthquakes. Appendix B gives the observed seismograms of fundamental and overtone Rayleigh waves for eleven large earthquakes.

Photographic investigations in molecular spectroscopy

The determination of the energy levels and the probabilities of transition between them, by the formal analysis of observed electronic, vibrational, and rotational band structures, forms the direct goal of all investigations of molecular spectra, but the significance of such data lies in the possibility of relating them theoretically to more concrete properties of molecules and the radiation field. From the well developed electronic spectra of diatomic molecules, it has been possible, with the aid of the non-relativistic quantum mechanics, to obtain accurate moments of inertia, molecular potential functions, electronic structures, and detailed information concerning the coupling of spin and orbital angular monenta with the angular momentum of nuclear rotation. The silicon fluori1e molecule has been investigated in this laboratory, and is found to emit bands whose vibrational and rotational structures can be analyzed in this detailed fashion.

Like silicon fluoride, however, the great majority of diatomic molecules are formed only under the unusual conditions of electrical discharge, or in high temperature furnaces, so that although their spectra are of great theoretical interest, the chemist is eager to proceed to a study of polyatomic molecules, in the hope that their more practically interesting structures might also be determined with the accuracy and assurance which characterize the spectroscopic determinations of the constants of diatomic molecules. Some progress has been made in the determination of molecule potential functions from the vibrational term values deduced from Raman and infrared spectra, but in no case can the calculations be carried out with great generality, since the number of known term values is always small compared with the total number of potential constants in even so restricted a potential function as the simple quadratic type. For the determination of nuclear configurations and bond distances, however, a knowledge of the rotational terms is required. The spectra of about twelve of the simpler polyatomic molecules have been subjected to rotational analyses, and a number of bond distances are known with considerable accuracy, yet the number of molecules whose rotational fine structure has been resolved even with the most powerful instruments is small. Consequently, it was felt desirable to investigate the spectra of a number of other promising polyatomic molecules, with the purpose of carrying out complete rotational analyses of all resolvable bands, and ascertaining the value of the unresolved band envelopes in determining the structures of such molecules, in the cases in which resolution is no longer possible. Although many of the compounds investigated absorbed too feebly to be photographed under high dispersion with the present infrared sensitizations, the location and relative intensities of their bands, determined by low dispersion measurements, will be reported in the hope that these compounds may be reinvestigated in the future with improved techniques.

On the determination of the properties of a medium from its reflection coefficient

This thesis demonstrates how the parameters of a slightly non-homogeneous medium can be derived approximately from the reflection coefficient.

Two types of media are investigated. The first is described by the one-dimensional wave equation, the second by the more complex Timoshenko beam equation. In both cases, the media are assumed to be infinite in extent, with the media parameters becoming homogeneous as the space variable approaches positive or negative infinity.

Much effort is placed in deriving properties of the reflection coefficient for both cases. The wave equation is considered primarily to introduce the techniques used to investigate the more complex Timoshenko equation. In both cases, an approximation is derived for one of the medium parameters involving the reflection coefficient.

Direct measurement of entrainment in plasma jets

The entrainment rate of ambient gas into a turbulent argon plasma jet generated by plasma torch is directly measured using a “porous-wall chamber” technique. It is shown that with the increase of the mass flow rates of argon at the jet inlet, the mass flow rate of entrained gas increases. The normalized mass flow rate decreases with the increasing inlet mass flow rates of plasma torch. The entrained gas mass flow rate increases with increasing chamber length, but less depends on the arc current of the plasma torch at higher flow rates. The effects of different ways of inflowing gas into plasma torch on entrainment characteristics of plasma jet are also examined in this paper.

Fluctuations in a direct current argon plasma jet at reduced pressure

Dynamic measurements of the ion saturation current in the plasma plume by a double-electrostatic probe system were carried out. Regular signals obtained by the electros- tatic probe show good agreement with the stable plasma flow state. Dependence of the flow steadiness on the plasma generation parameters was discussed. As a fast response method, the double-electrostatic probe system is feasible to characterize the fluctuations in the plasma jet.

Measurement of the direct CP asymmetry in b-->s+gamma via sum of exclusive B Meson decays using the BABAR detector

We perform a measurement of direct CP violation in b to s+gamma Acp, and the measurement of a difference between Acp for neutral B and charged B mesons, Delta A_{X_s\gamma}, using 429 inverse femtobarn of data recorded at the Upsilon(4S) resonance with the BABAR detector. B mesons are reconstructed from 16 exclusive final states. Particle identification is done using an algorithm based on Error Correcting Output Code with an exhaustive matrix. Background rejection and best candidate selection are done using two decision tree-based classifiers. We found $\acp = 1.73%+-1.93%+-1.02% and Delta A_X_sgamma = 4.97%+-3.90%+-1.45% where the uncertainties are statistical and systematic respectively. Based on the measured value of Delta A_X_sgamma, we determine a 90% confidence interval for Im C_8g/C_7gamma, where C_7gamma and C_8g are Wilson coefficients for New Physics amplitudes, at -1.64 < Im C_8g/C_7gamma < 6.52.