32 resultados para Data Structure Operations


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To obtain accurate information from a structural tool it is necessary to have an understanding of the physical principles which govern the interaction between the probe and the sample under investigation. In this thesis a detailed study of the physical basis for Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy is presented. A single scattering formalism of EXAFS is introduced which allows a rigorous treatment of the central atom potential. A final state interaction formalism of EXAFS is also discussed. Multiple scattering processes are shown to be significant for systems of certain geometries. The standard single scattering EXAFS analysis produces erroneous results if the data contain a large multiple scattering contribution. The effect of thermal vibrations on such multiple scattering paths is also discussed. From symmetry considerations it is shown that only certain normal modes contribute to the Debye-Waller factor for a particular scattering path. Furthermore, changes in the scattering angles induced by thermal vibrations produces additional EXAFS components called modification factors. These factors are shown to be small for most systems.

A study of the physical basis for the determination of structural information from EXAFS data is also presented. An objective method of determining the background absorption and the threshold energy is discussed and involves Gaussian functions. In addition, a scheme to determine the nature of the scattering atom in EXAFS experiments is introduced. This scheme is based on the fact that the phase intercept is a measure of the type of scattering atom. A method to determine bond distances is also discussed and does not require the use of model compounds or calculated phase shifts. The physical basis for this method is the absence of a linear term in the scattering phases. Therefore, it is possible to separate these phases from the linear term containing the distance information in the total phase.

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The structure and the electrical and magnetic properties of an amorphous alloy containing approximately 80 at .% iron, 13 at.% phos phorus and 7 at.% carbon (Fe_(80)Fe_(13)C_7) obtained by rapid quenching from the liquid state have been studied. Transmission electron diffraction data confirm the amorphous nature of this alloy. An analysis of the radial distribution function obtained from X-ray diffraction data indicates that the number of nearest neighbors is approximately seven, at a distance of 2.6A. The structure of the alloy can be related to that of silicate glasses and is based on a random arrangement of trigonal prisms of Fe_2P and Fe_3C types in which the iron atoms have an average ligancy of seven. Electrical resistance measurements show that the alloys are metallic. A minimum in the electrical resistivity vs. temperature curve is observed between 10° K to 50° K depending on the specimen, and the temperature at which the minimum occurs is related to the degree of local ordering. The Fe-P-C amorphous alloys are ferromagnetic. The Curie temperature measured by the induction method and by Mossbauer spectroscopy is 315° C. The field dependence of the magneto-resistance at temperatures from liquid helium to room temperature is similar to that found in crystalline iron. The ordinary Hall coefficient is approximately 10^(-11) volt-cm/amp-G. The spontaneous Hall coefficient is about 0.6 x 10^(-9) volt-cm/amp-G and is practically independent of temperature from liquid helium temperature up to 300° c.

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In the cell, the binding of proteins to specific sequences of double helical DNA is essential for controlling the processes of protein synthesis (at the level of DNA transcription) and cell proliferation (at the level of DNA replication). In the laboratory, the sequence-specific DNA binding/cleaving properties of restriction endonuclease enzymes (secreted by microorganisms to protect them from foreign DNA molecules) have helped to fuel a revolution in molecular biology. The strength and specificity of a protein:DNA interaction depend upon structural features inherent to the protein and DNA sequences, but it is now appreciated that these features (and therefore protein:DNA complexation) may be altered (regulated) by other protein:DNA complexes, or by environmental factors such as temperature or the presence of specific organic molecules or inorganic ions. It is also now appreciated that molecules much smaller than proteins (including antibiotics of molecular weight less than 2000 and oligonucleotides) can bind to double-helical DNA in sequence-specific fashion. Elucidation of structural motifs and microscopic interactions responsible for the specific molecular recognition of DNA leads to greater understanding of natural processes and provides a basis for the design of novel sequence-specific DNA binding molecules. This thesis describes the synthesis and DNA binding/cleaving characteristics of molecules designed to probe structural, stereochemical, and environmental factors that regulate sequence-specific DNA recognition.

Chapter One introduces the DNA minor groove binding antibiotics Netropsin and Distamycin A, which are di- and tri(N-methylpyrrolecarboxamide) peptides, respectively. The method of DNA affinity cleaving, which has been employed to determine DNA binding properties of designed synthetic molecules is described. The design and synthesis of a series of Netropsin dimers linked in tail-to-tail fashion (by oxalic, malonic, succinic, or fumaric acid), or in head-to-tail fashion (by glycine, β-alanine, and γ-aminobutanoic acid (Gaba)) are presented. These Bis(Netropsin)s were appended with the iron-chelating functionality EDTA in order to make use of the technique of DNA affinity cleaving. Bis(Netropsin)-EDTA compounds are analogs of penta(N-methylpyrrolecarboxamide)-EDTA (P5E), which may be considered a head-to-tail Netropsin dimer linked by Nmethylpyrrolecarboxamide. Low- and high-resolution analysis of pBR322 DNA affinity cleaving by the iron complexes of these molecules indicated that small changes in the length and nature of the linker had significant effects on DNA binding/cleaving efficiency (a measure of DNA binding affinity). DNA binding/cleaving efficiency was found to decrease with changes in the linker in the order β-alanine > succinamide > fumaramide > N-methylpyrrolecarboxamide > malonamide >glycine, γ-aminobutanamide > oxalamide. In general, the Bis(Netropsin)-EDTA:Fe compounds retained the specificity for seven contiguous A:T base pairs characteristic of P5E:Fe binding. However, Bis(Netropsin)Oxalamide- EDTA:Fe exhibited decreased specificity for A:T base pairs, and Bis(Netropsin)-Gaba-EDT A:Fe exhibited some DNA binding sites of less than seven base pairs. Bis(Netropsin)s linked with diacids have C2-symmmetrical DNA binding subunits and exhibited little DNA binding orientation preference. Bis(Netropsin)s linked with amino acids lack C2-symmetrical DNA binding subunits and exhibited higher orientation preferences. A model for the high DNA binding orientation preferences observed with head-to-tail DNA minor groove binding molecules is presented.

Chapter Two describes the design, synthesis, and DNA binding properties of a series of chiral molecules: Bis(Netropsin)-EDTA compounds with linkers derived from (R,R)-, (S,S)-, and (RS,SR)-tartaric acids, (R,R)-, (S,S)-, and (RS,SR)-tartaric acid acetonides, (R)- and (S)-malic acids, N ,N-dimethylaminoaspartic acid, and (R)- and (S)-alanine, as well as three constitutional isomers in which an N-methylpyrrolecarboxamide (P1) subunit and a tri(N-methylpyrrolecarboxamide)-EDTA (P3-EDTA) subunit were linked by succinic acid, (R ,R)-, and (S ,S)-tartaric acids. DNA binding/cleaving efficiencies among this series of molecules and the Bis(Netropsin)s described in Chapter One were found to decrease with changes in the linker in the order β-alanine > succinamide > P1-succinamide-P3 > fumaramide > (S)-malicamide > N-methylpyrrolecarboxamide > (R)-malicamide > malonamide > N ,N-dimethylaminoaspanamide > glycine = Gaba = (S,S)-tartaramide = P1-(S,S)-tanaramide-P3 > oxalamide > (RS,SR)-tartaramide = P1- (R,R)-tanaramide-P3 > (R,R)-tartaramide (no sequence-specific DNA binding was detected for Bis(Netropsin)s linked by (R)- or (S)-alanine or by tartaric acid acetonides). The chiral molecules retained DNA binding specificity for seven contiguous A:T base pairs. From the DNA affinity cleaving data it could be determined that: 1) Addition of one or two substituents to the linker of Bis(Netropsin)-Succinamide resulted in stepwise decreases in DNA binding affinity; 2) molecules with single hydroxyl substituents bound DNA more strongly than molecules with single dimethylamino substituents; 3) hydroxyl-substituted molecules of (S) configuration bound more strongly to DNA than molecules of (R) configuration. This stereochemical regulation of DNA binding is proposed to arise from the inherent right-handed twist of (S)-enantiomeric Bis(Netropsin)s versus the inherent lefthanded twist of (R)-enantiomeric Bis(Netropsin)s, which makes the (S)-enantiomers more complementary to the right-handed twist of B form DNA.

Chapter Three describes the design and synthesis of molecules for the study of metalloregulated DNA binding phenomena. Among a series of Bis(Netropsin)-EDTA compounds linked by homologous tethers bearing four, five, or six oxygen atoms, the Bis(Netropsin) linked by a pentaether tether exhibited strongly enhanced DNA binding/cleaving in the presence of strontium or barium cations. The observed metallospecificity was consistent with the known affinities of metal cations for the cyclic hexaether 18-crown-6 in water. High-resolution DNA affinity cleaving analysis indicated that DNA binding by this molecule in the presence of strontium or barium was not only stronger but of different sequence-specificity than the (weak) binding observed in the absence of metal cations. The metalloregulated binding sites were consistent with A:T binding by the Netropsin subunits and G:C binding by a strontium or barium:pentaether complex. A model for the observed positive metalloregulation and novel sequence-specificity is presented. The effects of 44 different cations on DNA affinity cleaving by P5E:Fe were examined. A series of Bis(Netropsin)-EDTA compounds linked by tethers bearing two, three, four, or five amino groups was also synthesized. These molecules exhibited strong and specific binding to A:T rich regions of DNA. It was found that the iron complexes of these molecules bound and cleaved DNA most efficiently at pH 6.0-6.5, while P5E:Fe bound and cleaved most efficiently at pH 7.5-8.0. Incubating the Bis(Netropsin) Polyamine-EDTA:Fe molecules with K2PdCl4 abolished their DNA binding/cleaving activity. It is proposed that the observed negative metalloregulation arises from kinetically inert Bis(Netropsin) Polyamine:Pd(II) complexes or aggregates, which are sterically unsuitable for DNA complexation. Finally, attempts to produce a synthetic metalloregulated DNA binding protein are described. For this study, five derivatives of a synthetic 52 amino acid residue DNA binding/cleaving protein were produced. The synthetic mutant proteins carried a novel pentaether ionophoric amino acid residue at different positions within the primary sequence. The proteins did not exhibit significant DNA binding/cleaving activity, but they served to illustrate the potential for introducing novel amino acid residues within DNA binding protein sequences, and for the development of the tricyclohexyl ester of EDTA as a superior reagent for the introduction of EDT A into synthetic proteins.

Chapter Four describes the discovery and characterization of a new DNA binding/cleaving agent, [SalenMn(III)]OAc. This metal complex produces single- and double-strand cleavage of DNA, with specificity for A:T rich regions, in the presence of oxygen atom donors such as iodosyl benzene, hydrogen peroxide, or peracids. Maximal cleavage by [SalenMn(III)]OAc was produced at pH 6-7. A comparison of DNA singleand double-strand cleavage by [SalenMn(III)]+ and other small molecules (Methidiumpropyl-EDTA:Fe, Distamycin-EDTA:Fe, Neocarzinostatin, Bleomycin:Fe) is presented. It was found that DNA cleavage by [SalenMn(III)]+ did not require the presence of dioxygen, and that base treatment of DNA subsequent to cleavage by [SalenMn(III)]+ afforded greater cleavage and alterations in the cleavage patterns. Analysis of DNA products formed upon DNA cleavage by [SalenMn(III)] indicated that cleavage was due to oxidation of the sugar-phosphate backbone of DNA. Several mechanisms consistent with the observed products and reaction requirements are discussed.

Chapter Five describes progress on some additional studies. In one study, the DNA binding/cleaving specificities of Distamycin-EDTA derivatives bearing pyrrole N-isopropyl substituents were found to be the same as those of derivatives bearing pyrrole N-methyl substituents. In a second study, the design of and synthetic progress towards a series of nucleopeptide activators of transcription are presented. Five synthetic plasmids designed to test for activation of in vitro run-off transcription by DNA triple helix-forming oligonucleotides or nucleopeptides are described.

Chapter Six contains the experimental documentation of the thesis work.

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Part I

Regression analyses are performed on in vivo hemodialysis data for the transfer of creatinine, urea, uric acid and inorganic phosphate to determine the effects of variations in certain parameters on the efficiency of dialysis with a Kiil dialyzer. In calculating the mass transfer rates across the membrane, the effects of cell-plasma mass transfer kinetics are considered. The concept of the effective permeability coefficient for the red cell membrane is introduced to account for these effects. A discussion of the consequences of neglecting cell-plasma kinetics, as has been done to date in the literature, is presented.

A physical model for the Kiil dialyzer is presented in order to calculate the available membrane area for mass transfer, the linear blood and dialysate velocities, and other variables. The equations used to determine the independent variables of the regression analyses are presented. The potential dependent variables in the analyses are discussed.

Regression analyses were carried out considering overall mass-transfer coefficients, dialysances, relative dialysances, and relative permeabilities for each substance as the dependent variables. The independent variables were linear blood velocity, linear dialysate velocity, the pressure difference across the membrane, the elapsed time of dialysis, the blood hematocrit, and the arterial plasma concentrations of each substance transferred. The resulting correlations are tabulated, presented graphically, and discussed. The implications of these correlations are discussed from the viewpoint of a research investigator and from the viewpoint of patient treatment.

Recommendations for further experimental work are presented.

Part II

The interfacial structure of concurrent air-water flow in a two-inch diameter horizontal tube in the wavy flow regime has been measured using resistance wave gages. The median water depth, r.m.s. wave height, wave frequency, extrema frequency, and wave velocity have been measured as functions of air and water flow rates. Reynolds numbers, Froude numbers, Weber numbers, and bulk velocities for each phase may be calculated from these measurements. No theory for wave formation and propagation available in the literature was sufficient to describe these results.

The water surface level distribution generally is not adequately represented as a stationary Gaussian process. Five types of deviation from the Gaussian process function were noted in this work. The presence of the tube walls and the relatively large interfacial shear stresses precludes the use of simple statistical analyses to describe the interfacial structure. A detailed study of the behavior of individual fluid elements near the interface may be necessary to describe adequately wavy two-phase flow in systems similar to the one used in this work.

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Part 1 of this thesis is about the 24 November, 1987, Superstition Hills earthquakes. The Superstition Hills earthquakes occurred in the western Imperial Valley in southern California. The earthquakes took place on a conjugate fault system consisting of the northwest-striking right-lateral Superstition Hills fault and a previously unknown Elmore Ranch fault, a northeast-striking left-lateral structure defined by surface rupture and a lineation of hypocenters. The earthquake sequence consisted of foreshocks, the M_s 6.2 first main shock, and aftershocks on the Elmore Ranch fault followed by the M_s 6.6 second main shock and aftershocks on the Superstition Hills fault. There was dramatic surface rupture along the Superstition Hills fault in three segments: the northern segment, the southern segment, and the Wienert fault.

In Chapter 2, M_L≥4.0 earthquakes from 1945 to 1971 that have Caltech catalog locations near the 1987 sequence are relocated. It is found that none of the relocated earthquakes occur on the southern segment of the Superstition Hills fault and many occur at the intersection of the Superstition Hills and Elmore Ranch faults. Also, some other northeast-striking faults may have been active during that time.

Chapter 3 discusses the Superstition Hills earthquake sequence using data from the Caltech-U.S.G.S. southern California seismic array. The earthquakes are relocated and their distribution correlated to the type and arrangement of the basement rocks. The larger earthquakes occur only where continental crystalline basement rocks are present. The northern segment of the Superstition Hills fault has more aftershocks than the southern segment.

An inversion of long period teleseismic data of the second mainshock of the 1987 sequence, along the Superstition Hills fault, is done in Chapter 4. Most of the long period seismic energy seen teleseismically is radiated from the southern segment of the Superstition Hills fault. The fault dip is near vertical along the northern segment of the fault and steeply southwest dipping along the southern segment of the fault.

Chapter 5 is a field study of slip and afterslip measurements made along the Superstition Hills fault following the second mainshock. Slip and afterslip measurements were started only two hours after the earthquake. In some locations, afterslip more than doubled the coseismic slip. The northern and southern segments of the Superstition Hills fault differ in the proportion of coseismic and postseismic slip to the total slip.

The northern segment of the Superstition Hills fault had more aftershocks, more historic earthquakes, released less teleseismic energy, and had a smaller proportion of afterslip to total slip than the southern segment. The boundary between the two segments lies at a step in the basement that separates a deeper metasedimentary basement to the south from a shallower crystalline basement to the north.

Part 2 of the thesis deals with the three-dimensional velocity structure of southern California. In Chapter 7, an a priori three-dimensional crustal velocity model is constructed by partitioning southern California into geologic provinces, with each province having a consistent one-dimensional velocity structure. The one-dimensional velocity structures of each region were then assembled into a three-dimensional model. The three-dimension model was calibrated by forward modeling of explosion travel times.

In Chapter 8, the three-dimensional velocity model is used to locate earthquakes. For about 1000 earthquakes relocated in the Los Angeles basin, the three-dimensional model has a variance of the the travel time residuals 47 per cent less than the catalog locations found using a standard one-dimensional velocity model. Other than the 1987 Whittier earthquake sequence, little correspondence is seen between these earthquake locations and elements of a recent structural cross section of the Los Angeles basin. The Whittier sequence involved rupture of a north dipping thrust fault bounded on at least one side by a strike-slip fault. The 1988 Pasadena earthquake was deep left-lateral event on the Raymond fault. The 1989 Montebello earthquake was a thrust event on a structure similar to that on which the Whittier earthquake occurred. The 1989 Malibu earthquake was a thrust or oblique slip event adjacent to the 1979 Malibu earthquake.

At least two of the largest recent thrust earthquakes (San Fernando and Whittier) in the Los Angeles basin have had the extent of their thrust plane ruptures limited by strike-slip faults. This suggests that the buried thrust faults underlying the Los Angeles basin are segmented by strike-slip faults.

Earthquake and explosion travel times are inverted for the three-dimensional velocity structure of southern California in Chapter 9. The inversion reduced the variance of the travel time residuals by 47 per cent compared to the starting model, a reparameterized version of the forward model of Chapter 7. The Los Angeles basin is well resolved, with seismically slow sediments atop a crust of granitic velocities. Moho depth is between 26 and 32 km.

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An automatic experimental apparatus for perturbed angular correlation measurements, capable of incorporating Ge(Li) detectors as well as scintillation counters, has been constructed.

The gamma-gamma perturbed angular correlation technique has been used to measure magnetic dipole moments of several nuclear excited states in the osmium transition region. In addition, the hyperfine magnetic fields, experienced by nuclei of 'impurity' atoms embedded in ferromagnetic host lattices, have been determined for several '4d' and '5d' impurity atoms.

The following magnetic dipole moments were obtained in the osmium transition region μ2+(190Os) = 0.54 ± 0.06 nm μ4+(190Os) = 0.88 ± 0.48 nm μ2+(192Os) = 0.56 ± 0.08 nm μ2+(192Pt) = 0.56 ± 0.06 nm μ2+’(192Pt) = 0.62 ± 0.14 nm.

These results are discussed in terms of three collective nuclear models; the cranking model, the rotation-vibration model and the pairing-plus-quadrupole model. The measurements are found to be in satisfactory agreement with collective descriptions of low lying nuclear states in this region.

The following hyperfine magnetic fields of 'impurities' in ferromagnetic hosts were determined; Hint(Cd Ni) = - (64.0 ± 0.8)kG Hint(Hg Fe) = - (440 ± 105)kG Hint(Hg Co) = - (370 ± 78)kG Hint(Hg Ni) = - (86 ± 22)kG Hint(Tl Fe) = - (185 ± 70)kG Hint(Tl Co) = - (90 ± 35)kG Hint(Ra Fe) = - (105 ± 20)kG Hint(Ra Co) = - (80 ± 16)kG Hint(Ra Ni) = - (30 ± 10)kG, where in Hint(AB); A is the impurity atom embedded in the host lattice B. No quantitative theory is available for comparison. However, these results are found to obey the general systematics displayed by these fields. Several mechanisms which may be responsible for the appearance of these fields are mentioned.

Finally, a theoretical expression for time-differential perturbed angular correlation measurement, which duplicates experimental conditions is developed and its importance in data analysis is discussed.

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Studies on the dissociation of histones from chromatin by increasing concentrations of sodium deoxycholate (DOC) have shown that histrone II is removed at lowest concentrations of DOC, while slightly higher concentrations remove histones III and IV. Still higher concentrations remove histone I.

The complete separation of chromatin and 14C-DOC by sucrose sedimentation indicated that the binding of DOC to chromatin is readily and completely reversible.

The dissociation of histones from chromatin by increasing concentrations of related cholanic acids and some of their conjugated derivatives were studied. The results suggested that the driving force for the interaction between the cholanic acid anion and histones is the lowering of the activity coefficient of the cholanic acid anion which occurs when it is partially removed from solution by interaction with hydrophobic regions of the positively charged histones.

The role of histones in the structure of chromatin has been studied by comparing the effects of selective removal of histones from chromatin by increasing concentrations of DOC with those caused by NaCl (removes histone I at lowest concentrations, while higher concentrations remove histones II, III, and IV). Properties studied included thermal denaturation, sedimentation velocity, flow dichroism, relaxation times of molecules oriented in a flow field, and the irreversible disruption of a 130 S, cross-linked component of sheared chromatin. The data indicated that none of the structural or chemical parameters with which these properties are correlated show a dependence on the presence of one particular histone fraction.

The template activity (ability to prime a 0.2 M KC1 DNA-dependent RNA synthesis system catalyzed by E. coli RNA polymerase) increases from that of native chromatin (approximately 25 per cent of that pure DNA) to that of pure DNA in a fashion which shows a nearly linear relationship to the amount of histone coverage of the template. The precipitability of partially dehistonized chromatin samples in 0.15 M NaCl shows a large dependence on the presence of histone I.

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I. THE CRYSTAL STRUCTURE OF A NEW DIMER OF TRIPHENYLFLUOROCYCLOBUTADIENE

The crystal structure of thermal isomer of the “head-to-head” dimer of triphenylfluorocyclobutadiene was determined by the direct method. The Σ2 relationship involving the low angle reflections with the largest E’s were found and solved for the signs by the symbolic method of Zachariasen. The structure was seen in the electron density map and the E-map, and was refined antisotropically by the method of least squares. The residual R was 0.065.

The structure is a gem-difluorohexaphenyldihydropentalene. All of the phenyl groups are planar as it is the cyclopentadiene ring of the dihydropentalene skeleton. Overcrowding at the position of the flourines causes some deviations from the normal bond angles in the cyclopentene ring.

The list of observed and calculated structure factors on pages 32-34 will not be legible on the microfilm. Photographic copies may be obtained from the California Institute of Technology.

II. A LOW TEMPERATURE REFINEMENT OF THE CYANURIC TRIAZIDE STRUCTURE

The structure of cyanuric triazide was refined anisotropically by the method of least squares. Three-dimensional intensity data, which has been collected photographically with MoKα radiation at -110˚C, were used in the refinement. The residual R was reduced to 0.081.

The structure is completely planar, and there is no significant bond alternation in the cyanuric ring. The packing of the molecules causes the azide groups to deviate from linearity by 8 degrees.

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Several types of seismological data, including surface wave group and phase velocities, travel times from large explosions, and teleseismic travel time anomalies, have indicated that there are significant regional variations in the upper few hundred kilometers of the mantle beneath continental areas. Body wave travel times and amplitudes from large chemical and nuclear explosions are used in this study to delineate the details of these variations beneath North America.

As a preliminary step in this study, theoretical P wave travel times, apparent velocities, and amplitudes have been calculated for a number of proposed upper mantle models, those of Gutenberg, Jeffreys, Lehman, and Lukk and Nersesov. These quantities have been calculated for both P and S waves for model CIT11GB, which is derived from surface wave dispersion data. First arrival times for all the models except that of Lukk and Nersesov are in close agreement, but the travel time curves for later arrivals are both qualitatively and quantitatively very different. For model CIT11GB, there are two large, overlapping regions of triplication of the travel time curve, produced by regions of rapid velocity increase near depths of 400 and 600 km. Throughout the distance range from 10 to 40 degrees, the later arrivals produced by these discontinuities have larger amplitudes than the first arrivals. The amplitudes of body waves, in fact, are extremely sensitive to small variations in the velocity structure, and provide a powerful tool for studying structural details.

Most of eastern North America, including the Canadian Shield has a Pn velocity of about 8.1 km/sec, with a nearly abrupt increase in compressional velocity by ~ 0.3 km/sec near at a depth varying regionally between 60 and 90 km. Variations in the structure of this part of the mantle are significant even within the Canadian Shield. The low-velocity zone is a minor feature in eastern North America and is subject to pronounced regional variations. It is 30 to 50 km thick, and occurs somewhere in the depth range from 80 to 160 km. The velocity decrease is less than 0.2 km/sec.

Consideration of the absolute amplitudes indicates that the attenuation due to anelasticity is negligible for 2 hz waves in the upper 200 km along the southeastern and southwestern margins of the Canadian Shield. For compressional waves the average Q for this region is > 3000. The amplitudes also indicate that the velocity gradient is at least 2 x 10-3 both above and below the low-velocity zone, implying that the temperature gradient is < 4.8°C/km if the regions are chemically homogeneous.

In western North America, the low-velocity zone is a pronounced feature, extending to the base of the crust and having minimum velocities of 7.7 to 7.8 km/sec. Beneath the Colorado Plateau and Southern Rocky Mountains provinces, there is a rapid velocity increase of about 0.3 km/sec, similar to that observed in eastern North America, but near a depth of 100 km.

Complicated travel time curves observed on profiles with stations in both eastern and western North America can be explained in detail by a model taking into account the lateral variations in the structure of the low-velocity zone. These variations involve primarily the velocity within the zone and the depth to the top of the zone; the depth to the bottom is, for both regions, between 140 and 160 km.

The depth to the transition zone near 400 km also varies regionally, by about 30-40 km. These differences imply variations of 250 °C in the temperature or 6 % in the iron content of the mantle, if the phase transformation of olivine to the spinel structure is assumed responsible. The structural variations at this depth are not correlated with those at shallower depths, and follow no obvious simple pattern.

The computer programs used in this study are described in the Appendices. The program TTINV (Appendix IV) fits spherically symmetric earth models to observed travel time data. The method, described in Appendix III, resembles conventional least-square fitting, using partial derivatives of the travel time with respect to the model parameters to perturb an initial model. The usual ill-conditioned nature of least-squares techniques is avoided by a technique which minimizes both the travel time residuals and the model perturbations.

Spherically symmetric earth models, however, have been found inadequate to explain most of the observed travel times in this study. TVT4, a computer program that performs ray theory calculations for a laterally inhomogeneous earth model, is described in Appendix II. Appendix I gives a derivation of seismic ray theory for an arbitrarily inhomogeneous earth model.

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Part I

Potassium bis-(tricyanovinyl) amine, K+N[C(CN)=C(CN)2]2-, crystallizes in the monoclinic system with the space group Cc and lattice constants, a = 13.346 ± 0.003 Å, c = 8.992 ± 0.003 Å, B = 114.42 ± 0.02°, and Z = 4. Three dimensional intensity data were collected by layers perpendicular to b* and c* axes. The crystal structure was refined by the least squares method with anisotropic temperature factor to an R value of 0.064.

The average carbon-carbon and carbon-nitrogen bond distances in –C-CΞN are 1.441 ± 0.016 Å and 1.146 ± 0.014 Å respectively. The bis-(tricyanovinyl) amine anion is approximately planar. The coordination number of the potassium ion is eight with bond distances from 2.890 Å to 3.408 Å. The bond angle C-N-C of the amine nitrogen is 132.4 ± 1.9°. Among six cyano groups in the molecule, two of them are bent by what appear to be significant amounts (5.0° and 7.2°). The remaining four are linear within the experimental error. The bending can probably be explained by molecular packing forces in the crystals.

Part II

The nuclear magnetic resonance of 81Br and 127I in aqueous solutions were studied. The cation-halide ion interactions were studied by studying the effect of the Li+, Na+, K+, Mg++, Cs+ upon the line width of the halide ions. The solvent-halide ion interactions were studied by studying the effects of methanol, acetonitrile, and acetone upon the line width of 81Br and 127I in the aqueous solutions. It was found that the viscosity plays a very important role upon the halide ions line width. There is no specific cation-halide ion interaction for those ions such as Mg++, Di+, Na+, and K+, whereas the Cs+ - halide ion interaction is strong. The effect of organic solvents upon the halide ion line width in aqueous solutions is in the order acetone ˃ acetonitrile ˃ methanol. It is suggested that halide ions do form some stable complex with the solvent molecules and the reason Cs+ can replace one of the ligands in the solvent-halide ion complex.

Part III

An unusually large isotope effect on the bridge hydrogen chemical shift of the enol form of pentanedione-2, 4(acetylacetone) and 3-methylpentanedione-2, 4 has been observed. An attempt has been made to interpret this effect. It is suggested from the deuterium isotope effect studies, temperature dependence of the bridge hydrogen chemical shift studies, IR studies in the OH, OD, and C=O stretch regions, and the HMO calculations, that there may probably be two structures for the enol form of acetylacetone. The difference between these two structures arises mainly from the electronic structure of the π-system. The relative population of these two structures at various temperatures for normal acetylacetone and at room temperature for the deuterated acetylacetone were calculated.

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I. The 3.7 Å Crystal Structure of Horse Heart Ferricytochrome C.

The crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 Å using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.

Although it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 Å electron density map. Among these was the fact that cytochrome c contains little or no α-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.

The heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.

The high resolution analysis of cytochrome c is now in progress and should be completed within the next year.

II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.

The Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.

The tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.

Pages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.

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The induced magnetic uniaxial anisotropy of Ni-Fe alloy films has been shown to be related to the crystal structure of the film. By use of electron diffraction, the crystal structure or vacuum-deposited films was determined over the composition range 5% to 85% Ni, with substrate temperature during deposition at various temperatures in the range 25° to 500° C. The phase diagram determined in this way has boundaries which are in fair agreement with the equilibrium boundaries for bulk material above 400°C. The (α+ ɤ) mixture phase disappears below 100°C.

The measurement of uniaxial anisotropy field for 25% Ni-Fe alloy films deposited at temperatures in the range -80°C to 375°C has been carried out. Comparison of the crystal structure phase diagram with the present data and those published by Wilts indicates that the anisotropy is strongly sensitive to crystal structure. Others have proposed pair ordering as an important source of anisotropy because of an apparent peak in the anisotropy energy at about 50% Ni composition. The present work shows no such peak, and leads to the conclusion that pair ordering cannot be a dominant contributor.

Width of the 180° domain wall in 76% Ni-Fe alloy films as a function of film thickness up to 1800 Å was measured using the defocused mode of Lorentz microscopy. For the thinner films, the measured wall widths are in good agreement with earlier data obtained by Fuchs. For films thicker than 800 Å, the wall width increases with film thickness to about 9000 Å at 1800 Å film thickness. Similar measurements for polycrystalline Co films with thickness from 200 to 1500 Å have been made. The wall width increases from 3000 Å at 400 Å film thickness to about 6000 Å at 1500 Å film thickness. The wall widths for Ni-Fe and Co films are much greater than predicted by present theories. The validity of the classical determination of wall width is discussed, and the comparison of the present data with theoretical results is given.

Finally, an experimental study of ripple by Lorentz microscopy in Ni-Fe alloy films has been carried out. The following should be noted: (1) the only practical way to determine experimentally a meaningful wavelength is to find a well-defined ripple periodicity by visual inspection of a photomicrograph. (2) The average wavelength is of the order of 1µ. This value is in reasonable agreement with the main wavelength predicted by the theories developed by others. The dependence of wavelength on substrate deposition temperature, alloy composition and the external magnetic field has been also studied and the results are compared with theoretical predictions. (3) The experimental fact that the ripple structure could not be observed in completely epitaxial films gives confirmation that the ripple results from the randomness of crystallite orientation. Furthermore, the experimental observation that the ripple disappeared in the range 71 and 75% Ni supports the theory that the ripple amplitude is directly dependent on the crystalline anisotropy. An attempt to experimentally determine the order of magnitude of the ripple angle was carried out. The measured angle was about 0.02 rad. The discrepancy between the experimental data and the theoretical prediction is serious. The accurate experimental determination of ripple angle is an unsolved problem.

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Let M be an Abelian W*-algebra of operators on a Hilbert space H. Let M0 be the set of all linear, closed, densely defined transformations in H which commute with every unitary operator in the commutant M’ of M. A well known result of R. Pallu de Barriere states that if ɸ is a normal positive linear functional on M, then ɸ is of the form T → (Tx, x) for some x in H, where T is in M. An elementary proof of this result is given, using only those properties which are consequences of the fact that ReM is a Dedekind complete Riesz space with plenty of normal integrals. The techniques used lead to a natural construction of the class M0, and an elementary proof is given of the fact that a positive self-adjoint transformation in M0 has a unique positive square root in M0. It is then shown that when the algebraic operations are suitably defined, then M0 becomes a commutative algebra. If ReM0 denotes the set of all self-adjoint elements of M0, then it is proved that ReM0 is Dedekind complete, universally complete Riesz spaces which contains ReM as an order dense ideal. A generalization of the result of R. Pallu de la Barriere is obtained for the Riesz space ReM0 which characterizes the normal integrals on the order dense ideals of ReM0. It is then shown that ReM0 may be identified with the extended order dual of ReM, and that ReM0 is perfect in the extended sense.

Some secondary questions related to the Riesz space ReM are also studied. In particular it is shown that ReM is a perfect Riesz space, and that every integral is normal under the assumption that every decomposition of the identity operator has non-measurable cardinal. The presence of atoms in ReM is examined briefly, and it is shown that ReM is finite dimensional if and only if every order bounded linear functional on ReM is a normal integral.

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The effect of intermolecular coupling in molecular energy levels (electronic and vibrational) has been investigated in neat and isotopic mixed crystals of benzene. In the isotopic mixed crystals of C6H6, C6H5D, m-C6H4D2, p-C6H4D2, sym-C6H3D3, C6D5H, and C6D6 in either a C6H6 or C6D6 host, the following phenomena have been observed and interpreted in terms of a refined Frenkel exciton theory: a) Site shifts; b) site group splittings of the degenerate ground state vibrations of C6H6, C6D6, and sym-C6H3D3; c) the orientational effect for the isotopes without a trigonal axis in both the 1B2u electronic state and the ground state vibrations; d) intrasite Fermi resonance between molecular fundamentals due to the reduced symmetry of the crystal site; and e) intermolecular or intersite Fermi resonance between nearly degenerate states of the host and guest molecules. In the neat crystal experiments on the ground state vibrations it was possible to observe many of these phenomena in conjunction with and in addition to the exciton structure.

To theoretically interpret these diverse experimental data, the concepts of interchange symmetry, the ideal mixed crystal, and site wave functions have been developed and are presented in detail. In the interpretation of the exciton data the relative signs of the intermolecular coupling constants have been emphasized, and in the limit of the ideal mixed crystal a technique is discussed for locating the exciton band center or unobserved exciton components. A differentiation between static and dynamic interactions is made in the Frenkel limit which enables the concepts of site effects and exciton coupling to be sharpened. It is thus possible to treat the crystal induced effects in such a fashion as to make their similarities and differences quite apparent.

A calculation of the ground state vibrational phenomena (site shifts and splittings, orientational effects, and exciton structure) and of the crystal lattice modes has been carried out for these systems. This calculation serves as a test of the approximations of first order Frenkel theory and the atom-atom, pair wise interaction model for the intermolecular potentials. The general form of the potential employed was V(r) = Be-Cr - A/r6 ; the force constants were obtained from the potential by assuming the atoms were undergoing simple harmonic motion.

In part II the location and identification of the benzene first and second triplet states (3B1u and 3E1u) is given.

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I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. The buoyant densities and sedimentation velocities of both intact (I) and singly nicked (II) SV 40 DNAs were measured as a function of free dye concentration. The buoyant density data were used to determine the binding isotherms over a dye concentration range extending from 0 to 600 µg/m1 in 5.8 M CsCl. At high dye concentrations all of the binding sites in II, but not in I, are saturated. At free dye concentrations less than 5.4 µg/ml, I has a greater affinity for dye than II. At a critical amount of dye bound I and II have equal affinities, and at higher dye concentration I has a lower affinity than II. The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions.

The free energy of superhelix formation is calculated as a function of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. The free energy estimates are used to calculate the pitch and radius of the superhelix as a function of the number of superhelical turns. The pitch and radius of the native I superhelix are 430 Å and 135 Å, respectively.

A buoyant density method for the isolation and detection of closed circular DNA is described. The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length.

II. The general theory is presented for the sedimentation equilibrium of a macromolecule in a concentrated binary solvent in the presence of an additional reacting small molecule. Equations are derived for the calculation of the buoyant density of the complex and for the determination of the binding isotherm of the reagent to the macrospecies. The standard buoyant density, a thermodynamic function, is defined and the density gradients which characterize the four component system are derived. The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and silver to DNA.