Sequence specific complexation of b DNA at sites containing g,c base pairs

A series of eight related analogs of distamycin A has been synthesized. Footprinting and affinity cleaving reveal that only two of the analogs, pyridine-2- car box amide-netropsin (2-Py N) and 1-methylimidazole-2-carboxamide-netrops in (2-ImN), bind to DNA with a specificity different from that of the parent compound. A new class of sites, represented by a TGACT sequence, is a strong site for 2-PyN binding, and the major recognition site for 2-ImN on DNA. Both compounds recognize the G•C bp specifically, although A's and T's in the site may be interchanged without penalty. Additional A•T bp outside the binding site increase the binding affinity. The compounds bind in the minor groove of the DNA sequence, but protect both grooves from dimethylsulfate. The binding evidence suggests that 2-PyN or 2-ImN binding induces a DNA conformational change.

In order to understand this sequence specific complexation better, the Ackers quantitative footprinting method for measuring individual site affinity constants has been extended to small molecules. MPE•Fe(II) cleavage reactions over a 10^5 range of free ligand concentrations are analyzed by gel electrophoresis. The decrease in cleavage is calculated by densitometry of a gel autoradiogram. The apparent fraction of DNA bound is then calculated from the amount of cleavage protection. The data is fitted to a theoretical curve using non-linear least squares techniques. Affinity constants at four individual sites are determined simultaneously. The distamycin A analog binds solely at A•T rich sites. Affinities range from 10^(6)- 10^(7)M^(-1) The data for parent compound D fit closely to a monomeric binding curve. 2-PyN binds both A•T sites and the TGTCA site with an apparent affinity constant of 10^(5) M^(-1). 2-ImN binds A•T sites with affinities less than 5 x 10^(4) M^(-1). The affinity of 2-ImN for the TGTCA site does not change significantly from the 2-PyN value. At the TGTCA site, the experimental data fit a dimeric binding curve better than a monomeric curve. Both 2-PyN and 2-ImN have substantially lower DNA affinities than closely related compounds.

In order to probe the requirements of this new binding site, fourteen other derivatives have been synthesized and tested. All compounds that recognize the TGTCA site have a heterocyclic aromatic nitrogen ortho to the N or C-terminal amide of the netropsin subunit. Specificity is strongly affected by the overall length of the small molecule. Only compounds that consist of at least three aromatic rings linked by amides exhibit TGTCA site binding. Specificity is only weakly altered by substitution on the pyridine ring, which correlates best with steric factors. A model is proposed for TGTCA site binding that has as its key feature hydrogen bonding to both G's by the small molecule. The specificity is determined by the sequence dependence of the distance between G's.

One derivative of 2-PyN exhibits pH dependent sequence specificity. At low pH, 4-dimethylaminopyridine-2-carboxamide-netropsin binds tightly to A•T sites. At high pH, 4-Me_(2)NPyN binds most tightly to the TGTCA site. In aqueous solution, this compound protonates at the pyridine nitrogen at pH 6. Thus presence of the protonated form correlates with A•T specificity.

The binding site of a class of eukaryotic transcriptional activators typified by yeast protein GCN4 and the mammalian oncogene Jun contains a strong 2-ImN binding site. Specificity requirements for the protein and small molecule are similar. GCN4 and 2-lmN bind simultaneously to the same binding site. GCN4 alters the cleavage pattern of 2-ImN-EDTA derivative at only one of its binding sites. The details of the interaction suggest that GCN4 alters the conformation of an AAAAAAA sequence adjacent to its binding site. The presence of a yeast counterpart to Jun partially blocks 2-lmN binding. The differences do not appear to be caused by direct interactions between 2-lmN and the proteins, but by induced conformational changes in the DNA protein complex. It is likely that the observed differences in complexation are involved in the varying sequence specificity of these proteins.

Chemical studies of viral entry mechanisms: I. Hydrophobic protein-lipid interactions during sendai virus membrane fusion. II. Kinetics of bacteriophage λ DNA injection.

Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage λ DNA injection.

Sendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125 )I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.

Examination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.

The kinetics of DNA injection by bacteriophage λ. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.

It is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.

Chemistry of low-valent platinum dimers

Physical and chemical properties of low-valent platinum dimers, namely [Pt_2(P_2O_5H_2)4]^(4-) and Pt_2(µ-dppm)_2Cl_2, have been investigated using a variety of structural and spectroscopic techniques.

Platinum(II) d^8-d^8 dimers have been shown to exhibit much thermal and photochemical reactivity. Chapter 2 describes studies aimed at elucidating the excited state reduction potenetial of [Pt_2(P_2O_5H_2)4]^(4-), Pt_2, in organic media. By conducting excited state electron transfer studies using derivatized pyridiniums and benzophenones, the excited state reduction potential has been estimated to be ~2 V. The Pt_2 complex undergoes partial oxidation to form Pt(II,III) linear chains. Chapter 3 describes the structural and spectroscopic techniques used to determine the translational symmetries of these [Pt_2(P_2O_5H_2)4]^(4-) (X = Cl, Br), Pt_2X, chains. Pt_2Br has been found to be intermediate between (AAB)_n and (AABCCB)_n, while, Pt_2Cl is of (AABCCB)_n translational symmetry. Investigations into the electronic transitions of Pt_2Cl and Pt_2Br were conducted using high pressure techniques and are presented in Chapter 4. The Pt_2X electronic spectrum exhibits bands attributable to the reduced Pt2 complex and the oxidized Pt_2X_2 complex [Pt_2(P_2O_5H_2)4]^(4-) along with an intervalence charge-tranfer band characteristic of a mixed-valence solid.

Photophysical investigations of a new luminescent chromophore, Pt_2(µ-dppm)_2Cl_2, a d^9-d^9 dimer, and its analogs are described in Chapter 5. The absorption band directly responsible for the observed emission is believed to be very weak and, as of yet, unobserved. Attempts to determine the spin multiplicty and approximate energy of this unobserved transition are described in Chapter 6. Excited-state energy transfer studies indicate that this absorption band is a triplet transition at -13,000 cm^(-1). Although, the Pt_2(µ-dppm)_2Cl_2 excited state is non-luminescent in fluid solution, it has been shown to undergo thermal electron transfer to tetracyanoethylene and photoinduced electron transfer to methylviologen. These experiments are presented in Chapter 7. Preliminary studies, described in Chapter 8, of non-bridged d^9-d^9 platinum(I) dimers have shown that [Pt_2(CNCH_3)_6]^(2+) serves as a versatile precursor in the synthesis of new d^8-d^8 A-frame complexes.

Optimal guidance of low-thrust interplanetary space vehicles

The low-thrust guidance problem is defined as the minimum terminal variance (MTV) control of a space vehicle subjected to random perturbations of its trajectory. To accomplish this control task, only bounded thrust level and thrust angle deviations are allowed, and these must be calculated based solely on the information gained from noisy, partial observations of the state. In order to establish the validity of various approximations, the problem is first investigated under the idealized conditions of perfect state information and negligible dynamic errors. To check each approximate model, an algorithm is developed to facilitate the computation of the open loop trajectories for the nonlinear bang-bang system. Using the results of this phase in conjunction with the Ornstein-Uhlenbeck process as a model for the random inputs to the system, the MTV guidance problem is reformulated as a stochastic, bang-bang, optimal control problem. Since a complete analytic solution seems to be unattainable, asymptotic solutions are developed by numerical methods. However, it is shown analytically that a Kalman filter in cascade with an appropriate nonlinear MTV controller is an optimal configuration. The resulting system is simulated using the Monte Carlo technique and is compared to other guidance schemes of current interest.

Computational modeling and psychophysics in low- and mid-level vision

This thesis addresses a series of topics related to the question of how people find the foreground objects from complex scenes. With both computer vision modeling, as well as psychophysical analyses, we explore the computational principles for low- and mid-level vision.

We first explore the computational methods of generating saliency maps from images and image sequences. We propose an extremely fast algorithm called Image Signature that detects the locations in the image that attract human eye gazes. With a series of experimental validations based on human behavioral data collected from various psychophysical experiments, we conclude that the Image Signature and its spatial-temporal extension, the Phase Discrepancy, are among the most accurate algorithms for saliency detection under various conditions.

In the second part, we bridge the gap between fixation prediction and salient object segmentation with two efforts. First, we propose a new dataset that contains both fixation and object segmentation information. By simultaneously presenting the two types of human data in the same dataset, we are able to analyze their intrinsic connection, as well as understanding the drawbacks of today’s “standard” but inappropriately labeled salient object segmentation dataset. Second, we also propose an algorithm of salient object segmentation. Based on our novel discoveries on the connections of fixation data and salient object segmentation data, our model significantly outperforms all existing models on all 3 datasets with large margins.

In the third part of the thesis, we discuss topics around the human factors of boundary analysis. Closely related to salient object segmentation, boundary analysis focuses on delimiting the local contours of an object. We identify the potential pitfalls of algorithm evaluation for the problem of boundary detection. Our analysis indicates that today’s popular boundary detection datasets contain significant level of noise, which may severely influence the benchmarking results. To give further insights on the labeling process, we propose a model to characterize the principles of the human factors during the labeling process.

The analyses reported in this thesis offer new perspectives to a series of interrelating issues in low- and mid-level vision. It gives warning signs to some of today’s “standard” procedures, while proposing new directions to encourage future research.

Measurement of the neutron (^3He) spin structure function at low Q^2 : a connection between the Bjorken and Drell-Hearn-Gerasimov sum rules

The spin dependent cross sections, σT_1/2 and σT_3/2 , and asymmetries, A_∥ and A_⊥ for ³He have been measured at the Jefferson Lab's Hall A facility. The inclusive scattering process ³He(e,e)X was performed for initial beam energies ranging from 0.86 to 5.1 GeV, at a scattering angle of 15.5°. Data includes measurements from the quasielastic peak, resonance region, and the deep inelastic regime. An approximation for the extended Gerasimov-Drell-Hearn integral is presented at a 4-momentum transfer Q² of 0.2-1.0 GeV².

Also presented are results on the performance of the polarized ³He target. Polarization of ³He was achieved by the process of spin-exchange collisions with optically pumped rubidium vapor. The ³He polarization was monitored using the NMR technique of adiabatic fast passage (AFP). The average target polarization was approximately 35% and was determined to have a systematic uncertainty of roughly ±4% relative.

Low-noise THz Niobium SIS Mixers

This thesis describes the development of low-noise heterodyne receivers at THz frequencies for submillimeter astronomy using Nb-based superconductor-insulator-superconductor (SIS) tunneling junctions. The mixers utilize a quasi-optical configuration which consists of a planar twin-slot antenna and antisymmetrically-fed two-junctions on an antireflection-coated silicon hyperhemispherical lens. On-chip integrated tuning circuits, in the form of microstrip lines, are used to obtain maximum coupling efficiency in the designed frequency band. To reduce the rf losses in the integrated tuning circuits above the superconducting Nb gap frequency (~ 700 GHz), normal-metal Al is used to replace Nb as the tuning circuits.

To account the rf losses in the micros trip lines, we calculated the surface impedance of the AI films using the nonlocal anomalous skin effect for finite thickness films. Nb films were calculated using the Mattis-Bardeen theory in the extreme anomalous limit. Our calculations show that the losses of the Al and Nb microstrip lines are about equal at 830 GHz. For Al-wiring and Nb-wiring mixers both optimized at 1050 GHz, the RF coupling efficiency of Al-wiring mixer is higher than that of Nb-wiring one by almost 50%. We have designed both Nb-wiring and Al-wiring mixers below and above the gap frequency.

A Fourier transform spectrometer (FTS) has been constructed especially for the study of the frequency response of SIS receivers. This FTS features large aperture size (10 inch) and high frequency resolution (114 MHz). The FTS spectra, obtained using the SIS receivers as direct detectors on the FTS, agree quite well with our theoretical simulations. We have also, for the first time, measured the FTS heterodyne response of an SIS mixer at sufficiently high resolution to resolve the LO and the sidebands. Heterodyne measurements of our SIS receivers with Nb-wiring or Al-wiring have yielded results which arc among the best reported to date for broadband heterodyne receivers. The Nb-wiring mixers, covering 400 - 850 GHz band with four separate fixed-tuned mixers, have uncorrected DSB receiver noise temperature around 5hv/k_b to 700 GHz, and better than 540 K at 808 GHz. An Al-wiring mixer designed for 1050 GHz band has an uncorrected DSB receiver noise temperature 840 K at 1042 GHz and 2.5 K bath temperature. Mixer performance analysis shows that Nb junctions can work well up to twice the gap frequency and the major cause of loss above the gap frequency is the rf losses in the microstrip tuning structures. Further advances in THz SIS mixers may be possible using circuits fabricated with higher-gap superconductors such as NbN. However, this will require high-quality films with low RF surface resistance at THz frequencies.

Optical properties of excited silicon and germanium at low temperatures

Part I of this thesis deals with 3 topics concerning the luminescence from bound multi-exciton complexes in Si. Part II presents a model for the decay of electron-hole droplets in pure and doped Ge.

Part I.

We present high resolution photoluminescence data for Si doped With Al, Ga, and In. We observe emission lines due to recombination of electron-hole pairs in bound excitons and satellite lines which have been interpreted in terms of complexes of several excitons bound to an impurity. The bound exciton luminescence in Si:Ga and Si:Al consists of three emission lines due to transitions from the ground state and two low lying excited states. In Si:Ga, we observe a second triplet of emission lines which precisely mirror the triplet due to the bound exciton. This second triplet is interpreted as due to decay of a two exciton complex into the bound exciton. The observation of the second complete triplet in Si:Ga conclusively demonstrates that more than one exciton will bind to an impurity. Similar results are found for Si:Al. The energy of the lines show that the second exciton is less tightly bound than the first in Si:Ga. Other lines are observed at lower energies. The assumption of ground state to ground-state transitions for the lower energy lines is shown to produce a complicated dependence of binding energy of the last exciton on the number of excitons in a complex. No line attributable to the decay of a two exciton complex is observed in Si:In.

We present measurements of the bound exciton lifetimes for the four common acceptors in Si and for the first two bound multi-exciton complexes in Si:Ga and Si:Al. These results are shown to be in agreement with a calculation by Osbourn and Smith of Auger transition rates for acceptor bound excitons in Si. Kinetics determine the relative populations of complexes of various sizes and work functions, at temperatures which do not allow them to thermalize with respect to one another. It is shown that kinetic limitations may make it impossible to form two-exciton complexes in Si:In from a gas of free excitons.

We present direct thermodynamic measurements of the work functions of bound multi-exciton complexes in Al, B, P and Li doped Si. We find that in general the work functions are smaller than previously believed. These data remove one obstacle to the bound multi-exciton complex picture which has been the need to explain the very large apparent work functions for the larger complexes obtained by assuming that some of the observed lines are ground-state to ground-state transitions. None of the measured work functions exceed that of the electron-hole liquid.

Part II.

A new model for the decay of electron-hole-droplets in Ge is presented. The model is based on the existence of a cloud of droplets within the crystal and incorporates exciton flow among the drops in the cloud and the diffusion of excitons away from the cloud. It is able to fit the experimental luminescence decays for pure Ge at different temperatures and pump powers while retaining physically reasonable parameters for the drops. It predicts the shrinkage of the cloud at higher temperatures which has been verified by spatially and temporally resolved infrared absorption experiments. The model also accounts for the nearly exponential decay of electron-hole-droplets in lightly doped Ge at higher temperatures.

Convex Relaxation for Low-Dimensional Representation: Phase Transitions and Limitations

There is a growing interest in taking advantage of possible patterns and structures in data so as to extract the desired information and overcome the curse of dimensionality. In a wide range of applications, including computer vision, machine learning, medical imaging, and social networks, the signal that gives rise to the observations can be modeled to be approximately sparse and exploiting this fact can be very beneficial. This has led to an immense interest in the problem of efficiently reconstructing a sparse signal from limited linear observations. More recently, low-rank approximation techniques have become prominent tools to approach problems arising in machine learning, system identification and quantum tomography.

In sparse and low-rank estimation problems, the challenge is the inherent intractability of the objective function, and one needs efficient methods to capture the low-dimensionality of these models. Convex optimization is often a promising tool to attack such problems. An intractable problem with a combinatorial objective can often be "relaxed" to obtain a tractable but almost as powerful convex optimization problem. This dissertation studies convex optimization techniques that can take advantage of low-dimensional representations of the underlying high-dimensional data. We provide provable guarantees that ensure that the proposed algorithms will succeed under reasonable conditions, and answer questions of the following flavor:

More specifically, i) Focusing on linear inverse problems, we generalize the classical error bounds known for the least-squares technique to the lasso formulation, which incorporates the signal model. ii) We show that intuitive convex approaches do not perform as well as expected when it comes to signals that have multiple low-dimensional structures simultaneously. iii) Finally, we propose convex relaxations for the graph clustering problem and give sharp performance guarantees for a family of graphs arising from the so-called stochastic block model. We pay particular attention to the following aspects. For i) and ii), we aim to provide a general geometric framework, in which the results on sparse and low-rank estimation can be obtained as special cases. For i) and iii), we investigate the precise performance characterization, which yields the right constants in our bounds and the true dependence between the problem parameters.

Observations of nitrogen and oxygen isotopes in the low energy cosmic rays

The isotopic composition of the enhanced low energy nitrogen and oxygen cosmic rays can provide information regarding the source of these particles. Using the Caltech Electron/Isotope Spectrometer aboard the IMP-7 satellite, a measurement of this isotopic composition was made. To determine the isotope response of the instrument, a calibration was performed, and it was determined that the standard range-energy tables were inadequate to calculate the isotope response. From the calibration, corrections to the standard range-energy tables were obtained which can be used to calculate the isotope response of this and similar instruments.

The low energy nitrogen and oxygen cosmic rays were determined to be primarily ^(14)N and ^(16)O. Upper limits were obtained for the abundances of the other stable nitrogen and oxygen isotopes. To the 84% confidence level the isotopic abundances are: ^(15)N/N ≤ 0.26 (5.6- 12.7 MeV/nucleon), ^(17)0/0 ≤ 0.13 (7.0- 11.8 MeV/nucleon), (18)0/0 ≤ 0.12 (7.0 - 11.2 MeV/nucleon). The nitrogen composition differs from higher energy measurements which indicate that ^(15)N, which is thought to be secondary, is the dominant isotope. This implies that the low energy enhanced cosmic rays are not part of the same population as the higher energy cosmic rays and that they have not passed through enough material to produce a large fraction of ^(15)N. The isotopic composition of the low energy enhanced nitrogen and oxygen is consistent with the local acceleration theory of Fisk, Kozlovsky, and Ramaty, in which interstellar material is accelerated to several MeV/nucleon. If, on the other hand, the low energy nitrogen and oxygen result from nucleosynthesis in a galactic source, then the nucleosynthesis processes which produce an enhancement of nitrogen and oxygen and a depletion of carbon are restricted to producing predominantly ^(14)N and ^(16)O.

Structural and clumped-isotope constraints on the mechanisms of displacement along low-angle detachments

Despite years of research on low-angle detachments, much about them remains enigmatic. This thesis addresses some of the uncertainty regarding two particular detachments, the Mormon Peak detachment in Nevada and the Heart Mountain detachment in Wyoming and Montana.

Constraints on the geometry and kinematics of emplacement of the Mormon Peak detachment are provided by detailed geologic mapping of the Meadow Valley Mountains, along with an analysis of structural data within the allochthon in the Mormon Mountains. Identifiable structures well suited to constrain the kinematics of the detachment include a newly mapped, Sevier-age monoclinal flexure in the hanging wall of the detachment. This flexure, including the syncline at its base and the anticline at its top, can be readily matched to the base and top of the frontal Sevier thrust ramp, which is exposed in the footwall of the detachment to the east in the Mormon Mountains and Tule Springs Hills. The ~12 km of offset of these structural markers precludes the radial sliding hypothesis for emplacement of the allochthon.

The role of fluids in the slip along faults is a widely investigated topic, but the use of carbonate clumped-isotope thermometry to investigate these fluids is new. Faults rocks from within ~1 m of the Mormon Peak detachment, including veins, breccias, gouges, and host rocks, were analyzed for carbon, oxygen, and clumped-isotope measurements. The data indicate that much of the carbonate breccia and gouge material along the detachment is comminuted host rock, as expected. Measurements in vein material indicate that the fluid system is dominated by meteoric water, whose temperature indicates circulation to substantial depths (c. 4 km) in the upper crust near the fault zone.

Slip along the subhorizontal Heart Mountain detachment is particularly enigmatic, and many different mechanisms for failure have been proposed, predominantly involving catastrophic failure. Textural evidence of multiple slip events is abundant, and include multiple brecciation events and cross-cutting clastic dikes. Footwall deformation is observed in numerous exposures of the detachment. Stylolitic surfaces and alteration textures within and around “banded grains” previously interpreted to be an indicator of high-temperature fluidization along the fault suggest their formation instead via low-temperature dissolution and alteration processes. There is abundant textural evidence of the significant role of fluids along the detachment via pressure solution. The process of pressure solution creep may be responsible for enabling multiple slip events on the low-angle detachment, via a local rotation of the stress field.

Clumped-isotope thermometry of fault rocks associated with the Heart Mountain detachment indicates that despite its location on the flanks of a volcano that was active during slip, the majority of carbonate along the Heart Mountain detachment does not record significant heating above ambient temperatures (c. 40-70°C). Instead, cold meteoric fluids infiltrated the detachment breccia, and carbonate precipitated under ambient temperatures controlled by structural depth. Locally, fault gouge does preserve hot temperatures (>200°C), as is observed in both the Mormon Peak detachment and Heart Mountain detachment areas. Samples with very hot temperatures attributable to frictional shear heating are present but rare. They appear to be best preserved in hanging wall structures related to the detachment, rather than along the main detachment.

Evidence is presented for the prevalence of relatively cold, meteoric fluids along both shallow crustal detachments studied, and for protracted histories of slip along both detachments. Frictional heating is evident from both areas, but is a minor component of the preserved fault rock record. Pressure solution is evident, and might play a role in initiating slip on the Heart Mountain fault, and possibly other low-angle detachments.

Part I: The abortive infection of bacteriophage øx174 at low temperatures. Part II: The early stages in the process of infection by bacteriophage øx174

Part I

The infection of E. coli by ΦX174 at 15°C is abortive; the cells are killed by the infection but neither mature phage nor SS (single-stranded) DNA are synthesized. Parental RF (replicative form) is formed and subsequently replicated at 15°C. The RF made at 15°C shows normal infectivity and full competence to act as precursor to progeny SS DNA after an increase in temperature to 37°C. The investigations suggest that all of the proteins required for SS DNA synthesis and phage maturation are present in the abortive infection at 15°C.

Three possible causes are suggested for the abortive infection at 15°C: (a) A virus-coded protein whose role is essential to the infection is made at 15°C and assumes its native conformation, but its rate of activity is too low at this temperature to sustain the infection process. (b) Virus maturation may involve the formation of a DNA-protein complex and conformational changes which have an energy threshold infrequently reached at 15°C. (c) A host-coded protein present in uninfected cells, and whose activity is essential to the infection at all temperatures, but not to the host at 15°C, is inactive at 15°C. An hypothesis of this type is offered which proposes that the temperature-limiting factor in SS DNA synthesis in vivo may reflect a temperature-dependent property of the host DNA polymerase.

Part II

Three distinct stages are demonstrated in the process whereby ΦX174 invades its host: (1) Attachment: The phage attach to the cell in a manner that does not irreversibly alter the phage particle and which exhibits "single-hit" kinetics. The total charge on the phage particle is demonstrated to be important in determining the rate at which stable attachment is effected. The proteins specified by ΦX cistrons II, III and VII play roles, which may be indirect, in the attachment reaction. (2) Eclipse: 'The attached phage undergo a conformational change. Some of the altered phage particles spontaneously detach from the cell (in a non-infective form) while the remainder are more tightly bound to the cell. The altered phage particles detached (spontaneously or chemically) from such complexes have at least 40% of their DNA extruded from the phage coat. It is proposed that this particle is, or derives from, a direct intermediate in the penetration of the viral DNA.

The kinetics for the eclipse of attached phage particles are first-order with respect to phage concentration and biphasic; about 85% of the phage eclipse at one rate (k = 0.86 min^-1) and the remainder do so at a distinctly lesser rate (k = 0.21 min^-1).

The eclipse event is very temperature-dependent and has the relatively high Arrhenius activation energy of 36.6 kcal/mole, indicating the cooperative nature of the process. The temperature threshold for eclipse is 17 to 18°C.

At present no specific ΦX cistron is identified as affecting the eclipse process. (3) DNA penetration: A fraction of the attached, eclipsed phage particles corresponding in number to the plaque-forming units complete DNA penetration. The penetrated DNA is found in the cell as RF, and the empty phage protein coat remains firmly attached to the exterior of the cell. This step is inhibited by prior irradiation of the phage with relatively high doses of UV light and is insensitive to the presence of KCN and NaN₃. Temporally excluded superinfecting phages do not achieve DNA penetration.

Both eclipsed phage particles and empty phage protein coats may be dissociated from infected cells; some of their properties are described.

Simulations and mechanisms of subtropical low-cloud response to climate change

This thesis focuses on improving the simulation skills and the theoretical understanding of the subtropical low cloud response to climate change.

First, an energetically consistent forcing framework is designed and implemented for the large eddy simulation (LES) of the low-cloud response to climate change. The three representative current-day subtropical low cloud regimes of cumulus (Cu), cumulus-over-stratocumulus, and stratocumulus (Sc) are all well simulated with this framework, and results are comparable to the conventional fixed-SST approach. However, the cumulus response to climate warming subject to energetic constraints differs significantly from the conventional approach with fixed SST. Under the energetic constraint, the subtropics warm less than the tropics, since longwave (LW) cooling is more efficient with the drier subtropical free troposphere. The surface latent heat flux (LHF) also increases only weakly subject to the surface energetic constraint. Both factors contribute to an increased estimated inversion strength (EIS), and decreased inversion height. The decreased Cu-depth contributes to a decrease of liquid water path (LWP) and weak positive cloud feedback. The conventional fixed-SST approach instead simulates a strong increase in LHF and deepening of the Cu layer, leading to a weakly negative cloud feedback. This illustrates the importance of energetic constraints to the simulation and understanding of the sign and magnitude of low-cloud feedback.

Second, an extended eddy-diffusivity mass-flux (EDMF) closure for the unified representation of sub-grid scale (SGS) turbulence and convection processes in general circulation models (GCM) is presented. The inclusion of prognostic terms and the elimination of the infinitesimal updraft fraction assumption makes it more flexible for implementation in models across different scales. This framework can be consistently extended to formulate multiple updrafts and downdrafts, as well as variances and covariances. It has been verified with LES in different boundary layer regimes in the current climate, and further development and implementation of this closure may help to improve our simulation skills and understanding of low-cloud feedback through GCMs.

I. The crystal structure of a new dimer of triphenylfluorocyclobutadiene. II. A low temperature refinement of the cyanuric triazide structure

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 MoK_α 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.

Dielectric recovery of short A-C arcs between low-boiling-point electrodes

The re-ignition characteristics (variation of re-ignition voltage with time after current zero) of short alternating current arcs between plane brass electrodes in air were studied by observing the average re-ignition voltages on the screen of a cathode-ray oscilloscope and controlling the rates of rise of voltage by varying the shunting capacitance and hence the natural period of oscillation of the reactors used to limit the current. The shape of these characteristics and the effects on them of varying the electrode separation, air pressure, and current strength were determined.

The results show that short arc spaces recover dielectric strength in two distinct stages. The first stage agrees in shape and magnitude with a previously developed theory that all voltage is concentrated across a partially deionized space charge layer which increases its breakdown voltage with diminishing density of ionization in the field-tree space. The second stage appears to follow complete deionization by the electric field due to displacement of the field-free region by the space charge layer, its magnitude and shape appearing to be due simply to increase in gas density due to cooling. Temperatures calculated from this second stage and ion densities determined from the first stage by means of the space charge equation and an extrapolation of the temperature curve are consistent with recent measurements of arc value by other methods. Analysis or the decrease with time of the apparent ion density shows that diffusion alone is adequate to explain the results and that volume recombination is not. The effects on the characteristics of variations in the parameters investigated are found to be in accord with previous results and with the theory if deionization mainly by diffusion be assumed.