Sputtering by multiply-charged ions, and preferential sputtering of isotopic mixtures

Collector-type experiments have been conducted to investigate two different aspects of sputtering induced by keV ions. The first study looked for possible ejection mechanisms related to the primary charge state of the projectile. Targets of CsI and LiNbO_3 were bombarded with 48 keV Ar^(q+), and a Au target was bombarded with 60 keV Ar^(q+), for q = 4, 8, and 11. The collectors were analyzed using heavy-ion Rutherford backscattering spectroscopy to determine the differential angular sputtering yields; these and the corresponding total yields were examined for variations as a function of projectile charge state. For the Au target, no significant changes were seen, but for the insulating targets slight (~10%) enhancements were observed in the total yields as the projectile charge state was increased from 4+ to 11+.

In the second investigation, artificial ^(92)Mo/^(100)Mo targets were bombarded with 5 and 10 keV beams of Ar^+ and Xe^+ to study the isotopic fractionation of sputtered neutrals as a function of emission angle and projectile fluence. Using secondary ion mass spectroscopy to measure the isotope ratio on the collectors, material ejected into normal directions at low bombarding fluences (~ 10^(15) ions cm^(-2)) was found to be enriched in the light isotope by as much as ~70‰ compared to steady state. Similar results were found for secondary Mo ions sputtered by 14.5 keV O^-. For low-fluence 5 keV Xe^+ bombardment, the light-isotope enrichment at oblique angles was ~20‰ less than the corresponding enrichment in the normal direction. No angular dependence could be resolved for 5 keV Ar^+ projectiles at the lowest fluence. The above fractionation decreased to steady-state values after bombarding fluences of a few times 10^(16) ions cm^(-2) , with the angular dependence becoming more pronounced. The fractionation and total sputtering yield were found to be strongly correlated, indicating that the above effects may have been related to the presence of a modified target surface layer. The observed effects are consistent with other secondary ion measurements and multiple-interaction computer simulations, and are considerably larger than predicted by existing analytic theory.

Effects of self energy of the ions on the double layer structure and properties at the dielectric interface

Although numerous theoretical efforts have been put forth, a systematic, unified and predictive theoretical framework that is able to capture all the essential physics of the interfacial behaviors of ions, such as the Hofmeister series effect, Jones-Ray effect and the salt effect on the bubble coalescence remain an outstanding challenge. The most common approach to treating electrostatic interactions in the presence of salt ions is the Poisson-Boltzmann (PB) theory. However, there are many systems for which the PB theory fails to offer even a qualitative explanation of the behavior, especially for ions distributed in the vicinity of an interface with dielectric contrast between the two media (like the water-vapor/oil interface). A key factor missing in the PB theory is the self energy of the ion.

In this thesis, we develop a self-consistent theory that treats the electrostatic self energy (including both the short-range Born solvation energy and the long-range image charge interactions), the nonelectrostatic contribution of the self energy, the ion-ion correlation and the screening effect systematically in a single framework. By assuming a finite charge spread of the ion instead of using the point-charge model, the self energy obtained by our theory is free of the divergence problems and gives a continuous self energy across the interface. This continuous feature allows ions on the water side and the vapor/oil side of the interface to be treated in a unified framework. The theory involves a minimum set of parameters of the ion, such as the valency, radius, polarizability of the ions, and the dielectric constants of the medium, that are both intrinsic and readily available. The general theory is first applied to study the thermodynamic property of the bulk electrolyte solution, which shows good agreement with the experiment result for predicting the activity coefficient and osmotic coefficient.

Next, we address the effect of local Born solvation energy on the bulk thermodynamics and interfacial properties of electrolyte solution mixtures. We show that difference in the solvation energy between the cations and anions naturally gives rise to local charge separation near the interface, and a finite Galvani potential between two coexisting solutions. The miscibility of the mixture can either increases or decreases depending on the competition between the solvation energy and translation entropy of the ions. The interfacial tension shows a non-monotonic dependence on the salt concentration: it increases linearly with the salt concentration at higher concentrations, and decreases approximately as the square root of the salt concentration for dilute solutions, which is in agreement with the Jones-Ray effect observed in experiment.

Next, we investigate the image effects on the double layer structure and interfacial properties near a single charged plate. We show that the image charge repulsion creates a depletion boundary layer that cannot be captured by a regular perturbation approach. The correct weak-coupling theory must include the self-energy of the ion due to the image charge interaction. The image force qualitatively alters the double layer structure and properties, and gives rise to many non-PB effects, such as nonmonotonic dependence of the surface energy on concentration and charge inversion. The image charge effect is then studied for electrolyte solutions between two plates. For two neutral plates, we show that depletion of the salt ions by the image charge repulsion results in short-range attractive and long-range repulsive forces. If cations and anions are of different valency, the asymmetric depletion leads to the formation of an induced electrical double layer. For two charged plates, the competition between the surface charge and the image charge effect can give rise to like- charge attraction.

Then, we study the inhomogeneous screening effect near the dielectric interface due to the anisotropic and nonuniform ion distribution. We show that the double layer structure and interfacial properties is drastically affected by the inhomogeneous screening if the bulk Debye screening length is comparable or smaller than the Bjerrum length. The width of the depletion layer is characterized by the Bjerrum length, independent of the salt concentration. We predict that the negative adsorption of ions at the interface increases linearly with the salt concentration, which cannot be captured by either the bulk screening approximation or the WKB approximation. For asymmetric salt, the inhomogeneous screening enhances the charge separation in the induced double layer and significantly increases the value of the surface potential.

Finally, to account for the ion specificity, we study the self energy of a single ion across the dielectric interface. The ion is considered to be polarizable: its charge distribution can be self-adjusted to the local dielectric environment to minimize the self energy. Using intrinsic parameters of the ions, such as the valency, radius, and polarizability, we predict the specific ion effect on the interfacial affinity of halogen anions at the water/air interface, and the strong adsorption of hydrophobic ions at the water/oil interface, in agreement with experiments and atomistic simulations.

The theory developed in this work represents the most systematic theoretical technique for weak-coupling electrolytes. We expect the theory to be more useful for studying a wide range of structural and dynamic properties in physicochemical, colloidal, soft-matter and biophysical systems.

Negative regulators of a growth factor-mediated signaling pathway in the nematode Caenorhabditis elegans

Vulval differentiation in C. elegans is mediated by an Epidermal growth factor (EGF)- EGF receptor (EGFR) signaling pathway. I have cloned unc-101, a negative regulator of vulval differentiation of the nematode C. elegans. unc-101 encodes a homolog of AP47, the medium chain of the trans-Golgi clathrin-associated protein complex. This identity was confirmed by cloning and comparing sequence of a C. elegans homolog of AP50, the medium chain of the plasma membrane clathrin-associated protein complex. I provided the first genetic evidence that the trans-Golgi clathrin-coated vesicles are involved in regulation of an EGF signaling pathway. Most of the unc-101 alleles are deletions or nonsense mutations, suggesting that these alleles severely reduce the unc-101 activity. A hybrid gene that contains parts of unc-101 and mouse AP4 7 rescued at least two phenotypes of unc-101 mutations, the Unc and the suppression of vulvaless phenotype of let-23(sy1) mutation. Therefore, the functions of AP47 are conserved between nematodes and mammals.

unc-101 mutations can cause a greater than wild-type vulval differentiation in combination with certain mutations in sli-1, another negative regulator of the vulval induction pathway. A mutation in a new gene, rok-1, causes no defect by itself, but causes a greater than wild-type vulval differentiation in the presence of a sli-1 mutation. The unc-101; rok-1; sli-1 triple mutants display a greater extent of vulval differentiation than any double mutant combinations of unc-101, rok-1 and sli-1. Therefore, rok-1 locus defines another negative regulator of the vulval induction pathway.

I analyzed a second gene encoding an AP47 homolog in C. elegans. This gene, CEAP47, encodes a protein 72% identical to both unc-101 and mammalian AP47. A hybrid gene containing parts of unc-101 and CEAP47 sequences can rescue phenotypes of unc-101 mutants, indicating that UNC- 101 and CEAP47 proteins can be redundant if expressed in the same set of cells.

Physical investigations of small particles : (I) aerosol particle charging and flux enhancement and (II) whispering gallery mode sensing

Part I

Particles are a key feature of planetary atmospheres. On Earth they represent the greatest source of uncertainty in the global energy budget. This uncertainty can be addressed by making more measurement, by improving the theoretical analysis of measurements, and by better modeling basic particle nucleation and initial particle growth within an atmosphere. This work will focus on the latter two methods of improvement.

Uncertainty in measurements is largely due to particle charging. Accurate descriptions of particle charging are challenging because one deals with particles in a gas as opposed to a vacuum, so different length scales come into play. Previous studies have considered the effects of transition between the continuum and kinetic regime and the effects of two and three body interactions within the kinetic regime. These studies, however, use questionable assumptions about the charging process which resulted in skewed observations, and bias in the proposed dynamics of aerosol particles. These assumptions affect both the ions and particles in the system. Ions are assumed to be point monopoles that have a single characteristic speed rather than follow a distribution. Particles are assumed to be perfect conductors that have up to five elementary charges on them. The effects of three body interaction, ion-molecule-particle, are also overestimated. By revising this theory so that the basic physical attributes of both ions and particles and their interactions are better represented, we are able to make more accurate predictions of particle charging in both the kinetic and continuum regimes.

The same revised theory that was used above to model ion charging can also be applied to the flux of neutral vapor phase molecules to a particle or initial cluster. Using these results we can model the vapor flux to a neutral or charged particle due to diffusion and electromagnetic interactions. In many classical theories currently applied to these models, the finite size of the molecule and the electromagnetic interaction between the molecule and particle, especially for the neutral particle case, are completely ignored, or, as is often the case for a permanent dipole vapor species, strongly underestimated. Comparing our model to these classical models we determine an “enhancement factor” to characterize how important the addition of these physical parameters and processes is to the understanding of particle nucleation and growth.

Part II

Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and non-specific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, \lambda_{R}, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored.

Charged pion contribution to the anomalous magnetic moment of the muon

The model dependence inherent in hadronic calculations is one of the dominant sources of uncertainty in the theoretical prediction of the anomalous magnetic moment of the muon. In this thesis, we focus on the charged pion contribution and turn a critical eye on the models employed in the few previous calculations of $a_\mu^{\pi^+\pi^-}$. Chiral perturbation theory provides a check on these models at low energies, and we therefore calculate the charged pion contribution to light-by-light (LBL) scattering to $\mathcal{O}(p^6)$. We show that the dominant corrections to the leading order (LO) result come from two low energy constants which show up in the form factors for the $\gamma\pi\pi$ and $\gamma\gamma\pi\pi$ vertices. Comparison with the existing models reveal a potentially significant omission - none include the pion polarizability corrections associated with the $\gamma\gamma\pi\pi$ vertex. We next consider alternative models where the pion polarizability is produced through exchange of the $a_1$ axial vector meson. These have poor UV behavior, however, making them unsuited for the $a_\mu^{\pi^+\pi^-}$ calculation. We turn to a simpler form factor modeling approach, generating two distinct models which reproduce the pion polarizability corrections at low energies, have the correct QCD scaling at high energies, and generate finite contributions to $a_\mu^{\pi^+\pi^-}$. With these two models, we calculate the charged pion contribution to the anomalous magnetic moment of the muon, finding values larger than those previously reported: $a_\mu^\mathrm{I} = -1.779(4)\times10^{-10}\,,\,a_\mu^\mathrm{II} = -4.892(3)\times10^{-10}$.

Measurement of the band bending and surface dipole at chemically functionalized Si(111)/vacuum interfaces

The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si-Br, Si-H, and Si-CH₃ groups, respectively. The surface termination influenced the band bending, with the Si 2p_3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)-Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)-H, followed by Si(111)-CH₃ (whose Fermi level was positioned near mid-gap at the surface). Si(111)-CH₃ surfaces exposed to Br₂(g) yielded the lowest binding energies, with the Fermi level positioned between mid-gap and the valence band. The Fermi level position of Br₂(g)-exposed Si(111)-CH₃ was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.

Negative regulation of transcription factors by Srb10 cyclin-dependent kinase

The ubiquitin-dependent proteolytic pathway plays an important role in a broad array of cellular processes, inducting cell cycle control and transcription. Biochemical analysis of the ubiquitination of Sic1, the B-type cyclin-dependent kinase (CDK) inhibitor in budding yeast helped to define a ubiquitin ligase complex named SCF^cdc4 (for Skp1, Cdc53/cullin, F-box protein). We found that besides Sic1, the CDK inhibitor Far1 and the replication initiation protein Cdc6 are also substrates of SCF^cdc4 in vitro. A common feature in the ubiquitination of the cell cycle SCF^cdc4 substrates is that they must be phosphorylated by the major cell cycle CDK, Cdc28. Gcn4, a transcription activator involved in the general control of amino acid biosynthesis, is rapidly degraded in an SCF^cdc4-dependent manner in vivo. We have focused on this substrate to investigate the generality of the SCF^cdc4 pathway. Through biochemical fractionations, we found that the Srb10 CDK phosphorylates Gcn4 and thereby marks it for recognition by SCF^cdc4 ubiquitin ligase. Srb10 is a physiological regulator of Gcn4 stability because both phosphorylation and turnover of Gcn4 are diminished in srb10 mutants. Furthermore, we found that at least two different CDKs, Pho85 and Srb10, conspire to promote the rapid degradation of Gcn4 in vivo. The multistress response transcriptional regulator Msn2 is also a substrate for Srb10 and is hyperphosphorylated in an Srb10-dependent manner upon heat stress-induced translocation into the nucleus. Whereas Msn2 is cytoplasmic in resting wild type cells, its nuclear exclusion is partially compromised in srb10 mutant cells. Srb10 has been shown to repress a subset of genes in vivo, and has been proposed to inhibit transcription via phosphorylation of the C-terminal domain of RNA polymerase II. Our results suggest a general theme that Srb10 represses the transcription of specific genes by directly antagonizing the transcriptional activators.

The Flocculation of E. coli with Polyethyleneimine

A comprehensive study was made of the flocculation of dispersed E. coli bacterial cells by the cationic polymer polyethyleneimine (PEI). The three objectives of this study were to determine the primary mechanism involved in the flocculation of a colloid with an oppositely charged polymer, to determine quantitative correlations between four commonly-used measurements of the extent of flocculation, and to record the effect of varying selected system parameters on the degree of flocculation. The quantitative relationships derived for the four measurements of the extent of flocculation should be of direct assistance to the sanitary engineer in evaluating the effectiveness of specific coagulation processes.

A review of prior statistical mechanical treatments of absorbed polymer configuration revealed that at low degrees of surface site coverage, an oppositely- charged polymer molecule is strongly adsorbed to the colloidal surface, with only short loops or end sequences extending into the solution phase. Even for high molecular weight PEI species, these extensions from the surface are theorized to be less than 50 Å in length. Although the radii of gyration of the five PEI species investigated were found to be large enough to form interparticle bridges, the low surface site coverage at optimum flocculation doses indicates that the predominant mechanism of flocculation is adsorption coagulation.

The effectiveness of the high-molecular weight PEI species 1n producing rapid flocculation at small doses is attributed to the formation of a charge mosaic on the oppositely-charged E. coli surfaces. The large adsorbed PEI molecules not only neutralize the surface charge at the adsorption sites, but also cause charge reversal with excess cationic segments. The alignment of these positive surface patches with negative patches on approaching cells results in strong electrostatic attraction in addition to a reduction of the double-layer interaction energies. The comparative ineffectiveness of low-molecular weight PEI species in producing E. coli flocculation is caused by the size of the individual molecules, which is insufficient to both neutralize and reverse the negative E.coli surface charge. Consequently, coagulation produced by low molecular weight species is attributed solely to the reduction of double-layer interaction energies via adsorption.

Electrophoretic mobility experiments supported the above conclusions, since only the high-molecular weight species were able to reverse the mobility of the E. coli cells. In addition, electron microscope examination of the seam of agglutination between E. coli cells flocculation by PEI revealed tightly- bound cells, with intercellular separation distances of less than 100-200 Å in most instances. This intercellular separation is partially due to cell shrinkage in preparation of the electron micrographs.

The extent of flocculation was measured as a function of PEl molecular weight, PEl dose, and the intensity of reactor chamber mixing. Neither the intensity of mixing, within the common treatment practice limits, nor the time of mixing for up to four hours appeared to play any significant role in either the size or number of E.coli aggregates formed. The extent of flocculation was highly molecular weight dependent: the high-molecular-weight PEl species produce the larger aggregates, the greater turbidity reductions, and the higher filtration flow rates. The PEl dose required for optimum flocculation decreased as the species molecular weight increased. At large doses of high-molecular-weight species, redispersion of the macroflocs occurred, caused by excess adsorption of cationic molecules. The excess adsorption reversed the surface charge on the E.coli cells, as recorded by electrophoretic mobility measurements.

Successful quantitative comparisons were made between changes in suspension turbidity with flocculation and corresponding changes in aggregate size distribution. E. coli aggregates were treated as coalesced spheres, with Mie scattering coefficients determined for spheres in the anomalous diffraction regime. Good quantitative comparisons were also found to exist between the reduction in refiltration time and the reduction of the total colloid surface area caused by flocculation. As with turbidity measurements, a coalesced sphere model was used since the equivalent spherical volume is the only information available from the Coulter particle counter. However, the coalesced sphere model was not applicable to electrophoretic mobility measurements. The aggregates produced at each PEl dose moved at approximately the same vlocity, almost independently of particle size.

PEl was found to be an effective flocculant of E. coli cells at weight ratios of 1 mg PEl: 100 mg E. coli. While PEl itself is toxic to E.coli at these levels, similar cationic polymers could be effectively applied to water and wastewater treatment facilities to enhance sedimentation and filtration characteristics.

Theoretical and experimental investigations of the flocculation of charged particles in aqueous solutions by polyelectrolytes of opposite charge

An electrostatic mechanism for the flocculation of charged particles by polyelectrolytes of opposite charge is proposed. The difference between this and previous electrostatic coagulation mechanisms is the formation of charged polyion patches on the oppositely charged surfaces. The size of a patch is primarily a function of polymer molecular weight and the total patch area is a function of the amount of polymer adsorbed. The theoretical predictions of the model agree with the experimental dependence of the polymer dose required for flocculation on polymer molecular weight and solution ionic strength.

A theoretical analysis based on the Derjaguin-Landau, Verwey- Overbeek electrical double layer theory and statistical mechanical treatments of adsorbed polymer configurations indicates that flocculation of charged particles in aqueous solutions by polyelectrolytes of opposite charge does not occur by the commonly accepted polymerbridge mechanism.

A series of 1, 2-dimethyl-5 -vinylpyridinium bromide polymers with a molecular weight range of 6x10^3 to 5x10^6 was synthesized and used to flocculate dilute polystyrene latex and silica suspensions in solutions of various ionic strengths. It was found that with high molecular weight polymers and/or high ionic strengths the polymer dose required for flocculation is independent of molecular weight. With low molecular weights and/or low ionic strengths, the flocculation dose decreases with increasing molecular weight.

Electrocatalytic activity of transition metal substituted heteropolytungstates

The electrochemical and electrocatalytic behavior of a series of heteropolytungstate anions in which a tungsten atom in the well known Keggin structure has been replaced by an iron atom is described. All of the iron substituted ions exhibit a one electron reversible couple associated with the Fe³⁺ center and a pair of two electron waves attributed to electron addition and removal from the tungsten oxo framework. The pH and ionic strength effects upon the various electrochemical processes are discussed and interpreted in terms of a competition between protonation and ion pairing of the highly negatively charged ions.

The anions are efficient catalysts for the electroreduction of hydrogen peroxide. A catalytic mechanism involving a formally Fe(IV) intermediate is proposed. Pulse radiolysis experiments were employed to detect the intermediate and evaluate the rate constants for the reactions in which it is formed and decomposed. A chain mechanism for the catalytic decomposition of hydrogen peroxide in which the Fe center shuttles between the +2, +3, and +4 oxidation states is proposed to explain the non-integral stoichiometry observed for the iron substituted polytungstate catalyzed electroreduction of hydrogen peroxide.

The anions are also efficient electrocatalyst for the electrochemical conversion of nitric oxide to ammonia. The catalyzed reduction does not produce hydroxylamine as an intermediate and appears to depend upon the ability of the multiply reduced heteropolytungstates to deliver several electrons to the bound NO group in a concerted step. A valuable feature of the heteropolytungstates is the ease at which the formal potentials of the several redox couples they exhibit may be shifted by changing the identity of the central heteroatom. Exploitation of this feature provided diagnostic information that was decisive in establishing the mechanism of electrocatalytic reduction.

The iron substituted heteropolytungstates are not degraded by repeated cycling between their oxidized and reduced states. They also show superior activity compared to their unsubstituted analogues, indicating that the Fe center acts as a binding site that facilitates inner-sphere electron transfer processes. The basic electrochemistry of several other transition metal substituted Keggin ions is also described.

I. A recirculating charged-couple device. II. The mercury selenide on N-silicon Schottky barrier

A recirculating charge-coupled device structure has been devised. Entrance and exit gates allow a signal to be admitted, recirculated a given number of times, and then examined. In this way a small device permits simulation of a very long shift register without passing the signal through input and output diffusions. An oscilloscope motion picture demonstrating degradation of an actual circulating signal has been made. The performance of the device in simulating degradation of a signal by a very long shift register is well fit by a simple model based on transfer inefficiency.

Electrical properties of the mercury selenide on n-type chemically-cleaned silicon Schottky barrier have been studied. Barrier heights measured were 0.96 volts for the photoresponse technique and 0.90 volts for the current-voltage technique. These are the highest barriers yet reported on n-type silicon.

Structure-, stereochemistry-, and metal-regulated DNA binding/cleaving molecules

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.

Stopping power of gases for heavy ions

Pulse-height and time-of-flight methods have been used to measure the electronic stopping cross sections for projectiles of ¹²C, ¹⁶O, ¹⁹F, ²³Na, ²⁴Mg, and ²⁷Al, slowing in helium, neon, argon, krypton, and xenon. The ion energies were in the range 185 keV ≤ E ≤ 2560 keV.

A semiempirical calculation of the electronic stopping cross section for projectiles with atomic numbers between 6 and 13 passing through the inert gases has been performed using a modification of the Firsov model. Using Hartree-Slater-Fock orbitals, and summing over the losses for the individual charge states of the projectiles, good agreement has been obtained with the experimental data. The main features of the stopping cross section seen in the data, such as the Z₁ oscillation and the variation of the velocity dependence on Z₁ and Z₂, are present in the calculation. The inclusion of a modified form of the Bethe-Bloch formula as an additional term allows the increase of the velocity dependence for projectile velocities above v_o to be reproduced in the calculation.

A search for fractionally charged particles in cosmic rays and a theoretical interpretation of the results

An array of two spark chambers and six trays of plastic scintillation counters was used to search for unaccompanied fractionally charged particles in cosmic rays near sea level. No acceptable events were found with energy losses by ionization between 0.04 and 0.7 that of unit-charged minimum-ionizing particles. New 90%-confidence upper limits were thereby established for the fluxes of fractionally charged particles in cosmic rays, namely, (1.04 ± 0.07)x10^-10 and (2.03 ± 0.16)x10^-10 cm^-2sr^-1sec^-1 for minimum-ionizing particles with charges 1/3 and 2/3, respectively.

In order to be certain that the spark chambers could have functioned for the low levels of ionization expected from particles with small fractional charges, tests were conducted to estimate the efficiency of the chambers as they had been used in this experiment. These tests showed that the spark-chamber system with the track-selection criteria used might have been over 99% efficient for the entire range of energy losses considered.

Lower limits were then obtained for the mass of a quark by considering the above flux limits and a particular model for the production of quarks in cosmic rays. In this model, which is one involving the multi-peripheral Regge hypothesis, the production cross section and a corresponding mass limit are critically dependent on the Regge trajectory assigned to a quark. If quarks are "elementary'' with a flat trajectory, the mass of a quark can be expected to be at least 6 ± 2 BeV/c². If quarks have a trajectory with unit slope, just as the existing hadrons do, the mass of a quark might be as small as 1.3 ± 0.2 BeV/c². For a trajectory with unit slope and a mass larger than a couple of BeV/c², the production cross section may be so low that quarks might never be observed in nature.

Energy loss of light ions channeling in silicon

Experimental measurements of rate of energy loss were made for protons of energy .5 to 1.6 MeV channeling through 1 μm thick silicon targets along the <110>, <111>, and <211> axial directions, and the {100}, {110}, {111}, and {211} planar directions. A .05% resolution automatically controlled magnetic spectrometer was used. The data are presented graphically along with an extensive summary of data in the literature. The data taken cover a wider range of channels than has previously been examined, and are in agreement with the data of F. Eisen, et al., Radd. Eff. 13, 93 (1972).

The theory in the literature for channeling energy loss due to interaction with local electrons, core electrons, and distant valence electrons of the crystal atoms is summarized. Straggling is analyzed, and a computer program which calculates energy loss and straggling using this theory and the Moliere approximation to the Thomas Fermi potential, V_TF, and the detailed silicon crystal structure is described. Values for the local electron density Z_loc in each of the channels listed above are extracted from the data by graphical matching of the experimental and computer results.

Zeroth and second order contributions to Z_loc as a function of distance from the center of the channel were computed from ∇²V_TF = 4πρ for various channels in silicon. For data taken in this work and data of F. Eisen, et al., Rad. Eff. 13, 93 (1972), the calculated zeroth order contribution to Z_loc lies between the experimentally extracted Z_loc values obtained by using the peak and the leading edge of the transmission spectra, suggesting that the observed straggling is due both to statistical fluctuations and to path variation.