High pressure states in condensed matter: I. High pressure behavior of the iron-sulphur system with applications to the earth's core. II. Empirical equation of state for organic compounds at high pressures

Part I:

The earth's core is generally accepted to be composed primarily of iron, with an admixture of other elements. Because the outer core is observed not to transmit shear waves at seismic frequencies, it is known to be liquid or primarily liquid. A new equation of state is presented for liquid iron, in the form of parameters for the 4th order Birch-Murnaghan and Mie-Grüneisen equations of state. The parameters were constrained by a set of values for numerous properties compiled from the literature. A detailed theoretical model is used to constrain the P-T behavior of the heat capacity, based on recent advances in the understanding of the interatomic potentials for transition metals. At the reference pressure of 10⁵ Pa and temperature of 1811 K (the normal melting point of Fe), the parameters are: ρ = 7037 kg/m³, K_S0 = 110 GPa, K_S' = 4.53, K_S" = -.0337 GPa-1, and γ = 2.8, with γ α ρ^-1.17. Comparison of the properties predicted by this model with the earth model PREM indicates that the outer core is 8 to 10 % less dense than pure liquid Fe at the same conditions. The inner core is also found to be 3 to 5% less dense than pure liquid Fe, supporting the idea of a partially molten inner core. The density deficit of the outer core implies that the elements dissolved in the liquid Fe are predominantly of lower atomic weight than Fe. Of the candidate light elements favored by researchers, only sulfur readily dissolves into Fe at low pressure, which means that this element was almost certainly concentrated in the core at early times. New melting data are presented for FeS and FeS₂ which indicate that the FeS₂ is the S-hearing liquidus solid phase at inner core pressures. Consideration of the requirement that the inner core boundary be observable by seismological means and the freezing behavior of solutions leads to the possibility that the outer core may contain a significant fraction of solid material. It is found that convection in the outer core is not hindered if the solid particles are entrained in the fluid flow. This model for a core of Fe and S admits temperatures in the range 3450K to 4200K at the top of the core. An all liquid Fe-S outer core would require a temperature of about 4900 K at the top of the core.

Part II.

The abundance of uses for organic compounds in the modern world results in many applications in which these materials are subjected to high pressures. This leads to the desire to be able to describe the behavior of these materials under such conditions. Unfortunately, the number of compounds is much greater than the number of experimental data available for many of the important properties. In the past, one approach that has worked well is the calculation of appropriate properties by summing the contributions from the organic functional groups making up molecules of the compounds in question. A new set of group contributions for the molar volume, volume thermal expansivity, heat capacity, and the Rao function is presented for functional groups containing C, H, and O. This set is, in most cases, limited in application to low molecular liquids. A new technique for the calculation of the pressure derivative of the bulk modulus is also presented. Comparison with data indicates that the presented technique works very well for most low molecular hydrocarbon liquids and somewhat less well for oxygen-bearing compounds. A similar comparison of previous results for polymers indicates that the existing tabulations of group contributions for this class of materials is in need of revision. There is also evidence that the Rao function contributions for polymers and low molecular compounds are somewhat different.

On Ultrafast Time-Domain TeraHertz Spectroscopy in the Condensed Phase: Linear Spectroscopic Measurements of Hydrogen-Bond Dynamics of Astrochemical Ice Analogs and Nonlinear TeraHertz Kerr Effect Measurements of Vibrational Quantum Beats

Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz (THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz, 3 cm^-1 to 300 cm^-1, or 3000 μm to 30 μm) has been shown to provide unique possibilities in the study of condensed-phase processes. The goal of this work is to expand the possibilities available in the THz region and undertake new investigations of fundamental interest to chemistry. Since we are fundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz spectroscopy can provide new understanding: astrochemistry and solvation science. To advance these fields, we had to develop new instrumentation that would enable the experiments necessary to answer new questions in either astrochemistry or solvation science. We first developed a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz (THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm^-1) and the mid-IR (400 - 4000 cm^-1). The importance of astrochemical ices lies in their key role in the formation of complex organic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of performing variety of spectroscopic studies that can provide especially relevant laboratory data to support astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric Observatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array (ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm plasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz (~0.3 cm^-1) resolution.

Using the above instrumentation, experimental spectra of astrochemical ice analogs of water and carbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high vacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a new feature in both amorphous solid water and crystalline water at 33 cm^-1 (1 THz). In addition, our studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide as it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz spectra of mixed and layered ices are further analyzed by fitting their spectra features to those of pure amorphous solid water and crystalline water ice to quantify the effects of temperature changes on structure. From the results of this work, it appears that THz spectroscopy is potentially well suited to study thermal transformations within the ice.

To advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear THz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy. We implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased THz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS), and high numerical aperture optics which generates THz electric field in excess of 300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz (THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar interaction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument improves on both the frequency coverage, and sensitivity previously reported; it also ensures a backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we observe a quantum beat at 3.66 THz (122 cm^-1), in exact agreement with the fundamental transition frequency of the υ4 vibration of the molecule. This result provides new insight into dipolar vs. Raman selection rules at terahertz frequencies.

To conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab. We report the first results from an experiment using a plasma-based THz source for nonlinear spectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal resolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping. Finally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz data and how such a scheme could be implemented in the Blake lab. The instruments developed herein will hopefully remain a part of the groups core competencies and serve as building blocks for the next generation of THz instrumentation that pushes the frontiers of both chemistry and the scientific enterprise as a whole.

I. Phosphorescence and the true lifetime of triplet states in fluid solutions. II. Why is condensed oxygen blue?

I. PHOSPHORESCENCE AND THE TRUE LIFETIME OF TRIPLET STATES IN FLUID SOLUTIONS

Phosphorescence has been observed in a highly purified fluid solution of naphthalene in 3-methylpentane (3-MP). The phosphorescence lifetime of C₁₀H₈ in 3-MP at -45 °C was found to be 0.49 ± 0.07 sec, while that of C₁₀D₈ under identical conditions is 0.64 ± 0.07 sec. At this temperature 3-MP has the same viscosity (0.65 centipoise) as that of benzene at room temperature. It is believed that even these long lifetimes are dominated by impurity quenching mechanisms. Therefore it seems that the radiationless decay times of the lowest triplet states of simple aromatic hydrocarbons in liquid solutions are sensibly the same as those in the solid phase. A slight dependence of the phosphorescence lifetime on solvent viscosity was observed in the temperature region, -60° to -18°C. This has been attributed to the diffusion-controlled quenching of the triplet state by residual impurity, perhaps oxygen. Bimolecular depopulation of the triplet state was found to be of major importance over a large part of the triplet decay.

The lifetime of triplet C₁₀H₈ at room temperature was also measured in highly purified benzene by means of both phosphorescence and triplet-triplet absorption. The lifetime was estimated to be at least ten times shorter than that in 3-MP. This is believed to be due not only to residual impurities in the solvent but also to small amounts of impurities produced through unavoidable irradiation by the excitation source. In agreement with this idea, lifetime shortening caused by intense flashes of light is readily observed. This latter result suggests that experiments employing flash lamp techniques are not suitable for these kinds of studies.

The theory of radiationless transitions, based on Robinson's theory, is briefly outlined. A simple theoretical model which is derived from Fano's autoionization gives identical result.

Il. WHY IS CONDENSED OXYGEN BLUE?

The blue color of oxygen is mostly derived from double transitions. This paper presents a theoretical calculation of the intensity of the double transition (a ¹Δ_g) (a ¹Δ_g)←(X ³Σ_g^-) (X ³Σ_g^-), using a model based on a pair of oxygen molecules at a fixed separation of 3.81 Å. The intensity enhancement is assumed to be derived from the mixing (a ¹Δ_g) (a ¹Δ_g) _~~~ (X ³Σ_g^-) (X ³Σ_u^-) and (a ¹Δ_g) (¹Δ_u) _~~~ (X ³Σ_g^-) (X ³Σ_g^-). Matrix elements for these interactions are calculated using a π-electron approximation for the pair system. Good molecular wavefunctions are used for all but the perturbing (B ³Σ_u^-) state, which is approximated in terms of ground state orbitals. The largest contribution to the matrix elements arises from large intramolecular terms multiplied by intermolecular overlap integrals. The strength of interaction depends not only on the intermolecular separation of the two oxygen molecules, but also as expected on the relative orientation. Matrix elements are calculated for different orientations, and the angular dependence is fit to an analytical expression. The theory therefore not only predicts an intensity dependence on density but also one on phase at constant density. Agreement between theory and available experimental results is satisfactory considering the nature of the approximation, and indicates the essential validity of the overall approach to this interesting intensity enhancement problem.

Proton transfers at the air-water interface

Proton transfer reactions at the interface of water with hydrophobic media, such as air or lipids, are ubiquitous on our planet. These reactions orchestrate a host of vital phenomena in the environment including, for example, acidification of clouds, enzymatic catalysis, chemistries of aerosol and atmospheric gases, and bioenergetic transduction. Despite their importance, however, quantitative details underlying these interactions have remained unclear. Deeper insight into these interfacial reactions is also required in addressing challenges in green chemistry, improved water quality, self-assembly of materials, the next generation of micro-nanofluidics, adhesives, coatings, catalysts, and electrodes. This thesis describes experimental and theoretical investigation of proton transfer reactions at the air-water interface as a function of hydration gradients, electrochemical potential, and electrostatics. Since emerging insights hold at the lipid-water interface as well, this work is also expected to aid understanding of complex biological phenomena associated with proton migration across membranes.

Based on our current understanding, it is known that the physicochemical properties of the gas-phase water are drastically different from those of bulk water. For example, the gas-phase hydronium ion, H₃O⁺(g), can protonate most (non-alkane) organic species, whereas H₃O⁺(aq) can neutralize only relatively strong bases. Thus, to be able to understand and engineer water-hydrophobe interfaces, it is imperative to investigate this fluctuating region of molecular thickness wherein the ‘function’ of chemical species transitions from one phase to another via steep gradients in hydration, dielectric constant, and density. Aqueous interfaces are difficult to approach by current experimental techniques because designing experiments to specifically sample interfacial layers (< 1 nm thick) is an arduous task. While recent advances in surface-specific spectroscopies have provided valuable information regarding the structure of aqueous interfaces, but structure alone is inadequate to decipher the function. By similar analogy, theoretical predictions based on classical molecular dynamics have remained limited in their scope.

Recently, we have adapted an analytical electrospray ionization mass spectrometer (ESIMS) for probing reactions at the gas-liquid interface in real time. This technique is direct, surface-specific,and provides unambiguous mass-to-charge ratios of interfacial species. With this innovation, we have been able to investigate the following:

1. How do anions mediate proton transfers at the air-water interface?

2. What is the basis for the negative surface potential at the air-water interface?

3. What is the mechanism for catalysis ‘on-water’?

In addition to our experiments with the ESIMS, we applied quantum mechanics and molecular dynamics to simulate our experiments toward gaining insight at the molecular scale. Our results unambiguously demonstrated the role of electrostatic-reorganization of interfacial water during proton transfer events. With our experimental and theoretical results on the ‘superacidity’ of the surface of mildly acidic water, we also explored implications on atmospheric chemistry and green chemistry. Our most recent results explained the basis for the negative charge of the air-water interface and showed that the water-hydrophobe interface could serve as a site for enhanced autodissociation of water compared to the condensed phase.

The interplay of localization and interactions in quantum many-body systems

Disorder and interactions both play crucial roles in quantum transport. Decades ago, Mott showed that electron-electron interactions can lead to insulating behavior in materials that conventional band theory predicts to be conducting. Soon thereafter, Anderson demonstrated that disorder can localize a quantum particle through the wave interference phenomenon of Anderson localization. Although interactions and disorder both separately induce insulating behavior, the interplay of these two ingredients is subtle and often leads to surprising behavior at the periphery of our current understanding. Modern experiments probe these phenomena in a variety of contexts (e.g. disordered superconductors, cold atoms, photonic waveguides, etc.); thus, theoretical and numerical advancements are urgently needed. In this thesis, we report progress on understanding two contexts in which the interplay of disorder and interactions is especially important.

The first is the so-called “dirty” or random boson problem. In the past decade, a strong-disorder renormalization group (SDRG) treatment by Altman, Kafri, Polkovnikov, and Refael has raised the possibility of a new unstable fixed point governing the superfluid-insulator transition in the one-dimensional dirty boson problem. This new critical behavior may take over from the weak-disorder criticality of Giamarchi and Schulz when disorder is sufficiently strong. We analytically determine the scaling of the superfluid susceptibility at the strong-disorder fixed point and connect our analysis to recent Monte Carlo simulations by Hrahsheh and Vojta. We then shift our attention to two dimensions and use a numerical implementation of the SDRG to locate the fixed point governing the superfluid-insulator transition there. We identify several universal properties of this transition, which are fully independent of the microscopic features of the disorder.

The second focus of this thesis is the interplay of localization and interactions in systems with high energy density (i.e., far from the usual low energy limit of condensed matter physics). Recent theoretical and numerical work indicates that localization can survive in this regime, provided that interactions are sufficiently weak. Stronger interactions can destroy localization, leading to a so-called many-body localization transition. This dynamical phase transition is relevant to questions of thermalization in isolated quantum systems: it separates a many-body localized phase, in which localization prevents transport and thermalization, from a conducting (“ergodic”) phase in which the usual assumptions of quantum statistical mechanics hold. Here, we present evidence that many-body localization also occurs in quasiperiodic systems that lack true disorder.

Electronic states in disordered topological insulators

We present a theoretical study of electronic states in topological insulators with impurities. Chiral edge states in 2d topological insulators and helical surface states in 3d topological insulators show a robust transport against nonmagnetic impurities. Such a nontrivial character inspired physicists to come up with applications such as spintronic devices [1], thermoelectric materials [2], photovoltaics [3], and quantum computation [4]. Not only has it provided new opportunities from a practical point of view, but its theoretical study has deepened the understanding of the topological nature of condensed matter systems. However, experimental realizations of topological insulators have been challenging. For example, a 2d topological insulator fabricated in a HeTe quantum well structure by Konig et al. [5] shows a longitudinal conductance which is not well quantized and varies with temperature. 3d topological insulators such as Bi₂Se₃ and Bi₂Te₃ exhibit not only a signature of surface states, but they also show a bulk conduction [6]. The series of experiments motivated us to study the effects of impurities and coexisting bulk Fermi surface in topological insulators. We first address a single impurity problem in a topological insulator using a semiclassical approach. Then we study the conductance behavior of a disordered topological-metal strip where bulk modes are associated with the transport of edge modes via impurity scattering. We verify that the conduction through a chiral edge channel retains its topological signature, and we discovered that the transmission can be succinctly expressed in a closed form as a ratio of determinants of the bulk Green's function and impurity potentials. We further study the transport of 1d systems which can be decomposed in terms of chiral modes. Lastly, the surface impurity effect on the local density of surface states over layers into the bulk is studied between weak and strong disorder strength limits.

Direct simulation of proton-coupled electron transfer reaction dynamics and mechanisms

Proton-coupled electron transfer (PCET) reactions are ubiquitous throughout chemistry and biology. However, challenges arise in both the the experimental and theoretical investigation of PCET reactions; the rare-event nature of the reactions and the coupling between quantum mechanical electron- and proton-transfer with the slower classical dynamics of the surrounding environment necessitates the development of robust simulation methodology. In the following dissertation, novel path-integral based methods are developed and employed for the direct simulation of the reaction dynamics and mechanisms of condensed-phase PCET.

Nonlinear Effects in Granular Crystals with Broken Periodicity

When studying physical systems, it is common to make approximations: the contact interaction is linear, the crystal is periodic, the variations occurs slowly, the mass of a particle is constant with velocity, or the position of a particle is exactly known are just a few examples. These approximations help us simplify complex systems to make them more comprehensible while still demonstrating interesting physics. But what happens when these assumptions break down? This question becomes particularly interesting in the materials science community in designing new materials structures with exotic properties In this thesis, we study the mechanical response and dynamics in granular crystals, in which the approximation of linearity and infinite size break down. The system is inherently finite, and contact interaction can be tuned to access different nonlinear regimes. When the assumptions of linearity and perfect periodicity are no longer valid, a host of interesting physical phenomena presents itself. The advantage of using a granular crystal is in its experimental feasibility and its similarity to many other materials systems. This allows us to both leverage past experience in the condensed matter physics and materials science communities while also presenting results with implications beyond the narrower granular physics community. In addition, we bring tools from the nonlinear systems community to study the dynamics in finite lattices, where there are inherently more degrees of freedom. This approach leads to the major contributions of this thesis in broken periodic systems. We demonstrate the first defect mode whose spatial profile can be tuned from highly localized to completely delocalized by simply tuning an external parameter. Using the sensitive dynamics near bifurcation points, we present a completely new approach to modifying the incremental stiffness of a lattice to arbitrary values. We show how using nonlinear defect modes, the incremental stiffness can be tuned to anywhere in the force-displacement relation. Other contributions include demonstrating nonlinear breakdown of mechanical filters as a result of finite size, and the presents of frequency attenuation bands in essentially nonlinear materials. We finish by presenting two new energy harvesting systems based on our experience with instabilities in weakly nonlinear systems.

Secondary Organic Aerosol Composition Studies Using Mass Spectrometry

Trace volatile organic compounds emitted by biogenic and anthropogenic sources into the atmosphere can undergo extensive photooxidation to form species with lower volatility. By equilibrium partitioning or reactive uptake, these compounds can nucleate into new aerosol particles or deposit onto already-existing particles to form secondary organic aerosol (SOA). SOA and other atmospheric particulate matter have measurable effects on global climate and public health, making understanding SOA formation a needed field of scientific inquiry. SOA formation can be done in a laboratory setting, using an environmental chamber; under these controlled conditions it is possible to generate SOA from a single parent compound and study the chemical composition of the gas and particle phases. By studying the SOA composition, it is possible to gain understanding of the chemical reactions that occur in the gas phase and particle phase, and identify potential heterogeneous processes that occur at the surface of SOA particles. In this thesis, mass spectrometric methods are used to identify qualitatively and qualitatively the chemical components of SOA derived from the photooxidation of important anthropogenic volatile organic compounds that are associated with gasoline and diesel fuels and industrial activity (C12 alkanes, toluene, and o-, m-, and p-cresols). The conditions under which SOA was generated in each system were varied to explore the effect of NO_x and inorganic seed composition on SOA chemical composition. The structure of the parent alkane was varied to investigate the effect on the functionalization and fragmentation of the resulting oxidation products. Relative humidity was varied in the alkane system as well to measure the effect of increased particle-phase water on condensed-phase reactions. In all systems, oligomeric species, resulting potentially from particle-phase and heterogeneous processes, were identified. Imines produced by reactions between (NH₄)₂SO₄ seed and carbonyl compounds were identified in all systems. Multigenerational photochemistry producing low- and extremely low-volatility organic compounds (LVOC and ELVOC) was reflected strongly in the particle-phase composition as well.

Numerical Studies of Topological Phases

The topological phases of matter have been a major part of condensed matter physics research since the discovery of the quantum Hall effect in the 1980s. Recently, much of this research has focused on the study of systems of free fermions, such as the integer quantum Hall effect, quantum spin Hall effect, and topological insulator. Though these free fermion systems can play host to a variety of interesting phenomena, the physics of interacting topological phases is even richer. Unfortunately, there is a shortage of theoretical tools that can be used to approach interacting problems. In this thesis I will discuss progress in using two different numerical techniques to study topological phases.

Recently much research in topological phases has focused on phases made up of bosons. Unlike fermions, free bosons form a condensate and so interactions are vital if the bosons are to realize a topological phase. Since these phases are difficult to study, much of our understanding comes from exactly solvable models, such as Kitaev's toric code, as well as Levin-Wen and Walker-Wang models. We may want to study systems for which such exactly solvable models are not available. In this thesis I present a series of models which are not solvable exactly, but which can be studied in sign-free Monte Carlo simulations. The models work by binding charges to point topological defects. They can be used to realize bosonic interacting versions of the quantum Hall effect in 2D and topological insulator in 3D. Effective field theories of "integer" (non-fractionalized) versions of these phases were available in the literature, but our models also allow for the construction of fractional phases. We can measure a number of properties of the bulk and surface of these phases.

Few interacting topological phases have been realized experimentally, but there is one very important exception: the fractional quantum Hall effect (FQHE). Though the fractional quantum Hall effect we discovered over 30 years ago, it can still produce novel phenomena. Of much recent interest is the existence of non-Abelian anyons in FQHE systems. Though it is possible to construct wave functions that realize such particles, whether these wavefunctions are the ground state is a difficult quantitative question that must be answered numerically. In this thesis I describe progress using a density-matrix renormalization group algorithm to study a bilayer system thought to host non-Abelian anyons. We find phase diagrams in terms of experimentally relevant parameters, and also find evidence for a non-Abelian phase known as the "interlayer Pfaffian".

Forced convection film boiling of subcooled water around a sphere

An experimental investigation was made of forced convection film boiling of subcooled water around a sphere at atmospheric pressure. The water was sufficiently cool that the vapor condensed before leaving the film with the result that no vapor bubbles left the film. The experimental runs were made using inductively heated spheres at temperatures above 740°C. and using inlet water temperatures between 15°C. and 27°C. The spheres used had diameters of 1/2 inch, 9/16 inch, and 3/8 inch and were supported by the liquid flow. Reynolds numbers between 60 and 700 were used.

Analysis of the collected non-condensables indicated that oxygen and nitrogen dissolved in the water accumulated within the vapor film and that hetrogeneous chemical reactions occurred at the sphere surface. An iron-steam reaction resulted in more than 20% by volume hydrogen in the film at wall temperatures above 900°C. At temperatures near 1100°C. more than 80% by volume of the film was composed of hydrogen. It was found that gold plating of the sphere could eliminate this reaction.

Material and energy balances were used to derive equations which may be used to predict the overall average heat transfer coefficients for subcooled film boiling around a sphere. These equations include the effect of dissolved gases in the water. Equations also were derived which may be used to predict the composition of the film for cases in which an equilibrium exists between the dissolved gases and the gases in the film.

The derived equations were compared to the experimental results. It was found that a correlation existed between the Nusselt number for heat transfer from the vapor-liquid interface into the liquid and the Reynolds number, liquid Prandtl number product. In addition, it was found that the percentage of dissolved oxygen removed during the film boiling could be predicted to within 10%.

Part I. Synchronization of the cell division cycle of HeLa cells in suspension cultures. Part II. Studies on chromosomal proteins of HeLa cells during the cell division cycle

Part I

These studies investigate the potential of single and double treatments with either 5-fluorodeoxyuridine of excess thymidine to induce cell division synchrony in suspension cultures of HeLa cells. The patterns of nucleic acid synthesis and cell proliferation have been analyzed in cultures thus synchronized. Several changes in cell population during long incubation with 5-fluorodeoxyuridine or excess thymidine are also described. These results are subjected to detailed evaluation in terms of the degree and quality of synchrony finally achieved.

Part II

Histones and non-histone proteins associated with interphase and metaphase chromosomes of HeLa cells have been qualitatively and quantitatively analyzed. Histones were fractionated by chromatography on Amberlite CG-50 and further characterized by analytical disc electrophoresis and amino acid analysis of each chromatographic fraction. It is concluded that histones of HeLa cells are comprised of only a small number of major components and that these components are homologous to those of other higher organisms. Of all the histones, arginine-rich histone III alone contains cysteine and can polymerize through formation of intermolecular disulfide bridges between histone III monomers.

A detailed comparison by chromatography and disc electrophoresis established that interphase and metaphase histones are made up of similar components. However, certain quantitative differences in proportions of different histones of interphase and metaphase cells are reported. Indirect evidence indicates that a certain proportion of metaphase histone III is polymerized through intermolecular disulfide links, whereas interphase histone III occurs mainly in the monomeric form.

Metaphase chromosomes are associated with an additional acid-soluble protein fraction which is absent from interphase chromosomes. All of these additional acid-soluble proteins of metaphase chromosomes are shown to be non-histones and it is concluded that the histone/DNA ratio is identical in interphase and metaphase chromosomes. The bulk of acid-soluble non-histone proteins of metaphase chromosomes were found to be polymerized through disulfide bridges; corresponding interphase non-histone proteins displayed no evidence of similar polymerization.

The factors responsible for the condensed configuration and metabolic inactivity of metaphase chromosomes are discussed in light of these findings.

The relationship between histone and DNA synthesis in nondividing differentiated chicken erythrocyte cells and in rapidly dividing undifferentiated HeLa cells is also investigated. Of all the histones, only arginine-rich histones are synthesized in mature erythrocytes. Histone synthesis in HeLa cells was studied in both unsynchronized and synchronized cultures. In HeLa cells, only part of the synthesis of all histone fractions is dependent on concurrent DNA synthesis, whereas all histones are synthesized in varying degrees even in the absence of DNA synthesis.

Development of a Cationic Mucic Acid Polymer-Based Nanoparticle siRNA Delivery System

Cancer chemotherapy has advanced from highly toxic drugs to more targeted treatments in the last 70 years. Chapter 1 opens with an introduction to targeted therapy for cancer. The benefits of using a nanoparticle to deliver therapeutics are discussed. We move on to siRNA in particular, and why it would be advantageous as a therapy. Specific to siRNA delivery are some challenges, such as nuclease degradation, quick clearance from circulation, needing to enter cells, and getting to the cytosol. We propose the development of a nanoparticle delivery system to tackle these challenges so that siRNA can be effective.

Chapter 2 of this thesis discusses the synthesis and analysis of a cationic mucic acid polymer (cMAP) which condenses siRNA to form a nanoparticle. Various methods to add polyethylene glycol (PEG) for stabilizing the nanoparticle in physiologic solutions, including using a boronic acid binding to diols on mucic acid, forming a copolymer of cMAP with PEG, and creating a triblock with mPEG on both ends of cMAP. The goal of these various pegylation strategies was to increase the circulation time of the siRNA nanoparticle in the bloodstream to allow more of the nanoparticle to reach tumor tissue by the enhanced permeation and retention effect. We found that the triblock mPEG-cMAP-PEGm polymer condensed siRNA to form very stable 30-40 nm particles that circulated for the longest time – almost 10% of the formulation remained in the bloodstream of mice 1 h after intravenous injection.

Chapter 3 explores the use of an antibody as a targeting agent for nanoparticles. Some antibodies of the IgG1 subtype are able to recruit natural killer cells that effect antibody dependent cellular cytotoxicity (ADCC) to kill the targeted cell to which the antibody is bound. There is evidence that the ADCC effect remains in antibody-drug conjugates, so we wanted to know whether the ADCC effect is preserved when the antibody is bound to a nanoparticle, which is a much larger and complex entity. We utilized antibodies against epidermal growth factor receptor with similar binding and pharmacokinetics, cetuximab and panitumumab, which differ in that cetuximab is an IgG1 and panitumumab is an IgG2 (which does not cause ADCC). Although a natural killer cell culture model showed that gold nanoparticles with a full antibody targeting agent can elicit target cell lysis, we found that this effect was not preserved in vivo. Whether this is due to the antibody not being accessible to immune cells or whether the natural killer cells are inactivated in a tumor xenograft remains unknown. It is possible that using a full antibody still has value if there are immune functions which are altered in a complex in vivo environment that are intact in an in vitro system, so the value of using a full antibody as a targeting agent versus using an antibody fragment or a protein such as transferrin is still open to further exploration.

In chapter 4, nanoparticle targeting and endosomal escape are further discussed with respect to the cMAP nanoparticle system. A diboronic acid entity, which gives an order of magnitude greater binding (than boronic acid) to cMAP due to the vicinal diols in mucic acid, was synthesized, attached to 5kD or 10kD PEG, and conjugated to either transferrin or cetuximab. A histidine was incorporated into the triblock polymer between cMAP and the PEG blocks to allow for siRNA endosomal escape. Nanoparticle size remained 30-40 nm with a slightly negative ca. -3 mV zeta potential with the triblock polymer containing histidine and when targeting agents were added. Greater mRNA knockdown was seen with the endosomal escape mechanism than without. The nanoparticle formulations were able to knock down the targeted mRNA in vitro. Mixed effects suggesting function were seen in vivo.

Chapter 5 summarizes the project and provides an outlook on siRNA delivery as well as targeted combination therapies for the future of personalized medicine in cancer treatment.