The theory of long distance electron transfer reactions

The rate of electron transport between distant sites was studied. The rate depends crucially on the chemical details of the donor, acceptor, and surrounding medium. These reactions involve electron tunneling through the intervening medium and are, therefore, profoundly influenced by the geometry and energetics of the intervening molecules. The dependence of rate on distance was considered for several rigid donor-acceptor "linkers" of experimental importance. Interpretation of existing experiments and predictions for new experiments were made.

The electronic and nuclear motion in molecules is correlated. A Born-Oppenheimer separation is usually employed in quantum chemistry to separate this motion. Long distance electron transfer rate calculations require the total donor wave function when the electron is very far from its binding nuclei. The Born-Oppenheimer wave functions at large electronic distance are shown to be qualitatively wrong. A model which correctly treats the coupling was proposed. The distance and energy dependence of the electron transfer rate was determined for such a model.

Biological electron transfer in copper proteins

Nature has used a variety of protein systems to mediate electron transfer. In this thesis I examine aspects of the control of biological electron transfer by two copper proteins that act as natural electron carriers.

In the first study, I have made a mutation to one of the ligand residues in the azurin blue copper center, methionine 121 changed to a glutamic acid. Studies of intramolecular electron transfer rates from that mutated center to covalently attached ruthenium complexes indicate that the weak axial methionine ligand is important not only for tuning the reduction potential of the blue copper site but also for maintaining the low reorganization energy that is important for fast electron transfer at long distances.

In the second study, I begin to examine the reorganization energy of the purple copper center in the CuA domain of subunit II of cytochrome c oxidase. In this copper center, the unpaired electron is delocalized over the entire binuclear site. Because long-range electron transfer into and out of this center occurs over long distances with very small driving forces, the reorganization energy of the CuA center has been predicted to be extremely low. I describe a strategy for measuring this reorganization energy starting with the construction of a series of mutations introducing surface histidines. These histidines can then be labeled with a series of ruthenium compounds that differ primarily in their reduction potentials. The electron transfer rates to these ruthenium compounds can then be used to determine the reorganization energy of the CuA site.

Functional evaluation of noncovalent interactions in neuroreceptors and progress toward the expansion of unnatural amino acid methodology

This dissertation primarily describes chemical-scale studies of G protein-coupled receptors and Cys-loop ligand-gated ion channels to better understand ligand binding interactions and the mechanism of channel activation using recently published crystal structures as a guide. These studies employ the use of unnatural amino acid mutagenesis and electrophysiology to measure subtle changes in receptor function.

In chapter 2, the role of a conserved aromatic microdomain predicted in the D3 dopamine receptor is probed in the closely related D2 and D4 dopamine receptors. This domain was found to act as a structural unit near the ligand binding site that is important for receptor function. The domain consists of several functionally important noncovalent interactions including hydrogen bond, aromatic-aromatic, and sulfur-π interactions that show strong couplings by mutant cycle analysis. We also assign an alternate interpretation for the linear fluorination plot observed at W6.48, a residue previously thought to participate in a cation-π interaction with dopamine.

Chapter 3 outlines attempts to incorporate chemically synthesized and in vitro acylated unnatural amino acids into mammalian cells. While our attempts were not successful, method optimizations and data for nonsense suppression with an in vivo acylated tRNA are included. This chapter is aimed to aid future researchers attempting unnatural amino acid mutagenesis in mammalian cells.

Chapter 4 identifies a cation-π interaction between glutamate and a tyrosine residue on loop C in the GluClβ receptor. Using the recently published crystal structure of the homologous GluClα receptor, other ligand-binding and protein-protein interactions are probed to determine the similarity between this invertebrate receptor and other more distantly related vertebrate Cys-loop receptors. We find that many of the interactions previously observed are conserved in the GluCl receptors, however care must be taken when extrapolating structural data.

Chapter 5 examines inherent properties of the GluClα receptor that are responsible for the observed glutamate insensitivity of the receptor. Chimera synthesis and mutagenesis reveal the C-terminal portion of the M4 helix and the C-terminus as contributing to formation of the decoupled state, where ligand binding is incapable of triggering channel gating. Receptor mutagenesis was unable to identify single residue mismatches or impaired protein-protein interactions within this domain. We conclude that M4 helix structure and/or membrane dynamics are likely the cause of ligand insensitivity in this receptor and that the M4 helix has an role important in the activation process.

The logic of receptor-ligand interactions in the Notch signaling pathway

The Notch signaling pathway enables neighboring cells to coordinate developmental fates in diverse processes such as angiogenesis, neuronal differentiation, and immune system development. Although key components and interactions in the Notch pathway are known, it remains unclear how they work together to determine a cell's signaling state, defined as its quantitative ability to send and receive signals using particular Notch receptors and ligands. Recent work suggests that several aspects of the system can lead to complex signaling behaviors: First, receptors and ligands interact in two distinct ways, inhibiting each other in the same cell (in cis) while productively interacting between cells (in trans) to signal. The ability of a cell to send or receive signals depends strongly on both types of interactions. Second, mammals have multiple types of receptors and ligands, which interact with different strengths, and are frequently co-expressed in natural systems. Third, the three mammalian Fringe proteins can modify receptor-ligand interaction strengths in distinct and ligand-specific ways. Consequently, cells can exhibit non-intuitive signaling states even with relatively few components.

In order to understand what signaling states occur in natural processes, and what types of signaling behaviors they enable, this thesis puts forward a quantitative and predictive model of how the Notch signaling state is determined by the expression levels of receptors, ligands, and Fringe proteins. To specify the parameters of the model, we constructed a set of cell lines that allow control of ligand and Fringe expression level, and readout of the resulting Notch activity. We subjected these cell lines to an assay to quantitatively assess the levels of Notch ligands and receptors on the surface of individual cells. We further analyzed the dependence of these interactions on the level and type of Fringe expression. We developed a mathematical modeling framework that uses these data to predict the signaling states of individual cells from component expression levels. These methods allow us to reconstitute and analyze a diverse set of Notch signaling configurations from the bottom up, and provide a comprehensive view of the signaling repertoire of this major signaling pathway.

Generation of strong quasistatic magnetic fields in interactions of ultraintense and short laser pulses with overdense plasma targets

An analytical fluid model is proposed for the generation of strong quasistatic magnetic fields during normal incidence of a short ultraintense Gaussian laser pulse with a finite spot size on an overdense plasma. The steepening of the electron density profile in the originally homogeneous overdense plasma and the formation of electron cavitation as the electrons are pushed inward by the laser are included self-consistently. It is shown that the appearance of the cavitation plays an important role in the generation of quasistatic magnetic fields: the strong plasma inhomogeneities caused by the formation of the electron cavitation lead to the generation of a strong axial quasistatic magnetic field B-z. In the overdense regime, the generated quasistatic magnetic field increases with increasing laser intensity, while it decreases with increasing plasma density. It is also found that, in a moderately overdense plasma, highly intense laser pulses can generate magnetic fields similar to 100 MG and greater due to the transverse linear mode conversion process.

High temperature transport properties of lead chalcogenides and their alloys

This thesis describes a series of experimental studies of lead chalcogenide thermoelectric semiconductors, mainly PbSe. Focusing on a well-studied semiconductor and reporting good but not extraordinary zT, this thesis distinguishes itself by answering the following questions that haven’t been answered: What represents the thermoelectric performance of PbSe? Where does the high zT come from? How (and how much) can we make it better? For the first question, samples were made with highest quality. Each transport property was carefully measured, cross-verified and compared with both historical and contemporary report to overturn commonly believed underestimation of zT. For n- and p-type PbSe zT at 850 K can be 1.1 and 1.0, respectively. For the second question, a systematic approach of quality factor B was used. In n-type PbSe zT is benefited from its high-quality conduction band that combines good degeneracy, low band mass and low deformation potential, whereas zT of p-type is boosted when two mediocre valence bands converge (in band edge energy). In both cases the thermal conductivity from PbSe lattice is inherently low. For the third question, the use of solid solution lead chalcogenide alloys was first evaluated. Simple criteria were proposed to help quickly evaluate the potential of improving zT by introducing atomic disorder. For both PbTe1-xSex and PbSe1-xSx, the impacts in electron and phonon transport compensate each other. Thus, zT in each case was roughly the average of two binary compounds. In p-type Pb1-xSrxSe alloys an improvement of zT from 1.1 to 1.5 at 900 K was achieved, due to the band engineering effect that moves the two valence bands closer in energy. To date, making n-type PbSe better hasn’t been accomplished, but possible strategy is discussed.

Cosmological consequences of dark matter interactions and vacuum fluctuations

This thesis is divided into two parts: interacting dark matter and fluctuations in cosmology. There is an incongruence between the properties that dark matter is expected to possess between the early universe and the late universe. Weakly-interacting dark matter yields the observed dark matter relic density and is consistent with large-scale structure formation; however, there is strong astrophysical evidence in favor of the idea that dark matter has large self-interactions. The first part of this thesis presents two models in which the nature of dark matter fundamentally changes as the universe evolves. In the first model, the dark matter mass and couplings depend on the value of a chameleonic scalar field that changes as the universe expands. In the second model, dark matter is charged under a hidden SU(N) gauge group and eventually undergoes confinement. These models introduce very different mechanisms to explain the separation between the physics relevant for freezeout and for small-scale dynamics.

As the universe continues to evolve, it will asymptote to a de Sitter vacuum phase. Since there is a finite temperature associated with de Sitter space, the universe is typically treated as a thermal system, subject to rare thermal fluctuations, such as Boltzmann brains. The second part of this thesis begins by attempting to escape this unacceptable situation within the context of known physics: vacuum instability induced by the Higgs field. The vacuum decay rate competes with the production rate of Boltzmann brains, and the cosmological measures that have a sufficiently low occurrence of Boltzmann brains are given more credence. Upon further investigation, however, there are certain situations in which de Sitter space settles into a quiescent vacuum with no fluctuations. This reasoning not only provides an escape from the Boltzmann brain problem, but it also implies that vacuum states do not uptunnel to higher-energy vacua and that perturbations do not decohere during slow-roll inflation, suggesting that eternal inflation is much less common than often supposed. Instead, decoherence occurs during reheating, so this analysis does not alter the conventional understanding of the origin of density fluctuations from primordial inflation.

Microstructure control and iodine doping of bismuth telluride

On the materials scale, thermoelectric efficiency is defined by the dimensionless figure of merit zT. This value is made up of three material components in the form zT = Tα²/ρκ, where α is the Seebeck coefficient, ρ is the electrical resistivity, and κ is the total thermal conductivity. Therefore, in order to improve zT would require the reduction of κ and ρ while increasing α. However due to the inter-relation of the electrical and thermal properties of materials, typical routes to thermoelectric enhancement come in one of two forms. The first is to isolate the electronic properties and increase α without negatively affecting ρ. Techniques like electron filtering, quantum confinement, and density of states distortions have been proposed to enhance the Seebeck coefficient in thermoelectric materials. However, it has been difficult to prove the efficacy of these techniques. More recently efforts to manipulate the band degeneracy in semiconductors has been explored as a means to enhance α.

The other route to thermoelectric enhancement is through minimizing the thermal conductivity, κ. More specifically, thermal conductivity can be broken into two parts, an electronic and lattice term, κ_e and κ_l respectively. From a functional materials standpoint, the reduction in lattice thermal conductivity should have a minimal effect on the electronic properties. Most routes incorporate techniques that focus on the reduction of the lattice thermal conductivity. The components that make up κ_l (κ_l = 1/3Cνl) are the heat capacity (C), phonon group velocity (ν), and phonon mean free path (l). Since the difficulty is extreme in altering the heat capacity and group velocity, the phonon mean free path is most often the source of reduction.

Past routes to decreasing the phonon mean free path has been by alloying and grain size reduction. However, in these techniques the electron mobility is often negatively affected because in alloying any perturbation to the periodic potential can cause additional adverse carrier scattering. Grain size reduction has been another successful route to enhancing zT because of the significant difference in electron and phonon mean free paths. However, grain size reduction is erratic in anisotropic materials due to the orientation dependent transport properties. However, microstructure formation in both equilibrium and nonequilibrium processing routines can be used to effectively reduce the phonon mean free path as a route to enhance the figure of merit.

This work starts with a discussion of several different deliberate microstructure varieties. Control of the morphology and finally structure size and spacing is discussed at length. Since the material example used throughout this thesis is anisotropic a short primer on zone melting is presented as an effective route to growing homogeneous and oriented polycrystalline material. The resulting microstructure formation and control is presented specifically in the case of In₂Te₃-Bi₂Te₃ composites and the transport properties pertinent to thermoelectric materials is presented. Finally, the transport and discussion of iodine doped Bi₂Te₃ is presented as a re-evaluation of the literature data and what is known today.

Eggs of British Meniscus midges (diptera;dixidae) observed by scanning electron microscopy

The egg of Dixella martinii is described for the first time. The eggs of the Dixidae are placed in three morphological groups: bulbous and meshed; streamlined and smooth; streamlined and minutely spiculated. Ten of the fourteen species known from Britain are placed in these groups. After a detailed description of the egg of D. martinii, the three morphological groups are described and scanning electron micrographs are provided.

Conduction-electron localized-moment interaction in palladium-silicon base amorphous alloys containing transition metals

The electrical and magnetic properties of amorphous alloys obtained by rapid quenching from the liquid state have been studied. The composition of these alloys corresponds to the general formula M_xPd<sub>80-xSi₂₀, in which M stands for a metal of the first transition series between chromium and nickel and x is its atomic concentration. The concentration ranges within which an amorphous structure could be obtained were: from 0 to 7 for Cr, Mn and Fe, from 0 to 11 for Co and from 0 to 15 for Ni. A well-defined minimum in the resistivity vs temperature curve was observed for all alloys except those containing nickel. The alloys for which a resistivity minimum was observed had a negative magnetoresistivity approximately proportional to the square of the magnetization and their susceptibility obeyed the Curie-Weiss law in a wide temperature range. For concentrated Fe and Co alloys the resistivity minimum was found to coexist with ferromagnetism. These observations lead to the conclusion that the present results are due to a s-d exchange interaction. The unusually high resistivity minimum temperature observed in the Cr alloys is interpreted as a result of a high Kondo temperature and a large s-d exchange integral. A low Fermi energy of the amorphous alloys (3.5 eV) is also responsible for the anomalies due to the s-d exchange interaction.

Acceleration of ultra-thin electron layer.Analytical treatment compared with 1D-PIC simulation

In this paper, we apply an analytical model [V.V. Kulagin et al., Phys. Plasmas 14, 113101 (2007)] to describe the acceleration of an ultra-thin electron layer by a schematic single-cycle laser pulse and compare with one-dimensional particle-in-cell (1D-PIC) simulations. This is in the context of creating a relativistic mirror for coherent backscattering and supplements two related papers in this EPJD volume. The model is shown to reproduce the 1D-PIC results almost quantitatively for the short time of a few laser periods sufficient for the backscattering of ultra-short probe pulses.

Silicide formation and the interaction of metals with polycrystalline Si

The main factors affecting solid-phase Si-metal interactions are reported in this work. The influence of the orientation of the Si substrates and the presence of impurities in metal films and at the Si-metal interface on the formation of nickel and chromium silicides have been demonstrated. We have observed that the formation and kinetic rate of growth of nickel silicides is strongly dependent on the orientation and crystallinity of the Si substrates; a fact which, up to date, has never been seriously investigated in silicide formation. Impurity contaminations in the Cr film and at the Si-Cr interface are the most dominant influencing factors in the formation and kinetic rate of growth of CrSi₂. The potentiality and use of silicides as a diffusion barrier in metallization on silicon devices were also investigated.

Two phases, Ni₂Si and NiSi, form simultaneously in two distinct sublayers in the reaction of Ni with amorphous Si, while only the former phase was observed on other substrates. On (111) oriented Si substrates the growth rate is about 2 to 3 times less than that on <100> or polycrystalline Si. Transmission electron micrographs establish-·that silicide layers grown on different substrates have different microcrystalline structures. The concept of grain-boundary diffusion is speculated to be an important factor in silicide formation.

The composition and kinetic rate of CrSi₂ formation are not influenced by the underlying Si substrate. While the orientation of the Si substrate does not affect the formation of CrSi₂ , the purity of the Cr film and the state of Si-Cr interface become the predominant factors in the reaction process. With an interposed layer of Pd<sub>2Si between the Cr film and the Si substrate, CrSi₂ starts to form at a much lower temperature (400°C) relative to the Si-Cr system. However, the growth rate of CrSi₂ is observed to be independent of the thickness of the Pd2Si layer. For both Si-Cr and Si-Pd<sub>2Si-Cr samples, the growth rate is linear with time with an activation energy of 1.7 ± 0.1 ev.

A tracer technique using radioactive ³¹Si (T_1/2 = 2.26 h) was used to study the formation of CrSi₂ on Pd<sub>2Si. It is established from this experiment that the growth of CrSi₂ takes place partly by transport of Si directly from the Si substrate and partly by breaking Pd<sub>2Si bonds, making free Si atoms available for the growth process.

The role of CrSi₂ in Pd-Al metallization on Si was studied. It is established that a thin CrSi₂ layer can be used as a diffusion barrier to prevent Al from interacting with Pd<sub>2Si in the Pd-Al metallization on Si.

As a generalization of what has been observed for polycrystalline-Si-Al interaction, the reactions between polycrystalline Si (poly Si) and other metals were studied. The metals investigated include Ni, Cr, Pd, Ag and Au. For Ni, Cr and Pd, annealing results in silicide formation, at temperatures similar to those observed on single crystal Si substrates. For Al, Ag and Au, which form simple eutectics with Si annealing results in erosion of the poly Si layer and growth of Si crystallites in the metal films.

Backscattering spectrometry with 2.0 and 2.3 MeV ⁴He ions was the main analytical tool used in all our investigations. Other experimental techniques include the Read camera glancing angle x-ray diffraction, scanning electron, optical and transmission electron microscopy. Details of these analytical techniques are given in Chapter II.

Influence of composition on the structure, electric and magnetic properties of Pd-Mn-P and Pd-Co-P amorphous alloys

The influence of composition on the structure and on the electric and magnetic properties of amorphous Pd-Mn-P and Pd-Co-P prepared by rapid quenching techniques were investigated in terms of (1) the 3d band filling of the first transition metal group, (2) the phosphorus concentration effect which acts as an electron donor and (3) the transition metal concentration.

The structure is essentially characterized by a set of polyhedra subunits essentially inverse to the packing of hard spheres in real space. Examination of computer generated distribution functions using Monte Carlo random statistical distribution of these polyhedra entities demonstrated tile reproducibility of the experimentally calculated atomic distribution function. As a result, several possible "structural parameters" are proposed such as: the number of nearest neighbors, the metal-to-metal distance, the degree of short-range order and the affinity between metal-metal and metal-metalloid. It is shown that the degree of disorder increases from Ni to Mn. Similar behavior is observed with increase in the phosphorus concentration.

The magnetic properties of Pd-Co-P alloys show that they are ferromagnetic with a Curie temperature between 272 and 399°K as the cobalt concentration increases from 15 to 50 at.%. Below 20 at.% Co the short-range exchange interactions which produce the ferromagnetism are unable to establish a long-range magnetic order and a peak in the magnetization shows up at the lowest temperature range . The electric resistivity measurements were performed from liquid helium temperatures up to the vicinity of the melting point (900°K). The thermomagnetic analysis was carried out under an applied field of 6.0 kOe. The electrical resistivity of Pd-Co-P shows the coexistence of a Kondo-like minimum with ferromagnetism. The minimum becomes less important as the transition metal concentration increases and the coefficients of ℓn T and T^2 become smaller and strongly temperature dependent. The negative magnetoresistivity is a strong indication of the existence of localized moment.

The temperature coefficient of resistivity which is positive for Pd- Fe-P, Pd-Ni-P, and Pd-Co-P becomes negative for Pd-Mn-P. It is possible to account for the negative temperature dependence by the localized spin fluctuation model and the high density of states at the Fermi energy which becomes maximum between Mn and Cr. The magnetization curves for Pd-Mn-P are typical of those resulting from the interplay of different exchange forces. The established relationship between susceptibility and resistivity confirms the localized spin fluctuation model. The magnetoresistivity of Pd-Mn-P could be interpreted in tenns of a short-range magnetic ordering that could arise from the Rudennan-Kittel type interactions.

Damping and saturation of a second order electron plasma wave echo

A description is given of experimental work on the damping of a second order electron plasma wave echo due to velocity space diffusion in a low temperature magnetoplasma. Sufficient precision was obtained to verify the theoretically predicted cubic rather than quadratic or quartic dependence of the damping on exciter separation. Compared to the damping predicted for Coulomb collisions in a thermal plasma in an infinite magnetic field, the magnitude of the damping was approximately as predicted, while the velocity dependence of the damping was weaker than predicted. The discrepancy is consistent with the actual non-Maxwellian electron distribution of the plasma.

In conjunction with the damping work, echo amplitude saturation was measured as a function of the velocity of the electrons contributing to the echo. Good agreement was obtained with the predicted J₁ Bessel function amplitude dependence, as well as a demonstration that saturation did not influence the damping results.

Theory of s-d exchange scattering in dilute magnetic alloys

The problem of s-d exchange scattering of conduction electrons off localized magnetic moments in dilute magnetic alloys is considered employing formal methods of quantum field theoretical scattering. It is shown that such a treatment not only allows for the first time, the inclusion of multiparticle intermediate states in single particle scattering equations but also results in extremely simple and straight forward mathematical analysis. These equations are proved to be exact in the thermodynamic limit. A self-consistent integral equation for electron self energy is derived and approximately solved. The ground state and physical parameters of dilute magnetic alloys are discussed in terms of the theoretical results. Within the approximation of single particle intermediate states our results reduce to earlier versions. The following additional features are found as a consequence of the inclusion of multiparticle intermediate states;

(i) A non analytic binding energy is pre sent for both, antiferromagnetic (J < o) and ferromagnetic (J > o) couplings of the electron plus impurity system.

(ii) The correct behavior of the energy difference of the conduction electron plus impurity system and the free electron system is found which is free of unphysical singularities present in earlier versions of the theories.

(iii) The ground state of the conduction electron plus impurity system is shown to be a many-body condensate state for J < o and J > o, both. However, a distinction is made between the usual terminology of "Singlet" and "Triplet" ground states and nature of our ground state.

(iv) It is shown that a long range ordering, leading to an ordering of the magnetic moments can result from a contact interaction such as the s-d exchange interaction.

(v) The explicit dependence of the excess specific heat of the Kondo systems is obtained and found to be linear in temperatures as T→ o and T ℓnT for 0.3 T_K ≤ T ≤ 0.6 T_K. A rise in (ΔC/T) for temperatures in the region 0 < T ≤ 0.1 T_K is predicted. These results are found to be in excellent agreement with experiments.

(vi) The existence of a critical temperature for Ferromagnetic coupling (J > o) is shown. On the basis of this the apparent contradiction of the simultaneous existence of giant moments and Kondo effect is resolved.