Recent experiments have shown that junctions consisting of individual single-molecule magnets (SMMs) bridged between two electrodes can be fabricated in three-terminal devices, and that the characteristic magnetic anisotropy of the SMMs can be affected by electrons tunneling through the molecule. Vibrational modes of the SMM can couple to electronic charge and spin degrees of freedom, and this coupling also influences the magnetic and transport properties of the SMM. The effect of electron-vibron coupling on transport has been extensively studied in small molecules, but not yet for junctions of SMMs. The goals of this thesis will be two-fold: to present a novel approach for studying the effects of this electron-vibron coupling on transport through SMMs that utilizes both density functional theory calculations and model Hamiltonian construction and analysis, and to present a software framework based on this hybrid approach for the simulation of transport across user-defined SMMs. The results of these simulations will indicate a characteristic suppression of the current at low energies that is strongly dependent on the overall electron-vibron coupling strength and number of molecular vibrational modes considered. / Master of Science

Single molecule magnets (SMMs) are molecules of mesoscopic scale which exhibit quantum properties such as quantum tunneling of magnetization, quantum interference, spin filtering effects, strong spin-phonon coupling and strong hyperfine Stark effects. These effects allow applications of SMMs to high-density information storage, molecular spintronics, and quantum information science. Therefore, SMMs are of interest to physicists, chemists, and engineers. Recently, experimental fabrication of individual SMMs within transistor set-ups have been achieved, offering a new method to examine magnetic properties of individual SMMs. In this thesis, two types of SMMs, specifically Eu2(C8H8)3 and Ni9Te6(PEt3)8, are theoretically investigated by simulating their electron transport properties within three-terminal transistor set-ups. An extended metal atom chain (EMAC) consists of a string of metallic atoms with organic ligands surrounding the string. EMACs are an important research field for nanoelectronics. Homometallic iron-based EMACs are especially attractive due to the high spin and large magnetic anisotropy of iron(II). We explore the exchange coupling of iron atoms in two EMACs: [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. Chapter 1 provides an introduction to SMMs, electron transport experiments via SMMs and an introduction to density functional theory (DFT). Chapter 2 presents a theoretical study of electron transport via Eu2(C8H8)3. This type of molecule is interesting since its magnetic anisotropy type changes with oxidation state. The unique magnetic properties lead to spin blockade effects at zero and low bias. In other words, the current through this molecule is completely suppressed until the bias voltage exceeds a certain value. Chapter 3 discusses a theoretical study of electron transport via Ni9Te6(PEt3)8. The magnetic anisotropy of this magnetic cluster has cubic symmetry, which is higher than most SMMs. With appropriate magnetic anisotropy parameters, in the presence of an external magnetic field, uncommon phenomena such as low-bias blockade effects, negative conductance and discontinuous conductance lines, are observed. In Chapter 2 and 3 DFT-calculated magnetic anisotropy parameters are used and electron transport properties are calculated by solving master equations at low temperature. Chapter 4 examines the exchange coupling between iron ions in EMACs [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. The exchange coupling constants are calculated by using the least-squares fitting method, based on the DFT-calculated energies from different spin configurations. / Ph. D. / Single molecule magnets (SMMs) are molecules of mesoscopic scale which exhibit quantum properties. Its quantum effects are used to describe the behavior of SMMs at the smallest scales. These quantum properties could also be used to reveal possible applications of SMMs to high-density information storage, molecular spintronics, and quantum information science. Thus SMMs are of interest to physicists, chemists, and engineers. Recently, electron transport via individual SMMs was achieved in experiments. Electron transport is obviously affected by the magnetic properties of the SMM, thus one can examine magnetic properties of an SMM indirectly by measuring electron transport via the SMM. In this thesis, two types of SMMs, Eu2(C8H8)3 and Ni9Te6(PEt3)8, are investigated theoretically by simulating their electron transport properties. An extended metal atom chain (EMAC) consists of a string of metallic atoms with organic ligands surrounding the string. EMACs are an important research field for nanoelectronics. Homometallic iron-based EMACs are especially attractive due to the high spin and large magnetic anisotropy of iron(II). If a molecule has magnetic anisotropy, its magnetic properties change with the direction of its magnetic moment. We explore how iron atoms interact with each other in the EMACs [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. Chapter 1 provides an introduction to SMMs, electron transport experiments via SMMs and an approximation method, density functional theory (DFT). DFT is a method to approximate electronic structure and magnetic properties of various many-body systems. Chapter 2 investigates theoretical electron transport via Eu2(C8H8)3. Eu2(C8H8)3 changes its type of magnetic anisotropy when it obtains an extra electron, which is different from most SMMs. If the Eu2(C8H8)3 is short of an extra electron, its magnetization direction is in-plane, that is, its magnetic energy is lowest when its magnetic moment is along any direction in a specific plane. If an extra electron is captured by Eu2(C8H8)3, its magnetization direction becomes out-of-plane, and its lowest energy is obtained when its magnetic moment is along the direction normal to the specific plane. The unique magnetic properties lead to blockade effects at low bias: the current through this molecule is completely suppressed until the bias voltage exceeds a certain value. The bias voltage on a molecule equals the electrical potential difference between two ends of the molecule. Chapter 3 investigates theoretical electron transport via Ni9Te6(PEt3)8. Magnetic anisotropy of Ni9Te6(PEt3)8 is cubic symmetric, and its symmetry is higher than most SMMs. With appropriate magnetic anisotropy parameters, in the presence of an external magnetic field, uncommon phenomena are observed. These phenomena include (1) current is completely suppressed when bias is low; (2) current via SMM decreases while bias on SMM increases; (3) there are discontinuous lines in the figures that describe electrical conductance of current. Chapter 4 examines the iron atoms’ interaction strength in both [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. Reasonable spin Hamiltonians are used to describe the energy of EMACs. Considering all possible directions of the spins of iron atoms in two EMACs, we calculate the energy of every possible spin configuration using DFT. The energy of each spin configuration can be expressed as an equation containing one or more coupling constants. We apply the least-squares fitting method to obtain the values of the coupling constants in the spin Hamiltonians.

published_or_final_version / Physics / Doctoral / Doctor of Philosophy

published_or_final_version / Physics / Doctoral / Doctor of Philosophy

Liposomes incorporating chlorophyll (Chl) have been used as a model system to study various aspects of photosynthesis (such as Chl photooxidation and acceptor reduction). Laser flash photolysis studies of this system have demonstrated that the Chl triplet state (Chl(t)) can transfer an electron to acceptors such as quinones, resulting in the formation of the Chl cation radical (Chl⁺.) and the semiquinone anion radical (Q¯.). Quenching of Chl(t) by quinones in liposomes is diffusion-controlled. The quenching rate is dependent upon bilayer viscosity. Chl(t) lifetimes in the absence of quinones also reflect bilayer viscosity. Radical decay occurs by reverse electron transfer. Although the decay is non-exponential, the decay rate is independent of laser intensity. This is presumably because radical pairs once formed do not become independent of one another and back react in a manner which can be likened to geminate recombination. The non-exponentiality is due to electron exchange between quinone molecules and the heterogeneity in the distribution of molecules among the vesicles. This electron exchange is also manifested in the radical formation process. At high quinone concentration the radical yield increases with quinone concentration in non-linear fashion with respect to the amount of triplet quenched. This positive cooperative effect is interpreted in terms of high quinone concentrations increasing the efficiency of radical production by providing a pathway (via electron hopping) for removal of the electron from the site of initial electron transfer. When ubiquinone is used, only a single fast decay is observed. However, when quinones which can partition between the aqueous and lipid phases are used, radical decay occurs via a fast and a slow process. This is interpreted in terms of electron transfers from Q¯. within the bilayer to Q at the bilayer-water interface which results in a stabilization of the electron transfer products and a slowly-decaying radical. The rate of this slow decay process is also quinone concentration dependent, which is a consequence of a facilitation of electron return to Chl⁺. by Q molecules within the bilayer via an electron hopping mechanism. That such a mechanism is, in fact, operative in radical production is shown also by the observation of electron transfer from UQ¯. to BQ molecules.

The axial ligands of the iron porphyrin in Cytochrome c, an electron transfer protein, are an imidazole group of a histidine residue and a methionine thioether. This ligand coordination sphere has been difficult to model and consequently the influence of these ligands on the properties of cytochrome c has been problematic. The electrochemical and spectroscopic study of a novel strapped porphyrin has been addressed toward this problem. Spectroscopic studies have demonstrated the ability of this porphyrin to hold a thioether ligand near the central metal atom. The influence of the thioether is not seen in the UV/visible spectrum of the iron complex of this porphyrin. The coordination of N-methyl imidazole to the iron complexes of several porphyrins has been studied by UV/visible spectroscopy. These studies indicate a reduced affinity of the strapped porphyrin for this ligand. Also, the oxidation products of several porphyrins were monitored by thin-layer spectroelectrochemistry. Cyclic voltammetry has been used to demonstrate the influence of the thioether on the Fe('+3)/Fe('+2) electron transfer reaction. It was found that the thioether stabilizes the lower oxidation state causing an anodic shift in the half-wave potential for the reaction. However, the stabilization seen with this model system is not sufficient to account for the large positive redox potential of Cytochrome c. The oxidations of a selected group of free base and metallo- porphyrins were also studied. It was found that the oxidation of strapped porphyrins was similar in many respects to those of non-strapped porphyrins. The notable acception to this generalization was the instability of the cation radical of the strapped porphyrins used in this work.

Dissertation Submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in the fulfillment of the requirement for the degree of Master of Science in Medicine by Research. Johannesburg, 2017 / Electron transport and respiration in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB) occurs through the use of the aa3 type cytochrome c oxidase (CcO) under normoxic conditions or cytochrome bd oxidase (CbdO) under microaerophillia. Using these oxidases, Mtb couples substrate level oxidation to generation of metabolic energy in the form of adenosine triphosphate (ATP) under aerobic conditions. The presence of the CbdO is expected to allow for growth and survival of Mtb in the oxygen restricted environment of the human TB granuloma, thus rendering it an important enzyme for further study. CbdO is comprised of two structural subunits, CydA (subunit I) and CydB (subunit II), which are encoded by the cydAB operon. Both subunits span the cytoplasmic membrane to form part of the mycobacterial electron transport chain. Notably, two other genes that are transcribed separately from the cydAB operon, the cydDC operon, have been proposed to be required for the synthesis of a functional CbdO. Based on amino acid sequence and structural predictions, the cydDC encode heterodimeric members of the ATP Binding Cassette ABC-type transporters. In other organisms, the cydDC functions to transport reducing agents to the periplasm, thus contributing to periplasmic redox homeostasis. In this study we aimed to analyze the function of the cydDC genes in Mycobacterium smegmatis. Through bioinformatics analyses, it was demonstrated that the CydDC subunits retain conserved residues associated with the ABC domain and adopt a three-dimensional fold that is similar to their counterparts in Escherichia coli. However, the published sequence of M. smegmatis suggests that cydC is a pseudogene, which was inconsistent with the demonstrated evidence of a functional CbdO in this organism. In this study, using standard DNA sequencing, it was demonstrated that the CBTBR laboratory strain of M. smegmatis does not harbor a cydC pseudogene but rather has a functional cydC gene. Next, we interrogated the function of the M. smegmatis and Mtb cydDC genes by heterologous expression in an E. coli cydD mutant. Heterologous expression of the Mtb cydDC genes restored CbdO biogenesis in the E. coli mutant. Using various microbiological approaches, we demonstrated that the mycobacterial cydDC was able to revert the stationary phase exit defect, high temperature sensitivity and increased oxidative stress susceptibility defects of the E. coli cydD mutant. Collectively, these data provided strong evidence that the mycobacterial cydDC genes encode a functional transporter that contributes to periplasmic redox homeostasis. Following this, we generated a double deletion mutant of the cydDC operon in M smegmatis. We confirmed the genetic integrity of the ΔcydDC strain by Southern Blot analysis and proved by absorption difference spectroscopy that this strain is defective in the ability to synthesize a functional CbdO, as measured by the lack of a heme d peak in membrane preparations from the mutant. In addition, the ΔcydDC mutant displayed increased sensitivity to oxidative stress and a reduced ability to exit stationary phase, phenotypic defects that were consistent with the lack of CbdO. In summary, this study provides the first evidence that loss of the M. smegmatis cydDC genes affects CbdO biogenesis. These data also confirm that the CydDC ABC-type transporter most likely transports reducing equivalents that allow for maturation of CbdO in the periplasm. Collectively, our observations advance the understanding of the mycobacterial electron transport chain and provide new evidence to assist in the development of CbdO as a TB drug target. / MT2017

A research report submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science. Johannesburg, 2015. / In this thesis electron transport properties of silicon nanowires are studied. The devices are synthesized using a laser ablation technique. The catalysts used in the synthesis are nickel nanoparticles. The silicon nanowires are characterized by scanning electron microscopy, transmission electron microscopy, atomic force microscopy and Raman spectroscopy. Dielectrophoresis is used to align and contact nanowires across two electrodes to create two-terminal devices. In addition four-terminal devices are fabricated using PMMA lift-off based electron beam lithography. Electron transport properties of the fabricated devices have been studied using dc measurement techniques. Resistance of the silicon nanowires has been measured as a function of temperature and magnetic field. These measurements have been accomplished using a Cryogenics system at low temperature, and high magnetic field. Temperature dependent studies reveal that Arrhenius type thermally activated transport behavior is the dominant transport mechanism in measurements at zero magnetic field. Magnetic field dependent measurements show a weak positive linear magnetoresistance. There are also strong oscillations in magnetoresistance curves. The temperature and field independence of the oscillations has been attributed to quantum interference effects.

by Cheng Fat-chi. / Bibliography: leaves 85-86 / Thesis (M.Ph.)--Chinese University of Hong Kong, 1984

by Chan Hing Nam = 壓力對La₀.₆₇Ca₀.₃₃MnO₃薄膜的導電能的效應 / 陳慶楠. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references. / Text in English; abstracts in English and Chinese. / by Chan Hing Nam = Ya li dui La₀.₆₇Ca₀.₃₃MnO₃ bo mo de dao dian neng de xiao ying / Chen Qingnan. / Acknowledgements --- p.i / Abstract --- p.ii / 論文摘要 --- p.iii / Table of contents --- p.iv / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Introduction to colossal magnetoresistance --- p.1-1 / Chapter 1.2 --- Effects of chemical pressure and strain on LCMO thin films --- p.1-7 / Chapter 1.3 --- Review of pressure effects on bulk LCMO --- p.1-11 / Chapter Chapter 2 --- Instrumentation and Characterization / Chapter 2.1 --- Preparation of LCMO thin films --- p.2-1 / Chapter 2.2 --- X-ray diffraction (XRD) --- p.2-3 / Chapter 2.3 --- Self-clamping pressure cell --- p.2-5 / Chapter 2.3.1 --- Electrical feedthroughs --- p.2-5 / Chapter 2.3.2 --- Teflon cell --- p.2-8 / Chapter 2.3.3 --- Pressure variations in the pressure-transmitting medium --- p.2-9 / Chapter Chapter 3 --- Pressure effect on LCMO thin films grown on different substrates / Chapter 3.1 --- Annealing effect --- p.3-1 / Chapter 3.2 --- Thickness effect --- p.3-4 / Chapter 3.3 --- Lattice effect and pressure effect --- p.3-5 / Chapter 3.4 --- Crystallinity effect --- p.3-13 / Chapter Chapter 4 --- Activation energy of small polaron in LCMO thin films / Chapter 4.1 --- Motivation --- p.4-1 / Chapter 4.2 --- Basic theory --- p.4-2 / Chapter 4.3 --- Activation energy --- p.4-4 / Chapter Chapter 5 --- Conclusion --- p.5-1