Alumni Dissertations

 

Alumni Dissertations

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  • EXPLORATION OF CsSnI3: UNCOVERING OPTICAL AND ELECTRICAL PROPERTIES FOR PHOTONIC DEVICE APPLICATIONS

    Author:
    Chonglong Yu
    Year of Dissertation:
    2013
    Program:
    Physics
    Advisor:
    Kai Shum
    Abstract:

    This thesis is about the exploration of the optical properties of perovskite compound CsSnI3 (CSI), a newly identified semiconductor material. Based on what have been discovered so far, we believe that it has a great potential for photonic device applications. The exploration starts with the determination of the atomic and electronic structures of CSI and continues with the fundamental understanding of the optical properties revealed by spectroscipic measurments. One of the most fascinating optical properties associated with the unique atomic structuture of CSI is the superfluorecence from the correlated two-dimensional excitons naturally formed in the planes of SnI4 tetragons. After a brief introduction on the prior and recent research activities on CSI, the atomic structures and structural phase transitions of CSI were investigated using the first-principles approach. With the detailed structural information, the full electronic eigen states of CSI in its  phase, commonly accessible by the full optical spectrum from near infrared to ultraviolet, have been calculated. A few key charcteristics of the electronic structure were identified and discussed in view of their optical consequences, such as the much larger effective mass of electrons than that of holes, and the existence of the two lowest parallel conduction bands with an energy separation of 64 meV. In the chapters of 4, 5 and 6, the exploration continues with the understanding of interesting optical properties and the associated physics processes. The abnormal temperature dependence of the energy band gap of CSI is explained by the two combined effects: 1) the neglegible contribution of direct electron-phonon interactions to the band gap change due to the unusual large electron effective mass, and 2) the positive thermal expansion effect to the band gap change calculated by the first-principle approach. Pronounced two-LO-phonon features in both Raman scattering and photoluminescence excitation spectra are interpreted as the resonantly enhanced two-LO-phonon emission processes, originated by the unique electronic band structure of CSI: the two lowest parallel conduction bands with the energy separation close to the energy of two LO phonons. The final part of my thesis in the chapters of 7 and 8 is devoted to the one of most exciting and abstruse phenomena in photonics: superfluorescence (SF). After revisiting Dicke's initial superradiance theory and combining the characteristics of SF, we have developed a model to capture the essential physics, especially on the dynamic time evolution of SF. This model predicts the bi-exponential decay behavior when considerable dephasing is present. Meanwhile, the intensity of SF burst, delay time, and decay rate are also studied with the model. The SF in CSI is revealed through the power and temperature dependences of time resolved photoluminescence. The measured photoluminescence characteristics are shown to match all the SF features predicted by our model, such as the bi-exponential decay, the inverse relation of delay time over the number of exciton (N), the linear relation of decay rate over N, and the temperature dependence of decay rate. The natural formation of two dimensional excitons in the parallel planes of SnI4 tetragons is argued to be the reason for the SF to occur in CSI.  

  • Engineering cofactor and ligand binding in an artificial neuroglobin

    Author:
    Lei Zhang
    Year of Dissertation:
    2012
    Program:
    Physics
    Advisor:
    Ronald Koder
    Abstract:

    HP-7 is one artificial mutated oxygen transport protein, which operates via a mechanism akin to human neuroglobin and cytoglobin. This protein destabilizes one of two heme- ligating histidine residues by coupling histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Replacement of these glutamate residues with alanine, which has a neutral hydrophobicity, slows gaseous ligand binding 22-fold, increases the affinity of the distal histidine ligand by a factor of thirteen, and decreases the binding affinity of carbon monoxide, a nonreactive oxygen analogue, three-fold. Paradoxically, it also decreases heme binding affinity by a factor of three in the reduced state and six in the oxidized state. Application of a two-state binding model, in which an initial pentacoordinate binding event is followed by a protein conformational change to hexacoordinate, provides insight into the mechanism of this seemingly counterintuitive result: the initial pentacoordinate encounter complex is significantly destabilized by the loss of the glutamate side chains, and the increased affinity for the distal histidine only partially compensates. These results point to the importance of considering each oxidation and conformational state in the design of functional artificial proteins. We have also examined the effects these mutations have on function. The Kd of the nonnreactive oxygen analogue carbon monoxide (CO) is only decreased three-fold, despite the large increase in distal histidine affinity engendered by the 22-fold decrease in the histidine ligand off-rate. This is a result of the four-fold increase in affinity for CO binding to the pentacoordinate state. Oxygen binds to HP7 with a Kd of 117 ┬ÁM, while the mutant rapidly oxidizes when exposed to oxygen. EPR analysis of both ferric hemoproteins demonstrates that the mutation increases disorder at the heme binding site. NMR-detected deuterium exchange demonstrates that the mutation causes a large increase in water penetration into the protein core. The inability of the mutant protein may thus either be due to increased water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors.

  • Nano-scale interactions of particles and drops with heterogenous surfaces

    Author:
    Rui Zhang
    Year of Dissertation:
    2013
    Program:
    Physics
    Advisor:
    Joel Koplik
    Abstract:

    Recent technological developments enable one to study the behavior and interactions of particles and drops with heterogeneous surfaces at microscopic resolution, and investigate their possible applications. In this thesis, we use the microscopic calculational technique of molecular dynamics simulation, augmented by other continuum methods as appropriate, to study some prototypical examples. For applications to particle separation, we consider on the transport of particles by flow through a narrow channel of which one side has a stripe pattern of alternating wettabilities. We first consider van der Waals forces alone. The particle-wall interaction can either trap particles on the attractive stripes or deflect the trajectories of mobile particles away from the mean flow direction. Using molecular dynamics we determine how the migration angle of finite-sized rigid particles differs from the imposed fluid flow. The effects of electrostatic interactions are considered by decorating the particles and walls with opposite charges, resulting in significantly more trapping and larger deflection angles. We then use Langevin equations to simulate larger particles in the van der Waals case, and compare the results to the MD simulations. From the analysis of the associated Fokker-Planck equation we further obtain bounds on the deflection angle. The second problem involving fluid-solid interactions is that of nano-sized drop impact on a surface, which are flat, curved or pillared, with either homogeneous interactions or cross-shaped patterns of wettability. From the simulations we observe drop bouncing, sticking, spreading or disintegrating, depending on impact velocity and surface properties. In contrast to macroscopic observation, MD shows that the presence or absence of vapor has no effect on the onset of splashing. We argue that this difference is a direct consequence of drop size. For low velocity impacts, we compare MD results with continuum lattice Boltzmann methods at the same Reynolds and Weber numbers. In most situations we observe similar drop behavior at both length scales, with the best quantitative agreement for low impact velocities on wettable surfaces. We attribute the discrepancy for relatively high impact velocities to compressibility effects, while the disagreement on non-wetting surfaces is associated with different treatments of the liquid-solid boundary conditions.

  • Nonlinear Transport Behavior of Low Dimensional Electron Systems

    Author:
    Jingqiao Zhang
    Year of Dissertation:
    2009
    Program:
    Physics
    Advisor:
    Sergey Vitkalov Vitkalov
    Abstract:

    The nonlinear behavior of low-dimensional electron systems attracts a great deal of attention for its fundamental interest as well as for potentially important applications in nanoelectronics. In response to microwave radiation and DC bias, strongly nonlinear electron transport that gives rise to unusual electron states has been reported in two-dimensional systems of electrons in high magnetic fields. There has also been great interest in the nonlinear response of quantum ballistic constrictions, where the effects of quantum interference, spatial dispersion and electron-electron interactions play crucial roles. In this thesis, experimental results of the research of low dimensional electron gas systems are presented. The first nonlinear phenomena were observed in samples of highly mobile two dimensional electrons in GaAs heavily doped quantum wells at different magnitudes of DC and AC (10 KHz to 20 GHz) excitations. We found that in the DC excitation regime the differential resistance oscillates with the DC current and external magnetic field, similar behavior was observed earlier in AlGaAs/GaAs heterostructures. At external AC excitations the resistance is found to be also oscillating as a function of the magnetic field. However the form of the oscillations is considerably different from the DC case. We show that at frequencies below 100 KHz the difference is a result of a specific average of the DC differential resistance during the period of the external AC excitations. Secondly, in similar samples, strong suppression of the resistance by the electric field is observed in magnetic fields at which the Landau quantization of electron motion occurs. The phenomenon survives at high temperatures at which the Shubnikov de Haas oscillations are absent. The scale of the electric fields essential for the effect, is found to be proportional to temperature in the low temperature limit. We suggest that the strong reduction of the longitudinal resistance is a result of a nontrivial distribution function of the electrons induced by the DC electric field. We compare our results with a theory proposed recently. The comparison allows us to find the quantum scattering time of 2D electron gas at high temperatures, in a regime, where previous methods were not successful. In addition, we observed a zero differential resistance state (ZDRS) in response to a direct current above a threshold value I>I_th applied to a two-dimensional system of electrons at low temperatures in a strong magnetic field. Entry into the ZDRS, which is not observable above several Kelvins, is accompanied by a sharp dip in the differential resistance. Additional analysis reveals instability of the electrons for I>I_th and an inhomogeneous, non-stationary pattern of the electric current. We suggest that the dominant mechanism leading to the new electron state is the redistribution of electrons in energy space induced by the direct current. Finally, we present the results of rectification of microwave radiation generated by an asymmetric, ballistic dot at different frequencies (1-40GHz), temperatures (0.3K-6K) and magnetic fields. A strong reduction of the microwave rectification is found in magnetic fields at which the cyclotron radius of electron orbits at the Fermi level is smaller than the size of the dot. With respect to the magnetic field, both symmetric and anti-symmetric contributions to the directed transport are presented in this thesis. The symmetric part of the rectified voltage changes significantly with microwave frequency &omega at &omega&tauf&ge 1, where &tauf is the time of a ballistic electron flight across the dot. The results lead consistently toward the ballistic origin of the effect, and can be explained by the strong nonlocal electron response to the microwave electric field, which affects both the speed and the direction of the electron motion inside the dot.

  • Growth of semiconductor nanostructures by MBE for the study of electron and nuclear spin enhancement and other physical phenomena

    Author:
    Qiang Zhang
    Year of Dissertation:
    2010
    Program:
    Physics
    Advisor:
    Maria Tamargo
    Abstract:

    Molecular beam epitaxy (MBE) is an extremely versatile thin film technique, which can produce single-crystal layers with atomic dimensional controls and thus permit the preparation of novel structures and devices tailored to meet specific needs. Spin relaxation time is one of the key features in spin-related phenomena and thus of great importance for spintronics. In this work, we prepare high quality samples, mainly of CdTe epilayers, by MBE, characterize their spin relaxation dynamics, and discuss the results theoretically. First, with the goal of understanding the mechanisms of electron relaxation dynamics and nuclear spin enhancement, we focus on the growth and characterization of CdTe epilayers. By changing the shutter sequences and inserting ZnSe buffer layer, we have reproducibly grown (111) and (100) CdTe epilayers of high crystalline qualities by MBE, despite the large lattice mismatch between CdTe and GaAs substrate. Then we investigate for the (111) and (100) CdTe epilayers. It is found that for the (111) CdTe, spin relaxation rate is significantly enhanced and shows no temperature dependence through 130K to 300K, while for the (100) CdTe it is strongly affected by the temperature. It is also found that it is dependent on material quality for both (111) and (100) CdTe. We theoretically discuss the effect of strain and defect on spin relaxation time of CdTe. It is the first experimental observation of the effect of strain on spin relaxation rate in a II-VI semiconductor material. Second, the growth and characterization of ZnTe/ZnSe related Type-II quantum structures, or quantum dots (QDs), are also presented in this work. The PL of Zn-Se-Te related Type-II quantum structures show blue shifts with higher intensities of exciting laser, an indication of type-II QDs. Besides being an attractive method to p-type dope wide bandgap materials, the resulting material may be a promising structure for spin enhancement properties. Third, we present the study of the enhancement of nuclear spin polarization through pumping laser. We find strong enhancement both in bulk CdTe as well as in CdTe epilayers, independent of the helicity of the laser, which is on the contrary to the prior reports by others. Compared with GaAs crystal, we ascribe this independence to the surface spin-dependent recombination. GaAs/AlAs and GaAs/GaAlAs multiple coupled double quantum wells (QWs), and CdTe/CdMgTe QW have also been grown and explored. The measurements show good quality of the material and are consistent with the designed structures. Last, we summary the work and propose the future directions. Samples are in-situ monitored by reflection high energy electron diffraction (RHEED). Post growth characterization techniques, such as time resolved Kerr rotation (TRKR), X-ray diffraction (XRD), photoluminescence (PL), and optical pumping nuclear magnetic resonance (OPNMR), are introduced and applied to the samples.

  • Statistical, DFT and Continuum Electrostatics Analysis of Histidine Ligated Hemes in the Non-redundant Heme Database in Model Complexes and in Cytochrome c Oxidase

    Author:
    Jun Zhang
    Year of Dissertation:
    2010
    Program:
    Physics
    Advisor:
    Marilyn Gunner
    Abstract:

    Heme plays an important role in biological oxidation--reduction chemistry. Important heme structural factors of are investigated here to understand how the redox potential is shifted when bound to proteins. A statistical analysis of a non-redundant heme database shows that the redox potentials of heme are significantly correlated with heme types and heme ligand types. The patterns of histidine ligand orientation, relative histidine orientations were investigated for the proteins in the database.The heme redox potential can be shifted by the existence of hydrogen bond partner to the axial histidine ligand of the heme. With the simplified model complex of Bis-Imidazole-Porphyrin, the redox potential shift due to the hydrogen bond was compared using DFT and Continuum electrostatics methods. Two models, with a representative hydrogen bond partner and point charges, are built for the simulation. The calculated final energy shift due to the hydrogen bond found by the two methods are within 15% of each other. Four different charge sets were compared in the electrostatics calculation. Simulation of Bis-Imidazole-Porphyrin complex using DFT method also revealed the energetic impact of relative orientation of imidazole ligands on either side of the porphryn is less than 1kcal/mol in a flat core porphyrin complex. Cytochrome c Oxidase is one of the essential proteins in the anaerobic electron transfer chain. In the protein from Rhodobactor sphaeroides, S44 makes a hydrogen bond to H102, the axial ligand of Heme a, a key cofactor on the reaction pathway electron transfer chain. The electrochemical behavior of Heme a is revisited with a comparison of wild type and S44D mutant using the continuum electrostatics program MCCE. At pH7, the partially ionized Asp44 lowers the Heme redox potential by 50mV. The free energy differnce between CuA and Heme a is more pH-dependant with Asp than Ser. Holding other cofactors oxidized, electron transfer from CuA to Heme a is coupled with uptake 0.6 and 1.1 protons in S44 and D44 structures respectively.

  • Conditions For Entanglement In Spin Systems And For Multipartite Entanglement

    Author:
    Hongjun Zheng
    Year of Dissertation:
    2012
    Program:
    Physics
    Advisor:
    Mark Hillery
    Abstract:

    This dissertation reports a series of studies of conditions for entanglement in spin systems and multipartite entanglement. There have been numerous studies of entanglement in spin systems. These have usually focused on examining the entanglement between individual spins or determining whether the state of the system is completely separable. Here we present conditions that allow us to determine whether blocks of spins are entangled. We show that sometime these conditions can detect entanglement better than conditions involving individual spins. We apply these conditions to study entanglement in spin wave states, both when there are only a few magnons present and also at finite temperature. We introduce two entanglement conditions that take the form of inequalities involving expectation values of operators. These conditions are sufficient conditions for entanglement that is if they are satisfied the state is entangled, but if they are not, one can say nothing about the entanglement of the state. These conditions are quite flexible, because the operators in them are not specified, and they are particularly useful in detecting multipartite entanglement. We explore the range of utility of these conditions by considering a number of examples of entangled states, and seeing under what conditions entanglement in them can be detected by the inequalities presented here. We explore the possibility of using quantum walks on graphs to find extra edges on a graph. We focus our attention on star graph, whose edges are like spokes coming out of a central hub. If there are N spokes, we show that a quantum walk can find an extra edge connecting two of the spokes or a spoke with a loop on it in square root of N steps.

  • Studying Heme Electrochemistry in Heme Proteins and Quinone Binding in Purple Bacterial Reaction Center Using Multi-Conformation Continuum Electrostatics

    Author:
    Zhong Zheng
    Year of Dissertation:
    2011
    Program:
    Physics
    Advisor:
    Marilyn Gunner
    Abstract:

    Hemes are important redox cofactors. They are found in a variety of proteins and show a diversity of functions. The free energy of heme reduction in different proteins is found to vary over more than 18 kcal/mol. It is a challenge to determine how proteins manage to achieve this enormous range of Ems with a single type of redox cofactor. Proteins containing 141 unique hemes of a-, b- and c-type, with bis-His, His-Met and aquo-His ligation were calculated using Multi-Conformation Continuum Electrostatics (MCCE). The experimental Ems range over 800 mV from -350 mV in cytochrome c3 to 450 mV in cytochrome c peroxidase (vs. SHE). The quantitative analysis of the factors that modulate heme electrochemistry includes the interactions of the heme with its ligands, the solvent, the backbone, and sidechains. MCCE calculated Ems are in good agreement with measured values. The overview of heme proteins with known structures and Ems shows the lowest and highest potential hemes are c-type, while the b-type hemes are found in the middle Em range. In solution, bis-His ligation lowers the Em by ≈205 mV relative to hemes with His-Met ligands. The bis-His, aquo-His and His-Met ligated b-type hemes all cluster about Ems which are ≈200 mV more positive in protein than in water. In contrast, the low potential bis-His c-type hemes are shifted little from in solution, while the high potential His-Met c-type hemes are raised by ≈300 mV from solution. The analysis shows that no single type of interaction can be identified as the most important in setting heme electrochemistry in proteins. Therefore, different proteins use different aspects of their structures to modulate the in situ heme electrochemistry. Quinones play important roles in mitochondrial and photosynthetic energy conversion acting as intramembrane, mobile electron and proton carriers between catalytic sites in various electron transfer proteins. They display different affinity, selectivity, functionality and exchange dynamics in different binding sites. The computational analysis of quinone binding sheds light on the requirements for quinone affinity and specificity. The affinities of ten oxidized, neutral benzoquinones (BQs) were measured for the high affinity QA site in the detergent solubilized Rhodobacter sphaeroides bacterial photosynthetic reaction center. Multi-Conformation Continuum Electrostatics (MCCE) was then used to calculate their relative binding free energies by Grand Canonical Monte Carlo sampling with a rigid protein backbone, flexible ligand and side chain positions and protonation states. Van der Waals and torsion energies, Poisson-Boltzmann continuum electrostatics and accessible surface area dependent ligand-solvent interactions are considered. The affinities are dominated by favorable protein-ligand van der Waals rather than electrostatic interactions. Each quinone appears in a closely clustered set of positions. Methyl and methoxy groups move into the same positions as found for the native quinone.