# Alumni Dissertations

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### Direct Growth of Graphene-like Films on Single Crystal Quartz Substrates

Author:Siarhei SamsonauYear of Dissertation:2013Program:PhysicsAdvisor:Alexander ZaitsevAbstract:Direct growth of graphene-like (GL) films (nano-crystalline graphite films) on single crystal quartz substrates by chemical vapor deposition (CVD) from methane and molecular beam growth (MBG) is reported. The GL films have been characterized by means of Raman spectroscopy, atomic force microscopy and electrical measurements. Raman spectroscopy reveals nanocrystalline structure of the films grown at different conditions. The thinnest CVD grown GL films obtained so far have a thickness of 1.5 nm, a relatively rough surface structure and electrical conductivity in the range of 20 kohm/square. Low temperature Hall-effect measurements performed on these films have revealed that the major charge carriers are holes with mobility of 40 cm²/Vs at room temperature. While inferior to graphene in terms of electronic properties, the graphene-like films possess very high chemical sensitivity. Study of MBG grown films revealed formation of a non-conductive carbon layer of low crystallinity on the initial stage of the growth process. In order to study the influence of the quartz substrate on the film formation process we performed ab initio simulation of the MBG process. For this simulation we used an atom-by-atom approach, which, we believe, is a closer approximation to the real molecular beam deposition process reported so far. The simulation showed that the initial formation of the film follows the atomic structure of the substrate. This leads to a high content of sp3 hybridized atoms at the initial stage of growth and explains formation of a non-conductive film. Additionally, we demonstrated how a non-conductive film becomes conductive with the increase of the film thickness. These results agree fairly well with the data obtained by AFM, electrical, and Raman measurements conducted on the films grown by MBG. High chemical sensitivity of GL films has been demonstrated by measuring the change in their conductance during exposure to a NO2-containing atmosphere. Sensitivity of CVD grown GL films have been shown to be superior to that of MBG grown GL films. The stimulating action of ultraviolet light illumination on the chemical sensitivity has been found to be comparable to that of carbon nanotubes. A detection limit of 40 ppb (parts-per-billion) of NO2 diluted in an inert atmosphere has been estimated from the signal-to-noise ratio analysis. The optimal electrical conductance, high chemical sensitivity as well as the simple growth method make the CVD grown GL films promising for practical applications as a chemically sensitive material. Results obtained during this work were presented on several conferences: Gotham-Metro Condensed Matter Meeting (New York, NY), April 2010 and November 2012; American Physical Society March Meeting (Dallas, TX), March 2011; Nanoelectronic Devices for Defense & Security (NANO-DDS) Conference (Brooklyn, NY), August 2011. Two papers (http://dx.doi.org/10.1016/j.snb.2013.02.067 and http://dx.doi.org/10.1016/j.snb.2013.06.023) were published based on the results presented in this thesis.

### Gauge/ Gravity Correspondence, Bulk Locality and Quantum Black Holes

Author:Debajyoti SarkarYear of Dissertation:2014Program:PhysicsAdvisor:Daniel KabatAbstract:The aim of this dissertation is threefold. We begin by the study of two parallel ideal cosmic strings in the presence of non-minimal scalar fields and spin- 1 gauge fields. We show that the contributions of the non-minimal term on the interaction energy between the strings are similar to that of the gauge field for a particular value of non-minimal coupling parameter. In this context we clarify some of the issues that arise when comparing the renormalization of black hole entropy and entanglement entropy using the replica trick. In the second part of the dissertation we study the process of bound state formation in clusters of Dp- brane collision and Dp shell/ Membrane collapse processes. We consider two mechanisms for bound state formation. The first, operative at weak coupling in the worldvolume gauge theory, is creation of W-bosons. The second, operative at strong coupling, corresponds to formation of a black hole in the dual supergravity. These two processes agree qualitatively at intermediate coupling, in accord with the correspondence principle of Horowitz and Polchinski. We show that the size of the bound state and timescale for formation of a bound state agree at the correspondence point, along with other relevant thermodynamic quantities. The timescale involves matching a parametric resonance in the gauge theory to a quasinormal mode in supergravity. Finally we study construction of local operators in AdS using the generalized AdS/ CFT correspondence. After briefly sketching previous works on this topic which involve massless and massive scalar fields, we present similar construction for spin- 1 and spin- 2 gauge fields. Working in holographic gauge in the bulk, at leading order in 1/N bulk gauge fields are obtained by smearing boundary currents over a sphere on the complexified boundary, while linearized metric fluctuations are obtained by smearing the boundary stress tensor over a ball. This representation respects AdS covariance up to a compensating gauge transformation. We also consider massive vector fields, where the bulk field is obtained by smearing a non-conserved current. We compute bulk two-point functions and show that bulk locality is respected. We show how to include interactions of massive vectors using 1/N perturbation theory, and we comment on the issue of general backgrounds. We point out some more recent works on interacting scalar and gauge fields and try to answer the question of what should be the CFT properties to have a dual gravitational descriptions on AdS space. We end with some speculations about finite N and when we have black holes in the bulk.

### Performance Physics Analysis and Synthesis of Communicative Bodies

Author:Anthony SchultzYear of Dissertation:2012Program:PhysicsAdvisor:Brian SchwartzAbstract:Human motion contains information like written or spoken language. Contemporary camera and computer technologies capture this information for gaming, animation, medical diagnostics and robotic control. In this thesis we model human performance recorded with motion capture and video. Beginning with a kinematic chain model of the human body we generate a metric for comparing different states of skeletal articulation. Applying this measure over motion data time series generates similarity spectra from which we identify and characterize body motions. We use the results to model the subject's underlying movement vocabulary with a network of connected recordings called a motion graph. We construct a set of motion graphs from video data and by assigning variable transition probabilities between recorded movement sequences we model the purposeful subject as a stochastic traversal process on the motion graph. Finally we present the application of a non-anatomical kinematic chain model to video data and derive the accompanying distance metrics. We discuss the results and possible applications of these techniques.

### Measuring the transmission matrix for microwave radiation propagating through random waveguides: fundamentals and applications

Author:Zhou ShiYear of Dissertation:2014Program:PhysicsAdvisor:Azriel GenackAbstract:This thesis describes the measurement and analysis of the transmission matrix (TM) for microwave radiation propagating through multichannel random waveguides in the crossover to Anderson localization. Eigenvalues of the transmission matrix and the associated eigenchannels are obtained via a singular value decomposition of the TM. The sum of the transmission eigenvalues yields the transmittance

T , which is the classical analog of the dimensionless conductanceg . The dimensionless conductanceg is the electronic conductance in units of the quantum conductance,G/(e^2/h) . For diffusive wavesg >1, approximatelyg transmission eigenchannels contribute appreciably to the transmittanceT . In contrast, for localized waves withg <1,T is dominated by the highest transmission eigenvalue, &tau&_{1}. For localized waves, the inverse of the localization lengths of different eigenchannels are found to be equally spaced. Measurement of the TM allows us to explore the statistics of the transmittanceT . A one-sided log-normal distribution ofT is found for a random ensemble withyour g =0.37 and explained using an intuitive Coulomb gas model for the transmission eigenvalues. Single parameter scaling (SPS) predicted for one dimension random system is approached in multichannel systems onceT is dominated by a single transmission eigenchannel. In addition to the statistics of the TM for ensembles of random samples, we investigated the statistics of a single TM. The statistics within a large single TM are found to depend upon a single parameter, the eigenchannel participation number,M . The variance of the total transmission normalized by its averaging in the TM is equal toM -1 . We found universal fluctuation ofM , reminiscent of the well known universal conductance fluctuations for diffusive waves. We demonstrate focusing of steady state and pulse transmission through a random medium via phase conjugation of the TM. The contrast between the focus and the background is determined byM and the size of the transmission matrixN . The spatio-temporal profile of focused radiation in the diffusive limit is shown to be the square of the field-field correlation function in space and time. We determine the density of states (DOS) of a disordered medium from the dynamics of transmission eigenchannels and from the quasi-normal modes of the medium for localized samples. The intensity profile of each eigenchannel within the random media is closely linked to the dynamics of transmission eigenchannels and an analytical expression for intensity profile of each of the eigenchannel based on numerical simulation was provided.### Self-consistent calculations of optical properties of type I and type II quantum heterostructures

Author:Vladimir ShuvayevYear of Dissertation:2009Program:PhysicsAdvisor:Lev DeychAbstract:In this Thesis the self-consistent computational methods are applied to the study of the optical properties of semiconductor nanostructures with one- and two-dimensional quantum confinements. At first, the self-consistent Schrodinger-Poisson system of equations is applied to the cylindrical core-shell structure with type~II band alignment without direct Coulomb interaction between carriers. The electron and hole states and confining potential are obtained from a numerical solution of this system. The photoluminescence kinetics is theoretically analyzed, with the nanostructure size dispersion taken into account. The results are applied to the radiative recombination in the system of ZnTe/ZnSe stacked quantum dots. A good agreement with both continuous wave and time-resolved experimental observations is found. It is shown that size distribution results in the photoluminescence decay that has essentially non-exponential behavior even at the tail of the decay where the carrier lifetime is almost the same due to slowly changing overlap of the electron and hole wavefunctions. Also, a model situation applicable to colloidal core-shell nanowires is investigated and discussed. With respect to the excitons in type I quantum wells, a new computationally efficient and flexible approach of calculating the characteristics of excitons, based on a self-consistent variational treatment of the electron-hole Coulomb interaction, is developed. In this approach, a system of self-consistent equations describing the motion of an electron-hole pair is derived. The motion in the growth direction of the quantum well is separated from the in-plane motion, but each of them occurs in modified potentials found self-consistently. This approach is applied to a shallow quantum well with the delta-potential profile, for which analytical expressions for the exciton binding energy and the ground state eigenfunctions are obtained, and to the quantum well with the square potential profile with several different well and barrier materials. The numerical results yield lower exciton binding energies in comparison to standard variational calculations, while the iterative scheme used to calculate the energies and respective wavefunctions is stable, rapidly convergent and requires reduced computational effort. Thus, the method can be an important computational tool in computing exciton characteristics in quantum wells exceeding currently existing approaches in accuracy and efficiency. The method can also be naturally generalized for quantum wires and dots.

### Fuzzy Field Theory as a Random Matrix Model

Author:Juraj TekelYear of Dissertation:2013Program:PhysicsAdvisor:V Parameswaran NairAbstract:This dissertation considers the theory of scalar fields on fuzzy spaces from the point of view of random matrices. First we define random matrix ensembles, which are natural description of such theory. These ensembles are new and the novel feature is a presence of kinetic term in the probability measure, which couples the random matrix to a set of external matrices and thus breaks the original symmetry. Considering the case of a free field ensemble, which is generalization of a Gaussian matrix ensemble, we develop a technique to compute expectation values of the observables of the theory based on explicit Wick contractions and we write down recursion rules for these. We show that the eigenvalue distribution of the random matrix follows the Wigner semicircle distribution with a rescaled radius. We also compute distributions of the matrix Laplacian of the random matrix given by the new term and demonstrate that the eigenvalues of these two matrices are correlated. We demonstrate the robustness of the method by computing expectation values and distributions for more complicated observables. We then consider the ensemble corresponding to an interacting field theory, with a quartic interaction. We use the same method to compute the distribution of the eigenvalues and show that the presence of the kinetic terms rescales the distribution given by the original theory, which is a polynomially deformed Wigner semicircle. We compute the eigenvalue distribution of the matrix Laplacian and the joint distribution up to second order in the correlation and we show that the correlation between the two changes from the free field case. Finally, as an application of these results, we compute the phase diagram of the fuzzy scalar field theory, we find multiscaling which stabilizes this diagram in the limit of large matrices and compare it with the results obtained numerically and by considering the kinetic part as a perturbation.

### Interactions between a Bacterial Tyrosine Kinase and its Cognate Phosphatase- A Solution NMR Study

Author:Deniz TemelYear of Dissertation:2012Program:PhysicsAdvisor:Ranajeet GhoseAbstract:Bacterial tyrosine kinases (BY-kinases) play a central role in a variety of physiological processes in bacterial cells. Most notable among these processes is the formation of antiphagocytic capsule and biofilm for survival under environmental stress conditions. BY-kinases constitute a unique class of prokaryotic enzymes sharing no sequence or structural homology with their eukaryal counterparts. BY-kinases are regulated by eukaryotic-like protein tyrosine phosphatases and several tyrosine kinase/phosphatase pairs, which have been identified in both gram-positive and gram-negative bacterial species. The Escherichia coli (K12) BY-kinase Wzc is regulated by a cytosolic Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) Wzb through the autophosphorylation/dephosphorylation of five phosphorylatable tyrosine residues (termed the tyrosine cluster, YC) located in the C-terminal tail of the cytosolic catalytic domain of Wzc. The cycling between autophosphorylated form of Wzc and the Wzb-catalyzed dephosphorylated state, rather than the quantitative phosphorylation state of the YC, appears to play a central role in the synthesis and export of the exopolysaccharide, colanic acid. Despite biochemical evidence that Wzb dephosphorylates YC-phosphorylated Wzc, the nature of the interactions between these two enzymes and the detailed regulatory mechanism has not been elucidated. The aim of this research was to identify the structural, dynamic and mechanistic aspects of the regulation of Wzc by Wzb. We used state-of-the-art solution-state Nuclear Magnetic Resonance (NMR) techniques in order to illuminate the interaction between Wzc and Wzb. We have obtained near-complete resonance assignments of the catalytic domain of Wzc, the first for a BY-kinase. Utilizing these assignments and chemical shift titrations, we demonstrate that Wzb prevents oligomerization of Wzc by occluding its intramolecular interaction surface, that lies on the opposite face to that housing the Wzc catalytic site, thus facilitating the dephosphorylation of the exposed YC. The YC would be buried, and shielded from Wzb, in oligomeric Wzc. Similar chemical shift titrations on Wzb reveals that Wzc docks onto Wzb using a site proximal to the catalytic site of the latter. NMR spin-relaxation measurements confirm this hypothesis in addition to revealing interesting dynamics in the key regulatory elements in Wzc and Wzb.

### Magnetic Resonance Studies of Energy Storage Materials

Author:Rafael Vazquez ReinaYear of Dissertation:2013Program:PhysicsAdvisor:Steven GreenbaumAbstract:Abstract Magnetic Resonance Studies of Energy Storage Materials by Rafael Vázquez Reina Adviser: Professor Steven G. Greenbaum In today's society there is high demand to have access to energy for portable devices in different forms. Capacitors with high performance in small package to achieve high charge/discharge rates, and batteries with their ability to store electricity and make energy mobile are part of this demand. The types of internal dielectric material strongly affect the characteristics of a capacitor, and its applications. In a battery, the choice of the electrolyte plays an important role in the Solid Electrolyte Interphase (SEI) formation, and the cathode material for high output voltage. Electron Paramagnetic Resonance (EPR) and Nuclear Magnetic Resonance (NMR) spectroscopy are research techniques that exploit the magnetic properties of the electron and certain atomic nuclei to determine physical and chemical properties of the atoms or molecules in which they are contained. Both EPR and NMR spectroscopy technique can yield meaningful structural and dynamic information. Three different projects are discussed in this dissertation. First, High energy density capacitors where EPR measurements described herein provide an insight into structural and chemical differences in the dielectric material of a capacitor. Next, as the second project, Electrolyte solutions where an oxygen-17 NMR study has been employed to assess the degree of preferential solvation of Li+ ions in binary mixtures of EC (ethylene carbonate) and DMC (dimethyl carbonate) containing LiPF6 (lithium hexafluo- rophosphate) which may be ultimately related to the SEI formation mechanism. The third project was to study Bismuth fluoride as cathode material for rechargeable batteries. The objective was to study 19F and 7Li MAS NMR of some nanocomposite cathode materials as a conversion reaction occurring during lithiation and delithation of the BiF3/C nanocomposite.

### An experimental investigation into the mechanisms of bacterial evolution

Author:Zhenmao WanYear of Dissertation:2014Program:PhysicsAdvisor:Mark HilleryAbstract:This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium

Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer inE. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation under two different conditions: i) in the absence of selection; ii) in the presence of negative selection pressure — bacteriophage infection. Last, I will investigate spontaneous mutation through qPCR assay of competition between wild-type and mutator phenotypeE. coli . Mutator phenotype has an elevated mutation rate due to defects in DNA proofreading and repairing system. By introducing antibiotic selective pressure, I will examine the fixation probability of mutators competing with wild-type in novel environment. I also will utilize simulations to study the impact of three parameters on the fixation probability.### POTENTIAL ENERGY LANDSCAPE OF PARTICULATE MATTER

Author:Kun WangYear of Dissertation:2012Program:PhysicsAdvisor:Hernan MakseAbstract:The application of concepts from equilibrium statistical mechanics to out of equilibrium systems has a long history of describing diverse systems ranging from glasses to granular materials. These systems are considered "complex" since equilibrium statistics is insufficient in its attempt to describe the system dynamics. An appealing approach for understanding these complex systems is to study the properties of the system's "potential energy landscape" (PEL), described by the 3N-coordinates of all particles in the multi-dimensional configuration space, or landscape, of the potential energy of the system (N is the number of particles). For dissipative jammed systems- granular materials or droplets- a key concept introduced by S. Edwards in 1989 is to replace the energy ensemble describing conservative systems by the volume ensemble. However, this approach is no able to describe the jamming critical point (J-point) for deformable particles like emulsions, whose geometric configurations are influenced by the applied external stress. Therefore, the volume ensemble requires augmentation by the ensemble of stresses. Just as volume fluctuations in the Edwards ensemble can be described by compactivity, the stress fluctuations give rise to an angoricity, another analogue of temperature in equilibrium systems. In this Thesis, we test the combined volume-stress ensemble for granular matter by comparing the statistical properties of jammed configurations obtained by dynamics with those averaged over the ensemble as a test of ergodicity. Agreement between both methods suggests the idea of "thermalization" at a given angoricity and compactivity. These intensive variables elucidate the thermodynamic order of the jamming phase transition by showing the absence of critical fluctuations above jamming in static observables like pressure and volume. Our results demonstrate the possibility of calculating important observables such as the entropy, volume, pressure, coordination number and the distribution of interparticle forces to fully characterize the scaling laws near the jamming transition from a statistical mechanics point of view. We also study the energy-landscape network. We find the stable basins and the first order saddles connecting them, and identify them with the network nodes and links, respectively. We analyze the network properties and model the system's evolution.