Recognition of double helical DNA by purine oligonucleotides via triple helix formation

Oligonucleotide-directed triple helix formation is one of the most versatile methods for the sequence specific recognition of double helical DNA. Chapter 2 describes affinity cleaving experiments carried out to assess the recognition potential for purine-rich oligonucleotides via the formation of triple helices. Purine-rich oligodeoxyribonucleotides were shown to bind specifically to purine tracts of double helical DNA in the major groove antiparallel to the purine strand of the duplex. Specificity was derived from the formation of reverse Hoogsteen G•GC, A•AT and T•AT triplets and binding was limited to mostly purine tracts. This triple helical structure was stabilized by multivalent cations, destabilized by high concentrations of monovalent cations and was insensitive to pH. A single mismatched base triplet was shown to destabilize a 15 mer triple helix by 1.0 kcal/mole at 25°C. In addition, stability appeared to be correlated to the number of G•GC triplets formed in the triple helix. This structure provides an additional framework as a basis for the design of new sequence specific DNA binding molecules.

In work described in Chapter 3, the triplet specificities and required strand orientations of two classes of DNA triple helices were combined to target double helical sequences containing all four base pairs by alternate strand triple helix formation. This allowed for the use of oligonucleotides containing only natural 3'-5' phosphodiester linkages to simultaneously bind both strands of double helical DNA in the major groove. The stabilities and structures of these alternate strand triple helices depended on whether the binding site sequence was 5'-(purine)_m (pyrimidine)_n-3' or 5'- (pyrimidine)_m (purine)_n-3'.

In Chapter 4, the ability of oligonucleotide-cerium(III) chelates to direct the transesterfication of RNA was investigated. Procedures were developed for the modification of DNA and RNA oligonucleotides with a hexadentate Schiff-base macrocyclic cerium(III) complex. In addition, oligoribonucleotides modified by covalent attachment of the metal complex through two different linker structures were prepared. The ability of these structures to direct transesterification to specific RNA phosphodiesters was assessed by gel electrophoresis. No reproducible cleavage of the RNA strand consistent with transesterification could be detected in any of these experiments.

Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

A high pressure xenon time projection chamber for double beta decay

This thesis describes the design, construction and performance of a high-pressure, xenon, gas time projection chamber (TPC) for the study of double beta decay in ^(136) Xe. The TPC when operating at 5 atm can accommodate 28 moles of 60% enriched ^(136) Xe. The TPC has operated as a detector at Caltech since 1986. It is capable of reconstructing a charged particle trajectory and can easily distinguish between different kinds of charged particles. A gas purification and xenon gas recovery system were developed. The electronics for the 338 channels of readout was developed along with a data acquistion system. Currently, the detector is being prepared at the University of Neuchatel for installation in the low background laboratory situated in the St. Gotthard tunnel, Switzerland. In one year of runtime the detector should be sensitive to a 0ν lifetime of the order of 10^(24) y, which corresponds to a neutrino mass in the range 0.3 to 3.3 eV.

Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

The application of metallointercalators in recognition of and charge transport in nucleic acids

Metal complexes that utilize the 9,10-phenanthrene quinone diimine (phi) moiety bind to DNA through the major groove. These metallointercalators can recognize DNA sites and perform reactions on DNA as a substrate. The site-specific metallointercalator Λ-1-Rh(MGP)_2phi^(5+) competitively disrupts the major groove binding of a transcription factor, yAP-1, from an oligonucleotide that contains a common binding site. The demonstration that metal complexes can prevent transcription factor binding to DNA site-specifically is an important step in using metallointercalators as therapeutics.

The distinctive photochemistry of metallointercalators can also be applied to promote long range charge transport in DNA. Experiments using duplexes with regions 4 to 10 nucleotides long containing strictly adenine and thymine sequences of varying order showed that radical migration is more dependent on the sequence of bases, and less dependent on the distance between the guanine doublets. This result suggests that mechanistic proposals of long range charge transport must involve all the bases.

RNA/DNA hybrids show charge migration to guanines from a remote site, thus demonstrating that nucleic acid stacking other than B-form can serve as a radical bridge. Double crossover DNA assemblies also provide a medium for charge transport at distances up to 100 Å from the site of radical introduction by a tethered metal complex. This radical migration was found to be robust to mismatches, and limited to individual, electronically distinct base stacks. In single DNA crossover assemblies, which have considerably greater flexibility, charge migration proceeds to both base stacks due to conformational isomers not present in the rigid and tightly annealed double crossovers.

Finally, a rapid, efficient, gel-based technique was developed to investigate thymine dimer repair. Two oligonucleotides, one radioactively labeled, are photoligated via the bases of a thymine-thymine interface; reversal of this ligation is easily visualized by gel electrophoresis. This assay was used to show that the repair of thymine dimers from a distance through DNA charge transport can be accomplished with different photooxidants.

Thus, nucleic acids that support long range charge transport have been shown to include A-track DNA, RNA/DNA hybrids, and single and double crossovers, and a method for thymine dimer repair detection using charge transport was developed. These observations underscore and extend the remarkable finding that DNA can serve a medium for charge transport via the heteroaromatic base stack.

Investigations of charge-carrier dynamics at semiconductor/liquid interfaces

Theoretical and experimental investigations of charge-carrier dynamics at semiconductor/liquid interfaces, specifically with respect to interfacial electron transfer and surface recombination, are presented.

Fermi's golden rule has been used to formulate rate expressions for charge transfer of delocalized carriers in a nondegenerately doped semiconducting electrode to localized, outer-sphere redox acceptors in an electrolyte phase. The treatment allows comparison between charge-transfer kinetic data at metallic, semimetallic, and semiconducting electrodes in terms of parameters such as the electronic coupling to the electrode, the attenuation of coupling with distance into the electrolyte, and the reorganization energy of the charge-transfer event. Within this framework, rate constant values expected at representative semiconducting electrodes have been determined from experimental data for charge transfer at metallic electrodes. The maximum rate constant (i.e., at optimal exoergicity) for outer-sphere processes at semiconducting electrodes is computed to be in the range 10^-17-10^-16 cm⁴ s^-1, which is in excellent agreement with prior theoretical models and experimental results for charge-transfer kinetics at semiconductor/liquid interfaces.

Double-layer corrections have been evaluated for semiconductor electrodes in both depletion and accumulation conditions. In conjuction with the Gouy-Chapman-Stern model, a finite difference approach has been used to calculate potential drops at a representative solid/liquid interface. Under all conditions that were simulated, the correction to the driving force used to evaluate the interfacial rate constant was determined to be less than 2% of the uncorrected interfacial rate constant.

Photoconductivity decay lifetimes have been obtained for Si(111) in contact with solutions of CH₃OH or tetrahydrofuran containing one-electron oxidants. Silicon surfaces in contact with electrolyte solutions having Nernstian redox potentials > 0 V vs. SCE exhibited low effective surface recombination velocities regardless of the different surface chemistries. The formation of an inversion layer, and not a reduced density of electrical trap sites on the surface, is shown to be responsible for the long charge-carrier lifetimes observed for these systems. In addition, a method for preparing an air-stable, low surface recombination velocity Si surface through a two-step, chlorination/alkylation reaction is described.

Mechanistic aspects of the Ziegler-Natta polymerization

The isotope effect on propagation rate was determined for four homogeneous ethylene polymerization systems. The catalytic system Cp_2Ti(Et)Cl + EtA1Cl_2 has a k^H_p/k^D_p = 1.035 ± 0.03. This result strongly supports an insertion mechanism which does not involve a hydrogen migration during the rate determining step of propagation (Cossee mechanism). Three metal-alkyl free systems were also studied. The catalyst I_2 (PMe_3)_3Ta(neopentylidene)(H) has a k^H_p/k^D_p = 1.709. It is interpreted as a primary isotope effect involving a non-linear a-hydrogen migration during the rate determining step of propagation (Green mechanism). The lanthanide complexes Cp*_2LuMe•Et_2O and Cp*_2YbMe•Et_2O have a k^H_p/k^D_p = 1.46 and 1.25, respectively. They are interpreted as primary isotope effects due to a partial hydrogen migration during the rate determining step of propagation.

The presence of a precoordination or other intermediate species during the polymerization of ethylene by the mentioned metal-alkyl free catalysts was sought by low temperature NMR spectroscopy. However, no evidence for such species was found. If they exist, their concentrations are very small or their lifetimes are shorter than the NMR time scale.

Two titanocene (alkenyl)chlorides (hexenyl 1 and heptenyl 2 were prepared from titanocene dichloride and a THF solution of the corresponding alkenylmagnesium chloride. They do not cyclize in solution when alone, but cyclization to their respective titanocene(methyl(cycloalkyl) chlorides occurs readily in the presence of a Lewis acid. It is demonstrated that such cyclization occurs with the alkenyl ligand within the coordination sphere of the titanium atom. Cyclization of 1 with EtAlCl_2 at 0°C occurs in less than 95 msec (ethylene insertion time), as shown by the presence of 97% cyclopentyl-capped oligomers when polymerizing ethylene with this system. Some alkyl exchange occurs (3%). Cyclization of 2 is slower under the same reaction conditions and is not complete in 95 msec as shown by the presence of both cyclohexyl-capped oligomers (35%) and odd number α-olefin oligomers (50%). Alkyl exchange is more extensive as evidenced by the even number n-alkanes (15%).

Cyclization of 2-d_1 (titanocene(hept-6-en-1-yl-1-d_1)chloride) with EtA1Cl_2 demonstrated that for this system there is no α-hydrogen participation during said process. The cyclization is believed to occur by a Cossee-type mechanism. There was no evidence for precoordination of the alkenyl double bond during the cyclization process.

Electronic and kinetic processes in the Cu/CuCl double pulse laser

Kinetic and electronic processes in a Cu/CuCl double pulsed laser were investigated by measuring discharge and laser pulse characteristics, and by computer modeling. There are two time scales inherent to the operation of the Cu/CuCl laser. The first is during the interpulse afterglow (tens to hundreds of microseconds). The second is during the pumping pulse (tens of nanoseconds). It was found that the character of the pumping pulse is largely determined by the initial conditions provided by the interpulse afterglow. By tailoring the dissociation pulse to be long and low energy, and by conditioning the afterglow, one may select the desired initial conditions and thereby significantly improve laser performance. With a low energy dissociation pulse, the fraction of metastable copper obtained from a CuCl dissociation is low. By maintaining the afterglow, contributions to the metastable state from ion recombinations are prevented, and the plasma impedance remains low thereby increasing the rate of current rise during the pumping pulse. Computer models for the dissociation pulse, afterglow, pumping pulse and laser pulse reproduced experimentally observed behavior of laser pulse energy and power as a function of time delay, pumping pulse characteristics, and buffer gas pressure. The sensitivity of laser pulse properties on collisional processes (e.g., CuCl reassociation rates) was investigated.

Spin dynamics of pulsed nuclear magnetic double resonance in solids

In the first part of this thesis, experiments utilizing an NMR phase interferometric concept are presented. The spinor character of two-level systems is explicitly demonstrated by using this concept. Following this is the presentation of an experiment which uses this same idea to measure relaxation times of off-diagonal density matrix elements corresponding to magnetic-dipole-forbidden transitions in a ^(13)C-^1H, AX spin system. The theoretical background for these experiments and the spin dynamics of the interferometry are discussed also.

The second part of this thesis deals with NMR dipolar modulated chemical shift spectroscopy, with which internuclear bond lengths and bond angles with respect to the chemical shift principal axis frame are determined from polycrystalline samples. Experiments using benzene and calcium formate verify the validity of the technique in heteronuclear (^(13)C-^1H) systems. Similar experiments on powdered trichloroacetic acid confirm the validity in homonuclear (^1H- ^1H) systems. The theory and spin dynamics are explored in detail, and the effects of a number of multiple pulse sequences are discussed.

The last part deals with an experiment measuring the ^(13)C chemical shift tensor in K_2Pt(CN)_4Br_(0.3) • 3H_2O, a one-dimensional conductor. The ^(13)C spectra are strongly affected by ^(14)N quadrupolar interactions via the ^(13)C - ^(14)N dipolar interaction. Single crystal rotation spectra are shown.

An appendix discussing the design, construction, and performance of a single-coil double resonance NMR sample probe is included.

Double injection: high frequency noise and temperature dependence

Noise measurements from 140°K to 350°K ambient temperature and between 10kHz and 22MHz performed on a double injection silicon diode as a function of operating point indicate that the high frequency noise depends linearly on the ambient temperature T and on the differential conductance g measured at the same frequency. The noise is represented quantitatively by〈i^2〉 = α•4kTgΔf. A new interpretation demands Nyquist noise with α ≡ 1 in these devices at high frequencies. This is in accord with an equivalent circuit derived for the double injection process. The effects of diode geometry on the static I-V characteristic as well as on the ac properties are illustrated. Investigation of the temperature dependence of double injection yields measurements of the temperature variation of the common high-level lifetime τ(τ ∝ T^2), the hole conductivity mobility µ_p (µ_p ∝ T^(-2.18)) and the electron conductivity mobility µ_n(µ_n ∝ T^(-1.75)).

Effects of self energy of the ions on the double layer structure and properties at the dielectric interface

Although numerous theoretical efforts have been put forth, a systematic, unified and predictive theoretical framework that is able to capture all the essential physics of the interfacial behaviors of ions, such as the Hofmeister series effect, Jones-Ray effect and the salt effect on the bubble coalescence remain an outstanding challenge. The most common approach to treating electrostatic interactions in the presence of salt ions is the Poisson-Boltzmann (PB) theory. However, there are many systems for which the PB theory fails to offer even a qualitative explanation of the behavior, especially for ions distributed in the vicinity of an interface with dielectric contrast between the two media (like the water-vapor/oil interface). A key factor missing in the PB theory is the self energy of the ion.

In this thesis, we develop a self-consistent theory that treats the electrostatic self energy (including both the short-range Born solvation energy and the long-range image charge interactions), the nonelectrostatic contribution of the self energy, the ion-ion correlation and the screening effect systematically in a single framework. By assuming a finite charge spread of the ion instead of using the point-charge model, the self energy obtained by our theory is free of the divergence problems and gives a continuous self energy across the interface. This continuous feature allows ions on the water side and the vapor/oil side of the interface to be treated in a unified framework. The theory involves a minimum set of parameters of the ion, such as the valency, radius, polarizability of the ions, and the dielectric constants of the medium, that are both intrinsic and readily available. The general theory is first applied to study the thermodynamic property of the bulk electrolyte solution, which shows good agreement with the experiment result for predicting the activity coefficient and osmotic coefficient.

Next, we address the effect of local Born solvation energy on the bulk thermodynamics and interfacial properties of electrolyte solution mixtures. We show that difference in the solvation energy between the cations and anions naturally gives rise to local charge separation near the interface, and a finite Galvani potential between two coexisting solutions. The miscibility of the mixture can either increases or decreases depending on the competition between the solvation energy and translation entropy of the ions. The interfacial tension shows a non-monotonic dependence on the salt concentration: it increases linearly with the salt concentration at higher concentrations, and decreases approximately as the square root of the salt concentration for dilute solutions, which is in agreement with the Jones-Ray effect observed in experiment.

Next, we investigate the image effects on the double layer structure and interfacial properties near a single charged plate. We show that the image charge repulsion creates a depletion boundary layer that cannot be captured by a regular perturbation approach. The correct weak-coupling theory must include the self-energy of the ion due to the image charge interaction. The image force qualitatively alters the double layer structure and properties, and gives rise to many non-PB effects, such as nonmonotonic dependence of the surface energy on concentration and charge inversion. The image charge effect is then studied for electrolyte solutions between two plates. For two neutral plates, we show that depletion of the salt ions by the image charge repulsion results in short-range attractive and long-range repulsive forces. If cations and anions are of different valency, the asymmetric depletion leads to the formation of an induced electrical double layer. For two charged plates, the competition between the surface charge and the image charge effect can give rise to like- charge attraction.

Then, we study the inhomogeneous screening effect near the dielectric interface due to the anisotropic and nonuniform ion distribution. We show that the double layer structure and interfacial properties is drastically affected by the inhomogeneous screening if the bulk Debye screening length is comparable or smaller than the Bjerrum length. The width of the depletion layer is characterized by the Bjerrum length, independent of the salt concentration. We predict that the negative adsorption of ions at the interface increases linearly with the salt concentration, which cannot be captured by either the bulk screening approximation or the WKB approximation. For asymmetric salt, the inhomogeneous screening enhances the charge separation in the induced double layer and significantly increases the value of the surface potential.

Finally, to account for the ion specificity, we study the self energy of a single ion across the dielectric interface. The ion is considered to be polarizable: its charge distribution can be self-adjusted to the local dielectric environment to minimize the self energy. Using intrinsic parameters of the ions, such as the valency, radius, and polarizability, we predict the specific ion effect on the interfacial affinity of halogen anions at the water/air interface, and the strong adsorption of hydrophobic ions at the water/oil interface, in agreement with experiments and atomistic simulations.

The theory developed in this work represents the most systematic theoretical technique for weak-coupling electrolytes. We expect the theory to be more useful for studying a wide range of structural and dynamic properties in physicochemical, colloidal, soft-matter and biophysical systems.

Topological strings, double affine Hecke algebras, and exceptional knot homology

In this thesis, we consider two main subjects: refined, composite invariants and exceptional knot homologies of torus knots. The main technical tools are double affine Hecke algebras ("DAHA") and various insights from topological string theory.

In particular, we define and study the composite DAHA-superpolynomials of torus knots, which depend on pairs of Young diagrams and generalize the composite HOMFLY-PT polynomials from the full HOMFLY-PT skein of the annulus. We also describe a rich structure of differentials that act on homological knot invariants for exceptional groups. These follow from the physics of BPS states and the adjacencies/spectra of singularities associated with Landau-Ginzburg potentials. At the end, we construct two DAHA-hyperpolynomials which are closely related to the Deligne-Gross exceptional series of root systems.

In addition to these main themes, we also provide new results connecting DAHA-Jones polynomials to quantum torus knot invariants for Cartan types A and D, as well as the first appearance of quantum E6 knot invariants in the literature.

Signatures of Topological Superconductors

Topological superconductors are particularly interesting in light of the active ongoing experimental efforts for realizing exotic physics such as Majorana zero modes. These systems have excitations with non-Abelian exchange statistics, which provides a path towards topological quantum information processing. Intrinsic topological superconductors are quite rare in nature. However, one can engineer topological superconductivity by inducing effective p-wave pairing in materials which can be grown in the laboratory. One possibility is to induce the proximity effect in topological insulators; another is to use hybrid structures of superconductors and semiconductors.

The proposal of interfacing s-wave superconductors with quantum spin Hall systems provides a promising route to engineered topological superconductivity. Given the exciting recent progress on the fabrication side, identifying experiments that definitively expose the topological superconducting phase (and clearly distinguish it from a trivial state) raises an increasingly important problem. With this goal in mind, we proposed a detection scheme to get an unambiguous signature of topological superconductivity, even in the presence of ordinarily detrimental effects such as thermal fluctuations and quasiparticle poisoning. We considered a Josephson junction built on top of a quantum spin Hall material. This system allows the proximity effect to turn edge states in effective topological superconductors. Such a setup is promising because experimentalists have demonstrated that supercurrents indeed flow through quantum spin Hall edges. To demonstrate the topological nature of the superconducting quantum spin Hall edges, theorists have proposed examining the periodicity of Josephson currents respect to the phase across a Josephson junction. The periodicity of tunneling currents of ground states in a topological superconductor Josephson junction is double that of a conventional Josephson junction. In practice, this modification of periodicity is extremely difficult to observe because noise sources, such as quasiparticle poisoning, wash out the signature of topological superconductors. For this reason, We propose a new, relatively simple DC measurement that can compellingly reveal topological superconductivity in such quantum spin Hall/superconductor heterostructures. More specifically, We develop a general framework for capturing the junction's current-voltage characteristics as a function of applied magnetic flux. Our analysis reveals sharp signatures of topological superconductivity in the field-dependent critical current. These signatures include the presence of multiple critical currents and a non-vanishing critical current for all magnetic field strengths as a reliable identification scheme for topological superconductivity.

This system becomes more interesting as interactions between electrons are involved. By modeling edge states as a Luttinger liquid, we find conductance provides universal signatures to distinguish between normal and topological superconductors. More specifically, we use renormalization group methods to extract universal transport characteristics of superconductor/quantum spin Hall heterostructures where the native edge states serve as a lead. Interestingly, arbitrarily weak interactions induce qualitative changes in the behavior relative to the free-fermion limit, leading to a sharp dichotomy in conductance for the trivial (narrow superconductor) and topological (wide superconductor) cases. Furthermore, we find that strong interactions can in principle induce parafermion excitations at a superconductor/quantum spin Hall junction.

As we identify the existence of topological superconductor, we can take a step further. One can use topological superconductor for realizing Majorana modes by breaking time reversal symmetry. An advantage of 2D topological insulator is that networks required for braiding Majoranas along the edge channels can be obtained by adjoining 2D topological insulator to form corner junctions. Physically cutting quantum wells for this purpose, however, presents technical challenges. For this reason, I propose a more accessible means of forming networks that rely on dynamically manipulating the location of edge states inside of a single 2D topological insulator sheet. In particular, I show that edge states can effectively be dragged into the system's interior by gating a region near the edge into a metallic regime and then removing the resulting gapless carriers via proximity-induced superconductivity. This method allows one to construct rather general quasi-1D networks along which Majorana modes can be exchanged by electrostatic means.

Apart from 2D topological insulators, Majorana fermions can also be generated in other more accessible materials such as semiconductors. Following up on a suggestion by experimentalist Charlie Marcus, I proposed a novel geometry to create Majorana fermions by placing a 2D electron gas in proximity to an interdigitated superconductor-ferromagnet structure. This architecture evades several manufacturing challenges by allowing single-side fabrication and widening the class of 2D electron gas that may be used, such as the surface states of bulk semiconductors. Furthermore, it naturally allows one to trap and manipulate Majorana fermions through the application of currents. Thus, this structure may lead to the development of a circuit that enables fully electrical manipulation of topologically-protected quantum memory. To reveal these exotic Majorana zero modes, I also proposed an interference scheme to detect Majorana fermions that is broadly applicable to any 2D topological superconductor platform.

DNA-mediated charge transport signaling within the cell

DNA possesses the curious ability to conduct charge longitudinally through the π-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.

Herein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.

In separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?

UvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters.

Understanding Micro- and Macro-Mechanics of Soil Liquefaction: A Necessary Step for Field-Scale Assessment

Liquefaction is a devastating instability associated with saturated, loose, and cohesionless soils. It poses a significant risk to distributed infrastructure systems that are vital for the security, economy, safety, health, and welfare of societies. In order to make our cities resilient to the effects of liquefaction, it is important to be able to identify areas that are most susceptible. Some of the prevalent methodologies employed to identify susceptible areas include conventional slope stability analysis and the use of so-called liquefaction charts. However, these methodologies have some limitations, which motivate our research objectives. In this dissertation, we investigate the mechanics of origin of liquefaction in a laboratory test using grain-scale simulations, which helps (i) understand why certain soils liquefy under certain conditions, and (ii) identify a necessary precursor for onset of flow liquefaction. Furthermore, we investigate the mechanics of liquefaction charts using a continuum plasticity model; this can help in modeling the surface hazards of liquefaction following an earthquake. Finally, we also investigate the microscopic definition of soil shear wave velocity, a soil property that is used as an index to quantify liquefaction resistance of soil. We show that anisotropy in fabric, or grain arrangement can be correlated with anisotropy in shear wave velocity. This has the potential to quantify the effects of sample disturbance when a soil specimen is extracted from the field. In conclusion, by developing a more fundamental understanding of soil liquefaction, this dissertation takes necessary steps for a more physical assessment of liquefaction susceptibility at the field-scale.