1 

A boolean QPQ using single photons
I propose an implementation of the quantum private query protocol
as described in an article using a photon to encode a question and reflectionor transmission of the photon as answer options. Each question is represented by a photon in a transmission line with both ends returning to the user, and the answer is represented by reflection or transmission of this photon caused by the single photon transistor as described in another article. By solving the quantum Langevin equations for the 32 × 32dimensional operators describing the single photon transistor the system is analysed. This analysis shows that the user privacy is maintained when the returning transmission lines are under the user's control. The probabilities for reflection and transmission are calculated to verify the behaviour of the answering mechanism. By using pulse trains instead of numbered lines to represent questions, the scalability of the system could be improved.

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2 

Electrical actuation and frequency tuning of 2D mechanical resonators
The electrical actuation of suspended membrane nanomechanical resonators incorporated into a laser interferometer displacement setup was investigated. Graphene and MoS2 membranes have been used to show electrical actuation of both metals and semiconductors. The method to fabricate devices was optimized and the properties of the fabricated devices are documented in order to make future device farication easier when speciﬁc properties are required. The ﬁrst experiment performed with the electrical actuation was done in order to investigate the frequency tuning the of the 2D resonators. Resonance frequencies in the range of 1555 MHz are observed without frequency tuning, where variations are due to differences in diameter and thickness of the suspended drums and the builtin tension. Applying a DC voltage caused both a decrease and an increase in the resonance frequency, depending on the device and the magnitude of the voltage. A maximum (increasing) frequency tuning sensitivity of 7.62 MHz/V was achieved. Furthermore, the model of interactions in 2D circular membrane due to electric actuation and DC gate voltage tuning in the linear resonator regime is compared to the measurement results. This comparison gives insight in the interaction between electrostatic spring softening and mechanically induced strain in membranes with different properties. The investigated model was insufﬁcient to explain the measured frequency changes due to the applied DC voltages.

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3 

Pulse optimization for multiqubit gates in transmon system
In transmon qubits, the leading source of errors for quantum gates is the existence of higher energy levels, besides the 0> and 1> states which form the computational subspace. Several methods have been developed to eliminate these errors systematically by clever use of the available experimental controls. In this bachelor thesis we focus on performing quantum gates on multiple qubits simultaneously, when transition frequencies of different qubits are close to each other. The existing solution is designed to perform a quantum gate on one qubit, while eliminating all the effects on the other one. We develop a procedure to create new analytic pulse shapes which produce lowerror gates for single qubits and we generalize this approach to multiqubit systems to apply multiple quantum gates at the same time. For both single and twoqubit gates these new pulses reduce errors by several orders of magnitude compared to simple driving pulses. In addition we combine these optimal analytical pulse shapes with multiparameter pulses. The parameters of this additional pulse are optimized numerically, to produce even lower gate errors.

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4 

Towards Fast Light at the Single Photon Level

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5 

Electrodynamics of strongly disordered superconductors
Thin films of superconducting materials with a high resistance in the normal state, such as TiN, NbTiN, NbN and InO, are intensively studied from both an application and a fundamental point of view. A spatially inhomogeneous superconducting state can arise in these materials as a result of the strong disorder. This Thesis provides an experimental study of the evolution of the electromagnetic response with increasing disorder of superconducting thin films.
We primarily investigate a series of disordered TiN films. The films are grown by means of plasmaenhanced atomiclayer deposition. We probe the electromagnetic response using superconducting microwave resonators. We find a gradual evolution of the electromagnetic response with disorder, deviating from the MattisBardeen equations.
This result might be attributed to changes in the quasiparticle density of states (DoS) induced by the disorder. We can describe the measured microwave response with a heuristic model which contains a disorderdependent effective pair breaking parameter that modifies the DoS.
Further, we compare the assumed DoS—used to describe the electrodynamics—to local tunnel spectra obtained using scanning tunneling spectroscopy. We find affirmative results for the lowest disordered film. However, we find a strong discrepancy for the most disordered film. Moreover, this film displays large variations in the local tunnel spectra. This result signals the breakdown of a model that is based on average properties, due to the emergence of a spatial inhomogeneous superconducting state.

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6 

Cl2/O2inductively coupled plasma etching of deep holetype photonic
crystals in InP

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7 

Charge inversion at high ionic strength studied by streaming currents

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8 

Superconducting flux qubits: Quantum chains and tunable qubits
This thesis presents results of theoretical and experimental work on superconducting persistentcurrent flux quantum bits. These qubits are promising candidates for the implementation of scalable quantum information processing. This work focuses on the study of one dimensional chains of inductively coupled flux qubits and on qubits with a tunable energy gap.
Chains of flux qubits can be used as models of quantum spin chains, one of the most basic systems in manybody physics that has been extensively studied theoretically. The ability to design and tune the qubit and coupling parameters enables exploration of different phase regimes during measurements, in parameter regimes that are not accessible with magnetic materials. The study of the dynamics of quantum waves in an artificial spin chain can also be used to explore novel quantum phenomena with possible applications in quantum computing.
Tunability of the minimal energy splitting (the gap) enables one to rapidly bring the flux qubit in and out of resonance with other quantum systems, including a harmonic oscillator. With tunable qubits it also becomes possible to create interqubit couplings of different vector nature, using magnetic fluxes. This permits the design of various interaction Hamiltonians for multiple qubit systems. These operations can be performed at the degeneracy point of the qubit, where coherence properties are optimal. Therefore the tunable flux qubit provides an attractive component for the implementation of scalable quantum computation.

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9 

Nuclear Spin Effects in Nanostructures
In this thesis we theoretically investigate effects of the interaction between electron spins and nuclear spins in different nanoscopic devices, quantum dots and spin valves.
A quantum dot is a tiny potential well in which one can trap single electrons. One of the proposed applications of the quantum dot is to use the spin of the trapped electrons as qubits, the computational units in a quantum computer. The main obstacle for this application is the fact that the electron spin in the dot is coupled via the hyperfine interaction to roughly one million randomly fluctuating nuclear spins (those in the host material of the quantum dot). These fluctuations manifest themselves as a small but unpredictable magnetic field, causing the spin state of the electron to be not stable enough to be useful for quantum computation.
The hyperfine interaction however works both ways: Several recent experiments have showed clear evidence that the nuclear spins, in turn, are also affected by the electron spin. So, it might be possible to suppress the fluctuations of the nuclear field by a clever manipulation of the electron spin in the dot. If so, this would bring the realization of the quantum dot spin qubit one big step closer.
In this thesis we investigate the coupled electronnuclear spin dynamics in several realistic experimental situations. We consider both single and double quantum dots, and concentrate on the combination of electronic transport (current) and electron spin resonance (a magnetic microwave field). We find that in these situations the fluctuations of the nuclear field indeed can be strongly suppressed, and we support this with experimental results.
Further, we investigate the effect of strong spinorbit coupling on the transport properties of a double quantum dot, and we also consider hyperfine effects in a metallic spin valve.

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10 

Modeling and simulation of phasetransitions in multicomponent aluminum alloy casting
The casting process of aluminum products involves the spatial distribution of alloying elements. It is essential that these elements are uniformly distributed in order to guarantee reliable and consistent products. This requires a good understanding of the main physical mechanisms that affect the solidification, in particular the thermodynamic description and its coupling to the transport processes of heat and mass that take place. The continuum modeling is reviewed and methods for handling the thermodynamics component of multielement alloys are proposed. Savings in datastorage and computing costs on the order of 100 or more appear possible, when a combination of datareduction and datarepresentation methods is used. To test the new approach a simplified model was proposed and shown to qualitatively capture the evolving solidification front.

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11 

Endjoining long nucleic acid polymers
Many experiments involving nucleic acids require the hybridization and ligation of multiple DNA or RNA molecules to form a compound molecule. When one of the constituents is single stranded, however, the efficiency of ligation can be very low and requires significant individually tailored optimization. Also, when the molecules involved are very long (>10 kb), the reaction efficiency typically reduces dramatically. Here, we present a simple procedure to efficiently and specifically endjoin two different nucleic acids using the wellknown biotin–streptavidin linkage. We introduce a twostep approach, in which we initially bind only one molecule to streptavidin (STV). The second molecule is added only after complete removal of the unbound STV. This primarily forms heterodimers and nearly completely suppresses formation of unwanted homodimers. We demonstrate that the joining efficiency is 50 plus/minus25% and is insensitive to molecule length (up to at least 20 kb). Furthermore, our method eliminates the requirement for specific complementary overhangs and can therefore be applied to both DNA and RNA. Demonstrated examples of the method include the efficient endjoining of DNA to singlestranded and doublestranded RNA, and the joining of two doublestranded RNA molecules. Endjoining of long nucleic acids using this procedure may find applications in bionanotechnology and in singlemolecule experiments.

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12 

Development of Quantitative electron nanodiffraction
This thesis is a step towards development of quantitative parallel beam electron nanodiffraction (PBED). It is focused on the superstructure determination of zigzag and zigzig NaxCoO2 and analysis of charge distribution in the two polymorphs Nb12O29 using PBED. It has been shown that quantitative electron nanodiffraction (parallel beam) has the potential of solving superstructures as well as charge distribution by taking the dynamicity of the data to its advantage.
The information contained in the electron diffraction data has never been doubted but the dynamicity of the data (arising from multiple scattering) makes the interpretation very complex.
First of all the superstructure information, which is difficult to be seen in Xray or neutron diffraction data specially when they occur in the nanometer regime, can be resolved by electron diffraction. This has been illustrated with chapters 2 and 3. Further, the charge information contained in the electron diffraction is much more than Xray diffraction due to the fact that Xrays are scattered by electron cloud only while electron scattering is a result electrostatic potential of the system. Hence electron diffraction can be used as a tool to study precisely the charge distribution or charge ordering which by other means is not possible. Though there are many skeptics to this argument, this thesis through chapters 4 and 5, is an attempt to prove that the future lies in the electron diffraction to study the type of systems described in here.

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13 

InSitu Reduction of Charge Noise in GaAs/AlxGa1xAs SchottkyGated Devices
We show that an insulated electrostatic gate can be used to strongly suppress ubiquitous background charge noise in Schottkygated GaAs=AlGaAs devices. Via a 2D selfconsistent simulation of the conduction band profile we show that this observation can be explained by reduced leakage of electrons from the Schottky gates into the semiconductor through the Schottky barrier, consistent with the effect of ‘‘bias cooling.’’ Upon noise reduction, the noise power spectrum generally changes from Lorentzian to 1/f type. By comparing wafers with different Al content, we exclude that DX centers play a dominant role in the charge noise.

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14 

Computation of mutual fitness by competing bacteria
Competing populations in shared spaces with nonrenewable resources do not necessarily wage a battle for dominance at the cost of extinction of the lessfit strain if there are fitness advantages to the presence of the other strain. We report on the use of nanofabricated habitat landscapes to study the population dynamics of competing wild type and a growth advantage in stationary phase (GASP) mutant strains of Escherichia coli in a sealed and heterogeneous nutrient environment. Although GASP mutants are competitors with wildtype bacteria, we find that the 2 strains cooperate to maximize fitness (longterm total productivity) via spatial segregation: despite their very close genomic kinship, wildtype populations associate with wildtype populations and GASP populations with GASP populations. Thus, wildtype and GASP strains avoid each other locally, yet fitness is enhanced for both strains globally. This computation of fitness enhancement emerges from the local interaction among cells but maximizes global densities. At present we do not understand how fluctuations in both spatial and temporal dimensions lead to the emergent computation and how multilevel aggregates produce this collective adaptation.

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15 

SingleMolecule Observation of Anomalous Electrohydrodynamic Orientation of Microtubules
We use fluorescence microscopy to measure the orientation and shape of microtubules—which serve as a model system for semiflexible rods—that are electrophoretically driven. Surprisingly, a bimodal orientation distribution is observed, with microtubules in either parallel or perpendicular orientations to the electric field. The occupancy of these states varies nonmonotonically with the microtubule length L and the electric field E. We also observe a surprising bending deformation of microtubules. Interestingly, all data collapse onto a universal scaling curve when the average alignment is plotted as a function of B  EL3, which reflects the ratio between the driving force and a restoring elastic force. Our results have important implications for the interpretation of electrical birefringence experiments and, more generally, for a better understanding of the electrokinetics of rods.

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16 

Conformation and Dynamics of DNA Confined in Slitlike Nanofluidic Channels
Using laser fluorescence microscopy, we study the shape and dynamics of individual DNA molecules in slitlike nanochannels confined to a fraction of their bulk radius of gyration. With a confinement size spanning 2 orders of magnitude, we observe a transition from the de Gennes regime to the Odijk regime in the scaling of both the radius of gyration and the relaxation time. The radius of gyration and the relaxation time follow the predicted scaling in the de Gennes regime, while, unexpectedly, the relaxation time shows a sharp decrease in the Odijk regime. The radius of gyration remains constant in the Odijk regime. Additionally, we report the first measurements of the effect of confinement on the shape anisotropy.

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17 

Entanglement in SolidState Nanostructures
The goal of this thesis is to investigate theoretically the generation and behaviour of multipartite entanglement for solidstate nanosystems, in particular electron spin quantum bits (socalled 'qubits') in quantum dots.
A quantum dot is a tiny potential well where a single electron can be trapped. A quantum bit can be implemented in this system by applying a magnetic field, and thereby lifting the degeneracy of the spin states of the electron. These spins can then be used as single qubits, and engineering many of these quantum dots next to each other gives as a register of qubits. In this scheme, the socalled LossDiVincenzo quantum computer, the single spins can be rotated e.g. by applying a time dependent magnetic field, and two spins can interact through controlling the potential barrier between them.
A qubit cannot only be in a superposition of the two computational states 0 and 1 at the same time, but an even stranger characteristic arises for multiple qubits: this phenomenon is called entanglement and refers to a strong correlation between two or more qubits, which can not be achieved within the framework of classical physics, and exponentially enlarges the possible states for a Nqubit system as compared to a classical Nbit system.
In this thesis we devise algorithms how to generate multipartite entangled states in
electron spin qubits in quantum dots. We compare which classes of entangled states can be generated efficiently in this system. Once the states are created, they decay due to a process called decoherence. We compare how entangled states can be generated and detected in a realistic experiment, and which classes of states are the most suitable. Furthermore, we compare which classes conserve the entanglement, and quantify the robustness of various classes of entangled states.
In the last chapter, we devise a scheme of how to execute a simple quantum algorithm, the DeutschJozsa algorithm, in a system containing another type of solidstate qubit, the socalled flux qubit.

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18 

Triplet Josephson Effect with Magnetic Feedback in a SuperconductorFerromagnet Heterostructure

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19 

Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I
The Type I restrictionmodification enzyme EcoR124I is an archetypical helicasebased dsDNA translocase that moves unidirectionally along the 3'–5' strand of intact duplex DNA. Using a combination of ensemble and singlemolecule measurements, we provide estimates of two physicochemical constants that are fundamental to a full description of motor protein activity—the ATP coupling efficiency (the number of ATP consumed per base pair) and the step size (the number of base pairs transported per motor step). Our data indicate that EcoR124I makes small steps along the DNA of 1 bp in length with 1 ATP consumed per step, but with some uncoupling of the ATPase and translocase cycles occurring so that the average number of ATP consumed per base pair slightly exceeds unity. Our observations form a framework for understanding energy coupling in a great many other motors that translocate along dsDNA rather than ssDNA.

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20 

Shotnoise detection in a carbon nanotube quantum dot

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