Universität Stuttgart

The translocation of DNA through nanopores is an intensively studied field as it can lead to a new perspective in DNA sequencing. During this process the DNA is electrophoretically driven through a nanoscale hole in a membrane, and use different sensing schemes to read out the sequence. Within the scope of nanopore sequencing two important sensing schemes relevant to this thesis are: 1.) Tunneling sequencers based on solid state nanopores embedded with gold electrodes 2.) 2D materials beyond graphene For scheme 1, an obvious improvement is to coat the gold electrode with molecules that have high conductance and can form instantaneous hydrogen bond bridges with the translocating polynucleotide thereby improving the transverse current signal. The molecule that we propose is the so called diamondoid which are diamond caged molecules with hydrogen termination. Before applying such a molecule to a nanopore electrode set up, one would like to understand their interaction with DNA and its nucleobases. For this purpose, hydrogen bonded complexes formed between nitrogen doped derivatives of smallest diamondoids (i.e. adamantane derivatives) and nucleobases were investigated using dispersion corrected density functional theory (DFT). Mutated and methylated nucleobases are also taken into consideration in these investigations. DFT calculations revealed that hydrogen bonds are of moderate strength. In addition, starting from the DFT predicted hydrogen bonding configuration for each complex, rotations, and translations along a reference axis was performed to capture variations in the interaction energies along the donor-acceptor groups of the hydrogen bonds. The electronic density of states analysis for the hydrogen bonded complexes revealed distinguishable signatures for each nucleobase, thereby showing the suitability for application in electrodes functionalised with such probe molecules. In the next step, an adamantane derivative is placed on one of the electrode and nucleotides are introduced in such a way that nucleobases form hydrogen bonds with the of the nitrogen group of the adamantane derivatives. Electronic transport calculations were performed for gold electrodes functionalised with 3 different adamantane derivatives. Four pristine nucleotides, one mutated, and one methylated nucleotides were considered. Analysis of the transmission spectra reveal that each of the nucleotides has a unique resonance peak far below the Fermi level. We have also proposed a gating voltage window to sample the resonance peaks of the nucleotide so that they can be distinguished from each other. An alternative to tunneling sequencers would be to use nanopores built in to ultra thin metallic nanoribbons such as graphene. The sequence can be read out from the in-plane current modulation resulting from the local field effect of the translocating nucleotides in the vicinity of the metallic pore edges. But the hydrophobicity of graphene makes it a difficult candidate in aqueous environment. Hence in scheme 2, the aim is to model an ultra thin material that can rectify the hydrophobicity of graphene and can be a very good candidate for current modulation sequencing. Ultra thin MoS2 (2H) monolayer exist as direct band gap semiconductor. Nanopores based on 2H phases have been reported in the literature and are not hydrophobic. By means of chemical exfoliation of the 2H phase, a meta stable 1T phase of MoS2 has also been synthesized by various experimental groups. The 1T phase of MoS2 is metallic. The aim of this thesis is to model a nano-biosensor template based on a hybrid MoS2 monolayer made up of a metallic (1T) phase sandwiched between semiconducting (2H) phase. The sensor that we propose, should have only metallic nanopore edges. As a first step, we have modeled the semiconductor-metal interface, and compared them with experiments. Then an investigation to understand the influence of the increase of the metallic unit on the electronic properties is performed. Since, point defects are highly relevant to electrochemical pore growth, a point sulfur defect analysis is provided to ascertain the weakest point in the sheet. Finally to understand the effect of the interface electronic transport calculations are performed. The transmission spectra reveals a clear asymmetry in the current flow across the interface by means of gating. In the end, the relevance of such a hybrid MoS2 material for nanopore sequencing is discussed.

This dissertation aims to shed light on the fundamental aspects of supercooled liquid gallium. First, the mechanical properties of the oxide skin encapsulating the supercooled liquid gallium droplet is investigated. By leveraging the supercooling behavior of gallium and the formation of its oxide skin, we characterized the emergence of wrinkling at the interface and adhesion energy between the liquid gallium and rigid substrate. An interfacial energy of 0.238 ± 0.008 J m-2 was measured between gallium droplet and flat glass. Second, seed induced crystallization of supercooled liquid gallium on the different substrate materials revealed the dependence of the kinetics of crystallization on thermal behavior of the substrate. Such approach further elucidates on the importance of interface temperature during crystallization with a preferred orientation. The third part of the dissertation reports an unprecedented liquid crystal structure in supercooled liquid gallium. By the use of techniques applied in liquid crystal (LC) research, observation of LC texture in supercooled liquid gallium was realized. Reflective polarized optical microscopy (R-POM) on liquid gallium sandwiched between glasses treated with rubbed polymers reveals the onset of an anisotropic reflection of possible dimer molecules or clusters at 120°C that increases on cooling and persists down to room temperature or below. On the other hand, when gallium is sandwiched between substrates that align conventional liquid crystal molecules normal to the surface, the reflection is isotropic. This observation of LC structure of a highly electrically conductive supercooled liquid gallium provides an unexpected new field of materials science and liquid crystal research.

Universität Stuttgart

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