Scanning tunneling microscopy on large bio-molecular systems on surfaces

The ever growing demand for the development of new technologies and materials has led to extensive studies inspired by biological functional complexes. Peptides with their outstanding ability to efficiently self-assemble can express a broad spectrum of intriguing functionalities. A key question in mimicking their assembly and function is the precise understanding of the specific interactions between the contained amino acids on the level of a sub-molecular length scale. An excellent tool to probe samples at these length scales is available with scanning tunneling microscopy (STM) and its operation under the controlled conditions of ultra-high vacuum (UHV) and low temperature. Within this thesis it is demonstrated how high-resolution studies by STMin combination with a controlled sample preparation by electrospray ion beam deposition (ES-IBD) under UHV conditions allows for the structural determination of peptides on surfaces. Furthermore the results presented here contribute to the development of a method capable of directly identifying individual amino acids within a peptide sequence. The structural and electronic properties of molecules on surfaces crucially depend on their interaction with the underlying substrate. Implementing a thin dielectric layer on the metallic surface, electronically decouples molecules from the substrate and enables an unperturbed observation of the molecular electronic structure. In Chapter 2 the properties of hexagonal boron nitride (h-BN) on Rh(111) as decoupling layer are assessed on behalf of the structural and electronic properties of the molecular model system pentacene adsorbed on it. In a second part of this chapter the discovery and the characterization of a new phase of h-BN/Rh(111) is described. In Chapter 3, we gained insight into the properties of amino acids on metal surfaces by utilizing the capability of the STM to probe the structure and the electronic characteristics in high resolution imaging and scanning tunneling spectroscopy (STS). As a second important aspect of this chapter, the modification of STM tips with amino acids is investigated as a method to enhance the structural and electronic resolution. An experimental protocol allowing to adhere amino acids on the STM tip be could developed. Using functional STM tips in STS experiments on amino acids enabled the observation of specific molecular resonances. An obstacle in investigating large bio-polymers, such as natural peptides, is their high structural complexity and conformational freedom. Therefore the utilization of custom designed synthetic sequences tailored towards a specific property is a good approach. In Chapter 4 studies performed on two synthetic peptide sequences deposited by ES-IBD on an Au(111) surface are discussed. The first sequence assembled in ordered two-dimensional networks. A folded gas-phase conformation could be utilized to rationalize the observed structures in the networks. Subsequently it was shown that the self-assembly behavior of the peptide could be steered towards chain-like assemblies by modifying the sequence at the peptide C-terminal. Using specific amino acid functionalized STM tips a sensitivity towards an amino acid of the same type in the peptide sequence could be observed. Thereby a partial sequencing of the synthetic peptide was enabled

DNA charge transfer: An atomistic model

In this work, we address the phenomenon of charge transport in DNA using a simple, but chemically specific, approach that is intimately related to the Su-Schrieffer-Heeger (SSH) model. The emerging potential energy surface for hole transport is analyzed using Marcus' theory of charge transfer. Our results are fully compatible with the conjecture of charge transfer in DNA via two competing mechanisms, and the computations provide the corresponding charge-transfer rates both in the short-range superexchange and in the long-range hopping regime as the output of a single atomistic theory. Finally, the model allows the computation of the transport properties of systems containing modified bases and of more complex arrangements of base pairs as an additional element of verification

Charge transfer through the nucleosome: A theoretical approach

In this work, we approach the problem of charge transfer in deoxyribonucleic acid (DNA) from a theoretical and numerical perspective. We focus on a DNA geometry characteristic of the eukaryotic genome and study transport along a superhelix that contains 292 nucleobases. The electronic structure is described within the Su-Schrieffer-Heeger model in an atomistic parameterization, which has been extended by a nonretarded reaction field to take dielectric polarization effects into account. The emerging potential energy surface is analyzed using the Marcus theory of electron transfer. The computed reaction coefficients are compared to their counterparts originating from idealized geometries and to experimental findings. This comparison and the palindromic nature of the DNA sequence used here permit the assessment of fluctuations in the local orientation of the bases and their impact upon transport properties

Wireless Networks In-the-Loop: Emulating an RF front-end in GNU Radio

The objective of this work is to emulate the behavior of the Universal Software Radio Peripheral as an example of an RF front-end hardware for software radios. The model includes digital and analog signal processing. The emulator is implemented in GNU Radio and is intended to be used as part of a wireless network simulator

Adsorption and electronic properties of pentacene on thin dielectric decoupling layers

With the increasing use of thin dielectric decoupling layers to study the electronic properties of organic molecules on metal surfaces, comparative studies are needed in order to generalize findings and formulate practical rules. In this paper we study the adsorption and electronic properties of pentacene deposited onto h-BN/Rh(111) and compare them with those of pentacene deposited onto KCl on various metal surfaces. When deposited onto KCl, the HOMO and LUMO energies of the pentacene molecules scale with the work functions of the combined KCl/metal surface. The magnitude of the variation between the respective KCl/metal systems indicates the degree of interaction of the frontier orbitals with the underlying metal. The results confirm that the so-called IDIS model developed by Willenbockel et al. applies not only to molecular layers on bare metal surfaces, but also to individual molecules on thin electronically decoupling layers. Depositing pentacene onto h-BN/Rh(111) results in significantly different adsorption characteristics, due to the topographic corrugation of the surface as well as the lateral electric fields it presents. These properties are reflected in the divergence from the aforementioned trend for the orbital energies of pentacene deposited onto h-BN/Rh(111), as well as in the different adsorption geometry. Thus, the highly desirable capacity of h-BN to trap molecules comes at the price of enhanced metal-molecule interaction, which decreases the HOMO-LUMO gap of the molecules. In spite of the enhanced interaction, the molecular orbitals are evident in scanning tunnelling spectroscopy (STS) and their shapes can be resolved by spectroscopic mapping

Distributed Localized Interference Avoidance for Dynamic Frequency Hopping ad hoc Networks

We present a cognitive spectrum access solution for FH-CDMA ad hoc networks. Building on a cluster-based split phase multi-channel MAC protocol, we propose a mechanism for local interference avoidance through distributed hopset adaptation. Its goal is to identify and substitute channels not suitable for reliable communication. Substitution rules replace channels by locally unused hopsets. This way, interference is mitigated while maintaining orthogonality between nodes’ hopsets. We evaluate the gains of the proposed method with a simplified system model

DySPAN Spectrum Challenge: situational awareness and opportunistic spectrum access benchmarked

In this paper, we describe the original problem statement and the two winning solutions to the IEEE DySPAN Challenge, organized in Baltimore in 2017. The idea of the challenge was to invite teams to propose as diverse as possible solutions to a well defined problem, and evaluate the performance of the proposed solutions in a realistic environment. The challenge is defined to enable benchmarking and comparison of multiple teams, possibly working on different parts of the system, in a real environment. The winning solutions represented a complete and working system, working robustly and adapting to both anticipated scenario changes, as well as random effects caused by the conference setting. The code for running the challenge along with the winning solutions is publicly available, so that interested teams can start from the code when designing or benchmarking solutions, as well as when setting up own challenges and competitions. As a result, the challenge can serve as a milestone towards the creation of a benchmarking series. This paper contains all the necessary details about the software repositories so that it becomes possible to rerun the challenge and start building novel solutions based on the winners in IEEE DySPAN 2017.status: publishe