@phdthesis{Mostafa2024,
  author    = {Mostafa, Amr},
  title     = {DNA origami nanoforks: A platform for cytochrome c single molecule surface enhanced Raman spectroscopy},
  doi       = {10.25932/publishup-63548},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-635482},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xi, 90, x},
  year      = {2024},
  abstract  = {This thesis presents a comprehensive exploration of the application of DNA origami nanofork antennas (DONAs) in the field of spectroscopy, with a particular focus on the structural analysis of Cytochrome C (CytC) at the single-molecule level. The research encapsulates the design, optimization, and application of DONAs in enhancing the sensitivity and specificity of Raman spectroscopy, thereby offering new insights into protein structures and interactions. The initial phase of the study involved the meticulous optimization of DNA origami structures. This process was pivotal in developing nanoscale tools that could significantly enhance the capabilities of Raman spectroscopy. The optimized DNA origami nanoforks, in both dimer and aggregate forms, demonstrated an enhanced ability to detect and analyze molecular vibrations, contributing to a more nuanced understanding of protein dynamics. A key aspect of this research was the comparative analysis between the dimer and aggregate forms of DONAs. This comparison revealed that while both configurations effectively identified oxidation and spin states of CytC, the aggregate form offered a broader range of detectable molecular states due to its prolonged signal emission and increased number of molecules. This extended duration of signal emission in the aggregates was attributed to the collective hotspot area, enhancing overall signal stability and sensitivity. Furthermore, the study delved into the analysis of the Amide III band using the DONA system. Observations included a transient shift in the Amide III band's frequency, suggesting dynamic alterations in the secondary structure of CytC. These shifts, indicative of transitions between different protein structures, were crucial in understanding the protein's functional mechanisms and interactions. The research presented in this thesis not only contributes significantly to the field of spectroscopy but also illustrates the potential of interdisciplinary approaches in biosensing. The use of DNA origami-based systems in spectroscopy has opened new avenues for research, offering a detailed and comprehensive understanding of protein structures and interactions. The insights gained from this research are expected to have lasting implications in scientific fields ranging from drug development to the study of complex biochemical pathways. This thesis thus stands as a testament to the power of integrating nanotechnology, biochemistry, and spectroscopic techniques in addressing complex scientific questions.},
  language  = {en}
}
@article{SchuermannTitovEbeletal.2022,
  author    = {Sch{\"u}rmann, Robin and Titov, Evgenii and Ebel, Kenny and Kogikoski Junior, Sergio and Mostafa, Amr and Saalfrank, Peter and Milosavljević, Aleksandar R. and Bald, Ilko},
  title     = {The electronic structure of the metal-organic interface of isolated ligand coated gold nanoparticles},
  series = {Nanoscale Advances},
  volume    = {4},
  journal   = {Nanoscale Advances},
  number    = {6},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {2516-0230},
  doi       = {10.1039/d1na00737h},
  pages     = {1599 -- 1607},
  year      = {2022},
  abstract  = {Light induced electron transfer reactions of molecules on the surface of noble metal nanoparticles (NPs) depend significantly on the electronic properties of the metal-organic interface. Hybridized metal-molecule states and dipoles at the interface alter the work function and facilitate or hinder electron transfer between the NPs and ligand. X-ray photoelectron spectroscopy (XPS) measurements of isolated AuNPs coated with thiolated ligands in a vacuum have been performed as a function of photon energy, and the depth dependent information of the metal-organic interface has been obtained. The role of surface dipoles in the XPS measurements of isolated ligand coated NPs is discussed and the binding energy of the Au 4f states is shifted by around 0.8 eV in the outer atomic layers of 4-nitrothiophenol coated AuNPs, facilitating electron transport towards the molecules. Moreover, the influence of the interface dipole depends significantly on the adsorbed ligand molecules. The present study paves the way towards the engineering of the electronic properties of the nanoparticle surface, which is of utmost importance for the application of plasmonic nanoparticles in the fields of heterogeneous catalysis and solar energy conversion.},
  language  = {en}
}
@article{SchneiderFritzschePuciulMalinowskaetal.2020,
  author    = {Schneider, Matthias and Fritzsche, Nora and Puciul-Malinowska, Agnieszka and Baliś, Andrzej and Mostafa, Amr and Bald, Ilko and Zapotoczny, Szczepan and Taubert, Andreas},
  title     = {Surface etching of 3D printed poly(lactic acid) with NaOH},
  series = {Polymers},
  volume    = {12},
  journal   = {Polymers},
  number    = {8},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4360},
  doi       = {10.3390/polym12081711},
  pages     = {16},
  year      = {2020},
  abstract  = {The article describes a systematic investigation of the effects of an aqueous NaOH treatment of 3D printed poly(lactic acid) (PLA) scaffolds for surface activation. The PLA surface undergoes several morphology changes and after an initial surface roughening, the surface becomes smoother again before the material dissolves. Erosion rates and surface morphologies can be controlled by the treatment. At the same time, the bulk mechanical properties of the treated materials remain unaltered. This indicates that NaOH treatment of 3D printed PLA scaffolds is a simple, yet viable strategy for surface activation without compromising the mechanical stability of PLA scaffolds.},
  language  = {en}
}
@misc{SchneiderFritzschePuciulMalinowskaetal.2020,
  author    = {Schneider, Matthias and Fritzsche, Nora and Puciul-Malinowska, Agnieszka and Balis, Andrzej and Mostafa, Amr and Bald, Ilko and Zapotoczny, Szczepan and Taubert, Andreas},
  title     = {Surface etching of 3D printed poly(lactic acid) with NaOH: a systematic approach},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {8},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52508},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-525088},
  pages     = {18},
  year      = {2020},
  abstract  = {The article describes a systematic investigation of the effects of an aqueous NaOH treatment of 3D printed poly(lactic acid) (PLA) scaffolds for surface activation. The PLA surface undergoes several morphology changes and after an initial surface roughening, the surface becomes smoother again before the material dissolves. Erosion rates and surface morphologies can be controlled by the treatment. At the same time, the bulk mechanical properties of the treated materials remain unaltered. This indicates that NaOH treatment of 3D printed PLA scaffolds is a simple, yet viable strategy for surface activation without compromising the mechanical stability of PLA scaffolds.},
  language  = {en}
}
@article{SchneiderFritzschePuciulMalinowskaetal.2020,
  author    = {Schneider, Matthias and Fritzsche, Nora and Puciul-Malinowska, Agnieszka and Balis, Andrzej and Mostafa, Amr and Bald, Ilko and Zapotoczny, Szczepan and Taubert, Andreas},
  title     = {Surface etching of 3D printed poly(lactic acid) with NaOH: a systematic approach},
  series = {Polymers},
  volume    = {12},
  journal   = {Polymers},
  number    = {8},
  publisher = {MDPI},
  address   = {Basel},
  pages     = {16},
  year      = {2020},
  abstract  = {The article describes a systematic investigation of the effects of an aqueous NaOH treatment of 3D printed poly(lactic acid) (PLA) scaffolds for surface activation. The PLA surface undergoes several morphology changes and after an initial surface roughening, the surface becomes smoother again before the material dissolves. Erosion rates and surface morphologies can be controlled by the treatment. At the same time, the bulk mechanical properties of the treated materials remain unaltered. This indicates that NaOH treatment of 3D printed PLA scaffolds is a simple, yet viable strategy for surface activation without compromising the mechanical stability of PLA scaffolds.},
  language  = {en}
}