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Micro-pollutants such as 17β-estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been demonstrated. It is essential to confirm the presence of micro-pollutants in different environments by biosensors and to remove these compounds. In this thesis, E2-binding target structures were used to investigate the underlying binding properties. E2-binding protein, DNA-, and PNA-aptamere (peptide nucleic acid) structures were used as targets to determine physicochemical interactions. The protein dataset consist of 35 publicly accessible three-dimensional structures of E2-protein complexes, from which six representative binding sites could be selected. There is no three-dimensional structure information for an E2-specific DNA aptamer, thus it was modeled using a coarse-grained modeling method. Using sequence information additional DNA aptamers were modeled. The E2 ligand was positioned close to the potential binding area of the aptamer structures, the underlying complexes were investigated by a molecular dynamics simulation, and the interactions were examined by an interaction profiler tool for each time step. A PNA generator was developed that can convert DNA and RNA in silico to more robust, but chemically equivalent PNA. This generator was used to transform the E2-specific DNA aptamer into PNA for binding studies with E2. All formed complexes were investigated with respect to the following non-covalent interaction types: hydrogen bonds, water-mediated hydrogen bonds, π-stacking, and hydrophobic interactions. Ten functional groups could be derived which formed the conserved interactions to E2. The study contributes to the understanding of the behavior of ligands that bind through different target structures in an aqueous solution and to the identification of binding specific interaction partners. The results of this thesis can be used to design novel synthetic receptor and filter systems.

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This thesis is an attempt to understand ways to improve thermo-mechanical and structural properties of nano-structured materials. A detailed study on computational design and analysis of metallic nanowires is carried out. Molecular dynamic simulation method is applied. In particular, FCC metallic nanowires, NiAl, and CuZr nanowires are studied. Various bottom-up approaches are suggested with improved structural and thermo¬mechanical properties. In the first part of the thesis, Cu nanowires are considered. Existence of a novel and stable pentagonal multi-shell nanobridge structure of Cu under high strain rate tensile loading is reported. Such a structure shows enhanced mechanical properties. A three-fold pseudo-elastic-plastic shape recovery mechanism in such nanowires is established. This study also shows that the length of the pentagonal nanobridge structures can be characterized by its inelastic strain. It is also reported that an initial FCC structure is transformed into a new HCP structure. The evidence of HCP structure is confirmed with the help of experimental data published in the literature. Subsequent to the above study, a novel mechanism involving coupled temperature-stress dependent reorientation in FCC nanowires is investigated. A detailed map is generated for size dependent stress-temperature induced solid-solid reorientation in Cu nanowires. In the second part of the thesis, deformation mechanisms in NiAl based intermetallic nanowires are studied. A novel mechanism of temperature and cross-section dependent pseudo-elastic/pseudo-plastic shape and strain recovery by an initial B2 phase of NiAl nanowire is reported. Such a recoverable strain, which is as high as ~ 30%, can potentially be utilized to realize various types of shape memory and strain sensing phenomena in nano-scale devices. An asymmetry in tensile and compressive yield strength behavior is also observed, which is due to the softening and hardening of the nanowires under tensile and compressive loadings, respectively. Two different deformation mechanisms dominated by twinning under tension and slip under compression are found. Most interestingly, a superplastic behavior with a failure strain of up to 700% in the intermetallic NiAl nanowires is found to exist at a temperature of 0.36Tm. Such superplastic behavior is attributed to the transformation of the nanowire from a crystalline phase to an amorphous phase after yielding of the nanowire. In the last part the work, another type of nanowires having Cu-Zr system is considered. A novel stress induced martensitic phase transformation from an initial B2 phase to BCT phase in a CuZr nanowire under tensile loading is reported. It is further shown that such a stress induced martenistic phase transformation can be achieved under both tensile as well as compressive loadings. Tensile-compressive asymmetry in the stress-strain behavior is observed due to two different phase transformation mechanisms having maximum transformation strains of ~ 5% under compressive loading and ~ 20% under tensile loading. A size and temperature dependent tensile phase transformation in the nanowire is also observed. Small nanowires show a single step tensile phase transformation whereas the nanowires with larger size show a two step deformation mechanism via an intermediate R-phase hardening followed by R-phase yielding. A study of energetic behavior of these nanowires reveals uniform distribution of stress over the nanowire cross-section and such stress distribution can lead to a significant improvement in its thermo-mechanical properties. Similar improvement is demonstrated by designing the nanowires via manipulating the surface configuration of B2-CuZr system. It is found that the CuZr nanowires with Zr atoms at the surface sites are energetically more stable and also give a uniform distribution of stresses across the cross-section. This leads to the improvement in yield strength as well as failure strain. An approach to design energetically stable nano-structured materials via manipulating the surface configurations with improved thermo-mechanical properties is demonstrated which can help in fundamental understanding and development of similar structures with more stability and enhanced structural properties. Further ab-initio and experimental studies on the confirmation of the stability of the nanowires via manipulating the surface site is an open area of research and related future scopes are highlighted in the closure.