Diphenylalanine (FF) is a dipeptide capable of self-assembly in aqueous solution into needle-like hollow micro- and nanocrystals that possess advantageous properties such as high stiffness and piezoelectricity and have emerged as attractive candidates for functional nanomaterials. In addition, these structures can be made conductive or used as scaffolds for organising functional entities which do not on their own possess a propensity towards self-assembly. At the start of this project, despite wide-ranging interest in the FF assemblies, many important and fundamental aspects of the system remained relatively unexplored. The scope of the present work ranges from nanomaterials science to the relevance of the dipeptide as a model system for the study of aromatic $\pi$-stacking interactions in amyloidogenesis. The basic thermodynamic parameters of FF assembly, the kinetics of that process, and the similarities with, and differences from, the process of fibrillogenesis in polypeptides are explored in detail. The solubility of diphenylalanine in a range of organic solvents and the role of cosolvents in the kinetics of structural assembly were systematically investigated. We find that not only the crystal habit depends on the solvent conditions, but indeed different solvomorphs, possibly differing greatly in mechanical properties, can be obtained from self-assembly in different solvents. The thermodynamics of the dipeptide self-assembly are calculated and placed in the context of earlier work on the free energy of fibril elongation for a range of amyloidogenic polypeptides. It is established that FF aggregation displays the temperature dependence typical of hydrophobic desolvation processes, and that as a model amyloid-forming peptide it displays greater aggregation propensity per amino acid than naturally-occurring polypeptides, due in part to its crystalline as opposed to fibrillar aggregate state. Transition-state measurements are made and the nature of the transition state is elucidated- at the highest-energy point on the aggregation pathway, it is thought that the hydrophobic substituents are still solvent-exposed. The kinetics of self-assembly as a function of solution concentration are quantified through the use of microfluidic techniques, enabling high precision, time-resolved monitoring of the growth process. This work represents the first systematic study of the dependence of the growth rate of diphenylalanine on solution supersaturation. It is found that the aggregation process occurs through established mechanisms of crystal growth. The detailed dependence is shown, and the applicability of the results is demonstrated through the control of the aspect ratio of populations of the assemblies.

Physical and functional properties of advanced nano-composite materials and biological structures are determined by self-organized atoms and molecules into nanostructures and in turn by microscopic organization of the nanostructures into assemblies of higher structural complexity. Therefore, microscopes are indispensable tools for structural investigations at various levels of organization. In this work, novel nonlinear optical microscopy methods were developed to non-invasively study structural organization at the nanoscopic and microscopic levels. Atomic organization of semiconductor nanowires, molecular organization of amylose biocrystallites in starch granules, and microscopic organization of several photosynthetic organisms was elucidated. The structure of ZnSe nanowires, key components in many modern nanodevices, was investigated using polarization harmonic generation microscopy. Based on nonlinear optical properties of the different crystal lattices, zinc blende and wurtzite nanowires were differentiated, and the three-dimensional orientation of the zinc blende nanowires could be found. The structure of starch granules, a model biocrystal, important in food as well as health sciences, was also investigated using polarization harmonic microscopy. The study was combined with ab initio calculations using the crystal structures of amylose A and B, revealing that second harmonic signals originate from the hydroxide and hydrogen bonds in the starch granules. Visualization of several photosynthetic organisms including the green algae, Chlamydomonas reinhardtii, two species of cyanobacteria, Leptolyngbya sp. and Anabaena sp., aggregates of light-harvesting pigment-protein complexes as well as chloroplasts from green plants were also explored, revealing that future nonlinear microscopy applications could include structural studies of cell walls, the Chlamydomonas eyespot, and photosynthetic membranes. In this study, several nonlinear optical microscopy modalities were developed for quantitative structural investigations of nano and micro-sized architectures. Non-invasive extraction of crystallographic information in microscopic samples will have a number of potential benefits, for example, in clinical applications, allowing observations of disease states inside tissues without the need for biopsy. Industrial nanotechnology will benefit from fast determination of nanostructures with nonlinear microscopy that will improve quality of nanodevices.

Physical and functional properties of advanced nano-composite materials and biological structures are determined by self-organized atoms and molecules into nanostructures and in turn by microscopic organization of the nanostructures into assemblies of higher structural complexity. Therefore, microscopes are indispensable tools for structural investigations at various levels of organization. In this work, novel nonlinear optical microscopy methods were developed to non-invasively study structural organization at the nanoscopic and microscopic levels. Atomic organization of semiconductor nanowires, molecular organization of amylose biocrystallites in starch granules, and microscopic organization of several photosynthetic organisms was elucidated. The structure of ZnSe nanowires, key components in many modern nanodevices, was investigated using polarization harmonic generation microscopy. Based on nonlinear optical properties of the different crystal lattices, zinc blende and wurtzite nanowires were differentiated, and the three-dimensional orientation of the zinc blende nanowires could be found. The structure of starch granules, a model biocrystal, important in food as well as health sciences, was also investigated using polarization harmonic microscopy. The study was combined with ab initio calculations using the crystal structures of amylose A and B, revealing that second harmonic signals originate from the hydroxide and hydrogen bonds in the starch granules. Visualization of several photosynthetic organisms including the green algae, Chlamydomonas reinhardtii, two species of cyanobacteria, Leptolyngbya sp. and Anabaena sp., aggregates of light-harvesting pigment-protein complexes as well as chloroplasts from green plants were also explored, revealing that future nonlinear microscopy applications could include structural studies of cell walls, the Chlamydomonas eyespot, and photosynthetic membranes. In this study, several nonlinear optical microscopy modalities were developed for quantitative structural investigations of nano and micro-sized architectures. Non-invasive extraction of crystallographic information in microscopic samples will have a number of potential benefits, for example, in clinical applications, allowing observations of disease states inside tissues without the need for biopsy. Industrial nanotechnology will benefit from fast determination of nanostructures with nonlinear microscopy that will improve quality of nanodevices.