Nonlinear optical characterisation of organic chromophores and aspects of molecular aggregation

The work presented in this thesis describes an investigation into the properties and behaviour of a new class of nonlinear optical organic chromophores. This study contributes to the optimisation of nonlinear optical molecules through an improved understanding of the relationships between the molecular nonlinear optical properties and the measured macroscopic quantities. A series of highly dipolar non-linear optical chromophores with absorption typically in the range of 350-500 nm have been synthesised by the reactions of amines with tetracyanoquinodimethane (TCNQ). One of the advantages of these materials is the large molecular figure of merit (μβ where μ is the molecular dipole moment and P is the second order polarisability), which theoretically allows large nonlinear optical coefficients to be obtained. The molecular dipole moments of these chromophores were determined both experimentally and theoretically, and were found to agree. The nonlinear optical properties of these compounds in solution were studied using an electric field induced second harmonic generation (EFISH) technique. The measurements of μβ at 1064 nm and 1907 nm in chloroform and acetone are presented. Moderate μβ values were obtained but β is found to be unexpectedly small in chloroform and shows unusual dispersion characteristics in this solvent compared to acetone. Further concentration investigations revealed features that suggest the presence of aggregates within solution. Optical spectroscopy measurements provide evidence of new species whose presence and conformation were found to be solvent-dependent. The results of this work highlight the need for an entire concentration range to be studied if accurate determination of molecular properties of highly dipolar molecules is required. Guest-host polymer films of these materials have been corona poled using a constant current corona triode. Detailed characterisation studies of the second order nonlinearities using second harmonic generation (SHG) were compared to a less dipolar molecule. These investigations showed that the highly dipolar TCNQ derivatives show severe aggregation within the polymer films. The magnitude of the SHG that can be obtained from such systems is therefore limited by this aggregation

The Application of Archival Concepts to a Data-Intensive Environment: Working with Scientists to Understand Data Management and Preservation Needs

The collection, organization, and long-term preservation of resources are the raison d’être of archives and archivists. The archival community, however, has largely neglected science data, assuming they were outside the bounds of their professional concerns. Scientists, on the other hand, increasingly recognize that they lack the skills and expertise needed to meet the demands being placed on them with regard to data curation and are seeking the help of “data archivists” and “data curators.” This represents a significant opportunity for archivists and archival scholars but one that can only be realized if they better understand the scientific context.National Science Foundation under Grant No. 0724300Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86738/1/Akmonetal2011.pd

Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Funder: EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health); doi: https://doi.org/10.13039/100011272; Grant(s): 305444, 305444Funder: Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness); doi: https://doi.org/10.13039/501100003329Funder: Generalitat de Catalunya (Government of Catalonia); doi: https://doi.org/10.13039/501100002809Funder: EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj); doi: https://doi.org/10.13039/501100008530Funder: Instituto Nacional de Bioinformática ELIXIR Implementation Studies Centro de Excelencia Severo OchoaFunder: EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics