Development and Characterization of a Dispersion-Encoded Method for Low-Coherence Interferometry

This Open Access book discusses an extension to low-coherence interferometry by dispersion-encoding. The approach is theoretically designed and implemented for applications such as surface profilometry, polymeric cross-linking estimation and the determination of thin-film layer thicknesses. During a characterization, it was shown that an axial measurement range of 79.91 µm with an axial resolution of 0.1 nm is achievable. Simultaneously, profiles of up to 1.5 mm in length were obtained in a scan-free manner. This marked a significant improvement in relation to the state-of-the-art in terms of dynamic range. Also, the axial and lateral measurement range were decoupled partially while functional parameters such as surface roughness were estimated. The characterization of the degree of polymeric cross-linking was performed as a function of the refractive index. It was acquired in a spatially-resolved manner with a resolution of 3.36 x 10-5. This was achieved by the development of a novel mathematical analysis approach

Development and Characterization of a Dispersion-Encoded Method for Low-Coherence Interferometry

This Open Access book discusses an extension to low-coherence interferometry by dispersion-encoding. The approach is theoretically designed and implemented for applications such as surface profilometry, polymeric cross-linking estimation and the determination of thin-film layer thicknesses. During a characterization, it was shown that an axial measurement range of 79.91 µm with an axial resolution of 0.1 nm is achievable. Simultaneously, profiles of up to 1.5 mm in length were obtained in a scan-free manner. This marked a significant improvement in relation to the state-of-the-art in terms of dynamic range. Also, the axial and lateral measurement range were decoupled partially while functional parameters such as surface roughness were estimated. The characterization of the degree of polymeric cross-linking was performed as a function of the refractive index. It was acquired in a spatially-resolved manner with a resolution of 3.36 x 10-5. This was achieved by the development of a novel mathematical analysis approach

Binding energy of localized biexcitons in quantum wells

A variational calculation of the ground state energy of a biexciton in a GaAs/AlGaAs quantum well is presented. The well width fluctuations leading to trapping of the biexcitons are modeled by a parabolic potential. The results obtained for different well widths are compared with recent experimental data. Good agreement is obtained both for the biexciton binding energy and for the Haynes factor. We find that the structure of a biexciton is similar to the one of the H_2 molecule.Comment: 9 pages, 4 figure

Hidden Markov models for the analysis of next-generation-sequencing data

Onderzoekers in de hedendaagse biologie zijn steeds meer afhankelijk van de productie en analyse van grote hoeveelheden digitale data. Deze data wordt geproduceerd met behulp van nieuwe experimentele technieken die grotere inzichten verschaffen over de manier waarop onze cellen werken. Eén van deze technieken is next-generation sequencing (NGS). Deze techniek werd ontwikkeld in het begin van de 21e eeuw, en wordt nu op brede wijze toegepast om alles omtrent de basepaarvolgorde (sequentie) van het DNA te bestuderen. Dit proefschrift beschrijft vier nieuwe algoritmes voor de analyse van NGS-data, welke zijn ontwikkeld voor verschillende NGS-experimenten die elk een uniek inzicht leveren in de cel. Hoofdstuk 1 dient als introductie voor NGS en legt in detail uit hoe dezelfde technologie gebruikt kan worden om verschillende soorten fenomenen gerelateerd aan de DNA-sequentie te onderzoeken. Hoofdstuk 2 behandelt een model voor de analyse van kopienummerveranderingen in individuele cellen aan de hand van NGS-data, en deze methode is toegepast om de rol van aneuploïdie in de ziekte van Alzheimer te bestuderen en de rol van kleine kopienummerveranderingen in kankercellen. In hoofdstuk 3 wordt uitgeweid over een uitbreiding van het in hoofdstuk 2 beschreven model. Hoofdstukken 4 en 5 beschrijven modellen voor de analyse van epigenetische wijzigingen van het DNA, en deze modellen kunnen helpen om onze kennis te vergroten over hoe totipotente stamcellen differentiëren in gespecialiseerde celtypen, en hoe de omgeving de expressie van genen kan beïnvloeden

Experimental measurement and numerical analysis of group velocity dispersion in cladding modes of an endlessly single-mode photonic crystal fiber

The optical properties of the guided modes in the core of photonic crystal fibers (PCFs) can be easily manipulated by changing the air-hole structure in the cladding. Special properties can be achieved in this case such as endless singlemode operation. Endlessly single-mode fibers, which enable single-mode guidance over a wide spectral range, are indispensable in the field of fiber technology. A two-dimensional photonic crystal with a silica central core and a micrometer-spaced hexagonal array of air holes is an established method to achieve endless single-mode properties. In addition to the guidance of light in the core, different cladding modes occur. The coupling between the core and the cladding modes can affect the endlessly single-mode guides. There are two possible ways to determine the dispersion: measurement and calculation. We calculate the group velocity dispersion (GVD) of different cladding modes based on the measurement of the fiber structure parameters, the hole diameter and the pitch of a presumed homogeneous hexagonal array. Based on the scanning electron image, a calculation was made of the optical guiding properties of the microstructured cladding. We compare the calculation with a method to measure the wavelength-dependent time delay. We measure the time delay of defined cladding modes with a homemade supercontinuum light source in a white light interferometric setup. To measure the dispersion of cladding modes of optical fibers with high accuracy, a time-domain white-light interferometer based on a Mach-Zehnder interferometer is used. The experimental setup allows the determination of the wavelengthdependent differential group delay of light travelling through a thirty centimeter piece of test fiber in the wavelength range from VIS to NIR. The determination of the GVD using different methods enables the evaluation of the individual methods for characterizing the cladding modes of an endlessly single-mode fiber

breakpointR:an R/Bioconductor package to localize strand state changes in Strand-seq data

MOTIVATION: Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data. RESULTS: Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique. AVAILABILITY: R/Bioconductor package https://bioconductor.org/packages/breakpointR