Single-molecule spectroscopy has become a powerful method for using organic fluorescent molecules in numerous applications.

Detecting nanoscopic objects plays an important role in nanoscience in particular, in the rapidly growing field of nanobiology. The forebear to modern super-resolution microscopy for single molecule investigation, is fluorescence microscopy.

Surface acoustic waves (SAWs) are mechanical waves that travel along the surface of a material and find many applications in modern technologies due to the ease of excitation on piezoelectric substrates via interdigital transducers (IDTs).

We investigate how radiation pressure can be used to influence the mechanical motion of a micro-mirror suspended from springs.

Promotor: Prof.dr. E. Eliel, Co-Promotor: M.J.A. de Dood

Promotores: Prof.dr. D. Bouwmeester, Prof.dr. A. Fiore (TU Eindhoven)

This dissertation explores how we can make anomaly detection—identifying unusual or faulty behavior in complex systems—more trustworthy and effective, with a focus on smart manufacturing.

Structural variants (SVs) are the hidden architecture of the human genome, and are critical for us to understand diseases, evolution, and so on.

In the era of big data, extracting insights from complex datasets is a key challenge. This thesis demonstrates the superiority of graph-based methods over traditional clustering (e.g., k-means, DBSCAN) and outlier detection for analyzing high-dimensional and noisy data.

In this thesis we investigated the ability of two-photon multifocal microscopy for single-molecule microscopy in live cells and organisms.

Single-Molecule Microscopy (SMM) techniques constitute a group of powerful imaging tools that enable researchers to study the dynamic behavior of individual molecules.

This dissertation revolves around the design and implementation of novel instrumentation and related measurement techniques, at the single molecule level, for use in biophysical research. Chapter 1 presents an introduction to the field of fluorescence-based single molecule measurements. In particular,…

The sequence-dependence of biomolecular interactions involving nucleic acids and proteins is essential for numerous processes inside the cell. Insights into the underlying molecular mechanisms have been obtained using various biochemical and biophysical methods on two different levels — bulk and sin…

Promotor: E. Bouwman, Co-Promotor: S. Bonnet

This thesis is a collection of experimental attempts to enhance photoluminescence of fluorescent molecules and quantum dots with single gold nanorods (GNRs) and relevant applications.

This thesis aims to improve the detection from ultra-weak single emitter by enhancing their emission properties with plasmonic nanostructures. We exploit the wet-chemically synthesized single crystalline gold nanorods (GNRs) as our basic frameworks in the whole studies, simply because of their unique…

Op 8 januari 2020 verdedigde Jelmer Brouwer zijn proefschrift 'Detection, detention, deportation'. Het promotieonderzoek is begeleid door promotoren prof.dr. J.P. van der Leun en prof.dr. M.A.H. van der Woude.

In this thesis, we study different curved single crystals because of the diversity of surface structures across their curvature.

In this work, we investigate the minute circular dichroism effects of single nanoparticles.To this aim, we apply photothermal imaging with a polarization-modulated heating beam.

The major and ultimate aim of metabolomics is to obtain an answer to a specific biological or clinical question.

Promotor: T. Schmidt, Co-promotor: S. J.T. van Noort

Spectroscopic studies on fluorescent single molecules in organic condensed matter does not only provide information about the molecule itself, but also its near environment. By suppression of phonon-induced broadening of spectral lines through cooling to low temperatures, small changes in the spectral…

Promotor: Prof.dr. M.A.G.J. Orrit

Promotor: I. Snellen, Co-Promotor: M. Kenworthy

In human cells, a meter-long DNA is condensed inside a micrometer-sized cell nucleus. Simultaneously, the genetic code must remain accessible for its replication and transcription to functional proteins.

Curved single crystals provide variable, but well-defined surface structures.

Promotores: Prof.dr. G.W. Canters, Prof.dr. T.J. Aartsma

Promotor: Thomas Hankemeier, Co-promotores: Heiko van der Linden, Paul Vulto

Cardiovascular diseases (CVDs) are the leading global cause of mortality. Endothelial dysfunction, an early reversible stage of CVD development, is marked by decreased nitric oxide production linked to Ca2+ influx in endothelial cells.

Early time-resolved experiments by Frauenfelder on the ensemble of the kinetic rebinding of CO to myoglobin molecules resulted in a stretched exponential relaxa-tion due to a very large spread of the reaction rates of individual molecules.

Gold nanorods are biocompatible nanoparticles that present an excellent two-photon signal that can be used to get high spatial resolution inside living cells. Gold nanorods are photostable and therefore can be followed inside cells for long time, with possible applications as trackers in live cells.

A single self-assembled semiconductor quantum dot in a high-finesse optical microcavity - the subject of this thesis - is an interesting quantum-mechanical system for future quantum applications. For instance, this system allows trapping of an extra electron and thus can serve as a spin quantum memory,…

Promotor: M.A.G.J. Orrit

Miles Kellerman, universitair docent aan de Universiteit Leiden, stelt dat overheden financiële criminaliteit beter kunnen opsporen door Licensed Detection Agents in te zetten, een soort bounty hunters die structurele tekortkomingen in bestaande detectiesystemen moeten oplossen.

Acute cardiovascular syndromes, including myocardial infarction or stroke, are the principal cause of death in the Western society. The main underlying pathology of cardiovascular diseases is atherosclerosis, which is caused by the accumulation of lipids and inflammatory cells in the vessel wall, in…

This thesis consists of two main parts. The first part (Chapters 2 and 3) deals with a class of Markov process called Quasi-Skipfree (QSF) processes.

The deeper understanding of an organism's pathology is important for developing treatments. Over centuries of systematic research, clinical researchers have demonstrated that the more information they acquire about the cellular properties and their organisation in the tissue, the better they can understand…

Despite being the object of intense study, embryonic development has been difficult to model due to a number of reasons. First, complex tissues can be comprised of many cell types, of which we probably only know a subset.

In this thesis, we describe the potential of cell mechanical phenotyping for immune cell characterization, diagnosis, drug testing, as well as treatment of disease.

The focus throughout this thesis will be on gathering fundamental studies of the detailed structure and composition of the electrode/electrolyte interface effect on the rate and mechanism of key electrocatalytic reactions.

Transport inspectorates are looking for novel methods to identify dangerous behavior, ultimately to reduce risks associated to the movements of people and goods. We explore a data-driven approach to arrive at smart inspections of vehicles.

Promotor: Prof.dr. T. Schmidt, Co-Promotor: S.J.T. van Noort

Promotor: M.T.M. Koper, Co-Promotor: L.B.F. Juurlink

In most applications, electrocatalysts exhibit a large surface area to volume ratio, for example using nanoparticles.

Promotor: A.W. van der Vaart

Promotor: Prof.dr. J.N. Kok, Co-promotor: A.J. Knobbe

Gold nanoparticles show surprisingly strong interactions with light in the visible range, which can be divided into scattering, absorption, and photoluminescence.

In this thesis, the focus lies on studying glucocorticoid receptor dynamics in living cells with the aim of understanding how this transcription factor finds its DNA target sites to regulate transcription.

Viral hemorrhagic fever (VHF) is a group of acute diseases caused by highly infectious viruses including Ebola, Lassa, Dengue viruses. Its high mortality rate poses high risk to public health, however, studies on VHF have been hampered due to the non-availability of proper models and incomplete knowledge…

Biopolymer sequencing with graphene edge-based tunnel junctions has the potential to overcome current limitations with the third generation of sequencing based on biological nanopores.