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

Since the early 1990s, one can isolate the optical signal of a single molecule and single-molecule spectroscopy has quickly grown into an important research field.

Intrigued by the way cells autonomously regulate their fate, we strive to understand and visualize cellular processes as the basis of Cell Signaling.

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.

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

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

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

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.

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.

Promotor: M.A.G.J. Orrit

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…

Can we find new chemical and biological sensing routes on the edge and surface of graphene to improve the potential of graphene to act as a sensor?

Optical detection of a single electron using a single molecule has never been done. Leiden physicist Michel Orrit and his team have now identified a molecule that is sensitive enough to detect an electron at a distance of hundreds of nanometers. The results are published as a cover article in ChemPh…

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

Leiden physicists have managed to detect a single molecule called dibenzoterrylene in a new crystal, and found that it is a candidate component for a quantum network. Future quantum computers will need such a network to work together while maintaining their advantages. Publication in ChemPhysChem jo…

Individual molecules are extremely hard to see through feeble fluorescence. Tiny gold nanorods serve as new antennas to intensify their signal 500 times. Publication on 24 February in Angewandte Chemie.

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

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.

We study cell-fate decision-making using embryonic stem cells as a model system. Stem cells integrate a large number of cues to direct their development into a great variety of cell types.

Bioactive Molecules is one of the four research themes of the Institute of Biology Leiden.

Visualization of biomolecules in living cells by tagging with gold nanoparticles.

Ariadne Schmidt, Isabelle Devos and Julie de Groot provide you with refreshing insights concerning the study on urban singles in the period between 1200 and 1900.

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

Michel Orrit has received an NWO-TTW Open Technology Programme grant. He will use it to image single molecules without the need for fluorescence.

Our DNA molecules are packaged by proteins in compact structures. The aim of this project is to understand how modern gene editing techniques nevertheless get access to their target in the DNA.

Lecture

Microbial Sciences' contribution to the Bioactive Molecules research theme is to discover new bioactive molecules and enzymes and unravel their mechanisms of action, regulatory networks, and the (bio)synthetic pathways required for their production.

Promotor: T. Schmidt, Co-Promotor: B.E. Snaar-Jagalska

The aim of the research presented in this thesis was to develop new methods forchallenging systems in liquid-state NMR using paramagnetic effects generated by thetwo-armed probe CLaNP-5.

Even a small quantum computer should be able to simulate exactly the properties and behaviour of new molecules. This would take chemistry to an entirely new level. Better solar panels, more powerful batteries, saving lots of energy in the chemical industry: the applications have the potential to transform…

Plant Sciences' contribution to the Bioactive Molecules research theme is to identify new plant bioactive molecules, and unravel their mechanisms of action in plant development or health, and the regulatory networks and (bio)synthetic pathways required for their production.

Animal Sciences’ contribution to the Bioactive Molecules research theme includes research on molecules from natural sources, such as plants, insects, and snake venom, with the aim to identify novel anti-cancer, anti-inflammatory, anti-microbial, and anti-diabetic agents.

Schneider

PhD defence

All life on earth contains DNA, which is used to store biological information. Organisms compact their DNA in order for it to fit inside their cell(s).

Atoms and molecules are the basic units of matter. If we keep dividing a bar of gold or a glass of water into smaller parts, at the end we are left with a single gold atom or a water molecule.

Visualising cell proteins without invasive techniques is possible with the help of fluorescence. During a lecture of the Natuurwetenschappelijk Gezelschap Leiden on 18 January, winner of the Spinoza Prize 2017 and founder of the field of single molecule optics Michel Orrit explained how this works.

This thesis revolves around the electronic spectroscopy of molecules in the laboratory and the search for the carriers of the diffuse interstellar bands (DIBs).

While bioinformatics methods deal with the analysis of sequence information (be it proteins or DNA), the field of cheminformatics is concerned with the analysis of small-molecule datasets.

Nucleoid associated proteins maintain the architecture of the bacterial chromosome and regulate gene expression, hinting that their role as transcription factors may involve local three-dimensional chromosome re-modelling.

John van Noort

Promotor: Prof.dr. E. F. van Dishoeck, Co-promotor: A. N. Heays

Research groups in the Biological & Soft Matter Programme unravel mechanisms in biological processes and develop novel bio-inspired soft materials.

Promotor: T. Schmidt