Promotor: Prof.dr. J.N. Kok, Co-promotor: F.J. Verbeek

Onderzoeksgroepen in het Biological & Soft Matter onderzoeksprogramma ontrafelen de mechanismen in biologische processen en ontwikkelen nieuwe zachte materialen die geïnspireerd zijn door de natuur.

Shape and biological function are tightly connected. Physical descriptions are used to connect the shape of a biological system with its function.

In deze master specialisatie ligt de focus op het begrijpen van biologische processen in hun natuurlijke context, zoals cellen en weefsels.

Promotores: H. Schiessel, G.T. Barkema

This thesis investigates how cell shape and collective behavior influence the dynamics and structure of biological tissues, which are crucial for understanding processes like embryonic development, tissue regeneration, and metastasis.

This dissertation contains four works during my PhD. Different biomaterials have been designed based on coiled-coil peptides. These biomaterials have a range of applications, inclusing drug delivery, cell sorting to cell-cell fusion.

It has been a long-standing mystery how complex biological structures emerge from such seemingly uncoordinated building blocks as cells and tissues, in the presence of only minimal environmental guidance.

Promotie

This PhD-thesis presents a study on micron-sized particles, so-called colloids. By controlling the chemical and physical properties of these particles, such as the interparticle interaction and the particles’ shape, colloids can act as building blocks that self-assembly into larger structures.

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

Promotor: Prof.dr. P.G.L Klinkhamer, Co-promotor: K. Vrieling

The emergence of complex diseases resulting from abnormal cell-cell signaling and the spread of infectious diseases caused by pathogens are significant threats to humanity. Unraveling the dynamic mechanisms underlying cell-cell signaling and infectious disease spreading is crucial for effective disease…

Parkinson's disease is the second most common neurodegenerative disease in the world. One of its symptoms is the loss of dopaminergic neurons in the substantia nigra pars compacta.

Vitamin A or retinol is essential in embryonic development, the visual cycle and the immune system.

Promotor: A. Kros

In this thesis, we show how MRFM can usefully contribute to the field of condensed-matter.

Promotor: Prof.dr. J.N. Kok

This work has described synthetic strategies towards well-defined structures resembling capsular polysaccharide (CPS) fragments, CPS mimics, teichoic acid (TA) fragments as well as a third-generation ring-closing tandem metathesis (RCM) linker to better exploit the potential of automated synthesis.

Advanced mass spectrometry of glycosphingolipids takes the central stage in this thesis. Investigations focus on characterization of glycosphingolipid metabolism in health and disease with emphasis to the detection and accurate quantitation of known and so far unknown glycosphingolipids and closely…

Promotor: J.G.E.M. Fraaije, Co-Promotor: A. Kros

Promotor: Prof.dr. T. Hankemeier

Marine sponges are important members of reef ecosystems, as they play ecological roles that are essential for the health of the reef.

The recently introduced nature-originated deep eutectic solvents, so-called natural deep eutectic solvents (NADES) are considered as truly green solvents, which composed of natural ingredients found abundantly in organisms.

Promotor: Prof.dr. T. Hankemeier, Co-promotor: Theo Reijmers

Neurodegenerative diseases, including Parkinson’s disease (PD), are increasing in prevalence due to the aging population. Despite extensive study, these diseases are still not fully understood and the lack of personalised treatment options that can target the cause of the diseases, rather than the symptoms,…

Glycoside hydrolases (glycosidases/GHs) are widely abundant enzymes in all kingdoms of life and are important biocatalysts that catalyze the hydrolysis of glycosidic linkages in oligo/polysaccharides, glycoproteins and glycolipids with tremendous efficiency

Due to their central physiological roles in living organisms, retaining beta-glycosidases have been the subject of tremendous research efforts to examine their structure/function relation using numerous biophysical and biochemical approaches.

Kleinere computerchips, smallere cameraatjes; ze worden steeds moeilijker om te maken. Maar wat als de bouwstenen zichzelf opbouwen? Natuurkundige Daniela Kraft bedacht een methode om deeltjes aan te sturen in samenklonteren. Publicatie in ACS Nano.

Op een ogenschijnlijk gewone kubus verschijnt onder druk een patroon van hollingen en bollingen. Er is nu een methode ontwikkeld om zulke 3 dimensionale structuren te ontwerpen en maken met eenvoudige bouwstenen. Publicatie in Nature.

Climate change is a challenge for both current and future generations. New biological resources have to be developed in order to meet the demand for energy as well as the demand for food.

In this thesis an activity-based probe was discovered that could visualize the activity of PLAATs. With an optimized gel-based ABPP assay in hand, screening of a compound library led to the discovery of alpha-ketoamides as a hit for PLAAT3.

Promotor: J. van der Greef; Co-promotor: E. van Wijk, M. Wang

Promotores: Prof.dr. H.S. Overkleeft, Prof.dr. G.A. van der Marel

De verklaring van natuurkundige Scott Waitukaitis voor de gillende en stuiterende hydrogelballetjes is door verschillende media overgenomen. Zo was Waitukaitis te zien op het RTL 4 journaal van maandag 24 juli.

Biological polymers, including proteins and the genome, undergo folding processes crucial for their proper functioning. Even slight changes in the folding structure of these biopolymers can have significant implications, leading to the development of various pathological conditions, such as neurodegenerative…

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.

Mechanical interactions between cells and their environment play an important role in many biological processes.

In this thesis I describe the results of Pulsed Interleaved Excitation and Fluorescence (Cross) Correlation Spectroscopy (PIE-F(C)CS) combined with single-pair Förster Resonance Energy Transfer (spFRET) used to study dynamics in single nucleosomes, which depends on subtle differences in the length of…

Als je een elastiekje uitrekt, wordt het langer. Maar stel je eens voor dat een materiaal juist korter wordt als je eraan trekt. Dat klinkt raar, niet? Toch is dat precies wat natuurkundigen van de Universiteit Leiden, AMOLF en ARCNL voor elkaar hebben gekregen.

Lipid signaling is an essential biological event/process in a plethora of pathophysiological conditions. The underlying idea of this thesis is that many of the roles and the complex interplay of the individual signaling lipids in inflammatory processes and related conditions in health and disease is…

Promotores: H.S. Overkleeft, G.A. van der Marel, Co-Promotor: J.D.C. Codee

There is a need for alternative methods to replace, reduce and refine (3R) animal experimentation. Combining experimental data from high-throughput in vitro studies with in silico modeling is a promising approach to unravel the effect of chemicals on living cells and to gain a better understanding of…

Promotor: G. A. van der Marel, Co-promotor: D. V. Filippov

Because thin systems can deform along the thickness with relative ease, the interplay between surface mechanics and geometry plays a fundamental role in sculpting their three-dimensional shape.

In the traditional theory of linear elasticity, superposition dictates that the response of a material does not depend on the sequence of the applied mechanical actuations.