This thesis mainly focuses on cross-modal retrieval and single-modal image retrieval via deep learning methods, i.e. by using deep convolutional neural networks.

Lezing, Studium Generale

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

Promotor: D. Bouwmeester, Co-promotor: D. Kraft

This thesis advances our understanding of lipid uptake, a vital first step in lipid metabolism, by developing innovative click chemistry-based tools to study how immune cells internalize lipids.

Understanding interactions in quantum many-body systems remains one of the most profound and difficult challenges in condensed matter physics.

Promotor: Prof.dr. T. Hankemeier, Prof.dr. J.C.T. Eijkel (Twente University)

Nierfalen is een serieus probleem omdat nieren zichzelf niet kunnen regenereren na ernstige beschadiging. Een mogelijke oplossing bestaat uit het kunstmatig laten groeien van gezond nierweefsel. Daarvoor moeten wetenschappers eerst de ontwikkeling begrijpen tijdens de allereerste fase, in de foetus.…

Leidse natuurkundigen hebben een manier ontwikkeld om na te gaan hoe nauwkeurig een superconducting single photon detector kan worden onderzocht.

De American Society of Pharmacognosy (ASP) heeft de Varro E. Tyler prijs toegekend aan Rob Verpoorte, voor zijn uitstekende bijdragen aan de wetenschap van de natuur als bron van geneesmiddelen.

Alireza Mashaghi en zijn onderzoeksteam hebben een nieuw kader gecreëerd om vormen van eiwitten en DNA te begrijpen. Met dit raamwerk kunnen veel ziekten beter worden begrepen.

Protein–protein complexes are formed via transient states called encounter complexes that greatly influence the formation of the stereospecific complex.

Every organisms in the tree of life faces the same challenge: the length of its DNA exceeds the volume of the cell it needs to fit in. Several strategies have evolved to solve this problem, one of them being the expression of proteins that bind and organize the DNA.

Lysosomal glycosidases are acid hydrolases that fragment glycoconjugates in lysosomes.

Phospholipase A/acyltransferase 3 (PLAAT3) and PLAAT4 are enzymes involved in the synthesis of bioactive lipids. Despite sequential and structural similarities, the two enzymes differ in activity and specificity.

Promotor: Prof.dr. M. Ubbink

The research described in this thesis centered on retaining exo-β-glucosidases implicated in health and disease, in particular the human inherited lysosomal storage disorder, Gaucher disease (GD).

Several single-stranded RNA viruses make use of Xrn1-resistant RNAs in their 3’ untranslated regions of their genome RNAs in order to increase their pathogenicity.

The research aims to explore the evolutionary adaptability of enzymes and the impact of temperature on protein evolution pathways, using M. tuberculosis β-lactamase BlaC as the object of study. Enzymes inherently embody a delicate balance between activity and stability, and the acquisition of new enzymatic…

Advanced UHF MRI techniques provide powerful tools for studying the zebrafish brain, an emerging model in neurological research. In this work, various MRI and localized MRS methods are optimized and employed for UHF strength for studying the zebrafish brain.

β-Lactamases are enzymes that can break down β-lactam substrates, such as antibiotics, preventing the use of these antibiotics for the treatment of various infectious diseases. However, some compounds, β-lactamase inhibitors, can block these enzymes allowing for possible treatments using a combination…

Promotor: A. Achúcarro, Co-Promotor: J.W. van Holten

Deelnemers aan een Learning My Way programma kunnen via learningmyway.nl het portfolio bereiken via beveiligde single-sign on. Ook na het afronden van je studie blijft je portfolio toegankelijk.

The four possible segments A, T, C and G that link together to form DNA molecules, and with their ordering encode genetic information, are not only different in name, but also in their physical and chemical properties.

Promotores: J.N. Kok, H.J. Hoogeboom

Biofysicus Alireza Mashaghi gaat samen met zijn collega’s de strijd aan tegen spierdystrofie: genetische aandoeningen die spierziektes veroorzaken. Ze zijn op zoek naar een oplossing voor het samenklonteren van eiwitten, waarbij gevaarlijke ophopingen ontstaan. Het team ontvangt hiervoor 550.000 euro…

Despite being the second largest transmembrane protein family after GPCRs, the SLC superfamily has only gained significant attention in early drug development over the past decade.

Promotor: Prof.dr. E.F. van Dishoeck, Prof.dr. F.F.S. van der Tak (RUG)

Metals surfaces form a group of effective catalysts for the reaction of small molecules such as hydrogen (H2).

The adenosine receptors are proteins that reside in the extracellular membranes of cells. Activation of adenosine receptors plays a role in many physiological and pathological processes, such as immune responses and cancers.

Over several decades, a variety of computational methods for drug discovery have been proposed and applied in practice. With the accumulation of data and the development of machine learning methods, computational drug design methods have gradually shifted to a new paradigm, i.e. deep learning methods…

Promotor: H.S. Overkleeft, J. Neefjes, Co-promotor: M. van der Stelt

Multicopper oxidase, laccase, can efficiently reduce oxygen to water and are mostly used in the enzymatic biofuel cells.

In this thesis, a system pharmacology approach, integrating metabolomics, pharmacology and chemical biology, was applied to understand and modulate the endocannabinoid system across different model systems (cells, zebrafish, mice and humans).

Promotor: Prof.dr. H.S. Overkleeft

Lysosomal storage disorders (LSDs) are a group of orphan diseases characterized by lysosomal dysfunction or impaired lysosomal catabolism and affect collectively about 1 in 5000 live births.

This thesis describes the structural and biochemical characterization of the β-lactamase BlaC from Mycobacterium tuberculosis (Mtb), and the Alr and YlmE proteins from Streptomyces coelicolor A3(2).Mtb is the main cause of tuberculosis.

Bacteria often experience external challenges, such as changes in environmental conditions or attacks by bacteriophages.

Promotor: A.P. IJzerman

Promotor: A.P. IJzerman

This thesis discusses the physical and chemical processes than influence the composition of forming planets.

Stars and planets form within cold, dense clouds of gas and dust drifting through interstellar space. Although dust makes up only a small fraction of this material, it plays a key role in shaping the chemical evolution of these environments.

Astronomical observations of cold regions in the universe show a rich inventory of ices. Part of these ices may end up on planets like our own, but in that journey they will be exposed to considerable amounts of radiation.

In this thesis, we developed new ways to use a technique called electroextraction (EE) to extract charged molecules from one liquid into another using an electric field.

In deep reinforcement learning, searching and learning techniques are two important components. They can be used independently and in combination to deal with different problems in AI, and have achieved impressive results in game playing and robotics. These results have inspired research into artificial…

SHINE-VR is een korte interventie in Virtual Reality (VR) die wordt toegevoegd aan een reguliere traumabehandeling (TF-CBT). We onderzoeken de effectiviteit ervan met een experimenteel ontwerp waarbij naar individuele gevallen wordt gekeken. Dit doen we specifiek met jongvolwassenen die seksueel misbruik…

Quantum computing is an emerging technology, which holds the potential to simulate complex quantum systems beyond the reach of classical numerical methods.Despite recent formidable advancements in quantum hardware, constructing a quantum computer capable of performing useful calculations remains challenging.In…

In this dissertation, we work towards an experiment in which we aim to bring a micrometer sized magnet at the tip of a soft cantilever into a superposition.

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.