This dissertation focused on computational methods based on first principles calculations using the Density Functional Theory (DFT) framework. Emphasis was laid on affordable methods that can provide a tradeoff between computational expense and accuracy.

LUMC Technology Focus Area (TFA) Data Analytics is een samenwerkingsverband van verschillende onderzoeksgroepen in het LUMC die nieuwe kwantitatieve en computationele methodologie ontwikkelen voor biomedisch en klinisch onderzoek.

Promotor: Roeland M.H. Merks

Epithelial-mesenchymal plasticity (EMP) and tumor cell migration play an important role in cancer progression, and an improved understanding of the mechanisms underlying these concepts is essential for developing new targeted approaches.

Carbohydrates, or sugars, are the most diverse and most abundant biomolecules known. However, the isolation of carbohydrate samples in sufficient amounts and purity is often impractical or even impossible, so the chemical synthesis of glycosides becomes relevant. The glycosylation reaction, in which…

The Minor Computational Approaches to Disease, Signaling and Drug Targets (CADSDT) is focused on fundamental scientific research required for discovery of new drug targets and development of new drugs.

This thesis investigates the contribution of quantum computers to machine learning, a field called Quantum Machine Learning. Quantum Machine Learning promises innovative perspectives and methods for solving complex problems in machine learning, leveraging the unique capabilities of quantum computers…

Optical projection tomography (OPT) is a tomographic 3D imaging technique used for specimens in the millimetre scale.

In this work we describe three methods to improve the performance of Quantum Field Theory calculations.

The long-held desire - to link structure directly to function and to explain molecular mechanisms based on basic chemical or physical principles - is finally coming closer, satisfying not only our scientific curiosity but also offering new solutions to the many challenges in the field of health, energy…

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…

In the current global context, there is a pressing need to address sustainable energy supplies to safeguard our Planet and its ecosystems. The choices made by human society have a significant impact on genetic evolution and climate.

Promotor: Prof.dr. J.N. Kok

Assessing the risks of engineered nanomaterials (ENMs) solely on the basis of experimental assays is time-consuming, resource intensive, and constrained by ethical considerations (such as the principles of the 3Rs of animal testing). The adoption of computational toxicology in this field is a high p…

Most of current public-key cryptography is considered insecure against attacks from sufficiently powerful quantum computers. Post-quantum cryptography studies methods to secure information resistant against such attacks. One proposal is isogeny-based cryptography, which bases its security on computational…

Wiskunde en Natuurwetenschappen, Leiden Academic Centre for Drug Research (LACDR)

The zebrafish is a promising vertebrate model organism in early drug discovery and development.

In this thesis, we consider various (electro)chemical phenomena at surfaces and nanoparticles and their underlying atomistic processes, which we studied using first-principles methods such as density functional theory.

Nature uses a special class of histone proteins, histone variants, to modulate the properties of chromatin at defined genomic locations.

This thesis systematically studies the physicochemical properties of non-planar, propeller-shaped, polycyclic aromatic hydrocarbons. The synthesis of several so-called propellerenes is described on a gram scale, using optimized procedures aimed at using less hazardous reagents and reducing the amount…

In this thesis it is posed that the central object of preference discovery is a co-creative process in which the Other can be represented by a machine. It explores efficient methods to enhance introverted intuition using extraverted intuition's communication lines.

Promotor: Prof.dr. H.V.J. Linnartz

At the moment, over 350.000 chemicals are registered worldwide for production and use. Their application, however, may harm human health and the environment.

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…

We study the interplay of topology and geometry with chirality for several passive and active systems, employing both analytical and numerical methods.

Promotor: S.J. Edixhoven, L.D.J. Taelman

This thesis introduces the concept of

Drug-target binding kinetics determine the time course of the central event in pharmacotherapy: Drug-target interaction.

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.

With increasing carbon dioxide levels in the atmosphere and their detrimental effect on the global climate, modern society needs to push for more renewable energy sources. Storing widely accessible and abundant solar energy in chemical bonds in the form of molecular fuel via artificial photosynthesis…

This thesis focuses on data found in the field of computational drug discovery. New insight can be obtained by applying machine learning in various ways and in a variety of domains. Two studies delved into the application of proteochemometrics (PCM), a machine learning technique that can be used to…

This thesis describes the importance of being able to control the selectivity of potential drug candidates.

A complex community of microbes develops in the infant gut shortly after birth. We call this community the infant gut microbiota. The microbiota influences the health of the infant, which makes the composition and function of the infant gut microbiota an important topic to study.

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…

This thesis describes the use of a combined approach of computational and experimental techniques to gain novel insights to understand the glycosylation reaction and its reactive intermediates.

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…

Integrating life cycle assessment (LCA) with life cycle costing (LCC) offers the opportunity to simultaneously analyze the environmental and economic aspects of product alternatives, for the integration of which a unified computational has been proposed by Heijungs et al. (2013) [1]. The project aims…

In this thesis, topics relating to the optimization of high-throughput pipelines used for imaging are discussed. In particular, different levels of implementation, i.e., conceptual, software, and hardware, are discussed and the thesis outlines how advances on each level need to be made to make gains…

This thesis focuses on two processes involved in fighting infections: metabolism and immune cell motility and navigation.

Immunotherapies for cancer are an emerging class of therapeutic strategies which aim to treat cancer via augmentation of the immune system.

Promotor: K.J. Batenburg, Co-promotor: A.W. van der Vaart, B. de Smit

A common method to solve expensive function evaluation problem is using Bayesian Global Optimization, instead of Evolutionary Algorithms.

Valetudo, zo hebben de astronomen het nieuw ontdekte Jupitermaantje genoemd. Het is een weerbarstig exemplaar dat dwars tegen haar soortgenoten in beweegt. In de Volkskrant reageert Leidse astronoom Simon Portegies Zwart op de bijzondere ontdekking.

Promotie

Sonja Boas ontwikkelde nieuwe technieken om het groeiproces van bloedvaten op computationele wijze te bestuderen. De resultaten van haar onderzoek geven een beter begrip van mechanismen in bloedvatgroei en dat is relevant voor de ontwikkeling van medische therapieën. Promotie op dinsdag 22 december…

Altijd al een grafheuvel willen ontdekken? Of zelf willen speuren naar archeologische resten op de Veluwe? Doe dan nu mee met Erfgoed Gezocht! De Veluwe bevat zo veel archeologische resten dat archeologen alleen deze onmogelijk allemaal in kaart kunnen brengen! Je kan nu meedoen met de speurtocht via…