Classical mathematical models treat space and time as a continuum, while it is sometimes more useful to regard it as granular. Hupkes is studying what this means for a number of important patterns that are often found in computer calculations and in nature.

Promotor: Prof.dr. J.N. Kok

An in-depth history of Large Language Models—and what their ubiquity, disruption, and creativity mean from a wider sociopolitical perspective.

Source: J Cheminform, Volume 7, Issue 1 (2015)

How might we include circularity into the models often used in IPCC reporting (in technical language, how can IAMs, dMFA models and CGE models be integrated?) What are possible futures for global resource use and what are the consequences for greenhouse gas emissions in these scenarios?

It is a common technique in global optimization with expensive black-box functions to learn a surrogate-model of the response function from past evaluations and use it to decide on the location of future evaluations.

Promotor: P.D. Grünwald

Promotor: Prof.dr. F. den Hollander

Business Process Model and Notation (BPMN) has become the standard for business processes diagrams.

Following their application to system biological models, control theory techniques have further potential to aid in the understanding and application of quantitative systems pharmacology models.

An integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules.

A main goal of MSBB research is to address the major bottle-necks in combatting viral diseases: the lack of experimental models that are representative of human pathology and are cost effective and versatile. Viral diseases such as those that cause viral hemorrhagic syndromes or severe acute respiratory…

The project Deconstructing Stability aims to improve reconstructions of late prehistoric landscapes and predictive models for the purpose of archaeological heritage management.

In this research project Rohana analyzes and reflects on taqsīm recordings by two leading figures of ‘ūd playing who were pillars of modern Arabic music, namely the Egyptians Muḥammad al-Qaṣabjī (1898-1964) and Riyāḍ al-Sunbāṭī (1906-1981).

A research goal for ABS is to develop miniaturized platforms for research in (stem)cell, in-vitro systems and application in clinical and preventive research. Combined with the high throughput, this development will make it possible to study the dynamics of pathogenesis in human and cellular models…

In surface science there is great effort to move from studying simple, flat model surfaces in vacuum to investigating more complex model catalysts in gas environments (in situ). This thesis gives three examples of such studies using microscopy and spectroscopy.

A novel mathematical model describes spatial-temporal drug distribution within one or more brain units, which are cubic representations of a piece of brain tissue with brain capillaries at the edges.

In this dissertation, we study partition-based models that can be used both for interpretable predictive modeling and for understanding data via interpretable patterns.

Promotores: Arjen Doelman, Jens Rademacher, Max Rietkerk

To limit the effects of climate change, global average temperature since pre-industrial measurements are to be kept well below 2 °C preferably even at 1.5 °C.

Sepsis is a life-threatening condition caused by a dysregulated host response to infection, it is associated with significant morbidity, mortality, and with a high financial burden on global healthcare systems. Bacterial infections are the primary cause of sepsis, but the growing prevalence of antimicrobial…

Gaucher disease is a rare metabolic disorder, in which a mutation of the enzyme glucocerebrosidase (GBA1) causes buildup of its substrate glucosylceramide and the deacylated counterpart glucosylsphingosine in lysosomes.

Every day, we make numerous decisions, from choosing what to eat to how we interpret the world around us. Traditionally, researchers have assumed that a key part of our decision-making process, namely the decision criterion, stays stable over time. However, increasing evidence suggests that instead…

Promotor: Prof.dr. B.R. Katzy, Co-promotor: R. Ortt

The growing demand of energy indicates that global energy resources in the form of fossil fuels will not be sufficient in the future. In order to solve potential future energy problems development of a sustainable hydrogen economy is highly desirable.

Promotores: J. Kok, M. Chaudron (Chalmers University)

Promotor: F.H.J. Redig, Co-Promotor: W.T.F. den Hollander

This thesis explores how bees and hoverflies are distributed across the Dutch landscape and how ecological and landscape factors shape their occurrence.

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…

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

The parabolic Anderson model (PAM), which is the Cauchy problem for the heat equation with random potential. The PAM is a mathematical model that describes how mass (i.e. matter or energy) flows in a medium in the presence of a field of sources and sinks.

In this thesis we study quantum transport phenomena on the nanometer scale, in two classes of materials: topological insulators with induced superconductivity and graphene superlattices.

Appropriate animal models for intradermal vaccine delivery are scarce. Given the high similarity of their skin anatomy to that of humans, minipigs may be a suitable model for dermal vaccine delivery.

In this PhD study, I aim to deepen our understanding of the influence of major mycorrhizal types, namely arbuscular mycorrhizae (AM) and ectomycorrhizae (EM), on the global soil carbon cycle and their potential distribution changes under future environmental shifts.

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

Synthetic microswimmers take an important place within the interdisciplinary field of active soft matter.

Accelerating the diagnosis and personalising the management of inherited metabolic diseases.

This thesis tackles the difficulty of predicting the liver’s clinical response to novel therapies, a challenge arising from interspecies differences and limitations of existing in vitro models.

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

Promotor: Prof.dr. G.R. de Snoo, Co-promotores: Dr. ing. M.G. Vijver, J.P.M. Vink

Pharmaceutical companies, governments and the general public have become increasingly aware that animal models used in drug testing lack vital aspects to serve as an accurate representation of human biology. As models of the human body should become more physiologically relevant, animal models no longer…

Beginning teachers often experience difficulties making activating lessons. This study investigates how and if the practical teaching model can offer them a hand in learning to design lessons.

Source: Structure , Volume 22, Issue 8, pp. 1120-1139 (2014)

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.

This paper describes two synthetic lipid models designed to replace human stratum corneum (SC) in studies of the impact of volatile organic chemicals on the molecular organization of the skin barrier lipids.

M. Danhof, Co-promotor: O.E. Della Pasqua

This PhD project investigates how language models can be used to extract structured knowledge from text in a way that is accurate, robust, and applicable to real-world use cases.

This dissertation is concerned with the development of grammar. Starting from a usage-based perspective, which holds that children use domain-general learning mechanisms to acquire the grammatical patterns of their mother tongue, Beekhuizen shows how to operationalize various concepts from this tradition…