Promotor: Prof.dr. W.J.G.M. Peijnenburg, Co-promotor: Dr. ing. M.G. Vijver

From surface science towards industrial practice using high-pressure scanning tunneling microscopy.

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.

Science, Leiden Academic Centre for Drug Research (LACDR)

In this research project child language phonology is studied from the perspective of a psycholinguistic speech-production model and this model is in turn studied from the perspective of developmental phonology.

A research agenda

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

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.

Are predictive archaeological maps a reliable tool to play an important role in the spatial planning? One of the goals of this project was to develop best practices for the production and application of the models.

The Agent Based Modelling for Archaeologists (ABMA) project is dedicated to developing Open Educational Resources (OERs) and accompanying materials for agent-based modelling (ABM) in Archaeology.

Uncertainty and noise are frequently-encountered obstacles in real-world applications of numerical optimization. The practice of optimization that deals with uncertainties and noise is commonly referred to as robust optimization.

In this thesis, mathematical modeling and simulation was applied as a tool to inform quantitative decision making in oncology drug discovery and development.

Chemical reactions go hand-in-hand with an energy exchange with the environment in which they take place. Surfaces offer a variety of energy dissipation channels, constituted by the nuclear and electronic degrees of freedom of the atoms at the interface. Aiming at an improved future harvesting of energy,…

Decarbonizing the building stock is critical for realizing the climate-neutral target for the Netherlands.

Accurate prediction of the unbound drug concentration-time profile at the CNS target site is crucial for the assessment of the right drug concentration-effect relationship. PBPK models have supported the PK prediction of the CNS target sites and the translation of PK data between species and between…

Promotor: M. Danhof, Co-promotores: J. Freijer, A. Yassen

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…

Growth hormone profiles are pulsatile and highly variable between individuals, limiting the implementation of mathemathical models to quantify an individual's secretion.

Our educational team has been awarded an ICTO-grant of €12000 for the LACDR for flipping the Biochemistry 2 classroom.

The Executive Board has decided that the classroom scanners (people counters) installed by Leiden University during the coronavirus period at the entrance to buildings and teaching rooms to count how many people are present in an area will be switched off until further notice.

In the first part, we introduce a new condition, called toric-additivity, on a family of abelian varieties degenerating to a semi-abelian scheme over a normal crossing divisor.

The aim of this project is to determine in which cases uncertainty statements resulting from a Bayesian statistical analysis can be trusted.

Promotor: Prof.dr. J.N. Kok

PhD defence

Promotor: Prof. dr. A.G.G.M. Tielens

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?

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

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.

The objective of this project is the development of a new psychometric model, called the Generalized Squared Distance Logistic Model (GSDLM). This model is an evolution of older psychometric approaches (such as PARELLA, GHCM, and GGUM) and the Gaussian Ordination Models (GOMs) used in environmental…

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

Promotor: P.D. Grünwald

Promotor: Prof.dr. F. den Hollander

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.

Describe and identify what dosimetry parameters are of importance to interpret dose-response relationships (eg., mortality, sub-lethal, growth or reproduction inhabitation, DNA damage and reactive oxygen species, etc. ) for metal-based nanoparticles? How to develop quantitative models that enable to…

How can zebrafish models be used to gain a better understanding of host-pathogen interaction mechanisms and to screen new drugs for infectious disease treatment?

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…

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 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…

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

The aim of this thesis is to present novel techniques for proving cryptographic schemes secure against quantum adversaries. Most results are within the context of an idealized model called the ‘quantum random-oracle model’.

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…

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.

Promotores: Arjen Doelman, Jens Rademacher, Max Rietkerk

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).

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.

Which traits did change due to the invasion process of plants and how do these traits contribute to the invasiveness of such species. What is the role of carbohydrate accumulation? What is the function of carbohydrate accumulation in plants? Is genetic variation depleted in invasive species under se…

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.

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

This dissertation addresses the different use of the same philosophical model: immanent teleology. In this work Aristotle, the founder of the study of final causes, is put in relation with the modern French evolutionary thinker Henri Bergson, the philosopher of time. The dissertation tackles the two…