Lipid formulations have demonstrated strong potential for nucleic acid delivery,particularly with the success of COVID-19 vaccines. Despite these advances, manyaspects of lipid formulations remain unclear.

To improve treatment of breast cancer patients it is important to understand all stages of breast cancer from initiation to in situ disease and progression to invasive disease. In this thesis we use intraductal injections of patient derived tissue to model ductal carcinoma in situ and invasive breast…

SDN (Software-Defined Networking) represents a revolutionary approach to network architecture that enables the dynamic and flexible management of network resources through software-based control. This dissertation introduces the idea of SDN and its southbound protocol OpenFlow, then presents the formal…

In this project, we aim to develop mathematical models to mechanistically and quantitatively predict the dynamics of cellular stress pathway activation and its relation with toxic effects when cells are exposed to various toxicants.

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.

In this thesis, we extend the concept of null models as canonical ensembles of multi-graphs with given constraints and present new metrics able to characterize real-world layered systems based on their correlation patterns.

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

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,…

Bispecific antibodies with one Fab arm binding to effector cells, such as T-cells and NK-cells, while the other Fab arm recognizing a tumor associated antigen (TAA) can be used to redirect these effector cells for tumor specific killing. Using bispecific antibodies to treat hematological cancers is…

Spectroscopic studies on fluorescent single molecules in organic condensed matter does not only provide information about the molecule itself, but also its near environment. By suppression of phonon-induced broadening of spectral lines through cooling to low temperatures, small changes in the spectral…

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.

ASLU 14

A research agenda

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

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

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

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

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: Prof.dr. V. Icke, Co-Promotor: T.I. Madura

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.

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.

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…

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.

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

Exoplanets close in to their host star receive high levels of extreme ultraviolet (EUV) irradiation, capable of heating and ultimately driving the hydrodynamic escape of their atmospheres.

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…

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).

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

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.

In cryptography, generic transformations are often used to strengthen simpler but weaker schemes, into more sophisticated and stronger ones.

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.

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.

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…

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.

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