Zilverling

ir. Y.J. Kraakman (Yanna)

PhD Candidate
EEMCS-AM-MOR
Zilverling 4006
y.j.kraakman@utwente.nl
+31534894719
Business card

Hi! As a PhD candidate, I work on the project ‘Capturing Higher-Order Interactions in Chemical Reaction Networks’, in collaboration with PhD candidate Éverton Fernandes da Cunha and supervised by dr. Clara Stegehuis and dr. Albert Wong.

With this project, we aim to develop a mathematical framework that can be used to model higher-order interactions in systems. We focus on Chemical Reaction Networks, since these systems naturally show higher-order interactions.

The scope of this project is twofold. First, we investigate higher-order networks (directed hypergraphs) and develop mathematical tools that we deem necessary to apply and analyze these networks. Second, we use these networks to model chemical reactions, and we predict the dynamical behavior of these reactions. These predictions are verified in a chemical laboratory.

Currently, we are working on configuration models for directed hypergraphs, and on linking directed hypergraphs to chemical reaction networks.

Expertise

  • Mathematics

    • Hypergraphs
    • Chemical Reaction Networks
    • Edge

  • Computer Science

    • Network Property
    • Random Graphs
    • Neural Network

  • Engineering

    • Equilibrium Reaction
    • Reaction Network

Organisations

Publications

2025

Identify structures underlying out-of-equilibrium reaction networks with random graph analysis (2025)Chemical science, 16(7), 3099-3106. Fernandes da Cunha, É., Kraakman, Y. J., Kriukov, D., van Poppel, T., Stegehuis, C. & Wong, A. S. Y.https://doi.org/10.1039/D4SC05234J

2024

Hypercurveball algorithm for sampling hypergraphs with fixed degrees (2024)[Working paper › Preprint]. ArXiv.org. Kraakman, Y. J. & Stegehuis, C.https://doi.org/10.48550/arXiv.2412.05100Identify structures underlying out-of-equilibrium reaction networks with random graph analysis (2024)[Working paper › Preprint]. ChemRxiv. Fernandes da Cunha, É., Kraakman, Y., Kriukov, D., van Poppel, T., Stegehuis, C. & Wong, A. S. Y.https://chemrxiv.org/engage/chemrxiv/article-details/667c7bd2c9c6a5c07a7826a3Configuration models for random directed hypergraphs (2024)[Working paper › Preprint]. ArXiv.org. Kraakman, Y. & Stegehuis, C.https://arxiv.org/abs/2402.06466Random graph models can determine important species in a Chemical Reaction Network (2024)[Contribution to conference › Poster] CHAINS 2024 (In preparation). Kraakman, Y. J., Fernandes da Cunha, É., Kriukov, D., van Poppel, T., Stegehuis, C. & Wong, A. S. Y.

2023

You can make random uniform directed hypergraphs (2023)[Contribution to conference › Poster] 21st INFORMS Applied Probability Society Conference 2023 (In preparation). Kraakman, Y. & Stegehuis, C.

Research profiles

Courses academic year 2024/2025

Courses in the current academic year are added at the moment they are finalised in the Osiris system. Therefore it is possible that the list is not yet complete for the whole academic year.

Address

University of Twente

Zilverling (building no. 11), room 4006
Hallenweg 19
7522 NH Enschede
Netherlands

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