dr. Senja Barthel

Assistant Professor, Faculty of Science, Mathematics

Assistant Professor, Amsterdam Sustainability Institute

Personal information

I was born and raised in Berlin, Germany. Before coming to Amsterdam, I lived in Switzerland, Austria, England, Japan (for a summer research stay), South Africa, and Germany. My scientific CV:

Since 2019 Assitant professor at Vrije Univeriteit Amsterdam (tenured 2022)
2015-2019 Postdoc at EPFL Valais/Wallis in Berend Smit's molecular simulations group (chemistry/chemical engineering department)
2015 PhD from Imperial College London (Geometric topology, some modelling in topological cystallography)
2009 Diplom Mathematics from TU Berlin (Differential topology, master thesis on Gravitational lensing joined with Astronomy)
2006 Vordiplom Physics from TU Berlin

In a parallel life I graduated in

2007 Diplom Music Pedagogics from UdK Berlin (thesis on mathematial music theory, and on the theory and pedagogics of musical temperaments)

and worked as instrumental teacher and general music educator at the Musikschule Fanny Hensel Berlin (2007-2009) and at the Keiskamma Music Academy in Hamburg, South Africa (for 6 months in 2010). I taught recorder in groups and individually, gave ensemble lessons, taught music theory, history, and improvisation. My students won the Grahamtown Eisteddfod and we toured South Africa in concert. I won the first price of the South African "Rising star" music competition. After returning to Europe, I co-founded a recorder ensemble. We were awarded a Yehudi Menuhin fellowship 2011-2015 and performed in concerts.

Research

- Geometric topology: Spatial graphs
- Mathematical chemistry: Shape modelling
Spatial graphs are embeddings of graphs in 3-manifolds. Properties of spatial graphs are dependent on both the abstract underlying graphs and their specific realizations in space, which places their study between graph theory and knot theory. I study entanglements in spatial graphs and their embeddings in surfaces, often motivated by applications where graph embeddings have long been used to describe molecular structures.

In interdisciplinary projects, I explore how shapes define material properties, advancing method development in computational chemistry and materials science using tools from geometry and topology and discrete math. In particular, I study nanoporous materials such as metal-organic frameworks and zeolites, as well as solid-state electrolytes for energy applications.
We are part of the Center for Topology and Applications Amsterdam, the Amsterdam Sustainability Institute, and of the NWO DIAMANT cluster.
Current projects:
- Topology of molecular braids (NWO M1 grant)
- Geometrical/topological analysis of scalar fields for mass transport (paritally funded by Center of Interdisciplinary Mathematics Uppsala)
- Exploring 3D dynamics with welded braid groups (Horizon Europe)
- Collaborator on NWA Emergence Consortium (Project WP4.3: Intelligent matter; Project WP4.4: Phase transitions in active matter)
Together with Magnus Botnan, I am organising the Dutch Applied Topology days.

Group members:
- Riya Dogra PhD student working on the topology of molecular braids.
- Hannes Gustafsson PhD student co-supervised with Amber Mace (Uppsala Universitet) developing a cost-efficient multi-scale model for diffusion in crystalline materials.
- Hannah Rocio Santa Cruz Baur joint CTA^2 postdoc working on applied topology
- Stavroula Makri ERC Marie Curie postdoc working on welded braids on 3D dynamics
Alumni:
- Fabio Buccoliero graduated 2025 with a PhD thesis titled Cellular embeddability, properties and symmetries of leveled spatial graphs
Possible master thesis topics, contact me if you are interested (ideally at the begin of your master studies):
- Studying knots formed from DNA in Bacteriophages
- Are all knotless leveled spatial graphs primitive?
- Deriving counts for independent sets in periodic graphs from their fundamental domain to predict grand ensemble quantities for simulating methane storage.
- Constructing filtrations on (periodic) graphs. To make the PH framework available to them.
- Setting-up and testing persistent homological computations for computing topology-based descriptors for materials.

Teaching

Teaching 2025\2026:

Topology for BSc Mathematics

Linear Algebra for BSc Mathematics and BSc Econometrics

Linear Algebra at AUC

In Amsterdam, I taught so far

Differential Topology for BSc Mathematics
Mathematics 2 for BSc Creative Technology
Mathematics 3 for BSc Creative Technology
Calculus at AUC
Calculus for mechanical engineering and Linear Algebra & Calculus 2 for BSc Mechanical Engineering for BSc Mechanical Engineering
Calculus 2 for BSc Business Analytics
Mentored several 1st year projects for BSc Mech Engs (developing a mechanical cutter for under water pipes, designing power plants)
Mentored 2nd year student projects for BSc Mech Engs (diagnostics and maintainance of the grinders in coffee machines)
Supervised seven 2nd year BSc Mathematics projects (Graph theory in Chemistry, tuning systems in music, geometric knot invariants)
Supervision BSc Mathematics bachelor project on Braids in neuro science
Supervision BSc Mathematics bachelor project on Cayley graphs
Supervision BSc Mathematics bachelor project on Analysing relations between musical scales and cycles using filtered point symmetry
Co-Supervision BSc Mathematics bachelor project on detecting symmetries of crystals using persistence homology based machine learning
Co-supervision master projects in MSc Business Analytics (Inventory level planning for Bols; Gate scheduling for Schiphol airport; Assortment planning at IKEA; Optimizing inventory management for Campina Friesland)