Publications

Precise Parameter Synthesis for Stochastic Biochemical Systems

Milan Ceska, Frits Dannenberg, Marta Kwiatkowska and Nicola Paoletti,
Acta Informatica, in press.
cdp16.pdf
cdp+16.bib

Modelling DNA origami self-assembly at the domain level

Frits Dannenberg, Katherine E. Dunn, Jonathan Bath, Marta Kwiatkowska, Andrew J. Turberfield and Thomas E. Ouldridge. The Journal of Chemical Physics, 2015.
theorypaper_origami.pdf
Link to publisher

Guiding the folding pathway of DNA origami

Katherine E. Dunn*, Frits Dannenberg*, Thomas E. Ouldridge, Marta Kwiatkowska, Andrew J. Turberfield and Jonathan Bath. Nature, 2015. (* equal contribution)
folding_pathway.pdf
Link to publisher

Computing Cumulative Rewards Using Fast Adaptive Uniformization

Frits Dannenberg, Ernst Moritz Hahn and Marta Kwiatkowska. ACM Transactions on Modeling and Computer Simulation, 2015.
acmmcs-fau.pdf
Link to publisher

DNA walker circuits: Computational potential, design, and verification

Frits Dannenberg, Marta Kwiatkowska, Chris Thachuk and Andrew J. Turberfield. Natural Computing, 2014.
natcomp-walkers.pdf
Link to publisher

DPhil thesis

Modelling and verification for DNA nanotechnology

Frits Dannenberg, 2016.
dannenberg16.pdf

Conference papers

Precise Parameter Synthesis for Stochastic Biochemical Systems

Milan Ceska, Frits Dannenberg, Marta Kwiatkowska and Nicola Paoletti. Computational Methods for Systems Biology, 2014.
cmsb14.pdf
Link to publisher

Computing Cumulative Rewards Using Fast Adaptive Uniformization

Frits Dannenberg, Ernst Moritz Hahn and Marta Kwiatkowska. Computational Methods for Systems Biology, 2013.
See above for revised journal version.

DNA walker circuits: Computational potential, design, and verification

Frits Dannenberg, Marta Kwiatkowska, Chris Thachuk and Andrew J. Turberfield.  DNA Computing and Molecular Programming – 19th International Conference, 2013.
See above for revised journal version.

Non-peer reviewed

Arithmetic Self-Similarity of Infinite Sequences

D. Hendriks, F.G.W. Dannenberg, J. Endrullis, M. Dow and J.W. Klop. 2012.
Link to arxiv

Software

My tool to simulate DNA origami. (github)

My tutorial on DNA walker models using the PRISM model checker, and the associated filesExpanded with section on Petri nets by Benoit Barbot.

I helped implement the fast adaptive uniformisation and parameter synthesis (non-GPU) routines in the PRISM model checker software.  I also contributed to the Visual DSD software.