Publications

Precise Parameter Synthesis for Stochastic Biochemical Systems

Milan Češka, Frits Dannenberg, Nicola Paoletti, Marta Kwiatkowska and Luboš Brim.
Acta Informatica, 2017.  
cdp16.pdf
cdp+16.bib
Link to publisher

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. (* equal contribution)
Nature, 2015.
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

 

Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates

Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon,
Joseph M Schaeffer, Mark Schmidt, Chris Thachuk, and Erik Winfree.
DNA Computing and Molecular Programming – 23th International Conference, 2017.
dna23_inference.pdf
Link to publisher

Precise Parameter Synthesis for Stochastic Biochemical Systems

Milan Češka, Frits Dannenberg, Nicola Paoletti, Marta Kwiatkowska, Luboš Brim.
Computational Methods for Systems Biology, 2014.
See above for revised journal version.
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.
Link to publisher

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.
Link to publisher

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

Since 2016 I am the maintainer of Multistrand, a tool for simulating interacting nucleic acids.

My tool to simulate DNA origami.

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.

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