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- Frits Dannenberg, Marta Z. Kwiatkowska, Chris Thachuk, Andrew J. Turberfield
- Natural Computing
- 2013

Unlike their traditional, silicon counterparts, DNA computers have natural interfaces with both chemical and biological systems. These can be used for a number of applications, including the precise arrangement of matter at the nanoscale and the creation of smart biosensors. Like silicon circuits, DNA strand displacement systems (DSD) can evaluate… (More)

The computation of transient probabilities for continuous-time Markov chains often employs uniformisation, also known as the Jensen’s method. The fast adaptive uniformisation method introduced by Mateescu approximates the probability by neglecting insignificant states, and has proven to be effective for quantitative analysis of stochastic models arising in… (More)

DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by… (More)

- Milan Ceska, Frits Dannenberg, Nicola Paoletti, Marta Z. Kwiatkowska, Lubos Brim
- Acta Informatica
- 2014

We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised or minimised. Our method is based on extending CSL model checking and standard uniformisation to… (More)

- J Hoffmann, L Neeb, +4 authors U Reuter
- Cephalalgia : an international journal of…
- 2009

The release of calcitonin gene-related peptide (CGRP) and sensitization of the trigeminal nerve system are important elements in migraine pathophysiology. Sensitization can be induced by topical meningeal administration of inflammatory soup (IS). CGRP release is a marker of trigeminal nerve activation. We examined the effect of intracisternal IS… (More)

- Frits Dannenberg, Ernst Moritz Hahn, Marta Z. Kwiatkowska
- ACM Trans. Model. Comput. Simul.
- 2013

The computation of transient probabilities for continuous-time Markov chains often employs uniformization, also known as the Jensen method. The fast adaptive uniformization method introduced by Mateescu et al. approximates the probability by neglecting insignificant states and has proven to be effective for quantitative analysis of stochastic models arising… (More)

- Frits Dannenberg, Katherine E Dunn, Jonathan Bath, Marta Kwiatkowska, Andrew J Turberfield, Thomas E Ouldridge
- The Journal of chemical physics
- 2015

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with… (More)

We define the arithmetic self-similarity (AS) of a one-sided infinite sequence σ to be the set of arithmetic subsequences of σ which are a vertical shift of σ. We study the AS of several families of sequences, viz. completely additive sequences, Toeplitz words and Keane’s generalized Morse sequences. We give a complete characterization of the AS of… (More)

We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised/minimised. We develop algorithms based on the computation of lower and upper bounds of the… (More)

- Frits Gerrit Willem Dannenberg, Andrew J. Turberfield, Moritz Hahn, Tom Ouldridge, Nicola Paoletti
- 2016

DNA nanotechnology is a rapidly developing field that creates nanoscale devices from DNA, which enables novel interfaces with biological material. Their therapeutic use is envisioned and applications in other areas of basic science have already been found. These devices function at physiological conditions and, owing to their molecular scale, are subject to… (More)