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Maria Bruna, Jonathan Chapman, and Matthew J Smith
The quasi-steady-state approximation (or stochastic averaging principle) is a useful tool in the study of multiscale stochastic systems, giving a practical method by which to reduce the number of degrees of freedom in a model. The method is extended here to slow–fast systems in which the fast variables exhibit metastable behaviour. The key parameter that determines the form of the reduced model is the ratio of the timescale for the switching of the fast variables between metastable states to the timescale...
Publication details
Date: 1 April 2014
Type: Article
Publisher: American Institute of Physics
Boyan Yordanov, Neil Dalchau, Paul Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, and Andrew Phillips
The ability to design and construct synthetic biological systems with predictable behavior could enable significant advances in medical treatment, agricultural sustainability, and bioenergy production. However, to reach a stage where such systems can be reliably designed from biological components, integrated experimental and computational techniques that enable robust component characterization are needed. In this paper we present a computational method for the automated characterization of genetic...
Publication details
Date: 14 March 2014
Type: Article
Publisher: American Chemical Society
James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg McInerny, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, and Charlotte Deane
Publication details
Date: 1 March 2014
Type: Article
Publisher: PLoS Computational Biology (Public Library of Science Computational Biology),
Number: 3
Rakesh Agrawal, Behzad Golshan, and Evimaria Terzi
Given a class of large number of students, each exhibiting a different ability level, how can we form teams of students so that the expected performance of team members improves due to team participation? We take a computational perspective and formally define two versions of such team-formation problem: the MaxTeam and the MaxPartition problems. The first asks for the identification of a single team of students that improves the performance of most of the participating team members. The second asks for a...
Publication details
Date: 1 March 2014
Type: Inproceeding
Publisher: ACM
Michael Pedersen, Nicolas Oury, Colin Gravill, and Andrew Phillips
A host of formal, textual languages for modeling cellular processes have recently emerged, but their simulation tools often require an installation process which can pose a barrier for use. Bio Simulators is a framework for easy online deployment of simulators, providing a uniform web-based user interface to a diverse pool of tools. The framework is demonstrated through two plugins based on the KaSim Kappa simulator, one running directly in the browser and another running in the cloud.Web tool:...
Publication details
Date: 1 February 2014
Type: Article
Publisher: Oxford University Press
Matthew J. Smith, Paul I. Palmer, Drew W. Purves, Mark C. Vanderwel, Vassily Lyutsarev, Ben Calderhead, Lucas N. Joppa, Christopher M. Bishop, and Stephen Emmott
New details about natural and anthropogenic processes are continually added to models of the Earth System, anticipating that the increased realism will increase the accuracy of their predictions. However perspectives differ about whether this approach will improve the value of the information the models provide to decision makers, scientists and societies. The present bias towards increasing realism leads to a range of updated projections, but at the expense of uncertainty quantification and model...
Publication details
Date: 1 February 2014
Type: Article
Publisher: American Meteorological Society
Joppe W. Bos, Craig Costello, Patrick Longa, and Michael Naehrig
We select a set of elliptic curves for cryptography and analyze our selection from a performance and security perspective. This analysis complements recent curve proposals that suggest (twisted) Edwards curves by also considering the Weierstrass model. Working with both Montgomery-friendly and pseudo-Mersenne primes allows us to consider more possibilities which improves the overall efficiency of base field arithmetic. Our Weierstrass curves are backwards compatible with current implementations of prime...
Publication details
Date: 1 February 2014
Type: Technical report
Number: MSR-TR-2014-19
Joppe W. Bos, J. Alex Halderman, Nadia Heninger, Jonathan Moore, Michael Naehrig, and Eric Wustrow
In this paper, we perform a review of elliptic curve cryptography (ECC), as it is used in practice today, in order to reveal unique mistakes and vulnerabilities that arise in implementations of ECC. We study four popular protocols that make use of this type of public-key cryptography: Bitcoin, secure shell (SSH), transport layer security (TLS), and the Austrian e-ID card. We are pleased to observe that about 1 in 10 systems support ECC across the TLS and SSH protocols. However, we find that despite the...
Publication details
Date: 1 January 2014
Type: Inproceeding
Publisher: Springer
Joppe W. Bos, Craig Costello, and Andrea Miele
Motivated by the advantages of using elliptic curves for discrete logarithm-based public-key cryptography, there is an active research area investigating the potential of using hyperelliptic curves of genus 2. For both types of curves, the best known algorithms to solve the discrete logarithm problem are generic attacks such as Pollard rho, for which it is well-known that the algorithm can be sped up when the target curve comes equipped with an efficiently computable automorphism. In this paper we...
Publication details
Date: 1 January 2014
Type: Inproceeding
Publisher: Springer
Publication details
Date: 1 January 2014
Type: Inproceeding
Publisher: Springer
Joppe W. Bos, Alina Dudeanu, and Dimitar Jetchev
We prove collision bounds for the Pollard rho algorithm to solve the discrete logarithm problem in a general cyclic group G. Unlike the setting studied by Kim et al., we consider additive walks: the setting used in practice to solve the elliptic curve discrete logarithm problem. Our bounds differ from the birthday bound O(sqrt(|G|)) by a factor of sqrt(\log(|\G|)) and are based on mixing time estimates for random walks on finite abelian groups due to Dou and Hildebrand. See also:...
Publication details
Date: 1 January 2014
Type: Article
Publisher: de Gruyter
Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer Chayes, Riccardo Zecchina, and Ernest Fraenkel
Advances in experimental techniques resulted in abundant genomic, transcriptomic, epigenomic, and proteomic data that have the potential to reveal critical drivers of human diseases. Complementary algorithmic developments enable researchers to map these data onto protein-protein interaction networks and infer which signaling pathways are perturbed by a disease. Despite this progress, integrating data across different biological samples or patients remains a substantial challenge because samples from the...
Publication details
Date: 1 January 2014
Type: Article
Publisher: World Scientific Publishing
Y.P.Wang, B.C.Chen, W.R.Weider, Y.Q.Luo, B.E.Medlyn, M.Rasmussen, M.J.Smith, F.B.Agusto, and F.Hoffman
A number of nonlinear models have recently been proposed for simulating soil carbon decomposition. Their predictions of soil carbon responses to fresh litter input and warming differ significantly from conventional linear models. Using both stability analysis and numerical 5 simulations, we showed that two of those nonlinear models (a two-pool model and a three-pool model) exhibit damped oscillatory responses to small perturbations. Stability analysis showed the frequency of oscillation is proportional to...
Publication details
Date: 1 December 2013
Type: Article
Publisher: European Geosciences Union
Matthew R Evans, Mike Bithell, Stephen J. Cornell, Sasha R. X. Dall, Sandra Diaz, Stephen Emmott, Bruno Ernande, Volker Grimm, David J. Hodgson, Simon L. Lewis, Georgina M. Mace, Michael Morecroft, Aristides Moustakas, Eugene Murphy, Tim Newbold, K. J. Norris, Owen Petchey, Matthew J. Smith, Justin M. J. Travis, and Tim G. Benton
Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable to be able to predict their future states. We present a proposal to develop the paradigm of predictive systems ecology, explicitly to understand and predict the...
Publication details
Date: 22 November 2013
Type: Article
Publisher: Royal Society
Sadia E. Ahmed, Robert M. Ewers, and Matthew J. Smith
There is burgeoning interest in predicting road development because of the wide ranging important socio-economic and environmental issues that roads present, including the close links between road development, deforestation, and biodiversity loss. This is especially the case in developing nations, which are high in natural resources, where road development is rapid and often not centrally managed. Characterisation of large scale spatio-temporal patterns in road network development has been greatly...
Publication details
Date: 1 October 2013
Type: Article
Isabel M D Rosa, Drew Purves, Carlos Souza Jr, and Robert M Ewers
Tropical forests are diminishing in extent due primarily to the rapid expansion of agriculture, but the future magnitude and geographical distribution of future tropical deforestation is uncertain. Here, we introduce a dynamic and spatially-explicit model of deforestation that predicts the potential magnitude and spatial pattern of Amazon deforestation. Our model differs from previous models in three ways: (1) it is probabilistic and quantifies uncertainty around predictions and parameters; (2) the overall...
Publication details
Date: 1 October 2013
Type: Article
Publisher: PLoS
Sadia E Ahmed, Carlos M Souza, J Riberio, and Rob M Ewers
The Brazilian Amazon is a globally important ecosystem that is undergoing rapid development and land-use change. Roads are a key spatial determinant of land-use conversion and strongly influence the rates and patterns of habitat loss and represent a key component of models that attempt to predict the spatio-temporal patterns of Amazonian land-use change and the consequences of such changes. However, the spatio-temporal patterns of road network development are poorly understood and seldom quantified. Here,...
Publication details
Date: 1 October 2013
Type: Article
Publisher: Springer
Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, and Georg Seelig
Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We...
Publication details
Date: 29 September 2013
Type: Article
Publisher: Nature Publishing Group
Antony N Dodd, Neil Dalchau, Michael J Gardner, Seong Jin Baek, and Alex AR Webb
• A circadian rhythm matched to the phase and period of the day–night cycle has measurable benefits for land plants. We assessed the contribution of circadian period to the phasing of cellular events with the light : dark cycle. We also investigated the plasticity of circadian period within the Arabidopsis circadian oscillator. • We monitored the circadian oscillator in wild-type and circadian period mutants under light : dark cycles of varying total duration. We also investigated changes in oscillator...
Publication details
Date: 24 September 2013
Type: Article
Boyan Yordanov, Christoph Wintersteiger, Youssef Hamadi, Andrew Phillips, and Hillel Kugler
We present a method for the analysis of functional properties of large-scale DNA strand displacement (DSD) circuits based on Satisfiability Modulo Theories that enables us to prove the functional correctness of DNA circuit designs for arbitrary inputs, and provides significantly improved scalability and expressivity over existing methods. We implement this method as an extension to the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root circuit, together with the components used...
Publication details
Date: 1 September 2013
Type: Article
Publisher: Springer
Matthew R. Lakin, Andrew Phillips, and Darko Stefanovic
DNA strand displacement gates can be used to emulate arbitrary chemical reactions, and a number of different schemes have been proposed to achieve this. Here we develop modular correctness proofs for strand displacement emulations of chemical reaction networks and show how they may be applied to two-domain strand displacement systems. Our notion of correctness is serializability of interleaved reaction encodings, and we infer this global property from the properties of the gates that emulate the individual...
Publication details
Date: 1 September 2013
Type: Article
Publisher: Springer Verlag
Joppe W. Bos, Peter L. Montgomery, Daniel Shumow, and Greg Zaverucha
In this paper we present a parallel approach to compute \emph{interleaved} Montgomery multiplication. This approach is particularly suitable to be computed on 2-way single instruction, multiple data platforms as can be found on most modern computer architectures in the form of vector instruction set extensions. We have implemented this approach for tablet devices which run the x86 architecture (Intel Atom Z2760) using SSE2 instructions as well as devices which run on the ARM platform (Qualcomm MSM8960,...
Publication details
Date: 1 September 2013
Type: Inproceeding
Publisher: Springer
Lucas Joppa, Piero Visconti, C.N. Jenkins, and S.L. Pimm
Identifying which areas capture how many species is the first question in conservation planning. The Convention on Biological Diversity (CBD) aspires to formal protection of at least 17% of the terrestrial world and, through the Global Strategy for Plant Conservation, 60% of plant species. Are these targets of protecting area and species compatible? We show that 67% of plant species live entirely within regions that comprise 17% of the land surface. Moreover, these regions include most terrestrial...
Publication details
Date: 1 September 2013
Type: Article
Publisher: American Association for the Advancement of Science
Eric L. Berlow, Roland A. Knapp, Steven M. Ostoja, Richard J. Williams, Heather McKenny, John R. Matchett, Qinghua Guo, Gary M. Fellers, Patrick Kleeman, Matthew L. Brooks, and Lucas Joppa

A central challenge of conservation biology is using limited data to predict rare species occurrence and identify conservation areas that play a disproportionate role in regional persistence. Where species occupy discrete patches in a landscape, such predictions require data about environmental quality of individual patches and the connectivity among high quality patches. We present a novel extension to species occupancy modeling that blends traditional predictions of individual patch environmental...

Publication details
Date: 1 August 2013
Type: Article
Publisher: Public Library of Science
Number: 8
Boyan Yordanov, Neil Dalchau, Paul Grant, Jim Haseloff, Stephen Emmott, and Andrew Phillips
Recent DNA assembly methods have enabled the physical construction of large-scale biological devices but designing systems with a given behavior remains a challenge in synthetic biology. To enable the engineering of complex and robust systems, integrated experimental and computational methods are needed that allow precise experimental data to be collected and used to construct reliable computational models, that serve to make accurate predictions, leading to the design of functionally correct...
Publication details
Date: 1 July 2013
Type: Inproceeding
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