John Wilson-Kanamori

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Rule-based modeling, an alternative to traditional reaction-based modeling, allows us to intuitively specify biological interactions while abstracting from the underlying combinatorial complexity. One such rule-based modeling formalism is Kappa, which we introduce to readers in this chapter. We discuss the application of Kappa to three modeling scenarios in(More)
Several molecular systems form large-scale objects. One would like to understand their assembly and how this assembly is regulated. As a first step, we investigate the phase transition structure of a class of simple cooperative assembly systems. We characterize which of these systems have a (probabilistic) equilibrium and find an explicit form for their(More)
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