27,340 research outputs found
Context in Synthetic Biology: Memory Effects of Environments with Mono-molecular Reactions
Synthetic biology aims at designing modular genetic circuits that can be
assembled according to the desired function. When embedded in a cell, a circuit
module becomes a small subnetwork within a larger environmental network, and
its dynamics is therefore affected by potentially unknown interactions with the
environment. It is well-known that the presence of the environment not only
causes extrinsic noise but also memory effects, which means that the dynamics
of the subnetwork is affected by its past states via a memory function that is
characteristic of the environment. We study several generic scenarios for the
coupling between a small module and a larger environment, with the environment
consisting of a chain of mono-molecular reactions. By mapping the dynamics of
this coupled system onto random walks, we are able to give exact analytical
expressions for the arising memory functions. Hence, our results give insights
into the possible types of memory functions and thereby help to better predict
subnetwork dynamics.Comment: 14 pages, 6 figures Accepted Versio
Modelling Cell Cycle using Different Levels of Representation
Understanding the behaviour of biological systems requires a complex setting
of in vitro and in vivo experiments, which attracts high costs in terms of time
and resources. The use of mathematical models allows researchers to perform
computerised simulations of biological systems, which are called in silico
experiments, to attain important insights and predictions about the system
behaviour with a considerably lower cost. Computer visualisation is an
important part of this approach, since it provides a realistic representation
of the system behaviour. We define a formal methodology to model biological
systems using different levels of representation: a purely formal
representation, which we call molecular level, models the biochemical dynamics
of the system; visualisation-oriented representations, which we call visual
levels, provide views of the biological system at a higher level of
organisation and are equipped with the necessary spatial information to
generate the appropriate visualisation. We choose Spatial CLS, a formal
language belonging to the class of Calculi of Looping Sequences, as the
formalism for modelling all representation levels. We illustrate our approach
using the budding yeast cell cycle as a case study
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