23,431 research outputs found
A Formal Framework for Clock-free Networks of Cells
International audienceno abstrac
Complementary approaches to understanding the plant circadian clock
Circadian clocks are oscillatory genetic networks that help organisms adapt
to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri
is the simplest plant clock discovered so far. Its many advantages as an
experimental system facilitate the testing of computational predictions.
We present a model of the Ostreococcus clock in the stochastic process
algebra Bio-PEPA and exploit its mapping to different analysis techniques, such
as ordinary differential equations, stochastic simulation algorithms and
model-checking. The small number of molecules reported for this system tests
the limits of the continuous approximation underlying differential equations.
We investigate the difference between continuous-deterministic and
discrete-stochastic approaches. Stochastic simulation and model-checking allow
us to formulate new hypotheses on the system behaviour, such as the presence of
self-sustained oscillations in single cells under constant light conditions.
We investigate how to model the timing of dawn and dusk in the context of
model-checking, which we use to compute how the probability distributions of
key biochemical species change over time. These show that the relative
variation in expression level is smallest at the time of peak expression,
making peak time an optimal experimental phase marker. Building on these
analyses, we use approaches from evolutionary systems biology to investigate
how changes in the rate of mRNA degradation impacts the phase of a key protein
likely to affect fitness. We explore how robust this circadian clock is towards
such potential mutational changes in its underlying biochemistry. Our work
shows that multiple approaches lead to a more complete understanding of the
clock
BlenX-based compositional modeling of complex reaction mechanisms
Molecular interactions are wired in a fascinating way resulting in complex
behavior of biological systems. Theoretical modeling provides a useful
framework for understanding the dynamics and the function of such networks. The
complexity of the biological networks calls for conceptual tools that manage
the combinatorial explosion of the set of possible interactions. A suitable
conceptual tool to attack complexity is compositionality, already successfully
used in the process algebra field to model computer systems. We rely on the
BlenX programming language, originated by the beta-binders process calculus, to
specify and simulate high-level descriptions of biological circuits. The
Gillespie's stochastic framework of BlenX requires the decomposition of
phenomenological functions into basic elementary reactions. Systematic
unpacking of complex reaction mechanisms into BlenX templates is shown in this
study. The estimation/derivation of missing parameters and the challenges
emerging from compositional model building in stochastic process algebras are
discussed. A biological example on circadian clock is presented as a case study
of BlenX compositionality
Formal Systems Architectures for Biology
When the word "systems" is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and "control" mechanisms, 
which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on the connection between top-down control mechanisms and bottom-up self-organizing mechanisms
The century of the incomplete revolution: searching for general relativistic quantum field theory
In fundamental physics, this has been the century of quantum mechanics and
general relativity. It has also been the century of the long search for a
conceptual framework capable of embracing the astonishing features of the world
that have been revealed by these two ``first pieces of a conceptual
revolution''. I discuss the general requirements on the mathematics and some
specific developments towards the construction of such a framework. Examples of
covariant constructions of (simple) generally relativistic quantum field
theories have been obtained as topological quantum field theories, in
nonperturbative zero-dimensional string theory and its higher dimensional
generalizations, and as spin foam models. A canonical construction of a general
relativistic quantum field theory is provided by loop quantum gravity.
Remarkably, all these diverse approaches have turn out to be related,
suggesting an intriguing general picture of general relativistic quantum
physics.Comment: To appear in the Journal of Mathematical Physics 2000 Special Issu
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