15 research outputs found
A Model for the Self-Organization of Microtubules Driven by Molecular Motors
We propose a two-dimensional model for the organization of stabilized
microtubules driven by molecular motors in an unconfined geometry. In this
model two kinds of dynamics are competing. The first one is purely diffusive,
with an interaction between the rotational degrees of freedom, the second one
is a local drive, dependent on microtubule polarity. As a result, there is a
configuration dependent driving field. Applying a molecular field
approximation, we are able to derive continuum equations. A study on the
solutions shows nonequilibrium steady states. The presence and stability of
such self-organized states are investigated in terms of entropy production.
Numerical simulations confirm analytical results.Comment: 23 pages, 10 figures, LaTeX, ep
Random Networks Tossing Biased Coins
In statistical mechanical investigations on complex networks, it is useful to
employ random graphs ensembles as null models, to compare with experimental
realizations. Motivated by transcription networks, we present here a simple way
to generate an ensemble of random directed graphs with, asymptotically,
scale-free outdegree and compact indegree. Entries in each row of the adjacency
matrix are set to be zero or one according to the toss of a biased coin, with a
chosen probability distribution for the biases. This defines a quick and simple
algorithm, which yields good results already for graphs of size n ~ 100.
Perhaps more importantly, many of the relevant observables are accessible
analytically, improving upon previous estimates for similar graphs
Hierarchy and Feedback in the Evolution of the E. coli Transcription Network
The E.coli transcription network has an essentially feedforward structure,
with, however, abundant feedback at the level of self-regulations. Here, we
investigate how these properties emerged during evolution. An assessment of the
role of gene duplication based on protein domain architecture shows that (i)
transcriptional autoregulators have mostly arisen through duplication, while
(ii) the expected feedback loops stemming from their initial cross-regulation
are strongly selected against. This requires a divergent coevolution of the
transcription factor DNA-binding sites and their respective DNA cis-regulatory
regions. Moreover, we find that the network tends to grow by expansion of the
existing hierarchical layers of computation, rather than by addition of new
layers. We also argue that rewiring of regulatory links due to
mutation/selection of novel transcription factor/DNA binding interactions
appears not to significantly affect the network global hierarchy, and that
horizontally transferred genes are mainly added at the bottom, as new target
nodes. These findings highlight the important evolutionary roles of both
duplication and selective deletion of crosstalks between autoregulators in the
emergence of the hierarchical transcription network of E.coli.Comment: to appear in PNA
Computational core and fixed-point organisation in Boolean networks
In this paper, we analyse large random Boolean networks in terms of a
constraint satisfaction problem. We first develop an algorithmic scheme which
allows to prune simple logical cascades and under-determined variables,
returning thereby the computational core of the network. Second we apply the
cavity method to analyse number and organisation of fixed points. We find in
particular a phase transition between an easy and a complex regulatory phase,
the latter one being characterised by the existence of an exponential number of
macroscopically separated fixed-point clusters. The different techniques
developed are reinterpreted as algorithms for the analysis of single Boolean
networks, and they are applied to analysis and in silico experiments on the
gene-regulatory networks of baker's yeast (saccaromices cerevisiae) and the
segment-polarity genes of the fruit-fly drosophila melanogaster.Comment: 29 pages, 18 figures, version accepted for publication in JSTA