547 research outputs found
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
Folding and cytoplasm viscoelasticity contribute jointly to chromosome dynamics
The chromosome is a key player of cell physiology, and its dynamics provides
valuable information about its physical organization. In both prokaryotes and
eukaryotes, the short-time motion of chromosomal loci has been described as a
Rouse model in a simple or viscoelastic medium. However, little emphasis has
been put on the role played by the folded organization of chromosomes on the
local dynamics. Clearly, stress-propagation, and thus dynamics, must be
affected by such organization, but a theory allowing to extract such
information from data, e.g.\ of two-point correlations, is lacking. Here, we
describe a theoretical framework able to answer this general polymer dynamics
question, and we provide a general scaling analysis of the stress-propagation
time between two loci at a given arclength distance along the chromosomal
coordinate. The results suggest a precise way to detect folding information
from the dynamical coupling of chromosome segments. Additionally, we realize
this framework in a specific theoretical model of a polymer with variable-range
interactions in a viscoelastic medium characterized by a tunable scaling
exponent, where we derive analytical estimates of the correlation functions.Comment: 14 pages including supplementary material
Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains
We present a combined mean-field and simulation approach to different models
describing the dynamics of classes formed by elements that can appear,
disappear or copy themselves. These models, related to a paradigm
duplication-innovation model known as Chinese Restaurant Process, are devised
to reproduce the scaling behavior observed in the genome-wide repertoire of
protein domains of all known species. In view of these data, we discuss the
qualitative and quantitative differences of the alternative model formulations,
focusing in particular on the roles of element loss and of the specificity of
empirical domain classes.Comment: 10 Figures, 2 Table
Feedback topology and XOR-dynamics in Boolean networks with varying input structure
We analyse a model of fixed in-degree Random Boolean Networks in which the
fraction of input-receiving nodes is controlled by a parameter gamma. We
investigate analytically and numerically the dynamics of graphs under a
parallel XOR updating scheme. This scheme is interesting because it is
accessible analytically and its phenomenology is at the same time under
control, and as rich as the one of general Boolean networks. Biologically, it
is justified on abstract grounds by the fact that all existing interactions
play a dynamical role. We give analytical formulas for the dynamics on general
graphs, showing that with a XOR-type evolution rule, dynamic features are
direct consequences of the topological feedback structure, in analogy with the
role of relevant components in Kauffman networks. Considering graphs with fixed
in-degree, we characterize analytically and numerically the feedback regions
using graph decimation algorithms (Leaf Removal). With varying gamma, this
graph ensemble shows a phase transition that separates a tree-like graph region
from one in which feedback components emerge. Networks near the transition
point have feedback components made of disjoint loops, in which each node has
exactly one incoming and one outgoing link. Using this fact we provide
analytical estimates of the maximum period starting from topological
considerations
Physical descriptions of the bacterial nucleoid at large scales, and their biological implications.
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation
Hydrodynamic Synchronisation of Model Microswimmers
We define a model microswimmer with a variable cycle time, thus allowing the
possibility of phase locking driven by hydrodynamic interactions between
swimmers. We find that, for extensile or contractile swimmers, phase locking
does occur, with the relative phase of the two swimmers being, in general,
close to 0 or pi, depending on their relative position and orientation. We show
that, as expected on grounds of symmetry, self T-dual swimmers, which are
time-reversal covariant, do not phase-lock. We also discuss the phase behaviour
of a line of tethered swimmers, or pumps. These show oscillations in their
relative phases reminiscent of the metachronal waves of cilia.Comment: 17 pages, 8 figure
Coherent Hydrodynamic Coupling for Stochastic Swimmers
A recently developed theory of stochastic swimming is used to study the
notion of coherence in active systems that couple via hydrodynamic
interactions. It is shown that correlations between various modes of
deformation in stochastic systems play the same role as the relative internal
phase in deterministic systems. An example is presented where a simple swimmer
can use these correlations to hunt a non-swimmer by forming a hydrodynamic
bound state of tunable velocity and equilibrium separation. These results
highlight the significance of coherence in the collective behavior of
nano-scale stochastic swimmers.Comment: 6 pages, 3 figure
On the basic computational structure of gene regulatory networks
Gene regulatory networks constitute the first layer of the cellular
computation for cell adaptation and surveillance. In these webs, a set of
causal relations is built up from thousands of interactions between
transcription factors and their target genes. The large size of these webs and
their entangled nature make difficult to achieve a global view of their
internal organisation. Here, this problem has been addressed through a
comparative study for {\em Escherichia coli}, {\em Bacillus subtilis} and {\em
Saccharomyces cerevisiae} gene regulatory networks. We extract the minimal core
of causal relations, uncovering the hierarchical and modular organisation from
a novel dynamical/causal perspective. Our results reveal a marked top-down
hierarchy containing several small dynamical modules for \textit{E. coli} and
\textit{B. subtilis}. Conversely, the yeast network displays a single but large
dynamical module in the middle of a bow-tie structure. We found that these
dynamical modules capture the relevant wiring among both common and
organism-specific biological functions such as transcription initiation,
metabolic control, signal transduction, response to stress, sporulation and
cell cycle. Functional and topological results suggest that two fundamentally
different forms of logic organisation may have evolved in bacteria and yeast.Comment: This article is published at Molecular Biosystems, Please cite as:
Carlos Rodriguez-Caso, Bernat Corominas-Murtra and Ricard V. Sole. Mol.
BioSyst., 2009, 5 pp 1617--171
Three Dimensional Annihilation Imaging of Antiprotons in a Penning Trap
We demonstrate three-dimensional annihilation imaging of antiprotons trapped
in a Penning trap. Exploiting unusual feature of antiparticles, we investigate
a previously unexplored regime in particle transport; the proximity of the trap
wall. Particle loss on the wall, the final step of radial transport, is
observed to be highly non-uniform, both radially and azimuthally. These
observations have considerable implications for the production and detection of
antihydrogen atoms.Comment: Invited Talk at NNP03, Workshop on Non-Neutral Plasmas, 200
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