arXiv subjects

P. Jona

Publications and source records attributed to P. Jona.

10 recordsLinked to original sources

arXiv2007

DIA-MCIS. An Importance Sampling Network Randomizer for Network Motif Discovery and Other Topological Observables in Transcription Networks

Transcription networks, and other directed networks can be characterized by some topological observables such as for example subgraph occurrence (network motifs). In order to perform such kind of analysis, it is necessary to be able to generate suitable randomized network ensembles. Typically, one considers null networks with the same degree sequences of the original ones. The commonly used algorithms sometimes have long convergence times, and sampling problems. We present here an alternative, based on a variant of the importance sampling Montecarlo developed by Chen et al. [1].

q-bio.QM↗

arXiv2007

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.

cond-mat.stat-mech↗

arXiv2007

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.

q-bio.MN↗

arXiv2006

Randomization and Feedback Properties of Directed Graphs Inspired by Gene Networks

Having in mind the large-scale analysis of gene regulatory networks, we review a graph decimation algorithm, called "leaf-removal", which can be used to evaluate the feedback in a random graph ensemble. In doing this, we consider the possibility of analyzing networks where the diagonal of the adjacency matrix is structured, that is, has a fixed number of nonzero entries. We test these ideas on a network model with fixed degree, using both numerical and analytical calculations. Our results are the following. First, the leaf-removal behavior for large system size enables to distinguish between different regimes of feedback. We show their relations and the connection with the onset of complexity in the graph. Second, the influence of the diagonal structure on this behavior can be relevant.

q-bio.MN↗

arXiv2005

The Logic Backbone of a Transcription Network

A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that the logic backbone underlying all dynamic descriptions has the structure of a computational optimization problem. It involves variables, which correspond to gene expression levels, and constraints, which describe the effect of \emph{cis-}regulatory signal integration functions. In the simple paradigmatic case of Boolean variables and signal integration functions, we derive and discuss phase diagrams. Notably, the model exhibits a connectivity transition between a regime of simple, but uncertain, gene control, to a regime of complex combinatorial control.

q-bio.MN↗

arXiv2005

The large-scale logico-chemical structure of a transcriptional regulation network

Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory machinery of the cell. At the transcriptional level, the cis-regulatory regions establish sets of interdependencies between transcription factors and genes, including other transcription factors. These ``transcription networks'' are too large to be approached globally with a detailed dynamical model. In this paper, we describe an approach to this problem that focuses solely on the compatibility between gene expression patterns and signal integration functions, discussing calculations carried on the simplest, Boolean, realization of the model, and a first application to experimental data sets.

q-bio.MN↗

arXiv2003

Metachronal wave and hydrodynamic interaction for deterministic switching rowers

We employ a model system, called rowers, as a generic physical framework to define the problem of the coordinated motion of cilia (the metachronal wave) as a far from equilibrium process. Rowers are active (two-state) oscillators interacting solely through forces of hydrodynamic origin. In this work, we consider the case of fully deterministic dynamics, find analytical solutions of the equation of motion in the long wavelength (continuum) limit, and investigate numerically the short wavelength limit. We prove the existence of metachronal waves below a characteristic wavelength. Such waves are unstable and become stable only if the sign of the coupling is reversed. We also find that with normal hydrodynamic interaction the metachronal pattern has the form of stable trains of traveling wave packets sustained by the onset of anti-coordinated beating of consecutive rowers.

physics.bio-ph↗

arXiv2002

Rowers coupled hydrodynamically. Modeling possible mechanisms for the cooperation of cilia

We introduce a model system of stochastic entities, called 'rowers' which include some essentialities of the behavior of real cilia. We introduce and discuss the problem of symmetry breaking for these objects and its connection with the onset of macroscopic, directed flow in the fluid. We perform a mean field-like calculation showing that hydrodynamic interaction may provide for the symmetry breaking mechanism and the onset of fluid flow. Finally, we discuss the problem of the metachronal wave in a stochastic context.

cond-mat.stat-mech↗

arXiv1999

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.

cond-mat.stat-mech↗

arXiv1995

Criticality of Lamellar Surfaces by Conformational Degrees of freedom

A new model for lamellar surfaces formed by anisotropic molecules is proposed. The molecules have internal degrees of freedom, associated with their flexible section of length $N$ at zero temperature. We obtain a 2D non-standard six vertex model, which is exactly soluble and exhibits a finite order transition. The order and the character of the transition are determined by the dominant term in the $1 \over N$-expansion of the interaction energy. The dependence of the critical temperatures on $N$ is, instead, determined by the non-leading terms in the same expansion.

cond-mat↗