M. Cosentino Lagomarsino

Metachronal waves for deterministic switching two-state oscillators with hydrodynamic interaction.

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.

Joint scaling laws in functional and evolutionary categories in prokaryotic genomes

We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model, numbers of genes in different functional categories are coupled to each other. For example, an increase in the number of metabolic enzymes in a genome is usually accompanied by addition of new transcription factors regulating these enzymes. Such coupling can be thought of as a proportional ‘recipe’ for genome composition of the type ‘a spoonful of sugar for each egg yolk’. The model jointly reproduces two known empirical laws: the distribution of family sizes and the non-linear scaling of the number of genes in certain functional categories (e.g. transcription factors) with genome size. In addition, it allows us to derive a novel relation between the exponents characterizing these two scaling laws, establishing a direct quantitative connection between evolutionary and functional categories. It predicts that functional categories that grow faster-than-linearly with genome size to be characterized by flatter-than-average family size distributions. This relation is confirmed by our bioinformatics analysis of prokaryotic genomes. This proves that the joint quantitative trends of functional and evolutionary classes can be understood in terms of evolutionary growth with proportional recipes.

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

Abstract:We introduce a model system of stochastic entities, called rowers which include some essentials 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 through an analytical calculation based on a path integral representation of our model equation.

A model for the self-organization of microtubules driven by molecular motors

Abstract: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, while 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 of these equations shows non-equilibrium inhomogeneous steady states in various regions of the parameter space. The presence and stability of such self-organized states are investigated in terms of entropy production. Numerical simulations confirm our analytic results.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, while 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 of these equations shows non-equilibrium inhomogeneous steady states in various regions of the parameter space. The presence and stability of such self-organized states are investigated in terms of entropy production. Numerical simulations confirm our analytic results.

Fluctuations of a driven membrane in an electrolyte

We develop a model for a driven cell or artificial membrane in an electrolyte. The system is kept far from equilibrium by the application of a DC electric field or by concentration gradients, which causes ions to flow through specific ion-conducting units (representing pumps, channels or natural pores). We consider the case of planar geometry and Debye-Huckel regime, and obtain the membrane equation of motion within Stokes hydrodynamics. At steady state, the applied field causes an accumulation of charges close to the membrane, which, similarly to the equilibrium case, can be described with renormalized membrane tension and bending modulus. However, as opposed to the equilibrium situation, we find new terms in the membrane equation of motion, which arise specifically in the out-of-equilibrium case. We show that these terms lead in certain conditions to instabilities.

DIA-MCIS

MOTIVATION Transcription networks, and other directed networks can be characterized by some topological observables (e.g. network motifs), that require a suitable randomized network ensemble, typically 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 Monte Carlo developed by (Chen et al.). AVAILABILITY The algorithm is available at http://wwwteor.mi.infn.it/bassetti/downloads.html

Cooperativity and hydrodynamic interactions in externally driven semiflexible filaments

We describe a simple simulation method that describes the hydrodynamics of semiflexible filaments immersed in a low Reynolds number fluid and analyze how multiple body cooperativity emerges due to the presence of hydrodynamic interactions (HI). We study the sedimentation of ensembles of filaments under an external force and also consider the propulsion of filaments subject to simple periodic driving. In both cases the dynamics shows qualitative differences due to the presence of HI. For sedimentation, the effects include cooperative velocity and instabilities that can be understood from the interplay of deformations due to flexibility and hydrodynamic forces. The motion of swimmers is more complex, and shows both positive and negative cooperation depending on distance, frequency of drive, and flexibility.

Current quantization and fractal hierarchy in a driven repulsive lattice gas

Driven lattice gases are widely regarded as the paradigm of collective phenomena out of equilibrium. While such models are usually studied with nearest-neighbor interactions, many empirical driven systems are dominated by slowly decaying interactions such as dipole-dipole and Van der Waals forces. Motivated by this gap, we study the nonequilibrium stationary state of a driven lattice gas with slow-decayed repulsive interactions at zero temperature. By numerical and analytical calculations of the particle current as a function of the density and of the driving field, we identify (i) an abrupt breakdown transition between insulating and conducting states, (ii) current quantization into discrete phases where a finite current flows with infinite differential resistivity, and (iii) a fractal hierarchy of excitations, related to the Farey sequences of number theory. We argue that the origin of these effects is the competition between scales, which also causes the counterintuitive phenomenon that crystalline states can melt by increasing the density.

Exchangeable random networks

We introduce and study a class of exchangeable random graph ensembles. They can be used as statistical null models for empirical networks, and as a tool for theoretical investigations. We provide general theorems that characterize the degree distribution of the ensemble graphs, together with some features that are important for applications, such as subgraph distributions and kernel of the adjacency matrix. A particular case of directed networks with power-law out–degree is studied in more detail, as an example of the flexibility of the model in applications.

Feedback topology and XOR -dynamics in Boolean networks with varying input structure

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the 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. 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 treelike 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.