arXiv subjects

Marco Cosentino Lagomarsino

Publications and source records attributed to Marco Cosentino Lagomarsino.

At least 37 records · Page 2Linked to original sources

arXiv2014

Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid

Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework combining solely these two ingredients, in order to characterize their joint effects. Specifically, we study a simple polymer physics computational model with weak ubiquitous short-ranged self attraction and stronger sparse bridging interactions. Combining theoretical arguments and simulations, we study the general phenomenology of polymer collapse induced by these dual contributions, in the case of regularly-spaced bridging. Our results distinguish a regime of classical Flory-like coil-globule collapse dictated by the interplay of excluded volume and attractive energy and a switch-like collapse where bridging interaction compete with entropy loss terms from the looped arms of a star-like rosette. Additionally, we show that bridging can induce stable compartmentalized domains. In these configurations, different "cores" of bridging proteins are kept separated by star-like polymer loops in an entropically favorable multi-domain configuration, with a mechanism that parallels micellar polysoaps. Such compartmentalized domains are stable, and do not need any intra-specific interactions driving their segregation. Domains can be stable also in presence of uniform attraction, as long as the uniform collapse is above its theta point.

cond-mat.soft↗

arXiv2014

Soft bounds on diffusion produce skewed distributions and Gompertz growth

Constraints can affect dramatically the behavior of diffusion processes. Recently, we analyzed a natural and a technological system and reported that they perform diffusion-like discrete steps displaying a peculiar constraint, whereby the increments of the diffusing variable are subject to configuration-dependent bounds. This work explores theoretically some of the revealing landmarks of such phenomenology, termed "soft bound". At long times, the system reaches a steady state irreversibly (i.e., violating detailed balance), characterized by a skewed "shoulder" in the density distribution, and by a net local probability flux, which has entropic origin. The largest point in the support of the distribution follows a saturating dynamics, expressed by the Gompertz law, in line with empirical observations. Finally, we propose a generic allometric scaling for the origin of soft bounds. These findings shed light on the impact on a system of such "scaling" constraint and on its possible generating mechanisms.

cond-mat.stat-mech↗

arXiv2013

Hard and soft bounds in the evolution of Ubuntu packages. A lesson for species body masses?

Open-source software is a complex system; its development depends on the self-coordinated action of a large number of agents. This study follows the size of the building blocks, called "packages", of the Ubuntu Linux operating system over its entire history. The analysis reveals a multiplicative diffusion process, constrained by size-dependent bounds, driving the dynamics of the package-size distribution. A formalization of this into a quantitative model is able to match the data without relying on any adjustable parameters, and generates definite predictions. Finally, we formulate the hypothesis that a similar non-stationary mechanism could be shaping the distribution of mammal body sizes.

physics.soc-ph↗

arXiv2013

Growth-rate-dependent dynamics of a bacterial genetic oscillator

Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular "chassis" in which the circuits are embedded. For example, the intracellular macromolecular composition of fast-growing bacteria changes with growth rate. As a consequence, important parameters of gene expression, such as ribosome concentration or cell volume, are growth-rate dependent, ultimately coupling the dynamics of genetic circuits with cell physiology. This work addresses the effects of growth rate on the dynamics of a paradigmatic example of genetic oscillator, the repressilator. Making use of empirical growth-rate dependences of parameters in bacteria, we show that the repressilator dynamics can switch between oscillations and convergence to a fixed point depending on the cellular state of growth, and thus on the nutrients it is fed. The physical support of the circuit (type of plasmid or gene positions on the chromosome) also plays an important role in determining the oscillation stability and the growth-rate dependence of period and amplitude. This analysis has potential application in the field of synthetic biology, and suggests that the coupling between endogenous genetic oscillators and cell physiology can have substantial consequences for their functionality.

q-bio.MN↗

arXiv2012

Speed of evolution in large asexual populations with diminishing returns

The adaptive evolution of large asexual populations is generally characterized by competition between clones carrying different beneficial mutations. This interference phenomenon slows down the adaptation speed and makes the theoretical description of the dynamics more complex with respect to the successional occurrence and fixation of beneficial mutations typical of small populations. A simplified modeling framework considering multiple beneficial mutations with equal and constant fitness advantage captures some of the essential features of the actual complex dynamics, and some key predictions from this model are verified in laboratory evolution experiments. However, in these experiments the relative advantage of a beneficial mutation is generally dependent on the genetic background. In particular, the general pattern is that, as mutations in different loci accumulate, the relative advantage of new mutations decreases, trend often referred to as "diminishing return" epistasis. In this paper, we propose a phenomenological model that generalizes the fixed-advantage framework to include in a simple way this feature. To evaluate the quantitative consequences of diminishing returns on the evolutionary dynamics, we approach the model analytically as well as with direct simulations. Finally, we show how the model parameters can be matched with data from evolutionary experiments in order to infer the mean effect of epistasis and derive order-of-magnitude estimates of the rate of beneficial mutations. Applying this procedure to two experimental data sets gives values of the beneficial mutation rate within the range of previous measurements.

q-bio.PE↗

arXiv2012

Influence of homology and node-age on the growth of protein-protein interaction networks

Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two objects are intrinsically linked. Here, we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach. We then employ this unified framework to address the specific issue of the age dependence of protein interactions, through the definition of three different node wiring/divergence schemes. Comparison with empirical data indicates that an age-dependent divergence move is necessary in order to reproduce the basic topological observables together with the age correlation between interacting nodes visible in empirical data. We also discuss the possibility of nontrivial joint partition/topology observables.

q-bio.MN↗

arXiv2012

Gene silencing and large-scale domain structure of the E. coli genome

The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, from genome-wide protein binding profiles to evolutionary information, exploring the connections between chromosomal organization, genesilencing, pseudo-gene localization and horizontal gene transfer. We report the existence of transcriptionally silent contiguous areas corresponding to large regions of H-NS protein binding along the genome, their position indicates a possible relationship with the known large-scale features of chromosome organization.

q-bio.GN↗

arXiv2012

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 organised at various length scales. This has implications on modulating (when not enabling) the core biological processes of replication, transcription, 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. We also discuss some attempts of interpretation that unify different results, highlighting the role that statistical and soft condensed matter physics, and in particular classic and more modern tools from the theory of polymers, plays in describing this system of fundamental biological importance, and pointing to possible directions for future investigation.

physics.bio-ph↗

arXiv2012

DnaA and the timing of chromosome replication in Escherichia coli as a function of growth rate

Background: In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory circuit that depends on the binding of a critical number of ATP-bound DnaA proteins at the origin of replication. The synthesis of DnaA in the cell is controlled by a growth-rate dependent, negatively autoregulated gene found near the origin of replication. Both the regulatory and initiation activity of DnaA depend on its nucleotide bound state and its availability. Results: In order to investigate the contributions of the different regulatory processes to the timing of initiation of DNA replication at varying growth rates, we formulate a minimal quantitative model of the initiator circuit that includes the key ingredients known to regulate the activity of the DnaA protein. This model describes the average-cell oscillations in DnaA-ATP/DNA during the cell cycle, for varying growth rates. We evaluate the conditions under which this ratio attains the same threshold value at the time of initiation, independently of the growth rate. Conclusions: We find that a quantitative description of replication initiation by DnaA must rely on the dependency of the basic parameters on growth rate, in order to account for the timing of initiation of DNA replication at different cell doubling times. We isolate two main possible scenarios for this. One possibility is that the basal rate of regulatory inactivation by ATP hydrolysis must vary with growth rate. Alternatively, some parameters defining promoter activity need to be a function of the growth rate. In either case, the basal rate of gene expression needs to increase with the growth rate, in accordance with the known characteristics of the dnaA promoter.

q-bio.GN↗

arXiv2011

Hydrodynamically synchronized states in active colloidal arrays

Colloidal particles moving in a fluid interact via the induced velocity field. The collective dynamic state for a class of actively forced colloids, driven by harmonic potentials via a rule that couples forces to configurations, to perform small oscillations around an average position, is shown by experiment, simulation and theoretical arguments to be determined by the eigenmode structure of the coupling matrix. It is remarkable that the dynamical state can therefore be predicted from the mean spatial configuration of the active colloids, or from an analysis of the fluctuations near equilibrium. This has the surprising consequence that while 2 particles, or polygonal arrays of 4 or more colloids, synchronize with the nearest neighbors in anti-phase, a system of 3 equally spaced colloids synchronizes in-phase. In the absence of thermal fluctuations, the stable dynamical state is predominantly formed by the eigenmode with longest relaxation time.

cond-mat.soft↗

arXiv2011

Patterns of synchronization in the hydrodynamic coupling of active colloids

A system of active colloidal particles driven by harmonic potentials to oscillate about the vertices of a regular polygon, with hydrodynamic coupling between all particles, is described by a piece-wise linear model which exhibits various patterns of synchronization. Analytical solutions are obtained for this class of dynamical systems. Depending only on the number of particles, the synchronization occurs into states in which nearest neighbors oscillate either in-phase, or anti-phase, or in phase-locked (time-shifted) trajectories.

cond-mat.stat-mech↗

arXiv2011

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 nonlinear 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 characterising 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 characterised 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.

q-bio.GN↗

arXiv2010

Typical rank of coin-toss power-law random matrices over GF(2)

Random linear systems over the Galois Field modulo 2 have an interest in connection with problems ranging from computational optimization to complex networks. They are often approached using random matrices with Poisson-distributed or finite column/row-sums. This technical note considers the typical rank of random matrices belonging to a specific ensemble wich has genuinely power-law distributed column-sums. For this ensemble, we find a formula for calculating the typical rank in the limit of large matrices as a function of the power-law exponent and the shape of the matrix, and characterize its behavior through "phase diagrams" with varying model parameters.

cond-mat.dis-nn↗

arXiv2010

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations

Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional regulation. By means of a novel multi-scale spatial aggregation analysis, we uncover the existence of contiguous clusters of nucleoid-perturbation sensitive genes along the genome, whose expression is affected by a combination of topological DNA state and nucleoid-shaping protein occupancy. The clusters correlate well with the macrodomain structure of the genome. The most significant of them lay symmetrically at the edges of the ter macrodomain and involve all of the flagellar and chemotaxis machinery, in addition to key regulators of biofilm formation, suggesting that the regulation of the physical state of the chromosome by the nucleoid proteins plays an important role in coordinating the transcriptional response leading to the switch between a motile and a biofilm lifestyle.

q-bio.GN↗

arXiv2010

Minimal two-sphere model of the generation of fluid flow at low Reynolds numbers

Locomotion and generation of flow at low Reynolds number are subject to severe limitations due to the irrelevance of inertia: the "scallop theorem" requires that the system have at least two degrees of freedom, which move in non-reciprocal fashion, i.e. breaking time-reversal symmetry. We show here that a minimal model consisting of just two spheres driven by harmonic potentials is capable of generating flow. In this pump system the two degrees of freedom are the mean and relative positions of the two spheres. We have performed and compared analytical predictions, numerical simulation and experiments, showing that a time-reversible drive is sufficient to induce flow.

cond-mat.soft↗

arXiv2009

Statistical Mechanics of the Chinese Restaurant Process: lack of self-averaging, anomalous finite-size effects and condensation

The Pitman-Yor, or Chinese Restaurant Process, is a stochastic process that generates distributions following a power-law with exponents lower than two, as found in a numerous physical, biological, technological and social systems. We discuss its rich behavior with the tools and viewpoint of statistical mechanics. We show that this process invariably gives rise to a condensation, i.e. a distribution dominated by a finite number of classes. We also evaluate thoroughly the finite-size effects, finding that the lack of stationary state and self-averaging of the process creates realization-dependent cutoffs and behavior of the distributions with no equivalent in other statistical mechanical models.

cond-mat.dis-nn↗

arXiv2007

Sedimentation of pairs of hydrodynamically interacting semiflexible filaments

We describe the effect of hydrodynamic interactions in the sedimentation of a pair of inextensible semiflexible filaments under a uniform constant force at low Reynolds numbers. We have analyzed the different regimes and the morphology of such polymers in simple geometries, which allow us to highlight the peculiarities of the interplay between elastic and hydrodynamic stresses. Cooperative and symmetry breaking effects associated to the geometry of the fibers gives rise to characteristic motion which give them distinct properties from rigid and elastic filaments.

cond-mat.soft↗

arXiv2005

Continuum Description of the Cytoskeleton: Ring Formation in the Cell Cortex

Motivated by the formation of ring-like filament structures in the cortex of plant and animal cells, we study the dynamics of a two-dimensional layer of cytoskeletal filaments and motor proteins near a surface by a general continuum theory. As a result of active processes, dynamic patterns of filament orientation and density emerge via instabilities. We show that self-organization phenomena can lead to the formation of stationary and oscillating rings. We present state diagrams which reveal a rich scenario of asymptotic behaviors and discuss the role of boundary conditions.

q-bio.SC↗