arXiv subjects

Francesc Sagués

Publications and source records attributed to Francesc Sagués.

33 records · Page 2Linked to original sources

arXiv2016

Probing the shear viscosity of an active nematic

In vitro reconstituted active systems, such as the ATP-driven microtubule bundle suspension developed by the Dogic group, provide a fertile testing ground for elucidating the phenomenology of active liquid crystalline states. Controlling such novel phases of matter crucially depends on our knowledge of their material and physical properties. In this letter, we show that the rheological properties of an active nematic film can be probed by varying its hydrodynamic coupling to a bounding oil layer. Using the motion of disclinations as intrinsic tracers of the flow field and a hydrodynamic model, we obtain an estimate for the as of now unknown shear viscosity of the nematic film. Knowing this now provides us with an additional handle for robust and precision tunable control of the emergent dynamics of active fluids.

cond-mat.soft↗

arXiv2016

Reconfigurable swarms of colloidal particles electrophoretically drivenin nematic liquid crystals

We present experiments where anisometric colloidal microparticles dispersed in a nematic liquid crystal cell with homeotropic anchoring conditions are dynamically assembled by means of liquid-crystal-enabled electrophoresis (LCEEP) using an AC electric field perpendicular to the confining plates. A nematic host with negative dielectric anisotropy leads to a driving force parallel to the cell plates. We take advantage of the resulting gliding anchoring conditions and the degeneracy in the direction of particle motion to design reconfigurable trajectories using a photosensitive anchoring layer (azosilane self-assembled monolayer), as the particle trajectory follows the local director orientation.

cond-mat.soft↗

arXiv2016

Nematic Colloidal Swarms Assembled and Transported on Photosensitive Surfaces

We demonstrate a novel method to assemble and transport swarms of colloidal particles by combining liquid crystals enabled electrophoresis and photo-sensitive surface patterning. Colloidal particles are propelled in a nematic liquid crystal via application of an alternating current electric field. Swarms of particles are assembled into a rotating mill cluster, or moved as a whole along predefined paths photo-imprinted on chemically functionalized substrates. This technique represents an alternative approach to fluid based lab-on-a-chip technologies guiding the motion of large ensembles of micrometer scale solid or liquid inclusions.

cond-mat.soft↗

arXiv2016

Detecting the Escherichia coli metabolic backbone

The heterogeneity of reaction fluxes present in a metabolic network within a single flux state can be exploited to construct the so-called backbone as a reduced version of metabolism. The backbone maintains all significant fluxes producing or consuming metabolites while displaying a substantially decreased number of interconnections and, hence, it becomes a useful tool to extract primary metabolic routes. Here, we disclose the metabolic backbone of Escherichia coli using the computationally predicted fluxes which maximize the growth rate in glucose minimal medium, and we compare it with the backbone of Mycoplasma pneumoniae, a much simpler organism. We find that the central core in both backbones is mainly composed of reactions in ancient pathways, still playing at present a key role in energy metabolism. In E. coli, the analysis of the backbone reveals that the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism; but not conversely. At the same time, an analysis of the dependence of this backbone on media composition leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful to trace simultaneously both its evolution and adaptation fingerprints.

q-bio.MN↗

arXiv2015

Patterning active materials with addressable soft interfaces

Motor-proteins are responsible for transport inside cells. Harnessing their activity is key towards developing new nano-technologies, or functional biomaterials. Cytoskeleton-like networks, recently tailored in vitro, result from the self-assembly of subcellular autonomous units. Taming this biological activity bottom-up may thus require molecular level alterations compromising protein integrity. Taking a top-down perspective, here we prove that the seemingly chaotic flows of a tubulin-kinesin active gel can be forced to adopt well-defined spatial directions by tuning the anisotropic viscosity of a contacting lamellar oil. Different configurations of the active material are realized, when the passive oil is either unforced or commanded by a magnetic field. The inherent instability of the extensile active fluid is thus spatially regularized, leading to organized flow patterns, endowed with characteristic length and time scales. Our finding paves the way for designing hybrid active/passive systems where ATP-driven dynamics can be externally conditioned.

cond-mat.soft↗

arXiv2015

Mapping high-growth phenotypes in the flux space of microbial metabolism

Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to the study of a single optimal state, like maximum biomass yield that is by far the most common assumption. Here we confront optimal growth solutions to the whole set of feasible flux phenotypes (FFP), which provides a benchmark to assess the likelihood of optimal and high-growth states and their agreement with experimental results. In addition, FFP maps are able to uncover metabolic behaviors, such as aerobic fermentation accompanying exponential growth on sugars at nutrient excess conditions, that are unreachable using standard models based on optimality principles. The information content of the full FFP space provides us with a map to explore and evaluate metabolic behavior and capabilities, and so it opens new avenues for biotechnological and biomedical applications.

q-bio.MN↗

arXiv2014

Reconfigurable assembly of nematic colloids commanded by photoactivated surface patterns

Different phoretic driving mechanisms have been proposed for the transport of solid or liquid microscopic inclusions in integrated chemical processes. However, the ability to reversibly address both the flow path, rate, and local reactant concentration has not yet been realized. Here we show that a substrate chemically modified with photosensitive self-assembled monolayers allows to directly command the assembly and transport of large ensembles of micron-size particles and drops dispersed in a thin layer of anisotropic fluid. Our strategy separates particle driving, realized via AC electrophoresis, and steering, achieved by elastic modulation of the host nematic fluid. Inclusions respond individually or in collective modes following arbitrary reconfigurable paths imprinted via UV/blue illumination. Relying solely on generic material properties, the proposed procedure is versatile enough for the development of applications involving either inanimate or living materials.

cond-mat.soft↗

arXiv2014

Essential plasticity and redundancy of metabolism unveiled by synthetic lethality analysis

We unravel how functional plasticity and redundancy are essential mechanisms underlying the ability to survive of metabolic networks. We perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in a minimal medium and we find that synthetic lethal pairs divide in two different groups depending on whether the synthetic lethal interaction works as a backup or as a parallel use mechanism, the first corresponding to essential plasticity and the second to essential redundancy. In E. coli, the analysis of pathways entanglement through essential redundancy supports the view that synthetic lethality affects preferentially a single function or pathway. In contrast, essential plasticity, the dominant class, tends to be inter-pathway but strongly localized and unveils Cell Envelope Biosynthesis as an essential backup for Membrane Lipid Metabolism. When comparing E. coli and Mycoplasma pneumoniae, we find that the metabolic networks of the two organisms exhibit a large difference in the relative importance of plasticity and redundancy which is consistent with the conjecture that plasticity is a sophisticated mechanism that requires a complex organization. Finally, coessential reaction pairs are explored in different environmental conditions to uncover the interplay between the two mechanisms. We find that synthetic lethal interactions and their classification in plasticity and redundancy are basically insensitive to medium composition, and are highly conserved even when the environment is enriched with nonessential compounds or overconstrained to decrease maximum biomass formation.

q-bio.MN↗

arXiv2014

Tracer diffusion inside fibrinogen layers

We investigate the obstructed motion of tracer (test) particles in crowded environments by carrying simulations of two-dimensional Gaussian random walk in model fibrinogen monolayers of different orientational ordering. The fibrinogen molecules are significantly anisotropic and therefore they can form structures where orientational ordering, similar to the one observed in nematic liquid crystals, appears. The work focuses on the dependence between level of the orientational order (degree of environmental crowding) of fibrinogen molecules inside a layer and non-Fickian character of the diffusion process of spherical tracer particles moving within the domain. It is shown that in general particles motion is subdiffusive and strongly anisotropic, and its characteristic features significantly change with the orientational order parameter, concentration of fibrinogens and radius of a diffusing probe.

physics.chem-ph↗

arXiv2013

Networks of noisy oscillators with correlated degree and frequency dispersion

We investigate how correlations between the diversity of the connectivity of networks and the dynamics at their nodes affect the macroscopic behavior. In particular, we study the synchronization transition of coupled stochastic phase oscillators that represent the node dynamics. Crucially in our work, the variability in the number of connections of the nodes is correlated with the width of the frequency distribution of the oscillators. By numerical simulations on Erdös-Rényi networks, where the frequencies of the oscillators are Gaussian distributed, we make the counterintuitive observation that an increase in the strength of the correlation is accompanied by an increase in the critical coupling strength for the onset of synchronization. We further observe that the critical coupling can solely depend on the average number of connections or even completely lose its dependence on the network connectivity. Only beyond this state, a weighted mean-field approximation breaks down. If noise is present, the correlations have to be stronger to yield similar observations.

cond-mat.dis-nn↗

arXiv2012

Assessing the significance of knockout cascades in metabolic networks

Complex networks have been shown to be robust against random structural perturbations, but vulnerable against targeted attacks. Robustness analysis usually simulates the removal of individual or sets of nodes, followed by the assessment of the inflicted damage. For complex metabolic networks, it has been suggested that evolutionary pressure may favor robustness against reaction removal. However, the removal of a reaction and its impact on the network may as well be interpreted as selective regulation of pathway activities, suggesting a tradeoff between the efficiency of regulation and vulnerability. Here, we employ a cascading failure algorithm to simulate the removal of single and pairs of reactions from the metabolic networks of two organisms, and estimate the significance of the results using two different null models: degree preserving and mass-balanced randomization. Our analysis suggests that evolutionary pressure promotes larger cascades of non-viable reactions, and thus favors the ability of efficient metabolic regulation at the expense of robustness.

q-bio.MN↗

arXiv2012

Predicting effects of structural stress in a genome-reduced model bacterial metabolism

We studied in silico effects of structural stress in Mycoplasma pneumoniae, a genome-reduced model bacterial organism, by tracking the damage propagating on its metabolic network after a deleterious perturbation. First, we analyzed failure cascades spreading from individual reactions and pairs of reactions and compared the results to those in Staphylococcus aureus and Escherichia coli. To alert to the potential damage caused by the failure of individual reactions, we propose a generic predictor based on local information that identifies target reactions for structural vulnerability. With respect to the simultaneous failure of pairs of reactions, we detected strong non-linear amplification effects that can be predicted by the presence of specific motifs in the intersection of single cascades. We further connected the metabolic and gene co-expression networks of M. pneumoniae through enzyme activities, and studied the consequences of knocking out individual genes and clusters of genes. Damage caused by single gene knockouts reveals a strong correlation between genome-scale cascades of large impact and gene essentiality. At the same time, we found that genes controlling high-damage reactions tend to operate in functional isolation, as a metabolic protection mechanism. We conclude that the architecture of M. pneumoniae, both at the level of metabolism and genome, seems to have evolved towards increased structural robustness, similarly to other more complex model bacterial organisms, despite its reduced genome size and its greater metabolic network linearity. Our approach, although motivated biochemically, is generic enough to be of potential use toward analyzing and predicting spreading of structural stress in any bipartite complex network.

q-bio.MN↗

arXiv2010

Network-based confidence scoring system for genome-scale metabolic reconstructions

Reliability on complex biological networks reconstructions remains a concern. Although observations are getting more and more precise, the data collection process is yet error prone and the proofs display uneven certitude. In the case of metabolic networks, the currently employed confidence scoring system rates reactions according to a discretized small set of labels denoting different levels of experimental evidence or model-based likelihood. Here, we propose a computational network-based system of reaction scoring that exploits the complex hierarchical structure and the statistical regularities of the metabolic network as a bipartite graph. We use the example of Escherichia coli metabolism to illustrate our methodology. Our model is adjusted to the observations in order to derive connection probabilities between individual metabolite-reaction pairs and, after validation, we integrate individual link information to assess the reliability of each reaction in probabilistic terms. This network-based scoring system breaks the degeneracy of currently employed scores, enables further confirmation of modeling results, uncovers very specific reactions that could be functionally or evolutionary important, and identifies prominent experimental targets for further verification. We foresee a wide range of potential applications of our approach given the natural network bipartivity of many biological interactions.

q-bio.MN↗

arXiv2002

Does ohmic heating influence the flow field in thin-layer electrodeposition?

In thin-layer electrodeposition the dissipated electrical energy leads to a substantial heating of the ion solution. We measured the resulting temperature field by means of an infrared camera. The properties of the temperature field correspond closely with the development of the concentration field. In particular we find, that the thermal gradients at the electrodes act like a weak additional driving force to the convection rolls driven by concentration gradients.

nlin.PS↗

arXiv2002

Experimental investigation of the initial regime in fingering electrodeposition: dispersion relation and velocity measurements

Recently a fingering morphology, resembling the hydrodynamic Saffman-Taylor instability, was identified in the quasi-two-dimensional electrodeposition of copper. We present here measurements of the dispersion relation of the growing front. The instability is accompanied by gravity-driven convection rolls at the electrodes, which are examined using particle image velocimetry. While at the anode the theory presented by Chazalviel et al. describes the convection roll, the flow field at the cathode is more complicated because of the growing deposit. In particular, the analysis of the orientation of the velocity vectors reveals some lag of the development of the convection roll compared to the finger envelope.

nlin.PS↗