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Active nematics are fluids in which the components have nematic symmetry and are driven out of equilibrium due to the microscopic generation of an active stress. When the active stress is high, it drives flows in the nematic and can lead to the proliferation of topological defects, a state we refer to as defect chaos. Using numerical simulations of active nematics, we observe energy transfer between length scales during defect chaos. We demonstrate that this energy transfer is driven by the exchange between variations in the orientation and degree of order in the nematic that predominantly occur during defect creation and annihilation. We then show that the primary features of energy transfer during defect chaos scale with the active length scale. Finally, we identify a second regime that features few defects, but rather bend walls. Similar to topological defects, these bend walls co-localize variations in the orientation with variations in the scalar order parameter leading to energy transfer., Comment: Submission includes SI file and 3 movies

Microfluidics involves the manipulation of flows at the microscale, typically requiring external power sources to generate pressure gradients. Alternatively, harnessing flows from active fluids, which are usually chaotic, has been proposed as a paradigm for the development of micro-machines. Here, by combining experimental realizations and simulations, we demonstrate that the addition of triangular-shaped inclusions into an active nematic gel can locally break the fore-aft symmetry of active turbulence and stabilize flow fields with self-pumping capabilities. The proposed strategy has enabled us to generate wall-free and self-powered microfluidic systems capable of both cargo transport and mixing along with the downstream flow. We analyze the performance of these active pumps, both isolated and within cooperative ensembles in terms of their output velocity and hydrostatic pressure buildup. Finally, we demonstrate strategies to incorporate them into specifically designed microfluidic platforms to advantageously tailor the geometry of active flows. Our results reveal new possibilities for leveraging the self-organized mechanodynamics of active fluids., Comment: Supplementary figures and videos at DOI 10.17605/OSF.IO/N8G4C

The field of active nematics has traditionally employed descriptions based on dipolar activity, with interactions that align along a single axis. However, it has been theoretically predicted that interactions with a substrate, prevalent in most biological systems, would require novel forms of activity, such as quadrupolar activity, that are governed by hydrodynamic screening. Here, by combining experiments and numerical simulations, we show that upon light-induced solidification of the underlying medium, microtubule-kinesin mixtures undergo a transformation that leads to a biphasic active suspension. Using an active lyotropic model, we prove that the transition is governed by screening effects that alter the dominant form of active stress. Specifically, the combined effect of friction and quadrupolar activity leads to a hierarchical folding that follows the intrinsic bend instability of the active nematic layer. Our results demonstrate the dynamics of the collapse of orientational order in active nematics and present a new route for controlling active matter by modifying the activity through changing the surrounding environment., Comment: 7 pages, 4 figures

We study a new mechanism of active matter confinement of a thin, active nematic sample consisting of microtubules, activated by Adenosine Triphosphate (ATP), placed between a slab of passive liquid crystal, the compound 8CB, and water. The 8CB slab is kept at a temperature below the phase transition value between the nematic and the smectic A phases. The smectic A molecules are horizontally aligned with an applied magnetic field, with their centers of mass arranged on equally spaced layers perpendicular to the field. The contact with the active nematic prompts flow in the smectic slab, along the direction parallel to the layers. This flow direction is transferred back to the active nematic. We set up a model of such contact flow and make predictions on the experimentally observed pattern, from the point of view of asymptotic, linear and nonlinear analyses. We examine such results within the scope of the principle of minimum energy dissipation of the flow. For analytic convenience, we consider the active nematic confined between two symmetric 8CB slabs, and show that the conclusions still hold when replacing the bottom smectic A substrate with water, as in the experimental setting.

We present a framework to take new measurements in nematic systems that contain active elements such as molecular motors. Spatio-temporal fields of stress, traction, velocity, pressure, and forces are estimated jointly from microscopy images alone. Our inverse-problem approach ensures that these fields comply with physical laws and are accurate at system boundaries. Our novel measurements in active biological materials provide new insight for the design of boundary-aware nematic systems. The shear stress at the wall unveils a correlation with the nucleation of topological defects. The pressure gradients and the velocity characterize how boundary effects drive system-wide dynamics. And the forces link the underlying fluid with the nematic tensor to reveal the time scales of the system. More broadly, our work establishes a generalizable approach to quantitatively study experimental systems that are inaccessible to measuring probes.

In this work, we report a direct measurement of the forces exerted by a tubulin/kinesin active nematic gel as well as its complete rheological characterization, including the quantification of its shear viscosity, {\eta}, and its activity parameter, {\alpha}. For this, we develop a novel method that allows us to rapidly photo-polymerize compliant elastic inclusions in the continuously remodelling active system. Moreover, we quantitatively settle long-standing theoretical predictions, such as a postulated relationship encoding the intrinsic time scale of the active nematic in terms of {\eta} and {\alpha}. In parallel, we infer a value for the nematic elasticity constant, K, by combining our measurements with the theorized scaling of the active length scale. On top of the microrheology capatilities, we demonstrate novel strategies for defect encapsulation, quantification of defect mechanics, and defect interactions, enabled by the versatility of the new microfabrication strategy that allows to combine elastic motifs of different shape and stiffness that are fabricated in-situ and on-time., Comment: Supplementary videos available at: https://tinyurl.com/activeUB

Cells are fundamental building blocks of living organisms displaying an array of shapes, morphologies, and textures that encode specific functions and physical behaviors. Elucidating the rules of this code remains a challenge. In this work, we create biomimetic structural building blocks by coating ellipsoidal droplets of a smectic liquid crystal with a protein-based active cytoskeletal gel, thus obtaining core-shell structures. By exploiting the patterned texture and anisotropic shape of the smectic core, we were able to mold the complex nematodynamics of the interfacial active material and identify new time-dependent states where topological defects periodically oscillate between rotational and translational regimes. Our nemato-hydrodynamic simulations of active nematics demonstrate that, beyond topology and activity, the dynamics of the active material are profoundly influenced by the local curvature and smectic texture of the droplet, as well as by external hydrodynamic forces. These results illustrate how the incorporation of these constraints into active nematic shells orchestrates remarkable spatio-temporal motifs, offering critical new insights into biological processes and providing compelling prospects for designing bio-inspired micro-machines., Comment: 16 pages, 8 figures

We investigate experimentally the dynamic phase transition of a two-dimensional active nematic layer interfaced with a passive liquid crystal. Under a temperature ramp that leads to the transition of the passive liquid into a highly anisotropic lamellar smectic-A phase, and in the presence of a magnetic field, the coupled active nematic reorganizes its flow and orientational patterns from the turbulent into a quasi-laminar regime aligned perpendicularly to the field. Remarkably, while the phase transition of the passive fluid is known to be continuous, our observations reveal intermittent dynamics of the order parameter and the coexistence of aligned and turbulent regions in the active nematic, a signature of discontinuous, or first order, phase transitions., Comment: 5 manuscript pages with 5 figures, and 7 SI pages with 4 SI figures and 4 SI video captions. Video files are available at: http://doi.org/10.17605/OSF.IO/CYXU7

Active fluids exhibit complex turbulent-like flows at low Reynolds number. Recent work predicted that 2d active nematic turbulence follows universal scaling laws. However, experimentally testing these predictions is conditioned by the coupling to the 3d environment. Here, we measure the spectrum of the kinetic energy, $E(q)$, in an active nematic film in contact with a passive oil layer. At small and intermediate scales, we find the scaling regimes $E(q)\sim q^{-4}$ and $E(q)\sim q^{-1}$, respectively, in agreement with the theoretical prediction for 2d active nematics. At large scales, however, we find a new scaling $E(q)\sim q$, which emerges when the dissipation is dominated by the 3d oil layer. In addition, we derive an explicit expression for the spectrum that spans all length scales, thus explaining and connecting the different scaling regimes. This allows us to fit the data and extract the length scale that controls the crossover to the new large-scale regime, which we tune by varying the oil viscosity. Overall, our work experimentally demonstrates the emergence of universal scaling laws in active turbulence, and it establishes how the spectrum is affected by external dissipation.

The role of boundary layers in conventional liquid crystals is commonly subsumed in their anchoring on confining walls. In the classical view, anchoring enslaves the orientational field of the passive material under equilibrium conditions. In this work, we experimentally explore the role of confining walls in the behavior of an active nematic. We find that, under slip boundary conditions, the wall induces the accumulation of negatively charged topological defects in its vicinity, resulting in the formation of a topological boundary layer that polarizes the wall. While the dynamics of wall and bulk defects are decoupled, we find that the active boundary layer influences the overall dynamics of the system, to the point of fully controlling the behavior of the active nematic in situations of strong confinement. Finally, we show that wall defects exhibit behaviors that are essentially different from those of their bulk counterparts, such as high motility or the ability to recombine with another defect of like-sign topological charge. These exotic behaviors result from a change of symmetry induced by the wall in the director field around the defect. Finally, we show that the collective dynamics of wall defects can be described in terms of a one-dimensional Kuramoto-Sivashinsky -like description of spatio-temporal chaos., Comment: 10 pages, 6 figures in main text, 5 figures in SI

In this manuscript we describe the realization of a minimal hybrid microswimmer, composed of a ferromagnetic nanorod and a paramagnetic microsphere. The unbounded pair is propelled in water upon application of a swinging magnetic field that induces a periodic relative movement of the two composing elements, where the nanorod rotates and slides on the surface of the paramagnetic sphere. When taken together, the processes of rotation and sliding describe a finite area in the parameter space, which increases with the frequency of the applied field. We develop a theoretical approach and combine it with numerical simulations, which allow us to understand the dynamics of the propeller and explain the experimental observations. Furthermore, we demonstrate a reversal of the microswimmer velocity by varying the length of the nanorod, as predicted by the model. Finally, we determine theoretically and in experiments the Lighthill's energetic efficiency of this minimal magnetic microswimmer., Comment: Published in Soft Matter

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of active matter in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines.

The realization of artificial microscopic swimmers able to propel in viscous fluids is an emergent research field of fundamental interest and vast technological applications. For certain functionalities, the efficiency of the microswimmer in converting the input power provided through an external actuation into propulsive power output can be critical. Here we use a microswimmer composed by a self-assembled ferromagnetic rod and a paramagnetic sphere and directly determine its swimming efficiency when it is actuated by a swinging magnetic field. Using fast video recording and numerical simulations we fully characterize the dynamics of the propeller and identify the two independent degrees of freedom which allow its propulsion. We then obtain experimentally the Lighthill's energetic efficiency of the swimmer by measuring the power consumed during propulsion and the energy required to translate the propeller at the same speed. Finally, we discuss how the efficiency of our microswimmer could be increased upon suitable tuning of the different experimental parameters., Comment: Accepted for publication in Nanoscale

Using novel micro-printing techniques, we develop a versatile experimental setup that allows us to study how lateral confinement tames the active flows and defect properties of the microtubule/kinesin active nematic system. We demonstrate that the active length scale that determines the self-organization of this system in unconstrained geometries loses its relevance under strong lateral confinement. Dramatic transitions are observed from chaotic to vortex lattices and defect-free unidirectional flows. Defects, which determine the active flow behavior, are created and annihilated on the channel walls rather than in the bulk, and acquire a strong orientational order in narrow channels. Their nucleation is governed by an instability whose wavelength is effectively screened by the channel width. All these results are recovered in simulations, and the comparison highlights the role of boundary conditions.

We combine experiments, theory, and simulations to investigate the coexistence of nonequilibrium phases emerging from interacting colloidal particles that are electrokinetically propelled in a nematic liquid crystal solvent. We directly determine the mechanical pressure within the radial assemblies and measure a non-equilibrium equation of state for this athermal driven system. A generic model combines phoretic propulsion with the interplay between electrostatic effects and liquid-crystal-mediated hydrodynamics, which are effectively cast into a long-range interparticle repulsion, while elasticity plays a subdominant role. Simulations based on this model explain the observed collective organization process and phase coexistence quantitatively. Our colloidal assemblies provide an experimental test-bed to investigate the fundamental role of phoretic pressure in the organization of driven out-of-equilibrium matter., Comment: 5 pages, 4 figures, submitted

The most frequent form of pairwise synthetic lethality (SL) in metabolic networks is known as plasticity synthetic lethality (PSL). It occurs when the simultaneous inhibition of paired functional and silent metabolic reactions or genes is lethal, while the default of the functional reaction or gene in the pair is backed up by the activation of the silent one. Based on a complex systems approach and by using computational techniques on bacterial genome-scale metabolic reconstructions, we found that the failure of the functional PSL partner triggers a critical reorganization of fluxes to ensure viability in the mutant which not only affects the SL pair but a significant fraction of other interconnected reactions forming what we call a SL cluster. Interestingly, SL clusters show a strong entanglement both in terms of silent coessential reactions, which band together to form backup systems, and of other functional and silent reactions in the metabolic network. This strong overlap, also detected at the level of genes, mitigates the acquired vulnerabilities and increased structural and functional costs that pay for the robustness provided by essential plasticity. Finally, the participation of coessential reactions and genes in different SL clusters is very heterogeneous and those at the intersection of many SL clusters could serve as supertargets for more efficient drug action in the treatment of complex diseases and to elucidate improved strategies directed to reduce undesired resistance to chemicals in pathogens., Comment: 10 pages, 4 figures, 15 supplementary figures

Active matter embraces systems that self-organize at different length and time scales, often exhibiting turbulent flows. Here, we use a quasi-two-dimensional nematically ordered layer of a protein-based active gel to experimentally demonstrate that the geometry of active flows, which we have characterized by means of the statistical distribution of eddy sizes, can be reversibly modified. To this purpose, the active material is prepared in contact with a thermotropic liquid crystal, whose lamellar smectic-A phase tiles the water/oil interface with a lattice of anisotropic domains that feature circular easy-flow directions. The active flow, which arises from the motion of parabolic folds within the filamentous active material, becomes effectively confined into circulating eddies that are in registry with the underlying smectic-A domains. Based on topological arguments applied to the circular confinement, together with well-known properties of the active material, we show that the structure of the active flow is determined by a single intrinsic length scale. The role of this length scale thus reemerges from setting the decay length in the exponential eddy size distribution of the free turbulent regime, to determining the minimum size of circulating eddies featuring a scale-free power law. Our results demonstrate that soft-confinement provides with an invaluable tool to probe the intrinsic length and time scales of active materials, and pave the way for further exploration looking for similarities and differences between active and passive two-dimensional turbulence., Comment: Main manuscript and Supplementary Material. Movies available in http://www.ub.edu/socsam/AGEddies/

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., Comment: 5 pages, 4 figures, a SI file, and a SI video

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., Comment: Molecular Crystals and Liquid Crystals Volume 610, Issue 1, 2015

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.

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., Comment: Manuscript with supplementary information (experimental methods, supplementary figures, and supplementary videos). Video files are available at http://www.ub.edu/socsam/AGSmA/

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.

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.

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., Comment: Supplementary material temporary available at: http://tinyurl.com/swarms-SI

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., Comment: 8 pages, 12 figures

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., Comment: 22 pages, 4 figures

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.

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 Erd\"os-R\'enyi 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., Comment: 6 pages, 2 figures

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.

Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function remains a major challenge. In particular, turning observed structural regularities into organizing principles underlying systemic functions is a crucial task that can be significantly addressed after endowing complex network representations of metabolism with the notion of geometric distance. Here, we design a cartographic map of metabolic networks by embedding them into a simple geometry that provides a natural explanation for their observed network topology and that codifies node proximity as a measure of hidden structural similarities. We assume a simple and general connectivity law that gives more probability of interaction to metabolite/reaction pairs which are closer in the hidden space. Remarkably, we find an astonishing congruency between the architecture of E. coli and human cell metabolisms and the underlying geometry. In addition, the formalism unveils a backbone-like structure of connected biochemical pathways on the basis of a quantitative cross-talk. Pathways thus acquire a new perspective which challenges their classical view as self-contained functional units.

We study the transversal motion of paramagnetic particles on a uniaxial garnet film, exhibiting a longitudinal ratchet effect in the presence of an oscillating magnetic field. Without the field, the thermal diffusion coefficient obtained by video microscopy is $D_{0}\approx 3\times 10^{-4}$ $\mu m^2/s$. With the field, the transversal diffusion exhibits a giant enhancement by almost four decades and a pronounced maximum as a function of the driving frequency. We explain the experimental findings with a theoretical interpretation in terms of random disorder effects within the magnetic film., Comment: 4 pages, 4 figures

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.

We consider an irreversible autocatalytic conversion reaction A+B -> 2A under subdiffusion described by continuous time random walks. The reactants' transformations take place independently on their motion and are described by constant rates. The analog of this reaction in the case of normal diffusion is described by the Fisher-Kolmogorov-Petrovskii-Piskunov (FKPP) equation leading to the existence of a nonzero minimal front propagation velocity which is really attained by the front in its stable motion. We show that for subdiffusion this minimal propagation velocity is zero, which suggests propagation failure.

A model of a phase-separating two-component Langmuir monolayer in the presence of a photo-induced reaction interconvering two components is formulated. An interplay between phase separation, orientational ordering and treaction is found to lead to a variety of nonequilibrium self-organized patterns, both stationary and traveling. Examples of the patterns, observed in numerical simulations, include flowing droplets, traveling stripes, wave sources and vortex defects., Comment: Submitted to the Physical Review E

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., Comment: minor changes: correct estimation of concentration at the anode, added Journal-ref

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., Comment: 11 pages, 15 figures, REVTEX 4; reference added