Self-organization and Mechanical Properties of Active Filament Bundles

A phenomenological description for active bundles of polar filaments is presented. The activity of the bundle results from crosslinks, that induce relative displacements between the aligned filaments. Our generic description is based on momentum conservation within the bundle. By specifying the internal forces, a simple minimal model for the bundle dynamics is obtained, capturing generic dynamic behaviors. In particular, contracted states as well as solitary and oscillatory waves appear through dynamic instabilities. The introduction of filament adhesion leads to self-organized persistent filament transport. Furthermore, calculating the tension, homogeneous bundles are shown to be able to actively contract and to perform work against external forces. Our description is motivated by dynamic phenomena in the cytoskeleton and could apply to stress-fibers and self-organization phenomena during cell-locomotion.Comment: 19 pages, 10 figure

Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds

The producibility of metabolites from available resources is investigated systematically using flux balance analysis (FBA) and network expansion. Calculations are performed for the genome-scale metabolic networks of Escherichia coli and Methanosarcina barkeri. Strict biological interpretation of the results obtained with FBA leads to the concept of sustainability, which reduces the set of producible metabolites by assuming a growing and dividing cell. A systematic comparison showed that applying network expansion in many cases results in exactly the set of all sustainable metabolites. The purely heuristic approach of allowing for certain cofactors to facilitate reactions during the process of network expansion dramatically helps to improve agreement of the results from the two different approaches. In conclusion, we state that network expansion, due to its enormous advantages in computational speed, is a valuable alternative to determining producible metabolites with FBA

Enhanced reaction kinetics in biological cells

The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular medium, as well as on its transport properties : a generic tracer particle freely diffuses as in a standard equilibrium medium, but also intermittently binds with random interaction times to motor proteins, which perform active ballistic excursions along cytoskeletal filaments. Here, we propose for the first time an analytical model of transport limited reactions in active media, and show quantitatively how active transport can enhance reactivity for large enough tracers like vesicles. We derive analytically the average interaction time with motor proteins which optimizes the reaction rate, and reveal remarkable universal features of the optimal configuration. We discuss why active transport may be beneficial in various biological examples: cell cytoskeleton, membranes and lamellipodia, and tubular structures like axons.Comment: 10 pages, 2 figure

Dense active matter model of motion patterns in confluent cell monolayers

Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes that are reminiscent of supercooled liquids and active nematics. We show that many observed features can be described within the framework of dense active matter, and argue that persistent uncoordinated cell motility coupled to the collective elastic modes of the cell sheet is sufficient to produce swirl-like correlations. We obtain this result using both continuum active linear elasticity and a normal modes formalism, and validate analytical predictions with numerical simulations of two agent-based cell models, soft elastic particles and the self-propelled Voronoi model together with in-vitro experiments of confluent corneal epithelial cell sheets. Simulations and normal mode analysis perfectly match when tissue-level reorganisation occurs on times longer than the persistence time of cell motility. Our analytical model quantitatively matches measured velocity correlation functions over more than a decade with a single fitting parameter.Comment: updated version accepted for publication in Nat. Com

Bloch Electrons in a Magnetic Field - Why Does Chaos Send Electrons the Hard Way?

We find that a 2D periodic potential with different modulation amplitudes in x- and y-direction and a perpendicular magnetic field may lead to a transition to electron transport along the direction of stronger modulation and to localization in the direction of weaker modulation. In the experimentally accessible regime we relate this new quantum transport phenomenon to avoided band crossing due to classical chaos.Comment: 4 pages, 3 figures, minor modifications, PRL to appea

Structure formation in active networks

Structure formation and constant reorganization of the actin cytoskeleton are key requirements for the function of living cells. Here we show that a minimal reconstituted system consisting of actin filaments, crosslinking molecules and molecular-motor filaments exhibits a generic mechanism of structure formation, characterized by a broad distribution of cluster sizes. We demonstrate that the growth of the structures depends on the intricate balance between crosslinker-induced stabilization and simultaneous destabilization by molecular motors, a mechanism analogous to nucleation and growth in passive systems. We also show that the intricate interplay between force generation, coarsening and connectivity is responsible for the highly dynamic process of structure formation in this heterogeneous active gel, and that these competing mechanisms result in anomalous transport, reminiscent of intracellular dynamics

Reduced level of arousal and increased mortality in adult acute medical admissions: a systematic review and meta-analysis

Abstract Background Reduced level of arousal is commonly observed in medical admissions and may predict in-hospital mortality. Delirium and reduced level of arousal are closely related. We systematically reviewed and conducted a meta-analysis of studies in adult acute medical patients of the relationship between reduced level of arousal on admission and in-hospital mortality. Methods We conducted a systematic review (PROSPERO: CRD42016022048), searching MEDLINE and EMBASE. We included studies of adult patients admitted with acute medical illness with level of arousal assessed on admission and mortality rates reported. We performed meta-analysis using a random effects model. Results From 23,941 studies we included 21 with 14 included in the meta-analysis. Mean age range was 33.4 - 83.8 years. Studies considered unselected general medical admissions (8 studies, n=13,039) or specific medical conditions (13 studies, n=38,882). Methods of evaluating level of arousal varied. The prevalence of reduced level of arousal was 3.1%-76.9% (median 13.5%). Mortality rates were 1.7%-58% (median 15.9%). Reduced level of arousal was associated with higher in-hospital mortality (pooled OR 5.71; 95% CI 4.21-7.74; low quality evidence: high risk of bias, clinical heterogeneity and possible publication bias). Conclusions Reduced level of arousal on hospital admission may be a strong predictor of in-hospital mortality. Most evidence was of low quality. Reduced level of arousal is highly specific to delirium, better formal detection of hypoactive delirium and implementation of care pathways may improve outcomes. Future studies to assess the impact of interventions on in-hospital mortality should use validated assessments of both level of arousal and delirium

Improved photobiological H-2 production in engineered green algal cells

Oxygenic photosynthetic organisms use solar energy to split water (H2O) into protons (H+), electrons (e(-)), and oxygen. A select group of photosynthetic microorganisms, including the green alga Chlamydomonas reinhardtii, has evolved the additional ability to redirect the derived H+ and e(-) to drive hydrogen (H-2) production via the chloroplast hydrogenases HydA1 and A2 (H(2)ase). This process occurs under anaerobic conditions and provides a biological basis for solar-driven H-2 production. However, its relatively poor yield is a major limitation for the economic viability of this process. To improve H-2 production in Chlamydomonas, we have developed a new approach to increase H+ and e(-) supply to the hydrogenases. In a first step, mutants blocked in the state 1 transition were selected. These mutants are inhibited in cyclic e(-) transfer around photosystem I, eliminating possible competition for e(-) with H(2)ase. Selected strains were further screened for increased H-2 production rates, leading to the isolation of Stm6. This strain has a modified respiratory metabolism, providing it with two additional important properties as follows: large starch reserves ( i.e. enhanced substrate availability), and a low dissolved O-2 concentration (40% of the wild type (WT)), resulting in reduced inhibition of H2ase activation. The H-2 production rates of Stm6 were 5 - 13 times that of the control WT strain over a range of conditions ( light intensity, culture time, +/- uncoupler). Typically, similar to 540 ml of H-2 liter(-1) culture ( up to 98% pure) were produced over a 10-14-day period at a maximal rate of 4 ml h(-1) ( efficiency = similar to 5 times the WT). Stm6 therefore represents an important step toward the development of future solar-powered H-2 production systems

Colloquium: Mechanical formalisms for tissue dynamics

The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes being expressed. This information suggests that ourunderstanding of the respective contributions of gene expression and mechanics, and of their crucialentanglement, will soon leap forward. Biomechanics increasingly benefits from models, which assistthe design and interpretation of experiments, point out the main ingredients and assumptions, andultimately lead to predictions. The newly accessible local information thus calls for a reflectionon how to select suitable classes of mechanical models. We review both mechanical ingredientssuggested by the current knowledge of tissue behaviour, and modelling methods that can helpgenerate a rheological diagram or a constitutive equation. We distinguish cell scale ("intra-cell")and tissue scale ("inter-cell") contributions. We recall the mathematical framework developpedfor continuum materials and explain how to transform a constitutive equation into a set of partialdifferential equations amenable to numerical resolution. We show that when plastic behaviour isrelevant, the dissipation function formalism appears appropriate to generate constitutive equations;its variational nature facilitates numerical implementation, and we discuss adaptations needed in thecase of large deformations. The present article gathers theoretical methods that can readily enhancethe significance of the data to be extracted from recent or future high throughput biomechanicalexperiments.Comment: 33 pages, 20 figures. This version (26 Sept. 2015) contains a few corrections to the published version, all in Appendix D.2 devoted to large deformation

Dynamical Coupling between a Bose-Einstein Condensate and a Cavity Optical Lattice

A Bose-Einstein condensate is dispersively coupled to a single mode of an ultra-high finesse optical cavity. The system is governed by strong interactions between the atomic motion and the light field even at the level of single quanta. While coherently pumping the cavity mode the condensate is subject to the cavity optical lattice potential whose depth depends nonlinearly on the atomic density distribution. We observe bistability already below the single photon level and strong back-action dynamics which tunes the system periodically out of resonance.Comment: 5 pages, 4 figure