Ontology, Matter and Emergence

“Ontological emergence” of inherent high-level properties with causal powers is witnessed nowhere. A non-substantialist conception of emergence works much better. It allows downward causation, provided our concept of causality is transformed accordingly

Bilayer elasticity at the nanoscale: the need for new terms

Continuum elastic models that account for membrane thickness variations are especially useful in the description of nanoscale deformations due to the presence of membrane proteins with hydrophobic mismatch. We show that terms involving the gradient and the Laplacian of the area per lipid are significant and must be retained in the effective Hamiltonian of the membrane. We reanalyze recent numerical data, as well as experimental data on gramicidin channels, in light of our model. This analysis yields consistent results for the term stemming from the gradient of the area per molecule. The order of magnitude we find for the associated amplitude, namely 13-60 mN/m, is in good agreement with the 25 mN/m contribution of the interfacial tension between water and the hydrophobic part of the membrane. The presence of this term explains a systematic variation in previously published numerical data.Comment: 34 pages, 9 figure

Revealing evolutionary constraints on proteins through sequence analysis

Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein, represented by an additive trait, can give rise to such a sector. As an illustration of a selected trait, we consider the elastic energy of an important conformational change within an elastic network model, and we show that selection acting on this energy leads to correlations among residues. For this concrete example and more generally, we demonstrate that the main signature of functional sectors lies in the small-eigenvalue modes of the covariance matrix of the selected sequences. However, secondary signatures of these functional sectors also exist in the extensively-studied large-eigenvalue modes. Our simple, general model leads us to propose a principled method to identify functional sectors, along with the magnitudes of mutational effects, from sequence data. We further demonstrate the robustness of these functional sectors to various forms of selection, and the robustness of our approach to the identification of multiple selected traits.Comment: 37 pages, 28 figure

Antibody-mediated cross-linking of gut bacteria hinders the spread of antibiotic resistance

The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a multiscale model of the interaction between antibiotic use and resistance spread in a host population, focusing on an important aspect of within-host immunity. Antibodies secreted in the gut enchain bacteria upon division, yielding clonal clusters of bacteria. We demonstrate that immunity-driven bacteria clustering can hinder the spread of a novel resistant bacterial strain in a host population. We quantify this effect both in the case where resistance pre-exists and in the case where acquiring a new resistance mutation is necessary for the bacteria to spread. We further show that the reduction of spread by clustering can be countered when immune hosts are silent carriers, and are less likely to get treated, and/or have more contacts. We demonstrate the robustness of our findings to including stochastic within-host bacterial growth, a fitness cost of resistance, and its compensation. Our results highlight the importance of interactions between immunity and the spread of antibiotic resistance, and argue in the favor of vaccine-based strategies to combat antibiotic resistance.Comment: 49 pages, 11 figure

Universal amplitudes of the Casimir-like interactions between four types of rods in fluid membranes

The fluctuation-induced, Casimir-like interaction between two parallel rods of length L adsorbed on a fluid membrane is calculated analytically at short separations d<<L. The rods are modeled as constraints imposed on the membrane curvature along a straight line. This allows to define four types of rods, according to whether the membrane can twist along the rod and/or curve across it. For stiff constraints, all the interaction potentials between the different types of rods are attractive and proportional to L/d. Two of the four types of rods are then equivalent, which yields six universal Casimir amplitudes. Repulsion can occur between different rods for soft constraints. Numerical results obtained for all ranges of d/L show that the attraction potential reaches kT for d/L\simeq0.2. At separations smaller than d_c \approx L(L/l_p)^(1/3), where l_p is the rod persistence length, two rods with fixed ends will bend toward each other and finally come into contact because of the Casimir interaction.Comment: 6 pages, 3 figure

Pairwise summation approximation for Casimir potentials and its limitations

We investigate the error made by the pairwise summation (PWS) approximation in three geometries where the exact formula for the Casimir interaction is known: atom-slab, slab-slab and sphere-slab configurations. For each case the interactions are calculated analytically by summing the van der Waals interactions between the two objects. We show that the PWS result is incorrect even for an infinitely thin slab in the atom-slab configuration, because of local field effects, unless the material is infinitely dilute. In the experimentally relevant case of dielectric materials, in all considered geometries the error made by the PWS approximation is much higher than the well-known value obtained for perfect reflectors in the long-range regime. This error is maximized for permittivities close to the one of Silicon

Fluctuations of the Casimir-like force between two membrane inclusions

Although Casimir forces are inseparable from their fluctuations, little is known about these fluctuations in soft matter systems. We use the membrane stress tensor to study the fluctuations of the membrane-mediated Casimir-like force. This method enables us to recover the Casimir force between two inclusions and to calculate its variance. We show that the Casimir force is dominated by its fluctuations. Furthermore, when the distance d between the inclusions is decreased from infinity, the variance of the Casimir force decreases as -1/d^2. This distance dependence shares a common physical origin with the Casimir force itself.Comment: 5 pages, 3 figure

Dynamical membrane curvature instability controlled by intermonolayer friction

International audienceWe study a dynamical curvature instability caused by a local chemical modification of a phospholipid membrane. In our experiments, a basic solution is microinjected close to a giant unilamellar vesicle, which induces a local chemical modification of some lipids in the external monolayer of the membrane. This modification causes a local deformation of the vesicle, which then relaxes. We present a theoretical description of this instability, taking into account both the change of the equilibrium lipid density and the change of the spontaneous membrane curvature induced by the chemical modification. We show that these two types of changes of the membrane properties yield different dynamics. In contrast, it is impossible to distinguish them when studying the equilibrium shape of a vesicle subjected to a global modification. In our model, the longest relaxation timescale is related to the intermonolayer friction, which plays an important part when there is a change in the equilibrium density in one monolayer. We compare our experimental results to the predictions of our model by fitting the measured time evolution of the deformation height to the solution of our dynamical equations. We obtain good agreement between theory and experiments. Our fits enable us to estimate the intermonolayer friction coefficient, yielding values that are consistent with previous measurements

Relational EPR

We study the EPR-type correlations from the perspective of the relational interpretation of quantum mechanics. We argue that these correlations do not entail any form of 'non-locality', when viewed in the context of this interpretation. The abandonment of strict Einstein realism implied by the relational stance permits to reconcile quantum mechanics, completeness, (operationally defined) separability, and locality.Comment: Revised, published versio