Monodisperse domains by proteolytic control of the coarsening instability

The coarsening instability typically disrupts steady-state cluster-size distributions. We show that degradation coupled to the cluster size, such as arising from biological proteolysis, leads to a novel fixed-point cluster size. Stochastic evaporative and condensative fluxes determine the width of the fixed-point size distribution. At the fixed-point, we show how the peak size and width depend on number, interactions, and proteolytic rate. This proteolytic size-control mechanism is consistent with the phenomenology of pseudo-pilus length control in the general secretion pathway of bacteria.Comment: Physical Review E: Statistical, Nonlinear, and Soft Matter Physics (2011) in pres

Stuttering Min oscillations within E. coli bacteria: A stochastic polymerization model

We have developed a 3D off-lattice stochastic polymerization model to study subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding, and fragmentation of MinD filaments due to MinE. Each of processivity, protection, and fragmentation reduces stuttering, speeds oscillations, and reduces MinD filament lengths. Neither processivity or tip-protection were, on their own, sufficient to produce fast stutter-free oscillations. While filament fragmentation could, on its own, lead to fast oscillations with infrequent stuttering; high levels of fragmentation degraded oscillations. The infrequent stuttering observed in standard Min oscillations are consistent with short filaments of MinD, while we expect that mutants that exhibit higher stuttering frequencies will exhibit longer MinD filaments. Increased stuttering rate may be a useful diagnostic to find observable MinD polymerization in experimental conditions.Comment: 21 pages, 7 figures, missing unit for k_f inserte

Emergence of tip singularities in dissolution patterns

Chemical erosion, one of the two major erosion processes along with mechanical erosion, occurs when a soluble rock like salt, gypsum or limestone is dissolved in contact with a water flow. The coupling between the geometry of the rocks, the mass-transfer and the flow leads to the formation of remarkable patterns, like scallop patterns in caves. We emphasize the common presence of very sharp shapes and spikes, despite the diversity of hydrodynamic conditions and the nature of the soluble materials. We explain the generic emergence of such spikes in dissolution processes by a geometrical approach. Singularities at the interface emerge as a consequence of the erosion directed in the normal direction, when the surface displays curvature variations, like those associated to a dissolution pattern. First, we demonstrate the presence of singular structures in natural interfaces shaped by dissolution. Then, we propose simple surface evolution models of increasing complexity demonstrating the emergence of spikes and allowing us to explain at long term by coarsening the formation of cellular structures. Finally, we perform a dissolution pattern experiment driven by solutal convection and we report the emergence of a cellular pattern following well the model predictions. Although the precise prediction of dissolution shapes necessitates to perform a complete hydrodynamic study, we show that the characteristic spikes which are reported ultimately for dissolution shapes are explained generically by geometrical arguments due to the surface evolution. These findings can be applied to other ablation patterns, reported for example in melting ice.Comment: 13 pages, 8 figure

Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences

During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life

Inhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis and Model

Conjugation is the main mode of horizontal gene transfer that spreads antibiotic resistance among bacteria. Strategies for inhibiting conjugation may be useful for preserving the effectiveness of antibiotics and preventing the emergence of bacterial strains with multiple resistances. Filamentous bacteriophages were first observed to inhibit conjugation several decades ago. Here we investigate the mechanism of inhibition and find that the primary effect on conjugation is occlusion of the conjugative pilus by phage particles. This interaction is mediated primarily by phage coat protein g3p, and exogenous addition of the soluble fragment of g3p inhibited conjugation at low nanomolar concentrations. Our data are quantitatively consistent with a simple model in which association between the pili and phage particles or g3p prevents transmission of an F plasmid encoding tetracycline resistance. We also observe a decrease in the donor ability of infected cells, which is quantitatively consistent with a reduction in pili elaboration. Since many antibiotic-resistance factors confer susceptibility to phage infection through expression of conjugative pili (the receptor for filamentous phage), these results suggest that phage may be a source of soluble proteins that slow the spread of antibiotic resistance genes

Valence, magnétisme et conduction dans les composés à valence intermédiaire : Le cas SmB6

SmB6 is one typical example of the exciting physics which can result from a quantum equilibrium between two valence configurations. The first configuration of Samarium (Sm2+) corresponds to an insulating and non magnetic state whereas the second one (Sm3+) would theoretically give a magnetic and metallic ground state. Specific heat measurements under pressure evidenced a new long range magnetic ordering for pressures higher than pc=10GPa. On another hand, transport measurements measured for the first time in good conditions of hydrostaticity found a reliable and reproducible critical pressure for the insulator to metal transition equal to pc. The phase diagram is now well known and the observation for the first time of a magnetic anomaly in the high pressure resistivity curves certifies that the onset of the magnetic phase really coincide with the closure of the gap. This change is discussed in a general frame taking into account the Kondo lattice temperature as a key parameter for the renormalization of the wavefunction from one integer configuration to the other whereas the valence itself is still intermediate. This general idea seems to be valid also for other systems studied in this dissertation like SmS or TmSe and could even be valid for more general cases.In the same time, resistivity measurements under uniaxial stress were undertaken. The result is a strong anisotropy effect observed on the pressure dependence of the residual resistivity in the compound SmB6. The comparison with the transport under hydrostatic conditions enables us to consider a new idea for the nature of the gap, considering only one anisotropic gap.Le composé SmB6 est un exemple typique de la physique étrange qui peut résulter d'un équilibre de valence. La première configuration du Samarium (Sm2+) correspond à un état isolant non magnétique alors que la seconde (Sm3+) donnerait théoriquement un état magnétique et conducteur. Des mesures de microcalorimétrie sous pression ont permis d'établir le diagramme de phase magnétique de SmB6 : une nouvelle phase magnétique ordonnée à longue distance a été mise en évidence pour des pressions supérieures à 10GPa. D'un autre coté, des mesures de transport réalisées sous pression hydrostatique permettent de situer la transition isolant-métal pour la même pression. Le diagramme de phase sous pression est désormais bien établi et l'observation pour la première fois d'une anomalie magnétique dans les courbes de résistivité au delà de 10GPa permet d'affirmer que la coïncidence des deux phénomènes a bien lieu. Ce changement de comportement du système est discuté dans un nouveau cadre théorique prenant en compte la température Kondo du réseau comme paramètre clef pour la renormalisation de la fonction d'onde vers l'une ou l'autre configuration de valence entière alors que la valence mesurée est toujours nettement intermédiaire. Cette idée générale semble par ailleurs s'appliquer à d'autres composés à valence intermédiaire étudiés (SmS, TmSe). En parallèle, des mesures de résistivité sous contraintes uniaxiales ont été réalisées. Elles mettent en évidence un fort effet d'anisotropie dans le composé SmB6. La comparaison de ces expériences avec les résultats obtenus dans des conditions de pression très hydrostatiques permettent de revisiter le problème de la nature du gap de SmB6

Valence, magnétisme et conduction dans les composés à valence intermédiaire : Le cas SmB6

SmB6 is one typical example of the exciting physics which can result from a quantum equilibrium between two valence configurations. The first configuration of Samarium (Sm2+) corresponds to an insulating and non magnetic state whereas the second one (Sm3+) would theoretically give a magnetic and metallic ground state. Specific heat measurements under pressure evidenced a new long range magnetic ordering for pressures higher than pc=10GPa. On another hand, transport measurements measured for the first time in good conditions of hydrostaticity found a reliable and reproducible critical pressure for the insulator to metal transition equal to pc. The phase diagram is now well known and the observation for the first time of a magnetic anomaly in the high pressure resistivity curves certifies that the onset of the magnetic phase really coincide with the closure of the gap. This change is discussed in a general frame taking into account the Kondo lattice temperature as a key parameter for the renormalization of the wavefunction from one integer configuration to the other whereas the valence itself is still intermediate. This general idea seems to be valid also for other systems studied in this dissertation like SmS or TmSe and could even be valid for more general cases.In the same time, resistivity measurements under uniaxial stress were undertaken. The result is a strong anisotropy effect observed on the pressure dependence of the residual resistivity in the compound SmB6. The comparison with the transport under hydrostatic conditions enables us to consider a new idea for the nature of the gap, considering only one anisotropic gap.Le composé SmB6 est un exemple typique de la physique étrange qui peut résulter d'un équilibre de valence. La première configuration du Samarium (Sm2+) correspond à un état isolant non magnétique alors que la seconde (Sm3+) donnerait théoriquement un état magnétique et conducteur. Des mesures de microcalorimétrie sous pression ont permis d'établir le diagramme de phase magnétique de SmB6 : une nouvelle phase magnétique ordonnée à longue distance a été mise en évidence pour des pressions supérieures à 10GPa. D'un autre coté, des mesures de transport réalisées sous pression hydrostatique permettent de situer la transition isolant-métal pour la même pression. Le diagramme de phase sous pression est désormais bien établi et l'observation pour la première fois d'une anomalie magnétique dans les courbes de résistivité au delà de 10GPa permet d'affirmer que la coïncidence des deux phénomènes a bien lieu. Ce changement de comportement du système est discuté dans un nouveau cadre théorique prenant en compte la température Kondo du réseau comme paramètre clef pour la renormalisation de la fonction d'onde vers l'une ou l'autre configuration de valence entière alors que la valence mesurée est toujours nettement intermédiaire. Cette idée générale semble par ailleurs s'appliquer à d'autres composés à valence intermédiaire étudiés (SmS, TmSe). En parallèle, des mesures de résistivité sous contraintes uniaxiales ont été réalisées. Elles mettent en évidence un fort effet d'anisotropie dans le composé SmB6. La comparaison de ces expériences avec les résultats obtenus dans des conditions de pression très hydrostatiques permettent de revisiter le problème de la nature du gap de SmB6

Valence, magnétisme et conduction dans les composés à valence intermédiaire (le cas SmB6)

Dans certains composés à base de terre rare, le niveau 4f se trouve si proche du niveau de Fermi que la valence du composé peut devenir intermédiaire. Le composé 5mBs est un exemple typique de la physique étrange qui peut résulter de cet équilibre quantique entre deux configurations de valence. L'état Sm2+ correspond à un état isolant non magnétique alors que l'état Sm3+ donnerait théoriquement un état magnétique et conducteur. Des mesures de microcalorimétrie et de NFS sous pression, ont permis d'établir le diagramme de phase magnétique de 5mB6 : Une nouvelle phase magnétique ordonnée à longue distance a été mise en évidence pour des pressions supérieures à une pression critique de 10GPa. D'un autre coté, des mesures de transport sous pression réalisées dans de bonnes conditions de pression hydrostatique permettent de situer la transition isolant-métal sans ambiguïté et de façon reproductible pour la même pression critique. Le diagramme de phase de 5mB6 sous pressions est désormais bien établit et l'observation pour la première fois d'une anomalie magnétique dans les courbes de résistivité permettent d'affirmer que la coïncidence des deux phénomènes a bien lieu. Ce changement de comportement du système se produit alors que la valence du Sm est toujours intermédiaire. Ce phénomène est discuté dans un nouveau cadre théorique prenant en compte la température Kondo du réseau comme paramètre clef. En parallèle, des mesures de résistivité sous contrainte uniaxiale ont mis en évidence un fort effet d'an isotropie dans le composé 5mB6. Ceci permet de revisiter le problème de la nature du gap de 5mB6. En particulier, l'idée d'un gap unique anisotrope semble réhabilité.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Underlying mechanisms in microbial solar cells: how modeling can help

Using modeling we uncoupled and quantified the different rate constants implicated in microbial solar cells: mediator fluxes in and out of microbes, oxidation at the electrode, photo-reduction inside the microbe, and degradation over time