Ref HAL: hal-03438826_v1
PMID 33861734
DOI: 10.1371/journal.pcbi.1008869
WoS: 000641474200004
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ParAB S , the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS , and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS -anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParB S complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS . In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (≥ 30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional “leaky” boundaries.

Ref HAL: hal-03197323_v1
Ref Arxiv: 2104.03753
DOI: 10.1088/1361-6382/ac1852
Ref. & Cit.: NASA ADS
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Minimal varying $\Lambda$ theories are defined by an action built from the Einstein-Cartan-Holst first order action for gravity with the cosmological constant $\Lambda$ as an independent scalar field, and supplemented by the Euler and Pontryagin densities multiplied by $1/\Lambda$. We identify the canonical structure of these theories which turn out to represent an example of irregular systems. We find five degrees of freedom on generic backgrounds and for generic values of parameters, whereas if the parameters satisfy a certain condition (which includes the most commonly considered Euler case) only three degrees of freedom remain. On de Sitter-like backgrounds the canonical structure changes, and due to an emergent conformal symmetry one degree of freedom drops from the spectrum. We also analyze the self-dual case with an holomorphic action depending only on the self-dual part of the connection. In this case we find two (complex) degrees of freedom, and further discuss the Kodama state, the restriction to de Sitter background and the effect of reality conditions.

Ref HAL: hal-03186214_v1
Ref Arxiv: 2103.06721
Ref INSPIRE: 1851112
DOI: 10.1103/PhysRevD.104.046003
Ref. & Cit.: NASA ADS
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We find a parametrically light dilaton in special confining theories in three dimensions. Their duals form what we call a scion of solutions to the supergravity associated with the large-$N$ limit of the Coulomb branch of the $\mathcal{N}=4$ Super-Yang-Mills theory. The supergravity description contains one scalar with bulk mass that saturates the Breitenlohner-Freedman unitarity bound. The new solutions are defined within supergravity, they break supersymmetry and scale invariance, and one dimension is compactified on a shrinking circle, yet they are completely regular. An approximate dilaton appears in the spectrum of background fluctuations (or composite states in the confining theory), and becomes parametrically light along a metastable portion of the scion of new supergravity solutions, in close proximity of a tachyonic instability. A first-order phase transition separates stable backgrounds, for which the approximate dilaton is not parametrically light, from metastable and unstable backgrounds, for which the dilaton becomes parametrically light, and eventually tachyonic.

Ref HAL: hal-03184640_v1
Ref Arxiv: 2102.13214
DOI: 10.1016/j.coastaleng.2021.103976
WoS: WOS:000702874300002
Ref. & Cit.: NASA ADS
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The Miles theory of wave amplification by wind is extended to the case of finite depth h and a shear flow with (constant) vorticity {\Omega}. Vorticity is characterised through the non-dimensional parameter {\nu} = {\Omega} U_1 /g, where g the gravitational acceleration, U_1 a characteristic wind velocity and k the wavenumber. The notion of 'wave age' is generalised to account for the effect of vorticity. Several widely used growth rates are derived analytically from the dispersion relation of the wind/water interface, and their dependence on both water depth and vorticity is derived and discussed. Vorticity is seen to shift the maximum wave age, similar to what was previously known to be the effect of water depth. At the same time, a novel effect arises and the growth coefficients, at identical wave age and depth, are shown to experience a net increase or decrease according to the shear gradient in the water flow.

Ref HAL: hal-03184622_v1
Ref Arxiv: 2102.02486
Ref. & Cit.: NASA ADS
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We extend the paradigmatic and versatile TASEP (Totally Asymmetric Simple Exclusion Process) for stochastic 1d transport to allow for two different particle species, each having specific entry and exit rates. We offer a complete mean-field analysis, including a phase diagram, by mapping this model onto an effective one-species TASEP. Stochastic simulations confirm the results, but indicate deviations when the particle species have very different exit rates. We illustrate that this is due to a phenomenon of intermittency, and formulate a refined 'intermittent' mean-field (iMF) theory for this regime. We discuss how non-stationary effects may further enrich the phenomenology.

Ref HAL: hal-03184607_v1
DOI: 10.1103/PhysRevD.103.023526
WoS: WOS:000609014700004
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We consider the possibility that the dark sector of our Universe contains a negative cosmological constant dubbed λ. For such models to be viable, the dark sector should contain an additional component responsible for the late-time accelerated expansion rate (X). We explore the departure of the expansion history of these models from the concordanceΛ cold dark matter (ΛCDM) model. For a large class of our models, the accelerated expansion is transient with a nontrivial dependence on the model parameters. All models with wX>−1 will eventually contract and we derive an analytical expression for the scale factor a(t) in the neighborhood of its maximal value. We find also the scale factor for models ending in a Big Rip in the regime where dustlike matter density is negligible compared to λ. We address further the viability of such models, in particular when a high H0 is taken into account. While we find no decisive evidence for a nonzero λ, the best models are obtained with a phantom behavior on redshifts z≳1 with a higher evidence for nonzero λ. An observed value for h substantially higher than 0.70 would be a decisive test of their viability.

Ref HAL: hal-03171939_v1
DOI: 10.1063/5.0038749
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We propose a novel model for a glass-forming liquid which allows to switch in a continuous manner froma standard three-dimensional liquid to a fully connected mean-field model. This is achieved by introducingk additional particle-particle interactions which thus augments the effective number of neighbors of eachparticle. Our computer simulations of this system show that the structure of the liquid does not changewith the introduction of these pseudo neighbours and by means of analytical calculations, we determine thestructural properties related to these additional neighbors. We show that the relaxation dynamics of thesystem slows down very quickly with increasing k and that the onset and the mode-coupling temperaturesincrease. The systems with high values of k follow the MCT power law behaviour for a larger temperaturerange compared to the ones with lower values of k. The dynamic susceptibility indicates that the dynamicheterogeneity decreases with increasing k whereas the non-Gaussian parameter is independent of it. Thus weconclude that with the increase in the number of pseudo neighbours the system becomes more mean-field like.By comparing our results with previous studies on mean-field like system we come to the conclusion that thedetails of how the mean-field limit is approached are important since they can lead to different dynamicalbehavior in this limit.