- Home

[hal-02468189] Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles (02/06/2020)
Moins

We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending-or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.

[hal-02537855] Monte Carlo and Molecular Dynamics Simulations to Explain Biomembrane Meso-Patterning by a Composition-Curvature Coupling Mechanism (10/04/2020)
Plus

[...]

[hal-02518096] Quantum tunneling rate of dilute axion stars close to the maximum mass (08/07/2020)
Plus

We compute the quantum tunneling rate of dilute axion stars close to the maximum mass [P.H. Chavanis, Phys. Rev. D {\bf 84}, 043531 (2011)] using the theory of instantons. We confirm that the lifetime of metastable states is extremely long, scaling as $t_{\rm life}\sim e^N\, t_D$ (except close to the critical point), where $N$ is the number of axions in the system and $t_D$ is the dynamical time ($N\sim 10^{57}$ and $t_D\sim 10\, {\rm hrs}$ for typical QCD axion stars; $N\sim 10^{96}$ and $t_D\sim 100\, {\rm Myrs}$ for the quantum core of a dark matter halo made of ultralight axions). Therefore, metastable equilibrium states can be considered as stable equilibrium states in practice. We develop a finite size scaling theory close to the maximum mass and predict that the collapse time at criticality scales as $t_{\rm coll}\sim N^{1/5}t_D$ instead of being infinite as when fluctuations are neglected. The collapse time is smaller than the age of the universe for QCD axion stars and larger than the age of the universe for dark matter cores made of ultralight axions. We also consider the thermal tunneling rate and reach the same conclusions. We compare our results with similar results obtained for Bose-Einstein condensates in laboratory, globular clusters in astrophysics, and quantum field theory in the early Universe.

[hal-02470203] Kinetic theory of one-dimensional homogeneous long-range interacting systems sourced by 1/N2 effects (28/02/2020)
Plus

[...]

[hal-02459834] Galaxy Formation with BECDM - II. Cosmic Filaments and First Galaxies (08/07/2020)
Plus

Bose–Einstein condensate dark matter (BECDM, also known as fuzzy dark matter) is motivated by fundamental physics and has recently received significant attention as a serious alternative to the established cold dark matter (CDM) model. We perform cosmological simulations of BECDM gravitationally coupled to baryons and investigate structure formation at high redshifts (z ≳ 5) for a boson mass m = 2.5 × 10^−22 eV, exploring the dynamical effects of its wavelike nature on the cosmic web and the formation of first galaxies. Our BECDM simulations are directly compared to CDM as well as to simulations where the dynamical quantum potential is ignored and only the initial suppression of the power spectrum is considered – a warm dark matter-like (‘WDM’) model often used as a proxy for BECDM. Our simulations confirm that ‘WDM’ is a good approximation to BECDM on large cosmological scales even in the presence of the baryonic feedback. Similarities also exist on small scales, with primordial star formation happening both in isolated haloes and continuously along cosmic filaments; the latter effect is not present in CDM. Global star formation and metal enrichment in these first galaxies are delayed in BECDM/‘WDM’ compared to the CDM case: in BECDM/‘WDM’ first stars form at z ∼ 13/13.5, while in CDM star formation starts at z ∼ 35. The signature of BECDM interference, not present in ‘WDM’, is seen in the evolved dark matter power spectrum: although the small-scale structure is initially suppressed, power on kpc scales is added at lower redshifts. Our simulations lay the groundwork for realistic simulations of galaxy formation in BECDM.

[hal-02416956] Energy balance of a Bose gas in a curved space-time (08/07/2020)
Plus

Classical solutions of the Klein–Gordon equation are used in astrophysics to model galactic halos of scalar field dark matter and compact objects such as cores of neutron stars. These bound solutions are interpreted as Bose–Einstein condensates whose particle number density is governed by the Gross–Pitaevskii (GP) equation. It is well known that the Gross–Pitaevskii–Poisson (GPP) system arises as the non-relativistic limit of the Klein–Gordon–Einstein (KGE) equations and, conversely, the KGE system may be interpreted as a generalization of the GPP equations in a curved space-time. In the present work, we consider a 3+1 ADM foliation of the space-time in order to construct a general-relativistic version of the GP equation. Besides, we derive a general energy balance equation for the boson gas in the hydrodynamic variables, where different energy potentials are identified as kinetic, quantum, electromagnetic and gravitational. In addition, we find a correspondence between the energy potentials in the balance equation and actual components of the scalar energy–momentum tensor. We also study the Newtonian limit of the hydrodynamic formulation and the balance equation. As an illustrative case, we study the effects in the energy potentials of a relativistic correction in the GP equation.

[hal-02393253] Collective Information Processing in Human Phase Separation (17/03/2020)
Plus

Social media filters combined with recommender systems can lead to the emergence of filter bubbles and polarized groups. In addition, segregation processes of human groups in certain social contexts have been shown to share some similarities with phase separation phenomena in physics. Here, we study the impact of information filtering on collective segregation behavior. We report a series of experiments where groups of 22 subjects have to perform a collective segregation task that mimics the tendency of individuals to bond with other similar individuals. More precisely, the participants are each assigned a color (red or blue) unknown to them, and have to regroup with other subjects sharing the same color. To assist them, they are equipped with an artificial sensory device capable of detecting the majority color in their ``environment'' (defined as their $k$ nearest neighbors, unbeknownst to them), for which we control the perception range, $k=1,3,5,7,9,11,13$. We study the separation dynamics (emergence of unicolor groups) and the properties of the final state, and show that the value of $k$ controls the quality of the segregation, although the subjects are totally unaware of the precise definition of the ``environment''. We also find that there is a perception range $k=7$ above which the ability of the group to segregate does not improve. We introduce a model that precisely describes the random motion of a group of pedestrians in a confined space, and which faithfully reproduces and allows to interpret the results of the segregation experiments. Finally, we discuss the strong and precise analogy between our experiment and the phase separation of two immiscible materials at very low temperature.

[hal-02338378] Implosion-explosion in supernovae (08/07/2020)
Plus

We sketch a scenario for the explosion of massive stars (supernovae) that differs from published scenarios of explosions as a two-step process, an initial gravitational core collapse followed by an expansion of matter after a bouncing on the core, which meet difficulties. Our simple model, based on fluid mechanics and stability properties of the equilibrium state, shows that one can have a simultaneous inward/outward motion in the early stage of the instability of the star. This shows up by slowly sweeping a saddle-center bifurcation found when considering equilibrium states associated with the constraint of energy conservation (microcanonical ensemble) instead of the constraint of a fixed temperature (canonical ensemble). After the weakly nonlinear Painlevé regime, we show that the strongly nonlinear regime displays a self-similar behavior of the core collapse. Finally, the expansion of the remnants is revisited as an isentropic process leading to shocks formation.

[hal-02338342] Supernova implosion-explosion in the light of catastrophe theory (09/07/2020)
Plus

The present understanding of supernova explosion of massive stars as a two-step process, with an initial gravitational collapse toward the center of the star followed by an expansion of matter after a bouncing on the core, meets several difficulties. We show that it is not the only possible one: a simple model based on fluid mechanics, catastrophe theory, and stability properties of the equilibrium state shows that one can have also a simultaneous inward/outward motion in the early stage of the instability of the supernova described by a dynamical saddle-center bifurcation. The existence of this simultaneous inward/outward motion is sensitive to the model in such systems with long-range interactions. If a constant temperature is assumed (canonical ensemble), an overall inward motion occurs, but if one imposes with the same equation of state the constraint of energy conservation (microcanonical ensemble) there is an inward velocity field near the center of the star together with an outward velocity field in the rest of the star. We discuss the expansion stage of the remnants away from the collapsed core, and propose a new explanation for the formation of shock waves in the ejecta which differs from the usual Sedov–Taylor self-similar description.

[hal-02337217] A data-driven method for reconstructing and modelling social interactions in moving animal groups (28/02/2020)
Plus

Group-living organisms that collectively migrate range from cells and bacteria to human crowds, and include swarms of insects, schools of fish and flocks of birds or ungulates. Unveiling the behavioural and cognitive mechanisms by which these groups coordinate their movements is a challenging task. These mechanisms take place at the individual scale and they can be described as a combination of pairwise interactions between individuals and interactions between these individuals and the physical obstacles in the environment. Thanks to the development of novel tracking techniques that provide large and accurate data sets, the main characteristics of indivi\-dual and collective behavioural patterns can be quantified with an unprecedented level of precision. However, in a large number of works, social interactions are usually described by force map methods that only have a limited capacity of explanation and prediction, being rarely suitable for a direct implementation in a concise and explicit mathematical model. Here, we present a general method to extract the interactions between individuals that are involved in the coordination of collective movements in groups of organisms. We then apply this method to characterize social interactions in two species of shoaling fish, the rummy-nose tetra (Hemigrammus rhodostomus) and the zebrafish (Danio rerio), which both present a burst-and-coast motion. The detailed quantitative description of microscopic individual-level interactions thus provides predictive models of the emergent dynamics observed at the macroscopic group-level. This method can be applied to a wide range of biological and social systems.

[hal-02337175] Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish (28/02/2020)
Plus

Coordinated motion and collective decision-making in fish schools result from complex interactions by which individuals integrate information about the behavior of their neighbors. However, little is known about how individuals integrate this information to take decisions and control their movements. Here, we combine experiments with computational and robotic approaches to investigate the impact of different strategies for a fish to interact with its neighbors on collective swimming in groups of rummy-nose tetra (Hemigrammus rhodostomus). By means of a data-based agent model describing the inter\-actions between pairs of H.~rhodostomus (Calovi et al., 2018), we show that the simple addition of the pairwise interactions with two neighbors quantitatively reproduces the collective behavior observed in groups of five fish. Increasing the number of interacting neighbors does not significantly improve the simulation results. Remarkably, we find that groups remain cohesive and polarized even when each agent only interacts with only one of its neighbors: the one that has the strongest contribution to the heading variation of the focal agent. However, group cohesion is lost when each agent only interacts with its nearest neighbor. We~then investigate by means of a swarm robotic platform the collective motion in groups of five robots. Our platform combines the implementation of the fish behavioral model and an engineering-minded control system to deal with real-world physical constraints. We find that swarms of robots are able to reproduce the behavioral patterns observed in groups of five fish when each robot only interacts with its neighbor having the strongest effect on its heading variation, whereas increasing the number of interacting neighbors does not significantly improve the group coordination. Overall, our results suggest that fish have to acquire only a minimal amount of information about their environment to coordinate their movements when swimming in groups.

[hal-02337096] La danse organisée des bancs de poissons (28/02/2020)
Plus

Grâce au développement de nouvelles techniques de suivi de trajectoires et d'analyse de données comportementales, les scientifiques parviennent à reconstruire et à modéliser les interactions sociales entre des poissons au sein d'un banc. Interactions qui gouvernent leurs déplacements collectifs.

[hal-02323999] Switching between individual and collective motility in B lymphocytes is controlled by cell-matrix adhesion and inter-cellular interactions (03/07/2020)
Plus

Lymphocytes alternate between phases of individual migration across tissues and phases of clustering during activation and function. The range of lymphocyte motility behaviors and the identity of the factors that govern them remain elusive. To explore this point, we here collected unprecedented statistics pertaining to cell displacements, cell:matrix and cell:cell interactions using a model B cell line as well as primary human B lymphocytes. At low cell density, individual B lymphocytes displayed a high heterogeneity in their speed and diffusivity. Beyond this intrinsic variability, B lymphocytes adapted their motility to the composition of extra-cellular matrix, adopting slow persistent walks over collagen IV and quick Brownian walks over fibronectin. At high cell density, collagen IV favored the self-assembly of B lymphocytes into clusters endowed with collective coordination, while fibronectin stimulated individual motility. We show that this behavioral plasticity is controlled by acto-myosin dependent adhesive and Arp2/3-dependent protrusive actin pools, respectively. Our study reveals the adaptive nature of B lymphocyte motility and group dynamics, which are shaped by an interplay between and cell:matrix and cell:cell interactions.

[hal-02309051] Gravitational phase transitions and instabilities of self-gravitating fermions in general relativity (08/07/2020)
Plus

We discuss the occurrence of gravitational phase transitions and instabilities in a gas of self-gravitating fermions within the framework of general relativity. In the classical (nondegenerate) limit, the system undergoes a gravitational collapse at low energies E<Ec and low temperatures T<Tc . This is called “gravothermal catastrophe” in the microcanonical ensemble and “isothermal collapse” in the canonical ensemble. When quantum mechanics is taken into account and when the particle number is below the Oppenheimer-Volkoff limit ( N<NOV ), complete gravitational collapse is prevented by the Pauli exclusion principle. In that case, the Fermi gas undergoes a gravitational phase transition from a gaseous phase to a condensed phase. The condensed phase represents a compact object like a white dwarf, a neutron star, or a dark matter fermion ball. When N>NOV , there can be a subsequent gravitational collapse below a lower critical energy E<Ec″ or a lower critical temperature T<Tc′ leading presumably to the formation of a black hole. The evolution of the system is different in the microcanonical and canonical ensembles. In the microcanonical ensemble, the system takes a “core-halo” structure. The core consists in a compact quantum object or a black hole while the hot halo is expelled at large distances. This is reminiscent of the red giant structure of low-mass stars or the implosion-explosion of massive stars (supernova). In the canonical ensemble, the system collapses as a whole towards a compact object or a black hole. This is reminiscent of the implosion of supermassive stars (hypernova).

Transition vitreuse Glass transition Wisdom of crowds Phase separation Phase transition Violent relaxation Random tilings Random process Adsorption Mouvement brownien Ions close to interfaces Dark matter halo 9862Gq 9535+d Gravitation Black hole Processus stochastique 9536+x Chemotaxie Entropy DNA Dark matter Statistical Mechanics AQUEOUS-SOLUTIONS Brownian motion AIR/WATER INTERFACE Structure Automatic Keywords Gravitation collapse Collapse Potential quantum Smoluchowski-Poisson Effondrement gravitationnel Nonrelativistic Competition Bose–Einstein condensates 9880Jk Scalar field theory Thermodynamics Statistical mechanics Stability Théorème du viriel Fokker-Planck Self-gravitating systems Physique statistique Fermi gas Euler-Maclaurin Diffusion 9880-k Quasicrystals Cosmology Asymptotic expansion Suppression Long-range interactions Bethe ansatz Computational modeling Interacting agents Generalized thermodynamics Metastable states Aboav law Formation Condensation Bose-Einstein Scalar field Axion star Denaturation Quantum mechanics Absorption ADN Self-organization Catastrophe theory Keller-Segel Smoluchowski equation Apprentissage par Projet General relativity Turbulence Perturbation theory TASEP Random walker Quantum chromodynamics axion Field theory scalar Gravitational collapse AQUEOUS-SOLUTION Evaporation Collisionless stellar-systems Membrane transport 0440-b Angle-action variables Polytrope Marcheur aléatoire Wave function Energy high Nanofiltration Game theory Astrophysics and astroparticle physics Persistence Virial theorem Critical phenomena Hydrodynamics Chemotaxis 9530Sf