Bacterial swarmer cells in confinement: A mesoscale hydrodynamic simulation study

A wide spectrum of Peritrichous bacteria undergo considerable physiological changes when they are inoculated onto nutrition-rich surfaces and exhibit a rapid and collective migration denoted as swarming. Thereby, the length of such swarmer cells and their number of flagella increases substantially. In this article, we investigated the properties of individual E. coli-type swarmer cells confined between two parallel walls via mesoscale hydrodynamic simulations, combining molecular dynamics simulations of the swarmer cell with the multiparticle particle collision dynamics approach for the embedding fluid. E. coli-type swarmer cells are three-times longer than their planktonic counter parts, but their flagella density is comparable. By varying the wall separation, we analyze the confinement effect on the flagella arrangement, on the distribution of cells in the gap between the walls, and on the cell dynamics. We find only a weak dependence of confinement on the bundle structure and dynamics. The distribution of cells in the gap changes from a geometry-dominated behavior for very narrow to fluid-dominated behavior for wider gaps, where cells are preferentially located in the gap center for narrower gaps and stay preferentially next to one of the walls for wider gaps. Dynamically, the cells exhibit a wide spectrum of migration behaviors, depending on their flagella bundle arrangement, and ranges from straight swimming to wall rolling

Hydrodynamics of polymers in an active bath

The conformational and dynamical properties of active polymers in solution are determined by the nature of the activity, and the behavior of polymers with self-propelled, active Brownian particle-type monomers differs qualitatively from that of polymers with monomers driven externally by colored noise forces. We present simulation and theoretical results for polymers in solution in the presence of external active noise. In simulations, a semiflexible bead-spring chain is considered, in analytical calculations, a continuous linear wormlike chain. Activity is taken into account by independent monomer/site velocities, with orientations changing in a diffusive manner. In simulations, hydrodynamic interactions (HI) are taken into account by the Rotne-Prager-Yamakawa tensor, or by an implementation of the active polymer in the multiparticle collision dynamics approach for fluids. To arrive at an analytical solution, the preaveraged Oseen tensor is employed. The active process implies a dependence of the stationary-state properties on HI via polymer relaxation times. With increasing activity, HI lead to an enhanced swelling of flexible polymers, and the conformational properties differ substantially from those of polymers with self-propelled monomers in presence of HI or free-draining polymers. The polymer mean square displacement is enhanced by HI. Over a wide range of time scales, hydrodynamics leads to a subdiffusive regime of the site mean square displacement for flexible active polymers, with an exponent of (5/7), larger than that of the Rouse (1/2) and Zimm (2/3) models of passive polymers.Comment: 16 pages, 11 figure

Hydrodynamics of Binary Fluid Mixtures - An Augmented Multiparticle Collison Dynamics Approach

The Multiparticle Collision Dynamics technique (MPC) for hydrodynamics simulations is generalized to binary fluid mixtures and multiphase flows, by coupling the particle-based fluid dynamics to a Ginzburg-Landau free-energy functional for phase-separating binary fluids. To describe fluids with a non-ideal equation of state, an additional density-dependent term is introduced. The new approach is verified by applying it to thermodynamics near the critical demixing point, and interface fluctuations of droplets. The interfacial tension obtained from the analysis of the capillary wave spectrum agrees well with the results based on the Laplace-Young equation. Phase-separation dynamics follows the Lifshitz-Slyozov law

Active Brownian filaments with hydrodynamic interactions: conformations and dynamics

The conformational and dynamical properties of active self-propelled filaments/polymers are investigated in the presence of hydrodynamic interactions by both, Brownian dynamics simulations and analytical theory. Numerically, a discrete linear chain composed of active Brownian particles is considered, analytically, a continuous linear semiflexible polymer with active velocities changing diffusively. The force-free nature of active monomers is accounted for - no Stokeslet fluid flow induced by active forces - and higher order hydrodynamic multipole moments are neglected. The nonequilibrium character of the active process implies a dependence of the stationary-state properties on HI via the polymer relaxation times. In particular, at moderate activities, HI lead to a substantial shrinkage of flexible and semiflexible polymers to an extent far beyond shrinkage of comparable free-draining polymers; even flexible HI-polymers shrink, while active free-draining polymers swell monotonically. Large activities imply a reswelling, however, to a less extent than for non-HI polymers, caused by the shorter polymer relaxation times due to hydrodynamic interactions. The polymer mean square displacement is enhanced, and an activity-determined ballistic regime appears. Over a wide range of time scales, flexible active polymers exhibit a hydrodynamically governed subdiffusive regime, with an exponent significantly smaller than that of the Rouse and Zimm models of passive polymers. Compared to simulations, the approximate analytical approach predicts a weaker hydrodynamic effect

Studi sui tratti di qualità negativa nelle nuove viti mediamente resistenti alle malattie fungine

The varieties of vines tolerant to the main fungal diseases are the object of growing interest because they require fewer treatments for the production of quality grapes. These varieties are considered qualitatively unsuitable especially for some characteristics such as the foxy aroma, the level of anthocyanin diglucosides and the level of methyl alcohol in wines. In the three-year period 2016-2018, from a population of 74 medium resistant varieties placed in a single collection, in Marlengo (BZ), young leaves were taken for DNA analysis; annually 2 surveys of the OIV 452 453, 455 and 456 descriptors were carried out, and, at 18° Brix, sombunches were collected for the analysis of different metabolites. Nano-vinifications were carried out for 32 genotypes. Genotypes with different levels of stacked loci associated with resistance to downy and powdery mildew were detected, with different resistance behaviors over the years. Only some genotypes have aromas of foxy and only 20% of the genotypes analyzed have levels of anthocyanin diglucosides higher than the levels required by current legislation. Some vinifications showed methanol levels higher than the legal limit set. High percentages of genotypes respected the legal levels of metabolites required by current regulations and only genotypes with the presence of V. labrusca showed the aroma of foxy

Microswimmers - from active brownian polymers to swarming bacteria

In this thesis, a theoretical approach is applied to study active matter systems. First, we investigate the collective behavior of linearly connected active Brownian particles within the framework of an analytic theory approach, and, second, we analyse the swimming characteristics of bacteria, such as E. coli, by means of computer simulations. We find a distinct influence of motility on semiflexible filaments. A chain of active particles results in more than just the sum of its parts and gives rise to novel phenomena. In particular, activity strongly influences the conformational properties. We find that flexible filaments stretch with increasing activity, whereas rather stiff filaments are softened due to the activity, which then leads to a contraction of the chain for intermediate activities. However, beyond a certain threshold, the filament starts to swell again, but in a flexible-chain-like manner. Moreover, activity changes drastically the relaxation behavior and, hence, the dynamics of the filament. Furthermore, hydrodynamic interactions change via the coupling with the activity the conformation of the chain, in contrast to passive polymers. Thereby, it appears to be important whether the activity is an intrinsic property of the chain, or is induced by an external field. Also the dynamics is strongly influenced by the hydrodynamic interactions and shows a distinctly different behaviour compared to a passive polymer in dilute solution. We study the swimming behavior of bacterial swarmer cells using a detailed simulation model for the bacterial body and the flagella. The embedding fluid is modelled via the multiparticle collision dynamics simulation approach. We consider fluid films of different thicknesses, and cells with various arrangements of flagella. Overall, we find rather heterogeneous flagellar bundle conformations and cell dynamics. Specifically, confinement influences the bundle structure and the swimming pattern of the cell. Thereby, we find a transition from curved to straight swimming trajectories for surface-separation distances below trice the body diameter. In addition, we find a slight increase of the swimming speed in narrow slits. Contrary to experimental observation, we find a lower migration speed for swarmer cells compared to planktonic swimmer cells. This aspect needs further investigations. Moreover, we study a raft of P. mirabilis-like swarmer cells, a bacterial strain of cells with extremely elongated bodies and hundreds of flagella. Thereby, we focus on cell-cell interactions, specifically on the inter-cell flagellar bundle formation. We find, for the first time using computer simulations bundling of flagella belonging to adjacent cells

Path integral description of semiflexible active Brownian polymers

Semiflexible polymers comprised of active Brownian particles (ABPOs) exhibit intriguing activity-driven conformational and dynamical features. Analytically, the generic properties of ABPOs can be obtained in a mean-field description applying the Gaussian semiflexi- ble polymer model. In this article, we derive a path integral representation of the stationary-state distribution function of such ABPOs, based on the stationary-state distribution function of the normal mode amplitudes following from the Langevin equation of motion. The path integral includes characteristic semiflexible polymer contributions from entropy and bending energy, with activity depen- dent coefficients, and, in addition, activity-induced torsional and higher order correlations along the polymer contour. Focusing on a semiflexible polymer approximation, we determine various properties such as the tangent-vector correlation function, effective persis- tence length, and the mean-square end-to-end distance. The latter reflects the characteristic features of ABPOs, and good quantitative agreement is obtained with the full solution for larger activities, specifically for flexible polymers. Moreover, the approximation indi- cates the relevance of torsional and higher order contour correlations for the ABPO conformations. In general, the ABPO path integral illustrates how colored noise (active fluctuations) affects semiflexible polymer conformations in comparison to white noise thermal fluctuations

Internal dynamics of semiflexible polymers with active noise

The intramolecular dynamics of flexible and semiflexible polymers in response to active noise is studied theoretically. The active noise may either originate from interactions of a passive polymer with a bath of active Brownian particles or the polymer itself is comprised of active Brownian particles. We describe the polymer by the continuous Gaussian semiflexible-polymer model, taking into account the finite polymer extensibility. Our analytical calculations predict a strong dependence of the polymer dynamics on the activity. In particular, active semiflexible polymers exhibit a crossover from a bending elasticity-dominated dynamics at weak activity to that of flexible polymers at strong activity. The end-to-end vector correlation function decays exponentially for times longer than the longest polymer relaxation time. Thereby, the polymer relaxation determines the decay of the correlation function for long and flexible polymers. For shorter and stiffer polymers, the relaxation behavior of individual active Brownian particles dominates the decay above a certain activity. The diffusive dynamics of a polymer is substantially enhanced by the activity. Three regimes can be identified in the mean square displacement for sufficiently strong activities: an activity-induced ballistic regime at short times, followed by a Rouse-type polymer-specific regime for any polymer stiffness, and free diffusion at long times, again determined by the activity

Conformational Properties of Active Semiflexible Polymers

The conformational properties of flexible and semiflexible polymers exposed to active noise are studied theoretically. The noise may originate from the interaction of the polymer with surrounding active (Brownian) particles or from the inherent motion of the polymer itself, which may be composed of active Brownian particles. In the latter case, the respective monomers are independently propelled in directions changing diffusively. For the description of the polymer, we adopt the continuous Gaussian semiflexible polymer model. Specifically, the finite polymer extensibility is taken into account, which turns out to be essential for the polymer conformations. Our analytical calculations predict a strong dependence of the relaxation times on the activity. In particular, semiflexible polymers exhibit a crossover from a bending elasticity-dominated dynamics to the flexible polymer dynamics with increasing activity. This leads to a significant activity-induced polymer shrinkage over a large range of self-propulsion velocities. For large activities, the polymers swell and their extension becomes comparable to the contour length. The scaling properties of the mean square end-to-end distance with respect to the polymer length and monomer activity are discussed