The behavior of semiflexible polymers under external fields is numerically studied.

The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions are investigated by Brownian multi-particle collision dynamics. Different scenarios will be considered: tethered polymers subject to an external force, chains under steady shear flow [1], and filaments with either both [2] or one fixed end [3] under oscillatory shear flow. The results of the numerical studies will be presented and discussed. [1] A. Lamura and R. G. Winkler, Semiflexible polymers under external fields confined to two dimensions, J. Chem. Phys. 137, 244909 (2012) [2] A. Lamura and R. G. Winkler, Tethered semiflexible polymer under large amplitude oscillatory shear, Polymers 11, 737 (2019) [3] A. Lamura, R. G. Winkler, and G. Gompper, Wall-anchored semiflexible polymer under oscillating shear flow, pre-print (2020)

The phase separation of a two-dimensional active binary mixture is studied under the action of an applied shear through numerical simulations. It is highlighted how the strength of the external flow modifies the initial shape of growing domains. The activity is responsible for the formation of isolated droplets which affect both the coarsening dynamics and the morphology of the system. The characteristic dimensions of domains along the flow and the shear direction are modulated in time by oscillations whose amplitudes are reduced when the activity increases. This induces a broadening of the distribution functions of domain lengths with respect to the passive case due to the presence of dispersed droplets of different sizes.

The properties of semiflexible polymers tethered by one end to an impenetrable wall and exposed to oscillatory shear flow are investigated by mesoscale simulations. A polymer, confined in two dimensions, is described by a linear bead-spring chain, and fluid interactions are incorporated by the Brownian multiparticle collision dynamics approach. At small strain, the polymers follow the applied flow field. However, at high strain, we find a strongly nonlinear response with major conformational changes. Polymers are stretched along the flow direction and exhibit U-shaped conformations while following the flow. As a consequence of confinement in the half-space, frequency doubling in the time-dependent polymer properties appears along the direction normal to the wall.

We numerically study by lattice Boltzmann simulations the rheological properties of an active emulsion made of a suspension of an active polar gel embedded in an isotropic passive background. We find that the hexatic equilibrium configuration of polar droplets is highly sensitive to both active injection and external forcing and may either lead to asymmetric unidirectional states which break top-bottom symmetry or symmetric ones. In this latter case, for large enough activity, the system develops a shear thickening regime at low shear rates. Importantly, for larger external forcing a regime with stable negative effective viscosity is found. Moreover, at intermediate activity a region of multistability is encountered and we show that a maximum entropy production principle holds in selecting the most favorable state.

The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions under oscillatory shear flow are investigated by Brownian multi-particle collision dynamics. Two different scenarios will be considered: Filaments with both fixed ends [1] and wall-anchored chains [2].The results of the numerical studies will be presented and discussed. 1] A. Lamura, R. G. Winkler, 'Tethered semiflexible polymer under large amplitude oscillatory shear', Polymers 11, 737 (2019) [2] A. Lamura, R. G. Winkler, G. Gompper, 'Wall-anchored semiflexible polymer under large oscillatory shear flow', pre-print (2021)

The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions under oscillatory shear flow are investigated by Brownian multi-particle collision dynamics. Two different scenarios will be considered: Filaments with both fixed ends [1] and wall-anchored chains [2]. The results of the numerical studies will be presented and discussed. References [1] A. Lamura, R. G. Winkler Polymers 2019, 11, 737. DOI:10.3390/polym11040737 [2] A. Lamura, R. G. Winkler, G. Gompper pre-print 2021

The use of a mathematical model is proposed in order to denoise X-ray two-dimensional patterns. The method relies on a generalized diffusion equation whose diffusion constant depends on the image gradients. The numerical solution of the diffusion equation provides an efficient reduction of pattern noise as witnessed by the computed peak of signal-to-noise ratio. The use of experimental data with different inherent levels of noise allows us to show the success of the method even in the case, experimentally relevant, when patterns are blurred by Poissonian noise. The corresponding MatLab code for the numerical method is made available.

The phase-separation process of a binary mixture with order-parameter-dependent mobility under shear flow is numerically studied. The ordering is characterized by an alternate stretching and bursting of domains which produce oscillations in the physical observables. The amplitude of such modulations reduce in time when the mobility vanishes in the bulk phase, disfavoring the growth of bubbles coming from bursted domains. We propose two equations for the typical sizesR(x)andR(y)of domains finding the long-time behaviorsR(x)similar to t(5/4)andR(y)similar to t(1/4)in the flow and shear directions, respectively, in the case of surface diffusion. A reduction of the excess viscosity with increasing shear rate is observed in simulations.

We use computer simulations to study the morphology and rheological properties of a bidimensional emulsion resulting from a mixture of a passive isotropic fluid and an active contractile polar gel, in the presence of a surfactant that favours the emulsification of the two phases. By varying the intensity of the contractile activity and of an externally imposed shear flow, we find three possible morphologies. For low shear rates, a simple lamellar state is obtained. For intermediate activity and shear rate, an asymmetric state emerges, which is characterized by shear and concentration banding at the polar/isotropic interface. A further increment in the active forcing leads to the self-assembly of a soft channel where an isotropic fluid flows between two layers of active material. We characterize the stability of this state by performing a dynamical test varying the intensity of the active forcing and shear rate. Finally, we address the rheological properties of the system by measuring the effective shear viscosity, finding that this increases as active forcing is increased-so that the fluid thickens with activity.

The rheological behaviour of an emulsion made of an active polar component and an isotropic passive fluid is studied by lattice Boltzmann methods. Different flow regimes are found by varying the values of the shear rate and extensile activity (occurring, e.g., in microtubule-motor suspensions). By increasing the activity, a first transition occurs from the linear flow regime to spontaneous persistent unidirectional macro-scale flow, followed by another transition either to a (low shear) intermittent flow regime with the coexistence of states with positive, negative, and vanishing apparent viscosity, or to a (high shear) symmetric shear thinning regime. The different behaviours can be explained in terms of the dynamics of the polarization field close to the walls. A maximum entropy production principle selects the most likely states in the intermittent regime.

The properties of a semiflexible polymer with fixed ends under oscillatory shear flow are investigated by numerical simulations. The polymer is confined in two dimensions and is modeled as a worm-like chain. The interaction with the fluid is taken into account by the Brownian multiparticle collision dynamics approach. For small shear rates, a linear oscillatory response appears. However, at high shear rates, we find a strongly nonlinear behavior with the polymer wrapping around the fixation points and shrinking. The polymer center of mass is distributed on a spatial curve resembling a lima\c{c}on with an inhomogeneous distribution. Normal-mode correlation functions are changed by shear and a frequency doubling is observed at high shear rates. An even-odd asymmetry for the Cartesian components of the correlation functions is found with rather similar spectra for odd $x$- and even $y$-modes and vice versa. Our study yields an interesting nonlinear behavior of anchored semiflexible polymers under oscillatory shear flow. Preliminary results for the case of a semiflexible polymer with one fixed end exposed to oscillatory shear will be also provided.

Abstract inviato a Conferenza Internazionale "Statistical Mechanics and Field Theory 2019" - Bari 11-13/12/2019

The properties of a semiflexible polymer with fixed ends exposed to oscillatory shear flow are investigated by simulations. The two-dimensionally confined polymer is modeled as a linear bead-spring chain, and the interaction with the fluid is described by the Brownian multiparticle collision dynamics approach. For small shear rates, the tethering of the ends leads to a more-or-less linear oscillatory response. However, at high shear rates, we found a strongly nonlinear reaction, with a polymer (partially) wrapped around the fixation points. This leads to an overall shrinkage of the polymer. Dynamically, the location probability of the polymer center-of-mass position is largest on a spatial curve resembling a limacon, although with an inhomogeneous distribution. We found shear-induced modifications of the normal-mode correlation functions, with a frequency doubling at high shear rates. Interestingly, an even-odd asymmetry for the Cartesian components of the correlation functions appears, with rather similar spectra for odd x- and even y-modes and vice versa. Overall, our simulations yielded an intriguing nonlinear behavior of tethered semiflexible polymers under oscillatory shear flow.

Cell motility is crucial to biological functions ranging from wound healing to immune response. The physics of cell crawling on a substrate is by now well understood, whilst cell motion in bulk (cell swimming) is far from being completely characterized. We present here a minimal model for pattern formation within a compressible actomyosin gel, in both 2D and 3D, which shows that contractility leads to the emergence of an actomyosin droplet within a low density background. This droplet then becomes self-motile for sufficiently large motor contractility. These results may be relevant to understand the essential physics at play in 3D cell swimming within compressible fluids. We report results of both 2D and 3D numerical simulations, and show that the compressibility of actomyosin plays an important role in the transition to motility.

The morphology of a mixture made of a polar active gel immersed in an isotropic passive fluid is studied numerically. Lattice Boltzmann method is adopted to solve the Navier-Stokes equation and coupled to a finite-difference scheme used to integrate the dynamic equations of the concentration and of the polarization of the active component. By varying the relative amounts of the mixture phases, different structures can be observed. In the contractile case, at moderate values of activity, elongated structures are formed when the active component is less abundant, while a dynamic emulsion of passive droplets in an active matrix is obtained for symmetric composition. When the active component is extensile, aster-like rotating droplets and a phase-separated pattern appear for asymmetric and symmetric mixtures, respectively. The relevance of space dimensions in the overall morphology is shown by studying the system in three dimensions in the case of extensile asymmetric mixtures where interconnected tube-like structures span the whole system.

We present here a comparison between collision-streaming and finite-difference lattice Boltzmann (LB) models. This study provides a derivation of useful formulae which help one to properly compare the simulation results obtained with both LB models. We consider three physical problems: the shock wave propagation, the damping of shear waves, and the decay of Taylor-Green vortices, often used as benchmark tests. Despite the different mathematical and computational complexity of the two methods, we show how the physical results can be related to obtain relevant quantities.

In this paper an in silico study of the behavior of an active polar emulsion is reported, focusing on the case of a highly off-symmetric ratio between the polar (active) and passive components, both for the extensile and contractile case. In absence of activity the system is characterized by an hexatic-ordered droplets phase. We find that small extensile activity is able to enhance the hexatic order in the array of droplets with respect to the passive case, while increasing activity aster-like rotating droplets appear. In contractile systems activity creates shear flows and elongated structures are formed.

We review the state of the art of active fluids with particular attention to hydrodynamic continuous models and to the use of Lattice Boltzmann Methods (LBM) in this field. We present the thermodynamics of active fluids, in terms of liquid crystals modelling adapted to describe large-scale organization of active systems, as well as other effective phenomenological models. We discuss how LBM can be implemented to solve the hydrodynamics of active matter, starting from the case of a simple fluid, for which we explicitly recover the continuous equations by means of Chapman-Enskog expansion. Going beyond this simple case, we summarize how LBM can be used to treat complex and active fluids. We then review recent developments concerning some relevant topics in active matter that have been studied by means of LBM: spontaneous flow, self-propelled droplets, active emulsions, rheology, active turbulence, and active colloids.

The dynamics of a quasi two-dimensional isotropic droplet in a cholesteric liquid crystal medium under symmetric shear flow is studied by lattice Boltzmann simulations. We consider a geometry in which the flow direction is along the axis of the cholesteric, as this setup exhibits a significant viscoelastic response to external stress. We find that the dynamics depends on the magnitude of the shear rate, the anchoring strength of the liquid crystal at the droplet interface and the chirality. While low shear rate and weak interface anchoring the system shows a non-Newtonian behavior, a Newtonian-like response is observed at high shear rate and strong interface anchoring. This is investigated both by estimating the secondary flow profile, namely a flow emerging along the out-of-plane direction (absent in fully-Newtonian fluids, such as water) and by monitoring defect formation and dynamics, which significantly alter the rheological response of the system.