arXiv subjects

Gerhard Gompper

Publications and source records attributed to Gerhard Gompper.

At least 55 records · Page 3Linked to original sources

arXiv2021

Erythrocyte sedimentation: Fracture and collapse of a high-volume-fraction soft-colloid gel

The erythrocyte sedimentation rate is one of the oldest medical diagnostic methods whose physical mechanisms remain debatable up to date. Using both light microscopy and mesoscale cell-level simulations, we show that erythrocytes form a soft-colloid gel. Furthermore, the high volume fraction of erythrocytes, their deformability, and weak attraction lead to unusual properties of this gel. A theoretical model for the gravitational collapse is developed, whose predictions are in agreement with detailed macroscopic measurements of the interface velocity.

cond-mat.soft↗

arXiv2021

Active turbulence in microswimmer suspensions -- the role of active hydrodynamic stress and volume exclusion

Microswimmers exhibit an intriguing, highly-dynamic collective motion with large-scale swirling and streaming patterns, denoted as active turbulence -- reminiscent of classical high-Reynolds-number hydrodynamic turbulence. Various experimental, numerical, and theoretical approaches have been applied to elucidate similarities and differences to inertial hydrodynamic and active turbulence. These studies reveal a wide spectrum of possible structural and dynamical behaviors of active mesoscale systems, not necessarily consistent with the predictions of the Kolmogorov-Kraichnan theory of turbulence. We use squirmers embedded in a mesoscale fluid, modeled by the multiparticle collision dynamics (MPC) approach, to explore the collective behavior of bacteria-type microswimmers. Our model includes the active hydrodynamic stress generated by propulsion, and a rotlet dipole characteristic for flagellated bacteria. We find emergent clusters, activity-induced phase separation, and swarming, depending on density, active stress, and the rotlet dipole strength. The analysis of the squirmer dynamics in the swarming phase yields Kolomogorov-Kraichnan-type hydrodynamic turbulence and energy spectra for sufficiently high concentrations and strong rotlet dipoles. This emphasizes the paramount importance of the hydrodynamic flow field for swarming and bacterial turbulence.

cond-mat.soft↗

arXiv2021

A generic self-stabilization mechanism for biomolecular adhesions under load

Mechanical loading generally weakens adhesive structures and eventually leads to their rupture. However, biological systems can adapt to loads by strengthening adhesions, which is essential for maintaining the integrity of tissue and whole organisms. Inspired by cellular focal adhesions, we suggest here a generic, molecular mechanism that allows adhesion systems to harness applied loads for self-stabilization under non-equilibrium conditions -- without any active feedback involved. The mechanism is based on conformation changes of adhesion molecules that are dynamically exchanged with a reservoir. Tangential loading drives the occupation of some stretched conformation states out of equilibrium, which, for thermodynamic reasons, leads to association of further molecules with the adhesion cluster. Self-stabilization robustly increases adhesion lifetimes in broad parameter ranges. Unlike for catch-bonds, bond dissociation rates do not decrease with force. The self-stabilization principle can be realized in many ways in complex adhesion-state networks; we show how it naturally occurs in cellular adhesions involving the adaptor proteins talin and vinculin.

physics.bio-ph↗

arXiv2021

Multi-Ciliated Microswimmers -- Metachronal Coordination and Helical Swimming

The dynamics and motion of multi-ciliated microswimmers with a spherical body and a small number N (with 5 < N < 60) of cilia with length comparable to the body radius, is investigated by mesoscale hydrodynamics simulations. A metachronal wave is imposed for the cilia beat, for which the wave vector has both a longitudinal and a latitudinal component. The dynamics and motion is characterized by the swimming velocity, its variation over the beat cycle, the spinning velocity around the main body axis, as well as the parameters of the helical trajectory. Our simulation results show that the microswimmer motion strongly depends on the latitudinal wave number and the longitudinal phase lag. The microswimmers are found to swim smoothly and usually spin around their own axis. Chirality of the metachronal beat pattern generically generates helical trajectories. In most cases, the helices are thin and stretched, i.e. the helix radius is about an order of magnitude smaller than the pitch. The rotational diffusion of the microswimmer is significantly smaller than the passive rotational diffusion of the body alone, which indicates that the extended cilia contribute strongly to the hydrodynamic radius. The swimming velocity vswim is found to increase with the cilia number N with a slightly sublinear power law, consistent with the behavior expected from the dependence of the transport velocity of planar cilia arrays on the cilia separation.

cond-mat.soft↗

arXiv2020

Stability of heterogeneous parallel-bond adhesion clusters under static load

Adhesion interactions mediated by multiple bond types are relevant for many biological and soft matter systems, including the adhesion of biological cells and functionalized colloidal particles to various substrates. To elucidate advantages and disadvantages of multiple bond populations for the stability of heterogeneous adhesion clusters of receptor-ligand pairs, a theoretical model for a homogeneous parallel adhesion bond cluster under constant loading is extended to several bond types. The stability of the entire cluster can be tuned by changing densities of different bond populations as well as their extensional rigidity and binding properties. In particular, bond extensional rigidities determine the distribution of total load to be shared between different sub-populations. Under a gradual increase of the total load, the rupture of a heterogeneous adhesion cluster can be thought of as a multistep discrete process, in which one of the bond sub-populations ruptures first, followed by similar rupture steps of other sub-populations or by immediate detachment of the remaining cluster. This rupture behavior is qualitatively independent of involved bond types, such as slip and catch bonds. Interestingly, an optimal stability is generally achieved when the total cluster load is shared such that loads on distinct bond populations are equal to their individual critical rupture forces. We also show that cluster heterogeneity can drastically affect cluster lifetime.

physics.bio-ph↗

arXiv2020

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.

cond-mat.soft↗

arXiv2020

Wall entrapment of peritrichous bacteria: A mesoscale hydrodynamics simulation study

Microswimmers such as E. Coli bacteria accumulate and exhibit an intriguing dynamics near walls, governed by hydrodynamic and steric interactions. Insight into the underlying mechanisms and predominant interactions demand a detailed characterization of the entrapment process. We employ a mesoscale hydrodynamics simulation approach to study entrapment of a E. coli-type cell at a no-slip wall. The cell is modeled by a spherocylindrical body with several explicit helical flagella. Three stages of the entrapment process can be distinguished: the approaching regime, where a cell swims toward the wall on a nearly straight trajectory; a scattering regime, where the cell touches the wall, with an reorientation; and a surface-swimming regime. Our simulations show that steric interactions may dominate the entrapment process, yet, hydrodynamic interactions slow down the adsorption dynamics close to the boundary and imply a circular motion on the wall. The locomotion of the cell is characterized by a strong wobbling dynamics, with cells preferentially pointing toward the wall.

cond-mat.soft↗

arXiv2020

The physics of active polymers and filaments

Active matter agents consume internal energy or extract energy from the environment for locomotion and force generation. Already rather generic models, such as ensembles of active Brownian particles, exhibit phenomena, which are absent at equilibrium, in particular motility-induced phase separation and collective motion. Further intriguing nonequilibrium effects emerge in assemblies of bound active agents as in linear polymers or filaments. The interplay of activity and conformational degrees of freedom gives rise to novel structural and dynamical features of individual polymers as well as in interacting ensembles. Such out-of-equilibrium polymers are an integral part of living matter, ranging from biological cells with filaments propelled by motor proteins in the cytoskeleton, and RNA/DNA in the transcription process, to long swarming bacteria and worms such as Proteus mirabilis and Caenorhabditis elegans, respectively. Even artificial active polymers have been synthesized. The emergent properties of active polymers or filaments depend on the coupling of the active process to their conformational degrees of freedom, aspects which are addressed in this article. The theoretical models for tangentially and isotropically self-propelled or active-bath driven polymers are presented, both in presence and absence of hydrodynamic interactions. The consequences for their conformational and dynamical properties are examined, emphasizing the strong influence of the coupling between activity and hydrodynamic interactions. Particular features of emerging phenomena, induced by steric and hydrodynamic interactions, are highlighted. Various important, yet theoretically unexplored, aspects are featured and future challenges are discussed.

cond-mat.soft↗

arXiv2020

A minimal model for structure, dynamics, and tension of monolayered cell colonies

The motion of cells in tissues is an ubiquitous phenomenon. In particular, in monolayered cell colonies in vitro, pronounced collective behavior with swirl-like motion has been observed deep within a cell colony, while at the same time, the colony remains cohesive, with not a single cell escaping at the edge. Thus, the colony displays liquid-like properties inside, in coexistence with a cell-free "vacuum" outside. How can adhesion be strong enough to keep cells together, while at the same time not jam the system in a glassy state? What kind of minimal model can describe such a behavior? Which other signatures of activity arise from the internal fluidity? We propose a novel active Brownian particle model with attraction, in which the interaction potential has a broad minimum to give particles enough wiggling space to be collectively in the fluid state. We demonstrate that for moderate propulsion, this model can generate the fluid-vacuum coexistence described above. In addition, the combination of the fluid nature of the colony with cohesion leads to preferred orientation of the cell polarity, pointing outward, at the edge, which in turn gives rise to a tensile stress in the colony -- as observed experimentally for epithelial sheets. For stronger propulsion, collective detachment of cell clusters is predicted. Further addition of an alignment preference of cell polarity and velocity direction results in enhanced coordinated, swirl-like motion, increased tensile stress and cell-cluster detachment.

physics.bio-ph↗

arXiv2020

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.

cond-mat.soft↗

arXiv2020

A Bayesian traction force microscopy method with automated denoising in a user-friendly software package

Adherent biological cells generate traction forces on a substrate that play a central role for migration, mechanosensing, differentiation, and collective behavior. The established method for quantifying this cell-substrate interaction is traction force microscopy (TFM). In spite of recent advancements, inference of the traction forces from measurements remains very sensitive to noise. However, suppression of the noise reduces the measurement accuracy and the spatial resolution, which makes it crucial to select an optimal level of noise reduction. Here, we present a fully automated method for noise reduction and robust, standardized traction-force reconstruction. The method, termed Bayesian Fourier transform traction cytometry, combines the robustness of Bayesian L2 regularization with the computation speed of Fourier transform traction cytometry. We validate the performance of the method with synthetic and real data. The method is made freely available as a software package with a graphical user-interface for intuitive usage.

q-bio.CB↗

arXiv2020

The role of thickness inhomogeneities in hierarchical cortical folding

For long it has been known that specific patterns of folding are necessary for an optimally functioning brain. For instance, lissencephaly and polymicrogyria can lead to severe mental retardation, short life expectancy, epileptic seizures, and tetraplegia. The construction of a quantitative model on how and why these folds appear is the first step in understanding the cause of these conditions. In recent years, there have been various attempts to understand and model the mechanisms of brain folding. Previous works have shown that mechanical instabilities play a crucial role in the formation of brain folds, and that the geometry of the fetal brain is one of the main factors in dictating the folding characteristics. However, modeling higher-order folding, one of the main characteristics of the human brain, has not been fully tackled. The effects of thickness inhomogeneity in the gyrogenesis of the mammalian brain are studied through finite-element simulations of rectangular slabs. The slabs are divided into two distinct regions, where the outer layer mimics the gray matter, and the inner layer the underlying white matter. Differential growth is introduced by only growing the top layer. The brain tissue is modeled as a neo-Hookean hyperelastic material. Simulations are performed with both, homogeneous and inhomogeneous cortical thickness. The homogeneous cortex is shown to fold into a single wavelength, as common for bilayered materials, while the inhomogeneous cortex folds into more complex conformations: In their early stages of development, structures reminiscent of the deep sulci in the brain are obtained. As the cortex continues to develop, secondary undulations, which are shallower and more variable than the structures obtained in earlier gyrification stage emerge, reproducing well-known characteristics of higher-order folding in the mammalian, and particularly the human, brain.

physics.bio-ph↗

arXiv2020

Effect of cytosol viscosity on the flow behavior of red blood cell suspensions in microvessels

The flow behavior of blood in microvessels is directly associated with tissue perfusion and oxygen delivery. Current efforts on modeling blood flow have primarily focused on the flow properties of blood with red blood cells (RBCs) having a viscosity ratio $C$ of unity between the cytosol and suspending medium, while under physiological conditions the cytosol viscosity is about five times larger than the plasma viscosity (i.e., $C\approx 5$). The importance of $C$ for the behavior of single RBCs in fluid flow has already been demonstrated, while the effect of $C$ on blood flow has only been sparsely studied. We employ mesoscopic hydrodynamic simulations to perform a systematic investigation of flow properties of RBC suspensions with different cytosol viscosities for various flow conditions in cylindrical microchannels. Our main aim is to link macroscopic flow properties such as flow resistance to single cell deformation and dynamics as a function of $C$. Starting from a dispersed cell configuration, we find that the flow convergence and the development of a RBC-free layer (RBC-FL) depend only weakly on $C$, and require a convergence length in the range of $25D-50D$, where $D$ is the channel diameter. The flow resistance for $C=5$ is nearly the same as that for $C=1$, which is facilitated by a slightly larger RBC-FL thickness for $C=5$. This effect is due to the suppression of membrane motion and dynamic shape deformations by a more viscous cytosol for $C=5$, resulting in a more compact cellular core of the flow in comparison to $C=1$. The weak effect of cytosol viscosity on the flow resistance and RBC-FL explains why cells can have a high concentration of hemoglobin for efficient oxygen delivery, without a pronounced increase in the flow resistance.

cond-mat.soft↗

arXiv2020

Instability and fingering of interfaces in growing tissue

Interfaces in tissues are ubiquitous, both between tissue and environment as well as between populations of different cell types. The propagation of an interface can be driven mechanically. % e.g. by a difference in the respective homeostatic stress of the different cell types. Computer simulations of growing tissues are employed to study the stability of the interface between two tissues on a substrate. From a mechanical perspective, the dynamics and stability of this system is controlled mainly by four parameters of the respective tissues: (i) the homeostatic stress (ii) cell motility (iii) tissue viscosity and (iv) substrate friction. For propagation driven by a difference in homeostatic stress, the interface is stable for tissue-specific substrate friction even for very large differences of homeostatic stress; however, it becomes unstable above a critical stress difference when the tissue with the larger homeostatic stress has a higher viscosity. A small difference in directed bulk motility between the two tissues suffices to result in propagation with a stable interface, even for otherwise identical tissues. Larger differences in motility force, however, result in a finite-wavelength instability of the interface. Interestingly, the instability is apparently bound by nonlinear effects and the amplitude of the interface undulations only grows to a finite value in time.

q-bio.TO↗

arXiv2020

Enhanced rotational motion of spherical squirmer in polymer solutions

The rotational diffusive motion of a self-propelled, attractive spherical colloid immersed in a solution of self-avoiding polymers is studied by mesoscale hydrodynamic simulations. A drastic enhancement of the rotational diffusion by more than an order of magnitude in the presence of activity is obtained. The amplification is a consequence of two effects, a decrease of the amount of adsorbed polymers by active motion and an asymmetric encounter with polymers on the squirmer surface, which yields an additional torque and random noise for the rotational motion. Our simulations suggest a way to control the rotational dynamics of squirmer-type microswimmers by the degree of polymer adsorption and system heterogeneity.

cond-mat.soft↗

arXiv2020

Hydrodynamic correlations of viscoelastic fluids by multiparticle collision dynamics simulations

The emergent fluctuating hydrodynamics of a viscoelastic fluid modeled by the multiparticle collision dynamics (MPC) approach is studied. The fluid is composed of flexible, Gaussian phantom polymers, which interact by local momentum-conserving stochastic MPC collisions. For comparison, the analytical solution of the linearized Navier-Stokes equation is calculated, where viscoelasticity is taken into account by a time-dependent shear relaxation modulus. The fluid properties are characterized by the transverse velocity autocorrelation function in Fourier space as well as in real space. Various polymer lengths are considered---from dumbbells to (near-)continuous polymers. Viscoelasticity affects the fluid properties and leads to strong correlations, which overall decay exponentially in Fourier space. In real space, the center-of-mass velocity autocorrelation function of individual polymers exhibits a long-time tail independent of polymer length, which decays as $t^{-3/2}$, similar to a Newtonian fluid, in the asymptotic limit $t \to \infty$. Moreover, for long polymers an additional power-law decay appears at time scales shorter than the longest polymer relaxation time with the same time dependence, but negative correlations, and the polymer length dependence $L^{-1/2}$. Good agreement is found between the analytical and simulation results.

cond-mat.soft↗

arXiv2019

The 2019 Motile Active Matter Roadmap

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of active matter in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines.

cond-mat.soft↗

arXiv2019

Vesicles with internal active filaments: self-organized propulsion controls shape, motility, and dynamical response

Self-propulsion and navigation due to the sensing of environmental conditions - such as durotaxis and chemotaxis - are remarkable properties of biological cells that cannot be reproduced by single-component self-propelled particles. We introduce and study "flexocytes", deformable vesicles with enclosed attached self-propelled pushing and pulling filaments that align due to steric and membrane-mediated interactions. Using computer simulations in two dimensions, we show that the membrane deforms under the propulsion forces and forms shapes mimicking motile biological cells, such as keratocytes and neutrophils. When interacting with walls or with interfaces between different substrates, the internal structure of a flexocyte adapts, resulting in a preferred angle of reflection or deflection, respectively. We predict a correlation between motility patterns, shapes, characteristics of the internal forces, and the response to micropatterned substrates and external stimuli. We propose that engineered flexocytes with desired mechanosensitive capabilities enable the construction of soft-matter robots.

cond-mat.soft↗