arXiv subjects

Markus Bär

Publications and source records attributed to Markus Bär.

At least 19 recordsLinked to original sources

arXiv2026

A simple model for conserved intracellular dynamics exhibits multiscale pattern formation, traveling protein domains and arrested coarsening of lipid domains

We model the spatiotemporal dynamics of cellular protein concentrations relevant to cell polarity near membranes composed of different lipids. Therefore, we consider a three-variable continuum model for membrane-bound protein, cytosolic protein, and the local composition of a binary lipid membrane. The model contains two globally conserved quantities: the total protein content and the average fractions of the two lipid species. It combines a conserved reaction-diffusion model for the protein dynamics, undergoing an active phase separation, with a Cahn-Hilliard equation for lipid demixing. Linear stability analysis of the homogeneous steady state and direct numerical simulations show that the lipid dynamics undergoes classical phase separation, whereas the protein dynamics exhibits oscillatory phase separation for intermediate total protein contents, associated with a long-wavelength instability and traveling domains. In parameter regions where both instabilities are present, we find multiscale patterns with larger-scale traveling and rotating protein domains coexisting with smaller-scale stationary lipid domains. In this regime, traveling protein domains coexist with arrested coarsening of stationary lipid domains above a critical coupling. We further show that the main instabilities and phase diagram are well captured by an extension of a recently proposed conserved FitzHugh-Nagumo model for non-reciprocal pattern formation. The extended model consists of two non-reciprocally coupled Cahn-Hilliard equations with different interface tensions, reflecting the distinct physical properties of lipids and proteins. This also explains the observed asymmetry between static lipid patterns and traveling protein patterns.

cond-mat.soft↗

arXiv2024

Pattern selection and the route to turbulence in incompressible polar active fluids

Active fluids, such as suspensions of microswimmers, are known to self-organize into complex spatio-temporal flow patterns. An intriguing example is mesoscale turbulence, a state of dynamic vortex structures exhibiting a characteristic length scale. Here, we employ a minimal model for the effective microswimmer velocity field to explore how the turbulent state develops from regular vortex patterns when the strength of activity resp. related parameters such as nonlinear advection or polar alignment strength - is increased. First, we demonstrate analytically that the system, without any spatial constraints, develops a stationary square vortex lattice in the absence of nonlinear advection. Subsequently, we perform an extended stability analysis of this nonuniform "ground state" and uncover a linear instability, which follows from the mutual excitement and simultaneous growth of multiple perturbative modes. This extended analysis is based on linearization around an approximation of the analytical vortex lattice solution and allows us to calculate critical activity parameters. Above these critical values, the vortex lattice develops into mesoscale turbulence in numerical simulations. Utilizing the numerical approach, we uncover an extended region of hysteresis where both patterns are possible depending on the initial condition. Here, we find that turbulence persists below the instability of the vortex lattice. We further determine the stability of square vortex patterns as a function of their wavenumber and represent the results analogous to the well-known Busse balloons known from classical pattern-forming systems. Here, the region of stable periodic patterns shrinks and eventually disappears with increasing activity parameters. Our results show that the strength of activity plays a similar role for active turbulence as the Reynolds number does in driven flow exhibiting inertial turbulence.

cond-mat.soft↗

arXiv2022

MedalCare-XL: 16,900 healthy and pathological 12 lead ECGs obtained through electrophysiological simulations

Mechanistic cardiac electrophysiology models allow for personalized simulations of the electrical activity in the heart and the ensuing electrocardiogram (ECG) on the body surface. As such, synthetic signals possess known ground truth labels of the underlying disease and can be employed for validation of machine learning ECG analysis tools in addition to clinical signals. Recently, synthetic ECGs were used to enrich sparse clinical data or even replace them completely during training leading to improved performance on real-world clinical test data. We thus generated a novel synthetic database comprising a total of 16,900 12 lead ECGs based on electrophysiological simulations equally distributed into healthy control and 7 pathology classes. The pathological case of myocardial infraction had 6 sub-classes. A comparison of extracted features between the virtual cohort and a publicly available clinical ECG database demonstrated that the synthetic signals represent clinical ECGs for healthy and pathological subpopulations with high fidelity. The ECG database is split into training, validation, and test folds for development and objective assessment of novel machine learning algorithms.

physics.med-ph↗

arXiv2022

Ising-like critical behavior of vortex lattices in an active fluid

Turbulent vortex structures emerging in bacterial active fluids can be organized into regular vortex lattices by weak geometrical constraints such as obstacles. Here we show, using a continuum-theoretical approach, that the formation and destruction of these patterns exhibit features of a continuous second-order equilibrium phase transition, including long-range correlations, divergent susceptibility, and critical slowing down. The emerging vorticity field can be mapped onto a two-dimensional (2D) Ising model with antiferromagnetic nearest-neighbor interactions by coarse-graining. The resulting effective temperature is found to be proportional to the strength of the nonlinear advection in the continuum model.

cond-mat.soft↗

arXiv2021

Biophysics underlying the swarm to biofilm transition

Bacteria organize in a variety of collective states, from swarming, which has been attributed to rapid surface exploration, to biofilms, which are highly dense immobile communities attributed to stress resistance. It has been suggested that biofilm and swarming are oppositely controlled, making this transition particularly interesting for understanding the ability of bacterial colonies to adapt to challenging environments. Here, the swarm to biofilm transition is studied experimentally by analyzing the bacterial dynamics both on the individual and collective scales. We show that both biological and physical processes facilitate the transition - a few individual cells that initiate the biofilm program cause nucleation of large, scale-free stationary aggregates of trapped swarm cells. Around aggregates, cells continue swarming almost unobstructed, while inside, trapped cells slowly transform to biofilm. While our experimental findings rule out previously suggested purely physical effects as a trigger for biofilm formation, they show how physical processes, such as clustering and jamming, accelerate biofilm formation.

physics.bio-ph↗

arXiv2021

Turbulence-induced clustering in compressible active fluids

We study a novel phase of active polar fluids, which is characterized by the continuous creation and destruction of dense clusters due to self-sustained turbulence. This state arises due to the interplay of the self-advection of the aligned swimmers and their defect topology. The typical cluster size is determined by the characteristic vortex size. Our results are obtained by investigating a continuum model of compressible polar active fluids, which incorporates typical experimental observations in bacterial suspensions by assuming a non-monotone dependence of speed on density.

cond-mat.soft↗

arXiv2020

Motility-Induced Clustering and Meso-Scale Turbulence in Active Polar Fluids

Meso-scale turbulence was originally observed experimentally in various suspensions of swimming bacteria, as well as in the collective motion of active colloids. The corresponding large-scale dynamical patterns were reproduced in a simple model of a polar fluid, assuming a constant density of active particles. Recent, more detailed experimental studies revealed additional interesting aspects, such as anomalous velocity statistics and clustering phenomena. Those phenomena cannot be explained by currently available models for active polar fluids. Herein, we extend the continuum model suggested by Dunkel et al. to include density variations and a feedback between the local density and self-propulsion speed of the active particles. If the velocity decreases strong enough with the density, a linear stability analysis of the resulting model shows that, in addition to the short-wavelength instability of the original model, a long-wavelength instability occurs. This is typically observed for high densities of polar active particles and is analogous to the well-known phenomenon of motility-induced phase separation (MIPS) in scalar active matter. We determine a simple phase diagram indicating the linear instabilities and perform systematic numerical simulations for the various regions in the corresponding parameter space. The interplay between the well understood short-range instability and the long-range instability leads to interesting dynamics and novel phenomena concerning nucleation and coarsening processes. Our simulation results display a rich variety of novel patterns, including phase separation into domains with dynamically changing irregularly shaped boundaries. Anomalous velocity statistics are observed in all phases where the system segregates into regions of high and low densities. This offers a simple explanation for their occurrence in recent experiments with bacterial suspensions.

cond-mat.soft↗

arXiv2020

Efficient Bayesian inversion for shape reconstruction of lithography masks

Background: Scatterometry is a fast, indirect and non-destructive optical method for quality control in the production of lithography masks. To solve the inverse problem in compliance with the upcoming need for improved accuracy, a computationally expensive forward model has to be defined which maps geometry parameters to diffracted light intensities. Aim: To quantify the uncertainties in the reconstruction of the geometry parameters, a fast to evaluate surrogate for the forward model has to be introduced. Approach: We use a non-intrusive polynomial chaos based approximation of the forward model which increases speed and thus enables the exploration of the posterior through direct Bayesian inference. Additionally, this surrogate allows for a global sensitivity analysis at no additional computational overhead. Results: This approach yields information about the complete distribution of the geometry parameters of a silicon line grating, which in return allows to quantify the reconstruction uncertainties in the form of means, variances and higher order moments of the parameters. Conclusion: The use of a polynomial chaos surrogate allows to quantify both parameter influences and reconstruction uncertainties. This approach is easy to use since no adaptation of the expensive forward model is required.

physics.data-an↗

arXiv2019

Self-Propelled Rods: Insights and Perspectives for Active Matter

A wide range of experimental systems including gliding, swarming and swimming bacteria, in-vitro motility assays as well as shaken granular media are commonly described as self-propelled rods. Large ensembles of those entities display a large variety of self-organized, collective phenomena, including formation of moving polar clusters, polar and nematic dynamic bands, mobility-induced phase separation, topological defects and mesoscale turbulence, among others. Here, we give a brief survey of experimental observations and review the theoretical description of self-propelled rods. Our focus is on the emergent pattern formation of ensembles of dry self-propelled rods governed by short-ranged, contact mediated interactions and their wet counterparts that are also subject to long-ranged hydrodynamic flows. Altogether, self-propelled rods provide an overarching theme covering many aspects of active matter containing well-explored limiting cases. Their collective behavior not only bridges the well-studied regimes of polar self-propelled particles and active nematics, and includes active phase separation, but also reveals a rich variety of new patterns.

cond-mat.stat-mech↗

arXiv2019

A phase diagram for bacterial swarming

Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize a surface. Physically, swarming is a natural example of active particles that use energy to generate motion. Accordingly, understanding the constraints physics imposes on the dynamics is essential to understand the mechanisms underlying the swarming phenomenon. We present new experiments of swarming Bacillus subtilis mutants with different aspect ratios and densities. Analyzing the dynamics reveals a rich phase diagram of qualitatively distinct swarming regimes, describing how the shape and density of cells govern the global dynamical characteristics of the entire swarm. Moreover, we show that under standard conditions bacteria inhabit a region of phase space that is associated with rapid mixing and robust dynamics, with homogeneous density and no preferred direction of motion. This contrasts characteristic clustering behavior of self-propelled rods that is recovered only for very elongated mutant species. Thus, bacteria have adapted their physics to optimize the principle functions assumed for swarming.

cond-mat.soft↗

arXiv2019

An efficient approach to global sensitivity analysis and parameter estimation for line gratings

Scatterometry is a fast, indirect and nondestructive optical method for the quality control in the production of lithography masks. Geometry parameters of line gratings are obtained from diffracted light intensities by solving an inverse problem. To comply with the upcoming need for improved accuracy and precision and thus for the reduction of uncertainties, typically computationally expansive forward models have been used. In this paper we use Bayesian inversion to estimate parameters from scatterometry measurements of a silicon line grating and determine the associated uncertainties. Since the direct application of Bayesian inference using Markov-Chain Monte Carlo methods to physics-based partial differential equation (PDE) model is not feasible due to high computational costs, we use an approximation of the PDE forward model based on a polynomial chaos expansion. The expansion provides not only a surrogate for the PDE forward model, but also Sobol indices for a global sensitivity analysis. Finally, we compare our results for the global sensitivity analysis with the uncertainties of estimated parameters.

physics.data-an↗

arXiv2018

Asymmetric pattern formation in microswimmer suspensions induced by orienting fields

This paper studies the influence of orienting external fields on pattern formation, particularly mesoscale turbulence, in microswimmer suspensions. To this end, we apply a hydrodynamic theory that can be derived from a microscopic microswimmer model [Phys. Rev. E 97, 022613 (2018)]. The theory combines a dynamic equation for the polar order parameter with a modified Stokes equation for the solvent flow. Here, we extend the model by including an external field that exerts an aligning torque on the swimmers (mimicking the situation in chemo-, photo-, magneto- or gravitaxis). Compared to the field-free case, the external field breaks the rotational symmetry of the vortex dynamics and leads instead to strongly asymmetric, traveling stripe patterns, as demonstrated by numerical solution and linear stability analysis. We further analyze the emerging structures using a reduced model which involves only an (effective) microswimmer velocity field. This model is significantly easier to handle analytically, but still preserves the main features of the asymmetric pattern formation. We observe an underlying transition between a square vortex lattice and a traveling stripe pattern. These structures can be well described in the framework of weakly nonlinear analysis, provided the strength of nonlinear advection is sufficiently weak.

cond-mat.soft↗

arXiv2018

Oscillatory motion of a droplet in an active poroelastic two-phase model

We investigate flow-driven amoeboid motility as exhibited by microplasmodia of Physarum polycephalum. A poroelastic two-phase model with rigid boundaries is extended to the case of free boundaries and substrate friction. The cytoskeleton is modeled as an active viscoelastic solid permeated by a fluid phase describing the cytosol. A feedback loop between a chemical regulator, active mechanical deformations, and induced flows gives rise to oscillatory and irregular motion accompanied by spatio-temporal contraction patterns. We cover extended parameter regimes of active tension and substrate friction by numerical simulations in one spatial dimension and reproduce experimentally observed oscillation periods and amplitudes. In line with experiments, the model predicts alternating forward and backward ectoplasmatic flow at the boundaries with reversed flow in the center. However, for all cases of periodic and irregular motion, we observe practically no net motion. A simple theoretical argument shows that directed motion is not possible with a spatially independent substrate friction.

cond-mat.soft↗

arXiv2018

Derivation of a hydrodynamic theory for mesoscale dynamics in microswimmer suspensions

In this paper we systematically derive a fourth-order continuum theory capable of reproducing mesoscale turbulence in a three-dimensional suspension of microswimmers. We start from overdamped Langevin equations for a generic microscopic model (pushers or pullers), which include hydrodynamic interactions on both, small length scales (polar alignment of neighboring swimmers) and large length scales, where the solvent flow interacts with the order parameter field. The flow field is determined via the Stokes equation supplemented by an ansatz for the stress tensor. In addition to hydrodynamic interactions, we allow for nematic pair interactions stemming from excluded-volume effects. The results here substantially extend and generalize earlier findings [Phys. Rev. E 94, 020601(R) (2016)], in which we derived a two-dimensional hydrodynamic theory. From the corresponding mean-field Fokker-Planck equation combined with a self-consistent closure scheme, we derive nonlinear field equations for the polar and the nematic order parameter, involving gradient terms of up to fourth order. We find that the effective microswimmer dynamics depends on the coupling between solvent flow and orientational order. For very weak coupling corresponding to a high viscosity of the suspension, the dynamics of mesoscale turbulence can be described by a simplified model containing only an effective microswimmer velocity.

cond-mat.soft↗

arXiv2017

Determining the Refractive Index of Human Hemoglobin Solutions by Kramers-Kronig Relations with an Improved Absorption Model

The real part of the refractive index (RI) of aqueous solutions of human hemoglobin is computed from their absorption spectra in the wavelength range $250\,{\rm nm} - 1100\,{\rm nm}$ using the Kramers-Kronig (KK) relations and the corresponding uncertainty analysis is provided. The strong ultraviolet (UV) and infrared absorbance of the water outside this spectral range were taken into account in a previous study employing KK relations. We improve these results by including the concentration dependence of the water absorbance as well as by modeling the deep UV absorbance of hemoglobin's peptide backbone. The two free parameters of the model for the deep UV absorbance are fixed by a global fit.

physics.bio-ph↗

arXiv2017

Extinction spectra of suspensions of microspheres: Determination of spectral refractive index and particle size distribution with nanometer accuracy

A method is presented to infer simultaneously the wavelength-dependent real refractive index (RI) of the material of microspheres and their size distribution from extinction measurements of particle suspensions. To derive the averaged spectral optical extinction cross section of the microspheres from such ensemble measurements, we determined the particle concentration by flow cytometry to an accuracy of typically 2% and adjusted the particle concentration to ensure that perturbations due to multiple scattering are negligible. For analysis of the extinction spectra we employ Mie theory, a series-expansion representation of the refractive index and nonlinear numerical optimization. In contrast to other approaches, our method offers the advantage to simultaneously determine size, size distribution and spectral refractive index of ensembles of microparticles including uncertainty estimation.

physics.optics↗

arXiv2016

Mesoscale pattern formation of self-propelled rods with velocity reversal

We study self-propelled particles with velocity reversal interacting by uniaxial (nematic) alignment within a coarse-grained hydrodynamic theory. Combining analytical and numerical continuation techniques, we show that the physics of this active system is essentially controlled by the reversal frequency. In particular, we find that elongated, high-density, ordered patterns, called bands, emerge via subcritical bifurcations from spatially homogeneous states. Our analysis reveals further that the interaction of bands is weakly attractive and, consequently, bands fuse upon collision in analogy with nonequilibrium nucleation processes. Moreover, we demonstrate that a renormalized positive line tension can be assigned to stable bands below a critical reversal rate, beyond which they are transversally unstable. In addition, we discuss the kinetic roughening of bands as well as their nonlinear dynamics close to the threshold of transversal instability. Altogether, the reduction of the multi-particle system onto the dynamics of bands provides a framework to understand the impact of the reversal frequency on the emerging nonequilibrium patterns in self-propelled particle systems. In this regard, our results constitute a proof-of-principle in favor of the hypothesis in microbiology that reversal of gliding rod-shaped bacteria regulates the occurrence of various self-organized pattens observed during life-cycle phases.

cond-mat.stat-mech↗

arXiv2016

Diffusion properties of active particles with directional reversal

The diffusion properties of self-propelled particles which move at constant speed and, in addition, reverse their direction of motion repeatedly are investigated. The internal dynamics of particles triggering these reversal processes is modeled by a stochastic clock. The velocity correlation function as well as the mean squared displacement is investigated and, furthermore, a general expression for the diffusion coefficient for self-propelled particles with directional reversal is derived. Our analysis reveals the existence of an optimal, finite rotational noise amplitude which maximizes the diffusion coefficient. We comment on the relevance of these results with regard to microbiological systems and suggest further experiments in this context.

physics.bio-ph↗