arXiv subjects

Sebastian Aland

Publications and source records attributed to Sebastian Aland.

At least 19 recordsLinked to original sources

arXiv2026

A phase-field model for viscoelastic compressible tumor growth

It is well known that growing tumors generate and respond to stress in their local microenvironment. Tissue re-arrangements can relax these mechanical stresses and make the tissue more fluid-like. Further, intricate coupling between mechanotransduction and biochemical signaling leads to complex patterns of growth. To predict the outcomes of these nonlinear interactions, we develop a phase-field model to simulate tumors growing into a surrounding medium taking into account their elastic and viscous properties as well as their compressibilities. We couple continuum modeling of the viscoelastic mechanics to the concentration of a diffusible growth-promoting nutrient in a mass conservative way. The phase-field method is a stable and flexible way to describe the dynamics of arbitrarily shaped tumors. We demonstrate convergence of the phase-field model to a sharp interface model in radially symmetric geometries and can observe progression to stationary tumors. However, our results show that these stationary symmetric tumors are subject to symmetry-breaking instabilities in 2D and 3D driven by two primary mechanisms: (i) elastic buckling instabiliies due to differential growth induced by the nutrient gradient and (ii) instabilities generated by apoptosis-related volumetric loss. Further, tissue fluidity and compressibility can lead to changes in tumor topologies. Our modeling framework provides a robust methodology for investigating how tissue mechanics and growth factor signaling influence the progression and invasive potential of solid tumors.

cond-mat.soft↗

arXiv2026

Disorder-induced persistent random motion and trapping of microswimmers

Microorganisms ofter move in confined, disordered environments, where hydrodynamic couplings can modify their transport behavior. Using extensive finite-element simulations, we investigate the dynamics of microswimmers -- modeled as squirmers -- in two-dimensional disordered porous media by resolving the full hydrodynamic interactions. We reveal that the deterministic coupling between activity, hydrodynamics, and disorder is sufficient to generate effective diffusive transport. Strong pushers and pullers become localised in the porous medium either by trapping at corners or dynamic trapping, depending on swimmer type and obstacle packing fraction. Squirmers can escape from dynamic traps, leading to a prominent ``hopping-and--trapping'' dynamics. Strikingly, we find a pusher-puller asymmetry in the trapping probability that can be reversed by short-range swimmer-obstacle interactions, highlighting the sensitivity of transport to near-field effects.

cond-mat.soft↗

arXiv2026

Roadmap for Condensates in Cell Biology

Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants, clarifies key concepts for researchers, funding bodies, and journals. After unifying terminology that often separates disciplines, we outline the core physics of condensate formation, review their biological roles, and identify outstanding challenges in nonequilibrium theory, multiscale simulation, and quantitative in-cell measurements. We close with a forward-looking outlook to guide coordinated efforts toward predictive, experimentally anchored understanding and control of biomolecular condensates.

physics.bio-ph↗

arXiv2025

A numerical approach for the dynamics of active viscoelastic surfaces

The dynamics of active viscoelastic surfaces plays an important role in biological systems. One prominent example is the actin cortex, a thin bio-polymer sheet underneath the outer membrane of biological cells which combines active molecular force generation with viscoelastic behavior characterized by elastic properties at short timescales and viscous properties at longer timescales. We consider a surface Maxwell model within dominant rheology and an additional active term to model the dynamics of the actin cortex. This captures both, shear and dilational surface dynamics. We propose a monolithic numerical approach based on the surface finite element method (SFEM), validate the results for special cases and experimentally demonstrate convergence properties. Moreover, imposing a ring-shaped region of an enhanced active stress mimicking the contractile ring during cytokinesis, we observe different types of emergent patterns and shape dynamics depending on the viscoelastic properties. While viscous surfaces show a ring, which slips to one side of the surface, viscoelasticity provides a stabilization mechanism of the ring, thus forming a requirement for subsequent cell division. This study provides an example that viscoelastic properties are key ingredients to understand biological materials.

physics.bio-ph↗

arXiv2025

Modes of Mechanical Guidance of Adhesion-Independent Cell Migration

Adhesion-independent migration is a prominent mode of cell motility in confined environments, yet the physical principles that guide such movement remain incompletely understood. We present a phase-field model for simulating the motility of deformable, non-adherent cells driven by contractile surface instabilities of the cell cortex. This model couples surface and bulk hydrodynamics, accommodates large shape deformations and incorporates a diffusible contraction-generating molecule (myosin) that drives cortical flows. These capabilities enable a systematic exploration of how mechanical cues direct cell polarization and migration. We first demonstrate that spontaneous symmetry breaking of cortical activity can lead to persistent and directed movement in channels. We then investigate how various physical cues - including gradients in friction, viscosity, and channel width as well as external flows and hydrodynamic interactions between cells - steer migration. Our results show that active surface dynamics can generate stimulus-specific cell behaviors, such as migration up friction gradients or escape from narrow regions. Beyond cell migration, the model offers a versatile platform for exploring the mechanics of active surfaces in biological systems.

physics.bio-ph↗

arXiv2025

Active viscoelastic condensates provide controllable mechanical anchor points

Many biological materials must couple mechanical strength with the ability to rapidly self-assemble at a specific location. In particular, biomolecular condensates readily self-assemble via phase separation, but may also need to resist external forces to fulfil their function. Spatial localisation of condensate formation can be controlled by active cores that preferentially drive the production of condensate material at a particular point, while resistance to external forces can be facilitated by viscoelastic material properties. To investigate the interplay of these two processes, we develop a continuum model of viscoelastic growth around an active core. We find that viscoelastic stresses restrict condensate growth, but also impart resistance to deformation. We investigate the effect of different incorporation schemes on growth dynamics, and test the influence of mechanical properties on condensate strength. Finally, we compare the predictions of our model to experimental data from centrosomes in C. elegans embryos, identifying a parameter regime in which rapid growth can be combined with appropriate mechanical strength, and studying how strain-dependent material incorporation may lead to isotropic growth of scaffold material. Our results provide general design principles for other materials that must reconcile rapid, localised self-assembly with mechanical strength, such as focal adhesions.

physics.bio-ph↗

arXiv2025

High-Throughput Mechanical Characterization of Giant Unilamellar Vesicles by Real-Time Deformability Cytometry

Real-time deformability cytometry (RT-DC) enables high-throughput, contact-free mechanical characterization of soft microscopic objects. Here we apply this technique to giant unilamellar vesicles (GUVs). To interpret vesicle deformation in RT-DC, we present a simulation-based model taking into account the area expansion modulus as the dominant mechanical parameter. Using phase-field simulations over a wide parameter space, we find GUV deformation to depend linearly on GUV area. Based on these results, we derive two complementary fitting strategies for extracting the area expansion modulus K from RT-DC data: a direct model-based fit for single-vesicle characterization and a noise-resistant collective approach that enables robust population-level estimates. Furthermore, we introduce a combined fitting method that integrates both approaches to filter outliers and improve accuracy in heterogeneous or noisy datasets. All methods scale across varying flow rates, channel geometries and buffer viscosities, and produce predictions of K consistent with literature values for different lipid compositions. Compared to traditional techniques such as micropipette aspiration, our approach offers orders of magnitude higher throughput without mechanical contact, making it particularly suitable for GUV population studies. Beyond mechanical phenotyping, this framework opens new avenues for sorting vesicle populations based on membrane mechanics, a capability of growing interest in synthetic biology and soft matter research.

physics.bio-ph↗

arXiv2024

A simulation method for the wetting dynamics of liquid droplets on deformable membranes

Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far little understood. Here, we present a first numerical method to simulate the continuum dynamics of droplets interacting with deformable membranes via wetting. The method combines the advantages of the phase-field method for multi-phase flow simulation and the arbitrary Lagrangian-Eulerian (ALE) method for an explicit description of the elastic surface. The model is thermodynamically consistent, coupling bulk hydrodynamics with capillary forces, as well as bending, tension, and stretching of a thin membrane. The method is validated by comparing simulations for single droplets to theoretical results of shape equations, and its capabilities are illustrated in 2D and 3D axisymmetric scenarios.

cond-mat.soft↗

arXiv2023

A phase-field model for active contractile surfaces

The morphogenesis of cells and tissues involves an interplay between chemical signals and active forces on their surrounding surface layers. The complex interaction of hydrodynamics and material flows on such active surfaces leads to pattern formation and shape dynamics which can involve topological transitions, for example during cell division. To better understand such processes requires novel numerical tools. Here, we present a phase-field model for an active deformable surface interacting with the surrounding fluids. The model couples hydrodynamics in the bulk to viscous flow along the diffuse surface, driven by active contraction of a surface species. As a new feature in phase-field modeling, we include the viscosity of a diffuse interface and stabilize the interface profile in the Stokes-Cahn-Hilliard equation by an auxiliary advection velocity, which is constant normal to the interface. The method is numerically validated with previous results based on linear stability analysis. Further, we highlight some distinct features of the new method, like the avoidance of re-meshing and the inclusion of contact mechanics, as we simulate the self-organized polarization and migration of a cell through a narrow channel. Finally, we study the formation of a contractile ring on the surface and illustrate the capability of the method to resolve topological transitions by a first simulation of a full cell division.

q-bio.CB↗

arXiv2023

A computational model of self-organized shape dynamics of active surfaces in fluids

Mechanochemical processes on surfaces such as the cellular cortex or epithelial sheets, play a key role in determining patterns and shape changes of biological systems. To understand the complex interplay of hydrodynamics and material flows on such active surfaces requires novel numerical tools. Here, we present a finite-element method for an active deformable surface interacting with the surrounding fluids. The underlying model couples surface and bulk hydrodynamics to surface flow of a diffusible species which generates active contractile forces. The method is validated with previous results based on linear stability analysis and shows almost perfect agreement regarding predicted patterning. Away from the linear regime we find rich non-linear behavior, such as the presence of multiple stationary states. We study the formation of a contractile ring on the surface and the corresponding shape changes. Finally, we explore mechanochemical pattern formation on various surface geometries and find that patterning strongly adapts to local surface curvature. The developed method provides a basis to analyze a variety of systems that involve mechanochemical pattern formation on active surfaces interacting with surrounding fluids.

cond-mat.soft↗

arXiv2023

Pulsatory patterns in active viscoelastic fluids with distinct relaxation time scales

Developing tissues need to pattern themselves in space and time. A prevalent mechanism to achieve this are pulsatile active stresses generated by the actin cytoskeleton. Active gel theory is a powerful tool to model the dynamics of cytoskeletal pattern formation. In theoretical models, the influence of the viscoelastic nature of the actin cytoskeleton has so far only been investigated by the incorporation of one viscoelastic relaxation time scale. Here, using a minimal model of active gel theory with a single molecular regulator, we show that distinct shear and areal relaxation times are sufficient to drive pulsatile dynamics in active surfaces.

physics.bio-ph↗

arXiv2022

Chiral flows can induce neck formation in viscoelastic surfaces

During division in animal cells, the actomyosin cortex has been found to exhibit counter-rotating cortical flows, also known as chiral flows, along the axis of division. Furthermore, such chiral surface flows were shown to influence cellular rearrangements and drive the left-right symmetry breaking in developing organisms. In spite of this prospective biological importance, at the current state, no numerical simulations have been done to study the influence of chiral flows on the cell cortex shape. To deepen the insight on that matter, we present here a numerical study of an axi-symmetric viscoelastic surface embedded in a viscous fluid. To investigate the influence of a chiral flow field on the surface shape and material transport, we impose a generic counter-rotating force field on this surface which induces a chiral flow field. Notably, we find that the building of a neck, as is observed during cell division, occurs if there is a strong shear elastic component. Furthermore we find that a large areal relaxation time results in flows towards the equator of the surface. These flows assist the transport of a surface concentration during the forming of a contractile ring. Accordingly, we show that chiral forces by themselves can drive pattern formation and stabilise contractile rings at the equator.

physics.bio-ph↗

arXiv2022

A New Hyperelastic Lookup Table for RT-DC

Real-time deformability cytometry (RT-DC) is an established method that quantifies features like size, shape, and stiffness for whole cell populations on a single-cell level in real time. To extract the cell stiffness, a lookup table (LUT) disentangles the experimentally derived steady state cell deformation and the projected area, yielding the Young's modulus. So far, two lookup tables exists, but are limited to simple linear material models and cylindrical channel geometries. Here, we present two new lookup tables for RT-DC based on a neo-Hookean hyperelastic material numerically derived by simulations based on the finite element method in square and cylindrical channel geometries. At the same time, we quantify the influence of the shear-thinning behaviour of the surrounding medium on the stationary deformation of cells in RT-DC and discuss the applicability and impact of the proposed LUTs regarding past and future RT-DC data analysis. Additionally, we provide insights about the cell strain and stresses, as well as the influence resulting from the rotational symmetric assumption on the cell deformation and volume estimation. The new lookup tables as well as the numerical cell shapes are made freely available.

q-bio.QM↗

arXiv2022

Stick-Slip Contact Line Motion on Kelvin-Voigt Model Substrates

The capillary traction of a liquid contact line causes highly localized deformations in soft solids, tremendously slowing down wetting and dewetting dynamics by viscoelastic braking. Enforcing nonetheless large velocities leads to the so-called stick-slip instability, during which the contact line periodically depins from its own wetting ridge. The mechanism of this periodic motion and, especially, the role of the dynamics in the fluid have remained elusive, partly because a theoretical description of the unsteady soft wetting problem is not available so far. Here we present the first numerical simulations of the full unsteady soft wetting problem, with a full coupling between the liquid and the solid dynamics. We observe three regimes of soft wetting dynamics: steady viscoelastic braking at slow speeds, stick-slip motion at intermediate speeds, followed by a region of viscoelastic braking where stick-slip is suppressed by liquid damping, which ultimately gives way to classical wetting dynamics, dominated by liquid dissipation.

cond-mat.soft↗

arXiv2022

Smart mechanically tunable surfaces with shape memory behavior and wetting-programmable topography

This contribution reports for the first time on fabrication and investigation of wetting properties of structured surfaces containing lamellae with an exceptionally high aspect ratio - height/width ratio demonstrated of 57:1. The lamellar surface was made using a polymer with tunable mechanical properties, and shape-memory behavior. It was found that wetting properties of such structured surfaces depend on temperature and thermal treatment history - lamellae are wetted easier at elevated temperature or after cooling to room temperature when the polymer is soft because of the easier deformability of lamellae. The shape of lamellae deformed by droplets can be temporarily fixed at low temperature and remains fixed upon heating to room temperature. Heating above the transition temperature of the shape-memory polymer restores the orginal shape. The high aspect ratio allows tuning of geometry not only manually, as it is done in most works reported previously, but can also be made by a liquid droplet and is controlled by temperature. The liquid in combination with thermoresponsive topography present a new kind of wetting behavior. Moreover, the mechanical properties can be controlled - the polymer can either be hard or soft at room temperature depending on thermal pre-history. This behavior opens new opportunities for the design of novel smart elements for microfluidic devices such as smart valves, whose state and behavior can be switched by thermal stimuli: valves can or cannot be opened, are able to close or can be fixed in an open or closed states.

cond-mat.soft↗

arXiv2021

Post-buckling Dynamics of Spherical Shells

We explore the intrinsic dynamics of spherical shells immersed in a fluid in the vicinity of their buckled state, through experiments and 3D axisymmetric simulations. The results are supported by a theoretical model that accurately describes the buckled shell as a two-variable-only oscillator. We quantify the effective "softening" of shells above the buckling threshold, as observed in recent experiments on interactions between encapsulated microbubbles and acoustic waves. The main dissipation mechanism in the neighboring fluid is also evidenced.

cond-mat.soft↗

arXiv2021

A numerical method for the simulation of viscoelastic fluid surfaces

Viscoelastic surface rheology plays an important role in multiphase systems. A typical example is the actin cortex which surrounds most animal cells. It shows elastic properties for short time scales and behaves viscous for longer time scales. Hence, realistic simulations of cell shape dynamics require a model capturing the entire elastic to viscous spectrum. However, currently there are no numerical methods to simulate deforming viscoelastic surfaces. Thus models for the cell cortex, or other viscoelastic surfaces, are usually based on assumptions or simplifications which limit their applicability. In this paper we develop a first numerical approach for simulation of deforming viscoelastic surfaces. To this end, we derive the surface equivalent of the upper convected Maxwell model using the GENERIC formulation of nonequilibrium thermodynamics. The model distinguishes between shear dynamics and dilatational surface dynamics. The viscoelastic surface is embedded in a viscous fluid modelled by the Navier-Stokes equation. Both systems are solved using Finite Elements. The fluid and surface are combined using an Arbitrary Lagrange-Eulerian (ALE) Method that conserves the surface grid spacing during rotations and translations of the surface. We verify this numerical implementation against analytic solutions and find good agreement. To demonstrate its potential we simulate the experimentally observed tumbling and tank-treading of vesicles in shear flow. We also supply a phase-diagram to demonstrate the influence of the viscoelastic parameters on the behaviour of a vesicle in shear flow. Finally, we explore cytokinesis as a future application of the numerical method by simulating the start of cytokinesis using a spatially dependent function for the surface tension.

physics.flu-dyn↗

arXiv2020

An ALE method for simulations of axisymmetric elastic surfaces in flow

The dynamics of membranes, shells and capsules in fluid flow has become an active research area in computational physics and computational biology. The small thickness of these elastic materials enables their efficient approximation as a hypersurface which exhibits an elastic response to in-plane stretching and out-of-plane bending, possibly accompanied by a surface tension force. In this work, we present a novel ALE method to simulate such elastic surfaces immersed in Navier-Stokes fluids. The method combines high accuracy with computational efficiency, since the grid is matched to the elastic surface and can therefore be resolved with relatively few grid points. The focus of this work is on axisymmetric shapes and flow conditions which are present in a wide range of biophysical problems. We formulate axisymmetric elastic surface forces and propose a discretization with surface finite-differences coupled to evolving finite elements. We further develop an implicit coupling strategy to reduce time step restrictions. We show in several numerical test cases that accurate results can be achieved at computational times on the order of minutes on a single core CPU. We demonstrate two state-of-the-art applications which to our knowledge cannot be simulated with any other numerical method so far: We present first simulations of the observed shape oscillations of novel microswimming shells and the uniaxial compression of the cortex of a biological cell during an AFM experiment.

physics.comp-ph↗