arXiv subjects

Andrej Kosmrlj

Publications and source records attributed to Andrej Kosmrlj.

16 recordsLinked to original sources

arXiv2022

Linear Viscoelastic Response of the Vertex Model with Internal and External Dissipation: Normal Modes Analysis

We use the normal mode formalism to study the shear rheology of the vertex model for epithelial tissue mechanics in the overdamped linear response regime. We consider systems with external (e.g., cell-substrate) and internal (e.g., cell-cell) dissipation mechanisms, and derive expressions for stresses on cells due to mechanical and dissipative forces. The semi-analytical method developed here is, however, general and can be directly applied to study the linear response of a broad class of soft matter systems with internal and external dissipation. It involves normal mode decomposition to calculate linear loss and storage moduli of the system. Specifically, displacements along each normal mode produce stresses due to elastic deformation and internal dissipation, which are in force balance with loads due to external dissipation. Each normal mode responds with a characteristic relaxation timescale, and its rheological behavior can be described as a combination of a standard linear solid element due to elastic stresses and a Jeffreys model element due to the internal dissipative stresses. The total response of the system is then fully determined by connecting in parallel all the viscoelastic elements corresponding to individual normal modes. This allows full characterization of the potentially complex linear rheological response of the system at all driving frequencies and identification of collective excitations. We show that internal and external dissipation mechanisms lead to qualitatively different rheological behaviors due to the presence or absence of Jeffreys elements, which is particularly pronounced at high driving frequencies. Our findings, therefore, underscore the importance of microscopic dissipation mechanisms in understanding the rheological behavior of soft materials and tissues, in particular.

cond-mat.soft↗

arXiv2022

Linear Viscoelastic Properties of the Vertex Model for Epithelial Tissues

Epithelial tissues act as barriers and, therefore, must repair themselves, respond to environmental changes and grow without compromising their integrity. Consequently, they exhibit complex viscoelastic rheological behavior where constituent cells actively tune their mechanical properties to change the overall response of the tissue, e.g., from solid-like to fluid-like. Mesoscopic mechanical properties of epithelia are commonly modeled with the vertex model. While previous studies have predominantly focused on the rheological properties of the vertex model at long time scales, we systematically studied the full dynamic range by applying small oscillatory shear and bulk deformations in both solid-like and fluid-like phases for regular hexagonal and disordered cell configurations. We found that the shear and bulk responses in the fluid and solid phases can be described by standard spring-dashpot viscoelastic models. Furthermore, the solid-fluid transition can be tuned by applying pre-deformation to the system. Our study provides insights into the mechanisms by which epithelia can regulate their rich rheological behavior.

cond-mat.soft↗

arXiv2020

Designing morphology of separated phases in multicomponent liquid mixtures

Phase separation of multicomponent liquid mixtures plays an integral part in many processes ranging from industry to cellular biology. In many cases the morphology of coexisting phases is crucially linked to the function of the separated mixture, yet it is unclear what determines morphology when multiple phases are present. We developed a graph theory approach to predict the topology of coexisting phases from a given set of surface energies (forward problem), enumerate all topologically distinct morphologies, and reverse engineer conditions for surface energies that produce the target morphology (inverse problem).

cond-mat.soft↗

arXiv2020

Buckling of thermalized elastic sheets

Steady progress in the miniaturization of structures and devices has reached a scale where thermal fluctuations become relevant and it is thus important to understand how such fluctuations affect their mechanical stability. Here, we investigate the buckling of thermalized sheets and we demonstrate that thermal fluctuations increase the critical buckling load due to the enhanced scale-dependent bending rigidity for sheets that are much larger than a characteristic thermal length scale. The presented results are universal and apply to a wide range of microscopic sheets. These results are especially relevant for atomically thin 2D materials, where thermal fluctuations can significantly increase the critical buckling load because the thermal length scale is on the order of nanometers at room temperature.

cond-mat.soft↗

arXiv2020

Method of image charges for describing linear deformation of bounded 2D solid structures with circular holes and inclusions

We present a method for predicting the linear response deformation of finite and semi-infinite 2D solid structures with circular holes and inclusions by employing the analogies with image charges and induction in electrostatics. Charges in electrostatics induce image charges near conductive boundaries and an external electric field induces polarization (dipoles, quadrupoles, and other multipoles) of conductive and dielectric objects. Similarly, charges in elasticity induce image charges near boundaries and external stress induces polarization (quadrupoles and other multipoles) inside holes and inclusions. Stresses generated by these induced elastic multipoles as well as stresses generated by their images near boundaries then lead to interactions between holes and inclusions and with their images, which induce additional polarization and thus additional deformation of holes and inclusions. We present a method that expands induced polarization in a series of elastic multipoles, which systematically takes into account the interactions of inclusions and holes with the external field, between them, and with their images. The results of our method for linear deformation of circular holes and inclusions near straight and curved boundaries show good agreement with both linear finite element simulations and experiments.

cond-mat.soft↗

arXiv2020

Elastic multipole method for describing linear deformation of infinite 2D solid structures with circular holes and inclusions

Elastic materials with holes and inclusions are important in a large variety of contexts ranging from construction material to biological membranes. More recently, they have also been exploited in mechanical metamaterials, where the geometry of highly deformable structures is responsible for their unusual properties, such as negative Poisson's ratio, mechanical cloaking, and tunable phononic band gaps. Understanding how such structures deform in response to applied external loads is thus crucial for designing novel mechanical metamaterials. Here we present a method for predicting the linear response of infinite 2D solid structures with circular holes and inclusions by employing analogies with electrostatics. Just like an external electric field induces polarization (dipoles, quadrupoles and other multipoles) of conductive and dielectric objects, external stress induces elastic multipoles inside holes and inclusions. Stresses generated by these induced elastic multipoles then lead to interactions between holes and inclusions, which induce additional polarization and thus additional deformation of holes and inclusions. We present a method that expands the induced polarization in a series of elastic multipoles, which systematically takes into account the interactions of inclusions and holes with the external stress field and also between them. The results of our method show good agreement with both linear finite element simulations and experiments.

cond-mat.soft↗

arXiv2019

Non-uniform growth and surface friction determine bacterial biofilm morphology on soft substrates

During development, organisms acquire three-dimensional shapes with important physiological consequences. While the basic mechanisms underlying morphogenesis are known in eukaryotes, it is often difficult to manipulate them in vivo. To circumvent this issue, here we present a study of developing Vibrio cholerae biofilms grown on agar substrates in which the spatiotemporal morphological patterns were altered by varying the agar concentration. Expanding biofilms are initially flat, but later experience a mechanical instability and become wrinkled. Whereas the peripheral region develops ordered radial stripes, the central region acquires a zigzag herringbone-like wrinkle pattern. Depending on the agar concentration, the wrinkles initially appear either in the peripheral region and propagate inward (low agar concentration) or in the central region and propagate outward (high agar concentration). To understand these experimental observations, we developed a model that considers diffusion of nutrients and their uptake by bacteria, bacterial growth/biofilm matrix production, mechanical deformation of both the biofilm and the agar, and the friction between them. Our model demonstrates that depletion of nutrients beneath the central region of the biofilm results in radially-dependent growth profiles, which in turn, produce anisotropic stresses that dictate the morphology of wrinkles. Furthermore, we predict that increasing surface friction (agar concentration) reduces stress anisotropy and shifts the location of the maximum compressive stress, where the wrinkling instability first occurs, toward the center of the biofilm, in agreement with our experimental observations. Our results are broadly applicable to bacterial biofilms with similar morphologies and also provide insight into how other bacterial biofilms form distinct wrinkle patterns.

physics.bio-ph↗

arXiv2018

Phase behavior and morphology of multicomponent liquid mixtures

Multicomponent systems are ubiquitous in nature and industry. While the physics of few-component liquid mixtures (i.e., binary and ternary ones) is well-understood and routinely taught in undergraduate courses, the thermodynamic and kinetic properties of $N$-component mixtures with $N>3$ have remained relatively unexplored. An example of such a mixture is provided by the intracellular fluid, in which protein-rich droplets phase separate into distinct membraneless organelles. In this work, we investigate equilibrium phase behavior and morphology of $N$-component liquid mixtures within the Flory-Huggins theory of regular solutions. In order to determine the number of coexisting phases and their compositions, we developed a new algorithm for constructing complete phase diagrams, based on numerical convexification of the discretized free energy landscape. Together with a Cahn-Hilliard approach for kinetics, we employ this method to study mixtures with $N=4$ and $5$ components. We report on both the coarsening behavior of such systems, as well as the resulting morphologies in three spatial dimensions. We discuss how the number of coexisting phases and their compositions can be extracted with Principal Component Analysis (PCA) and K-Means clustering algorithms. Finally, we discuss how one can reverse engineer the interaction parameters and volume fractions of components in order to achieve a range of desired packing structures, such as nested `Russian dolls' and encapsulated Janus droplets.

cond-mat.soft↗

arXiv2017

Non-Hookean statistical mechanics of clamped graphene ribbons

Thermally fluctuating sheets and ribbons provide an intriguing forum in which to investigate strong violations of Hooke's Law: large distance elastic parameters are in fact not constant, but instead depend on the macroscopic dimensions. Inspired by recent experiments on free-standing graphene cantilevers, we combine the statistical mechanics of thin elastic plates and large-scale numerical simulations to investigate the thermal renormalization of the bending rigidity of graphene ribbons clamped at one end. For ribbons of dimensions $W\times L$ (with $L\geq W$), the macroscopic bending rigidity $κ_R$ determined from cantilever deformations is independent of the width when $W<\ell_\textrm{th}$, where $\ell_\textrm{th}$ is a thermal length scale, as expected. When $W>\ell_\textrm{th}$, however, this thermally renormalized bending rigidity begins to systematically increase, in agreement with the scaling theory, although in our simulations we were not quite able to reach the system sizes necessary to determine the fully developed power law dependence on $W$. When the ribbon length $L > \ell_p$, where $\ell_p$ is the $W$-dependent thermally renormalized ribbon persistence length, we observe a scaling collapse and the beginnings of large scale random walk behavior.

cond-mat.soft↗

arXiv2016

Statistical mechanics of thin spherical shells

We explore how thermal fluctuations affect the mechanics of thin amorphous spherical shells. In flat membranes with a shear modulus, thermal fluctuations increase the bending rigidity and reduce the in-plane elastic moduli in a scale-dependent fashion. This is still true for spherical shells. However, the additional coupling between the shell curvature, the local in-plane stretching modes and the local out-of-plane undulations, leads to novel phenomena. In spherical shells thermal fluctuations produce a radius-dependent negative effective surface tension, equivalent to applying an inward external pressure. By adapting renormalization group calculations to allow for a spherical background curvature, we show that while small spherical shells are stable, sufficiently large shells are crushed by this thermally generated "pressure". Such shells can be stabilized by an outward osmotic pressure, but the effective shell size grows non-linearly with increasing outward pressure, with the same universal power law exponent that characterizes the response of fluctuating flat membranes to a uniform tension.

cond-mat.soft↗

arXiv2015

Response of thermalized ribbons to pulling and bending

Motivated by recent free-standing graphene experiments, we show how thermal fluctuations affect the mechanical properties of microscopically thin solid ribbons. A renormalization group analysis of flexural phonons reveals that elongated ribbons behave like highly anisotropic polymers, where the two dimensional nature of ribbons is reflected in non-trivial power law scalings of the persistence length and effective bending and twisting rigidities with the ribbon width. With a coarse-grained transfer matrix approach, we then show how thermalized ribbons respond to pulling and bending forces over a wide spectrum of temperatures, forces and ribbon lengths.

cond-mat.soft↗

arXiv2014

Glucagon stop-go kinetics supports a monomer-trimer fibrillation model

We investigate in vitro fibrillation kinetics of the hormone peptide glucagon at various concentrations using confocal microscopy and determine the glucagon fibril persistence length $60 μ\textrm{m}$. At all concentrations we observe that periods of individual fibril growth are interrupted by periods of stasis. The growth probability is large at high and low concentrations and is reduced for intermediate glucagon concentrations. To explain this behavior we propose a simple model, where fibrils come in two forms, one built entirely from glucagon monomers and one entirely from glucagon trimers. The opposite building blocks act as fibril growth blockers, and this generic model reproduces experimental behavior well.

physics.bio-ph↗

arXiv2013

Thermal Excitations of Warped Membranes

We explore thermal fluctuations of thin planar membranes with a frozen spatially-varying background metric and a shear modulus. We focus on a special class of $D$-dimensional ``warped membranes'' embedded in a $d-$dimensional space with $d\ge D+1$ and a preferred height profile characterized by quenched random Gaussian variables $\{h_α({\bf q})\}$, $α=D+1,\ldots, d$, in Fourier space with zero mean and a power law variance $\overline{ h_α({\bf q}_1) h_β({\bf q}_2) } \sim δ_{α, β} \, δ_{{\bf q}_1, -{\bf q}_2} \, q_1^{-d_h}$. The case $D=2$, $d=3$ with $d_h = 4$ could be realized by flash polymerizing lyotropic smectic liquid crystals. For $D < \max\{4, d_h\}$ the elastic constants are non-trivially renormalized and become scale dependent. Via a self consistent screening approximation we find that the renormalized bending rigidity increases for small wavevectors ${\bf q}$ as $κ_R \sim q^{-η_f}$, while the in-hyperplane elastic constants decrease according to $λ_R,\ μ_R \sim q^{+η_u}$. The quenched background metric is relevant (irelevant) for warped membranes characterized by exponent $d_h > 4 - η_f^{(F)}$ ($d_h < 4 - η_f^{(F)}$), where $η_f^{(F)}$ is the scaling exponent for tethered surfaces with a flat background metric, and the scaling exponents are related through $η_u + η_f = d_h - D$ ($η_u + 2 η_f=4-D$).

cond-mat.soft↗

arXiv2013

Mechanical Properties of Warped Membranes

We explore how a frozen background metric affects the mechanical properties of planar membranes with a shear modulus. We focus on a special class of "warped membranes" with a preferred random height profile characterized by random Gaussian variables $h({\bf q})$ in Fourier space with zero mean and variance $<|h({\bf q})|^2> \sim q^{-d_h}$ and show that in the linear response regime the mechanical properties depend dramatically on the system size $L$ for $d_h \ge 2$. Membranes with $d_h=4$ could be produced by flash polymerization of lyotropic smectic liquid crystals. Via a self consistent screening approximation we find that the renormalized bending rigidity increases as $κ_R \sim L^{(d_h-2)/2}$ for membranes of size $L$, while the Young and shear modulii decrease according to $Y_R,\ μ_R \sim L^{-(d_h-2)/2}$ resulting in a universal Poisson ratio. Numerical results show good agreement with analytically determined exponents.

cond-mat.soft↗

arXiv2011

The influence of T cell development on pathogen specificity and autoreactivity

T cells orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors on their surface to short peptides derived from foreign proteins bound to protein products of the major histocompatibility (MHC) gene products, which are displayed on the surface of antigen presenting cells. T cells can also interact with peptide-MHC complexes, where the peptide is derived from host (self) proteins. A diverse repertoire of relatively self-tolerant T cell receptors is selected in the thymus. We study a model, computationally and analytically, to describe how thymic selection shapes the repertoire of T cell receptors, such that T cell receptor recognition of pathogenic peptides is both specific and degenerate. We also discuss the escape probability of autoimmune T cells from the thymus.

physics.bio-ph↗

arXiv2009

Thymic selection of T-cell receptors as an extreme value problem

T lymphocytes (T cells) orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors (TCRs) on their surface to short peptides (p) derived from foreign proteins, which are bound to major histocompatibility (MHC) gene products (displayed on antigen presenting cells). A diverse and self-tolerant T cell repertoire is selected in the thymus. We map thymic selection processes to an extreme value problem and provide an analytic expression for the amino acid compositions of selected TCRs (which enable its recognition functions).

physics.bio-ph↗