Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport.

The interior of a eukaryotic cell is a highly complex composite material which consists of water, structural scaffoldings, organelles, and various biomolecular solutes. All these components serve as obstacles that impede the motion of vesicles. Hence, it is hypothesized that any alteration of the cytoskeletal network may directly impact or even disrupt the vesicle transport. A disruption of the vesicle-mediated cell transport is thought to contribute to several severe diseases and disorders, such as diabetes, Parkinson's and Alzheimer's disease, emphasizing the clinical relevance. To address the outlined objective, a multiscale finite element model of the diffusive vesicle transport is proposed on the basis of the concept of homogenization, owed to the complexity of the cytoskeletal network. In order to study the microscopic effects of specific nanoscopic actin filament network alterations onto the vesicle transport, a parametrized three-dimensional geometrical model of the actin filament network was generated on the basis of experimentally observed filament densities and network geometries in an adenocarcinomic human alveolar basal epithelial cell. Numerical analyzes of the obtained effective diffusion properties within two-dimensional sampling domains of the whole cell model revealed that the computed homogenized diffusion coefficients can be predicted statistically accurate by a simple two-parameter power law as soon as the inaccessible area fraction, due to the obstacle geometries and the finite size of the vesicles, is known. This relationship, in turn, leads to a massive reduction in computation time and allows to study the impact of a variety of different cytoskeletal alterations onto the vesicle transport. Hence, the numerical simulations predicted a 35% increase in transport time due to a uniformly distributed four-fold increase of the total filament amount. On the other hand, a hypothetically reduced expression of filament cross-linking proteins led to sparser filament networks and, thus, a speed up of the vesicle transport.

Multiscale homogenisation of diffusion in enzymatically-calcified hydrogels.

Hydrogels are a promising class of material in biomedical and industrial applications, where both the mechanical and diffusion properties play an important role. The wide range of polymers that can be used and the different production methods allows these properties to be specifically tuned to a high degree for their application. Producing tough hydrogels with high stiffness has been a long-standing challenge that has recently been addressed by mineralisation methods. Those methods modify the hydrogel into one with a supporting mineral microstructure that is highly heterogeneous. This work investigates methods to determine the macroscopic diffusion behaviour of heterogeneous gels by a homogenisation method implemented in a finite element framework. This is applied to two recently developed materials by calcifying poly-dimethyl-acrylamide (PDMA) and polyacrylamide hydrogels (PAAm). The former has porous, spherical inclusions obstructing diffusion, while the latter has spherical pores enabling it. For both gels the unobstructed volume can be used as the primary parameter to tune the diffusivity. In PDMA the porosity of the obstructions is shown by multiscale analysis to give a strong, non-linear dependence of the diffusivity on the solute molecule radius. The framework is extended to other materials and comparisons are made to experimental works from the literature.

Review paper: The importance of consideration of collagen cross-links in computational models of collagen-based tissues.

Collagen as the main protein in Extra Cellular Matrix (ECM) is the main load-bearing component of fibrous tissues. Nanostructure and architecture of collagen fibrils play an important role in mechanical behavior of these tissues. Extensive experimental and theoretical studies have so far been performed to capture these properties, but none of the current models realistically represent the complexity of network mechanics because still less is known about the collagen's inner structure and its effect on the mechanical properties of tissues. The goal of this review article is to emphasize the significance of cross-links in computational modeling of different collagen-based tissues, and to reveal the need for continuum models to consider cross-links properties to better reflect the mechanical behavior observed in experiments. In addition, this study outlines the limitations of current investigations and provides potential suggestions for the future work.

Thermomechanical Modeling of Microstructure Evolution Caused by Strain-Induced Crystallization.

The present contribution deals with the thermomechanical modeling of the strain-induced crystallization in unfilled polymers. This phenomenon significantly influences mechanical and thermal properties of polymers and has to be taken into consideration when planning manufacturing processes as well as applications of the final product. In order to simultaneously capture both kinds of effects, the model proposed starts by introducing a triple decomposition of the deformation gradient and furthermore uses thermodynamic framework for material modeling based on the Coleman-Noll procedure and minimum principle of the dissipation potential, which requires suitable assumptions for the Helmholtz free energy and the dissipation potential. The chosen setup yields evolution equations which are able to simulate the formation and the degradation of crystalline regions accompanied by the temperature change during a cyclic tensile test. The boundary value problem corresponding to the described process includes the balance of linear momentum and balance of energy and serves as a basis for the numerical implementation within an FEM code. The paper closes with the numerical examples showing the microstructure evolution and temperature distribution for different material samples.

Determination of the geometry of the RVE for cancellous bone by using the effective complex shear modulus.

This contribution deals with the application of the inverse homogenization method to the determination of geometrical properties of cancellous bone. The approach represents a combination of an extended version of the Marquardt-Levenberg method with the multiscale finite element method. The former belongs to the group of gradient-based optimization strategies, while the latter is a numerical homogenization method, suitable for the modeling of materials with a highly heterogeneous microstructure. The extension of the Marquardt-Levenberg method is concerned with the selection strategy for distinguishing the global minimum from the plethora of local minima. Within the numerical examples, the bone is modeled as a biphasic viscoelastic medium and three different representative volume elements are taken into consideration. Different models enable the simulation of the bone either as a purely isotropic or as a transversally anisotropic medium. Main geometrical properties of trabeculae are determined from data on effective shear modulus but alternative schemes are also possible.

Investigation of the influence of reflection on the attenuation of cancellous bone.

The model proposed in this paper is based on the fact that the reflection might have a significant contribution to the attenuation of the acoustic waves propagating through the cancellous bone. The numerical implementation of the mentioned effect is realized by the development of a new representative volume element that includes an infinitesimally thin 'transient' layer on the contact surface of the bone and the marrow. This layer serves to model the amplitude transformation of the incident wave by the transition through media with different acoustic impedances and to take into account the energy loss due to the reflection. The proposed representative volume element together with the multiscale finite element is used to simulate the wave propagation and to evaluate the attenuation coefficient for samples with different effective densities in the dependence of the applied excitation frequency. The obtained numerical values show a very good agreement with the experimental results. Moreover, the model enables the determination of the upper and the lower bound for the attenuation coefficient.