Related papers: Developing an unfolding-incorporated coarse-graine…
Mechanical stress plays an intricate role in gene expression in individual cells and sculpting of developing tissues. However, systematic methods of studying how mechanical stress and feedback help to harmonize cellular activities within a…
This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths,…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
A novel numerical approach to analyze the mechanical behavior within composite materials including the inelastic regime up to final failure is presented. Therefore, a second-gradient theory is combined with phase-field methods to fracture.…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
Microstructural evolution in structural materials is known to occur in response to mechanical loading and can often accommodate substantial plastic deformation through the coupled motion of grain boundaries (GBs). This can produce desirable…
Graphene is susceptible to morphological instabilities such as wrinkles and folds, which result from the imposition of thermo-mechanical stresses upon cooling from high temperatures and/ or under biaxial loading. A particular pattern…
A curious feature of organ and organoid morphogenesis is that in certain cases, spatial oscillations in the thickness of the growing "film" are out-of-phase with the deformation of the slower-growing "substrate," while in other cases, the…
Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs 'A' and 'B' in the central nodule of fibrin monomer to complementary holes 'a' and 'b' in the beta- and gamma-nodules,…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Using a coarse-grained bead-spring model for semi-flexible macromolecules forming a polymer brush, structure and dynamics of the polymers is investigated, varying chain stiffness and grafting density. The anchoring condition for the grafted…
We propose a predictive model for the mechanical behavior of biodegradable polymers of interest for biomedical applications. Starting from a detailed description of the network behavior of the copolymer material, taking care of bonds…
We study the homogenization of a novel microscopic tridomain system, allowing for a more detailed analysis of the properties of cardiac conduction than the classical bidomain and monodomain models. In (Acta Appl.Math. 179 (2022) 1--35), we…
We report a simulation study for bottle-brush polymers grafted on a rigid backbone. Using a standard coarse-grained bead-spring model extensive molecular dynamics simulations for such macromolecules under good solvent conditions are…
Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Both animal and plant tissue exhibit a nonlinear rheological phenomenon known as compression stiffening, or an increase in moduli with increasing uniaxial compressive strain. Does such a phenomenon exist in single cells, which are the…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…