Related papers: Modeling generic aspects of ideal fibril formation
A unifying framework to describe dense flows of dry, deformable grains is proposed. Perturbative analysis of a granular temperature equation describing flows with contact stresses, supported by the recovery of the nonlocal granular fluidity…
This chapter reviews the different methodological aspects of the ab ini-tio modeling of dislocations. Such simulations are now frequently used to study the dislocation core, i.e. the region in the immediate vicinity of the line defect where…
During the application of mass-action equation models to the study of amyloid fiber formation, time-consuming numerical calculations constitute a major bottleneck when no analytical solution is available. To conquer this difficulty, here an…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
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…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
We introduce an individual-based model for fiber elements having the ability to cross-link or unlink each other and to align with each other at the cross links. We first formally derive a kinetic model for the fiber and cross-links…
A new model is suggested and used to mimic various spatial or temporal designs in biological or non biological formations where the focus is on the normal or irregular electrical signals coming from human heart (ECG) or brain (EEG). The…
Ample experimental evidence has been accumulated demonstrating that the formation of monodispersed colloids proceeds through a more complex mechanism, than the generally excepted diffusional "burst nucleation" process. Instead, the…
Analytical expressions for the elastic and dynamic form factors (FFs) are derived in the shell model (SM) with a potential well of finite depth. The consideration takes into account the motion of the target-nucleus center of mass (CM).…
Structure formation and constant reorganization of the actin cytoskeleton are key requirements for the function of living cells. Here we show that a minimal reconstituted system consisting of actin filaments, crosslinking molecules and…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most…
Matrix stiffness expressions are derived for the particle movements in an assembly of rigid granules having compliant contacts. The derivations include stiffness terms that arise from the particle shapes at their contacts. These geometric…
In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to…
Context. A porous and/or fractal description can generally be applied where particles have undergone coagulation into aggregates. Aims. To characterise finite-sized, porous and fractal particles and to understand the possible limitations of…
Amyloid fibers are aggregates of proteins. They are built out of a peptide called $\beta$--amyloid (A$\beta$) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the…
The lysyl oxidase (LOX) enzyme that catalyses cross-link formation during the assembly of collagen fibrils in vivo is too large to diffuse within assembled fibrils, and so is incompatible with a fully equilibrium mechanism for fibril…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…