Related papers: Modeling generic aspects of ideal fibril formation
Aims: We examine the movements of mass elements within dense fibrils using passive tracer particles (corks) in order to understand fibril creation and destruction processes. Methods: Simulated fibrils were selected at times when they were…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
In physics we often use very simple models to describe systems with many degrees of freedom, but it is not clear why or how this success can be transferred to the more complex biological context. We consider models for the joint…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
Recent experimental studies have shown that amyloid fibril formed by aggregation of {\beta} peptide exhibits excellent mechanical properties comparable to other protein materials such as actin filaments and microtubules. These excellent…
We consider a fibrillar medium with a continuous distribution of two-level atoms coupled to quantized electromagnetic fields. Perturbation theory is developed based on the current algebra satisfied by the atomic operators. The one-loop…
Filaments are crucial intermediaries in the star formation process. Recent observations of filaments show that - \textbf{(i)} a number of them are non-singular entities, and rather a bundle of velocity coherent fibres, and \textbf{(ii)}…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature; diverse biological materials, such as bone, cellulose, and muscle, have as many as ten hierarchical levels. Structural…
Deformation modeling of cardiac muscle is an important issue in the field of cardiac analysis. For this reason, many approaches have been developed to best estimate the cardiac muscle deformation, and to obtain a practical model to use in…
Mineralized collagen microfibrils in human bone provide its mechanical properties (stiffness, elasticity, ductility, energy dissipation and strength). However, detailed 3D finite element models describing the mechanical behaviour of the…
A model to describe the arising of new structures in an initial homogeneous biological system is proposed. The essay is motivated by the intention to work on a non-equilibrium situation grouping together several mechanisms and processes as:…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Type I collagen fibrils have circular cross sections with radii mostly distributed in between 50 and 100 nm and are characterized by an axial banding pattern with a period of 67 nm. The constituent long molecules of those fibrils, the…
The constitutive behaviors of materials are often modeled using a network of different rheological elements. These rheological models are mostly developed within a one-dimensional small strain framework. One of the key impediments of…
Recent advances in classical density functional theory are combined with stochastic process theory and rare event techniques to formulate a theoretical description of nucleation, including crystallization, that can predict nonclassical…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and non-measurable parameters, which have to be…
Recent experimental results on the static or quasistatic response of granular materials have been interpreted to suggest the inapplicability of the traditional engineering approaches, which are based on elasto-plastic models (which are…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…