Related papers: Comparative analysis of rigidity across protein fa…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
Dispersed colloidal particles within a suspension can aggregate and spontaneously self-organize into a robust, percolating structure known as a gel. These network-like structures are prevalent in nature and play a critical role in many…
The paper presents a new stiffness modelling method for multi-chain parallel robotic manipulators with flexible links and compliant actuating joints. In contrast to other works, the method involves a FEA-based link stiffness evaluation and…
We consider mechanically-induced pattern formation within the framework of a growing, planar, elastic rod attached to an elastic foundation. Through a combination of weakly nonlinear analysis and numerical methods, we identify how the shape…
We summarize ideas and methods that apply to rigidity and connectivity percolation. These include: constraint counting concepts, exact calculations on diluted trees and numerical results on diluted lattices using matching algorithms. The…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
We study the cooperative rupture of multiple adhesion bonds under shared linear loading. Simulations of the appropriate Master equation are compared with numerical integration of a rate equation for the mean number of bonds and its scaling…
In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Predicting protein-ligand binding affinity is an essential part of computer-aided drug design. However, generalisable and performant global binding affinity models remain elusive, particularly in low data regimes. Despite the evolution of…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
A theoretical scaling law for the size effect of the strength of brittle materials is presented. To some extend, it can be seen as an extension of the well known Weibull law. For that a correlated Random Fields is used to model the…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
New definitions of the structural susceptibilities based on the fluctuations of distances to the native state of toy protein models are proposed. The calculation of such susceptibilities does not require the basin of native state and the…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…
Various kinds of heterogeneity in solids including atomistic discreteness affect the fracture strength as well as the failure dynamics remarkably. Here we study the effects of an initial crack in a discrete model for fracture in…