Related papers: Residue mobility has decreased during protein evol…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
We present a set of evolutionary computations for binaries with a B-type primary at birth. Some liberal computations including loss of mass and angular momentum during binary evolution are added to an extensive grid of conservative…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
A correlation is established between the macro-scale friction regimes of metals and a transition between two dominant atomistic mechanisms of deformation. Metals tend to exhibit bi-stable friction behavior -- low and converging or high and…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
Recently acoustic signature of dislocation avalanches in HCP materials was found to be long tailed in size and energy, suggesting critical dynamics. Even more recently, the intermittent plastic response was found to be generic for micro-…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
The key to understanding a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility and function of…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
Plastic deformation of crystals is a physical phenomenon, which has immensely driven the development of human civilisation since the onset of the Chalcolithic period. This process is primarily governed by the motion of line defects, called…
Crystal plasticity is the result of the motion and interaction of dislocations. There is, however, still a major gap between microscopic and mesoscopic simulations and continuum crystal plasticity models. Only recently a higher dimensional…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Cells exhibit qualitatively different behaviors on substrates with different rigidities. The fact that cells are more polarized on the stiffer substrate motivates us to construct a two-dimensional cell with the distribution of focal…
In this paper we study the asymptotic behavior of a structure made of curved rods of thickness 2\delta when \delta rightarrow 0. This study is carried on within the frame of linear elasticity by using the unfolding method. It is based on…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
Pattern formation in drying protein droplets continues to attract considerable research attention because it can be linked to specific protein-protein interactions. An extensive study of the drying evolution and the final crack patterns are…