Related papers: Residue mobility has decreased during protein evol…
Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and bio-film formation. We use a novel two-colour, three-dimensional Lagrangian tracking technique, to follow simultaneously the body…
Beta-diversity has been repeatedly shown to decline with increasing elevation, but the causes of this pattern remain unclear, partly because they are confounded by coincident variation in alpha- and gamma-diversity. We used 8,795 forest…
Mobility properties inside and around degenerate domains of an elastic lattice partially pinned on a square array of traps are explored by means of a fully controllable model system of macroscopic particles. We focus on the different…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular…
We present the results of a set of N-body simulations following the long-term evolution of the rotational properties of star cluster models evolving in the external tidal field of their host galaxy, after an initial phase of violent…
The mechanical properties of cells, which influence the properties of the tissue they belong to, are controlled by various mechanisms. Bi et al. theoretically demonstrated that density-independent rigidity transition occurs in…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
The study of growth-induced surface wrinkling in constrained bilayers comprising a thin film attached to a thick substrate is a canonical model for understanding pattern formation in many biological systems. While the bilayer model has…
The $\beta$-relaxation associated with the sub-glass transition temperature ($T_{\text{g},\beta}$) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature ($T_{g\alpha}$). Despite…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
The effect of an order-parameter dependent mobility (or kinetic coefficient), on the phase-ordering dynamics of a system described by an n-component vector order parameter is addressed at zero temperature in the large-n limit. We consider…
Considering all the PDB annotated allosteric proteins (from ASD - AlloSteric Database) belonging to four different classes (kinases, nuclear receptors, peptidases and transcription factors), this work has attempted to decipher certain…
We analyze a bubble forming system composed of particles with competing long range repulsive and short range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a…
We investigate the dynamics of polymer translocation through nanopores under external driving by 3D Langevin Dynamics simulations, focusing on the scaling of the average translocation time $\tau$ versus the length of the polymer, $\tau\sim…
We have investigated the influence of the plasma membrane environment on the molecular evolution of G protein-coupled receptors (GPCRs), the largest receptor family in Metazoa. In particular, we have analyzed the site-specific rate…
We perform extensive molecular dynamics simulations of dense liquids composed of bidisperse dimer- and ellipse-shaped particles in 2D that interact via repulsive contact forces. We measure the structural relaxation times obtained from the…
Phi-values are experimental measures of the effects of mutations on the folding kinetics of a protein. A central question is which structural information Phi-values contain about the transition state of folding. Traditionally, a Phi-value…
Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish.…