Related papers: Residue mobility has decreased during protein evol…
We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very…
We present results on the evolution in the last 6 Gyr of the structural parameters of two samples of brightest cluster galaxies (BCGs). The nearby sample of BCGs consist on 69 galaxies from the WINGS survey spanning a redshift range of…
Animal behavior is shaped by a myriad of mechanisms acting on a wide range of scales, which hampers quantitative reasoning and the identification of general principles. Here, we combine data analysis and theory to investigate the…
This paper thoroughly investigates a range of popular DE configurations to identify components responsible for the emergence of structural bias - recently identified tendency of the algorithm to prefer some regions of the search space for…
It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
We study the phenomenon of migration of the small molecular weight component of a binary polymer mixture to the free surface using mean field and self-consistent field theories. By proposing a free energy functional that incorporates…
We carry out a detailed study of the orbital dynamics and structural evolution of over 6000 subhalos in the Via Lactea II simulation, from infall to present. By analyzing subhalos with masses down to m = 4e5 Msun, we find that lower mass…
This work presents a new modeling approach to macroscopic, polycrystalline elasto-plasticity starting from first principles and a few well-defined structural assumptions, incorporating the mildly rate-dependent (viscous) nature of plastic…
We simulate binary soft disk systems in two dimensions, and investigate how the dynamics slow as the area fraction is increased toward the glass transition. The "fragility" quantifies how sensitively the relaxation time scale depends on the…
A mesoscopic continuum model is employed to analyse the transport mechanisms and structure formation during the redistribution stage of deposition experiments where organic molecules are deposited on a solid substrate with periodic…
Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness…
Molecular dynamics simulations were used to quantify mechanically-induced structural evolution in nanocrystalline Al with an average grain size of 5 nm. A polycrystalline sample was cyclically strained at different temperatures, while a…
When adhesive elastomeric materials slide over hard rough surfaces at low velocities, there are two primary dissipative mechanisms that control how friction changes with sliding velocity: viscoelastic dissipation and adhesive dissipation.…
Fracture processes in multi-phase solids are inherently complex due to multiple competing mechanisms. Here, we investigate the elastic and fracture behaviour of two-phase solids, comprising a fragile phase and a tough phase using a…
Finite size effects on dynamical heterogeneity are studied in liquid silica with Molecular Dynamics simulations using the BKS potential model. When the system size decreases relaxation times are found to increase in accordance with previous…
We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…