Related papers: Sidechain Dynamics and Protein Folding
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
This short review covers a wide selection of topics from a multidisciplinary area of dynamics of nonequilibrium systems in physics, chemistry, biology. Theoretical models of colloid particle and protein deposition and adhesion at surfaces,…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
A model is derived for the viscoelastic response of glasses at isothermal uniaxial deformation with small strains. A glass is treated as an ensemble of relaxing units with various activation energies for rearrangement. With reference to the…
The microcanonical analysis is shown to be a powerful tool to characterize the protein folding transition and to neatly distinguish between good and bad folders. An off-lattice model with parameter chosen to represent polymers of these two…
An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
We consider the problem of relaxation in a one-dimensional system of interacting electrons. In the limit of weak interactions, we calculate the decay rate of a single-electron excitation, accounting for the nonlinear dispersion. The leading…
A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This…
Low-energy excitations play a key role in all condensed-matter systems, yet there is limited understanding of their nature in glasses, where they correspond to local rearrangements of groups of particles. Here we introduce an algorithm to…
We present a study of orientational relaxation dynamics in thin films of a low-molecular-weight glass-former as a function of temperature and film thickness. The relaxation is probed by second-harmonic generation after release of a poling…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
This article is devoted to the long-time dynamics of point-vortex type systems near thermal equilibrium and to the possible emergence of collisional relaxation. More precisely, we consider a tagged particle coupled to a large number of…
If quenched fast enough, a liquid is able to avoid crystallization and will remain in a metastable supercooled state down to the glass transition, with an important increase in viscosity upon further cooling. There are important differences…
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real…
The interplay between the structural relaxation and the rheological response of a binary LJ glass former is studied via MD simulations. In the quiescent state, the model is well known for its sluggish dynamics and a two step relaxation of…