Related papers: Glassy Dynamics of Protein Folding
We study the low temperature dynamics of a two dimensional short-range spin system with uniform ferromagnetic interactions, which displays glassiness at low temperatures despite the absence of disorder or frustration. The model has a dual…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…
We identify a link between the glass transition and percolation of mobile regions in configuration space. We find that many hallmarks of glassy dynamics, for example stretched-exponential response functions and a diverging structural…
We study theoretically and numerically a family of multi-point dynamic susceptibilities that quantify the strength and characteristic lengthscales of dynamic heterogeneities in glass-forming materials. We use general theoretical arguments…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
By means of molecular dynamics, we study the structure and the dynamics of a microscopic model for colloidal gels at low volume fractions. The presence of directional interactions leads to the formation of a persistent interconnected…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
We report results of molecular-dynamics simulations of a model polymer melt consisting of short non-entangled chains in the supercooled state above the critical temperature of mode-coupling theory (MCT). To analyse the dynamics of the…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
A general matrix-based scheme for analyzing the long-time dynamics in kinetically constrained models such as the East model is presented. The treatment developed here is motivated by the expectation that slowly-relaxing spin domains of…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
We analyze data from confocal microscopy experiments of a colloidal suspension to validate predictions of rapid sporadic events responsible for structural relaxation in a glassy sample. The trajectories of several thousand colloidal…
We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…
We study the dynamics of the East model, comprising a chain of uncoupled spins in a downward-pointing field. Glassy effects arise at low temperatures $T$ from the kinetic constraint that spins can only flip if their left neighbour is up. We…
We introduce a simple two-dimensional spin model with short-range interactions which shows glassy behavior despite a Hamiltonian which is completely homogeneous and possesses no randomness. We solve exactly for both the static partition…