Related papers: Glassy Dynamics of Protein Folding
We represent the slow, glassy equilibrium dynamics of a line in a two-dimensional random potential landscape as driven by an array of asymptotically independent two-state systems, or loops, fluctuating on all length scales. The assumption…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We study glassy dynamics using a simulation of three soft Brownian particles confined to a two-dimensional circular region. If the circular region is large, the disks freely rearrange, but rearrangements are rarer for smaller system sizes.…
The dynamical behavior of a kind of models with hierarchically constrained dynamics is investigated. The models exhibit many properties resembling real structural glasses. In particular, we focus on the study of time-dependent temperature…
The description of activated relaxation of glassy systems in the multidimensional configurational space is a long-standing open problem. We develop a phenomenological description of the out-of-equilibrium dynamics of a model with a rough…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
Elastic models of the glass transition relate the relaxation dynamics and the elastic properties of structural glasses. They are based on the assumption that the relaxation dynamics occurs through activated events in the energy landscape…
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…
We investigate the statistics of the fluctuations of the energy transfer between an overdamped Brownian particle, whose motion is confined by a stationary harmonic potential, and a surrounding viscoelastic fluid at constant temperature. We…
In this paper we propose a short range generalization of the $p$-spin interaction spin-glass model. The model is well suited to test the idea that an entropy collapse is at the bottom-line of the dynamical singularity encountered in…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
Activity-mediated unjamming of a confluent glassy system is crucial for several biological processes, such as embryogenesis and cancer metastasis. During these processes, the cells progressively change their junction properties,…
We describe a model for the thermodynamics and dynamics of glass-forming liquids in terms of excitations from an ideal glass state to a Gaussian manifold of configurationally excited states. The quantitative fit of this three parameter…
We present a Brownian dynamics theory with full hydrodynamics (Stokesian dynamics) for a Gaussian polymer chain embedded in a liquid membrane which is surrounded by bulk solvent and walls. The mobility tensors are derived in Fourier space…
Supercooled liquids undergo complicated structural relaxation processes, which have been a long-standing problem in both experimental and theoretical aspects of condensed matter physics. In particular, past experiments universally observed…
Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress relaxation in hydrated lysozyme…
An extended Molecular-Dynamics study of the short-time "glassy" elasticity exhibited by a polymer melt of linear fully-flexible chains above the glass transition is presented. The focus is on the infinite-frequency shear modulus $G_\infty$…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load…
We review a new theory of viscoelasticity of a glass-forming viscous liquid near and below the glass transition. In our model we assume that each point in the material has a specific viscosity, which varies randomly in space according to a…