Related papers: Relaxation in a perfect funnel
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
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…
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…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We study the jamming transition in a model of elastic particles under shear at zero temperature. The key quantity is the relaxation time $\tau$ which is obtained by stopping the shearing and letting energy and pressure decay to zero. At…
We study the condensation phenomenon in a zero range process on scale-free networks. We show that the stationary state property depends only on the degree distribution of underlying networks. The model displays a stationary state phase…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
We have investigated the relaxational dynamics for a protein model at various temperatures. Theoretical analysis of this model in conjunction with numerical simulations suggests several relaxation regimes, including a single exponential, a…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Landau's theory of phase transitions is adapted to treat independently relaxing regions in complex systems using nanothermodynamics. The order parameter we use governs the thermal fluctuations, not a specific static structure. We find that…
We investigate relaxation dynamics along the entire first-order phase transition line by analyzing the time evolution of the free energy landscape in the three-dimensional kinetic Ising model. Near the critical temperature $T_{\rm c}$, the…
Energy landscapes are high-dimensional surfaces representing the dependence of system energy on variable configurations, which determine crucially the system's emergent behavior but are difficult to be analyzed due to their high-dimensional…
The role of the potential energy landscape in determining the relaxation dynamics of model clusters is studied using a master equation. Two types of energy landscape are examined: a single funnel, as exemplified by 13-atom Morse clusters,…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
We analyze the density and size dependence of the relaxation time $\tau$ for kinetically constrained spin systems. These have been proposed as models for strong or fragile glasses and for systems undergoing jamming transitions. For the one…
The relaxation of temperatures and velocities of the components of a quasi-equilibrium two-component homogeneous completely ionized plasma is investigated on the basis of a generalization of the Chapman-Enskog method applied to the Landau…
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…
Stress relaxation following deformation of an entangled polymeric liquid is thought to be affected by transient reforming of chain entanglements. In this work, we use single molecule techniques to study the relaxation of individual polymers…