Related papers: Sidechain Dynamics and Protein Folding
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
Nearly all glass forming liquids display secondary relaxations, dynamical modes seemingly distinct from the primary alpha relaxations. We show that accounting for driving force fluctuations and the diversity of reconfiguring shapes in the…
The step motions considered are those in which crystallization is controlled by a single diffusion process, either the substance diffusion for growth from solution or the flow of latent heat from the step for growth from melt. Quasi-static…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
Understanding the realization of thermal equilibrium through the thermalization process in a many-body system is a fundamental and complex scientific question, bridging thermodynamics and classical dynamics and connecting to a host of…
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motions. Model-free types…
Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is…
The glass transition refers to the non-equilibrium process by which an equilibrium liquid is transformed to a non-equilibrium disordered solid, or vice versa. Associated response functions, such as heat capacities, are markedly different on…
Non-equilibrium molecular dynamics simulations are performed to investigate the dynamic behavior of three-dimensional binary glasses prepared via an instantaneous quench across the glass transition. We found that with increasing strain…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
Aligning self-propelled particles undergo a nonequilibrium flocking transition from apolar to polar phases as their interactions become stronger. We propose a thermodynamically consistent lattice model, in which the internal state of the…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
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…
A fundamental question in many-body physics is how closed quantum systems reach equilibrium. We address this question experimentally and theoretically in an ultracold large-spin Fermi gas where we find a complex interplay between internal…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
Poly(ethylene oxide) is an important polymer with many applications, e.g., as solid-state electrolyte in batteries. Its relaxation dynamics, characterizing its molecular and submolecular motions, which is relevant for many of these…
We study one-dimensional sideband cooling of Cesium atoms strongly confined in a far-detuned optical lattice. The Lamb-Dicke regime is achieved in the lattice direction whereas the transverse confinement is much weaker. The employed…