相关论文: Sidechain Dynamics and Protein Folding
The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
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,…
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprised of two…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Dynamics of a polymer chain in solution gets significantly affected by the temperature and the frictional forces arising due to solvent viscosity. Here, using an explicit solvent framework for polymer simulation with the liberty to tune the…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
While deeply supercooled liquids exhibit divergent viscosity and increasingly heterogeneous dynamics as the temperature drops, their structure shows only seemingly marginal changes. Understanding the nature of relaxation processes in this…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
Cold atoms, loaded into an optical lattice with double-well sites, are considered. Pseudospin representation for an effective Hamiltonian is derived. The system in equilibrium displays two phases, ordered and disordered. The second-order…
We use computer simulations to investigate the static properties of a simple glass-forming fluid in which the positions of a finite fraction of the particles has been frozen in. By probing the equilibrium distribution of the overlap between…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…