相关论文: Sidechain Dynamics and Protein Folding
The glass transition, extensively studied in dense fluids, polymers, or colloids, corresponds to a dramatic evolution of equilibrium transport coefficients upon a modest change of control parameter, like temperature or pressure. A similar…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
Relaxation dynamics in reversible catalytic reaction networks is studied, revealing two salient behaviors that are reminiscent of glassy behavior: slow relaxation with log(time) dependence of the correlation function, and emergence of a few…
Slowing down of the relaxation of the fluctuations around equilibrium is investigated both by stochastic simulations and by analysis of Master equation of reversible reaction networks consisting of resources and the corresponding products…
Isotropization occurs on time scales much shorter than the thermal equilibration time. This is a crucial ingredient for the understanding of collision experiments of heavy nuclei or other nonequilibrium phenomena in complex many body…
We have investigated the nature of the dynamical behaviour in low autocorrelation binary sequences. These models do have a glass transition $T_G$ of a purely dynamical nature. Above the glass transition the dynamics is not fully ergodic and…
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
In stark contrast with the conventional understanding of the glass transition, where the transition from glass to liquid appears as a dynamic process where atoms/molecules cooperatively relax into the equilibrium phase, we experimentally…
We uncover an unforeseen asymmetry in relaxation -- for a pair of thermodynamically equidistant temperature quenches, one from a lower and the other from a higher temperature, the relaxation at the ambient temperature is faster in case of…
We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…
We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
Diffusion-coagulation can be simply described by a dynamic where particles perform a random walk on a lattice and coalesce with probability unity when meeting on the same site. Such processes display non-equilibrium properties with strong…
Using Langevin dynamics complemented by Wang-Landau Monte Carlo simulations, we study the phase behavior of single and multiple semiflexible polymer chains in solution under poor-solvent conditions. In the case of a single chain, we obtain…
Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
Systems with long-range interactions when quenced into a metastable state near the pseudo-spinodal exhibit nucleation processes that are quite different from the classical nucleation seen near the coexistence curve. In systems with…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…