449 research outputs found
Droplets and the configurational entropy crisis for random first order transitions
We consider the effect of droplet excitations in the random first order
transition theory of glasses on the configurational entropy. The contribution
of these excitations is estimated both at and above the ideal glass transition
temperature. The temperature range where such excitations could conceivably
modify or `round-out' an underlying glass transition temperature is estimated,
and found to depend strongly on the surface tension between locally metastable
phases in the supercooled liquid. For real structural glasses this temperature
range is found to be very narrow, consistent with the quantitative success of
the theory. For certain finite-range spin-glass models, however, the surface
tension is estimated to be significantly lower leading to much stronger entropy
renormalizations, thus providing an explanation for the lack of a strict
thermodynamic glass transition in simulations of these models.Comment: 5 page
Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins
Within the frame of an effective, coarse-grained hydrophobic-polar protein
model, we employ multicanonical Monte Carlo simulations to investigate
free-energy landscapes and folding channels of exemplified heteropolymer
sequences, which are permutations of each other. Despite the simplicity of the
model, the knowledge of the free-energy landscape in dependence of a suitable
system order parameter enables us to reveal complex folding characteristics
known from real bioproteins and synthetic peptides, such as two-state folding,
folding through weakly stable intermediates, and glassy metastability.Comment: 10 pages, 1 figur
Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels
The quantitative description of model protein folding kinetics using a
diffusive collective reaction coordinate is examined. Direct folding kinetics,
diffusional coefficients and free energy profiles are determined from Monte
Carlo simulations of a 27-mer, 3 letter code lattice model, which corresponds
roughly to a small helical protein. Analytic folding calculations, using simple
diffusive rate theory, agree extremely well with the full simulation results.
Folding in this system is best seen as a diffusive, funnel-like process.Comment: LaTeX 12 pages, figures include
The Origin of the Boson Peak and the Thermal Conductivity Plateau in Low Temperature Glasses
We argue that the intrinsic glassy degrees of freedom in amorphous solids
giving rise to the thermal conductivity plateau and the ``boson peak'' in the
heat capacity at moderately low temperatures are directly connected to those
motions giving rise to the two-level like excitations seen at still lower
temperatures. These degrees of freedom can be thought of as strongly anharmonic
transitions between the local minima of the glassy energy landscape that are
accompanied by ripplon-like domain wall motions of the glassy mosaic structure
predicted to occur at by the random first order transition theory. The
energy spectrum of the vibrations of the mosaic depends on the glass transition
temperature, the Debye frequency and the molecular length scale. The resulting
spectrum reproduces the experimental low temperature Boson peak. The
``non-universality'' of the thermal conductivity plateau depends on and arises from calculable interactions with the phonons.Comment: 4 pages, submitted to PR
Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics
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 coordinates are identified as collective growth modes of the
unstable fluctuations about the saddle-points in the free energy surface. The
description of the chain dynamics incorporates internal friction (independent
of the solvent viscosity) arising from the elementary isomerizations of the
backbone dihedral angles. We find that the folding rate depends linearly on the
solvent friction for high viscosity, but saturates at low viscosity because of
internal friction. For -repressor, the calculated folding rate
prefactor, along with the free energy barrier from the variational theory,
gives a folding rate that agrees well with the experimentally determined rate
under highly stabilizing conditions, but the theory predicts too large a
folding rate at the transition midpoint. This discrepancy obtained using a
fairly complete quantitative theory inspires a new set of questions about chain
dynamics, specifically detailed motions in individual contact formation.Comment: 18 pages, 8 figure
- …