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 $T_g$ 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 $k_B T_g/\hbar \omega_D$ 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 $\lambda$-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