Warm and Cold Denaturation in the Phase Diagram of a Protein Lattice Model

Studying the properties of the solvent around proteins, we propose a much more sophisticated model of solvation than temperature-independent pairwise interactions between monomers, as is used commonly in lattice representations. We applied our model of solvation to a 16-monomer chain constrained on a two-dimensional lattice. We compute a phase diagram function of the temperature and a solvent parameter which is related to the pH of the solution. It exhibits a native state in which the chain coalesces into a unique compact conformation as well as a denatured state. Under certain solvation conditions, both warm and cold denaturations occur between the native and the denatured states. A good agreement is found with the data obtained from calorimetric experiments, thereby validating the proposed model.Comment: 7 pages, 2 figure

The superheated Melting of Grain Boundary

Based on a model of the melting of Grain Boundary (GB), we discuss the possibility of the existence of superheated GB state. A Molecular Dynamics simulation presented here shows that the superheated GB state can realized in the high symmetric tilt GB. Whether the sizes of liquid nuclei exceed a critical size determined the superheating grain boundary melting or not. Our results also indicate that the increase of melting point due to pressure is smaller than the superheating due to nucleation mechanism.Comment: Accepted by PRB, 7 pages and 5 figure

Elasticity and metastability limit in supercooled liquids: a lattice model

We present Monte Carlo simulations on a lattice system that displays a first order phase transition between a disordered phase (liquid) and an ordered phase (crystal). The model is augmented by an interaction that simulates the effect of elasticity in continuum models. The temperature range of stability of the liquid phase is strongly increased in the presence of the elastic interaction. We discuss the consequences of this result for the existence of a kinetic spinodal in real systems.Comment: 8 pages, 5 figure

Kinetic glass behavior in a diffusive model

Three properties of the Edwards-Anderson model with mobile bonds are investigated which are characteristic of kinetic glasses. First is two-time relaxation in aged systems, where a significant difference is observed between spin and bond autocorrelation functions. The spin subsystem does not show two-time behavior, and the relaxation is stretched exponential. The bond subsystem shows two-time behavior, with the first relaxation nearly exponential and the second similar to the spin one. Second is the two-temperature behavior, which can be tuned by bond dilution through the full range reported in the literature. Third is the rigid-to-floppy transition, identified as a function of bond dilution. Simple Glauber Monte Carlo evolution without extraneous constraints reproduces the behavior of classical kinetic simulations, with the bond (spin) degree of freedom corresponding to configurational (orientational) disorder.Comment: 4 pages, 3 figures, minimal corrections, to appear in Phys. Rev. B (RC

Dynamical heterogeneity in a glass forming ideal gas

We conduct a numerical study of the dynamical behavior of a system of three-dimensional crosses, particles that consist of three mutually perpendicular line segments rigidly joined at their midpoints. In an earlier study [W. van Ketel et al., Phys. Rev. Lett. 94, 135703 (2005)] we showed that this model has the structural properties of an ideal gas, yet the dynamical properties of a strong glass former. In the present paper we report an extensive study of the dynamical heterogeneities that appear in this system in the regime where glassy behavior sets in. On the one hand, we find that the propensity of a particle to diffuse is determined by the structure of its local environment. The local density around mobile particles is significantly less than the average density, but there is little clustering of mobile particles, and the clusters observed tend to be small. On the other hand, dynamical susceptibility results indicate that a large dynamical length scale develops even at moderate densities. This suggests that propensity and other mobility measures are an incomplete measure of dynamical length scales in this system.Comment: 11 pages, 7 figure

Glassy Mean-Field Dynamics of the Backgammon model

In this paper we present an exact study of the relaxation dynamics of the backgammon model. This is a model of a gas of particles in a discrete space which presents glassy phenomena as a result of {\it entropy barriers} in configuration space. The model is simple enough to allow for a complete analytical treatment of the dynamics in infinite dimensions. We first derive a closed equation describing the evolution of the occupation number probabilities, then we generalize the analysis to the study the autocorrelation function. We also consider possible variants of the model which allow to study the effect of energy barriers.Comment: 21 pages, revtex, 4 uuencoded figure

Solidity of viscous liquids. IV. Density fluctuations

This paper is the fourth in a series exploring the physical consequences of the solidity of highly viscous liquids. It is argued that the two basic characteristics of a flow event (a jump between two energy minima in configuration space) are the local density change and the sum of all particle displacements. Based on this it is proposed that density fluctuations are described by a time-dependent Ginzburg-Landau equation with rates in k-space of the form $\Gamma_0+Dk^2$ with $D\gg\Gamma_0a^2$ where $a$ is the average intermolecular distance. The inequality expresses a long-wavelength dominance of the dynamics which implies that the Hamiltonian (free energy) may be taken to be ultra local. As an illustration of the theory the case with the simplest non-trivial Hamiltonian is solved to second order in the Gaussian approximation, where it predicts an asymmetric frequency dependence of the isothermal bulk modulus with Debye behavior at low frequencies and an $\omega^{-1/2}$ decay of the loss at high frequencies. Finally, a general formalism for the description of viscous liquid dynamics, which supplements the density dynamics by including stress fields, a potential energy field, and molecular orientational fields, is proposed

Free Energy Landscape Of Simple Liquids Near The Glass Transition

Properties of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form are investigated numerically. A considerable number of glassy local minima of the free energy are located and the distribution of an appropriately defined ``overlap'' between minima is calculated. The process of transition from the basin of attraction of a minimum to that of another one is studied using a new ``microcanonical'' Monte Carlo procedure, leading to a determination of the effective height of free energy barriers that separate different glassy minima. The general appearance of the free energy landscape resembles that of a putting green: deep minima separated by a fairly flat structure. The growth of the effective free-energy barriers with increasing density is consistent with the Vogel-Fulcher law, and this growth is primarily driven by an entropic mechanism.Comment: 10 pages, 6 postscript figures, uses iopart.cls and iopart10.clo (included). Invited talk at the ICTP Trieste Conference on "Unifying Concepts in Glass Physics", September 1999. To be published in J. Phys. Cond. Ma

Replica symmetry breaking in long-range glass models without quenched disorder

We discuss mean field theory of glasses without quenched disorder focusing on the justification of the replica approach to thermodynamics. We emphasize the assumptions implicit in this method and discuss how they can be verified. The formalism is applied to the long range Ising model with orthogonal coupling matrix. We find the one step replica-symmetry breaking solution and show that it is stable in the intermediate temperature range that includes the glass state but excludes very low temperatures. At very low temperatures this solution becomes unstable and this approach fails.Comment: 6 pages, 2 figure

Properties of a continuous-random-network model for amorphous systems

We use a Monte Carlo bond-switching method to study systematically the thermodynamic properties of a "continuous random network" model, the canonical model for such amorphous systems as a-Si and a-SiO$_2$. Simulations show first-order "melting" into an amorphous state, and clear evidence for a glass transition in the supercooled liquid. The random-network model is also extended to study heterogeneous structures, such as the interface between amorphous and crystalline Si.Comment: Revtex file with 4 figure