Evaluation of configurational entropy of a model liquid from computer simulations

Computer simulations have been employed in recent years to evaluate the configurational entropy changes in model glass-forming liquids. We consider two methods, both of which involve the calculation of the `intra-basin' entropy as a means for obtaining the configurational entropy. The first method involves the evaluation of the intra-basin entropy from the vibrational frequencies of inherent structures, by making a harmonic approximation of the local potential energy topography. The second method employs simulations that confine the liquid within a localized region of configuration space by the imposition of constraints; apart from the choice of the constraints, no further assumptions are made. We compare the configurational entropies estimated for a model liquid (binary mixture of particles interacting {\it via} the Lennard-Jones potential) for a range of temperatures, at fixed density.Comment: 10 pages, 5 figures, Proceedings of "Unifying Concepts in Glass Physics" Trieste 1999 (to appear in J. Phys. Cond. Mat.

Diffusion in simple fluids

Computed self diffusion coefficients for the Lennard-Jones and hard sphere fluids are related by Dej = DNs(aB) exp (--e/2kB T) where σB=σLJ(2/[1+ii(1+2kBT/ε)])1/6, the effective hard sphere diameter, is the (average) distance of closest approach in collisions between molecules which interact with the positive part of the LJ potential, and the Arrhenius term reflects the influence of the negative part. σLJ and ε are the size and well depth parameters. Measured diffusion coefficients of the halomethane liquids are reproduced by the equation over wide ranges of temperature and density and do not reveal any influence of the inelastic effects associated with molecular anisotropy

Inherent Structure Entropy of Supercooled Liquids

We present a quantitative description of the thermodynamics in a supercooled binary Lennard Jones liquid via the evaluation of the degeneracy of the inherent structures, i.e. of the number of potential energy basins in configuration space. We find that for supercooled states, the contribution of the inherent structures to the free energy of the liquid almost completely decouples from the vibrational contribution. An important byproduct of the presented analysis is the determination of the Kauzmann temperature for the studied system. The resulting quantitative picture of the thermodynamics of the inherent structures offers new suggestions for the description of equilibrium and out-of-equilibrium slow-dynamics in liquids below the Mode-Coupling temperature.Comment: 11 pages of Latex, 3 figure

Potential energy landscape-based extended van der Waals equation

The inherent structures ({\it IS}) are the local minima of the potential energy surface or landscape, $U({\bf r})$, of an {\it N} atom system. Stillinger has given an exact {\it IS} formulation of thermodynamics. Here the implications for the equation of state are investigated. It is shown that the van der Waals ({\it vdW}) equation, with density-dependent $a$ and $b$ coefficients, holds on the high-temperature plateau of the averaged {\it IS} energy. However, an additional ``landscape'' contribution to the pressure is found at lower $T$. The resulting extended {\it vdW} equation, unlike the original, is capable of yielding a water-like density anomaly, flat isotherms in the coexistence region {\it vs} {\it vdW} loops, and several other desirable features. The plateau energy, the width of the distribution of {\it IS}, and the ``top of the landscape'' temperature are simulated over a broad reduced density range, $2.0 \ge \rho \ge 0.20$, in the Lennard-Jones fluid. Fits to the data yield an explicit equation of state, which is argued to be useful at high density; it nevertheless reproduces the known values of $a$ and $b$ at the critical point

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

X-ray Diffraction and Molecular Dynamics Study of Medium-range Order in Ambient and Hot Water

We have developed x-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows a precise oxygen-oxygen pair correlation function (PCF) to be directly derived from the Fourier transform of the experimental data resolving shell structure out to ~12 {\AA}, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell-structure in the range 4-12 {\AA} although less agreement is seen for the first peak in the PCF. The Local Structure Index [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the intermediate-range oscillations in the PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water, even at high temperatures, can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water postulated in the liquid-liquid phase transition hypothesis.Comment: Submitted to Phys. Chem. Chem. Phy

Freezing by Monte Carlo Phase-Switch

We describe a Monte Carlo procedure which allows sampling of the disjoint configuration spaces associated with crystalline and fluid phases, within a single simulation. The method utilises biased sampling techniques to enhance the probabilities of gateway states (in each phase) which are such that a global switch (to the other phase) can be implemented. Equilibrium freezing-point parameters can be determined directly; statistical uncertainties prescribed transparently; and finite-size effects quantified systematically. The method is potentially quite general; we apply it to the freezing of hard spheres.Comment: 5 pages, 2 figure

Characterization of prion disease associated with a two-octapeptide repeat insertion

Genetic prion disease accounts for 10–15% of prion disease. While insertion of four or more octapeptide repeats are clearly pathogenic, smaller repeat insertions have an unclear pathogenicity. The goal of this case series was to provide an insight into the characteristics of the 2-octapeptide repeat genetic variant and to provide insight into the risk for Creutzfeldt–Jakob disease in asymptomatic carriers. 2-octapeptide repeat insertion prion disease cases were collected from the National Prion Disease Pathology Surveillance Center (US), the National Prion Clinic (UK), and the National Creutzfeldt–Jakob Disease Registry (Australia). Three largescale population genetic databases were queried for the 2-octapeptide repeat insertion allele. Eight cases of 2-octapeptide repeat insertion were identified. The cases were indistinguishable from the sporadic Creutzfeldt–Jakob cases of the same molecular subtype. Western blot characterization of the prion protein in the absence of enzymatic digestion with proteinase K revealed that 2-octapeptide repeat insertion and sporadic Creutzfeldt–Jakob disease have distinct prion protein profiles. Interrogation of large-scale population datasets suggested the variant is of very low penetrance. The 2-octapeptide repeat insertion is at most a low-risk genetic variant. Predictive genetic testing for asymptomatic blood relatives is not likely to be justified given the low risk

Instantaneous Normal Mode Analysis of Supercooled Water

We use the instantaneous normal mode approach to provide a description of the local curvature of the potential energy surface of a model for water. We focus on the region of the phase diagram in which the dynamics may be described by the mode-coupling theory. We find, surprisingly, that the diffusion constant depends mainly on the fraction of directions in configuration space connecting different local minima, supporting the conjecture that the dynamics are controlled by the geometric properties of configuration space. Furthermore, we find an unexpected relation between the number of basins accessed in equilibrium and the connectivity between them.Comment: 5 pages, 4 figure

The potential energy landscape of a model glass former: thermodynamics, anharmonicities, and finite size effects

It is possible to formulate the thermodynamics of a glass forming system in terms of the properties of inherent structures, which correspond to the minima of the potential energy and build up the potential energy landscape in the high-dimensional configuration space. In this work we quantitatively apply this general approach to a simulated model glass-forming system. We systematically vary the system size between N=20 and N=160. This analysis enables us to determine for which temperature range the properties of the glass former are governed by the regions of the configuration space, close to the inherent structures. Furthermore, we obtain detailed information about the nature of anharmonic contributions. Moreover, we can explain the presence of finite size effects in terms of specific properties of the energy landscape. Finally, determination of the total number of inherent structures for very small systems enables us to estimate the Kauzmann temperature