Non-Gaussian energy landscape of a simple model for strong network-forming liquids: Accurate evaluation of the configurational entropy.

We present a numerical study of the statistical properties of the potential energy landscape of a simple model for strong network-forming liquids. The model is a system of spherical particles interacting through a square-well potential, with an additional constraint that limits the maximum number of bonds Nmax per particle. Extensive simulations have been carried out as a function of temperature, packing fraction, and Nmax. The dynamics of this model are characterized by Arrhenius temperature dependence of the transport coefficients and by nearly exponential relaxation of dynamic correlators, i.e., features defining strong glass-forming liquids. This model has two important features: (i) Landscape basins can be associated with bonding patterns. (ii) The configurational volume of the basin can be evaluated in a formally exact way, and numerically with an arbitrary precision. These features allow us to evaluate the number of different topologies the bonding pattern can adopt. We find that the number of fully bonded configurations, i.e., configurations in which all particles are bonded to Nmax neighbors, is extensive, suggesting that the configurational entropy of the low temperature fluid is finite. We also evaluate the energy dependence of the configurational entropy close to the fully bonded state and show that it follows a logarithmic functional form, different from the quadratic dependence characterizing fragile liquids. We suggest that the presence of a discrete energy scale, provided by the particle bonds, and the intrinsic degeneracy of fully bonded disordered networks differentiates strong from fragile behavior.

Energy landscape of a simple model for strong liquids.

We calculate the statistical properties of the energy landscape of a minimal model for strong network-forming liquids. Dynamic and thermodynamic properties of this model can be computed with arbitrary precision even at low temperatures. A degenerate disordered ground state and logarithmic statistics for the local minima energy distribution are the landscape signatures of strong liquid behavior. Differences from fragile liquid properties are attributed to the presence of a discrete energy scale, provided by the particle bonds, and to the intrinsic degeneracy of topologically disordered networks.

Model for reversible colloidal gelation.

We report a numerical study, covering a wide range of packing fraction Phi and temperature T, for a system of particles interacting via a square well potential supplemented by an additional constraint on the maximum number n(max) of bonded interactions. We show that, when n(max)<6, the liquid-gas coexistence region shrinks, giving access to regions of low Phi where dynamics can be followed down to low T without an intervening phase separation. We characterize these arrested states at low densities (gel states) in terms of structure and dynamical slowing down, pointing out features which are very different from the standard glassy states observed at high Phi values.

Liquid stability in a model for ortho-terphenyl.

We report an extensive study of the phase diagram of a simple model for ortho-terphenyl, focusing on the limits of stability of the liquid state. Reported data extend previous studies of the same model to both lower and higher densities and to higher temperatures. We estimate the location of the homogeneous liquid-gas nucleation line and of the spinodal locus. Within the potential energy landscape formalism, we calculate the distributions of depth, number, and shape of the potential energy minima and show that the statistical properties of the landscape are consistent with a Gaussian distribution of minima over a wide range of volumes. We report the volume dependence of the parameters entering in the Gaussian distribution (amplitude, average energy, variance). We finally evaluate the locus where the configurational entropy vanishes, the so-called Kauzmann line, and discuss the relative location of the spinodal and Kauzmann loci.

Test of nonequilibrium thermodynamics in glassy systems: the soft-sphere case.

The scaling properties of the soft-sphere potential allow the derivation of an exact expression for the pressure of a frozen liquid, i.e., the pressure corresponding to configurations which are local minima in its multidimensional potential energy landscape. The existence of such a relation offers the unique possibility for testing the recently proposed extension of the liquid free energy to glassy out-of-equilibrium conditions and the associated expression for the temperature of the configurational degrees of freedom. We demonstrate that the nonequilibrium free energy provides an exact description of the soft-sphere pressure in glass states.

Dynamics and configurational entropy in the Lewis-Wahnström model for supercooled orthoterphenyl.

We study thermodynamic and dynamic properties of a rigid model of the fragile glass-forming liquid orthoterphenyl. This model, introduced by Lewis and Wahnström in 1993, collapses each phenyl ring to a single interaction site; the intermolecular site-site interactions are described by the Lennard-Jones potential whose parameters have been selected to reproduce some bulk properties of the orthoterphenyl molecule. A system of N=343 molecules is considered in a wide range of densities and temperatures, reaching simulation times up to 1 micros. Such long trajectories allow us to equilibrate the system at temperatures below the mode coupling temperature T(c) at which the diffusion constant reaches values of order 10(-10) cm(2)/s and thereby to sample in a significant way the potential energy landscape in the entire temperature range. Working within the inherent structures thermodynamic formalism, we present results for the temperature and density dependence of the number, depth and shape of the basins of the potential energy surface. We evaluate the total entropy of the system by thermodynamic integration from the ideal-noninteracting-gas state and the vibrational entropy approximating the basin free energy with the free energy of 6N-3 harmonic oscillators. We evaluate the configurational part of the entropy as a difference between these two contributions. We study the connection between thermodynamical and dynamical properties of the system. We confirm that the temperature dependence of the configurational entropy and of the diffusion constant, as well as the inverse of the characteristic structural relaxation time, are strongly connected in supercooled states; we demonstrate that this connection is well represented by the Adam-Gibbs relation, stating a linear relation between logD and the quantity 1/TS(c). This relation is found to hold both above and below the critical temperature T(c)-as previously found in the case of silica-supporting the hypothesis that a connection exists between the number of basins and the connectivity properties of the potential energy surface.

Water and its energy landscape.

We present an overview of the recent studies on the properties of the potential energy surface for a simple model of water. We emphasize the relations between PES properties and dynamics in supercooled states for the model and discuss possible future application of the PES studies.

Dynamics of supercooled water in configuration space.

We study the potential energy surface (PES) sampled by a liquid modeled via the widely studied extended simple point charge (SPC/E) model for water. We characterize the curvature of the PES by calculating the instantaneous normal mode (INM) spectrum for a wide range of densities and temperatures. We discuss the information contained in the INM density of states, which requires additional processing to be unambiguously associated with the long-time dynamics. For the SPC/E model, we find that the slowing down of the dynamics in the supercooled region-where the ideal mode coupling theory has been used to describe the dynamics-is controlled by the reduction in the number of directions in configuration space that allow a structural change. We find that the fraction f(dw) of the double-well directions in configuration space determines the value of the diffusion constant D, thereby relating a property of the PES to a macroscopic dynamic quantity; specifically, it appears that square root D is approximately linear in f(dw). Our findings are consistent with the hypothesis that, at the mode coupling crossover temperature, dynamical processes based on the free exploration of configuration space vanish, and processes requiring activation dominate. Hence, the reduction of the number of directions allowing free exploration of configuration space is the mechanism of diffusion implicitly implemented in the ideal mode coupling theory. Additionally, we find a direct relationship between the number of basins sampled by the system and the number of free directions. In this picture, diffusion appears to be related to geometrical properties of the PES, and to be entropic in origin.

Thermodynamic and structural aspects of the potential energy surface of simulated water.

Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition is a topic of considerable interest. The potential energy surface of model liquids has been increasingly studied, since it provides a connection between the configurational component of the partition function on the one hand, and the system dynamics on the other. This connection is most obvious at low temperatures, where the motion of the system can be partitioned into vibrations within a basin of attraction and infrequent interbasin transitions. In this work, we present a description of the potential energy surface properties of supercooled liquid water. The dynamics of this model have been studied in great detail in recent years. We locate the minima sampled by the liquid by "quenches" from equilibrium configurations generated via molecular dynamics simulations, and then calculate the temperature and density dependence of the basin energy, degeneracy, and shape. The temperature dependence of the energy of the minima is qualitatively similar to simple liquids, but has anomalous density dependence. The unusual density dependence is also reflected in the configurational entropy, the thermodynamic measure of degeneracy. Finally, we study the structure of simulated water at the minima, which provides insight on the progressive tetrahedral ordering of the liquid on cooling.

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 mode-coupling theory. We find that the diffusion constant depends on the fraction of directions in configuration space connecting different local minima, supporting the hypothesis that the dynamics are controlled by the geometric properties of configuration space. Furthermore, we find a relation between the number of basins accessed in equilibrium and the connectivity between them.

Radiation damage to triplex DNA induced by gamma-rays: a footprinting study and Monte Carlo simulation.

PURPOSE: This study is aimed at comparing the radiosensitivity of a 21-mer DNA fragment in duplex and triplex form (Py x Pu duplex and Py x Pu:Py triplex) and to give insights into the fine structural features due to the different strandedness. MATERIALS AND METHODS: The triplex sample was characterized by means of electrophoretic mobility, circular dichroism spectra and UV melting experiments. Triplex and duplex, labelled on the homopyrimidine or homopurine strand, were irradiated with 60Co gamma-rays. The samples were analysed by sequencing gel electrophoresis and the patterns of relative probabilities of frank strand breakage (FSB) and alkali-revealed breakage (ARB) at each nucleotide site were determined. Relative probabilities of OH* radical attack to duplex and triplex DNA built up with a molecular modelling software were calculated using a previously reported simulation procedure (Sy et al. 1997). The experimental data were compared with the results of the theoretical simulations of OH* radical attack to DNA. RESULTS: Globally, the duplex is more attacked than the triplex, mainly in the Pu strand. Sequence-dependent variations of FSB and FSB+ARB probabilities in both duplex and triplex were revealed. No significant differences between the patterns of damage in the triplex and in the duplex were observed. CONCLUSIONS: The presence of the third Py strand located in the major groove of the DNA duplex modifies the total yields of radiation-induced DNA damage, but not the sequence-dependent patterns of relative probability of damage at each nucleotide site.

Configurational entropy and diffusivity of supercooled water

As a liquid approaches the glass transition, its properties are dominated by local potential minima in its energy landscape. The liquid experiences localized vibrations in the basins of attraction surrounding the minima, and rearranges via relatively infrequent inter-basin jumps. As a result, the liquid dynamics at low temperature are related to the system's exploration of its own configuration space. The 'thermodynamic approach' to the glass transition considers the reduction in configuration space explored as the system cools, and predicts that the configurational entropy (a measure of the number of local potential energy minima sampled by the liquid) is related to the diffusion constant. Here we report a stringent test of the thermodynamic approach for liquid water (a convenient system to study because of an anomalous pressure dependence in the diffusion constant). We calculate the configurational entropy at points spanning a large region of the temperature-density plane, using a model that reproduces the dynamical anomalies of liquid water. We find that the thermodynamic approach can be used to understand the characteristic dynamic anomalies, and that the diffusive dynamics are governed by the configurational entropy. Our results indicate that the thermodynamic approach might be extended to predict the dynamical behaviour of supercooled liquids in general.

Free energy surface of supercooled water

We present a detailed analysis of the free energy surface of a well characterized rigid model for water in supercooled states. We propose a functional form for the liquid free energy, supported by recent theoretical predictions [Y. Rosenfeld and P. Tarazona, Mol. Phys. 95, 141 (1998)], and use it to locate the position of a liquid-liquid critical point at T(C')=130+/-5 K, P(C')=290+/-30 MPa, and rho(C')=1.10+/-0.03 g/cm(3). The observation of the critical point strengthens the possibility that the extended simple point charge model of water may undergo a liquid-liquid phase transition. Finally, we discuss the possibility that the approach to the liquid-liquid critical point could be pre-empted by the glass transition.

Solution of lattice gas models in the generalized ensemble on the Bethe lattice.

We present the exact Bethe lattice solution for a lattice gas Potts model defined in the generalized ensemble which was previously studied in elucidating the anomalous thermodynamic properties of water. For this model the locus of density maxima (TMD), the locus of isothermal compressibility extrema, (TEC), the spinodal curve, and the percolation curve for four hydrogen bonded molecules are calculated using the Bethe lattice solution. The results confirm qualitative relationships between the TMD, the TEC, and the percolation curve obtained previously from a mean field calculation.