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.Comment: RevTeX 4, 8 pages, 8 eps figure

Supersymmetric Langevin equation to explore free energy landscapes

The recently discovered supersymmetric generalizations of Langevin dynamics and Kramers equation can be utilized for the exploration of free energy landscapes of systems whose large time-scale separation hampers the usefulness of standard molecular dynamics techniques. The first realistic application is here presented. The system chosen is a minimalist model for a short alanine peptide exhibiting a helix-coil transition.Comment: 9 pages, 9 figures, RevTeX 4 v2: conclusive section enlarged, references adde

Cut-off nonlinearities in the low-temperature vibrations of glasses and crystals

We present a computer simulation study of glassy and crystalline states using the standard Lennard-Jones interaction potential that is truncated at a finite cut-off distance, as is typical of many computer simulations. We demonstrate that the discontinuity at the cut-off distance in the first derivative of the potential (corresponding to the interparticle force) leads to the appearance of cut-off nonlinearities. These cut-off nonlinearities persist into the very-low-temperature regime thereby affecting low-temperature thermal vibrations, which leads to a breakdown of the harmonic approximation for many eigen modes, particularly for low-frequency vibrational modes. Furthermore, while expansion nonlinearities which are due to higher order terms in the Taylor expansion of the interaction potential are usually ignored at low temperatures and show up as the temperature increases, cut-off nonlinearities can become most significant at the lowest temperatures. Anharmonic effects readily show up in the elastic moduli which not only depend on the eigen frequencies, but are crucially sensitive to the eigen vectors of the normal modes. Whereas, those observables that rely mainly on static structural information or just the eigen frequencies, such as the vibrational density of states, total potential energy, and specific heat, show negligible dependence on the presence of the cut-off. Similar aspects of nonlinear behavior have recently been reported in model granular materials, where the constituent particles interact through finite-range, purely-repulsive potentials. These nonlinearities have been ascribed to the nature of the sudden cut-off at contact in the force-law, thus we demonstrate that cut-off nonlinearities emerge as a general feature of ordered and disordered solid state systems interacting through truncated potentials.Comment: 20 pages, 16 figures, 2 table

Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation

We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average dissipated work and the average hopping number in two state systems. It is shown how these quantities only depend on two parameters that characterize the folding/unfolding kinetics of the molecule: the fragility and the coexistence hopping rate. The latter has to be rescaled to take into account the appropriate experimental setup. Finally we carry out pulling experiments with optical tweezers in a specifically designed DNA hairpin that shows two-state cooperative folding. We then use these experimental results to validate our theoretical predictions.Comment: 28 pages, 12 figure

Equilibrium and out of equilibrium thermodynamics in supercooled liquids and glasses

We review the inherent structure thermodynamical formalism and the formulation of an equation of state for liquids in equilibrium based on the (volume) derivatives of the statistical properties of the potential energy surface. We also show that, under the hypothesis that during aging the system explores states associated to equilibrium configurations, it is possible to generalize the proposed equation of state to out-of-equilibrium conditions. The proposed formulation is based on the introduction of one additional parameter which, in the chosen thermodynamic formalism, can be chosen as the local minima where the slowly relaxing out-of-equilibrium liquid is trapped.Comment: 7 pages, 4 eps figure

Kovacs effects in an aging molecular liquid

We study by means of molecular dynamics simulations the aging behavior of a molecular model of ortho-terphenyl. We find evidence of a a non-monotonic evolution of the volume during an isothermal-isobaric equilibration process, a phenomenon known in polymeric systems as Kovacs effect. We characterize this phenomenology in terms of landscape properties, providing evidence that, far from equilibrium, the system explores region of the potential energy landscape distinct from the one explored in thermal equilibrium. We discuss the relevance of our findings for the present understanding of the thermodynamics of the glass state.Comment: RevTeX 4, 4 pages, 5 eps figure

A phytosociological study of the deciduous oak woods of Sardinia (Italy)

We present here the results from a phytosociological and synchorological study of the deciduous oak woods of Sardinia. This vegetation analysis has allowed the individuation of three new associations: Lonicero implexae-Quercetum virgilianae, Ornithogalo pyrenaici-Quercetum ichnusae and Glechomo sardoae-Quercetum congestae. The Lonicero implexae-Quercetum virgilianae association includes the woods on calcareous substrata spread throughout Northern Sardinia, which can occasionally be found in southern areas; the first of these are rich in mesophilous species and are attributed to the subassociation cyclaminetosum repandi, while the others are referred to quercetosum virgilianae. The Ornithogalo pyrenaici-Quercetum ichnusae association, more widely distributed in Central-Northern Sardinia, includes the climatophilous deciduous woods that are found on lithological substrata of a non-carbonatic nature, and in particular, on andesites, trachytes and metarenites. The typical aspect is referred to the subassociation cytisetosum villosi, while the subassociation ilicetosum aquifolii includes the more mesophilous woods on basaltic substrata. The Glechomo sardoae- Quercetum congestae association always includes the woods found on the non-carbonatic substrata in the higher altitude areas with an oceanic pluviseasonal temperate bioclimate. Of this, the subassociation quercetosum congestae, on the granite areas, and oenanthetosum pimpinelloidis, on those metamorphic and of basalt, are proposed. At the higher hierarchical levels, the association Lonicero implexae-Quercetum virgilianae is referred to the endemic Sardinian-Corsican suballiance Clematido cirrhosae-Quercenion ilicis, of the alliance Fraxino orni-Quercion ilicis, while for the other associations the new suballiance Paeonio morisii-Quercenion ichnusae, (holotypus: Glechoma sardoae-Quercetum congestae ass. nova) particular to the Sardinian biogeographic subprovince, is proposed, of the alliance Pino calabricae-Quercion congestae, the order Quercetalia pubescentipetraeae, and the class Querco roboris-Fagetea sylvaticae

Glassy behavior of a homopolymer from molecular dynamics simulations

We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the theta point, and the structure factor, as a function of time. The observation of these quantities show a close resemblance to those measured in structural glasses and suggest that the polymer chain in its low temperature phase is in a glassy phase, with its dynamics dominated by traps. In equilibrium, at low temperature, we observe the trapping of the monomers and a slowing down of the overall motion of the polymer as well as non-exponential relaxation of the structure factor. In out-of-equilibrium, at low temperatures, we compute the two-time quantities and observe breaking of ergodicity in a range of waiting times, with the onset of aging.Comment: 11 pages, 4 figure