Locally preferred structure in simple atomic liquids

We propose a method to determine the locally preferred structure of model liquids. This latter is obtained numerically as the global minimum of the effective energy surface of clusters formed by small numbers of particles embedded in a liquid-like environment. The effective energy is the sum of the intra-cluster interaction potential and of an external field that describes the influence of the embedding bulk liquid at a mean-field level. Doing so we minimize the surface effects present in isolated clusters without introducing the full blown geometrical frustration present in bulk condensed phases. We find that the locally preferred structure of the Lennard-Jones liquid is an icosahedron, and that the liquid-like environment only slightly reduces the relative stability of the icosahedral cluster. The influence of the boundary conditions on the nature of the ground-state configuration of Lennard-Jones clusters is also discussed.Comment: RevTeX 4, 17 pages, 6 eps figure

Finite TYCZ expansions and cscK metrics

Let $(M, g)$ be a Kaehler manifold whose associated Kaehler form $\omega$ is integral and let $(L, h)\rightarrow (M, \omega)$ be a quantization hermitian line bundle. In this paper we study those Kaehler manifolds $(M, g)$ admitting a finite TYCZ expansion. We show that if the TYCZ expansion is finite then $T_{mg}$ is indeed a polynomial in $m$ of degree $n$, $n=dim M$, and the log-term of the Szeg\"{o} kernel of the disc bundle $D\subset L^*$ vanishes (where $L^*$ is the dual bundle of $L$). Moreover, we provide a complete classification of the Kaehler manifolds admitting finite TYCZ expansion either when $M$ is a complex curve or when $M$ is a complex surface with a cscK metric which admits a radial Kaehler potential

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

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

Molecular dynamics simulation study of the high frequency sound waves in the fragile glass former ortho-terphenyl

Using a realistic flexible molecule model of the fragile glass former orthoterphenyl, we calculate via molecular dynamics simulation the collective dynamic structure factor, recently measured in this system by Inelastic X-ray Scattering. The comparison of the simulated and measured dynamic structure factor, and the study of its properties in an extended momentum, frequency and temperature range allows: i) to conclude that the utilized molecular model gives rise to a dynamic structure factor in agreement with the experimental data, for those thermodynamic states and momentum values where the latter are available; ii) to confirm the existence of a slope discontinuity on the T-dependence of the sound velocity that, at finite Q, takes place at a temperature T_x higher than the calorimetric glass transition temperature T_g; iii) to find that the values of T_x is Q-dependent and that its vanishing Q limit is consistent with T_g. The latter finding is interpreted within the framework of the current description of the dynamics of supercooled liquids in terms of exploration of the potential energy landscape.Comment: RevTex, 9 pages, 10 eps figure

Vibrational origin of the fast relaxation processes in molecular glass-formers

We study the interaction of the relaxation processes with the density fluctuations by molecular dynamics simulation of a flexible molecule model for o-terphenyl (oTP) in the liquid and supercooled phases. We find evidence, besides the structural relaxation, of a secondary vibrational relaxation whose characteristic time, few ps, is slightly temperature dependent. This i) confirms the result by Monaco et al. [Phys. Rev, E 62, 7595 (2000)] of the vibrational nature of the fast relaxation observed in Brillouin Light Scattering (BLS) experiments in oTP; and ii) poses a caveat on the interpretation of the BLS spectra of molecular systems in terms of a purely center of mass dynamics.Comment: RevTeX, 5 pages, 4 eps figure

Effective temperature of active matter

We follow the dynamics of an ensemble of interacting self-propelled motorized particles in contact with an equilibrated thermal bath. We find that the fluctuation-dissipation relation allows for the definition of an effective temperature that is compatible with the results obtained using a tracer particle as a thermometer. The effective temperature takes a value which is higher than the temperature of the bath and it is continuously controlled by the motor intensity