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

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

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

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 Simple Theory of Condensation

A simple assumption of an emergence in gas of small atomic clusters consisting of $c$ particles each, leads to a phase separation (first order transition). It reveals itself by an emergence of ``forbidden'' density range starting at a certain temperature. Defining this latter value as the critical temperature predicts existence of an interval with anomalous heat capacity behaviour $c_p\propto\Delta T^{-1/c}$. The value $c=13$ suggested in literature yields the heat capacity exponent $\alpha=0.077$.Comment: 9 pages, 1 figur

Oscillating flames in open tubes

When a flame passes along a tube that is open at both ends a self induced fluctuating pressure/flow field is created which the flame has to traverse. Here fuel rich (1.1 < ϕ < 1.4) propane-air flames have been filmed travelling along a 20 mm internal diameter quartz tube. Fluctuations in the flame’s progression were observed to increase as the flame propagated, achieving a maximum oscillation amplitude of ±10 mm at 220 Hz that decayed as the flame progressed further towards the end of the tube. The impact of the periodic pressure gradients on the flame shape could be discerned with tongues of unburned reactants pushed into the products as well as the corresponding rapid acceleration of the flame into the unburned mixture. The impact of the fluctuations on flame chemistry was monitored by capturing the CH∗ and C2 chemiluminescence using a high speed colour camera. The CH∗/C2∗ ratio was observed to decrease as the flame was pulled back towards the burned mixture; and increased when the flame was pushed forwards. This was consistent throughout the flame progress even when small oscillations in the flame position were measured. This could be a significant feature of flames in this environment

early nutritional programming and progeny performance is reproductive success already set at birth

Compelling evidence indicates that the environment encountered dur-ing fetal life exerts a profound influence on development, physiological function, and risk of disease in adult mammals (Barker, 2007; Langley-Evans and McMullen, 2010). Development is a plastic process, wherein a range of different phenotypes can be expressed from a given genotype. The developing conceptuses respond to conditions in the environment during sensitive periods of cellular proliferation, differentiation, and maturation, resulting in structural and functional changes in cells, tissues, and organ systems. These changes may have short- and/or long-term consequences for health and disease susceptibility. Hence, the term "programming" has been adopted to describe the process whereby a stimulus or an insult at a critical and sensitive period of fetal or perinatal life has permanent effects on the structure, physiology, and metabolism of different organs and sys-tems. Despite many studies investigating the associations between mater-nal environment during fetal development and the onset of cardiovascular disease, obesity, and diabetes in offspring as adults (McMillen and Robin-son, 2005), few studies have investigated the impact of maternal environ-ment on the reproductive potential of offspring. This paper reviews the existing literature on the effects of prenatal and perinatal nutrition on the development and function of the reproductive system in female and male domestic mammals, with particular emphasis on cattle and sheep

Programming scale-free optics in disordered ferroelectrics

Using the history-dependence of a dipolar glass hosted in a compositionally-disordered lithium-enriched potassium-tantalate-niobate (KTN:Li) crystal, we demonstrate scale-free optical propagation at tunable temperatures. The operating equilibration temperature is determined by previous crystal spiralling in the temperature/cooling-rate phase-space

Potential Energy Landscape Equation of State

Depth, number, and shape of the basins of the potential energy landscape are the key ingredients of the inherent structure thermodynamic formalism introduced by Stillinger and Weber [F. H. Stillinger and T. A. Weber, Phys. Rev. A 25, 978 (1982)]. Within this formalism, an equation of state based only on the volume dependence of these landscape properties is derived. Vibrational and configurational contributions to pressure are sorted out in a transparent way. Predictions are successfully compared with data from extensive molecular dynamics simulations of a simple model for the fragile liquid orthoterphenyl.Comment: RevTeX4, 4 pages, 5 figure