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

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

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

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

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

On the Yang-Lee and Langer singularities in the O(n) loop model

We use the method of `coupling to 2d QG' to study the analytic properties of the universal specific free energy of the O(n) loop model in complex magnetic field. We compute the specific free energy on a dynamical lattice using the correspondence with a matrix model. The free energy has a pair of Yang-Lee edges on the high-temperature sheet and a Langer type branch cut on the low-temperature sheet. Our result confirms a conjecture by A. and Al. Zamolodchikov about the decay rate of the metastable vacuum in presence of Liouville gravity and gives strong evidence about the existence of a weakly metastable state and a Langer branch cut in the O(n) loop model on a flat lattice. Our results are compatible with the Fonseca-Zamolodchikov conjecture that the Yang-Lee edge appears as the nearest singularity under the Langer cut.Comment: 38 pages, 16 figure

Direct single-molecule observation of calcium-dependent misfolding in human neuronal calcium sensor-1

Neurodegenerative disorders are strongly linked to protein misfolding, and crucial to their explication is a detailed understanding of the underlying structural rearrangements and pathways that govern the formation of misfolded states. Here we use single-molecule optical tweezers to monitor misfolding reactions of the human neuronal calcium sensor-1, a multispecific EF-hand protein involved in neurotransmitter release and linked to severe neurological diseases. We directly observed two misfolding trajectories leading to distinct kinetically trapped misfolded conformations. Both trajectories originate from an on-pathway intermediate state and compete with native folding in a calcium-dependent manner. The relative probability of the different trajectories could be affected by modulating the relaxation rate of applied force, demonstrating an unprecedented real-time control over the free-energy landscape of a protein. Constant-force experiments in combination with hidden Markov analysis revealed the free-energy landscape of the misfolding transitions under both physiological and pathological calcium concentrations. Remarkably for a calcium sensor, we found that higher calcium concentrations increased the lifetimes of the misfolded conformations, slowing productive folding to the native state. We propose a rugged, multidimensional energy landscape for neuronal calcium sensor-1 and speculate on a direct link between protein misfolding and calcium dysregulation that could play a role in neurodegeneration

Finite-Size Effects in a Supercooled Liquid

We study the influence of the system size on various static and dynamic properties of a supercooled binary Lennard-Jones liquid via computer simulations. In this way, we demonstrate that the treatment of systems as small as N=65 particles yields relevant results for the understanding of bulk properties. Especially, we find that a system of N=130 particles behaves basically as two non-interacting systems of half the size.Comment: Proceedings of the III Workshop on Non Equilibrium Phenomena in Supercooled Fluids, Glasses and Amorphous Materials, Sep 2002, Pis

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