Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

Entropy, non-ergodicity and non-Gaussian behaviour in ballistic transport

Ballistic transportation introduces new challenges in the thermodynamic properties of a gas of particles. For example, violation of mixing, ergodicity and of the fluctuation-dissipation theorem may occur, since all these processes are connected. In this work, we obtain results for all ranges of diffusion, i.e., both for subdiffusion and superdiffusion, where the bath is such that it gives origin to a colored noise. In this way we obtain the skewness and the non-Gaussian factor for the probability distribution function of the dynamical variable. We put particular emphasis on ballistic diffusion, and we demonstrate that in this case, although the second law of thermodynamics is preserved, the entropy does not reach a maximum and a non-Gaussian behavior occurs. This implies the non-applicability of the central limit theorem.Comment: 9 pages, 2 figure

Changes in toxins, intracellular and dissolved free amino acids of the toxic dinoflagellate Gymnodinium catenatum in response to changes in inorganic nutrients and salinity

19 páginas, 7 figuras, 2 tablas.The paralytic shellfish poison prducing dinoflagellate Gymnodiniun catemrum was subjected to changes in salinity, phosphate, ammonium and nitrate using continuous culture and batch culture methods. In contrast with other algae, this species showed very slow changes in the concentration of intracellular amino acids, in the Gln:Glu ratio, and, in contrast with Alrsandnum spp., only slow changes in toxin content, during such events as N-feeding of Ndeprived cells or during nutrient deprivation. This organism was found to be very susceptible to disturbance; maximum growth rates around 0.25–0.3 day–1 with a minimum C:N mass ratio of 5.5, were attained when cultures were only disturbed by sampling once a day. P-deprived cells were larger (twice the usual C content of 4 ng C cell–1 and volume of 20 pl). The content of free amino acids was always low (5% of cell-N), with low contributions made by arginine (the precursor for paralytic shellfish toxins). Cells growing using ammonium had the lowest C:N ratios and the highest proportion of intracellular amino acids as arginine. The toxin profile (equal mole ratios of dcSTX, GTX5, dcGT2/3 C1 and C2, and half those values for C3 and C4) was stable and the toxin concentration varied between 0.2 and 1 mM STX equivalents (highest when ammonium was not limiting, lowest in P-deprived cells, though as the latter were larger toxin per cell was not so variable). Decreased salinity did not result in increases in toxin content. Significant amounts of amino acids (mainly serine and glycine, with a total often exceeding 4 µM) accumulated in the growth medium during batch growth even though the cultures were not bacteria free.This work was funded by the Natural Environment Research Council (UK) through grants to K.J.F. and a studentship to E.H J. We also acknowledge funding received from the Spanish CICYT: projects MAR95-1791 to B.R. and ALI95- 1012-C05-01 to J.M.F.; the IEO-ESF grant to M.I.R., and the scholarship from Xunta de Galicia which funded M.I.R.'s visit to Swansea.Peer reviewe

The record of a high-energy event in a mud entrapment on the inner shelf off the Guadiana river

Recent environmental changes associated with high-energy events and human impacts were investigated in a mud entrapment confined in the paleo-Guadiana incised valley. Those changes were recorded in a gravity core during the last 2500 years. An erosional event seems to have occurred at ca. 500 cal yr BP but it is not clear how much sediment was removed. This event was followed by an increase in river discharges until ca. 465 cal yr BP while the benthic foraminiferal faunas were dominated by species associated with shallow-water sandy sediments. Upward, sedimentological and benthic foraminiferal variations indicated environmental changes, promoted by variable sediment supplies to the shelf.info:eu-repo/semantics/publishedVersio

Bulk and surface switching in Mn-Fe-based Prussian Blue Analogues

Many Prussian Blue Analogues are known to show a thermally induced phase transition close to room temperature and a reversible, photo-induced phase transition at low temperatures. This work reports on magnetic measurements, X-ray photoemission and Raman spectroscopy on a particular class of these molecular heterobimetallic systems, specifically on Rb0.81Mn[Fe(CN)6]0.95_1.24H2O, Rb0.97Mn[Fe(CN)6]0.98_1.03H2O and Rb0.70Cu0.22Mn0.78[Fe(CN)6]0.86_2.05H2O, to investigate these transition phenomena both in the bulk of the material and at the sample surface. Results indicate a high degree of charge transfer in the bulk, while a substantially reduced conversion is found at the sample surface, even in case of a near perfect (Rb:Mn:Fe=1:1:1) stoichiometry. Thus, the intrinsic incompleteness of the charge transfer transition in these materials is found to be primarily due to surface reconstruction. Substitution of a large fraction of charge transfer active Mn ions by charge transfer inactive Cu ions leads to a proportional conversion reduction with respect to the maximum conversion that is still stoichiometrically possible and shows the charge transfer capability of metal centers to be quite robust upon inclusion of a neighboring impurity. Additionally, a 532 nm photo-induced metastable state, reminiscent of the high temperature Fe(III)Mn(II) ground state, is found at temperatures 50-100 K. The efficiency of photo-excitation to the metastable state is found to be maximized around 90 K. The photo-induced state is observed to relax to the low temperature Fe(II)Mn(III) ground state at a temperature of approximately 123 K.Comment: 12 pages, 8 figure

Driven diffusion in a periodically compartmentalized tube: homogeneity versus intermittency of particle motion

We study the effect of a driving force F on drift and diffusion of a point Brownian particle in a tube formed by identical ylindrical compartments, which create periodic entropy barriers for the particle motion along the tube axis. The particle transport exhibits striking features: the effective mobility monotonically decreases with increasing F, and the effective diffusivity diverges as F → ∞, which indicates that the entropic effects in diffusive transport are enhanced by the driving force. Our consideration is based on two different scenarios of the particle motion at small and large F, homogeneous and intermittent, respectively. The scenarios are deduced from the careful analysis of statistics of the particle transition times between neighboring openings. From this qualitative picture, the limiting small-F and large-F behaviors of the effective mobility and diffusivity are derived analytically. Brownian dynamics simulations are used to find these quantities at intermediate values of the driving force for various compartment lengths and opening radii. This work shows that the driving force may lead to qualitatively different anomalous transport features, depending on the geometry design

Diffusion in Stationary Flow from Mesoscopic Non-equilibrium Thermodynamics

We analyze the diffusion of a Brownian particle in a fluid under stationary flow. By using the scheme of non-equilibrium thermodynamics in phase space, we obtain the Fokker-Planck equation which is compared with others derived from kinetic theory and projector operator techniques. That equation exhibits violation of the fluctuation dissipation-theorem. By implementing the hydrodynamic regime described by the first moments of the non-equilibrium distribution, we find relaxation equations for the diffusion current and pressure tensor, allowing us to arrive at a complete description of the system in the inertial and diffusion regimes. The simplicity and generality of the method we propose, makes it applicable to more complex situations, often encountered in problems of soft condensed matter, in which not only one but more degrees of freedom are coupled to a non-equilibrium bath.Comment: 10 pages, accepted in Phys. Rev.

Diffusion in Stationary Flow from Mesoscopic Non-equilibrium Thermodynamics

We analyze the diffusion of a Brownian particle in a fluid under stationary flow. By using the scheme of non-equilibrium thermodynamics in phase space, we obtain the Fokker-Planck equation which is compared with others derived from kinetic theory and projector operator techniques. That equation exhibits violation of the fluctuation dissipation-theorem. By implementing the hydrodynamic regime described by the first moments of the non-equilibrium distribution, we find relaxation equations for the diffusion current and pressure tensor, allowing us to arrive at a complete description of the system in the inertial and diffusion regimes. The simplicity and generality of the method we propose, makes it applicable to more complex situations, often encountered in problems of soft condensed matter, in which not only one but more degrees of freedom are coupled to a non-equilibrium bath.Comment: 10 pages, accepted in Phys. Rev.