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

Fractional diffusion in periodic potentials

Fractional, anomalous diffusion in space-periodic potentials is investigated. The analytical solution for the effective, fractional diffusion coefficient in an arbitrary periodic potential is obtained in closed form in terms of two quadratures. This theoretical result is corroborated by numerical simulations for different shapes of the periodic potential. Normal and fractional spreading processes are contrasted via their time evolution of the corresponding probability densities in state space. While there are distinct differences occurring at small evolution times, a re-scaling of time yields a mutual matching between the long-time behaviors of normal and fractional diffusion

ONGOING RESEARCH ON SPECIES OF DINOPHYSIS: ALTERNATIVES WITH UNCULTURABLE DINOFLAGELLATES

Dinophysis 200

A dynamic explanation for the origin of the western Mediterranean organic-rich layers

The eastern Mediterranean sapropels are amongst the most intensively investigated phenomena in the palaeoceanographic record , but relatively little has been written regarding the origin of the equivalent of the sapropels in the western Mediterranean, the Organic Rich Layers (ORL's). ORL's are recognised as sediment layers containing enhanced Total Organic Carbon that extend throughout the deep basins of the Western Mediterranean, and are associated with enhanced total barium concentration and a reduced diversity (dysoxic but not anoxic) benthic foraminiferal assemblage. Consequently, it has been suggested that ORL's represent periods of enhanced productivity coupled with reduced deep ventilation, presumably related to increased continental runoff, in close analogy to the sapropels. We demonstrate that despite their superficial similarity, the timing of the deposition of the most recent 1 ORL in the Alboran Sea is different to that of the approximately coincident sapropel, indicating that there are important differences between their modes of formation. We go on to demonstrate, through physical arguments, that a likely explanation for the origin of the Alboran ORLs lies in the response of the Western Mediterranean basin to a strong reduction in surface water density and a shoaling of the interface between intermediate and deep water during the deglacial period. Furthermore, we provide evidence that deep convection had already slowed by the time of Heinrich Event 1, and explore this event as a potential agent for preconditioning deep convection collapse. Important differences between Heinrich-like and deglacial-like influences are highlighted, giving new insights into the response of the western Mediterranean system to external forcing

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