Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Teleutomyrmex schneideri Kutter, 1950 en España (Hymenoptera, Formicidae)

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Catastrophic regime shifts in model ecological communities are true phase transitions

Ecosystems often undergo abrupt regime shifts in response to gradual external changes. These shifts are theoretically understood as a regime switch between alternative stable states of the ecosystem dynamical response to smooth changes in external conditions. Usual models introduce nonlinearities in the macroscopic dynamics of the ecosystem that lead to different stable attractors among which the shift takes place. Here we propose an alternative explanation of catastrophic regime shifts based on a recent model that pictures ecological communities as systems in continuous fluctuation, according to certain transition probabilities, between different micro-states in the phase space of viable communities. We introduce a spontaneous extinction rate that accounts for gradual changes in external conditions, and upon variations on this control parameter the system undergoes a regime shift with similar features to those previously reported. Under our microscopic viewpoint we recover the main results obtained in previous theoretical and empirical work (anomalous variance, hysteresis cycles, trophic cascades). The model predicts a gradual loss of species in trophic levels from bottom to top near the transition. But more importantly, the spectral analysis of the transition probability matrix allows us to rigorously establish that we are observing the fingerprints, in a finite size system, of a true phase transition driven by background extinctions.Comment: 19 pages, 11 figures, revised versio

Imperfect Imitation Can Enhance Cooperation

The promotion of cooperation on spatial lattices is an important issue in evolutionary game theory. This effect clearly depends on the update rule: it diminishes with stochastic imitative rules whereas it increases with unconditional imitation. To study the transition between both regimes, we propose a new evolutionary rule, which stochastically combines unconditional imitation with another imitative rule. We find that, surprinsingly, in many social dilemmas this rule yields higher cooperative levels than any of the two original ones. This nontrivial effect occurs because the basic rules induce a separation of timescales in the microscopic processes at cluster interfaces. The result is robust in the space of 2x2 symmetric games, on regular lattices and on scale-free networks.Comment: 4 pages, 4 figure

A theorem on the absence of phase transitions in one-dimensional growth models with onsite periodic potentials

We rigorously prove that a wide class of one-dimensional growth models with onsite periodic potential, such as the discrete sine-Gordon model, have no phase transition at any temperature $T>0$. The proof relies on the spectral analysis of the transfer operator associated to the models. We show that this operator is Hilbert-Schmidt and that its maximum eigenvalue is an analytic function of temperature.Comment: 6 pages, no figures, submitted to J Phys A: Math Ge

Historical warming and climate sensitivity

In this dissertation, we study the climate sensitivity of the Earth. The climate sensitivity quantifies the response of the Earth system to radiative forcing, in particular, the radiative forcing induced by humans. We use both complex climate modelling and observations from the historical record for this endeavour. We analyse these data sources from the perspective of a conceptual framework based on the Earth’s energy budget. The foci of our study are on two wide topics. The first topic estimates how sensitive the Earth’s climate is to carbon dioxide using the historical warming. We use two quantities to measure the sensitivity: the transient climate response (TCR) and the long-term equilibrium climate sensitivity (ECS). Past studies analysed the historical observations of warming and forcing in the light of the Earth’s energy budget to estimate TCR and ECS. We ascertain that some of these calculations underestimate TCR and ECS. First, we analyse the disadvantages of past observational estimates concerning the uncertainties in the anthropogenic radiative forcing. Based on this analysis, we select the post-1970s period. Then we link the modelled warming in this period in complex climate models with the corresponding modelled TCR and ECS. This relationship between warming and sensitivity, and the observed post-1970s warming allow us to estimate TCR and ECS. Our TCR estimate is higher than the past estimates, and we find that this difference can be explained by past studies assuming that the ocean mixed-layer is equilibrated. Our ECS estimate is also higher than some past estimates and is in line with other studies that accounted for the effects of an evolving sea-surface temperature pattern. The evolving sea surface temperature pattern changes the feedback mechanisms on the warming and temporarily counteract the radiative forcing. The second topic explores the role of clouds in this temporary dampening of the transient global warming. We find that the cloud feedback not only acts directly with the sea surface temperature patterns that arise when the climate system is out of equilibrium, but clouds also affect other relevant feedback mechanisms. Past studies found that the evolving sea surface temperature pattern changes the radiative response between decadal and centennial timescales. A proposed mechanism connects clouds with the evolving pattern. They also show in observations the relationship between the decadal cloud variations and the corresponding variations in the radiative response of the Earth. Assisted by a complex climate model, we find that not only clouds link the evolving pattern with the radiative response, but also that they influence the remaining relevant mechanisms. To unravel the role of clouds, we use a cloud-locking technique which inhibits cloud feedback. We find that: a) clouds explain almost half of the difference in the radiative response between decadal and centennial timescales, and b) a synergy between cloud processes, lapse-rate and water-vapour feedback provides the tropical free-tropospheric warming that the proposed physical mechanism needs.In dieser Dissertation untersuchen wir die Klimasensitivität der Erde. Die Klimasensitivität misst die Reaktion des Erdsystems auf den Strahlungsantrieb unter besonderer Berücksichtigung des anthropogenen Strahlungantriebes. Dazu verwenden wir sowohl komplexe Klimamodelle, als auch historische Beobachtungen. Wir analysieren beide Datenquellen im physikalisch-konzeptuellen Rahmen des Wärmehaushaltes der Erde. Die Schwerpunkte unserer Untersuchung liegen auf zwei großen Themengebieten. Das erste Thema schätzt basierend auf der historischen Erwärmung ab wie sensibel das Klima der Erde auf Kohlendioxyd reagiert. Wir verwenden zwei Maße, um die Sensitivität zu messen: die kurzfristige emph{Transient Climate Response} (TCR) und die langfristige emph{Equilibrium Climate Sensitivity} (ECS). Vorherige Untersuchungen analysieren historische Beobachtungen der Erwärmung und des Strahlungsantriebes mit dem Wärmehaushalt der Erde, um die TCR und die ECS zu berechnen. Wir stellen fest, dass einige dieser früheren Berechnungen die TCR und die ECS unterschätzen. In dieser Dissertation analysieren wir zuerst die Nachteile dieser früheren Schätzungen in Bezug auf die Messunsicherheit des anthropogenen Strahlungsantriebs. Aufgrund der niedriegeren Messunsicherheit des anthropogenen Aerosolstrahlungsantriebes wählen wir für unsere Analyse den Zeitraum ab den 1970-iger Jahren aus. Dann verbinden wir die modellierte Erwärmung in diesem Zeitraum mit den entsprechenden modellierten TCRs und ECSs. Die ermittelte Beziehung zwischen Erwärmung und Sensitivität und die tatsächliche Erwärmung seit den 1970-iger Jahren macht eine neue Schätzungen der tatsächliche TCR und ECS möglich. Unsere Schätzung der TCR ist höher als die früheren Schätzungen. Wir stellen fest, dass der Unterschied auf eine Annahme vorheriger Schätzungen zurückführbar ist: Bezüglich des Wärmeaustausches ist der gutgemischte Ozean stationär. Unsere Schätzung der ECS ist ebenfalls höher als diejenigen einiger vorheriger Schätzungen. Unsere Schätzung stimmt mit anderen Schätzungen, die die Effekte eines sich entwickelnden Musters der Meeresoberlfächnetemperatur berücksichtigen, überein. Dieses Muster verändert die Rückkopplungsmechanismen und wirkt dem Strahlungsantrieb vorläufig entgegen. Das zweite Thema handelt von der Rolle der Wolken in dieser vorläufigen Dämpfung der transienten globalen Erwärmung. Wir entdecken, dass die Wolkenrückkopplung nicht nur eine direkte Wirkung hat, sondern auch, dass die Wolken andere relevante Rückkopplungen beeinflussen. Vorherige Untersuchungen stellten fest, dass das sich entwickelnde Muster der Meeresoberflächentemperatur die Strahlungsreaktion zwischen zehn- und hundertjährigen Zeitskalen verändert. Ein möglicher physikalischer Mechanismus, der die Wolken mit dem sich entwickelnden Muster verknüpft, wurde vorgeschlagen. Die Beziehung zwischen den zehnjährigen Schwankungen der Wolken und den entsprechenden Änderungen in der Strahlungsreaktion der Erde konnte bereits durch Beobachtungen verifiziert werden. Mit Hilfe eines komplexen Kimamodells finden wir, dass nicht nur die Wolken das sich entwickelnde Muster mit der Strahlungsreaktion verknüpfen, sondern auch, dass die Wolke die übrigen relevanten Mechanismen beeinflussen. Um die Rolle der Wolken zu untersuchen, verwenden wir eine ''cloud-locking'' Technik, die die Wolkenrückkopplung unterbindet. Unser Resultat ist: a) die Wolken erklären fast die Hälfte der Änderung der Strahlungsreaktion zwischen zehn- und hundertjährigen Zeitskalen und b) eine Synergie zwischen Wolkenprozessen, die Temperatur-Gradient- und die Wasserdampfrückkopplung liefert die tropische frei-troposphärische Erwärmung, die der vorgeschlagene physikalische Mechanismus benötigt

Environmental enrichment results in both brain connectivity efficiency and selective improvement in different behavioral tasks

Exposure to environmental enrichment (EE) has been a useful model for studying the effects of experience on brain plasticity, but to date, few is known about the impact of this condition on the brain functional networks that probably underlies the multiple behavioral improvements. Hence, we assessed the effect of an EE protocol in adult Wistar rats on the performance in several behavioral tasks testing different domains (Open field (OP): locomotor activity; Elevated-zero maze (EZM): anxiety-related behaviors; 5-choice serial reaction time task (5-CSRTT): attentional processes; 4-arm radial water maze (4-RAWM): spatial memory) in order to check its effectiveness in a wide range of functions. After this, we analyzed the functional brain connectivity underlying each experimental condition through cytochrome C oxidase (COx) histochemistry. Our EE protocol reduced both locomotor activity in the OP and anxiety-related behaviors in the EZM. On the other hand, enriched rats showed more accuracy in the 4-RAWM, whereas 5-CSRTT performance was not significantly ameliorated by EE condition. In relation to COx functional connectivity, we found that EE reduced the number of strong positive correlations both in basal and training conditions, suggesting a modulating effect on specific brain connections. Our results suggest that EE seems to have a selective effect on specific brain regions, such as prefrontal cortex and hippocampus, leading to a more efficient brain connectivity.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. PPIT.UMA.B1.2017/3