Dynamics of driven three-dimensional thin films: from hdrophilic to superhydrophobic substrates

We study the forced displacement of a thin film of fluid in contact with vertical and inclined substrates of different wetting properties, that range from hydrophilic to hydrophobic, using the lattice-Boltzmann method. We study the stability and pattern formation of the contact line in the hydrophilic and superhydrophobic regimes, which correspond to wedge-shaped and nose-shaped fronts, respectively. We find that contact lines are considerably more stable for hydrophilic substrates and small inclination angles. The qualitative behavior of the front in the linear regime remains independent of the wetting properties of the substrate as a single dispersion relation describes the stability of both wedges and noses. Nonlinear patterns show a clear dependence on wetting properties and substrate inclination angle. The effect is quantified in terms of the pattern growth rate, which vanishes for the sawtooth pattern and is finite for the finger pattern. Sawtooth shaped patterns are observed for hydrophilic substrates and low inclination angles, while finger-shaped patterns arise for hydrophobic substrates and large inclination angles. Finger dynamics show a transient in which neighboring fingers interact, followed by a steady state where each finger grows independently.

Pattern selection in a lattice of pulse-coupled oscillators

We study spatio-temporal pattern formation in a ring of N oscillators with inhibitory unidirectional pulselike interactions. The attractors of the dynamics are limit cycles where each oscillator fires once and only once. Since some of these limit cycles lead to the same pattern, we introduce the concept of pattern degeneracy to take it into account. Moreover, we give a qualitative estimation of the volume of the basin of attraction of each pattern by means of some probabilistic arguments and pattern degeneracy, and show how they are modified as we change the value of the coupling strength. In the limit of small coupling, our estimative formula gives a pefect agreement with numerical simulations.

Dynamics of driven three-dimensional thin films: from hdrophilic to superhydrophobic substrates

We study the forced displacement of a thin film of fluid in contact with vertical and inclined substrates of different wetting properties, that range from hydrophilic to hydrophobic, using the lattice-Boltzmann method. We study the stability and pattern formation of the contact line in the hydrophilic and superhydrophobic regimes, which correspond to wedge-shaped and nose-shaped fronts, respectively. We find that contact lines are considerably more stable for hydrophilic substrates and small inclination angles. The qualitative behavior of the front in the linear regime remains independent of the wetting properties of the substrate as a single dispersion relation describes the stability of both wedges and noses. Nonlinear patterns show a clear dependence on wetting properties and substrate inclination angle. The effect is quantified in terms of the pattern growth rate, which vanishes for the sawtooth pattern and is finite for the finger pattern. Sawtooth shaped patterns are observed for hydrophilic substrates and low inclination angles, while finger-shaped patterns arise for hydrophobic substrates and large inclination angles. Finger dynamics show a transient in which neighboring fingers interact, followed by a steady state where each finger grows independently.

Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

Background: Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion: Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution.

dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes

H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address these questions, we have analyzed the contribution of dKDM5/LID, the main H3K4me3 demethylase in Drosophila, to the regulation of the pattern of H3K4me3. ChIP-seq results show that, at developmental genes, dKDM5/LID localizes at TSS and regulates H3K4me3. dKDM5/LID target genes are highly transcribed and enriched in active RNApol II and H3K36me3, suggesting a positive contribution to transcription. Expression-profiling show that, though weakly, dKDM5/LID target genes are significantly downregulated upon dKDM5/LID depletion. Furthermore, dKDM5/LID depletion results in decreased RNApol II occupancy, particularly by the promoter-proximal Pol lloser5 form. Our results also show that ASH2, an evolutionarily conserved factor that locates at TSS and is required for H3K4me3, binds and positively regulates dKDM5/LID target genes. However, dKDM5/LID and ASH2 do not bind simultaneously and recognize different chromatin states, enriched in H3K4me3 and not, respectively. These results indicate that, at developmental genes, dKDM5/LID and ASH2 coordinately regulate H3K4me3 at TSS and that this dynamic regulation contributes to transcription.

Unraveling dynamics of human physical activity patterns in chronic pain conditions.

Chronic pain is a complex disabling experience that negatively affects the cognitive, affective and physical functions as well as behavior. Although the interaction between chronic pain and physical functioning is a well-accepted paradigm in clinical research, the understanding of how pain affects individuals' daily life behavior remains a challenging task. Here we develop a methodological framework allowing to objectively document disruptive pain related interferences on real-life physical activity. The results reveal that meaningful information is contained in the temporal dynamics of activity patterns and an analytical model based on the theory of bivariate point processes can be used to describe physical activity behavior. The model parameters capture the dynamic interdependence between periods and events and determine a 'signature' of activity pattern. The study is likely to contribute to the clinical understanding of complex pain/disease-related behaviors and establish a unified mathematical framework to quantify the complex dynamics of various human activities.

Dynamics of transient domain structures in nematic liquid crystals: The splay Fréedericksz transition

We discuss the dynamics of the transient pattern formation process corresponding to the splay Fréedericksz transition. The emergence and subsequent evolution of the spatial periodicity is here described in terms of the temporal dependence of the wave numbers corresponding to the maxima of the structure factor. Situations of perpendicular as well as oblique field-induced stripes relative to the initial orientation of the director are both examined with explicit indications of the time scales needed for their appearance and posterior development.

Transient patterns in nematic liquid crystals: Domain-wall dynamics

We study the dynamics of the late stages of the Fréedericksz transition in which a periodic transient pattern decays to a final homogeneous state. A stability analysis of an unstable stationary pattern is presented, and equations for the evolution of the domain walls are obtained. Using results of previous theories, we analyze the effect that the specific dynamics of the problem, incorporating hydrodynamic couplings, has on the expected logarithmic domain growth law.

Effects of fire on soil nitrogen dynamics and microbial biomass in savannas of Central Brazil

The objective of this work was to study the effects of fire on net N mineralization and soil microbial biomass in burned and unburned cerrado stricto sensu sites. The study was carried out from April 1998 to April 2000. The pH values were significantly higher in the burned site while soil moisture content was significantly higher in the unburned site (P<0.05). The soil C/N ratio was 22/1 and the available NO3-N ranged between 1.5 and 2.8 mg kg-¹ dry weight. However, the NH4-N concentration ranged between 3 and 34 mg kg-1 dry weight in the burned site and between 3 and 22 mg kg-1 dry weight in the unburned site. The NH4-N increased after fire, but no significant changes were observed for NO3-N (P<0.05). The NO3-N accumulation occurred in short periods during the rainy season. The rates of net N mineralization increased during the rainy season while reductions in soil microbial biomass were observed at both sites. This suggested that the peak in microbial activities occurred with the first rain events, with an initial net immobilization followed by net mineralization. Both sites presented the same pattern for mineralization/immobilization, however, the amount of inorganic-N cycled annually in unburned site was 14.7 kg ha-1 per year while the burned site presented only 3.8 kg ha-¹ of inorganic-N, one year after the burning.

Influence on present-day coastal dynamics and evolution of a relict subaqueous delta lobe: Sol de Riu lobe, Ebro Delta. Continental Shelf Research, 74: 94-104. doi:10.1016/j.csr.2013.11.021

We used high-resolution swath-bathymetry data to characterise the morphology of the abandoned subaqueous Sol de Riu delta lobe in the Ebro Delta, Western Mediterranean Sea. This study aims to assess the influence of an abandoned delta lobe on present-day coastal dynamics in a micro-tidal environment. Detailed mapping of the relict Sol de Riu lobe also showed a set of bedforms interpreted as footprints of human activities: seasonal V-shaped depressions on the middle shoreface due to boat anchoring and old trawling marks between 16 and 18 m water depth. Estimations of the mobility of bottom sediment showed that the shallowest shoreface (i.e. less than 7 m depth) is the most dynamic part of the relict lobe, while the middle shoreface experienced significant morphological changes since the lobe was abandoned. The deepest shoreface (i.e. water depth in excess of 15 m), which corresponds to the front of the lobe, is defined by a very small potential for morphological change. Simulations showed that while the relict lobe does not significantly affect the typical short period waves (Tp ≈4 s) in the study area, it does interfere with the most energetic wave conditions (Tp ≥ 7 s) acting as a shoal leading to the concentration of wave energy along the shoreline northwest of the lobe. The consequence of such modification of the high-energy wave propagation pattern by the relict lobe is an alteration of the wave-induced littoral sediment dynamics with respect to a situation without the lobe.

Metabolic activation pattern of distinct hippocampal subregions during spatial learning and memory retrieval.

Activation dynamics of hippocampal subregions during spatial learning and their interplay with neocortical regions is an important dimension in the understanding of hippocampal function. Using the (14C)-2-deoxyglucose autoradiographic method, we have characterized the metabolic changes occurring in hippocampal subregions in mice while learning an eight-arm radial maze task. Autoradiogram densitometry revealed a heterogeneous and evolving pattern of enhanced metabolic activity throughout the hippocampus during the training period and on recall. In the early stages of training, activity was enhanced in the CA1 area from the intermediate portion to the posterior end as well as in the CA3 area within the intermediate portion of the hippocampus. At later stages, CA1 and CA3 activations spread over the entire longitudinal axis, while dentate gyrus (DG) activation occurred from the anterior to the intermediate zone. Activation of the retrosplenial cortex but not the amygdala was also observed during the learning process. On recall, only DG activation was observed in the same anterior part of the hippocampus. These results suggest the existence of a functional segmentation of the hippocampus, each subregion being dynamically but also differentially recruited along the acquisition, consolidation, and retrieval process in parallel with some neocortical sites.

dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes

H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address these questions, we have analyzed the contribution of dKDM5/LID, the main H3K4me3 demethylase in Drosophila, to the regulation of the pattern of H3K4me3. ChIP-seq results show that, at developmental genes, dKDM5/LID localizes at TSS and regulates H3K4me3. dKDM5/LID target genes are highly transcribed and enriched in active RNApol II and H3K36me3, suggesting a positive contribution to transcription. Expression-profiling show that, though weakly, dKDM5/LID target genes are significantly downregulated upon dKDM5/LID depletion. Furthermore, dKDM5/LID depletion results in decreased RNApol II occupancy, particularly by the promoter-proximal Pol lloser5 form. Our results also show that ASH2, an evolutionarily conserved factor that locates at TSS and is required for H3K4me3, binds and positively regulates dKDM5/LID target genes. However, dKDM5/LID and ASH2 do not bind simultaneously and recognize different chromatin states, enriched in H3K4me3 and not, respectively. These results indicate that, at developmental genes, dKDM5/LID and ASH2 coordinately regulate H3K4me3 at TSS and that this dynamic regulation contributes to transcription.

Analysis of a finite volume method for a cross-diffusion model in population dynamics

The main goal of this paper is to propose a convergent finite volume method for a reactionâeuro"diffusion system with cross-diffusion. First, we sketch an existence proof for a class of cross-diffusion systems. Then the standard two-point finite volume fluxes are used in combination with a nonlinear positivity-preserving approximation of the cross-diffusion coefficients. Existence and uniqueness of the approximate solution are addressed, and it is also shown that the scheme converges to the corresponding weak solution for the studied model. Furthermore, we provide a stability analysis to study pattern-formation phenomena, and we perform two-dimensional numerical examples which exhibit formation of nonuniform spatial patterns. From the simulations it is also found that experimental rates of convergence are slightly below second order. The convergence proof uses two ingredients of interest for various applications, namely the discrete Sobolev embedding inequalities with general boundary conditions and a space-time $L^1$ compactness argument that mimics the compactness lemma due to Kruzhkov. The proofs of these results are given in the Appendix.

Analysis of flow dynamics in right ventricular outflow tract.

BACKGROUND: The mechanism behind early graft failure after right ventricular outflow tract (RVOT) reconstruction is not fully understood. Our aim was to establish a three-dimensional computational fluid dynamics (CFD) model of RVOT to investigate the hemodynamic conditions that may trigger the development of intimal hyperplasia and arteriosclerosis. METHODS: Pressure, flow, and diameter at the RVOT, pulmonary artery (PA), bifurcation of the PA, and left and right PAs were measured in 10 normal pigs with a mean weight of 24.8 ± 0.78 kg. Data obtained from the experimental scenario were used for CFD simulation of pressure, flow, and shear stress profile from the RVOT to the left and right PAs. RESULTS: Using experimental data, a CFD model was obtained for 2.0 and 2.5-L/min pulsatile inflow profiles. In both velocity profiles, time and space averaged in the low-shear stress profile range from 0-6.0 Pa at the pulmonary trunk, its bifurcation, and at the openings of both PAs. These low-shear stress areas were accompanied to high-pressure regions 14.0-20.0 mm Hg (1866.2-2666 Pa). Flow analysis revealed a turbulent flow at the PA bifurcation and ostia of both PAs. CONCLUSIONS: Identified local low-shear stress, high pressure, and turbulent flow correspond to a well-defined trigger pattern for the development of intimal hyperplasia and arteriosclerosis. As such, this real-time three-dimensional CFD model may in the future serve as a tool for the planning of RVOT reconstruction, its analysis, and prediction of outcome.

Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa.

The production of beneficial public goods is common in the microbial world, and so is cheating - the exploitation of public goods by nonproducing mutants. Here, we examine co-evolutionary dynamics between cooperators and cheats and ask whether cooperators can evolve strategies to reduce the burden of exploitation, and whether cheats in turn can improve their exploitation abilities. We evolved cooperators of the bacterium Pseudomonas aeruginosa, producing the shareable iron-scavenging siderophore pyoverdine, together with cheats, defective in pyoverdine production but proficient in uptake. We found that cooperators managed to co-exist with cheats in 56% of all replicates over approximately 150 generations of experimental evolution. Growth and competition assays revealed that co-existence was fostered by a combination of general adaptions to the media and specific adaptions to the co-evolving opponent. Phenotypic screening and whole-genome resequencing of evolved clones confirmed this pattern, and suggest that cooperators became less exploitable by cheats because they significantly reduced their pyoverdine investment. Cheats, meanwhile, improved exploitation efficiency through mutations blocking the costly pyoverdine-signalling pathway. Moreover, cooperators and cheats evolved reduced motility, a pattern that likely represents adaptation to laboratory conditions, but at the same time also affects social interactions by reducing strain mixing and pyoverdine sharing. Overall, we observed parallel evolution, where co-existence of cooperators and cheats was enabled by a combination of adaptations to the abiotic and social environment and their interactions.