Weakly coupled, antiparallel, totally asymmetric simple exclusion processes

We study a system composed of two parallel totally asymmetric simple exclusion processes with open boundaries, where the particles move in the two lanes in opposite directions and are allowed to jump to the other lane with rates inversely proportional to the length of the system. Stationary density profiles are determined and the phase diagram of the model is constructed in the hydrodynamic limit, by solving the differential equations describing the steady state of the system, analytically for vanishing total current and numerically for nonzero total current. The system possesses phases with a localized shock in the density profile in one of the lanes, similarly to exclusion processes endowed with nonconserving kinetics in the bulk. Besides, the system undergoes a discontinuous phase transition, where coherently moving delocalized shocks emerge in both lanes and the fluctuation of the global density is described by an unbiased random walk. This phenomenon is analogous to the phase coexistence observed at the coexistence line of the totally asymmetric simple exclusion process, however, as a consequence of the interaction between lanes, the density profiles are deformed and in the case of asymmetric lane change, the motion of the shocks is confined to a limited domain.Comment: 14 pages, 15 figures, to appear in Phys. Rev.

Oils Colored with Wood-Staining Fungal Pigments : Color Loss, Oxidation, and Structural Breakdown

Wood-staining fungal pigments have potential uses as colorants for wood and textiles. Traditionally, organic solvents have been used as carriers for these pigments. However, other environmentally-friendly and more readily available carriers must be found. Natural oils have the potential to carry these pigments but have demonstrated color loss over relatively short periods of time, possibly due to oxidation and/or polymerization of both the oils and pigments. The current study examined therapeutic and food grade oils (instead of finishing oils) for their potential to carry draconin red, the pigment from Scytalidium cuboideum. To track color loss over time for treated and untreated pigmented oils, a colorimeter and the CIE2000 L*a*b* color space were used. It was determined that hemp oil was a potential carrier for draconin red, as were flax seed oil and cold-pressed linseed oil when treated with β-carotene as the pigment did not degrade over time in these oils. FTIR analysis was used to determine if oxidation was occurring in the oils and if changes in draconin red could be tracked. Based on the FTIR analysis, oxidation was not likely the cause of color loss in the pigmented oils and the pigment could not be distinguished from the oils in the IR spectra. Finally, SEM was employed to determine if crystal degradation was contributing to color loss. The SEM analysis indicated, surprisingly, that the crystals of draconin red formed rather than degraded over time, so crystal breakdown was also not likely the cause of color loss. Further in-depth chemical studies are needed to determine the mechanism of color loss in pigmented natural oils

Assessing the effects of different land-use/land-cover input datasets on modelling and mapping terrestrial ecosystem services - Case study Terceira Island (Azores, Portugal)

Modelling ecosystem services (ES) has become a new standard for the quantification and assessment of various ES. Multiple ES model applications are available that spatially estimate ES supply on the basis of land-use/land-cover (LULC) input data. This paper assesses how different input LULC datasets affect the modelling and mapping of ES supply for a case study on Terceira Island, the Azores (Portugal), namely: (1) the EU-wide CORINE LULC, (2) the Azores Region official LULC map (COS.A 2018) and (3) a remote sensing-based LULC and vegetation map of Terceira Island using Sentinel-2 satellite imagery. The InVEST model suite was applied, modelling altogether six ES (Recreation/Visitation, Pollination, Carbon Storage, Nutrient Delivery Ratio, Sediment Delivery Ratio and Seasonal Water Yield). Model outcomes of the three LULC datasets were compared in terms of similarity, performance and applicability for the user. For some InVEST modules, such as Pollination and Recreation, the differences in the LULC datasets had limited influence on the model results. For InVEST modules, based on more complex calculations and processes, such as Nutrient Delivery Ratio, the output ES maps showed a skewed distribution of ES supply. Yet, model results showed significant differences for differences in all modules and all LULCs. Understanding how differences arise between the LULC input datasets and the respective effect on model results is imperative when computing model-based ES maps. The choice for selecting appropriate LULC data should depend on: 1) the research or policy/decision-making question guiding the modelling study, 2) the ecosystems to be mapped, but also on 3) the spatial resolution of the mapping and 4) data availability at the local level. Communication and transparency on model input data are needed, especially if ES maps are used for supporting land use planning and decision-making

Direct observation of the tube model in F-actin solutions

Mutual uncrossability of polymers generates topological constraints on their conformations and dynamics, which are generally described using the tube model. We imaged confinement tubes for individual polymers within a F-actin solution by sampling over many successive micrographs of fluorescently labeled probe filaments. The resulting average tube width shows the predicted scaling behavior. Unexpectedly, we found an exponential distribution of tube curvatures which is attributed to transient entropic trapping in network void spaces.Comment: 6 pages, 4 figure

Molecular Spiders in One Dimension

Molecular spiders are synthetic bio-molecular systems which have "legs" made of short single-stranded segments of DNA. Spiders move on a surface covered with single-stranded DNA segments complementary to legs. Different mappings are established between various models of spiders and simple exclusion processes. For spiders with simple gait and varying number of legs we compute the diffusion coefficient; when the hopping is biased we also compute their velocity.Comment: 14 pages, 2 figure

Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Greedy Solution of Ill-Posed Problems: Error Bounds and Exact Inversion

The orthogonal matching pursuit (OMP) is an algorithm to solve sparse approximation problems. Sufficient conditions for exact recovery are known with and without noise. In this paper we investigate the applicability of the OMP for the solution of ill-posed inverse problems in general and in particular for two deconvolution examples from mass spectrometry and digital holography respectively. In sparse approximation problems one often has to deal with the problem of redundancy of a dictionary, i.e. the atoms are not linearly independent. However, one expects them to be approximatively orthogonal and this is quantified by the so-called incoherence. This idea cannot be transfered to ill-posed inverse problems since here the atoms are typically far from orthogonal: The ill-posedness of the operator causes that the correlation of two distinct atoms probably gets huge, i.e. that two atoms can look much alike. Therefore one needs conditions which take the structure of the problem into account and work without the concept of coherence. In this paper we develop results for exact recovery of the support of noisy signals. In the two examples in mass spectrometry and digital holography we show that our results lead to practically relevant estimates such that one may check a priori if the experimental setup guarantees exact deconvolution with OMP. Especially in the example from digital holography our analysis may be regarded as a first step to calculate the resolution power of droplet holography

Effect of molecular and electronic structure on the light harvesting properties of dye sensitizers

The systematic trends in structural and electronic properties of perylene diimide (PDI) derived dye molecules have been investigated by DFT calculations based on projector augmented wave (PAW) method including gradient corrected exchange-correlation effects. TDDFT calculations have been performed to study the visible absorbance activity of these complexes. The effect of different ligands and halogen atoms attached to PDI were studied to characterize the light harvesting properties. The atomic size and electronegativity of the halogen were observed to alter the relaxed molecular geometries which in turn influenced the electronic behavior of the dye molecules. Ground state molecular structure of isolated dye molecules studied in this work depends on both the halogen atom and the carboxylic acid groups. DFT calculations revealed that the carboxylic acid ligands did not play an important role in changing the HOMO-LUMO gap of the sensitizer. However, they serve as anchor between the PDI and substrate titania surface of the solar cell or photocatalyst. A commercially available dye-sensitizer, ruthenium bipyridine (RuBpy), was also studied for electronic and structural properties in order to make a comparison with PDI derivatives for light harvesting properties. Results of this work suggest that fluorinated, chlorinated, brominated, and iyodinated PDI compounds can be useful as sensitizers in solar cells and in artificial photosynthesis.Comment: Single pdf file, 14 pages with 7 figures and 4 table