Reduced kinetic models of facilitative transport

AbstractIn spite of the highly complex structural dynamics of globular proteins, the processes mediated by them can usually be described in terms of relatively simple kinetic diagrams. How do complex proteins, characterized by undergoing transitions among a possibly very large number of intermediate states, exhibit functional properties that can be interpreted in terms of kinetic diagrams consisting of only a small number of states? One possible way of explaining this apparent contradiction is that, under some conditions, a reduction of the actual complete kinetic diagram that describes all of the macromolecular states and transitions takes place. In this work, we contribute with a formal basis to this interpretation, by generalizing the procedure of diagram reduction to the case of multicyclic kinetic diagrams. As an example, we apply the procedure to a complex kinetic model of facilitative transport. We develop Monte Carlo simulations to obtain the kinetic parameters of the complex model and we compare them with the ones analytically obtained from the reduced model. We confirm that, under some conditions, the kinetic behavior of the complex transporter is indistinguishable from the one of a four-state simple carrier model, derived from the former by diagram reduction. Besides introducing some novel methodological aspects, this work further contributes to the idea that, under many physiological and experimental conditions, a reduction occurs of the complete kinetic diagram that describes the dynamics of a globular protein

Scaling of the conductance in gold nanotubes

A new form of gold nanobridges has been recently observed in ultrahigh-vacuum experiments, where the gold atoms rearrange to build helical nanotubes, akin in some respects to carbon nanotubes. The good reproducibility of these wires and their unexpected stability will allow for conductance measurements and make them promising candidates for future applications . We present here a study of the transport properties of these nanotubes in order to understand the role of chirality and of the different orbitals in quantum transport observables. The conductance per atomic row shows a light decreasing trend as the diameter grows, which is also shown through an analytical formula based on a one-orbital model.Comment: 5 pages, 6 figure

FERTILIZATION OF ARRACACHA IN AN ULTISOL

FERTILIZATION OF ARRACACHA IN AN ULTISO

Genome skimming and microsatellite analysis reveal contrasting patterns of genetic diversity in a rare sandhill endemic (Erysimum teretifolium, Brassicaceae)

Barriers between islands often inhibit gene flow creating patterns of isolation by distance. In island species, the majority of genetic diversity should be distributed among isolated populations. However, a self-incompatible mating system leads to higher genetic variation within populations and very little between-population subdivision. We examine these two contrasting predictions in Erysimum teretifolium, a rare self-incompatible plant endemic to island-like sandhill habitats in Santa Cruz County, California. We used genome skimming and nuclear microsatellites to assess the distribution of genetic diversity within and among eight of the 13 remaining populations. Phylogenetic analyses of the chloroplast genomes revealed a deep separation of three of the eight populations. The nuclear ribosomal DNA cistron showed no genetic subdivision. Nuclear microsatellites suggest 83% of genetic variation resides within populations. Despite this, 18 of 28 between-population comparisons exhibited significant population structure (mean FST = 0.153). No isolation by distance existed among all populations, however when one outlier population was removed from the analysis due to uncertain provenance, significant isolation by distance emerged (r2 = 0.5611, p = 0.005). Population census size did not correlate with allelic richness as predicted on islands. Bayesian population assignment detected six genetic groupings with substantial admixture. Unique genetic clusters were concentrated at the periphery of the species’ range. Since the overall distribution of nuclear genetic diversity reflects E. tereifolium’s self-incompatible mating system, the vast majority of genetic variation could be sampled within any individual population. Yet, the chloroplast genome results suggest a deep split and some of the nuclear microsatellite analyses indicate some island-like patterns of genetic diversity. Restoration efforts intending to maximize genetic variation should include representatives from both lineages of the chloroplast genome and, for maximum nuclear genetic diversity, should include representatives of the smaller, peripheral populations

Simple theory for scotogenic dark matter with residual matter-parity

Dark matter stability can result from a residual matter-parity symmetry surviving spontaneous breaking of an extended gauge symmetry. We propose the simplest scotogenic dark matter completion of the original SVS theory (Phys.Rev. D22 (1980) 738), in which the "dark sector" particles as well as matter-parity find a natural theoretical origin in the model. We briefly comment on its main features.Comment: 14 pages, 2 figures. Matches published version in PL

Discriminating the occurrence of inundation in tsunami early warning with one-dimensional convolutional neural networks

Tsunamis are natural phenomena that, although occasional, can have large impacts on coastal environments and settlements, especially in terms of loss of life. An accurate, detailed and timely assessment of the hazard is essential as input for mitigation strategies both in the long term and during emergencies. This goal is compounded by the high computational cost of simulating an adequate number of scenarios to make robust assessments. To reduce this handicap, alternative methods could be used. Here, an enhanced method for estimating tsunami time series using a one-dimensional convolutional neural network model (1D CNN) is considered. While the use of deep learning for this problem is not new, most of existing research has focused on assessing the capability of a network to reproduce inundation metrics extrema. However, for the context of Tsunami Early Warning, it is equally relevant to assess whether the networks can accurately predict whether inundation would occur or not, and its time series if it does. Hence, a set of 6776 scenarios with magnitudes in the range Mw 8.0–9.2 were used to design several 1D CNN models at two bays that have different hydrodynamic behavior, that would use as input inexpensive low-resolution numerical modeling of tsunami propagation to predict inundation time series at pinpoint locations. In addition, different configuration parameters were also analyzed to outline a methodology for model testing and design, that could be applied elsewhere. The results show that the network models are capable of reproducing inundation time series well, either for small or large flow depths, but also when no inundation was forecast, with minimal instances of false alarms or missed alarms. To further assess the performance, the model was tested with two past tsunamis and compared with actual inundation metrics. The results obtained are promising, and the proposed model could become a reliable alternative for the calculation of tsunami intensity measures in a faster than real time manner. This could complement existing early warning system, by means of an approximate and fast procedure that could allow simulating a larger number of scenarios within the always restricting time frame of tsunami emergencies.Tide gauge data were obtained from the Sea Level Station Monitoring Facility of the Intergovernmental Oceanographic Commission (http://www.ioc-sealevelmonitoring.org/list.php). The coarser bathymetric and topographic data from the General Bathymetric Chart of the Ocean (https://www.gebco.net/data_and_products/gridded_bathymetry_data/). The authors acknowledge SHOA for providing nautical charts and coastal zone plans used to generate high resolution topo-bathymetric grids for research purposes. We are deeply grateful with A. Gubler that prepared a first version of the high resolution bathymetry grids. The authors acknowledge the computer resources at CTE-POWER (https://www.bsc.es/supportkc/docs/CTE-POWER/overview) and the technical support provided by BSC. We are greatly thankful the EDANYA Group at Málaga University for sharing the Tsunami-HySEA code. Most figures were generated with Python91,92,93 and Global Mapping Tools94. JN deeply thanks support of Mitiga Solutions during his secondment. PAC would like to thank funding by ANID, Chile Grants FONDEF ID19I10048, Centro de Investigación para la Gestión Integrada del Riesgo de Desastres (CIGIDEN) ANID/FONDAP/15110017, and Centro Científico Tecnológico de Valparaíso, ANID PIA/APOYO AFB180002. NZ has received funding from the Marie Skłodowska-Curie grant agreement H2020-MSCA-COFUND-2016-75443.Peer ReviewedPostprint (published version