Resonant and Non-Resonant Modulated Amplitude Waves for Binary Bose-Einstein Condensates in Optical Lattices

We consider a system of two Gross-Pitaevskii (GP) equations, in the presence of an optical-lattice (OL) potential, coupled by both nonlinear and linear terms. This system describes a Bose-Einstein condensate (BEC) composed of two different spin states of the same atomic species, which interact linearly through a resonant electromagnetic field. In the absence of the OL, we find plane-wave solutions and examine their stability. In the presence of the OL, we derive a system of amplitude equations for spatially modulated states which are coupled to the periodic potential through the lowest-order subharmonic resonance. We determine this averaged system's equilibria, which represent spatially periodic solutions, and subsequently examine the stability of the corresponding solutions with direct simulations of the coupled GP equations. We find that symmetric (equal-amplitude) and asymmetric (unequal-amplitude) dual-mode resonant states are, respectively, stable and unstable. The unstable states generate periodic oscillations between the two condensate components, which is possible only because of the linear coupling between them. We also find four-mode states, but they are always unstable. Finally, we briefly consider ternary (three-component) condensates.Comment: 16 pages, 4 figures (some of which have multiple parts), to appear in Physica D; streamlined paper; added some references and discussion concerning experimental realizations of this work; higher-resolution copies of a couple figures are available on the version of the document downloadable from http://www.math.gatech.edu/~mason

Landscape genomics of a widely distributed snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia

Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius

Solar energetic particle transport near a heliospheric current sheet

Solar energetic particles (SEPs), a major component of space weather, propagate through the interplanetary medium strongly guided by the interplanetary magnetic field (IMF). In this work, we analyze the implications that a flat Heliospheric Current Sheet (HCS) has on proton propagation from SEP release sites to the Earth. We simulate proton propagation by integrating fully 3D trajectories near an analytically defined flat current sheet, collecting comprehensive statistics into histograms, fluence maps, and virtual observer time profiles within an energy range of 1–800 MeV. We show that protons experience significant current sheet drift to distant longitudes, causing time profiles to exhibit multiple components, which are a potential source of confusing interpretations of observations. We find that variation of the current sheet thickness within a realistic parameter range has little effect on particle propagation. We show that the IMF configuration strongly affects the deceleration of protons. We show that in our model, the presence of a flat equatorial HCS in the inner heliosphere limits the crossing of protons into the opposite hemisphere

Dark-in-Bright Solitons in Bose-Einstein Condensates with Attractive Interactions

We demonstrate a possibility to generate localized states in effectively one-dimensional Bose-Einstein condensates with a negative scattering length in the form of a dark soliton in the presence of an optical lattice (OL) and/or a parabolic magnetic trap. We connect such structures with twisted localized modes (TLMs) that were previously found in the discrete nonlinear Schr{\"o}dinger equation. Families of these structures are found as functions of the OL strength, tightness of the magnetic trap, and chemical potential, and their stability regions are identified. Stable bound states of two TLMs are also found. In the case when the TLMs are unstable, their evolution is investigated by means of direct simulations, demonstrating that they transform into large-amplitude fundamental solitons. An analytical approach is also developed, showing that two or several fundamental solitons, with the phase shift $\pi$ between adjacent ones, may form stable bound states, with parameters quite close to those of the TLMs revealed by simulations. TLM structures are found numerically and explained analytically also in the case when the OL is absent, the condensate being confined only by the magnetic trap.Comment: 13 pages, 7 figures, New Journal of Physics (in press

Few-cycle laser driven reaction nanoscopy on aerosolized silica nanoparticles

Nanoparticles offer unique properties as photocatalysts with large surface areas. Under irradiation with light, the associated near-fields can induce, enhance, and control molecular adsorbate reactions on the nanoscale. So far, however, there is no simple method available to spatially resolve the near-field induced reaction yield on the surface of nanoparticles. Here we close this gap by introducing reaction nanoscopy based on three-dimensional momentum-resolved photoionization. The technique is demonstrated for the spatially selective proton generation in few-cycle laser-induced dissociative ionization of ethanol and water on SiO2 nanoparticles, resolving a pronounced variation across the particle surface. The results are modeled and reproduced qualitatively by electrostatic and quasi-classical mean-field Mie Monte-Carlo (M3C) calculations. Reaction nanoscopy is suited for a wide range of isolated nanosystems and can provide spatially resolved ultrafast reaction dynamics on nanoparticles, clusters, and droplets

Few-cycle laser driven reaction nanoscopy on aerosolized silica nanoparticles

Nanoparticles offer unique properties as photocatalysts with large surface areas. Under irradiation with light, the associated near-fields can induce, enhance, and control molecular adsorbate reactions on the nanoscale. So far, however, there is no simple method available to spatially resolve the near-field induced reaction yield on the surface of nanoparticles. Here we close this gap by introducing reaction nanoscopy based on three-dimensional momentum-resolved photoionization. The technique is demonstrated for the spatially selective proton generation in few-cycle laser-induced dissociative ionization of ethanol and water on SiO2 nanoparticles, resolving a pronounced variation across the particle surface. The results are modeled and reproduced qualitatively by electrostatic and quasi-classical mean-field Mie Monte-Carlo ((MC)-C-3) calculations. Reaction nanoscopy is suited for a wide range of isolated nanosystems and can provide spatially resolved ultrafast reaction dynamics on nanoparticles, clusters, and droplets

Here and there, now

A textile installation shaped by traditional embroidery, geographical differences, technology and novel natural dye is the focus of this paper. ‘Through the globe’ [Através do globo] is the result of a six week artist in residency at Contextile 2016 in Guimarães, Portugal.1 It builds upon environmental pest invasive weed dye research, interprets ‘traditional’ embroidery illustrating the poetics of place.2 The essence of Guimarães embroidery provides the narrative along the fourteen metre length and is the physical embodiment of the antipodal link between and Wellington, New Zealand. The challenge offered by Contextile 2016 was to collaborate with Oficina embroiderers to learn, then use traditional Guimarães embroidery, and, then exhibit the work at Residências Artistícas at Casa da Memória [House of Memory] in the Contextile 2016 triennial.3 During a period in the late nineteenth century a desire for the creation of national identity existed and the documentation of Guimarães embroidery began to ensure it gained visibility.4 The embroidery arose from a range of other factors including human will, sensibility, and dexterity to create a united unique style. Traditionally, rural women’s waistcoats were richly embroidered, such as one included in the University of Aberdeen Needlework Development Scheme collection. 5 Now, Guimarães embroidery is mostly used to adorn home ware products for the tourist market

Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates

<p>Abstract</p> <p>Background</p> <p>The knowledge about proteins with specific interaction capacity to the protein partners is very important for the modeling of cell signaling networks. However, the experimentally-derived data are sufficiently not complete for the reconstruction of signaling pathways. This problem can be solved by the network enrichment with predicted protein interactions. The previously published <it>in silico </it>method PAAS was applied for prediction of interactions between protein kinases and their substrates.</p> <p>Results</p> <p>We used the method for recognition of the protein classes defined by the interaction with the same protein partners. 1021 protein kinase substrates classified by 45 kinases were extracted from the Phospho.ELM database and used as a training set. The reasonable accuracy of prediction calculated by leave-one-out cross validation procedure was observed in the majority of kinase-specificity classes. The random multiple splitting of the studied set onto the test and training set had also led to satisfactory results. The kinase substrate specificity for 186 proteins extracted from TRANSPATH^®database was predicted by PAAS method. Several kinase-substrate interactions described in this database were correctly predicted. Using the previously developed ExPlain™ system for the reconstruction of signal transduction pathways, we showed that addition of the newly predicted interactions enabled us to find the possible path between signal trigger, TNF-alpha, and its target genes in the cell.</p> <p>Conclusions</p> <p>It was shown that the predictions of protein kinase substrates by PAAS were suitable for the enrichment of signaling pathway networks and identification of the novel signaling pathways. The on-line version of PAAS for prediction of protein kinase substrates is freely available at <url>http://www.ibmc.msk.ru/PAAS/</url>.</p

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species

Correlated Evolution of Nearby Residues in Drosophilid Proteins

Here we investigate the correlations between coding sequence substitutions as a function of their separation along the protein sequence. We consider both substitutions between the reference genomes of several Drosophilids as well as polymorphisms in a population sample of Zimbabwean Drosophila melanogaster. We find that amino acid substitutions are “clustered” along the protein sequence, that is, the frequency of additional substitutions is strongly enhanced within ≈10 residues of a first such substitution. No such clustering is observed for synonymous substitutions, supporting a “correlation length” associated with selection on proteins as the causative mechanism. Clustering is stronger between substitutions that arose in the same lineage than it is between substitutions that arose in different lineages. We consider several possible origins of clustering, concluding that epistasis (interactions between amino acids within a protein that affect function) and positional heterogeneity in the strength of purifying selection are primarily responsible. The role of epistasis is directly supported by the tendency of nearby substitutions that arose on the same lineage to preserve the total charge of the residues within the correlation length and by the preferential cosegregation of neighboring derived alleles in our population sample. We interpret the observed length scale of clustering as a statistical reflection of the functional locality (or modularity) of proteins: amino acids that are near each other on the protein backbone are more likely to contribute to, and collaborate toward, a common subfunction