Dynamical description of vesicle growth and shape change

We systematize and extend the description of vesicle growth and shape change using linear nonequilibrium thermodynamics. By restricting the study to shape changes from spheres to axisymmetric ellipsoids, we are able to give a consistent formulation which includes the lateral tension of the vesicle membrane. This allows us to generalize and correct a previous calculation. Our present calculations suggest that, for small growing vesicles, a prolate ellipsoidal shape should be favored over oblate ellipsoids, whereas for large growing vesicles oblates should be favored over prolates. The validity of this prediction is examined in the light of the various assumptions made in its derivation.Comment: 6 page

Cosmological perturbations on local systems

We study the effect of cosmological expansion on orbits--galactic, planetary, or atomic--subject to an inverse-square force law. We obtain the laws of motion for gravitational or electrical interactions from general relativity--in particular, we find the gravitational field of a mass distribution in an expanding universe by applying perturbation theory to the Robertson-Walker metric. Cosmological expansion induces an ($\ddot a/a) \vec r$ force where $a(t)$ is the cosmological scale factor. In a locally Newtonian framework, we show that the $(\ddot a/a) \vec r$ term represents the effect of a continuous distribution of cosmological material in Hubble flow, and that the total force on an object, due to the cosmological material plus the matter perturbation, can be represented as the negative gradient of a gravitational potential whose source is the material actually present. We also consider the effect on local dynamics of the cosmological constant. We calculate the perihelion precession of elliptical orbits due to the cosmological constant induced force, and work out a generalized virial relation applicable to gravitationally bound clusters.Comment: 10 page

Excited Baryon Decay Widths in Large N_c QCD

We study excited baryon decay widths in large N_c QCD. It was suggested previously that some spin-flavor mixed-symmetric baryon states have strong couplings of O(N_c^{-1/2}) to nucleons [implying narrow widths of O(1/N_c)], as opposed to the generic expectation based on Witten's counting rules of an O(N_c^0) coupling. The calculation obtaining these narrow widths was performed in the context of a simple quark-shell model. This paper addresses the question of whether the existence of such narrow states is a general property of large N_c QCD. We show that a general large N_c QCD analysis does not predict such narrow states; rather they are a consequence of the extreme simplicity of the quark model.Comment: 9 page

Excited Baryons in Large N_c QCD Revisited: The Resonance Picture Versus Single-Quark Excitations

We analyze excited baryon properties via a 1/N_c expansion from two perspectives: as resonances in meson-nucleon scattering, and as single-quark excitations in the context of a simple quark model. For both types of analysis one can derive novel patterns of degeneracy that emerge as N_c --> \infty, and that are shown to be compatible with one another. This helps justify the single-quark excitation picture and may give some insight into its successes. We also find that in the large N_c limit one of the S_{11} baryons does not couple to the pi-N channel but couples to the eta-N channel. This is empirically observed in the N(1535), which couples very weakly to the pi-N channel and quite strongly to the eta-N channel. The comparatively strong coupling of the N(1650) to the pi-N channel and weak coupling to eta-N channel is also predicted. In the context of the simple quark model picture we reproduce expressions for mixing angles that are accurate up to O(1/N_c) corrections and are in good agreement with mixing angles extracted phenomenologically.Comment: 13 pages, ReVTeX

Efam: an expanded, metaproteome-supported HMM profile database of viral protein families

Motivation: Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Results: Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from 'conservative' to 'eXtremely Conservative' resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem

Modeling Transport in Gas Chromatography Columns for the Micro-ChemLab

The gas chromatography (GC) column is a critical component in the microsystem for chemical detection ({mu}ChemLab{trademark}) being developed at Sandia. The goal is to etch a meter-long GC column onto a 1-cm{sup 2} silicon chip while maintaining good chromatographic performance. Our design strategy is to use a modeling and simulation approach. We have developed an analytical tool that models the transport and surface interaction process to achieve an optimized design of the GC column. This analytical tool has a flow module and a separation module. The flow module considers both the compressibility and slip flow effects that may significantly influence the gas transport in a long and narrow column. The separation module models analyte transport and physico-chemical interaction with the coated surface in the GC column. It predicts the column efficiency and performance. Results of our analysis will be presented in this paper. In addition to the analytical tool, we have also developed a time-dependent adsorption/desorption model and incorporated this model into a computational fluid dynamics (CFD) code to simulate analyte transport and separation process in GC columns. CFD simulations can capture the complex three-dimensional flow and transport dynamics, whereas the analytical tool cannot. Different column geometries have been studied, and results will be presented in this paper. Overall we have demonstrated that the modeling and simulation approach can guide the design of the GC column and will reduce the number of iterations in the device development

Pion-Nucleon Scattering in a Large-N Sigma Model

We review the large-N_c approach to meson-baryon scattering, including recent interesting developments. We then study pion-nucleon scattering in a particular variant of the linear sigma-model, in which the couplings of the sigma and pi mesons to the nucleon are echoed by couplings to the entire tower of I=J baryons (including the Delta) as dictated by large-N_c group theory. We sum the complete set of multi-loop meson-exchange \pi N --> \pi N and \pi N --> \sigma N Feynman diagrams, to leading order in 1/N_c. The key idea, reviewed in detail, is that large-N_c allows the approximation of LOOP graphs by TREE graphs, so long as the loops contain at least one baryon leg; trees, in turn, can be summed by solving classical equations of motion. We exhibit the resulting partial-wave S-matrix and the rich nucleon and Delta resonance spectrum of this simple model, comparing not only to experiment but also to pion-nucleon scattering in the Skyrme model. The moral is that much of the detailed structure of the meson-baryon S-matrix which hitherto has been uncovered only with skyrmion methods, can also be described by models with explicit baryon fields, thanks to the 1/N_c expansion.Comment: This LaTeX file inputs the ReVTeX macropackage; figures accompany i

Species and population specific gene expression in blood transcriptomes of marine turtles

Background: Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. Results: We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance. Conclusions: Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles