508 research outputs found
Draft Nuclear Genome Sequence of the Liquid Hydrocarbon-Accumulating Green Microalga Botryococcus braunii Race B (Showa).
Botryococcus braunii has long been known as a prodigious producer of liquid hydrocarbon oils that can be converted into combustion engine fuels. This draft genome for the B race of B. braunii will allow researchers to unravel important hydrocarbon biosynthetic pathways and identify possible regulatory networks controlling this unusual metabolism
Quasiparticle energies for large molecules: a tight-binding GW approach
We present a tight-binding based GW approach for the calculation of
quasiparticle energy levels in confined systems such as molecules. Key
quantities in the GW formalism like the microscopic dielectric function or the
screened Coulomb interaction are expressed in a minimal basis of spherically
averaged atomic orbitals. All necessary integrals are either precalculated or
approximated without resorting to empirical data. The method is validated
against first principles results for benzene and anthracene, where good
agreement is found for levels close to the frontier orbitals. Further, the size
dependence of the quasiparticle gap is studied for conformers of the polyacenes
() up to n = 30.Comment: 10 pages, 5 eps figures submitted to Phys. Rev.
Importance of electronic self-consistency in the TDDFT based treatment of nonadiabatic molecular dynamics
A mixed quantum-classical approach to simulate the coupled dynamics of
electrons and nuclei in nanoscale molecular systems is presented. The method
relies on a second order expansion of the Lagrangian in time-dependent density
functional theory (TDDFT) around a suitable reference density. We show that the
inclusion of the second order term renders the method a self-consistent scheme
and improves the calculated optical spectra of molecules by a proper treatment
of the coupled response. In the application to ion-fullerene collisions, the
inclusion of self-consistency is found to be crucial for a correct description
of the charge transfer between projectile and target. For a model of the
photoreceptor in retinal proteins, nonadiabatic molecular dynamics simulations
are performed and reveal problems of TDDFT in the prediction of intra-molecular
charge transfer excitations.Comment: 9 pages, 8 figures. Minor changes in content wrt older versio
Atomistic simulations of self-trapped exciton formation in silicon nanostructures: The transition from quantum dots to nanowires
Using an approximate time-dependent density functional theory method, we
calculate the absorption and luminescence spectra for hydrogen passivated
silicon nanoscale structures with large aspect ratio. The effect of electron
confinement in axial and radial directions is systematically investigated.
Excited state relaxation leads to significant Stokes shifts for short nanorods
with lengths less than 2 nm, but has little effect on the luminescence
intensity. The formation of self-trapped excitons is likewise observed for
short nanostructures only; longer wires exhibit fully delocalized excitons with
neglible geometrical distortion at the excited state minimum.Comment: 10 pages, 4 figure
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed
High-throughput Comparison, Functional Annotation, and Metabolic Modeling of Plant Genomes using the PlantSEED Resource
There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes
Revival of the magnetar PSR J1622-4950: observations with MeerKAT, Parkes, XMM-Newton, Swift, Chandra, and NuSTAR
New radio (MeerKAT and Parkes) and X-ray (XMM-Newton, Swift, Chandra, and
NuSTAR) observations of PSR J1622-4950 indicate that the magnetar, in a
quiescent state since at least early 2015, reactivated between 2017 March 19
and April 5. The radio flux density, while variable, is approximately 100x
larger than during its dormant state. The X-ray flux one month after
reactivation was at least 800x larger than during quiescence, and has been
decaying exponentially on a 111+/-19 day timescale. This high-flux state,
together with a radio-derived rotational ephemeris, enabled for the first time
the detection of X-ray pulsations for this magnetar. At 5%, the 0.3-6 keV
pulsed fraction is comparable to the smallest observed for magnetars. The
overall pulsar geometry inferred from polarized radio emission appears to be
broadly consistent with that determined 6-8 years earlier. However, rotating
vector model fits suggest that we are now seeing radio emission from a
different location in the magnetosphere than previously. This indicates a novel
way in which radio emission from magnetars can differ from that of ordinary
pulsars. The torque on the neutron star is varying rapidly and unsteadily, as
is common for magnetars following outburst, having changed by a factor of 7
within six months of reactivation.Comment: Published in ApJ (2018 April 5); 13 pages, 4 figure
'To live and die [for] Dixie': Irish civilians and the Confederate States of America
Around 20,000 Irishmen served in the Confederate army in the Civil War. As a result, they left behind, in various Southern towns and cities, large numbers of friends, family, and community leaders. As with native-born Confederates, Irish civilian support was crucial to Irish participation in the Confederate military effort. Also, Irish civilians served in various supporting roles: in factories and hospitals, on railroads and diplomatic missions, and as boosters for the cause. They also, however, suffered in bombardments, sieges, and the blockade. Usually poorer than their native neighbours, they could not afford to become 'refugees' and move away from the centres of conflict. This essay, based on research from manuscript collections, contemporary newspapers, British Consular records, and Federal military records, will examine the role of Irish civilians in the Confederacy, and assess the role this activity had on their integration into Southern communities. It will also look at Irish civilians in the defeat of the Confederacy, particularly when they came under Union occupation. Initial research shows that Irish civilians were not as upset as other whites in the South about Union victory. They welcomed a return to normalcy, and often 'collaborated' with Union authorities. Also, Irish desertion rates in the Confederate army were particularly high, and I will attempt to gauge whether Irish civilians played a role in this. All of the research in this paper will thus be put in the context of the Drew Gilpin Faust/Gary Gallagher debate on the influence of the Confederate homefront on military performance. By studying the Irish civilian experience one can assess how strong the Confederate national experiment was. Was it a nation without a nationalism
Preimplant factors affecting postimplant CT-determined prostate volume and the CT/TRUS volume ratio after transperineal interstitial prostate brachytherapy with 125I free seeds
<p>Abstract</p> <p>Background</p> <p>The aim was to identify preimplant factors affecting postimplant prostate volume and the increase in prostate volume after transperineal interstitial prostate brachytherapy with <sup>125</sup>I free seeds.</p> <p>Methods</p> <p>We reviewed the records of 180 patients who underwent prostate brachytherapy with <sup>125</sup>I free seeds for clinical T1/T2 prostate cancer. Eighty-one (45%) of the 180 patients underwent neoadjuvant hormonal therapy. No patient received supplemental external beam radiotherapy. Postimplant computed tomography was undertaken, and postimplant dosimetric analysis was performed. Univariate and multivariate analyses were performed to identify preimplant factors affecting postimplant prostate volume by computed tomography and the increase in prostate volume after implantation.</p> <p>Results</p> <p>Preimplant prostate volume by transrectal ultrasound, serum prostate-specific antigen, number of needles, and number of seeds implanted were significantly correlated with postimplant prostate volume by computed tomography. The increase in prostate volume after implantation was significantly higher in patients with neoadjuvant hormonal therapy than in those without. Preimplant prostate volume by transrectal ultrasound, number of needles, and number of seeds implanted were significantly correlated with the increase in prostate volume after implantation. Stepwise multiple linear regression analysis showed that preimplant prostate volume by transrectal ultrasound and neoadjuvant hormonal therapy were significant independent factors affecting both postimplant prostate volume by computed tomography and the increase in prostate volume after implantation.</p> <p>Conclusions</p> <p>The results of the present study show that preimplant prostate volume by transrectal ultrasound and neoadjuvant hormonal therapy are significant preimplant factors affecting both postimplant prostate volume by computed tomography and the increase in prostate volume after implantation.</p
- …