Proton Drip-Line Calculations and the Rp-process

One-proton and two-proton separation energies are calculated for proton-rich nuclei in the region $A=41-75$. The method is based on Skyrme Hartree-Fock calculations of Coulomb displacement energies of mirror nuclei in combination with the experimental masses of the neutron-rich nuclei. The implications for the proton drip line and the astrophysical rp-process are discussed. This is done within the framework of a detailed analysis of the sensitivity of rp process calculations in type I X-ray burst models on nuclear masses. We find that the remaining mass uncertainties, in particular for some nuclei with $N=Z$, still lead to large uncertainties in calculations of X-ray burst light curves. Further experimental or theoretical improvements of nuclear mass data are necessary before observed X-ray burst light curves can be used to obtain quantitative constraints on ignition conditions and neutron star properties. We identify a list of nuclei for which improved mass data would be most important.Comment: 20 pages, 9 figures, 2 table

Metassembler: merging and optimizing de novo genome assemblies

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for meta-assembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source at http://metassembler.sourceforge.net

AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation

The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy AFM experiments. The oligorotaxanes consist of cyclobis(paraquat-\emph{p}-phenylene) rings threaded onto an oligomer of 1,5-dioxynaphthalenes linked by polyethers. The simulations are performed in a high dielectric medium using MM3 as the force field. The resulting force vs. extension isotherms show a mechanically unstable region in which the molecule unfolds and, for selected extensions, blinks in the force measurements between a high-force and a low-force regime. From the force vs. extension data the molecular potential of mean force is reconstructed using the weighted histogram analysis method and decomposed into energetic and entropic contributions. The simulations indicate that the folding of the oligorotaxanes is energetically favored but entropically penalized, with the energetic contributions overcoming the entropy penalty and effectively driving the self-assembly. In addition, an analogy between the single-molecule folding/unfolding events driven by the AFM tip and the thermodynamic theory of first-order phase transitions is discussed and general conditions, on the molecule and the cantilever, for the emergence of mechanical instabilities and blinks in the force measurements in equilibrium isometric pulling experiments are presented. In particular, it is shown that the mechanical stability properties observed during the extension are intimately related to the fluctuations in the force measurements.Comment: 42 pages, 17 figures, accepted to the Journal of Chemical Physic

Calculating Nonlocal Optical Properties of Structures with Arbitrary Shape

In a recent Letter [Phys. Rev. Lett. 103, 097403 (2009)], we outlined a computational method to calculate the optical properties of structures with a spatially nonlocal dielectric function. In this Article, we detail the full method, and verify it against analytical results for cylindrical nanowires. Then, as examples of our method, we calculate the optical properties of Au nanostructures in one, two, and three dimensions. We first calculate the transmission, reflection, and absorption spectra of thin films. Because of their simplicity, these systems demonstrate clearly the longitudinal (or volume) plasmons characteristic of nonlocal effects, which result in anomalous absorption and plasmon blueshifting. We then study the optical properties of spherical nanoparticles, which also exhibit such nonlocal effects. Finally, we compare the maximum and average electric field enhancements around nanowires of various shapes to local theory predictions. We demonstrate that when nonlocal effects are included, significant decreases in such properties can occur.Comment: 30 pages, 12 figures, 1 tabl

Neutron star cooling after deep crustal heating in the X-ray transient KS 1731-260

We simulate the cooling of the neutron star in the X-ray transient KS 1731-260 after the source returned to quiescence in 2001 from a long (>~ 12.5 yr) outburst state. We show that the cooling can be explained assuming that the crust underwent deep heating during the outburst stage. In our best theoretical scenario the neutron star has no enhanced neutrino emission in the core, and its crust is thin, superfluid, and has the normal thermal conductivity. The thermal afterburst crust-core relaxation in the star may be not over.Comment: 5 pages, 2 figures, accepted by MNRAS. In v.2, two references added and typos correcte

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Since any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our distribution predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.Comment: 20 pages, including Appendi