The interaction-strength interpolation method for main-group chemistry: benchmarking, limitations, and perspectives

We have tested the original interaction-strength-interpolation (ISI) exchange-correlation functional for main group chemistry. The ISI functional is based on an interpolation between the weak and strong coupling limits and includes exact-exchange as well as the G\"orling-Levy second-order energy. We have analyzed in detail the basis-set dependence of the ISI functional, its dependence on the ground-state orbitals, and the influence of the size-consistency problem. We show and explain some of the expected limitations of the ISI functional (i.e. for atomization energies), but also unexpected results, such as the good performance for the interaction energy of dispersion-bonded complexes when the ISI correlation is used as a correction to Hartree-Fock.Comment: 20 pages, 20 figure

Strictly correlated uniform electron droplets

We study the energetic properties of finite but internally homogeneous D-dimensional electron droplets in the strict-correlation limit. The indirect Coulomb interaction is found to increase as a function of the electron number, approaching the tighter forms of the Lieb-Oxford bound recently proposed by Rasanen et al. [Phys. Rev. Lett. 102, 206406 (2009)]. The bound is satisfied in three-, two-, and one-dimensional droplets, and in the latter case it is reached exactly - regardless of the type of interaction considered. Our results provide useful reference data for delocalized strongly correlated systems, and they can be used in the development and testing of exchange-correlation density functionals in the framework of density-functional theory

Decidability of the Monadic Shallow Linear First-Order Fragment with Straight Dismatching Constraints

The monadic shallow linear Horn fragment is well-known to be decidable and has many application, e.g., in security protocol analysis, tree automata, or abstraction refinement. It was a long standing open problem how to extend the fragment to the non-Horn case, preserving decidability, that would, e.g., enable to express non-determinism in protocols. We prove decidability of the non-Horn monadic shallow linear fragment via ordered resolution further extended with dismatching constraints and discuss some applications of the new decidable fragment.Comment: 29 pages, long version of CADE-26 pape

On Functionality of Visibly Pushdown Transducers

Visibly pushdown transducers form a subclass of pushdown transducers that (strictly) extends finite state transducers with a stack. Like visibly pushdown automata, the input symbols determine the stack operations. In this paper, we prove that functionality is decidable in PSpace for visibly pushdown transducers. The proof is done via a pumping argument: if a word with two outputs has a sufficiently large nesting depth, there exists a nested word with two outputs whose nesting depth is strictly smaller. The proof uses technics of word combinatorics. As a consequence of decidability of functionality, we also show that equivalence of functional visibly pushdown transducers is Exptime-Complete.Comment: 20 page

Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of nextgeneration sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBiogenerated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome sanalyses to facilitate functional studies into an organism’s biology

Absorption and photoluminescence spectroscopy on a single self-assembled charge-tunable quantum dot

We have performed detailed photoluminescence (PL) and absorption spectroscopy on the same single self-assembled quantum dot in a charge-tunable device. The transition from neutral to charged exciton in the PL occurs at a more negative voltage than the corresponding transition in absorption. We have developed a model of the Coulomb blockade to account for this observation. At large negative bias, the absorption broadens as a result of electron and hole tunneling. We observe resonant features in this regime whenever the quantum dot hole level is resonant with two-dimensional hole states located at the capping layer-blocking barrier interface in our structure.Comment: 6 pages, 6 figure

Enforcing Termination of Interprocedural Analysis

Interprocedural analysis by means of partial tabulation of summary functions may not terminate when the same procedure is analyzed for infinitely many abstract calling contexts or when the abstract domain has infinite strictly ascending chains. As a remedy, we present a novel local solver for general abstract equation systems, be they monotonic or not, and prove that this solver fails to terminate only when infinitely many variables are encountered. We clarify in which sense the computed results are sound. Moreover, we show that interprocedural analysis performed by this novel local solver, is guaranteed to terminate for all non-recursive programs --- irrespective of whether the complete lattice is infinite or has infinite strictly ascending or descending chains

Alpha-particle emitting 213Bi-anti-EGFR immunoconjugates eradicate tumor cells independent of oxygenation

Hypoxia is a central problem in tumor treatment because hypoxic cells are less sensitive to chemo- and radiotherapy than normoxic cells. Radioresistance of hypoxic tumor cells is due to reduced sensitivity towards low Linear Energy Transfer (LET) radiation. High LET α-emitters are thought to eradicate tumor cells independent of cellular oxygenation. Therefore, the aim of this study was to demonstrate that the cell-bound α-particle emitting 213Bi immunoconjugates efficiently kill hypoxic just like normoxic CAL33 tumor cells. For that purpose CAL33 cells were incubated with 213Bianti- EGFR-MAb or irradiated with photons with a nominal energy of 6 MeV both under hypoxic and normoxic conditions. Oxygenation of cells was checked via the hypoxia-associated marker HIF-1α. Survival of cells was analysed using the clonogenic assay. Cell viability was monitored with the WST colorimetric assay. Results were evaluated statistically using a t-test and a Generalized Linear Mixed Model (GLMM). Survival and viability of CAL33 cells decreased both after incubation with increasing 213Bi-anti-EGFR-MAb activity concentrations (9.25 kBq/ml – 1.48 MBq/ml) and irradiation with increasing doses of photons (0.5 – 12 Gy). Following photon irradiation survival and viability of normoxic cells were significantly lower than those of hypoxic cells at all doses analysed. In contrast, cell death induced by 213Bianti- EGFR-MAb turned out to be independent of cellular oxygenation. These results demonstrate for the first time that α-particle emitting 213Bi-immunoconjugates eradicate hypoxic tumor cells as effective as normoxic cells. Therefore, 213Biradioimmunotherapy seems to be an appropriate strategy for treatment of hypoxic tumors.JRC.E.5-Nuclear chemistr

Irradiation of Materials with Short, Intense Ion pulses at NDCX-II

We present an overview of the performance of the Neutralized Drift Compression Experiment-II (NDCX-II) accelerator at Berkeley Lab, and report on recent target experiments on beam driven melting and transmission ion energy loss measurements with nanosecond and millimeter-scale ion beam pulses and thin tin foils. Bunches with around 10^11 ions, 1-mm radius, and 2-30 ns FWHM duration have been created with corresponding fluences in the range of 0.1 to 0.7 J/cm^2. To achieve these short pulse durations and mm-scale focal spot radii, the 1.1 MeV He+ ion beam is neutralized in a drift compression section, which removes the space charge defocusing effect during final compression and focusing. The beam space charge and drift compression techniques resemble necessary beam conditions and manipulations in heavy ion inertial fusion accelerators. Quantitative comparison of detailed particle-in-cell simulations with the experiment play an important role in optimizing accelerator performance.Comment: 15 pages, 7 figures. revised manuscript submitted to Laser and Particle Beam