2,365 research outputs found
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
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