2,353 research outputs found
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
Streaming Tree Transducers
Theory of tree transducers provides a foundation for understanding
expressiveness and complexity of analysis problems for specification languages
for transforming hierarchically structured data such as XML documents. We
introduce streaming tree transducers as an analyzable, executable, and
expressive model for transforming unranked ordered trees in a single pass.
Given a linear encoding of the input tree, the transducer makes a single
left-to-right pass through the input, and computes the output in linear time
using a finite-state control, a visibly pushdown stack, and a finite number of
variables that store output chunks that can be combined using the operations of
string-concatenation and tree-insertion. We prove that the expressiveness of
the model coincides with transductions definable using monadic second-order
logic (MSO). Existing models of tree transducers either cannot implement all
MSO-definable transformations, or require regular look ahead that prohibits
single-pass implementation. We show a variety of analysis problems such as
type-checking and checking functional equivalence are solvable for our model.Comment: 40 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
Fermionic statistics in the strongly correlated limit of Density Functional Theory
Exact pieces of information on the adiabatic connection integrand
, which allows to evaluate the exchange-correlation energy
of Kohn-Sham density functional theory, can be extracted from the leading terms
in the strong coupling limit (, where is the
strength of the electron-electron interaction). In this work, we first compare
the theoretical prediction for the two leading terms in the strong coupling
limit with data obtained via numerical implementation of the exact Levy
functional in the simple case of two electrons confined in one dimension,
confirming the asymptotic exactness of these two terms. We then carry out a
first study on the incorporation of the fermionic statistics at large coupling
, both numerical and theoretical, confirming that spin effects enter
at orders
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
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
Integer Vector Addition Systems with States
This paper studies reachability, coverability and inclusion problems for
Integer Vector Addition Systems with States (ZVASS) and extensions and
restrictions thereof. A ZVASS comprises a finite-state controller with a finite
number of counters ranging over the integers. Although it is folklore that
reachability in ZVASS is NP-complete, it turns out that despite their
naturalness, from a complexity point of view this class has received little
attention in the literature. We fill this gap by providing an in-depth analysis
of the computational complexity of the aforementioned decision problems. Most
interestingly, it turns out that while the addition of reset operations to
ordinary VASS leads to undecidability and Ackermann-hardness of reachability
and coverability, respectively, they can be added to ZVASS while retaining
NP-completness of both coverability and reachability.Comment: 17 pages, 2 figure
The spatial coverage of dairy cattle urine patches in an intensively grazed pasture system
Accurate field data on the paddock area affected by cow urine depositions are critical to the estimation and modelling of nitrogen (N) losses and N management in grazed pasture systems. A new technique
using survey-grade global positioning system (GPS) technology was developed to precisely measure the paddock spatial area coverage, diversity and distribution of dairy cattle urine patches in grazed paddocks over time. A 4-year study was conducted on the Lincoln University Dairy Farm (LUDF), Canterbury, New Zealand, from 2003 to 2007. Twelve field plots, each 100m² in area, were established
on typical grazing areas of the farm. All urine and dung deposits within the plots were visually identified, the pasture response area (radius) measured and position marked with survey-grade GPS. The plots were grazed as part of the normal grazing rotation of the farm and urine and dung deposits measured at 12-week intervals. The data were collated using spatial (GIS) software and an assessment of annual urine patch coverage and spatial distribution was made. Grazing intensities ranged from
17645 to 30295 cow grazing h/ha/yr. Mean annual areas of urine patches ranged from 0·34 to 0·40m² (4-year mean 0·37±0·009m²), with small but significant variation between years and seasons. Mean annual urine patch numbers were 6240±124 patches/ha/yr. The mean proportional area coverage for a single sampling event or season was 0·058 and the mean proportional annual urine patch coverage was 0·232±0·0071. There was a strong linear relationship between annual cow grazing h/ha and urine patch numbers/ha (R²=0·69) and also annual urine patch area coverage (R²=0·77). Within the stocking densities observed in this study, an annual increase of 10 000 cow grazing h/ha increased urine patch numbers by 1800 urine patches/ha/yr and annual urine patch area coverage by 0·07. This study presents new quantitative data on urine patch size, numbers and the spatial coverage of patches on a temporal basis
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