Functional Derivative of the Zero Point Energy Functional from the Strong Interaction Limit of Density Functional Theory

We derive an explicit expression for the functional derivative of the subleading term in the strong interaction limit expansion of the generalized Levy--Lieb functional for the special case of two electrons in one dimension. The expression is derived from the zero point energy (ZPE) functional, which is valid if the quantum state reduces to strongly correlated electrons in the strong coupling limit. The explicit expression is confirmed numerically and respects the relevant sum-rule. We also show that the ZPE potential is able to generate a bond mid-point peak for homo-nuclear dissociation and is properly of purely kinetic origin. Unfortunately, the ZPE diverges for Coulomb systems, whereas the exact peaks should be finite.Comment: 12 pages, 7 figure

Rat Monoclonal Antibodies Specific for LST1 Proteins

The LST1 gene is located in the human MHC class III region and encodes transmembrane and soluble isoforms that have been suggested to play a role in the regulation of the immune response and are associated with inflammatory diseases such as rheumatoid arthritis. Here we describe the generation and characterization of the first monoclonal antibodies against LST1. Two hybridoma lines secreting monoclonal antibodies designated 7E2 and 8D12 were established. The 7E2 antibody detects recombinant and endogenous LST1 by Western blot analysis while 8D12 reacts with recombinant and endogenous LST1 in immunoprecipitation and flow cytometry procedures. The newly established antibodies were used to survey LST1 protein expression in human cell lines, which was found to be tightly regulated, allowing the expression of transmembrane isoforms but suppressing soluble isoforms

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

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 $W_{\lambda}[\rho]$, 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 ($\lambda\to\infty$, where $\lambda$ 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 $\lambda$, both numerical and theoretical, confirming that spin effects enter at orders $\sim e^{-\sqrt{\lambda}}$

Synthesis for Polynomial Lasso Programs

We present a method for the synthesis of polynomial lasso programs. These programs consist of a program stem, a set of transitions, and an exit condition, all in the form of algebraic assertions (conjunctions of polynomial equalities). Central to this approach is the discovery of non-linear (algebraic) loop invariants. We extend Sankaranarayanan, Sipma, and Manna's template-based approach and prove a completeness criterion. We perform program synthesis by generating a constraint whose solution is a synthesized program together with a loop invariant that proves the program's correctness. This constraint is non-linear and is passed to an SMT solver. Moreover, we can enforce the termination of the synthesized program with the support of test cases.Comment: Paper at VMCAI'14, including appendi

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