The Pocket Reasoner -- Automatic Reasoning on Small Devices

Automated reasoning in classical first-order logic is a core research field in Artificial Intelligence. Most of the fully automated reasoning tools are large and complex systems implementing proof search methods that have significant memory requirements. This paper presents an automated reasoning tool implemented on an iPod Nano. It is based on leanCoP, a very compact Prolog implementation of the connection calculus, which operates on the structure of the given formula without generating new subformula instances. Hence, the memory requirements are significantly lower, allowing leanCoP to run on devices with only little (random-access) memory. The paper presents details of the proof search calculus, its implementation, and a practical evaluation of the presented reasoning tool

leanCoP: lean connection-based theorem proving

AbstractThe Prolog programimplements a theorem prover for classical first-order (clausal) logic which is based on the connection calculus. It is sound and complete (provided that an arbitrarily large I is iteratively given), and demonstrates a comparatively strong performance

Converting ALC Connection Proofs into ALC Sequents

The connection method has earned good reputation in the area of automated theorem proving, due to its simplicity, efficiency and rational use of memory. This method has been applied recently in automatic provers that reason over ontologies written in the description logic ALC. However, proofs generated by connection calculi are difficult to understand. Proof readability is largely lost by the transformations to disjunctive normal form applied over the formulae to be proven. Such a proof model, albeit efficient, prevents inference systems based on it from effectively providing justifications and/or descriptions of the steps used in inferences. To address this problem, in this paper we propose a method for converting matricial proofs generated by the ALC connection method to ALC sequent proofs, which are much easier to understand, and whose translation to natural language is more straightforward. We also describe a calculus that accepts the input formula in a non-clausal ALC format, what simplifies the translation.Comment: In Proceedings PxTP 2019, arXiv:1908.08639. Thanks to CAPES: Coordination for the Improvement of Higher Level Personne

Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining

<p>Abstract</p> <p>Background</p> <p>GFP-fusion proteins and immunostaining are methods broadly applied to investigate the three-dimensional organization of cells and cell nuclei, the latter often studied in addition by fluorescence in situ hybridization (FISH). Direct comparisons of these detection methods are scarce, however.</p> <p>Results</p> <p>We provide a quantitative comparison of all three approaches. We make use of a cell line that contains a transgene array of lac operator repeats which are detected by GFP-lac repressor fusion proteins. Thus we can detect the same structure in individual cells by GFP fluorescence, by antibodies against GFP and by FISH with a probe against the transgene array. Anti-GFP antibody detection was repeated after FISH. Our results show that while all four signals obtained from a transgene array generally showed qualitative and quantitative similarity, they also differed in details.</p> <p>Conclusion</p> <p>Each of the tested methods revealed particular strengths and weaknesses, which should be considered when interpreting respective experimental results. Despite the required denaturation step, FISH signals in structurally preserved cells show a surprising similarity to signals generated before denaturation.</p

Computation and Stability of TravelingWaves in Second Order Evolution Equations

The topic of this paper are nonlinear traveling waves occuring in a system of damped waves equations in one space variable. We extend the freezing method from first to second order equations in time. When applied to a Cauchy problem, this method generates a comoving frame in which the solution becomes stationary. In addition it generates an algebraic variable which converges to the speed of the wave, provided the original wave satisfies certain spectral conditions and initial perturbations are sufficiently small. We develop a rigorous theory for this effect by recourse to some recent nonlinear stability results for waves in first order hyperbolic systems. Numerical computations illustrate the theory for examples of Nagumo and FitzHugh-Nagumo type

Freezing traveling and rotatingwaves in second order evolution equations

In this paper we investigate the implementation of the so-called freezing method for second order wave equations in one and several space dimensions. The method converts the given PDE into a partial differential algebraic equation which is then solved numerically. The reformulation aims at separating the motion of a solution into a co-moving frame and a profile which varies as little as possible. Numerical examples demonstrate the feasability of this approach for semilinear wave equations with sufficient damping. We treat the case of a traveling wave in one space dimension and of a rotating wave in two space dimensions. In addition, we investigate in arbitrary space dimensions the point spectrum and the essential spectrum of operators obtained by linearizing about the profile, and we indicate the consequences for the nonlinear stability of the wave

Constricted Boron Nanotubes

The recent discovery of pure boron nanotubes raises questions about their detailed atomic structure. Previous simulations predicted tubular structures with smooth or puckered surfaces. Here, we present some novel results based on ab initio simulations of bundled single-wall zigzag boron nanotubes (ropes). Besides the known smooth and puckered modifications, we found new forms that are radially constricted, and which seem to be energetically superior to the known isomers. Furthermore, those structures might be interpreted as intermediate states between ideal tubular phases and the known bulk phases based on boron icosahedra.Comment: 11 pages, 4 figure

Structural characterization of the thermostable <i>Bradyrhizobium japonicum</i> D-sorbitol dehydrogenase

Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is d-glucitol (a synonym for d-sorbitol), although l-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Å resolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain dehydrogenases, including the search model, could be reconstructed by applying crystallographic symmetry operations. The active site contains electron density consistent with d-glucitol and phosphate, but there was not clear evidence for the binding of NADH. In a search for the features that determine the thermostability of the enzyme, the T (m) for the orthologue from Rhodobacter sphaeroides, for which the structure was already known, was also determined, and this enzyme proved to be considerably less thermostable. A continuous β-sheet is formed between two monomers in the tetramer of the B. japonicum enzyme, a feature not generally shared by short-chain dehydrogenases, and which may contribute to thermostability, as may an increased Pro/Gly ratio