One-dimensional quasi-relativistic particle in the box

Two-term Weyl-type asymptotic law for the eigenvalues of one-dimensional quasi-relativistic Hamiltonian (-h^2 c^2 d^2/dx^2 + m^2 c^4)^(1/2) + V_well(x) (the Klein-Gordon square-root operator with electrostatic potential) with the infinite square well potential V_well(x) is given: the n-th eigenvalue is equal to (n pi/2 - pi/8) h c/a + O(1/n), where 2a is the width of the potential well. Simplicity of eigenvalues is proved. Some L^2 and L^infinity properties of eigenfunctions are also studied. Eigenvalues represent energies of a `massive particle in the box' quasi-relativistic model.Comment: 40 pages, 4 figures; minor correction

In Silico Approaches and the Role of Ontologies in Aging Research

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin

Computing the shortest elementary flux modes in genome-scale metabolic networks

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic networks. Our method was applied to find the K-shortest EFMs that produce lysine in the genome-scale metabolic networks of Escherichia coli and Corynebacterium glutamicum. A detailed analysis of the biological significance of the K-shortest EFMs was conducted, finding that glucose catabolism, ammonium assimilation, lysine anabolism and cofactor balancing were correctly predicted. The work presented here represents an important step forward in the analysis and computation of EFMs for large-scale metabolic networks, where traditional methods fail for networks of even moderate size. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp564/DC1).Fundação Calouste Gulbenkian, Fundação para a Ciência e a Tecnologia (FCT) and Siemens SA Portugal

Gearing motion in cogwheel pairs of molecular rotors: weak-coupling limit

Variable-​temp. (VT) crystal structures, VT 1H spin-​lattice relaxation in static crystals, and DFT modeling of the rotational barriers of BCP rotators in cryst. arrays of a rod-​like mol. contg. two 1,​3-​bis(ethynyl)​bicyclo[1.1.1]​pentane (BCP) units demonstrate that a correlated gearing motion occurs in the limit of a weak coupling between two rotors in a pair

Serological surveillance reveals patterns of exposure to H5 and H7 influenza A viruses in European poultry

Influenza A viruses of H5 and H7 subtype in poultry can circulate subclinically, and subsequently mutate from low to high pathogenicity with potentially devastating economic and welfare consequences. European Union Member States undertake surveillance of commercial and backyard poultry for early detection and control of subclinical H5 and H7 influenza A infection. This surveillance has moved towards a risk‐based sampling approach in recent years; however quantitative measures of relative risk associated with risk factors utilised in this approach are necessary for optimisation. This study describes serosurveillance for H5 and H7 influenza A in domestic and commercial poultry undertaken in the European Union from 2004 to 2010, where a random sampling and thus representative approach to serosurveillance was undertaken. Using these representative data, this study measured relative risk of seropositivity across poultry categories and spatially across the EU. Data were analysed using multivariable logistic regression. Domestic waterfowl, game birds, fattening turkeys, ratites, backyard poultry and the “other” poultry category holdings had relatively increased probability of H5 and/or H7 influenza A seropositivity, compared to laying‐hen holdings. Amongst laying‐hen holdings, free‐range rearing was associated with increased probability of H7 seropositivity. Spatial analyses detected ‘hotspots’ for H5 influenza A seropositivity in western France and England, and H7 influenza A seropositivity in Italy and Belgium, which may be explained by the demographics and distribution of poultry categories. Findings suggest certain poultry category holdings are at increased risk of subclinical H5 and/or H7 influenza A circulation, and free‐range rearing increases the likelihood of exposure to H7 influenza A. These findings may be used in further refining risk‐based surveillance strategies, and prioritising management strategies in influenza A outbreaks

Structure and photophysics of indigoids for singlet fission: Cibalackrot

We report an investigation of structure and photophysics of thin layers of cibalackrot, a sturdy dye derived from indigo by double annulation at the central double bond. Evaporated layers contain up to three phases, two crystalline and one amorphous. Relative amounts of all three have been determined by a combination of X-ray diffraction and FT-IR reflectance spectroscopy. Initially, excited singlet state rapidly produces a high yield of a transient intermediate whose spectral properties are compatible with charge-transfer nature. This intermediate more slowly converts to a significant yield of triplet, which, however, does not exceed 100% and may well be produced by intersystem crossing rather than singlet fission. The yields were determined by transient absorption spectroscopy and corrected for effects of partial sample alignment by a simple generally applicable procedure. Formation of excimers was also observed. In order to obtain guidance for improving molecular packing by a minor structural modification, calculations by a simplified frontier orbital method were used to find all local maxima of singlet fission rate as a function of geometry of a molecular pair. The method was tested at 48 maxima by comparison with the ab initio Frenkel-Davydov exciton model. Published under license by AIP Publishing

A new computational method to split large biochemical networks into coherent subnets

<p>Abstract</p> <p>Background</p> <p>Compared to more general networks, biochemical networks have some special features: while generally sparse, there are a small number of highly connected metabolite nodes; and metabolite nodes can also be divided into two classes: internal nodes with associated mass balance constraints and external ones without. Based on these features, reclassifying selected internal nodes (separators) to external ones can be used to divide a large complex metabolic network into simpler subnetworks. Selection of separators based on node connectivity is commonly used but affords little detailed control and tends to produce excessive fragmentation.</p> <p>The method proposed here (Netsplitter) allows the user to control separator selection. It combines local connection degree partitioning with global connectivity derived from random walks on the network, to produce a more even distribution of subnetwork sizes. Partitioning is performed progressively and the interactive visual matrix presentation used allows the user considerable control over the process, while incorporating special strategies to maintain the network integrity and minimise the information loss due to partitioning.</p> <p>Results</p> <p>Partitioning of a genome scale network of 1348 metabolites and 1468 reactions for <it>Arabidopsis thaliana </it>encapsulates 66% of the network into 10 medium sized subnets. Applied to the flavonoid subnetwork extracted in this way, it is shown that Netsplitter separates this naturally into four subnets with recognisable functionality, namely synthesis of lignin precursors, flavonoids, coumarin and benzenoids. A quantitative quality measure called <it>efficacy </it>is constructed and shows that the new method gives improved partitioning for several metabolic networks, including bacterial, plant and mammal species.</p> <p>Conclusions</p> <p>For the examples studied the Netsplitter method is a considerable improvement on the performance of connection degree partitioning, giving a better balance of subnet sizes with the removal of fewer mass balance constraints. In addition, the user can interactively control which metabolite nodes are selected for cutting and when to stop further partitioning as the desired granularity has been reached. Finally, the blocking transformation at the heart of the procedure provides a powerful visual display of network structure that may be useful for its exploration independent of whether partitioning is required.</p

Crystalline Arrays of Pairs of Molecular Rotors: Correlated Motion, Rotational Barriers, and Space-Inversion Symmetry Breaking Due to Conformational Mutations

The rod-like molecule bis 4-(4-pyridyl)ethynyl)bicyclo[2.2.2]oct-1-yl)buta-1,3-diyne, 1, contains two 1,4-bis(ethynyl)bicyclo[2.2.2]octane (ethynyl) chiral rotators linked by a diyne fragment and self assembles in a one-dimensional, monoclinic C2/c centrosymmetric structure where two equilibrium positions with large occupancy imbalance (88% versus 12%) are identified on a single rotor site Combining variable temperature (70-300 K) proton spin-lattice relaxation, H-1 T-1(-1), at two different H-1 Larmor frequencies (55 and 210 MHz) and DFT calculations of rotational barriers, we were able to assign two types of Brownian rotators with different activation energies, 1.85 and 6.1 kcal mol(-1), to the two H-1 spin-lattice relaxation processes on the single rotor site. On the basis of DFT calculations, the low-energy process has been assigned to adjacent rotors in a well-correlated synchronous motion, whereas the high-energy process is the manifestation of an abrupt change in their kinematics once two blades of adjacent rotors are seen to rub together. Although crystals of 1 should be second harmonic inactive, a large second-order optical response is recorded when the electric field oscillates in a direction parallel to the unique rotor axle director. We conclude that conformational mutations by torsional interconversion of the three blades of the BCO units break space-inversion symmetry in sequences of mutamers in dynamic equilibrium in the crystal in domains at a rnesoscopic scale comparable with the wavelength of light used A control experiment was performed with a crystalline film of a similar tetrayne molecule, 1,4-bis(3-((trimethylsilyl)ethynyl)bicyclo-[1.1.1]pent-1-yObuta-1,3-diyne, whose bic-ydopentane units can rotate but are achiral and produce no second-order optical response