Direct and indirect effect of bt cotton and no bt cotton on the development and reproduction of the predator Podisus nigrispinus (Dallas, 1851) (Hemiptera: Pentatomidae).

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Poincaré on the Foundation of Geometry in the Understanding

This paper is about Poincaré’s view of the foundations of geometry. According to the established view, which has been inherited from the logical positivists, Poincaré, like Hilbert, held that axioms in geometry are schemata that provide implicit definitions of geometric terms, a view he expresses by stating that the axioms of geometry are “definitions in disguise.” I argue that this view does not accord well with Poincaré’s core commitment in the philosophy of geometry: the view that geometry is the study of groups of operations. In place of the established view I offer a revised view, according to which Poincaré held that axioms in geometry are in fact assertions about invariants of groups. Groups, as forms of the understanding, are prior in conception to the objects of geometry and afford the proper definition of those objects, according to Poincaré. Poincaré’s view therefore contrasts sharply with Kant’s foundation of geometry in a unique form of sensibility. According to my interpretation, axioms are not definitions in disguise because they themselves implicitly define their terms, but rather because they disguise the definitions which imply them

Conformations of Linear DNA

We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link number. We derive a fundamental relation between the Euler angles that describe the curve and the topological linking number. Analytical expressions for the spatial configurations of the molecule in the infinite- length limit were obtained. A unique configuraion minimizes the energy for a given set of physical conditions. An elastic model incorporating thermal fluctuations provides excellent agreement with experimental results on the plectonemic transition.Comment: 5 pages, RevTeX; 6 postscript figure

Influence of a knot on the strength of a polymer strand

Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on the properties of polymers has become of great interest, in part because of their effect on mechanical properties. Knot theory applied to the topology of macromolecules indicates that the simple trefoil or `overhand' knot is likely to be present with high probability in any long polymer strand. Fragments of DNA have been observed to contain such knots in experiments and computer simulations. Here we use {\it ab initio} computational methods to investigate the effect of a trefoil knot on the breaking strength of a polymer strand. We find that the knot weakens the strand significantly, and that, like a knotted rope, it breaks under tension at the entrance to the knot.Comment: 3 pages, 4 figure

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.

Histone tails and their epigenetic modifications play crucial roles in gene expression regulation by altering the architecture of chromatin. However, the structural mechanisms by which histone tails influence the interconversion between active and inactive chromatin remain unknown. Given the technical challenges in obtaining detailed experimental characterizations of the structure of chromatin, multiscale computations offer a promising alternative to model the effect of histone tails on chromatin folding. Here we combine multimicrosecond atomistic molecular dynamics simulations of dinucleosomes and histone tails in explicit solvent and ions, performed with three different state-of-the-art force fields and validated by experimental NMR measurements, with coarse-grained Monte Carlo simulations of 24-nucleosome arrays to describe the conformational landscape of histone tails, their roles in chromatin compaction, and the impact of lysine acetylation, a widespread epigenetic change, on both. We find that while the wild-type tails are highly flexible and disordered, the dramatic increase of secondary-structure order by lysine acetylation unfolds chromatin by decreasing tail availability for crucial fiber-compacting internucleosome interactions. This molecular level description of the effect of histone tails and their charge modifications on chromatin folding explains the sequence sensitivity and underscores the delicate connection between local and global structural and functional effects. Our approach also opens new avenues for multiscale processes of biomolecular complexes.This work was supported by the European Union Seventh Framework Programme (FP7/2007–2013) [275096 to R.C.-G. and M.O.]; the European Union’s Horizon 2020 research and innovation programme under a Marie Sklodowska-Curie grant [654812 to G.P. and M.V.]; Sara Borrell Fellowships [to G.P. and M.O.]; the Spanish MINECO [BIO2012–32868 to M.O.]; the Spanish National Institute of Bioinformatics (INB) [to M.O.]; the European Research Council (ERC) [Advanced Investigator Grant to M.O.]; the National Science Foundation [MCB0316771 to T. S.]; the National Institutes of Health [R01 GM55164 to T. S.]; Philip Morris USA [to T. S.]; and Philip Morris International [to T.S.]. M.O. is an ICREA-Academia fellow