Exact and efficient calculation of Lagrange multipliers in constrained biological polymers: Proteins and nucleic acids as example cases

In order to accelerate molecular dynamics simulations, it is very common to impose holonomic constraints on their hardest degrees of freedom. In this way, the time step used to integrate the equations of motion can be increased, thus allowing, in principle, to reach longer total simulation times. The imposition of such constraints results in an aditional set of Nc equations (the equations of constraint) and unknowns (their associated Lagrange multipliers), that must be solved in one way or another at each time step of the dynamics. In this work it is shown that, due to the essentially linear structure of typical biological polymers, such as nucleic acids or proteins, the algebraic equations that need to be solved involve a matrix which is banded if the constraints are indexed in a clever way. This allows to obtain the Lagrange multipliers through a non-iterative procedure, which can be considered exact up to machine precision, and which takes O(Nc) operations, instead of the usual O(Nc3) for generic molecular systems. We develop the formalism, and describe the appropriate indexing for a number of model molecules and also for alkanes, proteins and DNA. Finally, we provide a numerical example of the technique in a series of polyalanine peptides of different lengths using the AMBER molecular dynamics package.Comment: 29 pages, 10 figures, 1 tabl

Cibermetría del Web: Las leyes de exponenciación.

An introduction to the power laws, enunciated by Michalis Faloutsos, is made and tbat allows us tu make a characterization of the Web through the analysis of their topology. Their most important characteristics are described and how calculate some of ihe values of thc most interesting functions.Se realiza una introducción a las leyes de exponenciación, enunciadas por Michalis Faloutsos y que nos permiten realizar una caracterización del Web a tra vés del análisis de su topología. Se describen sus características más importantes y cómo se calculan algunos de los valores de las funciones más interesantes

Salvia guaneorum (Labiatae), a new species from the Chicamocha Canyon, Colombia

[EN] A new species of Salvia subgen. Calosphace from the Chicamocha Canyon, in the Eastern Cordillera of Colombia is described and illustrated. The morphological affinities and putative relatives with other Colombian species of the sections Angulatae and Longipes are discussed. [ES] Se describe e ilustra una especie nueva de Salvia subgen. Calosphace, procedente del Cañón del Chicamocha, en la Cordillera Oriental de Colombia. Se discuten sus afinidades morfológicas y posible relación con otras especies colombianas de las secciones Angulatae y Longipes.National University of Colombia and the Ministry of Agriculture and Rural Development of Colombia by financing the project "Conservation and identification of promising native species for their content of essential oils", during which collections of Labiatae were made in Colombia, and experimental plots of the genus Salvia were established on the National University campus. At the Consejo Superior de Investigaciones Científicas (CSIC) and the Ministerio de Ciencia e Innovación of Spain for financing the project CGL 2010-19747, which facilitated the visits to Colombia and the study of the species discussed here.Peer reviewe

Expansión de Dittrichia graveolens (L.) Greuter (Asteraceae) por las carreteras del Pirineo y su relación con el uso de glifosfato

Damos cuenta de la rápida expansión de la compuesta Dittrichia graveolens por las carreteras del Pirineo aragonés occidental, especie de fenología otoñal que estaba ausente hasta el momento de su flora. Ligamos esta súbita aparición al uso primaveral del herbicida glifosato para el mantenimiento de las cunetas.We describe the rapid expansion of Dittrichia graveolens (Compositae) on the roads of Western Aragonese Pyrenees.This species has an autumnal phenology and was absent at the time of the West Pyrenean flora. This sudden appearance we believe that is due to the use of the herbicide glyphosate in the spring, for removing herbs of drainage ditches

Epilobium ciliatum Rafin. (Onagraceae), a new adventive species potentially invasive in the Iberian Peninsula

Epilobium ciliatum Rafin. (Onagraceae), a new adventive species potentially invasive in the Iberian Peninsula Palabras clave. Epilobium ciliatum, especies adventicias, Flora vascular, Onagraceae, Península Ibérica. Key words. Epilobium ciliatum, Iberian Peninsula, adventive species, Onagraceae, vascular flor

Epilobium ciliatum Rafin. (Onagraceae), una nueva adventicia potencialmente invasora en la Península Ibérica

Peer reviewe

Una nueva especie de Salvia (Labiatae) de Colombia

Se describe e ilustra una nueva especie del género Salvia, sea. Rubescentes (Epl.) Epl. (Labiatae), que vive en la franja paramuna del departamento de Santander (Colombia).Peer reviewe