Essential Tools: Version Control Systems

Did you ever wish you\u27d made a backup copy of a file before changing it? Or before applying a collaborator\u27s modifications? Version control systems make this easier, and do a lot more

Functional modes of proteins are among the most robust ones

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result should prove helpful in the context of several applications proposed recently, like for solving difficult molecular replacement problems or for fitting atomic structures into low-resolution electron density maps. Moreover, it may also pave the way for the development of methods allowing to predict such motions accurately.Comment: 4 pages, 5 figure

Archiving and referencing source code with Software Heritage

Software, and software source code in particular, is widely used in modern research. It must be properly archived, referenced, described and cited in order to build a stable and long lasting corpus of scientic knowledge. In this article we show how the Software Heritage universal source code archive provides a means to fully address the first two concerns, by archiving seamlessly all publicly available software source code, and by providing intrinsic persistent identifiers that allow to reference it at various granularities in a way that is at the same time convenient and effective. We call upon the research community to adopt widely this approach.Comment: arXiv admin note: substantial text overlap with arXiv:1909.1076

Plasmon tunability in metallodielectric metamaterials

The dielectric properties of metamaterials consisting of periodically arranged metallic nanoparticles of spherical shape are calculated by rigorously solving Maxwell's equations. Effective dielectric functions are obtained by comparing the reflectivity of planar surfaces limiting these materials with Fresnel's formulas for equivalent homogeneous media, showing mixing and splitting of individual-particle modes due to inter-particle interaction. Detailed results for simple cubic and fcc crystals of aluminum spheres in vacuum, silver spheres in vacuum, and silver spheres in a silicon matrix are presented. The filling fraction of the metal f is shown to determine the position of the plasmon modes of these metamaterials. Significant deviations are observed with respect to Maxwell-Garnett effective medium theory for large f, and multiple plasmons are predicted to exist in contrast to Maxwell-Garnett theory.Comment: 6 pages, 4 figure

Модификация атактического полипропилена малеиновым ангидридом

International audienceAn efficient scheme is presented for the numerical calculation of hydrodynamic interactions of many spheres in Stokes flow. The spheres may have various sizes, and are freely moving or arranged in rigid arrays. Both the friction and mobility matrix are found from the solution of a set of coupled equations. The Stokesian dynamics of many spheres and the friction and mobility tensors of polymers and proteins may be calculated accurately at a modest expense of computer memory and time. The transport coefficients of suspensions can be evaluated by use of periodic boundary conditions

Universal behavior of localization of residue fluctuations in globular proteins

Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.Comment: 4 pages, 3 figures. To appear in Phys. Rev.

On the origin of the Boson peak in globular proteins

We study the Boson Peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean Random Matrix theory, whose predictions can be numerically tested on real proteins structures. We find that the emergence of the Boson Peak is strictly related to an intrinsic mechanical instability of the protein, in close similarity to what is thought to happen in glasses. The biological implications of this conclusion are also discussed by focusing on a representative case study.Comment: Proceedings of the X International Workshop on Disordered Systems, Molveno (2006