Hierarchy and assortativity as new tools for affinity investigation: the case of the TBA aptamer-ligand complex

Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic applications is very challenging. Usually they are in vitro generated, but, recently, computational approaches have been developed for the in silico selection, with a higher affinity for the specific target. Anyway, the mechanism of aptamer-ligand formation is not completely clear, and not obvious to predict. This paper aims to develop a computational model able to describe aptamer-ligand affinity performance by using the topological structure of the corresponding graphs, assessed by means of numerical tools such as the conventional degree distribution, but also the rank-degree distribution (hierarchy) and the node assortativity. Calculations are applied to the thrombin binding aptamer (TBA), and the TBA-thrombin complex, produced in the presence of Na+ or K+. The topological analysis reveals different affinity performances between the macromolecules in the presence of the two cations, as expected by previous investigations in literature. These results nominate the graph topological analysis as a novel theoretical tool for testing affinity. Otherwise, starting from the graphs, an electrical network can be obtained by using the specific electrical properties of amino acids and nucleobases. Therefore, a further analysis concerns with the electrical response, which reveals that the resistance sensitively depends on the presence of sodium or potassium thus posing resistance as a crucial physical parameter for testing affinity.Comment: 12 pages, 5 figure

A Taste of Cosmology

This is the summary of two lectures that aim to give an overview of cosmology. I will not try to be too rigorous in derivations, nor to give a full historical overview. The idea is to provide a "taste" of cosmology and some of the interesting topics it covers. The standard cosmological model is presented and I highlight the successes of cosmology over the past decade or so. Keys to the development of the standard cosmological model are observations of the cosmic microwave background and of large-scale structure, which are introduced. Inflation and dark energy and the outlook for the future are also discussed. Slides from the lectures are available from the school website: physicschool.web.cern.ch/PhysicSchool/CLASHEP/CLASHEP2011/.Comment: 16 pages, contribution to the 2011 CERN-Latin-American School of High-Energy Physics, Natal, Brazil, 23 March-5 April 2011, edited by C. Grojean, M. Mulders and M. Spiropul

Hierarchical Structure of Magnetohydrodynamic Turbulence In Position-Position-Velocity Space

Magnetohydrodynamic turbulence is able to create hierarchical structures in the interstellar medium that are correlated on a wide range of scales via the energy cascade. We use hierarchical tree diagrams known as dendrograms to characterize structures in synthetic Position-Position-Velocity (PPV) emission cubes of optically thin isothermal magnetohydrodynamic turbulence. We show that the structures and degree of hierarchy observed in PPV space are related to the physics of the gas, i.e. self-gravity and the global sonic and Alfvenic Mach number. Simulations with higher Alfvenic Mach number, self-gravity and supersonic flows display enhanced hierarchical structure. We observed a strong sonic and Alfvenic dependency when we apply the the statistical moments (i.e. mean, variance, skewness, kurtosis) to the dendrogram distribution. Larger magnetic field and sonic Mach number correspond to larger values of the moments. Application of the dendrogram to 3D density cubes, also known as Position-Position-Position cubes (PPP), reveals that the dominant emission contours in PPP and PPV are related for supersonic gas but not for subsonic. We also explore the effects of smoothing, thermal broadening and velocity resolution on the dendrograms in order to make our study more applicable to observational data. These results all point to hierarchical tree diagrams as being a promising additional tool for studying ISM turbulence and star forming regions in the direction of obtaining information on the degree of self-gravity, the Mach numbers and the complicated relationship between PPV and PPP.Comment: submitted to Ap