Preliminary calculations of flow in channel with triangular and rectangular obstacle

The paper presents the results of preliminary numerical calculations of a fluid flow in a channel with an obstacle. The flow problem was solved with an application of the finite elements method. Various geometries of obstacles were considered

RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

Abstract Background The structures of biological macromolecules provide a framework for studying their biological functions. Three-dimensional structures of proteins, nucleic acids, or their complexes, are difficult to visualize in detail on flat surfaces, and algorithms for their spatial superposition and comparison are computationally costly. Molecular structures, however, can be represented as 2D maps of interactions between the individual residues, which are easier to visualize and compare, and which can be reconverted to 3D structures with reasonable precision. There are many visualization tools for maps of protein structures, but few for nucleic acids. Results We developed RNAmap2D, a platform-independent software tool for calculation, visualization and analysis of contact and distance maps for nucleic acid molecules and their complexes with proteins or ligands. The program addresses the problem of paucity of bioinformatics tools dedicated to analyzing RNA 2D maps, given the growing number of experimentally solved RNA structures in the Protein Data Bank (PDB) repository, as well as the growing number of tools for RNA 2D and 3D structure prediction. RNAmap2D allows for calculation and analysis of contacts and distances between various classes of atoms in nucleic acid, protein, and small ligand molecules. It also discriminates between different types of base pairing and stacking. Conclusions RNAmap2D is an easy to use method to visualize, analyze and compare structures of nucleic acid molecules and their complexes with other molecules, such as proteins or ligands and metal ions. Its special features make it a very useful tool for analysis of tertiary structures of RNAs. RNAmap2D for Windows/Linux/MacOSX is freely available for academic users at http://iimcb.genesilico.pl/rnamap2d.html</p

Solvers for Systems of Nonlinear Algebraic Equations - Their Sensitivity to Starting Vectors

In this note we compare the sensitivity of six advanced solvers for systems of nonlinear algebraic equations to the choice of starting vectors. We will report on results of our experiments in which, for each test problem, the calculated solution was used as the center from which we have moved away in various directions and observed the behavior of each solver attempting to find the solution. We are particularly interested in determining the best global starting vectors. Experimental results are presented and discussed