Implementing efficient concerted rotations using Mathematica and C code

In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second

High-level classification of the Fungi and a tool for evolutionary ecological analyses

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.Peer reviewe

Structure of binary polymer blends: Multiple time step hybrid Monte Carlo simulations and self-consistent integral-equation theory

This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder

Investigation of compound formation sequence in Al/Ni/…/Al/Ni multilayer system under conditions of an excessive amount of one component and its prediction using the analogy with gas system behavior

Interaction processes in Al/Ni/.../Al/Ni multilayer systems with an excess of one of the components are studied by of DSC, XRD and TEM methods. It is shown that the compounds formation sequence differs depending on which component is excessive. There is proposed a rule for compounds formation sequence in systems with an excess of one of the initial phases. It is based on the assumption that behaviour of two contacting solid phases system is analogical to that of a gas system: energy density change in a solid-state system is analogical to pressure change in gas system. The prediction is built on the calculation of parameter ΔH0/νV, where ΔH0 and νV are enthalpy change and volume of new phase forming as a result of the reaction

Relationship between polymer chain conformation and phase boundaries in a supercritical fluid

This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder