ABSTRACT
Inspired by experiments on topologically linked DNA networks, we consider the connectivity of Borromean networks, in which no two rings share a pairwise-link, but groups of three rings form inseparable triplets. Specifically, we focus on square lattices at which each node is embedded a loop which forms a Borromean link with pairs of its nearest neighbors. By mapping the Borromean link network onto a lattice representation, we investigate the percolation threshold of these networks (the fraction of occupied nodes required for a giant component), as well as the dissolution properties: the spectrum of topological links that would be released if the network were dissolved to varying degrees. We find that the percolation threshold of the Borromean square lattice occurs when approximately 60.75% of nodes are occupied, slightly higher than the 59.27% typical of a square lattice. Compared to the dissolution of Hopf-linked networks, a dissolved Borromean network will yield more isolated loops, and fewer isolated triplets per single loop. Our simulation results may be used to predict experiments from Borromean structures produced by synthetic chemistry.
ABSTRACT
Photon-HDF5 is an open-source and open file format for storing photon-counting data from single molecule microscopy experiments, introduced to simplify data exchange and increase the reproducibility of data analysis. Part of the Photon-HDF5 ecosystem, is phconvert, an extensible python library that allows converting proprietary formats into Photon-HDF5 files. However, its use requires some proficiency with command line instructions, the python programming language, and the YAML markup format. This creates a significant barrier for potential users without that expertise, but who want to benefit from the advantages of releasing their files in an open format. In this work, we present a GUI that lowers this barrier, thus simplifying the use of Photon-HDF5. This tool uses the phconvert python library to convert data files originally saved in proprietary data formats to Photon-HDF5 files, without users having to write a single line of code. Because reproducible analyses depend on essential experimental information, such as laser power or sample description, the GUI also includes (currently limited) functionality to associate valid metadata with the converted file, without having to write any YAML. Finally, the GUI includes several productivity-enhancing features such as whole-directory batch conversion and the ability to re-run a failed batch, only converting the files that could not be converted in the previous run.