SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Synthesis and characterisation of metal oxyhydroxide and oxide nanomaterials

In this work, a range of nanomaterials have been synthesised based on metal oxyhydroxides MO(OH), where M=Al, Co, Cr, etc. Through a self-assembly hydrothermal route, metal oxyhydroxide nanomaterials with various morphologies were successfully synthesised: one dimensional boehmite (AlO(OH)) nanofibres, zero dimensional indium hydroxide (In(OH)3) nanocubes and chromium oxyhydroxide (CrO(OH)) nanoparticles, as well as two dimensional cobalt hydroxide and oxyhydroxide (Co(OH)2 & CoO(OH)) nanodiscs. In order to control the synthetic nanomaterial morphology and growth, several factors were investigated including cation concentration, temperature, hydrothermal treatment time, and pH. Metal ion doping is a promising technique to modify and control the properties of materials by intentionally introducing impurities or defects into the material. Chromium was successfully applied as a dopant for fabricating doped boehmite nanofibres. The thermal stability of the boehmite nanofibres was enhanced by chromium doping, and the photoluminescence property was introduced to the chromium doped alumina nanofibres. Doping proved to be an efficient method to modify and functionalize nanomaterials. The synthesised nanomaterials were fully characterised by X-ray diffraction (XRD), transmission electron microscopy (TEM) combined with selected area electron diffraction (SAED), scanning electron microscopy (SEM), BET specific surface area analysis, X-ray photoelectron spectroscopy (XPS) and thermo gravimetric analysis (TGA). Hot-stage Raman and infrared emission spectroscopy were applied to study the chemical reactions during dehydration and dehydroxylation. The advantage of these techniques is that the changes in molecular structure can be followed in situ and at the elevated temperatures.

Diels-Alder reactions as an efficient route to high purity cyclic polymers

A simple and efficient route for the synthesis of cyclic polymer systems is presented. Linear furan protected α-maleimide-ω-cyclopentadienyl functionalized precursors (poly(methyl methacrylate) and poly(tert-butyl acrylate)) were synthesized via atom transfer radical polymerization (ATRP) and subsequent substitution of the bromine end-group with cyclopentadiene. Upon heating at high dilution, deprotection of the dieneophile occurs followed by an intramolecular Diels–Alder reaction yielding a high purity cyclic product.

Chain scission resists for extreme ultraviolet lithography based on high performance polysulfone-containing polymers

A series of polymers with a comb architecture were prepared where the poly(olefin sulfone) backbone was designed to be highly sensitive to extreme ultraviolet (EUV) radiation, while the well-defined poly(methyl methacrylate) (PMMA) arms were incorporated with the aim of increasing structural stability. It is hypothesized that upon EUV radiation rapid degradation of the polysulfone backbone will occur leaving behind the well-defined PMMA arms. The synthesized polymers were characterised and have had their performance as chain-scission EUV photoresists evaluated. It was found that all materials possess high sensitivity towards degradation by EUV radiation (E0 in the range 4–6 mJ cm−2). Selective degradation of the poly(1-pentene sulfone) backbone relative to the PMMA arms was demonstrated by mass spectrometry headspace analysis during EUV irradiation and by grazing-angle ATR-FTIR. EUV interference patterning has shown that materials are capable of resolving 30 nm 1:1 line:space features. The incorporation of PMMA was found to increase the structural integrity of the patterned features. Thus, it has been shown that terpolymer materials possessing a highly sensitive poly(olefin sulfone) backbone and PMMA arms are able to provide a tuneable materials platform for chain scission EUV resists. These materials have the potential to benefit applications that require nanopattering, such as computer chip manufacture and nano-MEMS.