Hydrogen-bond topology and the ice VII/VIII and ice Ih/XI proton-ordering phase transitions

The existence of an ice Ih/XI proton-ordering transition to a low-temperature ferroelectric phase has sparked considerable debate in the literature. Electronic density functional theory calculations, extended using graph invariants, confirm that a transition to a low-temperature ferroelectric phase should occur. The predicted transition at 98 K is in qualitative agreement with the observed transition at 72 K, and the low-temperature phase is the ferroelectric phase determined in diffraction experiments. The theoretical methods used to predict the phase transition are validated by comparing their prediction to the well-characterized ice VII/VIII proton-ordering transition.     

Spatial chaos aspects of laser-material interaction

In the past decade the understanding of stability and chaotic behaviour of nonlinear systems has made significant progress. Such systems include: structure of turbulence, oscillations in mechanical structures, multistable biological systems, etc. Laser machining is now an established industrial production method for: prototyping, small batch manufacture, cutting refractory materials and specialist applications such as micromachining. Within narrowly bounded limits, many models exist that can be used to predict the necessary machining control parameters such as cutting rate, power, pulse repetition frequency, etc. However, in an unconstrained machining process, chaotic phenomena can be observed to occur. The objective of this paper is to prove the existence of chaos, for the laser-material interaction, which can be described by Poincaré-Birkhoff-Smale horseshoes. Furthermore, to exploit the phase portrait of the process to predict the optimal laser machining control parameters.     

Thermodynamically stable phases of carbon at multiterapascal pressures

Phases of carbon are studied up to pressures of 1 petapascal (PPa) using first-principles density-functional-theory methods and a structure searching algorithm. Our extensive search over the potential energy surface supports the sequence of transitions diamond → BC8 → simple cubic under increasing pressure found in previous theoretical studies. At higher pressures we predict a soft-phonon driven transition to a simple hexagonal structure at 6.4 terapascals (TPa), and further transitions to the face centered cubic electride structure at 21 TPa, a double hexagonal close packed structure at 270 TPa, and the body centered cubic structure at 650 TPa.     

Low-energy termination of graphene edges via the formation of narrow nanotubes

We demonstrate that free graphene sheet edges can curl back on themselves, reconstructing as nanotubes. This results in lower formation energies than any other nonfunctionalized edge structure reported to date in the literature. We determine the critical tube size and formation barrier and compare with density functional simulations of other edge terminations including a new reconstructed Klein edge. Simulated high resolution electron microscopy images show why such rolled edges may be difficult to detect. Rolled zigzag edges serve as metallic conduction channels, separated from the neighboring bulk graphene by a chain of insulating sp(3)-carbon atoms, and introduce van Hove singularities into the graphene density of states.     

Elastic connection disk subjected to periodically fluctuating transmitted torque and rotational speed

Involving the intrinsic power transmission torque/speed coupling characteristics of prime-movers, a rotating elastic connection disk subjected to periodically fluctuating transmitted torque and rotational speed generated by the fluctuation of external loads is investigated. Using Galerkin's method, the rotating elastic connection disk is modeled as a parametrically excited gyroscopic system. The effects of the torque/speed coupling, transmitted torque fluctuation amplitude and frequency, and constant parts of the transmitted torque and the rotational speed on the system dynamic stability are explored for the disk modes possessing different nodal diameters. The rotational speed, transmitted torque and their fluctuations can all result in system instability of the elastic connection disk. The instability can be suppressed or avoided by operating at small amplitude and low frequency of the transmitted torque fluctuation, and by operating in the weakly coupled torque/speed regime of the prime-movers. Low rotational speed avoids the instability in the case of a small transmitted torque, but medium rotational speed operation is valuable to suppress the instability induced by a large transmitted torque and its fluctuation. Instability parameter regions for the positive and negative torque/speed coupling coefficient are roughly similar in shape, but there are some differences in the value of the instability coefficient.     

Unsupervised cell identification on multidimensional X‐ray fluorescence datasets

A novel approach to locate, identify and refine positions and whole areas of cell structures based on elemental contents measured by X‐ray fluorescence microscopy is introduced. It is shown that, by initializing with only a handful of prototypical cell regions, this approach can obtain consistent identification of whole cells, even when cells are overlapping, without training by explicit annotation. It is robust both to different measurements on the same sample and to different initializations. This effort provides a versatile framework to identify targeted cellular structures from datasets too complex for manual analysis, like most X‐ray fluorescence microscopy data. Possible future extensions are also discussed.     

Reverse fingerprinting, similarity searching by group fusion and fingerprint bit importance

Summary Recent research has shown that using data fusion rules in fingerprint-based similarity searching can improve results over traditional searches. Group fusion scores, which use multiple reference compounds, have in particular been shown to be quite effective in increasing enrichment rates over single reference structure based searches. In this paper, the effectiveness of using data fusion with multiple reference compounds to increase similarity search recall rates was investigated using 44 biological targets and four different 2D fingerprinting systems, including a new 2D typed triangle fingerprinting system introduced here. Scaffold-hopping abilities using data fusion rules were investigated using eight (8) different classes of scaffolds active against cGMP phosphodiesterase isoform 5 (PDE5). An approach to using the reference group for ranking and visualizing important fingerprints bits, or reverse fingerprinting, was presented, and used to score and visualize important pharmacophore features within sample active molecules. Finally, similarity statistics within the reference groups were investigated and compared to recall rates.