Modelling the atomic structure of very high-density amorphous ice

The structure of very high-density amorphous (VHDA) ice has been modelled by positionally disordering three crystalline phases, namely ice IV, VI and XII. These phases were chosen because only they are stable or metastable in the region of the ice phase diagram where VHDA ice is formed, and their densities are comparable to that of VHDA ice. An excellent fit to the medium range of the experimentally observed pair-correlation function g(r) of VHDA ice was obtained by introducing disorder into the positions of the H2O molecules, as well as small amounts of molecular rotational disorder, disorder in the O--H bond lengths and disorder in the H--O--H bond angles. The low-k behaviour of the experimental structure factor, S(k), is also very well reproduced by this disordered-crystal model. The fraction of each phase present in the best-fit disordered model is very close to that observed in the probable crystallization products of VHDA ice. In particular, only negligible amounts of ice IV are predicted, in accordance with experimental observation.Comment: 4 pages, 3 figures, 1 table, v2: changes made in response to referees' comments, the justification for using certain ice phases is improved, and ice IV is now disordered as wel

Pressure-induced amorphization and polyamorphism in one-dimensional single crystal TiO2 nanomaterials

The structural phase transitions of single crystal TiO2-B nanoribbons were investigated in-situ at high-pressure using the synchrotron X-ray diffraction and the Raman scattering. Our results have shown a pressure-induced amorphization (PIA) occurred in TiO2-B nanoribbons upon compression, resulting in a high density amorphous (HDA) form related to the baddeleyite structure. Upon decompression, the HDA form transforms to a low density amorphous (LDA) form while the samples still maintain their pristine nanoribbon shape. HRTEM imaging reveals that the LDA phase has an {\alpha}-PbO2 structure with short range order. We propose a homogeneous nucleation mechanism to explain the pressure-induced amorphous phase transitions in the TiO2-B nanoribbons. Our study demonstrates for the first time that PIA and polyamorphism occurred in the one-dimensional (1D) TiO2 nanomaterials and provides a new method for preparing 1D amorphous nanomaterials from crystalline nanomaterials.Comment: 4 figure

Radiation attenuation by single-crystal diamond windows

As artificial diamond becomes more cost effective it is likely to see increasing use as a window for sample environment equipment used in diffraction experiments. Such windows are particularly useful as they exhibit exceptional mechanical properties in addition to being highly transparent to both X-ray and neutron radiation. A key application is in high-pressure studies, where diamond anvil cells (DACs) are used to access extreme sample conditions. However, despite their utility, an important consideration when using single-crystal diamond windows is their interaction with the incident beam. In particular, the Bragg condition will be satisfied for specific angles and wavelengths, leading to the appearance of diamond Bragg spots on the diffraction detectors but also, unavoidably, to loss of transmitted intensity of the beam that interacts with the sample. This effect can be particularly significant for energy-dispersive measurements, for example, in time-of-flight neutron diffraction work using DACs. This article presents a semi-empirical approach that can be used to correct for this effect, which is a prerequisite for the accurate determination of diffraction intensities

Ab initio van der Waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like

The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations using van der Waals (vdW) density-functional theory, i.e. using the new exchange-correlation functionals optPBE-vdW and vdW-DF2. Inclusion of the more isotropic vdW interactions counteracts highly directional hydrogen-bonds, which are enhanced by standard functionals. This brings about a softening of the microscopic structure of water, as seen from the broadening of angular distribution functions and, in particular, from the much lower and broader first peak in the oxygen-oxygen pair-correlation function (PCF), indicating loss of structure in the outer solvation shells. In combination with softer non-local correlation terms, as in the new parameterization of vdW-DF, inclusion of vdW interactions is shown to shift the balance of resulting structures from open tetrahedral to more close-packed. The resulting O-O PCF shows some resemblance with experiment for high-density water (A. K. Soper and M. A. Ricci, Phys. Rev. Lett., 84:2881, 2000), but not directly with experiment for ambient water. However, an O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from experiment on low-density liquid water reproduces near-quantitatively the experimental O-O PCF for ambient water, indicating consistency with a two-liquid model with fluctuations between high- and low-density regions

A quantitative assay to study the lipid selectivity of membrane-associated systems using solution NMR

The activity of membrane proteins and compounds that interact with the membrane is modulated by the surrounding lipid composition. However, there are no simple methods that determine the composition of these annular phospholipids in eukaryotic systems. Herein, we describe a simple methodology that enables the identification and quantification of the lipid composition around membrane-associated compounds using SMA-nanodiscs and routine $^1H-^{31}P NMR$

Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined

Chloride channels of intracellular membranes

Proteins implicated as intracellular chloride channels include the intracellular ClC proteins, the bestrophins, the cystic fibrosis transmembrane conductance regulator, the CLICs, and the recently described Golgi pH regulator. This paper examines current hypotheses regarding roles of intracellular chloride channels and reviews the evidence supporting a role in intracellular chloride transport for each of these proteins