Hydrogen bonding in cubic (H_2O)_8 and OH∙(H_2O)_7 clusters

A systematic study is presented for OH∙(H_2O)_7 clusters derived from the cubic (H_2O)_8 octamer by replacing one water with a hydroxyl radical. The system is a prototype for atmospheric water clusters containing the environmentally important OH species, and for OH adsorbed at the surface of ice. The full set of 39 symmetry-distinct cubic OH∙(H_2O)_7 clusters is enumerated, and the structures are determined using ab initio quantum chemical methods. Graph invariants are employed to obtain a unified analysis of the stability and structure of cubic (H_2O)_8 and OH∙(H_2O)_7, relating these physical properties to the various hydrogen-bond topologies present in these clusters. To accomplish this the graph invariant formalism is extended to treat a hydrogen bonding impurity within a pure water network

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

Ice Ih, ordinary ice at atmospheric pressure, is a proton-disordered crystal that when cooled under special conditions is believed to transform to ferroelectric proton-ordered ice XI, but this transformation is still subject to controversy. Ice VII, also proton disordered throughout its region of stability, transforms to proton-ordered ice VIII upon cooling. In contrast to the ice Ih/XI transition, the VII/VIII transition and the crystal structure of ice VIII are well characterized. In order to shed some light on the ice Ih proton ordering transition, we present the results of periodic electronic density functional theory calculations and statistical simulations. We are able to describe the small energy differences among the innumerable H-bond configurations possible in a large simulation cell by using an analytic theory to extrapolate from electronic DFT calculations on small unit cells to cells large enough to approximate the thermodynamic limit. We first validate our methods by comparing our predictions to the well-characterized ice VII/VIII proton ordering transition, finding agreement with respect to both the transition temperature and structure of the low-temperature phase. For ice Ih, our results indicate that a proton-ordered phase is attainable at low temperatures, the structure of which is in agreement with the experimentally proposed ferroelectric Cmc2_1 structure. The predicted transition temperature of 98 K is in qualitative agreement with the observed transition at 72 K on KOH-doped ice samples

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

What’s special about the ethical challenges of studying disorders with altered brain activity?

Where there is no viable alternative, studies of neuronal activity are conducted on animals. The use of animals, particularly for invasive studies of the brain, raises a number of ethical issues. Practical or normative ethics are enforced by legislation, in relation to the dominant welfare guidelines developed in the UK and elsewhere. Guidelines have typically been devised to cover all areas of biomedical research using animals in general, and thus lack any specific focus on neuroscience studies at the level of the ethics, although details of the specific welfare recommendations are different for invasive studies of the brain. Ethically there is no necessary distinction between neuroscience and other biomedical research in that the brain is a final common path for suffering, irrespective of whether this involves any direct experience of pain. One exception arises in the case of in vitro studies, which are normally considered as an acceptable replacement for in vivo studies. However, to the extent sentience is possible, maintaining central nervous system tissue outside the body naturally raises ethical questions. Perhaps the most intractable challenge to the ethical use of animals in order to model neuronal disorder is presented by the logical impasse in the argument that the animal is similar enough to justify the validity of the experimental model, but sufficiently different in sentience and capacity for suffering, for the necessary experimental procedures to be permissible

Localized Mode Analysis Of Zeolite Complex Vibrational Motion

Author Institution: Department of Chemistry, The Ohio State University; Department of Chemistry, The Ohio State UniversityUsually we strive to understand vibrational modes as built from elementary ``zero-order'' motions such as bending and stretches. However, it is difficult to elucidate these localized motions for large molecules and solids with large unit cells. We have determined methods to obtain local vibrational motions from normal modes for large systems. These procedures have their roots the local orbital concept of Edmiston and Ruedenberg, the theory of localized electronic states in the context of Anderson localization, and in the group theoretic equivalent orbital approach of Lennard-Jones. One example of where our approach is useful is the analysis of zeolite normal modes. Experimentalists have long speculated on the relationship between the structure and spectral properties of zeolites. We find that spectral features can be associated with localized motion on the rings that comprise these silicates