Equation of State for Macromolecules of Variable Flexibility in Good Solvents: A Comparison of Techniques for Monte Carlo Simulations of Lattice Models

The osmotic equation of state for the athermal bond fluctuation model on the simple cubic lattice is obtained from extensive Monte Carlo simulations. For short macromolecules (chain length N=20) we study the influence of various choices for the chain stiffness on the equation of state. Three techniques are applied and compared in order to critically assess their efficiency and accuracy: the repulsive wall method, the thermodynamic integration method (which rests on the feasibility of simulations in the grand canonical ensemble), and the recently advocated sedimentation equilibrium method, which records the density profile in an external (e.g. gravitation-like) field and infers, via a local density approximation, the equation of state from the hydrostatic equilibrium condition. We confirm the conclusion that the latter technique is far more efficient than the repulsive wall method, but we find that the thermodynamic integration method is similarly efficient as the sedimentation equilibrium method. For very stiff chains the onset of nematic order enforces the formation of isotropic-nematic interface in the sedimentation equilibrium method leading to strong rounding effects and deviations from the true equation of state in the transition regime.Comment: 32 pages, 18 figures, submitted to Phys.Rev.E; one paragraph added to conclusions sectio

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

Electronic writing support in secondary and higher education : approaches, ideas, and examples

Although, today, electronic approaches to support the teaching/learning of writing are created in many places, discussions are more technology-driven rather than pedagogical. We feel that writing pedagogy needs to know and discuss these new developments and their applications in HE. While previous reviews and meta-analyses (for instance, Allen Jacovina & McNamara, 2015; Stenberger-Hu & Cooper 2015) focused mainly on such approaches as Automatic Essay Scoring (AES), Automated Writing Evaluation (AWE), or Intelligent Tutoring Systems (ITS) in general we will discuss these and additional approaches such as commented templates, real-time corpus search tools and uses of phrase books by explicitly linking them to pedagogical practices in HE. We will also offer an overview, based on a currently conducted systematic review. The final discussion will be devoted to the usefulness and usability of such electronic support measures and their pedagogical applications. It will allow the audience to report from their own experiences or developments