The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

The Opinion Editorial: teaching physiology outside the box

Improving the public understanding of science is an important challenge for the future professional scientists who are our current undergraduates. In this paper, we present a conceptual model that explores the role of mass media as community gatekeepers of new scientific findings. This model frames the benefits for undergraduate science students to learn about media genres so that they can learn to communicate science more effectively to nonprofessional audiences. Informed by this Media Role model, we then detail a novel writing task for undergraduate physiology students, the Opinion Editorial (Op-Ed), and an accompanying Peer Review. The Op-Ed genre was directly taught to the students by a professional journalist. As an assessment task, students presented a recent, highly technical paper as an Op-Ed. This was assessed by both faculty members and peers using a detailed assessment rubric. Most students were able to replicate the features of Op-Eds and attained high grades on their writing tasks. Survey data from final-year physiology students (n = 230) were collected before and after the implementation of the Op-Ed/Peer Review. These indicated that most students were aware of the importance of scientists to effectively communicate their knowledge to nonprofessional audiences, that the Op-Ed writing task was challenging, and that they believed that their ability to write to nonprofessional audiences was improved after explicit teaching and feedback.

Queensland's music outcomes: building pedagogical bridges

This paper discusses the challenges surrounding the implementation of the Music strand of the new syllabus for secondary teachers within the context of emerging trends in pedagogical reform in Queensland, and identifies several areas where research is needed to inform classroom music teaching practice and to guide teacher training programs. Secondary music teachers (Years 8-10) have not had the same systemic, school-based curriculum guidance that was given to teachers in years 1-7. This has resulted in a plethora of teaching and learning practices in lower secondary classrooms, many of which may be more experiential than developmental in approach and which may have little reference to the types of music programs common in primary classrooms.