Coarse-Grained Simulations of RNA and DNA Duplexes

Although RNAs play many cellular functions, little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities, these simulations have been limited to small RNAs and to short times. HiRe-RNA, a recently proposed high-resolution coarse-grained RNA that captures many geometric details such as base pairing and stacking, is able to fold RNA molecules to near-native structures in a short computational time. So far, it had been applied to simple hairpins, and here we present its application to duplexes of a couple dozen nucleotides and show how with replica exchange molecular dynamics (REMD) we can easily predict the correct double helix from a completely random configuration and study the dissociation curve. To show the versatility of our model, we present an application to a double stranded DNA molecule as well. A reconstruction algorithm allows us to obtain full atom structures from the coarse-grained model. Through atomistic molecular dynamics (MD), we can compare the dynamics starting from a representative structure of a low temperature replica or from the experimental structure, and show how the two are statistically identical, highlighting the validity of a coarse-grained approach for structured RNAs and DNAs

Poster Session with Peer Grading

<p>Scientific article reading is an important competence for undergraduate students in sciences. To help acquire this skill we chose to propose students a poster session with peer evaluation. </p><p>Students are grouped in teams to which subjects are assigned. Each team prepares a poster during the semester and prints it before the exam. Students then enter a rotation system in which they alternatively present their poster to their peers and one teacher, or evaluate the posters of other groups. Each session is composed of a presentation, questions and evaluation. The evaluation is performed both by the teachers and the peers. Students are also evaluated for their ability to evaluate their peers, comparing their evaluations to those performed by others (teachers and/or peers). The evaluation is normalised thanks to a dedicated evaluation grid. </p><p>After 2 years of manual management, the need to scale up our approach to larger cohorts of students lead to the development of a digital system. This article details our motives and method/protocol. Finally observations, limits and improvements are reported.</p

Screenshot of Phylo illustrating the high level of information that can be provided to the player through graphics.

<p>Screenshot of Phylo illustrating the high level of information that can be provided to the player through graphics.</p

Example of an augmented reality application (Pangu).

<p>Players build their tangible model of the expected molecule with a standard molecular model kit (or draw it on paper) and scan it with a mobile device, which validates that the correct molecule was built.</p