| Biography | |
|---|---|
 Prof. Marc Baaden Institut de Biologie Physico-Chimique, France |
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| Title: New computational tools for exploring and assembling macro- and supramolecular models | |
| Abstract: My team pursues the goal to study complex molecular assemblies through interactive visualization, manipulation and analysis approaches to aid hypothesis generation and exploration of such complex datasets. We are interested in molecular aggregation and assemblies, as well as the properties of supramolecular constructs in membrane environments. The UnityMol framework [1] forms a central tool for these investigations and is based on the Unity3D game engine. A first line of research tries to help with the 3D context, for instance through content-guided navigation, exploded views and semantic links between molecular objects and their analysis data [2]. Concerning the molecular representations, we extended the UnityMol repertoire to include specific visualizations for sugar molecules [3] and electrostatic properties [4]. We have now also included coarse-grained systems particularly relevant for the simulation of membrane systems by default. These levels of reduced representation are particularly apt for interactive simulations, even in the classroom or via crowdsourcing. A particular focus lies on the integration of dedicated hardware such as large, high-resolution display walls, or more recently head-mounted virtual reality headsets or augmented reality setups. [1] Lv et al., Game on, Science - how video game technology may help biologists tackle visualization challenges, PLoS ONE 8(3):e57990, 2013 (http://unitymol.sourceforge.net) [2] Trellet et al., Interactive Visual Analytics of Molecular Data in Immersive Environments via a Semantic Definition of the Content and the Context, IEEE VR 2016/VR 2016 Workshop on Immersive Analytics [3] Pérez et al., Three-Dimensional Representations of Complex Carbohydrates and Polysaccharides. SweetUnityMol: A Video Game Based Computer Graphic Software, Glycobiology 25, 2015, 483-491; doi: 10.1093/glycob/cwu133 [4] Laureanti et al., Visualizing biomolecular electrostatics in virtual reality with UnityMol(APBS) and APBS, Protein Science, arXiv:1908.11261 [q-bio.BM] and https://doi.org/10.1002/pro.3773 | |
| Biography: Dr. Marc Baaden (MB) is internationally recognized for research characterizing membrane proteins via high performance computing, comprising the development of novel bioinformatics methods. His research focuses on biological systems and phenomena at membranes and interfaces, related to diseases and medical conditions (dystrophies, channelopathies, rare diseases). The association of bioinformatics, high performance computing and scientific visualization with experimental and clinical biomedical research is a distinctive feature. Research on membrane proteins constitutes a major pilar of MB’s research since 2008, with many high-impact publications, for instance in Nature, NSMB, PNAS and Embo J. Strategic objectives are to create simulation algorithms to reproduce and predict physical properties of biomolecules either in vitro or in the cell, and understand the molecular or conformational factors responsible for the biological function of living systems and their roles in disease. Such computer simulations provide guidance for molecular medicine through insights on dynamics and mechanisms at the atomic scale. | |
