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Mathieu Linares

Profile picture of Mathieu Linares


About me

I am a Application Expert at the supecomputer center PDC working on the interoperability of computational chemistry tools. In particular, I am focusing on improving the workflow for users between GROMACS and VeloxChem.

I received his PhD degree from Paul Cézanne University, Marseille, France, in 2005. My research activities have been focusing on self-assembly, chirality, organic electronics, and protein-molecule interaction. From 2018 to June 2023, I held an associate professor position in the Group of Scientific Visualization at Linköping University, helping bridge the gap between theoretical chemistry and scientific visualization and leading to the development of VIAMD.

Graphical TOC VIAMD

VIAMD, or Visual Interactive Analysis of Molecular Dynamics, is a software that is specifically designed for the analysis of Molecular Dynamics (MD). It uniquely combines a 3D visualization of molecular trajectories with flexible analysis components. One of its key features is an interactive scripting interface that allows for property definition and evaluation. It also provides context-aware suggestions and expression feedback through information and visualizations. Users can explore and analyze user-defined properties through various components. This software enables correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties such as spatial distribution functions. Developed in collaboration with the Department for Media and Information Technology (LIU, Norrköping) and the PDC Center for High Performance Computing (KTH, Stockholm), VIAMD is written in C/C++ and is seen as a promising solution for improving the workflow of MD visualization and analysis. It has the potential to advance research in many scientific disciplines. More information about VIAMD can be found on its Github page and in the article published in JCIM.

You will find more informations about my research, CV and publications in the portfolio on the right.