Analysis of molecular simulations with 2D and 3D visualisations
A pioneering technology to improve driving assistance systems
October 1, 2018
Production of hydrogen with solar light
October 1, 2018Molecular dynamic simulations are computer simulations of the physical movements of atoms and molecules and the interactions between them. They are used in various areas such as physics, chemistry, material sciences and modelling of biomolecules.
In drug design, simulations of the molecular dynamic predict the type of bond and the affinity of the combination of a small molecule (the drug) with a biomolecule (protein). The result, if successful, is a drug that has therapeutic benefits for the patient.
The ViRVIG group has worked on molecular visualisation to address various aspects, such as the generation of realistic lighting in models of very large molecules or the visualisation of extremely long simulations of molecular dynamics. To meet these objectives, the group has developed tools for visual exploration of molecular simulations, which has facilitated the analysis and saved time, particularly in the visualisation of trajectories.
An example of applications are compact molecular simulations that abstract a 3D structure into a 2D design. Based on a web application that offers rapid, intuitive exploration of complete simulations, many physical properties are represented such as energy, index of flow of waste products or hydrogen bridges, among others.
A second example tackles the challenge of exploring extremely large molecular trajectories (of hundreds of thousands of steps). To achieve this, simulation data are analysed automatically, and relevant characteristics are extracted. Subsequently, through a set of coordinated views in 2D and 3D, an application is obtained that facilitates the progressive exploration of molecular simulation in a very efficient, intuitive way. The result is a graphic application that could be executed on a PC with a graphics card.
The developments have been made in collaboration with the Barcelona Supercomuting Center (BSC), the University of Ulm, Masaryk University, the Czech Republic and the Laboratory of Loschmidt in Masaryk University.
Related Projects
- The Centre for Sensors, Instruments and Systems Development (CD6) at the Universitat Politècnica de Catalunya - BarcelonaTech (UPC) is taking part in PhotonHub Europe. This is a European project to establish a single pan-European hub for innovation in photonics as a one-stop shop solution that brings together the pioneering photonics solutions, facilities, knowledge and experience of 53 European partners.
- MobilitApp is an application capable of predicting the mode of transport used by citizens using a deep learning tool based on three mobile phone sensors.
- The aim of the Muvity project in which the Multimedia Applications and ICTs Laboratory (LAM) of the Universitat Politècnica de Catalunya - BarcelonaTech (UPC) participates, is to develop a gamified physical telerehabilitation application for people with chronic injuries. The user carries out exercises and plays games designed with therapists that lead them to move their arms and legs and thus achieve the established goals.
- Researchers from the Advanced Broadband Communications Centre (CCABA) and the Optical Communications Group (GCO) of the Universitat Politècnica de Catalunya - BarcelonaTech (UPC) participate in the B5G-OPEN (Beyond 5G – OPtical nEtwork coNtinuum) project. This project is funded by the European Union, in the framework of which a new end-to-end integrated packet-optical transport architecture based on multiband optical transmission and switching networks is being designed and prototyped.
