Welcome to the Multiscale lab
Applied computational sciences in biomedicine and more
The group research interests are rooted in computational sciences, currently with an application focus on biomedicine. Specifically, we develop new computational methods and algorithms, we apply them to simulate and understand biological data and we design molecules with therapeutic applications in mind.
The group and the spin-off company Acellera has collaborated with major industries worldwide like Sony, Nvidia, HTC mobile, UCB, Pfizer, etc.
Biomedicine. Using large distributed computational resources (GPUGRID.net) we search novel therapeutic molecules. We are particularly active in molecular dynamics simulations, binding prediction, binding kinetics, Markov state models, online sampling methods, and software development (ACEMD, HTMD). The approach is completely computational driven for hypothesis generation, then experimentally validated. We also collaborate with experimental laboratories and industries where we work by rationalizing experimental results.
Machine Intelligence. In this new research line we develop machine learning approaches applied to the biological data that we generate. We are particularly interested in dimensionality reduction methods, artificial neural networks, unsupervised learning. We also look at new computational intelligence approaches in general.
- HTMD - HTMD is a Python platform for computational biology, including molecular simulations, docking, Markov state models, molecule manipulation, build tools for Amber and Charmm, visualization (webGL and VMD), adaptive sampling and more. Imagine setting up an entire computational experiment in a single, simple Python script.
- ACEMD - ACEMD has pioneered the use of GPUs for molecular simulations allowing for high-throughput simulations and ultimately leading to HTMD. ACEMD is still one of top molecular dynamics code, simple to use with a NAMD like syntax and compatible with input files from Charmm and Amber.
- Scientific publications - A complete list of our publications with PDFs
- The youtube channel of GPUGRID.net - We post here interesting video on the research done with GPUGRID.net
- Multiscale Laboratory GitHub - More tools are available in our github account. Follow us there.
- Acellera GitHub - Acellera publishes software in the company github page.
- The youtube channel of Acellera - Acellera posts a lot of material here
Current member of our research group
In our group we always value having the best people from different background and expertises
- Gianni De Fabritiis - Head of multiscale laboratory, Icrea research professor
- Matt J. Harvey - CTO at Acellera Ltd and High Performance Computing Systems Analyst at Imperial College London
- Dr Toni Giorgino - Researcher at the national research council, Italy
- Jose Jimenez - Phd student at University Pompeu Fabra
- Miha Skalic - Phd student at University Pompeu Fabra
- Pablo Herrera Nieto - Phd student at University Pompeu Fabra
- Gerard Martinez - Phd student at University Pompeu Fabra
- Stefan Doerr - Postdoc at University Pompeu Fabra and staff at Acellera
- Joao M. Damas - Staff scientist at Acellera
- Franck Chevalier - Scientific and business developer at Acellera
Apply for a position
We are always looking for talented people who would like to join our laboratory. We praise on diversity of expertises, e.g. mathematics, chemistry, computer science, statistics, physics, biology, biotechnology, etc. If you are a passionate, hard working, self-motivated person with the ambition to do great science, send us an email at email@example.com.
Gianni De Fabritiis, GRIB, Barcelona Biomedical Research Park (PRBB), C/ Dr. Aiguader 88, 08003, Barcelona, Spain.
Email: gianni.defabritiis at upf.edu