Zurich 02-03 June 2014

Parallel session on Life Sciences


Reference PASC Community


Invited Talks

Day 2 - June 3, 2014

09:50 – 10:40  HG F 30 - Invited Plenary

Feedback, lineages and cancer; John Lowengrub, University of California at Irvine, USA (Abstract
(Chair: Petros Koumoutsakos, ETH Zurich)

John Lowengrub is a Chancellor's Professor at the University of California at Irvine with appointments in the departments of Mathematics, Biomedical Engineering, Chemical Engineering and Materials Science. His research interests include mathematical and computational biology, applied and computational mathematics, mathematical oncology, complex fluids and materials science


15:20 – 16:10  HG F 30 - Invited Plenary

HPC & The Inventor’s Dilemma: Abandoing 20 years of Molecular Simulation Knowledge and Moving to GPUs; Eric Lindahl, SciLifeLab Stockholm, KTH, Sweden (Abstract)
(Chair: Olaf Schenk, Universita della Svizzera italiana)

Eric Lindahl heads a research division as professor of biophysics at the Department of Biochemistry & Biophysics at Stockholm University, with a dual appointment as professor of theoretical biophysics at the KTH Royal Institute of Technology. Since 2011 he is a member of the Swedish Young Academy. He completed undergraduate studies in engineering physics at Lund University, after which he received a PhD in theoretical biophysics at the KTH Royal Institute of Technology in Stockholm in 2001. He has been a visiting research scholar with Hermann Berendsen & Alan Mark at Groningen University (NL), Michael Levitt & Vijay Pande at Stanford University (USA) and Mark Delarue at the Pasteur Institute (FR). In 2004 he started as assistant professor and later associate professor at Stockholm University. The team’s main research theme concerns ion channels, in particular molecular simulations – and they have written the GROMACS molecular simulation package.

Day 1 - June 2, 2014


14:25 - 15:45 HG F 26.3
Chair: Petros Koumoutsakos, ETH Zurich

14:25 - 14:45 HPC-ABGEM: High-performance agent-based general ecosystems modeling; Simone Callegari (University of Zurich) (Abstract)

14:45 - 15:05 Bone structure analysis on multiple GPGPUs; Peter Arbenz (ETH Zurich) (Abstract)

15:05 - 15:25 Computational simulation of heart function with an orthotropic active strain model of electromechanics; Toni Lassila (EPFL) (Abstract)

15:25 - 15:45 Red blood cells and related functions of the human spleen; Igor V. Pivkin (Università della Svizzera italiana) (Abstract)


16:15 - 17:15 HG F 26.3
Chair: Igor Pivkin, Università della Svizzera italiana

16:15 - 16:35 LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems ; Simon Tanaka (ETH Zurich) (Abstract)

16:35 - 16:55 SEM++: a particle model of cellular mechanics, growth, signaling and migration; Gerardo Tauriello (ETH Zurich) (Abstract)

16:55 - 17:15 Exploring the unfolded ensemble of proteins; Albert Ardevol (ETH Zürich) (Abstract)


18:30 - 20:00 Gallery of HG F-Floor
Poster Session

Day 2 - June 3, 2014


11:05 - 12:05 HG F 26.3
Chair: Petros Koumoutsakos, ETH Zurich

11:05 - 11:25 Protein-ligand unbinding kinetics and pathways through metadynamics; Pratyush Tiwary (ETH Zurich and Università della Svizzera italiana) (Abstract)

11:25 - 11:45  Improving I/O Performance of ClustalW-MPI Multiple Sequence Alignment Software; Soon-Heum Ko (Linkoping University, Sweden) (Abstract)

11:45 - 12:05 OmicABEL: Story of a successful interdisciplinary collaboration; Diego Fabregat-Traver (AICES, RWTH Aachen, Germany) (Abstract)