ComputaonalScience at+the+ UniversitàdellaSvizzeraitaliana€¦ · Computational Electrophysiology...
Transcript of ComputaonalScience at+the+ UniversitàdellaSvizzeraitaliana€¦ · Computational Electrophysiology...
Computa(onal Science at the
Università della Svizzera italiana
Lugano November 18, 2014
Ins6tute of Computa6onal Science Faculty of Informa6cs
Università della Svizzera italiana
R. Krause
M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk,
�2R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk 4
Theory Physical Experimentation
Computational Science
21st Century Science
Computational Science
2005 Report of the US President's Information Technology Advisory Committee „Computational Science: Ensuring America's Comptetitiveness“
�3R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk 3ICS, wetterjournal.wordpress.com, lbl.gov, research.nokia.com
The 21st century’s first great scientific breakthrough was a triumph of large-‐scale computational science.. PITAC Report
Engineering and Manufacturing
Meteorology/Climatology and Geosciences
Finance
Biology
Physical Sciences
Political and Social Sciences
Neuroscience
Medicine
�4R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Science (physics, chemistry,
Mathematics
Informatics
Computational Science
Computational science, may be defined as the intellectual discipline concerned with the study, development, and use of algorithms, methods and simulations tools implemented on computing devices for scientific discovery and applications in science, engineering,
medicine, and technology.
�5R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Numerical Simulation in Science, Medicine, and Engineering (Krause)
Computational Shape Analysis (Bronstein)
Computational Fluid Dynamics (Pivkin)
Advanced Computing Laboratory (Schenk)
Cardiac Electrophysiology (Potse)
Computational Time Series Analysis (Horenko)
Computational Biology & Material Science (Parrinello)
8 Research Groups > 60 members
Master Program "Computa(onal Science” PhD in “Computa(onal Science”
PhD Program FOMICS
Medicinal Chemistry & Drug Design (Limongelli)
�6R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Center for Computational Medicine in Cardiology CCMCInstitute of Computational Science ICSFaculty of Informatics
UniversitàdellaSvizzeraitaliana
!
Center for Computational Medicine in Cardiology Auricchio (CCT), Krause (ICS/USI), Potse (ICS/USI)
�7R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
CSCS
Engineering
MedicineHealth
VisualData
EnvironmentClimateSociety
Energy
BiologyDrugs
DataAnalysisShape &
ImageAnalysis
Solid and Fluid
Mechanics
Geo Science
EngineeringOptimization
Material Science
Biology
Medicinal Chemistry
& Drug design
MedicineCardiology
EconomicsSocial
Sciences
Life Sciences
HPC
ICSApplied Mathematics
Master and PhD inComputational Science
Computational Science
Simulation tools and software
Graduate School FOMICS
Numerical Methods
CCMCCenter for
Computational Medicine in Cardiology
�8R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
CSCS
Engineering
MedicineHealth
VisualData
EnvironmentClimateSociety
Energy
BiologyDrugs
DataAnalysisShape &
ImageAnalysis
Solid and Fluid
Mechanics
Geo Science
EngineeringOptimization
Material Science
Biology
Medicinal Chemistry
& Drug design
MedicineCardiology
EconomicsSocial
Sciences
Life Sciences
IRBIOR
Cardiocentro Ticino
EPFL
EPFL
U Basel
ETH
U Bern
ETH
EPFL
HS Luzern
ETH
ETH
FU Berlin
CSIROU Tel-Aviv
TechnionDuke
KIT
U Bern
USI Eco
U BernISTB
U MaastrichtPolitecnico
HPC
ICSApplied Mathematics
Master and PhD inComputational Science
Computational Science
Simulation tools and software
Graduate School FOMICS
Numerical Methods
ETH
U Chicago
FZ JÜLICH
CCMCCenter for
Computational Medicine in Cardiology
SPP 1748
SCCER SoE
SPP SPPEXASCCER FURIESNCCR MARVEL
PASC
PASC
ERC
ERCPASC
NFP 70
�9R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Designed for Computa6onal Science
Interdisciplinary educa6on is more than just pu_ng together lectures from different disciplines
�10R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. SchenkDickopf, Krause, Krause, Potse SISC Journal for Scientific Computing, 2014
Center for Computational Medicine in CardiologyComputational Electrophysiology
(Potse, Krause (USI) Auricchio (CCT))
Potse, 2014
Computations done at CSCS
�11R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk 5Computational Science
Coupled Systems: Fluid Structure Interaction Fast solution methods and tailored discretization schemes
Computations done at CSCSSteiner, K’, 2014
�12R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Stochastic Platelet Model (more details) • Platelets can be in three biological states: passive, triggered, activated • The key component is an activation delay time – the time it takes for
platelet to go through the activation process ( Richardson, PD. (1973) Nature 245, 103–104)
• The activation delay time was estimated from experimental data to be about 0.2 seconds
Pivkin, Richardson, Karniadakis PNAS 103, 17164–17169
PASSIVE non-adhesive
TRIGGERED non-adhesive
ACTIVATED adhesive
Exposure to high concentration of
activation chemicals
Activation delay time, chosen RANDOMLY
for each platelet
If not adhered after 5 s
Activation corona
High concentration of activation chemicals, time dependent region
Stochastic Platelet Aggregation Model Group Pivkin
Computations done at CSCS
�13R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Research Highlight 2014 – Real-‐Fme StochasFc OpFmizaFon of Complex Energy Systems on High Performance Computers, Leadership CompuFng, IEEE Journal CompuFng in Science and Engineering
Computations done at CSCS
Wave propagation and adjoint optimization with focus on numerical methods transfer of knowledge into the earth science community
Group Schenk
�14R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Parrinello Groupatomistic simulations of complex systems
Materials Biomolecules
Calculation of the unbinding rate of drug from protein:!!A!new!way!for!effec-ve!drug!design!
Characterisation of the self-assembly of complex materials:!
!Ra-onal!design!of!crystalliza-on!processes
Method Development
Rates from MetadynamicsWell Tempered Metadynamics
MetadynamicsCar-Parrinello Molecular Dynamics
Variational Approach to Enhanced Sampling
⌦[V ] =
1
�log
Rds e��[F (s)+V (s)]
Rds e��F (s)
+
Zds p(s)V (s)Sampling rare events
in complex molecular systems
Breaking the millisecond
barrier in fully atomistic
simulations
Computations done at CSCS
�15R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Binding mechanism to cellular membrane of the multiple sclerosis (MS) biomarker CSF114(Glc). Using these simulations, complemented by a number of experiments, we have elucidating its functional mechanism. Our findings provide the molecular tools to develop new MS diagnostic and therapeutic agents.
Investigating peptide/membrane binding Group Limongelli
�16R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Visual Shape Analysis Group Bronstein
�17R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Computations done at CSCS
Contact of soft elastic material with
rough hard substrate
Rigazzi, K’ 2014
�18R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
Group KrauseHigh Performance Methods for Numerical Simulation in
Science, Medicine and EngineeringConclusions and Outlook
Surface e�ects (Bio)mechanics
Coupled models Parallel computing
Models,Methods,Software
R. Krause Parallel Methods 41
Computations done at CSCS
�19R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
PASC - Swiss Platform for Advanced Scientific ComputingPASC is a structuring project jointly supported by the Swiss University Conference (SUC) and the ETH Board.
PASC is coordinated by USI in collaboration with CSCS and with the other Swiss universities and EPFL.
Physics Climate
Solid Earth
Material
Life Sciences
PASCICS
CSCSApplied Mathematics
Computational ScienceNumerical Methods
Co-Design
CADMOS
Social Sciences
ICS participates in 6 projects in 4 networkshttp://www.pasc-ch.org
ETHZ
ETHZ
Meteoswiss
EPFL
Geneva Basel
Fribourg
Zürich
USI
ETHZ
ETHZ
EPFLUSI
Geneva
Zürich
Zürich
EPFL
USIBasel Geneva
Bern
USI
ETHZ
�20R. Krause, M. Bronstein, I. Horenko, V. Limongelli, M. Parrinello, I. Pivkin, M. Potse, O. Schenk
• 2 ERC Grants (Bronstein, Parrinello) 2013• Participation in NCCR MARVEL (Parrinello) 2014• 18 snf projects at ICS since 2009• Participation in NFP 70 (K’) 2014• Participation via “Dachabkommen” in 2 SPPs and “Forschergruppe” (Horenko, K’)
2012,2013,2014• Mercator Professorship DFG (Horenko) 2014• Participation in “Energy Swiss Competence Center of Energy Research (SCCER)”
FURIES and SoE (Schenk, K’, Malek (ALARI)) 2014• Platform for Advanced Scientific Computing (PASC): Swiss National High
Performance Strategy (Parrinello, Pivkin, Schenk, K’) 2013• PhD School FOMICS 2012• PhD in Computational Science 2014• Master Program in Computational Science 2012• Center for Computational Medicine in Cardiology 2014• Local cooperations: CCT, SUPSI, ALARI, IDSIA, industry, … since 2009• (Inter-)national cooperations (PASC, SCCER, snf, CTI, snf/DFG,…) since 2009• More than 60% of annual salaries are third party funding since 2009• …