Computational Biophysics: currenttrends, needs and challenges in termsof HPCMauricio Carrillo-Tripptrippm@langebio.cinvestav.mxUnidad LANGEBIO
Computational Biophysics: what is it? Bringing Physics to Life! • Apply the rigorous tools of physics to help uncover the fundamental mechanisms of life Theoretical & Computational Biophysics researchers have probed how cells do some of their fundamental tasks at the molecular level
Computational Biophysics: what does itdo?• Interested in the physical mechanisms by which cellular processes function by combining theoretical and modeling methods, and by collaborating with experimental biologists.• Detailed three-dimensional structures of cells macromolecules, pinpointing the position of the thousands of component atoms.• Those structures offer clues about how molecules act as motors, channels, solar cells, genetic switches, etc... All functions in life!
Computational Biophysics: how does it doit?• To begin explaining how a molecule functions, it is important to see it move!• Researchers have created software that simulates cell´s macromolecules at work.• Molecular-dynamics programs enable simulations using large-scale parallel machines with hundred to thousands of processors.• By developing algorithms and computing tools that help scientists visualize the movement of large biological molecules.
Computational Biophysics: Trends • Computer simulations of the biomolecular processes in human cells guide better understanding of health and disease. • Such simulations are extremely demanding and, in fact, all too often still limited by technological feasibility. • However, new Molecular Dynamics programs enable hundred- million-atom simulations in atomic detail, using the full capabilities of supercomputers due to parallel programming innovations and new technologies.
Computational Biophysics: Trends System size Use of GPUs Time
Computational Biophysics: Trends &highlights200020K atoms G-proteins; Signaling, involved in numerous diseases and related to many targets of drugs.
Computational Biophysics: Trends &highlights 2001 100K atomsAquaporins are channel proteins abundantly present in all life forms,defective forms are known to cause diseases.
Computational Biophysics: Trends &highlights 2003 220K atomsMechanosensitive channel of small conductance (MscS), protects thecell against osmotic stress.
Computational Biophysics: Trends &highlights 2004 300K atoms Ankyrin, protein acting as an elastic spring in hearing.
Computational Biophysics: Trends &highlights2005400K atomsTranslocation of DNA through alpha-hemolysin, a membrane proteinwith a narrow pore.
Computational Biophysics: Trends &highlights A new era in2006 computational1M atoms biology started!Satellite tobacco mosaic virus: the capsid (a protein shell), and agenome, consisting of either DNA or RNA.
Computational Biophysics: Trends &highlights20093M atomsComplex between the ribosome and a protein-conducting channelthat directs proteins into and across membranes.
Computational Biophysics: Needs Faster CPUs
Computational Biophysics: Needs • Solid state disk (SSD) technology is a extremely fast and large computer memory: storage medium to view and analyze on the fly Gigabytes-to-Terabytes of simulation data at the rate of up to 4 Gigabytes per second • Graphics Processing Units (GPUs) are increasingly being used, enabling computationally demanding simulation, visualization and analysis tasks. • Faster connection between processor nodes and high performance I/O nodes: Ultra fast switched fabric communications link with high throughput, low latency, quality of service, failover and scalable (InfiniBand).
Computational Biophysics: Challenges New frontier of physical life sciences - how individual components of the cell work together: Simulate a complete organelle or cell?? Engineering - by understanding the design principles of cellular machinery : "we are learning from nature how to design new bio-devices" Education - constructing a stronger bridge in Latin America - EU between people with expertise in Biology, Physics and Computing Sciences. Training.
HPC in GuanajuatoComputational centers (cores):• Unidad Langebio - Cinvestav (600+3000)• CIMAT Gto (200+GPU)• Universidad de Guanajuato (2000)Grid projectInternational SupercomputingConference (2012)