2. 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
3. Computational Biophysics: what does it
do?
• 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 cell's 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!
4. Computational Biophysics: how does it do
it?
• 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.
5. 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.
7. Computational Biophysics: Trends &
highlights
2000
20K atoms
G-proteins; Signaling, involved in numerous diseases and related
to many targets of drugs.
8. Computational Biophysics: Trends &
highlights
2001
100K atoms
Aquaporins are channel proteins abundantly present in all life forms,
defective forms are known to cause diseases.
9. Computational Biophysics: Trends &
highlights
2003
220K atoms
Mechanosensitive channel of small conductance (MscS), protects the
cell against osmotic stress.
11. Computational Biophysics: Trends &
highlights
2005
400K atoms
Translocation of DNA through alpha-hemolysin, a membrane protein
with a narrow pore.
12. Computational Biophysics: Trends &
highlights
A new era in
2006 computational
1M atoms biology started!
Satellite tobacco mosaic virus: the capsid (a protein shell), and a
genome, consisting of either DNA or RNA.
13. Computational Biophysics: Trends &
highlights
2009
3M atoms
Complex between the ribosome and a protein-conducting channel
that directs proteins into and across membranes.
15. 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).
16. 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.
17. HPC in Guanajuato
Computational centers (cores):
• Unidad Langebio -
Cinvestav (600+3000)
• CIMAT Gto (200+GPU)
• Universidad de Guanajuato
(2000)
Grid project
International Supercomputing
Conference (2012)
