Introduction
Computational
Biophysics is a new research group in the School of Physics
(established in 2004).
There have been tremendous advances in molecular biology in the last few decades, resulting in
thousands of new molecular structures for proteins. Understanding
the
function of biomolecules in terms of their structure (the so called
structure-function relationships) is one of the grand challenges for
science in the
21st century. It holds the key to a wide range
applications from biotechnology to pharmacology and medicine.
Physicists have a lot to contribute to this interdisciplinary research
area that requires modeling of biological systems at different time
scales using quantum, classical and stochastic dynamics. While
access to supercomputers have made this task feasible, brute force
number crunching is not likely to yield any useful answers. Judicious
modeling that links vastly different space-time domains (e.g. nano and
micro domains) is essential in achieving this aim. The focus of
our research is, therefore, to develop hierarchical schemes that will
allow description
of
biomolecular processes with
the available computational resources. The methods involved -
from most phenomenological to fundamental - are:
- Low resolution methods (e.g.
Brownian dynamics) are employed in model studies to make contact with
experimental phenomena that occur at long time scales and large space
dimensions.
- Microscopic methods (e.g.
molecular dynamics, Monte Carlo) are used to justify the
phenomenological models and derive the parameters employed in them.
- Ab initio methods (e.g. density functional theory, Car-Parinello
MD) are used to derive/justify the force fields in MD simulations.
Details of research projects that
apply the above scheme to ion channels and protein interactions can be
found in the Research page. Most of the projects require
substantial computational power and we make use of the supercomputers
in Sydney (AC3) and Canberra (APAC). Recently we
have acquired a beowulf cluster for the group, which has boosted our
capacity to perform long simulations by an order of magnitude
- Contact
details:
- Dr Serdar Kuyucak
Computational Biophysics
Group
- School of Physics A28
- University of Sydney
- NSW
2006, Australia
- Phone.
: (+61) 02-9036 5306
- Fax
: (+61) 02-9351 7726
- E-mail :
serdar@physics.usyd.edu.au