Speaker
Osvaldo Gervasi
(Department of Mathematics and Computer Science, University of Perugia)
Description
The understanding of the behavior of molecular systems is important for the
progress of life sciences and industrial applications. In both cases is increasingly
necessary to perform a study of the relevant molecular systems by using simulations
and computational procedures which heavily demand computational resources. In
some of these studies it is mandatory to put together the resource and complementary
competencies of various laboratories. The Grid is indeed the infrastructure
that allows such a cooperative modality of work. In particular for scientific
purposes
the EGEE Grid is the proper environment. For this reason a Virtual Organization
(VO) called CompChem has been created within EGEE. Its goal is to support the
computational needs of the Chemistry and Molecular Science community and pivot
the user access to the EGEE Grid facilities.
Using the simulator being implemented in CompChem the study of molecular
systems is carried out by adopting various computational approaches bearing
approximations of different levels.
These computational approaches can be grouped into three categories:
1. Classical and Quasiclassical: these are the less rigorous approaches.
They are, however, the most popular. The main characteristic of these
computational procedures is that the related computer codes are naturally
parallel. They consist in fact of a set of independent tasks, with few
communications at the beginning and at the end of each task.
Related computational codes are suitable to exploit the power of the Grid
in terms of the high number of computing elements (CEs) available.
2. Semi-classical: these approaches introduce appropriate corrections the
deviations of quasiclassical estimates from quantum ones. The Grid
infrastructure is exploited for massive calculations by varying the initial
conditions of the simulation and performing the statistical analysis of the
results.
3. Quantum: this is the most accurate computational approach heavily demanding
in terms of computational and storage resources. Grid facilities and
services will be only seldomly able to support them in a proper way using
present
hardware and middleware utilities. Therefore they will represent a real
challenge for Grid service development.
The computational codes presently used are mainly produced by the laboratories
member of the VO. However some popular commercial programs (DL POLY, Venus,
MolPro, GAMESS, Columbus, etc) are also being implemented. These packages are
at present executed only on the computing element (CE) owning the license. We are
planning to implement in the Resource Broker (RB) the mapping of the licensed
sites via the Job Description Language (JDL). In this way the RB will be able to
schedule properly the jobs requiring licensed software. The VO is implementing[1]
an algorithm to reward each participating laboratory for contributions given to the
VO providing hardware resources, licensed software and specific competences.
One of the most advanced activities we are carrying out in EGEE is the simulation
on the Grid of the ionic permeability of some cellular micropores. To this
end we use molecular dynamics simulations to mimic the behavior of a solvated
ion when driven by an electronic field through a simple model of the channel. As a
model channel a carbon nanotube (CNT) was used as done in a recent molecular
dynamics simulation of water filling and emptying of the interior of an open-end
carbon nanotube[3-6]. In this way we have been able to calculate the ionic
permeability
of several solvated ions (Na+, Mg++, K+, Ca++, Cs+) by counting the
ions forced to flow into the nanotube by the applied potential diffence along
z-axis.
References
1. Lagana', A., Riganelli, A., and Gervasi, O.: Towards Structuring Research
Laboratories
as Grid Services; submitted (2006).
2. Kalra, A., Garde, S., Hummer, G.: Osmotic water transport through carbon nanotube
membranes. Proc Natl Acad Sci USA 100 (2003) 10175-10180.
3. Berezhkovskii, A., Hummer, G.: Single-file transport of water molecules through a
carbon nanotube. Phys Rev Lett 89 (2002) 064503.
4. Mann, D.J., Halls, M.D.: Water alignment and proton conduction inside carbon
nanotubes.
Phys Rev Lett 90 (2003) 195503.
5. Zhu, F., Schulten, K.: Water and proton conduction through carbon nanotubes as a
models for biological channels. Biophys J 85 (2003) 236-244.
Primary authors
Antonio Lagana`
(Department of Chemistry, University of Perugia)
Cristian Dittamo
(Department of Mathematics and Computer Science, University of Perugia)
Leonardo Arteconi
(Department of Chemistry, University of Perugia)
Osvaldo Gervasi
(Department of Mathematics and Computer Science, University of Perugia)
