Concurrent Simulation of Diffusion in Biomembranes
This project centers around developing a concurrent extension of an
existing serial code (developed
by Dr. Juyang Huang) that
performs Monte Carlo simulations of lipid mixtures in biomembranes.
The target platform for the concurrent code is
a 16-node Beowulf cluster
located in the physics department.
Issues that must be addressed include:
- Problem decomposition for large scale simulations.
- Efficient internode communication using the standard message passing
- Implementation of a long-cycle, concurrent pseudo-random number
generator sufficient to pass the standard tests for "randomness."
- Simulation verification, where possible, by comparison to the existing
serial code and to laboratory measurement.
Useful Background Sources
- Naeem Jan, Turab Lookman, and David A. Pink, "On Computer Simulation
Methods Used To Study Models of Two-Component Lipid Bilayers,"
Biochemistry 23, 3227-3231 (1984).
- Juyang Huang and Gerald W. Feigenson, "Monte Carlo Simulation of
Lipid Mixtures: Finding Phase Separation," Biophysical
Journal 65, 1788-1794 (1993).
- Donald E. Knuth, "The Art of Computer Programming," Vol II, Chapter 3,
- Barry Wilkinson and Michael Allen, "Parallel Programming: Techniques and
Applications Using Networked Workstations and Parallel Computers," (Prentice
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