Design of Complex Fluid Simulation DPD code for mesoscopic simulations

1. Dissipative Particle Dynamics
Simulation Code
Julian C Shillcock
ComplexFluidSimulations.com

2. Outline
• Code purpose
• Major Features
• Executable environment
• Frameworks in the code
• Publications

3. Code purpose
• Simulate the material properties of complex fluids on the
1 nm - 200 nm length-scale for up to 100 microseconds
• Visualize molecular rearrangements during biophysical
processes such as vesicle fusion
• Quantitatively model the structure and kinetics of drug
delivery vehicles such as vesicles and polymersomes

4. Major Features
• Box size and number of bead and molecule types limited only by hardware
(RAM); approximately 0.5 kB required per bead
• Largest system so far is a planar bilayer containing 28,000 amphiphiles and a
vesicle containing 5800 amphiphiles in a box 100 x 100 x 42 nm3
• Wide range of initial state builders: random, restart, planar bilayer, vesicle,
vesicle-bilayer fusion, two-vesicle fusion, wormlike micelle, ...
• A simulation requires only a single ASCII input file (except for restarts)
• Commands can be issued to a running simulation to modify its evolution;
currently there are over 200 commands implemented

5. Executable
environment
• Written in ANSII standard C++ making extensive use of the
STL
• Single, stand-alone executable
• Runs under Windows, Linux (Intel 7.0 compiler) and
Macintosh
• RAM footprint linear in system size: ~ 0.5 KB/particle
• (42 nm)3 fusion event lasting 320 ns takes 40 cpu-hours*
* Run time depends on system complexity, e.g. commands

6. Frameworks

7. Infrastructure
frameworks
• Experiment - wraps the complete code
• Simulation - evolves the system’s dynamics
• Monitor - extracts observables for analysis
• Security - restricts access to licensed features
• Messages - Logs command execution and significant events
• Active Elements - dynamically-created molecules
Red frameworks not fully implemented yet

8. State frameworks
• Initial - contains complete information on the initial
configuration of a simulation
• Restart - contains complete information to continue a
simulation from a saved state
• Rebuild - allows extraction of geometric entities (e.g., a
vesicle) from one run and insertion into another
• Targets - allows user to select entities during a simulation
and to analyse them or send commands to them

9. Control frameworks
• Processes - allow user to control and monitor specified
behaviour, e.g., vesicle fusion
• Events - used by processes to watch for specified
simulation states and take action when they occur
• Commands - used to control aspects of the experiment’s
behaviour before and during a run; commands may modify
the simulation’s evolution or just change analysis options

10. Publications
• Equilibrium structure and lateral stress distribution of amphiphilic bilayers from
dissipative particle dynamics simulations
Shillcock, J.C., and Lipowsky, R. J. Chem. Phys. 117:5048 (2002)
• Tension-induced fusion of bilayer membranes and vesicles
Shillcock, J. C. and Lipowsky, R. Nature Mat. 4:225 (2005)
• Effect of chain length and asymmetry on material properties of bilayer
membranes
Illya, G., Lipowsky, R. and Shillcock, J. C. J. Chem. Phys. 122:244901 (2005)
• Dissipative particle dynamics of polymersomes
Ortiz,V. et al., J. Phys. Chem. B (Web release date August 30, 2005; doi 10.1021/
jp0512762 S1089-5647(05)01276-9