Codes written in C for Molecular Dynamics simulation of Brownian particles with programmable "specific" and "dynamic" inter-particle interactions. (e.g. DNA colloids) You can assign distinct "species" for each particle and define "interaction matrix" to characterize time-dependent inter-particle interactions among them.
main.h: Declare various constants and functions to be used
func.c: Define functions
main.c: Put the functions together to complete iterations
Python codes in Jupyter notebooks for data analysis and visualization. Main figures presented in the above paper are reproduced.
Main Brownian Dynamics simulation codes in C-files can be compiled with makefile.
While running, it outputs trajectory of all particles traj---.dat and number of self-replicated clusters with each species NumCl---.dat. Examples of data analysis and visualization using the output data are presented in the Jupyter notebook.
Rapid developments in DNA nanotechnology opened up the new paradigm of "programmable materials" in nano/micron scales. The DNA mediated "specific" and "dynamic" inter-particle interactions are hard to implement with existing molecular dynamics libraries. To explore the design space, and investigate possibilities for realizing self-replicating artificial living materials, I have developed this molecular dynamics simulation that implements the above self-replication scheme. Finally, this highly efficient codes allowed us to observe hundreds of self-replicating colloidal clusters, and thus we conducted the first study of "evolutionary dynamics" of artificial materials.
Part of this repository presents codes written by Hidenori Tanaka for
H. Tanaka, Z. Zeravcic, M.P. Brenner “Mutation at Expanding Front of Self-Replicating Colloidal Clusters.”
Physical Review Letters, 117, 238004, (2016).