NERDSS
Core simulation engine for nonequilibrium, multibody self-assembly with user-defined reaction rules, diffusion, and spatially-resolved kinetics.
NERDSS : A nonequilibrium simulator for multibody self-assembly at the cellular scale
Try NERDSS online
Try NERDSS on the webserver at nerdssdemo.org without local installation.
Go to NERDSSdemo.org →
ioNERDSS
Python tools for building models, running simulations, and analyzing NERDSS outputs with reproducible workflows.
Please cite
For NERDSS:
Varga, M., Fu, Y., Loggia, S., Yogurtcu, O.N., & Johnson, M.E.
NERDSS: a nonequilibrium simulator for multibody self-assembly at the cellular scale.
Biophysical Journal 118, 3026–3040 (2020).
Article
For ioNERDSS:
Ying, Y.M., Sang, M., Au, G., Chhibber, S., Du, Y., Fischer, J.A., Foley, S.L., Guo, S., Herzog-Pohl, I., Liu, Z., Roscom, H., Sohail, H., Takeshita, S.S., & Johnson, M.E.
Transforming macromolecular structures into simulations of self-assembly bioRxiv (2026).
Article