Software & Data
Hagan Group's Github Repository:
https://github.com/hagan-group
Recent open source software and data published with our research
Trubiano, Anthony, and Michael F. Hagan. "Markov State Model Approach to Simulate Self-Assembly." Physical Review X (accepted), arXiv preprint arXiv:2405.02467 (2024).
Paper: https://doi.org/10.48550/arXiv.2405.02467
Code:
https://github.com/onehalfatsquared/SAASH
https://github.com/onehalfatsquared/MultiMSM
Frechette, Layne B., Aparna Baskaran, and Michael F. Hagan. "Active noise-induced dynamic clustering of passive colloids." arXiv preprint arXiv:2410.05555 (2024).
Paper: https://doi.org/10.48550/arXiv.2410.05555
Code:
https://github.com/Layne28/ AnalysisTools
https://github.com/Layne28/ ActiveNoise
https://github.com/Layne28/ ActiveNoiseHoomd
https://github.com/Layne28/ active-assembly-hoomd
Ghosh, Saptorshi, Aparna Baskaran, and Michael F. Hagan. "Achieving designed texture and flows in bulk active nematics using optimal control theory." arXiv preprint arXiv:2408.14596 (2024).
Paper: https://doi.org/10.48550/arXiv.2408.14596
Code: https://github.com/ghoshsap/active_nematics_optimalcontrol
Tran, Phu N., Sattvic Ray, Linnea Lemma, Yunrui Li, Reef Sweeney, Aparna Baskaran, Zvonimir Dogic, Pengyu Hong, and Michael F. Hagan. "Deep-learning optical flow for measuring velocity fields from experimental data." Soft Matter 20, no. 36 (2024): 7246-7257.
Paper: https://doi.org/10.1039/D4SM00483C
Code: https://github.com/tranngocphu/opticalflow-activenematics
Li, Yunrui, Zahra Zarei, Phu N. Tran, Yifei Wang, Aparna Baskaran, Seth Fraden, Michael F. Hagan, and Pengyu Hong. "A machine learning approach to robustly determine director fields and analyze defects in active nematics." Soft Matter 20, no. 8 (2024): 1869-1883.
Paper: https://doi.org/10.1039/D3SM01253K
Code: https://github.com/siriusxiao62/Orientation-Finder
Ghosh, Saptorshi, Chaitanya Joshi, Aparna Baskaran, and Michael F. Hagan. "Spatiotemporal control of structure and dynamics in a polar active fluid." Soft Matter 20, no. 35 (2024): 7059-7071.
Paper: https://doi.org/10.1039/D4SM00547C
Code: https://github.com/ghoshsap/optimal-control-activepolarfluid
Hagan, Michael F., and Farzaneh Mohajerani. "Self-assembly coupled to liquid-liquid phase separation." PLoS Computational Biology 19, no. 5 (2023): e1010652.
Paper: https://doi.org/10.1371/journal.pcbi.1010652
Code: https://osf.io/mr9a3/
Trubiano, Anthony, and Michael F. Hagan. "Optimization of non-equilibrium self-assembly protocols using Markov state models." The Journal of Chemical Physics 157, no. 24 (2022).
Paper: https://doi.org/10.1063/5.0130407
Code:
https://github.com/onehalfatsquared/CPfold
https://github.com/onehalfatsquared/protocolOptMSM
Joshi, Chaitanya, Sattvic Ray, Linnea M. Lemma, Minu Varghese, Graham Sharp, Zvonimir Dogic, Aparna Baskaran, and Michael F. Hagan. "Data-driven discovery of active nematic hydrodynamics." Physical Review Letters 129, no. 25 (2022): 258001.
Paper: https://doi.org/10.1103/PhysRevLett.129.258001
Code: https://github.com/ joshichaitanya3/actnempy
Peterson, Matthew SE, Aparna Baskaran, and Michael F. Hagan. "Vesicle shape transformations driven by confined active filaments." Nature Communications 12, no. 1 (2021): 7247.
Paper: https://doi.org/10.1038/s41467-021-27310-8Code: https://osf.io/7s9jp/
Norton, Michael M., Piyush Grover, Michael F. Hagan, and Seth Fraden. "Optimal control of active nematics." Physical Review Letters 125, no. 17 (2020): 178005.
Paper: https://doi.org/10.1103/PhysRevLett.125.178005
Code: https://osf.io/qyk9t/
Duclos, Guillaume, Raymond Adkins, Debarghya Banerjee, Matthew SE Peterson, Minu Varghese, Itamar Kolvin, Arvind Baskaran et al. "Topological structure and dynamics of three-dimensional active nematics." Science 367, no. 6482 (2020): 1120-1124.
Paper: https://doi.org/10.1126/science.aaz4547
Code: https://datadryad.org/stash/dataset/doi:10.25349/D9CS31