Citations#
T.M. Earnest, J.A. Cole, and Z. Luthey-Schulten. “Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies.” Rep. Prog. Phys., 81(5), 2018, 052601. doi:10.1088/1361-6633/aaae2c
J.R. Peterson, M.J. Hallock, J.A. Cole, and Z. Luthey-Schulten. “A Problem Solving Environment for Stochastic Biological Simulations.” PyHPC 2013 at Supercomputing 2013, 2013. doi:10.13140/2.1.3207.7440
E. Roberts, J.E. Stone, L. Sepulveda, W.W. Hwu, and Z. Luthey-Schulten.” Long time-scale simulations of in vivo diffusion using GPU hardware.” In Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009. doi:10.1109/ipdps.2009.5160930
E. Roberts, J.E. Stone, and Z. Luthey-Schulten. “Lattice microbes: high-performance stochastic simulation method for the reaction-diffusion master equation.” J. Comp. Chem., 32(3), 245-55, 2013. doi:10.1002/jcc.23130
M.J. Hallock, J.E. Stone, E. Roberts, C. Fry and Z. Luthey-Schulten. “Simulation of reaction diffusion processes over biologically-relevant size and time scales using multi-GPU workstations.” Parallel Comput. 40:86-99, 2014. doi:10.1016/j.parco.2014.03.009
Z.R. Thornburg, D.M. Bianchi, T.A. Brier, B.R. Gilbert, T.M. Earnest, M.C.R. Melo, N. Safronova, J.P. Sáenz, A.T. Cook, K.S. Wise, C.A. Hutchison III, H.O. Smith, J.I. Glass, and Z. Luthey-Schulten. “Fundamental behaviors emerge from simulations of a living minimal cell.” Cell, 185(2):345-360.e28, 2022. doi:10.1016/j.cell.2021.12.025
Z.R. Thornburg, A. Maytin, J. Kwon, T.A. Brier, B.R. Gilbert, E. Fu, Y.-L. Gao, J. Quenneville, T. Wu, H. Li, T. Long, W. Pezeshkian, L. Sun, J.I. Glass, A. Mehta, T. Ha, and Z. Luthey-Schulten. “Bringing the Genetically Minimal Cell to Life on a Computer in 4D.” bioRxiv, 2025. doi:10.1101/2025.06.10.658899
E. Fu, Z.R. Thornburg, T.A. Brier, R. Wei, B. Yuan, B.R. Gilbert, S. Wang, and Z. Luthey-Schulten. “Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.” bioRxiv, 2025. doi:10.1101/2025.07.02.662439
T. Wu, M.-C. Spindler, E. Earnest, A.T. Apsley, H. Li, Z.R. Thornburg, J. Mahamid, and Z. Luthey-Schulten. “Spatial Heterogeneity Alters the Dynamics of the Yeast Galactose Switch: Insights from 4D RDME–ODE Hybrid Simulations.” bioRxiv, 2025. (Preprint)