Citations
=========

.. [EARN2018] 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 <https://doi.org/10.1088/1361-6633/aaae2c>`_

.. [PETE2013] 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 <https://doi.org/10.13140/2.1.3207.7440>`_

.. [ROBE2009] 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 <https://doi.org/10.1109/ipdps.2009.5160930>`_

.. [ROBE2013] 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 <https://doi.org/10.1002/jcc.23130>`_

.. [HALL2014] 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 <https://doi.org/10.1016/j.parco.2014.03.009>`_

.. [THORNBURG2022] 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 <https://doi.org/10.1016/j.cell.2021.12.025>`_

.. [THORNBURG2025a] 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 <https://doi.org/10.1101/2025.06.10.658899>`_

.. [FU2025] 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 <https://doi.org/10.1101/2025.07.02.662439>`_

.. [WU2025] 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)