Publications: 2015 - 2014

J.R. Peterson*, J.A. Cole*, J. Fei, T.J. Ha and Z. Luthey-Schulten
Effects of DNA Replication on mRNA Noise
Proc. Nat. Acad. Sci., 2015, Nov 11, 112(52): 15886-15891 doi:10.1073/pnas.1516246112.

T. M. Earnest, J. Lai, K. Chen, M. J. Hallock, J. R. Williamson, and Z. Luthey-Schulten
Towards a whole-cell model of ribosome biogenesis: Kinetic modeling of SSU assembly
Biophysical Journal, 2015, Sep 15, 109(6): 1117-35 doi:10.1016/j.bpj.2015.07.030
Files for the simulation can be found: here

J. A. Cole, L. Kohler L, J. Hedhli, Z. Luthey-Schulten
Spatially-Resolved Metabolic Cooperativity Within Dense Bacterial Colonies
BMC Syst Biol, 2015, 9(15), doi:10.1186/s12918-015-0155-1

H. Zhao, A. Palencia, E. Seiradake, Z. Ghaemi, S. Cusack, Z. Luthey-Schulten, S. Martinis
Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism
ACS Chem. Biol., 2015, 10(10): 2277-2285, doi:10.1021/acschembio.5b00291

I. Guzman, Z. Ghaemi, A. Baranger, Z. Luthey-Schulten, M. Gruebele
Native Conformational Dynamics of the Spliceosomal U1A Protein
J. Phys. Chem. B, 2015, 119 (9): 3651-3661, doi:10.1021/jp511760m

J. A. Cole, Z. Luthey-Schulten
Whole Cell Modeling: From Single Cells to Colonies
Isr. J. Chem., 2014, 54(8-9): 1219--1229, doi: 10.1002/ijch.201300147

Hajin Kim, Sanjaya C. Abeysirigunawarden, Ke Chen, Megan Mayerle, Kaushik Ragunathan, Zaida Luthey-Schulten, Taekjip Ha & Sarah A. Woodson
Protein-guided RNA dynamics during early ribosome assembly
Nature, 2014, 506, 7488, 334--338, http://dx.doi.org/10.1038/nature13039

M. J. Hallock, J. E. Stone, E. Roberts, C. Fry, Z. Luthey-Schulten
Simulation of reaction diffusion processes over biologically-relevant size and time scales using multi-GPU workstations
Parallel Comput. 2014, 40, 86-99, doi: 10.1016/j.parco.2014.03.009.

J.R. Peterson, P. Labhsetwar, J.R. Ellermeier, P.R.A.Kohler, A. Jain, T. Ha, W.W. Metcalf, Z. Luthey-Schulten
Towards a Computational Model of a Methane Producing Archaeum
Archaea, Article ID 898453, 18 pages, 2014, http://dx.doi.org/10.1155/2014/898453

J. A. Cole, M. J. Hallock, P. Labhsetwar, J. R. Peterson, J. E. Stone, Z. Luthey-Schulten
Stochastic Simulations of Cellular Processes: From Single Cells to Colonies
in Computational Systems Biology 2nd Edition: From Molecular Mechanisms to Disease, Eds. Kriete and Eils, Elsevier, 2014.