Publications: 2017 - 2016

T.M. Earnest, R. Watanabe, J.E. Stone, J. Mahamid, W. Baumeister, E. Villa, Z. Luthey-Schulten
Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations
J. Phys. Chem. B, 2017, Mar 14, 121(15):3871-3881 doi:10.1021/acs.jpcb.7b00672

J.R. Peterson, J.A. Cole, Z. Luthey-Schulten
Parametric Studies of Metabolic Cooperativity in Escherichia coli Colonies: Strain and Geometric Confinement Effects
Great Lakes Bioinformatics Conference (GLBIO 2017), 2017, Accepted

S. Thor, J.R. Peterson, Z. Luthey-Schulten
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function
Archaea, 2017, Jan 4, vol. 2017, Article ID: 9763848, 18 pages, doi: 10.1155/2017/9763848

J.R. Peterson, S. Thor, L. Kohler, P.R.A. Kohler, W.W. Metcalf, Z. Luthey-Schulten
Genome-Wide Gene Expression and RNA Half-Life Measurements allow Predictions of Regulation and Metabolic Behavior in Methanosarcina acetivorans
BMC Genomics, 2016, Nov 16, 17(1):924 doi: 10.1186/s12864-016-3219-8

Z. Ghaemi, I. Guzman, J.J. Baek, M. Gruebele, Z. Luthey-Schulten
Estimation of Relative Protein--RNA Binding Strengths from Fluctuations in the Bound State
J. Chem. Theory Comput., 2016, Aug 16, doi:10.1021/acs.jctc.6b00418

P. Labhsetwar, J.A Cole, M. Melo, Z. Luthey-Schulten
"Population Flux Balance Analysis Reveals Metabolic Phenotypes in Yeast" (submitted 2016)

T.M. Earnest, J.A. Cole, J.R. Peterson, T.E. Kuhlman, Z. Luthey-Schulten
Ribosome biogenesis in replicating cells: integration of experiment and theory
Biopolymers, 2016, Jul 22, 105(10): 735-751 doi:10.1002/bip.22892

M.J. Hallock, Z. Luthey-Schulten
Improving reaction kernel performance in Lattice Microbes: particle-wise propensities and run-time generated code
2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), May 2016, 428-434 doi:10.1109/IPDPSW.2016.118

J.E. Stone, M.J. Hallock, J.C. Phillips, J.R. Peterson, Z. Luthey-Schulten, K. Schulten
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads
2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), May 2016, 89-100 doi:10.1109/IPDPSW.2016.130