Publications: 2017 - 2016

J. Lai, Z. Ghaemi, Z. Luthey-Schulten
Conformational change in Elongation factor-Tu involves separation of its domains
Biochem., 2017, Accepted.

S.C. Abeysirigunawardena, H. Kim, J. Lai, K. Ragunathan, M.C. Rappe, Z. Luthey-Schulten, T. Ha, S. A. Woodson
Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes
Nat. Commun., 2017, Sep 8, 8(1):492, doi: 10.1038/s41467-017-00536-1

P. Labhsetwar*, M.C.R. Melo*, J.A. Cole*, Z. Luthey-Schulten
Population FBA Predicts Metabolic Phenotypes in Yeast
PLoS Comput. Biol. 2017, Sep 8, 13(9):e1005728. doi: 10.1371/journal.pcbi.1005728

J.R. Peterson, J.A. Cole, Z. Luthey-Schulten
Parametric Studies of Metabolic Cooperativity in Escherichia coli Colonies: Strain and Geometric Confinement Effects
PLoS ONE, 2017, Aug 18, 12(8):e0182570. doi: 10.1371/journal.pone.0182570

Z. Ghaemi, I. Guzman, D. Gnutt, Z. Luthey-Schulten, M. Gruebele
Role of Electrostatics in Protein-RNA binding: The Global vs. the Local Energy Landscape
J. Phys. Chem. B, 2017, Aug 14. doi: 10.1021/acs.jpcb.7b04318

J.A. Cole, Z. Luthey-Schulten
A Careful Accounting of Extrinsic Noise in Protein Expression Reveals Correlations Among its Sources
Phys. Rev. E. 2017, May 12, 95(6):062418. doi: 10.1103/PhysRevE.95.062418

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

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

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