Publications: 2017 - 2016

M. C. R. Melo, R. C. Bernardi, T. Rudack, M. Scheurer,C. Riplinger, J. C. Phillips, J. D. C. Maia, G. B. Rocha, J. V. Ribeiro, J. E. Stone, F. Neese, K. Schulten, and Z. Luthey-Schulten
NAMD goes quantum: A new integrative suite for QM/MM simulations
Nature Methods- In revisions, 2017.

D. M. Bianchi, J. R. Peterson, T. M. Earnest, M. J. Hallock, and Z. Luthey-Schulten
A Hybrid CME-ODE Method for Efficient Simulation of the Galactose Switch in Yeast
IET Systems Biology, 2017, Submitted.

J. Lai, Z. Ghaemi, Z. Luthey-Schulten
Conformational change in Elongation factor-Tu involves separation of its domains
Biochem., 2017, Accepted., doi: 10.1021/acs.biochem.7b00591

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