CPLC Publications

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  1. Breuer, M., Earnest, T.M., Merryman, C., Wise, K.S., Sun, L., Lynott, M.R., Hutchison III, C.A., Smith, H.O., Lapek Jr., J.D., Gonzalez, D.J., de Crecy-Lagard, V., Haas, D., Hanson, A.D., Labhsetwar, P., Glass, J.I., Luthey-Schulten, Z. Essential Metabolism for a Minimal Cell eLife (2018), submitted (2018).
  2. Figiel, M., Krepl, M., Park, S., Poznanski, J., Skowronek, K., Golab, A., Ha, T., Šponer, J., Nowotny, M., Mechanism of Polypurine Tract Primer Generation by HIV-1 Reverse Transcriptase. J. Biol. Chem. DOI: 10.1074/jbc.M117.798256 (2018).
  3. Karig, D., Martini, K.M., Lu, T., DeLateur, N., Goldenfeld, N., Weiss, R. Stochastic Turing Patterns in a Synthetic Bacterial Population. Proc. Natl. Acad. Sci. (2018).
  4. Lee, G., Sherer, N., Kim, N., Rajic, E., Kaur, D., Urriola, N., Martini, K.M., Xue, C., Goldenfeld, N., Kuhlman, T. Testing the Retroelement Invasion Hypothesis for the Emergence of the Ancestral Eukaryotic Cell. Proc. Natl. Acad. Sci., submitted(2018).
  5. Ma, W., Whitley, K.D., Chemla, Y.R., Luthey-Schulten, Z., Schulten, K. Free Energy Simulations Reveal Molecular Mechanism for Functional Switch of a DNA Helicase. Elife. DOI: 10.7554/eLife.34186 (2018).
  6. Merritt, J. and Kuehn, S. Frequency and Amplitude Dependent Microbial Population Dynamics During Cycles of Feast and Famine. The ISME Journal (2018).
  7. Shih, H.Y., Mickalide, H., Fraebel, D.T., Goldenfeld, N., Kuehn, S. Biophysical Constraints Determine the Selection of Phenotypic Fluctuations During Directed Evolution. Phys. Biol. (2018).
  8. Singh, D. and Ha, T. Understanding the Molecular Mechanisms of the CRISPR Toolbox Using Single Molecule Approaches. ACS Chem. Biol. DOI: 10.1021/acschembio.7b00905 (2018).
  9. Singh, D., Mallon, J., Poddar, A., Wang, Y.B., Tippana, R., Yang, O., Bailey, S., Ha, T. Real-Time Observation of DNA Target Interrogation and Product Release by the RNA-Guided Endonuclease CRISPR Cpf1 (Cas12a). Proc. Natl. Acad. Sci. USA. DOI: 10.1073/pnas.1718686115 (2018).
  10. Zhu, W., Kim, B.C., Wang, M.Y., Huang, J., Isak, A., Bexiga, N.M., Monticone, R., Ha, T., Lakatta, E.G. An, S.S. TGF Beta 1 Reinforces Arterial Aging in the Vascular Smooth Muscle Cell Through a Long-Range Regulation of the Cytoskeletal Stiffness. Sci. Rep. DOI: 10.1038/s41598-018-20763-w (2018).
  11. T. Perlova, M. Gruebele and Y. Chemla. Blue light is a universal tactic signal for Escherichia coli. J. Bact., submitted (2018).
  12. C. Davis and M. Gruebele. When is Cell Lysate Chemically and Sterically Like a Cell? Angew. Chem. Int. Ed., submitted (2018).
  13. C. Davis and M. Gruebele. Labeling for quantitative comparison of imaging measurements in vitro and in cells. Biochemistry 57, 1929-1938 (2018).
  14. Ma W, Whitley KD, Chemla YR, Luthey-Schulten Z, Schulten K. Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase. Elife7. pii: e34186. doi: 10.7554/eLife.34186. [Epub ahead of print]
  15. Whitley KD, Comstock MJ, Chemla YR. Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects. Phys Rev Lett.120(6):068102. doi: 10.1103/PhysRevLett.120.068102 (2018).
  16. Christopher R. Bensona, Chris Maffeo, Elisabeth M. Fatilaa, Yun Liu, Edward G. Sheetz, Aleksei Aksimentiev, Abhishek Singharoy, Amar H. Inchworm movements of two rings switching onto a thread by biased Brownian diffusion: a three-body problem. Proceedings of the National Academy of Sciences USA.doi: 10.1073/pnas.1719539115 (2018).
  17. D. Singh, Y. Wang, J. Mallon, O. Yang, A. Poddar, D Ceylan, S. Bailey, and T. Ha. Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. Nature Structural & Molecular Biology, 25, 347–354. doi:10.1038/s41594-018-0051-7 (2018)
  18. B. Hua, Y. Wang, S. Park, K.Y. Han, D. Singh, J.H. Kim, W. Cheng, and T. Ha. The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays. Biochemistry, 57 (10), pp 1572–1576 DOI: 10.1021/acs.biochem.7b01293 <2018)
  19. Y. Youn, Y. Ishitsuka, C. Jin, and P.R. Selvin. Thermal nanoimprint lithography for drift correction in super-resolution fluorescence microscopy. Opt Express. 22;26(2):1670-1680. doi: 10.1364/OE.26.001670 (2018)
  20. 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, doi:10.1049/iet-syb.2017.0070. In press. (2018)
  21. T.M. Earnest, J.A. Cole, and Z. Luthey-Schulten. Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies. Reports on Progress in Physics, doi:10.1088/1361-6633/aaae2c (2018)
  22. 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: An integrative suite for hybrid simulations. Nature Methods, online, doi:10.1038/nmeth.4638. (2018)
  23. T. Perlova, M. Gruebele and Y. Chemla. Blue light is a universal tactic signal for Escherichia coli. J. Bact., under revision (2018).
  24. E.A. Hemmig, C. Fitzgerald, C. Maffeo, L. Hecker, A. Aksimentiev, P. Tinnefeld, U.F. Keyser. Optical voltage sensing using DNA origami. Nano Letters 18:1962–1971 (2018).
  25. J. Yoo and A. Aksimentiev. New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Physical Chemistry Chemical Physics 20, 8432 – 8449 (2018).


  1. Doganay, S., Lee, M.Y., Baum, A., Peh, J., Hwang, S.Y., Yoo, J.Y., Hergenrother, P.J., Garcia-Sastre, A., Myong, S., Ha, T. Single-Cell Analysis of Early Antiviral Gene Expression Reveals a Determinant of Stochastic IFNB1 Expression. Integr. Biol. DOI: 10.1039/c7ib00146k (2017).
  2. Fei, J., Jadaliha, M., Harmon, T.S., Li, I.T.S., Hua, B., Hao, Q., Holehouse, A. S., Reyer, M., Sun, Q., Freier, S.M., Pappu, R.V., Prasanth, K.V., Ha, T. Quantitative Analysis of Multilayer Organization of Proteins and RNA in Nuclear Speckles at Super Resolution. J. Cell Sci. DOI: 10.1242/jcs.206854 (2017).
  3. Lee, H.T., Bose, A., Lee, C.Y., Opresko, P.L., Myong, S. Molecular Mechanisms by Which Oxidative DNA Damage Promotes Telomerase Activity. Nucl. Acids Res. DOI: 10.1093/nar/gkx789 (2017).
  4. Lin, C.T., Tritschler, F., Lee, K.S., Gu, M.G., Rice, C.M., Ha, T. Single-Molecule Imaging Reveals the Translocation and DNA Looping Dynamics of Hepatitis C Virus NS3 Helicase. Protein Sci. DOI: 10.1002/pro.3136 (2017).
  5. Qiu, Y.P., Levendosky, R.F., Chakravarthy, S., Patel, A., Bowman, G.D., Myong, S. The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer. Mol. Cell. DOI: 10.1016/j.molcel.2017.08.018 (2017).
  6. Singh, P., Ramachandran, K., Zhu, J., Kim, B.C., Biswas, D., Ha, T. Iglesias, P.A., Li, R. Sphingolipids Facilitate Age Asymmetry of Membrane Proteins in Dividing Yeast Cells. Molec. Biol. Cell. DOI: 10.1091/mbc.E17-05-0335 (2017).
  7. Zanetti-Polzi, L., Davis, C.M., Gruebele, M., Dyer, R.B., Daidone, I. Amadei, A., Daidone, I. Parallel Folding Pathways of Fip35 WW Domain Revealed by Infrared Spectra and Their Computer Simulation. FEBS Lett. DOI: 10.1002/1873-3468.12836 (2017).
  8. Y. Sun, G. Tortarolo, K.W. Teng, Y. Ishitsuka, U.C. Coskun, S.J. Liao, A. Diaspro, G. Vicidomini, P.R. Selvin, B. Barbieri. A novel pulsed STED microscopy method using FastFLIM and the phasor plots. Proc. SPIE 10069, Multiphoton Microscopy in the Biomedical Sciences XVII, 100691C; DOI:10.1117/12.2267880. <2017)
  9. S.H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K.W. Teng, A.A. de Thomaz, D.L. Nall, M. Baday, O. Jeyifous, D. Demonte, C.M. Dundas, S. Park, W.N. Green, P.R. Selvin. Super-resolution Imaging of Synaptic and Extra-synaptic Pools of AMPA Receptors with Different- sized Fluorescent Probes. eLife 2017;6:e27744 DOI: 10.7554/eLife.27744 (2017)
  10. J.A. Cole, Z. Luthey-Schulten. A Careful Accounting of Extrinsic Noise in Protein Expression Reveals Correlations Among its Sources. Physical Review E, 95(6):062418. doi: 10.1103/PhysRevE.95.062418 (2017)
  11. 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. Journal of Physical Chemistry B, doi: 10.1021/acs.jpcb.7b04318 (2017)
  12. 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, 12(8):e0182570. doi: 10.1371/journal.pone.0182570 (2017)
  13. P. Labhsetwar, M.C.R. Melo, J.A. Cole, Z. Luthey-Schulten. Population FBA Predicts Metabolic Phenotypes in Yeast. PLoS Computational Biology, 13(9):e1005728. doi: 10.1371/journal.pcbi.1005728 (2017)
  14. 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. Nature Communications, 8(1):492, doi: 10.1038/s41467-017-00536-1 (2017)
  15. C. Maffeo and A. Aksimentiev. Molecular mechanism of DNA association with single-stranded DNA binding protein. Nucleic Acids Research 45: 12125–12139 (2017)
  16. D.T. Fraebel, H. Mickalide, D. Schnitkey, J. Merritt, T.E. Kuhlman, S. Kuehn. Environment determines evolutionary trajectory in a constrained phenotypic space. eLife 6:e24669. DOI: 10.7554/eLife.24669 (2017).
  17. V.C. Luca, B.C. Kim, C. Ge, S. Kakuda, D. Wu, M. Roein-Peikar, R.S. Haltiwanger, C. Zhu, T. Ha, K.C. Garcia. Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity. Science 355(6331), 1320–1324. DOI: 10.1126/science.aaf9739 (2017).
  18. I.T.S. Li, T. Ha, Y.R. Chemla. Mapping cell surface adhesion by rotation tracking and adhesion footprinting. Sci. Rep. 7:44502. DOI: 10.1038/srep44502 (2017).
  19. J.A. Englaender, J.A. Jones, B.F. Cress, T.E. Kuhlman, R.J. Linhardt, M.A.G. Koffas. Effect of genomic integration location on heterologous protein expression and metabolic engineering in E. coli. ACS Synth. Biol. 6(4), 710–720. DOI: 10.1021/acssynbio.6b00350 (2017).