CPLC Publications

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2012

  1. A.  Jain,  R.  Liu,  Y.  K.  Xiang  and  T.  Ha.  “Single-molecule  pull-down  for  studying  protein interactions,” Nature Protocols 7, 445-452 2012).
  2. B.H. Blehm, T. A. Schroer, K. M. Trybus, Y. R. Chemla and P. R. Selvin. “In vivo optical trapping indicates kinesin’s stall force is reduced by dynein during intracellular transport,” Proc. Natl. Acad. Sci. USA 10.1073, 1219961110 (2012).
  3. C. Maffeo, B. Luan and A. Aksimentiev. “End-to-end attraction of short duplex DNA,” Nucleic Acids Research 40: 3812-3821 (2012).
  4. C. Maffeo, S. Bhattacharya, J. Yoo, D. Wells and A. Aksimentiev. “Modeling and simulation of ion channels,” Chemical Reviews 112:6250-6284 (2012). Cover.
  5. G. Lee, M. Bratkowski, F. Ding, A. Ke and T. Ha. “Elastic coupling between RNA degradation and unwinding by an exoribonuclease,” Science 336, 1726-1729 (2012).
  6. H. Gelman, M. Platkov and M. Gruebele. “Rapid perturbation of free energy landscapes: from in vitro to in vivo,” Chemistry: A Eur. J. 18, 6420-6427 (2012).
  7. H. Hwang, N. Buncher, P. L. Opresko and S. Myong. “POT1-TPP1 regulates telomeric overhang structural dynamics,” Structure 20, 1872-1880 2012).
  8. I. A. Solov’yov and K. Schulten. “Reaction kinetics and mechanism of magnetic field effects in cryptochrome,” J. Phys. Chem. B 116:1089-1099 (2012).
  9. I. A. Solov’yov,  P.-Y.  Chang  and  K.  Schulten.  “Vibrationally  assisted  electron  transfer mechanism of olfaction: Myth or reality?” Phys. Chem. Chem. Phys. 14:13861-13871 (2012).
  10. I. A. Solov’yov, T. Domratcheva, A. R. M. Shahi and K. Schulten. “Decrypting cryptochrome: Revealing the molecular identity of the photoactivation reaction,” Chem. Soc. 134:18046-18052 (2012).
  11. I. Cisse, H. Kim and T. Ha. “A rule of seven in Watson-Crick base pairing of mismatchedsequences,” Nature Structural & Molecular Biology 19, 623-627 (2012).
  12. J. C. Gumbart, E. Schreiner, D. N. Wilson, R. Beckmann and K. Schulten. “Mechanisms of SecM-mediated stalling in the ribosome,” Biophysics Journal 103:331-341 (2012).
  13. J. Comer, A. Ho and A. Aksimentiev. “Toward detection of DNA-bound proteins using solid- state nanopores: insights from computer simulations,” Electrophoresis 33:3466-3479 (2012).
  14. J. D. Kessler, K. T. Kahle, T. Sun, K. L. Meerbrey, M. R. Schlabach, E. M. Schmitt, S. O. Skinner, Q. Xu, M. Z. Li, Z. C. Hartman, M. Rao, P. Yu, R. Dominguez-Vidana, A. Liang, N. Solimini, R. J. Bernardi, B. Yu, T. Hsu, I. Golding, J. Luo, C. K. Osborne, C. J. Creighton, S. G. Hilsenbeck, R. Schiff, C. A. Shaw, S. J. Elledge and T. F. Westbrook. “A sumoylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis,” Science 335(6066):348-353 (2012).
  15. J.  Eargle  and  Z.  Luthey-Schulten.  “Chapter  11:  Simulating  Dynamics   in  RNA-Protein Complexes,” In RNA 3D Structure Analysis and Prediction Edited by N. Leontis and E. Westhof (2012).
  16. J.  Eargle  and  Z.  Luthey-Schulten.  “NetworkView: 3D display and  analysis of  RNA:Protein interaction networks,” Bioinformatics 28(22), 3000-3001 (2012).
  17. J. Strümpfer and K. Schulten. “Excited state dynamics in photosynthetic reaction center and light harvesting complex 1,” J. Chem. Phys. 137:065101, 8pp (2012).
  18. J. Strümpfer and K. Schulten. “Open quantum dynamics calculations with the hierarchy equations of motion on parallel computers,” J. Chem. Theor. Comp. 8:2808-2816 (2012).
  19. J. Strümpfer, M. Sener and K. Schulten. “How quantum coherence assists photosynthetic light harvesting,” J. Phys. Chem. Lett. 3:536-542 (2012).
  20. J. Yoo and A. Aksimentiev. “Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations,” Journal of Physical Chemistry B 116:12946-12954 (2012).
  21. J. Yoo and A. Aksimentiev. “Improved parameterization of Li+, Na+, K+, and Mg2+  ions for all- atom molecular dynamics simulations of nucleic acid systems,” Journal of Physical Chemistry Letters 3: 45-50 (2012).
  22. K. Chen, J. Eargle, J. Lai, H, Kim, T. Ha, T. Abeysirigunawardena, M. Mayerle, S. Woodson and Z. Luthey-Schulten. “Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Go simulations,” J. Phys. Chem. B., Harold A. Scheraga Festschrift, 116(23), 6819-6831 (2012).
  23. K. Ragunathan, C. Liu and T. Ha. “RecA filament sliding on DNA facilitates homology search,” eLife 1, e00067 (2012).
  24. K. Shen, S. Arslan, D. Akopian, T. Ha and S. Shan. “Activated GTPase movement on an RNA scaffold drives cotranslational protein targeting,” Nature 492, 271-275 (2012).
  25. K.-Y. Chan, L. G. Trabuco, E. Schreiner and K. Schulten. “Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method,” Biopolymers 97:678-686 (2012).
  26. L. Li, P. Ge, P. R. Selvin and Y. Lu. “Direct detection of adenosine in undiluted serum using a luminescent   aptamer  sensor   attached   to   a   terbium   complex,”    Analytical Chemistry.dx.doi.org/10.1021/ac302167d (2012).
  27. L. Li, R. Zhang, L. Yin, K. Zheng, W. Qin, P. R. Selvin and Y. Lu. “Biomimetic surface engineering of lanthanide-doped upconversion nanoparticles as versatile bioprobes,” Angewandte Chemie (International ed. in English). doi:10.1002/anie.201109156 (2012).
  28. M. Aghtar, J. Liebers, J. Strümpfer, K. Schulten and U. Kleinekathöfer. “Juxtaposing density matrix and classical path-based wave packet dynamics,” J. Chem. Phys. 136:214101 (2012).
  29. M. Assaf, L. Angheluta and N. Goldenfeld. “Effect of weak rotation on large-scale circulation cessations in turbulent convection,” Phys. Rev. Lett. 109, 074502-06 (2012).
  30. M. Baday, A. Cravens, A. Hastie, H. Kim, D. Kudeki, P. Kwok, M. Xiao and P. R. Selvin. “Multicolor super-resolution DNA imaging for genetic analysis,” Nano Letters 12, 3861-3866 (2012).
  31. M.  Mir,  S.  D.  Babacan,  M.  Bednarz,  M.  N.  Do,  I.  Golding  and  G.  Popescu.  “Visualizing Escherichia  coli  sub-cellular  structure  using  sparse  deconvolution  spatial  light  interference tomography,” PLoS One 7(6):e39816 (2012).
  32. N. Friedman, S. Ito, B.A.W. Brinkman, M. Shimono, R.E.L. DeVille, K. A. Dahmen and J. M. Beggs. “Universal critical dynamics in high resolution neuronal avalanche data,” Phys. Rev. Lett.  108 (20), 208102 (2012).
  33. Q. Gao, Y. Y. Chou, S. Doganay, R. Vafabakhsh, T. Ha and P. Palese. “The influenza A Virus PB2, PA, NP and M segments play a pivotal role during genome packaging,” J. Virology 86, 7043-51 (2012).
  34. R. Vafabakhsh and T. Ha. “Extreme bendability of DNA less than 100 base pairs long revealed by single molecule cyclization,” Science 337, 1097-1101 (2012).
  35. R. Zhou and T. Ha. “Single-molecule analysis of SSB dynamics on single-stranded DNA,” Methods Mol. Biol. 922, 85-100 (2012).
  36. S. Lee, M. Baday, M. Tjioe, P. D. Simonson, R. Zhang, E. Cai and P. R. Selvin. “Using fixed fiduciary markers for stage drift correction,” Optics Express 20(11), 12177-12183 (2012).
  37. W.  Kowalczyk,  D  B.  Wells,  A.  Aksimentiev  and  C.  Dekker.  “Slowing  down  DNA translocation through a nanopore in lithium chloride,” Nano Letters 12:1038-1044 (2012).
  38. T. Ha and P. Tinnefeld. “Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging,” Annual Review of Physical Chemistry 63, 595-617 (2012).
  39. T. Ha, A. G. Kozlov and T. M. Lohman. “Single-molecule views of protein movement on single- stranded DNA,” Annual Review of Biophysics 41, 295-319 (2012).
  40. T. L. Min, P. J. Mears, I. Golding and Y. R. Chemla. “Chemotactic adaptation kinetics of individual Escherichia coli cells,” Proc. Natl. Acad. Sci. USA 109(25):9869-74 (2012).
  41. X. Agirrezabala, H. Liao, E. Schreiner, J. Fu, R. Ortiz-Meoz, K. Schulten, R. Green and J. Frank. “Structural characterization of mRNA-tRNA translocation intermediates,” Proc. Natl. Acad. Sci.USA 109:6094-6099 (2012).
  42. X. Shi, Y. Jung, L.J. Lin, C. Liu, C. Wu, I.K.O. Cann and T. Ha. “Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging,” Nature Methods 9, 499-503 (2012).
  43. X. Zou, W. Ma, I. Solov’yov, C. Chipot and K. Schulten. “Recognition of methylated DNA through methyl-CpG binding domain proteins,” Nucleic Acids Res. 40:2747-2758 (2012).
  44. Y. Chen, E. R. Cruz-Chu, J. Woodard, M. R. Gartia, K. Schulten and L. Liu. “Electrically induced conformational change of peptides on metallic nano-surfaces,” ACS Nano 6:8847-8856 (2012).
  45. Y. Liu, J. Strümpfer, P. L. Freddolino, M. Gruebele and K. Schulten. “Structural characterization of l-repressor folding from all-atom molecular dynamics simulations,” J. Phys. Chem. Lett. 3:1117-1123 (2012).
  46. Y. Y. Chou, R. Vafabakhsh, S. Doğanay, Q. Gao, T. Ha and P. Palese. “One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis,” Proc. Natl. Acad. Sci. USA 109, 9101-9106 (2012).
  47. Z. Shen, A. Chakraborty, A. Jain, S. Giri, T. Ha, K. V. Prasanth and S. G. Prasanth. “Dynamic association of ORCA with pre-RC components regulates DNA replication initiation,” Mol. Cell. Biol. 32, 3107-20 (2012).