CPLC Publications

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2011

  1. A. D. Radadia, C. J. Stavis, R. Carr, H. Zeng, W. King, J. A. Carlisle, A. Aksimentiev, R. J. Hamers and R. Bashir. “Control of nanoscale environment to improve stability of immobilized proteins on diamond surfaces,” Advanced Functional Materials 21:1040-1050 (2011).
  2. A. Dhar, K. Girdhar, D. Singh, H. Gelman, S. Ebbinghaus and M. Gruebele. “Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of living cells,” Biophys. J. 101, 421-430 (2011).
  3. A. Jain, R. Liu, B. Ramani, E. Arauz, Y. Ishitsuka, K. Ragunathan, J. Park, J. Chen, Y. K. Xiang and T. Ha. “Probing cellular protein complexes using single-molecule pull-down,” Nature 473, 484-488 (2011).
  4. B. M. Venkatesan, J. Polans, J. Comer, S. Sridhar, D. Wendell, A. Aksimentiev and R. Bashir. “Lipid bilayer coated Al2O3 nanopore sensors: Towards a hybrid biological solid-state nanopore,” Biomedical Microdevices 13:671-682 (2011).
  5. C. K. Means, B. Lygren, L. K. Langeberg, A. Jain, R. E. Dixon, A. L. Vega, M. G. Gold, S Petrosyan, S. S. Taylor, A. N. Murphy, T. Ha, L. F. Santana, K. Tasken and J. D. Scott. “An entirely specific type I A-kinase anchoring protein that can sequester two molecules of PKA holoenzyme,” Proc. Natl. Acad. Sci. USA 108, E1227-35 (2011).
  6. C. Liu. M. C. McKinney, Y. H. Chen, T. M. Earnest, X. Shi, Li. J. Lin, Y. Ishino, K. Dahmen, I. K.O. Cann and T. Ha. “Reverse-chaperoning activity of an AAA+ protein,” Biophysical J. 100, 1344-1352 (2011).
  7. C. Olbrich, J. Strümpfer, K. Schulten and U. Kleinekathoefer. “Quest for spatially Correlated fluctuations in the FMO light-harvesting complex,” J. Phys. Chem. B 115:758-764 (2011).
  8. C. Olbrich, J. Strümpfer, K. Schulten and U. Kleinekathoefer. “Theory and simulation of the environmental effects on FMO electronic transitions,” J. Phys. Chem. Lett. 2:1771-1776 (2011).
  9. C.  Wang,  B.  Harrison,  K.  Schulten  and  J.  A.  McCammon.  “Implementation  of  accelerated molecular dynamics in NAMD,” Comput. Sci. Discov. 4:015002 (2011).
  10. C. Sathe, X. Zou, J-P. Leburton and K. Schulten. “Computational investigation of DNA Detection using graphene nanopores,” ACS Nano 5:8842-8851 (2011).
  11. C. Olbrich, T. L. C. Jansen, J. Liebers, M. Aghtar, J. Strümpfer, K. Schulten, J. Knoester and U. Kleinekathoefer. “From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex,” J. Phys. Chem. B 115(26):8609-8621 (2011).
  12. D. E. Tanner, K.-Y. Chan, J. C. Phillips and K. Schulten. “Parallel generalized Born implicit solvent calculations with NAMD,” J. Chem. Theor. Comp. 7:3635-3642 (2011).
  13. D. E. Tanner, W. Ma, Z. Chen and K. Schulten. “Theoretical and computational investigation Of flagellin translocation and bacterial flagellum growth,” Biophys. J. 100:2548-2556 (2011).
  14. E. Roberts, A. Magis, J. O. Ortiz, W. Baumeister and Z. Luthey-Schulten. “Noise contributions In an inducible genetic switch: A whole-cell simulation study,” PLoS Comp. Bio. 7(3):e1002010 (2011).
  15. E. Rothenberg, L. A. Sepúlveda, S. O. Skinner, L. Zeng, P. R. Selvin and I. Golding. “Single-virus tracking reveals a spatial receptor-dependent search mechanism,” Biophysical Journal 100(12), 2875-82 (2011).
  16. E. Schreiner, L. G. Trabuco, P. L. Freddolino and K. Schulten. “Stereochemical errors and their implications for molecular dynamics simulations,” BMC Bioinform 12:190 (2011).
  17. G. Lee, J. Yoo, B. J. Leslie and T. Ha. “Single molecule analysis reveals three phases of DNA degradation by an exonuclease,” Nature Chemical Biology 7, 367-374 (2011).
  18. G. Timp, U. Mirsaidov, W. Timp, J. Shim, D. Wang, V. Dimitrov, J. Scrimgeour, C. Lin, J. Comer, A. Ho, X. Zou, A. Aksimentiev and K. Schulten. “3rd generation DNA sequencing with a nanopore,” In Samir M. Iqbal and Rashid Bashir, editors, Nanopores: Sensing and Fundamental Biological Interactions, chapter 12, pp. 287-312. Springer, Berlin (2011).
  19. H. Kim, G. Q. Tang, S. S. Patel and T. Ha. “Opening-closing dynamics of the mitochondrial transcription pre-initiation complex,” Nucleic Acids Research 40, 371-380 (2011).
  20. I. Golding. “Decision making in living cells: Lessons from a simple system,” Annual Review of Biophysics 40:63-80 (2011).
  21. J. A. Lamboy, H. Kim, K. Lee, T. Ha and E. A. Komives. “Visualization of the nanospring dynamics of the IκBα ankyrin repeat domain in real time,” Proc. Natl. Acad. Sci. USA 108, 10178-10183 (2011).
  22. J.  C.  Gumbart,  C.  Chipot  and  K.  Schulten.  “Free  energy  of  nascent-chain  folding  in  the translocon,” J. Am. Chem. Soc. 133:7602-7607 (2011).
  23. J. C. Gumbart, C. Chipot and K. Schulten. “Free-energy cost for translocon-assisted insertion of membrane proteins,” Proc. Natl. Acad. Sci. USA 108:3596-3601 (2011).
  24. J.  C.  Gumbart,  E.  Schreiner,  L.  G.  Trabuco,  K-Y.  Chan  and  K.  Schulten.  “Viewing  the mechanisms of translation through the computational microscope,” In Joachim Frank, editor, Molecular Machines in Biology, chapter 8, pp. 142-157. Cambridge University Press (2011).
  25. J. Frauenfeld, J. C. Gumbart, E. O. van der Sluis, S. Funes, M. Gartmann, B. Beatrix, T. Mielke, O.  Berninghausen,  T.  Becker,  K.  Schulten  and  R.  Beckmann.  “Cryo-EM  structure  of  the ribosome-SecYE complex in the membrane environment,” Nature Struct. Mol. Biol. 18:614-621 (2011)
  26. J. Hsin, J. Strümpfer, E. H. Lee and K. Schulten. “Molecular origin of the hierarchical Elasticity of titin: Simulation, experiment and theory,” Annu. Rev. Biophys. 40:187-203 (2011).
  27. J. Strümpfer, J. Hsin, M. Sener, D. Chandler and K. Schulten. “The light-harvesting apparatus in purple photosynthetic bacteria, introduction to a quantum biological device,” In Benoit Roux, editor, Molecular Machines, chapter 2, 19-48. World Scientific Press (2011).
  28. K. Girdhar, G. Scott, Y.R. Chemla and M. Gruebele. “Better biomolecule thermodynamics from kinetics,” J. Chem. Phys. 135(1):015102. (2011).
  29. K. Ragunathan, C. Joo and T. Ha. “Real time observation of strand exchange reaction with high spatiotemporal resolution,” Structure 19, 1064-1073 (2011).
  30. K.-Y. Chan, J. C. Gumbart, R. McGreevy, J. M. Watermeyer, B. T. Sewell and K. Schulten. “Symmetry-restrained flexible fitting for symmetric EM maps,” Structure 19:1211-1218 (2011).
  31. L. G. Trabuco, E. Schreiner, J. C. Gumbart, J. Hsin, E. Villa and K. Schulten. “Applications of the molecular dynamics flexible fitting method,” J. Struct. Biol. 173:420-427 (2011).
  32. L. H. So, A. Ghosh, C. Zong, L. A. Sepulveda, R. Segev and I. Golding. “General properties of the transcriptional time series in Escherichia coli,” Nature Genetics 43:554-560 (2011).
  33. L. Zeng and I. Golding. “Following cell-fate in E. coli after infection by phage lambda,” JoVE Oct 14;(56) (2011).
  34. M. Assaf, E. Roberts and Z. Luthey-Schulten. “Determining the stability of genetic switches: Explicitly accounting for mRNA noise,” Phys. Rev. Lett. 106, 248102 (2011).
  35. M.  J.  Comstock,  T.  Ha  and  Y.  R.  Chemla.  “Ultra-high  resolution  optical  trap  with  single fluorophore sensitivity,” Nature Methods 8, 335-340 (2011).
  36. M. D. Brenner, R. Zhou and T. Ha. “Forcing a connection: Impacts of single-molecule force spectroscopy on in vivo tension sensing,” Biopolymers 95(5), 332-344 (2011).
  37. M. Mir, Z. Wang, Z. Shen, M. Bednarz, R. Bashir, I. Golding, S. G. Prasanth and G. Popescu. “Optical   measurement   of   cycle-dependent   cell   growth,”   Proc.   Natl.   Acad.   Sci.   USA 108(32):13124-9 (2011).
  38. M. Wanunu, S. Bhattacharya, Y. Xie, Y. Tor, A. Aksimentiev and M. Drndic. “Nanopore analysis of individual RNA/antibiotic complexes,” ACS Nano 5: 9345-9353 (2011).
  39. N. Goldenfeld and C. R. Woese. “Life is Physics: evolution as a collective phenomenon far from equilibrium,” Ann. Rev. Cond. Matt. Phys. 2, 375-399 (2011).
  40. D. Simonson, E. Rothenberg and P. R. Selvin. “Single-molecule-based super-resolution images in the presence of multiple fluorophores,” Nano Letters 11, 5090-5096 (2011).
  41. P. M. D. Severin, X. Zou, H. E. Gaub and K. Schulten. “Cytosine methylation alters DNA mechanical properties,” Nucleic Acids Res. 39:8740-8751 (2011).
  42. R. Carr, J. Comer, M. Ginsberg and A. Aksimentiev. “Modeling pressure-driven transport Of proteins through a nanochannel,” IEEE Transactions on Nanotechnology 10:75-82 (2011).
  43. R. Zhang, E. Rothenberg, G. Fruhwirth, P. D. Simonson, F. Ye, I. Golding, T. Ng, W. Lopes and P. R. Selvin. “Two-photon 3D FIONA of individual quantum dots in an aqueous environment,” Nano Letters 11, 4074-4078 (2011).
  44. R. Zhou, A. G. Kozlov, R. Roy, J. Zhang, S. Korolev, T. M. Lohman and T. Ha. “SSB functions as a sliding platform that migrates on DNA via reptation, Cell 146, 222-232 (2011).
  45. R. Zhou, S. Kunzelmann, M. R. Webb and T. Ha. “Detecting intramolecular conformational dynamics of single molecules in short distances range with sub-nanometer sensitivity,” Nano Letters 11, 5482-5488 (2011).
  46. S. Ebbinghaus and M. Gruebele. “Protein folding landscapes in the living cell,” J. Phys. Chem. Lett. 2, 314-319 (2011).
  47. S. K. Yang, X. Shi, S. Park, S. Doganay, T. Ha and S. C. Zimmerman. “Monovalent And clickable,   uncharged   water-soluble   perylenediimide-cored   dendrimers   for   target-specific, fluorescent biolabeling,” J. Am. Chem. Soc. 133, 9964-9967 (2011).
  48. W.  Li,  L.  G.  Trabuco,  K.  Schulten  and  J.  Frank.  “Molecular  dynamics  of  EF-G  duringtranslocation,” Proteins: Struct., Func., Bioinf. 79:1478-1486 (2011).
  49. X. Agirrezabala, E. Schreiner, L. G. Trabuco, J. Lei, R. F. Ortiz-Meoz, K. Schulten, R. Green and J. Frank. “Structural insights into cognate vs. near-cognate discrimination during decoding,” EMBO J. 30:1497-1507 (2011).
  50. Y. Liu, J. Hsin, H. Kim, P. R. Selvin and K. Schulten. “Extension of a three-helix bundle Domain of myosin VI and key role of calmodulins,” Biophysical Journal 100(12), 2964-2973 (2011).
  51. Z. Zhang, K. Vishal, R. Vafabakhsh, L. Dai, Y. R. Chemla, T. Ha and V. Rao. “A Promiscuous DNA packaging machine from bacteriophage T4,” PLoS Biology 9, e1000592 (2011).