The Zocchi Group: Publications

1. P. Tabeling, G. Zocchi and A. Libchaber, "An experimental study of the Saffman-Taylor instability," J. Fluid Mech. 177, 67 (1987).

2. M. Jensen, A. Libchaber, P. Pelce’ and G. Zocchi, "Effect of gravity on the Saffmann-Taylor meniscus: theory and experiment," Phys. Rev. A 35, 2221 (1987).

3. G. Zocchi, B. Shaw, A. Libchaber and L. Kadanoff, "Finger narrowing under local perturbations in the Saffmann-Taylor problem," Phys. Rev. A 36, 1894 (1987).

4. S. Gross, G. Zocchi and A. Libchaber, "Ondes et plumes de couche limite thermique," C. R. Acad. Sci. Paris, t. 307 Serie II, 447 (1988).

5. G. Zocchi, E. Moses, and A. Libchaber, "Coherent structures in turbulent convection, an experimental study," Physica A 166, 387 (1990).

6. E. Moses, G. Zocchi, I. Procaccia and A. Libchaber, "The dynamics and interactions of laminar thermal plumes," Europhys. Lett. 14, 55 (1991).

7. L. Kadanoff, A. Libchaber, E. Moses, and G. Zocchi, "Turbulence dans une boite," La Recherche 232, 628 (1991).

8. E. Moses, G. Zocchi, and A. Libchaber, "An experimental study of laminar plumes," J. Fluid Mech. 251, 581 (1993).

9. G. Zocchi, P. Tabeling, and M. Benamar, "Saffman-Taylor plumes," Phys. Rev. Lett. 69, 601 (1992).

10. J. Maurer, P. Tabeling, and G. Zocchi, "Statistics of turbulence between two counterrotating disks in low temperature Helium gas," Europhys. Lett. 26, 31 (1994).

11. G. Zocchi, P. Tabeling, J. Maurer, H. Willaime, "Measurement of the scaling of the dissipation at high Reynolds numbers," Phys. Rev. E 50, 3693 (1994).

12. P. Tabeling, G. Zocchi, F. Belin, J. Maurer, H. Willaime, "Probability density functions, skewness and flatness in large Reynolds number turbulence," Phys. Rev. E 53, 1613 (1996).

13. G. Zocchi, "Mechanical measurement of the unfolding of a protein," Europhys. Lett. 35, 633 (1996).

14. G. Zocchi, "Proteins unfold in steps," Proc. Natl. Acad. Sci. USA 94, 10647 (1997).

15. A. Hansen, M. Jensen, K. Sneppen, and G. Zocchi, "A hierarchical scheme for cooperativity and folding in proteins," Physica A 250, 355 (1998).

16. H. Jensenius and G. Zocchi, "Measuring the spring constant of a single polymer chain," Phys. Rev. Lett. 79, 5030 (1997).

17. A. Hansen, M. Jensen, K. Sneppen, and G. Zocchi, "Statistical mechanics of warm and cold unfolding in proteins," Eur. Phys. J. B 6, 157 (1998).

18. M. Singh-Zocchi, A. Andreasen, and G. Zocchi, "Osmotic pressure contribution of albumin to colloidal interactions," Proc. Natl. Acad. Sci. USA 96, 6711 (1999).

19. A. Hansen, M. Jensen, K. Sneppen, and G. Zocchi, "Hot and cold denaturation of proteins: critical aspects," Eur. Phys. J. B 10, 193 (1999).

20. A. Hansen, M. Jensen, K. Sneppen, and G. Zocchi, "A model for the thermodynamics of globular proteins," Physica A 270, 278 (1999).

In The New Millennium

21. A. Hansen, M. H. Jensen, K. Sneppen and G. Zocchi, "Proteins Top-Down: A Statistical Mechanics Approach," Physica A, 288, 21 (2000).

22. A. Hansen, M. Jensen, K. Sneppen, and G. Zocchi, "Modeling molecular motors as folding-unfolding cycles," Europhys. Lett. 50, 120 (2000).

23. A. Hansen, M. H. Jensen, K. Sneppen and G. Zocchi, "A Model for the Thermodynamics of Proteins," in Soft Condensed Matter: Configurations, Dynamics and Functionality, edited by A. T. Skjeltorp and S. F. Edwards (Kluwer, Dordrecht, 2000).

24. G. Zocchi, "Force measurements on single molecular contacts through evanescent wave microscopy," Biophys. J. 81, 2946 (2001).

25. M. Singh-Zocchi, J. Hanne, and G. Zocchi, "Plastic deformation of protein layers," Biophys. J. 83, 2211-18 (2002).

26. A. Montrichok, G. Gruner, and G. Zocchi, "Trapping intermediates in the melting transition of DNA oligomers," Europhys. Lett. 62, 452 (2003).

27. G. Zocchi, A. Omerzu, T. Kuriabova, J. Rudnick, G. Gruner, "Duplex-single strand denaturing transition in DNA oligomers," cond-mat/0304567 (2003).

28. M. Singh-Zocchi, S. Dixit, V. Ivanov, and G. Zocchi, "Single molecule detection of DNA hybridization," Proc. Natl. Acad. Sci. USA 100, 7605-10 (2003).

29. Y. Zeng, A. Montrichok, and G. Zocchi, "Length and statistical weight of bubbles in DNA melting," Phys. Rev. Lett. 91, Number 14, 148101 (2003).

30. V. Ivanov, K. Grzeskowiak, and G. Zocchi, "Evidence for an intermediate state in the B to Z transition of DNA," J. Phys. Chem. B 107, 12847-50 (2003).

31. Y. Zeng, A. Montrichok, and G. Zocchi, "Bubble nucleation and cooperativity in DNA melting," J. Mol. Biol. 339, 67-75 (2004).

32. V. Ivanov, Y. Zeng, and G. Zocchi, "Statistical mechanics of base stacking and pairing in DNA melting," Phys. Rev. E 70, 051907 (2004).

33. B. Choi, G. Zocchi, S. Canale, Y. Wu, S. Chan, L. Jeanne Perry, "Artificial allosteric control of Maltose Binding Protein," Phys. Rev. Lett. 94, 038103 (2005).

34. S. Dixit, M. Singh-Zocchi, J. Hanne, and G. Zocchi, "Mechanics of Binding of a Single Integration-Host-Factor Protein to DNA," Phys. Rev. Lett. 94, 118101 (2005).

35. V. Ivanov, D. Piontkovski, and G. Zocchi, "Local Cooperativity Mechanism in the DNA Melting Transition," Phys. Rev. E 71, 041909 (2005).

36. B. Choi, G. Zocchi, Y. Wu, S. Chan, L. Jeanne Perry, "Allosteric control through mechanical tension," Phys. Rev. Lett. 95, 078102 (2005).

37. G. Zocchi, "Analytical assays based on detecting conformational changes of single molecules," ChemPhysChem 7, 555-60 (2006).

38. Y. Zeng and G. Zocchi, "Mismatches and bubbles in DNA," Biophys. J. 90, 4522-29 (2006).

39. B. Choi and G. Zocchi, "Mimicking cAMP Dependent Allosteric Control of Protein Kinase A through Mechanical Tension," JACS 128, 8541-48 (2006).

40. B. Choi and G. Zocchi, "Guanylate Kinase, Induced Fit, and the Allosteric Spring Probe," Biophys. J. 92, 1651-58 (2007).

41. J. Hanne, G. Zocchi, N. K. Voulgarakis, A. R. Bishop and K. Ø. Rasmussen, "Opening rates of DNA hairpins: experiment and model," Phys. Rev. E 76, 011909-916 (2007).

42. A. Wang and G. Zocchi, "Elastic energy driven polymerization," Biophys. J. 96, 2344-52 (2009).

43. R. Gonzalez, Y. Zeng, V. Ivanov, and G. Zocchi, "Bubbles in DNA melting," J. Phys. Condens. Matter 21, 034102 (2009) (special issue on "DNA melting").

44. G. Zocchi, "Controlling proteins through molecular springs," Ann. Rev. Biophys. 38, 75-88 (2009).

45. Y. Wang, A. Wang, H. Qu, and G. Zocchi, "Protein-DNA chimeras: synthesis of two-arms chimeras and non-mechanical effects of the DNA spring," J. Phys.: Condens. Matter 21, 335103 (2009).

46. C-Y. Tseng, A. Wang, G. Zocchi, B. Rolih, A. J. Levine, "The elastic energy of protein-DNA chimeras," Phys. Rev. E 80, 061912 (2009).

47. Y. Wang and G. Zocchi, "The shape of fair weather clouds," Phys. Rev. Lett. 104, 118502 (2010).

48. H. Qu, C-Y. Tseng, Y. Wang, A. J. Levine, and G. Zocchi, "The elastic energy of sharply bent nicked DNA," Europhys. Lett. 90, 18003 (2010).

49. C-Y. Tseng, A. Wang, and G. Zocchi, "Mechano-chemistry of the enzyme Guanylate Kinase," Europhys. Lett. 91, 18005 (2010).

50. Y. Wang and G. Zocchi, "Elasticity of globular proteins measured from the AC susceptibility," Phys. Rev. Lett. 105, 238104 (2010).

51. Hao Qu and Giovanni Zocchi, "The complete bending energy function for nicked DNA," Europhys. Lett. 94, 18003 (2011).

52. A. Wang and G. Zocchi, "Artificial modulation of the gating behavior of a K+ channel in a KvAP-DNA chimera," PLoS ONE 6(4), e18598 (2011).

53. Y. Wang and G. Zocchi, "The folded protein as a visco-elastic solid," Europhys. Lett. 96, 18003 (2011).

54. Y. Wang and G. Zocchi, "Viscoelastic transition and yield strain of the folded protein," PLoS ONE 6(12), e28097 (2011).

55. H. Qu, Y. Wang, C-Y. Tseng, and G. Zocchi, "Critical torque for kink formation in double stranded DNA," Phys. Rev. X 1, 021008 (2011).

56. H. Qu, J. Landy, and G. Zocchi, "Cracking phase diagram for the dynamics of an enzyme," Phys. Rev. E 86, 041915 (2012).

57. H. Qu and G. Zocchi, "How Enzymes Work: A Look through the Perspective of Molecular Viscoelastic Properties," Phys. Rev. X 3, 011009 (2013).

58. A. Ariyaratne and G. Zocchi, "Nonlinearity of a voltage gated potassium channel revealed by the mechanical susceptibility," Phys. Rev. X 3, 011010 (2013).

59. D. Sanchez, H. Qu, D. Bulla and G. Zocchi, "DNA kinks and bubbles: Temperature dependence of the elastic energy of sharply bent 10-nm-size DNA molecules," Phys. Rev. E 87, 022710 (2013).

60. J. Wang, H. Qu, and G. Zocchi, "Critical bending torque of DNA is a materials parameter independent of local base sequence," Phys. Rev. E 88, 032712 (2013).

61. C-Y. Tseng and G. Zocchi, "Mechanical control of Renilla Luciferase," J. Am. Chem. Soc. 135, 11879 (2013).

62. C-Y. Tseng and G. Zocchi, "Equilibrium softening of an enzyme explored with the DNA spring," Appl. Phys. Lett. 104, 153702 (2014).

63. C. Joseph, C-Y. Tseng, G. Zocchi and T. Tlusty, "Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme," PLoS ONE 9, e101442 (2014).

64. A. Ariyaratne, C. Wu, C-Y. Tseng, and G. Zocchi, "Dissipative Dynamics of Enzymes," Phys. Rev. Lett. 113, 198101 (2014).

65. A. Ariyaratne and G. Zocchi, "Plasmon resonance enhanced mechanical detection of ligand binding," Appl. Phys. Lett. 106, 013702 (2015).

66. A. Ariyaratne and G. Zocchi, “Artificial phosphorylation sites modulate the activity of a voltage gated potassium channel”, Phys. Rev. E Phys. Rev. E 91, 032701 (2015).

67. Z. Alavi, A. Ariyaratne and G. Zocchi, “Nano-rheology measurements reveal that the hydration layer of enzymes partially controls conformational dynamics”, Appl. Phys. Lett. 106, 203702 (2015).

68. D. Sanchez and G. Zocchi, “EcoRV catalysis with a pre-bent substrate”, AIP Advances 5, 057153 (2015).