Journal publications

Biophysics papers:

    2023:

  1. Y. Niu, R. Zhang*, J. Yuan* (2023) Flagellar motors of swimming bacteria contain an incomplete set of stator units to ensure robust motility. Science Advances 9:eadi6724.
  2. X. Zhang†, C. Zhang†, R. Zhang*, J. Yuan* (2023) Differential Bending Stiffness of the Bacterial Flagellar Hook under Counterclockwise and Clockwise Rotations. Phys. Rev. Lett. 130:138401.
  3. A. Tao†, G. Liu†, R. Zhang*, J. Yuan* (2023) Precise Measurement of the Stoichiometry of the Adaptive Bacterial Flagellar Switch. mBio 14:e00189-23.
  4. C. Yue†, C. Zhang†*, R. Zhang*, J. Yuan* (2023) Tethered particle motion of the adaptation enzyme CheR in bacterial chemotaxis. iScience 26:107950.
  5. G. Yue, R. Zhang, J. Yuan* (2023) Timescale separation in the coordinated switching of bacterial flagellar motors. Phys. Biol. 20:046002.
  6. G. Yue, R. Zhang, J. Yuan* (2023) Stochastic fluctuations in the rotation of the bacterial flagellar motor. Chin. Phys. B 32:068703.

    7. 2022:

  7. M. Tian†, Z. Wu†, R. Zhang*, J. Yuan* (2022) A new mode of swimming in singly flagellated Pseudomonas aeruginosa. PNAS 119:e2120508119.
  8. B. Wang†, G. Yue†, R. Zhang*, J. Yuan* (2022) Direct Measurement of the Stall Torque of the Flagellar Motor in Escherichia coli with Magnetic Tweezers. mBio 13:e00782-22.
  9. X. Liu, R. Zhang*, J. Yuan* (2022) Suppression of cell-cell variation by cooperative interaction of phosphatase and response regulator. Biophys. J. 121:319-326.
  10. X. Liu†, C. Zhang†, R. Zhang*, J. Yuan* (2022) The Effect of the Second Messenger c-di-GMP on Bacterial Chemotaxis in Escherichia coli. Appl. Environ. Microbiol. 88:e00373-22.
  11. S. Ma, R. Zhang*, J. Yuan* (2022) Observation of broken detailed balance in polymorphic transformation of bacterial flagellar filament. Biophys. J. 121:2345-2352.
  12. L. Zhang†, Z. Wu†, R. Zhang*, J. Yuan* (2022) FliL Differentially Interacts with Two Stator Systems To Regulate Flagellar Motor Output in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 88:e01539-22.
  13. Y. Yang, C. Yue, C. Zhang*, J. Yuan* (2022) Chemotactic response of Escherichia coli to polymer solutions. Phys. Biol. 19:046004.
  14. R. Gupta, J. Yuan, P.P. Lele* (2022) Bacterial Proprioception: Can a Bacterium Sense Its Movement? Front. Microbiol. 13:928408.

    15. 2021:

  15. B. Wang†, Y. Niu†, R. Zhang*, J. Yuan* (2021) Dynamics of Switching at Stall Reveals Nonequilibrium Mechanism in the Allosteric Regulation of the Bacterial Flagellar Switch. Phys. Rev. Lett. 127:268101.
  16. Z. Wu, M. Tian, R. Zhang*, J. Yuan* (2021) Dynamics of the Two Stator Systems in the Flagellar Motor of Pseudomonas aeruginosa Studied by a Bead Assay. Appl. Environ. Microbiol. 87:e01674–21.
  17. G. Liu†, Z. Liu†, L. Zhu, R. Zhang*, J. Yuan* (2021) Upcoming flow promotes the bundle formation of bacterial flagella. Biophys. J. 120:4391-4398.
  18. M. Tian†, C. Zhang†, R. Zhang*, J. Yuan* (2021) Collective motion enhances chemotaxis in a two-dimensional bacterial swarm. Biophys. J. 120:1615-1624.
  19. H. Huo, R. He*, R. Zhang, J. Yuan* (2021) Swimming Escherichia coli Cells Explore the Environment by Lévy Walk. Appl. Environ. Microbiol. 87:e02429–20.

    20. 2020:

  20. A. Tao, R. Zhang*, J. Yuan* (2020) Direct Mapping from Intracellular Chemotaxis Signaling to Single-Cell Swimming Behavior. Biophys. J. 119:2461–2468.
  21. Z. Wu†, R. He†, R. Zhang*, J. Yuan* (2020) Swarming Motility Without Flagellar Motor Switching by Reversal of Swimming Direction in E. coli. Front. Microbiol. 11:1042.
  22. R. Wang†, Q. Chen†, R. Zhang*, J. Yuan* (2020) Measurement of the Internal Frictional Drag of the Bacterial Flagellar Motor by Fluctuation Analysis. Biophys. J. 118:2718–2725.
  23. G. Liu, A. Tao, R. Zhang*, J. Yuan* (2020) Robustness in an Ultrasensitive Motor. mBio 11:e03050-19.
  24. A. Tao, R. Zhang, J. Yuan* (2020) Characterization of Photophysical Properties of Photoactivatable Fluorescent Proteins for Super-Resolution Microscopy. J. Phys. Chem. B 124:1892-1897.
  25. W. Nie†, S. Wang†, R. He†, Q. Xu, P. Wang, Y. Wu, F. Tian, J. Yuan, B. Zhu*, G. Chen* (2020) A-to-I RNA editing in bacteria increases pathogenicity and tolerance to oxidative stress. PLoS Pathog. 16(8):e1008740.

    26. 2019:

  26. H. Shi†, S. Ma†, R. Zhang, J. Yuan* (2019) A hidden state in the turnover of a functioning membrane protein complex. Science Advances 5:eaau6885.

    27. 2018:

  27. R. Wang†, F. Wang†, R. He, R. Zhang*, and J. Yuan* (2018) The Second Messenger c-di-GMP Adjusts Motility and Promotes Surface Aggregation of Bacteria. Biophys. J. 115:2242-2249.
  28. C. Zhang†, R. He†, R. Zhang*, and J. Yuan* (2018) Motor adaptive remodeling speeds up bacterial chemotactic adaptation. Biophys. J. 114:1225-1231.
  29. X. Hua, C. Guo, J. Wang, D. Kim-Holzapfel, B. Schroeder, W. Liu, J. Yuan, J. French, S. Jia* (2018) Depth-extended, high-resolution fluorescence microscopy: whole-cell imaging with double-ring phase (DRiP) modulation. Biomed. Opt. Express 10(1):83-91.

    30. 2017:

  30. B. Wang, R. Zhang, and J. Yuan* (2017) Limiting (zero-load) speed of the rotary motor of Escherichia coli is independent of the number of torque-generating units. PNAS 114:12478-12482.
  31. C. Zhang, R. Zhang, and J. Yuan* (2017) Growth-dependent behavioral difference in bacterial chemotaxis. Phys. Rev. E. 95:062404.
  32. F. Wang†, H. Shi†, R. He†, R. Wang, R. Zhang*, J. Yuan* (2017) Nonequilibrium effect in the allosteric regulation of the bacterial flagellar switch. Nature Physics 13:710-714. (†:co-first authors)

    33. 2016:

  33. R. He, R. Zhang*, and J. Yuan* (2016) Noise-induced increase of sensitivity in bacterial chemotaxis. Biophys. J. 111:430-437.
  34. T. Si, J. Yuan, Y. Wu, J.X. Tang* (2016) Physical biology of bacterial motility. Acta Physica Sinica 65(17):178703.

    35. 2015:

  35. Y. Yuan et al. (2015) Bridging cells of three colors with two bio-orthogonal click reactions. Chemical Science 6(11):6425-6431.

    36. 2014:

  36. F. Wang, J. Yuan* and H.C. Berg* (2014) Switching dynamics of the bacterial flagellar motor near zero load. PNAS 111:15752-15755.
  37. J. Yuan* (2014) 细菌运动行为及趋化信号转导网络的研究. (invited review in Chinese) 中国科学技术大学学报 44:382-388.

    38. 2013 and before(@Harvard):

  38. J. Yuan and H.C. Berg (2013) Ultrasensitivity of an adaptive bacterial motor. J. Mol. Biol. 425:1760-1764.
  39. J. Yuan and H.C. Berg (2012) Characteriaztion of the adaptation module of the signaling network in bacterial chemotaxis by measurement of step responses. Biophys. J. 103:L31-L33 (Biophysical Letters).
  40. J. Yuan, R.W. Branch, B.G. Hosu and H.C. Berg (2012) Adaptation at the output of the chemotaxis signaling pathway. Nature 484:233-236.
  41. J. Yuan, K.A. Fahrner, L. Turner and H.C. Berg (2010) Asymmetry in the clockwise and counter-clockwise rotation of the bacterial flagellar motor. PNAS 107:12846-12949.
  42. J. Yuan and H.C. Berg (2010) Temperature and solvent-isotope effects on the flagellar rotary motor near zero load. Biophys. J. 98:2121-2126.
  43. J. Yuan and H.C. Berg (2010) Following the behavior of the flagellar rotary motor near zero load. Exp. Mech. 50:1263-1265.
  44. J. Yuan, K.A. Fahrner and H.C. Berg (2009) Switching of the bacterial flagellar motor near zero load. J. Mol. Biol. 390:394-400.
  45. J. Yuan and H.C. Berg (2008) Resurrection of the flagellar rotary motor near zero load. PNAS 105:1182-1185.

Nuclear & Particle Physics(@Caltech):

  1. B. Plaster et al. (2012) Measurement of the neutron β-asymmetry parameter A0 with ultracold neutrons. Phys. Rev. C 86:055501.
  2. R.W Pattie, et al. (2009) First Measurement of the Neutron β Asymmetry with Ultracold Neutrons. Phys. Rev. Lett. 102:012301.
  3. B. Plaster, et al. (2008) A solenoidal electron spectrometer for a precision measurement of the neutron β-asymmetry with ultracold neutrons. Nucl. Intrum. Meth. A595:587-598.
  4. T.M Ito, et al. (2007) A multiwire proportional chamber for precision studies of neutron β decay angular correlations. Nucl. Intrum. Meth. A571:676-686.
  5. J.W. Martin, J. Yuan, et al. (2006) New measurements and quantitative analysis of electron backscattering in the energy range of neutron β-decay. Phys. Rev. C 73:015501.
  6. A. Saunders, et al. (2004) Demonstration of a Solid Deuterium Source of Ultra-Cold Neutrons. Phys. Lett. B 593:55-60.
  7. T.M Ito, et al. (2004) Parity-Violating Electron Deuteron Scattering and the Proton’s Neutron Weak Axial Vector From Factor. Phys. Rev. Lett. 92:102003.
  8. J.W. Martin, J. Yuan, et al. (2003) Measurement of Electron Backscattering in the Energy Range of Neutron Beta Decay. Phys. Rev. C 68:055503.
  9. C.L Morris, et al. (2002) Measurements of Ultracold Neutron Lifetimes in Solid Deuterium. Phys. Rev. Lett. 89:272501.
  10. J. Yuan, et al. (2001) A Double-Focusing Helmholtz-Coil Spectrometer. Nucl. Intrum. Meth. A465:404.
  11. R.E. Hill, et al. (2000) Performance of the prototype LANL solid deuterium ultra-cold neutron source. Nucl. Intrum. Meth. A440:674-681.