Theoretical and Computational Biophysics Group
Beckman Institute, Room 3115
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801

Home Department: Physics


Phone: 217-244-5883
Fax: 217-244-6078

My CV (cv.pdf; 58k )

      Me with a flower


Research Projects:

BAR Domain Proteins Sculpting Cellular Membranes.

Living cells are characterized by intricately curved internal membranes forming organelles. The membrane curvature is sculpted by proteins that act through concerted action. A key sculpting mechanism is furnished by proteins, so-called BAR domains, that form lattice-like scaffolds adhering to membrane surfaces. We have investigated the membrane sculpting by BAR domains at different levels of resolutions (from an atomic to a continuum level). These studies have resulted in a coarse-graining (CG) model, which allowed us to reach time scales of 100 microseconds-1 millisecond. Using this CG model, we have sampled various lattices of BAR domains and observed complete membrane tubulation.

Coarse-Graining Methods for Biomolecular simulations. One of the main unresolved problems in biological science is the time-scale and length-scale gap between computational and experimental methods of studying biological systems. This project is aimed to bridge computational studies with experimental techniques by developing coarse-graining (CG) method, which represents a system by a reduced (in comparison with an all-atom description) number of degrees of freedom. We have developed such a CG method that leads to an increase of orders of magnitude in the simulated time and length scales. This method has been applied successfully to a varieties of systems including BAR domain-membrane system.

Conformational Changes in Lactose Permease.

Lactose permease (LacY) is a membrane protein that translocates the sugar, lactose, across cell's membrane utilizing an electrical potential maintained in the form of a trans-membrane proton gradient. We have investigated one step of the proton-sugar translocation, namely, how binding and unbinding of the proton activates a spring-like bond, a so-called salt bridge, that closes and opens the inner channel exit of the protein. We have also probed the molecular and energetic details of lactose translocation across LacY. During translocation, lactose was found to undergo a rotation and to induce a widening of the narrowest part of the protein's channel.

Modeling Carbon Nanotube-Biomolecular Assemblies. Carbon nanotubes (CNTs) are hexagonal lattices of carbon atoms rolled up into seamless cylinders. Due to their unique electronic, thermal, chemical, and mechanical properties, they are of great interest for many nanotechnological applications such as biosensors to detect various biomolecules. We have been developing computational methodologies for simulating CNT in complex with biomolecules.


  1. Publications Database Membrane-bending mechanism of amphiphysin N-BAR domains. Anton Arkhipov, Ying Yin, and Klaus Schulten. Biophysical Journal, 97:2727-2735, 2009.
  2. Publications Database
  3. Publications Database Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains. Ying Yin, Anton Arkhipov, and Klaus Schulten. Structure, 17:882-892, 2009.
  4. Publications Database Four-scale description of membrane sculpting by BAR domains. Anton Arkhipov, Ying Yin, and Klaus Schulten. Biophysical Journal, 95:2806-2821, 2008.
  5. Publications Database Using VMD - an introductory tutorial. Jen Hsin, Anton Arkhipov, Ying Yin, John E. Stone, and Klaus Schulten. Current Protocols - Bioinformatics, 5:Unit 5.7, 2008. (48 pages).
  6. Publications Database Application of residue-based and shape-based coarse graining to biomolecular simulations. Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Yin, Zhongzhou Chen, and Klaus Schulten. In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase and Biomolecular Systems, chapter 20, pp. 299-315. Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
  7. Publications Database Computer modeling in biotechnology, a partner in development. Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and Klaus Schulten. In Protocols in Nanostructure Design, Methods in Molecular Biology, pp. 181-234. Humana Press, 2008.
  8. Publications Database Sugar transport across lactose permease probed by steered molecular dynamics. Morten Ø. Jensen, Ying Yin, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 93:92-102, 2007.
  9. Publications Database Sugar binding and protein conformational changes in lactose permease. Ying Yin, Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 91:3972-3985, 2006.

  10. Not from the Theoretical and Computational Biophysics Group: Measurement of Upsilon Production for p+p and p+d Interactions at 800 GeV/c. L. Y. Zhu, P. E. Reimer, B. A. Mueller, T. C. Awes, M. L. Brooks, C. N. Brown, J. D. Bush, T. A. Carey, T. H. Chang, W. E. Cooper, C. A. Gagliardi, G. T. Garvey, D. F. Geesaman, E. A. Hawker, X. C. He, D. E. Howell, L. D. Isenhower, D. M. Kaplan, S. B. Kaufman, S. A. Klinksiek, D. D. Koetke, D. M. Lee, W. M. Lee, M. J. Leitch, N. Makins, P. L. McGaughey, J. M. Moss, P. M. Nord, V. Papavassiliou, B. K. Park, G. Petitt, J. C. Peng, M. E. Sadler, W. E. Sondheim, P. W. Stankus, T. N. Thompson, R. S. Towell, R. E. Tribble, M. A. Vasiliev, J. C. Webb, J. L. Willis, P. Winter, D. K. Wise, Y. Yin and G. R. Yong. Physical Review Letters, 100:062301, 2008.

Conferences and Presentations

  • Simulations of Membrane Sculpting by N-BAR domains,
    Biophysical Society Annual Meeting, 2009, Boston
  • Multiscale Simulations of Membrane Tubulation by BAR domains,
    Biophysical Society Annual Meeting, 2008, Long Beach
  • Sugar transport across lactose permease probed by molecular dynamics simulations,
    Biophysical Society Annual Meeting, 2007, Baltimore
  • The mechanism of sugar transport across E. coli lactose permease,
    Biophysical Society Annual Meeting, 2006, Salt Lake City
  • Coupling of Proton Translocation and Protein Conformational Changes in Lactose Permease,
    Biophysical Society Annual Meeting, 2006, Salt Lake City