Yu-Shan Lin

Yu-Shan Lin

Department of Chemistry
Pearson Chemistry Laboratory
62 Talbot Avenue
Tufts University 
Medford, MA 02155 

Office: 103X

Tel: 617-627-3689   Fax: 617-627-3443

E-mail: Yu-Shan.Lin@tufts.edu  

Research Homepage

Current Appointment


Associate Professor of Chemistry, Department of Chemistry




Postdoctoral Fellow, 2009-12, Stanford University, Stanford, CA (Vijay Pande)
Ph.D., 2009, University of Wisconsin – Madison, Madison WI (James Skinner)
M.S., 2007, University of Wisconsin – Madison, Madison WI (James Skinner)
B.S., 2004, National Taiwan University (Pi-Tai Chou)


Research Interests

Theoretical and Biophysical Chemistry. The Lin group aims to elucidate the structures and functions of biomolecules by integrating the power of advanced computations with the elegance of chemical theory. Our focus is to develop and apply computational methodology to significant biological problems that are difficult to address experimentally. To ensure that our simulation results are trustworthy, we leverage the tools of theoretical and experimental spectroscopy to integrate selected experimental results with our advanced simulations. This integration enables us to experimentally optimize our new theoretical methods. Optimized simulations are then applied to make predictions and understand biological problems in ways that are difficult or impossible to achieve experimentally. Two major research projects in the Lin lab are (1) to elucidate the structural and functional roles of post-translational modifications on protein folding and (2) to understand the underlying molecular mechanisms of how proteins manipulate their aqueous environment. In both projects, we employ state-of-the-art simulation techniques — parallel computing and graphics processing units simulations – combined with advanced chemical theory (e.g. Markov state models, theoretical vibrational spectroscopy, and normal mode analysis) to provide direct links to experimental results — for example, from infrared and terahertz spectroscopy.


Selected Recent Publications


“Computational methods to design cyclic peptides,” S. M. McHugh,† J. R. Rogers,† S. A. Solomon,† H. Yu,† Y.-S. Lin Curr. Opin. Chem. Biol. 2016, 34, 95.
†Equal contributions.


“D-amino acid scan of two small proteins,” M. D. Simon, Y. Maki, A. A. Vinogradov, C. Zhang, H. Yu, Y.-S. Lin, Y. Kajihara, B. L. Pentelute, J. Am. Chem. Soc. 2016, 138, 12099.


“Mapping the effect of Gly mutations in collagen on α2β1 integrin binding,” S. Yigit,† H. Yu,† B. An, S. Hamaia, R. W. Farndale, D. L. Kaplan, Y.-S. Lin,* B. Brodsky,*  J. Biol. Chem. 2016, 291, 19196.
†Equal contributions. *Co-corresponding authors.


“Insights into how cyclic peptides switch conformations,” S. M. McHugh,† J. R. Rogers,† H. Yu, Y.-S. Lin, J. Chem. Theory Comput. 2016, 12, 2480.
†Equal contributions.


“Collagen interactions: Drug design and delivery,” B. An, Y.-S. Lin, B. Brodsky, Adv. Drug Deliv. Rev. 97, 69 (2016).


“Toward structure prediction of cyclic peptides,” H. Yu and Y.-S. Lin, Phys. Chem. Chem. Phys. 2015, 17, 4210. We thank Prof. Wu for kindly providing us with the RSFF1 force field parameters!


“A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake,” J. S. Quartararo, M. R. Eshelman, L. Peraro, H. Yu, J. D. Baleja, Y.-S. Lin, J. A. Kritzer, Bioorg. Med. Chem. 2014, 22, 6387.


“Convergent diversity-oriented side-chain macrocyclization scan for unprotected polypeptides,” Y. Zou, A. M. Spokoyny, C. Zhang, M. D. Simon, H. Yu, Y.-S. Lin, B. L. Pentelute, Org. Biomol. Chem. 2014, 12, 566. Cover article.


“A perfluoroaryl-cysteine SNAr chemistry approach to unprotected peptide stapling,” A. M. Spokoyny, Y. Zou, J. J. Ling, H. Yu, Y.-S. Lin, B. L. Pentelute, J. Am. Chem. Soc. 2013, 135, 5946. Featured on the Science & Technology Concentrates in the C&EN.

“Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements”, K. A. Beauchamp, Y.-S. Lin, R. Das, V. S. Pande, J. Chem. Theory Comput. 2012, 8, 1409.


“Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer”, Y.-S. Lin, G. R. Bowman, K. A. Beauchamp, V. S. Pande, Biophys. J. 2012, 102, 315.


“Robust three-body water simulation model”, C. J. Tainter, P. A. Pieniazek, Y.-S. Lin, J. L. Skinner, J. Chem. Phys. 2011, 134, 184501.


“On the calculation of rotational anisotropy decay, as measured by ultrafast polarization-resolved pump-probe experiments”, Y.-S. Lin, P. A. Pieniazek, M. Yang, J. L. Skinner, J. Chem. Phys. 2010, 132, 174505.


“2D IR lineshapes probe ovispirin peptide conformation and depth in lipid bilayers”, A. M. Woys, Y.-S. Lin, A. S. Reddy, J. J. de Pablo, J. L. Skinner, M. T. Zanni, J. Am. Chem. Soc. 2010, 132, 2832.


“Solution structures of rat amylin peptide: Simulation, theory, and experiment”, A. S. Reddy, L. Wang, Y.-S. Lin, Y. L. Ling, M. T. Zanni, J. L. Skinner, J. J. de Pablo, Biophys. J. 2010, 98, 443.


“Vibrational spectroscopy and dynamics of water confined inside reverse micelles”, P. A. Pieniazek, Y.-S. Lin, J. L. Skinner, J. Phys. Chem. B 2009, 113, 15017.


“Water structure, dynamics, and vibrational spectroscopy in sodium bromide solutions”, Y.-S. Lin, B. M. Auer, J. L. Skinner, J. Chem. Phys. 2009, 131, 144511.


“Gating mechanism of the influenza A M2 channel revealed by 1D and 2D IR spectroscopies”, J. Manor, P. Mukherjee, Y.-S. Lin, H. Leonov, J. L. Skinner, M. T. Zanni, I. T. Arkin, Structure 2009, 17, 247.


“Empirical amide I vibrational frequency map: Applications to isotope-edited membrane peptide bundles”, Y.-S. Lin, J. M. Shorb, P. Mukherjee, M. T. Zanni, J. L. Skinner, J. Phys. Chem. B 2009, 113, 592.


“Vibrational line shapes and spectral diffusion in liquid water”, J. L. Skinner, B. M. Auer, Y.-S. Lin, Adv. Chem. Phys. 2009, 142, 59.


“Water inertial reorientation: Hydrogen bond strength and the angular potential”, D. E. Moilanen, E. E. Fenn, Y.-S. Lin, J. L. Skinner, B. Bagchi, M. D. Fayer, Proc. Nat. Acad. Sci. U.S.A 2008, 105, 5295.


“Vibrational energy relaxation of the bend fundamental of dilute water in liquid chloroform and d-chloroform”, Y.-S. Lin, S. G. Ramesh, J. M. Shorb, E. L. Sibert III, J. L. Skinner, J. Phys. Chem. B 2008, 112, 390.


Additional publications can be found HERE