Publications

Lei, J., Zhou, Y., Xie, D., and Zhang, Y. Mechanistic insights into a classic wonder drug-aspirin. J. Am. Chem. Soc. 137, 70-73 (2015)

Ozer, G., Collepardo-Guevara, R., and Schlick, T. Forced unraveling of chromatin fibers with nonuniform linker DNA lengths. J. Phys. Condens. Matter. 27, 064113 (2015)

Li, M., Zhang, J. Z. H., and Xia, F. Heterogeneous elastic network model improves description of slow motions of proteins in solution. Chem. Phys. Lett. 618, 102-107 (2015)

Gao, Y., Li, Y., Mou, L., Lin, B., Zhang, J. Z. H., and Mei, Y. Correct folding of an alpha-helix and a beta-hairpin using a polarized 2D torsional potential. Sci. Rep. 5, 10359 (2015)

Swails, J., Zhu, T., He, X., and Case, D. A. AFNMR: Automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR. 63, 125-139 (2015)

Wang, X., Ji, C., and Zhang, J. Z. H. Glycosylation modulates human CD2-CD58 adhesion via conformational adjustment. J. Phys. Chem. B. 119, 6493–6501 (2015)

Ozer, G., Luque, A., and Schlick, T. The chromatin fiber: Multiscale problems and approaches. Curr. Opin. Struct. Biol. 31, 124-139 (2015)

Freudenthal, B. D., Beard, W. A., Perera, L., Shock, D. D., Kim, T., Schlick, T., and Wilson, S. H. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature. 517, 635–639 (2015)

Sodt, A. J., Mei, Y., König, G., Tao, P., Steele, R. P., Brooks, B. R., and Shao, Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. J. Phys. Chem. A. 119, 1511–1523 (2015)

Sirin, G. S. and Zhang, Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J. Phys. Chem. A. 118, 9132-9139 (2014)

He, X., Zhu, T., Wang, X., Liu, J., and Zhang, J. Z. H. Fragment quantum mechanical calculation of proteins and its applications. Acc. Chem. Res. 47, 2748-2757 (2014)

Mou, L., Jia, X., Gao, Y., Li, Y., Zhang, J. Z. H., and Mei, Y. Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions. J. Theor. Comput. Chem. 13, 1450026 (2014)

Wang, X., Li, Y., He, X., Chen, S., and Zhang, J. Z. H. Effect of strong electric field on the conformational integrity of insulin. J. Phys. Chem. A. 117, 6015−6023 (2014)

Duan, L. L., Mei, Y., Zhang, Q. G., Tang, B., and Zhang, J. Z. H. Protein's native structure is dynamically stabilized by electronic polarization. J. Theor. Comput. Chem. 13, 1440005 (2014)

Ji, C. G., Mei, Y., & John Z. H. Zhang (2014, August). Protein structure and dynamics-polarization in MD simulation. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY (Vol. 248). 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC.

Lin, B., Gao, Y., Li, Y., Zhang, J. Z. H., and Mei, Y. Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin. J. Mol. Model. 20, 2189 (2014)

Duan, L. L., Zhu, T., Zhang, Q. G., Tang, B., Zhang, J. Z. H. Electronic polarization stabilizes tertiary structure prediction of HP-36. J. Mol. Model. 20, 2195 (2014)

Jia, X., Zeng, J., Zhang, J. Z. H., and Mei, Y. Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. J. Comput. Chem. 35, 737–747 (2014)

Marsalek, O., Chen, P., Dupuis, R., Benoit, M., Méheut, M., Bačić, Z., and Tuckerman​, M. E. Efficient calculation of free energy differences associated with isotopic substitution using path-integral molecular dynamics. J. Chem. Theory Comput. 10, 1440–1453​ (2014)

Yu, T. Q., Chen, P. Y., Chen, M., Samanta, A., Vanden-Eijnden, E., and Tuckerman, M. Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions. J. Chem. Phys. 140, 214109 (2014)

Li, M., Xu, W., Zhang, J. Z. H., and Xia, F. Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J Mol. Model. 20, 2530 (2014)

Shimshovitz, A., Bačić, Z., and Tannor, D. J. The von Neumann basis in non-Cartesian coordinates: Application to floppy triatomic molecules. J. Chem. Phys. 141, 2341061 (2014)

Samanta, A., Tuckerman, M. E., Yu, T. Q. Weinan, E. Microscopic mechanisms of equilibrium melting of a solid. Science. 346, 729-732 (2014)

Samanta, A., Chen, M., Yu, T. Q., Tuckerman, M. E., and Weinan, E. Sampling saddle points on a free energy surface. J. Chem. Phys. 140, 164109 (2014)

Duan, L. L., Gao, Y., Ji, C. G., Mei, Y., Zhang, Q. G., Tang, B., and Zhang, J. Z. H. Energetics of protein backbone hydrogen bonds and their local electrostatic environment. Sci. China Chem. 57, 1708 (2014)

Li, Y., Zhang, J. Z. H., and Mei, Y. Molecular dynamics simulation of protein crystal with polarized protein-specific force field. J. Phys. Chem. B. 118, 12326−12335 (2014)

Colognesi, D., Powers, A., Celli, M., Xu, M., Bačić, Z., and Ulivi, L. The HD molecule in small and medium cages of clathrate hydrates: Quantum dynamics studied by neutron scattering measurements and computation. J. Chem. Phys. 141, 134501 (2014)

Xu, M., Jiménez-Ruiz, M., Johnson, M. R., Rols, S., Ye, S., Carravetta, M., Denning, M. S., Lei, X., Bačić, Z., and Horsewill, A. J. Confirming a predicted selection rule in inelastic neutron scattering spectroscopy: The quantum translator-rotator H₂ entrapped inside C₆₀. Phys. Rev. Lett. 113, 123001 (2014)

Zhou, N., Lu, Z., Wu, Q., and Zhang, Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. J. Chem. Phys. 140, 214117 (2014)

Xiao, X., Kallenbach, N., and Zhang, Y. Peptide conformation analysis using an integrated Bayesian approach. J. Chem. Theory Comput. 10, 4152-4159 (2014)

Liu, J., He, X., and Zhang, J. Z. H. Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine. J. Mol. Model. 20, 2451 (2014)

Zhu, T., Zhang, J. Z. H., and He, X. Correction of erroneously packed protein’s side chains in the NMR structure based on ab initio chemical shift calculations. Phys. Chem. Chem. Phys. 16, 18163-18169 (2014)

Ji, C. and Mei, Y. Some practical approaches to treating electrostatic polarization of proteins. Acc. Chem. Res. 47, 2795-2803 (2014)

Jia, X., Wang, X., Liu, J., Zhang, J. Z. H., Mei, Y., and He, X. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins. J. Chem. Phys. 139, 214104 (2013)

Xiao, X., Zhu, T., Ji, C. G., and Zhang, J. Z. H. Development of an effective polarizable bond method for biomolecular simulation. J. Phys. Chem. B. 117, 14885-93 (2013)

Song, J., Ji, C., and Zhang, J. Z. H. Unveiling the gating mechanism of ECF transporter RibU. Sci. rep. 3, 3566 (2013)