Publications by Type: Journal Article

2018
F. Meng, Jing, Z., Ferreira, R., Ren, P., and Zhang, F., “Investigating the Association Mechanism between Rafoxanide and Povidone,” Langmuir, 2018.
R. Qi, Jing, Z., Liu, C., Piquemal, J. - P., Dalby, K. N., and Ren, P., “Elucidating the Phosphate Binding Mode of PBP: The Critical Effect of Buffer Solution,” The Journal of Physical Chemistry B, 2018.
J. A. Rackers, Wang, Z., Lu, C., Laury, M. L., Lagardere, L., Schnieders, M. J., Piquemal, J. - P., Ren, P., and Ponder, J. W., “Tinker 8: software tools for molecular design,” Journal of chemical theory and computation, vol. 14, pp. 5273–5289, 2018.
Z. Jing, Liu, C., Qi, R., and Ren, P., “Many-body effect determines the selectivity for Ca2+ and Mg2+ in proteins,” Proceedings of the National Academy of Sciences, vol. 115, pp. E7495–E7501, 2018.
J. A. Rackers, Liu, C., Ren, P., and Ponder, J. W., “A physically grounded damped dispersion model with particle mesh Ewald summation,” The Journal of chemical physics, vol. 149, pp. 084115, 2018.
L. Lagardère, Jolly, L. - H., Lipparini, F., Aviat, F., Stamm, B., Jing, Z. F., Harger, M., Torabifard, H., Cisneros, A. G., Schnieders, M. J., and others,Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields,” Chemical science, vol. 9, pp. 956–972, 2018.
C. Zhang, Lu, C., Jing, Z., Wu, C., Piquemal, J. - P., Ponder, J. W., and Ren, P., “AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids,” Journal of chemical theory and computation, vol. 14, pp. 2084–2108, 2018.
J. Zhao, Wang, G., del Mundo, I. M., McKinney, J. A., Lu, X., Bacolla, A., Boulware, S. B., Zhang, C., Zhang, H., Ren, P., and others,Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes,” Cell reports, vol. 22, pp. 1200–1210, 2018.
2017
Z. Jing, Liu, C., Cheng, S., Qi, R., Walker, B., Piquemal, J. - P., and Ren, P., “Polarizable force fields for biomolecular simulations: Recent advances and applications,” annual review of biophysics, 2017.
S. Deng, Wang, Q., and Ren, P., “Estimating and modeling charge transfer from the SAPT induction energy,” Journal of computational chemistry, vol. 38, pp. 2222–2231, 2017.
X. Han, Jing, Z., Wu, W., Zou, B., Peng, Z., Ren, P., Wikramanayake, A., Lu, Z., and Leblanc, R. M., “Biocompatible and blood–brain barrier permeable carbon dots for inhibition of A$\beta$ fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862–12866, 2017.
M. Harger, Li, D., Wang, Z., Dalby, K., Lagardère, L., Piquemal, J. - P., Ponder, J., and Ren, P., “Tinker-OpenMM: absolute and relative alchemical free energies using AMOEBA on GPUs,” Journal of computational chemistry, vol. 38, pp. 2047–2055, 2017.
B. S. Wendel, He, C., Qu, M., Wu, D., Hernandez, S. M., Ma, K. - Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., and others,Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature communications, vol. 8, pp. 531, 2017.
C. Zhang, Bell, D., Harger, M., and Ren, P., “Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases,” Journal of chemical theory and computation, vol. 13, pp. 666–678, 2017.
R. Edupuganti, Taliaferro, J. M., Wang, Q., Xie, X., Cho, E. J., Vidhu, F., Ren, P., Anslyn, E. V., Bartholomeusz, C., and Dalby, K. N., “Discovery of a potent inhibitor of MELK that inhibits expression of the anti-apoptotic protein Mcl-1 and TNBC cell growth,” Bioorganic & medicinal chemistry, vol. 25, pp. 2609–2616, 2017.
D. R. Bell, Cheng, S. Y., Salazar, H., and Ren, P., “Capturing RNA folding free energy with coarse-grained molecular dynamics simulations,” Scientific Reports, vol. 7, pp. 45812, 2017.
J. M. Obliosca, Cheng, S. Y., Chen, Y. - A., Llanos, M. F., Liu, Y. - L., Imphean, D. M., Bell, D. R., Petty, J. T., Ren, P., and Yeh, H. - C., “LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature,” Journal of the American Chemical Society, vol. 139, pp. 7110–7116, 2017.
C. Liu, Qi, R., Wang, Q., Piquemal, J. - P., and Ren, P., “Capturing many-body interactions with classical dipole induction models,” Journal of chemical theory and computation, vol. 13, pp. 2751–2761, 2017.
C. Wang, Ren, P., and Luo, R., “Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling,” The Journal of Physical Chemistry B, vol. 121, pp. 11169–11179, 2017.
Z. Jing, Qi, R., Liu, C., and Ren, P., “Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field,” The Journal of Chemical Physics, vol. 147, pp. 161733, 2017.

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