Published/in press/submitted 2017-2019

Our Citation Profile at Google Scholar


260. Free Energy Profile Is Less Sensitive to QM Size in QM/MM Simulations than Electronic Structural Properties, D. Demapan, Q. Cui∗, Submitted (2019)

259. A chemical perspective on environmental impacts of nanomaterials, C. J. Murphy*, J. A. Pedersen, R. J. Hamers, M. P. Schwartz, J. C. White, W. Elmer, D. H. Fairbrother, R. Hernandez, Z. V. Feng, G. Orr, Q. Cui, S. E. Mason, J. W. Bennett, E. E. Carlson, C. L. Haynes, R. D. Klaper, Z. Rosenzweig, J. Pablo Giraldo, Nat. Rev. Mater., Submitted (2019)

258. Artificial Intracellular Peptide Filaments, Z. Q. Feng, H. M. Wang, F. B. Wang, C. Berciu, Y. H. Oh, Q. Cui, E. H. Egelman, B. Xu*, Submitted (2019)

257. Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation, M. Leander, Y. C. Yuan, A. Meger, Q. Cui and S. Raman∗, Submitted (2019)

256. Molecular Simulation of Mechanical Properties and Membrane Activities of the ESCRT-III complexes, T. Mandel, W. Lough, S. E. Spagnolie, A. Audhya and Q. Cui∗, Biophys. J., Submitted (2019)

255. Photo-Disassembly of Membrane Microdomains Revives Conventional Antibiotics against MRSA, J. Hui, P-T, Dong, L. Liang, T. Mandal, J. Li, C. Ulloa, Y. W. Zhan, S. Jusuf, C. Zong, M. Seleem, G. Liu, Q. Cui, J-X, Cheng*, Submitted (2019)

254. Direct readout of heterochromatic H3K9me3 and H4K20me3 regulates DNMT1-mediated maintenance DNA methylation, W. D. Ren, H. T. Fan, S. A. Grimm, H. Uryu, J. J. Kim, L. H. Li, C. J. Petell, X-F, Tan, Z-M. Zhang, J. P. Coan, J. K. Yin, D. L. Chen, L. F. Gao, L. Cai, B. Detrick, B. Cetin, Y. S. Wang, Q. Cui, B. Strahl, O. Gozani, K. M. Miller, S. O’Leary, P. A. Wade, G. G. Wang, J. K. Song*, Submitted (2019)

253. Electrostatics, Hydrogen Bonding, and Molecular Structure at Polycation and Peptide:Lipid Membrane Interfaces, N. Dalchand, Q. Cui* and F. M. Geiger*, ACS Applied Mater. & Interfaces, In press (2019)

252. Proper Thermal Equilibration of Simulations with Drude Polarizable Models : Temperature Grouped Dual-Nos ́e-Hoover Thermostat, C. Y. Son, J. G. McDaniel, Q. Cui, A. Yethiraj∗, J. Phys. Chem. Lett., 10, 7523-7530 (2019)

251. Molecular Dynamics Simulation of Interaction between Functionalized Nanoparticles with Lipid Membranes: Analysis of Coarse-grained Models, M. Das, U. Dahal, O. Mesele, D. Y. Liang and Q. Cui*, J. Phys. Chem. B 123, 10547-10561 (2019)

250. Extensive Free Energy Simulations Identify Water as the Base in Nucleotide Addition by DNA Polymerase, D. Roston, D. Demapan, Q. Cui*, Proc. Natl. Acad. Sci. USA, 116, 25048-25056 (2019)

249. Analysis of Density Functional Tight Binding (DFTB) with Natural Bonding Orbitals (NBOs), X. Lu, J. Duchimaza-Heredia, and Q. Cui*, J. Phys. Chem. A 123, 7439-7453 (2019)

248. NMR structural analysis of isolated Shake voltage-sensing domain in LPPD micelles, H. B. Chen, J. K. Pan, Q. Cui, B. Chanda, K. Henzler-Wildman*, Biophys. J., 117, 388-398 (2019)

247. Quantitative analysis and correction of QM/MM boundary artifacts in adaptive QM/MM methods, H. C. Watanabe* and Q. Cui, J. Chem. Theory Comput., 15, 3917-3928 (2019) Cover

246. A Systematic Determination of Hubbard U using the GBRV Ultrasoft Pseudopotential Set, J. W. Bennett, B. G. Hudson, I. K. Metz, D. Y. Liang, S. Spurgeon, Q. Cui, S. E. Mason*, Comput. Mater. Sci., 170, 109137 (2019)

245. Gating and Inactivation of Mechanosensitive Channels of Small Conductance: A Continuum Mechanics Study, L. L. Zhu, Q. Cui, H. Xiao, X. B. Liao and X. Chen*, J. Mech. Behavior Biomed. Mater. 90, 502-514 (2019)

244. Exploring the Applicability of Density Functional Tight Binding to Transition Metal Ions: Parametrization for Nickel with the Spin-polarized DFTB3 model, M. Vujovic, M. Huynh, S. Steiner, P. Garcia-Fernandez, M. Elstner*, Q. Cui*, M. Gruden*, J. Comp. Chem., Special memorial issue for Keiji Morokuma , 40, 400-413 (2019)

243. N6-methyldeoxyadenosine directs nucleosome positioning in eukaryotic DNA, G. Z. Luo, Z. Y. Hao, M. R. Shen, D. Sparvoli, Y. Q. Zheng, Z. J. Zhang, X. C. Weng, K. Chen, Q. Cui, A. Turkewitz and C. He*, Genome Biol. 19, 200 (2018)

242. Specificity Landscapes unmask differential sequence preferences of homologous transcription factors, D. Bhimsaria, J. A. Rodriguez-Martinez, J. K. Pan, D. Roston, E. N. Korkmaz, Q. Cui, P. Ramanathan, and A. Z. Ansari*, Proc. Natl. Acad. Sci. USA , 115, E10586-10595 (2018)

241. Structural and Mechanistic Basis for Preferential Deadenylation of U6 snRNA by Usb1, Y. Nomura, D. Roston, E. J. Montemayor, Q. Cui*, and S. E. Butcher*, Nuc. Acids Res. 46, 11488-11501 (2018)

240. Lipid Corona Formation from Nanoparticle Interactions with Bilayers and Membrane-Specific Biological Outcomes, L. L. Olenick, J. M. Troiano, A. Vartanian, E. S. Melby, A. Mensch, L. L. Zhang, J. Hong, O. Mesele, T. Qiu, J. Bozich, S. Lohse, X. Zhang, T. R. Kuech, A. Millevolte, I. Gunsolus, A. C. McGeachy, M. Dogang\”un, T. Z. Li, D. H. Hu, S. R. Walter, A. Mohaimani, A. Schmoldt, M. D. Torelli, K. R. Hurley, J. Dalluge, G. Chong, Z. V. Feng, C. L. Haynes, R. J. Hamers, J. A. Pedersen, Q. Cui, R. Hernandez, R. Klaper, G. Orr, C. J. Murphy, and F. M. Geiger*, Chem , 4, 2709-2723 (2018)

239. Conformational and Dynamic Properties of Poly(ethylene oxide) in BMIM+$BF4 : A Microsecond Computer Simulation Study Using First Principles-Based Force Fields, C. Y. Son, J. G. McDaniel, Q. Cui, and A. Yethiraj*, Macromolecules, 51, 5336-5345 (2018)

238. Network Analysis of a Proposed Exit Pathway for Protons to the P-side of Cytochrome c Oxidase, X. H. Cai, K. Haider, J. X. Lu, S. Radik, C. Y. Son, Q. Cui and M. Gunner*, BBA Bioener. 1859, 997-1005 (2018)

237. Analysis of Phosphoryl Transfer Enzymes with QM/MM Free Energy Simulations, D. Roston, X. Lu, D. Fang, D. Demapan and Q. Cui*, Methods in Enzymology: Phosphatases , 607, 53-90 (2018) Invited contribution

236. Molecular Dynamics-Decorated Finite Element Method (MDeFEM): Application to the Gating Mechanism of Mechanosensitive Channels, L. L. Zhu, Q. Cui, Y. L. Liu, Y. Yan, H. Xiao, and X. Chen*, Handbook of Nonlocal Continuum Mechanics for Materials and Structure, 1-52 (2018)

235. Comment: Membrane Mediated Interaction Drives Mitochondria ATPase Assembly and Cristae Formation, Q. Cui*, J. Gen. Physiol. , 150, 777-780 (2018)

234. Hydrogen Bond Networks Near Supported Lipid Bilayers from Vibrational Sum Frequency Generation Experiments and Atomistic Simulations, M. Dogangun, P. E. Ohno, D. Y. Liang, A. C. McGeachy, N. Dalchand, T. Li, Q. Cui* and F. M. Geiger*, J. Phys. Chem. B 122, 4870-4879 (2018)

233. Counting Charges on Membrane-bound Peptides, A. C. McGeachy, E. Caudill, D. Y. Liang, Q. Cui, J. A. Pedersen and F. M. Geiger*, Chem. Sci. 9, 4285-4298 (2018)

232. Specific Substates of Ras to Interact with GAPs and Effectors: Revealed by Theoretical Simulations and FTIR Experiments, Y. Li, Y. W. Zhang, F. Groberuschkamp, S. Stephan, Q. Cui, C. Kottig, F. Xia* and K. Gerwert*, J. Phys. Chem. Lett. 9, 1312-1317 (2018)

231. Essence of Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations of amino acid side chain analogs, Z. J. Xu*, Q. C. Wei, W. L. Zhao, Q. Cui and N. Sahai*, J. Phys. Chem. C , 122, 4372-4380 (2018)

230. Inspiring Molecular Quantum Chemist, Obituary for Professor Keiji Morokuma, Q. Cui*, S. Irle and J. Musaev, Angew Chim. Intl. Ed. 57, 2288-2289 (2018)

229. Multiple Pathways and Timescales for Conformational Transitions in apo-Adenylate Kinase, Y. Q. Zheng and Q. Cui*, J. Chem. Theory Comput. 14, 1716-1726 (2018)

228. Dynamics and number of trans-SNARE complexes determine nascent fusion pore properties, H. Bao, D. Das, N. A. Courtney, Y. H. Jiang, J. Briguglio, X. C. Lou, D. Roston, Q. Cui, B. Chanda and E. R. Chapman*, Nature , 554, 260-263 (2018)

227. Iron starvation inhibits late stages of bacterial cytokinesis, T. M. A. Santos, M. G. Lammers, M. Q. Zhou, I. L. Sparks, M. Rajendran, D. Fang, C. L. Y. De Jesus, G. F. R. Carneiro, Q. Cui and D. B. Weibel*, ACS Chem. Bio , 13, 235-246 (2018)

226. Structural and functional analysis of the FtsLB tetrameric complex of the bacterial divisome, D. A. Mahbuba, S. G. F. Condon, C. R. Armstrong, G. Diaz-Vazquez, S. J. Craven, L. M. LaPointe, A. S. Khadria, R. Chadda, J. A. Crooks, N. Rangarajan, D. B. Weibel, A. A. Hoskins, J. L. Robertson, Q. Cui, A. Senes*, J. Biol. Chem. , 293, 1623-1641 (2018)

225. Analysis of Conformational Properties of Amine Ligands at the Gold/Water Interface with QM, MM and QM/MM simulations, D. Y. Liang, J. W. Hong, F. Dong, J. W. Bennett, S. E. Mason, R. J. Hamers and Q. Cui*, Phys. Chem. Chem. Phys. , 20, 3349-3362 (2018)

224. Cavity Hydration Dynamics in Cytochrome c Oxidase and Functional Implications, C. Y. Son, A. Yethiraj and Q. Cui*, Proc. Natl. Acad. Sci. USA 114, E8830-E8836 (2017)

223. Benchmarking Density Functional Tight Binding Models for Barrier Heights and Reaction Energetics of Organic Molecules, M. Gruden*, L. Andjelkovic, J. A. Kuriappan, S. Stepanovic, M. Zlatar, Q. Cui*, M. Elstner*, J. Comput. Chem., 38, 2171-2185 (2017)

222. Intermolecular Interactions in the Condensed Phase: Evaluation of Semi-empirical Quantum Mechanical Methods, A. S. Christensen, J. C. Kromann, J. H. Jensen and Q. Cui, J. Chem. Phys., Special Issue on “ From Quantum Mechanics to Force Fields“, 147, 161704 (2017)

221. Quantifying the Electrostatics of Polycation-Lipid Bilayer Interactions, J. M. Troiano, A. C. McGeachy, L. L. Olenick, D. Fang, D. Y. Liang, J. W. Hong, T. R. Kuech, J. A. Pedersen, Q. Cui and F. M. Geiger*, J. Am. Chem. Soc., 139, 5808-5816 (2017)

220. A Hybrid Molecular Dynamics/Multi Conformer Continuum Electrostatics (MD/MCCE) Approach for the Determination of Surface Charge of Nanomaterials, J. W. Hong, R. J. Hamers, J. A. Pedersen and Q. Cui*, J. Phys. Chem. C 121, 3584-3596 (2017)

219. Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical
Coupling in Myosin, X. Lu, V. Ovchinnikov and Q. Cui*, Biochem., 56, 1482-1497 (2017)

218. Microscopic Mechanisms that Govern the Titration Response and pK$_a$ Values of Buried Residues in Staphylococcal Nuclease Mutants, Y. Q. Zheng and Q. Cui*, Proteins , 85, 268-281 (2017) Cover