Published/in press/submitted 2013-2017

Our Citation Profile at Google Scholar

228. Cavity Hydration Dynamics in Cytochrome c Oxidase and Functional Implications, C. Y. Son, A. Yethiraj and Q. Cui*, Submitted (2017)

227. Contact Ion Pairing Drives Lipid Corona Formation from Nanoparticle Interactions with Bilayer Membranes, L. L. Olenick, J. M. Troiano, A. Vartanian, E. S. Melby, A. Mensch, L. L. Zhang, T. Qiu, S. Lohse, X. Zhang, T. R. Kuech, A. Millevolte, I. Gunsolus, A. C. McGeachy, M. Dogang\"un, D. H. Hu, S. R. Walter, S. Lovern, H. Owen, M. D. Torelli, Z. V. Feng, K. R. Hurley, J. Dalluge, G. Chong, C. L. Haynes, R. J. Hamers, J. A. Pedersen, Q. Cui, R. Hernandez, G. Orr, C. J. Murphy, and F. M. Geiger, Submitted (2017)

226. 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, mBio, submitted (2017)

225. 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., Submitted (2017)

224. 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", Submitted (2017)

223. SNARE copy number determines the size and kinetic properties of fusion pores, 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*, Submitted (2017)

222. Differential Specificity and Energy Landscapes (Di-SEL) Unmask Sequence Preferences of Transcription Factors that Bind Indistinguishably to DNA Consensus Motifs D. Bhimsaria, J. A. Rodriguez-Martinez, N. E. Korkmaz, Q. Cui, P. Ramanathan, and A. Z. Ansari*, Submitted

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

217. Structure and dynamics underlying elementary ligand binding events in pacemaking channels, M. P. Goldschen-Ohm, V. A. Klenchin, D. S. White, J. B. Cowgill, Q. Cui, R. H. Goldsmith, B. Chanda*, eLife 5, e20797 (2016)

216. Perspective: Quantum Mechanical Methods in Biochemistry and Biophysics, Q. Cui*, J. Chem. Phys., 145, 140901 (2016) Cover

215. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects, D. Roston*, Q. Cui*, J. Am. Chem. Soc., 138, 11946-11957 (2016)

214. Predicting the Structure-activity Relationship of Hydroxyapatite-binding Peptides by Enhanced-sampling Molecular Simulation, W. L. Zhao, Z. J. Xu, Q. Cui and N. Sahai*, Langmuir, 32, 7009-7022 (2016)

213. Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies, Q. Cui*, R. Hernandez*, S. E. Mason*, T. Frauenheim, J. A. Pedersen, F. M. Geiger, J. Phys. Chem., B., 120, 7297-7306 (2016) Invited Review, Cover

212. Intrinsic structural preferences of the L7P Neuropeptide Y signal peptide revealed by ion mobility-mass spectrometry, C. B. Lietz, Z. Chen, C. Son, Q. Cui and L. Li*, Analyst, 141, 4863-4869 (2016)

211. Leaving Group Ability Affects Transition State Structure for Phosphoryl Transfer in a Single Enzyme Active Site, D. Roston, D. Demapan and Q. Cui*, J. Am. Chem. Soc. 138, 7386-7394 (2016)

210. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes, D. Roston* and Q. Cui*, in Methods in Enzymology, Issue on ``Computational Approaches for Studying Enzyme Mechanism", Ed. G. A. Voth, Vol. 577, 213-250 (2016) Invited contribution

209. Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multi-component Lipid Bilayers, L. L. Zhang, M. Rajendram, D. B. Weibel, A. Yethiraj and Q. Cui*, J. Phys. Chem., Andy McCammon Festschrift, 120, 8424-8437 (2016)

208. Towards a Barrier Height Benchmark Set for Biologically Relevant Systems, J. C. Kromann, A. S. Christensen, Q. Cui and J. H. Jensen*, Peer J., e1994 (2016)

207. First Principles United Atom Force Field for the Ionic Liquid [BMIM+][BF4-] : An Alternative to Charge Scaling, C. Y. Son, J. McDaniel, J. R. Schmidt, Q. Cui and A. Yethiraj*, J. Phys. Chem. B, 120, 3560-3568 (2016)

206. A Computational Investigation on the Substrate Preference of TET2, J. Y. Lu, L. L. Hu, J. D. Cheng, D. Fang, C. Wang, K. Q. Yu, H. L. Jiang, Q. Cui, Y. H. Xu* and C. Luo*, Phys. Chem. Chem. Phys., 18, 4728-4738 (2016)

205. Gating Mechanism of Mechanosensitive Channel of Large Conductance: A Coupled Continuum Mechanical-Continuum Solvation Approach, L. Zhu, J. Wu, Y. Liu, Y. Yan, Q. Cui and X. Chen*, Biomechan.& Modeling in Mechanobio., 1-20 (2016)

204. QM/MM free energy simulations: recent progress and challenges, X. Lu, D. Fang, S. Ito, Y. Okamoto, V. Ovchinnikov and Q. Cui*, Mol. Simul. Special Issue on ``Free Energy Simulations", 42, 1056-1078 (2016) Invited review

203. Semi-empirical Quantum Mechanical Methods for Non-covalent Interactions for Chemical and Biochemical Applications, A. S. Christensen, T. Kubar, Q. Cui* and M. Elstner*, Chem. Rev., 116, 5301-5337 (2016)

202. Copper oxidation/reduction in water and protein: studies with DFTB3/MM and VALBOND molecular dynamics simulations, H. Jin, P. Goyal, A. Kumar Das, M. Gaus, M. Meuwly* and Q. Cui*, J. Phys. Chem. B Bruce Garrett Festschrift, 120, 1894-1910 (2016)

201. Different States of Synaptotagmin Regulate Evoked versus Spontaneous Release, B. Hua, R. H. Xue, H. Bao, L. Zhang, A. Yethiraj, Q. Cui and E. R. Chapman*, Nat. Comm., 7, 10971 (2016)

200. Structural insight into substrate preference for TET-mediated oxidation, L. L. Hu, J. Y. Lu, J. D. Cheng, Q. H. Rao, Z. Li, H. F. Hou, Z. Y. Lou, L. Zhang, W. Li, W. Gong, M. J. Liu, C. Sun, X. T. Yin, J. Li, X. S. Tan, P. C. Wang, Y. S. Wang, D. Fang, Q. Cui, P. Y. Yang, C. He, H. L. Jiang, C. Luo* and Y. H. Xu*, Nature, 527, 118-122 (2015)

199. Comparison of Native and Non-native Ubiquitin Oligomers Reveals Analogous Structures and Reactivities, G. H. Pham, A. S.J.B. Rana, E. N. Korkmaz, V. H. Trang, Q. Cui, and E. R. Strieter*, Prot. Sci., 25, 456-471 (2016)

198. A composite approach to a complete model of the myosin rod, E. H. Korkmaz, K. C. Taylor, M. P. Anreas, G. Ajay, N. T. Heinz, Q. Cui* and I. Rayment*, Proteins, 84, 172-189 (2016)

197. Electronic polarization effects in cation interactions with first and second coordination shell ligands in metalloproteins, V. Ngo, M. C. da Silva, M. Kubillus, M. Elstner, H. Li, B. Roux, Q. Cui*, D. R. Salahub* and S. Noskov*, J. Chem. Theory Comp. 11, 4992-5001 (2015)

196. Anionic phospholipids interact with RecA and stabilize nucleoprotein filaments in Escherichia coli, M. Rajendram, L. Zhang, H. H. Tuson, B. J. Reynolds, K. N. Ngo, M. M. Cox, A. Yethiraj, Q. Cui and D. B. Weibel*, Mol. Cell, 60, 374-384 (2015)

195. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization, A. S. Christensen, M. Elstner and Q. Cui*, J. Chem. Phys. 143, 084123 (2015)

194. DFTB3 Parametrization for Copper: the importance of orbital angular momentum dependence of Hubbard parameters, M. Gaus, H. Jin, D. Demapan, A. S. Christensen, P. Goyal, M. Elstner and Q. Cui*, J. Chem. Theory Comp. 11, 4205-4219 (2015)

193. Interplay of electrostatics and hydrophobic effects in the metamorphic protein human lymphotactin, N. Korkmaz, B. Volkman and Q. Cui*, J. Phys. Chem. B 119, 9547-9558 (2015)

192. Skip Residues Modulate the Structural Properties of the Myosin Rod and Guide Thick Filament Assembly, K. C. Taylor, M. Buvoli, N. Korkmaz, A. Buvoli, Y. Q. Zheng, N. T. Heinz, Q. Cui*, L. A. Leinwand*, and I. Rayment*, Proc. Natl. Acad. Sci. USA E3806-E3815 (2015)

191. Biological Responses to Engineered Nanomaterials: Needs for the Next Decade, C. J. Murphy*, A. M. Vartanian, FM. Geiger, R. J. Hamers, J. Pederson, Q. Cui, C. L. Haynes, E. E. Carlson, R. Hernandez, R. D. Klaper, G. Orr and Z. Rosenzweig, ACS Central, 1, 117-123 (2015)

190. Electrostatics and Many-body effects in Biomolecular simulations, Eds. Q. Cui, M. Meuwly and P. Ren, Pan Stanford Publishing (2015)

189. Histone H3 N-terminal tail: a computational analysis of free energy landscape and kinetics, Y. Zheng and Q. Cui*, Phys. Chem. Chem. Phys., 17, 13689-13698 (2015)

188. Atomic-level Mechanisms for Intrafibrillar Bone Mineralization, Z. Xu, Y. Yang, W. Zhao, Z. Wang, W. J. Landis, Q. Cui and N. Sahai*, Biomaterials, 39, 59-66 (2015)

187. Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis, P. Goyal, S. Yang and Q. Cui*, Chem. Sci., 6, 826-841 (2015)

186. Parameterization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Ap- plications, X. Lu, M. Gaus, M. Elstner and Q. Cui*, J. Phys. Chem. B, Special Issue: Bill Jorgensen Festschrift, 119,1062-82 (2015)

185. Elastic models of biomolecules, Q. Cui, in Coarse-grained Modeling of Biomolecules, Ed. G. Papoian, CRC Press (2014) Invited Book Chapter

184. Integration of FTIR spectroscopy and biomolecular simulations resolves the structure of a transient water wire in a membrane protein, S. Wolf, E. Freier, Q. Cui and K. Gerwert, J. Chem. Phys. Special Issue on "Biological Water" , 141, 22D524 (2014)

183. UO2+ Uptake by Proteins: Understanding the Binding Features of the Super Uranyl-Binding Protein (SUP) and Design of a Protein with Higher Affinity, S. O. Odoh, G. C. Bondarevsky, J. Karpus, Q. Cui, C. He, R. Spezia, L. Gagliardi*, J. Am. Chem. Soc. 136, 17484-17494 (2014)

182. Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models, P. Goyal, H-J. Qian, S. Irle, X. Lu, D. Roston, T. Mori, M. Elstner and Q. Cui*, J. Phys. Chem. B Featured Articles, 118, 11007-11027 (2014)

181. Free energy calculations for the peripheral binding of proteins/peptides to an anionic membrane. I. Implicit membrane models, L. Zhang, A. Yethiraj and Q. Cui*, J. Chem. Theo. Comp., Special issue on ``Free energy calculations: three decades of adventure in chemistry and biophysics", 10, 2845-2859 (2014)

180. Editorial: Making Biomolecular Simulations Accessible in the post-Nobel prize era. Q. Cui* and R. Nussinov*, PLoS Comp. Biol. 10, e1003786 (2014)

179. Density Functional Tight Binding: values of semi-empirical methods in an ab initio era, Q. Cui*, M. Elstner*, PCCP, Thematic issue on ``Density Functional Theory and Its Applications", 16, 14368-14377 (2014)

178. Integrated Hamiltonian Sampling: a simple and versatile method for free energy simulations and conformational sampling, T. Mori, R. J. Hamers, J. A. Pederson and Q. Cui*, J. Phys. Chem. B Special Issue: Jim Skinner Festschrift, 118, 8210-8220 (2014)

177. Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly, Q. T. Shen, A. L. Schuh, Y. Q. Zheng, K. Quinney, L. Wang, M. Hanna, J. C. Mitchell, M. S. Otegui, P. Ahlquist, Q. Cui, and A. Audhya J. Cell Biol. , 206, 763-777 (2014)

176. Parameterization of DFTB3 for Sulfur and Phosphorus for biological applications, M. Gaus, X. Lu, M. Elstner* and Q. Cui*, J. Chem. Theo. Comp., 10, 1518-1537 (2014)

175. Quantum Mechanical/Molecular Mechanical Studies of Zinc Hydrolases, D. G. Xu*, Q. Cui and Hua Guo*, Int. Rev. Phys. Chem., 33, 1-41 (2014)

174. Gas-phase Fragment Ion Isomer Analysis Reveals the Mechanism of Peptide Sequence Scrambling, C. Jia, Z. Wu, C. B. Lietz, Z. Liang, Q. Cui and L. Li*, Anal. Chem. 86, 2917-2924 (2014) Cover

173. Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations Benchmarked to Density Functional Theory, Z. J. Xu, Y. Yang, Z. Q. Wang, D. Mkhonto, C. Shang, Z. P. Liu, Q. Cui and N. Sahai*, J. Comp. Chem. 35, 70-81 (2014)

172. Density Functional Tight Binding (DFTB): Application to organic and biological molecules, M. Gaus, Q. Cui and M. Elstner, WIREs Comput. Mol. Sci., 4, 49-61 (2014)

171. Tethered spectroscopic probes as chemical calipers to estimate dynamic distances with sub-nanometer resolution, B. W. Jarecki, S. Q. Zheng, L. L. Zhang, X. C. Li, X. Zhou, Q. Cui, W. P. Tang and B. Chanda*, Biophys. J. 105, 2724-2732 (2013)

170. Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in Cytochrome c Oxidase, P. Goyal, J. Lu, S. Yang, M. R. Gunner* and Q. Cui*, Proc. Natl. Acad. Sci. USA, 110, 18886-18891 (2013)

169. An explicit consideration of desolvation is critical to binding free energy calculations of charged molecules at ionic surfaces, T. Mori, R. J. Hamers, J. A. Pedersen and Q. Cui*, J. Chem. Theo. Comp., 9, 5059-5069 (2013)

168. Why do Arginine and Lysine organize lipids differently? Insights from coarse-grained and atomistic simulations, Z. Wu, Q. Cui*, A. Yethiraj*, J. Phys. Chem. B 117, 12145-12156 (2013)

167. Generation and sensing of membrane curvature: where materials science and biophysics meet, Q. Cui*, L. Zhang, Z. Wu and A. Yethiraj*, Curr. Opin. Solid State Mater. Sci. 17, 164-174 (2013) Invited Review

166. Contribution of Electrostatics to the Binding of Pancreatic-Type Ribonucleases to Membranes, N. K. Sundlass, C. H. Eller, Q. Cui and R. T. Raines*, Biochem. 52, 6304-6312 (2013)

165. Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily, G. Hou, Q. Cui*, J. Am. Chem. Soc. 135, 10457-10469 (2013)

164. A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: test of force field models and application to proteins in the AlkB family, X. Pang, K. Han and Q. Cui*, J. Comp. Chem. 34, 1620-1635 (2013) Cover

163. Molecular Simulation of Biomineral Nucleation and Crystal Growth: Modern Computational Challenges and Approaches, Y. Yang, Z. J. Xu, Q. Cui and N. Sahai, Characterization of Biominerals and Biomimetic Materials, Eds. L. Gower, E. DiMasi, Taylor & Francis Invited Review p265 (2014)

162. Toward quantitative analysis of metalloenzyme function using MM and hybrid QM/MM methods: challenges, methods and recent applications, M. Gaus, P. Goyal, G. Hou, X. Lu, X. Pang, J. Zienau, X. Xu, M. Elstner and Q. Cui*, ``Quantitative Computations in Biology", Ed. Ruhong Zhou Invited Review p33 (2014)

161. FTO-Mediated Formation of N6-Hydroxymethyladenosine and N6-Formyladenosine in Mammalian RNA, Y. Fu, G. Jia, X. Pang, R. Wang, X. Wang, C. Li, Q. Dai, K. Han, Q. Cui, C. He*, Nat. Comm., 4, 1798 (2013)

160. Conformational Disorder Enhances Electron Transfer Through Alkyl Monolayers: Ferrocene on Conductive Diamond, R. E. Ruther, Q. Cui and R. J. Hamers*, J. Am. Chem. Soc., 135, 5751-5761 (2013)

159. Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: a comparative analysis using ion solvation and reduction potential in proteins, X. Lu and Q. Cui*, J. Phys. Chem. B 117, 2005-2018 (2013)

158. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores, J. Yoo, M. Jackson and Q. Cui*, Biophys. J., 104, 841-852 (2013)

157. Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association, J. Yoo and Q. Cui*, Biophys. J., 104, 128-138 (2013) Cover

156. Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A, J. Yoo and Q. Cui*, Biophys. J., 104, 117-127 (2013)

155. Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations, M. Daily, H. Yu, G. N. Phillips, Jr. and Q. Cui*, Special Issue of Topics in Current Chemistry, ``Macromolecular Dynamics in Biological Catalysis", Eds. S. Hammes-Schiffer and J. Klinman, 337, 139-164 (2013) Invited Review