l  L. Cong, Ruhong Zhou, Y. C. Kuo, M. Cunniff, and F. Zhang*, Comprehensive Interrogation of Natural TALE DNA Binding Modules and Transcriptional Repressor Domains,Nature Commun.3, 968, 2012

l   S. G. Kang, G. Q. Zhou, P. Yang, Y. Liu, B. Y. Sun, T. Huynh, H. Meng, L. Zhao, G. M. Xing, C. Y. Chen*, Y. L. Zhao*, Ruhong Zhou*, Molecular Mechanism of Pancreatic Tumor Metastases Inhibition by Metallofullerenol Gd@C82(OH)22: Implication for de novo Design of Nanomedicine, Proc. Natl. Acad. Sci., 109, 15431-15436, 2012 (featured article)

l  Z. Xia, P. Das, E. I. Shakhnovich*, and Ruhong Zhou*, Collapse of Unfolded Proteins in a Mixture of Denaturants, J. Am. Chem. Soc.134, 18266-18274, 2012

l  C. Guo, Y. Luo,Ruhong Zhou*, and G. H. Wei*,Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes, ACS Nano, 6, 3907-3918, 2012

l  S.G. Kang, H. Li, T. Huynh, F. Zhang, Z. Xia, Y. Zhang* andRuhong Zhou*,Molecular Mechanism of Surface-Assisted Epitaxial Self-Assembly of Amyloid-like Peptides, ACS Nano, 6, 9276-9282, 2012

l  B. Q. Luan* and Ruhong Zhou*,Nanopore-Based Sensors for Detecting Toxicity of a Carbon Nanotube to Proteins, J. Phys. Chem. Lett. 3, 2337-2341, 2012

l   P. Xiu, Y. Tu,X. L. Tian,H. P. Fang*, and Ruhong Zhou*, Molecular Wire of Urea in Carbon Nanotube: A Molecular Dynamics Study, Nanoscale, 4, 652-658, 2012

l   Amanda Barnard, Changming Li, Ruhong Zhou, Y. L. Zhao, Modeling of nanoscale, Nanoscale, 4, 1042-1043, 2012

l   S. C. Flores*, J. Bernauer*, S. Shin,Ruhong Zhou, and X. H. Huang*, Multiscale modeling of macromolecular biosystems, Briefings in Bioinformatics, 13, 395-405, 2012 

l   T. Y. Yoo, A. Adhikari, Z. Xia, T. Huynh, K. F. Freed*, Ruhong Zhou*, T. R. Sosnick*, The folding transition state of protein L is extensive with non-native interactions,J. Mol. Biol., 420, 220-234, 2012

l  Z. Xia, P. Clark, T. Huynh, P. Loher, Y. Zhao, H.W. Chen, P. Y. Ren, I. Rigoutsos*, and Ruhong Zhou*, Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets, Sci. Rep., 2, 569, 2012

l   S. G. Kang, T. Huynh, and Ruhong Zhou*,Non-destructive Inhibition of Metallofullerenol Gd@C82(OH)22 on WW domain: Implication on Signal Transduction Pathway, Sci. Rep.2, 957, 2012

l  C. J. Tian, P. Xiu, Y. Meng,W. Y. Zhao,Z. G. Wang, and Ruhong Zhou,Mechanism of Chiral Inversion of Thalidomide and the Role of Water and Hydroxide Ion, Chem. Eur. J. 18, 14305-14313, 2012 (cover article)

l  L. Zhao, Y. L. Zhao*, and Ruhong Zhou*, Novel design of a nanoflowmeter based on carbon nanotubes, J. Phys. Chem. C, 116, 13429-13434, 2012

l  Z. X. Yang, P. Xiu,B. Y. Shi, L. Hua, andRuhong Zhou*,A coherent microscopic picture for urea-induced denaturation of proteins, J. Phys. Chem. B 116, 8856-8862, 2012

l  W. F. Li, Ruhong Zhou, and Y. G. Mu*, Salting Effects on Protein Components in Aqueous NaCl and Urea Solutions: Toward Understanding of Urea-Induced Protein Denaturation, J. Phys. Chem. B 116, 1446-1451, 2012

l  Z. X. Yang^#, Z. Wang^#,X. L. Tian,P. Xiu*,andRuhong Zhou*, Amino Acid Analogues Bind to Carbon Nanotube via π-π interactions: Comparison of Molecular Mechanical and Quantum Mechanical Calculations, J. Chem. Phys. 136, 025103, 2012

l  X. Y. Li, Y. C. Shi, Y. L. Yang, H. L. Du, Ruhong Zhou*, and Y. L. Zhao*, How does water-nanotube interaction influence water flow through the nanochannel?J. Chem. Phys., 136, 175101, 2012

l  Z. Xia, T. Huynh, S. G. Kang, and Ruhong Zhou*, Free Energy Simulations Reveal Both Hydrophobic and Polar Interactions are Important to Influenza Hemagglutinin Antibody Binding, Biophys. J. 102, 1453-1461, 2012

l   B. Q. Luan^#*,D. Q. Wang^#,Ruhong Zhou, S. Harrer, H. B. Peng, andG. Stolovitzky, Dynamics of DNA Translocation in a Solid-StateNanopore Immersed in Aqueous Glycerol, Nanotechnology, 23, 455102, 2012

l  Ruhong Zhou, Protein folding: Bridging the gap between theory and experiment,Editorial for Hot-topic Special Issue, Curr. Phys. Chem., 2, 2-3, 2012

l  G. Zuo, P. Xiu, X. Zhou, Ruhong Zhou*, and H. P. Fang*, Conformational Changes of the Protein Domains Upon Binding with Carbon Nanotubes Studied by Molecular Dynamics Simulations,Curr. Phys. Chem., 2, 12-22, 2012

l  Z. Xia, P. Xiu, and Ruhong Zhou, Small Molecules and Peptides inside Carbon Nanotubes: Impact of Nanoscale Confinement, Editor A. Lazinica, Recent Progress in Carbon Nanotube Research, ISBN 980-953-307-485-1, InTech Publisher, 2012