Yildiz, I., Yildiz, B. S., Kirmizialtin, S.,Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods” ACS Omega, 3, 14689, (2018)

Plumridge, A., Katz, A.M., Calvey, G.D., Elber, R., Kirmizialtin, S., Pollack, L.“Revealing the distinct folding phases of an RNA three-helix junction” Nucleic Acid Res. 45,1 (2018) 

Dinesh Shetty, Tina Skorjanc, Jesus Raya, Sudhir Kumar Sharma, Ilma Jahovic, Kyriaki Polychronopoulou, Zouhair Asfari, Dong Suk Han, Sajeewa Dewage, John-Carl Olsen, Ramesh Jagannathan, Serdal Kirmizialtin*, Ali Trabolsi*, "Calix[4]arene-based Porous Organic Nanosheets", ACS Appl. Mater. Interfaces, (2018)

Tina Skorjanc, Dinesh Shetty, Sudhir Sharma, Jesus Raya, Hassan Traboulsi, Dong-Suk Han, Jayesh Lalla, Ryan Newlon, Ramesh Jagannathan, Serdal Kirmizialtin, John-Carl Olsen, Ali Trabolsi, "Redox‐responsive Covalent Organic Nanosheets from Viologens and Calix[4]arene for Iodine and Toxic Dye Capture", Chemistry–A European Journal, (2018)

Nawaz, H., Ferreira, J., Nedyalkova, L., Zhu, H., Carrasco-López, C., Kirmizialtin, S., W. Rabeh, ”The Catalytic Inactivation of the N-half of Human Hexokinase 2 and Structural and Biochemical Characterization of its Mitochondrial Conformation” , Bioscience Rep., (2018)

Kirmizialtin, S., Yildiz, I., Yildiz, S. B, “A DFT-based Mechanistic Study on the Formation of Oximes”, J. of Organic Chemistry", e3711, 1-10, (2017).

Gulay, S.P., Bista, S., Varshney, A., Kirmizialtin, S., Sanbonmatsu, K. ,Dinman, J. “Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle”, Nucleic Acid Res. 45,4958 (2017)

Riansari, I., Benyettou, F., Sharma, SK, Blanton, T., Kirmizialtin, S.*, Jagannathan, R.* “A Chemical Template for Synthesis of Molecular Sheets of Calcium Carbonate”, Scientific Reports, 6, 25393, (2016)

Eom K., Kirmizialtin, S., Lui, Y., Xu, Zhiping, “Nanoscale Biological Materials”, 2016, 5403560, Journal of Nanomaterials, (2016)

Jijakli, K., Khraiwesh, B., Fu, W., Luo, L., Alzahmi, A., Koussa, J., Chaiboonchoe, A., Kirmizialtin, S., Yen, L., Salehi-Ashtiani, K., “The In Vitro Selection World”, Methods Journal, S1046, 16, (2016)

Kirmizialtin, S., Loerke, J., Behrmann, E., Spahn, C. M. T., Sanbonmatsu, K. Y.,”Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions”, Meth. In. Enzym., 558, 497, (2015

Kirmizialtin, S*., Hennelly, S. P., Schug, A., Onuchic, J. N., Sanbonmatsu, K. Y., “Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT”, Meth. In. Enzym., 553, 215, (2015)

Kirmizialtin, S., Johnson KA, Elber, R.," Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition", J. Phys. Chem. B, 119, 11513, (2015)

Yingying J., Kirmizialtin, S.*, Sanchez, I.*, “Dynamic Void Distribution in Myoglobin and five Mutants”, Scientific Reports, 4, 4011 (2014)

Steve P. Meisburger, Julie L. Sutton, Huimin Chen, Suzette A. Pabit, Serdal Kirmizialtin, Ron Elber, and Lois Pollack, “Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model”Biopolymers, 99, 12, 1032 (2013)

Elber R., Kirmizialtin, S., “Molecular Machines”, Curr. Opin. in Stru. Bio. 23, 1-6, (2013)

Kirmizialtin, S., Nguyen, V., Johnson. K. A., Elber R., “How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations”, Structure, 20, 618-627, (2012)

Kirmizialtin, S. ϒ, Silalahi, A. R. J. ϒ, Elber R., Fenley, M. O., “Ionic atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations”, Biophysical J., 102,829-838, (2012)

Kirmizialtin, Sϒ, Suzetteϒ, A. P., Steve, P. M., Pollack, L., Elber R., “RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations”, Biophysical J., 102, 819-828, (2012)

Kirmizialtin, S., Elber R., “Revisiting and Computing Reaction Coordinate with Directional Milestoning”, J. Phys. Chem. A, 115, 6137, (2011)

Kirmizialtin, S.*, Elber R., “Computational Exploration of Mobile Ion Distributions around RNA duplex”, J. Phys. Chem. B, 114, 8207, (2010)

Kirmizialtin, S., Makarov D.E., “Simulations of the untying of molecular friction knots between individual polymer strands”, J. Chem. Phys., 128, 094901, (2008)

C. P. Goodrich, S. Kirmizialtin, B. M. Huyghues-Despointes, A. P. Zhu, J. M. Scholtz, and D. E. Makarov, Movileanu, L., “Single-molecule electrophoresis of beta-hairpin peptides by electrical recordings and Langevin dynamics simulations”, J. Phys. Chem. B, 111, 3332, (2007)

Kirmizialtin, S., Huang L, Makarov D.E., “Computer simulations of protein translocation”, Phys. Stat. Solidi B, 243, 2038, (2006)

Huang L, Kirmizialtin, S., Makarov D.E., “Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore”, J. Chem. Phys., 123, 124903, (2005)

Kirmizialtin, S. ϒ, Huang L. ϒ, Makarov D.E., “Topography of the free-energy landscape probed via mechanical unfolding of proteins”, J. Chem. Phys., 122, 2349, (2005)

Kirmizialtin, S., Ganesan V., Makarov D.E., “Translocation of a beta-hairpin-forming peptide through a cylindrical tunnel”, J. Chem. Phys., 121, 10268, (2004)

Kirmizialtin, S., Baysal. C., Erman, B., “Conformational properties of the bacterial polyester poly (3-hydroxy-5,8-decadienoate)”, Macromolecules 36, 1132, (2003)

Kirmizialtin, S., Menceloglu YZ., Baysal, C., “New surfactants design for CO2 applications: Molecular dynamics simulations of fluorocarbon-hydrocarbon oligomers”, J. Chem. Phys., 119, 4953, (2003)

Yurtsever, E., Kirmizialtin, S., “Vibrational spectroscopy of structural defects in oligothiophenes”, Mol. Phys. 101, 2725, (2003)