PUBLICATIONS
contact at serdal@nyu.edu for preprints
Weiwei He, Josue San Emeterio, Michael T Woodside, Serdal Kirmizialtin, and Lois Pollack, "Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics", Nucleic Acids Research, (2023)
Weiwei He, Xiangyun Qiu, and Serdal Kirmizialtin, "Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA–DNA Interactions", J. Chem. Theory Comput., (2023)
Nawavi Naleem, Charlles R. A. Abreu, Krzysztof Warmuz, Muchen Tong, Serdal Kirmizialtin, Mark E. Tuckerman, "An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions", The Journal of Chemical Physics, (2023)
Gobinda Das, Thirumurugan Prakasam, Nour Alkhatib, Rasha G. AbdulHalim, Falguni Chandra, Sudhir Kumar Sharma, Bikash Garai, Sabu Varghese, Matthew A. Addicoat, Florent Ravaux, Renu Pasricha, Ramesh Jagannathan, Na’il Saleh, Serdal Kirmizialtin, Mark A. Olson, Ali Trabolsi, "Light-driven self-assembly of spiropyran-functionalized covalent organic framework", Nature Communications, (2023)
Chang Liu, Anja Henning-Knechtel, Nicklas Osterlund, Jinming Wu, Guangshun Wang, Ruth Astrid Olivia Graslund, Serdal Kirmizialtin, Jinghui Luo, "Oligomer Dynamics of LL-37 Truncated Fragments Probed by α-Hemolysin Pore and Molecular Simulations", Small, (2023)
Turan Selman Erkal, Norazanita Shamsuddin, Serdal Kirmizialtin, and A. Ozgur Yazaydin. 'Computational Investigation of Structure–Function Relationship in Fluorine-Functionalized MOFs for PFOA Capture from Water', J. Phys. Chem. C (2023)
Tina Skorjanc, Dinesh Shetty, Felipe Gándara, Simon Pascal, Nawavi Naleem, Salma Abubakar, Liaqat Ali, Abdul Khayum Mohammed, Jesus Raya, Serdal Kirmizialtin, Olivier Siri, and Ali Trabolsi. 'Covalent Organic Framework Based on Azacalix[4] arene for the Efficient Capture of Dialysis Waste Products', ACS Appl. Mater. Interfaces (2022)
Anja Henning-Knechtel, D. Thirumalai, Serdal Kirmizialtin. "Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts", Science Advances, (2022)
Yen-Lin Chen, Weiwei He, Serdal Kirmizialtin, and Lois Pollack. "Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations", Cell Reports Physical Science, (2022)
Weiwei He, Nawavi Naleem, Diego Kleiman, and Serdal Kirmizialtin,
"Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA", J. Phys. Chem. Lett. (2022)
Tyler L Dangerfield, Serdal Kirmizialtin and Kenneth A Johnson. "Substrate specificity and proposed structure of the proofreading complex of T7 DNA polymerase", J. Biol. Chem. (2022)
Tyler L Dangerfield, Serdal Kirmizialtin and Kenneth A Johnson. "Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid", J. Biol. Chem. (2022)
Weiwei He, Anja Henning-Knechtel and Serdal Kirmizialtin. "Visualizing RNA Structures by SAXS-driven MD Simulations", Frontiers in Bioinformatics, (2022)
Weiwei He, Yen-Lin Chen, Lois Pollack, and Serdal Kirmizialtin."The structural plasticity of nucleic acid duplexes revealed by WAXS and MD", Science Advances, (2021)
Bikash Garai, Dinesh Shetty*, Tina Skorjanc, Felipe Gándara, Nawavi Naleem, Sabu Varghese, Sudhir Kumar Sharma, Maria Baias, Ramesh Jagannathan, Mark A. Olson, Serdal Kirmizialtin*, and Ali Trabolsi*, "Taming the Topology of Calix[4]arene-Based 2D-Covalent Organic Frameworks: Interpenetrated vs Noninterpenetrated Frameworks and Their Selective Removal of Cationic Dyes", J. Am. Chem. Soc. (2021)
Shanzhong Gong, Serdal Kirmizialtin, Adrienne Chang, Joshua E. Mayfield, Yan Jessie Zhang and Kenneth A. Johnson " Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis", Journal of Biological Chemistry, (2020)
Serdal Kirmizialtin, Felicia Pitici, Alfredo E. Cardenas, Ron Elber, D. Thirumalai. "Dramatic shape changes occur as Cytochrome c folds", The Journal of Physical Chemistry B, (2020)
Dinesh Shetty, Ilma Jahović, Tina Skorjanc, Turan Selman Erkal, Liaqat Ali, Jesus Raya, Zouhair Asfari, Mark A. Olson, Serdal Kirmizialtin, A. Ozgur Yazaydin, and Ali Trabolsi, "Rapid and Efficient Removal of Perfluorooctanoic Acid from Water with Fluorine-Rich Calixarene-Based Porous Polymers", ACS Applied Materials & Interfaces, (2020)
Amit Srivastava, Raju Timsina, Seung Heo, Sajeewa W Dewage, Serdal Kirmizialtin, Xiangyun Qiu, "Structure-guided DNA–DNA attraction mediated by divalent cations", Nucleic Acids Research, 499, (2020)
Weiwei He, Serdal Kirmizialtin, "Exploring Cation Mediated DNA Interactions Using Computer Simulations",Advances in Bionanomaterials II, 51-63, (2020)
Henning-Knechtel, A., Sunil Kumar, S., Krol, S., Wallin, C., Wärmländer, S., Jarvet, J., Esposito, Kirmizialtin S., G., Gräslund, A., Hamilton, A. D., Magzoub, M” Designed cell-penetrating peptide inhibitors of amyloid-beta aggregation and cytotoxicity”, Cell Reports Physical Science, 100014, (2020)
Doo Nam Kim, Nigel W Moriarty, Serdal Kirmizialtin, Pavel V Afonine, Billy Poon, Oleg V Sobolev, Paul D Adams, Karissa Sanbonmatsu,”Cryo_fit: Democratization of flexible fitting for cryo-EM”, Journal of Structural Biology,208, 1,(2019)
Gobinda Das, Sudhir Kumar Sharma, Thirumurugan Prakasam, Felipe Gándara, Renny Mathew, Nour Alkhatib, Na’il Saleh, Renu Pasricha, John-Carl Olsen, Maria Baias, Serdal Kirmizialtin, Ramesh Jagannathan, Ali Trabolsi,”A polyrotaxanated covalent organic network based on viologen and cucurbit [7] uril”, Communications Chemistry, 2,1,(2019)
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. , Silalahi, A. R. J. , Elber R., Fenley, M. O., “Ionic atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations”, Biophysical J., 102,829-838, (2012)
Kirmizialtin, S., Suzette, 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., Huang L., 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)