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Serdal Kirmizialtin

Assistant Professor of Chemistry

    20032019
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    Research Output 2003 2019

    2019

    A polyrotaxanated covalent organic network based on viologen and cucurbit[7]uril

    Das, G., Sharma, S. K., Prakasam, T., Gándara, F., Mathew, R., Alkhatib, N., Saleh, N., Pasricha, R., Olsen, J. C., Baias, M., Kirmizialtin, S., Jagannathan, R. & Trabolsi, A., Dec 1 2019, In : Communications Chemistry. 2, 1, 106.

    Research output: Contribution to journalArticle

    Open Access
    Viologens
    Rotaxanes
    liquid
    Covalent bonds
    Imines

    Cryo_fit: Democratization of flexible fitting for cryo-EM

    Kim, D. N., Moriarty, N. W., Kirmizialtin, S., Afonine, P. V., Poon, B., Sobolev, O. V., Adams, P. D. & Sanbonmatsu, K., Jan 1 2019, (Accepted/In press) In : Journal of Structural Biology.

    Research output: Contribution to journalArticle

    Cryoelectron Microscopy
    Molecular Dynamics Simulation
    Software
    Professional Competence
    Computer Simulation
    2018

    Calix[4]arene-Based Porous Organic Nanosheets

    Shetty, D., Skorjanc, T., Raya, J., Sharma, S. K., Jahovic, I., Polychronopoulou, K., Asfari, Z., Han, D. S., Dewage, S., Olsen, J. C., Jagannathan, R., Kirmizialtin, S. & Trabolsi, A., May 23 2018, In : ACS Applied Materials and Interfaces. 10, 20, p. 17359-17365 7 p.

    Research output: Contribution to journalArticle

    Calixarenes
    Nanosheets
    Electron energy levels
    Polymers
    Supramolecular chemistry

    Comparative Computational Approach to Study Enzyme Reactions Using QM and QM-MM Methods

    Yildiz, I., Yildiz, B. S. & Kirmizialtin, S., Nov 2 2018, In : ACS Omega. 3, 11, p. 14689-14703 15 p.

    Research output: Contribution to journalArticle

    Betaines
    Choline
    Hydrides
    choline oxidase
    Enzymes

    Corrigendum to: Redox-Responsive Covalent Organic Nanosheets from Viologens and Calix[4]arene for Iodine and Toxic Dye Capture (Chemistry - A European Journal, (2018), 24, 34, (8648-8655), 10.1002/chem.201800623)

    Skorjanc, T., Shetty, D., Sharma, S. K., Raya, J., Traboulsi, H., Han, D. S., Lalla, J., Newlon, R., Jagannathan, R., Kirmizialtin, S., Olsen, J. C. & Trabolsi, A., Jan 1 2018, (Accepted/In press) In : Chemistry - A European Journal.

    Research output: Contribution to journalArticle

    Viologens
    Nanosheets
    Poisons
    Iodine
    Coloring Agents

    Redox-Responsive Covalent Organic Nanosheets from Viologens and Calix[4]arene for Iodine and Toxic Dye Capture

    Skorjanc, T., Shetty, D., Sharma, S. K., Raya, J., Traboulsi, H., Han, D. S., Lalla, J., Newlon, R., Jagannathan, R., Kirmizialtin, S., Olsen, J. C. & Trabolsi, A., Jun 18 2018, In : Chemistry - A European Journal. 24, 34, p. 8648-8655 8 p.

    Research output: Contribution to journalArticle

    Viologens
    Organic polymers
    Nanosheets
    Poisons
    Iodine

    Revealing the distinct folding phases of an RNA three-helix junction

    Plumridge, A., Katz, A. M., Calvey, G. D., Elber, R., Kirmizialtin, S. & Pollack, L., Jan 1 2018, In : Nucleic Acids Research. 46, 14, p. 7354-7365 12 p.

    Research output: Contribution to journalArticle

    RNA Folding
    RNA
    Microfluidics
    X-Rays
    Ions

    The catalytic inactivation of the N-half of human hexokinase 2 and structural and biochemical characterization of its mitochondrial conformation

    Nawaz, M. H., Ferreira, J. C., Nedyalkova, L., Zhu, H., Carrasco-López, C., Kirmizialtin, S. & Rabeh, W., Feb 21 2018, In : Bioscience Reports. 38, 1, BSR20171666.

    Research output: Contribution to journalArticle

    Hexokinase
    Conformations
    Enzyme Stability
    Glucose
    Mitochondria
    2017

    A DFT-based mechanistic study on the formation of oximes

    Kirmizialtin, S., Yildiz, B. S. & Yildiz, I., Dec 1 2017, In : Journal of Physical Organic Chemistry. 30, 12, e3711.

    Research output: Contribution to journalArticle

    Oximes
    Discrete Fourier transforms
    aniline
    aldehydes
    ketones

    Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

    Gulay, S. P., Bista, S., Varshney, A., Kirmizialtin, S., Sanbonmatsu, K. Y. & Dinman, J. D., Jan 1 2017, In : Nucleic Acids Research. 45, 8, p. 4958-4971 14 p.

    Research output: Contribution to journalArticle

    Ribosomes
    Yeasts
    Peptide Elongation Factors
    Ricin
    Energy Transfer
    2016

    A Chemical Template for Synthesis of Molecular Sheets of Calcium Carbonate

    Rianasari, I., Benyettou, F., Sharma, S. K., Blanton, T., Kirmizialtin, S. & Jagannathan, R., May 5 2016, In : Scientific Reports. 6, 25393.

    Research output: Contribution to journalArticle

    calcium acetate
    Calcium Carbonate
    carbopol 940
    Nacre
    Polymers

    Nanoscale Biological Materials

    Eom, K., Kirmizialtin, S., Liu, Y. & Xu, Z., Jan 1 2016, In : Journal of Nanomaterials. 2016, 5403560.

    Research output: Contribution to journalEditorial

    Biological materials

    The in vitro selection world

    Jijakli, K., Khraiwesh, B., Fu, W., Luo, L., Alzahmi, A., Koussa, J., Chaiboonchoe, A., Kirmizialtin, S., Yen, L. & Salehi-Ashtiani, K., Aug 15 2016, In : Methods. 106, p. 3-13 11 p.

    Research output: Contribution to journalReview article

    Mutagenesis
    Molecules
    Nucleic Acids
    Amplification
    Experiments
    2015

    Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition

    Kirmizialtin, S., Johnson, K. A. & Elber, R., Sep 3 2015, In : Journal of Physical Chemistry B. 119, 35, p. 11513-11526 14 p.

    Research output: Contribution to journalArticle

    HIV Reverse Transcriptase
    human immunodeficiency virus
    Catalyst selectivity
    Free energy
    Conformations

    Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

    Kirmizialtin, S., Hennelly, S. P., Schug, A., Onuchic, J. N. & Sanbonmatsu, K. Y., Jan 1 2015, In : Methods in Enzymology. 553, p. 215-234 20 p.

    Research output: Contribution to journalArticle

    Acylation
    Molecular Dynamics Simulation
    Hydroxyl Radical
    Molecular dynamics
    Computer simulation

    Using molecular simulation to model high-resolution cryo-EM reconstructions

    Kirmizialtin, S., Loerke, J., Behrmann, E., Spahn, C. M. T. & Sanbonmatsu, K. Y., Jan 1 2015, In : Methods in Enzymology. 558, 1, p. 497-514 18 p.

    Research output: Contribution to journalArticle

    Cryoelectron Microscopy
    Electron microscopy
    Molecular Dynamics Simulation
    Ribosomes
    Molecular dynamics
    2014

    Dynamic void distribution in myoglobin and five mutants

    Jiang, Y., Kirmizialtin, S. & Sanchez, I. C., Feb 6 2014, In : Scientific Reports. 4, 04011.

    Research output: Contribution to journalArticle

    Myoglobin
    Proteins
    Ion Transport
    Molecular Dynamics Simulation
    Heme
    2013

    Molecular machines

    Elber, R. & Kirmizialtin, S., Apr 1 2013, In : Current Opinion in Structural Biology. 23, 2, p. 206-211 6 p.

    Research output: Contribution to journalReview article

    Cellular Structures
    Thermodynamics
    Direction compound

    Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model

    Meisburger, S. P., Sutton, J. L., Chen, H., Pabit, S. A., Kirmizialtin, S., Elber, R. & Pollack, L., Dec 1 2013, In : Biopolymers. 99, 12, p. 1032-1045 14 p.

    Research output: Contribution to journalReview article

    Single-Stranded DNA
    Polyelectrolytes
    Poly T
    Nucleic Acids
    Nucleic acids
    2012

    How conformational dynamics of DNA polymerase select correct substrates: Experiments and simulations

    Kirmizialtin, S., Nguyen, V., Johnson, K. A. & Elber, R., Apr 4 2012, In : Structure. 20, 4, p. 618-627 10 p.

    Research output: Contribution to journalArticle

    DNA-Directed DNA Polymerase
    Nucleotides
    HIV Reverse Transcriptase
    Catalytic Domain
    Carrier Proteins

    RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations

    Kirmizialtin, S., Pabit, S. A., Meisburger, S. P., Pollack, L. & Elber, R., Feb 22 2012, In : Biophysical Journal. 102, 4, p. 819-828 10 p.

    Research output: Contribution to journalArticle

    RNA
    Ions
    Molecular Dynamics Simulation
    Gene Expression Regulation
    Theoretical Models

    The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations

    Kirmizialtin, S., Silalahi, A. R. J., Elber, R. & Fenley, M. O., Feb 22 2012, In : Biophysical Journal. 102, 4, p. 829-838 10 p.

    Research output: Contribution to journalArticle

    Molecular Dynamics Simulation
    Atmosphere
    RNA
    Ions
    Strontium
    2011

    Revisiting and computing reaction coordinates with directional milestoning

    Kirmizialtin, S. & Elber, R., Jun 16 2011, In : Journal of Physical Chemistry A. 115, 23, p. 6137-6148 12 p.

    Research output: Contribution to journalArticle

    Fluxes
    Adenosine
    Molecular dynamics
    adenosines
    Trajectories
    2010

    Computational exploration of mobile ion distributions around RNA duplex

    Kirmizialtin, S. & Elber, R., Jun 24 2010, In : Journal of Physical Chemistry B. 114, 24, p. 8207-8220 14 p.

    Research output: Contribution to journalArticle

    ion distribution
    RNA
    Ions
    ions
    replicas
    2008

    Simulations of the untying of molecular friction knots between individual polymer strands

    Kirmizialtin, S. & Makarov, D. E., Mar 14 2008, In : Journal of Chemical Physics. 128, 9, 094901.

    Research output: Contribution to journalArticle

    strands
    Polymers
    friction
    Friction
    polymers
    2007

    Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations

    Goodrich, C. P., Kirmizialtin, S., Huyghues-Despointes, B. M., Zhu, A., Scholtz, J. M., Makarov, D. E. & Movileanu, L., Apr 5 2007, In : Journal of Physical Chemistry B. 111, 13, p. 3332-3335 4 p.

    Research output: Contribution to journalArticle

    electrophoresis
    Electrophoresis
    peptides
    recording
    Peptides
    2006

    Computer simulations of protein translocation

    Kirmizialtin, S., Huang, L. & Makarov, D. E., Jul 1 2006, In : Physica Status Solidi (B) Basic Research. 243, 9, p. 2038-2047 10 p.

    Research output: Contribution to journalArticle

    computerized simulation
    proteins
    Proteins
    Computer simulation
    porosity
    2005

    Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore

    Huang, L., Kirmizialtin, S. & Makarov, D. E., Sep 22 2005, In : Journal of Chemical Physics. 123, 12, 124903.

    Research output: Contribution to journalArticle

    computerized simulation
    proteins
    porosity
    pulling
    Computer simulation

    Topography of the free-energy landscape probed via mechanical unfolding of proteins

    Kirmizialtin, S., Huang, L. & Makarov, D. E., Jun 15 2005, In : Journal of Chemical Physics. 122, 23, 234915.

    Research output: Contribution to journalArticle

    Topography
    Free energy
    topography
    free energy
    proteins
    2004

    Translocation of a β-hairpin-forming peptide through a cylindrical tunnel

    Kirmizialtin, S., Ganesan, V. & Makarov, D. E., Nov 22 2004, In : Journal of Chemical Physics. 121, 20, p. 10268-10277 10 p.

    Research output: Contribution to journalArticle

    peptides
    tunnels
    Tunnels
    Peptides
    ribosomes
    2003

    Conformational properties of the bacterial polyester poly(3-hydroxy-5,8-decadienoate)

    Kirmizialtin, S., Baysal, C. & Erman, B., Feb 25 2003, In : Macromolecules. 36, 4, p. 1132-1137 6 p.

    Research output: Contribution to journalArticle

    Polyesters
    Molecular dynamics
    Computer simulation
    Gaussian distribution
    Dihedral angle

    New surfactants design for CO2 applications: Molecular dynamics simulations of fluorocarbon-hydrocarbon oligomers

    Kirmizialtin, S., Menceloglu, Y. Z. & Baysal, C., Sep 1 2003, In : Journal of Chemical Physics. 119, 9, p. 4953-4961 9 p.

    Research output: Contribution to journalArticle

    Fluorocarbons
    fluorocarbons
    Hydrocarbons
    oligomers
    Oligomers

    Vibrational spectroscopy of structural defects in oligothiophenes

    Yurtsever, E. & Kirmizialtin, S., Sep 10 2003, In : Molecular Physics. 101, 17, p. 2725-2729 5 p.

    Research output: Contribution to journalArticle

    Vibrational spectroscopy
    Raman scattering
    Spectrum Analysis
    infrared spectra
    Raman spectra