Publications

At Yale

22. Force-Detected Nanoscale Absorption Spectroscopy in Water at Room Temperature using an Optical Trap

Jacob W. Black, Maria Kamenetska, Ziad Ganim
J. Chem. Phys., 2018, 148(14), 144201 [link: 10.1063/1.5017853]

21. An Optical Tweezers Platform for Single Molecule Force Spectroscopy in Organic Solvents

Jacob W. Black, Maria Kamenetska, Ziad Ganim
Nano Lett., 2017, 17(11), 6598-6605 [link: 10.1021/acs.nanolett.7b02413]


20. Mechanically Switching Single Molecule Fluorescence of GFP by Unfolding and Refolding

Ziad Ganim, Matthias Rief
Proc. Natl. Acad. Sci. USA, 2017, 114(42), 11052-11056 [link: 10.1073/pnas.1704937114]


19. Octave-spanning mid-infrared pulses by plasma generation in air pumped with an Yb:KGW source

Jinqing Huang, Alexander Parobek, Ziad Ganim
Opt. Lett., 2016, 41, 4855-4858 [link: 10.1364/OL.41.004855]

 

Prior to Yale

18. Correction: Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

Ziad Ganim, Kevin C. Jones, Andrei Tokmakoff
Phys. Chem. Chem. Phys., 2017, 19, 18773-3588 [link: 10.1039/c7cp90151h]

17. Single-Molecule Vibrational Spectroscopy Adds Structural Resolution to the Optical Trap (New and Notable Commentary)

Ziad Ganim
Biophys. J., 2013, 104, 4-5 [link: 10.1016/j.bpj.2012.09.044]


16. Vibrational excitons in ionophores; Experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels

Ziad Ganim, Andrei Tokmakoff, Alipasha Vaziri
New. J. Phys., 2011, 13, 113030 [link: 10.1088/1367-2630/13/11/113030]


15. Transient Two-Dimensional Spectroscopy with Linear Absorption Corrections Applied to Temperature Jump 2D IR

Kevin Jones, Ziad Ganim, Chunte Sam Peng, Andrei Tokmakoff
J. Opt. Soc. Am. B., 2012, 29, 118-129 [link: 10.1364/JOSAB.29.000118]


14. Solvent and Conformation Dependence of Amide I Vibrations in Peptides and Proteins Containing Proline

Santanu Roy, Joshua Lessing, Georg Meisl, Ziad Ganim, Andrei Tokmakoff, Jasper Knoester, Thomas L. C. Jansen
J. Chem. Phys., 2011, 135, 234507[link: 10.1063/1.3665417]


13. Melting of a β-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations

Adam W. Smith, Joshua Lessing, Ziad Ganim, Chunte Sam Peng, Andrei Tokmakoff, Santanu Roy, Thomas L. C. Jansen, Jasper Knoester
J. Phys. Chem. B, 2010, 114, 10913-10924 [link: 10.1021/jp104017h]


12. Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

Ziad Ganim, Kevin C. Jones, Andrei Tokmakoff
Phys. Chem. Chem. Phys., 2010, 12, 3579-3588 [link: 10.1039/b923515a]


11. Heterodyne-Detected Dispersed Vibrational Echo Spectroscopy

Kevin C. Jones, Ziad Ganim, Andrei Tokmakoff
J. Phys. Chem. A, 2009, 113 (51), 14060-14066 [link: 10.1021/jp906256s]


10. Amide I'-II' 2D IR Spectroscopy Provides Enhanced Protein Secondary Structural Sensitivity

Lauren P. DeFlores, Ziad Ganim, Rebecca A. Nicodemus, Andrei Tokmakoff
J. Am. Chem. Soc., 2009, 131 (9), 3385-3391 [link: 10.1021/ja8094922]


9. Amide I 2D IR Spectroscopy of Proteins

Ziad Ganim, Hoi Sung Chung, Adam W. Smith, Lauren P. DeFlores, Kevin C. Jones, and Andrei Tokmakoff
Acc. Chem. Res., 2008, 41 (3), 432-441 [link: 10.1021/ar700188n]


8. Transient 2D IR Spectroscopy of Ubiquitin Unfolding Dynamics

Hoi Sung Chung*, Ziad Ganim*, Kevin C. Jones, and Andrei Tokmakoff
Proc. Natl. Acad. Sci. USA, 2007, 104 (36), 14237-14242 [link: 10.1073/pnas.0700959104]


7. Spectral Signatures of Heterogeneous Protein Ensembles Revealed by MD Simulations of 2DIR Spectra

Ziad Ganim and Andrei Tokmakoff
Biophys. J., 2006, 91 (7), 2636-2646 [link: 10.1529/biophysj.106.088070]


6. The Anharmonic Vibrational Potential and Relaxation Pathways of the Amide I and II Modes of N-Methylacetamide

Lauren P. Deflores, Ziad Ganim, Sarah F. Ackley, Hoi Sung Chung, and Andrei Tokmakoff
J. Phys. Chem. B, 2006, 110 (38), 18973-18980 [link: 10.1021/jp0603334]


5. Residual Native Structure in a Thermally Denatured β-Hairpin

Adam W. Smith, Hoi Sung Chung, Ziad Ganim, and Andrei Tokmakoff
J. Phys. Chem. B, 2005, 109 (36), 17025-17027 [link: 10.1021/jp053949m]


4. Conformational Changes During the Nanosecond-To-Millisecond Unfolding of Ubiquitin

Hoi Sung Chung, Munira Khalil, Adam W. Smith, Ziad Ganim, and Andrei Tokmakoff
Proc. Natl. Acad. Sci. USA, 2005, 102 (3), 612-617 [link: 10.1073/pnas.0408646102]


3. Resonance Raman Analysis of the Mechanism of Energy Storage and Chromophore Distortion in the Primary Visual Photoproduct

Elsa C. Y. Yan, Ziad Ganim, Manija A. Kazmi, Belinda S. W. Chang, Thomas P. Sakmar, Richard A. Mathies
Biochemistry, 2004, 43 (34), 10867-10876 [link: 10.1021/bi0400148]


2. Retinal Counterion Switch in the Photoactivation of the G Protein-Coupled Receptor Rhodopsin

Elsa C. Y. Yan, Manija A. Kazmi, Ziad Ganim, Jian-Min Hoi, Douhai Pan, Belinda S. W. Chang, Thomas P. Sakmar, and Richard A. Mathies
Proc. Natl. Acad. Sci. USA, 2003, 100 (16), 9262-9267 [link: 10.1073/pnas.1531970100]


1. Time-Resolved Resonance Raman Analysis of Chromophore Structural Changes in the Formation and Decay of Rhodopsin's BSI Intermediate

Duohai Pan, Ziad Ganim, Judy E. Kim, Michiel A. Berhoeven, Johan Lugtenburg, Richard A. Mathies
J. Am. Chem. Soc., 2002, 124 (17), 4857-4864 [link: 10.1021/ja0126663]