Publications

Publications

Edited Books:

[1] Natural Biomarkers for Cellular Metabolism: Biology, Techniques, and Applications. Vladimir V. Ghukasyan and Ahmed A. Heikal (Editors), Taylor & Francis, CRC Press (October 7, 2014, 408 Pages, ISBN: 9781466509986), Series in Cellular and Clinical Imaging (Senior Editor: Ammasi Periasamy).

Ghukasyan and Heikal_Book (2014)

Invited Reviews:

[1] Heikal, A.A. Intracellular coenzymes as natural biomarkers for metabolic activities and mitochondrial anomalies. Biomarkers in Medicine, 4(2): 241-263 (2010). https://www.futuremedicine.com/doi/10.2217/bmm.10.1

Invited Book Chapters:

[4] Wickramasinghe, D., R. Timerman, J. Bartusek, and A.A. Heikal. “Partitioning and diffusion dynamics of fluorescently labeled FTY720 in resting epithelial cells”. In “Advanced Time-Correlated Single-Photon Counting Applications”, Wolfgang Becker (Editor), Springer Series in Chemical Physics 111, Springer (ISBN: 978-3-319-14928-8, DOI: 10.1007/978-3-319-14929-5), Chapter 10, pp 339 - 355 (May 2015).

[3] Vishwasrao, H.D., Q. Yu, K. Hewawasam, A.A. Heikal. “Polarization Imaging of Cellular Autofluorescence”. In “Natural Biomarkers for Cellular Metabolism: Biology, Techniques, and Applications, Ghukasyan, V. and Ahmed A. Heikal (Editors), Series in Cellular and Clinical Imaging, Dr. Ammasi Periasamy (Senior Editor), Taylor & Francis Books, (October 2014).

[2] Heikal, A.A. A Multiparametric fluorescence approach for biomembrane studies. In, “Advances in Planar Lipid Bilayers and Liposomes”, Editor: Iglic A, Volume 13, Elsevier, Inc.; p. 169-197 (May 2011).

[1] Heikal, A.A. A Multiparametric imaging of cellular coenzymes for monitoring metabolic and mitochondrial activities. In, “Annual Review in Fluorescence 2010”, Editor: Chris D.Geddes, Springer, (2011).

Publications in Peer-Review Journals:

[42] Mersch, S.A., Bergman, B., Sheets, E.D., Boersma, A.J., and Heikal, A.A.. 2024. Two-photon excited-state dynamics of mEGFP- linker-mScarlet-I crowding biosensor in controlled environments. Phys. Chem. Chem. Phys., DOI: 10.1039/d3cp04733d.

[41] Kay T.M., C.P. Aplin, R. Simonet, J. Beenken, R.C. Miller, C. Libal, A.J. Boersma, E.D. Sheets, and A.A. Heikal. 2021. Molecular Brightness Approach for FRET Analysis of Donor-Linker- Acceptor Constructs at the Single Molecule Level: A Concept. Front. Mol. Biosci. 8:730394. DOI: 10.3389/fmolb.2021.730394

[40] Cong, A.T. Q., R.M.L. Pimenta, J. Holy  and A.A. Heikal. 2021. Associated anisotropy of intrinsic NAD(P)H for monitoring changes in the metabolic activities of breast cancer cells (4T1) in three-dimensional collagen matrix. Phys. Chem. Chem. Phys., 2021, 23, 12692. DOI: https://doi.org/10.1039/D0CP06635D

[39] Aplin, C.P., R.C. Miller, T.M. Kay, A.A. Heikal, A.J. Boersma, and E.D. Sheets. 2021. Fluorescence depolarization dynamics of ionic strength sensors using time-resolved anisotropy. Biophys. J., 120, 1417–1430. https://doi.org/10.1016/j.bpj.2021.01.035.

[38] Miller, R.C., C.P. Aplin, T.M. Kay, R. Leighton, C. Libal, R. Simonet, A. Cembran, A.A. Heikal, A.J. Boersma, and E.D. Sheets. 2020. FRET Analysis of Ionic Strength Sensors in the Hofmeister Series of Salt Solutions Using Fluorescence Lifetime Measurements. J. Phys. Chem. B, 124, 3447−3458. https://dx.doi.org/10.1021/acs.jpcb.9b10498

[37] Schwarz, J., H.J. Leopold, R. Leighton, R. C. Miller, C. P. Aplin, A. J. Boersma, A. A. Heikal, and E. D. Sheet. 2019. “Macromolecula Crowding Effects on Energy Transfer Efficiency and Donor-Acceptor Distance of Hetero-FRET Sensors using Time-Resolved Fluorescence.” Methods and Applications in Fluorescence, 7(2): 025002 (2019). DOI: 10.1088/2050-6120/ab0242.

[36] Leopold, H.J., R. Leighton, J. Schwarz, A. J. Boersma, E. D. Sheets, and A. A. Heikal. "Crowding Effects on Energy Transfer Efficiencies of hetero-FRET Probes as Measured using Time-Resolved Fluorescence Anisotropy". J. Phys. Chem. (B), 2019, 123, 379 - 393. DOI: 10.1021/acs.jpcb.8b09829.

[35] Cong, A., R.M.L. Pimenta, H.B. Lee, V. Mereddy, J. Holy, A.A. Heikal. 2018. "Two-Photon Fluorescence Lifetime Imaging of Intrinsic NAD(P)H in Three-Dimensional Tumor Models". Cytometry (Part A), 95A, 80 – 92, 2019. DOI: 10.1002-cyto.a.23632.

[34] Lee, H.B., A. Cong, H. Leopold, M. Currie, A.J. Boersma, E.D. Sheets,  and A.A. Heikal. 2018. "Rotational and Translational Diffusion of Size-Dependent Fluorescent Probes in Homogeneous and Heterogeneous Environments". Phys. Chem. Chem. Phys.,  20, 24045 – 24057. DOI: 10.1039/c8cp03873b.

[33] Currie, M., H. Leopold, J. Schwarz, A. J. Boersma, E.D. Sheets, and A.A. Heikal. 2017. Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies. The Journal of Physical Chemistry B, 121 (23), 5688-5698. DOI: 10.1021/acs.jpcb.7b01306.

[32] Xu, Z., F. Gao, E. Makarova, A.A. Heikal, and V. Nemykin. 2015. "Energy Transfer from Colloidal Quantum Dots to Near Infrared Absorbing Tetraazaporphyrins for Enhanced Light Harvesting", The Journal of Physical Chemistry (C); 119(18): 9754 - 9761 (DOI: 10.1021/acs.jpcc.5b01603).

[31] Heikal, A.A. 2014. Time-resolved fluorescence anisotropy and fluctuation correlation analysis of major histocompatibility complex class I proteins in fibroblast cells. Methods; Volume 66: 283 - 291.

[30] Solntsev P.V., K.L. Spurgin, J.R. Sabin, A.A. Heikal, V.N. Nemykin. 2012. Photoinduced charge transfer in short-distance ferrocenylsubphthalocyanine dyads. Inorg. Chem., 51(12): 6537-6547.

[29] Yu, Q. and A.A. Heikal. 2009. Two-photon autofluorescence dynamics imaging reveals sensitivity of intracellular NADH concentration and conformation to cell physiology at the single-cell level. Journal of Photochemistry and Photobiology (B): Biology, 95: 46–57; Press Release.

[28] Ariola, F.S., Z. Li, C. Cornejo, R. Bittman, and A.A. Heikal. 2009. Membrane fluidity and lipid order in ternary giant unilamellar vesicles using a new Bodipy-cholesterol derivative. Biophysical Journal, April Issue, 96(7), 2696–2708.

[27] Davey, A.M., K.M. Krise, E.D. Sheets, and A.A. Heikal.  2008.  Molecular perspective of antigen-mediated mast cell signaling. Journal of Biological Chemistry, 283:7117-7127. Press Release.

[26] Davey, A.M., R.P. Walvick, Y. Liu, A.A. Heikal, and E.D. Sheets.  2007.  Membrane order and molecular dynamics associated with IgE receptor crosslinking in mast cells.  Biophysical Journal, 92: 343-355. 

[25] Yu, Q., M. Proia, and A.A. Heikal. 2008. Integrated biophotonics approach for noninvasive, multiscale studies of biomolecular and cellular biophysics. Journal of Biomedical Optics, 13: 04131.

[24] Larson, D.R., H. Ow, H.D. Vishwasrao, and A.A. Heikal, U. Wiesner, and W.W. Webb. 2008. Silica nanoparticle architecture determines radiative properties of encapsulated fluorophores. Chemistry of Materials, 20: 2677-2684.

[23] Liu, Y., H.-R. Kim, and A.A. Heikal. 2006. Structural basis of fluorescence fluctuation dynamics of green fluorescent proteins in acidic environments. Journal of Physical Chemistry (B), 110: 24138-24146.

[22] Ariola, F.S., Mudaliar, D.J., R.P. Walvick, and A.A. Heikal. 2006. Dynamics of lipid phases and lipid-marker interactions in model biomembranes. Physical Chemistry Chemical Physics, 8(39): 4517-4529.

[21] Shi, K., A.A. Heikal, and Z. Liu. 2006. A single-shot approach for measuring two-photon action cross-section of fluorescent markers. Optics Express, 14(19): 8722-8727.

[20] Vishwasrao, H.D., A.A. Heikal, K.A. Kasischke, and W.W. Webb.  2005.  Conformational dependence of intracellular NADH on metabolic state revealed by associated fluorescence anisotropy.  Journal of Biological Chemistry, 208(26): 25119-252126; Issue cover and Press Release.

Vischwasrao et al_JBC (2005) Issue Cover

[19] Hess, S.T., A.A. Heikal, and W.W. Webb. 2004. Fluorescence photoconversion kinetics in novel green fluorescent protein pH sensors (pHluorins).  Journal of Physical Chemistry (B), 108(28): 10138-10148; Issue cover.

Hess et al_JPC(B) Issue Cover (2004)

[18] Korlach, J., D. Baird, A.A. Heikal, K.R. Gee, G.R. Hoffman, and W.W. Webb.  2004. Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled g-phosphate linked GTP analogs. Proceedings of the National Academy of Sciences (USA), 101(9): 2800-2805.

[17] Hess, S.T., E.D. Sheets, A. Wagenknecht-Wiesner, and A.A. Heikal. 2003. Quantitative analysis of the fluorescence properties of intrinsically fluorescent proteins in living cells. Biophysical Journal, 85: 2566–2580.

[16] Huang, S., A.A. Heikal, and W.W. Webb. 2002. Two-photon fluorescence spectroscopy and microscopy on NAD(P)H and flavoprotein. Biophysical Journal, 82(5):2811-2825.

[15] Hess, S.T., S. Huang, A.A. Heikal, and W.W. Webb. 2002. Biological and chemical applications of fluorescence correlation spectroscopy: a review. Biochemistry, 41(3):697-705.

[14] Heikal, A.A., S.T. Hess, and W.W. Webb. 2001.  Multiphoton spectroscopy and excited state dynamics of enhanced green fluorescent protein (EGFP): acid-base specificity. Chemical Physics, 274(1): 37-55.

[13] Heikal, A.A., S.T. Hess, G.S. Baird, R.Y. Tsien, and W.W. Webb. 2000. Molecular spectroscopy and dynamics of intrinsically fluorescent proteins: coral red (dsRed) and yellow (Citrine). Proceedings of the National Academy of Sciences (USA), 97(22): 11996-12001

[12] Schwille, P., S. Kummer, A.A. Heikal, W.E. Moerner, and W.W. Webb.  2000. Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins. Proceedings of the National Academy of Sciences (USA), 97(1): 151-156. 

[11] Kuebler, S.M., M. Rumi, T. Watanabe, K. Braun, B.H. Cumpston, A.A. Heikal, L.L. Erskine, S. Thayumanavan, S. Barlow, S.R. Marder, and J.W. Perry.  2001. Optimizing two-photon initiators and exposure conditions for three-dimensional lithographic microfabrication.  Journal of Photopolymer Science and Technology, 14(4): 657-668.

[10] Rumi, M., J.E. Ehrlich, A.A. Heikal, J.W. Perry, S. Barlow, Z. Hu, D. McCord-Maughon, T.C. Parker, H. Roeckel, S. Thayumanavan, S.R. Marder, D. Beljonne, and J.-L. Bredas. 2000.  Structure-property relationships for two-photon absorbing chromophores: bis-donor diphenylpolyene and bis(styryl)benzene derivatives. Journal of the American Chemical Society, 122(39): 9500-9510.

[9] Cumpston, B.H., S.P. Ananthavel, S. Barlow, D.L. Dyer, J.E. Ehrlich, L.L. Erskine, A.A. Heikal, S.M. Kuebler, I.-Y.S. Lee, D. McCord-Maughon, J. Qin, H. Rockel, M. Rumi, X.-L. Wu, S.R. Marder, and J.W. Perry. 1999.  Two-photon polymerization initiators for three-dimensional optical data storage and microfabrication. Nature (London), 398(6722): 51-54.

[8] Albota, M., D. Beljonne, J.-L. Bredas, J.E. Ehrlich, J-Y. Fu, A.A. Heikal, S.T. Hess, T. Kogej, M.D. Levin, S.R. Marder, D. McCord-Maughon, J.W. Perry, H. Rockel, M. Rumi, G. Subramaniam, W.W. Webb, X.-L. Wu, and C. Xu.  1998.  Design of organic molecules with large two-photon absorption cross sections. Science, 281(5383): 1653-1656.

[7] Heikal, A.A., J.S. Baskin, L. Banares, and A.H. Zewail. 1997.  Structural effects on the isomerization dynamics of trans-stilbenes: IVR, microcanonical reaction rates, and the nature of the transition state. Journal of Physical Chemistry (A), 101(4): 572-590.

[6] Heikal, A.A., S.H. Chong, J.S. Baskin, and A.H. Zewail. 1995. Microscopic friction and solvation in barrier crossing: isomerization of stilbene in size-selected hexane clusters, Chemical Physics Letters, 242(4,5): 380-389.

[5] Kim, S.K., J.J. Breen, D.M. Willberg, L.W. Peng, A.A. Heikal, J.A. Syage, and A.H. Zewail.  1995. Solvation ultrafast dynamics of reactions. 8. Acid-base reactions in finite-sized clusters of naphthol in ammonia, water, and piperidine. Journal of Physical Chemistry, 99(19): 7421-7435.

[4] Lienau, C., A.A. Heikal, and A.H. Zewail. 1993.  Picosecond dynamics of hexane-solvated trans-stilbene. Chemical Physics, 175(1): 171-191.

[3] Banares, L., A.A. Heikal, and A.H. Zewail. 1992. Ultrafast dynamics of isomerization reactions: structural effects in stilbene(s). Journal of Physical Chemistry, 96(11): 4127-4130.

[2] Heikal, A.A., L. Banares, D.H. Semmes, and A.H. Zewail. 1991. Real-time dynamics of vibrational predissociation in anthracene-argonn (n = 1, 2, 3). Chem. Phys, 156(2): 231-250.

[1] Breen, J.J., L.W. Peng, D.M. Willberg, A.A. Heikal, P. Cong, and A.H. Zewail. 1990.  Real-time probing of reactions in clusters. Journal of Physical Chemistry, 92(1): 805-807.

Papers Published in Books or Proceedings:

[14] Clint McCue, Sarah A. Mersch, Sarah Bergman, Erin D. Sheets, Ahmed A. Heikal, Conformational equilibrium analysis of mCerulean3–linker–mCitrine constructs using time-resolved fluorescence measurements in controlled environments. Proc. SPIE 12681, Ultrafast Nonlinear Imaging and Spectroscopy XI, 1268107 (5 October 2023); doi: 10.1117/12.2679719

[13] S. Mersch, M. Brink, R. Simonet, A.J. Boersma, E.D. Sheets, A.A. Heikal. Integrated laser-induced fluorescence spectroscopy of donor-linker-acceptor constructs for bioenvironmental sensing. Proc. SPIE 12228, Ultrafast Nonlinear Imaging and Spectroscopy X, 1222804 (3 October 2022); doi: 10.1117/12.2635951.

[12] C.P. Aplin, T.M. Kay, J. Beenken, C. Nwachuku, E.Tetteh-Jada, A.A. Heikal, A.J. Boersma, and E.D. Sheets. 2020. Comparative studies of the fluorescence spectroscopy and dynamics of mCerulean3 and mTurquoise2.1 as donors in FRET pairing with mCitrine. Ultrafast Nonlinear Imaging and Spectroscopy VIII, Zhiwen Liu, Demetri Psaltis, and Kebin Shi (Editors), Proceedings of SPIE, Vol. 11497, 114970T1-11; doi: 10.1117/12.2571138.

[11] C.P. Aplin, T.M. Kay, R.C. Miller, A.J. Boersma, E.D. Sheets, A.A. Heikal. 2019. Integrated fluorescence approach for FRET analysis of environmental sensors, Proc. SPIE 11122, Ultrafast Nonlinear Imaging and Spectroscopy VII, 111220E (9 September 2019).

[10] Jacob Schwarz, Ryan Leighton*, Hannah J. Leopold, Megan Currie, Arnold J. Boersma, Erin D. Sheets, and Ahmed A. Heikal. 2017.“Kinetics model for the wavelength-dependence of excited-state dynamics of hetero-FRET sensors.”  Proc. SPIE 10380, Ultrafast Nonlinear Imaging and Spectroscopy V, 103800S; doi: 10.1117/12.2274793.

[9] Spencer Gardeen, Joseph L. Johnson, and Ahmed A. Heikal. 2016. Fluorescence Fluctuation Analysis of BACE1-GFP Fusion Protein in Cultured HEK293 Cells". Proc. SPIE 9956, Ultrafast Nonlinear Imaging and Spectroscopy IV, 99560K, doi: 10.1117/12/2237183.

[8] Megan Currie, Chang Thao, Randi Timerman, Robb Welty, Brenden Berry, Erin D. Sheets, and Ahmed A. Heikal. 2015. Multiscale diffusion of a molecular probe in a crowded environment: A concept. Proc. SPIE 9584, Ultrafast Nonlinear Imaging and Spectroscopy III, 95840E (August 31, 2015), doi:10.1117/12.2188746."

[7] John Alfveby, Randi Timerman, Monica P. Soto Velasquez, Dhanushka W.P.M. Wickramasinghe, Jillian Bartusek, and Ahmed A. Heikal. 2014. "Time- and polarization-resolved cellular autofluorescence towards quantitative biochemistry on living cells". Ultrafast Nonlinear Imaging and Spectroscopy II, Zhiwen Liu, Iam Choon Khoo, Demetri Psaltis (Editors), Proc. of SPIE Vol. 9198 91980U, Pages 1-15 (invited paper).

[6] Liu, Y. F.S. Ariola, H.-R. Kim, Q. Yu, R. Walvick, and A.A. Heikal. 2006. Two-photon excited-state and conformation dynamics of NADH binding with dehydrogenases. Femtochemistry and Femtobiology, VII, William Castlemann (Editor), Elsevier B.V. Ltd. 396-401.

[5] Walvick, R.P., D.J. Mudaliar, and A.A. Heikal. Quantitative analysis of biomolecular concentration in living cells with high spatial resolution. Institute of Electrical and Electronics Engineers (IEEE), pp 37 (2005).

[4] Cumpston, B.H., S.P. Ananthavel, S. Barlow, D.L. Dyer, J.E. Ehrlich, L.L. Erskine, A.A. Heikal, S.M. Kuebler, I.-Y.S. Lee, D. McCord-Maughon, J. Qin, H. Rockel, M. Rumi, X.-L. Wu, S.R. Marder, and J.W. Perry. Two-photon polymerization initiators for three-dimensional optical data storage and microfabrication. Multiphoton Excitation Microscopy, Editors: B.J. Thompson, SPIE Optical Engineering Press, 175:212-215 (2003).

[3] Albota, M., D. Beljonne, J.-L. Bredas, J.E. Ehrlich, J.-Y. Fu, A.A. Heikal, S.E. Hess, T. Kogej, M.D. Levin, S.R. Marder, D. McCord-Maughon, J.W. Perry, H. Rocket, M. Rumi, G. Subramaniam, W.W. Webb, X.-L. Wu, and C. Xu.  Design of organic molecules with large two-photon absorption cross sections.  Multiphoton Excitation Microscopy, Editors:  B.J. Thompson, SPIE Optical Engineering Press, 175:507-510 (2003).

[2] Heikal, A.A., S.T. Hess, E.D. Sheets, and W.W. Webb. Mutation-photophysics relationship in intrinsically fluorescent proteins. Femtochemistry and Femtobiology: Ultrafast Dynamics in Molecular Science, Editors: A. Douhal and J. Santamaria, World Scientific, Singapore, pp 774-781 (2002).

[1] Heikal, A.A. and W.W. Webb. Multiphoton fluorescence microscopy for functional imaging of biomolecules. Nonlinear Optics: Materials, Fundamentals and Applications (NLO), Bio-Chemical Nonlinear Optics (ThA4-1): 321-323 (2002).