Publications

S.K. Sharma, B.J. Al-Hourani, M. Wuest, J.Y. Mane, J.A. Tuszynski, V. Baracos, M. Suresh and F. Wuest, Synthesis and evaluation of fluorobenzoylated di- and tripeptides as inhibitors of cyclooxygenase-2 (COX-2), Bioorganic and Medicinal Chemistry 20:2221-2226 (2012).

P. Davies, L. Demetrius and J.A. Tuszynski, Implications of quantum metabolism and natural selection for the origin of cancer cells and tumor progression, AIP Advances, Special Issue on the Physics of Cancer 2:011101 [14 pages] (2012). doi:10.1063/1.3697850

T.J.A. Craddock, J.A. Tuszynski, D. Chopra, N. Casey, L.E. Goldstein, S.R. Hameroff and R. Tanzi, The Zinc Dyshomeostasis Hypothesis of Alzheimer's Disease, PLoS ONE 7(3):e33552 (2012). doi:10.1371/journal.pone.0033552

T.J.A. Craddock, S.R. Hameroff and J.A. Tuszynski, Cytoskeletal signaling: Is molecular memory encoded in microtubule lattices by CaMKII phosphorylation, PloS Computational Biology 8:e1002421 (2012).

M.V. Satarić, S. Zdravković and J.A. Tuszyński, Modeling of Relay Helix Functional Dynamics and Feasibility of Experimental Verification by Neutron Scattering, Chaos: An Interdisciplinary Journal of Nonlinear Science 21(4):043135 (2011). doi:10.1063/1.3665091

T.J.A. Craddock and J.A. Tuszynski, Molecular Models of Information Processing at the Level of Individual Neurons and Their Significance (invited paper), Journal Paritantra- Journal of System Science and Engineering 20(1):15-31 (2012).

A.A. Saha, T.J.A. Craddock and J.A. Tuszynski, An investigation of the plausibility of stochastic resonance in tubulin dimers, Biosystems 107:81-87 (2012).

K. Barakat, B.B. Issack, M. Stepanova and J.A. Tuszynski, Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: Comparing the wild type to the R248Q mutant, PLoS One 6:e27651 (2011). doi:10.1371/journal.pone.0027651

M. Ashrafuzzaman, M. Duszyk and J.A. Tuszynski, Chemotherapy Drugs Thiocolchicoside and Taxol Permeabilize Lipid Bilayer Membranes by Forming Ion Pores, Journal of Physics: Conference Series 329:012029 (2011). doi:10.1088/1742-6596/329/1/012029

H. Freedman, T. Luchko, R.F. Luduena and J.A. Tuszynski, Molecular Dynamics Modeling of C-terminal Tail Interactions with the Microtubule Surface, Proteins: Structure, Function, Bioinformatics 79(10):2968-2982 (2011). doi:10.1002/prot.23155

L. Alisaraie and J.A. Tuszynski, Determination of Noscapine’s Localization and Interaction with the Tubulin-α/β Heterodimer, Chemical Biology & Drug Design, 78:535-546 (2011). doi:10.1111/j.1747-0285.2011.01189.x

P. Hinow, V. Rezania, M. Lopus, M.A. Jordan and J.A. Tuszynski, Modeling the effects of drug binding on the dynamic instability of microtubules, Physical Biology 8:056004 (2011) doi:10.1088/1478-3975/8/5/056004

E.B. Kelly, J.A. Tuszynski, and M. Klobukowski, QM and QM/MD Simulations of the Vinca Alkaloids Docked to Tubulin, Journal of Molecular Graphics and Modelling 30:54-66 (2011). doi:10.1016/j.jmgm.2011.06.005

E.A. Rietman, J.Z. Colt and J.A. Tuszynski, Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems, Theoretical Biology and Medical Modeling 8:19 (2011). doi:10.1186/1742-4682-8-19

E.A. Rietman, R.L. Karp and J.A. Tuszynski, Review and application of group theory to molecular systems biology, Theoretical Biology and Medical Modeling 8:21 (2011). doi:10.1186/1742-4682-8-21

P.C. Davies, L. Demetrius and J.A. Tuszynski, Cancer as a dynamical phase transition, Theoretical Biology and Medical Modeling 8:30 (2011). doi:10.1186/1742-4682-8-30

A. Samarbakhsh and J. A. Tuszynski, Vibrational Dynamics of bio- and nano-filaments in viscous solution subjected to ultrasound: implications for microtubules, European Biophysics Journal 40: 937-946 (2011). doi:10.1007/s00249-011-0709-0

D.L. Sekulić, B.M. Satarić, J.A. Tuszynski and M.V. Satarić, Nonlinear Ionic Pulses Along Microtubules, European Physical Journal E Soft Matter and Biological Physics 34:49-60 (2011). doi:10.1140/epje/i2011-11049-0

A. Samarbakhsh and J.A. Tuszynski, Resonance Condition in  Microtubules Using Ultrasound Plane Waves, Journal of Computational and Theoretical Nanoscience 9:1-5 (2011).

V. Salari, J.A. Tuszynski, I. Bokkon, M. Rahnama and M. Cifra, On the Photonic Cellular Interaction and the Electric Activity of Neurons in the Human Brain, Journal of Physics: Conference Series 329:012006 (2011). doi:10.1088/1742-6596/329/1/012006

C-Y Tseng, M. Ashrafuzzaman, J.Y. Mane, J. Kapty, J.R. Mercer, and J.A. Tuszynski, Entropic fragment based approach to aptamer design, Chemical Biology and Drug Design 78:1-13 (2011). doi:10.1111/j.1747-0285.2011.01125.x

B.J. Al-Hourani, S.K. Sharma, J.Y. Mane, J.A. Tuszynski, V. Baracos, T. Kniess, M. Suresh, J. Pietzsch and F. Wuest, Synthesis and evaluation of 1,5-diaryl-substituted tetrazoles as novel selective cyclooxygenase-2 (COX-2) inhibitors, Bioorganic & Medicinal Chemistry Letters 21:1823-1826 (2011). doi:10.1016/j.bmcl.2011.01.057

M. Rahnama, J.A. Tuszynski, I. Bokkon, M. Cifra, P. Sardar, S. Bosman, and V. Salari, Emission of mitochondrial Biophotons and their effect on electrical activity of membrane via microtubules, Journal of Integrative Neuroscience 10(1):65-88 (2011).

C-Y Tseng and J.A. Tuszynski, Using Entropy Leads to a Better Understanding of Biological Systems, Entropy 12(12):2450-2469 (2010). doi:10.3390/e12122450

P.S. Agutter and J.A. Tuszynski, Analytic Theories of Allometric Scaling, Journal of Experimental Biology 214:1055-1062 (2011). doi:10.1242/jeb.054502

K. Barakat and J.A. Tuszynski, Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta, Journal of Molecular Graphics and Modelling 29(5):702-716  (2011). doi:10.1016/j.jmgm.2010.12.003

S.R. Hameroff, T.J.A. Craddock and J.A. Tuszynski, “Memory bytes”—A molecular match for CaMKII phosphorylation encoding of microtubule lattices, Journal of Integrative Neuroscience 9(3):253-267 (2010).

I. Bokkon, V. Salari and J.A. Tuszynski, Emergence of Intrinsic Representations of Images by Feedforward and Feedback Processes and Bioluminescent Photons in Early Retinopic Areas, Journal of Integrative Neuroscience, 10(1):47-64 (2011).

R.E. Marsh, J.A. Tuszynski, M. Sawyer and K.J.E. Vos, A model of competing saturable kinetic processes with application to the pharmacokinetics of the anticancer drug paclitaxel, Mathematical Biosciences and Engineering 8(2):325-355 (2011).

A.A. Saha and J.A. Tuszynski, Signal Transmission in Carbon Nanotube Arrays, Journal of Computational and Theoretical Nanoscience, 8:60-88 (2011). doi:10.1166/jctn.2011.1659

C-Y Tseng, J.Y. Mane, P. Winter, L. Johnson, T. Huzil, E. Izbicka, R.F. Luduena and J.A. Tuszynski, Quantitative analysis of the effect of tubulin isotype expression on sensitivity of cancer cell lines to a set of novel colchicine derivatives, Molecular Cancer 9:131 (2010) doi:10.1186/1476-4598-9-131

Bókkon, V. Salari, J.A. Tuszynski, I. Antal, Estimation of the number of biophotons involved in the visual perception of a single-object image: biophoton intensity can be considerably higher inside cells than outside, Journal of Photochemistry and Photobiology B: Biology, 100:160-166 (2010). doi:10.1016/j.jphotobiol.2010.06.001

T.J.A. Craddock, J.A. Tuszynski, A. Priel and H. Freedman, Microtubule Ionic Conduction and its Implications for Higher Cognitive Functions, Journal of Integrative Neuroscience 9(2):103-122 (2010).

M. Bennett, K. Barakat, T. Huzil, J.A. Tuszynski and D.C. Schriemer, Discovery and Characterization of the Laulimalide-Microtubule Binding Mode by Mass Shift Perturbation Mapping, Chemistry and Biology 17:725-734 (2010) doi:10.1016/j.chembiol.2010.05.019

H. Freedman, V. Rezania, A. Priel, E. Carpenter, S. Noskov and J.A. Tuszynski, Model of ionic currents through microtubule nanopores and the lumen, Physical Review E 81:051912 [11 pages] (2010), also selected for the May 24, 2010 issue of Virtual Journal of Nanoscale Science & Technology, also selected for the May 15, 2010 issue of Virtual Journal of Biological Physics Research.

J.T. Huzil, P. Winter, L. Johnson, A.L. Weis, T. Bakos, A. Banerjee, R.F. Luduena, S. Damaraju and J.A. Tuszynski, Computational design and biological testing of highly cytotoxic colchicine ring A modifications, Chemical Biology and Drug Design 75(6):541-550 (2010). doi:10.1111/j.1747-0285.2010.00970.x

T. Luchko, S. Gusarov, D. Roe, C. Simmerling, D. Case, J.A. Tuszynski, and A. Kovalenko, Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber, Journal of Chemical Theory and Computation 6(3):607-624 (2010). doi:10.1021/ct900460m

L. Demetrius, J. Coy and J.A. Tuszynski, Cancer Proliferation and Therapy: the Warburg Effect and Quantum Metabolism, Theoretical Biology and Medical Modelling 7:2 (2010). doi:10.1186/1742-4682-7-2

N.J. Woolf, T.J.A. Craddock, D.E. Friesen, and J.A. Tuszynski, Neuropsychiatric Illness: A Case for Impaired Neuroplasticity and Possible Quantum Processing Derailment in Microtubules, Neuroquantology, 8(1):13-28 (2010).

K. Barakat, J. Mane, D. Friesen and J.A. Tuszynski, Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions, Journal of Molecular Graphics and Modelling 28(6):555-568 (2010). doi:10.1016/j.jmgm.2009.12.003

H. Freedman, L.P. Huynh, L. Le, T.E. Cheatham III, J.A. Tuszynski, and T.N. Truong, Explicitly Solvated Ligand Contribution to Continuum Solvation Models for Binding Free Energies:  Selectivity of Theophylline Binding to an RNA Aptamer, Journal of Physical Chemistry B 114(6):2227-2237 (2010). doi:10.1021/jp9059664

D. Bartusik, B. Tomanek, E. Lattová, H. Perreault, J. Tuszynski, and G. Fallone, Derivatives of thiocolchicine and its applications to CEM cells treatment using 19F magnetic resonance ex vivo, Bioorganic Chemistry 38(1):1-6 (2010). doi:10.1016/j.bioorg.2009.10.002

J.L.P. Velazquez, J.A. Tuszynski and L.G. Dominguez, Boundaries of brain information processing, Journal of Biological Physics, 36(1):1 (2010). doi:10.1007/s10867-009-9179-3

J.T. Huzil, J. Mane, and J.A. Tuszynski, Computer assisted design of second generation colchicine derivatives, Interdisciplinary Sciences- Computational Life Sciences 2(2):169-174 (2010). doi:10.1007/s12539-010-0076-z

D. Bartusik, B. Tomanek, E. Lattová, H. Perreault , J.A. Tuszynski and G. Fallone, The efficacy of new colchicine derivatives and viability of the T-lymphoblastoid cells in three-dimensional culture using 19F MRI and HPLC-UV ex vivo, Bioorganic Chemistry 37(6):193-201 (2009). doi:10.1016/j.bioorg.2009.07.007

M. Rahnama , V. Salari and J.A. Tuszynski, How Can the Visual Quantum Information be Transferred to The Brain Intact, Collapsing There and Causing Consciousness?, Neuroquantology 7(4): 491-499 (2009).

L. Demetrius and J.A. Tuszynski, Quantum metabolism explains the allometric scaling of metabolic rates, Journal of the Royal Society Interface 7:507-514 (2010). doi:10.1098/rsif.2009.0310

P. Chelminiak, J.M. Dixon and J.A. Tuszynski, Torsional Elastic Deformations of Microtubules Within Continuous Sheet Model, European Physical Journal E Soft Matter and Biological Physics 31(2):215-227 (2010). doi:10.1140/epje/i2010-10562-x

P. Hinow, V. Rezania and J.A. Tuszynski, A continuous model for microtubule dynamics with catastrophe, rescue and nucleation processes, Physical Review E 80(3):031904 (2009), also selected for the September 15, 2009 issue of Virtual Journal of Biological Physics Research. doi:10.1103/PhysRevE.80.031904

A. Samarbakhsh and J.A. Tuszynski, Viscous drag effect in the flexural rigidity and cantilever stiffness of bio- and nano-filaments measured with the shooting-bead method, Physica Review E 80:011903 [9 pages] (2009), also selected for the July 13, 2009 issue of Virtual Journal of Nanoscale Science & Technology. doi:10.1103/PhysRevE.80.011903

M. Bennett, J.K. Chik, G.W. Slysz, T. Luchko, J.A. Tuszynski, D.L. Sackett and D.C. Schriemer, Structural mass spectrometry of the alpha beta-tubulin dimer supports a revised model of microtubule assembly, Biochemistry 48(22):4858-4870 (2009). doi:10.1021/bi900200q Correction to Structural Mass Spectrometry of the αβ-Tubulin Dimer Supports a Revised Model of Microtubule Assembly, Biochemistry 48(40):9704 (2009).

K. Barakat, J.T. Huzil, C. Dumontet, L. Jordheim and J.A. Tuszynski, Characterization of an Inhibitory Dynamic Pharmacophore for the ERCC1-XPA Interaction Using a Combined Molecular Dynamics and Virtual Screening Approach, Journal of Molecular Graphics and Modelling 28(2):113-130 (2009). doi:10.1016/j.jmgm.2009.04.009

T.J.A. Craddock, C. Beauchemin and J.A. Tuszynski, Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests, Biosystems 97(1):28-34 (2009). doi:10.1016/j.biosystems.2009.04.001

J.T. Huzil, K. Barakat and J.A. Tuszynski, Electrostatic Contributions to Colchicine Binding within Tubulin Isotypes, Electromagnetic Biology and Medicine, 28(4): 355-364 (2009). doi:10.3109/15368370903206606

A. Priel, J.A. Tuszynski and N.J. Woolf, Neural Cytoskeleton Correlates for Learning and Memory, Journal of Biological Physics, 36(1):3-21 (2010). doi:10.1007/s10867-009-9153-0

T.J.A. Craddock and J.A. Tuszynski, A Critical Assessment of the Information Processing Capabilities of Neuronal Microtubules Using Coherent Excitations, Journal of Biological Physics 36(1):53-70 (2010). doi:10.1007/s10867-009-9158-8

M.V. Sataric, D.I. Ilic, N. Ralevic and J.A. Tuszynski, A Nonlinear Model of Ionic Wave Propagation along Microtubules, European Journal of Biophysics 38(5):637-647 (2009). doi:10.1007/s00249-009-0421-5 Erratum: European Journal of Biophysics 38(8):1147

P. Chelminiak, J.A. Tuszynski and J.M. Dixon, Effects of C-Termini Distribution on Ion Transport Along Microtubules, Interdisciplinary Sciences- Computational Life Sciences 1(2): 108-112 (2009). doi:10.1007/s12539-009-0010-9

H. Freedman, J.T. Huzil, T. Luchko, R.F. Luduena, and J.A. Tuszynski, Identification and Characterization of an Intermediate Taxol Binding Site Within Microtubule Nanopores and a Mechanism for Tubulin Isotype Binding Selectivity, Journal of Chemical Informatics and Modeling. 49:424-436 (2009). doi:10.1021/ci8003336

V. Rezania and J.A. Tuszynski, A first principle (3+1)-dimensional model for microtubule polymerization, Physics Letters A 372(47): 7051-7056 (2008). doi:10.1016/j.physleta.2008.10.038

V. Rezania and J.A. Tuszynski, A Stochastic Model for Microtubule Dynamicity Involving Mixtures of Tubulin isotypes, International Journal of Quantum Chemistry 109(14):3430-3440 (2009). doi:10.1002/qua.21986

R.E. Marsh, J.A. Tuszynski, M.B. Sawyer and K. Vos, Emergence of power laws in the pharmacokinetics of paclitaxel due to competing saturable processes, Journal of Pharmacy and Pharmaceutical Science 11(3):77-96 (2008).

A. Priel and J.A. Tuszynski, A nonlinear cable-like model of amplified ionic wave propagation along microtubules, European Physics Letters 83: 68004 (2008). doi:10.1209/0295-5075/83/68004

K. Chen, J.T. Huzil, H. Freedman, P. Ramachandran, A. Antoniou, J.A. Tuszynski and L. Kurgan, Identification of tubulin drug binding sites and prediction of relative differences in binding affinities to tubulin isotypes using digital signal processing, Journal of Molecular Graphics and Modelling 27(4): 497-505 (2008). doi:10.1016/j.jmgm.2008.09.001

J.A. Tuszynski, S. Portet, J.M. Dixon, M. Nishino and L.Y. Yu-Lee, Propagation of Localized Bending Deformations in Microtubules, Journal of Computational and Theoretical Nanoscience 6:525-532 (2009). doi:10.1166/jctn.2009.1064

A. Priel, A.J. Ramos, J.A. Tuszynski and H.F. Cantiello, Effect of calcium on electrical energy transfer by microtubules, Journal of Biological Physics 34(5): 475-485 (2008). doi:10.1007/s10867-008-9106-z

V. Rezania and J.A. Tuszynski, Modeling polymerization of microtubules: A semi-classical nonlinear field theory approach, Physica A 387(23): 5795-5809 (2008). doi:10.1016/j.physa.2008.06.023

J.T. Huzil, J.K. Chik, G.W. Slysz, H. Freedman, J.A. Tuszynski, R.E. Taylor, D.L. Sackett, D.C. Schriemer, A unique mode of microtubule stabilization induced by peloruside A, Journal of Molecular Biology, 378(5): 1016-1030 (2008). doi:10.1016/j.jmb.2008.03.026

J. Mátrai, A. Jonckheer, E. Joris, P. Krüger, E. Carpenter, G. Verheyden, J.A. Tuszynski, M. De Maeyer and Y. Engelborghs, Exploration of the activation pathway of Δα-Chymotrypsin with molecular dynamics simulations and correlation with kinetic experiments, European Journal of Biophysics 38:13-23 (2008). doi:10.1007/s00249-008-0348-2

C.J. Foley, H. Freedman, S.L. Choo, C. Onyskiw, N.Y. Fu, V.C. Yu, J.A. Tuszynski, J.L. Pratt and S. Baksh, Dynamics of RASSF1A/MOAP-1 Association with Death Receptors, Molecular and Cellular Biology 28(14):4520-4535 (2008). doi:10.1128/MCB.02011-07

M.V. Sataric, L. Budinski-Petkovic, I. Loncarevic and J.A. Tuszynski, Modelling the role of intrinsic electric fields in microtubules as an additional control mechanism of bi-directional intracellular transport, Cell Biochemistry and Biophysics 52(2):113-124 (2008). doi:10.1007/s12013-008-9028-1

V. Rezania, O. Azarenko, M.A. Jordan, H. Bolterauer, R.F. Ludueña , J.T. Huzil and J.A. Tuszynski, Microtubule Assembly of Isotypically Purified Tubulin and Its Mixtures, Biophysical Journal  95:1993-2008 (2008). doi:10.1529/biophysj.108.132233

J.Y. Mane, M. Klobukowski, J.T. Huzil and J.A. Tuszynski, Free energy calculations on the binding of colchicine and its derivatives with the alpha/beta-tubulin isoforms, Journal of Chemical  Information and Modeling 48(9):1824-1832 (2008). doi:10.1021/ci800054n

J.M. Dixon, P. Chelminiak, and J.A. Tuszynski, Surface conductance in seamless microtubules, Physica A 387(16-17):4183-4194 (2008). doi:10.1016/j.physa.2008.02.044

C. Nouri, R. Luppes, A.E.P. Veldman, J.A. Tuszynski and R. Gordon, Rayleigh instability of the inverted one-cell amphibian embryo [Invited: “Physical Aspects of Developmental Biology” special issue, Guest Editor Shane Hutson, Vanderbilt University], Physical Biology, 5:015006 [12 pages] (2008). doi:10.1088/1478-3975/5/1/015006

M. Gajewski, J. Tuszynski, H. Mori, E. Miyoshi and M. Klobukowski, DFT studies of the electronic structure and geometry of 18-crown-6, hexaaza[18]annulene, and their complexes with cations of the heavier alkali and alkaline earth metals, Inorganica Chimica Acta 361:2166-2171 (2008). doi:10.1016/j.ica.2007.10.033

J.A. Tuszynski, T.J.A. Craddock and E.J. Carpenter, Bio-ferroelectricity at the Nanoscale, Journal of Computational and Theoretical Nanoscience 5(10):2022-2032 (2008). doi:10.1166/jctn.2008.1008

A. Samarbakhsh and J.A. Tuszynski, A “Shooting Bead” Method for Finding the Flexural Rigidity of Semiflexible Rodlike Biological Filaments, Journal of Computational and Theoretical Nanoscience 5(10):2041-2044 (2008). doi:10.1166/jctn.2008.1011

H. Freedman, L. Le, J.A. Tuszynski, and T.N. Truong, Improving the Performance of the Coupled Reference Interaction Site Model-Hyper-netted Chain (RISM-HNC)/ Simulation Method for Free Energy of Solvation, Journal of Physical Chemistry B, 112(8):2340-2348 (2008). doi:10.1021/jp077179l

T. Luchko, J.T. Huzil, M. Stepanova and J.A. Tuszynski, Conformational Analysis of the Carboxy-Terminal Tails of Human β-Tubulin Isotypes, Biophysical Journal 94:1971-1982 (2008). doi:10.1529/biophysj.107.115113

J.A. Tuszynski, W. Malinski, E.J. Carpenter, T. Luchko and J.T. Huzil and R.F. Luduena, Tubulin electrostatics and isotype specific drug binding, Canadian Journal of Physics 86(4):635-640 (2008). doi:10.1139/P07-199