References
- Acbas, G., K. A. Niessen, E. H. Snell, A. G. Markelz, et al. 2014. Optical measurements of long-range protein vibrations. Nat. Commun. 5. 3076. Nature Publishing Group. doi:https://doi.org/10.1038/ncomms4076.
- Agarwal, P. K. 2006. Enzymes: An integrated view of structure, dynamics and function. Microb. Cell Fact. doi:https://doi.org/10.1186/1475-2859-5-2.
- Animalu, A. O. E. 1977. Intermediate quantum theory of crystalline solids. Prentice-Hall.
- Austin, R. H., A. Xie, D. Fu, W. W. Warren, B. Redlich, L. van der Meer, et al. 2009. Tilting after dutch windmills: Probably no long-lived davydov solitons in proteins. J. Biol. Phys. 35:91–101. doi:https://doi.org/10.1007/s10867-009-9130-7.
- Balu, R., H. Zhang, E. Zukowski, J.-Y. Chen, A. G. Markelz, S. K. Gregurick, et al. 2008. Terahertz spectroscopy of bacteriorhodopsin and rhodopsin: similarities and differences. Biophys. J. 94:3217–26. doi:https://doi.org/10.1529/biophysj.107.105163.
- Bellissent-Funel, M.-C., A. Hassanali, M. Havenith, R. Henchman, P. Pohl, F. Sterpone, D. van der Spoel, Y. Xu, A. E. Garcia, et al. 2016. Water determines the structure and dynamics of proteins. Chem. Rev. 116. 7673–97. American Chemical Society. doi:https://doi.org/10.1021/acs.chemrev.5b00664.
- Bolterauer, H., and J. A. Tuszyński. 1989. Fröhlich’s condensation in a biological membrane viewed as a Davydov soliton. J. Biol. Phys. 17:41–50. Kluwer Academic Publishers. doi:https://doi.org/10.1007/BF00393325.
- Bolterauer, H., J. A. Tuszyński, and M. V. Satarić. 1991. Fröhlich and Davydov regimes in the dynamics of dipolar oscillations of biological membranes. Phys. Rev., A 44:1366–81. American Physical Society. doi:https://doi.org/10.1103/PhysRevA.44.1366.
- Chenu, A., N. Christensson, H. F. Kauffmann, T. Mančal, et al. 2013. Enhancement of vibronic and ground-state vibrational coherences in 2D spectra of photosynthetic complexes. Sci Rep 3. 2029. Nature Publishing Group. doi:https://doi.org/10.1038/srep02029.
- Columbus, L., Kálai, T., Jekö, J., Hideg, K., Hubbell, W.L. 2001. Molecular motion of spin labeled side chains in α-helices: Analysis by variation of side chain structure. Biochemistry. doi:https://doi.org/10.1021/bi002645h.
- Columbus, L., and W. L. Hubbell. 2002. A new spin on protein dynamics. Trends Biochem. Sci. 27:288–95. Accessed: 14 April 2019. http://www.ncbi.nlm.nih.gov/pubmed/12069788.
- Conti Nibali, V., and M. Havenith. 2014. New insights into the role of water in biological function: studying solvated biomolecules using terahertz absorption spectroscopy in conjunction with molecular dynamics simulations. J. Am. Chem. Soc. 136:12800–07. American Chemical Society. doi:https://doi.org/10.1021/ja504441h.
- Davydov, A. S. 1977. Solitons and energy transfer along protein molecules. J. Theor. Biol. 66:379–87. Academic Press. doi:https://doi.org/10.1016/0022-5193(77)90178-3.
- Davydov, A. S. 1985. Solitons in molecular systems. Dordrecht: Springer Netherlands (Mathematics and Its Applications). doi:https://doi.org/10.1007/978-94-017-3025-9.
- Del Giudice, E. Doglia, S., Milani, M., Vitiello, G.. 1986. Collective properties of biological systems. In Modern bioelectrochemistry F. Gutmann and H. Keyzer (Eds.), 263–87, Boston, MA: Springer US. doi: https://doi.org/10.1007/978-1-4613-2105-7_9
- Doster, W. 2010. The protein-solvent glass transition. Biochimica Et Biophysica Acta (BBA) - Proteins and Proteomics 1804:3–14. doi:https://doi.org/10.1016/j.bbapap.2009.06.019.
- Duan, H.-G., V. I. Prokhorenko, R. J. Cogdell, K. Ashraf, A. L. Stevens, M. Thorwart, R. J. D. Miller, et al. 2017. Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer. Proc. Natl. Acad. Sci. U.S.A. 114. 8493–98. National Academy of Sciences. doi:https://doi.org/10.1073/pnas.1702261114.
- Engel, G. S., T. R. Calhoun, E. L. Read, T.-K. Ahn, T. Mančal, Y.-C. Cheng, R. E. Blankenship, G. R. Fleming, et al. 2007. Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446. 782–86. Nature Publishing Group. doi:https://doi.org/10.1038/nature05678.
- Foletti, A., Grimaldi, S., Lisi, A., Ledda, M., Liboff, A.R. 2013. Bioelectromagnetic medicine: The role of resonance signaling. Electromagn Biol Med 32:484–99. doi:https://doi.org/10.3109/15368378.2012.743908.
- Freedman, H., and G. Hanna. 2016. Mixed quantum–classical Liouville simulation of vibrational energy transfer in a model α-helix at 300 K. Chem Phys. doi:https://doi.org/10.1016/j.chemphys.2016.08.015.
- Fröhlich, H. 1968a. Long-range coherence and energy storage in biological systems. Int J Quantum Chem 2:641–49. John Wiley & Sons, Inc. doi:https://doi.org/10.1002/qua.560020505.
- Fröhlich, H. 1968b. Storage of Light Energy and Photosynthesis. Nature 219:743–44. Nature Publishing Group. doi:https://doi.org/10.1038/219743a0.
- Fröhlich, H. 1970. Long range coherence and the action of enzymes. Nature. 228:1093. Accessed: 7 June 2019. http://www.ncbi.nlm.nih.gov/pubmed/5483165.
- Fröhlich, H. 1980. The Biological Effects of Microwaves and Related Questions. Adv. Electron. Electron Phys. 53:85–152. Academic Press. doi:https://doi.org/10.1016/S0065-2539(08)60259-0.
- Fröhlich, H. 1988. Biological coherence and response to external stimuli. Springer: Berlin, Heidelberg.
- Ghosh, T., S. Garde, and A. E. García. 2003. Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution. Biophys. J. 85:3187–93. The Biophysical Society. doi:https://doi.org/10.1016/S0006-3495(03)74736-5.
- Glauber, R. J. 2006. Quantum theory of optical coherence. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA. doi:https://doi.org/10.1002/9783527610075.
- Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. U.S.A. 80:3696–700. National Academy of Sciences. doi:https://doi.org/10.1073/PNAS.80.12.3696.
- Goncharuk, V. V., A. V. Syroeshkin, T. V. Pleteneva, E. V. Uspenskaya, O. V. Levitskaya, V. A. Tverdislov, et al. 2017. On the possibility of chiral structure-density submillimeter inhomogeneities existing in water. J. Water Chem. Technol. 39. 319–24. Pleiades Publishing. doi:https://doi.org/10.3103/S1063455X17060029.
- Haken, H. 1983. Synergetics: An introduction : Nonequilibrium phase transitions and self-organization in physics, chemistry, and biology. Springer: Berlin, Heidelberg. Accessed: 14 January 2018. https://books.google.co.uk/books?id=KHn1CAAAQBAJ&source=gbs_similarbooks
- Issa, S., C. B. Tabi, H. P. Ekobena Fouda, T. C. Kofané, et al. 2018. Fluctuations of polarization induce multisolitons in α -helix protein. Nonlinear Dyn 91. 679–86. Springer. doi:https://doi.org/10.1007/s11071-017-3902-6.
- Kadantsev, V., and A. Savin. 1997. Resonance effects of microwaves are caused by their interaction with solitons in A-helical proteins. Electro- Magnetobiol. 16:95–106. Taylor & Francis. doi:https://doi.org/10.3109/15368379709009835.
- Kadantsev, V. N., and А. N. Goltsov. 2018. Collective excitations in α-helical protein structures. Russ. Technol.l J. 6:32–45. doi:https://doi.org/10.32362/2500-316X-2018-6-2-32-45.
- Kadantsev, V. N., L. N. Lupichcv, and A. V. Savin. 1994. Electrosoliton dynamics in a thermalized chain. Phys. Status Solidi B 183:193–99. Wiley-Blackwell. doi:https://doi.org/10.1002/pssb.2221830115.
- Kadantsev, V. N., L. N. Lupichov, and A. V. Savin. 1987. Intramolecular excitation dynamics in a thermalized chain. I. Formation of autolocalized states in a cyclic chain. Phys. Status Solidi B 143:569–79. Wiley-Blackwell. doi:https://doi.org/10.1002/pssb.2221430217.
- Kamerlin, S. C. L., and A. Warshel. 2010. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins Struct. Funct. Bioinf. 78:NA–NA. doi:https://doi.org/10.1002/prot.22654.
- Kolli, A., E. J. O’Reilly, G. D. Scholes, A. Olaya-Castro, et al. 2012. The fundamental role of quantized vibrations in coherent light harvesting by cryptophyte algae. J. Chem. Phys. 137. 174109. American Institute of Physics. doi:https://doi.org/10.1063/1.4764100.
- Kuramochi, H., Takeuchi, S., Kamikubo, H., Kataoka, M., Tahara, T. 2019. Fifth-order time-domain Raman spectroscopy of photoactive yellow protein for visualizing vibrational coupling in its excited state. Sci. Adv 5. eaau4490. American Association for the Advancement of Science. doi:https://doi.org/10.1126/sciadv.aau4490.
- Kurian, P., A. Capolupo, T. J. A. Craddock, G. Vitiello, et al. 2018a. Water-mediated correlations in DNA-enzyme interactions. Phys Lett A 382. 33–43. North-Holland. doi:https://doi.org/10.1016/J.PHYSLETA.2017.10.038.
- Kurian, P., A. Capolupo, T. J. A. Craddock, G. Vitiello, et al. 2018b. Water-mediated correlations in DNA-enzyme interactions. Phys Lett A 382. 33–43. North-Holland. doi:https://doi.org/10.1016/J.PHYSLETA.2017.10.038.
- Lambert, N., Y.-N. Chen, Y.-C. Cheng, C.-M. Li, G.-Y. Chen, F. Nori, et al. 2013. Quantum biology. Nat Phys 9. 10–18. Nature Publishing Group. doi:https://doi.org/10.1038/nphys2474.
- Lawrence, A. F., J. C. McDaniel, D. B. Chang, R. R. Birge, et al. 1987. The nature of phonons and solitary waves in alpha-helical proteins. Biophys. J. 51. 785–93. Cell Press. doi:https://doi.org/10.1016/S0006-3495(87)83405-7.
- Lindorff-Larsen, K., R. B. Best, M. A. DePristo, C. M. Dobson, M. Vendruscolo, et al. 2005. Simultaneous determination of protein structure and dynamics. Nature 433. 128–32. Nature Publishing Group. doi:https://doi.org/10.1038/nature03199.
- Liu, D., X.-Q. Chu, M. Lagi, Y. Zhang, E. Fratini, P. Baglioni, A. Alatas, A. Said, E. Alp, S.-H. Chen, et al. 2008. Studies of phononlike low-energy excitations of protein molecules by inelastic X-ray scattering. Phys. Rev. Lett. 101:135501. doi:https://doi.org/10.1103/PhysRevLett.101.135501.
- Lundholm, I. V., H. Rodilla, W. Y. Wahlgren, A. Duelli, G. Bourenkov, J. Vukusic, R. Friedman, J. Stake, T. Schneider, G. Katona, et al. 2015. Terahertz radiation induces non-thermal structural changes associated with Fröhlich condensation in a protein crystal.. Struct. Dyn. 2. 054702. American Institute of Physics. doi:https://doi.org/10.1063/1.4931825.
- Lupas, A. N., and J. Bassler. 2017. Coiled Coils – A Model System for the 21st Century. Trends Biochem. Sci. 42:130–40. doi:https://doi.org/10.1016/j.tibs.2016.10.007.
- Lupichev, L. N., A. V. Savin, and V. N. Kadantsev. 2015. Synergetics of molecular systems. Cham: Springer International Publishing (Springer Series in Synergetics). doi:https://doi.org/10.1007/978-3-319-08195-3.
- Markov, M., and S. Marko. 2015. Electromagnetic fields in biology and medicine, electromagnetic fields in biology and medicine. doi: https://doi.org/10.1201/b18148.
- Mesquita, M. V., Á. R. Vasconcellos, and R. Luzzi. 2004. Considerations on undistorted-progressive X-waves and Davydov solitons, Fröhlich-Bose-Einstein condensation, and Cherenkov-like effect in biosystems. Braz. J. Phys. 34:489–503. Sociedade Brasileira de Física. doi:https://doi.org/10.1590/S0103-97332004000300028.
- Mohseni, M. Omar, Y., Engel, G.S., Plenio, M.B. (Eds.). 2014. Quantum effects in biology, Cambridge: Cambridge University Press. doi: https://doi.org/10.1017/CBO9780511863189
- Nardecchia, I., J. Torres, M. Lechelon, V. Giliberti, M. Ortolani, P. Nouvel, M. Gori, Y. Meriguet, I. Donato, J. Preto, et al. 2018. Out-of-equilibrium collective oscillation as phonon condensation in a model protein. Phys. Rev. X 8. 031061. American Physical Society. doi:https://doi.org/10.1103/PhysRevX.8.031061.
- Niessen, K. A., M. Xu, A. Paciaroni, A. Orecchini, E. H. Snell, A. G. Markelz, et al. 2017a. Moving in the right direction: protein vibrations steering function. Biophys. J. 112. 933–42. Cell Press. doi:https://doi.org/10.1016/J.BPJ.2016.12.049.
- Niessen, K. A., M. Xu, A. Paciaroni, A. Orecchini, E. H. Snell, A. G. Markelz, et al. 2017b. Moving in the right direction: protein vibrations steering function. Biophys. J. 113:2573. doi:https://doi.org/10.1016/j.bpj.2017.10.038.
- Oldfield, C. J. , Cheng, Y., Cortese, M.S., Romero, P., Uversky, V.N., Dunker, A.K. 2005. Coupled folding and binding with α-helix-forming molecular recognition elements. Biochemistry 44: 12454–12470. doi: https://doi.org/10.1021/BI050736E
- Pokorný, J. 1999. Conditions for coherent vibrations in the cytoskeleton. Bioelectrochem. Bioenerg. 48:267–71. Elsevier. doi:https://doi.org/10.1016/S0302-4598(99)00016-1.
- Pokorný, J. 2004. Excitation of vibrations in microtubules in living cells. Bioelectrochemistry 63:321–26. doi:https://doi.org/10.1016/j.bioelechem.2003.09.028.
- Preto, J. 2017. Semi-classical statistical description of Fröhlich condensation. J. Biol. Phys. 43:167–84. doi:https://doi.org/10.1007/s10867-017-9442-y.
- Prigogine, I., and R. Lefever. 1973. Theory of dissipative structures. In Synergetics, H. Haken (Ed.), 124–35. Wiesbaden: Vieweg+Teubner Verlag. doi:https://doi.org/10.1007/978-3-663-01511-6_10.
- Reimers, J. R., McKemmish, L.K., McKenzie, R.H., Mark, A.E., Hush, N.S. 2009. Weak, strong, and coherent regimes of Fröhlich condensation and their applications to terahertz medicine and quantum consciousness. Proc. Natl. Acad. Sci. U.S.A. 106. 4219–24. National Academy of Sciences. doi:https://doi.org/10.1073/pnas.0806273106.
- Rolczynski, B. S., H. Zheng, V. P. Singh, P. Navotnaya, A. R. Ginzburg, J. R. Caram, K. Ashraf, A. T. Gardiner, S.-H. Yeh, S. Kais, et al. 2018. Correlated protein environments drive quantum coherence lifetimes in photosynthetic pigment-protein complexes. Chem 4. 138–49. Cell Press. doi:https://doi.org/10.1016/J.CHEMPR.2017.12.009.
- Salari, V., Tuszynski, J., Rahnama, M., Bernroider, G. 2011. Plausibility of quantum coherent states in biological systems. J Phys Conf Ser 306. 012075. IOP Publishing. doi:https://doi.org/10.1088/1742-6596/306/1/012075.
- Shibata, F., and N. Hashitsume. 1978. Generalized phase-space method in the langevin-equation approach. J. Physi. Soc. Jpn. 44:1435–48. The Physical Society of Japan. doi:https://doi.org/10.1143/JPSJ.44.1435.
- Siegel, P. H. 2004. Terahertz technology in biology and medicine. IEEE Trans. Microw. Theory Tech. 52:2438–47. doi:https://doi.org/10.1109/TMTT.2004.835916.
- Sivaramakrishnan, S., B. J. Spink, A. Y. L. Sim, S. Doniach, J. A. Spudich, et al. 2008. Dynamic charge interactions create surprising rigidity in the ER/K -helical protein motif. Proc. Natl. Acad. Sci. U.S.A. 105:13356–61. doi:https://doi.org/10.1073/pnas.0806256105.
- Squire, R. H., N. H. March, R. A. Minnick, R. Turschmann, et al. 2013. Comparison of various types of coherence and emergent coherent systems. Int J Quantum Chem 113. 2181–99. Wiley-Blackwell. doi:https://doi.org/10.1002/qua.24423.
- Takeno, S. 1984. Vibron solitons in one-dimensional molecular crystals. Prog. Theor. Phys. 71:395–98. Oxford University Press. doi:https://doi.org/10.1143/PTP.71.395.
- Tchinang Tchameu, J. D., A. B. Togueu Motcheyo, and C. Tchawoua. 2014. Mobility of discrete multibreathers in the exciton dynamics of the Davydov model with saturable nonlinearities. Phys. Rev. E 90:043203. doi:https://doi.org/10.1103/PhysRevE.90.043203.
- Tsivlin, D. V., and V. May. 2007. Multidimensional wave packet dynamics in polypeptides: Coupled amide-exciton chain-vibrational motion in an α-helix. Chem Phys 338:150–59. doi:https://doi.org/10.1016/j.chemphys.2007.03.010.
- Turton, D. A., H. M. Senn, T. Harwood, A. J. Lapthorn, E. M. Ellis, K. Wynne, et al. 2014. Terahertz underdamped vibrational motion governs protein-ligand binding in solution. Nat. Commun. 5. 3999. Nature Publishing Group. doi:https://doi.org/10.1038/ncomms4999.
- Vasconcellos, Á. R., F. S. Vannucchi, S. Mascarenhas, R. Luzzi, et al. 2012. Fröhlich condensate: emergence of synergetic dissipative structures in information processing biological and condensed matter systems. Information 3. 601–20. Molecular Diversity Preservation International. doi:https://doi.org/10.3390/info3040601.
- Venema, L., B. Verberck, I. Georgescu, G. Prando, E. Couderc, S. Milana, M. Maragkou, L. Persechini, G. Pacchioni, L. Fleet, et al. 2016. The quasiparticle zoo. Nat Phys 12. 1085–89. Nature Publishing Group. doi:https://doi.org/10.1038/nphys3977.
- Wang, W. B., Liang, Y., Zhang, J., Wu, Y.D., Du, J.J., Li, Q.M., Zhu, J.Z., Su, J.G. 2018. Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model. Sci Rep. doi:https://doi.org/10.1038/s41598-018-27745-y.
- Weightman, P. 2014. Investigation of the Frohlich hypothesis with high intensity terahertz radiation. In Optical interactions with tissue and cells XXV; and terahertz for biomedical applications, E. D. Jansen , Thomas, R.J., Wilmink, G.J., Ibey, B.L. (Eds.), 89411F. San Francisco, California, United States. doi: https://doi.org/10.1117/12.2057397
- Wu, T. M., and S. J. Austin. 1981. Fröhlich’s model of bose condensation in biological systems. J. Biol. Phys. 9:97–107. Kluwer Academic Publishers. doi:https://doi.org/10.1007/BF01987286.
- Xie, A., L. van der Meer, and R. H. Austin. 2002. Excited-state lifetimes of far-infrared collective modes in proteins. J. Biol. Phys. 28:147–54. Kluwer Academic Publishers. doi:https://doi.org/10.1023/A:1019986321524.
- Xie, L., Y. Yao, and Y. Ying. 2014. The application of terahertz spectroscopy to protein detection: a review. Appl. Spectrosc. Rev. 49:448–61. Taylor & Francis. doi:https://doi.org/10.1080/05704928.2013.847845.