[1] A. Ghaffari, A. Shokuhfar, R. Hasanzadeh Ghasemi (2012) Capturing and releasing a nano cargo by Prefoldin nano actuator, Sensors and Actuators B: Chemical, Vol. 171, pp. 1199-1206.
[2] Mavroidis C. (2006) Bio-Nano-Machines for Space Applications, Phase II NIAC Grant, Final Report.
[3] M. Askarian, M. Moavenian, R. H. Ghasemi (2013) Prefoldin β1: A New Bio-Nanorobots component, advanced science, Engineering and Medicine, Vol. 5, No. 9, pp. 895-904.
[4] Howard J. (1996) The movement of kinesin along microtubules. Annu. Rev. Physiol. 58: 703–729.
[5] Wang M.D., Schnitzer M.J., Yin H., Landick R., Gelles J., Block S. M. (1998) “Force and Velocity Measured for Single Molecules of RNA Polymerase”, Science, 282, 902-907.
[6] Sellers J.R. (2000) Myosins: a diverse superfamily. Biochimica et Biophys. Acta (BBA) — Mol. Cell Res. 1496: 3–22.
[7] Sack S.,Muller J.,Marx A., Thormahlen M.,Mandelkow E.M. et al. (1997) X-ray structure of motor and neck domains from rat brain kinesin. Biochemistry 36: 16155
[8] Berg H.C. and Anderson R.A. (1973) Bacteria swim by rotating their flagellar filaments. Nature 245:380–382.
[9] Schalley C.A., Beizai K. and Vogtle F.K., (2001) “On the Way to Rotaxane-Based Molecular Motors: Studies in Molecular Mobility and Topological Chirality”, Accounts of Chemical Research, 34, 465-476.
[10] Erickson, H.P. (1997) “Stretching Single Protein Molecules: Titin is a Weird spring”, Science, 276,1090-1092.
[11] Mahadevan L. and Matsudaira P. (2000) “Motility Powered by Supramolecular Springs and Ratchets”, Science, 288, 95-99.
[12] M. Keramati, R. Hasanzadeh Ghasemi (2016) Study of interaction between Prefoldin nano actuator and amyloid beta dimeric pathogenetic cargo with MD simulation, Modares Mechanical Engineering, Vol. 16, No. 7, pp. 385-391. (in Persian )
[13] A. Ghaffari, A. Shokuhfar, R. Hasanzadeh Ghasemi (2011) Prefoldin: a nano actuator for carrying the various size nano drugs, Journal of Computational and Theoretical Nanoscience, Vol. 8, No. 10, pp. 2078-2086.
[14] Akinori Kuzuya, Yuichi Ohya (2014) Nanomechanical Molecular Devices made of DNA Origami, 1742-1749.
[15] David M. Smith, Verena Sch¨uller, Carsten Forthmann, Robert Schreiber, Philip Tinnefeld & Tim Liedl (2011) A Structurally Variable Hinged Tetrahedron Framework from DNA Origami, Journal of Nucleic Acids doi:10.4061/2011/360954.
[16] Douglas, S. M.; Bachelet, I.; Church, G. M. (2012) A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads. Science 335, 831−834.
[17] Ke Y.; Meyer T.; Shih W. M. & Bellot G. (2016 )Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator. Nature Communications.
[18] Sharma R., Schreck J. S., Romano F., Louis Ard A., and Jonathan P. K. Doye, (2017),
“Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model”,
ACS Nano, 11, 12426-12435.
[19] Lee Ch., Lee J. Y., and Kim D.-N., (2017) “Polymorphic design of DNA origami
structures through mechanical control of modular components”, NATURE COMMUNICATIONS.
[20] Khosravi, R., Ghasemi, R.H. & Soheilifard, R., (2020) Design and Simulation of a DNA Origami Nanopore for Large Cargoes. Mol Biotechnol 62, 423–432. https://doi.org/10.1007/s12033-020-00261-z
[21] Mogheiseh, M., Hasanzadeh Ghasemi, R. and Soheilifard, R. (2021), “The effect of crossovers on the stability of DNA origami type nanocarriers”, Multidiscipline Modeling in Materials and Structures, Vol. 17 No. 2, pp. 426-436. https://doi.org/10.1108/MMMS-05-2020-0094
[22] Dastorani, S., Mogheiseh, M., Ghasemi, R. H., & Soheilifard, R.(2020). “Modeling and Structural investigation of a new DNA origami based flexible bio-nano joint”. Molecular Simulation. https://doi.org/10.1080/08927022.2020.1797019
[23] Dastorani, S., Ghasemi, R. H., & Soheilifard, R.(2021). “A Study on the Bending Stiffness of a New DNA Origami Nano-Joint”. Molecular Biotechnology. https://doi.org/10.1007/s12033-021-00367-y.
[24] Seeman, N. C. Nanomaterials Based on DNA. Annu. Rev.Biochem. 2010, 79, 65–87.
[25] Han, D.; Pal, S.; Nangreave, J.; Deng, Z.; Liu, Y.; Yan, H. DNA Origami with Complex Curvatures in Three-Dimensional Space. Science, 332, 342–346, 2011.
[26] Dastorani, S.,(2020). Design and simulation of biologically joints using DNA origami by molecular dynamics method, Degree of Master of Science (M.Sc.) in Mechanical Engineering, Hakim Sabzevari University.
[27] Rothemund, P. W. K. (2006) Folding DNA To Create Nanoscale Shapes and Patterns. Nature, 440, 297–302,.
[28] Castro, C. E.; Kilchherr, F.; Kim, D.-N.; Shiao, E. L.; Wauer, T.; Wortmann, P.; Bathe, M.; Dietz, H. A (2011) Primer to Scaffolded DNA Origami. Nat. Methods, 8, 221–229,.
[29] Linko, V.; Dietz, H. (2013) The Enabled State of DNA Nanotechnology. Curr. Opin. Biotechnol., 24, 555–561,.
[30] Langecker, M.; Arnaut, V.; Martin, T. G.; List, J.; Renner, S.; Mayer, M.; Dietz, H.; Simmel, F. C. (2012) Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures. Science, 338, 932–936,.
[31] Douglas, S. M.; Bachelet, I.; Church, G. M. A (2012) Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads. Science, 335, 831–834,.
[32] Zadegan, R. M.; Jepsen, M. D. E.; Thomsen, K. E.; Okholm, A. H.; Schaffert, D. H.; Andersen, E. S.; Birkedal, V.; Kjems, J. (2012) Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami. ACS Nano, 6, 10050–10053.
[33] Zhou, L., Marras, A. E., Su, H.-J., and Castro, C. E., (2014), “DNA Origami Compliant Nanostructures with Tunable Mechanical Properties,” ACS Nano, 8(1), pp. 27–34.
[34] Tinland, B.; Pluen, A.; Sturm, J.; Weill, G. (1997) Persistence Length of Single-Stranded DNA. Macromolecules, 30, 5763–5765.
[35] Fajer, M., Swift, R., McCammon, J.: (2009) Using multistate free energy techniques to improve
the efficiency of replica exchange accelerated molecular dynamics. J. Comp. Chem. 30,
1719–1725
[36] Brooks, C.L., Karplus, M., Pettit, B.M.: (1989) Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. Wiley, New York
[37] Karplus, M.: Molecular dynamics: applications to proteins. In: J.L. Rivail (ed.) (1990) Modelling of Molecular Structures and Properties, Studies in Physical and Theoretical Chemistry, vol. 71, pp. 427–461. Elsevier Science Publishers, Amsterdam. Proceedings of an International Meeting
[38] McCammon, J.A., Harvey, S.C.: (1987) Dynamics of Proteins and Nucleic Acids. Cambridge
University Press, Cambridge
[39] Wang, Y., McCammon, J.A. (2012). Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling. In: Dokholyan, N. (eds) Computational Modeling of Biological Systems. Biological and Medical Physics, Biomedical Engineering. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-2146-7_1
[40] M. Talab F., Arab S. Sh., Mohammadian J. (2020) “Structural investigation of bacteriorhodopsin protein due to absorption of microwaves using molecular dynamics simulation”, Madras Journal , Vol. 7, Num. 2, P. 1-13, , (in Persian).
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