Engineering Topology of Photonic Systems for Sustainable Molecular Structure: Autopoiesis Systems

Authors: Moustafa Osman Mohammed

Abstract:

This paper introduces topological order in descried social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. Topological order is important in describing the physical systems for exploiting optical systems and improving photonic devices. The stats of topologically order have some interesting properties of topological degeneracy and fractional statistics that reveal the entanglement origin of topological order, etc. Topological ideas in photonics form exciting developments in solid-state materials, that being; insulating in the bulk, conducting electricity on their surface without dissipation or back-scattering, even in the presence of large impurities. A specific type of autopoiesis system is interrelated to the main categories amongst existing groups of the ecological phenomena interaction social and medical sciences. The hypothesis, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for exchange photon energy with molecules without changes in topology (i.e., chemical transformation into products do not propagate any changes or variation in the network topology of physical configuration). The engineering topology of a biosensor is based on the excitation boundary of surface electromagnetic waves in photonic band gap multilayer films. The device operation is similar to surface Plasmonic biosensors in which a photonic band gap film replaces metal film as the medium when surface electromagnetic waves are excited. The use of photonic band gap film offers sharper surface wave resonance leading to the potential of greatly enhanced sensitivity. So, the properties of the photonic band gap material are engineered to operate a sensor at any wavelength and conduct a surface wave resonance that ranges up to 470 nm. The wavelength is not generally accessible with surface Plasmon sensing. Lastly, the photonic band gap films have robust mechanical functions that offer new substrates for surface chemistry to understand the molecular design structure, and create sensing chips surface with different concentrations of DNA sequences in the solution to observe and track the surface mode resonance under the influences of processes that take place in the spectroscopic environment. These processes led to the development of several advanced analytical technologies, which are automated, real-time, reliable, reproducible and cost-effective. This results in faster and more accurate monitoring and detection of biomolecules on refractive index sensing, antibody–antigen reactions with a DNA or protein binding. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other in order to form unique spatial structure and dynamics of biological molecules for providing the environment mutual contribution in investigation of changes due the pathogenic archival architecture of cell clusters.

Keywords: autopoiesis, engineering topology, photonic system molecular structure, biosensor

References:

[1] Roli A, Villani M, Filisetti A, and Serra R, (2018), “Dynamical Criticality: Overview and Open Questions”, Journal of Systems Science and Complexity, Vol. 31 (3): pp.647663, Iune 2018. https://doi.org/10.1007/s11424-017-6117-5
[2] Maximilian Zander, (2005) “Molecular Topology and Chemical Reactivity of Polynuclear Benzenoid Hydrocarbons”, Advances in the Theory of Benzenoid Hydrocarbons, 10.1007/3-540-51505-4_20, (101-122), (2005).
[3] Xiao-Gang Wen, (2017) “An Introduction of Topological Orders”, archived from the original (PDF) on 9 January 2020; https://web.archive.org/web/20170829201814
[4] Francl M, (2009) “Stretching Topology”, Nat. Chem., Vol. 1: pp.334–335, 2009.
[5] Manoil C, and Beckwith J, (1986) “A Genetic Approach to Analyzing Membrane Protein Topology”, Science, Vol. 233: pp. 1403–1408, 1986.
[6] Rapp M, Granseth E, Seppälä S and von Heijne G, (2006) “Identification and Evolution of Dual-Topology Membrane Proteins”, Nat. Struct. Mol. Biol., Vol. 13: pp. 112–116, 2006.
[7] von Heijne G, (2006) “Membrane-protein Topology”, Nat. Rev. Mol. Cell Biol., Vol. 7: pp. 909–918, 2006.
[8] MacBeath G, Kast P, and Hilvert D, (1998) “Redesigning Enzyme Topology by Directed Evolution”, Science, Vol. 279: pp.1958–1961, 1998.
[9] Shortle D, and Ackerman M S, (2001) “Persistence of Native-Like Topology in a Denatured Protein in 8 M Urea”, Science, Vol. 293: pp. 487–489, 2001.
[10] Claverie P and Jona-Lasinio G, (1986) “Instability of Tunneling and the Concept of Molecular Structure in Quantum Mechanics: The Case of Pyramidal Molecules and the Enantiomer Problem”, Physical Review A, 10.1103/PhysRevA.33.2245, 33, 4, (2245-2253), (1986).
[11] Meyer C D, (2000) “Matrix Analysis and Applied Linear Algebra”, (Philadelphia: Society for Industrial and Applied Mathematics), 2000.
[12] Shank E A, Cecconi C, Dill J W, Marqusee S, and Bustamante C, (2010) “The Folding Cooperativity of a Protein is Controlled by Its Chain Topology”, Nature, Vol. 465: pp. 637–640, 2010.
[13] Lu Ling, Joannopoulos John D, Soljačić Marin, (November 2014) “Topological Photonics”, Nature Photonics, Vol. 8 (11): pp.821–829, 2014; https://doi.org/10.1038/nphoton.2014.248, ISSN 1749-4893
[14] Ozawa Tomoki, Price Hannah M, Amo Alberto, Goldman, Nathan, Hafezi Mohammad, Lu Ling, Rechtsman Mikael C, Schuster David, Simon Jonathan, Zilberberg Oded, Carusotto Iacopo, (25 March 2019) “Topological Photonics”, Reviews of Modern Physics, Vol. 91(1): pp. 015006, https://doi.org/10.1103/RevModPhys.91.015006
[15] Duarte F J, (2014) “Quantum Optics for Engineers”, New York: CRC, ISBN 978-1439888537.
[16] Thirumalai D, Klimov D, (1999) “Deciphering the Time Scales and Mechanisms of Protein Folding Using Minimal off-lattice Models”, Curr. Opin. Struct. Biol., Vol. 9: pp. 197–207, 1999.
[17] Zhaxylyk A. Kudyshev, Alexander V. Kildishev, Alexandra Boltasseva, and Vladimir M. Shalaev, (2019) “Photonic Topological Phase Transition on Demand”, Nanophotonics, Volume 8 (8): pp. 1349–1356, 09 April, 2019. https://doi.org/10.1515/nanoph-2019-0043
[18] Yoshikawa, H. (1981) “General Design Theory and a CAD System”, In Sata, T. and Warman, E., editors, Man-Machine Communication in CAD/CAM, Proceedings of The IFIP WG5.2-5.3 Working Conference 1980 (Tokyo), pages 35{57, North-Holland, Amsterdam.
[19] Tomiyama, T. and Yoshikawa, H. (1985) “Knowledge Engineering and CAD”, In Yoshikawa H, editor, Design and Synthesis, Proceedings of The International Symposium on Design and Synthesis, pages 3{8, North-Holland, Tokyo, Japan.
[20] Tomiyama, T. (1994) “From General Design Theory To Knowledge Intensive Engineering”, Articial Intelligence for Engineering Design, Analysis, and Manufacturing, Vol. 8(4): pp. 319-333, 1994.
[21] Tomiyama T, and Yoshikawa H, (1986) “Extended General Design Theory”, Technical Report CS-R8604, Centre for Mathematics and Computer Science, Amsterdam.
[22] Tang Z Z, and Pan S L, (2016) “A Compact Image-Reject and Single-Sideband Mixer with Suppression of LO Leakage Based on A Dual-Polarization Dual-Drive Mach-Zehnder Modulator”, in the Avionics and Vehicle Fiber-Optics and Photonic Conference and the International Topical Meeting on Microwave Photonics 2016 (AVFOP&MWP 2016), Long Beach, California, USA, Oct.31-Nov.3, 2016,
[23] Xie C. X., Zhu D., Chen W. J., Liu J., Pan S. L., (2019) “Microwave Channelizer based on Polarization Multiplexing and Photonic Image-Reject Mixing”, IEEE International Topical Meeting on Microwave Photonics, Ottawa, Canada, Oct. 7-10, 2019.
[24] Levin, Michael; Wen, Xiao-Gang (2005) “Colloquium: Photons and Electrons as Emergent Phenomena”, Reviews of Modern Physics, Vol. 77 (3): pp. 871–879, 2005.
[25] Denis Arm`elle, Pesquera Luis and Claverie Pierre, (1981) “Linear Response of Stochastic Multi periodic Systems in Stationary States with Application to Stochastic Electrodynamics”, Physica A: Statistical Mechanics and its Applications, 10.1016/0378-4371(81)90043-1, 109, 1-2, (178-192), (1981).
[26] Sabato J A, (1970) “Topology and Metallurgy”, Nature, Vol. 227: pp. 757, 1970.
[27] Senyuk B, Liu Q, He S, Kamien R D, Kusner R B, Lubensky T C, and Smalyukh I I, (2013) “Topological Colloids”, Nature, Vol. 493: pp. 200–205, 2013.
[28] Terentjev E, (2013) “Liquid Crystals: Interplay of Topologies”, Nat. Mater., Vol. 12: pp.187–189, 2013.
[29] Mizuguchi K, and Go N, (1995) “Seeking Significance in Three-Dimensional Protein Structure Comparisons”, Curr. Opin. Struct. Biol., Vol. 5: pp. 377–382, 1995.
[30] Xue M and Pan S L, (2018) “Measurement, Analysis and Calibration of Analog Response for Photonic Integrated Chips”, Asia Communications and Photonics Conference (ACP), Hangzhou, China, Oct. 26-29, 2018.
[31] EmmanuelFrancalanza, Mark Mercieca, Alec Fenech, (2018) "Modular System Design Approach for Cyber Physical Production Systems", Elsevier, Volume 72: Pages 486-491, 2018. https://doi.org/10.1016/j.procir.2018.03.090
[32] Rogers J A, Someya T, Huang Y, (2010) Science, Vol. 327: pp. 1603-1607, 2010.
[33] Ko H C, Stoykovich M P, Song J, Malyarchuk V, Choi W M, Yu C-J, Geddes J B, Xiao J, Wang, Huang Y, Rogers J A, (2008) Nature, Vol. 454: pp. 748-753, 2008.
[34] Gelinck G H, Huitema H E A, Veenendaal E, Cantatore E, Schrijnemakers L, van der Putten J B P H, Geuns T C T, Beenhakkers M, Giesbers J B, Huisman B-H, Meijer E J, Benito E M, Touwslager F J, Marsman A W, van Rens B J E, de Leeuw. D M, (2004) Nat. Mater, Vol. 3: pp.106–110, 2004.
[35] Hu J J, Li L, Lin H T, Zhang P, Zhou W D, Ma Z Q, (2013) Opt. Express, Vol. 3: pp. 1313-1331, 2013.
[36] Li L, Lin H T, Qiao S T, Zou Y, Danto S, Richardson K, Musgraves J D, Lu N S, Hu J J, (2014) Nat. Photon., Vol. 8: pp. 643-649, 2014.
[37] Xu C, Subbaraman H, Chakravarty S, Hosseini A, Covey J, Yu Y L, Kwong D, Zhang Y, Lai W C, Zou Y, Lu N S, Chen R T, (2014) ACS Nano, Vol. 8: pp.12265-12271, 2014.
[38] Chen Y, Li H, Li M, (2012) Sci. Rep., Vol. 2: pp. 622, 2012.
[39] Aksu S, Huang M, Artar A, Yanik A A, Selvarasah S, Dokmeci M R, Altug H, (2011) Adv. Mater., Vol. 23: pp. 4422-4430, 2011.
[40] Shen X P, Cui T J, Martin-Cano D, Garcia-Vidal F J, Proc. Natl. Acad. Sci. 2013, Vol. 110: pp. 40-45, 2013.
[41] Muthukumar M, (1999) “Chain Entropy: Spoiler or Benefactor in Pattern Recognition?” Proc. Natl. Acad. Sci. U S A, Vol. 96: pp.11690–11692, 1999.
[42] Pauling L, and Corey R B, (1951a) “Configurations of Polypeptide Chains with Favored Orientations around Single Bonds: Two New Pleated Sheets”, Proc. Natl.Acad. Sci. U S A, Vol. 37: pp.729–740, 1951a,
[43] Pauling L, and Corey R B, (1951b) “The Pleated Sheet, A New Layer Configuration of Polypeptide Chains”, Proc. Natl. Acad. Sci. U S A, Vol. 37: pp. 251–256,1951b
[44] Kirimaya T, Tomiyama T, and Yoshikawa H, (1991) “The use of Qualitative Physics for Integrated Design Object Modeling”, In Proceeding ASME Design Theory and Methodology Conference, pp. 53–60, 1991.
[45] Fernández Nelson, Maldonado C, and Gershenson C, (2014), “Information Measures of Complexity, Emergence, Self-organization, Homeostasis, and Autopoiesis”, In Guided Self-Organization: Inception, pages 1951. Springer, Berlin, Heidelberg, 2014.
[46] Vanderstraeten R, (2000) “Autopoiesis and Socialization: on Luhmann’s reconceptualization of communication and socialization”, British Journal of Sociology Vol. 51: pp. 581–598, 2000.
[47] Mingers J, (1989), “An Introduction to Autopoiesis - Implications and Applications”, Systems Practice, Vol.2 (2): pp.159-180, 1989.
[48] Christenson C O, and Voxman W L, (1977) “Aspects of Topology”, Marcel Dekker, New York, 1977
[49] Angelique Chettiparamb, (2019) “Autopoietic Interaction Systems: Micro-Dynamics of Participation and Its Limits”, International Planning Studies, https://doi.org/10.1080/13563475.2019.1627185
[50] Holm L, and Sander C, (1996) “Mapping the Protein Universe”, Science Vol. 273: pp. 595–603, 1996.
[51] Richardson J S, (1981) “The Anatomy and Taxonomy of Protein Structure”, Adv. Protein Chem. 34, 167–339.
[52] Milner-White E .J, and Poet R, (1986) “Four Classes of Beta-Hairpins in Proteins”, Biochem. J., Vol. 240: pp. 289–292, 1986.
[53] Moutevelis, E., and Woolfson D N, (2009) “A ‘periodic table’ of Coiled-Coil Protein Structures”, J. Mol. Biol. 385, 726–732.
[54] Taylor W R, (2002) “A ‘periodic table’ for Protein Structures”, Nature 416,657–660, 2002.
[55] Sara Rahiminejad, Mano R. Maurya, and Shankar Subramaniam, (2019) "Topological and Functional Comparison of Community Detection Algorithms in Biological Networks", BMC Bioinformatics, Vol. 20: Article no. 212, 27 April, 2019. https://doi.org/10.1186/s12859-019-2746-0
[56] Brown I D, (2002) “Topology and Chemistry”, Structural Chemistary, Vol. 13: pp. 339–355, 2002.
[57] Flapan, E. (2000). “When Topology Meets Chemistry: A Topological Look at Molecular Chirality”, (New York: Cambridge University Press).
[58] Liang C, and Mislow K, (1995) “Topological Features of Human Chorionic Gonadotropin”, Biopolymers, Vol. 35: pp. 343–345, 1995.
[59] Yamamoto T, (2013) “Synthesis of Cyclic Polymers and Topology Effects on Their Diffusion and Thermal Properties”, Polym. J., Vol.45: pp.711–717, 2013.
[60] Ayme J F, Beves J E, Leigh D A, McBurney R T, Rissanen K, and Schultz D, (2012) “A Synthetic Molecular Pentafoil Knot”, Nat. Chem., Vol. 4: pp. 15–20, 2012.
[61] Blankenship J W and Dawson P E, (2007) “Threading A Peptide through A Peptide: Protein Loops, Rotaxanes, and Knots”, Protein Sci., Vol. 16: pp. 1249–1256, 2007.
[62] Coskun A, Banaszak M, Astumian R D, Stoddart J F, and Grzybowski, B A, (2012) “Great Expectations: Can Artificial Molecular Machines Deliver on their Promise?”, Chem. Soc. Rev., Vol. 41: pp. 19–30, 2012.
[63] Harada A, (2012) “Supramolecular Polymer Chemistry”, (Weinheim, Germany: Wiley-VCH), 2012.
[64] Yan H, Zhang X, Shen Z, and Seeman N C, (2002) “A Robust DNA Mechanical Device Controlled by Hybridization Topology”, Nature, Vol. 415: pp. 62–65, 2002.
[65] Kamien R D, (2003) “Physics: Topology from the bottom up”, Science Vol. 299: pp. 1671–1673, 2003
[66] Siegel J S, (2004) “Chemistry: Chemical Topology and Interlocking Molecules”, Science, Vol. 304: pp.1256–1258, 2012.
[67] Guan Z, Cotts P M, Mc Cord E F, and McLain S J, (1999). “Chain Walking: A New Strategy to Control Polymer Topology”, Science Vol. 283: pp. 2059–2062, 1999.
[68] Tezuka Y, and Oike H, (2001) “Topological Polymer Chemistry: Systematic Classification of Nonlinear Polymer Topologies”, J. Am. Chem. Soc., Vol. 123: pp. 11570–11576, 2001.
[69] Doboli A and Vemuri R, (2003) “Exploration-Based High-Level Synthesis of Linear Analog Systems operating at low/medium Frequencies”, IEEE Trans. CADICS, 2003.
[70] Sripramong T, and Toumazou C, (2002) “The Invention Of CMOS Amplifiers Using Genetic Programming and Current-Flow Analysis”, IEEE Trans. CADICS, 2002.
[71] McConaghy T and et al., (2009) “Variation-Aware Structural Synthesis of Analog Circuits via Hierarchical Building Blocks and Structural Homotopy”, IEEE Trans. CADICS, 2009.
[72] Xiao-Liang Qi, Edward Witten, Shou-Cheng Zhang, (2012) “Axion Topological Field Theory of Topological Superconductors”, Physical Review B. Vol. 87 (13): pp. 134519, 2012. doi:10.1103/PhysRevB.87.134519
[73] Levin Michael, Wen Xiao-Gang, (24 March 2006) “Detecting Topological Order in a Ground State Wave Function”, Physical Review Letters, Vol. 96 (11): pp. 110405, 2006. doi:10.1103/physrevlett.96.11040. ISSN 0031-9007. PMID 16605803
[74] Levin, Michael; Wen, Xiao-Gang (2006) “Quantum Ether: Photons and Electrons from A Rotor Model”, Physical Review B, Vol. 73 (3): pp. 035122, 2006.https://doi.org/10.1103/PhysRevB.73.035122
[75] Holling, C S, (1973) "Resilience and Stability of Ecological Systems", Annual Review of Ecological Systematics, Vol. 4: pp. 1-23, 1973.
[76] Stephenson C, Lyon D, and Hübler A, (2017). “Topological Properties of a Self-Assembled Electrical Network via ab initio Calculation”, Sci. Rep. 7: pp. 41621, 2017. doi:10.1038/srep41621, PMID 28155863Chen,
[77] Schreiber, Roy E.; Avram, Liat; Neumann, Ronny (2018) “Self-Assembly through Noncovalent Preorganization of Reactants: Explaining the Formation of a Polyfluoroxometalate”, Chemistry - A European Journal, Vol. 24 (2): pp. 369–379, 2018.
[78] Franklin S, Strain S, Snaider J, McCall R, and Faghihi U, (2012) “Global Workspace Theory, its LIDA Model and the Underlying Neuroscience”, Biologically Inspired Cognitive Architectures, Vol.1: pp.32–43, 2012.
[79] Friston K, (2012) “Self-organization, Inference and Cognition: Comment on “Consciousness, Crosstalk, and the Mereological Fallacy: An Evolutionary Perspective”, by Rodrick Wallace, Physics of Life Reviews, Vol. 9(4): pp. 456–457, 2012.
[80] Moreno A, (2016) “Some Conceptual Issues in the Transition from Chemistry to Biology”, History and Philosophy of the Life Sciences, Vol. 38(4): pp. 1-16, 2016.
[81] Luisi PL, (2015) “The Minimal Autopoietic Unit”, Origins of Life and Evolution of Biospheres, Vol.44 (4): pp.335-338, 2015.
[82] Nyman R A, Scheel S, and Hinds E A, (2011) “Prospects for using Integrated Atom-Photon Junctions for Quantum Information Processing”, Quantum Information Processing, Vol. 10: no. 941, 2011. https://doi.org/10.1007/s11128-011-0298-y
[83] Xie, Gu Zheng-Cheng, Wen Xiao-Gang, (2010) “Local Unitary Transformation, Long-Range Quantum Entanglement, Wave Function Renormalization, and Topological Order”, Phys. Rev. B., Vol. 82 (15): pp. 155138, 2010. doi:10.1103/physrevb.82.15513800
[84] Belkin A, Hubler A, and Bezryadin A, (2015) “Self-Assembled Wiggling Nano-Structures and the Principle of Maximum Entropy Production”, Sci. Rep., Vol. 5: pp. 8323, 2015. doi:10.1038/srep08323. PMID 25662746.
[85] Lundgaard Christian, Alexandersen Joe, Zhou Mingdong, Andreasen Casper Schousboe, Sigmund Ole, (2018) “Revisiting Density-Based Topology Optimization for Fluid-Structure-Interaction Problems”, Structural and Multidisciplinary Optimization, Vol. 58 (3): pp.969–995, 2018. doi:10.1007/s00158-018-1940-4
[86] Siegel J S, Liang C Z, Mislow K, and Am J, (2012) “Driving the Formation of Molecular Knots”, Science, Vol. 338: pp. 752–753, 2012.
[87] Lei Liu, Yu Liu, Tianxun Gong, Wen Huang, Junxiong Guo, Xiaosheng Zhang, Shifeng Zhou and Bin Yu, (2019) "Graphene-Based Polarization-Sensitive Longwave Infrared Photodetector", IOP Publishing Ltd, Nanotechnology, Volume 30 (43), 13 August, 2019.
[88] Salas L D and Arce J C, (2017) “Potential Energy Surfaces in Atomic Structure: The Role of Coulomb Correlation in the Ground State of Helium”, Physical Review A, 10.1103/PhysRevA.95.022502, 95, 2, (2017).
[89] Hamidi S M, Ramezani R, Bananej A, (2016) “Hydrogen Gas Sensor based on Long-Range Surface Plasmons in Lossy Palladium Film Placed on Photonic Crystal Stack”, Elsevier, Vol. 53: pp.201-208, 2016. https://doi.org/10.1016/j.optmat.2016.01.050
[90] Moore, Joel E, (2010) “The Birth of Topological Insulators”, Nature, Vol. 464 (7286): pp. 194–198, 2010. https://doi.org/10.1038/nature08916. PMID 20220837.
[91] Adam Farmer, Andrienne C, Friedli, Stephen M, Wright, William M. Robertson, (2012) “Biosensing using Surface Electromagnetic Waves In Photonic Band Gap Multilayers”, Elsevier, Vol. 173: pp.79-84, 2012. https://doi.org/10.1016/j.snb.2012.06.015.
[92] Matthias Fischer, (2015) “Fit for the future? A New Approach in the Debate about what Makes healthcare Systems Really Sustainable”, Sustainability (Switzerland), Vol.7 (1): pp.294–312, 2015.
[93] Jeffrey Braithwaite, Luke Testa, Gina Lamprell, Jessica Herkes, Kristiana Ludlow, Elise McPherson, Margie Campbell, and Joanna Holt, (2017) “Built to last? The Sustainability of Health System Improvements, Interventions and Change Strategies: A Study Protocol for a Systematic Review”, BMJ open, Vol. 7, no. 11, 2017.
[94] West G B, and Brown J H, (2005) “The Origin of Allometric Scaling Laws in Biology from Genomes to Ecosystems: Towards A Quantitative Unifying Theory of Biological Structure and Organization”, Journal of experimental biology, Vol. 208(9):15751592, 2005; https://doi.org/10.1242/jeb.01589 PMID: 15855389
[95] Göppl M. et al., (2008) “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics”, Jounal of Applied Physics, 2008. https://doi.org/10.1063/1.3010859.
[96] Simons, Rainee N, (2001) “Coplanar Waveguide Circuits, Components, and Systems”, John Wiley & Sons Inc., 2001. ISBN 0-471-16121-7.
[97] Wallraff A et al., (2004) “Strong Coupling of A Single Photon to a Superconducting Qubit Using Circuit Quantum Electrodynamics”, Nature. Nature Publishing Group. 431 (7005): 162–167, 2004. https://doi.org/10.1038/nature02851. PMID 15356625.
[98] Tiwari S C, (1999) “Rebirth of the Electron: Electromagnetism an Unorthodox New Approach to Fundamental Problems in Physics”, (http://www.lulu.com/content/439658, 2006) J. Mod. Opt., Vol. 46: pp.1721, (1999).
[99] Yuta Tsuji, Mikiya Hori, Kazunari Yoshizawa, (2020) “Theoretical Study on the Electronic Structure of Heavy Alkali-Metal Suboxides”, Inorganic Chemistry Vol. 59 (2): pp. 1340-1354, 2020. https://doi.org/10.1021/acs.inorgchem.9b03046.
[100] Tang Z Z and Pan S L, (2019) “Simultaneous Measurement of Doppler-Frequency-Shift and Angle-of-Arrival of Microwave Signals for Automotive Radars", IEEE International Topical Meeting on Microwave Photonics, Ottawa, Canada, Oct. 7-10, 2019.
[101] Cui Z Z, Tang Z Z, Li S M, He Z Q and Pan S L, (2019) “ On-chip Photonic Method for Doppler Frequency Shift Measurement”, IEEE International Topical Meeting on Microwave Photonics, Ottawa, Canada, Oct. 7-10, 2019.
[102] Chen W, Xue M, Zhu D and Pan S L, (2019) “High-Precision Optical Time Delay Measurement based on Carrier-Suppressed Optical Double-Sideband Modulation,” the 24th Optoelectronics and Communications Conference (OECC 2019), pp. 1-2, Fukuoka, Japan, July 7-11, 2019.
[103] Yao Wang, Yong-Heng Lu, Feng Mei, Jun Gao, Zhan-Ming Li, Hao Tang, Shi-Liang Zhu, Suotang Jia, and Xian-Min Jin, (2019) “Direct Observation of Topology from Single-Photon Dynamics on a Photonic Chip”, Physical Review Letters, Vol. 122 (19): no.193903 – Published 16 May 2019. https://doi.org/10.1103/PhysRevLett.122.193903
[104] François Léonard, Catalin D. Spataru, Michael Goldflam, David W. Peters & Thomas E. Beechem, (2017) “Dynamic Wavelength-Tunable Photodetector Using Subwavelength Graphene Field-Effect Transistors”, Sci Rep 7, 45873 (2017). https://doi.org/10.1038/srep45873.
[105] Catalin D. Spataru and François Léonard, (2019) “Quantum Dynamics of Single-Photon Detection Using Functionalized Quantum Transport Electronic Channels”, Phys. Rev. Research 1, 013018 – Published 30 August 2019. https://doi.org/10.1103/PhysRevResearch.1.013018.
[106] De la Peña L and Cetto A M, (2008) “The Physics of Stochastic Electrodynamics”, Il Nuovo Cimento B, 10.1007/BF02732647, 92, 2, (189-217), (2008).
[107] Ole Keller, (2000) “Space-time Description of Photon Emission from an Atom”, Phys. Rev. A 62, 022111 – Published 18 July 2000. https://doi.org/10.1103/PhysRevA.62.022111.
[108] Dietrich A, Doherty M W, Aharonovich I, and Kubanek A, (2020) “Solid-State Single Photon Source with Fourier Transform Limited Lines at Room Temperature”, Phys. Rev. B, Vol. 101: 081401(R) – Published 5 February 2020. https://doi.org/10.1103/PhysRevB.101.081401
[109] Boyer M, and Stewart N F, (1991) “Modeling Space for Toleranced Objects”, International Journal of Robotics Research, Volume 10 (5): pp. 270 – 582, 1991.
[110] Boyer M, and Stewart N F, (1992) “Imperfect from Tolerancing on Manifold Object”, International Journal of Robotics Research, Volume 11 (5): pp. 482 – 490, 1992.
[111] Stewart N F, (1993) “A Sufficient Condition for Correct Topological form in Tolerance Specification”, Computer – Aided Design”, January Vol. 25 (1): pp. 39 – 48, 1993.
[112] Andresson L-E, Dorney S M, Peters T J, and Stewart N F, (1994) “Polyhedral Perturbations that Preserve Topological form”, CT Technical Report CSE-TR-94-09, University of Connecticut, Storrs. To appear in Computer – Aided Geometry Design.
[113] Rosen D W, and Peter T J, (1992) “Topological Prosperities that Mode Feature-Based Representation Conversions within Concurrent Engineering”, Research in Engineering Design, Vol. 4(4): pp.147–158, 1992.
[114] Peters T J, Rosen D W, and Shapiro V, (1994 c) “A Topological Model of Limitations in Design for Manufacturing”, Research in Engineering Design, Vol. 6 (4): pp. 223 – 233, 1994.
[115] David B. Lindenmayer, Joern Fischer, Adam Felton, Mason Crane, Damian Michael, Christopher Macgregor, Rebecca Montague-Drake, Adrian Manning, and Richard J. Hobbs, (2008). “Novel Ecosystems Resulting from Landscape Transformation Create Dilemmas for Modern Conservation Practice”, Conservation Letters, Vol. 1 (3): pp.129–135, 2008. http:///doi.org/10.1111/j.1755-263X.2008.00021.x
[116] Blersh D M, Kangas P C, (2012) “Autonomous Behavior of a Wetland Soil Technoecosystem”, Environmental Engineering Science, Vol. 23 (2): pp. 156–166, 2012. Archived from the original (PDF) on 2012-03-25. Retrieved 2020-06-16.
[117] Nicholson D J, (2014) “The Return of the Organism as a Fundamental Explanatory Concept in Biology”, Philosophy Compass, Vol.9 (5): pp.347-359, 2014.
[118] Hickman GJ, Hodgman TC, (2009) "Inference of Gene Regulatory Networks using Boolean Network Inference Methods", J Bioinform Comput Biol, Vol.7: pp.1013—1029, 2009.
[119] Sachs K, Perez O, Peter D, Lauffenburger D, Nolan G, (2005) “Causal Protein Signaling Networks Derived from Multi-parameter Single-Cell Data”, Science, Vol. 308: pp.523—529, 2005.
[120] Mukherjee S, Speed TP: Network inference using informative priors. PNAS 2008, 105:14313—14318.
[121] Hartemink A (2005) “Reverse Engineering Gene Regulatory Networks”, Nat Biotechnol, Vol.23: pp.554—55, 2005.
[122] Bansal M, Belcastro V, Ambesi-Impiombato A, Bernardo D, (2007) "How to Infer Gene Networks from Expression Profiles", Mol Syst Biol, Vol. 3: pp.78, 2007.
[123] Gardner T, di Bernardo D, Lorenz D, Collins J, (2003) “Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling”, Science, Vol.301: pp.102—105, 2003.
[124] Rogers S, Girolami M, (2005) “A Bayesian Regression Approach to The Inference of Regulatory Networks from Gene Expression Data”, Bioinformatics, Vol.21: pp.3131—3137, 2005.
[125] de la Fuente A, Makhecha D, (2006) “Unravelling Gene Networks From Noisy Under-Determined Experimental Perturbation Data”, IEE Proc.-Syst. Biol., Vol.153: pp. 256—261, 2006.
[126] Kimura S, Shiraishi Y, Hatakeyama M, (2009) “Inference of Genetic Networks Using Linear Programming Machines: Application of a Priori Knowledge”, In Proceedings of International Joint Conference on Neural Networks, IEEE, Atlanta, Georgia, USA, pp.1617—1624, June 14-19, 2009.
[127] D’Haeseleer P, Liang S, Somogyi R, (2002) “Reverse Engineering of Regulatory Networks: Simulation Studies on A Genetic Algorithm Approach for Ranking Hypotheses", Biosystems, Vol.66: pp.31—41, 2002.
[128] Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Favera RD, Califano A, (2006) “Aracne: An Algorithm for The Reconstruction Of Gene Regulatory Networks In Amammalian Cellular Context", BMC Bioinformatics, Vol.7: S7, 2006.
[129] Peng L, Zhang C, Perkins EJ, Gong P, Deng Y, (2007) “Comparison of Probabilistic Boolean Network and Dynamic Bayesian Network Approaches for Inferring Gene Regulatory Networks", BMC Bioinformatics, Vol. 8: S13, 2007.
[130] Grimbleby J B, (1995) “Automatic Analogue Network Synthesis Using Genetic Algorithms”, in Proc. 1st Int. Conf. Genetic Algorithms in Engineering Systems: Innovations and Applications (GALESIA), pp. 53–58, 1995.
[131] Zebulum R S, Pacheco M A, and Vellasco M, (1998) “Comparison of Different Evolutionary Methodologies Applied to Electronic Filter Design,” in 1998 IEEE International Conference on Evolutionary Computation. Piscataway, NJ: IEEE Press, pp. 434–439, 1998.
[132] Markowitz F, Spang R: Inferring cellular networks - a review. BMC Bioinformatics, 8: S5, 2007.
[133] Crisona N J, Weinberg R L, Peter B J, Sumners D W, Cozzarelli N R, (1999) “The Topological Mechanism of Phage Lambda Integrase”, Journal of Molecular Biology, Vol. 289(4): pp. 747–775, 1999.
[134] Darcy I K, Scharein R G, (2006) “Topoice-R: 3D Visualization Modeling the Topology of DNA Recombination”, Bioinformatics, Vol. (22) 14: pp. 1790 – 1791, 2006
[135] Jorge B. Schvartzman, Pablo Hernandez, Dora B. Krimer, Julien Dorier, and Andrzej Stasiak (2019) “Closing the DNA Replication Cycle: from Simple Circular Molecules to Supercoiled and Knotted DNA Catenanes”, Nucleic Acids Research, Vol. 47 (14): pp. 7182–7198, Published online 5 July 2019. http\\doi.org\10.1093/nar/gkz586
[136] Klöpffer W, (1997) “Life Cycle Assessment”, Environmental Science and Pollution Research, 4 (4), 223–8, 1997.
[137] Selkoe DJ (December 2003) “Folding Proteins in Fatal Ways”, Nature. 426 (6968): 900–4, 2003. doi:10.1038/nature02264.
[138] Alberts B, Bray D, Hopkin K, Johnson A, Lewis J, Raff M, Roberts K, Walter P, (2010) “Protein Structure and Function”, Essential cell biology (Third ed.). New York, NY: Garland Science. pp. 120–70, 2010 ISBN 978-0-8153-4454-4.
[139] Tainter J A, (2011) “Energy, Complexity, and Sustainability: A Historical Perspective”, Environmental Innovation and Societal Transitions, Vol.1 (1): pp.89–95, 2011.
[140] Friston K J, Mechelli A, Turner R, Price C J, (2000) “Nonlinear Responses in fMRI: The Balloon Model”, Volterra kernels, and another hemodynamics, Neuroimage, Vol (12): pp. 466–477, 2000.
[141] Pearson L J, and Pearson C J, (2012) “Societal Collapse or Transformation, and Resilience”, Proceedings of the National Academy of Sciences, Vol.109 (30): E2030–E2031, 2012.
[142] Picelli, R.; Vicente, W.M.; Pavanello, R. (2017). “Evolutionary Topology Optimization for Structural Compliance Minimization Considering Design-Dependent FSI Loads”, Finite Elements in Analysis and Design. 135: 44–55, 2017 doi: 10.1016/j.finel.2017.07.005
[143] Nicholas Jenkins, Kurt Maute, (2016) “An Immersed Boundary Approach for Shape and Topology Optimization of Stationary Fluid-Structure Interaction Problems”, Structural and Multidisciplinary Optimization. 54 (5): 1191–1208. doi:10.1007/s00158-016-1467-5.
[144] Ponnuswamy N, Cougnon F B L, Clough J M, Pantosx G D, and Sanders J K M , (2012) “Discovery of an Organic Trefoil Knot”, Science, Vol. 338: pp.783–785, 2012.
[145] Stelniec-Klotz I, Legewie S, Tchernitsa O, Witzel F, Klinger B, Sers C, Herzel H, Bluthgen N, Schafer R, (2012) "Reverse Engineering a Hierarchical Regulatory Network Downstream of Oncogenic KRAS", Mol Cell Biol., Vol.8: pp.6012012, 2012.
[146] Qi Xiaodong, Zhang Fei, Su Zhaoming, Jiang Shuoxing, Han Dongran, Ding Baoquan, Liu Yan, Chiu Wah, Yin Peng, YanHao, (2018-11-02) “Programming Molecular Topologies from Single-Stranded Nucleic Acids”, Nature Communications, Vol. 9 (1): pp. 4579, 2018. Bibcode: 2018NatCo...9.4579Q. doi:10.1038/s41467-018-07039-7. ISSN 2041-1723. PMC 6214983. PMID 30389935.
[147] Faísca, Patrícia F N, (2015-01-01) “Knotted Proteins: A Tangled Tale of Structural Biology”, Computational and Structural Biotechnology Journal, Vol. 13: pp. 459–468, 2015. doi:10.1016/j.csbj.2015.08.003. ISSN 2001-0370. PMC 4556803. PMID 26380658.
[148] Gao Z, Gao F, Zhang Y M, Xu H Y, Luo Y, Zhang B L, (2017) Adv. Mater., Vol.29: pp. 1700018, 2017.
[149] Gao Z, Xu H, Gao F, Zhang Y, Luo Y, Zhang B, (2018) Phys. Rev. Appl., Vol. 9: pp. 044019, 2018.
[150] Mathew Stracy, Adam J M Wollman, Elzbieta Kaja, Jacek Gapinski, Ji-Eun Lee, Victoria A Leek, Shannon J McKie, Lesley A Mitchenall, Anthony Maxwell, David J Sherratt, Mark C Leake, Pawel Zawadzki, (2018) “Single-Molecule Imaging of DNA gyrase activity in Living Escherichia coli”, Nucleic Acids Research, Vol. 47(1): Pages 210–220, 10 January 2019, https://doi.org/10.1093/nar/gky1143
[151] Darcy I K, Luecke J, Vazquez M, (2009) “Tangle Analysis of Different Topology Experiments: Applications to a Mu Protein–DNA Complex”, Algebra. Geome. Topology, Vol. 9(4): pp. 2247–2309, 2019.
[152] Fersht A R, (1998) “Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding”,San Francisco: Freeman, 1998 .
[153] Onuchic J, Luthey-Schulten A, Wolynes P G, (1997) “Theory of Protein Folding: The Energy Landscape Perspective”, Annu. Rev. Phys. Chem., Vol. 48: pp.545–600, 1997.
[154] Gan H H, Pasquali S, and Schlick T, (2003) “Exploring The Repertoire of RNA Secondary Motifs Using Gsraph Theory; Implications for RNA Design”, Nucleic Acids Res., Vol. 31: pp. 2926–2943, 2003.
[155] Young S M, Sarovar M, and Léonard F, Phys. Rev. A 97, 033836 (2018).
[156] Stobinska M, Alber G, and Leuchs G, ´ Europhys. Lett. 86, 14007 (2009).
[157] Wang Y, Mináˇr J, Sheridan L, and Scarani V, Phys. Rev. A 83, 063842 (2011).
[158] Gough J E, James M R, Nurdin H I, and Combes J, Phys. Rev. A 86, 043819 (2012).
[159] Domokos P, Horak P, and Ritsch H, Phys. Rev A 65, 033832 (2002).
[160] Spataru C D, Ismail-Beigi S, Benedict L X, and Louie S G, Phys. Rev. Lett. 92, 077402 (2004).
[161] Capaz R B, Spataru C D, Ismail-Beigi S, and Louie S G, Phys. Status Solidi B 244, 4016 (2007).
[162] Feliciano Giustino, (2014) “Materials Modelling using Density Functional Theory”, Oxford University Press, 2014.
[163] Schrödinger E, (1926) “Quantizierung als Eigenwertproblem (Erste Mitteilung) / Quantization as a Problem of Proper Values”, Part I. Annalen der Physik, Leipzig 79 (1926) 361.
[164] Schrödinger E, (1926) “An Undulatory Theory of the Mechanics of Atoms and Molecules”, Phys. Rev., Vol. 28 (6): pp. 1049–1070, Published 1 December 1926. https:///doi.org/10.1103/PhysRev.28.1049
[165] Dmitri Yerchuck, Alla Dovlatova, Felix Borovik, Yauhen Yerchak, Vyacheslav Stelmakh, (2014) “To Principles of Quantum Mechanics Development”, International Journal of Physics, Vol. 2(5): pp.129-145, 2014. doi: 10.12691/ijp-2-5-2.
[166] Rosen R, (1958) “A Relational Theory of Biological Systems”, Bull. Math. Biophys. Vol. 20: pp. 245–341, 1958.
[167] Varela F, (1979), “Principles of Biological Autonomy”, New York: North Holland/Elsevier, 1979.
[168] Hieulle J, Carbonell-Sanrom E, Vilas-Varela M, Garcia-Lekue A, Guitin E, Peña D and Pascual J I, (2018) “On-surface Route for Producing Planar Nanographenes with Azulene Moieties”, Nano Lett., Vol. 18: pp 418, (2018).
[169] Xin H and Gao X, (2017) “Application of Azulene in Constructing Organic Optoelectronic Materials: New Tricks for an Old Dog”, Chem. Plus Chem., Vol. 82: pp. 945, 2017.
[170] Yamaguchi Y, Takubo M, Ogawa K, Nakayama K-i, Koganezawa T, and Katagiri H, (2016) “Terazulene Isomers: Polarity Change of OFETs through Molecular Orbital Distribution Contrast”, J. Am. Chem. Soc. Vol. 138: pp. 11335, 2016.
[171] Murai M, Iba S, Ota H and Takai K, (2017) “Azulene-fused Linear Polycyclic Aromatic Hydrocarbons with Small Bandgap, High Stability, and Reversible Stimuli Responsiveness”, Org. Lett. Vol. 19: pp. 5585m 2017.
[172] Peter Monk, (2003) “Finite Element Methods for Maxwell's Equations”, Oxford UK, Oxford University Press, p. 1 ff. ISBN 978-0-19-850888-5
[173] Gibson J J, (1979) “The Ecological Approach to Visual Perception”,. Boston: Houghton Mifflin, 1979.
[174] Varela F J & Frenk S, (1987) “The Organ of form: Towards a Biological Theory of Shape”, Journal of Social Biology and Structure, Vol. 10: pp. 73–83, 1987.
[175] Varela FG, Maturana HR, Uribe R, (1974) “Autopoiesis: the organization of living systems, its characterization and a model”, Curr Mod Biol. Vol.5: pp. 187–196, 1974.
[176] David O, Kilner J M, Friston K J, (2000) “Mechanisms of Evoked and Induced Responses in MEG/EEG. Neuroimage”, Vol. 31: pp. 1580–1591, 2000.
[177] Buxton R B, Wong E C, Frank L R, (1998) “Dynamics of Blood Flow and Oxygenation Changes During Brain Activation: The Balloon Model”, Magn Reson Med. Vol. 39: pp. 855–864, 1998.
[178] Hamalainen M, Hari R, Ilmoniemi R, Knuutila J, Lounasmaa O, (1993) “Magnetoencephalography. Theory, Instrumentation and Applications to Tne Noninvasive Study of Brain Function”, Rev Mod Phys. Vol. 65: pp.413–497, 1993.
[179] Nunez P L, Srinivasan R, (2005) “Electric fields of the Brain”, Oxford University Press; New York: 2005.
[180] Athanasiadis I N, Rizzoli A E, Donatelli M, Carlini L, (2011) “Enriching Environmental Software Model interfaces through Ontology-based tools”, Int. J. Advanced Systemic Studies, Vol. (4): pp.94-105, (2011).
[181] Manuel González de Molina, Víctor M. Toledo, (2014) “The Social Metabolism: A Socio-Ecological Theory of Historical Change”, Book, August, 2014. http:/// doi.org/10.1007/978-3319-06358-4. https://www.researchgate.net/publication/270817639
[182] Urrestarazu H, (2011) “Autopoeisis System: A Generalized Explanatory Approach”, Part I, Constructivist Foundation, Vol. 6(3): pp.307-324, 2011. Available at http://www.univie.ac.at/constructivism/journal/6/3/307.
[183] Romesh G. Abeysuriya , Jonathan Hadida, Stamatios N. Sotiropoulos, Saad Jbabdi, Robert Becker, Benjamin A. E. Hunt, Matthew J. Brookes and Mark W Woolrich, (2018) “A Biophysical Model of Dynamic Balancing of Excitation and Inhibition in Fast Oscillatory Large-Scale Networks”, PLoS Comput Biol., Vol. 14(2): e1006007. https://doi.org/10.1371/journal.pcbi.1006007
[184] Gálvez J, Gálvez-Llompart M and García-Domenech R, (2012) “Introduction to Molecular Topology: Basic Concepts and Application to Drug Design”, Current Computer Aided Drug Design, Vol.8 (3):pp.196-223. 2012 Sep. http:///doi.org/10.2174/157340912801619094 PMID: 22734705.
[185] SonaliShinde, Vineetha Mandlik and ShailzaSingh, (2015) “Integrating Bioinformatics and Systems Biology for Exploring Novel Lipid Pathways in Infectious Diseases”, Advances in Mathematical Chemistry and Applications, Volume 2 : Pages 191-220, 2015. https://doi.org/10.1016/B978-1-68108-053-6.50009-0
[186] DanailBonchev, (2015) “On the Concept for Overall Topological Representation of Molecular Structure”, Advances in Mathematical Chemistry and Applications, Volume 1: Pages 42-75, 2015. https:///doi.org/10.1016/B978-1-68108-198-4.50003-5