From quasispecies to quasispaces: coding and cooperation in chemical and electronic systems

Review

Abstract

This contribution addresses the physical roles of spatial structures, either externally imposed or generated through self-assembly, either passive or active, on the physical chemistry of evolution. Starting with simple diffusion in closed capillaries, a one-dimensional space, it covers eight aspects of experimental and theoretical research into the interaction of evolution with spatial structures: in various dimensions, including hitherto unexplored ones, spanning from externally defined physical spaces to actively tailored spaces, assembled by the evolving components themselves. As such, it contains some original research by the author as well as tracing how other insights grew over three decades out of the mentorship of Manfred Eigen in the 1980s. Much of the early interest in spatial structures centres on its role in stabilizing higher order cooperative structures involving the coevolution of different molecules, as the genetic coding system exemplifies. Modern nanotechnology enables the design and construction of genetically encoded variants of smart components that can actively control both the proliferation of molecules and the structuring of space. A key role for this article is to show the continuity in this line of enquiry, beginning with quasispecies and projecting to autonomous microparticles with electronic genomes able to form programmable quasispaces.

Keywords

Evolution Reaction diffusion Microfluidics cooperation Synthetic biology Lablets 

Abbreviations

CATCH

Cooperative amplification of templates by cross-hybridization

CCD

Charge-coupled device

DNA

Deoxyribose nucleic acid

ECCell

Electronic chemical cell (also an EU Project with this name)

EU

European Union

FPGA

Field-programmable gate array: a form of reconfigurable digital electronics

GPU

Graphics processing unit

imb

Former Institute for Molecular Biotechnology in Jena, Germany

MPIbpc

Max Planck Institute for Biophysical Chemistry (in Göttingen, Germany)

MICREAgents

Microscale chemically reactive electronic agents (also an EU project)

NGEN

Computer designed for many (N) generations

NTP

Nucleotide triphosphate: activated ribose or deoxyribose monomers with base either A,C,G,T,U

A virus infecting bacteria and used in early molecular evolution experiments

RNA

Ribose nucleic acid

SRAM

Static random-access memory (here as dedicated chips next to an FPGA)

TO

Thiazole orange

TOTO

Bis-intercalator made of two covalently linked TO molecules

UTP

Uracil triphosphate

UV

Ultraviolet light

ZNA

Zip nucleic acid (synthetic DNA with artificial spermidine phosphoramidite residues at defined monomer positions in the sequence)

Notes

Acknowledgements

This work was supported in part by the European Commission under Grant #318671. It was also made possible through the support of a Grant from the John Templeton Foundation provided through the Earth-Life Science Institute of Tokyo Institute of Technology. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation or the Earth-Life Science Institute. The author wishes to acknowledge the generous inspiration and support of Manfred Eigen, also through the yearly Biophysical Winterseminar in Klosters on “Molecules, Memory and Mind”, and especially his untiring excitement in the high-dimensionality of sequence space that brings innovation in quasispecies closer. Quasispaces, as described here, can take this one step further in allowing cooperative innovation in evolution. Especially, in this place, the author would also like to thank his scientific team BioMIP in Göttingen, Jena, Sankt Augustin and Bochum for thirty years (since 1987) of important contributions and their loyal willingness to participate in this journey.

References

  1. Adlam B, Chatterjee K, Nowak MA (2015) Amplifiers of selection. Proc R Soc A Math Phys Eng Sci 471:20150112–20150114.  https://doi.org/10.1098/rspa.2015.0114 CrossRefGoogle Scholar
  2. Agerschou ED, Mast CB, Braun D (2017) Emergence of life from trapped nucleotides? Non-equilibrium -behavior of oligonucleotides in thermal gradients. Synlett.  https://doi.org/10.1055/s-0036-1588653 Google Scholar
  3. Allen B, Lippner G, Chen Y-T, Fotouhi B, Momeni N, Yau S-T, Nowak MA (2017) Evolutionary dynamics on any population structure. Nature 544:227–230.  https://doi.org/10.1038/nature21723 CrossRefPubMedGoogle Scholar
  4. Altmeyer S, McCaskill JS (2001) Error threshold for spatially resolved evolution in the quasispecies model. Phys Rev Lett 86:5819–5822.  https://doi.org/10.1103/PhysRevLett.86.5819 CrossRefPubMedGoogle Scholar
  5. Altmeyer S, Fuchslin RM, McCaskill JS (2004) Folding stabilizes the evolution of catalysts. Artif Life 10:23–38.  https://doi.org/10.1162/106454604322875896 CrossRefPubMedGoogle Scholar
  6. Anderson PW (1983) Suggested model for prebiotic evolution: the use of chaos. Proc Natl Acad Sci 80:3386–3390.  https://doi.org/10.1073/pnas.80.11.3386 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bauer GJ, McCaskill JS, Oten H, Schwienhorst A (1989a) Evolution im Laboratorium. Nachr Chem Tech Lab 37:484–488.  https://doi.org/10.1002/nadc.19890370508 CrossRefGoogle Scholar
  8. Bauer GJ, McCaskill JS, Otten H (1989b) Traveling waves of in vitro evolving RNA. Proc Natl Acad Sci USA 86:7937–7941.  https://doi.org/10.1073/pnas.86.20.7937 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Biebricher CK, Eigen M, Gardiner WC (1983) Kinetics of ribonucleic acid replication. Biochemistry 22:2544–2559.  https://doi.org/10.1021/bi00279a036 CrossRefPubMedGoogle Scholar
  10. Biebricher CK, Eigen M, Gardiner WC (1984) Kinetics of RNA replication: plus-minus asymmetry and annealing. Biochemistry 23:3186–3194.  https://doi.org/10.1021/bi00309a012 CrossRefPubMedGoogle Scholar
  11. Biebricher CK, Eigen M, Gardiner WC (1985) Kinetics of RNA replication: competition and selection among self-replicating RNA species. Biochemistry 24:6550–6560.  https://doi.org/10.1021/bi00344a037 CrossRefPubMedGoogle Scholar
  12. Biebricher CK, Eigen M, Luce R (1986) Template-free RNA synthesis by Q[beta] replicase. Nature 321:89–91.  https://doi.org/10.1038/321089a0 CrossRefPubMedGoogle Scholar
  13. Biebricher CK, Eigen M, McCaskill JS (1993) Template-directed and template-free RNA-synthesis by Q-Beta replicase. J Mol Biol 231:175–179.  https://doi.org/10.1006/jmbi.1993.1271 CrossRefPubMedGoogle Scholar
  14. Boerlijst MC, Hogeweg P (1991) Spiral wave structure in pre-biotic evolution: hypercycles stable against parasites. Phys D 48:17–28.  https://doi.org/10.1016/0167-2789(91)90049-F CrossRefGoogle Scholar
  15. Borrelli V, Jabrane S, Lazarus F, Thibert B (2012) Flat tori in three-dimensional space and convex integration. Proc Natl Acad Sci USA 109:7218–7223.  https://doi.org/10.1073/pnas.1118478109 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Braich RS, Chelyapov N, Johnson C, Rothemund PWK, Adleman L (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296:499–502.  https://doi.org/10.1126/science.1069528 CrossRefPubMedGoogle Scholar
  17. Bresch C, Niesert U, Harnasch D (1980) Hypercycles, parasites and packages. J Theor Biol 85:399–405.  https://doi.org/10.1016/0022-5193(80)90314-8 CrossRefPubMedGoogle Scholar
  18. Castets V, Dulos E, Boissonade J, De Kepper P (1990) Experimental evidence of a sustained standing Turing-type nonequilibrium chemical pattern. Phys Rev Lett 64:2953–2956.  https://doi.org/10.1103/PhysRevLett.64.2953 CrossRefPubMedGoogle Scholar
  19. Chemnitz S, Tangen U, Wagler PF, Maeke T, McCaskill JS (2008) Electronically programmable membranes for improved biomolecule handling in micro-compartments on-chip. Chem Eng J 135:S276–S279.  https://doi.org/10.1016/j.cej.2007.07.061 CrossRefGoogle Scholar
  20. Cronhjort MB, Blomberg C (1994) Hypercycles versus parasites in a two dimensional partial differential equations model. J Theor Biol 169:31–49.  https://doi.org/10.1006/jtbi.1994.1128 CrossRefGoogle Scholar
  21. Cronhjort MB, Blomberg C (1997) Cluster compartmentalization may provide resistance to parasites for catalytic networks. Phys D 101:289–298.  https://doi.org/10.1016/S0167-2789(97)87469-6 CrossRefGoogle Scholar
  22. Dapprich J, McCaskill JS, Volker S, Krause F (1994) Fluorescence imaging of evolving RNA in capillaries. Berichte Der Bunsen-Gesellschaft-Phys Chem Chem Phys 98:1202.  https://doi.org/10.1002/bbpc.19940980927 CrossRefGoogle Scholar
  23. Edwards BF, Timperman AT, Carroll RL, Jo K, Mease JM, Schiffbauer JE (2009) Traveling-wave electrophoresis for microfluidic separations. Phys Rev Lett 102:076103.  https://doi.org/10.1103/PhysRevLett.102.076103 CrossRefPubMedGoogle Scholar
  24. Ehricht R, Ellinger T, McCaskill JS (1997a) Cooperative amplification of templates by cross-hybridization (CATCH). Eur J Biochem 243:358–364.  https://doi.org/10.1111/j.1432-1033.1997.0358a.x CrossRefPubMedGoogle Scholar
  25. Ehricht R, Kirner T, Ellinger T, Foerster P, McCaskill JS (1997b) Monitoring the amplification of CATCH, a 3SR based cooperatively coupled isothermal amplification system, by fluorimetric methods. Nucleic Acids Res 25:4697–4699.  https://doi.org/10.1093/nar/25.22.4697 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Eigen M (1971) Selforganization of matter and evolution of biological macromolecules. Naturwissenschaften 58:465–523.  https://doi.org/10.1007/BF00623322 CrossRefPubMedGoogle Scholar
  27. Eigen M, Schuster P (1977) Hypercycle: a principle of natural self-organization. Part A. Emergence of the hypercycle. Naturwissenschaften 64:541–565.  https://doi.org/10.1007/BF00450633 CrossRefPubMedGoogle Scholar
  28. Eigen M, Schuster P (1978) Hypercycle: a principle of natural self-organization. Part C The realistic hypercycle. Naturwissenschaften 65:341–369.  https://doi.org/10.1007/BF00439699 CrossRefGoogle Scholar
  29. Eigen M, McCaskill JS, Schuster P (1988) Molecular quasi-species. J Phys Chem 92:6881–6891.  https://doi.org/10.1021/j100335a010 CrossRefGoogle Scholar
  30. Eigen M, McCaskill JS, Schuster P (1989) The molecular quasi-species. Adv Chem Phys 75:149–263.  https://doi.org/10.1002/9780470141243.ch4 Google Scholar
  31. Ellinger T, Ehricht R, McCaskill JS (1998) In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system. Chem Biol 5:729–741.  https://doi.org/10.1016/s1074-5521(98)90665-2 CrossRefPubMedGoogle Scholar
  32. Fife PC (1979) Mathematical aspects of reacting and diffusing systems. Lecture Notes in Biomathematics, vol 28. Springer, Berlin. ISBN 978-3-642-93111-6Google Scholar
  33. Fisher RA (1937) The wave of advance of advantageous genes. Ann Eugenics 7:353–369.  https://doi.org/10.1111/j.1469-1809.1937.tb02153.x Google Scholar
  34. Foerster P, Wlotzka B, McCaskill JS (1994) Spatially-resolved evolution studies in an open reactor. Berichte Der Bunsen-Gesellschaft-Phys Chem Chem Phys 98:1203.  https://doi.org/10.1002/bbpc.19940980928 CrossRefGoogle Scholar
  35. Fontana W (1992) Algorithmic chemistry: a model for functional self-organization. vol 10. Artificial life II. ISBN 0-201-52571-2Google Scholar
  36. Fontana W, Schuster P (1987) A computer model of evolutionary optimization. Biophys Chem 26:123–147.  https://doi.org/10.1016/0301-4622(87)80017-0 CrossRefPubMedGoogle Scholar
  37. Frasconi M, Tel-Vered R, Riskin M, Willner I (2010) Electrified selective “Sponges” made of Au nanoparticles. J Am Chem Soc 132:9373–9382.  https://doi.org/10.1021/ja102153f CrossRefPubMedGoogle Scholar
  38. Fuchslin RM, McCaskill JS (2001) Evolutionary self-organization of cell-free genetic coding. Proc Natl Acad Sci USA 98:9185–9190.  https://doi.org/10.1073/pnas.151253198 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Füchslin RM, Altmeyer S, McCaskill JS (2004) Evolutionary stabilization of generous replicases by complex formation. Eur Phys J B 38:103–110.  https://doi.org/10.1140/epjb/e2004-00105-2 CrossRefGoogle Scholar
  40. Fuechslin RM, Maeke T, Tangen U, McCaskill JS (2006) Evolving inductive generalization via genetic self-assembly. Adv Complex Syst 9:1–29.  https://doi.org/10.1142/s0219525906000598 CrossRefGoogle Scholar
  41. Fuechslin RM, Maeke T, McCaskill JS (2009) Spatially resolved simulations of membrane reactions and dynamics: multipolar reaction DPD. Eur Phys J E 29:431–448.  https://doi.org/10.1140/epje/i2009-10482-x CrossRefGoogle Scholar
  42. Funke DA, Hillger P, Oehm J, Mayr P, Straczek L, Pohl N, McCaskill JS (2017) A 200 µm by 100 µm smart submersible system with an average current consumption of 1.3 nA and a compatible voltage converter. IEEE Trans Circuits Syst Online.  https://doi.org/10.1109/tcsi.2017.2750905
  43. Garcia-Schwarz G, Rogacs A, Bahga SS, Santiago JG (2012) On-chip isotachophoresis for separation of ions and purification of nucleic acids. JoVE:e3890.  https://doi.org/10.3791/3890
  44. Holland JH (1976) Studies of the spontaneous emergence of self-replicating systems using cellular automata and formal grammars. In: Lindenmayer A, Rozenberg G (eds) Automata, languages, development. North-Holland, Amsterdam, pp 385–404. ISBN 9780720404746Google Scholar
  45. Hoogerbrugge PJ, Koelman JMVA (1992) Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. EPL (Eur Lett) 19:155.  https://doi.org/10.1209/0295-5075/19/3/001 CrossRefGoogle Scholar
  46. Jo KD, Schiffbauer JE, Edwards BE, Lloyd Carroll R, Timperman AT (2012) Fabrication and performance of a microfluidic traveling-wave electrophoresis system. Analyst 137:875.  https://doi.org/10.1039/c1an15669a CrossRefPubMedGoogle Scholar
  47. Kahn JS, Trifonov A, Cecconello A, Guo W, Fan C, Willner I (2015) Integration of switchable DNA-based hydrogels with surfaces by the hybridization chain reaction. Nano Lett 15:7773–7778.  https://doi.org/10.1021/acs.nanolett.5b04101 CrossRefPubMedGoogle Scholar
  48. Kirner T, Ackermann J, Ehricht R, McCaskill JS (1999) Complex patterns predicted in an in vitro experimental model system for the evolution of molecular cooperation. Biophys Chem 79:163–186.  https://doi.org/10.1016/s0301-4622(99)00049-6 CrossRefPubMedGoogle Scholar
  49. Kirner T, Ackermann J, Steen D, Ehricht R, Ellinger T, Foerster P, McCaskill JS (2000) Complex patterns in a trans-cooperatively coupled DNA amplification system. Chem Eng Sci 55:245–256.  https://doi.org/10.1016/s0009-2509(99)00320-6 CrossRefGoogle Scholar
  50. Kolmogorov A, Petrovskii I, Piskunov N (1991) A study of the diffusion equation with increase in the amount of substance, and its application to a biological problem (from Bull. Moscow Univ., Math. Mech. 1, 1–25, 1937). In: Tikhomirov VM (ed) Selected works of A N Kolmogorov I. Kluwer, Dordrecht, pp 248–270. ISBN 90-277-2796-1Google Scholar
  51. Li T, Nicolaou KC (1994) Chemical self-replication of palindromic duplex DNA. Nature 369:218–221.  https://doi.org/10.1038/369218a0 CrossRefPubMedGoogle Scholar
  52. Lieberman E, Hauert C, Nowak MA (2005) Evolutionary dynamics on graphs. Nature 433:312–316.  https://doi.org/10.1038/nature03204 CrossRefPubMedGoogle Scholar
  53. Maeke T, McCaskill JS, Funke D, Mayr P, Sharma A, Tangen U, Oehm J (2018) Autonomous programmable microscopic electronic lablets optimized with digital control. (in preparation).Google Scholar
  54. McCaskill JS (1984a) A localization threshold for macromolecular quasispecies from continuously distributed replication rates. J Chem Phys 80:5194–5202.  https://doi.org/10.1063/1.446590 CrossRefGoogle Scholar
  55. McCaskill JS (1984b) A stochastic-theory of macromolecular evolution. Biol Cybern 50:63–73.  https://doi.org/10.1007/bf00317940 CrossRefGoogle Scholar
  56. McCaskill JS (1988) Polymer chemistry on tape: a computational model for emergent genetics. Max-Planck-Institut for Biophysical Chemistry, Göttingen.  https://doi.org/10.17617/2.2525422
  57. McCaskill JS (1990) The equilibrium partition-function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105–1119.  https://doi.org/10.1002/bip.360290621 CrossRefPubMedGoogle Scholar
  58. McCaskill JS (1992) How is genetic information generated? In: Andersson SI, Andersson AE, Ottoson U (eds) Theory and control of dynamical systems: applications to systems in biology. World Scientific, Singapore, pp 137–164.  https://doi.org/10.1142/9789814537957
  59. McCaskill JS (1994a) A massively parallel computer with user configurable hardware. In: Schuster P, Wagner H (eds) Annual Report, Institute of Molecular Biotechnology, vol 2. imb Jena, Jena, pp 118–124.  https://doi.org/10.17617/2.2554120
  60. McCaskill JS (1994b) Ursprünge der molekularen Kooperation: Theorie und Experiment. In: Schuster P (ed) Antriitsvorlesungen and der Friedrich-Schiller-Universtät Jena. Institut für Molekulare Biotechnologie IMB, Jena, Germany. Friedrich Schiller Universität, Jena, Jena, pp 27–40.  https://doi.org/10.17617/2.2554115
  61. McCaskill JS (1997) Spatially resolved in vitro molecular ecology. Biophys Chem 66:145–158.  https://doi.org/10.1016/s0301-4622(97)00073-2 CrossRefPubMedGoogle Scholar
  62. McCaskill JS (2001) Optically programming DNA computing in microflow reactors. Biosystems 59:125–138.  https://doi.org/10.1016/s0303-2647(01)00099-5 CrossRefPubMedGoogle Scholar
  63. McCaskill JS, Bauer GJ (1993) Images of evolution—origin of spontaneous RNA replication waves. Proc Natl Acad Sci USA 90:4191–4195.  https://doi.org/10.1073/pnas.90.9.4191 CrossRefPubMedPubMedCentralGoogle Scholar
  64. McCaskill JS, Niemann U (2000) Graph replacement chemistry for DNA processing. DNA Comput 2054:103–116.  https://doi.org/10.1007/3-540-44992-2_8 (Condon A, Rozenberg G, editors) Google Scholar
  65. McCaskill JS, Chorongiewski H, Mekelburg K, Tangen U, Gemm U (1994) NGEN—Configurable computer hardware to simulate long-time self-organization of biopolymers. Berichte Der Bunsen-Gesellschaft-Physical Chemistry Chem Phys 98:1114.  https://doi.org/10.1002/bbpc.19940980906 CrossRefGoogle Scholar
  66. McCaskill JS, Packard NH, Rasmussen S, Bedau MA (2007) Evolutionary self-organization in complex fluids. Philos Trans R Soc B Biol Sci 362:1763–1779.  https://doi.org/10.1098/rstb.2007.2069 CrossRefGoogle Scholar
  67. McCaskill JS et al (2012) Microscale chemically reactive electronic agents. Int J Unconv Comput 8:289–299 (ISSN 1548-7202) Google Scholar
  68. Mills DR, Peterson RL, Spiegelman S (1967) An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc Natl Acad Sci USA 58:217–224.  https://doi.org/10.1073/pnas.58.1.217 CrossRefPubMedPubMedCentralGoogle Scholar
  69. Minero GKA (2016) Electronically controlled DNA processing on a chip. Ph.D. Thesis., Ruhr Universität BochumGoogle Scholar
  70. Minero GAS, Wagler PF, Oughli AA, McCaskill JS (2015a) Electronic pH switching of DNA triplex reactions. RSC Adv 5:27313–27325.  https://doi.org/10.1039/c5ra02628h CrossRefGoogle Scholar
  71. Minero GAS, Wagler PF, Oughli AA, McCaskill JS (2015b) Electronic pH switching of DNA triplex reactions. (Correction: vol 5, pg 27313, 2015). RSC Adv 5:52321.  https://doi.org/10.1039/c5ra90057c CrossRefGoogle Scholar
  72. Möller FM, Kriegel F, Kieß M, Sojo V, Braun D (2017) Steep pH gradients and directed colloid transport in a microfluidic alkaline hydrothermal pore. Angew Chem Int Ed 56:2340–2344.  https://doi.org/10.1002/anie.201610781 CrossRefGoogle Scholar
  73. Niesert U, Harnasch D, Bresch C (1981) Origin of life between Scylla and Charybdis. J Mol Evol 17:348–353.  https://doi.org/10.1007/BF01734356 CrossRefPubMedGoogle Scholar
  74. Noir R, Kotera M, Pons B, Remy J, Behr J (2008) Oligonucleotide—oligospermine conjugates (Zip Nucleic Acids): a convenient means of finely tuning hybridization temperatures. 130:13500–13505.  https://doi.org/10.1021/ja804727a Google Scholar
  75. Patzke V, McCaskill JS, von Kiedrowski G (2014) DNA with 3′-5′-disulfide links-rapid chemical ligation through isosteric replacement. Angew Chem Int Ed 53:4222–4226.  https://doi.org/10.1002/anie.201310644 CrossRefGoogle Scholar
  76. Penchovsky R, McCaskill JS (2001) Cascadable hybridisation transfer of specific DNA between microreactor selection modules. Paper presented at the DNA Computing. In: 7th International workshop on DNA-based computers, DNA7, June 10–13, 2001, Tampa, Florida, USA.  https://doi.org/10.1007/3-540-48017-x_5
  77. Rocheleau T, Rasmussen S, Nielsen PE, Jacobi MN, Ziock H (2007) Emergence of protocellular growth laws. Philos Trans R Soc B Biol Sci 362:1841–1845.  https://doi.org/10.1098/rstb.2007.2076 CrossRefGoogle Scholar
  78. Rücker T (2004) Biomolekulare Informationsverarbeitung in vernetzten Mikroflussreaktoren. Ph. D. Thesis., University of Bonn ISBN-13: 978-3898259590Google Scholar
  79. Schmidt K, McCaskill JS (1996) Open Flow Microreactors. In: Gumpert J (ed) Annual Report, Institute of Molecular Biotechnology, vol 4. imb Jena, Jena, pp 92–100.  https://doi.org/10.17617/2.2554111
  80. Schmidt K, Foerster P, Bochmann A, McCaskill JS (1998) A microflow reactor for two dimensional investigations of in vitro amplification systems. Paper presented at the First International Conference on Microreaction Technology, 1998/01/01 ISBN: 9783540638834Google Scholar
  81. Schnitzler T, Herrmann A (2012) DNA block copolymers: functional materials for nanoscience and biomedicine. Acc Chem Res 45:1419–1430.  https://doi.org/10.1021/ar200211a CrossRefPubMedGoogle Scholar
  82. Schober A, Walter N, Tangen U, Strunk G, Ederhof T, Dapprich J, Eigen M (1995) Multichannel PCR and serial transfer machine as a future tool in evolutionary biotechnology. Biotechniques 18:652–661 (ISSN: 0736-6205) PubMedGoogle Scholar
  83. Segré D, Ben-Eli D, Deamer D, Lancet D (2001) The lipid world. Orig Life Evol Biosph.  https://doi.org/10.1023/A:1006746807104 PubMedGoogle Scholar
  84. Straczek L, Maeke T, Funke D, Shar-ma A, Mc-Cas-kill JS, Oehm J (2016) A CMOS 16 K microelectrode array as docking platform for autonomous microsystems. Paper presented at the Nordic Circuits and Systems Conference (NORCAS), 2016 IEEE, 1–2 Nov. 2016 ISBN: 978-1-5090-1095-0.  https://doi.org/10.1109/norchip.2016.7792908
  85. Szathmary E, Demeter L (1987) Group selection of early replicators and the origin of life. J Theor Biol 128(4):463–486.  https://doi.org/10.1016/s0022-5193(87)80191-1 CrossRefPubMedGoogle Scholar
  86. Tangen U, Schulte L, McCaskill JS (1997) A parallel hardware evolvable computer POLYP. Paper presented at the FCCM 97 (IEEE Transactions).  https://doi.org/10.1109/fpga.1997.624625
  87. Tangen U, Maeke T, McCaskill JS (2002) Advanced simulation in the configurable massively parallel hardware MereGen. In: Hoffmann KH (ed) Coupling of biological and electronic systems, vol 2nd Caesarium 2000. Springer, New York, pp 107–118. (ISBN: 3-540-43699-5)Google Scholar
  88. Tangen U, Wagler PF, Chemnitz S, Goranovic G, Maeke T, McCaskill JS (2006) An electronically controlled microfluidic approach towards artificial cells. ComPlexUs 3:48–57.  https://doi.org/10.1159/000094187 CrossRefGoogle Scholar
  89. Thürk M (1993) A model of self-organising automata algorithms describing molecular evolution. (German title: Ein Modell zur Selbstorganisation von Automatenalgorithmen zum Studium molekularer Evolution). Ph.D. Thesis., Friedrich-Schiller-Universität. https://books.google.de/books/about/Ein_Modell_zur_Selbstorganisation_von_Au.html?id=bePgGwAACAAJ&redir_esc=y
  90. Varela FJ (1979) Principles of biological autonomy. General Systems Research, vol 2. Elsevier North-Holland Inc, New York.  https://doi.org/10.1002/bs.3830260110 Google Scholar
  91. Vasas V, Szathmary E, Santos M (2010) Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life. Proc Natl Acad Sci 107:1470–1475.  https://doi.org/10.1073/pnas.0912628107 CrossRefPubMedPubMedCentralGoogle Scholar
  92. von Kiedrowski G (1993) Minimal replicator theory I: parabolic versus exponential growth. In: Dugas H, Schmidtchen FP (eds) Bioorganic chemistry frontiers. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 113–146.  https://doi.org/10.1007/978-3-642-78110-0_4
  93. von Neumann J (1966) Theory of Self-Reproducing Automata. (Edited posthume by Arthur W. Burks.). University of Illinois Press, Champaign (ISBN-13: 978-0252727337)Google Scholar
  94. Wagler P et al (2015) Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations. Electrophoresis 36:2451–2464.  https://doi.org/10.1002/elps.201400489 CrossRefPubMedGoogle Scholar
  95. Widom B (1986) Lattice model of microemulsions. J Chem Phys 84:6943–6954.  https://doi.org/10.1063/1.450615 CrossRefGoogle Scholar
  96. Wills PR (1993) Self-organization of genetic coding. J Theor Biol 162:267–287.  https://doi.org/10.1006/jtbi.1993.1087 CrossRefPubMedGoogle Scholar
  97. Wills PR (2016) The generation of meaningful information in molecular systems. Philos Trans R Soc A Math Phys Eng Sci.  https://doi.org/10.1098/rsta.2015.0066 Google Scholar
  98. Wlotzka B, McCaskill JS (1997) A molecular predator and its prey: coupled isothermal amplification of nucleic acids. Chem Biol 4:25–33.  https://doi.org/10.1016/s1074-5521(97)90234-9 CrossRefPubMedGoogle Scholar
  99. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159 (ISSN: 0016-6731) Google Scholar
  100. Yin J, McCaskill JS (1992) Replication of viruses in a growing plaque—a reaction-diffusion model. Biophys J 61:1540–1549.  https://doi.org/10.1016/s0006-3495(92)81958-6 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© European Biophysical Societies' Association 2018

Authors and Affiliations

  1. 1.Microsystems Chemistry and BioITRuhr-Universität BochumBochumGermany
  2. 2.European Centre for Living Technology, Ca’ Foscari UniversitasVeniceItaly

Personalised recommendations