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  • Featured in Physics
  • Open Access

Design Principles for Fast and Efficient Self-Assembly Processes

Florian M. Gartner1 and Erwin Frey1,2,*

  • 1Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 Munich, Germany
  • 2Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 Munich, Germany

  • *frey@lmu.de

Phys. Rev. X 14, 021004 – Published 3 April, 2024

DOI: https://doi.org/10.1103/PhysRevX.14.021004

Abstract

Self-assembly is a fundamental concept in biology and of significant interest to nanotechnology. Significant progress has been made in characterizing and controlling the properties of the resulting structures, both experimentally and theoretically. However, much less is known about kinetic constraints and determinants of dynamical properties like time efficiency, although these constraints can become severe limiting factors of self-assembly processes. Here, we investigate how the time efficiency and other dynamical properties of reversible self-assembly depend on the morphology (shape) of the building blocks for systems in which the binding energy between the constituents is large. As paradigmatic examples, we stochastically simulate the self-assembly of constituents with triangular, square, and hexagonal morphology into two-dimensional structures of a specified size. We find that the constituents’ morphology critically determines the assembly time and how it scales with the size of the target structure. Our analysis reveals three key structural parameters defined by the morphology: the nucleation size and attachment order, which describe the effective order of the chemical reactions by which clusters nucleate and grow, respectively, and the growth exponent, which determines how the growth rate of an emerging structure scales with its size. Using this characterization, we formulate an effective theory of the self-assembly kinetics, which we show exhibits an inherent scale invariance. This allows us to identify general scaling laws that describe the minimal assembly time as a function of the size of the target structure. We show how these insights on the kinetics of self-assembly processes can be used to design assembly schemes that could significantly increase the time efficiency and robustness of artificial self-assembly processes.

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synopsis

Shape Matters in Self-Assembly

Published 3 April, 2024

A theoretical study of self-assembly finds that hexagon-shaped building blocks can form large structures faster than triangular or square blocks.

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References (87)

  1. D. Kushner, Self-assembly of biological structures, Bacteriological reviews 33, 302 (1969).
  2. G. M. Whitesides and B. Grzybowski, Self-assembly at all scales, Science 295, 2418 (2002).
  3. G. M. Whitesides, J. P. Mathias, and C. T. Seto, Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures, Science 254, 1312 (1991).
  4. S. Zhang, Fabrication of novel biomaterials through molecular self-assembly, Nat. Biotechnol. 21, 1171 (2003).
  5. A. C. Mendes, E. T. Baran, R. L. Reis, and H. S. Azevedo, Self-assembly in nature: using the principles of nature to create complex nanobiomaterials, Wiley Interdiscip. Rev. 5, 582 (2013).
  6. C. Sigl, E. M. Willner, W. Engelen, J. A. Kretzmann, K. Sachenbacher, A. Liedl, F. Kolbe, F. Wilsch, S. A. Aghvami, U. Protzer, M. F. Hagan, S. Fraden, and H. Dietz, Programmable icosahedral shell system for virus trapping, Nat. Mater. 20, 1281 (2021).
  7. M. G. Mateu, Assembly, stability and dynamics of virus capsids, Arch. Biochem. Biophys. 531, 65 (2013).
  8. I. G. Johnston, A. A. Louis, and J. P. Doye, Modelling the self-assembly of virus capsids, J. Phys. Condens. Matter 22, 104101 (2010).
  9. F. M. Menger, The structure of micelles, Acc. Chem. Res. 12, 111 (1979).
  10. G. M. Whitesides and M. Boncheva, Beyond molecules: Self-assembly of mesoscopic and macroscopic components, Proc. Natl. Acad. Sci. U.S.A. 99, 4769 (2002).
  11. R. Freeman, M. Han, Z. Álvarez, J. A. Lewis, J. R. Wester, N. Stephanopoulos, M. T. McClendon, C. Lynsky, J. M. Godbe, H. Sangji, E. Luijten, and S. I. Stupp, Reversible self-assembly of superstructured networks, Science 362, 808 (2018).
  12. P. Ceres and A. Zlotnick, Weak protein-protein interactions are sufficient to drive assembly of hepatitis B virus capsids, Biochemistry 41, 11525 (2002).
  13. J. Grant, R. L. Jack, and S. Whitelam, Analyzing mechanisms and microscopic reversibility of self-assembly, J. Chem. Phys. 135, 214505 (2011).
  14. A. Zlotnick, Are weak protein-protein interactions the general rule in capsid assembly?, Virology 315, 269 (2003).
  15. D. C. Rapaport, Role of reversibility in viral capsid growth: A paradigm for self-assembly, Phys. Rev. Lett. 101, 186101 (2008).
  16. M. F. Hagan, Modeling viral capsid assembly, Adv. Chem. Phys. 155, 1 (2014).
  17. J. D. Perlmutter and M. F. Hagan, Mechanisms of virus assembly, Annu. Rev. Phys. Chem. 66, 217 (2015).
  18. W. M. Gelbart, A. Ben-Shaul, and D. Roux, Micelles, Membranes, Microemulsions, and Monolayers (Springer Science & Business Media, New York, 2012).
  19. D. Endres and A. Zlotnick, Model-based analysis of assembly kinetics for virus capsids or other spherical polymers, Biophys. J. 83, 1217 (2002).
  20. M. F. Hagan, O. M. Elrad, and R. L. Jack, Mechanisms of kinetic trapping in self-assembly and phase transformation, J. Chem. Phys. 135, 104115 (2011).
  21. E. J. Deeds, J. A. Bachman, and W. Fontana, Optimizing ring assembly reveals the strength of weak interactions, Proc. Natl. Acad. Sci. U.S.A. 109, 2348 (2012).
  22. S. Whitelam and R. L. Jack, The statistical mechanics of dynamic pathways to self-assembly, Annu. Rev. Phys. Chem. 66, 143 (2015).
  23. W. M. Jacobs and D. Frenkel, Self-assembly of structures with addressable complexity, J. Am. Chem. Soc. 138, 2457 (2016).
  24. K. Baek, I. Hwang, I. Roy, D. Shetty, and K. Kim, Self-assembly of nanostructured materials through irreversible covalent bond formation, Acc. Chem. Res. 48, 2221 (2015).
  25. A. Murugan, J. Zou, and M. P. Brenner, Undesired usage and the robust self-assembly of heterogeneous structures, Nat. Commun. 6, 6203 (2015).
  26. F. M. Gartner, I. R. Graf, and E. Frey, The time complexity of self-assembly, Proc. Natl. Acad. Sci. U.S.A. 119, e2116373119 (2022).
  27. K. F. Wagenbauer, C. Sigl, and H. Dietz, Gigadalton-scale shape-programmable DNA assemblies, Nature (London) 552, 78 (2017).
  28. S. Katen and A. Zlotnick, Methods in Enzymology, 1st ed. (Elsevier, New York, 2009), Vol. 455, pp. 395–417.
  29. B. A. Grzybowski, C. E. Wilmer, J. Kim, K. P. Browne, and K. J. Bishop, Self-assembly: From crystals to cells, Soft Matter 5, 1110 (2009).
  30. A. Zlotnick, To build a virus capsid: An equilibrium model of the self assembly of polyhedral protein complexes, J. Mol. Biol. 241, 59 (1994).
  31. L. O. Hedges, R. V. Mannige, and S. Whitelam, Growth of equilibrium structures built from a large number of distinct component types, Soft Matter 10, 6404 (2014).
  32. M. F. Hagan and G. M. Grason, Equilibrium mechanisms of self-limiting assembly, Rev. Mod. Phys. 93, 025008 (2021).
  33. J. N. Israelachvili, D. J. Mitchell, and B. W. Ninham, Theory of self-assembly of hydrocarbon amphiphiles into micelles and bilayers, J. Chem. Soc., Faraday Trans. 2 72, 1525 (1976).
  34. P. C. Hiemenz and T. P. Lodge, Polymer Chemistry (CRC Press, Boca Raton, 2007).
  35. C. G. Evans and E. Winfree, Physical principles for DNA tile self-assembly, Chem. Soc. Rev. 46, 3808 (2017).
  36. M. Lenz and T. A. Witten, Geometrical frustration yields fibre formation in self-assembly, Nat. Phys. 13, 1100 (2017).
  37. P. Masson, C. Hulo, E. De Castro, H. Bitter, L. Gruenbaum, L. Essioux, L. Bougueleret, I. Xenarios, and P. Le Mercier, ViralZone: Recent updates to the virus knowledge resource, Nucl. Acids Res. 41, D579 (2012).
  38. C. A. Kerfeld and M. R. Melnicki, Assembly, function and evolution of cyanobacterial carboxysomes, Curr. Opin. Plant Biol. 31, 66 (2016).
  39. M. F. Hagan, Modeling viral capsid assembly, Adv. Chem. Phys. 155, 1 (2014).
  40. Y. Ke, L. L. Ong, W. M. Shih, and P. Yin, Three-dimensional structures self-assembled from DNA bricks, Science 338, 1177 (2012).
  41. B. Alberts, Molecular Biology of the Cell (Garland Science, New York, 2017).
  42. A. Ianiro, H. Wu, M. M. van Rijt, M. P. Vena, A. D. Keizer, A. C. C. Esteves, R. Tuinier, H. Friedrich, N. A. Sommerdijk, and J. P. Patterson, Liquid-liquid phase separation during amphiphilic self-assembly, Nat. Chem. 11, 320 (2019).
  43. S. Li, P. Roy, A. Travesset, and R. Zandi, Why large icosahedral viruses need scaffolding proteins, Proc. Natl. Acad. Sci. U.S.A. 115, 10971 (2018).
  44. X. Ye, J. Chen, M. Engel, J. A. Millan, W. Li, L. Qi, G. Xing, J. E. Collins, C. R. Kagan, J. Li et al., Competition of shape and interaction patchiness for self-assembling nanoplates, Nat. Chem. 5, 466 (2013).
  45. H. Fang, M. F. Hagan, and W. B. Rogers, Two-step crystallization and solid-solid transitions in binary colloidal mixtures, Proc. Natl. Acad. Sci. U.S.A. 117, 27927 (2020).
  46. S. Auer and D. Frenkel, Prediction of absolute crystal-nucleation rate in hard-sphere colloids, Nature (London) 409, 1020 (2001).
  47. D. Hayakawa, T. E. Videbaek, D. M. Hall, H. Fang, C. Sigl, E. Feigl, H. Dietz, S. Fraden, M. F. Hagan, G. M. Grason et al., Geometrically programmed self-limited assembly of tubules using DNA origami colloids, Proc. Natl. Acad. Sci. U.S.A. 119, e2207902119 (2022).
  48. M. F. Hagan and D. Chandler, Dynamic pathways for viral capsid assembly, Biophys. J. 91, 42 (2006).
  49. C. G. Evans, J. O’Brien, E. Winfree, and A. Murugan, Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly, Nature (London) 625, 500 (2024).
  50. B. Wei, M. Dai, and P. Yin, Complex shapes self-assembled from single-stranded DNA tiles, Nature (London) 485, 623 (2012).
  51. W. M. Jacobs, A. Reinhardt, and D. Frenkel, Rational design of self-assembly pathways for complex multicomponent structures, Proc. Natl. Acad. Sci. U.S.A. 112, 6313 (2015).
  52. A. Reinhardt, C. P. Ho, and D. Frenkel, Effects of co-ordination number on the nucleation behaviour in many-component self-assembly, Faraday Discuss. 186, 215 (2016).
  53. F. M. Gartner, I. R. Graf, P. Wilke, P. M. Geiger, and E. Frey, Stochastic yield catastrophes and robustness in self-assembly, eLife 9, e51020 (2020).
  54. C. Chen, C. C. Kao, and B. Dragnea, Self-assembly of brome mosaic virus capsids: Insights from shorter time-scale experiments, J. Phys. Chem. A 112, 9405 (2008).
  55. A. Ben-Shaul and W. M. Gelbart, Statistical thermodynamics of amphiphile self-assembly: Structure and phase transitions in micellar solutions, in Micelles, Membranes, Microemulsions, and Monolayers (Springer, New York, 1994), pp. 1–104.
  56. S. Arrhenius, Über die reaktionsgeschwindigkeit bei der inversion von rohrzucker durch säuren, Z. Phys. Chem. 4U, 226 (1889).
  57. K. J. Laidler, The development of the Arrhenius equation, J. Chem. Ed. 61, 494 (1984).
  58. A. Ben-Ari, L. Ben-Ari, and G. Bisker, Nonequilibrium self-assembly of multiple stored targets in a dimer-based system, J. Chem. Phys. 155, 234113 (2021).
  59. M. Faran and G. Bisker, Nonequilibrium self-assembly time forecasting by the stochastic landscape method, J. Phys. Chem. B 127, 6113 (2023).
  60. P. L. Krapivsky, S. Redner, and E. Ben-Naim, A Kinetic View of Statistical Physics (Cambridge University Press, Cambridge, England, 2010).
  61. D. T. Gillespie, Stochastic simulation of chemical kinetics, Annu. Rev. Phys. Chem. 58, 35 (2007).
  62. Note that, in the system with triangle-shaped monomers, the attachment order for the first assembly step following nucleation is larger, γ=4, compared to all subsequent assembly steps, where γ=3.

  63. Since cluster growth is by the addition of monomers, stochastic effects result in some interface roughness (akin to Eden growth [87]) leading to a larger surface-to-volume ratio than given by ps=as and, hence, to an effective growth exponent ω>1/2. Since this affects only the system with hexagon-shaped monomers, we do not discuss this additional effect here further and simply approximate ω by 1/2 for hexagon-shaped monomers.

  64. Unlike for hexagon-shaped building blocks, in the case of square and triangular building blocks, the prefactor a additionally includes the multiplicity qs of the seed-forming reaction pathways. For example, the multiplicity considers that the seed can typically grow in two directions unless it forms directly at the corner of an edge.

  65. The combinatorial factors fs for clusters of small size s typically deviate from the asymptotic form asω. Note, however, that, for increasing target size S, the approximation becomes ever more accurate, as the asymptotic form of fs applies to an increasingly large fraction of all assembly steps.

  66. In general, β>α holds if σ>γ+1 and ω<3/2, meaning that this must be true, in general.

  67. The latter is particularly pronounced in the system with hexagonal monomers, where, due to the absence of a domino effect that fills up the edges of a cluster after an initial seed has formed, the typical morphologies of the cluster exhibit some interface roughness during growth. Note that the assembly time obtained from integrating the effective model in which we use ω=1/2 coincides with the analytic estimate θth=1/2 for the system with hexagonal building blocks. Furthermore, using a value of ω slightly larger than 1/2 in Eq. (17) (which would be plausible due to the roughening effect) consistently results in a value of θ smaller than 1/2 as observed from the simulation data. For example, the measured value θ≈0.4 is obtained with ω=0.6 according to Eq. (17).

  68. A. Zlotnick, J. M. Johnson, P. W. Wingfield, S. J. Stahl, and D. Endres, A theoretical model successfully identifies features of hepatitis B virus capsid assembly, Biochemistry 38, 14644 (1999).
  69. A. Y. Morozov, R. F. Bruinsma, and J. Rudnick, Assembly of viruses and the pseudo-law of mass action, J. Chem. Phys. 131, 155101 (2009).
  70. Note that some of the approximations used here actually become exact in the limit of large S. For example, neglecting the diffusion term and higher-order terms in the advection equation is irrelevant in the limit S→∞, as their contribution becomes negligible against the leading-order advection term [see Eqs. (c4) and (c5)], showing that the advective contribution to cluster growth equals the square of the diffusive contribution. Similarly, neglecting the nucleation term in Eq. (22) becomes increasingly irrelevant as S increases.

  71. A. Zlotnick and S. Mukhopadhyay, Virus assembly, allostery and antivirals, Trends Microbiol. 19, 14 (2011).
  72. C. Packianathan, S. P. Katen, C. E. Dann III, and A. Zlotnick, Conformational changes in the hepatitis B virus core protein are consistent with a role for allostery in virus assembly, J. Virol. 84, 1607 (2010).
  73. E. Bekyarova, Y. Ni, E. B. Malarkey, V. Montana, J. L. McWilliams, R. C. Haddon, and V. Parpura, Applications of carbon nanotubes in biotechnology and biomedicine, J. Biomed. Nanotechnol. 1, 3 (2005).
  74. M. F. De Volder, S. H. Tawfick, R. H. Baughman, and A. J. Hart, Carbon nanotubes: Present and future commercial applications, Science 339, 535 (2013).
  75. S. K. Kulkarni and S. K. Kulkarni, Nanotechnology: Principles and Practices (Springer, New York, 2015).
  76. We remark that the precondition for the applicability of our theory is that the growth rate of large clusters consistently scales as r˜s→s+1∼sω with some arbitrary growth exponent ω.

  77. J. E. Baschek, H. C. R Klein, and U. S. Schwarz, Stochastic dynamics of virus capsid formation: Direct versus hierarchical self-assembly, BMC Biophys. 5, 1 (2012).
  78. C. Li, J. C.-Y. Wang, M. W. Taylor, and A. Zlotnick, In vitro assembly of an empty picornavirus capsid follows a dodecahedral path, J. Virol. 86, 13062 (2012).
  79. S. Flasinski, A. Dzianott, J. A. Speir, J. E. Johnson, and J. J. Bujarski, Structure-based rationale for the rescue of systemic movement of brome mosaic virus by spontaneous second-site mutations in the coat protein gene, J. Virol. 71, 2500 (1997).
  80. S. J. Hanslip, N. R. Zaccai, A. P. Middelberg, and R. J. Falconer, Assembly of human papillomavirus type-16 virus-like particles: Multifactorial study of assembly and competing aggregation, Biotechnol. Prog. 22, 554 (2006).
  81. D. Willits, X. Zhao, N. Olson, T. Baker, A. Zlotnick, J. Johnson, T. Douglas, and M. Young, Effects of the cowpea chlorotic mottle bromovirus β-hexamer structure on virion assembly, Virology 306, 280 (2003).
  82. M. A. Boettcher, H. C. Klein, and U. S. Schwarz, Role of dynamic capsomere supply for viral capsid self-assembly, Phys. Biol. 12, 016014 (2015).
  83. There are either no or only a small number of successive lower-order processes for the assembly steps immediately following nucleation. Hence, the growth rates for small clusters behave a bit differently, as we discuss below, specifically for triangle-shaped building blocks. In the other cases, however, good agreement with the simulation data can be obtained even if we do not treat the initial assembly steps separately and assume the same growth rate for them as for larger clusters.

  84. P. E. Prevelige, Jr., D. Thomas, and J. King, Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells, Biophys. J. 64, 824 (1993).
  85. Note also that explicit boundaries violate the equivalence between homogeneous and heterogeneous systems (cf. Appendix pp10-s1) due to the distinct properties of the boundary species.

  86. C. J. Jones and S.-I. Aizawa, The bacterial flagellum and flagellar motor: Structure, assembly and function, Advances in Microbial Physiology 32, 109 (1991).
  87. E. Murray, A two-dimensional growth process, in Proceedings of the 4th Berkeley Symposium on Mathematical Statistics and Probability (University of California Press, Berkeley, 1960), Vol. 4, p. 223.

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