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Lessons from simulation regarding the control of synthetic self-assembly

  • Jack F. Douglas (a1) and Kevin Van Workum (a1)


We investigated the role of particle potential symmetry on self-assembly by Monte Carlo simulation with a particular view toward synthetically creating structures of prescribed form and function. First, we established a general tendency for the rotational potential symmetries of the particles to be locally preserved upon self-assembly. Specifically, we found that a dipolar particle potential, having a continuous rotational symmetry about the dipolar axis, gives rise to chain formation, while particles with multipolar potentials (e.g., square quadrupole) having discrete rotational symmetries lead to the self-assembly of “random surface” polymers preserving the rotational symmetries of the particles within these sheet structures. Surprisingly, these changes in self-assembly geometry with the particle potential symmetry are also accompanied by significant changes in the thermodynamic character and in the kinetics of the self-assembly process. Linear chain growth involves a continuous chain growth process in which the chains break and reform readily, while the growth of the two-dimensional polymers only occurs after an “initiation” or “nucleation” time that fluctuates from run to run. We show that the introduction of artificial seeds provides an effective method for controlling the structure and growth kinetics of sheet-like polymers. The significance of these distinct modes of polymerization on the functional character of self-assembly growth is illustrated by constructing an artificial centrosome structure derived from particles having continuous and discrete rotational potential symmetries.


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a) Address all correspondence to this author. e-mail: This paper was selected as the Outstanding Meeting Paper for the F2005 MRS Fall Meeting Symposium J Proceedings, Vol. 897E.


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1Klug, A.: Macromolecular order in biology, Proc. R. Soc. London Ser. A 348, 167 (1994).
2Oosawa, F. and Asakura, S.: Thermodynamics of the Polymerization of Protein (Academic Press, New York, 1975).
3Caspar, D.L.D. and Klug, A.: Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 27, 1 (1962).
4Caspar, D.L.D.: Movement and self-control in protein assemblies: Quasi-equivalence revisited. Biophys. J. 32, 103 (1980).
5Makowski, L.: An unreasonable man in a quasi-equivalent world. Biophys. J. 74, 534 (1998).
6Klug, A.: Molecular structure: Architectural design of spherical viruses. Nature 303, 378 (1983).
7Johnson, J.J. and Spier, J.A.: Quasi-equivalent viruses: A paradigm for protein assemblies. J. Mol. Biol. 269, 665 (1997).
8Chapman, M.S.: Watching one’s p’s and q’s: Promiscuity, plasticity, and quasi-equivalence in a T = 1 virus. Biophys. J. 74, 639 (1998).
9Philp, D. and Stoddart, J.F.: Self-assembly in natural and unnatural systems. Angew. Chem., Int. Ed. Engl. 35, 1155 (1996).
10Moore, J.S.: Supramolecular polymers. Current Opinion Coll. Int. Sci. 4, 108 (1999).
11Lehn, J.M.: Supramolecular Chemistry (VCH, Weinheim, Germany, 1995).
12Alivisatos, A.P., Johnsson, K.P., Peng, X.G., Wilson, T.E., Loweth, C.J., Bruchez, M.P., and Schultz, P.G.: Organization of ‘nanocrystal molecules’ using DNA. Nature 382, 609 (1996).
13Jeneke, S.A. and Chen, X.L.: Self-assembly of ordered microporous materials from rod-coil block copolymers. Science 283, 372 (1999).
14Brunsveld, L., Folmer, B.J.B., Meijer, E.W., and Sijbesma, R.P.: Supramolecular polymers. Chem. Rev. 101, 4071 (2001).
15de Gans, B.J., Wiegand, S., Zubarev, E.R., and Stupp, S.I.: A light scattering study of the self-assembly of dendron rod-coil molecules. J. Phys. Chem. B 106, 9730 (2002).
16Stupp, S.I., Son, S., Lin, H.C., and Li, L.S.: Synthesis of two-dimensional polymers. Science 259, 59 (1993).
17Stupp, S.I., LeBonheur, V., Walker, K., Li, L.S., Huggins, K.E., Keser, M., and Amstutz, A.: Supramolecular materials: Self-organized nanostructures. Science 276, 384 (1997).
18Mirkin, C.A., Letsinger, R.L., Mucic, R.C., and Storhoff, J.J.: A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607 (1996).
19Schnur, J.: Lipid tubules: A paradigm for molecularly engineered structures. Science 262, 1669 (1993).
20Ghadiri, M.R., Granja, J.R., Milligan, R.A., McRee, D.E., and Khazanovich, N.: Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 366, 324 (1993).
21Furhop, J.H. and Helfrich, W.: Fluid and solid fibers made of lipid molecular bilayers. Chem. Rev. 93, 1565 (1993).
22Lawrence, D.S., Jiang, T., and Levelt, M.: Self-assembling supramolecular complexes. Chem. Rev. 95, 2229 (1995).
23Crick, F.H.C. and Watson, J.D.: Structure of small viruses. Nature 177, 473 (1956).
24Finch, J.T. and Klug, A.: Structure of poliomyelitis virus. Nature 183, 1709 (1959).
25Bancroft, J.B.: Advances in Virus Research (Academic, New York, 1970).
26Rossmann, M.G. and Johnson, J.E.: Icosahedral RNA virus structure. Annu. Rev. Biochem. 58, 533 (1989).
27Van Workum, K. and Douglas, J.F.: Equilibrium polymerization in the Stockmayer fluid as a model of supermolecular self-organization. Phys. Rev. E 71, 031502 (2005).
28Staumbaugh, J., Van Workum, K., Douglas, J.F., and Losert, W.: Polymerization transition in two-dimensional systems of dipolar spheres. Phys. Rev. E 72, 031301 (2005).
29Shelley, J.C., Patey, G.N., Levesque, D., and Weis, J.J.: Liquid-vapor coexistence in fluids of dipolar hard dumbbells and spherocylinders. Phys. Rev. E 59, 3065 (1999).
30Chen, B. and Siepmann, J.I.: Improving the efficiency of the aggregation-volume-bias Monte Carlo algorithm. J. Phys. Chem. B 105, 11275 (2001).
31Dudowicz, J., Freed, K.F., and Douglas, J.F.: Lattice model of equilibrium polymerization. I. Basic thermodynamic properties. J. Chem. Phys. 111, 7116 (1999).
32Dudowicz, J., Freed, K.F., and Douglas, J.F.: Lattice model of equilibrium polymerization. II. Interplay between polymerization and phase stability. J. Chem. Phys. 112, 1002 (2000).
33Dudowicz, J., Freed, K.F., and Douglas, J.F.: Lattice model of equilibrium polymerization. III. Evidence for particle clustering from phase separation properties and ‘rounding’ of the dynamical clustering transition. J. Chem. Phys. 113, 434 (2000).
34Dudowicz, J., Freed, K.F., and Douglas, J.F.: Lattice model of equilibrium polymerization. IV. Influence of activation, chemical initiation, chain scission and fusion, and chain stiffness on polymerization and phase separation. J. Chem. Phys. 119, 12645 (2003).
35Staumbaugh, J.: The self-assembly of particles with multipolar interactions. Ph.D. Thesis, University of Maryland, College Park, MD (2004).
36Van Workum, K. and Douglas, J.F.: Schematic models of molecular self-organization. Macromol. Symp. 227, 1 (2005).
37Van Workum, K. and Douglas, J.F.: Symmetry, equivalence, and molecular self-assembly. Phys. Rev. E 73, 031502 (2006).
38Wolde, P.R. ten, Oxtoby, D.W., and Frenkel, D.: Coil-globule transition in gas-liquid nucleation of polar liquids. Phys. Rev. Lett. 81, 3695 (1988).
39Dijkstra, M., Hansen, J.P., and Madden, P.A.: Gelation of a clay colloid suspension. Phys. Rev. Lett. 75, 2236 (1995).
40Dijkstra, M., Hansen, J.P., and Madden, P.A.: Statistical model for the structure and gelation of smectite clay suspensions. Phys. Rev. E 55, 3044 (1997).
41Cao, Z. and Ferrone, F.A.: Homogeneous nucleation in sickle hemoglobin: Stochastic measurements with a parallel method. Biophys. J. 72, 343 (1997).
42King, J. and Casjens, S.: Catalytic head assembling protein in virus morphogenesis. Nature 251, 112 (1974).
43Klug, A.: From macromolecules to biological assemblies. Angew. Chem., Int. Ed. Engl. 22, 565 (1983).
44Fygenson, D.K., Braun, E., and Libchaber, A.: Phase diagram of microtubules. Phys. Rev. E 50, 1579 (1994).
45Flyvbjerg, H., Holy, T.E., and Leibler, S.: Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis. Phys. Rev. E 54, 5538 (1996).
46Holy, T.E., Dogterom, M., Yurke, B., and Leibler, S.: Assembly and positioning in microtube asters in microfabricated channels. Proc. Natl. Acad. Sci. U.S.A. 94, 6228 (1997).
47Nédélec, F.J., Surrey, T., Maggs, A.C., and Leibler, S.: Self-organization of microtubules and motors. Nature 389, 305 (1997).
48Rodionov, V., Nadezhdina, E., and Borisy, G.: Centrosomal control of microtubule dynamics. Proc. Natl. Acad. Sci. U.S.A. 96, 115 (1999).
49Watts, N.R., Sackett, D.L., Ward, R.D., Miller, M.W., Wingfield, P.T., Stahl, S.S., and Steven, A.C.: HIV-1 Rev depolymerizes microtubules to form stable bilayered rings. J. Cell Biol. 150, 349 (2000).


Lessons from simulation regarding the control of synthetic self-assembly

  • Jack F. Douglas (a1) and Kevin Van Workum (a1)


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