A brief comment on self-assembly

There is good reason to take a closer look at the concept of self-assembly to understand how nanotechnology differs from conventional technology and how these differences connects nanotechnology to biological systems. This post will be a brief comment on self-assembly in nanotechnology and will hopefully serve as an introduction to a more in-depth discussion on self-assembly and how different aspects of self-assembly interrelates.

My starting point for this post is the doctoral thesis by Erik Lundberg “Bottom-up Fabrication of Functional DNA Nanostructures” (Lundberg, 2012), which has recently been published. Lundberg describes the construction of nanometer-scale DNA-assemblies along the lines described in the “DNA, genes and nanotechnologies” post.  What is striking about DNA nanotechnology is how it combines programmability, offered through sequence design, and self-assembly, when the individual strands come together to form the final structure. However, this post won’t discuss DNA nanotechnology, but instead focus on the organizational principles that govern it.

A system that self-assembles is characterized by a tendency to form spontaneous order. The emergence of spontaneous order is driven by the interactions of the individual constituting objects without an imposed external driving force. However, as Lundberg notes

It is important to bear in mind that the spontaneous organization of the components is an apparent decrease of disorder of the system; self-assembly must obey the second law of thermodynamics. (Lundberg, 2012: 32)

This means that the increased order of the self-organizing system must be associated with and increased disorder of the surroundings. This notion might be trivial when dealing with molecular self-assembly, but its implication are important to bear in mind when we later on expand the discussion to involve self-assembly in societies of objects – both living and non-living.

From a chemical point of view, there is a need to set up certain criteria to what can actually be called self-assembly. Not all spontaneous processes can be described using the term self-assembly and not all molecules are self-assembled systems. George M. Whitesides has been one of the leading figures when it comes to defining what is meant by self-assembly. Based on the work by Whitesides (Whitesides and Boncheva, 2002), Lundberg puts up five criteria for a system to be defined as self-assembling

(1) The components that are involved in the process are initially in a state of disorder but have specific properties that favor constructive interactions between the components at a local level. […] (2) Interactions between the components are of relatively weak nature, i.e. hydrogen bonds, van der Waals and dispersion forces. Furthermore, (3) the assembly process must be reversible which is correlated with the weaker interactions between components. (4) The environment of the process plays a key part, mainly for entropic reasons […]. Finally, (5) components must have free mobility in order to interact properly. (Lundberg, 2012: 32)

Thus, a self-assembling system is one where the interacting objects move freely through the environment, continuously forming and breaking weak associations with each other. This interrelation, which features constantly developing associations, is likely a common feature for any self-assembling systems, whether they being molecular assemblies or a human societies.

When looking at the criteria for when a process can be defined as self-assembling a fundamental question arises? The weak interactions between the different objects and the unhindered mobility required for the process, are they not also typical for any gaseous or liquid system? Systems that by no means can be ascribed a spontaneous order. In the gaseous or liquid phase, there is no transition between free and disordered individual molecules to the consolidated and ordered assembly.  What drives the emergence of spontaneous order in the self-assembling system?

These questions can be approached using the term molecular recognition. Lundberg describes molecular recognition as

[…] the phenomenon describing specificity of non-covalent interactions between molecules, yielding distinct intermolecular coupling. (Lundberg, 2012: 33)

Molecular recognition allows interacting entities to form multiple associations that act in cooperation. When this multitude of chemical interactions follows a defined pattern, the assembly of an ordered system is facilitated. In biology, self-assembly through molecular recognition is norm, perhaps most prominently seen in DNA duplex formation or protein folding. In nanotechnology relying on self-assembly, it is the molecular recognition pattern of the individual components in a constructed assembly that is the main design feature. By careful design of the recognition pattern the assembly can be controlled from the bottom-up.

We are now back where we started, with the realm of nanotechnology copying the engineering principles of molecular biology.  The main questions still remain. How is self-assembly in biology and nanotechnology related to other types of self-assembly? How does things like molecular recognition apply outside chemistry? Is the growing focus on self-assembly in technology related to increased interest for issues related to spontaneous organization outside the realm of natural sciences? These questions will be elaborated on in forthcoming posts.

References

Lundberg, E. (2012). Bottom-up Fabrication of Functional DNA Nanostructures. In Department of Chemical and Biological Engineering (Göteborg: Chalmers University of Technology).

Whitesides, G.M., and Boncheva, M. (2002). Beyond Molecules: Self-Assembly of Mesoscopic and Macroscopic Components. Proc. Natl. Acad. Sci. U.S.A. 99, 4769-4774.

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