Accessing Semi-Addressable Self Assembly with Efficient Structure Enumeration

• Published in: arXiv.org
• Main Authors: Hübl, Maximilian C, Goodrich, Carl P
• Format: Paper
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 22.05.2024
• Subjects: Algorithms; Enumeration; Inverse design; Inverse problems; Robustness; Self-assembly
• ISSN: 2331-8422

Modern experimental methods enable the creation of self-assembly building blocks with tunable interactions, but optimally exploiting this tunability for the self-assembly of desired structures remains an important challenge. Many studies of this inverse problem start with the so-called fully-addressable limit, where every particle in a target structure is different. This leads to clear design principles that often result in high assembly yield, but it is not a scaleable approach -- at some point, one must grapple with ``reusing'' building blocks, which lowers the degree of addressability and may cause a multitude of off-target structures to form. While the existence of off-target structures does not necessarily preclude high yield assembly of the target structure(s), it massively complicates the design process because it is often unclear if or how these off-target structures can be controlled. Here, we solve a key obstacle preventing robust inverse design in the ``semi-addressable regime'' by developing a highly efficient algorithm that enumerates all structures that can be formed from a given set of building blocks. By combining this with established partition-function-based yield calculations, we successfully inverse design for target structures while minimizing the required number of distinct building block species. Furthermore, we show that it is almost always possible to find semi-addressable designs where the entropic gain from reusing building blocks outweighs the presence of off-target structures and even increases the yield of the target. Thus, not only does our enumeration algorithm enable robust and scalable inverse design in the semi-addressable regime, our results demonstrate that it is possible to operate in this regime while maintaining the level of control often associated with full addressability.