Intellectual Merits: DNA has been suggested as an effective way to program collections of microscopic particles to self-assemble into desired structures. The idea is appealingly simple: particle species bearing complementary DNA strands will stick together, and the ordered structure that maximizes such contacts between complementary species will self-assemble spontaneously from the mixture. Unfortunately, the notion of pre-programmed structure is not appropriate for realizing a broad array of useful DNA-linked particle materials, or DLPMs. It is not, for instance, how real atomic materials work: there are typically several different crystal structures that are local minima of a systems free energy, and what structure actually forms under prescribed conditions depends on relative nucleation and growth rates, and possible solid-solid transformations between different phases. Moreover, the quality of any resulting ordered structure, as defined by the density of morphological and compositional defects, is strongly influenced by a variety of processing variables such as the thermal history during nucleation and growth. Here, the PIs propose that the correct pathway to establish DLPMs as a practical material class is to consider simultaneously both materials and processes in the context of an expanded design paradigm. The overarching intellectual goals of this proposal are therefore (1) to establish a quantitative understanding of the nucleation and growth thermodynamics and kinetics of binary DLPMs using experiments and predictive computer simulations (2) to demonstrate the ability to process DLPMs much in the same way as any other material, i.e. by developing approaches for controlling nucleation, growth, and any potential solid-solid transformations using thermal or chemical stimuli to achieve these goals, we aim to develop an experimental system to enable real time real space optical microscopy for dynamical analysis of binary DLPMs with tunable interparticle interactions. The experimental work will be coupled closely to a comprehensive computer simulation effort that will elucidate fundamental mechanisms and provide high-throughput analysis of material-process combinations.

Broader Impacts:

In principle, new materials called metamaterials, formed of organized arrays and circuits of optically active nanoparticles instead of atoms, promise to allow the manipulation of photons with the same density and versatility that microelectronics brings to computation. This would alleviate the current optoelectronic technology bottleneck between microelectronics and fiber optic telecommunications as well as enable new information technologies. The primary challenge is building these revolutionary new materials. This project will develop and validate a general self-assembly design and material processing platform for producing complex, ordered particle composite materials. It is anticipated that the design rules that emerge from this project will be directly applicable to the making useful metamaterialsif optically active particles are assembled with DNA, the resulting material can be used as is for prototyping and proof of concept studies, or alternatively, as a template for conversion into a solid composite material more appropriate for applications.

This interdisciplinary project will provide ample opportunities for student training at both the graduate and undergraduate levels. The two graduate students principally involved in this project will be expected to be actively involved in both the computational and experimental facets. Students will be exposed to a state-of-the-art toolkit which includes nanoparticle and colloidal functionalization, advanced microscopy and various numerical modeling and simulation techniques. Moreover, the rich, visual nature of the simulation and experimental data, and their potential application in remarkable technology. directed self-assembly will facilitate outreach efforts to high-school students in the Philadelphia public schools and convey the excitement of scientific research. Both Sinno and Crocker are increasingly active in various outreach activities at Penn and neighboring institutions and this project will provide additional materials for continuing these efforts.

Project Report

Engineers have long tried to realize directed self-assembly---coaxing a device's constituent parts to assemble themselves into a useful device. The key is to precisely specify which parts stick to which others, so that they will only assemble into a specific desired structure. Researchers at the University of Pennsylvania have studied such a self-assembly technology based on microscopic plastic spheres covered with strands of synthetic single-stranded DNA. When spheres bearing complementary DNA strands come in contact, their DNA strands link together into double helixes, sticking them together; spheres bearing sequences that are not complementary just bounce off each other. In this way, it is possible to create a periodic table of 'artificial atoms', only some of which will stick to others, as determined by their DNA sequences. With careful choice of the DNA sequences, these toy atoms will self-assemble into a variety of different structures that are analogous to atomic crystals and molecules. This project sought to better understand the details of the self-assembly processes of these DNA covered artificial atoms in both experiment and simulation. Specifically, we wanted to understand how particle crystals grew from particle vapor, how some crystals could transform into other crystals having different structures, and develop methods for processing these materials with the same ease as atomic materials into useful quantities of large crystals and purified molecule-like assemblies. We had six primary accomplishments, which together signfiicantly increase the utility and versatility of these materials, as well as providing a deepeer understanding of self-assemebly processes in general. 1. Unlike earlier studies, we developed methods for forming crystalline materials on a light micrscope. This allows us to watch the formation, growth and transformation processes as they occur. This advance is key to understanding these complex processes 2. We developed methods to 'reprogram' the interactions between the spheres 'on the fly', by adding soluble DNA strands and used this technique to convert the particle crystals into molecule-like clusters of particles having novel and desirable shape. 3. We further learned how to reprogram the DNA bridges to make them permanent, making the molecules above stable enough for storage, handling and purification. We also demonstrated techniques for separating the molecules/clusters according to their size and shape using a centrifuge. This will enable them to be used as building blocks in future projects. 4. In simulation studies of crystals that transform from one structure to another, we found that the hydrodynamic forces the particles exert on each other must be considered to reproduce the results of experiment. The particles can move in many different directions with equal energy penalty, but we find that they move colectively in such a way as to slip-stream on each other, leading them to a specific end-state. This is the first time that such slip-streaming has been shown to control such a process. 5. Software developed for the preceding project suggested a spin-off technology: a method for converting particle trajectories into the corresponding forces betwen particles, including complicated hydrodynamic forces. We expect that this method will find wide utility in both experiements studying micrscopic particles, and as a simulation tool to enable faster and more powerful simulations in a wide variety of applications. 6. We explored the use of genetic algorithms to explore the myriad possibilites for how particles can form into different crystals, in an attempt to develop a powerful discovery tool. In the end we have decided to shelve this approach in favor of other methods.

Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Pennsylvania
United States
Zip Code