Behavior-based robotics was established around the idea that robots could be constructed by connecting elementary sensor and actuator modules, without the need to form any internal representation of the world in which they operate. When designed appropriately, such robots, both as individuals and as groups, exhibit complex and seemingly ?intelligent? behaviors, solving challenging tasks in real time, while reacting only to their local environment and obeying sets of local rules. In part, this approach to robotics was inspired by considering natural systems, such as self-organization and adaptability of social insects in their colonies. An analogous approach to initiate the development of the field of behavior-based molecular robotics will be performed over the next three years, leading to groups of molecules that would appear to an observer to show a variety of task-oriented behaviors or some form of purposeful and dynamic self-organization.
Individual behavior-based molecular robots are single molecules displaying multiple sensors-actuators. When exposed to artificial landscapes displaying substrates keyed to their sensors-actuators, the molecules start executing elementary steps, determined, in a stochastic sense, by their constantly changing local environments. On some landscapes, called prescriptive, individual molecular robots and their collectives will execute algorithms mimicking wound-up automata with sequence control mechanisms. In contrast, on non-deterministic landscapes, the robots and their collectives will demonstrate properties emerging from internal organization of individual sensors and actuators and through local interactions between molecules and their environments. Importantly, these new interpretations of molecular behaviors will allow radically different experiments from all previous approaches to molecular robotics, while keeping experimental designs realistic, leading to embodiment in the physical world.
This proposal for construction of molecular robots was initially inspired by macroscopic experiments such as this: A simple robot is released in a room with a floor randomly covered with empy cans. The robot picks up and drops off cans based on trivial counting rules, but within a short period of time all cans are arranged in a neat pile. We say that the robot was programmed to execute a set of local rules, which led to self-organizing and useful behavior. Similar processes in Nature are observed, e.g., in collectives of ants and bees; complex structures and adaptive behaviors that we associate with these insects and their collective intelligence are, to a large extent, results of implementations of straightforward local rules along with feedback from a dynamically changing environment. Moving away from robots and insects into the realm at the interface between chemistry and computer science, we proposed to start asking experimentally the following basic science questions: Can a molecule that walks over the surface based on the affinity interactions with surface elements implement local rules that would lead to an increase in self-organization, that is, to a deviation from random behavior? In order to be able to ask this question at all experimentally, we needed a large team that had to develop a series of new techniques and protocols. Our primary focus was walking molecules known as molecular spiders. These spiders have legs made of catalytic nucleic acids that cleave other oligonucleotides. Spider legs bind to both substrates and products of that cleavage. They execute a set of local residency rules on the landscapes covered with substrates, leading to rapid directed movement in the direction of new substrates at the rate proportional to the rate of catalytic cleavage. Both spiders and their landscapes are made of nucleic acid components, and we can take advantage of these components to define precisely the interactions between a spider and its landscape, or between two (or more) spiders sharing the same landscape. Such interactions and initial experimental demonstrations were the topic of this grant. As an example of the research pursued, one important demonstration was made using Rothemund’s scaffolded 2D rectangular origami as a landscape for spiders to walk on. Scaffolded origami are DNA structures in which a single long strand of DNA is folded so that it runs through every double helix. We used it in our experiment to precisely control positions of hundreds of elements at a resolution of 5-6 nm in fields of rectangular shape and 100x60 nm size. We showed, using methods for monitoring processes at the single molecule level, that substrates deposited on origami in lanes can lead spiders from one corner to another along arbitrary paths. Based on this and other results, we moved the field of molecular robotics to the stage where we can now ask next generation questions such as: Can collectives of walking molecules execute well-defined local rules leading to a characterizable increase in self-organization (i.e., non-random behaviors) of a system?; and in the longer term: Can we learn to program macroscopic effects by defining the rules of interaction between walking molecules, and between molecules and their environment?
