Design of Autonomous DNA Cellular Automata

Abstract

Abstract. Recent experimental progress in DNA lattice construction, DNA robotics, and DNA computing provides the basis for designing DNA cellular computing devices, i.e. autonomous nano-mechanical DNA computing devices embedded in DNA lattices. Once assembled, DNA cellular computing devices can serve as reusable, compact computing devices that perform (universal) computation, and programmable robotics devices that demonstrate complex motion. As a prototype of such devices, we recently reported the design of an Autonomous DNA Turing Machine, which is capable of universal sequential computation, and universal translational motion, i.e. the motion of the head of a single tape universal mechanical Turing machine. In this paper, we describe the design of an Autonomous DNA Cellular Automaton (ADCA), which can perform parallel universal computation by mimicking a one-dimensional (1D) universal cellular automaton. In the computation process, this device, embedded in a 1D DNA lattice, also demonstrates well coordinated parallel motion. The key technical innovation here is a molecular mechanism that synchronizes pipelined "molecular reaction waves" along a 1D track, and in doing so, realizes parallel computation. We first describe the design of ADCA on an abstract level, and then present detailed DNA sequence level implementation using commercially available protein enzymes. We also discuss how to extend the 1D design to 2D.

Direct Design of an Energy Landscape with Bistable DNA Origami Mechanisms

“…Structural DNA nanotechnology − has enabled the precise design of 2D and 3D static and dynamic structures including smiley faces, , twisted and bent bars, spheres, , linkages with complex motion, and nanorobots. − Recent studies have demonstrated promising applications that utilize DNA origami nanostructures as templates to organize proteins or nanoparticles , in 2D and 3D space, vehicles for drug delivery, ,, nanopores, − and biosensors. , Although the majority of DNA nanostructure applications utilize objects with static geometry, important strides have been made to design dynamic DNA devices (i.e., DNA nanomachines). Early DNA nanomachines − involved configurations of DNA strands that could be triggered to undergo conformational changes, usually via DNA strand displacement, to achieve, for example, rotational or translational motion or even measure molecular binding energies . The development of scaffolded DNA origami ,, enabled greater control over geometry and stiffness of nanostructure components, which has expanded the possibilities to design complex mechanical behavior.…”

Programmable pattern formation in cellular systems with local signaling

“…An elementary CA with the programmable rule 90 has already been implemented with DNA tiles 31,32 albeit not in a way that permits inputs from an organizer. Other DNA-based implementations, which are more complex but offer more flexibility, have also been proposed 10 . On the basis of these proposed designs, a biomolecular CA that allows for input signals controlling its patterning process could be implemented as described in Suppl.…”

“…Such models would provide a conceptual framework for programmable pattern formation, and could reveal design principles, e.g., for synthetic molecular systems. DNA-based molecular systems, in particular, are readily programmable via the sequence-dependent interaction between DNA strands, which has been exploited to design self-assembling dynamic DNA devices 7 , neural network-like molecular computation 8 , coupled regulatory circuits 9 , and schemes for constructing molecular-scale cellular automata 10 . Here, we use a minimal model to study the concept of programmable pattern formation using theoretical and computational tools.…”

Integral biomathics: A post-Newtonian view into the logos of bios

“…Biomolecular computation ventured into the domains of game theory, neuroscience and design automation to investigate utilization aspects such as RNA solutions to chess problems (Faulhammer et al, 2000), experimental DNA neural computation (Mills et al, 2001) and bottom-up circuit patterning based on DNA self-assembly (Dwyer, 2005). Other prominent developments were autonomous DNA nanomechanical computation and motion devices (Yin et al, 2005), as well as autonomous DNA cellular automata (Yin et al, 2006). The challenges and applications for selfassembled DNA nanostructures were thoroughly reviewed in (Reif et al, 2001).…”