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Universal computing by DNA origami robots in a living animal.

ABSTRACT: Biological systems are collections of discrete molecular objects that move around and collide with each other. Cells carry out elaborate processes by precisely controlling these collisions, but developing artificial machines that can interface with and control such interactions remains a significant challenge. DNA is a natural substrate for computing and has been used to implement a diverse set of mathematical problems, logic circuits and robotics. The molecule also interfaces naturally with living systems, and different forms of DNA-based biocomputing have already been demonstrated. Here, we show that DNA origami can be used to fabricate nanoscale robots that are capable of dynamically interacting with each other in a living animal. The interactions generate logical outputs, which are relayed to switch molecular payloads on or off. As a proof of principle, we use the system to create architectures that emulate various logic gates (AND, OR, XOR, NAND, NOT, CNOT and a half adder). Following an ex vivo prototyping phase, we successfully used the DNA origami robots in living cockroaches (Blaberus discoidalis) to control a molecule that targets their cells.

SUBMITTER: Amir Y

PROVIDER: S-EPMC4012984 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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Universal computing by DNA origami robots in a living animal.

Amir Yaniv Y Ben-Ishay Eldad E Levner Daniel D Ittah Shmulik S Abu-Horowitz Almogit A Bachelet Ido I

Nature nanotechnology 20140406 5

Biological systems are collections of discrete molecular objects that move around and collide with each other. Cells carry out elaborate processes by precisely controlling these collisions, but developing artificial machines that can interface with and control such interactions remains a significant challenge. DNA is a natural substrate for computing and has been used to implement a diverse set of mathematical problems, logic circuits and robotics. The molecule also interfaces naturally with liv ...[more]

PMID: 24705510

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Project description:The theory of computer science is based around universal Turing machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of classical UTMs. For the most important class of problem in computer science, non-deterministic polynomial complete problems, non-deterministic UTMs (NUTMs) are theoretically exponentially faster than both classical UTMs and quantum mechanical UTMs (QUTMs). However, no attempt has previously been made to build an NUTM, and their construction has been regarded as impossible. Here, we demonstrate the first physical design of an NUTM. This design is based on Thue string rewriting systems, and thereby avoids the limitations of most previous DNA computing schemes: all the computation is local (simple edits to strings) so there is no need for communication, and there is no need to order operations. The design exploits DNA's ability to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that the design works using both computational modelling and in vitro molecular biology experimentation: the design is thermodynamically favourable, microprogramming can be used to encode arbitrary Thue rules, all classes of Thue rule can be implemented, and non-deterministic rule implementation. In an NUTM, the resource limitation is space, which contrasts with classical UTMs and QUTMs where it is time. This fundamental difference enables an NUTM to trade space for time, which is significant for both theoretical computer science and physics. It is also of practical importance, for to quote Richard Feynman 'there's plenty of room at the bottom'. This means that a desktop DNA NUTM could potentially utilize more processors than all the electronic computers in the world combined, and thereby outperform the world's current fastest supercomputer, while consuming a tiny fraction of its energy.

Project description:BackgroundVarious technological interventions have been proposed and studied to address the growing demand for care of residents in assisted living facilities, in which a preexisting shortage of professional caregivers has been exacerbated by the COVID-19 pandemic. Care robots are one such intervention with the potential to improve both the care of older adults and the work life of their professional caregivers. However, concerns about efficacy, ethics, and best practices in the applications of robotic technologies in care settings remain.ObjectiveThis scoping review aimed to examine the literature on robots used in assisted living facilities and identify gaps in the literature to guide future research.MethodsOn February 12, 2022, following the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) protocol, we searched PubMed, CINAHL Plus with Full Text, PsycINFO, IEEE Xplore digital library, and ACM Digital Library using predetermined search terms. Publications were included if they were written in English and focused on the use of robotics in assisted living facilities. Publications were excluded if they did not provide peer-reviewed empirical data, focused on user needs, or developed an instrument to study human-robot interaction. The study findings were then summarized, coded, and analyzed using the Patterns, Advances, Gaps, Evidence for practice, and Research recommendations framework.ResultsThe final sample included 73 publications from 69 unique studies on the use of robots in assisted living facilities. The findings of studies on older adults were mixed, with some studies suggesting positive impacts of robots, some expressing concerns about robots and barriers to their use, and others being inconclusive. Although many therapeutic benefits of care robots have been identified, methodological limitations have weakened the internal and external validity of the findings of these studies. Few studies (18/69, 26%) considered the context of care: most studies (48/69, 70%) collected data only on recipients of care, 15 studies collected data on staff, and 3 studies collected data on relatives or visitors. Theory-driven, longitudinal, and large sample size study designs were rare. Across the authors' disciplines, a lack of consistency in methodological quality and reporting makes it difficult to synthesize and assess research on care robotics.ConclusionsThe findings of this study call for more systematic research on the feasibility and efficacy of robots in assisted living facilities. In particular, there is a dearth of research on how robots may change geriatric care and the work environment within assisted living facilities. To maximize the benefits and minimize the consequences for older adults and caregivers, future research will require interdisciplinary collaboration among health sciences, computer science, and engineering as well as agreement on methodological standards.

Dataset Information

Universal computing by DNA origami robots in a living animal.

Publications

Universal computing by DNA origami robots in a living animal.

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