April 20, 2024

Biological computing of the future, thanks to DNA |OpenMind

Supercomputers have already surpassed exascale barrier of 1018 operations per second. Artificial intelligence has has been hidden for a long time on our devicesand has recently come to the fore through large language models such as ChatGPT and image generators. We have been hearing about the progress of quantum computing for years, although its promises have not yet materialized. These are some of the trends in advanced technology, along with more daring proposals such as chemical computing. But there are frontiers that some researchers are exploring and that are still a long way from producing practical systems, although they are already offering concrete applications along the way. This is where the future of DNA computing fits.

BBVA-OpenMind-Yanes-The biological computing of the future thanks to DNA_1 Quantum computing takes advantage of the alternative values ​​of the properties of subatomic particles, but its promises have not yet materialized.  Credit: Daniel Karmann/Picture Alliance via Getty Images.
Quantum computing exploits alternative values ​​of the properties of subatomic particles, although its promises have yet to be realized. Credit: Daniel Karmann/Picture Alliance via Getty Images.

A computer is a device that can execute a program by following instructions, an algorithm. A machine capable of doing this needs logic gates, a type of device that can receive a data input and perform a logical operation to generate a result. In today’s computers, this is done using semiconductors, which can give a binary response in the movement of electrons. Quantum computing Exploits alternative values ​​of the properties of subatomic particles. And certain chemical reactions can also be modulated, allowing molecules to act as logic gates; this is the basis of chemical computing.

From test tube to SAT problem solving

The idea of ​​using molecules and their reactions as logic gates has a long theoretical history. In 1959, physicist Richard Feynman proposed the creation of submicroscopic computers, and molecules offered the ideal substrate. Among them, DNA It is particularly versatile: it can form strings of variable length and contains a code that allows them to be paired. The use of DNA opens a particular field within chemical informatics, that of biological informatics or biocomputing.

BBVA-OpenMind-Yanes-The biological computing of the future thanks to DNA_2 The use of DNA opens a particular field within chemical computing, that of biological computing or biocomputing.  Credit: WLADIMIR BULGAR/SCIENCE PHOTO LIBRARY/Getty Images.
The use of DNA opens a particular field within chemical informatics, that of biological informatics or biocomputing. Credit: WLADIMIR BULGAR/SCIENCE PHOTO LIBRARY/Getty Images.

In 1994, University of Southern California computer scientist Leonard Adleman, who is also a He is credited with coining the term “computer virus.”published the fundamental study on DNA computing in Science. His computer, called the TT-100 (from Test Tube 100), was simply a test tube containing 100 microliters of DNA strands specially designed to react with each other in steps (an algorithm) to complete a logical process. hamiltonian path; In its graphic version, this problem consists of drawing a line that passes once through all the vertices of a figure. A typical case is the problem of the traveler who has to visit several cities by the shortest route. In Adleman’s experiment, the DNA fragments represented the cities, and they were joined together in different possible orders to finally reach the optimum by chemical means.

BBVA-OpenMind-Yanes-The biological computing of the future thanks to DNA_3 The Boston startup Catalog is developing a DNA computer.  Compared to traditional computing, DNA offers greater information density, lower energy consumption and parallel processing.  Credit: David L. Ryan/The Boston Globe via Getty Images.
Boston startup Catalog is developing a DNA-based computer. Compared to conventional computing, DNA offers higher information density, lower power consumption, and parallel processing. Credit: David L. Ryan/The Boston Globe via Getty Images.

Adleman’s study was just a proof of concept; It took seven days to solve a trivial problem that could be solved in minutes with pencil and paper. But he showed the way: “In the long term, we can only speculate about the prospects for molecular computing,” he wrote. In 2002, the scientist and his collaborators used DNA computing to solve a type of computer problem called HE SAT, which the authors described as “the largest yet solved by non-electronic means” and which, with more than a million possible solutions, could not be solved without computational help. Before Adleman, other scientists such as Richard Lipton of Princeton University had already addressed this type of problem using DNA calculations.

The dream of DNA computing

Compared to conventional computing, DNA offers higher information density, lower power consumption and parallel processing, which would provide a speed advantage. But while the first prototypes of DNA computers date back to the 1990s and advances have been made in the use DNA as a digital storage medium.computing is still in the proof-of-concept stage.

Although operating in parallel saves time, the speed is still very slow: according to a computer scientist at the University of Oxford Marta Kwiatkowska, finding the square root of a four-digit number takes several hours. Furthermore, the material, DNA, is single-use. According to Kwiatkowska, it is the biological nature of DNA that makes it particularly interesting, allowing its use in “the field of environmental biosensing or the administration of drugs and therapies within living organisms.” An advantage in this field is the ability to combine computing with the use of DNA in the form of mechanical nanorobots.

BBVA-OpenMind-Yanes-The biological computing of the future thanks to DNA_4 An advantage of biocomputing is being able to couple computing to the use of DNA in the form of mechanical nanorobots that can be used to carry medications and therapies inside living organisms.  Credit: Matthias A. Fenner /CC BY-SA 4.0
An advantage of biocomputing is being able to combine computing with the use of DNA in the form of mechanical nanorobots that can be used to deliver drugs and therapies within living organisms. Credit: Matthias A. Fenner /CC BY-SA 4.0

In 2023 there was impressive progress in China. Researchers at Shanghai Jiao Tong University have created a DNA integrated circuit whose logic gates can form 100 billion circuits, all working in parallel. As his study published in nature explains, it is a general-purpose computer, which is not limited to very specific algorithms as in the pioneering experiments; “Programmability allows specification of the device to perform various algorithms, while scalability allows handling an increasing amount of work by adding resources to the system,” write the authors, led by scientists Fei Wang and Chunhaimake Fan.

The system has been used to solve simple problems such as square roots or quadratic equations, but it has also been tested to identify RNA molecules associated with kidney cancer in different samples. In this sense, the authors talk about future applications in which a device of this type would be able to diagnose a disease and release a DNA chain with therapeutic effects: a DNA computer to diagnose and cure at the same time. It’s still a dream, but that’s how many advances begin.

Javier Yanes

Main image credit: CIFotos/Getty Images

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