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DNA computer performs calculations in a water droplet

ZME Science reports that Maynooth University researchers programmed DNA strands to rearrange toward a stable structure that encodes an answer.

Owen GregorianOG
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ZME Science reports that Maynooth University researchers built a programmable computer from DNA strands that bind to a longer scaffold. They tested more than 700 computations across 10 programs, including multiplication and parity detection, and demonstrated a calculation involving 100 bits. Larger calculations took up to 14 hours, far slower than silicon computing.

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Owen Gregorian@OwenGregorianScientists Created a Computer Inside a Water Drop Using Billions of DNA Molecules and It Worked | Rupendra Brahambhatt, ZME Science To you or me, a tiny drop of water looks ordinary. There seems to be nothing special about it. However, some researchers see a whole computing device inside a drop. There is no silicon processor inside, but they claim that the billions of DNA molecules in a water drop can interact, process information, and produce an answer. The researchers at Maynooth University have turned these interactions into a programmable Scaffolded DNA Computer (SDC) that can perform calculations, including 100-bit computations. Molecular computing that uses genetic material, chemical reactions, and proteins (instead of silicon chips and electricity) to store and process information has existed for decades. What sets this SDC apart is how it makes molecules calculate. Instead of forcing molecules through a fixed sequence of steps, the researchers designed a system such that the correct answer is its most energetically favorable state. In this approach, as the DNA molecules compete and rearrange themselves, they naturally move toward this state, which is the most stable and has low energy. “The molecules interact, form a structure, and that structure is the answer. One key innovation is that the system naturally finds that answer without needing continuous energy inputs,“ Damien Woods, one of the study authors and a professor at Maynooth University, said. Programming a molecular computer with DNA The SDC starts with a longer DNA strand that acts as a scaffold. Shorter DNA strands, called compute tiles, can attach at specific positions along it. The researchers program these strands by choosing DNA sequences that determine which neighboring strands can bind correctly. The trick is what happens when the strands get it wrong. Each position on the scaffold can have competing DNA tiles. When neighboring tiles have matching sequences, their binding is energetically favorable. When they do not match, the arrangement carries an energetic penalty. A mismatched tile can eventually detach and be replaced by another one. As this continues, the molecular structure moves toward the configuration with the fewest mismatches. This created a molecular landscape where the answer sits at the bottom. The researchers prepare a mixture containing the scaffold, the appropriate compute strands, and reporting molecules, then heat and cool it. A typical experiment dropped the temperature from 80 °C (~353 K) to 20 °C (~293 K) over three hours, followed by a 45-minute hold. As the DNA strands rearrange, the system moves toward its thermodynamically favored state, which is basically the arrangement that is most stable and requires the least energy to maintain. Unlike many molecular computers that have to carefully control the order of chemical reactions, the SDC lets the DNA strands explore different possible arrangements at the same time. If two neighboring strands do not fit together correctly, that arrangement is less stable, so the strands can separate and make room for a better match. This means the system can correct many mistakes on its own, without needing a separate error-correction mechanism. The researchers tested the system with more than 700 computations across 10 programs, including multiplication by three, division by two, 8-bit parity detection, and other logic problems. In the four-position tests, about 95 percent of the computations produced the expected result on average. Think of the DNA computer as an enormous molecular jigsaw puzzle in which the shapes of the pieces encode the rules of arithmetic. Numbers are first written in binary, as strings of 0s and 1s. Along a long DNA scaffold, each position represents one place in that binary number, and several short DNA “tiles” compete to occupy it. Crucially, the DNA sequences on the sides of those tiles encode not just a 0 or 1, but the rules needed to carry information from one position to the next. In addition, for instance, a tile effectively asks: given these two input bits and the carry from the previous column, what should the next output bit and carry be? Tiles representing wrong answers can still attach, but they make poor matches with their neighbors and are therefore less stable. They tend to fall off and get replaced. Correct tiles fit their neighbors more snugly, so as billions of molecules attach, detach and try again, the system gradually settles into a chain with no mismatches. Read the bits encoded by that final arrangement and you have the answer. A computer that can reuse itself The SDC could handle calculations of different sizes. In one demonstration, the DNA computer was given the numbers 10 and 3 and correctly worked out their sum, 13. Some smaller calculations were completed in about 30 seconds. The researchers then tested how far they could scale up the system. Using a longer DNA strand, they added two much larger numbers, with the calculation involving 100 bits of information. The more difficult examples took up to 14 hours to complete. As the calculations became larger, the researchers had to make some changes to help the DNA molecules reach the correct answer reliably. In other words, making the right answer the most stable outcome was not enough by itself; the researchers also had to make it easier for the molecules to get there. Also, “the reaction happens fast in the test tube, but not as fast as silicon, nor is it intended to be. But compared to other DNA computers, ours is the fastest,” Abeer Eshra, study co-author and a computer science professor at Maynooth University, said. The more surprising result was that the DNA computer could be used again and again. The team successfully reused three different programs between 9 and 25 times, with each new calculation taking about 12 minutes to prepare and run. The researchers also found that the system could survive for a surprisingly long time. When they returned to one experiment one and a half years later, the sample had partly dried out. After they added water, the DNA computer was able to perform the experiment again. What a water-drop computer could eventually become The researchers see this approach as a possible alternative to the energy demands of conventional computing. “Silicon-based computers use so much energy – 23% of Ireland’s electricity goes into computing and data storage. We’ve been blinkered by only seeing one type of computer, but there are other examples around us, including our brain,” Woods said. The DNA computer takes a very different approach. Its molecules interact in water and settle into a stable arrangement (which represents the answer) rather than being continuously driven through a sequence of electronic operations. However, it is still far too slow to compete with silicon. Some of the larger calculations performed using the DNA computer took up to 14 hours, and the experiments required heating and cooling the DNA. For now, the achievement is less about making a faster computer than about showing that computation can emerge from molecules simply moving toward a favorable physical state. Read more: https://zmescience.com/science/news-science/computer-water-drop-dna9h
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    Owen Gregorian@OwenGregorianScientists Created a Computer Inside a Water Drop Using Billions of DNA Molecules and It Worked | Rupendra Brahambhatt, ZME Science To you or me, a tiny drop of water looks ordinary. There seems to be nothing special about it. However, some researchers see a whole computing device inside a drop. There is no silicon processor inside, but they claim that the billions of DNA molecules in a water drop can interact, process information, and produce an answer. The researchers at Maynooth University have turned these interactions into a programmable Scaffolded DNA Computer (SDC) that can perform calculations, including 100-bit computations. Molecular computing that uses genetic material, chemical reactions, and proteins (instead of silicon chips and electricity) to store and process information has existed for decades. What sets this SDC apart is how it makes molecules calculate. Instead of forcing molecules through a fixed sequence of steps, the researchers designed a system such that the correct answer is its most energetically favorable state. In this approach, as the DNA molecules compete and rearrange themselves, they naturally move toward this state, which is the most stable and has low energy. “The molecules interact, form a structure, and that structure is the answer. One key innovation is that the system naturally finds that answer without needing continuous energy inputs,“ Damien Woods, one of the study authors and a professor at Maynooth University, said. Programming a molecular computer with DNA The SDC starts with a longer DNA strand that acts as a scaffold. Shorter DNA strands, called compute tiles, can attach at specific positions along it. The researchers program these strands by choosing DNA sequences that determine which neighboring strands can bind correctly. The trick is what happens when the strands get it wrong. Each position on the scaffold can have competing DNA tiles. When neighboring tiles have matching sequences, their binding is energetically favorable. When they do not match, the arrangement carries an energetic penalty. A mismatched tile can eventually detach and be replaced by another one. As this continues, the molecular structure moves toward the configuration with the fewest mismatches. This created a molecular landscape where the answer sits at the bottom. The researchers prepare a mixture containing the scaffold, the appropriate compute strands, and reporting molecules, then heat and cool it. A typical experiment dropped the temperature from 80 °C (~353 K) to 20 °C (~293 K) over three hours, followed by a 45-minute hold. As the DNA strands rearrange, the system moves toward its thermodynamically favored state, which is basically the arrangement that is most stable and requires the least energy to maintain. Unlike many molecular computers that have to carefully control the order of chemical reactions, the SDC lets the DNA strands explore different possible arrangements at the same time. If two neighboring strands do not fit together correctly, that arrangement is less stable, so the strands can separate and make room for a better match. This means the system can correct many mistakes on its own, without needing a separate error-correction mechanism. The researchers tested the system with more than 700 computations across 10 programs, including multiplication by three, division by two, 8-bit parity detection, and other logic problems. In the four-position tests, about 95 percent of the computations produced the expected result on average. Think of the DNA computer as an enormous molecular jigsaw puzzle in which the shapes of the pieces encode the rules of arithmetic. Numbers are first written in binary, as strings of 0s and 1s. Along a long DNA scaffold, each position represents one place in that binary number, and several short DNA “tiles” compete to occupy it. Crucially, the DNA sequences on the sides of those tiles encode not just a 0 or 1, but the rules needed to carry information from one position to the next. In addition, for instance, a tile effectively asks: given these two input bits and the carry from the previous column, what should the next output bit and carry be? Tiles representing wrong answers can still attach, but they make poor matches with their neighbors and are therefore less stable. They tend to fall off and get replaced. Correct tiles fit their neighbors more snugly, so as billions of molecules attach, detach and try again, the system gradually settles into a chain with no mismatches. Read the bits encoded by that final arrangement and you have the answer. A computer that can reuse itself The SDC could handle calculations of different sizes. In one demonstration, the DNA computer was given the numbers 10 and 3 and correctly worked out their sum, 13. Some smaller calculations were completed in about 30 seconds. The researchers then tested how far they could scale up the system. Using a longer DNA strand, they added two much larger numbers, with the calculation involving 100 bits of information. The more difficult examples took up to 14 hours to complete. As the calculations became larger, the researchers had to make some changes to help the DNA molecules reach the correct answer reliably. In other words, making the right answer the most stable outcome was not enough by itself; the researchers also had to make it easier for the molecules to get there. Also, “the reaction happens fast in the test tube, but not as fast as silicon, nor is it intended to be. But compared to other DNA computers, ours is the fastest,” Abeer Eshra, study co-author and a computer science professor at Maynooth University, said. The more surprising result was that the DNA computer could be used again and again. The team successfully reused three different programs between 9 and 25 times, with each new calculation taking about 12 minutes to prepare and run. The researchers also found that the system could survive for a surprisingly long time. When they returned to one experiment one and a half years later, the sample had partly dried out. After they added water, the DNA computer was able to perform the experiment again. What a water-drop computer could eventually become The researchers see this approach as a possible alternative to the energy demands of conventional computing. “Silicon-based computers use so much energy – 23% of Ireland’s electricity goes into computing and data storage. We’ve been blinkered by only seeing one type of computer, but there are other examples around us, including our brain,” Woods said. The DNA computer takes a very different approach. Its molecules interact in water and settle into a stable arrangement (which represents the answer) rather than being continuously driven through a sequence of electronic operations. However, it is still far too slow to compete with silicon. Some of the larger calculations performed using the DNA computer took up to 14 hours, and the experiments required heating and cooling the DNA. For now, the achievement is less about making a faster computer than about showing that computation can emerge from molecules simply moving toward a favorable physical state. Read more: https://zmescience.com/science/news-science/computer-water-drop-dna9h
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