While DNA-based computing may not be taking over silicon quite so soon, there is progress in the works. In a paper published by Small, researchers from the University of Rochester demonstrate a molecular computing system capable of calculating square roots of integers up to 900. The computer is built from synthetic biochemical logic gates using hybridization, a process where two strands of DNA join to form double-stranded DNA, and strand displacement reactions.
DNA-based circuits have already been shown to implement complex logic functions, but most existing circuits prior to the recent paper were unable to calculate square root operations. This required 4-bit binary numbers – the new prototype implements a 10-bit square root logic circuit, operating up to the decimal integer 900.
The computer uses 32 strands of DNA for storing and processing information. The process uses three modules, starting off with encoding a number on the DNA. Each combination is attached to a florescent marker, which changes signal during hybridization in the second module. The process for calculating the square root controls the signals, with the results deducted from the final color according to a threshold set in the third module.
We’re beginning to see the end of Moore’s Law approaching, with companies like Intel and AMD struggling to shrink transistors 10 nm wide. Nevertheless, with DNA molecules still about 10 time smaller than the best transistors today and DNA computing systems continuing to gain in sophistication, biochemical circuits could potentially be holding solutions to increasing the speed of computing beyond silicon computing.
OSM stands for Oligonucleotide Synthesizer designed for use in Microgravity, meaning that it’s a device that makes arbitrary DNA strands (of moderate length) in space. Cool eh? I’ve been working on this project for the last eight months with a wonderful team of fellow hackers as part of the Stanford Student Space Initiative, and I’d like to share what we’re doing, what we’ve already done, and where we’re going.
Why space? Well, first of all, space is cool. But more seriously, access to arbitrary DNA in space could accelerate research in a plethora of fields, and the ability to genetically engineer bacteria to produce substances (say on a martian colony) could mean the difference between death and a life-saving shot. In short, it’s hard to predict the exact DNA one might need for research or practical use before hand.
First, as Hackaday tends to be a little light on biology terminology, we need to get a little vocabulary out of the way to grease the ways of communication. If you have a Ph.D. in synthetic biology, you might want to skip this section. Otherwise, here are five quick terms that will make your brain bigger so stay with me!
Continue reading “OSM (Pronounced Awesome) Hardware Makes DNA In Space”
Microfluidics, the precise control and manipulation of small volumes of liquids, is heavily used in any field that does small-scale experiments with expensive reagents (We’re looking at you, natural sciences.) However, the process commonly used to create microfluidic devices is time and experience intensive. But, worry not: the Uppsala iGEM team has created Chipgineering: A manual for manufacturing a microfluidic chip.
Used while developing everything from inkjet print heads to micro-thermal technologies, microfluidic systems are generally useful. Specifically, Uppsala’s microfluidic device performs a simple biological procedure, a heat-shock transformation, as a proof of concept. Moreover, Uppsala uses commonly available materials: ready to pour PDMS (a biologically compatible silicon) and a 3D printed mold. Additionally, while the team used a resin 3D printer, there seems to be little reason that a fused deposition modeling (FDM) printer wouldn’t work just as well. Particularly interesting is how they sandwich their PDMS between two plates, potentially allowing easy removal and replacement of reagents without external mechanisms. And, to put the cherry on top, Uppsala’s well-illustrated documentation is a joy to read.
This isn’t the first time we’ve covered microfluidic devices, and if you’re still in the prototyping phase, these microfluidic LEGO-like blocks might be what you need. But, if you prefer macrofluidics, this waste shark that aims to clean our oceans might be more your style.
Years ago, prototyping microfluidic systems was a long, time-intensive task. With inspiration from DIY PCB fabrication techniques, that time is now greatly reduced. However, even with the improvements, it still takes a full day to go from an idea to a tangible implementation. However, progress creeps in this petty pace from day to day, and in accordance, a group of researchers have found a way to use 3D printed molds to create microfluidic LEGO bricks that make microfluidic prototyping child’s play.
For the uninitiated, microfluidics is the study and manipulation of very small volumes of water, usually a millionth of a liter and smaller (nL-pL). Interestingly, the behavior of fluids at small scales differs greatly from its larger scale brethren in many key ways. This difference is due to the larger role surface tension, energy dissipation, and fluidic resistance play when distances and volumes are minimized.
By using 3D printed molds to create microfluidic bricks that fit together like LEGOs, the researchers hope to facilitate medical research. Even though much research relies on precise manipulation of minuscule amounts of liquid, most researchers pipette by hand (or occasionally by robot), introducing a high level of human error. Additionally, rather than needing multiple expensive micropipettes, a DIY biohacker only needs PDMS (a silicon-based chemical already used microfluidics) and 3D printed molds to get started in prototyping biological circuits. However, if you prefer a more, ahem, fluid solution, we’ve got you covered.
High-altitude balloons are used to perform experiments in “near space” at 60,000-120,000 ft. (18000-36000m). However, conditions at such altitude are not particularly friendly and balloons have to compete with ultraviolet radiation, bad weather and the troubles of long distance communication. The trick is to send up a live entity to make repairs as needed. A group of students from Stanford University and Brown University repurposed nature in their solution. Enter Bioballoon: a living high-altitude research balloon.
Instead of using inorganic materials, the Stanford-Brown International Genetically Engineered Machine (iGEM) team designed microbes that grow the components required to build various tools and structures with the hope of making sustained space research feasible. Being made of living material, Bioballoon can be grown and re-grown with the same bacteria, lowering the cost of manufacturing and improving repeatability.
Bioballoon is engineered to be modular, with different strains of bacteria satisfying different requirements. One strain of bacteria has been modified to produce hydrogen in order to inflate the balloon while the balloon itself is made of a natural Kevlar-latex mix created by other cells. Additionally, the team is using Melanin, the molecule responsible for skin color and our personal UV protection to introduce native UV resistance into the balloon’s structure. And, while the team won’t be deploying a glider, they’ve designed biological thermometers and small molecule sensors that can be grown on the balloon’s surface. They don’t have any logging functionality yet, but these cellular hacks could amalgamate as a novel scientific instrument: cheap, light and durable.
Living things too organic for your taste? Don’t worry, we’ve got some balloons that won’t grow on you.
Continue reading “Living High-Altitude Balloon”
Few things have managed to capture the imagination of hackers and engineers around the world the way Synthetic Biology did over the last couple of years. The promise of “applying engineering principles to designing new biological devices and systems” just seemed way too sci-fi to missed out on, and everyone jumped on the bandwagon. All of a sudden, the field which used to be restricted to traditional research organizations and startups found itself crowded with all sorts of enthusiasts, biohackers, and weirdos alike. Competitions such as the International Genetically Engineered Machine (iGEM) paved the way, and the emergence of community spaces like GenSpace and BioCurious finally made DNA experimentation accessible to anyone who dares to try. As it often happens, the Sci-Fi itself did not go untouched, and a whole new genre called “Biopunk” emerged, further fueling people’s imagination and extrapolating worlds to come.
Continue reading “Mediated Matter At The MIT Media Lab”
There’s still time to enter io9’s Build a Lifeform contest. Synthetic biologists, get cracking on the design of that synthetic lifeform or BioBricks lifeform! The rules are pretty straightforward; you need to propose a lifeform design that would be scientifically viable. The BioBricks lifeform part of the contest requires that your design needs to not only be scientifically viable, you have to explain how you would create it in a lab, and you get extra points if you already have an organism. The deadline is August 25, 2008. You could win the opportunity to attend an all-expenses-paid trip to the Synthetic Biology Conference in Hong Kong or $1000 and a chance to get your creature drawn by a cool comic book artist.