A DNA-Based Computer Calculates Square Roots Up To 900

January 12, 2020 by Sharon Lin 20 Comments

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.

Engineering Your Way To Better Sourdough (and Other Fermented Goods)

January 8, 2020 by Kristina Panos 23 Comments

Trent Fehl is an engineer who has worked for such illustrious outfits as SpaceX and Waymo. When he got into baking, he brought those engineering skills home to solve a classic problem in the kitchen: keeping a sourdough starter within the ideal, somewhat oppressive range of acceptable temperatures needed for successful fermentation.

A sourdough starter is a wad of wild yeasts that you make yourself using flour, water, and patience. It’s good for a lot more than just sourdough bread — you can scoop some out of the jar and use it to make pancakes, waffles, pretzels, and a host of other bread-y delights. A starter is a living thing, a container full of fermentation that eats flour and has specific temperature needs. Opinions differ a bit, but the acceptable temperature range for active growth is about 60 F to 82 F. Too cold, and the starter will go dormant, though it can be revived with a little love. But if the starter gets too hot, all the yeasts and bacteria will die.

While there are of course commercial products out there that attempt to solve this problem of temperature control, most of them seem to be aimed at people who live in some wonderland that never gets warmer than 80F. Most of these devices can’t cool, they only provide heat. But what if you live in a place with seasons where the climate ranges from hot and humid to cold and dry?

The answer lies within Chamber, a temperature-regulated haven Trent created that lets these wild yeasts grow and thrive. It uses a Peltier unit to heat and cool the box as needed to keep the mixture fermenting at 26°C /78.8°F.

Thanks to the Peltier unit, Trent can change the temperature inside the chamber simply by alternating the direction of current flow through the Peltier. He’s doing this with an H-bridge module driven by a Raspberry Pi Zero. When it starts to get too warm in the chamber, the fan on the outside wall vents the heat away. A second fan inside the chamber pulls warm air in when it gets too cold.

Trent says that Chamber performs really well, and he’s recorded temperatures as low as 60F and as high as 82F. He mostly uses it for sourdough, but it could work for other temperature-sensitive food sciences like pickling, growing mushrooms, or making yogurt. We think it could be ideal for fermenting kombucha, too.

Chamber works well enough that Trent has put further development on the back burner while he makes use of it. He does have several ideas for improvements, so if you want to help, check out his website and Github repo.

Continue reading “Engineering Your Way To Better Sourdough (and Other Fermented Goods)” →

A Car That Runs On Homemade Chemical Reactions

December 25, 2019 by Sharon Lin 11 Comments

The race for chemical engineering is quite literally on. Every year, the American Institute of Chemical Engineers (AlChE) brings together hundreds of university students to face-off to design the fastest car using techniques they’ve learned from chemical engineering courses.

The Chem-E-Car competition races cars which are only powered by chemical reactions. The goal is to come up with an elegant solution – you can’t simply jettison matter out the back as the method of locomotion. In particular, the rules don’t allow the use of liquid or obnoxious odor discharge, commercial batteries, brakes, or electrical/mechanical timing devices. However, this doesn’t mean that electronics are absent from these designs. Many teams must gather data in order to design a control system to improve the performance of their car.

Students have to build a power system, stopping mechanism, circuitry, and mechanical assembly for the body of the car, all to fit in a size constraint not much bigger than a shoebox. The competition primarily judges the accuracy of the chemical reaction for stopping the car more so than speed or power. Given that the load the car must carry is typically unknown until the day of the competition, this is a significant challenge, allowing teams to find a way to design a flexible reaction that can accommodate a range of loads and distances.

For example, this 2015 entry from the Rice University team (PDF) uses a fuel cell for locomotion and an iodine clock reaction as a timer for braking. The fuel cell powers an Arduino which monitors a light-dependent resistor. In between the LED and that LDR, the clock reaction turns opaque at a predictable time and triggers the motors to stop turning.

While many schools choose not to disclose their designs in order to gain a competitive edge, we applaud the teams who have shared the story of their builds. Kudos to the Rice team mentioned above, to the 2014 Rutger’s team whose white paper outlines the construction of aluminum air batteries worthy of Walter White, to the car from the Universitas Negeri Semarang, Indonesia powered by a thermoelectric generator (PDF), the UC Berkeley team for outlining numerous approaches to developing their power system, and the two Ohio State team’s entries seen winning the regional competition in the video below.

If you were on a team that compete the the Chem-E-Car, we want to hear about it!

Continue reading “A Car That Runs On Homemade Chemical Reactions” →

The Story Of The Quickening: Mercurial Metal

December 11, 2019 by Maya Posch 49 Comments

Of all known metals, mercury is probably one of the most famous, if only for its lustrous, liquid form at room temperature. Over the centuries, it has been commonly used in a wide variety of applications, including industrial chemical processes, in cosmetics, for telescope mirrors, thermometers, fluorescent lamps, dental fillings, bearings, batteries, switches and most recently in atomic clocks.

Though hardly free from the controversy often surrounding a toxic heavy metal, it’s hard to argue the myriad ways in which mercury has played a positive role in humanity’s technological progress and scientific discoveries. This article will focus both on its historical, current, and possible future uses, as well as the darker side of this fascinating metal.

Continue reading “The Story Of The Quickening: Mercurial Metal” →

Using Glow-in-the-Dark Fish Gut Bacteria To Make Art

December 7, 2019 by Sharon Lin 3 Comments

In New Orleans, a Loyola University professor has been creating original art out of glow-in-the-dark fish gut bacteria, enough to fill 1000 Petri dishes. Her first major foray into art was biomorphic abstractions, inspired by Impressionist painters, with her current work reflecting much of the abstraction of the earlier style.

The bacteria comes from the Pacific Rock Fish and glows a vibrant electric-blue. It is typically kept in a freezer and has a texture and color similar to water when it’s being used. The luminescence only lasts for 24 hours, presenting timing challenges when preparing artwork for a photoshoot, as artist [Hunter Cole] often does. With a Q-tip, [Cole] paints roses, lilies, and insects onto the Petri dishes and arranges them for surreal photography shoots. In addition to painting shapes in agar, she uses a light painting technique by filling clear water bottles with the bacteria for long-exposure shots.

[Cole] is planning on presenting her work at an art exhibit in New Orleans, along with showcasing a performance piece featuring models clad in chandelier-like costumes glowing with bioluminescent bacteria in petri dishes.

A Self-Healing, Stretchable Electronic Skin

December 4, 2019 by Sharon Lin 4 Comments

In a report published by Science Advances, a research team from the United States and Korea revealed a strain-sensitive, stretchable, and autonomous self-healing semiconductor film. In other words, they’ve created an electronic skin that’s capable of self-regulation. Time to cue the ending track from Ex Machina? Not quite.

Apart from the inevitable long timeline it will take to see the material in production, there are still challenges to improve sensing for active semiconductors. The methods used by the team – notably using a dynamically cross-linked blend of polymer semiconductor and self-healing elastomer – have created a film with a gauge factor of 5.75×10^5 at full strain. At room temperature, even with fracture strains, the material demonstrated self healing.

The technique mimics the self healing properties of human skin, accelerating the development of biomedical devices and soft robots. While active-matrix transistor array-based sensors can provide signals that reduce crosstalk between individual pixels in electronic skin, embedding these rigid sensors and transistors into stretchable systems causes mechanical mismatch between rigid and soft components. A strain-sensing transistor simplifies the process of fabrication, while also improving mechanical conformability and the lifetime of the electronic skin.

The synthetic skin was also shown to operate within a medically safe voltage and to be waterproof, which will prevent malfunctions when placed in contact with ionic human sweat.

[Thanks Qes for the tip!]

A Single-Digit-Micrometer Thickness Wood Speaker

November 27, 2019 by Sharon Lin 22 Comments

Researchers have created an audio speaker using ultra-thin wood film. The new material demonstrates high tensile strength and increased Young’s modulus, as well as acoustic properties contributing to higher resonance frequency and greater displacement amplitude compared to a commercial polypropylene diaphragm in an audio speaker.

Typically, acoustic membranes have to remain very thin (on the micron scale) and robust in order to allow for a highly sensitive frequency response and vibrational amplitude. Materials made from plastic, metal, ceramic, and carbon have been used by engineers and physicists in an attempt to enhance the quality of sound. While plastic thin films are most commonly manufactured, they have a pretty bad impact on the environment. Meanwhile, metal, ceramic, and carbon-based materials are more expensive and less attractive to manufacturers as a result.

Cellulose-based materials have been making an entrance in acoustics research with their environmentally friendly nature and natural wooden structure. Materials like bagasse, wood fibers, chitin, cotton, bacterial cellulose, and lignocellulose are all contenders for effective alternatives to parts currently produced from plastics.

The process for building the ultra-thin film involved removing lignin and hemicellulose from balsa wood, resulting in a highly porous material. The result is hot pressed for a thickness reduction of 97%. The cellulose nano-fibers remain oriented but more densely packed compared to natural wood. In addition, the fibers required higher energy to be pulled apart while remaining flexible and foldable.

At one point in time, plastics seemed to be the hottest new material, but perhaps wood is making a comeback?

[Thanks Qes for the tip!]