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Category Archives: chemistry

Origin of life researchers figure out how to build bigger RNAs

A close up of the active site of a catalytic RNA.
UCB

We'll probably never know exactly how life on Earth got its start. The conditions in which it began have long since been lost, and there are simply too many precursor molecules and potential environments that could have gotten the process going. Nevertheless, researchers hope to put together a pathway that's at least plausible, starting from simple molecules that were present on the early Earth and building up to an enclosed system with basic inheritance (from there, evolution can take over).

A lot of progress has been made in understanding how a simple chemical, like hydrogen cyanide, can be built up through a series of reactions into a nucleotide, the basic building block of molecules like DNA and RNA. And we've learned quite a bit about how larger RNAs (more than 100 nucleotides long) can fold into complex structures that can catalyze reactions and undergo the chemical equivalent of Darwinian evolution. The challenge has been bridging the gap between the two, going from a handful of linked nucleotides to a large molecule that's potentially capable of catalyzing chemical reactions.

Now, the team that developed the earlier results is back with another publication. Their latest work shows how short molecules that are composed of just a handful of nucleotides can be linked together, eventually building longer, more complex chains. Once again, the chemistry is simple enough to occur on the early Earth, and the reaction might explain a curious bias in how DNA and RNA are built into long chains of nucleotides.

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Making HIV tests visible to the naked eye

One of the recurring themes in healthcare is that a lot of what works in the developed world doesn't work in the developing world. There may be limited access to basics like power or communications facilities, never mind the medical technologies that make a hospital one of the modern wonders of the world. Beyond simple access to expensive technologies and medicines, even something as basic as a diagnostic test might be too expensive or require skilled technicians to use.

Though cures might remain expensive—drug companies like their profits—every dime saved on diagnosis is a dime more for prevention and cure. That makes cheap, accurate, and simple diagnostic tests very, very desirable.

I was thinking about this when I came across an older paper that somehow didn't attract any attention when it came out. Last year, a group of researchers showed that they could detect HIV at extremely low concentrations. That by itself is nothing special: people are always improving diagnostic tests. What is special is that the test is very much like a pregnancy test, in that a simple visible color change indicates a positive result. Even better, it seems to work in real-life tests.

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Inside science: Selling and upsizing the meal

Aurich Lawson / Thinkstock

By now, everyone who cares is aware of exactly what I want to do: you can't shut me up about this stuff. The application for funding is on its way in. But does the project really fit the institutional boundary conditions, and does it stand a chance of being funded?

If we recall part one of this series, I said that the science needs to be broken up into bite-sized chunks, each of which will turn out a good PhD or provide support for a post doc. I've done that: three good projects, each of which should succeed no matter what experimental results they obtain. In that sense, they are "safe." But, they also have elements that allow us to go for gold, producing results that will turn heads. In short, I think I've got a good balanced program in the works.

On the other hand, the laser system that enables it all seems... complicated. Certainly, the early work is going to involve a lot of set up time. And that should worry me, the funding agency, and the institution. I'm not going into this blind, however. I can't walk into a showroom and order a laser system, like you might a car. "Hi, I'd like the red M3 with the boy-racer body kit, low profile tires, mags, and red brakes. Oh, and because this is on the government ticket, please make it a diesel."

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From idea to science: Pouring concrete for an experiment and securing funds

Aurich Lawson / Thinkstock

"From idea to science" is a process, and as such, it's become a series here. We've discussed what I perceive to be the institutional boundary conditions that constrain my academic success, then followed that with a long exposition on the science that gets me out of bed in the morning. But now it's time to get specific. This is the part that I admittedly have difficulty with: turning ideas and desires into concrete plans. Or, at least making them into plans that are acceptable to people who provide money.

Today, let's take the general idea from last time and break it up into individual, graduate-student-sized projects. In one sense, this is easy—just come up with three sets of experiments. Unfortunately, they need to tie together intellectually. It isn't necessary that the students need to work together on everything, but, thematically, they should be sufficiently related. That way, the students can assist each other when problems arise.

Getting specific also means thinking about who I am going to ask for money and how much. The European Research Council is offering up to €2 million (about $2.59 million) over five years to a few clever and competent researchers fitting a certain profile. I need to be relatively young—you must have held your PhD for less than 12 years—and you should be looking to strengthen an existing research group. There are other criteria, but those are the two that give you the essence of what they are looking for: new researchers trying to get more independence. As for the money, it sounds like a lot, but, for what I want to do, it will provide for three PhD students over the entire period.

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Making industrial chemistry green: catalysts, chemicals, and lifecycle

The Earth has finite resources and they're not evenly distributed. As we use up the easy-to-access sources of ores and fossil fuels, some of the key foundations of modern society risk becoming rare and prohibitively expensive. Until we actually perfect fusion and asteroid mining, these are realities driving our push to develop sustainable practices.

At the meeting of the American Association for the Advancement of Science, researchers talked about the progress they're making when attempting to put industrial chemistry on a sustainable path. The overall belief of the panel is that it's not simply enough to make any one part of the process sustainable. Using a cheap and easily available catalyst to drive reactions that require fossil fuels will only buy us so much. It's only when we make every step of the process sustainable—including what happens to the chemicals when we're done with them—that we can really make progress.

The session's organizer, UCSB's Susannah Scott, set out the scale of the problem. Industrial chemistry needs account for something like a quarter of US energy use. The metals Ru, Te, Pd, Rh, Au, Pt, Re, Os, and Ir are all fantastic catalysts, but they are the least common elements in the crust relative to silicon. Princeton's Paul Chirik added a few more details: the current US lifestyle requires something like 80 different elements (GE, for example, uses 72 of the first 82 in the periodic chart). Right now, 19 of them come exclusively from different countries.

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Sodium-air battery shows potential

With battery technology being critical for so many things, interest in building better batteries just keeps on growing. The recent Tesla Model S testing debacle, explosive laptop batteries, and Boeing battery problems give us hints at how close to the edge engineers operate batteries. Volume, weight, and energy are key. Minimize the first two and maximize the last to obtain energy storage nirvana.

Lithium-ion batteries rule the roost at the moment, but as capacities are already on the order of 200Wh/kg, we're pushing up against their limits—basic chemical reactions provide a fixed amount of energy. The search for alternatives is being pursued by a rapidly growing field of eyebrow-less engineers (just kidding; battery mishaps don't happen that often). A recent publication on a sodium-air battery shows promise, but it also demonstrates what a huge amount of work still needs to be done.

The key to a battery is a simple chemical reaction that, at its heart, is the exchange of an electron. During the exchange, a certain amount of energy is released, usually in the form of heat. That's why, when you drop some sodium metal in water, the energy released is enough to cause explosions. The role of the battery is to intercept that electron and release its energy in the form of useful work.

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Synthetic particles that flock like birds

A flock of starlings is called a murmuration.
Walter Baxter

Scientists have built a self-organizing system of synthetic particles that assemble into clusters in a way that mimics the complicated organization of flocks of birds or colonies of bacteria. The particles form a “living crystal” that moves, swirls, and adjusts to heal cracks.

Self-assembly is a common way to build materials. Often, individual building blocks stick together due to inherent attractions, like bases of DNA bonding to form a nanotube, proteins gathering to form a helical virus coat, or nanospheres gathering to form a photonic crystal.

But what draws flocks of starlings, schools of fish, or rafts of ants together? Flocking or schooling can be a social behavior. However, the similarities among these phenomena, regardless of the creatures involved, led NYU's Jérémie Palacci and his colleagues to wonder if an underlying physical principle could also govern the organization process.

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Synthetic particles that flock like birds

A flock of starlings is called a murmuration.
Walter Baxter

Scientists have built a self-organizing system of synthetic particles that assemble into clusters in a way that mimics the complicated organization of flocks of birds or colonies of bacteria. The particles form a “living crystal” that moves, swirls, and adjusts to heal cracks.

Self-assembly is a common way to build materials. Often, individual building blocks stick together due to inherent attractions, like bases of DNA bonding to form a nanotube, proteins gathering to form a helical virus coat, or nanospheres gathering to form a photonic crystal.

But what draws flocks of starlings, schools of fish, or rafts of ants together? Flocking or schooling can be a social behavior. However, the similarities among these phenomena, regardless of the creatures involved, led NYU's Jérémie Palacci and his colleagues to wonder if an underlying physical principle could also govern the organization process.

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Single-molecule motor sits on a single-atom ball bearing

The base of the device holds a Ru atom, and the five-armed device can rotate on top of it.
Image from Perera et. al., Nature Nanotechnology

For some time now, researchers have been managing to craft ever-smaller devices, though they're approaching the problem from two directions. Some researchers are etching small features into chips to carve out nanoscale versions of familiar devices. But others are taking advantage of our ability to synthesize and interact with individual molecules to create systems that are only a few dozen atoms across. And, in many cases, these single-molecule devices look disturbingly like their full-scale counterparts.

When last we left single-molecule motors, they were four wheeling across a sheet of copper, powered by electrons fed in by an atomic force microscope. In the latest iteration, researchers have managed to create a reversible rotor that sits atop a ball bearing—but in this case, the bearing is a single ruthenium atom.

Again, the tricky part comes in building the molecules required. The base of the system involves a boron atoms that coordinates three ringed structures that are chemically similar to the bases of DNA. Nitrogens at a corner of these ringed structures coordinate the ruthenium atom, placing it at the peak of a three-sided pyramid. (This compound has the succinct name [n5-1-(4- tolyl )-2,3,4,5-tetra(4-ferrocenylphenyl) cyclopentadienyl hydrotris [6-((ethylsulphanyl)methyl)indazol-1-yl] borate ruthenium(II)], which should provide some sense of its complexity.)

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Earthworm guts become factory for nanoparticles

Enlarge / Meet the latest quantum dot assembly factory.
Colorado State

Quantum dots are nanoscale-sized pieces of semiconductor. Their small size ensures that quantum effects, like the Pauli exclusion principle, influence the behavior of electrons within them. This gives the dots properties that a bulk material with the same composition lacks, and it makes them appealing candidates for things like tiny lasers, photovoltaic materials, and LEDs.

Another area where they've shown promise is medical imaging. In terms of absorbing and emitting light, quantum dots behave much like the fluorescent molecules we can use to label cells of interest. But, since their fluorescent properties depend on the shape of the particles rather than the chemical structure of a molecule, they are much less prone to undergoing reactions that destroy their fluorescence. The problem is that most semiconductors aren't especially biocompatible, meaning additional chemical reactions need to be performed before the dots can attach to or enter cells.

Some researchers have started to look towards making the dots in biological systems, figuring that the output would necessarily be biocompatible. After some successes with bacteria and yeast, they've moved on to a larger target: the earthworm. And it appears to work very well.

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