Tag Archives: Technische Universitaet Muenchen

An entire chemistry lab (nanofactory) in a droplet

I love the blue in this image, which illustrates the thousand-droplets test, research suggesting the possibility of a nanofactory or laboratory within a droplet ,

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction - Photo: Maximilian Weitz / TUM

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction – Photo: Maximilian Weitz / TUM

A Feb. 19, 2014 news item on Azonano reveals more,

An almost infinite number of complex and interlinked reactions take place in a biological cell. In order to be able to better investigate these networks, scientists led by Professor Friedrich Simmel, Chair of Systems Biophysics and Nano Biophysics at the Technische Universitaet Muenchen (TUM) try to replicate them with the necessary components in a kind of artificial cell.

This is also motivated by the thought of one day using such single-cell systems for example as “nanofactories” for the production of complex organic substances or biomaterials.

All such experiments have so far predominantly worked with very simple reactions, however. NIM Professor Friedrich Simmel and his team have now for the first time managed to let a more complex biochemical reaction take place in tiny droplets of only a few micrometers in size. Together with co-authors from the University of California Riverside and the California Institute of Technology in Pasadena, USA, the scientists are presenting their findings in the current edition of Nature Chemistry.

The Feb. 18, 2014 TUM press release, which originated the news item, details the experiements,

Shaking once – investigating thousands of times

The experiment is conducted by putting an aqueous reaction solution into oil and shaking the mixture vigorously. The result is an emulsion consisting of thousands of droplets. Employing only a tiny amount of material, the scientists have thus found a cost-efficient and quick way of setting up an extremely large number of experiments simultaneously.

As a test system, the researchers chose a so-called biochemical oscillator. This involves several reactions with DNA and RNA, which take place repetitively one after the other. Their rhythm becomes visible because in one step two DNA strands bind to each other in such a way that a fluorescent dye shines. This regular blinking is then recorded with special cameras.

Small droplets – huge differences

In the first instance, Friedrich Simmel and his colleagues intended to investigate the principal behavior of a complex reaction system if scaled down to the size of a cell. In addition, they specifically wondered if all droplet systems displayed an identical behavior and what factors would cause possible differences.

Their experiments showed that the oscillations in the individual droplets differed strongly, that is to say, much stronger than might have been expected from a simple statistical model. It was above all evident that small drops display stronger variations than large ones. “It is indeed surprising that we could witness a similar variability and individuality in a comparatively simple chemical system as is known from biological cells”, explains Friedrich Simmel the results.

Thus, it is currently not possible to realize systems which are absolutely identical. This de facto means that researchers have to either search for ways to correct these variations or factor them in from the start. On the other hand, the numerous slightly differing systems could also be used specifically to pick out the one desired, optimally running set-up from thousands of systems.

Investigating complex biosynthetic systems in artificial cells opens up many other questions, as well. In a next step, Friedrich Simmel plans to address the underlying theoretical models: “The highly parallel recording of the emulsion droplets enabled us to acquire plenty of interesting data. Our goal is to use these data to review and improve the theoretical models of biochemical reaction networks at small molecule numbers.”

Here’s link to and a citation for the paper,

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator by Maximilian Weitz, Jongmin Kim, Korbinian Kapsner, Erik Winfree, Elisa Franco, & Friedrich C. Simmel. Nature Chemistry (2014) doi:10.1038/nchem.1869 Published online 16 February 2014

This paper is behind a paywall.

RoboEarth (robot internet) gets examined in hospital

RoboEarth sometimes referred to as a robot internet or a robot world wide web is being tested this week by a team of researchers at Eindhoven University of Technology (Technische Universiteit Eindhoven, Netherlands) and their colleagues at Philips, ETH Zürich, TU München and the universities of Zaragoza and Stuttgart according to a Jan. 14, 2014 news item on BBC (British Broadcasting Corporation) news online,

A world wide web for robots to learn from each other and share information is being shown off for the first time.

Scientists behind RoboEarth will put it through its paces at Eindhoven University in a mocked-up hospital room.

Four robots will use the system to complete a series of tasks, including serving drinks to patients.

It is the culmination of a four-year project, funded by the European Union.

The eventual aim is that both robots and humans will be able to upload information to the cloud-based database, which would act as a kind of common brain for machines.

There’s a bit more detail in Victoria Turk’s Jan. 13 (?), 2014 article for motherboard.vice.com (Note: A link has been removed),

A hospital-like setting is an ideal test for the project, because where RoboEarth could come in handy is in helping out humans with household tasks. A big problem for robots at the moment is that human environments tend to change a lot, whereas robots are limited to the very specific movements and tasks they’ve been programmed to do.

“To enable robots to successfully lend a mechanical helping hand, they need to be able to deal flexibly with new situations and conditions,” explains a post by the University of Eindhoven. “For example you can teach a robot to bring you a cup of coffee in the living room, but if some of the chairs have been moved the robot won’t be able to find you any longer. Or it may get confused if you’ve just bought a different set of coffee cups.”

And of course, it wouldn’t just be limited to robots working explicitly together. The Wikipedia-like knowledge base is more like an internet for machines, connecting lonely robots across the globe.

A Jan. 10, 2014 Eindhoven University of Technology news release provides some insight into what the researchers want to accomplish,

“The problem right now is that robots are often developed specifically for one task”, says René van de Molengraft, TU/e  [Eindhoven University of Technology] researcher and RoboEarth project leader. “Everyday changes that happen all the time in our environment make all the programmed actions unusable. But RoboEarth simply lets robots learn new tasks and situations from each other. All their knowledge and experience are shared worldwide on a central, online database. As well as that, computing and ‘thinking’ tasks can be carried out by the system’s ‘cloud engine’, so the robot doesn’t need to have as much computing or battery power on‑board.”

It means, for example, that a robot can image a hospital room and upload the resulting map to RoboEarth. Another robot, which doesn’t know the room, can use that map on RoboEarth to locate a glass of water immediately, without having to search for it endlessly. In the same way a task like opening a box of pills can be shared on RoboEarth, so other robots can also do it without having to be programmed for that specific type of box.

There’s no word as to exactly when this test being demonstrated to a delegation from the European Commission, which financed the project, using four robots and two simulated hospital rooms is being held.

I first wrote abut RoboEarth in a Feb. 14, 2011 posting (scroll down about 1/4 of the way) and again in a March 12 2013 posting about the project’s cloud engine, Rapyuta.

Carbon nanotubes one way: gas and other flexible sensors

A Sept. 24, 2013 Technische Universitaet Muenchen (TUM) press release (also on EurekAlert) promises that flexible sensors are on the horizon,

Carbon nanotube-based gas sensors created at TUM offer a unique combination of characteristics that can’t be matched by any of the alternative technologies. They rapidly detect and continuously respond to extremely small changes in the concentrations of gases including ammonia, carbon dioxide, and nitrogen oxide. They operate at room temperature and consume very little power. Furthermore, as the TUM researchers report in their latest papers, such devices can be fabricated on flexible backing materials through large-area, low-cost processes.

Thus it becomes realistic to envision plastic food wrap that incorporates flexible, disposable gas sensors, providing a more meaningful indicator of food freshness than the sell-by date. Measuring carbon dioxide, for example, can help predict the shelf life of meat. “Smart packaging” – assuming consumers find it acceptable and the devices’ non-toxic nature can be demonstrated – could enhance food safety and might also vastly reduce the amount of food that is wasted. Used in a different setting, the same sort of gas sensor could make it less expensive and more practical to monitor indoor air quality in real time.

Dexter Johnson in a Sept. 26, 2013 posting on Nanoclast (an IEEE [Institute of Electrical and Electronics Engineers] blog) warns (Note: Links have been removed),

While this sounds great, the obstacle preventing this from becoming a reality has always been cost. Thin-film sensory packaging may make sense for a high-cost item, but for an inexpensive grocery store product, it’s hard to justify an additional cost that may be as much as the product itself. I made this point nearly a decade ago in report I authored titled, “The Future of Nanotechnology in Printing and Packaging”.

This doesn’t even take into account the often biased opinion people have about nanotechnology in relation to food.

Dexter recommends the researchers focus their commercialization efforts on robotic skins and other high ticket applications.

In reading the description of how the researchers created these flexible sensors, Dexter’s concerns are brought int high relief,

The most basic building block for this technology is a single cylindrical molecule, a rolled-up sheet of carbon atoms that are linked in a honeycomb pattern. This so-called carbon nanotube could be likened to an unimaginably long garden hose: a hollow tube just a nanometer or so in diameter but perhaps millions of times as long as it is wide. Individual carbon nanotubes exhibit amazing and useful properties, but in this case the researchers are more interested in what can be done with them en masse.

Laid down in thin films, randomly oriented carbon nanotubes form conductive networks that can serve as electrodes; patterned and layered films can function as sensors or transistors. “In fact,” Prof. Lugli [Prof. Paolo Lugli, director of TUM's Nanoelectronics Institute] explains, “the electrical resistivity of such films can be modulated by either an applied voltage (to provide a transistor action) or by the adsorption of gas molecules, which in turn is a signature of the gas concentration for sensor applications.” And as a basis for gas sensors in particular, carbon nanotubes combine advantages (and avoid shortcomings) of more established materials, such as polymer-based organic electronics and solid-state metal-oxide semiconductors. What has been lacking until now is a reliable, reproducible, low-cost fabrication method.

Spray deposition, supplemented if necessary by transfer printing, meets that need. An aqueous solution of carbon nanotubes looks like a bottle of black ink and can be handled in similar ways. Thus devices can be sprayed – from a computer-controlled robotic nozzle – onto virtually any kind of substrate, including large-area sheets of flexible plastic. There is no need for expensive clean-room facilities.

“To us it was important to develop an easily scalable technology platform for manufacturing large-area printed and flexible electronics based on organic semiconductors and nanomaterials,” Abdellah says. “To that end, spray deposition forms the core of our processing technology.”

Remaining technical challenges arise largely from application-specific requirements, such as the need for gas sensors to be selective as well as sensitive.

Here are citations for and links to three of the researchers’ papers,

Fabrication of carbon nanotube thin films on flexible substrates by spray deposition and transfer printing. Ahmed Abdelhalim, Alaa Abdellah, Giuseppe Scarpa, Paolo Lugli. Carbon, Vol. 61, September 2013, 72-79. DOI: 10.1016/j.carbon.2013.04.069

Flexible carbon nanotube-based gas sensors fabricated by large-scale spray deposition.
Alaa Abdellah, Zubair Ahmad, Philipp Köhler, Florin Loghin, Alexander Weise, Giuseppe Scarpa, Paolo Lugli. IEEE Sensors Journal, Vol. 13 Issue 10, October 2013, 4014-4021. DOI: 10.1109/JSEN.2013.2265775

Scalable spray deposition process for high performance carbon nanotube gas sensors. Alaa Abdellah, Ahmed Abdelhalim, Markus Horn, Giuseppe Scarpa, and Paolo Lugli. IEEE Transactions on Nanotechnology 12, 174-181, 2013. DOI: 10.1109/TNANO.2013.2238248

All three papers are behind paywalls.

In one of those coincidences that take place from time to time, I wrote about an upcoming event taking place in the Guardian’s London offices, a panel discussion on nanotechnology and food,in a Sept.  26, 2013 posting.

Breakthroughs with self-assembling DNA-based nanoscaled structures

With all the talk about self-assembling DNA nanotechnology, it’s possible to misunderstand the stage of development this endeavour occupies as the title, Reality check for DNA Nanotechnology, for a Dec. 13, 2012 news release on EurekAlert suggests,

… This emerging technology employs DNA as a programmable building material for self-assembled, nanometer-scale structures. Many practical applications have been envisioned, and researchers recently demonstrated a synthetic membrane channel made from DNA. Until now, however, design processes were hobbled by a lack of structural feedback. Assembly was slow and often of poor quality.

In fact, the news release is touting two breakthroughs,

Now researchers led by Prof. Hendrik Dietz of the Technische Universitaet Muenchen (TUM) have removed these obstacles.

One barrier holding the field back was an unproven assumption. Researchers were able to design a wide variety of discrete objects and specify exactly how DNA strands should zip together and fold into the desired shapes. They could show that the resulting nanostructures closely matched the designs. Still lacking, though, was the validation of the assumed subnanometer-scale precise positional control. This has been confirmed for the first time through analysis of a test object designed specifically for the purpose. A technical breakthrough based on advances in fundamental understanding, this demonstration has provided a crucial reality check for DNA nanotechnology.

In a separate set of experiments, the researchers discovered that the time it takes to make a batch of complex DNA-based objects can be cut from a week to a matter of minutes, and that the yield can be nearly 100%. They showed for the first time that at a constant temperature, hundreds of DNA strands can fold cooperatively to form an object — correctly, as designed — within minutes. Surprisingly, they say, the process is similar to protein folding, despite significant chemical and structural differences. “Seeing this combination of rapid folding and high yield,” Dietz says, “we have a stronger sense than ever that DNA nanotechnology could lead to a new kind of manufacturing, with a commercial, even industrial future.” And there are immediate benefits, he adds: “Now we don’t have to wait a week for feedback on an experimental design, and multi-step assembly processes have suddenly become so much more practical.”

Dexter Johnson comments in his Dec. 18, 2012 posting (which includes an embedded video) on the Nanoclast blog (located on the Institute of Electrical and Electronics Engineers [IEEE] website),

The field of atomically precise manufacturing—or molecular manufacturing—has taken a big step towards realizing its promise with this latest research.  We may still be a long way from realizing the “nanotech rapture”  but certainly knowing that the objects built meet their design specifications and can be produced in minutes rather than weeks has to be recognized as a significant development.

Three papers have been published on these breakthroughs, here are the citations,

Xiao-chen Bai, Thomas G. Martin, Sjors H. W. Scheres, Hendrik Dietz. Cryo-EM structure of a 3D DNA-origami object. Proceedings of the National Academy of Sciences of the USA, Dec. 4, 2012, 109 (49) 20012-20017; on-line in PNAS Early Edition, Nov. 19, 2012. DOI: 10.1073/pnas.1215713109

Jean-Philippe J. Sobczak, Thomas G. Martin, Thomas Gerling, Hendrik Dietz. Rapid folding of DNA into nanoscale shapes at constant temperature. Science, vol. 338, issue 6113, pp. 1458-1461. DOI: 10.1126/science.1229919

See also: Martin Langecker, Vera Arnaut, Thomas G. Martin, Jonathan List, Stephan Renner, Michael Mayer, Hendrik Dietz, and Friedrich C. Simmel. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science, vol. 338, issue 6109, pp. 932-936. DOI: 10.1126/science.1225624