Tag Archives: self-assembling

Self-organizing nanotubes and nonequilibrium systems provide insights into evolution and artificial life

If you’re interested in the second law of thermodynamics, this Feb. 10, 2015 news item on ScienceDaily provides some insight into the second law, self-organized systems, and evolution,

The second law of thermodynamics tells us that all systems evolve toward a state of maximum entropy, wherein all energy is dissipated as heat, and no available energy remains to do work. Since the mid-20th century, research has pointed to an extension of the second law for nonequilibrium systems: the Maximum Entropy Production Principle (MEPP) states that a system away from equilibrium evolves in such a way as to maximize entropy production, given present constraints.

Now, physicists Alexey Bezryadin, Alfred Hubler, and Andrey Belkin from the University of Illinois at Urbana-Champaign, have demonstrated the emergence of self-organized structures that drive the evolution of a non-equilibrium system to a state of maximum entropy production. The authors suggest MEPP underlies the evolution of the artificial system’s self-organization, in the same way that it underlies the evolution of ordered systems (biological life) on Earth. …

A Feb. 10, 2015 University of Illinois College of Engineering news release (also on EurekAlert), which originated the news item, provides more detail about the theory and the research,

MEPP may have profound implications for our understanding of the evolution of biological life on Earth and of the underlying rules that govern the behavior and evolution of all nonequilibrium systems. Life emerged on Earth from the strongly nonequilibrium energy distribution created by the Sun’s hot photons striking a cooler planet. Plants evolved to capture high energy photons and produce heat, generating entropy. Then animals evolved to eat plants increasing the dissipation of heat energy and maximizing entropy production.

In their experiment, the researchers suspended a large number of carbon nanotubes in a non-conducting non-polar fluid and drove the system out of equilibrium by applying a strong electric field. Once electrically charged, the system evolved toward maximum entropy through two distinct intermediate states, with the spontaneous emergence of self-assembled conducting nanotube chains.

In the first state, the “avalanche” regime, the conductive chains aligned themselves according to the polarity of the applied voltage, allowing the system to carry current and thus to dissipate heat and produce entropy. The chains appeared to sprout appendages as nanotubes aligned themselves so as to adjoin adjacent parallel chains, effectively increasing entropy production. But frequently, this self-organization was destroyed through avalanches triggered by the heating and charging that emanates from the emerging electric current streams. (…)

“The avalanches were apparent in the changes of the electric current over time,” said Bezryadin.

“Toward the final stages of this regime, the appendages were not destroyed during the avalanches, but rather retracted until the avalanche ended, then reformed their connection. So it was obvious that the avalanches correspond to the ‘feeding cycle’ of the ‘nanotube inset’,” comments Bezryadin.

In the second relatively stable stage of evolution, the entropy production rate reached maximum or near maximum. This state is quasi-stable in that there were no destructive avalanches.

The study points to a possible classification scheme for evolutionary stages and a criterium for the point at which evolution of the system is irreversible—wherein entropy production in the self-organizing subsystem reaches its maximum possible value. Further experimentation on a larger scale is necessary to affirm these underlying principals, but if they hold true, they will prove a great advantage in predicting behavioral and evolutionary trends in nonequilibrium systems.

The authors draw an analogy between the evolution of intelligent life forms on Earth and the emergence of the wiggling bugs in their experiment. The researchers note that further quantitative studies are needed to round out this comparison. In particular, they would need to demonstrate that their “wiggling bugs” can multiply, which would require the experiment be reproduced on a significantly larger scale.

Such a study, if successful, would have implications for the eventual development of technologies that feature self-organized artificial intelligence, an idea explored elsewhere by co-author Alfred Hubler, funded by the Defense Advanced Research Projects Agency [DARPA]. [emphasis mine]

“The general trend of the evolution of biological systems seems to be this: more advanced life forms tend to dissipate more energy by broadening their access to various forms of stored energy,” Bezryadin proposes. “Thus a common underlying principle can be suggested between our self-organized clouds of nanotubes, which generate more and more heat by reducing their electrical resistance and thus allow more current to flow, and the biological systems which look for new means to find food, either through biological adaptation or by inventing more technologies.

“Extended sources of food allow biological forms to further grow, multiply, consume more food and thus produce more heat and generate entropy. It seems reasonable to say that real life organisms are still far from the absolute maximum of the entropy production rate. In both cases, there are ‘avalanches’ or ‘extinction events’, which set back this evolution. Only if all free energy given by the Sun is consumed, by building a Dyson sphere for example, and converted into heat then a definitely stable phase of the evolution can be expected.”

“Intelligence, as far as we know, is inseparable from life,” he adds. “Thus, to achieve artificial life or artificial intelligence, our recommendation would be to study systems which are far from equilibrium, with many degrees of freedom—many building blocks—so that they can self-organize and participate in some evolution. The entropy production criterium appears to be the guiding principle of the evolution efficiency.”

I am fascinated

  • (a) because this piece took an unexpected turn onto the topic of artificial life/artificial intelligence,
  • (b) because of my longstanding interest in artificial life/artificial intelligence,
  • (c) because of the military connection, and
  • (d) because this is the first time I’ve come across something that provides a bridge from fundamental particles to nanoparticles.

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

Self-Assembled Wiggling Nano-Structures and the Principle of Maximum Entropy Production by A. Belkin, A. Hubler, & A. Bezryadin. Scientific Reports 5, Article number: 8323 doi:10.1038/srep08323 Published 09 February 2015

Adding to my delight, this paper is open access.

Watching buckyballs (buckminsterfullerenes) self-assemble in real-time

For the 5% or less of the world who need this explanation, the reference to a football later in this post is, in fact, a reference to a soccer ball. Moving on to a Nov. 5, 2014 news item on Nanowerk (Note: A link has been removed),

Using DESY’s ultrabright X-ray source PETRA III, researchers have observed in real-time how football-shaped carbon molecules arrange themselves into ultra-smooth layers. Together with theoretical simulations, the investigation reveals the fundamentals of this growth process for the first time in detail, as the team around Sebastian Bommel (DESY and Humboldt Universität zu Berlin) and Nicola Kleppmann (Technische Universität Berlin) reports in the scientific journal Nature Communications (“Unravelling the multilayer growth of the fullerene C60 in real-time”).

This knowledge will eventually enable scientists to tailor nanostructures from these carbon molecules for certain applications, which play an increasing role in the promising field of plastic electronics. The team consisted of scientists from Humboldt-Universität zu Berlin, Technische Universität Berlin, Universität Tübingen and DESY.

Here’s an image of the self-assembling materials,

Caption: This is an artist's impression of the multilayer growth of buckyballs. Credit: Nicola Kleppmann/TU Berlin

Caption: This is an artist’s impression of the multilayer growth of buckyballs.
Credit: Nicola Kleppmann/TU Berlin

A Nov. 5, 2014 DESY (Deutsches Elektronen-Synchrotron) press release (also on EurekAlert), describes the work further,

The scientists studied so called buckyballs. Buckyballs are spherical molecules, which consist of 60 carbon atoms (C60). Because they are reminiscent of American architect Richard Buckminster Fuller’s geodesic domes, they were christened buckminsterfullerenes or “buckyballs” for short. With their structure of alternating pentagons and hexagons, they also resemble tiny molecular footballs. [emphasis mine]

Using DESY’s X-ray source PETRA III, the researchers observed how buckyballs settle on a substrate from a molecular vapour. In fact, one layer after another, the carbon molecules grow predominantly in islands only one molecule high and barely form tower-like structures..“The first layer is 99% complete before 1% of the second layer is formed,” explains DESY researcher Bommel, who is completing his doctorate in Prof. Stefan Kowarik’s group at the Humboldt Universität zu Berlin. This is how extremely smooth layers form.

“To really observe the growth process in real-time, we needed to measure the surfaces on a molecular level faster than a single layer grows, which takes place in about a minute,” says co-author Dr. Stephan Roth, head of the P03 measuring station, where the experiments were carried out. “X-ray investigations are well suited, as they can trace the growth process in detail.”

“In order to understand the evolution of the surface morphology at the molecular level, we carried out extensive simulations in a non-equilibrium system. These describe the entire growth process of C60 molecules into a lattice structure,” explains Kleppmann, PhD student in Prof. Sabine Klapp’s group at the Institute of Theoretical Physics, Technische Universität Berlin. “Our results provide fundamental insights into the molecular growth processes of a system that forms an important link between the world of atoms and that of colloids.”

Through the combination of experimental observations and theoretical simulations, the scientists determined for the first time three major energy parameters simultaneously for such a system: the binding energy between the football molecules, the so-called “diffusion barrier,” which a molecule must overcome if it wants to move on the surface, and the Ehrlich-Schwoebel barrier, which a molecule must overcome if it lands on an island and wants to hop down from that island.

“With these values, we now really understand for the first time how such nanostructures come into existence,” stresses Bommel. “Using this knowledge, it is conceivable that these structures can selectively be grown in the future: How must I change my temperature and deposition rate parameters so that an island of a particular size will grow. This could, for example, be interesting for organic solar cells, which contain C60.” The researchers intend to explore the growth of other molecular systems in the future using the same methods.

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

Unravelling the multilayer growth of the ​fullerene C60 in real time by S. Bommel, N. Kleppmann, C. Weber, H. Spranger, P. Schäfer, J. Novak, S.V. Roth, F. Schreiber, S.H.L. Klapp, & S. Kowarik. Nature Communications 5, Article number: 5388 doi:10.1038/ncomms6388 Published 05 November 2014

This article is open access.

I was not able to find any videos of these buckyballs assembling in real-time. Presumably, there are technical issues with recording the process, financial issues, or some combination thereof. Still, I can’t help but feel teased (tongue in cheek) by these scientists who give me an artist’s concept instead. Hopefully, budgets and/or technology will allow the rest of us to view this process at some time in the future.

Self-assembling and disassembling nanotrain network

A Nov. 11, 2013 University of Oxford news release (also on EurekAlert dated as Nov. 10, 2013) highlights the first item I’ve seen about a nanostructure which both assembles and disassembles itself,

Tiny self-assembling transport networks, powered by nano-scale motors and controlled by DNA, have been developed by scientists at Oxford University and Warwick University.

The system can construct its own network of tracks spanning tens of micrometres in length, transport cargo across the network and even dismantle the tracks.

Researchers were inspired by the melanophore, used by fish cells to control their colour. Tracks in the network all come from a central point, like the spokes of a bicycle wheel. Motor proteins transport pigment around the network, either concentrating it in the centre or spreading it throughout the network. Concentrating pigment in the centre makes the cells lighter, as the surrounding space is left empty and transparent.

The researchers have provided an image,

Nanotrain network created by scientists at Oxford University: green dye-carrying shuttles after 'refuelling' with ATP travel towards the center of the network with their cargoes of green dye. Credit: Adam Wollman/Oxford University

Nanotrain network created by scientists at Oxford University: green dye-carrying shuttles after ‘refuelling’ with ATP travel towards the center of the network with their cargoes of green dye. Credit: Adam Wollman/Oxford University

The news release goes on to describe the system,

The system developed by the Oxford University team is very similar [to the melanophore used by fish cells], and is built from DNA and a motor protein called kinesin. Powered by ATP fuel, kinesins move along the micro-tracks carrying control modules made from short strands of DNA. ‘Assembler’ nanobots are made with two kinesin proteins, allowing them to move tracks around to assemble the network, whereas the ‘shuttles’ only need one kinesin protein to travel along the tracks.

‘DNA is an excellent building block for constructing synthetic molecular systems, as we can program it to do whatever we need,’ said Adam Wollman, who conducted the research at Oxford University’s Department of Physics. ‘We design the chemical structures of the DNA strands to control how they interact with each other. The shuttles can be used to either carry cargo or deliver signals to tell other shuttles what to do.

‘We first use assemblers to arrange the track into ‘spokes’, triggered by the introduction of ATP. We then send in shuttles with fluorescent green cargo which spread out across the track, covering it evenly. When we add more ATP, the shuttles all cluster in the centre of the track where the spokes meet. Next, we send signal shuttles along the tracks to tell the cargo-carrying shuttles to release the fluorescent cargo into the environment, where it disperses. We can also send shuttles programmed with ‘dismantle’ signals to the central hub, telling the tracks to break up.’

This demonstration used fluorescent green dyes as cargo, but the same methods could be applied to other compounds. As well as colour changes, spoke-like track systems could be used to speed up chemical reactions by bringing the necessary compounds together at the central hub. More broadly, using DNA to control motor proteins could enable the development of more sophisticated self-assembling systems for a wide variety of applications.

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

Transport and self-organization across different length scales powered by motor proteins and programmed by DNA by Adam J. M. Wollman, Carlos Sanchez-Cano, Helen M. J. Carstairs, Robert A. Cross, & Andrew J. Turberfield. Nature Nanotechnology (2013) doi:10.1038/nnano.2013.230 Published online 10 November 2013

This article is behind a paywall although you can preview it for free via ReadCube Access.

Self-assembling chains of nanoparticles

The Argonne National Laboratory (US) has announced that their researchers have for the first time watched nanoparticles assemble into chains in real-time. From the Apr. 20, 2013 news item on Nanowerk (Note: Links have been removed),

In a new study performed at the Center for Nanoscale Materials at the U.S. Department of Energy’s (DOE) Argonne National Laboratory, researchers have for the first time seen the self-assembly of nanoparticle chains in situ, that is, in place as it occurs in real-time (“In Situ Visualization of Self-Assembly of Charged Gold Nanoparticles”).

The Apr. 19, 2013 Argonne National Laboratory press release by Jared Sagoff, which originated the news item, provides more detail,

The scientists exposed a tiny liquid “cell” or pouch that contained gold nanoparticles covered with a positively charged coating to an intense beam of electrons generated with a transmission electron microscope. Some of the electrons that penetrated the outside of the cell became trapped in the fluid medium in the cell. These “hydrated” electrons attracted the positively charged nanoparticles, which in time reduced the intensity of charge of the positive coating.

As the hydrated electrons reduced the coating’s positive charge, the nanoparticles no longer repelled each other as strongly.  Instead, their newfound relative attraction led the nanoparticles to “jump around” and eventually stick together in long chains. This self-assembly of nanoparticle chains had been detected before in different studies, but this technique allowed researchers, for the first time, to observe the phenomenon as it occurred.

“The moment-to-moment behavior of nanoparticles is something that’s not yet entirely understood by the scientific community,” said Argonne nanoscientist Yuzi Liu, the study’s lead author. “The potential of nanoparticles in all sorts of different applications and devices – from tiny machines to harvesters of new sources of energy – requires us to bring all of our resources to bear to look at how they function on the most basic physical levels.”

Self-assembly is particularly interesting to scientists because it could lead to new materials that could be used to develop new, energy-relevant technologies. “When we look at self-assembly, we’re looking to use nature as a springboard into man-made materials,” said Argonne nanoscientist Tijana Rajh, who directed the group that carried out the study.

Because the particles under study were so tiny – just a few dozen nanometers in diameter – an optical microscope would not have been able to resolve, or see, individual nanoparticles. By using the liquid cell in the transmission electron microscope at the Center for Nanoscale Materials, Liu and his colleagues could create short movies showing the quick movement of the nanoparticles as their coatings contacted the hydrated electrons.

Here’s a video of the self-assembling nanoparticles, provided by the Argonne National Laboratory,

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

In Situ Visualization of Self-Assembly of Charged Gold Nanoparticles by Yuzi Liu, Xiao-Min Lin, Yugang Sun, and Tijana Rajh. J. Am. Chem. Soc., [Journal of the American Chemical Socieyt] 2013, 135 (10), pp 3764–3767
DOI: 10.1021/ja312620e Publication Date (Web): February 22, 2013
Copyright © 2013 American Chemical Society


Virtual lego used to simulate self-assembling crystal structures

The Jan. 17, 2013 news release on EurekAlert describes a ‘soft’ or virtual lego computer simulation developed at the University of Vienna (Austria),

In developing these novel self-assembling materials, postdoc Barbara Capone has focused on the design of organic and inorganic building blocks, which are robust and can be produced at large scale. Capone has put forward, together with her colleagues at the Universities of Vienna and Mainz, a completely new pathway for the construction of building blocks at the nanoscale.

The team of researchers has shown that so-called block copolymer stars – that means polymers that consist of two different blocks and they are chemically anchored on a common point – have a robust and flexible architecture and they possess the ability to self-assemble at different levels. At the single-molecule level, they first order as soft patchy colloids which serve then as “soft Lego” for the emergence of larger structures. At the next level of self-assembly, the colloids form complex crystal structures, such as diamond or cubic phases.

The spatial ordering in the crystals can be steered through the architecture of the “soft Lego” and opens up the possibility for the construction of new materials at the macroscopic scale with desired structure. In this way, crystals can be built that have applications in, e.g., photonics, acting as filters for light of certain frequencies or as light guides.

You can find illustrations of the ‘diamond’ and the ‘cube’ produced by Capone and her colleagues with the news release on EurekAlert or here at the University of Vienna’s media portal where you may be able to find more information if you can read German. Alternatively, you can read the research paper,

Telechelic Star Polymers as Self-Assembling Units from the Molecular to the Macroscopic Scale by Barbara Capone, Ivan Coluzza, Federica LoVerso, Christos N. Likos, and Ronald Blaak in Physical Review Letters 109 [issue no. 23], 238301 (2012) [5 pages]DOI:10.1103/PhysRevLett.109.238301

This article is behind a paywall.

Turning my world upside down: a new view on entropy

Entropy as a state of increasing disorder (or everything falls apart) is a concept introduced to me during a high school chemistry class. I think the teacher was having a bad day because the concept was couched in the most depressive terms possible. However, that may the reason a very strong impression was made, so news that entropy may lead to organization definitely piqued my interest. From the July 26, 2012 news item on Nanowerk (Note: I have removed a link),

Researchers trying to herd tiny particles into useful ordered formations have found an unlikely ally: entropy, a tendency generally described as “disorder.”

Computer simulations by University of Michigan scientists and engineers show that the property can nudge particles to form organized structures. By analyzing the shapes of the particles beforehand, they can even predict what kinds of structures will form.

The findings, published in this week’s edition of Science (“Predictive Self-Assembly of Polyhedra into Complex Structures”), help lay the ground rules for making designer materials with wild capabilities such as shape-shifting skins to camouflage a vehicle or optimize its aerodynamics.

More information can be found in the University of Michigan July 26, 2012 news release by Nicole Casal Moore,

One of the major challenges is persuading the nanoparticles to create the intended structures, but recent studies by Glotzer’s [professor Sharon Glotzer] group and others showed that some simple particle shapes do so spontaneously as the particles are crowded together. The team wondered if other particle shapes could do the same.

“We studied 145 different shapes, and that gave us more data than anyone has ever had on these types of potential crystal-formers,” Glotzer SAID. “With so much information, we could begin to see just how many structures are possible from particle shape alone, and look for trends.”

Using computer code written by chemical engineering research investigator Michael Engel, applied physics graduate student Pablo Damasceno ran thousands of virtual experiments, exploring how each shape behaved under different levels of crowding. The program could handle any polyhedral shape, such as dice with any number of sides.

Left to their own devices, drifting particles find the arrangements with the highest entropy. That arrangement matches the idea that entropy is a disorder if the particles have enough space: they disperse, pointed in random directions. But crowded tightly, the particles began forming crystal structures like atoms do—even though they couldn’t make bonds. These ordered crystals had to be the high-entropy arrangements, too.

However, this isn’t a simple reversal of the  entropy concept at the nanoscale (from the Moore news release),

Glotzer explains that this isn’t really disorder creating order—entropy needs its image updated. Instead, she describes it as a measure of possibilities. If you could turn off gravity and empty a bag full of dice into a jar, the floating dice would point every which way. However, if you keep adding dice, eventually space becomes so limited that the dice have more options to align face-to-face. The same thing happens to the nanoparticles, which are so small that they feel entropy’s influence more strongly than gravity’s.

“It’s all about options. In this case, ordered arrangements produce the most possibilities, the most options. It’s counterintuitive, to be sure,” Glotzer said.

The simulation results showed that nearly 70 percent of the shapes tested produced crystal-like structures under entropy alone. But the shocker was how complicated some of these structures were, with up to 52 particles involved in the pattern that repeated throughout the crystal.

Here’s an illustration the scientists have provided,

Shapes can arrange themselves into crystal structures through entropy alone, new research from the University of Michigan shows. Image credit: P. Damasceno, M. Engel, S. Glotzer

This excerpt includes a bit more about the crystals and two of the remaining mysteries (from the Moore news release),

The particle shapes produced three crystal types: regular crystals like salt, liquid crystals as found in some flat-screen TVs and plastic crystals in which particles can spin in place. By analyzing the shape of the particle and how groups of them behave before they crystallize, Damasceno said that it is possible to predict which type of crystal the particles would make.

“The geometry of the particles themselves holds the secret for their assembly behavior,” he said.

Why the other 30 percent never formed crystal structures, remaining as disordered glasses, is a mystery.

“These may still want to form crystals but got stuck. What’s neat is that for any particle that gets stuck, we had other, awfully similar shapes forming crystals,” Glotzer said.

In addition to finding out more about how to coax nanoparticles into structures, her team will also try to discover why some shapes resist order.

Plenty of Room at the Bottom’s 50th anniversary; new advance in nanoassembly; satirizing the copyright wars; China’s social media map

There’s plenty of room at the bottom, Richard Feynman’s December 29, 1959 talk for the American Physical Society is considered to be the starting point or origin for nanotechnology and this December marks its 50th anniversary. Chris Toumey, a cultural anthropologist at the University of South Carolina NanoCenter, has an interesting commentary about it (on Nanowerk) and he poses the question, would nanotechnology have existed without Richard Feynman’s talk? Toumey answers yes. You can read the commentary here.

In contrast to Toumey’s speculations, there’s  Colin Milburn (professor at University of California, Davis) who in his essay, Nanotechnology in the Age of Posthuman Engineering: Science Fiction as Science, suggests that nanotechnology originated in science fiction. You can read more about Milburn, find the citations for the essay I’ve mentioned, and/or download three of his other essays from here.

Ting Xu and her colleagues at the US Dept. of Energy’s Lawrence Berkeley National Laboratory have developed a new technique for self-assembling nanoparticles. From the news item on Physorg.com,

“Bring together the right basic components – nanoparticles, polymers and small molecules – stimulate the mix with a combination of heat, light or some other factors, and these components will assemble into sophisticated structures or patterns,” says Xu. “It is not dissimilar from how nature does it.”

More details are available here.

TechDirt featured a clip from This hour has 22 minutes, a satirical Canadian comedy tv programme, which pokes fun at the scaremongering which features mightily in discussions about copyright. You can find the clip here on YouTube.

I’ve been meaning to mention this tiny item from Fast Company (by Noah Robischon) about China’s social media. From the news bit,

The major players in the U.S. social media world can be counted on one hand: Facebook, MySpace, Twitter, LinkedIn. Not so in China, where the country’s 300 million online users have a panoply of popular social networks to choose from–and Facebook doesn’t even crack the top 10.

Go here to see the infographic illustrating China’s social media landscape.

Happy weekend!

Doing the impossible (superconductorwise) and self-assembling gold

They made the electrons behave. Of course, it will be written up in much loftier terms but that’s what it comes down to. (For purists who think that you can’t end a sentence in a preposition, you are wrong. One of these days I will dig up the appropriate references.) A team at the University of British Columbia (‘UBC] yes, there is Canadian nanotechnology) have found a way to manipulate electrons on ultra thin material, in this case, potassium atoms were laid over a a piece of superconductive copper oxide. (superconductive = no resistance to conducting electricity)

As to why this is good news, here’s what the lead researcher, Dr. Andrea Damascelli has to say, “The development of future electronics, such as quantum computer chips, hinges on extremely thin layers of material.”  Sounds reasonable, so what’s the problem? He goes on, “Extremely thin layers and surfaces of superconducting material take on very different properties from the rest of the material. Electrons have been observed to rearrange, making it impossible for scientists to study.” Until recently. Damascelli adds, “The new technique opens the door to systematic studies not just of high-temperature superconductors, but many other materials where surfaces and interfaces control the physical properties.” He mentions fuel cells and lossless power lines as two potential applications. The journal, Nature Physics, is publishing Damascelli and team’s paper this week. (I imagine that you won’t be able to access the article unless you have a subscription or permission to use someone else’s subscription.) For more details you will find the press release here or at Phys.org here.

There is self-assembling gold according to Dr. Pulickel M. Ajayan at Rice University. His study will be published next month in Nano Letters. With the right conditions (exposure to magnets, chemicals, and light) Ajayan’s team coaxed nanorods into self-assembling as a giant structure (like a grain of rice). Go here for more details about the paper and an image of a giant gold droplet.