Nanodot: the original nanotechnology weblog

It is difficult to imagine any design for a mature molecular manufacturing system that does not require molecular motors. Now, as part of a plan to build more complex automated molecular machines, an international team has designed and built a molecular motor powered by electrons from a scanning tunneling microscope tip that uses a single atom as a bearing. A hat tip to KurzweilAI.net for reprinting this Ohio University news release “Scientists design, control movements of molecular motor“:

An international team of scientists has taken the next step in creating nanoscale machines by designing a multi-component molecular motor that can be moved clockwise and counterclockwise.

Although researchers can rotate or switch individual molecules on and off, the new study is the first to create a stand-alone molecular motor that has multiple parts, said Saw-Wai Hla, an Ohio University professor of physics and astronomy who led the study with Christian Joachim of A*Star in Singapore and CEMES/CNRS in France and Gwenael Rapenne of CEMES/CNRS.

It’s an essential step in creating nanoscale devices—quantum machines that operate on different laws of physics than classical machines—that scientists envision could be used for everything from powering quantum computers to sweeping away blood clots in arteries.

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One of the core concepts of molecular manufacturing is that nanotechnology will evolve to the point that it will become possible to position small groups of reactive atoms at atomically precise desired locations on a work piece in order to build arbitrarily complex atomically precise structures. For several decades optical tweezers have been used to trap and manipulate micrometer-size objects, like bacteria, molecules attached to micrometer size beads, and organelles within eukaryotic cells. They have been limited in precision by the wavelength of light (about 400 to 700 nm) so that they have been unable to manipulate nanometer-scale objects. Two recently published papers raise the possibility that this technology might evolve through the use of surface plasmon polaritons to enable atomically precise positioning. One paper presents a theoretical proposal for extending optical trapping to particles smaller than 2 nm. The second presents an experimental demonstration of highly efficient nanofocusing.

A hat tip to Phys.org for reprinting this Stanford Engineering news release by Kelly Servick “New Optical Tweezers Trap Specimens Just A Few Nanometers Across“:

To grasp and move microscopic objects, such as bacteria and the components of living cells, scientists can harness the power of concentrated light to manipulate them without ever physically touching them.

Now, doctoral student Amr Saleh and Assistant Professor Jennifer Dionne, researchers at the Stanford School of Engineering, have designed an innovative light aperture that allows them to optically trap smaller objects than ever before – potentially just a few atoms in size.

The process of optical trapping – or optical tweezing, as it is often known – involves sculpting a beam of light into a narrow point that produces a strong electromagnetic field. The beam attracts tiny objects and traps them in place, just like a pair of tweezers.

Unfortunately, there are natural limits to the technique. The process breaks down for objects significantly smaller than the wavelength of light. Therefore, optical tweezers cannot grasp super-small objects like individual proteins, which are only a couple of nanometers in diameter.

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Think about the smartest teenager (under 20) you know. Is this person passionate about science, technology, or entrepreneurship? If so, talk to him or her about starting a business or developing an invention or breakthrough. The 20 under 20 Thiel Fellowship offers $100,000 grants and lots of advice to smart innovators who are ready to pursue their dreams. It costs nothing to apply, and the deadline is December 31.

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http://www.nytimes.com/2012/09/16/business/the-thiel-fellows-forgoing-college-to-pursue-dreams.html

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Before this year the best way to build complex 3D nanostructures from DNA was to use scaffolded DNA origami (see, for example, this post). Last May scientists at the Wyss Institute introduced a DNA tile method for fabricating complex DNA objects that was much faster and much less expensive, and just two weeks ago we posted news that they had extended this method to make arbitrarily complex 3D DNA nanostructures from DNA bricks. Now scientists at the Technische Universität München have published two papers documenting major enhancements to scaffolded DNA origami. From “Reality check for DNA nanotechnology“:

Two major barriers to the advancement of DNA nanotechnology beyond the research lab have been knocked down. 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. 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.

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Biology uses various types of molecular machines to produce movement, all of which are candidates to be mimicked for use in nanotechnology. Muscles produce movement through the contraction of systems of polymers, powered by the release of chemical energy. Now scientists from France’s CNRS have developed an artificial muscle that produces micrometer-scale movement through the coordinated action of thousands of individual molecular machines each producing nanometer-scale movement. A hat tip to Gene Ostrovsky at MedGadget for a story on this CNRS press release “Assembly of nano-machines mimics human muscle“:

For the first time, an assembly of thousands of nano-machines capable of producing a coordinated contraction movement extending up to around ten micrometers, like the movements of muscular fibers, has been synthesized by a CNRS team from the Institut Charles Sadron. This innovative work, headed by Nicolas Giuseppone, professor at the Université de Strasbourg, and involving researchers from the Laboratoire de Matière et Systèmes Complexes (CNRS/Université Paris Diderot), provides an experimental validation of a biomimetic approach that has been conceptualized for some years in the field of nanosciences. This discovery opens up perspectives for a multitude of applications in robotics, in nanotechnology for the storage of information, in the medical field for the synthesis of artificial muscles or in the design of other materials incorporating nano-machines (endowed with novel mechanical properties). This work has been published in the on-line version of the journal Angewandte Chemie International Edition [abstract].

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One issue in designing molecular machine systems to do nanoscale work, such as molecular manufacturing, is how to transfer energy to implement guided molecular motions, to move components or to make or break chemical bonds. In Chemistry World Philip Ball comments on recent research that provides fresh insights into how this process is optimized in biology, and which could prove useful in designing artificial molecular machine systems. From “Make or break: the laws of motion“:

… the question biology has to face is: what is the optimal bond strength for a given mechanical function? This issue is tackled by Henry Hess of Columbia University, US, in a paper that is stimulating fresh thinking about molecular machines [abstract]. Consider a kinesin motor protein ‘walking’ along a tubulin track. The objective is to transfer impulse from the protein’s motor stroke – a conformational change driven by hydrolysis of adenosine triphospate – to the protein–tubule interface, propelling the molecule forward. Hess compares it to a car (kinesin) stuck in mud (tubulin). Anyone who has ever faced this situation knows how delicately the coupling must be managed, by engaging the clutch to just the right degree. Too much and the wheel just spins: the bond snaps. Too little, and the wheel’s coupling to the engine is insufficient to generate movement. The optimal point is found where the wheel–mud adhesion is just about to cease.

… Hess shows that as the load on a bond is increased, the transfer of impulse across the bond has a peak. The position of this peak depends on the distance to the transition state for bond rupture along the reaction coordinate. In other words, here is a design criterion for the ideal molecular machine that transfers energy during reversible binding: the bond should be just strong enough to be likely to survive during the power stroke. …

Proposals of how to advance from current nanotechnology to atomically precise manufacturing (see, for example, the Technology Roadmap for Productive Nanosystems) embody a range of proposals for different stages of development, from biological molecular machines based on networks of weak noncovalent bonds, to nanoscale versions of macroscopic machines constructed from hard materials like diamond comprising dense networks of strong covalent bonds. An important question to be clarified is how (or if) the design rules for molecular machine systems change at various points along this continuum.
—James Lewis, PhD

This past May we posted news of a major advance in the toolkit for DNA nanotechnology. Researchers led by Wyss Institute core faculty member Peng Yin developed a very versatile, rapid, and inexpensive way to assemble arbitrarily complex 150-nm two-dimensional DNA nanostructures from 42-nucleotide DNA tiles. A hat tip to ScienceDaily for reprinting this Wyss Institute news release of another major advance from the same research group aided by another Wyss Core Faculty member William Shih “Researchers Create Versatile 3D Nanostructures Using DNA ‘Bricks’”:

Researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University have created more than 100 three-dimensional (3D) nanostructures using DNA building blocks that function like Lego® bricks — a major advance from the two-dimensional (2D) structures the same team built a few months ago.

In effect, the advance means researchers just went from being able to build a flat wall of Legos®, to building a house. The new method, featured as a cover research article in the 30 November issue of Science [abstract], is the next step toward using DNA nanotechnologies for more sophisticated applications than ever possible before, such as “smart” medical devices that target drugs selectively to disease sites, programmable imaging probes, templates for precisely arranging inorganic materials in the manufacturing of next generation computer circuits, and more. …

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Mechanochemistry is the process of using mechanical force to effect bulk chemical reactions with small (catalytic) amounts of solvent. Although the process lacks any form of the positional control that is a cornerstone capability of productive nanosystems, understanding how chemical reactions proceed under mechanical force will help lessen the gap between current and future machine-phase synthesis. Recently featured at Phys.org, an international research collaboration led at McGill University is using high-energy synchrotron Xrays to study the chemical transformations that take place during ball milling.

In recent years, ball milling has become increasingly popular in the production of highly complex chemical structures. In such synthesis, steel balls are shaken with the reactants and catalysts in a rapidly vibrating jar. Chemical transformations take place at the sites of ball collision, where impact causes instant “hot spots” of localized heat and pressure. This is difficult to model and, without access to real time reaction monitoring, mechanochemistry remained poorly understood.
…
The team of scientists chose to study mechanochemical production of the metal-organic framework ZIF-8 from the simplest and non-toxic components. Materials such as ZIF-8 are rapidly gaining popularity for their ability to capture large amounts of CO2; if manufactured cheaply and sustainably, they could become widely used for carbon capture and storage, catalysis and even hydrogen storage.

“The team came to the ESRF because of our high-energy X-rays capable of penetrating 3 mm thick walls of a rapidly moving reaction jar made of steel, aluminium or plastic. The X-ray beam must get inside the jar to probe the mechanochemical formation of ZIF-8, and then out again to detect the changes as they happened”, says Simon Kimber, a scientist at the European Synchrotron Radiation Facility (ESRF) in Grenoble, who is a member of the team. This unprecedented methodology enabled the real-time observation of reaction kinetics, reaction intermediates and the development of their respective nanoparticles.

The work, published in Nature Chemistry (Abstract), allowed the research team to see differences in reaction pathways and kinetics relative to traditional solvent-phase processes.

An excellent introduction to mechanosynthesis and mechanochemistry (and their important distinctions) by Damian Allis of Syracuse University can be found in the Productive Nanosystems Technology Roadmap (see Part 3 Proceedings of the Roadmap Working Group, Atomically Precise Fabrication: 02 Mechanosynthesis).
-Posted by Stephanie C

Yet another milestone along the protein design molecular engineering path to advanced nanotechnology has been reached, thanks to the efforts of the laboratory of David Baker, one of the 2004 winners of the Foresight Feynman Prize in Nanotechnology for Theoretical work. From KurzweilAI “How to design proteins from scratch“:

… By following a set of rules, they designed five proteins from scratch that fold reliably into predicted conformations. In a blind test, the team showed that the synthesized proteins closely match the predicted structures.

“What you have now is a flexible set of building blocks for nanoscale assembly,” says Jeremy England, a molecular biophysicist at the Massachusetts Institute of Technology in Cambridge, who was not involved in the work. …

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One of the major applications currently driving the development of atomically precise manufacturing technologies is the quest for a quantum computer (see for example, this PDF “Atomically Precise, No Interface, Device Regime Workshop“). Another group of Australian researchers has achieved another milestone in this quest. A hat tip to ScienceDaily for reprinting this news release provided by the University of New South Wales, via EurekAlert!, a service of AAAS. “Single-atom writer a landmark for quantum computing“:

A research team led by Australian engineers has created the first working quantum bit based on a single atom in silicon, opening the way to ultra-powerful quantum computers of the future.

In a landmark paper published today in the journal Nature [abstract], the team describes how it was able to both read and write information using the spin, or magnetic orientation, of an electron bound to a single phosphorus atom embedded in a silicon chip.

“For the first time, we have demonstrated the ability to represent and manipulate data on the spin to form a quantum bit, or ‘qubit’, the basic unit of data for a quantum computer,” says Scientia Professor Andrew Dzurak. “This really is the key advance towards realising a silicon quantum computer based on single atoms.”

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One possible pathway from current technology to advanced nanotechnology that will comprise atomically precise manufacturing implemented by atomically precise machinery is through adaptation and extension of the complex molecular machine systems evolved by biology. Synthetic biology, which engineers new biological systems and function not evolved in nature, is an intermediate stage along this path. An article on KurzweilAI-net describes a recent achievement by MIT scientists in constructing a synthetic genetic circuit that responds to control signals from four molecules without any one molecule interfering with the responses to any other molecules. From “The most complex synthetic biology circuit yet“:

Christopher Voigt, an associate professor of biological engineering at MIT,.and his students have developed circuit components that don’t interfere with one another, allowing them to produce the most complex synthetic circuit ever built.

The circuit integrates four sensors for different molecules. Such circuits could be used in cells to precisely monitor their environments and respond appropriately.

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Imagine that there exists a two-dimensional (single-layer) crystal that is made of a commonly available element, is stronger than steel yet lighter weight and flexible, displays ballistic electron mobility (for comparison, two orders of magnitude greater mobility than silicon, at room temperature), and is sufficiently optically active to see with the naked eye (though far more practically, using an optical microscope). Prospective applications include flexible, high-speed electronic devices and new composite materials for aircraft.

Would this sound like a potentially world-changing substance worthy of scientific attention and funding?
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Nanoparticle-based research remains at the forefront of nanoscale approaches to targeted drug delivery and gene therapy (see related posts highlighting achievements in targeting specificity and enhanced delivery owed to high nanoparticle surface area). Recently reprinted by KurzweilAI.net, a news release from Johns Hopkins University entitled “Scientists Discover That Shape Matters in DNA Nanoparticle Therapy” describes the new findings, in which researchers from JHU and Northwestern University developed a set of DNA-copolymer nanoparticles that differ significantly in shape and in transfection efficiency.

The shapes were achieved first by mixing solutions of DNA and copolymer under varying solvent polarity conditions, allowing the micellar nanoparticles to adopt preferred configurations. The resulting shapes were similar to those observed in viral particles, with a worm-like shape predominating at higher polarities (i.e. higher water ratios). A reversible disulfide crosslinking method was then used to replicate the shapes under aqueous conditions, using cryo-TEM imaging to verify shape fidelity.

Notably, molecular dynamics simulations were conducted to model the shape transitions, providing experimentalists with time-saving predictive power.

“Our computer simulations and theoretical model have provided a mechanistic understanding, identifying what is responsible for this shape change,” Luijten said. “We now can predict precisely how to choose the nanoparticle components if one wants to obtain a certain shape. The use of computer models allowed Luijten’s team to mimic traditional lab experiments at a far faster pace.

In rat liver, the worm-like shapes, with average length of 581 nm, showed the highest gene expression, over 1,600-fold higher than that observed for spherical shapes of approximately 40 nm diameter.

While the variation in particle size may have an impact, co-corresponding author Hai-Quan Mao of JHU notes that the range of particles are similar in volume and weight, with fixed amounts of DNA. The full study, published in Advanced Materials, can be viewed in advance on line.
-Posted by Stephanie C

Among the recommendations of the 2007 Technology Roadmap for Productive Nanosystems is the development of modular molecular composite nanosystems (MMCNs), such as systems in which million-atom-scale DNA frameworks are used to organize various functional molecular components in ways to accomplish specific functions, eventually including atomically precise manufacturing. A step in this direction was taken by Harvard University scientists who used a DNA origami framework as a chasis on which to assemble and test the biological molecular motors that maintain subcellular organization in eukaryotic cells through the organized transport of various molecular cargos. In cells these molecular motors dynein and kinesin transport cargos in opposite directions along a hollow 25-nm-diameter protein track—the microtubule component of the cytoskeleton. In this work, the molecular motors carried a DNA chasis cargo along microtubules for a few tens of micrometers—comparable to the length of a eukaryotic cell. “Tug-of-War in Motor Protein Ensembles Revealed with a Programmable DNA Origami Scaffold” was published online in Science last week [abstract, PDF made available by corresponding author].

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The American Chemical Society and its partners foster flexible volunteer programs that enable scientists, engineers, and enthusiasts to share their expertise and passion with local communities. Foresight members can add tremendous value to these programs by bringing unique insight and experience in nanotechnology concepts and directions. Highlighted here are four great options for direct involvement on a variety of levels.

National Chemistry Week 2012: Nanotechnology, Oct. 21-27th
The focus of the 25th National Chemistry Week is “Nanotechnology – The Smallest BIG Idea In Science.” Use the link to find events scheduled for your area, connect with NCW coordinators and other like-minded thinkers, and/or learn how to set up your own event.

NanoDays 2013: March 30 – April 7th
Organized by participants in the Nanoscale Informal Science Education Network, NanoDays is

a nationwide festival of educational programs about nanoscale science and engineering and its potential impact on the future.

Events are held at science museums, observatories, universities, and more. Kits are available to applicants, providing experiments and tips for anyone interested in hosting an event, or find out about designing your own.

Science Coaches Program: Apply By October 30th
This remarkable program gives you the opportunity to team-up with a like-minded middle- or high school teacher in your community to bring nanotechology-oriented concepts and experiences to students. The ACS Science Coaches program is entering its third academic year.

Kids & Chemistry Program
The ACS Kids & Chemistry program is aimed at younger students and offers broad flexibility regarding the size of your volunteer commitment.

Volunteer efforts can be implemented as a full program administered by an ACS local section or by an individual as a one-time classroom visit.

Already participating in any of these programs? Know of other programs worth pointing at? Leave a Comment to let us know.
-Posted by Stephanie C

Metal-organic frameworks (MOFs) are back in the news again. A few months ago we cited the use of MOFs by Canadian chemists to self-assemble a molecular wheel on an axis in a solid material. More recently chemists at Northwestern University have used MOFs to set a world record for surface area. From “A world record for highest-surface-area materials“:

Northwestern University researchers have broken a world record by creating two new synthetic materials with the greatest amount of surface areas reported to date.

Named NU-109 and NU-110, the materials belong to a class of crystalline nanostructure known as metal-organic frameworks (MOFs) that are promising vessels for natural-gas and hydrogen storage for vehicles, and for catalysts, chemical sensing, light harvesting, drug delivery, and other uses requiring a large surface area per unit weight.

The materials’ promise lies in their vast internal surface area. If the internal surface area of one NU-110 crystal the size of a grain of salt could be unfolded, the surface area would cover a desktop. …

MOFs are composed of organic linkers held together by metal atoms, resulting in a molecular cage-like structure. The researchers believe they may be able to more than double the surface area of the materials by using less bulky linker units in the materials’ design. …

Beyond their near-term practical applications, Eric Drexler has cited MOFs as potentially useful building blocks in the molecular machine path to molecular manufacturing. Near-term applications may drive the technology development to produce more choices for molecular machine system components.
—James Lewis, PhD

Targeted drug delivery is one of the most important contributions of current and near-term nanotechnology to medicine. New research shows that specifically targeting one component of the cell makes nanoparticle-mediated drug delivery much more effective for a variety of applications. A hat tip to KurzweilAI.net for reprinting this University of Georgia news release “UGA researchers boost efficacy of drugs by using nanoparticles to target ‘powerhouse of cells’“:

Nanoparticles have shown great promise in the targeted delivery of drugs to cells, but researchers at the University of Georgia have refined the drug delivery process further by using nanoparticles to deliver drugs to a specific organelle within cells.

By targeting mitochondria, often called “the powerhouse of cells,” the researchers increased the effectiveness of mitochondria-acting therapeutics used to treat cancer, Alzheimer’s disease and obesity in studies conducted with cultured cells.

“The mitochondrion is a complex organelle that is very difficult to reach, but these nanoparticles are engineered so that they do the right job in the right place,” said senior author Shanta Dhar, an assistant professor of chemistry in the UGA Franklin College of Arts and Sciences.

Dhar and her co-author, doctoral student Sean Marrache, used a biodegradable, FDA-approved polymer to fabricate their nanoparticles and then used the particles to encapsulate and test drugs that treat a variety of conditions. Their results were published this week in early edition of the journal Proceedings of the National Academy of Sciences [abstract].

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The RSC web site features an article on molecular machines written by Josh Howgego that gives a very good brief introduction to the topic: Rise of the molecular machines. A downloadable PDF of the article as it originally appeared in Education in Chemistry provides better images of the figures than does the HTML version. The article explains how chemists have worked to mimic the function of biological molecular machine like muscles, by using intermolecular forces to control movements of mechanically interlocked molecules. The first example given is from the work of Fraser Stoddart, winner of the 2007 Feynman Prizes in Nanotechnology for Experimental work and Co-Chair of the January 2013 Foresight Technical Conference: Illuminating Atomic Precision, which will feature a session on “Molecular Machines and Non-Equilibrium Processes,” which Prof. Stoddart will chair. The article goes on to explain that harnessing simple molecular shuttles of the type pioneered by Stoddart to do real work like muscles has proved difficult, and cites as a prototype solution a molecular machine that works in a different way: a walker that sequentially makes and breaks different types of covalent bonds, developed by David Leigh, winner of the 2007 Feynman Prizes in Nanotechnology in the Theory category. The article finishes with a description of a nanocar developed by Ben Feringa that uses electricity to move across a metal surface by rotating paddle-like wheels.
—James Lewis, PhD

Four years ago we cited a report by a German research group of a single molecule cut and paste technology to assemble molecular building blocks on a DNA scaffold. The advance was noteworthy because it combined self-assembly of atomically precise components with the ability to use a manipulator (an atomic force microscope) to place those components at arbitrary positions in a larger structure, analogous to the way in which we use our hands to assemble parts macroscopically. These researchers have extended this technology to arrange single protein molecules. A hat tip to ScienceDaily.com and KurzweilAI.net for pointing to this press release from Ludwig-Maximilians University in Munich “All systems go at the biofactory“:

In order to assemble novel biomolecular machines, individual protein molecules must be installed at their site of operation with nanometer precision. LMU researchers have now found a way to do just that. Green light on protein assembly!

The finely honed tip of the atomic force microscope (AFM) allows one to pick up single biomolecules and deposit them elsewhere with nanometer accuracy. The technique is referred to as Single-Molecule Cut & Paste (SMC&P), and was developed by the research group led by LMU physicist Professor Hermann Gaub. In its initial form, it was only applicable to DNA molecules. However, the molecular machines responsible for many of the biochemical processes in cells consist of proteins, and the controlled assembly of such devices is one of the major goals of nanotechnology. A practical method for doing so would not only provide novel insights into the workings of living cells, but would also furnish a way to develop, construct and utilize designer nanomachines.

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