Nanodot: the original nanotechnology weblog

Computer-generated 3D models (top) and corresponding 2D projection microscopy images (bottom) of nanostructures self-assembled from synthetic DNA strands called DNA bricks. (Image Credit: Yonggang Ke, Wyss Institute, Harvard University.)

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

Comparison of computational models with experimentally determined structure: design model (left) and NMR structure (right). Credit: Nobuyasu Koga et al./Nature)

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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This is an artist's impression of a phosphorus atom (red sphere surrounded by electron cloud, with arrow showing the spin direction) coupled to a silicon single-electron transistor. A burst of microwaves (blue) is used to 'write' information on the electron spin. (Credit: Tony Melov)

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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The protein–protein and protein–DNA interactions that can lead to crosstalk between gates are shown as red rectangles. (Credit: Tae Seok Moon et al./Nature)

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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Credits: Wei Qu, Northwestern University, simulation cartoons; Xuan Jiang, Johns Hopkins University, microscopic images.

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

(credit: Reck-Peterson Lab, Harvard Medical School)

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

Shanta Dhar, right, an assistant professor of chemistry in the UGA Franklin College of Arts and Sciences, and doctoral student Sean Marrache have fabricated nanoparticles that boost the effectiveness of drugs by delivering them to the mitochondria of cells (credit: University of Georgia).

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

Walk traffic man icon assembled by using an atomic force microscope to place molecules of green fluorescent protein (credit: Ludwig-Maximilians University)

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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Robert D. Cormia of Foothill College passes along this information on a program to help professionals transition into nanotechnology:

Foothill College is starting a prototype program with NASA-ASL (NASA-Ames) to train working professionals (incumbent) and transitional workers to use FE-SEM (Field Emission SEM) and Transmission Electron Microscopy (TEM) plus exposure to Design of Experiments (DOE) in thin film deposition and nanocarbon synthesis.

I have attached the flier in hope that you might be able to promote this through the Foresight Institute. The training at NASA-ASL is funded through my NSF-ATE grant (but we do want people to consider our online course NANO53 to learn the material characterization techniques.

Robert D. Cormia, Foothill College

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Noncontact AFM with a carbon monoxide-functionalized tip was used to image C-C bonds of different length and bond order in a nanographene molecule. The molecules used were synthesized by Centro de Investigacion en Quimica Bioloxica e Materiais Moleculares (CIQUS) at the Universidade de Santiago de Compostela and Centre National de la Recherche Scientifique (CNRS) in Toulouse. (Credit: IBM Research-Zurich)

Scanning probe microscopy (SPM) is one of the principal paths to atomically precise manufacturing (molecular manufacturing). One of the varieties of SPM that shows great promise is noncontact atomic force microscopy (NC-AFM). In a significant milestone, a team of scientists at IBM has greatly expanded the capabilities of NC-AFM by providing unprecedented information about the length and strength of individual chemical bonds within molecules. A hat tip to ScienceDaily for reprinting this IBM press release “IBM Scientists First to Distinguish Individual Molecular Bonds“:

IBM (NYSE: IBM) scientists have been able to differentiate the chemical bonds in individual molecules for the first time using a technique known as noncontact atomic force microscopy (AFM).

The results push the exploration of using molecules and atoms at the smallest scale and could be important for studying graphene devices, which are currently being explored by both industry and academia for applications including high-bandwidth wireless communication and electronic displays.

“We found two different contrast mechanisms to distinguish bonds. The first one is based on small differences in the force measured above the bonds. We expected this kind of contrast but it was a challenge to resolve,” said IBM scientist Leo Gross. “The second contrast mechanism really came as a surprise: Bonds appeared with different lengths in AFM measurements. With the help of ab initio calculations we found that the tilting of the carbon monoxide molecule at the tip apex is the cause of this contrast.”

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Bartosz A. Grzybowski (credit: Northwestern University)

From the standpoint of the development of advanced nanotechnology, the most useful type of machine intelligence is AI that facilitates scientific and engineering design. A computer network described in this news release from Northwestern University could greatly facilitate chemical synthesis useful for the development of molecular manufacturing. From “Northwestern Scientists Create Chemical Brain“, by Megan Fellman:

Northwestern University scientists have connected 250 years of organic chemical knowledge into one giant computer network — a chemical Google on steroids. This “immortal chemist” will never retire and take away its knowledge but instead will continue to learn, grow and share.

A decade in the making, the software optimizes syntheses of drug molecules and other important compounds, combines long (and expensive) syntheses of compounds into shorter and more economical routes and identifies suspicious chemical recipes that could lead to chemical weapons.

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Predicted structure of the cyclic nonamer proposed by the theorists, shown to match the actual folded structure with remarkable accuracy (credit: Lawrence Berkeley National Laboratory).

Peptoids are chemical cousins of proteins that present opportunities for molecular engineering comparable to but different from those presented by biomolecular systems (reviewed by Drexler here). Progress toward rational design of peptoids has been reported by a team of scientists at New York University, Lawrence Berkeley National Laboratory, Simprota Corporation, Stony Brook University, and Temple University. A hat tip to KurzweilAI.net for describing this news release from Lawrence Berkeley National Laboratory “Form, Function and Folding: In collaboration with Berkeley Lab, a team of scientists move toward rational design of artificial proteins“:

In the world of proteins, form defines function. Based on interactions between their constituent amino acids, proteins form specific conformations, folding and twisting into distinct, chemically directed shapes. The resulting structure dictates the proteins’ actions; thus accurate modeling of structure is vital to understanding functionality.

Peptoids, the synthetic cousins of proteins, follow similar design rules. Less vulnerable to chemical or metabolic breakdown than proteins, peptoids are promising for diagnostics, pharmaceuticals, and as a platform to build bioinspired nanomaterials, as scientists can build and manipulate peptoids with great precision. But to design peptoids for a specific function, scientists need to first untangle the complex relationship between a peptoid’s composition and its function-defining folded structure.

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The first Design Night at the Autodesk Gallery has the theme “Small is the next big thing: Exploring the frontiers of bio and nano technology”. From Instructables and the Autodesk Gallery:

September 6, 2012
6-10 p.m.
Autodesk Gallery, 2nd Floor
1 Market Street, San Francisco

Introducing Design Night, a new event series in the Autodesk Gallery at One Market held on the first Thursday of every month. At each event, guests will explore a different theme – such as biomimicry, light, or robotics – that challenges the conventionally narrow definition of design. The theme will be reflected in all aspects of the event, from the activities guests enjoy to the food they eat to the music they hear. Design is all about experience, so why limit that experience to just talk?

Please join us as we launch the Design Night series on Thursday, September 6, 6-10 p.m.The theme is “Small is the Next Big Thing” where we will explore the frontiers of bio and nano technology.

General admission to Design Night is $20 and student admission is $10. Admission fees include access to the exhibits, content such as a speaker, music, a hosted bar, and hands-on activities.

FIND OUT MORE INFORMATION & PURCHASE TICKETS HERE

Come explore what great design can do.

Nanotechnologically Yours,
Instructables and the Autodesk Gallery

The conceptual history of nanotechnology is usually traced to a classic talk “There’s Plenty of Room at the Bottom” that Richard Feynman gave on December 29th 1959 at the annual meeting of the American Physical Society at the California Institute of Technology (Caltech), which was first published in Caltech Engineering and Science, Volume 23:5, February 1960, pp 22-36. Feynman gave an updated version of that talk on October 25, 1984 during a weeklong experiential seminar at the Esalen Institute, Big Sur, California, called “Idiosyncratic Thinking”. He called the talk “Tiny Machines”. A video of Feynman’s 1984 talk has surfaced on YouTube (with an appropriate bongo drum introduction). A hat tip to Wayne Radinsky for passing this along. This 1 hour 19 minute updated speech is similar in content to an updated speech Feynman had given on February 23, 1983 at the Jet Propulsion Laboratory in Pasadena, California to reconsider his 1959 talk in light of subsequent developments. The JPL speech was titled “Infinitesimal Machinery”, edited from a video by Stephen D. Senturia, and published ten years after it was given in the Journal of Microelectromechanical Systems Volume 2:1 March 1993. I found a copy of the article here.
—James Lewis, PhD