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Carbyne: the strongest, stiffest carbon chain

Posted by Stephanie C on October 11th, 2013

Carbyne ropes and rods. Credit: Vasilii Artyukhov/Rice University

Carbyne – a straight line of carbon atoms linked by double bonds or by alternating single and triple bonds — is the next stiff, carbon-based structure with unusual and desirable properties. It has been observed under limited natural and experimental conditions, is expected to be difficult to synthesize and store, and now has been theoretically characterized.

Researchers at Rice University recently published DFT characterizations of carbyne ropes and rods, and overviews of the findings and prospects are reprinted at Phys.org:

According to the portrait drawn from calculations by Yakobson and his group:

  • Carbyne’s tensile strength – the ability to withstand stretching – surpasses “that of any other known material” and is double that of graphene. (Scientists had already calculated it would take an elephant on a pencil to break through a sheet of graphene.)
  • It has twice the tensile stiffness of graphene and carbon nanotubes and nearly three times that of diamond.
  • Stretching carbyne as little as 10 percent alters its electronic band gap significantly.
  • If outfitted with molecular handles at the ends, it can also be twisted to alter its band gap. With a 90-degree end-to-end rotation, it becomes a magnetic semiconductor.
  • Carbyne chains can take on side molecules that may make the chains suitable for energy storage.
  • The material is stable at room temperature, largely resisting crosslinks with nearby chains.

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Nanotubes aren't stiff if they aren't straight

Posted by Stephanie C on October 3rd, 2013

"This montage includes images of carbon nanotube forests. New research explains why the CNT forests have less stiffness than expected. (Credit: Images courtesy of Justin Chow)"

Materials scientists have pursued the question of why vertically aligned carbon nanotube forests show much lower modulus values than expected. Now researchers from Georgia Tech have found that the nanotubes they fabricate contain kinks that dramatically diminish modulus value. In other words, the nanotubes are not straight; therefore, they are not stiff.

The government-funded research was recently published in Carbon, and the first sentence of the Abstract reads, “Waviness is invariably present in vertically-aligned Carbon Nanotubes (CNTs) regardless of how controlled the fabrication process is.”  As described in the journal article, and in a reprinted news article at ScienceDaily.com, the inescapably wavy nanotube forests afford possible heat management applications:

Carbon nanotubes provide many attractive properties, including high electrical and thermal conductivity, and high strength. Individual carbon nanotubes have a modulus ranging from 100 gigapascals to 1.5 terapascals. Arrays of vertically-aligned carbon nanotubes with a low density would be expected to a have an effective modulus of at least five to 150 gigapascals, Sitaraman said, but scientists have typically measured values that are four orders or magnitude less — between one and 10 megapascals.

To look for potential explanations, the researchers examined the carbon nanotubes using scanning electron microscopes located in Georgia Tech’s Institute for Electronics and Nanotechnology facilities. At magnification of 10,000 times, they saw the waviness in sections of the nanotubes.

“We found very tiny kinks in the carbon nanotubes,” said Sitaraman. “Although they appeared to be perfectly straight, there was waviness in them. The more waviness we saw, the lower their stiffness was.”
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Foresight Invitational Workshop: Nanotechnology for Developing Countries

Posted by Jim Lewis on September 30th, 2013

Nanotechnology for Developing Countries: the 2014 Foresight Invitational Workshop
February 7-9, 2014
Crowne Plaza Cabana Hotel, Palo Alto
Silicon Valley, California, USA

TO REQUEST AN INVITATION, EMAIL TO developing@foresight.org
DEADLINE OCTOBER 16

Nanoscale technologies have the potential to bring immense benefits to developing countries, in areas ranging from water and energy to health and environmental restoration. But the challenges are correspondingly large; required steps include:

• Identify nanotechnologies that can make a difference near-term
• Design and build products that will actually be useful
• Bring these to market at affordable price points
• Balance intellectual property interests
• Speed enterprises past the “Valley of Death”
• Solve support and maintenance issues
• Avoid solving problems that local economies are already handling well

It’s time to gather the major players to tackle these in an invitational workshop, held in the center of high-tech entrepreneurship: Silicon Valley. Researchers, product developers, IP specialists, funders, and those with experience tackling real-world problems in developing countries will come together to find ways to “fast track” nanotechnologies to make a positive difference.

Once candidate research advances, technologies, or products are identified, vigorous efforts will be made to connect innovators with funders having experience in nano-based products. Additionally, it is understood that developing country markets have special requirements and new companies will need targeted advice to succeed.

This meeting is being held in parallel with Foresight’s “Integration Conference” to enable us to take advantage of the technical expertise gathered there.

The goal is to keep this initial workshop relatively small to enable intense interaction. Those requesting an invitation should send an email to developing@foresight.org by October 16 with name and contact info.

We look forward to hearing from you soon!

John Allen
President, i-Nano LLC
Co-Chairman, Nanotechnology for Developing Countries

Paul Melnyk
Co-Chairman, Nanotechnology for Developing Countries
President, Foresight Institute

Christine Peterson
Co-Founder, Foresight Institute

Computational design of protein-small molecule interactions

Posted by Jim Lewis on September 26th, 2013

Digoxigenin, from the Wikimedia Commons

The modular molecular composite nanosystems (MMCNs) approach to developing atomically precise manufacturing, as described in the Technology Roadmap for Productive Nanosystems envisions million-atom-scale DNA frameworks with dense arrays of atomically precise binding sites for various functional components, with specially engineered proteins binding specific functional components to specific sites on the DNA frameworks. We have frequently highlighted here improvements in DNA nanotechnology to precisely position individual components, but until now a general purpose method to engineer proteins to bind specific small molecules has been elusive. A hat tip to Phys.org for reprinting this University of Washington press release describing recent work from the laboratory of David Baker, who shared the 2004 Foresight Feynman Prize for Theoretical Nanotechnology. From “Pico-world dragnets: Computer-designed proteins recognize and bind small molecules“:

Computer-designed proteins that can recognize and interact with small biological molecules are now a reality. Scientists have succeeded in creating a protein molecule that can be programmed to unite with three different steroids.

The achievement could have far wider ranging applications in medicine and other fields, according to the Protein Design Institute at the University of Washington.

“This is major step toward building proteins for use as biosensors or molecular sponges, or in synthetic biology — giving organisms new tools to perform a task,” said one of the lead researchers, Christine E. Tinberg, a postdoctoral fellow in biochemistry at the UW.

The approach they took appears in the Sept. 4 online issue of Nature. Tinberg and Sagar D. Khare headed the study under the direction of David Baker, UW professor of biochemistry and Howard Hughes Medical Institute investigator. Khare is currently an assistant professor at Rutgers University.

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Building a hub for nanotech advancement

Posted by Stephanie C on September 17th, 2013

"An artist's rendering of what a possible computer chip manufacturing site might look like in Marcy." credit: UticaOD.com

Nanotechnology draws from physics, chemistry, engineering, computation, etc., and this multi-disciplinary nature has served as a major speed bump in achievement of envisioned nanotech goals. There has been substantial concern that the U.S. is lagging behind other countries in nanotech R&D. Now researchers, companies, and politicians are coming together to create a much-needed physical hub for promoting and funding multi-disciplinary progress toward advanced technologies. The location: New York. The focus: chips.

Recently described at UticaOD.com in an article entitled New York State: Building a Nano Empire :

For at least a decade, major nanotechnology players have been attracted by the intellectual center SUNY’s College of Nanoscale Science and Engineering has created in Albany. And now, Gov. Andrew Cuomo’s 2011 announcement of a $4.8 billion partnership with private companies — including Intel, Samsung, TSMC, IBM and Global Foundries — to develop the next generation of computer chip manufacturing is gaining traction.

“The biggest companies are behind it,” Singer said. “They really believe it will give them the competitive edge that will make it unbeatable, and they have the wherewithal to make it happen.”

And biotech is getting in on the action. Earlier this summer, SUNY CNSE announced a biotech partnership aimed at “nanotech-enabled cancer research”:

Albany, NY and Pittsfield, MA – Underscoring the strategic blueprint of Governor Andrew M. Cuomo in fueling New York’s growing reputation as a hub for nanotechnology-enabled innovation, SUNY’s College of Nanoscale Science and Engineering (CNSE) and Pittsfield, Massachusetts-based Nuclea Biotechnologies, Inc. (Nuclea) today announced the launch of a $1 million research partnership to enable the development and commercialization of a high-throughput nanochip to accelerate the diagnosis and treatment of breast, colon, prostate and other cancers.

“Driven by the vision and leadership of Governor Andrew Cuomo, New York is recognized as the leading global hub for nanotechnology education and innovation, including an expanding footprint in critical 21st century fields such as life sciences,” said Dr. Alain E. Kaloyeros, CNSE Senior Vice President and CEO. “This public-private partnership with Nuclea Biotechnologies expands CNSE’s cutting-edge research in the nanobioscience arena, and further illustrates its role in accelerating advanced technologies and attracting high-tech companies to New York.”

“This research agreement is a perfect marriage of biotechnology and nanotechnology,” said Patrick Muraca, President and CEO of Nuclea. “CNSE’s global reputation as the world leader in nanoscale engineering will lend critical expertise in developing the miniature version of our protein chip, which is an important element for us as we work toward commercialization. We’ve assembled a great team and look forward to this collaboration with CNSE.”

Chips, which are for the most part continuing on cycles of iterative miniaturization and are still on the millimeter (bulk) scale despite the use of the term ‘nanotechnology’, remain indisputably relevant to near-term advanced technologies. Do these NY-based efforts help restore the standing of the US in global nanotech R&D?
-Posted by Stephanie C

Circuits of graphitic nanoribbons grown from aligned DNA templates

Posted by Jim Lewis on September 17th, 2013

Representation of DNA Assembly of Graphene Transistor. To the right is a honeycomb of graphene atoms. To the left is a double strand of DNA. The white spheres represent copper ions integral to the chemical assembly process. The fire represents the heat that is an essential ingredient in the technique. (Credit: Anatoliy Sokolov of the Bao Group)

The “molecular threading” technique disclosed by Aeon Biowares that was the topic of our previous post was presented as a great improvement over earlier bulk methods for stretching DNA, such as “molecular combing”, and the researchers speculated that it might also be useful for fabricating arrays of nanowires. As a starting point to thinking about what molecular threading might make possible, it might be useful to consider what current methods like molecular combing can accomplish. A hat tip to Josh Hall for pointing to this example of what can already be done in terms of using DNA strands to assemble functional arrays “Stanford scientists use DNA to assemble a transistor from graphene“.

DNA is the blueprint for life. Could it also become the template for making a new generation of computer chips based not on silicon, but on an experimental material known as graphene?

That’s the theory behind a process that Stanford chemical engineering professor Zhenan Bao reveals in Nature Communications [abstract]. …

Graphene has the physical and electrical properties to become a next-generation semiconductor material – if researchers can figure out how to mass-produce it.

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Precise mechanical manipulation of individual long DNA molecules

Posted by Jim Lewis on September 12th, 2013

Electron micrographs demonstrating Aeon Biowares' patented Molecular Threading technology. Left: DNA molecules threaded onto an electron microscopy grid with an amorphous carbon surface; right: DNA molecules threaded onto a graphene coated grid (credit: Aeon Biowares and KurzweilAI)

Those Nanodot readers who heard very interesting research results from Halcyon Molecular discussed at the Foresight Institute 25th Anniversary Reunion Conference (see here and here and these videos) will be interested in this update on the “Molecular Threading” portion of that technology found on KurzweilAI.net:

Teams of researchers from Harvard University and Halcyon Molecular, Inc. have disclosed “Molecular Threading,” the first technology to allow single DNA molecules to be drawn from solution and precisely manipulated, allowing for faster, cheaper, more accurate DNA sequencing.

This novel technology pulls single high-molecular weight DNA molecules from solution into air and then places them onto any surface. Halcyon Molecular developed the processes and the intellectual property is now owned by Palo Alto-based biotechnology firm Aeon Biowares.

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THE SINGULARITY film premiere at The Castro Theatre 09.16.13

Posted by Jim Lewis on September 6th, 2013

THE SINGULARITY, a documentary directed by Doug Wolens

Just off special screenings at NASA and Yerba Buena Center for the Arts, Doug Wolens’s documentary THE SINGULARITY will premiere on the giant silver screen at San Francisco’s historic Castro Theatre. An awesome venue for the premiere of the most comprehensive and insightful documentary film about the singularity to date.

Synopsis:
Within the coming decades we will be able to create computers with greater than human intelligence, bio-engineer our species and re-design matter through nanotechnology. How will these technologies change what it means to be human? Director Doug Wolens speaks with leading futurists, computer scientists, artificial intelligence experts, and philosophers who turn over the question like a Rubik’s Cube. Ultimately, if we become more machine-like, and machines more like us, will we sacrifice our humanity to gain something greater? Or will we engineer our own demise?

Q&A with filmmaker Doug Wolens to follow the screening.
Show times: 4pm and 8pm — 75 minutes

THE SINGULARITY will be shown together with Doug’s earlier films BUTTERFLY (2000) and WEED (1996)

Tickets now available through Brown Paper
Tickets: http://thesingularity.brownpapertickets.com/ One ticket is good for all 3 films!

For more information go to: http://www.thesingularityfilm.com
Official event listing: http://www.thesingularityfilm.com/castro
The Castro Theatre listing: http://www.castrotheatre.com/s-events.html#sep16
Facebook page: http://www.facebook.com/thesingularityfilm

Among those featured in this documentary well-known in the Foresight community are Ray Kurzweil, Christine Peterson, Ben Goertzel, Eliezer Yudkowsky, Aubrey De Grey, Ralph Merkle, Brad Templeton, and Chris Phoenix.

Conference video: Assembly and Manipulation of Molecules at the Atomic Scale

Posted by Jim Lewis on August 29th, 2013

Credit: Leonhard Grill

A select set of videos from the 2013 Foresight Technical Conference: Illuminating Atomic Precision, held January 11-13, 2013 in Palo Alto, have been made available on vimeo. Videos have been posted of those presentations for which the speakers have consented. Other presentations contained confidential information and will not be posted.

The second speaker at the Atomic Scale Devices session, the winner of the 2011 Feynman Prize for Experimental work, Leonhard Grill, presented his prize-winning work “Assembly and Manipulation of Molecules at the Atomic Scale: ‘Stiching and Switching’biography and abstract, http://vimeo.com/62028034 – video length 27:43. He addressed two topics: (1) the manipulation of single molecules on surfaces to gain fundamental understanding of their function by triggering their function, which could be mechanical, optical, or electronic, directly on the surface; (2) how to build molecular architectures on a surface in a very controlled way with pre-defined topography using different kinds of interactions on the surface. The work he presented was done using a scanning tunneling microscope (STM) under high vacuum to keep things clean, and at the very low temperature of 5 K to minimize molecular movement. The first example illustrated a mechanical function, a rolling motion of a molecule on a surface. Previous demonstrations of lateral movement of a single molecule as a result of STM manipulation relied on getting the molecule to hop from one point on the surface to another. A molecular wheel made from a triptycene dimer was manipulated with the STM, causing the molecule to move across the surface. However, monitoring electric current through the tip in real time as the molecule moved, yielding a saw-tooth pattern, showed the motion to be hopping rather than rolling. So they changed the substrate from copper (100), which is very flat, to copper (110), which consists of atomic lines of copper atoms. Because of these corrugations on the surface, the molecular wheel was able to roll over the surface.

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Next Foresight Conference on Nanotechnology in February 2014

Posted by Jim Lewis on August 28th, 2013

17th Foresight Conference: ”The Integration Conference

February 7-9, 2014
Crowne Plaza Cabana Hotel, Palo Alto
Silicon Valley, California, USA

Over 20 speakers will present their research and vision within the realm of groundbreaking atomic- and molecular-scale science and engineering with application across a wide range of advanced technologies, including materials, electronics, energy conversion, biotechnology and more. Events will include presentation of the annual Foresight Institute Feynman Prize, one of the most prestigious awards in nanoscale science and technology.

Integration: The development and proliferation of nanotechnology through its applications in diverse fields are dependent upon the successful integration of nano-engineered devices and materials (“nanosystems”) into more complex micro- and macro-systems. Thus, this year the concept of Integration is highlighted, for the successful integration of nanosystems can impact the rate of development, application, and ultimately benefit.

Analysis, simulation, synthesis, and mass production are challenges for nanotechnology integration in such diverse applications as biotechnology, medicine, microelectronics, defense, energy conversion and storage, coatings, textiles, pharmaceuticals, cosmetics, and even food and food security.

Conference Co-Chairs
Robert P. Meagley, CEO/CTO, ONE Nanotechnologies
William A. Goddard III, Director, Materials and Process Simulation Center, Caltech

Planned Sessions include:

  • Analysis and Simulation
  • Bionano Systems
  • Commercially Implemented Nanotechnology
  • Electronic and Optical Nanosystems
  • Self-Organizing & Adaptive Systems

Look for further details on the conference, speakers, and events in the coming weeks and months. Registration will open in mid-September.

Warped graphene molecules offer new building blocks for nanotechnology

Posted by Jim Lewis on August 26th, 2013

Credit: Boston College

There has been a great deal of interest over the past few years in the properties of graphene, one-atom-thick sheets of trigonal carbon atoms. For the most part, the graphene sheets that have been studied are large on the molecular scale, irregular in their extent, and flat. Chemists have now synthesized distinct molecular species of grossly distorted graphene, somewhat more than one nanometer across, comprising 80 carbon atoms and 30 hydrogen atoms. A hat tip to KurzweilAI for highlighting this Boston College news release “Chemists at Boston College, Nagoya University Synthesize First Example of New Carbon Form“:

Chemists at Boston College and Nagoya University have together synthesized the first example of a new form of carbon, the team reports in the most recent edition of the journal Nature Chemistry [abstract]. This new material consists of many identical piece of grossly warped graphene, each containing exactly 80 carbon atoms joined together in a network of 26 rings, with 30 hydrogen atoms decorating the rim. These individual molecules, because they measure somewhat more than a nanometer across, are referred to generically as “nanocarbons,” or more specifically in this case as “grossly warped nanographenes.” …

Graphene sheets prefer planar, 2-dimensional geometries as a consequence of the hexagonal, chicken wire-like, arrangements of trigonal carbon atoms comprising their two-dimensional networks. The new form of carbon just reported in Nature Chemistry, however, is wildly distorted from planarity as a consequence of the presence of five 7-membered rings and one 5-membered ring embedded in the hexagonal lattice of carbon atoms.

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Illuminating Atomic Precision Conference videos

Posted by Jim Lewis on August 23rd, 2013

Credit: John Randall, Zyvex Labs

A select set of videos from the 2013 Foresight Technical Conference: Illuminating Atomic Precision, held January 11-13, 2013 in Palo Alto, have been made available on vimeo. Videos have been posted of those presentations for which the speakers have consented. Other presentations contained confidential information and will not be posted.

In his introductory comments, Conference Co-Chair Larry S. Millstein stressed that the five sessions of the Conference were designed to bring together five research communities that have until now not had close contacts, in the hope that their interactions would accelerate progress. Similarly, the Conference’s restrictive media policy was designed to accelerate progress by encouraging speakers to share with Conference participants unpublished research by assuring them that sharing these results would not interfere with their future publication. http://vimeo.com/62028032 video length 3:49.

In his introductory comments, Conference Co-Chair J. Fraser Stoddart observed that for a quarter of a century nanotechnology has been bringing together physicists, chemists, biologists, material scientists, engineers, and computational people under the banner of “nano”. He referred to his own recent work as an example of the self-assembly of simple structures to produce emergent complex behavior, and expressed the desire that this assembly bringing together widely divergent scientific, technological and engineering perspectives would inspire new knowledge. http://vimeo.com/62028033 video length 7:36.

John Randall introduced the session on Atomic Scale Devices and discussed work at Zyvex Labs on “Atomically Precise Manufacturing”. http://vimeo.com/62119582 – video length 28:52. Randall made clear at the onset that by atomic precision, he is not talking about a precision of plus or minus one atom, but rather about absolute precision in manufacturing—no size variation. You put the atoms where you want them so everything is the same and matter can be dealt with as though it is digital. There is no accumulation of error and eventually materials can be defect free. He proposed that once absolute precision is achieved that the volume of material that could be produced cost effectively would increase exponentially, making an “educated guess” that using techniques that they are working on today, they will reach one cubic micrometer before 2020. He described the Atomically Precise Manufacturing Consortium and their commitment to bring atom-by-atom manufacturing tools to market. Their approach uses an STM to precisely remove individual hydrogen atoms from the surface of a passivated crystal, followed by atomic layer epitaxy to build three-dimensional structures with top-down control, “putting every atom where we want it.” Randall emphasized that the STM tip is not used to drag Si or H atoms around and into place; it is only used to image and for electron-stimulated desorption of passivated hydrogen atoms. Examples of products that might start this proposed exponential manufacturing trend include a nanometrology standard consisting of a wall of silicon a know number of atoms wide and a known number of atoms tall, NEMS resonators that operate in the terahertz regime, master templates for nanoimprinting, devices for quantum computing, and nanopores for ultra-high-speed DNA sequencing.
—James Lewis, PhD

Nanocrystal-in-glass composite controlled by voltage

Posted by Jim Lewis on August 23rd, 2013

Nanocrystals of indium tin oxide (shown here in blue) embedded in a glassy matrix of niobium oxide (green) form a composite material that can switch between NIR-transmitting and NIR-blocking states with a small jolt of electricity. A synergistic interaction in the region where glassy matrix meets nanocrystal increases the potency of the electrochromic effect. (Credit: Lawrence Berkeley National Laboratory)

The most fundamental dimension in the transition from current nanotechnology, which is mostly materials science and simple devices, to the advanced nanotechnology of productive nanosystems and atomically precise manufacturing will be the dimension of greater control of the structure of matter leading to atomic precision. But another important dimension is imbuing matter with intelligence. Ultimately that intelligence will be embodied in control by atomically precise digital computers, but steps toward that goal are resulting from nanocomposites that combine a sensing and an effecting function. A hat tip to ScienceDaily for reprinting this Lawrence Berkeley National Laboratory news release written by Alison Hatt “Raising the IQ of Smart Windows“:

Researchers at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have designed a new material to make smart windows even smarter. The material is a thin coating of nanocrystals embedded in glass that can dynamically modify sunlight as it passes through a window. Unlike existing technologies, the coating provides selective control over visible light and heat-producing near-infrared (NIR) light, so windows can maximize both energy savings and occupant comfort in a wide range of climates.

“In the US, we spend about a quarter of our total energy on lighting, heating and cooling our buildings,” says Delia Milliron, a chemist at Berkeley Lab’s Molecular Foundry who led this research. “When used as a window coating, our new material can have a major impact on building energy efficiency.”

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Improved molecular targeting via cellular automata

Posted by Stephanie C on August 12th, 2013

In simplest terms, cellular automata can be thought of as groups of ‘cells’ in which the state of an individual cell will flip depending on the states of its neighbors. A ‘cell’ can be a pixel, a molecule, etc. The mathematical rules associated with cellular automation are complex and have been applied to fields as diverse as computation and cryptography to patterns of pigment in seashells. Now researchers at Hospital for Special Surgery (HSS) in New York City and Columbia University have used an analogous system of molecular cascades to select for particular biological surfaces, taking new steps towards medical therapeutics that use multiple recognition events to improve molecular targeting. The work is published in Nature Nanotechnology, and the press release was reprinted at MedicalXpress.com:

Many drugs such as agents for cancer or autoimmune diseases have nasty side effects because while they kill disease-causing cells, they also affect healthy cells. Now a new study has demonstrated a technique for developing more targeted drugs, by using molecular “robots” to hone in on more specific populations of cells.

Drugs can target disease-causing cells by binding to a receptor, but in some cases, disease-causing cells do not have unique receptors and therefore drugs also bind to healthy cells and cause “off-target” side effects.

Rituximab (Rituxan, Genentech), for example, is used to treat rheumatoid arthritis, non-Hodgkin’s lymphoma and chronic lymphocytic leukemia by docking on CD20 receptors of aberrant cells that are causing the diseases. However, certain immune cells also have CD20 receptors and thus the drug can interfere with a person’s ability to mount a fight against infection.

In the new study, scientists have designed molecular robots that can identify multiple receptors on cell surfaces, thereby effectively labeling more specific subpopulations of cells. The molecular robots, called molecular automata, are composed of a mixture of antibodies and short strands of DNA.
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Molecular sponges give atomic structures of trace substances

Posted by Jim Lewis on August 8th, 2013

Ever since Richard Feynman lamented in his 1959 talk “There’s Plenty of Room at the Bottom” that the electron microscope failed by two orders of magnitude to image individual atoms, a general method of imaging nanostructures to atomic resolution has been an integral part of the Feynman vision of what was later called nanotechnology: the construction of atomically-precise products through the use of molecular machine systems. Imaging proteins to atomic resolution is a necessary subgoal of Eric Drexler’s 1981 proposal that protein design could provide an approach to develop general capabilities for molecular engineering and molecular manipulation. X-ray crystallography has been the gold standard for obtaining atomically precise structures for proteins and other nanostructures, but this method requires substantial amounts of crystalline material, and not all proteins, and certainly not all nanostructures, are available in crystalline form. Nadrian C. Seeman, the pioneer of DNA nanotechnology, one of the most promising roads to atomically precise manufacturing (APM), has said that “The first goal is to use our branched DNA system to scaffold the organization of biological macromolecules into crystalline arrays, thus overcoming the crystallization problem of biological crystallography. This will enable the 3D structural characterization of potential drug targets, leading to rational drug design.” The electron microscope has been greatly improved since Feynman’s time and some success has been obtained in using DNA nanotechnology to organize proteins for structure determination. However, another option is now available. A blog by Derek Lowe discusses a paper from a group at the University of Tokyo published in Nature earlier this year [abstract] that uses porous metal-organic frameworks (MOFs) as ‘chemical sponges’ as ‘hosts’ to soak up very small quantities of small to mid-sized molecules as ‘guests’ so that X-ray crystallography of the host-guest complex provides the structure of the guest molecule. From “X-Ray Structures Of Everything. Without Crystals. Holy Cow“:.

… This latest paper demonstrates that if you soak a solution of some small molecule in a bit of crystalline porous “molecular sponge”, you can get the x-ray structure of the whole complex [emphasis in the original], small molecules and all. If you’re not a chemist you might not feel the full effect of that statement, but so far, every chemist I’ve tried it out on has reacted with raised eyebrows, disbelief, and sometimes a four-letter exclamation for good measure. …

The crystalline stuff in question turns out to be two complexes with tris(4-pyridyl)triazine and either cobalt isothiocyanate or zinc iodide. These form large cage-like structures in the solid state, with rather different forms, but each of them seems to be able to pick up small molecules and hold them in a repeating, defined orientation. Shown is a lattice of santonin molecules in the molecular cage, to give you the idea.

Just as impressive is the scale that this technique works on. They demonstrate that by solving the structure of a marine natural product, miyakosyne A, using a 5-microgram sample. I might add that its structure certainly does not look like something that is likely to crystallize easily on its own, and indeed, no crystal is known. By measuring the amount of absorbed material in other examples and extrapolating down to their X-ray sample size, the authors estimate that they can get a structure on as little as 80 nanograms of actual compound. …

With the help of Google Scholar, I found full text PDFs of the original Nature article here and here. Nature News also comments on the research article.

Although the pores used in this paper are not large enough to accept protein molecules as guests, Lowe points to a recent paper in Science on a series of MOFs with pore apertures ranging from 1.4 to 9.8 nm—large enough to accept proteins or other interesting nanostructures or molecular building blocks. As often the case with advances in the molecular sciences, the motivation for the research appears to be basic science or biotechnology. Nevertheless, the ability to obtain atomically precise structural information for minute quantities of difficult or impossible to crystallize molecules and nanostructures could greatly facilitate developments leading to APM. Last year we cited the potential of MOFs as “building blocks in the molecular machine path to molecular manufacturing”. At the very least, they appear likely to indirectly accelerate progress by providing structural information for a wide variety of useful nanostructures. Whether or not they could eventually supplement DNA scaffolds as ways to organize a complex set of components of molecular machine systems could depend upon whether methods can be found to address individual pores within the MOFs.
—James Lewis, PhD

Nanoscale box aids single-molecule optical detection

Posted by Stephanie C on July 29th, 2013

Credit: Jerome Wenger, Fresnel Institute

Good old fashioned boxes are here to stay, even in the context of nanoscale devices. Across a broad range of technologies and size regimes, boxes serve as containers for components, barriers against contaminants and/or radiation, and, as in the case of cell membranes, can be permeable to allow selected interactions between the interior and exterior. In a recent advance in optical detection, a nanoscale box-like housing was used to create an aperture that greatly enhanced the ability of antenna structures to detect single molecules at physiological concentrations. As reprinted at Phys.org:

Researchers at the Fresnel Institute in Marseille and ICFO-the Institute for Photonic Sciences in Barcelona report in Nature Nanotechnology the design and fabrication of the smallest optical device, capable of detecting and sensing individual biomolecules at concentrations that are similar to those found in the cellular context. The device called “antenna-in-a-box” consists of a tiny dimer antenna made out of two gold semi-spheres, separated from each other by a gap as small as 15nm. Light sent to this antenna is enormously amplified in the gap region where the actual detection of the biomolecule of interest occurs. Because amplification of the light is confined to the dimensions of the gap, only molecules present in this tiny region are detected. A second trick that the researchers used to make this device work was to embed the dimer antennas inside boxes also of nanometric dimensions. “The box screens out the unwanted “noise” of millions of other surrounding molecules, reducing the background and improving as a whole the detection of individual biomolecules.”, explains Jerome Wenger from Fresnel Institute. When tested under different sample concentrations, this novel antenna-in-box device allowed for 1100-fold fluorescence brightness enhancement together with detection volumes down to 58 zeptoliters (1 zL = 10-21L), i.e., the smallest observation volume in the world.

IFCO researcher and coauthor Maria Garcia-Parajo notes that the platform could also serve as a very bright, nanoscale light source.

Because the optical benefits come from the inner dimensions of the box (i.e. the aperture), the outer dimensions can vary, opening possibilities for customized sizes and shapes, as well as possible detection arrays.

-Posted by Stephanie C

DNA nanotechnology positions components to optimize single-molecule fluorescence

Posted by Jim Lewis on July 19th, 2013

Credit: Technische Universität Braunschweig

Recently we noted an extensive review of the use of DNA scaffolds to orient molecules for molecular studies, as this capability could lead to organizing functional components for atomically precise manufacturing (APM). An excellent example of this capability of DNA scaffolds, published last year in Science [abstract] has been made available for open access: “Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas” (pdf). A press release from the Technische Universität Braunschweig (in German, translated by http://translate.google.com/):

Light on the nanoscale focus: Researchers present tiny lenses from nanoparticles and DNA

Conventional lenses may focus light only to a volume of about one femtoliters (10-15 liters), which corresponds to a cubic micron. This limitation is a result of diffraction, which is inherent in all conventional lenses, and prevents many applications in the field of nanotechnology. The research group led by Prof. Philip Tinnefeld, Institute of Physical and Theoretical Chemistry, Technical University of Braunschweig, now has developed a method, are produced in parallel with the millions of so-called nano-lenses of metallic nanoparticles and DNA. These nano-lenses allow us to investigate even single molecules up to one hundred times more precise.

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Nanotechnology, optical lithography, and petabyte data storage media

Posted by Jim Lewis on July 16th, 2013

Credit: Nature Communications

Foresight’s interest is in advancing nanotechnology to the point of developing high-throughput atomically precise manufacturing, but it is worth noting occasionally the potential applications of nanoscale technologies that achieve less than atomic precision. These two examples point toward several-orders-of-magnitude improvement in data storage technology. A hat tip to Phys.org for reprinting this article written by researchers at Australia’s Swinburne University of Technology “More data storage? Here’s how to fit 1,000 terabytes on a DVD” by M Gu, Y Cao, and Z Gan:

In Nature Communications [open access article] today, we, along with Richard Evans from CSIRO, show how we developed a new technique to enable the data capacity of a single DVD to increase from 4.7 gigabytes up to one petabyte (1,000 terabytes). This is equivalent of 10.6 years of compressed high-definition video or 50,000 full high-definition movies. …

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Recent highlights and discussions of APM concepts

Posted by Stephanie C on July 12th, 2013

The release of Eric Drexler’s new book Radical Abundance has sparked a resurgence of discussion about nanotechnology and the global future.

Last month, Nanowerk reprinted Drexler’s blog write-up entitled The Physical Basis of High-Throughput Atomically Precise Manufacturing, a reader-friendly overview highlighting parallels between molecular manufacturing and conventional chemistry and manufacturing.

Over the last couple months, Robin Hanson, associate professor of economics at George Mason and a well-known name to many in the broader Foresight community, has been posting his critiques of various aspects of Radical Abundance, leading to some response and conversation that Drexler has featured on his blog site metamodern.com.
-Posted by Stephanie C

Reviews of DNA nanotechnology-atomically precise microscale objects

Posted by Jim Lewis on July 9th, 2013

Recently we noted the use of DNA nanotechnology to build a solar energy antenna as another example of progress in the modular molecular composite nanosystems (MMCNs) approach to developing atomically precise manufacturing. Structural DNA nanotechnology is currently the only way we have to manufacture large (million-atom, 100-nm-scale) arbitrarily complex atomically precise objects, so it plays a central role in the MMCN approach. Two very useful recent overviews of structural DNA nanotechnology have been made freely available on the web.

DNA nanotechnology: a curiosity or a promising technology? by Thomas Tørring and Kurt V. Gothelf, Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark, nicely covers the most important results of this extensive and rapidly progressing field in a very brief and accessible article.

A more detailed and technical review emphasizes the use of DNA scaffolds to orient molecules for single-molecule studies: “Single-Molecule Analysis Using DNA Origami” by Arivazhagan Rajendran, Masayuki Endo, and Hiroshi Sugiyama of Kyoto University and Japan Science and Technology Corporation [abstract] has been made available by the authors as a full-text PDF here. This extensive review covers single-molecule biomolecular recognition, conformational analysis, chemical reactions, enzymatic reactions, single molecule fluorescence studies, and cargo transporters and DNA robots. As documented by this review, the volume of work in this field has expanded to the point that we can cover only a small part of it here, so this review is a good place to get some appreciation of what is happening. The part that struck me as most relevant to atomically precise manufacturing was the example of “click chemistry” on a DNA origami surface (section 4.2, Fig. 7) since this might represent a path toward positional control of chemical synthesis.
—James Lewis, PhD