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Nanodot: the original nanotechnology weblog

What kind of nanomachines will advanced nanotechnology use?

Posted by Jim Lewis on August 31st, 2014

Dr. Richard Jones

Dr. Richard Jones

Long-term readers of Nanodot will be familiar with the work of Richard Jones, a UK physicist and author of Soft Machines: Nanotechnology and Life, reviewed in Foresight Update Number 55 (2005) page 10. Basically Jones follows Eric Drexler’s lead in Engines of Creation in arguing that the molecular machinery found in nature provides an existence proof of an advanced nanotechnology of enormous capabilities. However, he cites the very different physics governing biomolecular machinery operating in an aqueous environment on the one hand, and macroscopic machine tools of steel and other hard metals, on the other hand. He then argues that rigid diamondoid structures doing atomically precise mechanochemistry, as later presented by Drexler in Nanosystems, although at least theoretically feasible, do not form a practical path to advanced nanotechnology. This stance occasioned several very useful and informative debates on the relative strengths and weaknesses of different approaches to advanced nanotechnology, both on his Soft Machines blog and here on Nanodot (for example “Debate with ‘Soft Machines’ continues“, “Which way(s) to advanced nanotechnology?“, “Recent commentary“). An illuminating interview of Richard Jones over at h+ Magazine not only presents Jones’s current views, but spotlights the lack of substantial effort since 2008 in trying to resolve these issues “Going Soft on Nanotech“:

… RJ: I’m both a fan of Eric Drexler and a critic — though perhaps it would be most correct to say I’m a critic of many of his fans. Like many people, I was inspired by the vision of Engines of Creation, in outlining what would be possible if we could make functional machines and devices at the nanoscale. If Engines set out the vision in general terms, Nanosystems was a very thorough attempt to lay out one possible concrete realisation of that vision. Looking back at it twenty years on, two things strike me about it. Read the rest of this entry »

Seeing and touching a single synthetic molecular machine

Posted by Jim Lewis on August 24th, 2014

a single synthetic molecular machine

Schematic illustration for single-molecule motion capturing and manipulation of 1-nm sized synthetic molecular machine by optical microscopy using a bead probe. A large bead attached to the rotor part of the synthetic molecular bearing (double decker porphyrin) traces its motion. credit Tomohiro Ikeda

Molecular machines are a central component of efforts to develop atomically precise manufacturing. Optical microscopy and optical trap manipulation of single molecules, made possible by attachment of micrometer-scale beads, have facilitated greater understanding of the workings of biomolecular machines. For example, a 2008 paper published in Cell (“Intramolecular Strain Coordinates Kinesin Stepping Behavior along Microtubules“) revealed how the kinesin molecular motor molecule coordinates its two motor domains to achieve one-way stepping along microtubule proteins. When additional peptides were inserted into the mechanical “neck linker” elements that span the two motor domains, tension was reduced, and as a result, the motor’s velocity was reduced. Motor velocity returned to near normal when external tension was applied via an optical trap operating on a 920 nm diameter bead attached via an antibody to the molecular motor. Nanotechnologists can use similar techniques to study a wide variety of biomolecular machines, including naturally occurring molecular motors with typical length scales of 10 nm. Until now, however, it has not been possible to use similar approaches to study smaller synthetic molecular machines, with typical length scales on the order of one nm. A hat tip to Asian Scientist for reprinting this press release from the University of Tokyo “Seeing and touching a single 1-nm-sized synthetic molecular machine“:

Single-molecule imaging and manipulation with optical microscopy using a bead probe as a marker (single–molecule “motion capturing”) unveils fundamental properties of biomolecular machines such as direction of motion, step size and force the molecule exerts, which cannot be resolved by whole-molecule measurements. As a result, it has become an essential method for research of biomolecular machines. In addition, single-molecule motion capturing could also become a powerful tool to develop “synthetic” molecular machines. However, it is difficult to apply the conventional method to individual molecules because the size of a typical synthetic molecular machine is only 1 nm, about one-tenth the size of a biomolecular machine. This miniaturization of the target molecule causes significant problems such as low efficiency of the bead probe immobilization reaction and undesired interaction between the surfaces of the bead and substrate.

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Recent cases of 'accessible' high-tech: Open source chips & Origami robots

Posted by Stephanie C on August 22nd, 2014

From MegaOm.com: "An origami robot transforming from flat to 3D. Photo courtesy of Seth Kroll, Wyss Institute."

Nanotech promises more commonplace access to advanced technology as material and fabrication costs fall and traditional barriers to innovation are removed. Examples are already being seen globally: more access to laptops and cell phones in developing countries, desktop 3D printers, a surge in establishment of shared-use research facilities, etc.

A couple recent cases getting attention on GigaOm.com include the latest release of RISC-based open source chip from UC Berkeley, and self-folding ‘origami’ robots developed at the Wyss Institute and published in Science.

About the chips:


Fed up with the limitations of current computer chips and their related intellectual property, a team of researchers at the University of California, Berkeley, is pushing an open source alternative. The RISC-V instruction set architecture was originally developed at the university to help teach computer architecture to students, but now its creators want to push it into the mainstream to help propel emerging markets such as cloud computing and the internet of things.
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Surprisingly real value from virtual reality

Posted by Stephanie C on August 21st, 2014

Looks can be deceiving -- these gamers may be engaged in highly cooperative, albeit remote, team objectives. Credit: Reuters

Speaking of big computation, cyberspace isn’t yet as potent as Neal Stephenson portrayed in Snow Crash and subsequent books, but it’s getting there. A new article in the Wall Street Journal online titled Can World of Warcraft Game Skills Help Land a Job? states that some job seekers are adding gaming skills to their resumes to indicate their ability to work productively in large, remote teams:

Gamers’ ability to accomplish complex tasks across virtual teams could be seen as a plus for some companies.

“This capability to engage in strategy-building, team-building, knowledge-sharing and problem-solving remotely is really important,” said, Ms. LeGoues, currently vice president of transformation at the YAI Network of nonprofits.

The topic was also featured on the Harvard Business Review blog, and was picked up at Yahoo Finance (video and article here), noting that skill-based hobbies such as chess and even golf have been touted in LinkedIn profiles for some time:

…Still, excluding people who work at video game companies, less than 2,000 have mentioned World of Warcraft on their resumes on LinkedIn. More than 250,000 people list chess on their LinkedIn profile, mostly in the fields of IT, computer software and finance. That beats the 116,000 who list golfing skills, mainly in the fields of finance, real estate and marketing and advertising. Poker is less common, listed on only 43,000 profiles, and about half are people who work in the gaming industry. The rest, about 22,000, are concentrated in IT, advertising, and marketing and finance.

MIT researcher Michael Schrage says a whole bunch of modern, digital pursuits such as fantasy baseball and Minecraft should eventually become appealing to hiring companies, since they signify modern skills.

Feeling skeptical? How about flight simulators, which have been used for decades
to help train pilots but have only recently achieved high enough levels of computational sophistication to effectively prepare pilots for dangerous flight conditions that were previously relegated to ‘on the job training’.
Read the rest of this entry »

Big computation brings your ideas into 3D

Posted by Stephanie C on August 14th, 2014

Hyve3D credit: University of Montreal

What 3D printers are doing to facilitate fabrication, 3D drawing programs are surpassing to facilitate design. As described at ScienceDaily.com, two systems referred to as “powerful” and “spectacular” are being highlighted at the SIGGRAPH 2014 conference in Vancouver this week:

True2Form (out of University of British Columbia) brings 2D sketches into 3D (excerpt from SD reprint):

…”In line-drawings, designers and artists use descriptive curves and informative viewpoints to convey the full shape of an object,” says Alla Sheffer, a professor in UBC’s Dept. of Computer Science. “Our system mimics the results of human three-dimensional shape inference to lift a sketch curve network into 3-D, while preserving fidelity to the original sketch.”

True2Form uses powerful mathematics to interpret artists’ strokes automatically lifting drawings off of the page. It produces convincing, complex 3-D shapes computed from individual sketches, automatically corrected to account for inherent drawing inaccuracy…

Hyve3D (out of University of Montreal) delivers collaborative, real-time 3D sketching (excerpt from SD reprint):

…For example, as the designers are immersed in their work, this could mean designing the outside of a car, and then actually getting into it to work on the interior detailing. Hyve-3D stands for “Hybrid Virtual Environment 3D.” Univalor, the university’s technology commercialization unit, is supporting the market launch of the system.

The 3D images are the result of an optical illusion created by a widescreen high-resolution projector, a specially designed 5m-diameter spherically concave fabric screen and a 16-inch dome mirror projecting the image onto the screen…

While industrial/commercial/military applications are pretty obvious, the potential for classrooms (remember trying to visualize molecular stereochemistry by pointing your fingers in unnatural directions?!), for emerging technologies, and for individual innovators (as these types of systems arrive in collaborative facilities or as costs/size come down to allow desktop versions) makes the imagination soar.
-Posted by Stephanie C

Tunable Assembly of Nanoparticles for (Photovoltaic) Devices

Posted by Stephanie C on August 13th, 2014

credit: Venkataraman et al., University of Massachusetts Amherst

Photovoltaics are an interesting case where atomic precision is not necessary to achieve potentially dramatic global impacts. Even an “ok efficiency” device that is easy to manufacture with reduced environmental hazard could have significant beneficial effects on energy resources and on device fabrication processes (which could, in turn, contribute to developments toward APM).

The struggle to balance ease of manufacture and device efficiency is a major driver behind current research efforts.  Two recent publications out of Massachusetts alone make the point: Research from University of Massachusetts Amherst describes the fabrication of (very low efficiency) photovoltaic devices via tunable self-assembly of aqueous nanoparticle dispersions (organic nanospheres). The work is published in NanoLetters and the press release is reprinted at Phys.org here (excerpt below), and research from MIT utilizes quantum dots to reach a notable 9% efficiency (high for QD-based devices). This work is published in ACSNano and the press release also reprinted at Phys.org here.

A team of materials chemists, polymer scientists, device physicists and others at the University of Massachusetts Amherst today report a breakthrough technique for controlling molecular assembly of nanoparticles over multiple length scales that should allow faster, cheaper, more ecologically friendly manufacture of organic photovoltaics and other electronic devices. Details are in the current issue of Nano Letters.

Lead investigator, chemist Dhandapani Venkataraman, points out that the new techniques successfully address two major goals for device manufacture: controlling molecular assembly and avoiding toxic solvents like chlorobenzene. “Now we have a rational way of controlling this assembly in a water-based system,” he says. “It’s a completely new way to look at problems. With this technique we can force it into the exact structure that you want.”

-Posted by Stephanie C

Nanotechnology-based next generation memory nears mass production

Posted by Jim Lewis on August 10th, 2014

This scanning electron microscope image and schematic show the design and composition of new RRAM memory devices based on porous silicon oxide that were created at Rice University. Credit: Tour Group/Rice University

Investment in the ultimate promise of advanced or molecular nanotechnology, that is, molecular manufacturing or atomically precise manufacturing, may well rest upon the success of current nanoscale science and incremental nanotechnology. Computation represents a major area of investment for current nanotechnology. One researcher who has contributed greatly to both atomically precise devices leading toward molecular manufacturing, on the one hand, and current commercializable nanotechnology, on the other hand, is James Tour of Rice University, winner of the 2008 Foresight Institute Feynman Prize in the Experimental category. A hat tip to KurzweilAI for reprinting this Rice University news release “Rice’s silicon oxide memories catch manufacturers’ eye“:

Rice University’s breakthrough silicon oxide technology for high-density, next-generation computer memory is one step closer to mass production, thanks to a refinement that will allow manufacturers to fabricate devices at room temperature with conventional production methods.

First discovered five years ago, Rice’s silicon oxide memories are a type of two-terminal, “resistive random-access memory” (RRAM) technology. In a new paper available online in the American Chemical Society journal Nano Letters [abstract], a Rice team led by chemist James Tour compared its RRAM technology to more than a dozen competing versions.

“This memory is superior to all other two-terminal unipolar resistive memories by almost every metric,” Tour said. “And because our devices use silicon oxide — the most studied material on Earth — the underlying physics are both well-understood and easy to implement in existing fabrication facilities.” Tour is Rice’s T.T. and W.F. Chao Chair in Chemistry and professor of computer science and of materials science and nanoengineering.

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Emergence of nanobiotechnology points to importance of deep collaboration

Posted by Jim Lewis on August 8th, 2014

(credit: Elicia Maine et al./Nature Nanotechnology)

We’ve suggested that biotechnology could serve as an enabling technology for the development of atomically precise manufacturing (through an opensource biological parts depository for building molecular machines and through a ground-breaking innovation to have robots do biotech experiments “in the cloud”). Whether or not the confluence of biotechnology and nanotech advances the development of atomically precise manufacturing, this confluence has already opened a path to new products and new markets. An article over at KurzweilAI reports two studies on opportunities in the emerging nanobiotechnology industry “Innovation management and the emergence of the nanobiotechnology industry“:

The confluence of nanotechnology and biotechnology is creating opportunities and an emerging industry, nanobiotechnology, with tremendous potential for economic and social value creation, according to an international research team at MIT, Simon Fraser University, and the University of New South Wales

The medical applications of nanobiotechnology are promising, including effectively targeted drug delivery — imagine highly efficacious cancer treatment with few side effects — and real time, minimally invasive diagnostics. But there is little known about the emergence of this industry or of ways to reap the possible benefits. …

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Biotech lab in the cloud lowers entry barrier to nanotech research

Posted by Jim Lewis on August 5th, 2014

credit The Emerald Cloud Laboratory

Recently we cited an alliance between Foresight and parts of the Bay Area biotech community to build an opensource biological parts repository, and we expressed the hope that spreading the meme that biological machines are indeed machines that can be engineered might seed efforts toward the open source development of molecular manufacturing. We thank Desiree D. Dudley of the Synthetic Neurobiology Group, MIT for letting us know of another Bay Area biotech initiative that might also speed development of molecular manufacturing (also known as atomically precise manufacturing). Emerald Therapeutics, whose co-founder DJ Kleinbaum spoke on “Democratizing Biotechnology” at the 2014 Foresight Technical Conference, has just announced The Emerald Cloud Laboratory, “a web-based life sciences lab, developed by scientists for scientists.” From Ashlee Vance at Bloomberg Businessweek “Emerald Therapeutics: Biotech Lab for Hire“:

There’s a basic formula these days for anyone looking to develop a cure for a disease. Along with a good idea, you need $20 million, a team of about 30 scientists, and a year to set up the lab equipment to start testing your theory. From there, the grunt work begins, as your team of well-paid researchers squirts fluid into test tubes, feeds chemicals into machines, and analyzes the results from thousands of experiments. If you luck out and discover something useful, then it’s time to pray that the desired result can be replicated.

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TED talk: A 30-Year History of the Future

Posted by Stephanie C on July 29th, 2014

credit: TED

Nicholas Negroponte, founder of the MIT media lab and the One Laptop Per Child program, gave a TED talk in March 2014 titled A 30-Year History of the Future. Click to access the talk or the TEDBlog article discussing the talk.

Negroponte highlights some cutting-edge technological developments of the past that had been openly scorned by nay-sayers, including early touch screens and the prediction that books and newspapers would be widely accessed via the internet.

Negroponte also describes some unexpected and inspiring results of giving tablets to children, with no training or instructions provided.

Of course hindsight is always 20/20, but some of the nay-sayers Negroponte encountered may have been viewing computation as competitive with the human experience, while in fact history is showing that, in many cases, computation is supporting and enhancing the human experience.

Building biological molecular machines as an open source path to advanced nanotechnology

Posted by Jim Lewis on July 24th, 2014

A popular added event at the February 2014 Foresight Conference was the B.R.AI.N.S Immortalist Audit focusing on what self-described “Life-Extensionists” are doing to cure disease and extend healthy human life, and how attendees could help. Photos from the Conference present a who’s who of principal players in biotechnology-, and life extension-related startups and research organizations. An April 16 B.R.AI.N.S salon on Human Biology and Freedom capped a successful Crowdtilt community fundraising campaign to build a strategic alliance between B.R.AI.N.S., Berkeley BioLabs and Foresight Institute to build an opensource biological parts repository and design and distribute a line of “How-to Build Biological Machines” educational kits.

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Discount to attend SENS Rejuvenation Biotechnology Conference

Posted by Jim Lewis on July 11th, 2014

Aubrey de Grey, Co-Founder and Chief Science Officer, SENS Research Foundation


Rejuvenation Biotechnology Conference

August 21-23, 2014 · Santa Clara, California
Conference brochure (pdf)
Registration details

We are in the midst of a transformation in the way we search for cures to the diseases of aging. The prevalence of age-related diseases is spiraling and the socioeconomic impacts are a constant source of debate. Subsequently, interest in preventing such diseases through novel approaches to drug development is at an all-time high.

The Rejuvenation Biotechnology Conference is the latest SENS Research Foundation Conference and will be held on August 21-23 at the Hyatt Regency in Santa Clara, California. Join the growing rejuvenation biotechnology industry and hear the latest scientific and policy developments from leading experts in research, industry, policy, finance and regulatory fields.

25% discount for the longevity research conference from SENS Foundation this Aug. 21-23 in Santa Clara, CA. Early rate Extended Until July 14th.

To Foresight members and friends,

Ever since the longevity research conference series called SENS — Strategies for Engineering Negligible Senescence, chaired by Aubrey de Grey — began in 2003, I’ve longed to attend, but never could, because it’s held at Cambridge University in the UK, putting the cost out of reach.

Now, finally, SENS Foundation has started a conference in the U.S., with the first one this August 21-23 here in Silicon Valley!

To get your costs down further, do two things:

  • Register by July 14 to get the early rate.
  • Use the discount code FORESIGHT25 to get an additional 25% off.

This is a ground-breaking meeting featuring true “rock stars” of longevity research, including George Church, Judith Campisi, Michael West, and 37 others.

To round out the event, there’s a keynote by Ajay Royan of Mithril Capital Management, and even appearances by leaders from the entertainment world: comedian Hal Sparks, actor Edward James Olmos, and Cecilia Noel, the “Latin Tina Turner.”

This promises to be the most informative and engaging longevity research event ever held.  I wouldn’t miss it, so please join Foresight president Paul Melnyk, Gayle Pergamit, Tanya Jones, myself, and other friends this August in Santa Clara.

Hope to see you there!

—Christine

Christine Peterson
Co-Founder, Foresight Institute

The NNI Debate of 2014

Posted by Stephanie C on July 11th, 2014

Credit: NNI at nano.gov

Just when it seemed like debate over the National Nanotechnology Initiative was a thing of the past (see Foresight’s disappointment in 2008 here), disagreements regarding re-authorization and budget cuts are prompting politicians and researchers to take a detailed look at what the program supports and what it is achieving.

Witnesses to the House Research Subcommittee hearing, held this past May, included Timothy Persons of US GAO, who spoke at Foresight’s 2014 Integration Conference (and whose work indicating shortfalls in US manufacturing and policy is highlighted in a recent Nanodot post here), and Lloyd Whitman of CNST who emphasized the great strides made in building collaborative facilities that support decentralization of technological advancement, also a key area of discussion at the Integration Conference.

Some highlights from the hearing appear in the American Institute of Physics online bulletin:

The Research Subcommittee of the House Science, Space and Technology Committee held a hearing on May 20 during which Members examined nanotechnology research and development and discussed the National Nanotechnology Initiative (NNI).   Both parties noted that the House of Representatives had previously passed a reauthorization of this Initiative but that the Senate did not.  There was bi-partisan interest from Members of the subcommittee to again attempt to reauthorize NNI.

Subcommittee Chairman Larry Bucshon (R-IN) opened the hearing by describing the development of nanomaterials and listing many products developed due to nanotechnology. “In 2013, the National Science Foundation (NSF) nanotechnology investment supported 5,000 active projects, over 30 research centers and several infrastructure networks for device development, computation, and education,” noted Bucshon as he highlighted the 150 small businesses that were funded through the Small Business Innovation Research (SBIR) and the Small Business Technology Transfer (STTR) Programs.  Bucshon was displeased at the President’s budget request for NSF directorates that support nanotechnology research, noting the $1.5 million decrease in the FY 2015 budget for those directorates.
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The atomically precise manufacture of quantum dots

Posted by Jim Lewis on July 5th, 2014

This image shows a quantum dot molecule consisting of three 6-atom indium chains. (Image: Stefan Fölsch/PDI)

One of the iconic milestones in the history of nanotechnology was the 1989 feat by Eigler and Schweizer at IBM (published the following April in Nature) of using an STM to arrange 35 xenon atoms on a nickel surface to spell IBM. The demonstration was done at 4 K and the atoms of the nickel crystal acted like an “egg carton” to hold the xenon atoms in place. For these and other reasons, although the symbolic impact of the accomplishment was enormous, it was not obvious that this could lead to practical atomically precise manufacturing. However, the recent accomplishment of using an STM at 5 K to make atomically precise quantum dots may turn out to have near-term practical applications. A hat tip to Nanowerk News for publishing this U.S. Naval Research Laboratory news release “Researchers Create Quantum Dots with Single-Atom Precision“:

A team of physicists from the Paul-Drude-Institut für Festkörperelektronik (PDI) in Berlin, Germany, NTT Basic Research Laboratories in Atsugi, Japan, and the U.S. Naval Research Laboratory (NRL) has used a scanning tunneling microscope to create quantum dots with identical, deterministic sizes. The perfect reproducibility of these dots opens the door to quantum dot architectures completely free of uncontrolled variations, an important goal for technologies from nanophotonics to quantum information processing as well as for fundamental studies. The complete findings are published in the July 2014 issue of the journal Nature Nanotechnology [full text, PDF].

Quantum dots are often regarded as artificial atoms because, like real atoms, they confine their electrons to quantized states with discrete energies. But the analogy breaks down quickly, because while real atoms are identical, quantum dots usually comprise hundreds or thousands of atoms – with unavoidable variations in their size and shape and, consequently, in their properties and behavior. External electrostatic gates can be used to reduce these variations. But the more ambitious goal of creating quantum dots with intrinsically perfect fidelity by completely eliminating statistical variations in their size, shape, and arrangement has long remained elusive.

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Lipid coat protects DNA nanorobot from immune attack

Posted by Jim Lewis on July 5th, 2014

An enveloped virus (left) coats itself with lipid as part of its life cycle. New lipid-coated DNA nanodevices (right) closely resemble those viruses and evade the immune defenses of mice. Credit: Steven Perrault/Harvard's Wyss Institute

In general one would not expect a close correlation between the nanoscience and nanomaterials R&D leading to near-term applications in medicine, energy, computation, and other fields, and the molecular nanotechnology that will eventually lead to productive nanosystems and atomically precise manufacturing. A counter example in which the correlation is looking close is structural DNA nanotechnology. A hat tip to KurzweilAI for showcasing this news release from Harvard’s Wyss Institute “Cloaked DNA nanodevices survive pilot mission“:

It’s a familiar trope in science fiction: In enemy territory, activate your cloaking device. And real-world viruses use similar tactics to make themselves invisible to the immune system. Now scientists at Harvard’s Wyss Institute for Biologically Inspired Engineering have mimicked these viral tactics to build the first DNA nanodevices that survive the body’s immune defenses.

The results pave the way for smart DNA nanorobots that could use logic to diagnose cancer earlier and more accurately than doctors can today; target drugs to tumors, or even manufacture drugs on the spot to cripple cancer, the researchers report in the April 22 online issue of ACS Nano [abstract, PDF available].

“We’re mimicking virus functionality to eventually build therapeutics that specifically target cells,” said Wyss Institute Core Faculty member William Shih, Ph.D., the paper’s senior author. Shih is also an Associate Professor of Biological Chemistry and Molecular Pharmacology at Harvard Medical School and Associate Professor of Cancer Biology at the Dana-Farber Cancer Institute.

The same cloaking strategy could also be used to make artificial microscopic containers called protocells that could act as biosensors to detect pathogens in food or toxic chemicals in drinking water.

DNA is well known for carrying genetic information, but Shih and other bioengineers are using it instead as a building material. To do this, they use DNA origami — a method Shih helped extend from 2D to 3D. In this method, scientists take a long strand of DNA and program it to fold into specific shapes, much as a single sheet of paper is folded to create various shapes in the traditional Japanese art.

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Photos from 2014 Foresight Technical Conference

Posted by Jim Lewis on June 24th, 2014

Courtesy of Joshua Lee at SunyataStudios.com

A collection of photos from the 2014 Foresight Technical Conference that highlighted the integration of nanosystems across a range of advanced technologies is now available. In addition to the speakers listed on the conference schedule, the photos present a who’s who of principal players in space-, biotechnology-, and life extension-related startups and research organizations. The photos are provided courtesy of Joshua Lee at SunyataStudios.com. The entire collection of 2014 Integration Conference photos, in a range of sizes up to 7360 x 4912 pixels, is available for viewing and purchase here.
—James Lewis, PhD

Robust triangular RNA brick adds to RNA nanotechnology toolkit

Posted by Jim Lewis on June 24th, 2014

Credit the Guo lab, University of Kentucky. An RNA triangle resistant to boiling assembles into a hexamer that assembles into a honeycomb-like array.

As we have frequently pointed out (for example), RNA has several properties different from those of its close cousin DNA that provide unique opportunities for RNA nanotechnology. One disadvantage of RNA nanostructures is that they are relatively easy to dissociate. RNA nanotechnology pioneer Peixuan Guo has now used rational design to further improve the stability of the unusually stable pRNA-3WJ3 motif to create new RNA triangular nanoparticles. A hat tip to Nanowerk for reprinting this University of Kentucky news release “RNA shows potential as boiling-resistant anionic polymer material for nanoarchitectures“:

A team of nanotechnology researchers at the University of Kentucky has discovered new methods to build heat resistant nanostructures and arrays using RNA.

The research, led by Peixuan Guo, professor and William Farish Endowed Chair in Nanobiotechnology at the UK College of Pharmacy and Markey Cancer Center, is reported in an article titled “RNA as a Boiling-Resistant Anionic Polymer Material To Build Robust Structures with Defined Shape and Stoichiometry,” coauthored by Emil F. Khisamutdinov and Daniel L. Jasinski.

The article, [appearing in] the journal ACS Nano, published by the American Chemical Society (ACS), was selected as an ACS “Editors’ Choice” and … is available for free download as a PDF through open access at http://dx.doi.org/10.1021/nn5006254.

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Novel properties for nanotechnology rebar-graphene reinforced with carbon nanotubes

Posted by Jim Lewis on June 9th, 2014

Nanotubes with added carbon side chains are spin coated onto a substrate and heated to form rebar graphene in a process invented at Rice University. The rebars add strength and electrical connectivity to the transparent, flexible sheet that could replace more expensive materials in displays and solar cells. (Credit: Tour Group/Rice University)

In keeping with the theme of February’s “The Integration Conference”, integration of two different types of nanostructure promises greatly improved functional devices. In research described at KurzweilAI.net from 2008 Feynman Prize winner James Tour’s group, a composite of carbon nanotubes and graphene has improved mechanical and electronic properties, and may provide an inexpensive substitute for a rare and expensive material. From a Rice University news release written by Mike Williams “Rebar technique strengthens case for graphene“:

Carbon nanotubes are reinforcing bars that make two-dimensional graphene much easier to handle in a new hybrid material grown by researchers at Rice University.

The Rice lab of chemist James Tour set nanotubes into graphene in a way that not only mimics how steel rebar is used in concrete but also preserves and even improves the electrical and mechanical qualities of both.

The technique should make large, flexible, conductive and transparent sheets of graphene much easier to manipulate, which should be of interest to electronics manufacturers, Tour said. He suggested the new hybrid could, upon stacking in a few layers, be a cost-effective replacement for expensive indium tin oxide (ITO) now used in displays and solar cells.

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DNA nanotechnology replicates enzyme cascade

Posted by Jim Lewis on June 4th, 2014

Photo by: Jason Drees, Biodesign Institute at ASU

Five years ago this blog pointed to progress in using DNA scaffolding to organize functional modules for use in the modular molecular composite nanosystems (MMCNs) route to atomically precise productive nanosystems. In another advance along this pathway to atomically precise manufacturing, researchers have arranged two enzymes on a DNA scaffold to replicate the organization of an enzyme cascade inside a cell, passing a substrate molecule from one enzyme to the next. From Arizona State University “DNA nanotechnology opens future to biomedical applications with 3-D artificial enzyme“:

Using molecules of DNA like an architectural scaffold, Arizona State University scientists, in collaboration with colleagues at the University of Michigan, have developed a 3-D artificial enzyme cascade that mimics an important biochemical pathway that could prove important for future biomedical and energy applications.

The findings were published in the journal Nature Nanotechnology [abstract]. Led by ASU professor Hao Yan, the research team included ASU Biodesign Institute researchers Jinglin Fu, Yuhe Yang, Minghui Liu, Professor Yan Liu and professor Neal Woodbury, along with colleagues professor Nils Walter and postdoctoral fellow Alexander Johnson-Buck at the University of Michigan.

Researchers in the field of DNA nanotechnology, taking advantage of the binding properties of the chemical building blocks of DNA, twist and self-assemble DNA into ever-more imaginative 2- and 3-dimensional structures for medical, electronic and energy applications.

In the latest breakthrough, the research team took up the challenge of mimicking enzymes outside the friendly confines of the cell. …

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Expanded DNA alphabet provides more options for nanotechnology

Posted by Jim Lewis on May 14th, 2014

Floyd E. Romesberg, associate professor at Scripps Research (Credit: The Scripps Research Institute)

Long-time readers of Nanodot may remember the section of Chapter 15 of Nanosystems in which Drexler explores options for producing easier to design proteins for the protein engineering path toward atomically precise manufacturing by incorporating specially chosen amino acids in addition to the 20 genetically encoded amino acids. Back in 1992 the only option for incorporating unnatural amino acids into proteins was Merrifield solid phase peptide synthesis, using the methods of organic chemistry rather than biological systems. However, this becomes problematic and expensive for longer chains. Consequently, finding ways to expand the repertoire of biologically encoded amino acids would be quite useful. One way to accomplish this goal would be to expand the DNA ‘alphabet’ from two to three base pairs (that is, from four to six ‘letters’). We noted progress in this direction back in February of 2008 when Floyd Romesberg, at the Scripps Research Institute, La Jolla, California created two artificial DNA letters that were accurately and efficiently replicated by a natural enzyme. In September of 2011 we noted a different approach taken by a team at the Salk Institute that keeps the current DNA alphabet but alters one three-letter word to mean an unnatural amino acid, increasing the amino acid repertoire by one. We noted in June of 2012 that continued work by Romesberg had revealed how the new base pair was efficiently replicated in the test tube by a natural enzyme. In a major advance, Romesberg and his collaborators have engineered a living organism to stably propagate the expanded genetic alphabet. The research was published in Nature [abstract] and was nicely described in a news article in Science by Robert F. Service “Designer Microbes Expand Life’s Genetic Alphabet“:

From bacteria to basketball players, all life as we know it encodes genetic information using two pairs of DNA letters. Not anymore. Now, along with the double helix’s two natural pairs—A bound to T and G bound to C—a bacterium growing in a California lab can incorporate and copy a third, artificial pair of letters. For now, the artificial bases—call them X and Y—don’t code for anything, unlike natural DNA base pairs, which in various combinations code for the 20 different amino acids that make up proteins. But the newly expanded genetic code opens the door for synthetic biologists to create microbes capable of building their proteins out of as many as 172 different amino acids, both natural and artificial—a potential boon to drug and materials developers. …

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