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Linking together small DNAs to build more diverse DNA nanostructures

Posted by Jim Lewis on July 2nd, 2015

DNA ligase is used to link varying amounts of repeated structural units A and B and unique addressable unit X together into a long DNA segment, which can then be amplified by DNA polymerase to make many copies. Credit: Sleiman's research group and McGill University.

A few months ago we cited a cheaper, easier way developed by researchers at McGill University to build long DNA scaffolds. A further substantial improvement, in which long DNA segments of up to 1000 base pairs are produced less expensively than the short 100-base strands they previously used is described at KurzweilAI.net “A new technique to build complex custom-designed DNA scaffolds“:

McGill University researchers have devised a new technique to produce long, custom-designed DNA strands to build nanoscale structures to deliver drugs to targets within the body or take electronic miniaturization to a new level.

Researchers have been assembling and experimenting with DNA structures or “DNA origami” for years, as KurzweilAI has reported. But as these applications continue to develop, they require increasingly large and complex strands of DNA. It can take hundreds of these short strands to assemble nanotubes for applications such as smart drug-delivery systems.

That poses a problem: automated systems used for making synthetic DNA can’t produce strands containing more than about 100 bases (the chemicals that link up to form the DNA strands). …

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Toward advanced nanotechnology: Working solid state molecular shuttle

Posted by Jim Lewis on July 1st, 2015

Credit: Loeb Research Group, University of Windsor

Two years ago we cited the demonstration by a group at the University of Windsor of a solid state molecular machine comprising a molecular wheel made from a rotaxane molecule held in place in a self-assembled metal organic framework. This work was widely recognized as a step toward solid state molecular machinery. A recent article at Phys.org written by Heather Zeiger explains the most recent step forward along that path, the creation of a molecular shuttle in which the ring around the axle of the rotaxane molecule shuttles back and forth between two positions. “Toward solid-state molecular circuitry: Molecular shuttle within a metal-organic framework“:

…Kelong Zhu, Christopher A. O’Keefe, V. Nicholas Vukotic, Robert W. Schurko and Stephen J. Loeb from the Department of Chemistry and Biochemistry at the University of Windsor have designed and characterized a molecular shuttle that functions both in solution and when placed within a rigid chemical structure called a metal-organic framework. Their work appears in Nature Chemistry [abstract].

This research makes use of the rotaxane architecture, a MIM [mechanically interlocked molecule] comprised of a ring-shaped molecule and two recognition sites. Rotaxanes have two components: A molecule is threaded through a macrocyclic ring, like a wheel with an axle. The macrocycle moves linearly along the axle between two recognition sites. Zhu, et al. used a 24-crown-8 macrocycle and benzimidazole recognition sites on the axle. …

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Wafer-scale atomically precise thin layers for nanotechnology

Posted by Jim Lewis on June 30th, 2015

A molybdenum disulphide device array on a transparent silica wafer. Credit: Kibum Kang, Cornell University

The path of progress in nanotechnology stretches from approximate control of the structure of matter—a precision of 1 to 100 nm in at least one dimension in which unique phenomena enable novel applications—to atomic precision in three dimensions. We at Foresight have been primarily interested in mechanical properties of systems of atomically precise machines. Progress along this path leads toward productive nanosystems and inexpensive high throughput atomically precise manufacturing. Current computer and other important technologies, however, rely upon electronic and optoelectrnic properties. For these applications, progress toward atomically precise thin films, especially thin films of semiconductors, looks very promising. A hat tip to ScienceDaily for reprinting this Cornell University news article written by Anne Ju “Chemists cook up three atom-thick electronic sheets“:

Making thin films out of semiconducting materials is analogous to how ice grows on a windowpane: When the conditions are just right, the semiconductor grows in flat crystals that slowly fuse together, eventually forming a continuous film.

This process of film deposition is common for traditional semiconductors like silicon or gallium arsenide – the basis of modern electronics – but Cornell scientists are pushing the limits for how thin they can go. They have demonstrated a way to create a new kind of semiconductor thin film that retains its electrical properties even when it is just atoms thick.

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DNA nanomachines more stable than expected in human serum and blood

Posted by Jim Lewis on June 29th, 2015

Credit: Boise State University and Sara Goltry et al.

Over the past several years we have cited substantial progress in making ever more complex molecular machinery using structural DNA nanotechnology. Much of this work is focused on eventual medical applications, so it becomes important to ask how fragile such machinery would be in human serum and blood. A year ago we cited work work showing that a Lipid coat protects DNA nanorobot from immune attack, and six months ago that Swarms of DNA nanorobots execute complex tasks in living animal. More recently researchers at Boise State University have demonstrated that some DNA nanomachines are surprisingly stable in human serum and blood. From a Boise State news article “Nanobots! – DNA Nanomachines Operating In Blood” (scroll down):

Everyone knows DNA is rapidly degraded by enzymes in serum; except it isn’t–at least not always. While most studies of DNA in serum use fetal bovine serum, which exhibits a high enzyme activity and does degrade DNA rapidly, few studies have looked at DNA nanostructures in human serum. With the aim of creating new tools for biomedical diagnostic applications in humans (sorry bovines!), Sara Goltry, a PhD student in Materials Science & Engineering at Boise State, and co-workers measured the lifetimes of DNA devices in human serum and blood. The results of their four-year study, published recently in Nanoscale [abstract], show that some DNA nanostructures survive in human serum for about two days while others last only about an hour. Interestingly, the device lifetime can be programmed by changing the shape of the molecule. Beyond lifetime studies, Goltry also demonstrated that a circular DNA nanomachine operates in human serum and blood just fine. The nanomachine can be made to open and close with DNA fuels, similar to the DNA tweezers first published by Yurke et al. in 2000. Demonstrating operation in serum and blood supports the goal of building programmable molecular machines as a means to engineer new DNA-based tools for biotechnology.

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Self-assembly of silicon metamaterial for nanoscale reflectors

Posted by Stephanie C on June 25th, 2015

A scanning electron micrograph shows a tilted view of a metamaterial mirror made of silicon cylinders patterned on a silicon wafer. Credit: ACS Photonic

Recently highlighted in a C&EN article titled Simple Process Creates Near-Perfect Mirrors Out of a Metamaterial, researchers out of Vanderbilt University developed a method to self-assemble silicon nanostructures to achieve highly (Bragg-like) reflective mirrors which capitalize on nanoscale properties not present in bulk structures. The self-assembly method is far simpler than previous, conventional electron beam lithography approaches.

…Metamaterials are engineered to have properties, typically derived from nanoscale patterning, that do not occur in the bulk material. They made their reflector by patterning a silicon wafer’s surface with an array of silicon cylinders a few hundred nanometers in diameter. Each of the cylinders acted like a tiny resonator for particular light frequencies—analogous to the way certain sound frequencies will make a tuning fork hum. By adjusting the size of the cylinders, Valentine could control how well they reflected light of a given frequency. This mirror reflected more than 99% of light at the peak wavelength.

Although the work showed that metamaterial mirrors could be effective, the method for making them was far from practical: The researchers painstakingly created the arrays using electron-beam lithography, which is difficult to scale up. So Valentine and his team adopted a simpler method to make bigger, near-perfect reflectors.
They started with off-the-shelf polystyrene beads 820 nm across and dropped them into a film of water. Driven by electrostatic forces, the beads self-assembled into a monolayer on the water’s surface with a repeated hexagonal pattern. Valentine’s group then drained the water, lowering the bead layer onto a submerged silicon wafer, and used a plasma etching process to shrink the beads to 560 nm. Finally, they used the bead layer as a lithographic mask to pattern the underlying silicon. The resulting 2-cm2 arrays were covered in silicon cylinders, each 335 nm tall and 480 nm across the top.

The arrays reflect 99.7% of incident infrared light at 1,530 nm. Valentine is now working on making larger area reflectors by patterning with silicon nanospheres.

“This is a phenomenal result, especially for something made by self-assembly,” says Michael B. Sinclair, who develops metamaterials at Sandia National Laboratories. Bragg reflectors are an established technology that will be difficult to compete with anytime soon, he says, but the work is “an impressive step forward for making large-area metamaterials.”

-Posted by Stephanie C

Google Tech Talk video by Feynman Prize Winner

Posted by Jim Lewis on June 24th, 2015

Christian Schafmeister Google Tech Talk June 10, 2015.

Christian Schafmeister, winner of the 2005 Foresight Institute Feynman Prize for Experimental work and participant in last year’s Foresight Institute Workshop on Directed/Programmable Matter for Energy, began programming at age 12 on a Radio Shack TRS-80, followed that interest into a career in chemistry, and is currently a chemistry professor at Temple University. Earlier this month he gave a Google Tech Talk that is available on You Tube “Clasp: Common Lisp using LLVM and C++ for Molecular Metaprogramming – Towards a Matter Compiler” (57:37).

Prof. Schafmeister’s goal is to build molecules as easily as he can write software; specifically he wants to build molecules that can do things, like go into the body and fix things. Inspired by Richard Feynman’s 1959 talk in which Feynman proposed building machines on a molecular scale that were atomically precise, where you know where every atom is in space, he went into biophysics, where he made proteins and solved crystal structures of proteins, and from there into chemistry.

We understand a great deal about proteins, the molecular machines that make us work. Explaining how proteins are made of chains of amino acids that fold into precise 3D shapes that do specific things, like catalyze chemical reactions, or like antibodies, which bind to specific structures to start the immune system attacking pathogens, or like channels that let specific molecules, and nothing else, pass through cellular membranes, Prof. Schafmeister asserted that we could solve most of humanity’s problems if we could build similar machines. He actually began this process as a graduate student, building one of the first unnatural proteins, called DHP1. He designed the protein on paper, designed a gene to make it, got bacteria to make it, and determined the crystal structure, showing it to be a four-helix bundle, a very common structural motif in proteins.

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US OSTP seeking suggestions for Nanotechnology Grand Challenges

Posted by Jim Lewis on June 23rd, 2015

The US White House Office of Science and Technology Policy (OSTP) is seeking suggestions for Nanotechnology Grand Challenges. As explained in the Federal Register for June 17, 2015 “Nanotechnology-Inspired Grand Challenges for the Next Decade“:

A Notice by the Science and Technology Policy Office on 06/17/2015

The purpose of this Request for Information (RFI) is to seek suggestions for Nanotechnology-Inspired Grand Challenges for the Next Decade: Ambitious but achievable goals that harness nanoscience, nanotechnology, and innovation to solve important national or global problems and have the potential to capture the public’s imagination. This RFI is intended to gather information from external stakeholders about potential grand challenges that will help guide the science and technology priorities of Federal agencies, catalyze new research activities, foster the commercialization of nanotechnologies, and inspire different sectors to invest in achieving the goals. Input is sought from nanotechnology stakeholders including researchers in academia and industry, non-governmental organizations, scientific and professional societies, and all other interested members of the public. …

Responses must be received by July 16, 2015 to be considered. …

The announcement continues with background information, instructions on how to submit a response, just what information is requested, questions to be addressed in proposals, and lastly examples of potential nanotechnology-inspired grand challenges for the next decade. All of the six examples given are worthy, but we find #4 the most interesting:

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Conference video: Regenesis: Bionano

Posted by Jim Lewis on June 9th, 2015

Credit: George Church

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 1st speaker at the Commercial Scale Devices session was George M. Church. His talk was titled “Regenesis: Bionano ” biography and abstracts, video – video length 51:19.

Prof. Church began with the immense drop in the cost of DNA sequencing from the production of the draft human genome sequence in 2000 at a cost of $3 billion to the early 2013 cost of $2000 to $4000 per genome. With whole genome sequencing becoming inexpensive, the question arises where are you going to store all of the data? Prof. Church’s answer is that DNA itself is a pretty good place to store that data, and other types of data as well. In fact, he encoded his book co-authored with Ed Regis Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves, into a 5.27 megabit bitstream that was written with DNA synthesis technologies and read with DNA sequencing technology, requiring about a picogram of DNA, implying about a MByte/femtoliter (“Next-Generation Digital Information Storage in DNA“). Church notes that DNA as old as 800,000 years has been sequenced, and that he personally made 70 billion copies of his book.

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Computational nanotechnology reveals complex interactions in double-walled carbon nanotubes

Posted by Jim Lewis on June 8th, 2015

In this example, the team analyzed a nanotube with two zigzag components. The individual nanotubes have band gaps and are semiconductors, but when combined, the band gaps overlap and make the double-walled a semimetal. (Illustration by Matías Soto/Rice University)

Last week we cited research reporting an efficient method to remove metallic single-walled carbon nanotubes from semiconducting single-walled carbon nanotubes, among other purposes, to facilitate studies of thin film transistors. Other researchers at Rice University have recently shown by extensive theoretical studies that it may be possible to tune double-walled carbon nanotubes for specific electronic properties, including those important for nanotube transistors. A hat tip to Kurzweil Accelerating Intelligence for an overview of this work and linking to this Rice University news release written by Mike Williams “Nanotubes with 2 walls have singular qualities“:

Rice University researchers have determined that two walls are better than one when turning carbon nanotubes into materials like strong, conductive fibers or transistors.

Rice materials scientist Enrique Barrera and his colleagues used atomic-level models of double-walled nanotubes to see how they might be tuned for applications that require particular properties. They knew from others’ work that double-walled nanotubes are stronger and stiffer than their single-walled cousins. But they found it may someday be possible to tune double-walled tubes for specific electronic properties by controlling their configuration, chiral angles and the distance between the walls.

The research reported in Nanotechnology was chosen as the journal’s “publisher’s pick” this month. The journal also published an interview with the study’s lead author, Rice graduate student Matías Soto.

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Computational nanotechnology to benefit from expanded first-principles molecular dynamics

Posted by Jim Lewis on June 7th, 2015

Snapshot structure from first-principles simulation of DNA in water medium using the calculation method developed by the research. The forces between atoms are calculated by first-principles calculation (joint research London Centre for Nanotechnology and RIKEN)

Historically, proposals for molecular nanotechnology by K. Eric Drexler and others, usually referred to these days as high-throughput atomically precise manufacturing, have been based upon physical law. The very earliest proposals (1981, 1986) argued that biological molecular machine systems provide an existence proof that artificial molecular machine systems could work together to built large atomically precise systems. However, serious study of what is possible, beginning with the book Nanosystems in 1992 and continuing with the 2005 animated short film “Productive Nanosystems: from Molecules to Superproducts”, described here and on Drexler’s web site, have been based on what physical law says is possible. Such studies have relied heavily on computational chemistry based on first-principles calculations. They have been limited by the fact that, even with substantial increases in available computer power over the past decade, it is difficult to study systems of more than a few hundred atoms. Foresight President Paul Melnyk sends this news that limitation may be disappearing soon. A hat tip to Nanowerk for reprinting this news from the London Centre for Nanotechnology “Large-scale simulations of atom dynamics“:

Researchers develop a new method for simulating previously unstudied complex matter

An international research team has developed a highly efficient novel method for simulating the dynamics of very large systems potentially containing millions of atoms, up to 1000 times more than current conventional methods. This advance will open up a range of possibilities for accurately studying complex matter, for example biomolecules in solution, and gaining a previously unattainable understanding of processes such as electron, water or ion transport or chemical reactions.

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Arrays of pure semiconducting carbon nanotubes for nanoelectronics

Posted by Jim Lewis on June 6th, 2015

Thermal gradients associated with mild heating of a metallic carbon nanotube induces thermocapillary flows in a thin organic overcoat. The result is an open trench with the tube at the base. Credit: J.Rogers/UIUC

Carbon nanotubes (CNT) have been widely known for more than 25 years, but a major impediment to their use in nanoscale electric circuits has always been the fact that they are prepared as mixtures of CNT differing somewhat in structure but with very different electrical properties. A major advance in purification made by researchers at the University of Illinois at Urbana-Champaign may be the crucial advance that will lead to widespread use of CNT in electronic devices. A hat tip to Kurzweil Accelerating Intelligence for reprinting this American Institute of Physics news release “Future Electronics Based on Carbon Nanotubes“:

A team at the University of Illinois at Urbana-Champaign finds way to purify arrays of single-walled carbon nanotubes (SWCNTs), possibly providing a step toward post-silicon circuits and devices

The exceptional properties of tiny molecular cylinders known as carbon nanotubes have tantalized researchers for years because of the possibility they could serve as a successors to silicon in laying the logic for smaller, faster and cheaper electronic devices.

First of all they are tiny — on the atomic scale and perhaps near the physical limit of how small you can shrink a single electronic switch. Like silicon, they can be semiconducting in nature, a fact that is essential for circuit boards, and they can undergo fast and highly controllable electrical switching.

But a big barrier to building useful electronics with carbon nanotubes has always been the fact that when they’re arrayed into films, a certain portion of them will act more like metals than semiconductors — an unforgiving flaw that fouls the film, shorts the circuit and throws a wrench into the gears of any potential electronic device.

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Dynamic nanomachines for DNA nanotechnology inspired by proteins

Posted by Jim Lewis on June 4th, 2015

This is an artist's impression of shape-complementary DNA components that self-assemble into nanoscale machinery. CREDIT C. Hohmann / NIM

Several of our most recent posts on DNA origami and structural DNA nanotechnology have cited research aimed at creating more mechanically dynamic structures (here, here, and here). Another approach to using DNA origami to make nanomachines with moving parts has been published by a German research group inspired by how proteins function by forming and reconfiguring relatively weak bonds. A hat tip to ScienceDaily for reprinting this Technische Universitaet Muenchen news release published on AAAS EurekAlert “Designer’s toolkit for dynamic DNA nanomachines: Arm-waving nanorobot signals new flexibility in DNA origami“:

The latest DNA nanodevices created at the Technische Universitaet Muenchen (TUM) – including a robot with movable arms, a book that opens and closes, a switchable gear, and an actuator – may be intriguing in their own right, but that’s not the point. They demonstrate a breakthrough in the science of using DNA as a programmable building material for nanometer-scale structures and machines. Results published in the journal Science [abstract] reveal a new approach to joining – and reconfiguring – modular 3D building units, by snapping together complementary shapes instead of zipping together strings of base pairs. This not only opens the way for practical nanomachines with moving parts, but also offers a toolkit that makes it easier to program their self-assembly.

The field popularly known as “DNA origami,” in reference to the traditional Japanese art of paper folding, is advancing quickly toward practical applications, according to TUM Prof. Hendrik Dietz. Earlier this month, Dietz was awarded Germany’s most important research award, the Gottfried Wilhelm Leibniz Prize, for his role in this progress.

In recent years, Dietz and his team have been responsible for major steps in the direction of applications: experimental devices including a synthetic membrane channel made from DNA; discoveries that cut the time needed for self-assembly processes from a week to a few hours and enable yields approaching 100%; proof that extremely complex structures can be assembled, as designed, with subnanometer precision.

Yet all those advances employed “base-pairing” to determine how individual strands and assemblies of DNA would join up with others in solution. What’s new is the “glue.”

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Preserving protein function in DNA-protein nanostructures

Posted by Jim Lewis on June 1st, 2015

(A) Single-stranded M13 DNA (dark blue) and complementary DNA oligonucleotides (golden-rods), two of which have been chemically linked to two different peptides, each containing a GGG site that identifies the N-terminal recognition site of sortase. (B) Annealing places each peptide one third of the way from one end of the M13 DNA. (C) Treatment with sortase and protein CDH23 containing the C-terminal recognition sequence for sortase links protein CDH23 to the GGG-modified oligonucleotide one third from the right of the M13. The other oligo is protected because its N terminus is blocked by the Flag-TEV sequence. (D) Addition of the TEV protease removes the block. (E) Addition of sortase and the PCDH15 protein, also containing the C-terminal recognition sequence for sortase, places that protein on the site at the left. Under conditions in which CDH23 and PCDH15 bind, the loop closes, producing a shorter end-to-end length of the nanoswitch. Credit: Koussa et al. Methods.

We have frequently cited (for example, here, here, and here) the importance of modular molecular composite nanosystems (MMCNs} for the development of atomically precise productive nanosystems and eventually atomically precise manufacturing. One of the recommendations made by the 2007 Productive Nanosystems Technology Roadmap (Executive Summary, p. xi) to support the development of MMCNs is to “Develop systematic methodologies for building MMCNs in which proteins bind specific functional components to specific sites on DNA structural frameworks.” Two months ago, while researching DNA nanoswitches developed by Wesley Wong’s research group to study molecular interactions, I noted on his lab’s publications page a major contribution to achieving this objective through addressing a practical problem that could occur when making DNA-protein nanostructures “Protocol for sortase-mediated construction of DNA-protein hybrids and functional nanostructures” (open access). The abstract of the paper:

Recent methods in DNA nanotechnology are enabling the creation of intricate nanostructures through the use of programmable, bottom-up self-assembly. However, structures consisting only of DNA are limited in their ability to act on other biomolecules. Proteins, on the other hand, perform a variety of functions on biological materials, but directed control of the self-assembly process remains a challenge. While DNA–protein hybrids have the potential to provide the best-of-both-worlds, they can be difficult to create as many of the conventional techniques for linking proteins to DNA render proteins dysfunctional. We present here a sortase-based protocol for covalently coupling proteins to DNA with minimal disturbance to protein function. To accomplish this we have developed a two-step process. First, a small synthetic peptide is bioorthogonally and covalently coupled to a DNA oligo using click chemistry. Next, the DNA–peptide chimera is covalently linked to a protein of interest under protein-compatible conditions using the enzyme sortase. Our protocol allows for the simple coupling and purification of a functional DNA–protein hybrid. We use this technique to form oligos bearing cadherin-23 and protocadherin-15 protein fragments. Upon incorporation into a linear M13 scaffold, these protein–DNA hybrids serve as the gate to a binary nanoswitch. The outlined protocol is reliable and modular, facilitating the construction of libraries of oligos and proteins that can be combined to form functional DNA–protein nanostructures. These structures will enable a new class of functional nanostructures, which could be used for therapeutic and industrial processes.

The introduction to the paper points out that many chemistries conventionally used to link proteins and DNA react with functional groups that are ubiquitous in biology so that the DNA oligo could react to amy of several sites on the protein, increasing the risk of interfering with protein function. This risk is avoided by coupling the DNA oligo to a small, synthetic peptide, so there is no need to optimize coupling protocols for each protein. The protein of interest is then coupled to this DNA-peptide chimera using sortase, a microbial enzyme that recognizes a short amino acid sequence LPX1TGX2 near the C-terminus of one protein and couples it to a GGG sequence at the N-terminus of another protein to produce a fusion of the two proteins. The variant of sortase used was evolved to optimize coupling under conditions favorable for protein stability. Thus all of the chemistry that might be damaging to proteins is front-loaded so that is performed on a small peptide designed to be compatible with those conditions. The peptide can also be designed to facilitate easy purification of the DNA oligo-synthetic peptide-fusion protein. The end result of this process is that it is straight-forward to systematically build a library of proteins linked to DNA oligos, which can then be used to bind any of those proteins to any desired site on a DNA origami structure.

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Single molecule pump concentrates small molecules

Posted by Jim Lewis on May 26th, 2015

Credit: Stoddart research group, Northwestern University

Among the classes of molecular machines that make life possible are the protein pumps that move ions and small molecules across membranes, from one compartment to another. These ions and molecules are driven uphill energetically, from low concentrations to high concentrations, forming systems that are high in energy and can perform work on their environments. Demonstration of this basic principle using a much smaller artificial molecular pump comes this month from the laboratory of Sir Fraser Stoddart, winner of the 2007 Feynman Prize in Nanotechnology in the Experimental category. Hat tips to Phys.org and ECN for reprinting this Northwestern University news release written by Megan Fellman “Nature inspires first artificial molecular pump“:

Using nature for inspiration, a team of Northwestern University scientists is the first to develop an entirely artificial molecular pump, in which molecules pump other molecules. This tiny machine is no small feat. The pump one day might be used to power other molecular machines, such as artificial muscles.

The new machine mimics the pumping mechanism of life-sustaining proteins that move small molecules around living cells to metabolize and store energy from food. For its food, the artificial pump draws power from chemical reactions, driving molecules step-by-step from a low-energy state to a high-energy state — far away from equilibrium.

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Conference video: Microscopic Reversibility: The Organizing Principle for Molecular Machines

Posted by Jim Lewis on May 13th, 2015

Credit: Dean Astumian

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 Molecular Machines and Non-Equilibrium Processes session, the winner of the 2011 Feynman Prize for Theoretical work, Dean Astumian, presented his prize-winning work “Microscopic Reversibility: The Organizing Principle for Molecular Machines” biography and abstract, https://vimeo.com/63008846 – video length 42:12. He addressed how we should think about molecular machines, and in particular, molecular machines inspired by biology, which operate in water at slightly more than room temperature. A molecule called kinesin converts chemical energy from the hydrolysis of ATP (adenosine triphosphate) to walk in one direction on a molecular track called a microtubule. We could try to think of it in terms of a macroscopic deterministic picture, as in mechanics, or we could think of it in probabilistic terms more consistent with chemistry.

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Conference video: Multi-Million Atom Simulations for Single Atom Transistor Structures

Posted by Jim Lewis on May 12th, 2015

Credit:Gerhard Klimeck

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 8th speaker at the Atomic Scale Devices session was Gerhard Klimeck. His talk was titled “Multi-Million Atom Simulations for Single Atom Transistor Structures” biography and abstracts, video – video length 26:37.

From an electrical engineer’s perspective, Prof. Klimeck began with the observation that over the years the number of transistors on a chip has increased exponentially to more than two billion transistors on a chip, but for the last six to eight year the clock speed has not increased beyond two gigahertz because the power consumption on the chip, about 100 watts per square centimeter, limits the clock speed. Currently the major contribution to this power consumption is “static power”—the power leaking through the transistor whether it is switching or not. The amount of leakage is a fundamental limit of the thermal distribution of charge carriers in the CMOS chip. A solution would be to develop a tunneling transistor that is no longer thermally limited, but instead gives current flow in a narrow energy window. Modeling potential solutions, such as a double gate or a nanowire, to see how current flow can be modulated by the gate of transistor requires an atomistic modeling tool. We and others have shown that nanowire gates can dramatically reduce voltage, so that tunneling transistors may be able to solve the power consumption problem, but perhaps only for a short time. One multi-gate device called a finFET depends on a thin silicon “fin”, so that although the device is nominally a 22-nm device, the active region is only 8 nm wide—64 atoms. In devices currently of interest the number of critical atoms can be as low as 14. This is the reason Klimeck’s group has been building their NEMO (NanoElectronicMOdeling) tool. Further, the number of electrons under the gate in today’s technology is already in the hundreds and is rapidly approaching the tens. So the regime of single electron and quantum dot devices is not so far away. Thus Klimeck’s NEMO tool spans the range from modeling current devices to designing single electron and quantum dot devices.

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Nanoparticles shepherd DNA into cells to regulate immune response

Posted by Jim Lewis on May 6th, 2015

Credit Mirkin research group

One of biotechnology’s most powerful tools is the introduction of nucleic acids of specific sequence into cells to implement a specific pre-determined change. Not surprisingly, nucleic acids incorporated into nanostructures are often much more functional than isolated nucleic acid molecules. It is sometimes not necessary for such nanostructures to be totally atomically precise, as has been demonstrated by Spherical Nucleic Acids (SNAs), dense conjugates of oriented nucleic acids on the surfaces of various nanoparticles, introduced by Chad Mirkin, winner of the 2002 Feynman Prize in Nanotechnology, Experimental. An informative animation available on the Mirkin group web site shows how SNAs are constructed and explains the advantages of SNAs, such as efficient entry into cells via endocytosis, resistance to nucleases, lack of unintended immunogenicity, and much better binding to intracellular nucleic acid targets. A recent success of the Mirkin group with SNAs is described over at KurzweilAI.net “Spherical nucleic acids train immune system to fight disease“:

A research team led by Northwestern University nanomedicine expert Chad A. Mirkin and Sergei Gryaznov of AuraSense Therapeutics has shown that spherical nucleic acids (SNAs) can be used as potent drugs to effectively train the immune system to fight disease, by either boosting or dampening the immune response. The initial treatment triggers a cell-specific immune response all over the body.

By increasing the body’s immune response toward a specific cell type, SNAs could be used to target anything from influenza to different forms of cancer. They also can be used to suppress the immune response, a tactic important in treating autoimmune disorders, such as rheumatoid arthritis and psoriasis, where the body’s immune system mistakenly attacks healthy tissues.

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Nanowires and bacteria harnessed for artificial photosynthesis

Posted by Jim Lewis on May 4th, 2015

This break-through artificial photosynthesis system has four general components: (1) harvesting solar energy, (2) generating reducing equivalents, (3) reducing CO2 to biosynthetic intermediates, and (4) producing value-added chemicals. Credit Berkeley Lab

One of the major areas in which improved precision in our control of matter is likely to deliver major benefits is the area of energy technology, as evidenced by Foresight Institute’s 2014 Workshop on Directed/Programmable Matter for Energy. Gayle Pergamit forwards this news of a major advance in artificial photosynthesis made possible by current-day nanotechnology. A hat tip to Controlled Environments for reprinting this Berkeley Lab news release written by Lynn Yarris “Major Advance in Artificial Photosynthesis Poses Win/Win for the Environment“:

A potentially game-changing breakthrough in artificial photosynthesis has been achieved with the development of a system that can capture carbon dioxide emissions before they are vented into the atmosphere and then, powered by solar energy, convert that carbon dioxide into valuable chemical products, including biodegradable plastics, pharmaceutical drugs and even liquid fuels.

Scientists with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley have created a hybrid system of semiconducting nanowires and bacteria that mimics the natural photosynthetic process by which plants use the energy in sunlight to synthesize carbohydrates from carbon dioxide and water. However, this new artificial photosynthetic system synthesizes the combination of carbon dioxide and water into acetate, the most common building block today for biosynthesis.

“We believe our system is a revolutionary leap forward in the field of artificial photosynthesis,” says Peidong Yang, a chemist with Berkeley Lab’s Materials Sciences Division and one of the leaders of this study. “Our system has the potential to fundamentally change the chemical and oil industry in that we can produce chemicals and fuels in a totally renewable way, rather than extracting them from deep below the ground.”

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Science and technology roadmaps for nanotechnology

Posted by Jim Lewis on May 3rd, 2015

From the cover of the European Science and Technology Roadmap for Graphene, Related Two-Dimensional Crystals, and Hybrid Systems.

A decade ago Foresight participated in a two-year effort to produce the first technology roadmap from current, incremental nanotechnology to productive nanosystems capable of general purpose, high-throughput atomically precise manufacturing (APM). The purpose of roadmaps, such as the well-known and extremely successful International Technology Roadmap for Semiconductors, is to define the future technology requirements for complex systems so that present-day research world-wide can be coordinated to develop all the necessary components for the future target system, be it a next generation semiconductor fabrication facility for computer chips, or a nanofactory.

With ITRS the challenge is to develop the next generation of a mature, commercially successful technology. With APM the first generation does not yet exist so the challenge is how to go from a set of disparate enabling technologies, including various molecular sciences and surface physics, to the first functional prototype of a nanofactory. With ITRS the current and earlier technology generations have enabled a flourishing industry that lies at the foundation of much of the world economy and has vast financial resources, providing ample incentive to develop the next generation of the technology. With APM there is no legacy of previous generations, so the incentive to develop the first generation has to come from industries and needs served by different technologies (molecular sciences like chemistry and biotechnology, materials science) that could benefit by extension or replacement of those technologies with APM.

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Nanothreads formed from smallest possible diamonds

Posted by Jim Lewis on May 2nd, 2015

Diamond nanothreads promise extraordinary properties, including strength and stiffness greater than that of today's strongest nanotubes and polymers. The core of the nanothreads is a long, thin strand of carbon atoms arranged just like the fundamental unit of a diamond structure -- zig-zag cyclohexane rings of six carbon atoms bound together, in which each carbon is surrounded by others in the strong triangular-pyramid shape of a tetrahedron. The threads, made for the first time by a team led by John V. Badding of Penn State University, have a structure that has never been seen before. Credit: Enshi Xu, Vincent Crespi lab, Penn State University

A few months ago we cited a report of a new form of carbon—penta-graphene—that had been computationally simulated but not yet synthesized. Foresight Co-Founder Christine Peterson forwarded a link to this publication a couple months ago that reported the mechanical properties of yet another form of carbon—diamond nanothreads. This Nano Letters abstract reports that, based on molecular dynamics simulations, diamond nanothreads have a stiffness comparable to carbon nanotubes and a tenacity (specific strength) exceeding carbon nanotubes and graphene.

A Penn State news release reported the first production of diamond nanothreads last September “Smallest Possible Diamonds Form Ultra-thin Nanothreads“:

21 September 2014 — For the first time, scientists have discovered how to produce ultra-thin “diamond nanothreads” that promise extraordinary properties, including strength and stiffness greater than that of today’s strongest nanotubes and polymers. A paper describing this discovery by a research team led by John V. Badding, a professor of chemistry at Penn State University, will be published in the 21 September 2014 issue of the journal Nature Materials [abstract].

“From a fundamental-science point of view, our discovery is intriguing because the threads we formed have a structure that has never been seen before,” Badding said. The core of the nanothreads that Badding’s team made is a long, thin strand of carbon atoms arranged just like the fundamental unit of a diamond’s structure — zig-zag “cyclohexane” rings of six carbon atoms bound together, in which each carbon is surrounded by others in the strong triangular-pyramid shape of a tetrahedron. “It is as if an incredible jeweler has strung together the smallest possible diamonds into a long miniature necklace,” Badding said. “Because this thread is diamond at heart, we expect that it will prove to be extraordinarily stiff, extraordinarily strong, and extraordinarily useful.”

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