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Designing novel protein backbones through digital evolution

Posted by Jim Lewis on January 17th, 2017

Overview of the SEWING method. Each panel, from left to right: parental structures with extracted substructures; Graph schematic - colored nodes indicate substructures contained in final design model, superimposed structures show structural similarity indicated by adjacent edges; Design model before sequence optimization and loop design; Final design models. Credit: Jacobs et al.

Continuing yesterday’s discussion of two complementary approaches to balance designing protein structures with novel functions with designing protein structures with maximum stability, we focus on a method to create novel proteins by stitching together pieces of existing proteins, developed by Brian Kuhlman, one of two co-winners of the 2004 Feynman Prize, Theory category, and his collaborators. From the University of North Carolina Medical School newsroom “Scientists digitally mimic evolution to create new proteins“:

… researchers at the University of North Carolina School of Medicine have developed a method that creates novel proteins by stitching together pieces of already existing proteins.

The technique, called SEWING, is inspired by natural evolutionary mechanisms that also recombine portions of known proteins to produce new structures and functions. This approach can generate a diverse set of protein structures with many of the distinctive features that proteins require to carry out specific biological functions.

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Adding modular hydrogen-bond networks to protein design

Posted by Jim Lewis on January 15th, 2017

Molecular recognition in DNA is built upon a small set of hydrogen-bonding interactions in the core of the DNA double helix. Specificity in protein folding depends largely on buried packing of hydrophobic amino acid side chains complemented by irregular interactions of specific polar groups. A general method is described to design a wide range of protein oligomers that specifically interact via a network of hydrogen bonds. Credit: Baker Lab, University of Washington.

Advances last year in the bottom-up design and fabrication of increasingly complex atomically precise nanostrutures were so rapid we were not able to cover as many as we wanted. Before we dive into this year’s advances, we are catching up on some of the important advances we missed last year. Perhaps the most active area of molecular engineering research last year was the de novo protein design area, originally proposed by Foresight co-founder K. Eric Drexler as “a path to the fabrication of devices to complex atomic specifications”. Our most recent post in this area cites five earlier posts last year about protein design.

Continuing our coverage of important advances in protein design, the two co-winners of the 2004 Feynman Prize, Theory category (for developing the Rosetta software suite for biomolecular modeling and design) both reported important protein design advances in adjacent papers in Science last May. A perspective commentary “Inspired by nature” in the same issue by Ravit Netzer and Sarel J. Fleishman of the Weizmann Institute of Science points out that the great success over the past decade of de novo designing proteins that folded exactly as designed and were very stable has not produced all of the “important structural features seen in protein interfaces and enzyme active sites”. They note that computer algorithms like Rosetta used to design proteins optimize stability. “By contrast, evolution selects proteins for their ability to perform a vital molecular function, often at the expense of stability.” They discuss the complementary approaches to this issue taken by David Baker and his collaborators (today’s post) and by Brian Kuhlman and his collaborators (tomorrow’s post).

Writing in Geekwire, Alan Boyle reports “Scientists add twists to protein designs“:

Biochemists from the University of Washington have engineered complex protein molecules with additional chemical bonds that make it possible to mix and match them like the base pairs of DNA.

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A brief history of nanotechnology

Posted by Jim Lewis on January 3rd, 2017

Richard Feynman teaches a special lecture on March 13, 1964. United States government work.

Our two most recent posts (here and here) have been about efforts by the Advanced Manufacturing Office of the U.S. Department of Energy to promote atomically precise manufacturing—a specific vision for the future of nanotechnology—a vision upon which the Foresight Institute has been focused since our founding 30 years ago. The vision was far removed from then current laboratory technologies, but those current technologies were entering a period of very rapid progress. Progress in several areas led to very useful functional nanomaterials and nanodevices. Enthusiasm for near-term commercial applications became conflated with a long-term technology vision and combined to bring forth ambitious new funding in the US and elsewhere. The differing visions of what nanotechnology is and can become, and the resulting conflicts over funding and over the public image of nanotechnology, are part of the story of Foresight’s first 30 years “Thirty Years of Nanotechnology and Foresight“. An engaging perspective on the history of nanotechnology written by W. Patrick McCray, a professor in the history department at the University of California–Santa Barbara, was published by Slate earlier this year as part of its Futurography series: “Gods of Small Things“.

The field may seem new—but it dates back more than 50 years

… Since the 21st century began, few emerging technologies have been so heavily promoted, funded, and debated as nanotechnology. Defined (currently) by the U.S. government as “the understanding and control of matter at the nanoscale”—a nanometer is one-billionth a meter—nanotechnology as a field and research community has received billions of funding dollars, making it one of the nation’s largest technology investments since the space race.

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New Funding Opportunity from U.S. DOE

Posted by Jim Lewis on January 1st, 2017

U.S. Department of Energy Mission Innovation - a joint effort by more than 20 nations to double clean energy R&D by 2020.

David Forrest, Technology Manager, Advanced Manufacturing Office, U.S. Department of Energy, writes with news of a new funding opportunity at DOE:

Dear Friends and Colleagues who have shown some interest in Atomically Precise Manufacturing (APM),

I am pleased to forward this funding opportunity announcement (FOA) to you from the Advanced Manufacturing Office. The FOA includes a range of topics in advanced materials and processes, and explicitly includes a subtopic on Atomically Precise Manufacturing.

Note: scroll down to the line “DE-FOA-0001465 – Advanced Manufacturing Projects for Emerging Research Exploration (Last Updated: 12/21/2016 05:28 PM ET)” Download the PDF and scroll down to page 11/91 – “Subtopic 1.5 – Atomically Precise Manufacturing”

As some of you know, we have been soliciting SBIR projects in this space for several years now but this is the first AMO R&D Projects FOA in this space. And the application space has been expanded from the SBIR offerings—responsive concept papers and proposals will include atomically precise membranes and catalysts, sensors, molecular electronic computer circuits, and also tools and systems to perform APM through positional assembly (whether tip-based, or molecular machine-based–aka molecular additive manufacturing). Announcement is [here].

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DOE office focusing on atomically precise manufacturing

Posted by Jim Lewis on December 31st, 2016

David Forrest ScD, PE, FASM
Technology Manager, Advanced Manufacturing Office,
U.S. Department of Energy

Longtime Foresight member David Forrest has been involved with nanotechnology development since his student days at MIT with Foresight co-founders Eric Drexler and Christine Peterson, and since October 2012 he has been Technology Manager, Advanced Manufacturing Office, U.S. Department of Energy. At Foresight Institute’s Breakthrough Technologies for Energy workshop this past spring, Dr. Forrest spoke about “Progress in Atomically Precise Manufacturing at the Advanced Manufacturing Office”. The strategic goals of this effort include developing a suite of manufacturing technologies capable of building a broad range of macroscopic atomically precise products, and transitioning these to commercial practice to transform the U.S. manufacturing base to APM-centric production. The motivation from the standpoint of DOE is to reduce energy use. Current efforts began with a DOE workshop held August 5-6, 2015 in Berkeley, CA “Workshop on Integrated Nanosystems for Atomically Precise Manufacturing“. The six plenary presentations that can be downloaded from the workshop web page comprise arguably the best overview of progress toward APM since Foresight Institute and Battelle unveiled a Technology Roadmap for Productive Nanosystems in 2007. When complete, the workshop report is expected to be available from this page.

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Nobel Prize in Chemistry recognizes molecular machines

Posted by Jim Lewis on October 10th, 2016

Sir Fraser receiving the 2007 Foresight Feynman Prize for Experiment

Sir J. Fraser Stoddart, joint winner of the 2016 Nobel Prize in Chemistry, accepting the 2007 Foresight Institute Feynman Prize for Experiment.

The 2016 Nobel Prize in Chemistry was awarded to three scientists who “developed the world’s smallest machines”. From the Royal Swedish Academy of Sciences “Press Release: The Nobel Prize in Chemistry 2016“:

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry 2016 to
Jean-Pierre Sauvage, University of Strasbourg, France
Sir J. Fraser Stoddart, Northwestern University, Evanston, IL, USA, and
Bernard L. Feringa, University of Groningen, the Netherlands
“for the design and synthesis of molecular machines” …

A tiny lift, artificial muscles and minuscule motors. The Nobel Prize in Chemistry 2016 is awarded to Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa for their design and production of molecular machines. They have developed molecules with controllable movements, which can perform a task when energy is added.

The development of computing demonstrates how the miniaturisation of technology can lead to a revolution. The 2016 Nobel Laureates in Chemistry have miniaturised machines and taken chemistry to a new dimension.

The first step towards a molecular machine was taken by Jean-Pierre Sauvage in 1983, when he succeeded in linking two ring-shaped molecules together to form a chain, called a catenane. Normally, molecules are joined by strong covalent bonds in which the atoms share electrons, but in the chain they were instead linked by a freer mechanical bond. For a machine to be able to perform a task it must consist of parts that can move relative to each other. The two interlocked rings fulfilled exactly this requirement.

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Assembling a large, stable, icosahedral protein molecular cage

Posted by Jim Lewis on September 9th, 2016

The design model of the icosahedral nano-cage shows its large, empty volume. UW Institute for Protein Design

It feels like progress in the design and fabrication of atomically precise nanostructures and molecular machines is accelerating along several different paths. A couple days ago we cited advances in molecular machines fabricated using organic synthesis. Earlier this year we cited a number of advances along the protein design pathway to atomically precise manufacturing (here, here, here, here, here). A hat tip to Nanowerk for reprinting this recent advance from the University of Washington Health Sciences news room, written by Leila Gray, and describing work from the University of Washington Institute for Protein Design directed by David Baker, co-winner of the 2004 Feynman Prize, Theory categorySelf-assembling protein icosahedral shell designed“:

The same 20-sided solid that was morphed into geodesic domes in the past century may be the shape of things to come in synthetic biology.

For University of Washington Institute of Protein Design scientists working to invent molecular tools, vehicles, and devices for medicine and other fields, the icosahedron’s geometry is inspiring. Its bird cage-like symmetry and spacious interior suggest cargo-containing possibilities.

The protein designers took their cue from the many viruses that, en route to living cells, transport their genomes inside protective icosahedral protein shells. These delivery packages, termed viral capsids, are formed to be tough enough to withstand the trip, efficiently use storage room, and break apart to release their contents when conditions are right.

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Chemical fuel keeps molecular motor moving

Posted by Jim Lewis on September 4th, 2016

Earlier this year we cited further progress on molecular machines, in this case transporting cargo, from the group of Professor David A Leigh FRS FRSE MAE and winner of the 2007 Feynman Prize in Nanotechnology, Theoretical category. Further molecular machine progress was recently reported by Belle Dumé at “Chemically powered nanomotor goes autonomous“:

Researchers at the University of Manchester, UK have made the first autonomous chemically powered synthetic small-molecule motor. The new device, which is very much like the protein motors found in biological cells, might be used to design artificial molecular machines similar to those found in nature. Such machines could be important for applications such as synthetic muscles, nano- and micro-robots and advanced mechanical motors.

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Rational improvement of DNA nanodevice function

Posted by Jim Lewis on August 13th, 2016

Left panel shows tweezers in the open position, with the enzyme (green) on the upper arm and the co-factor (gold) on the lower arm. Supplying a complementary fuel strand causes the tweezers to close, producing the reaction of the enzyme-cofactor pair. (Right panel) while a set strand restores the tweezers to their open position. Image credit: Biodesign Institute, Arizona State University

We have frequently cited examples of the artificial molecular machines that can be built from DNA. An open question is whether these prototype molecular machines can be improved toward practical applications. For example, can simple machines for manipulating molecules be improved to the point of implementing atomically precise manufacturing? A recent publication provides an example of rational improvement of a simple DNA machine reported three years ago. Three years ago a news release from the Biodesign Institute of Arizona State University reported “Tiny tweezers allow precision control of enzymes“:

Tweezers are a handy instrument when it comes to removing a splinter or plucking an eyebrow.

In new [2013] research, Hao Yan and his colleagues at Arizona State University’s Biodesign Institute describe a pair of tweezers shrunk down to an astonishingly tiny scale. When the jaws of these tools are in the open position, the distance between the two arms is about 16 nanometers—over 30,000 times smaller than a single grain of sand.

The group demonstrated that the nanotweezers, fabricated by means of the base-pairing properties of DNA, could be used to keep biological molecules spatially separated or to bring them together as chemical reactants, depending on the open or closed state of the tweezers.

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Atomically precise location of dopants a step toward quantum computers

Posted by Jim Lewis on August 4th, 2016

An STM image showing the atomic level detail of the electron wave function of a sub-surface phosphorus dopant. Through highly precise matching with theoretical calculations the exact lattice site position and depth of the dopant can be determined. Credit: University of Melbourne

A couple months ago we cited the demonstration of a quantum simulator with dopant atoms placed in silicon with atomic precision. The same Australian and New Jersey teams have since further advanced the prospects for tomorrow’s silicon-based quantum computers. A hat tip to Nanowerk for reprinting this University of Melbourne news release “World-first pinpointing of atoms at work for quantum computers“:

Scientists can now identify the exact location of a single atom in a silicon crystal, a discovery that is key to greater accuracy in the operation of tomorrow’s silicon-based quantum computers.

It’s now possible to track and see individual phosphorus atoms in a silicon crystal allowing confirmation of quantum computing capability but which also has use in nano detection devices.

Quantum computing has the potential for enormous processing power in the future. Your current laptop has transistors that use a binary code, an on or off state (bits). But tomorrow’s quantum computer will use quantum bits ‘qubits’, which have multiple states.

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Watching individual chemical bonds during a reaction

Posted by Jim Lewis on August 2nd, 2016

Identification of reactants, transient intermediates, and products in a bimolecular enediyne coupling and cyclization cascade on a silver surface by non-contact atomic force microscopy. The corresponding chemical structures are depicted below the nc-AFM images. Image credit: A. Riss, adapted from DOI: 10.1038/nchem.2506

One path to advanced nanotechnologies begins with using scanning probe microscopes (SPM) to make atomically precise surface modifications—see, for example p. xii of Productive Nanosystems: A Technology Roadmap. The more precisely the SPM tip can image and manipulate atoms on a surface, the more rationally this path can be planned and implemented. Some of the most impressive progress along this path has come from using noncontact-atomic force microscopy (NC-AFM), such as measuring individual chemical bonds using a carbon monoxide-functionalized tip. Now researchers have succeeded in seeing changes in bond configurations as an organic reaction is catalyzed on a surface. A hat tip to Nanowerk for reprinting this press release from the Max Planck Institute for the Structure and Dynamics of Matter “Viewing a catalytic reaction in action“:

To be able to follow and directly visualize how the structure of molecules changes when they undergo complex chemical transformations has been a long-standing goal of chemistry. While reaction intermediates are particularly difficult to identify and characterize due to their short lifetimes, knowledge of the structure of these species can give valuable insights into reaction mechanisms and therefore impact fields beyond the chemical industry, such as materials science, nanotechnology, biology and medicine. Now an international team of researchers led by Felix R. Fischer, Michael F. Crommie (University of California at Berkeley and Lawrence Berkeley National Laboratory), and Angel Rubio (Max Planck Institute for the Structure and Dynamics of Matter at CFEL in Hamburg and University of the Basque Country in San Sebastián) has imaged and resolved the bond configuration of reactants, intermediates and final products of a complex and technologically relevant organic surface reaction at the single-molecule level. The findings are published in the journal Nature Chemistry [abstract].

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Peptoid nanosheets assemble by different design rule

Posted by Jim Lewis on July 31st, 2016

Snakes on a plane: This atomic-resolution simulation of a peptoid nanosheet reveals a snake-like structure never seen before. The nanosheet’s layers include a water-repelling core (yellow), peptoid backbones (white), and charged sidechains (magenta and cyan). The right corner of the nanosheet’s top layer has been “removed” to show how the backbone’s alternating rotational states give the backbones a snake-like appearance (red and blue ribbons). Surrounding water molecules are red and white. Image courtesy of Ranjan V. Mannige, Molecular Foundry, Berkeley.

The earliest proposal to “open a path to the fabrication of devices to complex atomic specifications” envisioned designing proteins to fold in predetermined ways. Over the years we have cited here numerous advances along this path, most recently here, here, here, here, and here. There has also been interest in polymers that are chemical cousins of proteins, for example, the peptoids, in which the side chains are appended to the nitrogen atom in the peptide bond joining the monomers, rather than to the alpha carbon atom, as is the case with proteins. Four years ago we cited a report of initial successes in the rational design of peptoids, speculated that it might be opening a path to advanced nanotechnology, but noted that their successful computer modeling had so far only produced structures composed of nine subunits. Now we can cite further work by a subset of that group reporting a peptoid nanosheet, two molecules thick but extending laterally for micrometers, based on a structural element not seen in the natural world. A hat tip to Nanowerk for reprinting this news release from the U.S. Dept.of Energy Office of Science “Understanding and Predicting Self-Assembly“:

To mimic complex natural proteins’ capabilities as sensors, catalysts, and more using synthetic materials that can withstand industrial conditions, scientists must first know how to finesse the building blocks they’ll use. Molecular Foundry staff worked with scientists to discover a new design rule that controls the way in which polymer building blocks adjoin to form the backbones that run the length of tiny biomimetic sheets.

Understanding the rules that govern how the nanosheets self-assemble could be used to piece together complex sheet structures and others, such as nanotubes and crystalline solids, that could be customized into incredibly sensitive chemical detectors or long-lasting catalysts, to name a few possibilities.

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Engineered protein assembles molecules into atomically precise lattice

Posted by Jim Lewis on July 30th, 2016

A buckyball, a sphere-like molecule composed of 60 carbon atoms shaped like a soccer ball. (Image credit: St Stev via / CC BY-NC-ND)

An important step as nanotechnology develops toward the ultimate goal of general purpose, high-throughput, atomically precise manufacturing is the use of molecules specifically designed to organize other molecules into precise orientations in space. Simple first steps would be to organize repeating lattices of one component to make novel functional materials; more complex further steps would be to precisely organize the multiple components of molecular machine systems. An early step in this process was reported this spring using a specially engineered protein. A hat tip to Nanowerk for reprinting this Dartmouth College news release “Researchers Create Artificial Protein to Control Assembly of Buckyballs“:

A Dartmouth College scientist and his collaborators have created an artificial protein that organizes new materials at the nanoscale.

“This is a proof-of-principle study demonstrating that proteins can be used as effective vehicles for organizing nano-materials by design,” says senior author Gevorg Grigoryan, an assistant professor of computer science at Dartmouth. “If we learn to do this more generally – the programmable self-assembly of precisely organized molecular building blocks — this will lead to a range of new materials towards a host of applications, from medicine to energy.”

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Another powerful nanoengine remembered

Posted by Jim Lewis on July 11th, 2016

A nanocrystal ram is sandwiched between two MWNT lever arms. On one nanotube a metal particle serves as an atom reservoir that can source or sink atoms to or from the nanocrystal ram. The nanotube conveys the thermally excited atoms between the atom reservoir and ram. Credit: Regan et al. 2005 Nano Letters DOI: 10.1021/nl0510659

Last month we posted a report of a powerful new type of nanoengine, able to deliver a force of ~5 nN (nanonewtons). The authors noted that “The resulting nanoscale forces are several orders of magnitude larger than any produced previously.” A couple weeks later Foresight Senior Fellow—Standards David R. Forrest wrote to challenge that comparison:

Just a quick note on

Cambridge claimed: “The forces exerted by these tiny devices are several orders of magnitude larger than those for any other previously produced device”

I don’t think that is true.

Zettl’s actuator force was 2.6 nN, vs. 5 nN for this “device.” See Reference 8

Given the similar sizes, and noting that the gold nanoparticles ALSO require the surrounding polymer mass as part of the actuation system, I think Zettl’s device has the edge regarding smallest total mass although it’s hard to beat Cambridge’s I/O (light). Also I would note that Zettl’s actuator was positioned on a fixed CNT surface, which allowed the force to be applied at a known location; not true for the particles in suspension. To get useful work out of the device there would need to be attached substrates/levers/something. (More mass, then.)

They probably don’t know about Zettl’s work.

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Simulation of quantum entanglement with subsurface dopant atoms

Posted by Jim Lewis on June 9th, 2016

Atomic resolution single-hole tunnelling probes the interacting states of coupled acceptor dopants. Interference of atomic orbitals directly contained in the quasi-particle wavefunction (QPWF) allows quantifying the electron–electron correlations and the entanglement entropy. Credit: Salfi et al. and Nature Communications

Based on their success reported here four years ago of creating a working transistor from a single atom placed in a silicon crystal with atomic precision, researchers from the University of New South Wales and the University of Melbourne in Australia, and from Purdue University in the US, have created a quantum simulator with dopant atoms placed in silicon with atomic precision. A hat tip to Nanowerk for reprinting this news release from the University of New South Wales written by Deborah Smith “Atoms placed precisely in silicon can act as quantum simulator“:

Coinciding with the opening of a new quantum computing laboratory at UNSW by Prime Minister Malcolm Turnbull, UNSW researchers have made another advance towards the development of a silicon-based quantum computer.

Coinciding with the opening of a new quantum computing laboratory at UNSW by Prime Minister Malcolm Turnbull, UNSW researchers have made another advance towards the development of a silicon-based quantum computer.

In a proof-of-principle experiment, they have demonstrated that a small group of individual atoms placed very precisely in silicon can act as a quantum simulator, mimicking nature – in this case, the weird quantum interactions of electrons in materials.

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Protein design provides a novel metabolic path for carbon fixation

Posted by Jim Lewis on June 8th, 2016

Overlay of the Des1 crystal structure (blue) and the FLS model (green, with mutated residues brown) with the docked DHA product (purple). The four active site mutations (BAL vs. Des1) are shown in sticks, conserved amino acids in lines. Credit: Siegel et al. PNAS March 24, 2015

More evidence that computational protein design can create not only novel proteins but also novel functions that do not exist in nature comes from the creation of an entire novel metabolic pathway. A large collaboration involving scientists from the University of California, Davis, two research groups at the University of Washington (including the lab of David Baker, who shared the 2004 Foresight Institute Feynman Prize for theoretical work), the Fred Hutchinson Cancer Research Center, and several other institutions in California and Israel published a paper last year in PNASComputational protein design enables a novel one-carbon assimilation pathway” that describes a novel computationally designed enzyme they designate “formolase” that catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxy acetone molecule. This complex project comprised many steps to create three novel enzyme functions, not previously known, in the process creating a microbial metabolic pathway that could be further optimized for enhanced production of desired products. This research demonstrates the feasibility of organizing multiple engineered enzymes into a sequence that does not exist in nature. In this particular case the goal is to address current challenges in energy storage and carbon sequestration by converting one carbon compounds, such as CO2, into multicarbon fuels and other high-value chemicals. One could also envision such systems as components along the path to productive nanosystems, leading eventually to general purpose, high throughput atomically precise manufacturing.

The authors note that the lack of one-carbon anabolic pathways in microbes suitable to address current needs in energy storage and carbon sequestration could arise from unfavorable chemical driving force at one or more pathway steps, the inherent complexity and inefficiency of the steps, or the environmental sensitivity of the steps (the ability to function efficiently under both aerobic and anaerobic conditions). Despite the lack of such a pathway in nature, they further note, the established electrochemical reduction of CO2 to formate provides an attractive starting point for a one-carbon fixation pathway. They describe in this paper the computational design of an enzyme that catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon molecule. The new enzyme enables the construction of the ‘formolase’ pathway, which converts formate into the centrally important metabolite dihydroxyacetone phosphate.

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Powerful nanoengine built from coated nanoparticles

Posted by Jim Lewis on June 5th, 2016

Expanding polymer-coated gold nanoparticles. Credit: Yu Ji/University of Cambridge NanoPhotonics

Discussions of complex molecular machine systems or nanorobots navigating through water frequently raise the issue of whether nanoscale engines can be powerful enough. Scientists at UK’s Cavendish Laboratory have provided one response. A hat tip to KurzweilAI for showcasing this University of Cambridge news release “Little ANTs: researchers build the world’s tiniest engine“:

Researchers have built a nano-engine that could form the basis for future applications in nano-robotics, including robots small enough to enter living cells.

Researchers have developed the world’s tiniest engine – just a few billionths of a metre in size – which uses light to power itself. The nanoscale engine, developed by researchers at the University of Cambridge, could form the basis of future nano-machines that can navigate in water, sense the environment around them, or even enter living cells to fight disease.

The prototype device is made of tiny charged particles of gold, bound together with temperature-responsive polymers in the form of a gel. When the ‘nano-engine’ is heated to a certain temperature with a laser, it stores large amounts of elastic energy in a fraction of a second, as the polymer coatings expel all the water from the gel and collapse. This has the effect of forcing the gold nanoparticles to bind together into tight clusters. But when the device is cooled, the polymers take on water and expand, and the gold nanoparticles are strongly and quickly pushed apart, like a spring. The results are reported in the journal PNAS [abstract].

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Foresight Co-Founder to speak on altruism, nanotechnology

Posted by Jim Lewis on May 28th, 2016

Foresight Co-Founder Christine Peterson will speak on “High-Leverage Altruism” at Effective Altruism Global 2016, August 5-7, 2016, Berkeley, California. This is the fourth annual conference of Effective Altruism, “a growing community based on using reason and evidence to improve the world as much as possible. This year, around 1000 attendees and over 50 speakers from around the world are expected to attend.” Featured topics include “CRISPR: Can and should we use it to end malaria?”, “How will philanthropy shape the development of breakthrough technologies?”, “Can we end global poverty within a generation? How?”, “Risks and benefit of advanced AI”, and “Replacing meat, reducing suffering”. EA Global 2016 is organized by the Effective Altruists of Berkeley in collaboration with the Centre for Effective Altruism. For more information on what Effective Altruism is, visit or

Peterson will also speak on nanotechnology a few weeks later at the Singularity University Global Summit, August 28-30, 2016, San Francisco, California. SU Global Summit is the definitive gathering for those who understand the critical importance of exponential technologies, the impact they’ll have on the future of humanity, and the disruption these technologies will cause across all industries. Other speakers include Peter Diamandis, Ray Kurzweil, and Melanie Swan; an unconference component is included as well.

If you do attend either of these meetings, Christine asks that you stop by and say hello!
—James Lewis, PhD

Foresight President to speak on Artificial Intelligence

Posted by Jim Lewis on May 10th, 2016

The TEDxEchoPark “Paradigm Shift” event on Saturday May 14, 2016, in Los Angeles, California, will “examine the most intriguing Paradigm Shifts unraveling in every field; from artificial intelligence to education, from branding to sexuality, from food to consciousness and many more. The event examines three key drivers that are sparking this change: ideas as impetus for change, combination as impetus for change and invention or discovery as impetus for change. Common to this colorful mix of Paradigm Shifts is their promise to deliver a roadmap that is superior to its predecessor in navigating us into a better future. At TEDxEchoPark we will take this map on a tour.” Foresight President Julia Bossmann will speak on Artificial Intelligence:

Julia Bossmann
President of Foresight Institute and Founder of Synthetic to speak on AI
Julia Bossmann is the president of Foresight Institute, the leading think tank on world­changing technologies such as nanotechnology and artificial intelligence (AI). Bossmann holds a Masters degree with highest honors in brain & behavioral sciences from the University of Dusseldorf and USC. Her professional experience includes scientific research in labs in Germany and in the USA, management consulting at McKinsey & Company, R&D at Bosch Research and Technology, and entrepreneurship at Anticip8 and Synthetic. Bossmann is a GSP alumna at Singularity University and a Global Shaper at the World Economic Forum. She has spoken at the World Economic Forum’s annual meeting in Davos on the role of Artificial Intelligence in the Fourth Industrial Revolution.

Tickets are available at the event web site.
—James Lewis, PhD

Triple helices stabilize macroscopic crystals for DNA nanotechnology

Posted by Jim Lewis on May 5th, 2016

To self-assemble macroscopic, porous DNA crystals suitable for use as structural scaffolds or molecular sieves, it was first necessary to show that macroscopic crystals could be self-assembled from atomically precise DNA nanostructures, and then to show that triple helix forming oligo nucleotides could target cargo molecules to each cavity in the crystal with sub-nanometer precision. A paper published last year from Prof. Chengde Mao of Purdue University and Prof. Nadrian C Seeman of New York University, and their collaborators tackles and resolves conflicting requirements for successful self assembly. The component nanostructures must attach to each other using interactions that are weak enough that a building block in an incorrect site can detach, but strong enough that the final structure is stable. They report success using another molecule that binds to the cohesive sites and stabilizes the interactions among the subunits: “Post-Assembly Stabilization of Rationally Designed DNA Crystals” (abstract, full text behind pay wall).

Each gray rod represents a DNA duplex, and the red line represents a triplex-forming DNA strand. Credit: Zhao et al. Angewandte Chemie

The authors explain that the triangular DNA motifs that they engineered to assemble into macroscopic 3D crystals bind weakly to adjacent motifs through a pair of two-nucleotide single-stranded overhangs (sticky ends). With such weak interactions, the crystals are stable only in high salt solutions (> 1.2M (NH4)2SO4), which however, greatly limit the applications for which they can be used. Their solution is to strength the inter-triangle interactions after self-assembly by adding a triplex-forming oligonucleotide at the inter-triangle cohesion region to enhance the interactions of the tensegrity triangle subunits.

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