Foresight Institute https://foresight.org Foresight Institute Wed, 17 Jan 2018 20:23:26 +0000 en-US hourly 1 https://foresight.org/wp-content/uploads/2017/04/cropped-foresight-logo-notext-2-32x32.png Foresight Institute https://foresight.org 32 32 Design of hyperstable constrained peptides https://foresight.org/design-hyperstable-constrained-peptides/ https://foresight.org/design-hyperstable-constrained-peptides/#respond Wed, 17 Jan 2018 20:23:26 +0000 https://foresight.org/?p=21099 Sixteen topologies of de novo designed hyperstable constrained peptides. Credit: Baker lab, University of Washington Protein design has been one of the major paths from current fabrication technology toward the goal of general purpose, high-throughput atomically precise manufacturing since Foresight co-founder Eric Drexler proposed it in 1981. It also produced some of the earliest [...]

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sixteen peptide topologies formed by different combinations of alpha-helices and beta strands

Sixteen topologies of de novo designed hyperstable constrained peptides. Credit: Baker lab, University of Washington

Protein design has been one of the major paths from current fabrication technology toward the goal of general purpose, high-throughput atomically precise manufacturing since Foresight co-founder Eric Drexler proposed it in 1981. It also produced some of the earliest promising results. Although de novo protein design was at first slow, progress has accelerated since David Baker (University of Washington) and Brian Kuhlman (University of North Carolina) won the 2004 Foresight Feynman Prize for Theoretical work for the creation of the RosettaDesign software for modeling and analysis of protein structures. Among recent successes: “From de novo protein design to molecular machine systems“, “Designing novel protein backbones through digital evolution“, and “Rational design of protein architectures not found in nature“. Another milestone accomplished the design of new backbone structures to fit into target binding, and opened up previously inaccessible regions of shape space to design and fabricate new parts for complex molecular machine systems. A September, 2016 news release from the Baker Lab “Accurate de novo design of hyperstable constrained peptides“:

Small constrained peptides combine the stability of small molecule drugs with the selectivity and potency of antibody-based therapeutics. However, peptide-based therapeutics have largely remained underexplored due to the limited diversity of naturally occurring peptide scaffolds, and a lack of methods to design them rationally.

In an article published in Nature this week [abstract, PDF courtesy of Baker lab], Baker lab scientists and collaborators describe the development of computational methods for de novo design of constrained peptides with exceptional stabilities. They used these computational methods to design 18-47 residue constrained peptides with diverse shapes and sizes. The designed peptides presented in the paper cover three broad categories: 1) genetically encodable disulfide cross-linked peptides, 2) synthetic disulfide cross-linked peptides with non-canonical sequences, and 3) cyclic peptides with non-canonical backbones and sequences. Experimentally determined structures for these peptides are nearly identical to their design models.

By including D-amino acids (mirror images of the L-amino acids), and thus expanding the palette of building blocks, Baker lab scientists designed peptides in a sequence and structure space sampled rarely by Nature. Indeed, the article describes successful design of a cyclic 2-helix peptide of mix chirality that represents a shape beyond natural secondary- and tertiary structure.

These designed peptides also exhibit exceptional stability to thermal and chemical denaturation, and thus could serve as attractive scaffolds for design of novel peptide-based therapeutics. More broadly, development of this new computational toolkit to precisely design constrained peptides opens the door for “on-demand” development of a new generation of peptide-based therapeutics.

This research begins with the observation that constrained peptides are an unexplored frontier for drug discovery that is made interesting by the fact that among the small number of examples known are some of the most potent pharmacologically active compounds known. these peptides are constrained by disulfide bonds or backbone cyclization to favor conformations that precisely complement their targets. The inability to achieve global shape complementarity with targets reveals the need for a method to create constrained peptides that provide precise control over the size and shape of the designed molecules. The desire of the researchers to access “broad regions of peptide structure and function space not explored by evolution” provides a motivation to incorporate non-canonical backbones and unnatural amino acids.

Of course, the computational design of covalently constrained peptides with new strutures and non-canonical backbones presents new challenges, including mixed chirality. The Rosetta software suite was used for all of the design calculations in this article. A diverse array of 18-47 residue peptides was designed. These included two classes of peptides: (1) genetically encodable (i.e., using only the 20 amino acids specified by the universal genetic code, often called the canonical amino acids) disulfide-rich peptides, (2) heterochiral peptides with non-canonical sequences. The authors note that genetic encodability has the advantage of compatibility with high-throughput selection methods like phage, ribosome, and yeast display, while incorporation of non-canonical components opens access to new types of structures. For the former class, they selected nine combinations of α-helices and β-strands. The latter class included α-helices and β-strands connected by loop segments containing D-amino acid residues, non-canonical amino acids, and cyclic structures.

Genetically encodable disulfide-constrained peptides

For the nine chosen topologies of genetically encodable disulfide-constrained peptides, Monte Carlo-based assembly of short protein fragments was used to construct backbone conformations, which were then scanned for sites capable of hosting disulfide bonds with nearly ideal geometry. One ot three disulfides bonds were incorporated and low energy sequences were designed and optimized using the Rosetta all-atom force field. Rosetta ab initio structure prediction calculations were carried out for each designed sequence, resulting in a diverse set of 130 designs for which the target structure was in a deep global free-energy minimum (i.e., the structure would be very stable). Genes were constructed for each design and expressed in the bacterium Escherichia coli or in cultured mammalian cells. Since disulfide bonds would be unlikely to form in the reducing environment of the cytoplasm, gene expression was engineered to secrete the designed proteins, which were analyzed for signs that the disulfide bond had formed consistent with the designed topology. 29 designs passed this test, and one representative design was chosen from each of the nine topologies for further biochemical characterization.

One of the nine designs produced a protein that could be crystallized. The structure was determined to a resolution of 0.209 nm. The details of the structure were in excellent agreement with the design model. The protein was thermostable and completely resistant to chemical denaturation.

The eight designs that could not be crystallized were expressed as isotopically labelled peptides and the structures determined by nuclear magnetic resonance (NMR) spectroscopy. The formation of the designed disulfide bonds was confirmed. “Taken together, the X-ray crystallographic and NMR structures demonstrate that our computational approach enables accurate design of protein main-chain conformation, disulfide bonds and core residue rotamers.”

Synthetic heterochiral disulfide-constrained peptides

To design shorter disulfide-constrained peptides incorporating
both l- and d-amino acids, the rosetta energy function was generalized to support D-amino acids and mixed chirality designs. Since chemical synthesis required to synthesize peptides that cannot be genetically encoded is laborious, automated computational screening techniques were developed to supplement Rosetta ab initio screening with molecular dynamics (MD) evaluation. Sequences were designed favoring D-amino acids at positions with positive main chain φ dihedral angle values. A single low energy design was selected for each of three topologies evaluated, chemically synthesized, and structurally characterized by NMR. All three gave NMR spectra consistent with the secondary structure of the design. High resolution NMR solution structures showed close agreement for two of the designs. The third differed from the design model by having an unwound carboxyl terminus, but a second design chosen for that topology had a structure very close to the design model. All three designs were very thermostable.

Synthetic backbone-cyclized peptides

A generalized kinematic loop closure method (named GenKIC) was implemented to samo arbitrary covalently linked atom chains capable of connecting the termini. Each GenKIC chain-closure attempt involved perturbing multiple chain degrees of freedom, then enforcing loop closure with ideal peptide bond geometry. “Sequence design, backbone relaxation, and in silico structure validation using MD simulation and Rosetta ab initio structure prediction were carried out with terminal bond geometry constraints”. Cyclic peptides were synthesized for three topologies, and their structures determined with NMR spectroscopy. All three peptides had structures very close to their design models, and all three were extremely stable to thermal denaturation and resistant to chemical denaturation. They were exceptionally stable given their small sizes.

Beyond natural secondary and tertiary structure

A “heterochiral, backbone-cyclized, two-helix topology with
one non-canonical left-handed α-helix and one canonical right-handed
α-helix” provided a final test of the design methodology. For validation by ab initio structure prediction, it was necessary to develop a new, GenKIC-based protocol since the standard Rosetta method uses uses fragments of native proteins, which typically do not contain left-handed helices. The selected design for this topology is a 26-residu protein with one D-cysteine,L-cysteine disulfide bond connecting the right-handed and left-handed α-helices. There was an excellent match between the NMR structure ensemble and the design model. This success demonstrated that the authors’ computational methods are general enough to design in a conformational space not explored by nature.

The authors point out that of the sixteen constrained peptide topologies designed, the twelve for which the strutures were experimentally determined were in close agreement with the design models. Unlike the natural constrained peptide families, these designed peptides are not limited to particular sizes, shapes, or disulfide connectivities.

Here we have focused on extending sampling and scoring methods to permit design with d-amino acids and cyclic backbones, but the new tools are fully generalizable to peptides containing more exotic building-blocks, such as amino acids with non-canonical sidechains or non-canonical backbones.

This research was clearly focused on extending de novo peptide design methods to provide a greater variety of protein components for drug discovery and therapeutic applications. Drugs and biotech therapies, whether small molecules or protein or other biomolecules, are all molecules sought to enhance or alter the functions of the complex natural molecular machine systems that comprise cells and organisms. Other complex molecular machine systems, as yet not designed, will play crucial roles along the paths to productive nanosystems and general purpose, high throughput atomically precise manufacturing.
—James Lewis, PhD

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Changing the world with a nanofabricator that could make anything https://foresight.org/changing-world-nanofabricator-make-anything/ https://foresight.org/changing-world-nanofabricator-make-anything/#respond Wed, 10 Jan 2018 17:31:14 +0000 https://foresight.org/?p=21046 Image Credit: 3DSculptor / Shutterstock.com The Foresight Institute was founded in 1986 on a vision presented by Eric Drexler in which the ultimate manufacturing technology uses a machine termed a nanofactory or nanofabricator to provide atom-by-atom control of the manufacturing process for complex objects, both large and small. Although initially controversial, this vision has [...]

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flower dissolving into constituent tiny cubes, conveying the idea of a nanofabricator building objects from molecular components, represented by tiny cubes

Image Credit: 3DSculptor / Shutterstock.com

The Foresight Institute was founded in 1986 on a vision presented by Eric Drexler in which the ultimate manufacturing technology uses a machine termed a nanofactory or nanofabricator to provide atom-by-atom control of the manufacturing process for complex objects, both large and small. Although initially controversial, this vision has been increasingly accepted over the past 32 years as progress in the underlying technologies leading in that direction has accelerated. Two essays published two weeks ago both point to Drexler’s vision and link it to a vision of the future put forward in September of 2013 by renowned British science historian James Burke, which predicts that nanofabricators will be common by 2042, and imagines the effects they will have had on the world by 2103, 90 years after Burke wrote. Burke’s September 2013 essay is available at RadioTimes “James Burke: I’ve seen the future“.

Burke bases his prediction that the world of 2103 will be unrecognizably different on the assumption that the year 2040 sees the beginning of worldwide distribution of kits to make a “nano-fabricator” able to take “dirt, air and water and a bit of cheap, carbon-rich acetylene gas”, manipulate atoms and molecules, and “produce anything you want, virtually free”. Since each of these can make a copy of itself, everyone has one by 2042.

… Sixty years later, we’ll have adapted to the new abundance and are living in small, no-pollution, autonomous communities, anywhere. Energy from spray-on photovoltaics makes any object (like a house) its own power source. So, here you are in your fabber-fabricated dwelling, filled with Mona Lisas if that’s your wish, with holographic reality transforming any room into anywhere (like: beach, sun, wind ruffling hair). So nobody travels any more. Want to see a pal, have dinner with your mother, join a discussion group? No problem: they’ll be there with you as 3D holograms, and you won’t know Stork from butter, unless you try to make physical contact (I’m avoiding sex and reproduction because that might have to be wild speculation).

The entire global environment will also be covered with quintillions of dust-sized nano-computers called motes. So your life will be constantly curated by an intelligent network of ubiquitous cyber-servants. The “motes” will know you need more food, or that it’s a bit chilly today, or that you’re supposed to call Charlie. And they’ll take the relevant action. Your shirt (motes in the fabric) will call Charlie. Either his avatar will appear, or you’ll hear his voice. Not sound waves, but brainwaves. Brain-to-brain communication (it happened for the first time in summer 2013). …

Burke continues, pointing out that nano-fabricators will thus eliminate the need for infrastructure and for government, and that the resulting abundance will eliminate the need for crime, and with it the need for privacy (“outside the boudoir”). Diseases would be eliminated. Without jobs to qualify for, education would be replaced by “learning-for-fun”. Entertainment will be “all in-brain, with accompanying holograms … Tailored to your most idiosyncratic wishes.”

In “How a Machine That Can Make Anything Would Change Everything” on SingularityHub, Thomas Hornigold comments on Burke’s prognostication (“It sounds like science fiction—although, with the advent of 3D printers in recent years, less so than it used to.”) and links the concept to Drexler’s work on “molecular assemblers” and Richard Feynman’s 1959 talk “Plenty of Room at the Bottom”.

Noting progress toward nanofabricators (citing the paper from David Leigh’s group that we recently cited), Hornigold speculates “It may well be that we make faster progress by mimicking the processes of biology, where individual cells, optimized by billions of years of evolution, routinely manipulate chemicals and molecules to keep us alive.”

After agreeing with Burke that the widespread availability of nanofabricators “will destroy the current social, economic, and political system, because it will become pointless,” Hornigold compares such a world with warnings about a world with superintelligent AI “We are limited to considering things in our own terms … there is no sense in comparing it to anything we know, because it is different in kind.”

Nanofabricators: The Creation Machine That Will Turn The World Upside Down Forever In 25 Years” by Gwyn D’Mello draws conclusions similar to those of Hornigold’s piece, and then concludes:

The thing is, the question itself is so vast, and rife with so many variables, we just can’t comprehend how it would play out. Perhaps, however, it’ll be the beginning of a new world, one where caring for everyday needs isn’t an odious task anymore. Perhaps the commotion this sort of invention will cause a new type of conflict on a global scale. Or perhaps the technology will prove impossible to accomplish after all. Either way, people like Burke believe the answer is almost at hand, and those of you reading this now might still be around to see it.

With James Burke’s five-year-old prediction of widespread use of general purpose nanofabricators able to easily copy themselves and almost anything else by 2042 simultaneously endorsed by two writers apparently on opposite sides of the world just two weeks ago, it’s difficult to avoid thinking about how long it might be until general purpose, high-throughput atomically precise manufacturing (APM) transforms the world and the entire human experience.

After Drexler’s ideas were published in 1986 and the Foresight Institute was founded, there was a general reluctance to avoid making predictions about when the ultimate manufacturing technology would arrive. About the clearest statement made during the first decade was made by Drexler in 1994. He gave two varieties of “conservative” estimates for the arrival of nanotechnology. If you are considering the benefits of nanotechnology, it is conservative to plan on 20 years. If you are concerned about competitors getting it first, it is conservative to plan on 10 years. Clearly, more than 23 years later there is no sign that anyone is close to perfecting such a device, although several paths have shown promising progress toward early, very limited, prototypes.

Closer to Burke’s timeline, in 2005 inventor, writer, and renowned futurist Ray Kurzweil predicted 2025 as the most likely year for the debut of advanced nanotechnology, and that one of the earliest applications will be advanced medical nanorobots. “By the late 2020s, nanotech-based manufacturing will be in widespread use, radically altering the economy as all sorts of products can suddenly be produced for a fraction of their traditional-manufacture costs. The true cost of any product is now the amount it takes to download the design schematics”. Kurzweil’s 2005 prediction could still conceivable[y be realized, but could it be that the advent of APM always appears to be about 20 years in the future? The Foresight Institute, in collaboration with Battelle and The Waitt Family Foundation studied the road from then current nanotechnology to APM and published a report in 2007 “Technology Roadmap for Productive Nanosystems“. Perhaps it is time for another look at paths, progress, and possible timelines?
—James Lewis, PhD

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Mechanical communication in a rotaxane molecular machine https://foresight.org/communication-mechanically-interlocked-molecular-machine/ https://foresight.org/communication-mechanically-interlocked-molecular-machine/#respond Tue, 09 Jan 2018 04:00:47 +0000 https://foresight.org/?p=21030 The structural formula of the rotaxane 1H3+. Above: The dibenzo[24]crown-8 macrocycle circles the dibenzylammonium site on the left end of the axle, which had been protonated by the addition of acid. Below: With the addition of a suitable base, the rotaxane is deprotonated to 1H2+, and the macrocycle translates over to the 4,4′-bipyridinium unit [...]

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Molecular structures of the protonated and deprotonated forms of the rotaxane, showing the macrocycle at each of the two alternate binding sites on the axle of the rotaxane.

The structural formula of the rotaxane 1H3+. Above: The dibenzo[24]crown-8 macrocycle circles the dibenzylammonium site on the left end of the axle, which had been protonated by the addition of acid. Below: With the addition of a suitable base, the rotaxane is deprotonated to 1H2+, and the macrocycle translates over to the 4,4′-bipyridinium unit at the right end of the axle. The bulky 1,3-Di-tert-butylbenzene groups at either end of the axle constrain the macrocycle to remain on the axle. (The “R” attached to one side of the macrocycle is a nitrile-terminated substituent irrelevant for this work.) Credit: Alberto Credi.

Mechanically interlocked molecules (MIMs), such as rotaxanes and catenanes, provide a fertile opportunity to study some of the complexities of large biological systems of molecular machines, composed of large protein molecules, with small molecular machines composed of small organic molecules containing components that can move relative to each other in response to external control. The Foresight Institute recognized the usefulness of MIMs for development of advanced nanotechnology with the award of the 2007 Feynman Prizes for Theoretical work to David Leigh FRS and for Experimental work to Sir J. Fraser Stoddart. The great potential of these small molecular machines was further recognized by the award of the 2016 Nobel Prize in Chemistry to Jean-Pierre Sauvage, Sir J. Fraser Stoddart, and Bernard L. Feringa. News of another way in which the dynamic properties of MIMs may lead, through mechanical communication of molecular information, to deeper insights into allosteric communication mechanisms of enzymes, and perhaps to the improvement of technology involving fuel cells, sensors, catalysts, and electrochemical devices comes in a press release from the University of Bologna, forwarded to Foresight by Giulio Ragazzon, the first author of the cited research “Hermes, The First Communication System For Molecules”:

It is the first artificial system in which remote parts of a molecule communicate by a dynamic mechanism. Nature uses an analogue strategy in the cellular respiration.

The unprecedented case of two different remote parts of a synthetic molecule that can dynamically exchange chemical information is described. This strategy is employed to change in a controlled manner the acidity of a molecule that becomes 10 million times less acidic: the biggest change ever obtained with an artificial molecule. In our body the process that converts nutrients in energy exploits a similar mechanism, which is still partly unknown and was never mimicked before.

As reported today in the prestigious journal PNAS [abstract, full text], the system — nicknamed Hermes — was designed, synthesized and operated by a research team based at the University of Bologna and National Research Council of Italy (CNR), led by professors Alberto Credi and Marco Lucarini.

Hermes

The key component of this communication system is a rotaxane, constituted by a ring-like molecule surrounding a thread-like molecule. The ring is free to shuttle along the thread, but it cannot escape because two “stoppers” prevent its dethreading. It is thanks to this shuttling ability that the ring enables the communication between the two extremities. One of these extremities is capable of receiving electric signals, whereas the other one is responsible for the acid/base properties. When an electron is caught by the first site, the ring transfers the information to the other extremity, causing a change of the acidity of the molecule. Therefore the ring acts as a messenger, from which the nickname Hermes (the messenger of the Greek Gods) derived. The absolute novelty of Hermes is that it can provide communication between two distant regions of a molecule that would otherwise be isolated in a rapid, efficient and selective manner. It represents an incredibly challenging task that Nature performs with highly sophisticated chemical structures. Hermes achieves the same result in a system of just a few atoms, easy to synthesize with common synthetic techniques. The rotaxane is one nanometer (a billionth of a meter) long.

An inexplicable experiment

Very similar systems were synthesized and investigated at the end of the 1990s in the area of molecular machines (a field awarded with the Nobel Prize in Chemistry last year), but nobody ever realized such a unique behavior. The discovery happened thanks to a surprising and initially inexplicable experiment: the only possibility to justify the experimental observations was that the molecule was able to put the two distal extremities in communication. “During the experiments I realized that the behavior of the rotaxane radically changed in the presence of different bases” — tells Giulio Ragazzon, the young researcher who participated in the work — “Thanks to the collaboration with the group of Prof. Lucarini, which studies the behavior of unpaired electrons with magnetic resonance techniques, it was possible to confirm our hypothesis, directly observing the ring position along the thread when the molecule receives an electron”.

Relevance and future developments

Hermes deals with two fundamental subjects for molecular systems: long range communication and the coupling of electrical and chemical signals. The operation of most enzymes, natural molecules at the basis of life, relies on the former subject. The latter one lies at the foundation of key biological processes like photosynthesis and respiration, as well as of technological areas like fuel cells, sensors and catalysis. For this reason the discovery may have an impact well beyond the chemistry domain; indeed, the study is published in PNAS (Proceedings of the National Academy of Sciences), an important journal which covers all areas of Science, and not in a specialized chemistry journal as it usually happens.

With Hermes the researchers convert an electric signal into an acidity change; the same strategy, however, may be applied to process light signals or to release at will other molecules. Therefore this work could be relevant for the fields of energy conversion and drug delivery.

The project

Hermes is the result of a project started about three years ago, in the framework of the activities of the Center for Light Activated Nanostructures (CLAN) leaded by Prof. Alberto Credi. CLAN is a joint research laboratory set up by the University of Bologna and the CNR, whose the mission is the development of nanoscale molecular systems and materials able to perform actions activated by light or related stimuli. This study is the result of collaboration between CLAN and the group of Chemistry of Free Radicals at the Chemistry Department “Ciamician” of the University of Bologna. …

The fundamental concept at the basis of this research is the mimicking in artificial systems of what Nature does to form structures, obtain mechanical movements and communicate using proteins and enzymes. In this specific case the focus is on the ability to communicate and convert a signal. In performing these studies, chemists operate like engineers and architects, however manipulating systems a billion times smaller, since their building blocks are molecules. The realization of artificial machines and motors of nanometer size is of great interest for the growth of nanotechnology, that is, a technology that allows the construction of highly miniaturized structures and devices. It is generally considered that nanotechnology will not only lead to lighter, tougher and smarter materials and to smaller and more powerful computer, but also revolutionize medicine and other areas of science and technology.

The results show that the protonation of an ammonium site at one end of the axle can be reversibly modulated through an electron transfer at the bipyridinium site at the opposite end of the axle, which can exist as either a radical cation (one unpaired electron spin and one positive charge) or a dication (two positive charges). The electron transfer (redox reaction) at the bipyridinium changes the affinity of the crown ether macrocycle for the bipyridinium site. The protonation state of the dibenzylammonium site will depend on whether the macrocycle resides there or on the bipyridinium site. Thus the movement of the ring between two sites on the axle carries information between the two distant sites because the chemical or electrochemical state of one site determines the affinity of the ring to that site, and thus whether it stays or moves to the other site.

Biological molecular machine systems, small organic molecular machines with mechanically interlocked molecules, DNA origami machine systems, and combinations of various types of chemical scaffolds and catalysts, or scanning probes have been demonstrated or can be envisioned to build complex structures with atomic precision. The variety of nanostructures and functions that exist or seem possible is impressive. How can they be combined and/or improved to fill specific technological roles? What will be the limit to what we can build with them? Is there a path (or paths) to general purpose, high throughput atomically precise manufacturing?
—James Lewis, PhD

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Funding announcements for Atomically Precise Manufacturing https://foresight.org/funding-announcements-atomically-precise-manufacturing/ https://foresight.org/funding-announcements-atomically-precise-manufacturing/#respond Wed, 27 Dec 2017 23:10:14 +0000 https://foresight.org/?p=21003 Credit - energy.gov/science-innovation Longtime Foresight member, and since October 2012 Technology Manager, Advanced Manufacturing Office, U.S. Department of Energy, David Forrest passes along these funding announcements about new opportunities at DOE: Those of you in the Atomically Precise Manufacturing community should be aware of new funding opportunities: ARPA-E The U.S. Department of Energy (DOE) [...]

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Science & Innovation logo US Dept. of Energy

Credit – energy.gov/science-innovation

Longtime Foresight member, and since October 2012 Technology Manager, Advanced Manufacturing Office, U.S. Department of Energy, David Forrest passes along these funding announcements about new opportunities at DOE:

Those of you in the Atomically Precise Manufacturing community should be aware of new funding opportunities:

ARPA-E

The U.S. Department of Energy (DOE) today [Dec. 13, 2017] announced up to $100 million in funding for new projects as part of the Advanced Research Projects Agency-Energy’s (ARPA‑E) latest OPEN funding opportunity. OPEN will support America’s top innovators through dozens of early-stage research and development projects as they build technologies to transform the nation’s energy system. …
The deadline to submit a concept paper is February 12, 2018 at 5:00 p.m. E.T.

Energy Frontier Research Center

Today, U.S. Secretary of Energy Rick Perry announced a proposed $99 million in Fiscal Year 2018 funding for Energy Frontier Research Centers (EFRCs) to accelerate transformative scientific advances for the most challenging topics in materials sciences, chemical sciences, geosciences, and biosciences. Research supported by this initiative will provide fundamental understanding to enable future advances in energy production and use. …

Between the work in atomically precise catalysts and atomically precise membranes, I think the transformative nature of APM and the energy impact could hit all the marks for these solicitations. Scanning probe molecular assembly and integrated nanosystems may be a harder sell but could perhaps be convincingly rationalized for these solicitations.

Good luck to all who decide to apply! And please spread the word about these opportunities.

David
==================================================================
David R. Forrest, Sc.D., PE, FASM david.forrest@ee.doe.gov
Technology Manager
Department of Energy
Energy Efficiency and Renewable Energy
Advanced Manufacturing Office

Almost exactly a year ago, David forwarded us a New Funding Opportunity from U.S. DOE announcement. We can hope these yearly funding announcements continue and grow, and that progress toward atomically precise manufacturing secures an abundant and sustainable energy future.
—James Lewis, PhD

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Building atom-by-atom on insulator at room temperature https://foresight.org/building-atom-by-atom-on-insulator-at-room-temperature/ https://foresight.org/building-atom-by-atom-on-insulator-at-room-temperature/#respond Wed, 27 Dec 2017 18:04:18 +0000 https://foresight.org/?p=20997 It’s not red and white, but the atoms are arranged in the shape of a Swiss cross (Credit: Physics department, University of Basel) If the above picture reminds you of something like it some 27 years ago when physicists announced a nanostructure built atom-by-atom, then it is important to recognize there are multiple crucial [...]

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Swiss cross of 20 atoms

It’s not red and white, but the atoms are arranged in the shape of a Swiss cross (Credit: Physics department, University of Basel)

If the above picture reminds you of something like it some 27 years ago when physicists announced a nanostructure built atom-by-atom, then it is important to recognize there are multiple crucial differences between the above 2014 image of a Swiss cross formed from 20 precisely placed bromine atoms and the 1990 image of the IBM logo formed from 35 precisely placed xenon atoms (Foresight Update 9 “Spelling IBM with 35 Atoms” June 30, 1990). The Swiss cross fabrication was reported in a University of Basel press release three summers ago “Smallest Swiss cross in the world made in Basel“:

Researchers at the University of Basel have made the smallest Swiss cross in the world, out of just 20 atoms. It’s the first time a structure of single atoms has been made at room temperature—it normally has to be much colder for the structure to be stable.

The international team in the university’s physics department used the tip of an atomic force microscope, which is extremely tiny and used in nanotechnology, to place the bromine atoms on an insulating surface.

The Swiss cross they constructed measures only 5.6 nanometres square.

Physicists have been able to move around and reposition single atoms since the 1990s, when done at very low temperatures. Attempts to create these types of structures at room temperature however, had produced disappointing results up until now as they were too difficult to control and properly manipulate.

The study, which was published in the journal, Nature Communications [“Atom manipulation on an insulating surface at room temperature“, OPEN ACCESS], states that the researchers have showed that the systematic manipulation of atoms at room temperature is now possible, demonstrating a key step towards a number of new developments, including new atomic-scale data storage devices.

The 1990 paper presenting the IBM logo was done using a scanning tunneling microscope (STM) in ultra high vacuum and very low temperature (4 K) to position individual xenon atoms on a single-crystal nickel surface with atomic precision. The Xenon atoms were adsorbates, not covalently bound to the surface, and so they could be manipulated by the force exerted by the STM tip. That force contains both van der Waals and electrostatic contributions, and adjusting the position and voltage of the tip determines both the magnitude of the force, and whether it is attractive or repulsive.

It generally takes less force to move an atom along the surface than to pull it away from the surface. Therefore, it is usually possible to adjust parameters so that an STM tip can pull an atom across the surface while the atom remains bound to the surface. The decision to study xenon on a Ni (110) surface was dictated by the requirement that corrugations of the surface potential be sufficiently large for the xenon atoms to be imaged without inadvertently moving them, but small enough that enough lateral force could be exerted to move xenon atoms across the surface. Note that although the STM tip is made from tungsten wire, the chemical identity of the tip apex is not known.

The statement in the above University of Basel press release that this demonstration is “the first time a structure of single atoms has been made at room temperature” is not true, although it is true that this was the first instance in which a structure was made on an insulating surface at room temperature. An earlier demonstration was on a semiconductor surface.

The 2009 Foresight Institute Feynman Prize for Experimental work was awarded to the team of Yoshiaki Sugimoto, Masayuki Abe, and Oscar Custance for the use of atomic resolution dynamic force microscopy — also known as non-contact atomic force microscopy (NC-AFM) — for vertical and lateral manipulation of single atoms on semiconductor surfaces at room temperature. This accomplishment was reported in a 2008 paper in Science “Complex Patterning by Vertical Interchange Atom Manipulation Using Atomic Force Microscopy” [abstract] and described in an article in ScienceDaily “Scientists ‘Write’ With Atoms Using An Atomic Force Microscope“.

In this 2008 work NC-AFM using commercial silicon cantilevers with very sharp tips were used to image a Sn/Si (111) reconstructed surface by detecting the short-range chemical interaction force between the closest tip and surface atoms. A vertical interchange of tip and surface atoms was observed controlled by the mechanical properties of a hybrid tip-surface structure formed in the repulsive regime of the tip-surface interaction force.

The surface appears initially as a single atomic layer of tin (Sn) atoms grown over a Si(111) single crystal substrate. The imaged surface exhibited atomic defects consisting of single Si atoms interspersed in the Sn monolayer. After imaging the surface and placing the AFM tip directly over a single Si atom, and moving the surface toward the oscillating AFM tip, at a certain tip-surface distance am instability in the oscillation frequency occurs. Imaging the surface after the tip was retracted showed the Si atom had been replaced by a Sn atom at the same lattice position. Repeating this process multiple times resulted in the atomic symbol for silicon—Si— constructed from 12 Si atoms on a surface of Sn atoms. These manipulations could be accomplished either at room temperature or at the low temperature of 80 K.

The process described above differs from the two other methods of controlled manipulation of isolated atoms by scanning probe microscopes that had been described previous to this publication: (1) using a bias voltage from an STM to drag a weakly bound atom across a metallic surface; (2) using the attractive part of the tip-surface interaction of an AFM to laterally manipulate atoms without any active participation of the AFM tip beyond tuning the interaction of the manipulated atom with the surface.

The bonding interaction between the closest tip and surface atoms in the repulsive regime is complex, involving several atoms and leading to a complex energy landscape that could result in three outcomes: (1) interchange of tip and surface atoms; (2) atom transfer to the tip; (3) deposition of tip atoms on the surface. Simulations based on density functional theory first-principles calculations rationalize the observed result that experiments with many individual tips fall into three classes: (1) some tips alternately deposit Sn and Si atoms; (2) others only deposit Sn atoms; (3) some only deposit Si atoms. The fact that specific classes of tip had to be identified for specific manipulations accounts for the fact that it took 1.5 h to build the ‘Si’ image shown.

The 2014 paper presenting the fabrication of the Swiss cross from 20 bromide ions on an insulator surface notes that since the 1990 atomic manipulation of xenon atoms on a nickel surface, the ultimate goal has been fabrication of next-generation atomic-scale electro-mechanical devices operating at room temperature (RT) on a dielectric surface (an electrical insulator that can be polarized by an electric field). The paper further notes that on fully insulating surfaces, the smaller diffusion barrier of adsorbed species compared to covalently bounded semiconductor surfaces makes room temperature mechanical manipulation by AFM more difficult than on semiconductor surfaces. This paper presents “the first systematic atomic manipulation on an insulating NaCl(001) surface under ultra-high vacuum (UHV) conditions at RT.”

These experiments use “the recently developed bimodal dynamic mode AFM (bimodal d-AFM, a 2009 paper with the same first and last authors as this 2014 paper), in which the vertical and lateral tip-sample interactions are simultaneously detected via frequency shifts of the flexural and torsional resonance modes, respectively.” These changes result in improved resolution at the atomic scale. The tip apex of a silicon cantilever was terminated with NaCl by prior indentation to the sample surface. Imaging a 28 nm x 28 nm area with the bimodal technique revealed the typical contrast pattern of a NaCl (100) surface, with a number of defects appearing as brighter atomic sites. These were attributed to contaminating bromide ions, whose presence in the crystal was confirmed by X-ray fluorescence analysis. The concentration of bromide ions estimated by AFM was one order of magnitude higher than the crystal concentration. This difference was attributed to the effect of annealing the NaCl crystal at 80 °C. FroM their AFM images, the authors conclude that the foremost atom on the tip apex must be a sodium ion (Na+) and that the corrugation amplitude of bromide ion is about three times higher than the corrugation amplitude of chloride ion, and that the position of the bromide ion is predicted to be 20 pm (picometers) above the surface. They further conclude that the bromide ions are not adsorbed on the surface, but instead incorporated into the NaCl(001) surface layer as substitutional species in the Cl sub-lattice. Further, the bromide ions were stable to repeated imaging over the time course of the experiment.

Upon scanning at smaller tip-sample separations, a class of novel lateral manipulations appears in which a bromide ion exchanges with a chloride ion while scanning in a specific direction. The diversity of this class of lateral manipulations indicated to the authors that the mechanism is more complicated than is the case with a standard lateral manipulation in which an adatom moves on top of the surface.

To achieve more control in manipulating bromide ions, an equivalent of dynamic force spectroscopy was attempted by sequentially approaching the surface to pick up the ion, and then approaching the surface again to implant the ion at the desired surface lattice location. 95 % of the implantations were successful. The experimental data reveal that implantation only occurs if the tip is approached 100 pm closer than the pickup approach.

Theoretical calculations of the manipulation mechanisms based on density functional theory (DFT) were performed In order to understand the detailed process of the atomic manipulation. The model system included a NaCl nanocluster tip and the NaCl surface with one substitutional bromide ion. Conventional lateral manipulation has too high a transition barrier to account for the extensive lateral manipulation observed experimentally. The authors suggest a more plausible model involving the tip temporarily picking up a bromide ion, allowing the vacancy underneath to diffuse before the bromide ion is dropped into a new site. They note that the barrier for vacancy diffusion is always low, and proximity to the tip reduces the barrier to lifting the bromide ion above the surface, especially if a polar model of the tip is used. Thus this process is only viable at large tip-sample separations and is not directionally controlled.

In contrast to the more random lateral manipulationprocess, the statistical preference for implanting ions over picking up ions at closer approach made i possible to perfectly align 20 broide ion in the NaCl surface, forming a 5.64 nm by 5.64 nm ‘Swiss cross’. The authors note that this was the largest number of atomic manipulations achieved at room temperature. They further note that bromide ions are positioned at every other chloride ion site on the surface, and that the fabricated cross is “relatively stable” in that no diffusion was observed during the six hours it took to build the structure. Thus, combining theory with the bimodal dynamic force microscopy they had published five years earlier, they were able to demonstrate “how systematic atomic manipulation at RT, on any class of surface, is now possible. This is an important step towards the fabrication of advanced electromechanical systems at the nanoscale, in a bottom-up manner.” This 2014 advance has capped a 24-year journey to build a larger variety of structures on a surface, atom-by-atom, but I expect that this will not be the end of the story, and that scanning probe microscopes will continue to figure prominently in the roadmap to productive nanosystems and atomically precise manufacturing.
—James Lewis, PhD

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Blockchains, Cryptoeconomics, and Emerging Technology Risks https://foresight.org/blockchains-cryptoeconomics-emerging-technology-risks/ https://foresight.org/blockchains-cryptoeconomics-emerging-technology-risks/#respond Wed, 20 Dec 2017 02:44:37 +0000 https://foresight.org/?p=20979 Blockchain formation. The main chain (black) consists of the longest series of blocks from the genesis block (green) to the current block. Orphan blocks (purple) exist outside of the main chain. Image Credit: Theymos from Bitcoin wiki. This file is licensed under the Creative Commons Attribution 3.0 Unported license. In writing for this [...]

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blockchain diagram

Blockchain formation. The main chain (black) consists of the longest series of blocks from the genesis block (green) to the current block. Orphan blocks (purple) exist outside of the main chain. Image Credit: Theymos from Bitcoin wiki. This file is licensed under the Creative Commons Attribution 3.0 Unported license.

In writing for this blog, I am accustomed to rapid changes from one technological area to another, such as from DNA origami to de novo protein design to scanning probe microscopy to molecular machinery based on mechanically interlocked molecular architectures. The DNA and protein work overlaps with biotechnology, and we have always seen all these molecular topics interlinked with computation, and with increasing frequency recently, with artificial intelligence. These relationships go back to Foresight Institute’s Founding Vision and Eric Drexler’s 1986 book Engines of Creation. But a year ago Foresight’s events and salons began to include concepts new to me, like Bitcoin, cryptocurrencies, and blockchains. The Great Debates of Our Time (November 19, 2016) included a panel (video) discussing “Blockchain, Alternative Societies, Universal Basic Income”; Building Better Futures on Blockchains (May 11, 2017); The Next Frontier: Blockchain meets Object Capabilities (July 3, 2017). In addition Foresight’s 2017 Vision Weekend included a keynote panel “Blockchains – Master Key To Unlock The Future?” on how to build better base realities block by block: Beyond crypto, ICO hype & hope, decentralized governance. Looking for a place to begin to understand what this is all about, I found the following a very useful introduction: “The Blockchain Economy: A beginner’s guide to institutional cryptoeconomics“:

Chris Berg, Sinclair Davidson and Jason Potts are from the RMIT Blockchain Innovation Hub, the world’s first social science research centre into the economics, politics, sociology, and law of blockchain technology.

The blockchain is a digital, decentralised, distributed ledger.

Most explanations for the importance of the blockchain start with Bitcoin and the history of money. But money is just the first use case of the blockchain. And it is unlikely to be the most important.

It might seem strange that a ledger—a dull and practical document associated mainly with accounting—would be described as a revolutionary technology. But the blockchain matters because ledgers matter.

Ledgers all the way down

Ledgers are everywhere. Ledgers do more than just record accounting transactions. A ledger consists simply of data structured by rules. Any time we need a consensus about facts, we use a ledger. Ledgers record the facts underpinning the modern economy. …

At their most fundamental level, ledgers map economic and social relationships.

Agreement about the facts and when they change—that is, a consensus about what is in the ledger, and a trust that the ledger is accurate—is one of the fundamental bases of market capitalism. …

After describing the function and evolution of ledgers, the article explains how the blockchain solves the principal shortcoming of ledgers:

… But a database still relies on trust; a digitised ledger is only as reliable as the organisation that maintains it (and the individuals they employ). It is this problem that the blockchain solves. The blockchain is a distributed ledgers that does not rely on a trusted central authority to maintain and validate the ledger. …

The above conclusion leads into exploring the place of the blockchain among the economic institutions of capitalism, based upon the realization that relative transaction costs determine how ledgers are maintained, and how firms and governments have assumed this function. But now the advent of cryptographically secure ledgers that do not need to be maintained by a trusted authority—a firm or a government— has opened the possibility that “Ledgers of identity, permission, privilege and entitlement can be maintained and enforced without the need for government backing.” this insight opens the field of institutional cryptoeconomics, the study of the institutional consequences of cryptographically secure and trustless ledgers.

After concluding that we can’t yet predict how the blockchain will affect the economy, but we can expect a substantial amount of disruption, the article emphasizes the role of smart contracts, and the distinction between complete and incomplete smart contracts. As smart contracts become more complete, the roles of firms and governments will be lessened. They conclude:

… The blockchain and associated technological changes will massively disrupt current economic conditions. The industrial revolution ushered in a world where business models were predicated on hierarchy and financial capitalism. The blockchain revolution will see an economy dominated by human capitalism and greater individual autonomy.

How that unfolds is unclear at present. Entrepreneurs and innovators will resolve uncertainty, as always, through a process of trial and error. No doubt great fortunes will be made and lost before we know exactly how this disruption will unfold. …

The recent rise in the value of BitCoin, whether a bubble or not, has stimulated great interest in the blockchain, and a recent opinion piece in the New York Times places it in the context of falling confidence in institutions and governments. From “The Bitcoin Boom: In Code We Trust” by Tim Wu, Dec. 18, 2017:

… Yet as Bitcoin continues to grow, there’s reason to think something deeper and more important is going on. Bitcoin’s rise may reflect, for better or worse, a monumental transfer of social trust: away from human institutions backed by government and to systems reliant on well-tested computer code. It is a trend that transcends finance: In our fear of human error, we are putting an increasingly deep faith in technology. …

Although it is too early to foresee what the effects of blockchains will be, it seems already clear that the blockchain is closely linked with long-term Foresight interests in computer security and managing the risks of powerful emerging technologies (see for example Cyber, Nano, and AGI Risks: Decentralized Approaches to Reducing Risks” by Christine Peterson, Mark S. Miller and Allison Duettmann.)
—James Lewis, PhD

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Cyber, Nano, and AGI Risks: Computer Security and Effective Altruism https://foresight.org/cyber-nano-agi-risks-computer-security-effective-altruism/ https://foresight.org/cyber-nano-agi-risks-computer-security-effective-altruism/#respond Sat, 25 Nov 2017 12:28:53 +0000 https://foresight.org/?p=20852 Christine Peterson, Foresight Institute Co-Founder and Projects Director Foresight Institute Co-Founder and Projects Director Christine Peterson (full biography) was interviewed recently by 80000 Hours, “an independent nonprofit funded by individual donors” and founded “because we couldn’t find any sources of advice on how to do good with our own working lives. Since 2011, [...]

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Christine Peterson interviewed at Effective Altruism Global

Christine Peterson, Foresight Institute Co-Founder and Projects Director

Foresight Institute Co-Founder and Projects Director Christine Peterson (full biography) was interviewed recently by 80000 Hours, “an independent nonprofit funded by individual donors” and founded “because we couldn’t find any sources of advice on how to do good with our own working lives. Since 2011, we’ve been on a mission to figure out how best to choose a career with high social impact.” Among their many activities in support of this goal, they offer free, one-on-one career advice, and an extensive blog that includes interviews with major thinkers and doers on this and related fascinating and important topics.

Christine’s interview, recorded by Robert Wiblin, director of research at 80,000 Hours, at Effective Altruism Global in San Francisco (August 13, 2017), provided content for two posts on the 80000 Hours blog. The first, posted on October 4, 2017, focused on a very current risk of advanced technology and what do about it: computer security and the risk of cyber warfare. One of three key points covered in the post:

Present day computer systems are fundamentally insecure, allowing hacking by state-level actors to take down almost any service on the internet, including essential services such as the electricity grid. Automated hacking by algorithms in future could allow computer systems around the world to be rapidly taken down. Christine believes the only way to effectively deal with this problem is to change the operating systems we all use to those that have been designed for maximum security from the ground up. Christine and two colleagues recently released a paper on tackling this issue.

Other topics addressed in the post include the importance of taking care “of your own health and welfare in order to be able to continue working hard on useful things for decades,” “life extension research, cryonics, and how to choose a life partner.”

The second post, on October 6, 2017, focused on space colonization and nanotechnology and the Silicon Valley community of the 1970s and 80s. Robert Wilbin explains:

One tricky thing about lengthy podcasts is that you cover a dozen issues, but when you give the episode a title you only get to tell people about one. With Christine Peterson’s interview I went with a computer security angle, which turned out to not be that viral a topic. But people who listened to the episode kept telling me how much they loved it. So I’m going to try publishing the interview in pieces, each focussed on a single theme we covered. Christine Peterson co-founded the Foresight Institute in the 90s. In the lightly edited transcript below we talk about a community she was part of in her youth, whose idealistic ambition bears some similarity to effective altruism today. We also cover a controversy from that time about whether nanotechnology would change the world or was impossible. Finally we think about what lessons we can learn from that whole era.

The podcast, included in the first post, upon which the two posts are based, runs 1 h and 45 minutes. Each post includes a transcript and the first also includes a list of extra resources to learn more, including the above-cited paper “Cyber, Nano, and AGI Risks: Decentralized Approaches to Reducing Risks” by Christine Peterson, Mark S. Miller and Allison Duettmann. This 34-page paper (single spaced) combines a look at Foresight’s beginnings with an insightful discussion of how those founding interests evolved into the current focus on cybersecurity, biotech-based opportunities and threats, and the connection with the more distant benefits and challenges of atomically precise nanotechnology and artificial general intelligence. From the abstract:

The aim of this paper, rather than attempting to present one coherent strategy for reducing existential risks, is to introduce a variety of possible options with the goal of broadening the discussion and inviting further investigation. Two themes appear throughout: (1) the proposed approaches for risk reduction attempt to avoid the dangers of centralized “solutions,” and (2) cybersecurity is not treated as a separate risk. Instead, trustworthy cybersecurity is a prerequisite for the success of our proposed approaches to risk reduction.

Our focus is on proposing pathways for reducing risks from advanced nanotechnology and artificial general intelligence.

A paper very well worth reading. On a personal note, I was glad to see the return of interest in one of my favorite sections of Engines of Creation, a proposal for “Inheritance Day.”
—James Lewis, PhD

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Prototype quantum computer gives small molecule quantum simulation https://foresight.org/prototype-quantum-computer-gives-small-molecule-quantum-simulation/ https://foresight.org/prototype-quantum-computer-gives-small-molecule-quantum-simulation/#respond Tue, 10 Oct 2017 00:26:24 +0000 https://foresight.org/?p=20785 Optical micrograph of the superconducting quantum processor with seven qubits. Image credit: Kandala et al. Nature We have pointed to examples of how atomically precise nanotechnology might open the road to developing quantum computers (Atomically precise location of dopants a step toward quantum computers, August 4th, 2016; Architecture for atomically precise quantum computer in [...]

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superconducting quantum processor with seven qubits

Optical micrograph of the superconducting quantum processor with seven qubits. Image credit: Kandala et al. Nature

We have pointed to examples of how atomically precise nanotechnology might open the road to developing quantum computers (Atomically precise location of dopants a step toward quantum computers, August 4th, 2016; Architecture for atomically precise quantum computer in silicon, November 9th, 2015; A nanotechnology route to quantum computers through hybrid rotaxanes, March 27th, 2009). The converse process of quantum computing facilitating the development of atomically precise nanotechnology by enabling quantum simulations too large to be tractable on a classical computer was noted by Richard Terra writing on this blog (Quantum computers for quantum physics calculations, July 5th, 2002). This converse process took a big step forward with an advance from IBM.

MIT Technology Review reports “IBM Has Used Its Quantum Computer to Simulate a Molecule—Here’s Why That’s Big News

We just got a little closer to building a computer that can disrupt a large chunk of the chemistry world, and many other fields besides. A team of researchers at IBM have successfully used their quantum computer, IBM Q, to precisely simulate the molecular structure of beryllium hydride (BeH2). It’s the most complex molecule ever given the full quantum simulation treatment.

Molecular simulation is all about finding a compound’s ground state—its most stable configuration. Sounds easy enough, especially for a little-old three-atom molecule like BeH2. But in order to really know a molecule’s ground state, you have to simulate how each electron in each atom will interact with all of the other atoms’ nuclei, including the strange quantum effects that occur on such small scales. This is a problem that becomes exponentially harder as the size of the molecule increases. …

The IBM team published in Nature a new algorithm to calculate the ground state of BeH2 “Hardware-efficient variational quantum eigensolver for small molecules and quantum magnets ” [abstract, full text preprint]. An IBM Research blog post by three of the seven authors of the Nature paper provides further explanation of the quantum algorithm they implemented with IBM’s seven qubit superconducting quantum hardware “How to measure a molecule’s energy using a quantum computer“:.

Simulating molecules on quantum computers just got much easier with IBM’s superconducting quantum hardware. In a recent research article published in Nature, … we implement a new quantum algorithm capable of efficiently computing the lowest energy state of small molecules. By mapping the electronic structure of molecular orbitals onto a subset of our purpose-built seven qubit quantum processor, we studied molecules previously unexplored with quantum computers, including lithium hydride (LiH) and beryllium hydride (BeH2). The particular encoding from orbitals to qubits studied in this work can be used to simplify simulations of even larger molecule and we expect the opportunity to explore such larger simulations in the future, when the quantum computational power (or “quantum volume”) of IBM Q systems has increased.

While BeH2 is the largest molecule ever simulated by a quantum computer to date, the considered model of the molecule itself is still simple enough for classical computers to simulate exactly. This made it a test case to push the limits of what our seven qubit processor could achieve, further our understanding of the requirements to enhance the accuracy of our quantum simulations, and lay the foundational elements necessary for exploring such molecular energy studies.

The best simulations of molecules today are run on classical computers that use complex approximate methods to estimate the lowest energy of a molecular Hamiltonian. A “Hamiltonian” is a quantum mechanical energy operator that describes the interactions between all the electron orbitals* and nuclei of the constituent atoms. The “lowest energy” state of the molecular Hamiltonian dictates the structure of the molecule and how it will interact with other molecules. Such information is critical for chemists to design new molecules, reactions, and chemical processes for industrial applications.…

Although our seven qubit quantum processor is not fully error-corrected and fault-tolerant, the coherence times of the individual qubits last about 50 µs. It is thus really important to use a very efficient quantum algorithm to make the most out of our precious quantum coherence and try to understand molecular structures. The algorithm has to be efficient in terms of number of qubits used and number of quantum operations performed.

Our scheme contrasts from previously studied quantum simulation algorithms, which focus on adapting classical molecular simulation schemes to quantum hardware – and in so doing not effectively taking into account the limited overheads of current realistic quantum devices.

So, instead of forcing classical computing methods onto quantum hardware, we have reversed the approach and asked: how can we extract the maximal quantum computational power out of our seven qubit processor?

Our answer to this combines a number of hardware-efficient techniques to attack the problem:

  • First, a molecule’s fermionic Hamiltonian is transformed into a qubit Hamiltonian, with a new efficient mapping that reduces the number of qubits required in the simulation.
  • A hardware-efficient quantum circuit that utilizes the naturally available gate operations in the quantum processor is used to prepare trial ground states of the Hamiltonian.
  • The quantum processor is driven to the trial ground state, and measurements are performed that allow us to evaluate the energy of the prepared trial state.
  • The measured energy values are fed to a classical optimization routine that generates the next quantum circuit to drive the quantum processor to, in order to further reduce the energy.
  • Iterations are performed until the lowest energy is obtained to the desired accuracy.

With future quantum processors, that will have more quantum volume, we will be able to explore the power of this approach to quantum simulation for increasingly complex molecules that are beyond classical computing capabilities. The ability to simulate chemical reactions accurately, is conductive to the efforts of discovering new drugs, fertilizers, even new sustainable energy sources.

The experiments we detail in our paper were not run on our currently publically available five qubit and 16 qubit processors on the cloud. But developers and users of the IBM Q experience can now access quantum chemistry Jupyter notebooks on the QISKit github repo. On the five qubit system, users can explore ground state energy simulation for the small molecules hydrogen and LiH. Notebooks for larger molecules are available for those with beta access to the upgraded 16-qubit processor.

Information about the physical implementation if IBM’s superconducting quantum hardware and qubits can be found on IBM Q experience under Frequently Asked Questions:

What is the qubit that you are physically using?

The qubit we use is a fixed-frequency superconducting transmon qubit. It is a Josephson-junction-based qubit that is insensitive to charge noise. For more information on this type of qubit please see here (Koch et al. 2007, abstract, arxiv preprint). We use fixed-frequency qubits, as opposed to tunable qubits, to minimize our sensitivity to external magnetic field fluctuations that could corrupt the quantum information.

How do you make the qubits?

The superconducting qubits are fabricated at IBM. The devices are made on silicon wafers with superconducting metals such as niobium and aluminum. Details about the fabrication processes are given in these references (Chow et al. 2014, Córcoles et al. 2015).

The qubits used in the work described here appear to be fabricated using optical lithography, so are far from requiring atomically precise fabrication technology. On the other hand, quantum algorithm advances as exemplified here may facilitate the computational analysis and design of general purpose high-throughput atomically precise manufacturing systems, as well as systems to implement artificial general intelligence. The opportunities for synergy among these emerging, world-shaping technologies would appear to be large and growing.
—James Lewis, PhD

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Molecular robot builds four types of molecules https://foresight.org/molecular-robot-builds-four-types-molecules/ https://foresight.org/molecular-robot-builds-four-types-molecules/#respond Sun, 01 Oct 2017 02:59:16 +0000 https://foresight.org/?p=20767 Since winning the 2007 Foresight Institute Feynman Prize in Nanotechnology, Theory category, Professor David Leigh FRS FRSE FRSC MAE, and since 2012 at the University of Manchester, has continued to achieve major milestones on the road to complex systems of molecular machinery. Contributions we have recently cited here: First direct measurement of force generated by [...]

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Since winning the 2007 Foresight Institute Feynman Prize in Nanotechnology, Theory category, Professor David Leigh FRS FRSE FRSC MAE, and since 2012 at the University of Manchester, has continued to achieve major milestones on the road to complex systems of molecular machinery. Contributions we have recently cited here:

The most recent achievement of his team has garnered much well-deserved attention. A hat tip to Nanowerk for pointing to this University of Manchester news release “Scientists create world’s first ‘molecular robot’ capable of building molecules“:

Scientists at The University of Manchester have created the world’s first ‘molecular robot’ that is capable of performing basic tasks including building other molecules.

The tiny robots, which are a millionth of a millimetre [that is, a nanometer] in size, can be programmed to move and build molecular cargo, using a tiny robotic arm.

Each individual robot is capable of manipulating a single molecule and is made up of just 150 carbon, hydrogen, oxygen and nitrogen atoms. To put that size into context, a pile of a billion billion of these robots would still only be the same size (volume/weight) as a few grains of salt.

The robots operate by carrying out chemical reactions in special solutions which can then be controlled and programmed by scientists to perform the basic tasks.

In the future such robots could be used for medical purposes, advanced manufacturing processes and even building molecular factories and assembly lines. The research, which was funded by the Engineering and Physical Sciences Research Council (EPSRC) will be published in Nature today (21st September) [“Stereodivergent synthesis with a programmable molecular machine”, by Kassem et al. Abstract; full text provided on Prof. Leigh’s web site].

Professor David Leigh, who led the research at University’s School of Chemistry, explains: ‘All matter is made up of atoms and these are the basic building blocks that form molecules. Our robot is literally a molecular robot constructed of atoms just like you can build a very simple robot out of Lego bricks. The robot then responds to a series of simple commands that are programmed with chemical inputs by a scientist.’

A schematic of the operation of a molecular robot shows the position of the cargo arm in seven stages of operation

Programmable operation of a molecular machine that synthesizes different products by moving a substrate between different activating sites. Image credit: Leigh group, School of Chemistry, University of Manchester

“Molecular robotics represents the ultimate in the miniaturisation of machinery. Our aim is to design and make the smallest machines possible. This is just the start but we anticipate that within 10 to 20 years molecular robots will begin to be used to build molecules and materials on assembly lines in molecular factories.”
—Professor David Leigh, Sir Samuel Hall Professor of Chemistry

‘It is similar to the way robots are used on a car assembly line. Those robots pick up a panel and position it so that it can be riveted in the correct way to build the bodywork of a car. So, just like the robot in the factory, our molecular version can be programmed to position and rivet components in different ways to build different products, just on a much smaller scale at a molecular level.’

The benefit of having machinery that is so small is it massively reduces demand for materials, can accelerate and improve drug discovery, dramatically reduce power requirements and rapidly increase the miniaturisation of other products. Therefore, the potential applications for molecular robots are extremely varied and exciting.

Prof Leigh says: ‘Molecular robotics represents the ultimate in the miniaturisation of machinery. Our aim is to design and make the smallest machines possible. This is just the start but we anticipate that within 10 to 20 years molecular robots will begin to be used to build molecules and materials on assembly lines in molecular factories.’

Whilst building and operating such tiny machine is extremely complex, the techniques used by the team are based on simple chemical processes.

Prof Leigh added: ‘The robots are assembled and operated using chemistry. This is the science of how atoms and molecules react with each other and how larger molecules are constructed from smaller ones.

‘It is the same sort of process scientists use to make medicines and plastics from simple chemical building blocks. Then, once the nano-robots have been constructed, they are operated by scientists by adding chemical inputs which tell the robots what to do and when, just like a computer program.’

Prof. Leigh’s web site has a page “Building with a Programmable Molecular Robot” that links to the full text of the paper, places this advance in the context of the ‘molecular assembler’ concept originally proposed by K Eric Drexler in 1986 and inspired by Richard Feynman’s 1959 lecture. The molecular machine design used in the recent paper, based upon their previous molecular robot, is illustrated to show how this molecular robot can be programmed to produce one of four possible molecules from a tandem reaction process, including molecules that cannot be made through conventional organic catalysis. The page speculates that “Future generations of programmable molecular machines may play significant roles in chemical synthesis and molecular manufacturing.”

It should be noted, however, that there is nothing in this report that points toward using molecular machines or systems of molecular machines to apply sufficient mechanical force to break strong covalent bonds, or to precisely manuever extremely reactive free radicals or similar fragments to form strong covalent bonds. Rather, larger, less reactive molecules are being used as building blocks:

This first generation machine augurs well for the development of small-molecule robots that can be programmed to manipulate substrates to control synthesis in a form of mechanosynthesis (that is, the use of mechanical constraints to direct reactive molecules to specific molecular sites), in a manner reminiscent of the way that molecular construction is carried out in biology.

A News & Views technical review of the paper published in the same issue of Nature presents much the same picture. “A molecular assembler,” by T. Ross Kelly and Marc L. Snapper, recalls both K. Eric Drexler’s 1986 vision of “molecular assemblers,” published in Engines of Creation: The Coming Era of Nanotechnology, which formed the Foresight Institute’s founding vision, and the censure the concept attracted, and positions the Kassem et al. paper as reporting “a non-biological example of what could be regarded as a molecular assembler”.

The review illustrates how this latest molecular robot from David Leigh’s group can be reversibly switched between a left-handed and a right handed assembly mode by the addition or removal of a proton. A process of typically seven steps begins with the attachment of a substrate to the assembler, followed by activation, then the attachment of two chemical groups to the substrate in separate steps, with the outcome dependent on whether the assembler has been switched to left- or right-handed mode. Four different products can be made, dependent on the sequence of reactions and switching steps. The reviewers see the chief appeal of the molecular assembler as “the long-term prospect of streamlining organic synthesis.” Since conventional organic synthesis commonly requires 10-30 reactions, the process is time-consuming, inefficient, and expensive, often taking months to years. By contrast, each product of the molecular assembler can be made in one flask without purification between steps. The reviewers speculate that this molecular assembler could bring to general organic synthesis, choosing from up to 100 million molecular building blocks, benefits comparable to the benefits that solid-phase synthesis brought to peptide (20 building blocks) and DNA synthesis (4 building blocks). It is too soon to tell whether this molecular assembler holds advantages compared to automated solid-phase organic synthesis. While acknowledging the limitations of this first generation molecular assembler, the reviewers caution:

… those who dismiss the concept of molecular assemblers should heed the lesson of Lord Kelvin’s infamous 1895 pronouncement that “heavier-than-air flying machines are impossible”. We look forward to seeing what other impossibilities take flight in the future.

Derek Lowe’s blog on drug discovery and the pharma industry presents a similar take on the Kassem et al. paper “Building Our Own Molecular Machines“:

Let’s talk about enzyme envy. That’s what we organic chemists experience when we stop to think about how every complex natural product in the world is synthesized so much more quickly and efficiently than we can do it. All those crazy multiple rings systems, those bizarre heterocycles, huge macrolides, and dense arrays of stereochemistry are cranked out at ambient temperature, under aqueous conditions, on a time scale of minutes to hours. Oh, and they’re made offhand, in the background, as time permits, while the cells and organisms themselves are otherwise occupied with the even more startling business of being living chemical systems. …

Now let’s talk about nanotechnology. … The dream of assembling molecules and materials to order, atom by atom, has been around for some years now, and it largely remains just that: a dream. Eric Drexler and others have taken a lot of grief for maintaining that such things are possible, and to be sure, I have trouble myself with the real atomic scale this-carbon-goes-right-here level of the idea. But what about “this acetyl group goes right here?” That is, small-molecular scale versus atomic scale? That is exactly what every living cell on the planet is doing right now — that’s enzymatic chemistry, and I see no reason why we can’t get smart and capable enough to do the same sorts of things ourselves, and more. That leads up to this new paper … which is basically a molecular-sized stereoselective synthesis machine. …

… this thing has been designed to give you such chiral products, in a programmable fashion, and that it can indeed switch states on command to give them to you. It’s a machine – a very small machine, with limited inputs, but the first computer circuits were also very small machines with limited inputs, too.

Continuing with the computer circuit analogy, Lowe suggest’s that a key step in improving molecular synthesis machines is to reduce the key steps to binary ones.

If we develop these and other spatiotemporal switches to be faster, more responsive, more reliable, and more orthogonal to other functional groups, we can adapt them (as this paper does) to do some fairly complicated chemistry by positioning our other reagents in the appropriate places. …

Referring to Lord Kelvin’s infamous 1895 pronouncement that “heavier-than-air flying machines are impossible”:

The attempt to make molecular assemblers — which is, after all, the attempt to make our own enzymes, when we know that enzymes exist — is the same sort of problem. The molecular-machine folks (last year’s Nobel!), who care about rendering fundamental ideas and processes into molecular form, and the more traditional synthetic organic chemists, who care about what products any new reaction or machine can produce for them, can find common ground in building such things. Bring on the molecular machines!

In contrast to the controversy that greeted Drexler’s original conceptual proposal for a molecular assembler, the report of Prof. Leigh’s implementation of an actual molecular assembler, albeit of a more limited type than Drexler’s proposal, has been well received, as exemplified by the coverage cited here. Additional links to news coverage of the paper are available on Prof. Leigh’s publications page (at the top of the page as accessed Sept.28, 2017).

This paper adds a substantial milestone to the general impression, confirmed by the award of the 2016 Nobel Prize in Chemistry to three scientists who pioneered the development of molecular machines, that systems of molecular machines will be developed to perform a wide range of useful tasks. The consensus of the comments cited here is that the most exciting application will be the synthesis of a wide arrange of organic molecules difficult or impossible to synthesize by conventional methods, including pharmaceuticals and medical devices. The challenge for future molecular machine work will be to build increasingly complex arrays of molecular machines, to exert increasingly strong forces on individual atoms and small clusters of very reactive atoms, to build increasingly complex, atomically precise products.

In addition to mechanically interlocked architectures of small organic molecules exemplified by the work cited here, other paths toward complex systems of molecular machines are being explored, also with substantial success, including structural DNA nanotechnology, protein design, and scanning probe microscopy. These paths featured prominently in a first roadmap of the paths from current nanotechnology to advanced systems published ten years ago by Foresight Institute and Battelle. During the past ten years there has been much progress along all of these paths, but it remains to be seen which paths or combinations of paths will lead to systems for general purpose, high throughput atomically precise manufacturing, capable of inexpensively fabricating any useful arrangement of atoms allowed by physical law, as originally proposed by Drexler. The issue raised in comments cited above as to whether systems of molecular machines will be able eventually to break strong covalent bonds and precisely manipulate very reactive groups of atoms has a long history. At a 1989 nanotechnology conference at which Nadrian C. Seeman introduced DNA nanotechnology as his approach to nanoscale construction, he added the following caveat:

I’d like to emphasize something about the interactions of these segments of DNA and of the slide that Eric showed last night of a protein bound to a stretch of DNA. This DNA-protein complex involved several thousand atoms and several thousand bonds. Moving the big protein off the DNA would take about 20 kcal/mol. I think that it is important to emphasize that that is a weak interaction. To break any one of the thousands of covalent bonds in the DNA or protein would take much more energy than to move the whole protein “blob” off the DNA. It is important when thinking about what can be made and what can’t be made to realize that there are two stages of what Eric is talking about as nanotechnology. In one case, he is talking about moving molecules away from or toward other molecules where you are making weak intermolecular contacts. Whereas making particular molecules (like the crankshaft) involves an order of magnitude more energy. I don’t see this second phase as coming during the remainder of my scientific career (which I hope will go on another third of a century), while the first phase should be feasible soon because we are talking about lower energies.

Eric Drexler was in the audience when Prof. Seeman made the above comment. His response: “I agree entirely.” How far can we go, with which varieties of molecular machine systems? We can hope the answer will be clear within another decade or two.
—James Lewis, PhD

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USA-Austrian and Swiss Nanocars finish first in first Nanocar race https://foresight.org/usa-austrian-swiss-nanocars-finish-first-first-nanocar-race/ https://foresight.org/usa-austrian-swiss-nanocars-finish-first-first-nanocar-race/#respond Sun, 11 Jun 2017 02:54:35 +0000 http://foresight.org/?p=20415 If the current is high enough, the molecule starts to move and can be steered over the racetrack (University of Basel) Our previous post announced a race around a 100 nm course of six NanoCars, each a unique concept created from only several dozen atoms and powered by electrical pulses. The race was [...]

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STM image from University of Basel

If the current is high enough, the molecule starts to move and can be steered over the racetrack (University of Basel)

Our previous post announced a race around a 100 nm course of six NanoCars, each a unique concept created from only several dozen atoms and powered by electrical pulses. The race was run a few weeks later and two winners declared, due to two different tracks being used. From Swiss news “Swiss team wins shortest car race in the world“:

“Swiss Nano Dragster”, driven by scientists from Basel, has won the first international car race involving molecular machines. The race involved four nano cars zipping round a pure gold racetrack measuring 100 nanometres – or one ten-thousandth of a millimetre.

The two Swiss pilots, Rémy Pawlak and Tobias Meier from the Swiss Nanoscience Institute and the Department of Physics at the University of Basel, had to reach the chequered flag – negotiating two curves en route – within 38 hours.

The winning drivers, who actually shared first place with a US-Austrian team, were not sitting behind a steering wheel but in front of a computer. They used this to propel their single-molecule vehicle with a small electric shock from a scanning tunnelling microscope.

During such a race, a tunnelling current flows between the tip of the microscope and the molecule, with the size of the current depending on the distance between molecule and tip. If the current is high enough, the molecule starts to move and can be steered over the racetrack, a bit like a hovercraft.

[Includes 24-frame video from Basel University]

The race track was maintained at a very low temperature (-268 degrees Celsius) so that the molecules didn’t move without the current.

What’s more, any nudging of the molecule by the microscope tip would have led to disqualification.

Miniature motors

The race, held in Toulouse, France, and organised by the National Centre for Scientific Research (CNRS), was originally going to be held in October 2016, but problems with some cars resulted in a slight delay. In the end, organisers selected four of nine applicants since there were only four racetracks.

The cars measured between one and three nanometres – about 30,000 times smaller than a human hair. The Swiss Nano Dragster is, in technical language, a 4′-(4-Tolyl)-2,2′:6′,2”-terpyridine molecule.

The Swiss and US-Austrian teams outraced rivals from the US and Germany.

The race is not just a bit of fun for scientists. The researchers hope to gain insights into how molecules move.

Christian Joachim, head of research at CNRS, said that if they managed to control molecule movement, “we could create extremely miniature motors that could have all sorts of uses”.

Twenty years ago Dr. Joachim shared the 1997 Foresight Feynman Prize in Nanotechnology for Experimental Work with two researchers then at IBM Research Zurich for work using scanning probe microscopes to manipulate molecules. Eight years later he won the 2005 Foresight Feynman Prize in Nanotechnology for Theory for developing theoretical tools and establishing the principles for design of a wide variety of single molecule functional nanomachines.

STM image from Rice and partner University of Graz

Image from 22-second video. Rice and partner University of Graz run fastest single-molecule car in international event (Rice University)

Additional details and perspectives are provided by a Rice University news release written by Mike Williams. “Rice vehicle tops all in Nanocar Race“:

Rice University chemist James Tour [winner of the 2008 Foresight Institute Feynman Prize for Experimental work] and his international team have won the first Nanocar Race. With an asterisk.

The Rice and University of Graz team finished first in the inaugural Nanocar Race in Toulouse, France, April 28, completing a 150-nanometer course — a thousandth of the width of a human hair — in about 1½ hours. (The race was declared over after 30 hours.)

The team led by Tour and Graz physicist Leonhard Grill [winner of the 2011 Foresight Institute Feynman Prize for Experimental work] deployed a two-wheeled, single-molecule vehicle with adamantane tires on its home track in Graz, Austria, achieving an average speed of 95 nanometers per hour. Tour said the speed ranged from more than 300 to less than 1 nanometer per hour, depending upon the location along the course.

The Swiss Nano Dragster team finished next, five hours later. But organizers at the French National Center for Scientific Research declared them a co-winner of first place as they were tops among teams that raced on a gold track.

Because the scanning tunneling microscope track in Toulouse could only accommodate four cars, two of the six competing international teams — Ohio University and Rice-Graz — ran their vehicles on their home tracks (Ohio on gold) and operated them remotely from the Toulouse headquarters.

Five cars were driven across gold surfaces in a vacuum near absolute zero by electrons from the tips of microscopes in Toulouse and Ohio, but the Rice-Graz team got permission to use a silver track at Graz. “Gold was the surface of choice, so we tested it there, but it turns out it’s too fast,” Grill said. “It’s so fast, we can’t even image it.”

The team got permission from organizers in advance of the race to use the slower silver surface, but with an additional handicap. “We had to go 150 nanometers around two pylons instead of 100 nanometers since our car was so much faster,” Tour said.

Tour said the race directors used the Paris-Rouen auto race in 1894, considered by some to be the world’s first auto race, as precedent for their decision April 29. “I am told there will be two first prizes regardless of the time difference and handicap,” he said.

The Rice-Graz car, called the Dipolar Racer, was designed by Tour and former Rice graduate student Victor Garcia-Lopez and raced by the Graz team, which included postdoctoral researcher and pilot Grant Simpson and undergraduate and co-pilot Philipp Petermeier.

The purpose of the competition, according to organizers, was to push the science of how single molecules can be manipulated as they interact with surfaces.

“We chose our fastest wheels and our strongest dipole so that it could be pulled by the electric field more efficiently,” said Tour, whose lab has been designing nanocars since 1998. ‘We gave it two (side-by-side) wheels to minimize interaction with the surface and to lower the molecular weight.

“We built in every possible design parameter that we could to optimize speed,” he said.

While details of the Dipolar Racer remained a closely held secret until race time, Tour and Grill said they will be revealed in a forthcoming paper.

“This is the beginning of our ability to demonstrate nanoscale manipulation with control around obstacles and speed and will pave the way for much faster paces and eventually for carrying cargo and doing bottom-up assembly.

“It’s a great day for nanotechnology,” Tour said. “And a great day for Rice University and the University of Graz.”

Additional coverage:

In Science, by Robert F. Service “Watch the world’s smallest cars race along tracks thinner than a human hair“:

… To propel the molecular machines forward on their silver and gold tracks, researchers use electric jolts provided by the tip of a scanning tunneling microscope. After nearly 8 hours, the Austrian-U.S. entry, Dipolar Racer, has already crossed the finish line. The car, which resembles a molecular Segway without a handle, has completed two runs down its 150-nanometer silver track at an average speed of 35 nanometers per hour. At that pace, it would take hundreds of years to drive the car across a €1 coin. The Nano Dragster, entered by the Swiss team, was the first to complete a shorter, 100-nanometer-long gold race track. But the other four teams have struggled to even cross the starting line …

From National Public Radio, written by Merrit Kennedy “Microscopic Cars Square Off In Big Race” [includes 6:22 video]:

… The Austrian-U.S. team, driving the Dipolar Racer, finished hours before any of its competitors.

However, the two-wheeled car raced on its home track in Austria, on a silver track rather than a gold one. The team controlled it remotely. Rice University, where some of the scientists hail from, say silver was a handicap because it’s a slower surface. Race scientific director Christian Joachim tells The Two-Way that “they were unable to compete on gold because on gold the molecule was not stable enough.”

The next finisher, the Swiss Nano Dragster, was declared a co-winner – because it was the first team to finish on gold. …

From Chemistry World, written by Fernando Gomollón-Bel “World’s first nanocar race a success for science and engagement“:

…Steve Goldup, who works on interlocked molecules and molecular machines at the University of Southampton, UK, but didn’t take part in the race, says that the dipolar racer is a ‘really nice design’. He notes that the team ’optimised it to maximise the dipole (maximises the force created by the electric field of the STM tip) and minimise the molecular weight. It will be interesting to find out – and the experiments to work this out will be interesting in themselves – if the car skids along or if the wheels roll. Either way would achieve the goal as the wheels prevent the aromatic body from sticking to the surface.’ …

It is interesting that a small collection of molecular cars, all driven by electric pulses from an STM tip, differing substantially in design details, show such a wide range of performances. Perhaps this is not only an iconic event in the developing story of molecular machines, but a beginning of a systematic effort to understand function and engineer improved performance?
—James Lewis, PhD

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