A video of my talk at the Moscow Polytechnical Museum is now on YouTube. I gave this talk on advanced nanotechnology prospects to an audience drawn from local technical universities during my recent Moscow visit.

I recently gave the Inaugural Lecture for the Programme on the Impacts of Future Technology at the Oxford Martin School, and the lecture video is now available.*

The talk describes the application of physical law and exploratory engineering to studies of the future potential of nanotechnology.

Summary here: News & Research Highlights.

* With thanks to Stuart Armstrong, researcher and occasional videographer

See also:

• Exploratory Engineering:
  Applying the predictive power of science
  to future technologies
• The Antiparallel Structures of Science and Engineering
• A Map of Science
• How to Learn About Everything

Here are two Monirobo robotic machines — radiation-hard, 2.4 km/hr, 600 kg robots, recently arrived on site:

These probably aren’t very good at exploring wrecked buildings, viewing fuel storage pools obscured explosion debris, sampling smoke plumes rising from (?), etc.

Here’s a Parrot AR.Drone — iPhone controlled, resistant to multiply-lethal radiation doses [update: > 10 times the human -lethal dose; see comments], and available for $300 from Amazon:

Parrot’s-eye view from on high:

Exploring a warehouse:

They can of course carry lights for exploring dark places:

Parrot drones would be useful.

They haven’t been used.

It seems that our civilization has difficulty recognizing and applying its own abilities, even when they are concrete, available, and widely known.

(As you may know, Japan has displayed a special sort of organizational paralysis in this crisis, but wouldn’t it be surprising if “toys” like these were used in an incident managed by Very Serious People anywhere in the world?)

The New York Times has an article, “Where Cinema and Biology Meet”, on the recent high-quality animations of biomolecular machines.

The author, Erik Olsen, highlights Drew Barry as the Steven Spielberg of the field:

Mr. Berry’s work is revered for artistry and accuracy within the small community of molecular animators, and has also been shown in museums, including the Museum of Modern Art in New York and the Centre Pompidou in Paris. In 2008, his animations formed the backdrop for a night of music and science at the Guggenheim Museum called “Genes and Jazz.”

I discuss some of Drew’s work here.

But beware! The videos lie because they must.
All of them.

1. Molecular Machine Assembly: The Movie
2. Productive Nanosystems: The Movies
3. Productive Nanosystems: The Ribosome Videos
4. Nanomachines: How the Videos Lie to Scientists
5. VIDEOS

Video: A digitally controlled
molecular machine
(>3 billion years of patchwork)

A few weeks ago, I highlighted some of the most popular posts in Metamodern’s first year (see “Knowledge about Knowledge…”). Posts that offer videos, documents, or talk slides also ranked high:

With downloadable documents and talk slides:

• Molecular Nanomachines: Physical Principles and Implementation Strategies
• My MIT dissertation — a draft of Nanosystems — is now online
• Slides for Talk on Nanotechnology and Computational Challenges
• Slides for Berkeley Talk on Molecular Nanosystems
• The Technology Roadmap Translated: Russian

With molecular videos:

• Productive Nanosystems: The Movies
• Productive Nanosystems: The Ribosome Videos

With videos of machines making things at blazing speeds:

• High-Throughput Nanomanufacturing: Small Parts
• High-Throughput Nanomanufacturing: Assembly
• High-Throughput Nanomanufacturing: Assembling larger products

• Knowledge about Knowledge:
  The most popular posts in the first year

A challenge question:
Measured by cumulative traffic, one post on Metamodern ranks well above the rest. It was neither very recent, nor very early, nor on any of the topics above. Which one is it, and why is it popular? (Actually, I’m baffled by the second part of the question.)

“Big Dog”: An agile quadruped robot
Climbing a hill.     Slipping on ice.
Climbing down.     The leap.
(See potentially disturbing video)

---

Brought to you by Boston Dynamics and DARPA

A fast, dexterous robotic hand
The hand.    Motion blur.
The toss.    The catch.
(See potentially disturbing video)

---

Brought to you by the Ishikawa Komuro Laboratory
at the University of Tokyo

Forget about clumsy, lumbering robots.
Think fast, precise, and acrobatic.

[Update: only potentially disturbing videos.]

• — Small Parts (with videos, no robots)
• — Assembly (with videos, no robots)
• — Assembling larger products (with video of a very fast robot)

And…

• Why I hate “nanobots”

The ribosome diagrammed

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The ribosome in reality
(see video below)

While browsing the literature on the catalysis of bond formation in protein synthesis by ribosomes*, I came across a wonderful set of videos of the ribosomal protein manufacturing system at work, shown in recent-state-of-the-art molecular detail. These videos were presented in a Chemical & Engineering News article online, but I missed seeing them at the time. (This shows a shortcoming of my habit of reading only the paper bundles that the ACS sends by post.)

…but beware of
Ornithological Aeronautics

Ribosomes are productive nanosystems, that is, machines that combine small molecular building blocks under digital control to build complex structures. They’re programmable by means of genetic engineering, and extraordinarily useful in emerging molecular technologies. However, when watching how ribosomes work — in strange, messy, and subtle ways — it’s wise to keep in mind the usual relationship between biological examples (horses, birds) and engineered, mechanical systems (cars, aircraft) that serve similar functions. Biological examples show that functions can be performed (ground transport, air transport), but they don’t necessarily suggest the best approach to building machines for human purposes. If aeronautical engineering had been a branch of ornithology, there would be extensive research on artificial feathers and the ongoing challenge of artificial muscle, but no passenger aircraft.

There’s a much learn from ribosomes, but also much that needn’t be imitated.

Video: A digitally controlled
molecular machine
(>3 billion years of patchwork)

The first video (from the MRC Laboratory of Molecular Biology in Cambridge, UK) is based on structures determined by x-ray crystallography and electron microscopy; these are animated, and rendered at a fine, molecular level of detail. The video shows the entire process of protein manufacture, from initiation to release. The frantic pace of the middle part of the video shows action in approximately real time.

Note, however, that the actual motions of these biological molecular machines are far less purposeful — depicting realistic molecular trajectories would either show a blur, or be excruciatingly boring. (See “The videos lie because they must” in Molecular Machine Assembly: The Movie.)

Video: A smoother view
of the elongation cycle

The second video, produced by researchers at the Howard Hughes Medical Institute, focuses on the repeating cycle that extends the amino acid chain. It, too, is based on real structural data, but is presented at more diagrammatic level of detail.

Video: Molecular dynamics
of tRNA binding
(>2 billion years; almost no change)

The final video, showing detail at a molecular level, is shows the results of a targeted molecular dynamics simulation; targeting is another way to give an unnatural degree of direction to molecular motion, avoiding both excruciating boredom and (here) consumption of inordinate amounts of computer time.

The video shows a key step in tRNA binding, the “accommodation” process, the step where the appendage carrying the next amino acid (green) swings across from right to left. This step is central to kinetic proofreading in ribosomal translation, a process that keeps error rates tolerably low. A landmark paper on this process was co-authored by the new U.S. Secretary of Energy, physicist and Nobel laureate, Steven Chu.

• Productive Nanosystems: The Movies
• Molecular Machine Assembly: The Movie
• Nanomachines: How the Videos Lie to Scientists

And of high-throughput manufacturing:

• High-Throughput Nanomanufacturing: Small Parts (with videos)
• High-Throughput Nanomanufacturing: Assembly (with videos)

A simple molecular chain

---

A 2D simplification of
its typical complex,
disordered, 3D structure

A scientist recently remarked to me that molecular modeling techniques cannot accurately predict the mechanical properties of typical polymers, even one as simple as polyethylene, a hydrocarbon consisting of long chains of –(CH₂)– units. He was, I think, suggesting that molecular modeling may tell us little about molecular technologies based on structures that would be far more complex.

It’s important to understand why this plausible line of reasoning is mistaken.

Where can molecular mechanics models give accurate predictions? One area includes precisely structured solids with stable, covalent bonding and no conformational degrees of freedom. Ideally structured, hydrogen-terminated silicon crystals provide examples, as does a large class of existing and potential polycyclic structures with modest strain and saturated bonds. The elements H, C, N, O, F, Si, P, S, and Cl provide a broad palette, and the higher adamantanes are hydrocarbons in this class.

[ Note: When operation of a device involves only low stresses and strains, the elastic responses of structures of this sort typically are nearly linear, which greatly simplifies (for example) calculations of entropic contributions to free energy.]

Where do molecular mechanics models encounter difficulties? One area includes disordered solids with extensive non-covalent interactions and conformational degrees of freedom, and polyethylene is a good example. Its deceptive simplicity stems from the simplicity of its molecules; its challenging complexity stems from the organization and interaction of those molecules.

At room temperature, polyethylene forms a disordered structure consisting of of small crystallites threaded by multiple, partly-folded chains. Under increasing tension, chains unfold and slide, distributing tension unevenly and breaking in more-or-less random patterns. The mechanical properties of the material (for example, stress-strain curves and maximum elongation to failure) depend on polymer chain lengths and processing history: both milk jugs and plastic bags are commonly made of polyethylene, but so is Dyneema, a polyethylene material in which the same repeating units — but in longer, highly oriented chains — form fibers that rival high-strength steel.

In short, polyethylene forms complex, disordered materials that are quite unlike well-ordered proteins or other components suitable for use in atomically precise systems. Noncrystalline solids that form spontaneously from simple molecules will often be more difficult to model than even quite complex molecular machinery, in part because they have no specific structure.

This example illustrates aspects of the contrasting perspectives of scientific inquiry and engineering design. I’ve recently written about the methodology of exploratory engineering as a basis for applying the predictive power of scientific knowledge to achieve a limited — yet powerful —set of insights into future technologies, and in an earlier post I described why the intricate molecular systems that can be made today are challenging to model, and why the intricate molecular systems that are easiest to model cannot (yet) be made.

I see many steps between where we are and what we can see ahead, several turns further along a winding road. I expect bionanotechnology to play a central role, and for design, biomolecular modeling is already surprisingly capable.

• Making vs. Modeling:
  A paradox of progress in nanotechnology
• Exploratory Engineering:
  Applying the predictive power of science
  to future technologies
• Macromolecular Modeling for Molecular Systems Engineering
• The Physical Basis of Atomically Precise Manufacturing