From the category archives:

Nanoscience

Molecular Electron Holography:
Progress toward atomic-resolution imaging?

October 20, 2009

Hans-Werner Fink’s group reports a remarkable advance in imaging individual biomolecules, with surprising physics, and (to me, at least) a somewhat mysterious date of publication.
The surprise is that it doesn’t destroy the molecules before imaging them.
The new generation of aberration-corrected electron microscopes achieve atomic resolution, but with a caveat — they succeed with robust, inorganic [...]

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Productive Nanosystems: The Ribosome Videos

July 16, 2009

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 [...]

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What is simple?
Polyethylene, molecular modeling,
and molecular machines

July 8, 2009

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 [...]

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Science and Engineering:
A Layer-Cake of Inquiry and Design

June 16, 2009

Inquiry is the essence of science, design is the essence of engineering, and in their pure forms, these activities are utterly different. Scientific inquiry draws observations from the world to reshape the mind; engineering design projects ideas from the mind to reshape the world. One is an eye, the other a hand, afferent and efferent [...]

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Machines Evolving to the Brink of Failure

April 30, 2009

While writing a post on molecular engineering for the Macromolecular Modeling Blog, I came across an EMBO Reports paper that provided new guidelines for protein engineering; It also illustrates a general principle that should be taken to heart by anyone thinking about molecular engineering from a biomolecular perspective:
Molecular machines tend to evolve toward the [...]

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The Casimir Effect and Nanomachines

April 20, 2009

The Casimir effect can be viewed as a manifestation of the quantum-mechanical zero-point energy of the vacuum, and has recently been hyped as if it were something new and mysterious that will assist or maybe ruin advanced nanomechanical systems. It has inflamed the minds of something-for-nothing energy enthusiasts, too.
In reality, what Casimir described is a [...]

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Macromolecular Modeling
for Molecular Systems Engineering

April 16, 2009

Nir London of the Macromolecular Modeling Blog has invited me to offer my perspective on the field. After patiently waiting for me to complete it, he’s posted the resulting essay, which I have cross-posted below.
The Macromolecular Modeling Blog is hosted by the Rosetta Design Group, which offers molecular modeling services based on the Rosetta protein [...]

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Mechanochemistry, Mechanosynthesis,
and Molecular Machinery

April 14, 2009

Volume 1, Number 1 of Nature Chemistry is now out, and the next issue will include an article titled “Activating catalysts with mechanical force”. This article reports a nice experimental result and helps to illustrate the broad range of physical processes included under the umbrella terms of “mechanochemistry” and “mechanosynthesis”.
The authors demonstrate two examples of [...]

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Graphene Nanotechnology
(and TEAM Microscopes)

April 2, 2009

I’ve intended to write about the wonders of graphene and related materials for nanotechnology, both as products and as a basis for building productive nanosystems, but there is so much to say that I didn’t know where to begin. As Rosa reminds me, though, a great virtue of a blog is that you can use [...]

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A Revolution
in de novo Protein Engineering Methodology

March 30, 2009

In a recent Nature article, researchers describe the design of a peptide foldamer device (a.k.a. “protein”) that binds and releases oxygen in a way that resembles the heme protein, neuroglobin — and they focus more on the design process than on the design product. They advocate an engineering approach that explicitly rejects aspects of the [...]

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Polyoxometalate Nanostructures

March 29, 2009

My technical talks often include a slide that shows several kinds of atomically precise components that may prove useful in composite nanosystems. One image is labeled “polyoxometalates”, a name that isn’t widely known. I think it should be.
Polyoxometalates (POMs) are molecular structures that are, in effect, atomically precise bits of metal oxide that contain [...]

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Effective Concentration in Self Assembly,
Catalysis, and Mechanosynthesis (2)

March 27, 2009

In my post on effective concentration, I noted that the concentration of water in water (about as high as a real concentration can be) is 55 M, while observed effective concentrations are often >55,000 M. This is puzzling until you realize that, for a molecular collision to result in a reaction, it must typically hit a target [...]

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