Software technologies

Serverification of molecular engineering tools

November 3, 2013

If you’re interested in RosettaDesign (see Learning practical atomically precise fabrication and Further notes…), you might want to look at this PLOS ONE paper: Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE) …This paper describes the ROSIE server infrastructure, a step-by-step ‘serverification’ protocol for use by Rosetta developers, and the […]

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Further notes on Rosetta, RosettaDesign
— and Rosie

October 31, 2013

In “Learning practical atomically precise fabrication”, I blogged a paper on the Rosetta software suite for protein modeling and design (you might want to skip quickly to page 2993, “Protein Design”). I’ve also done a guest post, “Macromolecular Modeling for Molecular Systems Engineering” for the Rosetta Design Group’s blog, and that post offers a deeper […]

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Learning practical atomically precise fabrication

October 30, 2013

If you’d like to learn about (and perhaps help advance) the state of the art in fabricating intricate, nanoscale, atomically precise objects, you might want to examine this paper: Practically Useful: What the ROSETTA Protein Modeling Suite Can Do for You (open-access pdf). The materials are peptide polymers, a diverse class of materials that can […]

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Nobel Prize for Computational Chemistry

October 9, 2013

Michael Levitt, Martin Karplus, and Arieh Warshel have been awarded the Nobel Prize in chemistry for their contributions to computational methods for molecular simulation. These are the methods that tell us how atomically precise covalent structures can serve as high-performance nanomachines, which will provide the basis for advanced high-throughput atomically precise manufacturing. (BBC)

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Software, trust, and proof

August 22, 2013

A recently developed high-performance OS microkernel supports the capability security model and comes with a formal specification and machine-checked proof: it’s called seL4. This is very, very, important. As the NICTA project notes: …software systems are increasingly trusted with critical operations. Yet, the traditional ways in which they are engineered provide limited or no assurance […]

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Quiz Question:
What is wrong with this model of computation?

August 3, 2011

In the news today: “Governments, IOC and UN hit by massive cyber attack” (BBC) How did the attack work? In a mind-numbingly ordinary way: “An email would be sent to an individual with the right level of access within the system; attached to the message was a piece of malware which would then execute and […]

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An advance in atomically precise
building-block assembly

May 27, 2011

A paper in Science reports a design method that substantially advances the macromolecular technology base for building atomically precise nanosystems. Background: foldamer engineering As many readers know, biology shows an effective way build large, intricate, atomically precise systems: Use covalent chemistry to build chains of small building blocks, and design these chains to fold into […]

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3D atomic imaging of nanoparticles
— a new technique

February 24, 2011

Image and atomic reconstruction From the abstract: Although atomic-resolution electron microscopy has been feasible for nearly four decades, neither electron tomography nor any other experimental technique has yet demonstrated atomic resolution in three dimensions. Here we report the 3D reconstruction of a complex crystalline nanoparticle at atomic resolution. To achieve this, we combined aberration-corrected scanning […]

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The 7th Peptoid Summit:
Progress in peptoid toolkit development

August 13, 2010

The 7th Peptoid Summit highlighted progress in design technology for one of the most promising toolkits in modular molecular systems engineering. I’ve outlined the submonomer method for peptoid synthesis as a powerful and convenient way to assemble diverse molecular components, and the recent development of crystalline peptoid nanosheets as a platform for extended atomically-precise structures. […]

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Needless Megadeaths:
A Suggestion for Science in the Public Interest

June 16, 2010


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How many minds produce knowledge
(and how they don’t)

December 11, 2009

How groups think and how to do it better A review of Infotopia I’ve been discussing problems with public information and ways to improve it with Michael Nielsen, and on this topic, he recommended Infotopia: how many minds produce knowledge by Cass Sunstein. Having just finished reading it, I recommend it too. With a solid […]

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Cybersecurity: Let’s try something that can work

November 25, 2009

Perimeter defense considered harmful William Wulf and Anita Jones have written a brief, tantalizing, and important article in Science: “Reflections on Cybersecurity”. They point the way out of a tangle of security problems (not all, of course) that costs billions of dollars in losses billions in countermeasures, and billions more in opportunity costs — some […]

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