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	<title>Comments on: Self assembly and nanomachines: Complexity, motion, and computational control</title>
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	<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/</link>
	<description>The Trajectory of Technology</description>
	<lastBuildDate>Wed, 28 Jul 2010 03:14:01 -0700</lastBuildDate>
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		<title>By: Self assembly and nanomachines: Complexity, motion, and computational control &#124; NanoLinxs</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-3044</link>
		<dc:creator>Self assembly and nanomachines: Complexity, motion, and computational control &#124; NanoLinxs</dc:creator>
		<pubDate>Sat, 27 Feb 2010 02:22:11 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-3044</guid>
		<description>[...] at 3:33 am UTC  { 18 comments… read them below or add one [...]</description>
		<content:encoded><![CDATA[<p>[...] at 3:33 am UTC  { 18 comments… read them below or add one [...]</p>
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		<title>By: Eniac</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-2979</link>
		<dc:creator>Eniac</dc:creator>
		<pubDate>Fri, 19 Feb 2010 14:23:17 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-2979</guid>
		<description>&lt;blockquote&gt;
Acoustic pressure can vary within any of several pressure bands, driving any of several pistons while leaving other differently-sprung pistons pinned at either end of their stroke. Thus, multiple dimensions of control.
&lt;/blockquote&gt;
Yes, but with wavelength to vary you get an additional signal dimension, so if there are n bands in intensity and m bands in wavelength, you have m x n dimensions of control.
&lt;blockquote&gt;
Photon absorption is probabilistic, so you would need to spend several times the energy per photon pulse to make sure that the pulse was received. Acoustic and photonic noise thus get handled similarly.
&lt;/blockquote&gt;
Good point, I hadn&#039;t thought this through. Still, you&#039;d be averaging over a (small) time interval only, not a volume, which should save space, at the very least. You get much more energy from photons than you could acoustically, I think, which could be good or bad, depending on how much you need.</description>
		<content:encoded><![CDATA[<blockquote><p>
Acoustic pressure can vary within any of several pressure bands, driving any of several pistons while leaving other differently-sprung pistons pinned at either end of their stroke. Thus, multiple dimensions of control.
</p></blockquote>
<p>Yes, but with wavelength to vary you get an additional signal dimension, so if there are n bands in intensity and m bands in wavelength, you have m x n dimensions of control.</p>
<blockquote><p>
Photon absorption is probabilistic, so you would need to spend several times the energy per photon pulse to make sure that the pulse was received. Acoustic and photonic noise thus get handled similarly.
</p></blockquote>
<p>Good point, I hadn&#8217;t thought this through. Still, you&#8217;d be averaging over a (small) time interval only, not a volume, which should save space, at the very least. You get much more energy from photons than you could acoustically, I think, which could be good or bad, depending on how much you need.</p>
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		<title>By: Eniac</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-2970</link>
		<dc:creator>Eniac</dc:creator>
		<pubDate>Thu, 18 Feb 2010 16:08:07 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-2970</guid>
		<description>This is fascinating stuff. I am still bothered, though, that for all the ingenuity we put into the design of these devices, there is currently no path to making them, nor is one obviously emerging in the near future. DNA origami are fine, but from there to something that could start putting atoms together is a long way.

There seem to be three distinct ways we can currently put atoms together: 1) old-fashioned synthetic chemistry, 2) programming organisms to make biopolymers, and 3) STM/AFM style methods of mechanosyntesis. Each of these is in the embryonic stages when it comes to atomically precise manufacturing, corresponding perhaps to chipping stone tools. No lathes, no drills, not even a screwdriver. The biological systems could be compared to animal husbandry. Useful, but a technological dead-end.

In contrast, if I wanted to roll up my sleeves and build a clanking replicator, I could go to a hobby/toy store, buy a few dozen R/C servos and Meccano kits and start putting together manipulators. Add some easily available controller boards and connect them to my PC. Next thing I know, I am sitting there losing hair over creating software to make the manipulators put parts together. Granted, that would not yet be a replicator, but it is still a long way from square one, where we are with nanosystems.</description>
		<content:encoded><![CDATA[<p>This is fascinating stuff. I am still bothered, though, that for all the ingenuity we put into the design of these devices, there is currently no path to making them, nor is one obviously emerging in the near future. DNA origami are fine, but from there to something that could start putting atoms together is a long way.</p>
<p>There seem to be three distinct ways we can currently put atoms together: 1) old-fashioned synthetic chemistry, 2) programming organisms to make biopolymers, and 3) STM/AFM style methods of mechanosyntesis. Each of these is in the embryonic stages when it comes to atomically precise manufacturing, corresponding perhaps to chipping stone tools. No lathes, no drills, not even a screwdriver. The biological systems could be compared to animal husbandry. Useful, but a technological dead-end.</p>
<p>In contrast, if I wanted to roll up my sleeves and build a clanking replicator, I could go to a hobby/toy store, buy a few dozen R/C servos and Meccano kits and start putting together manipulators. Add some easily available controller boards and connect them to my PC. Next thing I know, I am sitting there losing hair over creating software to make the manipulators put parts together. Granted, that would not yet be a replicator, but it is still a long way from square one, where we are with nanosystems.</p>
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		<title>By: Chris Phoenix</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-2957</link>
		<dc:creator>Chris Phoenix</dc:creator>
		<pubDate>Tue, 16 Feb 2010 22:01:04 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-2957</guid>
		<description>Eniac, 

First, let me congratulate you and thank you for stepping up with an idea that may be genuinely new: broadcast control via singlet/triplet conversions. I don&#039;t know if it&#039;ll work - I&#039;ve written to a physicist who&#039;s interested in nanotech - but it&#039;s a great idea.

Now some details: as proposed in &lt;a href=&quot;http://www.molecularassembler.com/KSRM/4.11.3.1.htm&quot; rel=&quot;nofollow&quot;&gt;this section of KSRM&lt;/a&gt;, the signaling frequency is 10 MHz, over 200 times better than 40 kHz. On the other hand, 100 pulses seems a bit low to place an atom. The device floats in a 2 micron chamber - rather small, but makes the high frequency plausible.

...OK, according to the numbers buried in &lt;a href=&quot;http://www.molecularassembler.com/KSRM/AppB.4.5.htm&quot; rel=&quot;nofollow&quot;&gt;Appendix B&lt;/a&gt;, the device seems to require 1 million seconds - about 1 month - to replicate. That implies 200 atoms per second, or 50,000 pulses per atom.

Acoustic pressure can vary within any of several pressure bands, driving any of several pistons while leaving other differently-sprung pistons pinned at either end of their stroke. Thus, multiple dimensions of control.

Photon absorption is probabilistic, so you would need to spend several times the energy per photon pulse to make sure that the pulse was received. Acoustic and photonic noise thus get handled similarly.

Rather than building a soup of devices, it would be more efficient to build a double-long device, which could then be used to build a double-wide device... it&#039;s not too many doublings till you attain a device large enough to be controlled and powered with direct physical links. This should be thought of as a bootstrapping stage, not a useful manufacturing system in itself.

I suspect that significantly faster devices will turn out to be possible in practice. For example, this device has rigid walls, which use most of its atoms. An inflated flexible-wall device, as Merkle originally proposed, would replicate much faster. It would have other problems that the present design aims to solve, but I don&#039;t think those problems are actually very important for bootstrapping devices. Also, I suspect that they may have gone farther than they needed to in simplifying the control system. 

Chris</description>
		<content:encoded><![CDATA[<p>Eniac, </p>
<p>First, let me congratulate you and thank you for stepping up with an idea that may be genuinely new: broadcast control via singlet/triplet conversions. I don&#8217;t know if it&#8217;ll work &#8211; I&#8217;ve written to a physicist who&#8217;s interested in nanotech &#8211; but it&#8217;s a great idea.</p>
<p>Now some details: as proposed in <a href="http://www.molecularassembler.com/KSRM/4.11.3.1.htm" rel="nofollow">this section of KSRM</a>, the signaling frequency is 10 MHz, over 200 times better than 40 kHz. On the other hand, 100 pulses seems a bit low to place an atom. The device floats in a 2 micron chamber &#8211; rather small, but makes the high frequency plausible.</p>
<p>&#8230;OK, according to the numbers buried in <a href="http://www.molecularassembler.com/KSRM/AppB.4.5.htm" rel="nofollow">Appendix B</a>, the device seems to require 1 million seconds &#8211; about 1 month &#8211; to replicate. That implies 200 atoms per second, or 50,000 pulses per atom.</p>
<p>Acoustic pressure can vary within any of several pressure bands, driving any of several pistons while leaving other differently-sprung pistons pinned at either end of their stroke. Thus, multiple dimensions of control.</p>
<p>Photon absorption is probabilistic, so you would need to spend several times the energy per photon pulse to make sure that the pulse was received. Acoustic and photonic noise thus get handled similarly.</p>
<p>Rather than building a soup of devices, it would be more efficient to build a double-long device, which could then be used to build a double-wide device&#8230; it&#8217;s not too many doublings till you attain a device large enough to be controlled and powered with direct physical links. This should be thought of as a bootstrapping stage, not a useful manufacturing system in itself.</p>
<p>I suspect that significantly faster devices will turn out to be possible in practice. For example, this device has rigid walls, which use most of its atoms. An inflated flexible-wall device, as Merkle originally proposed, would replicate much faster. It would have other problems that the present design aims to solve, but I don&#8217;t think those problems are actually very important for bootstrapping devices. Also, I suspect that they may have gone farther than they needed to in simplifying the control system. </p>
<p>Chris</p>
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		<title>By: Eniac</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-2948</link>
		<dc:creator>Eniac</dc:creator>
		<pubDate>Mon, 15 Feb 2010 16:51:29 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-2948</guid>
		<description>Has any work been done to investigate light as the source of energy and broadcast signal? Pressure is inherently noisy at the nanoscale, due to Brownian motion. Light is not. Pressure requires (comparably) huge volumes and parts, light can be transduced into mechanical work by something as small as a retinal chromophore. Pressure has only one useable variable, intensity, light has two: wavelength and intensity. Retinal can be tuned to different frequencies, as happens to give us color vision. Hybrid approaches are also possible, perhaps pressure for energy and light for control.

Perhaps even more promising could be nuclear or electron magnetic resonance. It permits extremely detailed control of spins at the atomic level, if only it could be made to have chemical/mechanical effects. I think it might be possible to do that using singlet/triplet conversions and associated radical reactions. Magnetic resonance can convert between singlet and triplet spin states of radicals, and the two have distinctly different reaction paths that could be used for control purposes, theoretically. The radical states can be created by light absorption, so we would have a hybrid optical/magnetic system: light for energy and magnetic resonance for control. The electron transfer chain in the photosynthetic reaction center is a good example of this kind of controlled radical reaction, albeit without external control.

 It is quite likely, I think, that nanocomputers will use spin states for computation, because that requires much less energy than electronic excitations or even mechanical interactions. This, too, would make magnetic resonance a natural way of interaction between nano and macro systems.</description>
		<content:encoded><![CDATA[<p>Has any work been done to investigate light as the source of energy and broadcast signal? Pressure is inherently noisy at the nanoscale, due to Brownian motion. Light is not. Pressure requires (comparably) huge volumes and parts, light can be transduced into mechanical work by something as small as a retinal chromophore. Pressure has only one useable variable, intensity, light has two: wavelength and intensity. Retinal can be tuned to different frequencies, as happens to give us color vision. Hybrid approaches are also possible, perhaps pressure for energy and light for control.</p>
<p>Perhaps even more promising could be nuclear or electron magnetic resonance. It permits extremely detailed control of spins at the atomic level, if only it could be made to have chemical/mechanical effects. I think it might be possible to do that using singlet/triplet conversions and associated radical reactions. Magnetic resonance can convert between singlet and triplet spin states of radicals, and the two have distinctly different reaction paths that could be used for control purposes, theoretically. The radical states can be created by light absorption, so we would have a hybrid optical/magnetic system: light for energy and magnetic resonance for control. The electron transfer chain in the photosynthetic reaction center is a good example of this kind of controlled radical reaction, albeit without external control.</p>
<p> It is quite likely, I think, that nanocomputers will use spin states for computation, because that requires much less energy than electronic excitations or even mechanical interactions. This, too, would make magnetic resonance a natural way of interaction between nano and macro systems.</p>
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		<title>By: Eric Drexler Talks about Self Assembly at Metamodern and Chris Phoenix does the same at CRNano &#124; NanoLinxs</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-2931</link>
		<dc:creator>Eric Drexler Talks about Self Assembly at Metamodern and Chris Phoenix does the same at CRNano &#124; NanoLinxs</dc:creator>
		<pubDate>Sun, 14 Feb 2010 03:33:39 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-2931</guid>
		<description>[...] for Nanoengineering: DNA, proteins, and search-intensive design  3. Self assembly and nanomachines: Complexity, motion, and computational control (See [...]</description>
		<content:encoded><![CDATA[<p>[...] for Nanoengineering: DNA, proteins, and search-intensive design  3. Self assembly and nanomachines: Complexity, motion, and computational control (See [...]</p>
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		<title>By: Eniac</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-2914</link>
		<dc:creator>Eniac</dc:creator>
		<pubDate>Fri, 12 Feb 2010 17:34:42 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-2914</guid>
		<description>Ah, the &quot;replicating brick&quot;. Explained here: http://www.zyvex.com/nanotech/nano4/merklePaper.html it appears to be the answer to the self-extrusion problem. That and the pressure actuated &quot;broadcast&quot; mechanism could work, I think. It would not be autonomously self-replicating, but self-replicating nevertheless. It would be challenging to get the transmission/actuation error rate down to where it belongs, but perhaps not impossible.

It would give you a soup of &quot;billions and billions&quot; of devices, which should be complex enough to cooperate to produce larger things, or self-organize into same.

Mmmh, however, there are 200,000,000 atoms to be placed. To move an atom from the I/O port to the workpiece will require hundreds, if not thousands of ratchet signals. If we use, say, a 40 kHz pressure transducer to generate those, it would take (optimistically assume 100 ratchets per atom placement)  about a week per generation. Not so bad, really...

The transmission/actuation error rate would have to be well below 10^-10, though, assuming a single missed signal will lead to failure, which I think is fair.

I should really go read that Nanosystems book...</description>
		<content:encoded><![CDATA[<p>Ah, the &#8220;replicating brick&#8221;. Explained here: <a href="http://www.zyvex.com/nanotech/nano4/merklePaper.html" rel="nofollow">http://www.zyvex.com/nanotech/nano4/merklePaper.html</a> it appears to be the answer to the self-extrusion problem. That and the pressure actuated &#8220;broadcast&#8221; mechanism could work, I think. It would not be autonomously self-replicating, but self-replicating nevertheless. It would be challenging to get the transmission/actuation error rate down to where it belongs, but perhaps not impossible.</p>
<p>It would give you a soup of &#8220;billions and billions&#8221; of devices, which should be complex enough to cooperate to produce larger things, or self-organize into same.</p>
<p>Mmmh, however, there are 200,000,000 atoms to be placed. To move an atom from the I/O port to the workpiece will require hundreds, if not thousands of ratchet signals. If we use, say, a 40 kHz pressure transducer to generate those, it would take (optimistically assume 100 ratchets per atom placement)  about a week per generation. Not so bad, really&#8230;</p>
<p>The transmission/actuation error rate would have to be well below 10^-10, though, assuming a single missed signal will lead to failure, which I think is fair.</p>
<p>I should really go read that Nanosystems book&#8230;</p>
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		<title>By: Eniac</title>
		<link>http://metamodern.com/2010/01/28/self-assembly-and-nanomachines-complexity-motion-and-computational-control/comment-page-1/#comment-2913</link>
		<dc:creator>Eniac</dc:creator>
		<pubDate>Fri, 12 Feb 2010 16:27:23 +0000</pubDate>
		<guid isPermaLink="false">http://metamodern.com/?p=7719#comment-2913</guid>
		<description>Chris,

Thanks for that link. I had not previously seen that. I will look more closely at that design, but just looking at the description in KSRM has given me more questions than answers. I have a hard time imagining how the device would produce and extrude some of its own parts, particularly the diamond hull. That one certainly does not fit through the extrusion hole, so it must be assembled outside. In what environment? By what other machines? Hopefully I will find answers when I look up the publication. Is there one? Any reference beyond the KSRM book would be greatly appreciated, I could not find one right away in the on-line book or via Google.</description>
		<content:encoded><![CDATA[<p>Chris,</p>
<p>Thanks for that link. I had not previously seen that. I will look more closely at that design, but just looking at the description in KSRM has given me more questions than answers. I have a hard time imagining how the device would produce and extrude some of its own parts, particularly the diamond hull. That one certainly does not fit through the extrusion hole, so it must be assembled outside. In what environment? By what other machines? Hopefully I will find answers when I look up the publication. Is there one? Any reference beyond the KSRM book would be greatly appreciated, I could not find one right away in the on-line book or via Google.</p>
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