Posts by Jim Logajan

    Looks promising - thanks for posting those news items.
    Though I found it a bit odd that climate change is mentioned as a motivator, considering the more profound impacts nanotechnology will have.

    I hope to retire mid-year from my decidedly non-nanotech related job, which will give me more time to devote to nanotech stuff. One task I'd like to do is try my hand at using some of the existing molecular modeling tools to determine their strong and weak points with respect to design of molecular machines. Probably someone has already done this, so that would be the first thing to check. As chemist Frank Westheimer once observed: "A couple of months in the laboratory can frequently save a couple of hours in the library."

    Saw this remotely related announcement today:
    Scientists create world’s first ‘molecular robot’ capable of building molecules


    The original article in Nature:
    Stereodivergent synthesis with a programmable molecular machine


    I say "remotely related" because it also looks to use a manufacturing system in a solution that can synthesize some kinds of molecules. But it appears to use a chemically positionable "arm" which would put it in a different class of machines/techniques than the previously mentioned approaches.

    I guess the one most widely known of these is the "Great Pyramid of Giza" best viewed form the perspective of "Pyramid of Menkaure". mrgris.com/projects/merc-extreme/#0b6b7dd3@29.97271,31.12854

    A good choice - Giza was the first place I thought of when I started thinking of well known but temporally distant things. But as you note, not much interesting in its vicinity.


    Maybe: Greece Athens "Sunken Lake" (with caves unexplored to this day).
    en.wikipedia.org/wiki/Vouliagmeni#Lake_Vouliagmeni
    Viewing coordinates: 37.807075,23.786131
    mrgris.com/projects/merc-extreme/#0b6b7dd3@37.80707,23.78613

    Looks interesting because it encompasses an area rather than a small object. But it is probably obscure enough to need a brief introduction (though any choice would need one.)


    I like this choice. The art is sufficiently arresting to the eye, though, that it might distract from the surrounding view which highlights the non-linear mapping. The copyright aspect is Interesting. Belgium's "freedom of panorama" copyright laws are new to me - U.S. copyright law is different. (It occurs to me that Google satellite maps must incorporate millions of copyright violations caused by photos of public buildings in countries whose laws don't allow publication of them without permission, which I doubt Google got.)

    I found an interactive version of nonlinear mapping:
    https://mrgris.com/projects/merc-extreme/
    (Tip: turn on satellite view)


    What would be the most visually interesting while least politically, religiously, ideologically problematic place to focus at for a screenshot demonstrating that kind of the mapping?


    This is already hard. Additionally asking for a place that can be easily identified by most of the worlds population is probably too much and likely leaves no results.

    "Least problematic focus" appears to be a goal without a solid reason. If the audience is presumed to be that emotionally sensitive, exposure to non-linear mapping is probably an effort in futility. That said, something like the most ancient extant building might be sufficiently distant from present-day disputes that it could serve the desired purpose. One list of such entities: https://en.wikipedia.org/wiki/List_of_oldest_buildings

    Sorry for the tardy reply. It looks like those URL pointers got messed up during the port to the new forum software. I'm not sure where the links were supposed to point. I'll do some more searching to see what I can find.

    I did send a message to Josh via my linkedin.com contact when I started this web site. I did not hear back from him. However, I see he has a Facebook page and is active there (he just posted today in fact.) After browsing his posts, it looks like he now has a pilot license certificate - earned about 5 years ago and still flying, so medically fit to fly per the FAA.


    (I do not have a Facebook account, but my wife does. We jointly use hers to keep in touch with family members who joined. Neither of us would have joined otherwise.)

    I did reply to Dr. Neil Sarkar saying I was interested in any information they could share. I indicated a general interest in scanning probe nanolithography since that seemed the most relevant use of their product given its resolution and what I would really attempt with such a device. I have not yet heard anything from them.


    I was not aware of the two efforts you found. The ISCPI AFM is about 2.6 times more expensive, but has about 40 times greater resolution, than the Stromlinet Nano AFM. I could not find any mention of cost for tips for the Stromlinet Nano AFM. The ISCPI AFM comes with 4 replacement chip tips.



    The OpenAFM project doesn't seem to have progressed since November 2015.


    I have found a fair number of articles on DIY STM projects. Most accomplished with under US$1000. Atomic resolution attained with some of them.


    Your 3D modeling skills are quite impressive. I have a Robo 3D R1+ but I followed a project that modified the bed after I managed to chip the glass on the original bed. I now have build area of 22 cm wide by 32 cm deep by 20 cm high. The new bed heater can get quite hot very fast. For design I started with the free DesignSpark Mechanical but I really wanted to draw some of the lines and planes of my projects with equations. I also wanted to be able to import and export several file types that the free programs didn't always support, so I finally ended paying as much for the Rhino 3D CAD system as I did for the printer (if I include the cost to upgrade the bed - otherwise the software cost more!) It was definitely a bit of a learning curve after DesignSpark but the free evaluation period for Rhino 3D is 90 days, giving me plenty of time to make sure it would work for me.


    I do have some ideas for an STM I'd like to try but have to work around my day job.

    I received a reply from the president, Dr. Neil Sarkar. I'm going to go out on a limb and assume he would have no objection to his response being published verbatim, so here it is:


    Hi Jim,

    Thank you for your interest in the nGauge AFM system, I'm happy to answer your questions (apologies for the delay).


    We have a conductive path to the tip in all of our AFM chips, but we do not yet support electrical modes. Our team has produced scanning microwave microscopes, which are on the product roadmap but no hard dates that we can disclose yet.


    We would be happy to share the electrical, mechanical and signal interface with customers that would like to build their own coarse approach mechanisms. One customer has built a wafer-scale multi-probe AFM tool, while another is interested in roll-to-roll metrology. Please feel free to tell us about the application you have in mind if you'd like some feedback.


    Best,
    Neil


    I think that is as good a response as can be expected. The price of the chips makes the idea of a hobbyist coarse approach mechanism quite appealing. I'm definitely going to look into it.

    Appended to this post is the content of an email I sent to their info@ address. If I get a response I'll post a summary of its content here. If they don't answer by the 8th I'll try to find another way to contact them.


    Since the chips are essentially consumables they should have priced them well above cost to manufacture. The patents on their web site all pertain to the technology in the chips and not to the stage. The assignee for each of the six patents they mention are Niladri Sarkar, Icspi Corp., and Zyvex Corp (4 of the 6.) This appears to be one of the results of a US DARPA funded APM project awarded to Zyvex back in 2008.



    I recently learned of your nGauge AFM and was hoping you would be willing to provide answers to two questions:


    Are there any plans or schedules to offer chips that allow scanning tunneling (STM) or other scanning modes in addition to the AFM mode chips?


    Under what conditions, if any, is documentation on the electrical, mechanical, and signal interface to the AFM chips available so others might develop their own equivalents of the nGauge stage?


    Thank you for your time!


    Regards,


    Jim Logajan

    I presume this is the firm's site (let me know if it isn't):
    http://www.icspicorp.com/


    Obviously the price is based on their expectations of number of units they hope to sell versus the cost they've so far spent in developing the microscope plus per-unit costs. And also what competitors are charging and getting away with - even though they claimed it was for the masses. I had not previously looked at the current market for AFMs but your post made me curious and I came across the following document which gives some estimates of its size and growth:


    http://www.nanotechmag.com/wp-…09/SPMicroscopes2014-.pdf


    According to this link that market analysis probably wasn't cheap to purchase either! I presume that issue is either out of date or was posted in violation of copyright (if the latter I would expect it to vanish eventually.) In any case, I believe the US$7900 price of the AFM is relatively inexpensive - compared to competitors.


    I know that the most common 3D printer plastics, PLA and ABS, are likely fine because their thermal expansion properties are similar to metals they would replace. This article has a reference to a 3D printed head that was compared to a plastic one (actually only partially plastic; I found a copy of the complete article here:(


    We have employed such a technique to manufacture an atomic force microscopy (AFM) head, and we compared its performance with a copy milled from aluminum. We tested both AFM heads for single molecule force spectroscopy applications and found little to no difference in the signal-to-noise ratio as well as in the thermal drift. The lower E modulus seems to be compensated by higher damping making this material well suited for low noise and low drift applications. Printing an AFM thus offers unparalleled freedom in the design and the rapid production of application-tailored custom instruments.

    But the cost to machine the AFM's head doesn't make it expensive, it is the content of the heads of the sellers that makes the AFM expensive.

    Welcome Diamondoid!


    It is difficult to say what approach will yield the quickest route, since only modest progress has been made in any of the approaches.


    When my time permits, I've been looking at using SPMs in the bootstrap phase. I suspect that DNA engineered bacteria are another approach that may be relatively fast. I'm not aware of anyone making any progress using any of the other techniques you mention to the extent that those two approaches have already demonstrated in the lab.

    So you mean like the Nanomedicine books by Robert Freitas (I haven't yet read them)?

    Yes, something along those lines. Getting older seems to have made me more interested in nanotech applications of medicine.

    There are two more possible usages for de novo foldamer engineering (foldamer being the most general case) B) as "simple" delivery vessels for drugs C) for bootstrapping advanced APM.

    Someone is likely to prove me wrong, but I'm not sure that that foldamer engineering will bootstrap advanced APM. At best I suspect it may be a dispensable tool, much like one can use a screwdriver to pound a nail - though a hammer would be the better tool. On the other hand, there is no easy way to use a hammer as a screwdriver.

    The reason I think that Eric Drexler has switched his focus is this video of a somewhat recent talk he gave:
    Eric Drexler - A Cambrian Explosion in Deep Learning

    Thanks for the video. I watched it (being impatient I played it at 1.5 times normal speed - just fast enough for me to still comprehend what is being said while saving some time.) As an aside, where I work, we have noticed that money and investments are flowing toward cyber security and more people are looking to get into it as a way to make money. Companies that can claim to have cyber security products have higher valuations per unit sales revenue than those that don't. I suspect this motivates a lot of interest in the area rather than a genuine interest in security. But maybe I'm being too cynical.


    One issue I have with predictions about AI is one that Eric mentions too briefly in his talk: goals and motivations of AI. All living things have a goal built into them due to the way life evolved: perpetuate oneself and one's offspring. Eric states we wont know or will be unsure of the goals AI will have. I don't see why we wouldn't, since unless we explicitly program goals in, the AI will have intelligence but it wont have any motivation to do anything with it. Without goals it wont have motivation to act for or against anything. Probably a good reason not to program in any goals.

    It would certainly be cool to make atoms visible in the livingroom but I gave up on this endeavour because:
    # I worked on a professional one (Omicron) and realized how hard it is to scan z steps greater than one or two atomic layers.
    # Playing around with structural DNA nanotechnology (and even more so for other stuff) requires a full-blown lab (automatic pipetting system ...)
    # I'm not sure whether larger DNA meshes can be scanned electrically with STM. If AFM is necessary it gets harder. DNA is strongly negatively charged due to its phosphate groups. If DNA structures sits dry on a surface I guess some alkali metal atoms (Na) remain on there cancelling the charge but I'm pretty sure they will be immobile.

    I think of SPMs as one tool of many that will be needed to bootstrap nanotechnology. That an STM has limitations is no different than other tools. Based on my reading of history, I think progress in nanotechnology will only take off once more "amateurs" can begin work on it.

    Lipid Rafts come to mind. I heard that they may not really exist but they are everywhere in the literature.
    I don't really see how that applies to advanced APM. There I more see that correct and useful old ideas have been and are still tragically misused to judge possibilities/impossibilities in a very different context where they are not applicable anymore.

    My read of history of chemistry suggests that debates like the Drexler/Smalley one have happened more than once and progress was held up by the more notable participant. Though it isn't clear to me (yet) whether history provides any lessons in how to avoid or mitigate such things.

    In one of the foresight conference videos there was one person presenting his companies goals to produce ultra cheap STM microscopes in masses to accelerate nanotechnology research by making the tools more widely and easily accessible - sadly I can't find that video anymore. I've also forgotten the name of the presenter. It might be "Saed"?? I'm not sure.

    There were discussions in the sci.nanotech newsgroup many years ago about developing a cheap STM. I recall discussing it with Steve Vetter and Jim Rice at a Foresight conference. I believe one issue that got in the way was lack of money or capital - and uncertain demand. While a determined amateur can build a marginally working inexpensive hobby STM, buyers of commercial systems have higher expectations and getting a refined product to market is not cheap. Of course, back then we didn't have Kickstarter, GoFundMe, IndieGoGo, or RocketHub as options to raise capital and establish a seed of potential customers.

    1) I was visiting the first ever Makerfaire in Vienna Austria showing of my collection of 3D prints.
    I also made a lot of graphical Infosheets for A4 flipcharts about 3D printing and APM.

    Sounds interesting!

    * that the visalisation pictures of cell membranes are basically all very wrong showing way to much lipid layer and way too few proteins going through and showing the size ratios very wrong too.

    Yes, the high percentage of membrane that is protein is mentioned in the better texts on the subject. But some definitely imply too much of the surface as lipid.

    It seems that only a tiny fraction of molecular biology is really directly applicable to even the early bioinspired stages of advanced APM bootstrapping. I think It'll still take some more time that topic dedicated resources and courses are made.

    My interest in the subject is more as an area of problems that can be better attacked by nano robots than as a source for bootstrapping nanotechnology. My impression is that most of the advances in things like DNA and RNA manipulation (e.g. CRISPR/Cas9) appear to be due to discoveries of ancient enzymes that can be turned into tools than clever de novo nucleotide protein engineering.

    You seem to have read a lot about history too. This not a place where I usually would spoop around since it is even further away from advanced APM than molecular biology. Since I'm unlikely to read this set of literature if you've found/find something that may suprisingly be applicable specifically to bootstrapping APM dont hold back telling us here. Even if its just a hunch.

    Only insight I can note at this point is that false theories held up progress for decades due to the human failing of judging the merit of ideas by who espoused them rather than objective analysis of the ideas. Well, some ideas sounded quite reasonable too and evidence to the contrary was considered due to experimental error, not due to an error in the theory. It seemed to take more evidence than necessary to get a theory in trouble.

    You say that you'd like to "design and build some nanotech related tools".
    Do you have anything specific in mind?
    I do have made quite a set of APM principle demonstration objects by now.
    (I need to post a picture)

    I'm thinking of a novel design for a scanning probe microscope that I can 3D print. At least the mechanical part. STMs have already been 3D printed and the common plastics like PLA and ABS have decent properties for the purpose (such as low thermal expansion coefficient.) There is at least one piezoelectric plastic that is available (Polyvinylidene fluoride) available from at least one source (http://www.3dogg.com/c-3265319/pvdf-filament/) but expensive. Though my idea doesn't employ piezoelectrics, though more traditional approaches do.

    With molecular sciences more and more on the right track and the recent advances in machine learning (deep learning / deep dream)
    I think Drexler has switched his main forcus to artificial intelligence (tensorflow & stuff?).

    Any reason you think that?

    Assuming anyone is still checking in here - I wonder what keeps people from posting. Here's what has kept me from posting:


    After I exercised some stock options in the client company that I've done work for the last 10 years and become part owner, I've found an extra incentive to make sure things go well there. We have had a major development project underway for the last year that has sucked my time. So work has kept me busy.


    The closest I've come to nanotechnology lately is that I started studying the Kindle edition of Molecular Biology of the Cell, 6th edition, by Alberts et al (MBoC) from beginning to end. I've had a copy of the third edition for about 15 years but had only ever used it as a reference; never tried to read it all the way through. As I started reading the 6th edition (to fill in gaps in my knowledge and get more up to date info) I became curious about the history of molecular biology, so I went looking for recommendations on books on the subject. Based on reviews, I bought a copy of Operators and Promoters: The Story of Molecular Biology and Its Creators, by Echols and Gross. Early on it said if I wanted to know more about the period it didn't cover, I should read The Double Helix by Watson and The Eighth Day of Creation: Makers of the Revolution in Biology, by Judson. (There is a commemorative edition of the latter that I only discovered later.)


    So I read Double Helix, then The Eighth Day, and am just now finishing Operators and Promoters. Once done I'll get back to finishing MBoC. Except I can't help it, I got curious about the history of chemistry, so a copy of The Development of Modern Chemistry by Ihde will be arriving soon.


    Lastly, not sure why it took me so long, but bought a 3D printer and downloaded a free copy of DesignSpark Mechanical so I could design the types of things I wanted to print. Fun stuff - if I had more time I'd be designing and building some nanotech related tools. It's amazing sometimes how much time one expends on the allegedly "trivial" aspect of mounting and arranging parts in some apparatus. Sure, it may take hours to print the needed parts, but it can take that long or even longer to do the same using the tools in a garage workshop.

    So the Set described in the there discussed tooltip paper ( molecularassembler.com/Papers/MinToolset.pdf ) is not reversible in the bond-topology-state.


    Since the goal of the study did not include the additional burden of that requirement, I am not surprised. Efficient reversibility would see a longer-term goal.


    I made a 3D model for visualizing the qualitative progression of the energy wells that is necessary for a energetically reversible mechanosynthetic operation. This model is quantitatively disconnect from any particular physical process like e.g. hydrogen abstraction.
    apm.bplaced.net/w/index.php?ti…nosynthesis_principle.jpg


    I'm afraid I don't know what the image is supposed to be showing me. None of the axis are labeled - do you have some additional context or discussion somewhere?




    I'm probably missing something, but I don't see how one can draw any inference about future tools from the first set of invented tools for molecular carbon mechanical synthesis. I skimmed sections 13.3.7, 13.3.8, and 8.5.2 of Nanosystems and it does not look to me like there are any dangers. Even if none of the released binding energy were stored for later re-use, the universe is awash in thermonuclear energy. I think it is something of a technical oddity that so much of it is temporarily inaccessible. Energetically inefficient nanotech production would still be, on a relative scale, far more efficient than current tech production.