Lighters, lighters, lighters!

I'm trying something new here: A Nina-esq blog post. Nina frequently posts work-in-progress from projects she's working on (e.g. partial scenes from her movie, possible character designs, etc). Well, I'm working on a new project too... Reactions, due out at the end of 2016, will be the sequel to Molecules, third in the trilogy of Elements, Molecules, Reactions.

Combustion is, of course, a very important class of reaction, and I plan to have a wide spectrum of combustion examples, from rusting (very slow) to gunpowder (pretty fast, but nowhere near as fast as some explosives). As a sort of warm-up project, I decided to see what it would look like if Nick photographed a model lighting a whole bunch of different cigarette lighters. The answer is this:

Frankly I'm a bit disappointed. They are all so...similar. But I guess that's to be expected since they are all burning butane in air. The only variety comes from "windproof" lighters that pre-mix the butane with air before it burns (and sometimes include little salt beads in the flame to color it red or green or whatever).

I'm not entirely sure what I was trying to achieve with this video, which probably explains why I didn't achieve it. Still, it has a certain pointless charm to it.

Dominating the bottom of the list!

Great news (for me and Nick): Our books now occupy the bottom two slots on the NYT Science Best Sellers list!

Molecules entered the list at #20 last month, and this month it has not only maintained its stellar position right at the very bottom, but has dragged its friend The Elements up to the #19 slot above it. (That makes The Elements something like the Dark Side of the Moon of books about the periodic table, since I hear that that particular record recently reentered the Billboard top-20 list.)

For my next trick, I plan to come in last at the next County Fair hot dog eating contest.

Hm, I need to start writing fewer shamelessly self-promotional blog posts. I think this will naturally start happening as I begin work on my next book, making the transition from promoting the last one to seeing if I can write another one. The next one will be the first book where I've been writing a regular blog while also writing a book, and I'm curious to see if I start posting odd facts I come across along the way, kind of like the way my girlfriend Nina Paley posts work-in-progress of her movies.

The Elements for All Devices! Sort of!

I regularly get questions from people wondering if The Elements or Molecules is, or will be, available as an app for Android devices, as it is for iPads. The answer so far is always no, sorry, there are no plans for an Android version. (The basic problem is that Android devices and stores are very fragmented, with hundreds of different versions to support. We just don't think we could recover the cost of making an Android version.)

But despite that, there is now a version of The Elements available for basically ALL tablet/ebook reader devices, including all Android devices. The catch is that it's a static, traditional ebook, not the fully interactive app version available for iPads. The main difference is that in the app version you can spin all the objects with your finger, while in the static ebook version each object gets just a single photo, like in the print book.

But other than that, it's the same book: Same text, same objects, same everything. Many people might actually prefer the static ebook to the app, because it is completely flexible with regards to font, font size, background color, etc. (It looks best on a black background, but if you find that hard on your eyes, most ebook readers let you adjust all kinds of things about how the text is displayed.)

Here are links to the English-language static ebook version in as many stores as I could find it in. If you have a different kind of device, or want it in a different language, you can probably find it by searching for "Elements Theodore" (or "Atomes Theodore" in French) in your store/torrent site. (If you intend to pirate it, OK, but I hope you're doing that because you hate me and don't want me to get any of your money, not just because you're cheap.)

For iPad/iPhone users, note that there are now two different versions you can get: The interactive app, and the static ebook. Which should you get? Well, the app takes up about 1.7GB of space,  lets you rotate all the samples and see them in stereo 3D, and includes The Elements song by Tom Lehrer in both English and Japanese. The static ebook is about 82MB (i.e. Way WAY smaller), includes all the same text, but just one image per object and no song. You buy the app in the App Store and the static ebook version in the iBookstore. (Sorry, there is no practical way we can offer you both for one price: Those are completely different stores, and completely different products.)

If you're wondering about my new book, Molecules, that is currently available only as a print book and as an iPad app, but some time in the future, can't promise when, it will also come out as a static ebook.

External Validation for Molecules

Being very insecure, I love it when other people tell me I'm not a screwup. For example, Apple just put my Molecules app in their latest TV Commercial, indicating that at least someone likes it. Granted, you can only see it for about half a second in a couple of places, but I'll take what I can get. It's also listed in the website about the commercial, so people have a way to find it.

And Molecules was also just listed in Apple's "Best of 2014" for iPad apps. It's not the best iPad app (that's some other dumb app) it's just one of the short list of not-quite-as-best best apps. That's pretty nice considering how many contenders there are, and even nicer when you add that three other Touchpress apps were also on the almost-best list: Beethoven's 9thIncredible Numbers, and Vivaldi's Four Seasons.

Shrinks call this external validation, and you're not supposed to rely on it for a sense of well-being. But it doesn't hurt.

Apple Store Appearance

I'm going to be at the Chicago (Michigan Avenue) Apple Store Monday evening (December 8th) for a talk in their "Meet the Developer" series. The event starts at 7PM, and I think you're supposed to reserve a spot, though it's a store open to the public so anyone can just walk in any time. This is the website for the event:

You have to scroll down and click the "View More" link to see the event. And they (currently at least) list it as lasting from 7:00 to 7:15PM, which is silly, it's actually about an hour long including Q&A. I'm going to talk about Mathematica, iPad apps, and automated quilting and embroidery.

And for those of you who are fans of my more-famous-than-me girlfriend Nina Paley, she's going to be there too, because we're on our way to London together. We're going to bring an example of the quilting work we've been doing together.


BAFTA stands for the British Academy of Film and Television Arts, and the BAFTA awards are basically the British equivalent of the Emmy and/or Oscar awards, except that fewer people outside the UK have heard of them. The other difference, as of last night, is that I haven't won on Emmy or an Oscar.

The Disney Animated app that I wrote/directed, produced by the great team at Touchpress in cooperation with Disney Interactive and Walt Disney Animation Studios, and released about a year ago, just won a BAFTA award in the Children's Interactive category!  (I think this is kind of like a Daytime Emmy, or perhaps a Technical Emmy in a category like advanced camera lubrication technology.) The award is shared with Dave Bossert at Disney, plus Louise Rice and Matt Aitken at Touchpress. And of course many, many other people were involved in, and crucial to, the success of the app.

There was a nice dinner.

The swag was a bit thin....

Yes, I wore an actual suit with an actual tie! That's Dave next to me.

I'll add a rotation video of the actual award after Nick has had a chance to photograph it. That thing is HEAVY! It's really got a serious amount of metal in it.

The Wonderful World of Molecules

 My new app Molecules is Editor's Choice as of today! (This lasts a week.) That means Apple thinks it's the best new iPad app this week, and who's to argue with them, eh? (Oh, and the print edition is currently #20 on the  New York Times Science best-seller list . OK, it's not the main list, and it's only #20, but is the NYT!)

My new app Molecules is Editor's Choice as of today! (This lasts a week.) That means Apple thinks it's the best new iPad app this week, and who's to argue with them, eh? (Oh, and the print edition is currently #20 on the New York Times Science best-seller list. OK, it's not the main list, and it's only #20, but is the NYT!)

Molecules exist on a scale far smaller than the wavelength of visible light: Seeing them is a physical impossibility. And the tempo of their dance, set by the vibrational frequency of a bonded hydrogen atom, is about a thousand million million beats per second. 

It seems like an untouchable world, but with clever software and clever devices, we can come close to dancing with the molecules, joining them in their world and learning their ways first hand.

This is what we've tried to do with the iPad/iPhone App edition of my book, Molecules.

The print edition of Molecules is a very nice thing indeed (and if you don't have a copy, that's a problem you might want to consider addressing). But the App version is something quite remarkable. I think it's going to change the way many people think about molecules, by making it possible for anyone with an iPad, iPhone, or iPod Touch to inhabit the world of molecules and relate to them on their own terms.

I should say first that the Molecules app is a full ebook edition of Molecules. It's got all the text and all the pictures from the print edition, and it's worth it just for that. Here's a gallery of screen shots from the app:

And here's a spiffy trailer video we made for it:

But what really sets the App edition of Molecules apart is the wiggling molecules.

How this aspect of the App came about is kind of a fun story. I'd been thinking that it would be really nice to let people see how molecules actually behave, and it seemed like iPads and iPhones should be powerful enough to simulate at least simple molecules. I considered having the excellent team at Touchpress write a very simple simulation engine that faked, in a semi-realistic way, the forces acting between atoms in a molecule. But I really didn't want to do that, because the resulting simulations would not be "real", and you could not rely on the intuitions gained from playing with them. Writing real molecular dynamics simulation code is not an afternoon project.

Then my girlfriend Nina forced me to go to a New Year's Eve party at the house of some people I didn't know (which is definitely not my thing, especially since I was told that dancing would be involved). But it was OK, they had carrots, and while chatting with a nice couple, Barry and Deanna, the conversation soon turned to molecular dynamics (it's that kind of town). I discovered that one of them worked in a research group at the University of Illinois that happened to work on just the kind of software I was looking for (this university being why it's that kind of town).

Several days later, after hours of further conversation, I discovered that this particular group was the Theoretical and Computational Biophysics Group, headed by none other than Klaus Schulten, who I randomly happen to have known for over 30 years, since he spent a summer living in my parent's house! For some reason it never clicked in my head to talk to him until I randomly ran into one of his associates, which made me really glad I randomly agreed to go to that party (and I didn't even have to dance!).

So thus it came to be that the Molecules iPad app contains a full, robust implementation of the NAMD simulation engine, one of the most sophisticated pieces of software in the world for modeling the behavior of molecular systems. Normally it is run on building-sized supercomputers, modeling the behavior of giant biological macromolecules with hundreds of thousands of connected atoms. But we use it to let you tie knots in much smaller molecules, up to a few hundred atoms.

NAMD simulations are "real" simulations. By that I mean that when you see them, you are seeing very close to the real behavior of actual molecules, just slowed down by a factor of about 10^12, and magnified by a factor of about 10^8. You can gain a lot of intuition and understanding of the properties of molecules by playing with them this way, and that intuition is real, that understanding useful.

Playing with molecules also turns out to be surprisingly fun. It was delightful each time we got a new molecule working, because I could try out things like how hard it is to flip around a double bond, or whether you could tie a knot in a molecule. (The answer is yes, you can, as long as it's one of those long thin ones. Maitotoxin is pretty easy to get into a knot, while some of the fatty acid esters in beeswax are trickier.)

Once you have a molecule in a knot you really appreciate the thing that our iPad implementation of NAMD has made possible for the first time ever (that we know of): Multi-touch interactive molecular dynamics. That means you can use two fingers to pull opposite ends of the molecule and tighten the knot!

You see, NAMD is generally run on workstation computers, and interactivity is through a mouse (just one) or a haptic feedback device (again, only one). The haptic devices are cool (they let you "feel" the molecule through virtual force feedback as you poke it), but it's really hard to tie a knot with just one "finger" at a time. Our iPad implementation lets you touch and pull on the molecule in up to 11 places at once (the maximum number of touch points supported by the iPad screen). No one has done that before, and it's every bit as cool as it sounds.

It's not just knot-tying that benefits from the multi-touch interface. For example, I was very eager to get my fingers on the indigo molecule:

See the double-bond in the middle that joins the two identical halves? Double bonds don't allow free rotation, but rotation is possible if enough force is applied. I wanted to see if I could pin down one half of the molecule with a few fingers (locking that half in place), then use my other hand to flip the other half of the molecule around. I could imagine this in my head, but would it actually work?

Yes, it works like a charm. You can quite easily flip this molecule so the two red oxygen atoms are both on the same side (which is not the way indigo is supposed to be). You can then use the temperature slider to heat the molecule up until it eventually flips back again: The orientation with one oxygen on each side is more stable because two hydrogen bonds form across the two halves of the molecule when it's arranged that way. (Don't worry if this doesn't mean anything to you, it's still lots of fun to play with the molecules anyway. I mention the bit about hydrogen bonds only to show off the fact that NAMD is actually simulating them correctly, which is pretty cool if you know what hydrogen bonds are.)

Members of the Theoretical and Computational Biophysics Group at the University of Illinois who all helped create the interactive molecular simulations in the Molecules app. Sadly not pictured are Klaus, the head of the group, and Barry and Deanna, all of whom were out of town on the release day.

The App has over 350 molecules you can play with, all drawn from the text of the book (which means in most cases there's also a photograph of what the substance looks like on a human scale). This doesn't just happen: Each molecule has to have a "force field" created for it, which encodes the unique profile of forces created by the quantum mechanical interactions of the electrons in the molecule. Sometimes this is easy, sometimes it's a real struggle, and I am tremendously grateful for all the work put in by members of the research group, Deanna, Barry, and Chris in particular, who created these force fields.

Being able to interact with individual molecules really drives home how much of chemistry boils down to mechanics. By getting a feel for how they work, you take a step towards understanding how they will behave in chemical reactions, which is the ultimate goal of most of chemistry (and, coincidentally, the subject of my next book, Reactions, due in 2016).

OK, to be perfectly blunt, what I'm saying here is that if you are at all interesting in understanding how chemistry works, you should really get this app. I'm not kidding: I learned more from ten minutes of playing with these simulations than I did from years of studying chemistry, which, incidentally, included a year in graduate school at Berkeley running molecular dynamics simulations on their Cray 1 (yes, I'm that old). Back then the output of the simulation was tables of numbers, not the living, breathing, wiggling, jiggling, dancing, delightful bundles of joyful atoms you see in this app. Sure, this technology will make it into other apps in the future, probably cheaper ones, but don't you want to see it now? Come on, be the first on the block with the new wiggling molecules! I guarantee you will think it was worth every penny. Plus, you get the complete ebook version of Molecules, which is easily worth the price by itself.

Here's a convenient link to the App Store.





A video chat with me and Nick about Molecules

I just got through a video interview/discussion/google hangout with Joanne Manaster, a science blogger and online personality, and her associate Jeff Shaumeyer. We talked about molecules and stuff. Unusually for my public appearances, this one included my photographer Nick Mann as well, in case you're wondering what he looks like.

You can watch it here:

A Cat Named Theodore

Last night I gave the first talk in the book tour promoting my new book Molecules, and I think it went pretty well, but forget about that, I have something much more exciting to tell you about!

I have a cat named after me!!

Just before my talk started, a kid named Owen came up and showed me this picture of his cat, who is named after me because Owen is such a big fan of my books! Wow. Just wow. I had another kid once who wanted me to sign his arm, and I thought that was pretty cool, but this is really an unprecedented honor. I guess the only thing left now is for someone to name a baby after me, but I'm not holding my breath on that one.

P.S. Here is the arm-signing kid. On an unrelated note, I'm reminded by this picture that at the same event (the USA Science & Engineering Festival several years ago) another kid came to see my talk even though he had no idea who I was or what my books were about, simply because his name is Gray Theodore, and he had to find out who this Theodore Gray character was. I guess there's about as much reason for me telling you this as there was for him coming to meet me.

First Molecules Fan Photo!

This whole being-an-author thing can be fun! Hot on the heals of the first public sighting of Molecules in a bookstore (see previous post), I just got my first fan photo from a happy new owner of Molecules! This is Danny, 10, who has constructed a model of gabapentin (a painkiller from page 21) using what looks like a very nice molecule construction kit. 

Tuesday should be fun too: That will be my first public talk about Molecules (at the Science on Tap event at the Alberta Rose Theater). See for a complete schedule of speaking events.

Really the only downside of today is that I'm currently sitting in the LA airport after a totally botched attempt to fly to San Jose.