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# Book - "A Course on Quantum Techniques for Stochastic Mechanics"

I'm getting back to work on the book I helped John out with. I want to use this thread to keep track of what's happening.

Normally I use SVN, but for some reason, this created a disaster on the windows based system John uses. Now I've created a dropbox folder for the book.

The issue with dropbox is that it does not have version control, such as SVN which merges changes made by two parties on commit. So in other words, multiple people can't work on the book concurrently, with the changes being merged. The advantage is that it keeps track of the current version, and typically your editor will let you know if the file was changed remotely---which avoids disaster.

• My plan for the summer is (i) to improve this book as much as possible and (ii) make a contribution to the area of reaction networks.

As you know, the book covers essentally two topics. The first is stochastic mechanics such as walks on graphs, and the second is reaction networks. I feel that I've made a research contribution to only the first topic, in these papers:

I need to make a contribution to the topic of reaction networks. Anyway, working on the book is a start towards that.

Source Text:hoidle

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1.

Here are some TODO's from John:

"Arjun Jain read most of the network theory series on the blog and added comments on the blog solving most of the exercises that didn't already have solutions. You can take these solutions and add them to the book. If you cut-and-paste them from the blog, the  surrounding equations will be lost, but that's all; it's pretty easy to stick them back in.

I would also still like you to write up a section that treats a model with spatial variations, i.e. one where we have a lattice (possibly 1d), species located at sites, and some nearest-neighbor interactions."

Just keeping track of everything here.

Source Text:Here are some TODO's from John: > "Arjun Jain read most of the network theory series on the blog and added comments on the blog solving most of the exercises that didn't already have solutions. You can take these solutions and add them to the book. If you cut-and-paste them from the blog, the  surrounding equations will be lost, but that's all; it's pretty easy to stick them back in. > I would also still like you to write up a section that treats a model with spatial variations, i.e. one where we have a lattice (possibly 1d), species located at sites, and some nearest-neighbor interactions." Just keeping track of everything here.
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2.

[[Allan Erskine]] set up a github cvs repo for Azimuth code but I can't find it. It's very easy to set up a github account and put your book under version control. HTH.

Source Text:[[Allan Erskine]] set up a github cvs repo for Azimuth code but I can't find it. It's very easy to set up a github account and put your book under version control. HTH.
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3.

Thanks! I'll look into it!

Source Text:Thanks! I'll look into it!
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4.

Here's another TODO:

another thing that needs to get written is a (short, sweet) introduction to software for simulating stochastic Petri nets. Jim Stuttard has listed a lot of such programs on the Azimuth Wiki article "Petri net". ...We don't need to talk about all ~30 programs he's found, just the best ones... especially freeware.

Source Text:Here's another TODO: > another thing that needs to get written is a (short, sweet) introduction to software for simulating stochastic Petri nets. Jim Stuttard has listed a lot of such programs on the Azimuth Wiki article "Petri net". ...We don't need to talk about all ~30 programs he's found, just the best ones... especially freeware.
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5.
edited August 2013

I've just found this animated Petri net written using a javascript library called jointJS. The engine code at first glance is similar to [[Dave Tanzer]]'s javascript. It's the nearest thing I've found so far to the sort of rendering engine people might want. I've knocked up a first UI for a Petri net editor with the aim of producing simulation results just as graphs using Haskell digestive-functors (to integrate with the prototype Azimuth Snap server in case anybody doesn't know it exists).

The half-dozen means of producing the necessary subforms in javascript I've tried are pretty kludgy but everything I'm doing should end up as htm5, css3, canvas and javascript in the browser.

Ian Ross's has published some excellent code for an animated ring oscillator, produced using the Fay haskell to javascript compiler and html canvas, so also runs in the browser.

This is relevant to a recent paper on Milankovitch cyles cited by Nathan showing improved correlation with the historical record by using a van der Poll oscillator circuit model. There is also a linear, bistable and chaotic circuit coded by an Azimuth member. The van der Pol oscillator is proof of concept Petri net test case. I must try and contact Ian as he's sent code to Mars craft, worked on climate modelling and writen excellent code on his blog (see Lyapunov exponents 1 & 2).

These are my benchmarks to cut down the slew down the current list of practicable options for a Petri net editor.

As an applications programmer I hate it when I'm desperately trying to code some algorithm, get a textbook and find just the 2 or 3 line description of what I''m after with the codicil "Left as an exercise for the reader".

So my reader's exercise is what does the Petri net representation of a quantum harmonic oscillator look like?

Source Text:I've just found [this](http://jointjs.com/demos/pn) animated Petri net written using a javascript library called jointJS. The engine code at first glance is similar to [[Dave Tanzer]]'s javascript. It's the nearest thing I've found so far to the sort of rendering engine people might want. I've knocked up a first UI for a Petri net editor with the aim of producing simulation results just as graphs using Haskell digestive-functors (to integrate with the [prototype Azimuth Snap server](stuttard.org) in case anybody doesn't know it exists). The half-dozen means of producing the necessary subforms in javascript I've tried are pretty kludgy but everything I'm doing should end up as htm5, css3, canvas and javascript in the browser. Ian Ross's has published some excellent code for an animated [ring oscillator](http://www.skybluetrades.net/blog/posts/2012/11/13/fay-ring-oscillator/index.html), produced using the Fay haskell to javascript compiler and html canvas, so also runs in the browser. This is relevant to a recent paper on Milankovitch cyles cited by Nathan showing improved correlation with the historical record by using a van der Poll oscillator circuit model. There is also a linear, bistable and chaotic circuit coded by an Azimuth member. The van der Pol oscillator is proof of concept Petri net test case. I must try and contact Ian as he's sent code to Mars craft, worked on climate modelling and writen excellent code on his blog (see Lyapunov exponents 1 & 2). These are my benchmarks to cut down the slew down the current list of practicable options for a Petri net editor. As an applications programmer I hate it when I'm desperately trying to code some algorithm, get a textbook and find just the 2 or 3 line description of what I''m after with the codicil "Left as an exercise for the reader". So my reader's exercise is what does the Petri net representation of a quantum harmonic oscillator look like?
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6.

I don't think there is a Petri net representation of a quantum harmonic oscillator. Not a stochastic Petri net, anyway. But replace the probabilities by amplitudes and you're doing quantum field theory! Then it's easy to get a harmonic oscillator. One species, and one transition going from that species to itself.

Source Text:I don't think there is a Petri net representation of a quantum harmonic oscillator. Not a _stochastic_ Petri net, anyway. But replace the probabilities by amplitudes and you're doing quantum field theory! Then it's easy to get a harmonic oscillator. One species, and one transition going from that species to itself.
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7.

[[John Baez]] wrote:

One species, and one transition going from that species to itself.

Thanks John, that wasn't obvious to me.

Source Text:[[John Baez]] wrote: > One species, and one transition going from that species to itself. Thanks John, that wasn't obvious to me.
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8.

Yes, it seems funny but the harmonic oscillator Hamiltonian is $a^\dagger a$. The number of quanta doesn't change, but the complex phase changes faster when you've got more quanta of energy.

Source Text:Yes, it seems funny but the harmonic oscillator Hamiltonian is $a^\dagger a$. The number of quanta doesn't change, but the complex phase changes faster when you've got more quanta of energy.
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9.
edited September 2013

I haven't thought about it but that's an interesting kind of invariant to try and specify.

Source Text:I haven't thought about it but that's an interesting kind of invariant to try and specify.
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10.

Jim Stuttard wrote

doing a Torino GreatSPN software evaluation?

Source Text:Adding to our list... Jim Stuttard wrote > doing a Torino GreatSPN software evaluation?
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11.

Jim Stuttard wrote

I’ve just found this animated Petri net written using a javascript library called jointJS.

Just to let you know. There is a bug in this animated Petri net. There is once in while a little red ball part appearing in the upper left corner.

Source Text:Jim Stuttard <a href="http://azimuth.mathforge.org/discussion/1236/book-a-course-on-quantum-techniques-for-stochastic-mechanics/?Focus=9379#Comment_9379">wrote</a> >>I’ve just found this animated Petri net written using a javascript library called jointJS. Just to let you know. There is a bug in this animated Petri net. There is once in while a little red ball part appearing in the upper left corner.
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12.

Thanks, why is your name nad though? I got rejected for using Jacob.Biamonte since it is not my real name!

Source Text:Thanks, why is your name nad though? I got rejected for using Jacob.Biamonte since it is not my real name!
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13.
edited September 2013

nad is Nadja Kutz, commenting on my post #6 about JointJS which has a Petri net animation example worth looking at. Thanks NAD I'll have another look at it.

Source Text:nad is Nadja Kutz, commenting on my post #6 about JointJS which has a Petri net animation example worth looking at. Thanks NAD I'll have another look at it.
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14.

Thanks, why is your name nad though? I got rejected for using Jacob.Biamonte since it is not my real name!

Amongst others I was allowed to use this short form because usually my last name Kutz gets easily mixed up with Kurtz.

Source Text:>Thanks, why is your name nad though? I got rejected for using Jacob.Biamonte since it is not my real name! Amongst others I was allowed to use this short form because usually my last name Kutz gets easily mixed up with Kurtz.
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15.

Sorry Nad I'm never noticed the absence of r :).

Source Text:Sorry Nad I'm never noticed the absence of r :).
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16.

Sorry Nad I’m never noticed the absence of r :).

it is a bit strange that you am never noticed - since finally kutz and kurtz would be pronounced rather differently in english (in contrast to german if you speak kutz as it is written, however the word has the pecularity that it is (at least in Berlin and surroundings) sometimes pronounced rather like qoots)

by the way you probably know that kurz (or an older way of writing: kurtz) means SHORT in german. But Kutz doesn't mean short. In fact it has sofar rather been unclear what it means.

Source Text:>Sorry Nad I’m never noticed the absence of r :). it is a bit strange that you am never noticed - since finally kutz and kurtz would be pronounced rather differently in english (in contrast to german if you speak kutz as it is written, however the word has the pecularity that it is (at least in Berlin and surroundings) sometimes pronounced rather like qoots) by the way you probably know that kurz (or an older way of writing: kurtz) means SHORT in german. But Kutz doesn't mean short. In fact it has sofar rather been unclear what it means.
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17.

kurz (or an older way of writing: kurtz) means SHORT in german. But Kutz doesn’t mean short. In fact it has sofar rather been unclear what it means.

maybe it means "shot" then ;).

Source Text:> kurz (or an older way of writing: kurtz) means SHORT in german. But Kutz doesn’t mean short. In fact it has sofar rather been unclear what it means. maybe it means "shot" then ;).
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18.

Btw, Nad you are right. In this JointJS Petri Net animation, there is a red ball blinking in the upper left corner.

Source Text:Btw, Nad you are right. In this [JointJS Petri Net](http://jointjs.com/demos/pn) animation, there is a red ball blinking in the upper left corner.
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19.

@Nad, I'm a very short-sighted touch typist who looks at the screen as seldom as possible when writing; I guess I might also suffer from considerable selective blindness as well :)

Source Text:@Nad, I'm a very short-sighted touch typist who looks at the screen as seldom as possible when writing; I guess I might also suffer from considerable selective blindness as well :)
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20.
edited September 2013

Zoltan Zimboras wrote:

maybe it means “shot” then ;).

No not that I know of. It is said that it may come from the german word Kotze, which is a kind of cowl. But especially since there is this other pronounciation, which is strangely preserved despite nowadays power of the written word, I think it has probably another origin. May be it is from a slavic word. Like an abbreviation of Kuznetz (Blacksmith). On the other hand the "z" is in german rather pronounced as "ts" and most other slavic languages the "z" in the corresponding slavic word of blacksmith is completely gone. However this part of my family is indeed actually quite tall and often rather strong. It is said that a Kutz ancestor made his living by offering fights on fairs, i.e. he was something like a human high striker.

But not that you get a false image: I am not that strong (last but not least because I sit too much in front of the screen....), although I am still rather tall, even for a german female. I made the experience that especially small men may sometimes perceive alone this fact as provoking. Like I was once in a foreign country within a region with on average shorter men and I was accused of having attacked a whole group of men (!), while I was just passively clinging to a bar and letting me not being pushed out of the way (I was actually taken into custody by the local police for that but luckily there were other travelers from other countries there as witnesses) so they let me go.

Source Text:Zoltan Zimboras wrote: >maybe it means “shot” then ;). No not that I know of. It is said that it may come from the german word <a href="http://de.wikipedia.org/wiki/Kotze_%28Kleidung%29">Kotze</a>, which is a kind of <a href="http://en.wikipedia.org/wiki/Cowl">cowl</a>. But especially since there is this other pronounciation, which is strangely preserved despite nowadays power of the written word, I think it has probably another origin. May be it is from a slavic word. Like an abbreviation of <a href="http://ru.wikipedia.org/wiki/%D0%9A%D1%83%D0%B7%D0%BD%D0%B5%D1%86">Kuznetz</a> (Blacksmith). On the other hand the "z" is in german rather pronounced as "ts" and most other slavic languages the "z" in the corresponding slavic word of blacksmith is completely gone. However this part of my family is indeed actually quite tall and often rather strong. It is said that a Kutz ancestor made his living by offering fights on <a href="http://en.wikipedia.org/wiki/Fair">fairs</a>, i.e. he was something like a human <a href="http://en.wikipedia.org/wiki/High_striker">high striker.</a> But not that you get a false image: I am not that strong (last but not least because I sit too much in front of the screen....), although I am still rather tall, even for a german female. I made the experience that especially small men may sometimes perceive alone this fact as provoking. Like I was once in a foreign country within a region with on average shorter men and I was accused of having attacked a whole group of men (!), while I was just passively clinging to a bar and letting me not being pushed out of the way (I was actually taken into custody by the local police for that but luckily there were other travelers from other countries there as witnesses) so they let me go.
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21.
edited September 2013

Hi @Zoltan,

Source Text:Hi @Zoltan, I've downloaded joint.shapes.pn.js for a look.
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22.
edited September 2013

Jacob: actually Nad joined us using a short username before we decided on the policy saying people had to use their whole real names. As part of this decision, we agreed that I would try to persuade existing users to switch their usernames to their whole real names, but not force them to do so.

Since I know her, I find it very strange to imagine someone accusing her of attacking a group of men. Maybe it could happen by accident in a country where the men were two inches tall.

Source Text:Jacob: actually Nad joined us using a short username before we [decided on the policy](http://azimuth.mathforge.org/discussion/394/use-of-real-names/) saying people had to use their whole real names. As part of this decision, we agreed that I would try to _persuade_ existing users to switch their usernames to their whole real names, but not _force_ them to do so. Since I know her, I find it very strange to imagine someone accusing her of attacking a group of men. Maybe it could happen by accident in a country where the men were two inches tall.
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23.
edited September 2013

I would try to persuade existing users to switch their usernames to their whole real names, but not force them to do so.

I already tried to explain to you why I do not always want to use may real name.

I find it very strange to imagine someone accusing her of attacking a group of men. Maybe it could happen by accident in a country where the men were two inches tall.

No in this case I wasn't sexually attacked. At least I didn't perceive it as such. I was standing in a line for a train ticket and waiting as everybody there and then when the ticket booth opened there was a turmoil and people started pushing. It may also that they didn't like me because I was a foreigner, but there were other foreigners in that line so the attack or more the accusations seemed to have to do with my specific appearance.

The worst physical sexual attack I luckily had sofar was that 4 men tore me violently into an entrance hallway here in Berlin, which end appeared to them then finally still to too visible from the pedestrain walk (on which there where still pedestrians), so they let me finally go. These men were way stronger then me and I would have had no chance of defense, I even couldn't yell for help.

Source Text:>I would try to persuade existing users to switch their usernames to their whole real names, but not force them to do so. I already tried to explain to you why I do not always want to use may real name. >I find it very strange to imagine someone accusing her of attacking a group of men. Maybe it could happen by accident in a country where the men were two inches tall. Was this a question wether I was sexually attacked? No in this case I wasn't sexually attacked. At least I didn't perceive it as such. I was standing in a line for a train ticket and waiting as everybody there and then when the ticket booth opened there was a turmoil and people started pushing. It may also that they didn't like me because I was a foreigner, but there were other foreigners in that line so the attack or more the accusations seemed to have to do with my specific appearance. The worst physical sexual attack I luckily had sofar was that 4 men tore me violently into an entrance hallway here in Berlin, which end appeared to them then finally still to too visible from the pedestrain walk (on which there where still pedestrians), so they let me finally go. These men were way stronger then me and I would have had no chance of defense, I even couldn't yell for help.
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24.

This message is for John and regarding our shared dropbox folder contianing our book.

Just finished a small list of corrections and adjustments in the book I've been saving for a while. The important ones are either inside of a command \yo{my remark here} or done as %% !!! so they should be easy to search for. Please do a search for \yo in the book to see what I've done.

Source Text:This message is for John and regarding our shared dropbox folder contianing our book. Just finished a small list of corrections and adjustments in the book I've been saving for a while. The important ones are either inside of a command \yo{my remark here} or done as %% !!! so they should be easy to search for. Please do a search for \yo in the book to see what I've done.
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25.

Thanks, I'll do that!

Source Text:Thanks, I'll do that!