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# Potential blog post series on quantum community detection

edited February 2015

Hi all!

I have an idea for a series of 3 posts on quantum community detection:

First two topic are standalone, general introduction to these topics. And I believe that they are of the general interest and benefit of the readers. The third one is about a paper arXiv:1310.6638, in which we are trying to predict the scale of quantum effects in a light-harvesting complex of green plants. It is an investigation in the same team (Jake Biamonte, Tomi Johnson and Mauro Faccin, Ville Bergholm and me) as the previous quantum network posts:

John, what do you think about it?

That is, is the concept of these blog post nice? Do you like the introduction to quantum superposition?

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1.

I'm happy to help edit your posts if John is happy to let us invade his amazing blog with quantum physics! The quantum bio stuff fits in and probably people want to know more about quantum stuff in general, which is why your first article on quantum states would likely be well received.

Comment Source:I'm happy to help edit your posts if John is happy to let us invade his amazing blog with quantum physics! The quantum bio stuff fits in and probably people want to know more about quantum stuff in general, which is why your first article on quantum states would likely be well received.
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edited September 2014

Just a side comment (LHCII is for you only a special application for your methods, so this is probably not so interesting for you):

Some community detection for you: There is another community mostly located in Arizona, which used serial time resolved investigations with femtosecond X-ray lasers of PSI. I don't have access to all those papers from them and [28] from the Fleming group and frankly also not the time to study them in detail, but it might be that there are still discussions about the concrete topology of the involved electron transfer channels. That is I was in particular irritated by one image (which is now shunned from public access), which somehow suggested another interpretation of the role of chlorophyll a. That is in the image it looked (if I remember correctly) as if chlorophyll a is sort of parallel to P680 (they seem to operate in different wavelengths (do they?)) in the transfer chain to pheophytin, however Wikipedia writes that

Chlorophyll a also transfers resonance energy in the antenna complex, ending in the reaction center where specific chlorophylls P680 and P700 are located.[5]

unfortunately Wikipedia contradicts itself by claiming also (a bit down the page) that chlorophyll a IS P680, which seems wrong since P680 is a dimer and it looks as if chlorophyll a is not (?)

Since the chlorophyll a molecules only capture certain wavelengths, organisms may use accessory pigments to capture a wider range of light energy shown as the yellow circles.[5] It then transfers captured light from one pigment to the next as resonance energy, passing energy one pigment to the other until reaching the special chlorophyll a molecules in the reaction center.[9] These special chlorophyll a molecules are located in both photosystem II and photosystem I. They are known as P680 for Photosystem II and P700 for Photosystem I.[12]

Links to the article and similar research here

Comment Source:Just a side comment (LHCII is for you only a special application for your methods, so this is probably not so interesting for you): Some community detection for you: There is another community mostly located in Arizona, which used serial time resolved investigations with femtosecond X-ray lasers of PSI. I don't have access to all those papers from them and [28] from the Fleming group and frankly also not the time to study them in detail, but it might be that there are still discussions about the concrete topology of the involved electron transfer channels. That is I was in particular irritated by one image (which is now shunned from public access), which somehow suggested another interpretation of the role of chlorophyll a. That is in the image it looked (if I remember correctly) as if chlorophyll a is sort of parallel to P680 (they seem to operate in different wavelengths (do they?)) in the transfer chain to pheophytin, however Wikipedia writes that >Chlorophyll a also transfers resonance energy in the antenna complex, ending in the reaction center where specific chlorophylls P680 and P700 are located.[5] unfortunately Wikipedia contradicts itself by claiming also (a bit down the page) that chlorophyll a IS P680, which seems wrong since P680 is a dimer and it looks as if chlorophyll a is not (?) >Since the chlorophyll a molecules only capture certain wavelengths, organisms may use accessory pigments to capture a wider range of light energy shown as the yellow circles.[5] It then transfers captured light from one pigment to the next as resonance energy, passing energy one pigment to the other until reaching the special chlorophyll a molecules in the reaction center.[9] These special chlorophyll a molecules are located in both photosystem II and photosystem I. They are known as P680 for Photosystem II and P700 for Photosystem I.[12] Links to the article and similar research <a href="http://www.randform.org/blog/?p=4922">here</a>
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edited September 2014

Hi!

Piotr wrote:

The first two topic articles are standalone, general introductions to these topics. And I believe that they are of the general interest and benefit of the readers. The third one is about a paper arXiv:1310.6638, in which we are trying to predict the scale of quantum effects in a the light-harvesting complex of green plants.

That sounds like a nice series! Please go ahead and write these posts... and please get Jacob Biamonte to edit the English, as I just did here. Then I'll edit his English, and by the end it will be okay.

There will be some people interested in learning about quantum superpositions, and others who know quantum mechanics interested in hearing how it's important in photosynthesis, so you'll have a fun challenge writing to multiple audiences. One good trick is to make sure the beginning of each post is easy, but then, if there's more advanced stuff, include it at the end with some warning like "Experts might be interested to hear that..."

Quantum mechanics is not really one of the main foci of Azimuth, but it's fun. Photosynthesis and the capture of solar energy really do fit into the main focus of Azimuth, so the more you can say about those topics, the better!

Comment Source:Hi! Piotr wrote: > <b>The</b> first two <del>topic</del> <b>articles</b> are standalone, general introduction<b>s</b> to these topics. And I believe that they are of <del>the</del> general interest and benefit of the readers. The third one is about a paper arXiv:1310.6638, in which we are trying to predict the scale of quantum effects in <del>a</del> <b>the</b> light-harvesting complex of green plants. That sounds like a nice series! Please go ahead and write these posts... and please get Jacob Biamonte to edit the English, as I just did here. Then I'll edit his English, and by the end it will be okay. <img src = "http://math.ucr.edu/home/baez/emoticons/tongue2.gif" alt = ""/> There will be some people interested in learning about quantum superpositions, and others who know quantum mechanics interested in hearing how it's important in photosynthesis, so you'll have a fun challenge writing to multiple audiences. One good trick is to make sure the beginning of each post is easy, but then, if there's more advanced stuff, include it at the end with some warning like "Experts might be interested to hear that..." Quantum mechanics is not really one of the main foci of Azimuth, but it's fun. Photosynthesis and the capture of solar energy really _do_ fit into the main focus of Azimuth, so the more you can say about those topics, the better!
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Hi John,

it is great to hear that you like it!

English - sure. When I read my stuff a few days after writing it, I can spot so many mistakes (except for articles, which are still a bit tricky for me).

With quantum mechanics - I know it is not the main focus of Azimuth, so my biggest doubt is what should be the level. Do you think that, as of now, it is OK?

Comment Source:Hi John, it is great to hear that you like it! English - sure. When I read my stuff a few days after writing it, I can spot so many mistakes (except for articles, which are still a bit tricky for me). With quantum mechanics - I know it is not the main focus of Azimuth, so my biggest doubt is what should be the level. Do you think that, as of now, it is OK?
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Hi Piotr,

I don't think there's any description of how to read quantum circuit diagrams on the Azimuth wiki. I'd need one :).

Comment Source:Hi Piotr, I don't think there's any description of how to read quantum circuit diagrams on the Azimuth wiki. I'd need one :).
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Hi Jim,

quantum circuits are another (and fascinating!) story. If there is need, I can write such (though, there are many much more competent persons to write it).

In general, there is an interesting notation of Penrose for tensors, which is often used (sometimes implicitly) in quantum many-body systems.

Comment Source:Hi Jim, quantum circuits are another (and fascinating!) story. If there is need, I can write such (though, there are many much more competent persons to write it). In general, there is an interesting [notation of Penrose for tensors](https://en.wikipedia.org/wiki/Penrose_graphical_notation), which is often used (sometimes implicitly) in quantum many-body systems.
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I think that formalising and explaining as many useful diagramming conventions as possible is an Azimuth goal. Do you know any good descriptions of quantum circuit diagrams, The Wikipedia entry is cursory and searching didn't come up with anything useful. How these relate to the Penrose notation which I could just about grasp in the Emperor's new clothes. I don't think that there's a guide to ladder diagrams which had struck me as another omission which I'm not the best person to write either.

I guess it's also off topic wrt. clustering techniques but I'd also like to know about how you specify applications for use with QIT?

Thanks for the reminder that Penrose notation exists.

Cheers

Comment Source:I think that formalising and explaining as many useful diagramming conventions as possible is an Azimuth goal. Do you know any good descriptions of quantum circuit diagrams, The Wikipedia entry is cursory and searching didn't come up with anything useful. How these relate to the Penrose notation which I could just about grasp in the Emperor's new clothes. I don't think that there's a guide to ladder diagrams which had struck me as another omission which I'm not the best person to write either. I guess it's also off topic wrt. clustering techniques but I'd also like to know about how you specify applications for use with QIT? Thanks for the reminder that Penrose notation exists. Cheers
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edited September 2014

Piotr wrote:

With quantum mechanics - I know it is not the main focus of Azimuth, so my biggest doubt is what should be the level. Do you think that, as of now, it is OK?

The big challenge of science writing is to carefully imagine a class of readers and always make sure what you write is comprehensible to that class. It doesn't matter so much what the class is, as long as it's much larger than "me, myself, and I".

Can you tell me what class of readers you are trying to be comprehensible to?

Let's see if I can guess from what you write. You write:

$$|\psi\rangle = \alpha |1\rangle + \beta |2\rangle \equiv \begin{bmatrix} \alpha \ \beta \end{bmatrix}$$ Someone who has taken a first course in quantum mechanics will understand the bra-ket notation here. Are you writing to that class of people? Or are you hoping that this equation will explain that notation to someone who has never seen it? That would be overoptimistic, I think.

A mathematically sophisticated reader might see that $\equiv$ sign, realize you're defining $|1 \rangle$ and $|2 \rangle$ by this equation, and take the vertical line and angle bracket in $1 \rangle$ to be undefined primitives. But most mathematicians who haven't seen bra-ket notation will wonder why you're writing things like $| 1 \rangle$ instead of $e_1$ for the standard basis vectors. They will have trouble believing that this vertical line and angle bracket are undefined primitives; they'll want to know the rules governing them. And later you spring the notation $|\psi \rangle$ on the reader, whose meaning cannot be guessed by knowing

$$|1 \rangle = \begin{bmatrix} 1 \ 0 \end{bmatrix}$$ Quantum mechanics typically takes a year to learn and is considered difficult. So, almost nobody will be able to learn it from a single blog post. Maybe your audience is people who have taken a course on it, or tried to read a book on it, but need more practice?

Will this audience be able to understand the next posts in the series?

Often people overestimate the ability of others to keep up with a rapid ascent from basics to more advanced material. To avoid this problem, sometimes it can be better to choose a fairly sophisticated audience from the start, and write to them. But the main thing is to make a clear choice. It can be very good to say at the start of a post who your intended audience is. If the second post is a lot harder than the first, say that. In a blog post you can do this in a jokey way, like

Now all of a sudden I'll assume you know quantum field theory. If you don't, goodbye - and I hope you had fun!

I do this kind of thing sometimes. It may sound cruel but it's less cruel than suddenly increasing the prerequisites without admitting it.

Comment Source:Piotr wrote: > With quantum mechanics - I know it is not the main focus of Azimuth, so my biggest doubt is what should be the level. Do you think that, as of now, it is OK? The big challenge of science writing is to carefully imagine a class of readers and always make sure what you write is comprehensible to that class. It doesn't matter so much what the class is, as long as it's much larger than "me, myself, and I". Can you tell me what class of readers you are trying to be comprehensible to? Let's see if I can guess from what you write. You write: $$|\psi\rangle = \alpha |1\rangle + \beta |2\rangle \equiv \begin{bmatrix} \alpha \\ \beta \end{bmatrix}$$ Someone who has taken a first course in quantum mechanics will understand the bra-ket notation here. Are you writing to that class of people? Or are you hoping that this equation will explain that notation to someone who has never seen it? That would be overoptimistic, I think. A mathematically sophisticated reader might see that $\equiv$ sign, realize you're defining $|1 \rangle$ and $|2 \rangle$ by this equation, and take the vertical line and angle bracket in $1 \rangle$ to be undefined primitives. But most mathematicians who haven't seen bra-ket notation will wonder why you're writing things like $| 1 \rangle$ instead of $e_1$ for the standard basis vectors. They will have trouble believing that this vertical line and angle bracket are undefined primitives; they'll want to know the rules governing them. And later you spring the notation $|\psi \rangle$ on the reader, whose meaning cannot be guessed by knowing $$|1 \rangle = \begin{bmatrix} 1 \\ 0 \end{bmatrix}$$ Quantum mechanics typically takes a year to learn and is considered difficult. So, almost nobody will be able to learn it from a single blog post. Maybe your audience is people who have taken a course on it, or tried to read a book on it, but need more practice? Will this audience be able to understand the next posts in the series? Often people overestimate the ability of others to keep up with a rapid ascent from basics to more advanced material. To avoid this problem, sometimes it can be better to choose a fairly sophisticated audience from the start, and write to them. But the main thing is to make a clear choice. It can be very good to say at the start of a post _who your intended audience is_. If the second post is a lot harder than the first, say that. In a blog post you can do this in a jokey way, like > Now all of a sudden I'll assume you know quantum field theory. If you don't, goodbye - and I hope you had fun! I do this kind of thing sometimes. It may sound cruel but it's less cruel than suddenly increasing the prerequisites without admitting it.
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Hi John,

thank you for your remarks. A few times I thought quantum mechanics from scratch (http://migdal.wikidot.com/en:quantum-outlines), but you are right that even braket notation needs some time, before one understands it and get used to it. And if 'decypher my mathematical notation' is a puzzle, then it is not the most enjoyable kind of puzzle.

Braket - I will delete it (or elaborate carefully).

For other stuff - my goal is explain off-diagonal elements in density matrix. Within this constraint, I want to make it as accessible as possible. Some matrix calculus is necessary. Popular-science level of quantum mechanics as well. It might be useful to be after some introduction to quantum mechanics, but I think it is not a requirement.

In any case, I will change some stuff and test it on some smart friends, who are not physicists.

Comment Source:Hi John, thank you for your remarks. A few times I thought quantum mechanics from scratch (http://migdal.wikidot.com/en:quantum-outlines), but you are right that even braket notation needs some time, before one understands it and get used to it. And if 'decypher my mathematical notation' is a puzzle, then it is not the most enjoyable kind of puzzle. Braket - I will delete it (or elaborate carefully). For other stuff - my goal is explain off-diagonal elements in density matrix. Within this constraint, I want to make it as accessible as possible. Some matrix calculus is necessary. Popular-science level of quantum mechanics as well. It _might_ be useful to be after some introduction to quantum mechanics, but I think it is not a requirement. In any case, I will change some stuff and test it on some smart friends, who are not physicists.
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Is it better now?

Comment Source:Is it better now?
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I'll check it out now.

Comment Source:I'll check it out now.
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edited October 2014

It looks good! I think it explains the ideas pretty clearly!

How about getting Jacob or someone to polish the English? I could do it too, but I'm sort of crazy-busy right now, and I'd prefer to make the next more sophisticated layer of improvements after the grammar and typos are fixed.

I'm talking about things like these:

"State of electron can be described as complex, two-dimensional vector" $\mapsto$

"A state of an electron can be described as a complex, two-dimensional vector"

"Energy, and evolution, of this state is described by a Hamiltionian:" $\mapsto$

"The energy, and evolution, of this state is described by a Hamiltonian:"

"How to add classically quantum things" $\mapsto$

"How to classically add quantum things" (This may not technically be grammatical, but it's what people would actually say. The other one makes me think you're talking about "classically quantum things".)

and so on (about 50 more). After these changes are made, I can make the more sophisticated edits while staying happy. There's nothing worse than a grumpy editor!

Comment Source:It looks good! I think it explains the ideas pretty clearly! How about getting Jacob or someone to polish the English? I could do it too, but I'm sort of crazy-busy right now, and I'd prefer to make the next more sophisticated layer of improvements _after_ the grammar and typos are fixed. I'm talking about things like these: "State of electron can be described as complex, two-dimensional vector" $\mapsto$ "**A** state of **an** electron can be described as **a** complex, two-dimensional vector" "Energy, and evolution, of this state is described by a Hamiltionian:" $\mapsto$ "**The** energy, and evolution, of this state is described by a **Hamiltonian**:" "How to add classically quantum things" $\mapsto$ "How to **classically add** quantum things" (This may not technically be grammatical, but it's what people would actually say. The other one makes me think you're talking about "classically quantum things".) and so on (about 50 more). After these changes are made, I can make the more sophisticated edits while staying happy. There's nothing worse than a grumpy editor!
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edited October 2014

I don't know if this'll help (I have the advantage of being a native English speaker) but I find sending text through a speech synthesis program helps me catch things like missing articles, etc. It's more dificult to start skimming when you're listening vs reading.

Comment Source:I don't know if this'll help (I have the advantage of being a native English speaker) but I find sending text through a speech synthesis program helps me catch things like missing articles, etc. It's more dificult to start skimming when you're listening vs reading.
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Hi John,

so now - is it OK? It went through some proofreading by my colleagues.

Comment Source:Hi John, so now - is it OK? It went through some proofreading by my colleagues.
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edited March 2015

Hi! I'm going through this post now, adding explanations of terms that are undefined, and fixing grammar and formatting:

A question: is it really wise to use $\psi_+$ as the name for the state whose energy is $E_0 - \Delta$, and $\psi_-$ as the name for the state whose energy is $E_0 + \Delta$? I guess I know why you're doing this, but it could be a bit confusing. Maybe I'll add an explanation.

By the way, the term 'superposition' is never defined. I'll add a definition, since that's the topic of the post!

Comment Source:Hi! I'm going through this post now, adding explanations of terms that are undefined, and fixing grammar and formatting: * [Blog - quantum superposition](http://www.azimuthproject.org/azimuth/show/Blog+-+Quantum+superposition) A question: is it really wise to use $\psi_+$ as the name for the state whose energy is $E_0 - \Delta$, and $\psi_-$ as the name for the state whose energy is $E_0 + \Delta$? I guess I know why you're doing this, but it could be a bit confusing. Maybe I'll add an explanation. By the way, the term 'superposition' is never defined. I'll add a definition, since that's the topic of the post!