Author Topic: density matrix simulation for parahydrogen induced polarization (PHIP)  (Read 5045 times)

Ronghui

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I wonder if there is an example for simulating PHIP?

I just downloaded SpinDynamica and am trying to get started, but no idea how.

Thanks.

Ronghui

MalcolmHLevitt

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Re: density matrix simulation for parahydrogen induced polarization (PHIP)
« Reply #1 on: August 14, 2012, 12:02:09 PM »
Hi Ronghui,
 here is a quick example notebook that I hope will help get you started.
 all the best
malcolm

ps. I've stripped out most of the graphics cells to reduce the file size but these should be restored when you execute the notebook.

MalcolmHLevitt

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Re: density matrix simulation for parahydrogen induced polarization (PHIP)
« Reply #2 on: August 19, 2012, 10:59:25 AM »
An improved example set for PHIP is included here. This includes an ALTADENA simulation using a linear field sweep. The graphic output has been stripped out of the file to reduce space but will be restored on execution.

Ronghui

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Re: density matrix simulation for parahydrogen induced polarization (PHIP)
« Reply #3 on: September 06, 2012, 08:26:50 PM »
Dr. Levitt,

Thank you very much for the examples.

I wonder if there is any limit on the size of spin system in this case? I guess I saw you stated somewhere it is not good for more than 5 spins.

I would like to include other spins in the substrate to simulate the magnetization/hyperpolarization transfer to coupled spins, and this will give me more than 5 spins in total.

For instance, in the following paper, they saw slight polarization of aromatic region during the para-hydrogenation of styrene.

http://pubs.rsc.org/en/content/articlehtml/2009/cp/b914188j#tab1
Para-hydrogen induced polarization in multi-spin systems studied at variable magnetic field

Thanks.
Ronghui

MalcolmHLevitt

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Re: density matrix simulation for parahydrogen induced polarization (PHIP)
« Reply #4 on: September 07, 2012, 08:04:17 AM »
The best thing is just to try, Ronghui. You can keep expanding the size of the spin system until you find the simulation is too slow to be practical. My guess is that 6 spins will be manageable with the latest code. However the ALTADENA-style simulations which require numerical integration of differential equations under a continuous variation in the Hamiltonian are likely to be much slower.

I expect to introduce truncated operator bases in a future version which should allow the approximate simulation of larger systems. But this is not going to happen soon with my current time constraints.

As an alternative you can try the SPINACH program of Ilya Kuprov which can handle much larger numbers of spins with good numerical efficiency.

Ronghui

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Re: density matrix simulation for parahydrogen induced polarization (PHIP)
« Reply #5 on: September 07, 2012, 02:47:05 PM »
Dr. Levitt,

Thanks for your suggestions.

I have been learning both Spinach and SpinDynamica. I like the easiness of finding the explanation of functions by just typing "?***" in SpinDynamica very much. And our group is much more familiar with Mathematica and  SpinDynamica as well. So it seems to be easier using SpinDanamica to familiarize myself with density matrix simulation as a beginner.

By the way, I am a graduate student working with Dr. Russ Bowers.

Ronghui

Ronghui

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Re: density matrix simulation for parahydrogen induced polarization (PHIP)
« Reply #6 on: September 07, 2012, 09:21:03 PM »
Dr. Levitt,

I am trying to expand the spin system to 3 spins for the calculation of parahydrogenation of propiolic acid to acrylic acid. The chemical shifts and J-coupling constants are taken from literature. Spin-1 and 2 are from parahydrogen.

Something is wrong, and especially I am not confident about the initial density operator.

I have attached the notebook here and I wonder if you could give me some suggestions.

Thank you very much.

Ronghui

MalcolmHLevitt

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Re: density matrix simulation for parahydrogen induced polarization (PHIP)
« Reply #7 on: September 07, 2012, 09:40:13 PM »
Hi Ronghui,
 I looked at this briefly. I agree that the initial density operator does not look right. If spins 1 and 2 come from parahydrogen the initial density operator should simply be opI[1].opI[2].

 In general, when asking for advice, it is not constructive to say "something is wrong". Please be more helpful and specific, and provide a highlighted comment in the .nb file.

good luck
malcolm