View source for Talk:Surface plasmon resonance

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==picture request==
Can someone please make a picture to go with the new example? I tried to make the example as simple as possible, but I think that it would easily benefit from a picture of a window and a picture of a window with a gold film behind it.

Maybe use a Picture of the SPR setup, in which the change of the angle of the incoming laserbeam is modulated by the laser position. In your image it looks like the splitting of the beam into beams of different angle is caused by the prism. In fact the prism is only used to ensure total reflection of the laserbeam.  <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/141.2.221.163|141.2.221.163]] ([[User talk:141.2.221.163|talk]]) 08:24, 21 April 2014 (UTC)</span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->

==scope of the article==
Not sure how to go about sorting it yet, but this description of SPR is really about the application of the phenomenum in biological analysis rather than SPR itself, which a property most often observed in gold nanoparticles.

A solution that immediately springs to ming is to have this page talk about the phenomenon of Surface Plasmon Resonance described here, and to create a new page for Surface Plasmon Resonance Biosensors for the utilisation of the phenomenon in optical biosensors. [[User:Dwayne Dibly|Dwayne Dibly]] 23:20, 20 December 2005 (UTC)

Besides, Surface Plasmon Resonance is propagative while Surface Plasmon Polaritons on nanoparticules are localized.

Tried to create an SPR page that describes both planar SPR and localized SPR.  Both are used for biosensing, but both can be used for other applications as well. User: Ucispr, 01 May 2006.

==units of RU==
What do the units of RU stand for?  These are sometimes given with data and relate to the amount of bound species.
- JamMan 4th Nov 06
:RU = Response Units. There is a formula to compute this quantity, but roughly 0.1° SPR angle change corresponds to 1000 RU. [[User:Axelve|Axelve]] 23:20, 8 November 2006 (UTC)
::Oh, and that relates to roughly 1 nanogram per square millimeter (ng/mm^2) bound protein. [[User:Axelve|Axelve]] 23:26, 8 November 2006 (UTC)

In fact, RU is a commercial unit that has been introduced and popularized by Biacore. RU stands for Resonance Unit. 1 RU relates roughly to 1 PICOgram (1E-12) per square millimeter (and not 1 nanogram as Axelve stated).  <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/129.175.96.79|129.175.96.79]] ([[User talk:129.175.96.79|talk]]) 12:58, 31 October 2008 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot-->

==law enforcement tag==
: I removed the Law Enforcement tag, after reading the article I don't see that it has anything to do with LE. If I am wrong, because the articel is over my head, please put the tag back  [[User:EMT1871|EMT1871]] 10:08, 20 January 2007 (UTC)

==reorganization==
Added a few things, some new figures as well. I did not remove anything, just reorganized. Feedback is welcome. ([[User:Tomio-|tomio-]] 20:40, 28 May 2007 (UTC))

==Kretschmann==
The pic with SPR setup uses a triangular prisma. Doesn't the Kretschmann setup us a semi-cylindrical prism? [[User:Benkeboy|Benkeboy]] 13:21, 1 February 2007 (UTC)

:I believe the Kretschmann configuration is defined by contact between the prism and the sample.
:([[User:JoeCarson|JoeCarson]] 19:11, 1 February 2007 (UTC))

:The Kretschmann configuration uses the metal film on a glass block, whatever shape it has. This result a shift in the dispersion relation (because the glass has a refractive index more than 1), and gives a possible resonance angle. This is reasonably described in the Raether book. Also, the plasmon propagates on the outer surface of the metal film in this setup, whilst in the Otto configuration -a gap between the glass block and the metal film- it propagates on the inner surface.
:A prism shape is easier to get, a half cylinder has no refraction, which alters the incident angle on the film -it can be easily calculated though.([[User:Tomio-|tomio-]] 14:06, 27 April 2007 (UTC))

==Example==
The example needs to be rewritten and should not be the first section of this article.  I may have some useful pictures but not enough time or motivation to add them right now.  If you give me an e-mail address here or on my talk page, I can send you a great book on surface plasmons with many useful diagrams.
[[User:JoeCarson|JoeCarson]] 13:50, 4 April 2007 (UTC)

:What's the problem with the example? Looks like it's quite clear to me. Cannot we add it? --[[User:Cyclopia|Cyclopia]] 11:30, 5 April 2007 (UTC)

::The quality of writing is poor and it's too long.  It also seems too oversimplified to do SPR justice.  A shorter example with a good diagram would be preferable.[[User:JoeCarson|JoeCarson]] 13:29, 5 April 2007 (UTC)

:::I agree, but itt's anyway better than nothing. It surely helps newbies on the subject even in its present state. I personally would readd it to the article, with a "not of encyclopedic quality" warning tag (don't remember the correct tag now, sorry).  --[[User:Cyclopia|Cyclopia]] 22:06, 5 April 2007 (UTC)

::::An example would be great.  However, we need a good diagram and decent writing to go along with it.  I believe leaving the page as is would be better than inserting that example.[[User:JoeCarson|JoeCarson]] 11:26, 8 April 2007 (UTC)

:::::I'm the guy who wrote the example. Personally, I understand your point. The main reason I added it was just to get "the ball rolling". Almost all of the Physics Wiki pages are too technical, and could easily benefit from an example. Anyways, my email address is tjm1@ualberta.ca. If you could send me that book, I can try to make the example better. I am not going to increase the english standard that its at, but I have no problem with someone else updating it. <small>—The preceding [[Wikipedia:Sign your posts on talk pages|unsigned]] comment was added by [[Special:Contributions/68.148.190.156|68.148.190.156]] ([[User talk:68.148.190.156|talk]]) 18:32, 15 April 2007 (UTC).</small><!-- HagermanBot Auto-Unsigned -->

:::::If I have some time, I can dig up some full resonance curves from my data. I would add that to the example, showing how the SPR data looks in general, then the given adsorpion response curve can be interpreted more clearly by the readers. I would also update a bit, if you do not mind 8). ([[User:Tomio-|tomio-]] 14:09, 27 April 2007 (UTC))

::::::I have absolutely no problem with that. I have been swamped by finals, and so have not been able to redo the example. I am definetly not an expert in this area, so any information you could add would be very beneficial.[[User talk:68.148.190.156|talk]]) 18:32, 15 April 2007 (UTC)

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==Electric/electronic/magnetic plasmons==
It would be nice if one could clear up the usage of electric or electronic for the SPR, and what is exactly the magnetic SPR.
* the light used for excitation is electromagnetic radiation
* the electron beam is an electron beam
* the plasmon is an oscillation phenomena of electrons (affected by both electric and magnetic fields)
([[User:Tomio-|tomio-]] 12:49, 2 June 2007 (UTC))

==Realisation==
I am not entirely sure but where it says "In the case of p-polarized light (polarization occurs parallel to the surface)" isn't p-polarized light parallel to the plane of incidence, not the surface.  I thought it would be perpendicular to the surface.  Let me know what you think.   P.s. this is my first Wikidiscussion.  Let me know if I screwed up.

[[User:Helicopter34234|Helicopter34234]] ([[User talk:Helicopter34234|talk]]) 19:03, 1 February 2008 (UTC)

:You were right, I had a look into it. It is corrected now. ([[User:Tomio-|tomio-]] ([[User talk:Tomio-|talk]]) 02:48, 30 April 2008 (UTC))

Also under this section, could you please define the variables more clearly? A mass-independent version (I assume mu refers to the mass-per-volume) of this equation is given in a nature article (k = k0 * sqrt(e1*e2 / (e1 + e2)).

[[User:Motrax|Motrax]] ([[User talk:Motrax|talk]]) 17:36, 6 April 2008 (UTC)

: No, mu is the magnetic permeability. In general it is left out, when the material it is close to 1, but in this case it is needed for keeping the story more opened. I added an explanation line. ([[User:Tomio-|tomio-]] ([[User talk:Tomio-|talk]]) 09:10, 13 April 2009 (UTC))


I think, 'impulse' should be replaced by 'momentum' throughout the paragraph. This would be the correct physical quantity in this context.

[[User:Criosx|Criosx]] ([[User talk:Criosx|talk]]) 21:14, 6 April 2010 (UTC)

I think a better title for the section would be "Implementations" rather than "Realization."  To a native English speaker, the use of "realization" in this context is confusing.  

This is a very common mistake made by non-native English speakers.  In Romance languages and in German, the equivalent words are often used interchangeably.  The English word "realization" is most commonly used in reference to an abstract concept, such as the "realization of a dream" or the "realization of a goal."  It is never used to describe the creation of a physical object (like a plasmon-resonance detector.)  For example, a Spanish real estate developer once described to me the realization of an office building, and I had no idea what he was talking about.  The correct English word in that context would have been the "construction" of the office building.  The building could accurately be described as the realization of his (abstract) *vision* for the site, but there's no such thing as the realization of a (concrete) *building*.   Likewise, in the context of this article, the article is describing concrete, physical implementations, as opposed to concepts.  A machine can be the realization of an idea (note that "realize" here refers to an abstract idea).  But you can't realize a machine (a machine is a physical object).  You make a machine, you don't realize a machine.  

See, for example, http://ell.stackexchange.com/questions/10749/realization-vs-implementation-of-a-computer-program[http://ell.stackexchange.com/questions/10749/realization-vs-implementation-of-a-computer-program] for a similar discussion in the context of computer programs.  [[User:Tpkaplan|Tpkaplan]] ([[User talk:Tpkaplan|talk]]) 18:55, 12 December 2015 (UTC)

==Moved from main article==
Provided examples below, are very specific to a particular application partially involving Surface Plasmon Resonance. The Section titled Applications gives a very fair broad overview of examples ranging from spectroscopy to bio sensors. The below discussion describes some specific work which is not relevant to this discussion thread. Infact the discussion dwells on getting correct data, correcting spikes, data processing etc more than SPR itself. So commenting this out before I add very short relevant examples which everybody can appreciate.

+++++++++++++++++++++++++++++++++++++++++++++++++
=== Protein-Protein interaction ===
{{Textbook|date=December 2007}}
SPR can be used to measure [[protein-protein interaction]].
Experience shows that one RU represents the binding of approximately 1 pg/mm². In practice more than 50 pg/mm² of analyte binding is needed (100 RU of binding should be adequate). SPR provides a good estimation of ''k''<sub>on</sub> and ''k''<sub>off</sub> if mass-transport and re-binding are insignificant, otherwise the apparent ''k''<sub>on</sub> and ''k''<sub>off</sub> values would be only lower estimates. There are two major ways to measure ''K''<sub>''D''</sub>:
#Equilibrium (use when ''K''<sub>''D''</sub> is high), and
#Kinetics (use when ''K''<sub>''D''</sub> is low).

A useful rule of thumb is that an interaction should reach 99% of the equilibrium level within 4.6/''k''<sub>off</sub> s. There are three main types of coupling chemistry, which utilize, respectively, amine (e.g. lysine), thiol (cysteine), or aldehyde (carbohydrate; if the protein is glycosylated, i.e., glycoprotein. All covalent coupling methods utilize free carboxymethyl groups on the sensor chip surface. As controls use:
#negative ligand control,
#negative analyte control,
#different ligand that is not expected to bind,
#reverse the order of analyte injection from lower to higher concentration and back,
#Use a Scatchard plot (RU bound in equilibrium/analyte concentration), it should be linear for 1:1 Langmuir interaction model.
#test effect of ligand immobilization level on the binding.
#repeat the experiment with ligand immobilized in a different way. <br>
Perform all measurements in physiological temperature. Ideally analyte concentration should be varied over four orders of magnitude, from 0.01''K''<sub>''D''</sub> to 100''K''<sub>''D''</sub>. You may use Biaevaluation, Scrubber, or any other software to analyze your data and prepare it for presentation. All buffers should be filtered through 0.2 micrometer filters and degassed at room temperature.

====Data processing for measuring binding affinity====
1) Zeroing: zero on the y-axis for start time of the injection;
2) Reference subtraction: subtract-out data from the reference spots;
3) Replication overlays and double Referencing;
4) Globally fitting data: numerically fit the data to 1:1 Langmuir interaction model.

====Possible artifacts while measuring binding affinity====
1) Spikes in the sensogram in the response to elevated temperatures that can occur due to outgassing of the buffer; 2) excluded-volume effects; 3) Protein immobilization affects affinity; 4) the injected analyte is not monomeric (use analytical ultracentrifugation to assure monomeric state, also use gel filtration), aggregation; 5) avidity effects; 6) both analyte and ligand should be chemically and conformationally pure; 7) instrument is not clean and should be primed; 8) baseline drift (use covalent immobilization); 9) check for non-specific binding;
10) surface heterogeneity (look at the shape of the 'SPR dip');
11) surface instability (baseline drift);
12) mass-transport effects, check whether ''k''<sub>on</sub> and ''k''<sub>off</sub> dependence on flow rate, use high flow rates (100 µL/min) and low levels of immobilized ligand;
13) one cannot measure association or dissociation rates which are faster than the machine sampling frequency (usually 1&nbsp;Hz);
14) If your concentrations are wrong then your affinity results would be wrong [concentration of correctly folded protein];
15) If your protein Lysine content is high you might consider conjugating the protein by a method other than amine chemistry [biotin is recommended];
16) degradarion of the protein on the chip during long measurements (several hours);
17) Biphasic sensogram is bad; lower concentration to achieve a monotonic curve of association and dissociation.

====Validation of measuring binding affinity====
1) Isothermal titration calorimetry;
2) Nuclear magnetic resonance;
3) using different machine (Biacore vs. ProteOn);
4) co-immunoprecipitation (less quantitative)

====Tips for achieving a good measurement of binding affinity====
1) To avoid using too much protein inject a small amount of sample only for a short time [even if you don't reach a steady-state]. That will help avoiding aggregation effects; 2) If the two binding partners are protein and short peptide, conjugate the peptide to the surface. Otherwise, several peptides would bind a single protein in mixed specific and non-specific binding; 3) Add 1% alignate top the buffer to reduce non-specific association; 4) protein must be fresh (i.e., not frozen), after gel-filtration, and kept on ice; 5) use as a reference measurement "empty but activated" surface; 6) chi-squared should be lower than 10% of ''R''<sub>max</sub>.

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== Added changes ==
I added some changes, trying to clarify some minor issues. I think, it is important to clarify, that SPR is not only a biosensor. That is perhaps the most popular application, but the method is more general.

I did not want to be offensive, but moved the ''Biosensor'' examample. It was not showing any concrete explanation to the readers, just a link to a nice paper. So I moved this link into the text, and removed the rest. It could be nice though to see a bit more detailed example on this, or using other absorption based diosensor data.

([[User:Tomio-|tomio-]] ([[User talk:Tomio-|talk]]) 09:24, 13 April 2009 (UTC))

== Dispersion Relation ==

On the equation for the dispersion relation K(w), could somebody please add text that defines K?  It was not obvious to me.  Thanks.  <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/201.116.80.51|201.116.80.51]] ([[User talk:201.116.80.51|talk]]) 14:38, 19 September 2011 (UTC)</span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->

== Intro ==

"It is the fundamental behind many color-based biosensor applications and different lab-on-a-chip sensors."

fundamental process?  <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/131.252.4.4|131.252.4.4]] ([[User talk:131.252.4.4|talk]]) 18:56, 17 November 2011 (UTC)</span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot-->

==Animation==

An animation of this process would easily illustrate many of the technical concepts included in this article. I have tagged this article with {{tlx|Video requested}}. A simple animated [[.gif]] may suffice, or a longer video animation with description/narration may fulfil this request. Kind regards, '''[[User:Captain-n00dle|<span style="color:green">Captain n00dle</span>]][[User:Captain-n00dle/status|<span style="margin-left:-1px">\</span>]]'''<sup>[[User talk:Captain-n00dle|<span style="color:#7cfc00;margin-left:-2px;cursor:help">Talk</span>]]</sup> 10:33, 8 April 2012 (UTC)

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