[3dem] (mean Inner potential) Re: 3dem Digest, Vol 142, Issue 38
Vladan Lucic
vladan at biochem.mpg.de
Thu Jun 27 10:08:51 PDT 2019
Hi Philip,
Thanks for digging deeper into this.
On 6/26/19 7:58 PM, Philip Köck wrote:
>
> The statement in Wanner et al. 2006 is very strange in my opinion.
>
> Shouldn't "perpendicular" be replaced by "parallel"?
>
I also thought the same when I read this statement the first time. But
now, my understanding is that the statement was meant to be this way,
please pay attention to the second part of this statement:
"Although only dipole moments with a component perpendicular to the
electron beam would contribute to a phase shift the irregular and
corrugated a-C surface will provide attachment sites for H2O molecules
to fulfill this condition."
Adsorbed H2O dipoles are oriented perpendicular to the surface. If the
surface is flat and perpendicular to the beam, the dipoles will be
parallel to the beam. However, an "irregular and corrugated a-C surface"
will cause some H2O dipoles to be oriented at an angle (or even
perpendicular) to the beam, thus providing the dipole component
perpendicular to the beam. Therefore, if an "irregular and corrugated
a-C surface" is needed to "fulfill this condition", the condition seem
to be that dipoles are perpendicular to the beam, as stated.
>
>
> I don't see how the potential can be proportional to the distance
> between the dipole layers. If we think of a slab of neutral matter (as
> a thought experiment), which is covered first by a layer of positive
> charges and then an equal amount of negative charges on top of that,
> the following should happen: The negative charge curves the potential
> upwards and the potential increases, then the positive charge curves
> the potential down again by an equal amount. The total effect is that
> the potential is constant inside the slab and independent of the
> slab's thickness and therefore the phase shift is proportional to the
> thickness.
> Maybe you meant that the potential is roughly proportional to the
> distance between the negative and positive layer (or more generally
> the dipole moment).
>
>
> I can imagine a constant phase shift coming from multiple layers of
> charge, at least 3, that are balanced. A bit like - + + -, for
> example. That could lead to a potential that's confined to the surface
> and a phase shift contribution that's independent of the thickness of
> the solid.
>
Let me try to expand on your model. Adsorbed H2O forms dipoles on the
surface, with positive charge towards the vacuum and the negative
towards the material. A potential arising from one dipole (having
electric dipole moment p, vector) that an electron at a distance
(vector) r sees is proportional to:
scalar_product(r, p) / magnitude(r)^3
So you're right that it is proportional to the distance between the
positive and the negative charge (contained in p), but that's not all.
H2O dipoles form on both sides of the material and they're oriented in
the opposite direction. The contribution to the potential from the
"other side dipol" has the same form, but r needs to be replaced by r+d,
where (vector) d is the thickness of the material. Adding the two terms
(with opposite signs because of the opposite orientation), when
(magnitudes) r>>d leaves in the first approximation a term proportional
to d. That's the reason for my proportionality statement.
In any case, we agree that it is clear why the phase should be
proportional to the thickness, at least for flat surfaces. The strange
thing is the thickness-independent part of the phase change. Perhaps I'm
wrong, but I don't see how multiple flat dipole layers could produce
this effect. That's why I'm thinking that dipoles having components
perpendicular to the beam, or some lateral rearrangement of electrons in
the material are needed (arising from rough surfaces or perhaps Volta
phase plate), even though I don't understand the mechanism.
Best,
Vladan
> All the best,
>
>
> Philip
>
> ------------------------------------------------------------------------
> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Vladan Lucic
> <vladan at biochem.mpg.de>
> *Sent:* Wednesday, 26 June 2019 17:57:58
> *To:* 3dem at ncmir.ucsd.edu
> *Subject:* Re: [3dem] (mean Inner potential) Re: 3dem Digest, Vol 142,
> Issue 38
> I agree that classically, the potential generated by two surface
> layers of dipoles oriented perpendicular to the surface is in the
> first approximation directly proportional to the distance between the
> layers, that is to the thickness, which argues against the
> thickness-independent phase shift. Perhaps that is the reason for
> Wanner et al 2006 (the paper recommended by Ben) to propose that
> dipoles perpendicular to the beam should be considered:
>
> "Although only dipole moments with a component perpendicular to the
> electron beam would contribute to a phase shift the irregular and
> corrugated a-C surface will provide attachment sites for H_2 O
> molecules to fulfill this condition."
>
> Interestingly, Hettler et al 2018, Charging of carbon thin films in
> scanning and phase-plate transmission electron microscopy (
> https://doi.org/10.1016/j.ultramic.2017.09.009
> <https://doi.org/10.1016/j.ultramic.2017.09.009> ) argue that the high
> surface roughness of the Volta phase plate is needed to generate the
> phase shift (at a high temperature). Furthermore, in their picture,
> surface dipoles are absent from the region of the direct beam, which
> causes lateral (perpendicular to the beam) redistribution of
> electrons. Both of these could provide the "perpendicular dipoles"
> proposed by Wanner et al 2006.
>
> Vladan
>
> On 6/18/19 9:26 AM, Philip Köck wrote:
>>
>> Thanks for the reference.
>>
>>
>> I can't make sense of a thickness-independent contribution to the
>> phase shift either. The way I see it even a surface layer of dipoles
>> would lead to a constant MIP and a phase shift proportional to the
>> thickness.
>>
>> One can think of a simple model: A slab of completely neutral
>> material (made of neutrons) covered in a layer of positive charge and
>> outside that a layer of negative charge that balances the positive
>> charge. The potential inside this slab will be constant and
>> independent of the thickness of the slab.
>>
>>
>> I wonder if we can get a comment from someone who knows more.
>>
>>
>> All the best,
>>
>>
>> Philip
>>
>> ------------------------------------------------------------------------
>> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu>
>> <mailto:3dem-bounces at ncmir.ucsd.edu> on behalf of Benjamin Himes
>> <himes.benjamin at gmail.com> <mailto:himes.benjamin at gmail.com>
>> *Sent:* Monday, 17 June 2019 20:45:48
>> *To:* 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>> *Subject:* [3dem] (mean Inner potential) Re: 3dem Digest, Vol 142,
>> Issue 38
>> Hi Philip,
>>
>> The mean inner potential (MIP) refers to a total "interaction"
>> potential that is considered a material property. It consists of all
>> the sources contributing to the potential well seen by an imaging
>> electron, including those you suggest (nuclear and electronic
>> contributions.)
>>
>> Yes, physical changes to the surface via adsorbed matter will
>> directly affect the MIP. I believe the working hypothesis for the
>> source of the "Volta" potential is through heat/exposure related
>> modification of surface adsorbates.
>>
>> It is also interesting to note that in addition to the electronic
>> character of the object, the surface contributions of adsorbates and
>> heating, there is another thickness independent phase shift (at least
>> for carbon) the source of which I am not clear on. Happy to hear an
>> explanation from anyone in the know : )
>>
>> Please have a look at this paper where all of the non-Volta
>> contributions are discussed and also measured.
>>
>> *"Electron holography of thin amorphous carbon films: Measurement of
>> the mean inner potential and a thickness-independent phase shift"*
>> *
>> *
>> *doi: j.ultramic.2005.10.004*
>> *
>> *
>> HTH
>>
>> Ben
>>
>> ------------------------
>> Benjamin Himes
>>
>> cryoEM methods development
>> Grigorieff lab
>> <https://mail.hhmi.org/owa/redir.aspx?C=SbsCefkcbOt75jDyr05lpd3OifVN_utmfvnhZrtXS7Bl2i2eOXXVCA..&URL=http%3a%2f%2fgrigoriefflab.janelia.org%2f>,
>> HHMI Janelia Research Campus
>>
>> cryoSTAC development @ emClarity
>> <https://mail.hhmi.org/owa/redir.aspx?C=8yDzXj54yTidMevTB7q5m3liEVwqAZ9LxuXQ4iYOVvtl2i2eOXXVCA..&URL=https%3a%2f%2fgithub.com%2fbHimes%2femClarity%2fwiki>
>>
>> -------------------------
>>
>>
>> On Mon, Jun 17, 2019 at 12:17 PM <3dem-request at ncmir.ucsd.edu
>> <mailto:3dem-request at ncmir.ucsd.edu>> wrote:
>>
>> Send 3dem mailing list submissions to
>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>> <https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem>
>> or, via email, send a message with subject or body 'help' to
>> 3dem-request at ncmir.ucsd.edu <mailto:3dem-request at ncmir.ucsd.edu>
>>
>> You can reach the person managing the list at
>> 3dem-owner at ncmir.ucsd.edu <mailto:3dem-owner at ncmir.ucsd.edu>
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of 3dem digest..."
>>
>>
>> Today's Topics:
>>
>> 1. mean inner potential of a solid (Philip K?ck)
>> 2. NYC Computational Cryo-EM Summer Workshop
>> (Cindy Rampersad-Phillips)
>> 3. side entry holder for autogrids? (Michael Elbaum)
>> 4. Re: side entry holder for autogrids? (Wim Hagen)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 17 Jun 2019 08:27:35 +0000
>> From: Philip K?ck <philip.koeck at ki.se <mailto:philip.koeck at ki.se>>
>> To: "3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>"
>> <3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>>,
>> "microscopy at microscopy.com
>> <mailto:microscopy at microscopy.com>" <microscopy at microscopy.com
>> <mailto:microscopy at microscopy.com>>
>> Subject: [3dem] mean inner potential of a solid
>> Message-ID:
>>
>> <HE1PR0802MB2586733E695E56B20FBCC6D183EB0 at HE1PR0802MB2586.eurprd08.prod.outlook.com
>> <mailto:HE1PR0802MB2586733E695E56B20FBCC6D183EB0 at HE1PR0802MB2586.eurprd08.prod.outlook.com>>
>>
>> Content-Type: text/plain; charset="utf-8"
>>
>>
>> Hi all.
>>
>> I've been wondering what the mean inner electrostatic potential
>> of a solid (for example the 10 V of carbon) is actually due to.
>> Is it purely caused by the distribution of nuclei and electrons
>> in the solid itself or could there be a contribution from
>> adsorbed surface charges?
>>
>> All the best,
>>
>> Philip
>>
>>
>>
>> N?r du skickar e-post till Karolinska Institutet (KI) inneb?r
>> detta att KI kommer att behandla dina personuppgifter. H?r finns
>> information om hur KI behandlar
>> personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>.
>>
>>
>> Sending email to Karolinska Institutet (KI) will result in KI
>> processing your personal data. You can read more about KI?s
>> processing of personal data
>> here<https://ki.se/en/staff/data-protection-policy>.
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20190627/5ecef449/attachment-0001.html>
More information about the 3dem
mailing list