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Hi Philip,<br>
<br>
Thanks for digging deeper into this.<br>
<br>
<div class="moz-cite-prefix">On 6/26/19 7:58 PM, Philip Köck wrote:<br>
</div>
<blockquote type="cite"
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<p style="margin-top:0;margin-bottom:0">The statement in Wanner
et al. 2006 is very strange in my opinion.</p>
<p style="margin-top:0;margin-bottom:0">Shouldn't
"perpendicular" be replaced by "parallel"?</p>
</div>
</blockquote>
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:<br>
<br>
"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."<br>
<br>
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.<br>
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cite="mid:HE1PR0802MB258608708FF7E2E5CA51605383E20@HE1PR0802MB2586.eurprd08.prod.outlook.com">
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<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">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.<br>
Maybe you meant that the potential is roughly proportional to
the distance between the negative and positive layer (or more
generally the dipole moment).</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">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.</p>
</div>
</blockquote>
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:<br>
<br>
scalar_product(r, p) / magnitude(r)^3 <br>
<br>
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. <br>
<br>
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.<br>
<br>
Best,<br>
Vladan<br>
<br>
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</p>
<p style="margin-top:0;margin-bottom:0">All the best,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Philip</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> 3dem
<a class="moz-txt-link-rfc2396E" href="mailto:3dem-bounces@ncmir.ucsd.edu"><3dem-bounces@ncmir.ucsd.edu></a> on behalf of Vladan Lucic
<a class="moz-txt-link-rfc2396E" href="mailto:vladan@biochem.mpg.de"><vladan@biochem.mpg.de></a><br>
<b>Sent:</b> Wednesday, 26 June 2019 17:57:58<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br>
<b>Subject:</b> Re: [3dem] (mean Inner potential) Re: 3dem
Digest, Vol 142, Issue 38</font>
<div> </div>
</div>
<div style="background-color:#FFFFFF">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:<br>
<br>
"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<sub>2</sub>O molecules to fulfill this condition."<br>
<br>
Interestingly, Hettler et al 2018, Charging of carbon thin films
in scanning and phase-plate transmission electron microscopy (
<a class="x_moz-txt-link-freetext"
href="https://doi.org/10.1016/j.ultramic.2017.09.009"
moz-do-not-send="true">
https://doi.org/10.1016/j.ultramic.2017.09.009</a> ) 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.<br>
<br>
Vladan<br>
<br>
<div class="x_moz-cite-prefix">On 6/18/19 9:26 AM, Philip Köck
wrote:<br>
</div>
<blockquote type="cite">
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<p style="margin-top:0; margin-bottom:0">Thanks for the
reference.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">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.</p>
<p style="margin-top:0; margin-bottom:0">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.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I wonder if we can
get a comment from someone who knows more.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">All the best,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Philip</p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> 3dem
<a class="x_moz-txt-link-rfc2396E"
href="mailto:3dem-bounces@ncmir.ucsd.edu"
moz-do-not-send="true"><3dem-bounces@ncmir.ucsd.edu></a>
on behalf of Benjamin Himes
<a class="x_moz-txt-link-rfc2396E"
href="mailto:himes.benjamin@gmail.com"
moz-do-not-send="true"><himes.benjamin@gmail.com></a><br>
<b>Sent:</b> Monday, 17 June 2019 20:45:48<br>
<b>To:</b> <a class="x_moz-txt-link-abbreviated"
href="mailto:3dem@ncmir.ucsd.edu" moz-do-not-send="true">
3dem@ncmir.ucsd.edu</a><br>
<b>Subject:</b> [3dem] (mean Inner potential) Re: 3dem
Digest, Vol 142, Issue 38</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div class="x_x_gmail_default" style="font-size:small">Hi
Philip,</div>
<div class="x_x_gmail_default" style="font-size:small"><br>
</div>
<div class="x_x_gmail_default" style="font-size:small">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.)</div>
<div class="x_x_gmail_default" style="font-size:small"><br>
</div>
<div class="x_x_gmail_default" style="font-size:small">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.</div>
<div class="x_x_gmail_default" style="font-size:small"><br>
</div>
<div class="x_x_gmail_default" style="font-size:small">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 :
)</div>
<div class="x_x_gmail_default" style="font-size:small"><br>
</div>
<div class="x_x_gmail_default" style="font-size:small">Please
have a look at this paper where all of the non-Volta
contributions are discussed and also measured.</div>
<div class="x_x_gmail_default" style="font-size:small"><br>
</div>
<div class="x_x_gmail_default" style="font-size:small"><b>"Electron
holography of thin amorphous carbon films:
Measurement of the mean inner potential and a
thickness-independent phase shift"</b></div>
<div class="x_x_gmail_default" style="font-size:small"><b><br>
</b></div>
<div class="x_x_gmail_default" style="font-size:small"><b>doi:
j.ultramic.2005.10.004</b></div>
<div class="x_x_gmail_default" style="font-size:small"><b><br>
</b></div>
<div class="x_x_gmail_default" style="font-size:small">HTH</div>
<div class="x_x_gmail_default" style="font-size:small"><br>
</div>
<div class="x_x_gmail_default" style="font-size:small">Ben</div>
<div class="x_x_gmail_default" style="font-size:small"><br
clear="all">
</div>
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<div dir="ltr">
<div dir="ltr">------------------------<br>
<font size="2" face="Tahoma"
color="black"><span dir="ltr"
style="font-size:10pt"><font
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style="font-size:13px"><font
face="Arial">Benjamin
Himes</font><font
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</font><font face="Arial"><br>
cryoEM methods
development </font><font
face="Arial"><br>
</font><a
href="https://mail.hhmi.org/owa/redir.aspx?C=SbsCefkcbOt75jDyr05lpd3OifVN_utmfvnhZrtXS7Bl2i2eOXXVCA..&URL=http%3a%2f%2fgrigoriefflab.janelia.org%2f"
target="_blank"
moz-do-not-send="true"><font
face="Arial">Grigorieff
lab</font></a><font
face="Arial">, HHMI
Janelia Research Campus</font><font
face="Arial"><br>
</font><font face="Arial"><br>
cryoSTAC development @ </font><a
href="https://mail.hhmi.org/owa/redir.aspx?C=8yDzXj54yTidMevTB7q5m3liEVwqAZ9LxuXQ4iYOVvtl2i2eOXXVCA..&URL=https%3a%2f%2fgithub.com%2fbHimes%2femClarity%2fwiki"
target="_blank"
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face="Arial">emClarity</font></a><font
face="Arial"><br>
<br>
-------------------------</font></span></font></span></font></div>
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<br>
<div class="x_x_gmail_quote">
<div dir="ltr" class="x_x_gmail_attr">On Mon, Jun 17,
2019 at 12:17 PM <<a
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Today's Topics:<br>
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1. mean inner potential of a solid (Philip K?ck)<br>
2. NYC Computational Cryo-EM Summer Workshop<br>
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Message: 1<br>
Date: Mon, 17 Jun 2019 08:27:35 +0000<br>
From: Philip K?ck <<a
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To: "<a href="mailto:3dem@ncmir.ucsd.edu"
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Subject: [3dem] mean inner potential of a solid<br>
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<br>
Hi all.<br>
<br>
I've been wondering what the mean inner electrostatic
potential of a solid (for example the 10 V of carbon)
is actually due to.<br>
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?<br>
<br>
All the best,<br>
<br>
Philip<br>
<br>
<br>
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