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		<id>https://en.formulasearchengine.com/index.php?title=Protein_pKa_calculations&amp;diff=13685</id>
		<title>Protein pKa calculations</title>
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		<updated>2013-01-11T17:23:37Z</updated>

		<summary type="html">&lt;p&gt;132.180.65.129: /* Software For Protein pKa Calculations */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;In [[mathematics]], a &#039;&#039;&#039;totally disconnected group&#039;&#039;&#039; is a [[topological group]] that is [[totally disconnected]]. Such topological groups are necessarily [[Hausdorff space|Hausdorff]].&lt;br /&gt;
&lt;br /&gt;
Interest centres on [[locally compact]] totally disconnected groups (variously referred to as groups of &#039;&#039;&#039;td-type&#039;&#039;&#039;,&amp;lt;ref&amp;gt;{{harvnb|Cartier|1979|loc=§1.1}}&amp;lt;/ref&amp;gt; [[locally profinite group]]s,&amp;lt;ref name=BushnellHenniart&amp;gt;{{harvnb|Bushnell|Henniart|2006|loc=§1.1}}&amp;lt;/ref&amp;gt; &#039;&#039;&#039;t.d. groups&#039;&#039;&#039;&amp;lt;ref&amp;gt;{{harvnb|Borel|Wallach|2000|loc=Chapter X}}&amp;lt;/ref&amp;gt;). The [[compact space|compact]] case has been heavily studied – these are the [[profinite group]]s – but for a long time not much was known about the general case. A theorem of [[David van Dantzig|van Dantzig]] from the 1930s, stating that every such group contains a compact [[open set|open]] [[subgroup]], was all that was known. Then groundbreaking work on this subject was done in 1994, when [[George Willis (mathematician)|George Willis]] showed that every locally compact totally disconnected group contains a so-called &#039;&#039;tidy&#039;&#039; subgroup and a special function on its automorphisms, the &#039;&#039;scale function&#039;&#039;, thereby advancing the knowledge of the local structure. Advances on the &#039;&#039;global structure&#039;&#039; of totally disconnected groups have been obtained in 2011 by Caprace and Monod, with notably a clasification of [[characteristically simple group]]s and of Noetherian groups.&lt;br /&gt;
&lt;br /&gt;
==Locally compact case==&lt;br /&gt;
{{main|Locally profinite group}}&lt;br /&gt;
&lt;br /&gt;
In a locally compact, totally disconnected group, every [[neighbourhood (mathematics)|neighbourhood]] of the identity contains a compact open subgroup. Conversely, if a group is such that the identity has a [[neighbourhood basis]] consisting of compact open subgroups, then it is locally compact and totally disconnected.&amp;lt;ref name=BushnellHenniart/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Tidy subgroups===&lt;br /&gt;
Let &#039;&#039;G&#039;&#039; be a locally compact, totally disconnected group, &#039;&#039;U&#039;&#039; a compact open subgroup of &#039;&#039;G&#039;&#039; and &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; a continuous automorphism of &#039;&#039;G&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
Define:&lt;br /&gt;
   &lt;br /&gt;
:&amp;lt;math&amp;gt;U_{+}=\bigcap_{n\ge 0}\alpha^n(U)&amp;lt;/math&amp;gt;&lt;br /&gt;
:&amp;lt;math&amp;gt;U_{-}=\bigcap_{n\ge 0}\alpha^{-n}(U)&amp;lt;/math&amp;gt;&lt;br /&gt;
:&amp;lt;math&amp;gt;U_{++}=\bigcup_{n\ge 0}\alpha^n(U_{+})&amp;lt;/math&amp;gt;&lt;br /&gt;
:&amp;lt;math&amp;gt;U_{--}=\bigcup_{n\ge 0}\alpha^{-n}(U_{-})&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;U&#039;&#039; is said to be &#039;&#039;&#039;tidy&#039;&#039;&#039; for &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; if and only if &amp;lt;math&amp;gt;U=U_{+}U_{-}=U_{-}U_{+}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;U_{++}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;U_{--}&amp;lt;/math&amp;gt; are closed.&lt;br /&gt;
&lt;br /&gt;
===The scale function===&lt;br /&gt;
The index of &amp;lt;math&amp;gt;\alpha(U_{+})&amp;lt;/math&amp;gt; in &amp;lt;math&amp;gt;U_{+}&amp;lt;/math&amp;gt; is shown to be finite and independent of the &#039;&#039;U&#039;&#039; which is tidy for &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt;. Define the scale function &amp;lt;math&amp;gt;s(\alpha)&amp;lt;/math&amp;gt; as this index. Restriction to [[inner automorphism]]s gives a function on &#039;&#039;G&#039;&#039; with interesting properties. These are in particular:&amp;lt;br&amp;gt;&lt;br /&gt;
Define the function &amp;lt;math&amp;gt;s&amp;lt;/math&amp;gt; on &#039;&#039;G&#039;&#039; by &lt;br /&gt;
&amp;lt;math&amp;gt;s(x):=s(\alpha_{x})&amp;lt;/math&amp;gt;, &lt;br /&gt;
where &amp;lt;math&amp;gt;\alpha_{x}&amp;lt;/math&amp;gt; is the inner automorphism of &amp;lt;math&amp;gt;x&amp;lt;/math&amp;gt; on &#039;&#039;G&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;s&amp;lt;/math&amp;gt; is continuous.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;math&amp;gt;s(x)=1&amp;lt;/math&amp;gt;, whenever x in &#039;&#039;G&#039;&#039; is a compact element.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;math&amp;gt;s(x^n)=s(x)^n&amp;lt;/math&amp;gt; for every integer &amp;lt;math&amp;gt;n&amp;lt;/math&amp;gt;.&amp;lt;br&amp;gt;&lt;br /&gt;
The modular function on &#039;&#039;G&#039;&#039; is given by &amp;lt;math&amp;gt;\Delta(x)=s(x)s(x^{-1})^{-1}&amp;lt;/math&amp;gt;.&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Calculations and applications===&lt;br /&gt;
The scale function was used to prove a conjecture by Hofmann and Mukherja and has been explicitly calculated for [[p-adic]] [[Lie group]]s and linear groups over local skew fields by Helge Glöckner.&lt;br /&gt;
&lt;br /&gt;
==Notes==&lt;br /&gt;
{{reflist}}&lt;br /&gt;
&lt;br /&gt;
==References==&lt;br /&gt;
*{{Citation&lt;br /&gt;
| last=Borel&lt;br /&gt;
| first=Armand&lt;br /&gt;
| author-link=Armand Borel&lt;br /&gt;
| last2=Wallach&lt;br /&gt;
| first2=Nolan&lt;br /&gt;
| author2-link=Nolan Wallach&lt;br /&gt;
| title=Continuous cohomology, discrete subgroups, and representations of reductive groups&lt;br /&gt;
| year=2000&lt;br /&gt;
| edition=Second&lt;br /&gt;
| publisher=[[American Mathematical Society]]&lt;br /&gt;
| location=Providence, Rhode Island&lt;br /&gt;
| series=Mathematical surveys and monographs&lt;br /&gt;
| volume=67&lt;br /&gt;
| isbn=978-0-8218-0851-1&lt;br /&gt;
| mr=1721403&lt;br /&gt;
}}&lt;br /&gt;
*{{Citation | last1=Bushnell | first1=Colin J. | last2=Henniart | first2=Guy | title=The local Langlands conjecture for GL(2) | publisher=[[Springer-Verlag]] | location=Berlin, New York | series=Grundlehren der Mathematischen Wissenschaften [Fundamental Principles of Mathematical Sciences] | isbn=978-3-540-31486-8 | doi=10.1007/3-540-31511-X | mr=2234120 | year=2006 | volume=335}}&lt;br /&gt;
*{{Citation | last1=Caprace | first1=Pierre-Emmanuel | last2=Monod | first2=Nicolas | title=Decomposing locally compact groups into simple pieces | journal=Math. Proc. Cambridge Philos. Soc.  | doi=10.1017/S0305004110000368 | mr=2739075 | year=2011 | volume=150 | pages=97–128}}&lt;br /&gt;
*{{Citation&lt;br /&gt;
| last=Cartier&lt;br /&gt;
| first=Pierre&lt;br /&gt;
| author-link=Pierre Cartier (mathematician)&lt;br /&gt;
| contribution=Representations of &amp;lt;math&amp;gt;\mathfrak{p}&amp;lt;/math&amp;gt;-adic groups: a survey&lt;br /&gt;
| year=1979&lt;br /&gt;
| title=Automorphic Forms, Representations, and L-Functions&lt;br /&gt;
| editor1-last=Borel&lt;br /&gt;
| editor1-first=Armand&lt;br /&gt;
| editor1-link=Armand Borel&lt;br /&gt;
| editor2-last=Casselman&lt;br /&gt;
| editor2-first=William&lt;br /&gt;
| editor2-link=William Casselman (mathematician)&lt;br /&gt;
| url=http://www.ams.org/online_bks/pspum331/pspum331-ptI-7.pdf&lt;br /&gt;
| publisher=[[American Mathematical Society]]&lt;br /&gt;
| publication-place=Providence, Rhode Island&lt;br /&gt;
| series=Proceedings of Symposia in Pure Mathematics&lt;br /&gt;
| volume=33, Part 1&lt;br /&gt;
| pages=111–155&lt;br /&gt;
| isbn=978-0-8218-1435-2&lt;br /&gt;
| mr=0546593&lt;br /&gt;
}}&lt;br /&gt;
*G.A. Willis - [http://gdz.sub.uni-goettingen.de/no_cache/dms/load/img/?IDDOC=167209 The structure of totally disconnected, locally compact groups], [[Mathematische Annalen]] 300, 341-363 (1994)&lt;br /&gt;
&lt;br /&gt;
[[Category:Topological groups]]&lt;/div&gt;</summary>
		<author><name>132.180.65.129</name></author>
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