Nonlocal electrostatics and Perron's method: Difference between pages

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Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.
'''Perron's method''', also known as the '''method of subharmonic functions''', is a technique originally introduced by Oskar Perron for the solution of the Dirichlet problem for Laplace's equation.<ref>{{Citation | last1=Perron | first1=O. |  title=Eine neue Behandlung der ersten Randwertaufgabe für Δu=0 | publisher=Springer Berlin / Heidelberg | doi=10.1007/BF01192395 | year=1923 | month=12 | journal=Mathematische Zeitschrift| issn=0025-5874 | volume=18 | issue=1 | pages=42–54}}
</ref> The Perron method works by finding the largest subharmonic function with boundary values below the desired values; the "Perron solution" coincides with the actual solution of the Dirichlet problem if the problem is soluble.  


Finding a drug for a specific purpose is without a doubt a very difficult task, and today it is largely a trial and error experimental process. A first screening that could simplify the process would be to automatically detect which molecules will stick to certain proteins. This effect is called ''protein docking''. If a molecule sticks to a protein, it is certainly more likely to affect it. In theory one can numerically compute the electric potential around a protein to see if it matches the corresponding potential generated by the molecule. If done naively, the predicted results do not coincide with the experiments. The underlying reason seems to be that the large molecules are surrounded by liquid, mostly water. Their potential interacts with the ions in the water. The ions change the orientation, which affects the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a more accurate model to predict protein docking.
The Perron method can be used [[viscosity solutions]] whenever a [[comparison principle]] is available and appropriate barriers can be constructed to assure the boundary conditions. The Perron solution is taken to be the largest viscosity subsolution, or the least viscosity supersolution.  


== Links ==
==References==
There is a group in the center for Bioinformatics in Saarland University doing research in this field actively. They have a webside describing the project
{{reflist}}
http://bioinf-www.bioinf.uni-sb.de/projects/solvation.html
 
== References ==
{{reflist|refs=
<ref name="ICH">{{Citation | last1=Ishizuka | first1=R | last2=Chong | first2=S-H | last3=Hirata | first3=F | title=An integral equation theory for inhomogeneous molecular fluids: the reference interaction site model approach. | url=http://www.ncbi.nlm.nih.gov/pubmed/18205507 | publisher=AIP | year=2008 | journal=The Journal of Chemical Physics | volume=128 | issue=3 | pages=034504}}</ref>
<ref name="HBRK">{{Citation | last1=Hildebrandt | first1=A. | last2=Blossey | first2=R. | last3=Rjasanow | first3=S. | last4=Kohlbacher | first4=O. | last5=Lenhof | first5=H.P. | title=Electrostatic potentials of proteins in water: a structured continuum approach | publisher=Oxford Univ Press | year=2007 | journal=Bioinformatics | volume=23 | issue=2 | pages=e99}}</ref>
<ref name="SBRF">{{Citation | last1=Scott | first1=R. | last2=Boland | first2=M. | last3=Rogale | first3=K. | last4=Fernández | first4=A. | title=Continuum equations for dielectric response to macro-molecular assemblies at the nano scale | publisher=IOP Publishing | year=2004}}</ref>
}}
 
 
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Latest revision as of 01:28, 29 January 2012

Perron's method, also known as the method of subharmonic functions, is a technique originally introduced by Oskar Perron for the solution of the Dirichlet problem for Laplace's equation.[1] The Perron method works by finding the largest subharmonic function with boundary values below the desired values; the "Perron solution" coincides with the actual solution of the Dirichlet problem if the problem is soluble.

The Perron method can be used viscosity solutions whenever a comparison principle is available and appropriate barriers can be constructed to assure the boundary conditions. The Perron solution is taken to be the largest viscosity subsolution, or the least viscosity supersolution.

References

  1. Perron, O. (12 1923), "Eine neue Behandlung der ersten Randwertaufgabe für Δu=0", Mathematische Zeitschrift (Springer Berlin / Heidelberg) 18 (1): 42–54, doi:10.1007/BF01192395, ISSN 0025-5874