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Last (?) paper available

wpmaster — Sun, 16 May 2010 20:41:42 +0000

The (most probably last) computational chemistry/modelling paper where I am involved is available now from the website of the American Chemical Society. It concerns the simulations of nucleation and freezing of surface contaminated water. You can use this direct link to access it or go through the journal articles section of this website (available in sidebar as well).

This is bringing the total (body) count to 23… :-D

Additional paper… or two :)

wpmaster — Sun, 10 Jan 2010 22:10:39 +0000

… bringing the total count to 21 – molecular dynamics study of the ion specific effects of sodium and potassium cations on the catalytic activity of the HIV-protease. The paper was published in Phys. Chem. Chem. Phys. and is available here.

The ‘Journal articles’ section contains the reference of the new article.

updated 15.01.2010 – another paper is now available online – “Ionic force field optimization based on single-ion and ion-pair solvation properties” in the Journal of Chemical Physics.

One more paper…

wpmaster — Tue, 20 Oct 2009 17:06:23 +0000

Results of my main project carried out at the University of Regensburg have finally been published, increasing the number of my papers to 20. The ‘Journal articles’ section contains the reference of the new article.

The paper describes our combined molecular dynamics / Monte Carlo / HNC study of aqueous electrolytes and a new method of evaluating the thermodynamic properties of such solutions. It also includes a thorough introduction to the HNC theory and further discussion of related topics, so don’t miss it out!

Update: our paper has been selected for the November 1, 2009 issue of the Virtual Journal of Biological Physics Research.

New publication

wpmaster — Fri, 11 Sep 2009 19:52:22 +0000

The ‘Journal articles’ section contains the reference of our new article (most probably one of my last publications in this field) concerning thermodynamically consistent nonpolarizable force fields for molecular simulations. It’s a very nice paper, so don’t forget to check it out!

The related parts of this web presentation were modified accordingly. I just need one more paper to reach the number of 20 – it’s on its way, actually…

pyOZ version 0.3 released

wpmaster — Wed, 12 Aug 2009 13:36:51 +0000

New (and very probably also the last) version (0.3) of my iterative solver of the Ornstein-Zernike equation – pyOZ – has been just released. More information is available on the project website http://pyoz.vrbka.net. You can access the download page directly. The code is also available through the Miscellaneous section.

Update of pyOZ available

wpmaster — Fri, 24 Jul 2009 09:08:41 +0000

Some changes had to be done to the code of the 0.2.1 release of my iterative Ornstein-Zernike equation solver pyOZ, among others to the Newton-Raphson/conjugate gradients solver which still doesn’t work as it should and was thus disabled in this version. I will now concentrate on the CG/NR stuff, so I hopefully will be able to finally come with final and working version (which would most probably be released as 0.3).

Some minor bugs were fixed as well. The handling of Python exceptions is consistent with the new versions of the language now, so you shouldn’t be getting deprecation warnings any more.

Please get the updated version on the pyOZ webpage – you can also access the download page directly.

LaTeX math display problem

wpmaster — Thu, 23 Jul 2009 08:54:37 +0000

Due to an unknown reason, part of the equations published on this website using the LatexRender plugin were damaged – minus signs were partially replaced with “8211;”. I tried to correct all occurences – if you find something that I missed, please let me know.

While doing the changes and trying to find easier way to handle them than changing all occurences per hand (there is no find-and-replace functionality built into Firefox), I found the following nifty plugin – FoxReplace for – for exactly this purpose.

prop_conv utility update available for download

wpmaster — Thu, 16 Jul 2009 15:48:33 +0000

First update (bugfixes, database) of the conversion utility prop_conv (conversion of concentrations, densities and osmotic coefficients of electrolyte solutions) is now available for download.

The code is available through the Miscellaneous section, or directly in the Downloads section of the pyOZ homepage.

Lindau

wpmaster — Tue, 07 Jul 2009 22:09:33 +0000

Minulý týden jsem se zúčastnil 59. setkání s laureáty Nobelovy ceny v Lindau u Bodamského jezera. Fotografie z prohlídky Linday a z výletu lodí na ostrov Mainau jsou v této galerii.

Last week I attended the 59th meeting of Nobel Laureates in Lindau, Lake Constance. Some photos from the city tour and from the boat trip to the Mainau island are available in this gallery.

Letzte Woche habe ich an der 59. Nobelpreisträgertagung in Lindau am Bodensee teilgenommen. Einige Fotos aus der Stadttour und aus dem Ausflug nach Mainau befinden sich in dieser Galerie.

prop_conv utility available for download

wpmaster — Tue, 16 Jun 2009 12:17:16 +0000

My conversion utility prop_conv (conversion of concentrations, densities and osmotic coefficients of electrolyte solutions) is now available for download. Similarly to pyOZ, an iterative solver of the Ornstein-Zernike equation, it is written in Python programming language and released under the BSD license.

Check it out, I hope it will be useful… the code is available through the Miscellaneous section, or directly in the Downloads section of the pyOZ homepage.