Surface Charges Generalized Born (SCGB) family of the polar solvation energy caclulation methods is a recently developed approach aimed at getting fast numerical solutions of the Poisson Boltzmann equation in linear time (and memory). SCGB combines the bests of the two worlds: the simplicity of Generalized Born models with the sound physics behind exact continuous electrostatics. Does not only SCGB provide accurate solvation energies for realistic systems, the surface charges obtained in the course of the calculation can be compared directly to those found using a boundary-element version of Poisson equation.

Recently we reported calculation of the Born radii. Now we can use SCGB model expressions for the surface charges density to obtain the solvation energies in linear time as well. The results are represented on the Figure below:

SCGB energies of 233 proteins are calculated first directly (in steps, the horizontal horizontal axis) and then compared with the same energies calculated using FFTw (in steps, the data along the vertical axis). Both energies correlate pretty well aside of the extreme solvation energies region. While the nature of such deviation remains unknown and needs to be fully accounted for, the proof of concept calculation shows the method potential in practical calculations

P.O. Fedichev, L.I. Menshikov
(Submitted on 7 Aug 2008 (v1), last revised 20 Dec 2009 (this version, v3))
We develop a series of approximations to calculate free energy of a polar liquid. We show that long range nature of dipole interactions between the molecules leads to para-electric state instability at low temperatures and to a second-order phase transition. We establish the transition temperature, T_{c}, both within mean field and ring diagrams approximation and show that the ferro-electric transition may play an important role explaining a number of peculiar properties of supercooled water, such as weak singularity of dielectric constant as well as to a large extent anomalous density behavior. Finally we discuss the role of fluctuations, shorter range forces and establish connections with phenomenological models of polar liquids.
Comments: 5 pages, 1 eps figure, density anomaly at T=4C analysis added
Subjects: Statistical Mechanics (cond-mat.stat-mech); Soft Condensed Matter (cond-mat.soft)
Cite as: arXiv:0808.0991v3 [cond-mat.stat-mech]

P. O. Fedichev, L.I. Menshikov
(Submitted on 5 Aug 2009 (v1), last revised 14 Dec 2009 (this version, v2))
We apply recently developed phenomenological theory of polar liquids to calculate the repulsive pressure between two hydrophilic membranes at nm-distances. We find that the repulsion does show up in the model and the solution to the problem fits the published experimental data well both qualitatively and quantitatively. Moreover, we find that the repulsion is practically independent on temperature, and thus put some extra weight in favour of the so called hydration over entropic hypothesis for the membranes interactions explanation. The calculation is a good proof of concept example a continuous water model application to non-trivial interactions on -size bodies in water arising from long-range correlations between the water molecules.
Comments: 4 pages, 1 png figure, massive update
Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci)
Cite as: arXiv:0908.0632v2 [cond-mat.soft]

P.O. Fedichev, E.G. Getmantsev, L.I. Men'shikov
(Submitted on 12 Aug 2009 (v1), last revised 9 Dec 2009 (this version, v2))
We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory requirements, is only a few percent wrong for any molecular configurations of arbitrary sizes, gives explicit value for the reaction field potential at any point, provides both the solvation energy and its derivatives suitable for Molecular Dynamics simulations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as solvation energies of molecular complex formation.
Comments: 6 pages, 4 figures, more results, examples and references added
Subjects: Quantitative Methods (q-bio.QM); Chemical Physics (physics.chem-ph)
Cite as: arXiv:0908.1708v2 [q-bio.QM]

The talk "Water as a segnetoelectric, anomalous properties and interactions of molecular sized objects at nm-distances" (in Russian).



The talk was a part of IAChPhys seminar held at the Institute of Molecular Physics, Russian Research Center "Kurchatov Institute". The talk in part mirrored the last year presentation at MIPT (Moscow) and contained all the new stuff we developed over the last year: the nature of phospholipid membranes repulsion at nm-distances, Molecular polarization on a polar liquid interface: the structure of a water surface, The nature of percolation phase transition in films of hydration water around immersed bodies (see publications on polar liquids for more info).