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).

Not only our recently introduced surface charges generalized Born (SCGB) models prove to be reasonable in terms of providing solutions to Poisson Boltzmann equation in complicated geometries, such as biomolecules. By getting rid of the standard expression for the solvation energy we are able to formulate SCGB models in terms of a fast algorithm using FFT. The comparison between the Born radii calculated with the help of the fast method and the standard approach is presented below:

The calculation was performed for 2ht7 H1N1 neuromidase protein. The radii match over a broad range of the atoms locations within the protein. The fast method involves an (large) computational overhead due to FFT calculation and breaks even with the usual approach for any molecule exceeding about a thousand atoms.

Up to now, there have been at least two schools of thoughts among those trying to calculate electrostatics part of solvation energies. Half of the folks believe that only an exact solution of the Poisson equation can be better than the solution of the Poisson equation. The other half believes that though the exact solution of the Poisson equation can be obtained, it is too slow and numerically unstable. Here in Quantum we attempt to give Generalized Born models almost infinite credit of trust and push for a direct link between the Poisson equation solutions and Generalized Born models.

The missing link between the two worlds is established by the equation linking the Born radii with the water polarization charges on a molecular interface. If the surface charges are then interpreted on their own, we can calculate the solvation energy using its direct definition, rather than an approximate Born formula. The question is of course if it all works in real life.

To proof the concept we attempted the calculation of the solvation energies for about 580 proteins from our Quantum Pharmaceuticals target list of proteins with available 3D structure. The results obtained with 4 different types of Surface Charges Generalized Born (SCGB) models are compared with the Surface Electrostatics solutions of the Poisson eqaution and are summarized below:

Here the surface electrostatics solvation energies are measured along the horizontal axis, the vertical axis is used for the SCGB solvation energies values. The green dots represent SCGB model with FSBE radii, yellow and red dots are SCGB models with respectively. All the three models give exact solvation energies for an arbitrary system of charges within a shpere and cope fairly well with the realistic proteins. SCGB with standard CFA Born radii (the blue dots) are completely off. Given tremendous speed advantage of SCGB models over SE we end up with an approximation worth to be employed!