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Our Recent Publications

Novel ab initio molecular modeling tools for drug discovery

P.O. Fedichev, L.I. Men'shikov, A.A. Vinnik

QUANTUM is new generation tool for biochemical modeling and drug discovery based on ab initio physical approaches. QUANTUM models molecular interactions and consists of three parts: a) vacuum force field for internal molecular interactions, b) the continuous water model, c) thermodynamic expressions for Gibbs energy. QUANTUM molecular modeling software has linear scaling both in speed and memory requirements, and can be used for both fundamental biological research and drug discovery on an industrial scale (download pdf).

Long-Range Order and Interactions of Macroscopic Objects in Polar Liquids

P.O. Fedichev, L.I. Men'shikov

We are developing a phenomenological vector model of polar liquids capable of describing aqueous interactions of macroscopic bodies. It is shown that a strong, long-range and orientationally dependent interaction between macroscopic objects occurs as a result of competition between short-range (hydrogen bonding) and the long-range dipole-dipole interactions of the solvent molecules. Spontaneous polarization of molecular dipoles next to hydrophobic boundaries leads to formation of a globally ordered network of hydrogen-bonded molecules with ferroelectric properties. The proposed vector model naturally describes topological excitations on the solute boundaries and can be used to explain the hydrogen bonds networks and order-disorder phase transitions in the hydration water layer (http://xxx.lanl.gov/abs/cond-mat/0601129).

The Figure above shows a network of water molecules (yellow arrows) surrounding a hydrophobic sphere of a macromolecular size. The cutting plane shows the average water polarization vector value. The Figure illustrates a sophistocated pattern of arrangement of water molecules with non-zero circulation of water polarization around a neutral impurity, exhibiting one of numerous possible vortex configurations.