We have published a scientific article titled Topological complexity of molecules in theprestigious publication Encyclopedia of Complexity and Systems Science, which provides an authoritative single source for understanding and applying the concepts of complexity theory together with the tools and measures for analyzing complex systems in all fields of science and engineering. This unique work will extend the influence of complexity and system science to a much wider audience than has been possible to date.
The second CHARMM paper was published. CHARMM is a computer program for macromolecular simulations mainly in the biochemistry field, but it is often a suitable tool in the new material research and other fields where the methods of computational chemistry are used to explain natural phenomena. The program is highly versatile and contains a large set of computational tools using force fields on the atomic or coarse grain levels. It is interfaced with several major ab intio quantum program packages so it is well suited to study enzyme reactions mechanisms by QM/MM methods.
Molecular dynamics simulations of cholesterol/sphingomyelin bilayers revealed structural features involved in formation of the liquid-ordered phase. The threshold cholesterol concentration at which the transition from the liquid-disordered phase to the liquid-ordered phase appears is approximately 30 mol %, which is in agreement with the experimental results. Hydrogen bonding was found to be important in the formation of the liquid-ordered phase. Our results suggest that cholesterol/sphingomyelin mixing below critical concentration is entropy driven, while above 30 mol % it is enthalpy-driven.
We have coupled atomistic and continuum descriptions of liquid water via a mesoscopic particle model. The triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. Our multiscale approach is designed for molecular simulations of open domains with relatively large molecules, either in the grand canonical ensemble or under nonequilibrium conditions.
Kinetic analysis of guanine alkylation by aflatoxin B1 exo-8,9-epoxide, the reactive form of the hepatocarcinogen aflatoxin B1, shows the reaction to be more than 2000 times more efficient in DNA than in aqueous solution, that is with free 2'-deoxyguanosine. Thermodynamic analysis reveals AFB1 exo-8,9-epoxide intercalation as the predominant source of the observed DNA catalytic effect. However, the known exo ) endo epoxide stereospecificity of the DNA alkylation is observed even with free deoxyguanosine, as predicted beforehand by our theoretical calculations.