Frozen-density embedding theory with average solvent charge densities from explicit atomistic simulations.

Besides molecular electron densities obtained within the Born-Oppenheimer approximation (ρB(r)) to represent the environment, the ensemble averaged density (〈ρB〉(r)) is also admissible in frozen-density embedding theory (FDET) [Wesolowski, Phys. Rev. A, 2008, 77, 11444].

A maximum likelihood approach to generate hypotheses on the evolution and historical biogeography in the Lower Volga Valley regions (southwest Russia).

The evolution of the diverse flora in the Lower Volga Valley (LVV) (southwest Russia) is complex due to the composite geomorphology and tectonic history of the Caspian Sea and adjacent areas. In the absence of phylogenetic studies and temporal information, we implemented a maximum likelihood (ML) approach and stochastic character mapping reconstruction aiming at recovering historical signals from species occurrence data. A taxon-area matrix of 13 floristic areas and 1018 extant species was constructed and analyzed with RAxML and Mesquite.

Pushing the frontiers of first-principles based computer simulations of chemical and biological systems.

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these methods to larger systems, longer time scales and increased accuracies. Their versatility is illustrated with a diverse range of applications, ranging from the determination of the gas phase structure of the cyclic decapeptide gramicidin S, to the study of G protein coupled receptors, the interaction of transition metal based anti-cancer agents with protein targets, the mechanism of action of DNA repair enzymes, the role of metal ions in neurodegenerative diseases and the computational design of dye-sensitized solar cells.

Mixed quantum mechanical/molecular mechanical (QM/MM) simulations of adiabatic and nonadiabatic ultrafast phenomena.

A thorough theoretical description of ultrafast phenomena that occur in complex systems constitutes a formidable challenge. It not only necessitates the use of quantum mechanical methods that can describe ground and possibly even electronically excited state potential energy surfaces with sufficient accuracy but also calls for approaches that can take the real-time dynamics of a system and the coupling between its electronic and nuclear degrees of freedom fully into account. Over the last years, our group has been active in the development of mixed quantum mechanical/molecular mechanical (QM/MM) methods for the in situ simulations of dynamical phenomena in ground and excited states within the adiabatic (Born-Oppenheimer) approximation.

Nonadiabatic coupling vectors for excited states within time-dependent density functional theory in the Tamm-Dancoff approximation and beyond.

Recently, we have proposed a scheme for the calculation of nonadiabatic couplings and nonadiabatic coupling vectors within linear response time-dependent density functional theory using a set of auxiliary many-electron wavefunctions [I. Tavernelli, E. Tapavicza, and U.