Various biochemical and biophysical processes, occurring on multiple time and length scales, can nowadays be studied using specialized software packages on supercomputer clusters. The complexity of such simulations often requires application of different methods in a single study and strong computational expertise. We have developed VIKING, a convenient web platform for carrying out multiscale computations on supercomputers. VIKING allows combining methods in standardized workflows, making complex simulations accessible to a broader biochemical and biophysical society.

The cytochrome bc complex is the third protein complex in the electron transport chain of mitochondria or photosynthetic bacteria, and it serves to create an electrochemical gradient across a cellular membrane, which is used to drive ATP synthesis. The purpose of this study is to investigate interactions involving an occasionally trapped oxygen molecule (O) at the so-called Q site of the bc complex, which is one of the central active sites of the protein complex, where redox reactions are expected to occur. The investigation focuses on revealing the possibility of the oxygen molecule to influence the normal operation of the bc complex and acquire an extra electron, thus becoming superoxide, a biologically toxic free radical. The process is modeled by applying quantum chemical calculations to previously performed classical molecular dynamics simulations. Investigations reveal several spontaneous charge transfer modes from amino acid residues and cofactors at the Q-site to the trapped O molecule.

Ion-beam cancer therapy has become increasingly favored worldwide in treatment of certain types of cancer over the last decade. Whereas the clinical effects of the therapy are well documented, the understanding of the underlying physical mechanisms is somewhat incomplete. The problem arises due to the multiscale nature of the effects involved in ion-beam cancer therapy, as the effects range from quantum-mechanical to macroscopic scales. The present study investigates the production of free electrons in the vicinity of the Bragg peak through quantum-mechanical simulations of the collision between a C 4+ ion with a cytosine-guanine nucleotide pair taken from a DNA double helix. Time-dependent density-functional theory was employed using the OCTOPUS 6.0 software. The results show that such a collision triggers the release of a large amount of electrons into the cellular environment, as only a fraction is captured by the C 4+ ion. Furthermore, it is demonstrated that the impact angle and projectile kinetic energy have much more influence on the number of ejected electrons than the impact parameter.

The presented investigation aims to establish a foundation for the study of ion beam cancer therapy employing time-dependent density functional theory for calculating collision cross-sections and energies of secondary electrons produced by a charged ion impacting on a biological target of arbitrary size and shape. The obtained collision cross-sections compare well to values obtained using the popular PASS code, which relies on the modified Bohr theory. Furthermore, we demonstrate that the differential cross-sections obtained in this study seem to be affected by post-collision electron recapture processes occurring inside the target.