This computational project is composed of two interrelated research areas of interests of the PI: (A) complex soft matter and (B) challenging biomedical problems requiring extensive amounts of computing time. A and B in turn are divided to several subprojects denoted P1-P8. (A) concerns ionic liquids (IL). ILs are notoriously among the most challenging molecular systems to study due to their complex and strong short-range and very long-range interactions, while they are highly heterogeneous with slowly converging liquid structures showing very intricate structural and dynamical correlations. As designable green solvents with numerous applications it is important to understand ILs to predict their properties using modelling and simulations. Projects P1-P3 are devoted to demanding multi-scale simulations also including method and model development to be tested. Projects P4&P5 are about ILs at interfaces and in constraint spaces. Concerning (B), the project P6 is modelling a gene therapy system by designing a non-viral vector of PEI and PEG polymers made stimuli-responsive. P7 is both about development a new constant pH simulation method and applications to study processes behind protein-protein and protein-virus interactions. P8 is about designing therapeutic peptides for SARS-Covid-19 infections.