Functionalized nanoparticles hold great potential as antitumor drug delivery carriers. They can change the pharmacokinetic and pharmacodynamic profile of carried drugs, which increases their therapeutic index. However, despite the advances and potentially great advantages over conventional therapy, only a small number of nanoparticle-based cancer treatments have been approved. The nanosystem design must be complex to overcome all the obstacles in the body. However, this significantly complicates their characterization as well as the prediction of their efficacy. Applying only the experimental approach to solve this problem is time-consuming and expensive. Also, due to the spatial and temporal resolution necessary to investigate some aspects of the physiological effect, an experimental approach, in some cases, is technically not possible.The general goal of this thesis is to develop models of selected nanosystems, and simulate their structure and physiological effect. The two main, specific objectives of this research were: 1. Obtaining useful structural and energetic data of the examined functionalized gold nanoparticles by theoretical calculations; 2. Modeling and simulation of their physiological effect. Models used in this thesis include several temporal and spatial scales (molecule level – molecular dynamics, cell level – stochastic reaction-diffusion reactions, tumor level – agent-based modeling). The general conclusion of this research is that the theoretical approach is complementary to experiments. This way we can obtain detailed information on aspects that are impossible to test experimentally. Simulations of several different levels can link different temporal and spatial resolutions, which can provide a preliminary assessment of the nanosystem’s efficacy in physiological conditions. This approach is much faster and requires much less resources than the purely experimental approach, which can increase efficiency and speed of bringing new nanosystems into clinical practice.