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The ideas of complexity are increasingly becoming an integral part in understanding natural and social sciences. Previous research indicates that involvement with modeling scientific phenomena and complex systems can play a powerful role in science learning. Some researchers argue with this view indicating that models and modeling do not contribute to understanding complexity concepts, since these increase the cognitive load on students. This study will investigate the effect of different modes of involvement in exploring scientific phenomena using computer modeling tools, on students' understanding of complexity concepts. Quantitative and qualitative methods are used to report about 121 freshmen students that engaged in participatory simulations about complex phenomena, showing emergent, self organized and decentralized patterns. Results show that Learning-by-Modeling (LbM) plays a major role in students' concept formation about complexity concepts.