This thesis proposes an innovative approach for the comprehensive and structured modeling of online open collaboration. By conceptualizing individuals, teams, and collaborative environments as social atoms, molecules, and mediums respectively, it employs concepts and tools from physics and chemistry to illustrate human interactions. This research introduces an analogical framework that retains the fundamental principles of select traditional natural science instruments while also integrating more probabilistic and dynamic elements to address the disparities between the physical and social systems. It applies and adapts two tools and one concept from physics and chemistry - namely the collaborative periodic table (inspired by the periodic table of elements), the probabilistic collaboration equation (based on the reaction equation), and the social superposition state (derived from quantum physics). These tools and concepts are employed to study open collaboration on GitHub, leveraging a dataset sourced from the GitHub open-source community that includes collaborative data from hundreds of thousands of users. The findings of this study not only provide deeper insights into the behavior patterns of open collaboration participants but also illuminate a bottom-up strategy for future sociophysical pursuits.