Exploring the theoretical foundation of molecular assembly: current status and opportunities

Molecular assembly (MA) is an essential approach to create novel substances and new functional materials beyond molecules. Improving the controllability of MA processes and the functionality of assemblies is the core target in this field. However, due to the limitation of methods and theories for complex MA systems, most of current researches are based on the “black box” paradigm, which can mostly focus on the initial and final state of MA. Such a paradigm has become a bottleneck that restricts the development of MA. Here, we review the current theoretical methods and models of MA systems from the molecular to subcellcular level. We try to measure the complexity of MA research from the dimension of matter, energy and information, and gradually explore the current status, opportunities and breakthrough of the theoretical research of MA: in the dimension of matter, we illuminate that the pathways of MA processes are multi-step, multi-pathway and multi-scale; in the integrated dimension of energy and matter, we demonstrate that MA systems are usually accompanied by the entropy-driven phenomena or the complementation of entropy and enthalpy. We further discuss how the MA systems far from the equilibrium can form an order spatiotemporal dissipated structure; in the integrated dimension of information, energy and matter, we demonstrate how the synergetic processes of positive or negative feedback facilitates the emergence of complex physiological functions of MA systems. To address these challenges in the development of MA theoretical researches, we probably need to establish a larger theoretical framework and synergistically develop the research methods of MA from the three dimensions of matter, energy and information. It seems to help us to explore its fundamental laws of MA comprehensively, then establish the new theory and promote the development of assisting methods with high efficiency, and finally elevate the complexity and functionality of MA system, which may provide new perspectives and methods for life science and soft matter science.