37 hkoyama@nibb.ac.jp. 38 39 Keywords 40 morphological diversity, mechanics, multi-cellular system, effective potential of cell-41 cell interaction, early embryogenesis 42 43 4 Abstract 44Physical properties of cell-cell interactions have been suggested to be critical for the 45 emergence of diverse three-dimensional morphologies of multicellular organisms. Their 46 direct evaluation in living systems, however, has been difficult due to technical 47 limitations. In this study, we developed a novel framework for analyzing and modeling 48 the physical properties of cell-cell interactions. First, by analogy to molecular and 49 colloidal sciences, cells were assumed to be particles, and the effective forces and 50 potentials of cell-cell interactions were statistically inferred from live imaging data. 51 Next, the physical features of the potentials were analyzed. Finally, computational 52 simulations based on these potentials were performed to test whether these potentials 53 can reproduce the original morphologies. Our results from various systems, including 54 Madin-Darby canine kidney (MDCK) cells, C.elegans early embryos, and mouse 55 blastocysts, suggest that the method can accurately capture the diverse 56 three-dimensional morphologies. Importantly, energy barriers were predicted to exist at 57 the distant regions of the interactions, and this physical property was essential for 58 formation of cavities, tubes, cups, and two-dimensional sheets. Collectively, these 59 structures constitute basic structural units observed during morphogenesis and 60 organogenesis. We propose that effective potentials of cell-cell interactions are 61 5 parameters that can be measured from living organisms, and represent a fundamental 62 principle underlying the emergence of diverse three-dimensional morphogenesis. 63 64 65 66 6 Introduction 67The physical properties of interactions between objects are among the most 68 fundamental parameters of various physical, chemical, and biological phenomena at a 69 wide range of spatial scales in the molecular, colloidal, cellular, and astrophysical 70 sciences. Interactions among particulate matter such as ions, molecules, and colloids are 71 primarily mediated by electromagnetic forces, and the properties of these interactions, 72 including attractive and repulsive forces, substantially affect the dynamics and stability 73 of systems 1,2 . In multi-cellular living systems, various three-dimensional morphologies 74 are observed. The emergence of these diverse morphologies is thought to be primarily 75 dependent on the physical properties of the constituent cells. In particular, mechanical 76 properties of cell-cell interactions are involved in morphogenetic events such as 77 epithelial cell movement and cell sorting [3][4][5][6][7] . However, the physical basis of 78 morphogenesis, which gives rise to a variety of structures, remains to be elucidated, and 79 it is not yet known whether any unifying principle can explain the morphological 80 diversity of organs and tissue...