Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

Computational modeling has become increasingly important in biophysics, but the great challenge in numerical simulations due to the multiscale feature of biological systems limits the capability of modeling in making discoveries in biology. Innovative multiscale modeling approaches are desired to bridge different scales from nucleic acids and proteins to cells and tissues. Although all-atom molecular dynamics has been successfully applied in many microscale biological processes such as protein folding, it is still prohibitively expensive for studying macroscale problems such as biophysics of cells and tissues. On the other hand, continuum-based modeling has become a mature procedure for analysis and design in many engineering fields, but new insights for biological systems in the microscale are limited when molecular details are missing in continuum-based modeling. In this context, mesoscale modeling approaches such as Langevin dynamics, lattice Boltzmann method, and dissipative particle dynamics have become popular by simultaneously incorporating molecular interactions and long-range hydrodynamic interactions, providing insights to properties on longer time and length scales than molecular dynamics. In this review, we summarized several mesoscale simulation approaches for studying two model systems in biophysics: red blood cells (RBCs) and deoxyribonucleic acids (DNAs). The RBC is a model system for cell mechanics and biological membranes, while the DNA represents a model system for biopolymers. We introduced the motivations of studying these problems and presented the key features of different mesoscale methods. Furthermore, we described the latest progresses in these methods and highlighted the major findings for modeling RBCs and DNAs. Finally, we also discussed the challenges and potential issues of different approaches.