Modeling Cooperative Nucleoprotein Assembly through Stochastic Simulation and Mass Photometry Analysis

RAD51 and RPA nucleoproteins play key roles in homologous recombination by dynamically binding and assembling on single-stranded DNA. To investigate their cooperative interactions, we developed a stochastic modeling framework that captures protein binding dynamics and oligomer formation on a DNA lattice. Using simulated data and single-molecule mass photometry measurements, we analyzed polymer distributions and assembly kinetics with custom statistical tools. The model reproduces experimental trends and provides a foundation for extracting kinetic and structural parameters relevant to nucleoprotein filament organization. Our approach links quantitative simulation with experimental observation while withholding specific mechanistic parameters.