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Virtual cell modeling aims to simulate cellular responses to drug perturbations in silico, but existing flow-matching models optimize only pixel-level reconstruction and can produce biologically implausible outputs like nuclei outside cytoplasm. CellFluxRL addresses this by post-training the state-of-the-art CellFlux model with reinforcement learning, using seven manually designed reward functions spanning biological function (mode of action), structural validity (nuclear containment), and morphological statistics (size/count). The approach reveals a systematic framework for enforcing physical constraints through differentiable optimization, achieving consistent improvements across all biological metrics while maintaining image quality.