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Pulsed Electric Fields (PEF) is a promising technology for the gentle and energy efficient disruption of microalgae cells such as Chlorella vulgaris. The technology is based on the exposure of cells to a high voltage electric field, which causes the permeabilization of the cell membrane. Due to the dependency of the effective treatment conditions on the specific design of the treatment chamber, it is difficult to compare data obtained in different chambers or at different scales, e.g., lab or pilot scale. This problem can be overcome by the help of numerical simulation since it enables the accessibility to the local treatment conditions (electric field strength, temperature, flow field) inside a treatment chamber. To date, no kinetic models for the cell membrane permeabilization of microalgae are available what makes it difficult to decide if and in what extent local treatment conditions have an impact on the permeabilization. Therefore, a kinetic model for the perforation of microalgae cells of the species Chlorella vulgaris was developed in the present work. The model describes the fraction of perforated cells as a function of the electric field strength, the temperature and the treatment time by using data which were obtained in a milliliter scale batchwise treatment chamber. Thereafter, the model was implemented in a CFD simulation of a pilot-scale continuous treatment chamber with colinear electrode arrangement. The numerical results were compared to experimental measurements of cell permeabilization in a similar continuous treatment chamber. The predicted values and the experimental data agree reasonably well what demonstrates the validity of the proposed model. Therefore, it can be applied to any possible treatment chamber geometry and can be used as a tool for scaling cell permeabilization of microalgae by means of PEF from lab to pilot scale. The present work provides the first contribution showing the applicability of kinetic modeling and numerical simulation for designing PEF processes for the purpose of biorefining microalgae biomass. This can help to develop new processes and to reduce the costs for the development of new treatment chamber designs.