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This paper presents an integrated approach to energy harvester modelling and performance optimisation where the complete mixed physical-domain energy harvester system (micro generator, voltage booster, storage element and load) can be modelled and optimised in a systematic manner using one simulation platform. We developed an accurate HDL model for the energy harvester and demonstrated its accuracy by validating it experimentally and comparing it with recently reported models. To address the performance loss due to the close mechanical-electrical interaction that takes place in energy harvesters, we proposed a holistic methodology to the energy harvester optimisation based on the HDL model. The effectiveness of employing such an approach has been demonstrated by showing that it is possible to improve vibration-based energy harvester efficiency (energy delivered to load/harvested energy) by 30% through optimising the micro-generator size and the voltage booster circuit components.