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arXiv · 2603.26974

Recent advances in modeling and simulation of biological phenomena in crowded and cellular environments

Apoorva Mathur·Vanessa Regina Miranda·Ariane Nunes-Alves
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Abstract

While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise recent computational methods to investigate crowded and cellular environments. Protein crowders, inert crowders and small molecules were used to mimic crowding. Simulations were performed for models of the cytoplasm. New methods were developed to simulate crowded systems, reaching up to 200 microseconds of simulation time. Apart from the challenges, modeling and simulations to investigate biological phenomena inside cells is a growing field, and has a lot of potential to improve our understanding of how such phenomena happen in vivo.

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Apoorva Mathur, Vanessa Regina Miranda, Ariane Nunes-Alves. 2026-03-27. Recent advances in modeling and simulation of biological phenomena in crowded and cellular environments. https://arxiv.org/abs/2603.26974

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