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

TL;DR

This paper reviews recent computational methods for simulating biological phenomena in crowded cellular environments, highlighting new approaches and their potential to enhance understanding of in vivo processes.

Contribution

It revises recent simulation techniques for crowded cellular environments and introduces new methods capable of long-timescale simulations up to 200 microseconds.

Findings

Simulations used protein crowders, inert crowders, and small molecules.

Models of the cytoplasm were simulated.

New methods enable longer simulation times, up to 200 microseconds.

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.