Biophysical Reviews

, Volume 9, Issue 6, pp 941–958 | Cite as

Molecular simulations of cellular processes

  • Fabio TrovatoEmail author
  • Giordano Fumagalli


It is, nowadays, possible to simulate biological processes in conditions that mimic the different cellular compartments. Several groups have performed these calculations using molecular models that vary in performance and accuracy. In many cases, the atomistic degrees of freedom have been eliminated, sacrificing both structural complexity and chemical specificity to be able to explore slow processes. In this review, we will discuss the insights gained from computer simulations on macromolecule diffusion, nuclear body formation, and processes involving the genetic material inside cell-mimicking spaces. We will also discuss the challenges to generate new models suitable for the simulations of biological processes on a cell scale and for cell-cycle-long times, including non-equilibrium events such as the co-translational folding, misfolding, and aggregation of proteins. A prominent role will be played by the wise choice of the structural simplifications and, simultaneously, of a relatively complex energetic description. These challenging tasks will rely on the integration of experimental and computational methods, achieved through the application of efficient algorithms.

Graphical abstract


Macromolecular crowding Coarse-graining Molecular dynamics Stochastic processes Diffusion in the cytoplasm Sub-diffusion Nuclear bodies Genetic material Facilitated diffusion Soft interactions Hydrodynamic interactions Integrative modeling 


Compliance with ethical standards

Conflict of interest

Fabio Trovato declares that he has no conflict of interest. Giordano Fumagalli declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Department of Mathematics and Computer ScienceFreie Universität BerlinBerlinGermany
  2. 2.Nephrology and Dialysis UnitUSL Toscana Nord OvestLido di CamaioreItaly

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