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Microscopic mechanics of biomolecules in living cells

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Scientific Modeling and Simulations

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 68))

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Abstract

The exporting of theoretical concepts and modelling methods from physics and mechanics to the world of biomolecules and cell biology is increasing at a fast pace. The role of mechanical forces and stresses in biology and genetics is just starting to be appreciated, with implications going from cell adhesion, migration, division, to DNA transcription and replication, to the mechanochemical transduction and operation of molecular motors, and more. Substantial advances in experimental techniques over the past 10 years allowed to get unprecedented insight into the elasticity and mechanical response of many different proteins, cytoskeletal filaments, nucleic acids, both in vitro and, more recently, directly inside the cell. In a parallel effort, also theoretical models and computational methods are evolving into a rather specialized toolbox. However, several key issues need to be addressed when applying to life sciences the theories and methods typically originating from the fields of condensed matter and solid mechanics. The presence of a solvent and its dielectric properties, the many subtle effects of entropy, the non-equilibrium thermodynamics conditions, the dominating role of weak forces such as Van der Waals dispersion, hydrophobic interactions, and hydrogen bonding, impose a special caution and a thorough consideration, up to possibly rethinking some basic physics concepts. Discussing and trying to elucidate at least some of the above issues is the main aim of the present, partial and non-exhaustive, contribution.

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  1. Institut d’Electronique, Microélectronique et Nanotechnologie, Université des Sciences et Technologies de Lille, Av. Poincaré, BP 60069, 59652, Villeneuve d’Ascq, France

    Fabrizio Cleri

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  1. Fabrizio Cleri
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  1. Department of Nuclear Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA

    Sidney Yip

  2. Lawrence Livermore National Laboratory, University of California, 7000 East Avenue, P.O. Box 808, CA, Livermore, 94551, USA

    Tomás Diaz de la Rubia

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Cleri, F. (2008). Microscopic mechanics of biomolecules in living cells. In: Yip, S., de la Rubia, T.D. (eds) Scientific Modeling and Simulations. Lecture Notes in Computational Science and Engineering, vol 68. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9741-6_18

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