The cytoplasm of a cell is sometimes jestingly called a Soup, since it contains many different ingredients. Indeed there is quite a bit of salt and glutamate, the well known flavour enhancing compoud that is used a lot in asian kitchen but also in broth. Read more here: https://en.wikipedia.org/wiki/Glutamate_flavoring
In order to study the cytoplasm of a cell one can use a variety of experimental biochemistry techniques, but also computer simulations, which is the focus of this page. Here we thererfore provide information and python scripts to run computer simulations using http://www.gromacs.org of (quite) realistic models of the cytoplasm.
The main work is done here by a few scripts, located in the aptly named scripts directory. They are described briefly in the README.md in that directory. The main content of this project is described here:
Leandro Oliveira Bortot, Zahedeh Bashardanesh and David van der Spoel: Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation J. Chem. Inf. Model. 60 pp. 322-331 (2020) https://pubs.acs.org/doi/10.1021/acs.jcim.9b00971
Some related papers from the same group are here:
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Zahadeh Bashardanesh, Johan Elf, Haiyang Zhang and David van der Spoel: Rotational and translational diffusion of proteins as a function of concentration ACS Omega 4 pp. 20654-20664 (2019) http://doi.org/10.1021/acsomega.9b02835
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Zahadeh Bashardanesh and David van der Spoel: Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids J. Phys. Chem. B 122 pp. 8018-8027 (2018) https://pubs.acs.org/doi/10.1021/acs.jpcb.8b05770