A continuum model of mechanosensation based on contractility kit assembly.
Dolgitzer, D., Plaza-Rodriguez, A.I., Iglesias, M.A., Jacob, M.A.C. , Todd, B.A., Robinson, D., Iglesias, P.
Biophys J. 2024 Nov 8:S0006-3495(24)00708-2.
PUBMED:39521955
https://doi.org/10.1016/j.bpj.2024.10.020
VCell BioModels referenced in the publication
user:Dolgitzer
biomodel name: Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly
2024-07-22-24. VCell and COPASI teams run 25th Annual Workshop on Computational Cell Biology. Nine students (one could not attend due to flights being cancelled) from Arkansas, Connecticut, New York, Ohio, Texas and Viginia worked with instructors for 3 days, developing their computational models. Thanks to NIH for the funding!
Multi-condensate state as a functional strategy to optimize the cell signaling output.
Chattaraj, A., & Shakhnovich, E. I.
Nat Commun. 2024 Jul 25;15(1):6268.
PUBMED:39054333
https://www.nature.com/articles/s41467-024-50489-5
VCell BioModels referenced in the publication
user:Ani
biomodel name: AC_public_OneCondensate_ARP_revised
Comparative Investigation of the Mechanisms of Calcium Response in Human and Murine Spermatozoa.
Korobkina, J. D., Panteleev, M. A., & Sveshnikova, A. N.
Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology, 18(2), 110-126.
https://link.springer.com/article/10.1134/S1990747824700132
VCell BioModels referenced in the publication
user:Juliajessica
biomodel name: MouseSpermCalcium
Reaction-diffusion modeling provides insights into biophysical carbon concentrating mechanisms in land plants.
Kaste, J. A., Walker, B. J., & Shachar-Hill, Y.
Plant Physiol. 2024 Jun 10:kiae324.
PUBMED:38857179
doi: 10.1093/plphys/kiae324
2024-06-10. The team of researchers from Michigan State University used reaction-diffusion modeling with VCell to provide insights into biophysical carbon concentrating mechanisms in land plants.
Kaste, J. A., Walker, B. J., & Shachar-Hill, Y. (2024). Reaction-diffusion modeling provides insights into biophysical carbon concentrating mechanisms in land plants. Plant Physiology, kiae324.
https://pubmed.ncbi.nlm.nih.gov/38857179/
2024-05-14. The team of researchers from Australia and Johns Hopkins University used VCell to design and simulate a model explaining the formation of endocytic nanoclusters driven by distinct recruitment of Dynamin1 long- and short-tail isoforms.
Jiang, A., Kudo, K., Gormal, R.S., Ellis, S., Guo, S., Wallis, T.P., Longfield, S.F., Robinson, P.J., Johnson, M.E., Joensuu, M. and Meunier, F.A., 2024. Dynamin1 long-and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters. Nature Communications, 15(1), p.4060.
https://pubmed.ncbi.nlm.nih.gov/38017688/ […]
Dynamin1 long-and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters.
Jiang, A., Kudo, K., Gormal, R.S., Ellis, S., Guo, S., Wallis, T.P., Longfield, S.F., Robinson, P.J., Johnson, M.E., Joensuu, M. and Meunier, F.A..
Nature Communications. 2024 May 14;15(1):4060.
PUBMED:38744819
doi: 10.1038/s41467-024-47677-8
VCell BioModels referenced in the publication
user:mejohnson81
biomodel name: DiffuseToCluster_WCoopDense
biomodel name: DiffuseToCluster_WithCoop
2024-04-10. Michael Blinov and Ion Moraru presented VCell tutorial at HARMONY 2024 at University College London. Other topics discussed include interoperability of multiple standards like SBML, SED-ML and COMBINE archive supported by VCell.
VCell, COPASI and SpringSalad were taught and used for projects at the 25th Annual Computational Cell Biology (CCB) workshop that took place online February 26-28th. The invited talks were given by Yulia Timofeeva (University of Warwick), James P Sluka (Indiana University) and Kevin Janes (University of Virginia). Sixteen participants were selected to work with VCell and COPASI instructors on their projects, and eight gave presentations on their projects at the Modeling Symposium.
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