2023-08-28. VCell collaborator Jason Haugh from North Carolina State University published a manuscript where experiments and VCell modeling demonstrated that G-actin diffusion is insufficient to achieve F-actin assembly in fast-treadmilling protrusions.
Appalabhotla, R., Butler, M.T., Bear, J.E. and Haugh, J.M. G-actin diffusion is insufficient to achieve F-actin assembly in fast-treadmilling protrusions. Biophys J. 2023 Aug 28;S0006-3495(23)00553-2. doi: 10.1016/j.bpj.2023.08.022. https://pubmed.ncbi.nlm.nih.gov/37644720/
See 5 biomodels and 14 mathmodels at https://vcell.org/appalabhotla-2023

Prof Margaret Johnson from John Hopkins University and Michael Blinov are hosting the Special Interest Subgroup session on Biophysical Modeling of the Cell at Cell Bio 2023 – an ASCB/EMBO (https://www.ascb.org/cellbio2023/) meeting in Boston, MA, December 2-6. The session will take place on Wednesday, December 6, 8:30 AM – 11:00 AM (https://www.ascb.org/cellbio2023/program/subgroups/).

2023-06-28. The  24th Annual Computational Cell Biology (CCB) workshop took place at the Center for Cell Analysis and Modeling (CCAM) on June 26-28th. 11 participants from all over the US (from Maryland to Illinois) came to Farmington to work on developing their modeling projects using VCell and COPASI software tools, designed and maintained at CCAM. The students were helped by a CCAM team consisting of Michael Blinov, Ann Cowan, Leslie Loew, Pedro Mendes, Ion Moraru, Kelvin Peterson, Jim Schaff, Nathan Schaumburger, and Boris Slepchenko.

2023-05-04. The interdisciplinary team consisting of CCAM modelers Drs. Blinov and Moraru and researchers from the Center on Aging Drs. Kuchel and Kositsawat, together with former undergrad students Schaumburger and Pally published a manuscript theoretically explaining the bistability of clinical outcomes: the likelihood of an individual remaining mobile over time either increases to almost 100% or decreases to almost zero. The VCell software was extensively used for parameter scans and fitting.

Schaumburger, N., Pally, J., Moraru, I. I., Kositsawat, J., Kuchel, G. A., & Blinov, M. L. (2023). Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes. Frontiers in Network Physiology, 3, 1079070.

https://www.frontiersin.org/articles/10.3389/fnetp.2023.1079070/full

2023-05-01. VCell 7.5 has been released. It features parameter estimation from the latest version of COPASI; model exchange via multiple standards, including, SBML, SEDML and OMEX; parameter scans in local client simulations; and hardening of unit handling including automatic unit transformations. Full specs available https://vcell.org/run-vcell-software.

2023-03-01.VCell was used to demonstrate that expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide. Find links to the paper on our published models page.

2023-02-20. The VCell team presented a poster at the Biophysical Society Annual Meeting in San Diego (https://www.biophysics.org/2023meeting#/).

2023-02-13. The 24th Annual Computational Cell Biology workshop was sponsored by Cell Analysis and Modeling Center at the UConn Health on February 13-15th. It was an intense online event designed to enable cell biologists and biphysicists to develop mathematical models of their experimental systems.Keynote speakers included Jason Haugh, Pablo Iglesias and Ursula Kummer.

SpringSaLaD software was used to model contractility kits, complexes in the cytoplasm of Dictyostelium cells consisting of myosin II and cortexillin I in the publication, Particle-based model of mechanosensory contractility kit assembly.

2022-09-28.VCell and COPASI were used together to study the kinetic behavior of antibiotic biosynthesis. The paper describes the same model designed in both COPASI (for parameter estimations) and VCell (for simulation reaction curves). Find links to the paper on our published models page.

2022-09-12. The VCell team will give a tutorial at the 21st International Conference on Systems Biology – the premier meeting on systems studies in biology, human evolution disease and planetary health. The meeting will take place in Berlin, Germany on October 8th-12th. The tutorial will be on October 9th at 12:30pm local time (https://www.icsb2022.berlin/satellite-events).

2022-05-25. The 23rd Computational Cell Biology workshop took place at R. D. Berlin Center for Cell Analysis and Modeling (CCAM) on May 23-25th. For 3 days more than 40 online participants learnt how to use VCell, COPASI and SpringSalad software tools for modeling of cell biology systems. 16 participants participated in the “project track”, working individually with CCAM staff on developing their modeling projects.

2022-04-14. A new compartmental VCell Model was used to explore nutrients transporter network in plants. Find links to the paper and BioModel on our published models page.

2022-02-10. VCell was used to analyze structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis in a new Nature paper (available on our published models page).

2021-12-8. A discussion of how to use a VCell MathModel to teach mathematical modeling in cellular systems has been published by the Carlier lab with contributions from Cowan and Loew. Find links to the paper and public VCell models on our published models page.

2021-11-24. A new VCell Model of actin dynamics was used to explore how phsophorylation of cofilin is involved in transmission of signals to the transcriptional machinery by depleting of nuclear G-actin. Find links to the paper on our published models page.

2021-10-05. A new publication by Martin et al. describes a VCell model of the lifecyle of LINE-1 RNA elements in order to understand their activation and propagation. Find links to the paper and public VCell models on our published models page.

2021-10-04. VCell was used to validate a new model for cAMP metabolism used to explore cAMP signaling in pulmonary microvascular endothelial cells. Find links to the paper and on our published models page.

2021-09-22. A new VCell model from the Carlier lab is combined with experiments to explore regulation of ion transport in the kidney proximal tubule. Find links to the paper and public VCell models on our published models page.

2021-09-10. VCell MathModels were used to explore how FAK activation influences YAP/TAZ translocation in a new publication by Eroume et al. in Biophysical Journal. Find links to the paper and public VCell models on our published models page.