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Development of a Virtual Cell Model to Predict Cell Response to Substrate Topography.
Heydari T, Heidari M, Mashinchian O, Wojcik M, Xu K, Dalby MJ, Mahmoudi M, Ejtehadi MR. Heydari T, et al. ACS Nano. 2017 Sep 26;11(9):9084-9092. doi: 10.1021/acsnano.7b03732. Epub 2017 Jul 30. ACS Nano. 2017. PMID: 28742318 Free article.
Here, we developed a unifying computational framework to create a multicomponent cell model, called the "virtual cell model" that has the capability to predict changes in whole cell and cell nucleus characteristics (in terms …
Here, we developed a unifying computational framework to create a multicomponent cell model, called the "virtual …
cellPACK: a virtual mesoscope to model and visualize structural systems biology.
Johnson GT, Autin L, Al-Alusi M, Goodsell DS, Sanner MF, Olson AJ. Johnson GT, et al. Nat Methods. 2015 Jan;12(1):85-91. doi: 10.1038/nmeth.3204. Epub 2014 Dec 1. Nat Methods. 2015. PMID: 25437435 Free PMC article.
cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analy …
cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and c …
Multiscale mechanobiology of de novo bone generation, remodeling and adaptation of autograft in a common ovine femur model.
Knothe Tate ML, Dolejs S, McBride SH, Matthew Miller R, Knothe UR. Knothe Tate ML, et al. J Mech Behav Biomed Mater. 2011 Aug;4(6):829-40. doi: 10.1016/j.jmbbm.2011.03.009. Epub 2011 Mar 16. J Mech Behav Biomed Mater. 2011. PMID: 21616464 Free PMC article. Review.
To address this, here we integrate insights from our previously published studies describing the mechanobiology on both de novo bone generation and graft healing in a common ovine femoral defect model. ...Furthermore, these insights provide a foundation to create …
To address this, here we integrate insights from our previously published studies describing the mechanobiology on both de novo bone …
Predicting Nano-Bio Interactions by Integrating Nanoparticle Libraries and Quantitative Nanostructure Activity Relationship Modeling.
Wang W, Sedykh A, Sun H, Zhao L, Russo DP, Zhou H, Yan B, Zhu H. Wang W, et al. ACS Nano. 2017 Dec 26;11(12):12641-12649. doi: 10.1021/acsnano.7b07093. Epub 2017 Nov 22. ACS Nano. 2017. PMID: 29149552 Free PMC article.
The resulting models were then used to predict and design nanoparticles with desired bioactivities. The experimental testing results of the designed nanoparticles were consistent with the model predictions. These findings demonstrate that rational design appr …
The resulting models were then used to predict and design nanoparticles with desired bioactivities. The experimental testing r …
Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria.
Gao M, Nakajima An D, Skolnick J. Gao M, et al. Elife. 2022 Dec 28;11:e82885. doi: 10.7554/eLife.82885. Elife. 2022. PMID: 36576775 Free PMC article.
The journey of an OMP from the center of the cell where it is made to the outer membrane is complicated. First, the OMP needs to pass through the cell's inner membrane. ...s work inspires new hypotheses about the mechanisms through which OMPs are transported to the …
The journey of an OMP from the center of the cell where it is made to the outer membrane is complicated. First, the OMP needs to pass …
Evolution of taxis responses in virtual bacteria: non-adaptive dynamics.
Goldstein RA, Soyer OS. Goldstein RA, et al. PLoS Comput Biol. 2008 May 23;4(5):e1000084. doi: 10.1371/journal.pcbi.1000084. PLoS Comput Biol. 2008. PMID: 18483577 Free PMC article.
This approach starts with a population of virtual bacteria that move in a virtual environment based on the dynamics of the simple biochemical pathways they harbour. ...We find that a certain dynamics evolves consistently under different model assumptio …
This approach starts with a population of virtual bacteria that move in a virtual environment based on the dynamics of …