John Jack | Searcharxiv

arXiv2009

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells.

cs.FL↗

arXiv2007

Modeling the effects of HIV-1 virions and proteins on Fas-induced apoptosis of infected cells

We report a first in modeling and simulation of the effects of the HIV proteins on the (caspase dependent) apoptotic pathway in infected cells. This work is novel and is an extension on the recent reports and clarifications on the FAS apoptotic pathway from the literature. We have gathered most of the reaction rates and initial conditions from the literature, the rest of the constants have been computed by fitting our model to the experimental results reported. Using the model obtained we have then run the simulations for the infected memory T cells, called also latent T cells, which, at the moment, represent the major obstacle to finding a cure for HIV. We can now report that the infected latent T cells have an estimated lifetime of about 42 hours from the moment they are re-activated. As far as we know this is the first result of this type obtained for the infected memory T cells.

q-bio.MN↗