Simple Stochastic Simulation in MatLab

Currently I am doing some Teaching Assistance for an advanced Math Biology / Biophysics class. Wanting to point our students towards a simple example of a Gillespie algorithm (check references by Gillespie and textbooks for a description of the algorithm)  in MatLab, I found that google served up one fully developed set of boxed functions … Continue reading Simple Stochastic Simulation in MatLab

Actin and Tropomyosin Isoforms in Smooth Muscle Molecular Mechanics

Yesterday PLoS Computational Biology published one of our studies. At PLoS Computational Biology, they have the nice speciality of a 'friendly abstract', called the Author Summary. It is supposed to be accessible to a general (educated) audience. As PLoS is all open access, I will shamelessly and righteously copy and paste from our paper: Dependent … Continue reading Actin and Tropomyosin Isoforms in Smooth Muscle Molecular Mechanics

Stress-Induced Hypermutation – a Physical Process?

Image: Simulation of colonies seeded from single lesion mutant cells and exposed to different levels of lesion stress. The cellular events in the colony are monitored till detectable colony size or colony extinction are reached. Graph adapted from Lennart Hilbert, 2013, Phys. Biol. 10:026001 doi:10.1088/1478-3975/10/2/026001 Over the past 30 and some years, an increasingly convincing … Continue reading Stress-Induced Hypermutation – a Physical Process?