How I Learned to Stop Worrying and Love Modelling The Biological Mesoscale

Computational Science seminar series

Speaker: Dr Rob Welch, University of Leeds

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Biology has changed. New imaging modalities and a new,multiscale view of biophysics has resulted in a wealth of new information about many biological systems. And yet, computational biophysics is dominated by anachronisms. Molecular dynamics is ubiquitous, and invaluable as a computational microscope - but it cannot be used to study the larger, more complex, longer-lived systems of the biological mesoscale. This talk will explore two coupled attempts to build algorithms and perform simulations at this scale: FFEA (Fluctuating Finite Element Analysis), and KOBRA (KirchOff Biological Rod Algorithm). FFEA attempts to model globular proteins on the continuum scale as viscoelastic finite element meshes. KOBRA attempts to model slender biological objects as elastic rods. Combined, these algorithms have novel applications to large,long-lived systems such as the kinetochore, cytoplasmic dynein, and the SMC complex. This talk will focus on KOBRA, and discuss the model,the parameterisation of KOBRA rods, connections between FFEA meshes and KOBRA rods, its applications to the kinetochore.