ICMCS Seminar - Geometry, Order Disorder in Chromatin

Title: Geometry, Order Disorder in Chromatin

Abstract: The human genome comprises approximately 3×10⁹ base pairs of DNA, encoding for proteins essential for every function in our lives. The challenge of efficiently storing this genetic material while allowing selective access by transcription machinery is a fundamental task for all living organisms. Evolution has optimised this process across multiple length scales. At the chromatin level, DNA is wrapped around histone proteins to form disk-like nucleosomes, which are connected by accessible linker DNA. While recent advances in experimental imaging have provided valuable insights into chromatin structure under controlled conditions, the precise organisation and dynamics of chromatin in living systems remain poorly understood. Hence, we introduce a polymer physics-informed model and conduct molecular dynamics simulations at the scale of individual nucleosomes. By precisely controlling input parameters, we systematically explore chromatin's physical behavior across various regions of its phase space. We derive an effective contour of the simulated chromatin fibers, enabling the measurement of effective persistence lengths and the calculation of a contour-space nematic order parameter. We further show that introducing quenched noise, in the form of irregular nucleosome positioning, induces a sharp order-to-disorder transition, akin to the effect of increasing temperature. This finding is validated through comparison with experimental data from our collaborators. We also contrast this behavior with the effects of adding quenched noise in the form of irregular linker angles. Finally, we discuss the underlying geometry of chromatin and use this to provide some insight towards explaining the behaviour observed.

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https://ed-ac-uk.zoom.us/j/81211470751

Meeting ID: 812 1147 0751
Passcode: ICMCS123