Kinetic model of DNA replication and the looping of semiflexible polymers

Biological systems are a rich source of new problems in physics, and solving them requires ideas from various fields. In this thesis, we focus on the specific biological phenomenon of DNA replication, which is tightly regulated by spatio-temporal "programs" during the cell cycle.;After developing the kinetic model, we show how underlying physical properties of chromatin, in particular its intrinsic stiffness, can explain various long-standing experimental observations. These include synchrony and correlations in the initiation of replication origins, as well as determination of the origin spacings in the absence of sequence requirements in early embryos.;Inspired by a formal analogy between DNA replication and one-dimensional nucleation-and-growth processes, we extend the 1D Kolmogorov-Johnson-Mehl-Avrami (KJMA) model to arbitrary nucleation rates I(t). We then use the KJMA model to extract kinetic parameters from data taken from molecular combing experiments. The analysis developed here can help biologists to understand and compare temporal programs of DNA replication of different organisms from a unified scheme.