Modelling transcriptional silencing and its coupling to 3D genome organisation.

Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation transcriptional activators has been extensively investigated, gene silencing remains understudied, especially by modelling. This study employs 3D simulations to study the biophysics of a chromatin fibre where active transcription factors compete with repressors for binding to transcription units along the fibre, and investigates how different silencing mechanisms affect 3D chromatin structure and transcription.

Oscillation in the SIRS model.

We study the SIRS epidemic model, both analytically and on a square lattice. The analytic model has two stable solutions, post outbreak/epidemic (no infected, I=0) and the endemic state (constant number of infected: I>0). When the model is implemented with noise, or on a lattice, a third state is possible, featuring regular oscillations.

Equilibrium phases and phase transitions in multicritical magnetic polymers.

Magnetic polymers are examples of composite soft materials in which the competition between the large configurational entropy of the soft substrate (polymer) and the magnetic interaction may give rise to rich equilibrium phase diagrams as well as non-standard critical phenomena. Here, we study a self-avoiding walk model decorated by Ising spins of value 0 and ±1 that interact according to a Blume-Emery-Griffith-like Hamiltonian. By using mean-field approximations and Monte Carlo simulations, we report the existence of three distinct equilibrium phases: swollen disordered, compact ordered, and compact disordered.

To promote network connectivity in colloidal rod suspensions, end with a tip.

Colloidal gels formed from patchy rods provide a promising platform to design novel functional materials and formulations. Yet, the case for localized interactions at the rod tips remains relatively unexplored. Here we probe the structure and dynamics of such systems by means of coarse-grained computer simulations, and show that the emerging tipped gel networks are fundamentally different to uniform ones.

Formation of Topological Bigels in Mixtures of Colloidal Rings and Polymers.

We study a spherically confined mixture of polymers and colloidal rings. Unlike in standard colloid-polymer mixtures, the polymers interact topologically with the rings by threading them. We find that, above a critical value of the ring radius, threading yields a topological transition from a fluid to a gel-like phase characterized by a space-spanning network of interlocked polymers and rings, which we refer to as a bicomponent gel, or bigel.