Condensed Matter Theory

Abstract:

We introduce oxNA, a new model for the simulation of DNA–RNA hybrids that is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA–RNA hydrogen bonding interaction, we fit the model’s thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model’s applicability, we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.

Abstract:

It is a matter of current debate whether the gate-tunable superconductivity in twisted bilayer graphene is phonon-mediated or arises from electron-electron interactions. The recent observation of the strong coupling of electrons to so-called K-phonon modes in angle-resolved photoemission spectroscopy experiments has resuscitated early proposals that K-phonons drive superconductivity. We show that the bandwidth-enhancing effect of interactions drastically weakens both the intrinsic susceptibility towards pairing as well as the screening of Coulomb repulsion that is essential for the phonon attraction to dominate at low temperature. This rules out purely K-phonon-mediated superconductivity with the observed transition temperature of ∼1 K. We conclude that the unflattening of bands by Coulomb interactions challenges any purely phonon-driven pairing mechanism, and must be addressed by a successful theory of superconductivity in moiré graphene

Abstract:

The presence of long-lived oscillations in the expectation values of local observables after quantum quenches has recently attracted considerable attention in relation to weak ergodicity breaking. Here, we focus on an alternative mechanism that gives rise to such oscillations in a class of systems that support kinematically protected gapped excitations at zero temperature. An open question in this context is whether such oscillations will ultimately decay. We provide strong support for the decay hypothesis by considering spin models that can be mapped to systems of weakly interacting fermions, which in turn are amenable to an analysis by standard methods based on the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy. We find that there is a time scale beyond which the oscillations start to decay that grows as the strength of the quench is made small.

Abstract:

Cell sorting, the segregation of cells with different properties into distinct domains, is a key phenomenon in biological processes such as embryogenesis. We use a phase-field model of a confluent cell layer to study the role of activity in cell sorting. We find that a mixture of cells with extensile or contractile dipolar activity, and which are identical apart from their activity, quickly sort into small, elongated patches which then grow slowly in time. We interpret the sorting as driven by the different diffusivity of the extensile and contractile cells, mirroring the ordering of Brownian particles connected to different hot and cold thermostats. We check that the free energy is not changed by either partial or complete sorting, thus confirming that activity can be responsible for the ordering even in the absence of thermodynamic mechanisms.