Condensed Matter Theory

Abstract:

We predict a novel conformational regime for DNA, where denaturation bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. For negative supercoiling, this regime lies between bubble-dominated and plectoneme-dominated phases, and explains the broad transition between the two observed in experiment. Tip bubbles cause localisation of plectonemes within thermodynamically weaker AT-rich sequences, and can greatly suppress plectoneme diffusion by a pinning mechanism. They occur for supercoiling densities and forces that are typically encountered for DNA in vivo, and may be exploited for biological control of genomic processes.

Abstract:

We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.

Abstract:

We report an entropy-driven orientational hopping transition in a magnetically confined colloidal Janus rod. In a magnetic field, the sedimented rod randomly hops between horizontal and vertical states: the latter state comes at a substantial gravitational cost at no reduction of magnetic potential energy. The probability distribution over the angles of the rod shows that the presence of an external magnetic field leads to the emergence of a metastable vertical state separated from the ground state by an effective barrier. This barrier does not come from the potential energy but rather from the vast gain in phase space available to the rod as it approaches the vertical state. The loss of rotational degree of freedom that gives rise to this effect is a statistical mechanical analogue of the phenomenon of gimbal lock from classical mechanics.

Abstract:

Detailed physical and mechanical characterization of the matrix as well as the interphases of polymer matrix composites can lead to a more complete understanding of failure mechanisms in polymer matrix composite (PMC). This study illustrates mechanical damage of polymers in both the bulk, as well as around the interphase region through integrated computation & experimentation approach. We have developed a quantum mechanics-molecular dynamics framework, which has enabled the prediction of bond scission under load, creation of intermittent free radicals, and exploration of the potential energy surface for possible secondary reactions immediately following bond scission. In parallel, we have conducted experiments with epoxy systems with varying molecular weight and cross-linker density at different load conditions to benchmark the simulation findings of the chemical species present on fracture surfaces of the polymer. In order to evaluate experimentally molecular level effects of mechanical load in epoxy-systems, detail characterizations were conducted combing spectroscopy (X-ray photoelectron spectroscopy, FT-Infrared spectroscopy), microscopy (HRTEM, AFM-IR, SEM), X-ray diffraction (SAXS) and mechanical testing (3-point bending). Similarly, the nanoscopic nature of interphases of PMCs in terms of topography, chemical mapping/bonding, fractography, and modulus are also studied in order to find a bridge between nanoscopic, microscopic and macroscopic mechanical properties.