Condensed Matter Theory

Abstract:

Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc.

Abstract:

We study the orientational dynamics of heavy silica microrods flowing through a microfluidic channel. Comparing experiments and Brownian dynamics simulations we identify different particle orbits, in particular in-plane tumbling behavior, which cannot be explained by classical Jeffery theory, and we relate this behavior to the rotational diffusion of the rods. By constructing the full, three-dimensional, orientation distribution, we describe the rod trajectories and quantify the persistence of Jeffery orbits using temporal correlation functions of the Jeffery constant. We find that our colloidal rods lose memory of their initial configuration in about a second, corresponding to half a Jeffery period.

Abstract:

I solve a quantum chain whose Hamiltonian is comprised solely of local four-fermi operators by constructing free-fermion raising and lowering operators. The free-fermion operators are both non-local and highly non-linear in the local fermions. This construction yields the complete spectrum of the Hamiltonian and an associated classical transfer matrix. The spatially uniform system is gapless with dynamical critical exponent z=3/2, while staggering the couplings gives a more conventional free-fermion model with an Ising transition. The Hamiltonian is equivalent to that of a spin-1/2 chain with next-nearest-neighbour interactions, and has a supersymmetry generated by a sum of fermion trilinears. The supercharges are part of a large non-abelian symmetry algebra that results in exponentially large degeneracies. The model is integrable for either open or periodic boundary conditions but the free-fermion construction only works for the former, while for the latter the extended symmetry is broken and the degeneracies split.