Condensed Matter Theory

Abstract:

Molecular dynamics simulation techniques are used to study the process of aggregation of highly charged stiff polyelectrolytes due to the presence of multivalent salt. The dominant kinetic mode of aggregation is found to be the case of one end of one polyelectrolyte meeting others at right angles, and the kinetic pathway to bundle formation is found to be similar to that of flocculation dynamics of colloids as described by Smoluchowski. The aggregation process is found to favor the formation of finite bundles of 10-11 filaments at long times. Comparing the distribution of the cluster sizes with the Smoluchowski formula suggests that the energy barrier for the aggregation process is negligible. Also, the formation of long-lived metastable structures with similarities to the raft-like structures of actin filaments is observed within a range of salt concentration.

Abstract:

Read-Rezayi fractional quantum Hall states are among the prime candidates for realizing non-Abelian anyons which, in principle, can be used for topological quantum computation. We present a prescription for efficiently finding braids which can be used to carry out a universal set of quantum gates on encoded qubits based on anyons of the Read-Rezayi states with k>2, k≠4. This work extends previous results which only applied to the case k=3 (Fibonacci) and clarifies why, in that case, gate constructions are simpler than for a generic Read-Rezayi state. © 2009 The American Physical Society.

Abstract:

We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy landscape structure of the assembling system. Even though the model is strongly coarse-grained, it exhibits a number of features also observed in experiments, such as sigmoidal assembly dynamics, hysteresis in capsid formation and numerous kinetic traps. We also investigate the effect of macromolecular crowding on the assembly dynamics. Crowding agents generally reduce capsid yields at optimal conditions for non-crowded assembly, but may increase yields for parameter regimes away from the optimum. Finally, we generalize the model to a larger triangulation number T = 3, and observe more complex assembly dynamics than that seen for the original T = 1 model.