Viscous fingering at ultralow interfacial tension
Soft Matter 9:44 (2013) 10599-10605
Abstract:
We experimentally study the viscous fingering instability in a fluid-fluid phase separated colloid-polymer mixture by means of laser scanning confocal microscopy and microfluidics. We focus on three aspects of the instability. (i) The interface between the two demixed phases has an ultralow surface tension, such that we can address the role of thermal interface fluctuations. (ii) We image the interface in three dimensions allowing us to study the interplay between interface curvature and flow. (iii) The displacing fluid wets all walls completely, in contrast to traditional viscous fingering experiments, in which the displaced fluid wets the walls. We also perform lattice Boltzmann simulations, which help to interpret the experimental observations. © 2013 The Royal Society of Chemistry.Zigzag transitions and nonequilibrium pattern formation in colloidal chains
ArXiv 1309.3442 (2013)
Abstract:
Paramagnetic colloidal particles that are optically trapped in a linear array can form a zigzag pattern when an external magnetic field induces repulsive interparticle interactions. When the traps are abruptly turned off, the particles form a nonequilibrium expanding pattern with a zigzag symmetry, even when the strength of the magnetic interaction is weaker than that required to break the linear symmetry of the equilibrium state. We show that the transition to the equilibrium zigzag state is always potentially possible for purely harmonic traps. For anharmonic traps that have a finite height, the equilibrium zigzag state becomes unstable above a critical anharmonicity. A normal mode analysis of the equilibrium line configuration demonstrates that increasing the magnetic field leads to a hardening and softening of the spring constants in the longitudinal and transverse directions, respectively. The mode that first becomes unstable is the mode with the zigzag symmetry, which explains the symmetry of nonequilibrium patterns. Our analytically tractable models help to give further insight into the way that the interplay of such factors as the length of the chain, hydrodynamic interactions, thermal fluctuations affect the formation and evolution of the experimentally observed nonequilibrium patterns.Coarse-graining DNA for simulations of DNA nanotechnology
ArXiv 1308.3843 (2013)
Abstract:
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
ACS Nano 7:3 (2013) 2479-2490
Abstract:
DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands. In this article, we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA walker that is designed to step along a reusable track, thereby offering the possibility of optimizing the design of such systems. We find that applying moderate tension to the track can have a large influence on the operation of the walker, providing a bias for stepping forward and helping the walker to recover from undesirable overstepped states. Further, we show that the process by which spent fuel detaches from the walker can have a significant impact on the rebinding of the walker to the track, strongly influencing walker efficiency and speed. Finally, using the results of the simulations, we propose a number of modifications to the walker to improve its operation.DNA hybridization kinetics: zippering, internal displacement and sequence dependence
ArXiv 1303.337 (2013)