Mechanical Folding of DNA Nanostructures

Using DNA as a building material for a nanostructure has been an attractive idea because DNA is small, rigid, programmable and easy to synthesize. In the seminal paper published in Nature in 2006, Rothemund introduced the DNA origami technique, a versatile tool to build DNA-based nanostructure with arbitrary shape and modification sites. However, the folding method involves time-consuming thermal annealing, which takes at least 1 day to assemble a structure.

We demonstrated rapid and efficient folding of a DNA nanostructure by using single molecule force spectroscopy without any thermal processes. Our mechanical folding of DNA origami structures exploits completely different pathway from that of the thermal folding. 1) To remove the secondary structures, we mechanically stretch the single scaffold DNAs by applying 5 pN tension with magnetic tweezers. Because this selective melting of the scaffold DNA is done essentially at room temperature, 2) hybridization of the scaffold DNA can be efficiently induced upon introduction of staple strands. When the mechanical tension is quenched, folding of the DNA nanostructures is completed through 3) displacement between the bound staple strands. Thus, in our mechanical folding pathway, the previous one-pot thermal reaction is replaced by an ordered and well-separated sequence of three molecular processes. Each step is well defined and free from kinetic traps, which permits de novo design of the folding process and enables us to complete one folding cycle within 10 minutes. Our mechanical folding pathway provides an avenue toward a programmed assembly of DNA nanostructures.

Fluid Dynamics of Liquid Droplet

The environment around us consists of matter in all forms, none more ubiquitous than the liquid state, especially in biological and industrial processes. In an effort to understand such processes in a piecewise manner, we developed a technique that uses a laser light focused onto the surface of a small liquid droplet. In contrast to other comparable methods, light is not a mechanical probe that applies a pressure on or pierces the droplets; rather, light manipulates them without complex moving parts. This technique, coupled with the pace at which light-based technology is advancing, may lead to further understanding of liquids, if only one small droplet at a time.

A deformable liquid droplet inside immiscible background fluids can create various flow instabilities due to the temperature gradient inside the droplet depending on the laser power, which would be used as a model system of convection surrounded with fully soft boundaries. We discovered that such droplets exhibit breathing, crawling, budding, and splitting modes. The dynamic transitions among these modes are explained with dynamic instabilities inside the liquid droplet. I expect that the understanding of the dynamic instabilities in a liquid droplet would be helpful in comprehension of the micro-scale flow dynamics in soft boundary systems as well as in developing new open microfluidic devices surrounded by soft boundaries, which have potential applications in chemical micro-reactors and biological assays.

Jamming Transition of Granular Matter

There has been much interest in the physics of noncohesive granular materials lying on a vertically vibrating surface. When the vibration intensity is large, the granular systems show the properties of fluids. When the vibration intensity is small, disordered granular materials become jammed, behaving like a system with infinite viscosity. Liu and Nagel suggested a scenario of unifying the glass transition and the jamming behavior. We experimentally studied the jamming process of a highly dense 3D granular system using a noninvasive optical technique called diffusing wave spectroscopy, which is very sensitive to very small relative motions of the particles in the medium. When the maximum acceleration of the external vibration was large, the granular system behaved like a fluid with the dynamic correlation function G(t) relaxing rapidly. As the acceleration of vibration approached the gravitational acceleration, the relaxation of G(t) slowed down dramatically, and eventually stopped like a solid. Each G(t) was well fitted by a stretched exponential decay function, and the characteristic relaxation time showed the scaling property in agreement with the mode coupling theory of the supercooled liquids close to the glass transition. These results were the strong evidence of the analogy between the dynamics of granular materials and the behavior of supercooled liquids close to the glass transition, in support of the idea embodied in the jamming phase diagram.

Pattern Formation and Dynamics of Granular Matter

As part of my Ph.D., I worked on ordering phenomena in granular physics. In particular, I experimentally studied the transient ordering dynamics of local orientation of the striped pattern in thin granular layers. The non-equilibrium and non-steady process shows dynamic scaling behavior and the growth exponent of the characteristic length scale of the ordered domain is 0.25, which agrees with that of the Swift-Hohenberg system.

We studied the transient spiral patterns in granular layers, and demonstrated that transient dynamics of spiral patterns depend on the ramping time of the oscillation amplitude. Also, by using a two-frequency forcing vertical vibration, various patterns are formed depending on the control parameters, and a Super Hexagonal Lattice pattern is observed under specific conditions.

We had also tested a two-dimensional crystal in the system with millimeter-sized polystyrene spheres, using triboelectrification through rubbing on the substrate plate. The Fourier transform spectra, the pair distribution, and the bond-orientation-correlation function data showed that the system was in near hexatic phase after fully charged, which was predicted by the KTHNY theory.