Person:

Manoharan, Vinothan

Although RNA interference (RNAi) has emerged as an important tool for studying the effects of gene knockdown, it is still difficult to predict the success of RNAi effectors in human systems. By examining the basic thermodynamic equations for RNA interactions in RNAi, we demonstrate how the free energies of RNA folding and phosphoester bond hydrolysis can drive RNAi without ATP. Our calculations of RNAi efficiency are close to actual values obtained from in vitro experimental data from 2 previous studies, for both silencing complex formation (2.50 vs. 2.40 for relative efficiency of RISC formation) and mRNA cleavage (0.50 vs. 0.56 for proportion cleaved). Our calculations are also in agreement with previous observations that duplex unwinding and target site folding are major energy barriers to RNAi.

We have built a simple holographic microscope completely out of consumer components. We obtain at least 2.8 micrometer resolution and depth of field greater than 200 micrometers from an instrument costing less than $1000.

Young's law predicts that a colloidal sphere in equilibrium with a liquid interface will straddle the two fluids, its height above the interface defined by an equilibrium contact angle. This equilibrium analysis has been used to explain why colloids often bind to liquid interfaces, an effect first observed a century ago by Ramsden and Pickering and later exploited in a wide range of material processes, including emulsification, water purification, mineral recovery, encapsulation, and the making of nanostructured materials. But little is known about the dynamics of binding. Here we show that the adsorption of polystyrene microspheres to a water-oil interface is characterized by a sudden breach and an unexpectedly slow relaxation. Particles do not reach equilibrium even after 100 seconds, and the relaxation appears logarithmic in time, suggesting that complete equilibration may take months. Surprisingly, viscous dissipation appears to play little role. Instead, the observed dynamics, which bear strong resemblance to aging in glassy systems, agree well with a model describing activated hopping of the contact line over nanoscale surface heterogeneities. These results may provide clues to longstanding questions on colloidal interactions at an interface.

We have developed a new method to produce hybrid particles with polyhedral shapes in very high yield (liter quantities at up to 70% purity) using a combination of emulsion polymerization and inorganic surface chemistry. The procedure has been generalized to create complex geometries, including hybrid line segments, triangles, tetrahedra, octahedra, and more. The optical properties of these particles are tailored for studying their dynamics and self-assembly. For example, we produce systems that consist of index-matched spheres allowing us to define the position of each elementary particle in three-dimensional space. We present some preliminary studies on the self-assembly of these complex shaped systems based on electron and optical microscopy.

We investigate how colloidal particles self-assemble in confined and nonequilibrium systems, including particles trapped at liquid-liquid interfaces (e.g. emulsion droplets) and inside spherical containers. Although common in industrial formulations and fundamental condensed matter studies, these systems remain poorly understood, primarily because no existing experimental probes, including confocal microscopy, can yield real-space data with sufficiently fast acquisition times to resolve 3D dynamics. We use a powerful interferometric technique, Digital Holographic Microscopy (DHM), in concert with particle synthesis and algorithm development to overcome these limitations. Preliminary data show that the technique is capable of tracking several micrometer-sized colloidal particles with 30 nm spatial precision in all three dimensions on millisecond time scales. DHM may be able to yield the most complete physical picture to date of dynamics, interactions, and assembly in colloidal suspensions.

Although the effects of kinetics on crystal growth are well understood, the role of substrate curvature is not yet established. We studied rigid, two-dimensional colloidal crystals growing on spherical droplets to understand how the elastic stress induced by Gaussian curvature affects the growth pathway. In contrast to crystals grown on flat surfaces or compliant crystals on droplets, these crystals formed branched, ribbon-like domains with large voids and no topological defects. We show that this morphology minimizes the curvature-induced elastic energy. Our results illustrate the effects of curvature on the ubiquitous process of crystallization, with practical implications for nanoscale disorder-order transitions on curved manifolds, including the assembly of viral capsids, phase separation on vesicles, and crystallization of tetrahedra in three dimensions.

Colloidal glasses, bird feathers, and beetle scales can all show structural colors arising from short-ranged spatial correlations between scattering centers. Unlike the structural colors arising from Bragg diffraction in ordered materials like opals, the colors of these photonic glasses are independent of orientation, owing to their disordered, isotropic microstructures. However, there are few examples of photonic glasses with angle-independent red colors in nature, and colloidal glasses with particle sizes chosen to yield structural colors in the red show weak color saturation. Using scattering theory, we show that the absence of angle-independent red color can be explained by the tendency of individual particles to backscatter light more strongly in the blue. We discuss how the backscattering resonances of individual particles arise from cavity-like modes and how they interact with the structural resonances to prevent red. Finally, we use the model to develop design rules for colloidal glasses with red, angle-independent structural colors.

Particle-doped thin films that are translucent and diffusive have applications in cosmetics, coatings, and display technologies, but finding material combinations that produce these effects simultaneously is challenging: formulations tend to be either transparent or opaque. Using a combination of Mie scattering calculations and spectral transmission measurements on monodisperse colloidal suspensions, we demonstrate that the two characteristic optical properties of the films, total transmittance and haze, scale with the effective backscattering and forward scattering cross sections, both of which are properties of single particles. These scalings enable an efficient computational search for combinations of particle sizes, concentrations, and refractive indices that break the trade-off between translucency and diffusion. The optimum particle sizes and concentrations obey power-law dependences on the refractive index difference, a result of the interference condition for resonances in the scattering cross sections. The power laws serve as design equations for formulating particle-doped thin films.

The optical theorem provides a powerful tool for calculating the extinction cross section of a particle from a solution to Maxwell’s equations, relating the cross section to the scattering amplitude in the forward direction. The theorem has been generalized by a number of other workers to consider a particle near an interface between media with different refractive indices. Here we present a derivation of the generalized optical theorem that is valid for a particle embedded in the interface, as well as an incident beam undergoing total internal reflection. We also obtain an additional useful physical result: we show that the far-field scattered field must be zero in the direction parallel to the interface. Our results enable the verification of computations of scattering by particles embedded in interfaces and may be relevant to experiments on colloidal particles at fluid interfaces.