Skanda Vivek

High-speed DNA-based rolling motors powered by RNase H

DNA-based machines that walk by converting chemical energy into controlled motion could be of use in applications such as next generation sensors, drug delivery platforms, and biological computing. Despite their exquisite programmability, DNA-based walkers are, however, challenging to work with due to their low fidelity and slow rates (~1 nm/min). Here, we report DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three-orders of magnitude greater than conventional DNA motors. The motors are made from DNA-coated spherical particles that hybridise to a surface modified with complementary RNA; motion is achieved through the addition of RNase H, which selectively hydrolyses hybridised RNA. Spherical motors move in a self-avoiding manner, whereas anisotropic particles, such as dimerised particles or rod-shaped particles travel linearly without a track or external force. Finally, we demonstrate detection of single nucleotide polymorphism by measuring particle displacement using a smartphone camera.

Long-wavelength fluctuations and the glass transition in two dimensions and three dimensions

Significance For phase transitions and fluid dynamics, there are significant qualitative differences between two dimensions and three dimensions. However, it has been long assumed that the glass transition is similar in two and three dimensions. Here, we present experimental data on 2D and 3D colloidal systems near their glass transitions. We demonstrate that the differences between two dimensions and three dimensions are due to long-wavelength fluctuations, precisely those that distinguish 2D and 3D phase transitions. We show that the influence of these fluctuations can be disentangled from the underlying dynamics, and that 2D and 3D glass transitions are otherwise similar. Phase transitions significantly differ between 2D and 3D systems, but the influence of dimensionality on the glass transition is unresolved. We use microscopy to study colloidal systems as they approach their glass transitions at high concentrations and find differences between two dimensions and three dimensions. We find that, in two dimensions, particles can undergo large displacements without changing their position relative to their neighbors, in contrast with three dimensions. This is related to Mermin–Wagner long-wavelength fluctuations that influence phase transitions in two dimensions. However, when measuring particle motion only relative to their neighbors, two dimensions and three dimensions have similar behavior as the glass transition is approached, showing that the long-wavelength fluctuations do not cause a fundamental distinction between 2D and 3D glass transitions.Phase transitions significantly differ between two-dimensional and three-dimensional systems, but the influence of dimensionality on the glass transition is unresolved. We use microscopy to study colloidal systems as they approach their glass transitions at high concentrations, and find differences between 2D and 3D. We find that in 2D particles can undergo large displacements without changing their position relative to their neighbors, in contrast with 3D. This is related to Mermin-Wagner longwavelength fluctuations that influence phase transitions in 2D. However, when measuring particle motion only relative to their neighbors, 2D and 3D have similar behavior as the glass transition is approached, showing that the long wavelength fluctuations do not cause a fundamental distinction between 2D and 3D glass transitions.

Programmable DNA Hydrogels Assembled from Multidomain DNA Strands.

Hydrogels are important in biological and medical applications, such as drug delivery and tissue engineering. DNA hydrogels have attracted significant attention due to the programmability and biocompatibility of the material. We developed a series of low‐cost one‐strand DNA hydrogels self‐assembled from single‐stranded DNA monomers containing multiple palindromic domains. This new hydrogel design is simple and programmable. Thermal stability, mechanical properties, and loading capacity of these one‐strand DNA hydrogels can be readily regulated by simply adjusting the DNA domains.

Measuring and Overcoming Limits of the Saffman-Delbrück Model for Soap Film Viscosities

We observe tracer particles diffusing in soap films to measure the two-dimensional (2D) viscous properties of the films. Saffman-Delbrück type models relate the single-particle diffusivity to parameters of the film (such as thickness h) for thin films, but the relation breaks down for thicker films. Notably, the diffusivity is faster than expected for thicker films, with the crossover at h/d = 5.2 ± 0.9 using the tracer particle diameter d. This indicates a crossover from purely 2D diffusion to diffusion that is more three-dimensional. We demonstrate that measuring the correlations of particle pairs as a function of their separation overcomes the limitations of the Saffman-Delbrück model and allows one to measure the viscosity of a soap film for any thickness.We observe tracer particles diffusing in soap films to measure the two-dimensional (2D) viscous properties of the films. We make soap films with a variety of water-glycerol mixtures and of differing thicknesses. The single-particle diffusivity relates closely to parameters of the film (such as thickness h) for thin films, but the relation breaks down for thicker films. Notably, the diffusivity is faster than expected for thicker films, with the transition at h/d = 5.2 ± 0.9 using the tracer particle diameter d. This indicates a transition from purely 2D diffusion to diffusion that is more three-dimensional. Additionally, we measure larger length scale flow fields from correlated particle motions and find good agreement with what is expected from theory of 2D fluids for all our films, thin and thick. We measure the effective 2D viscosity of a soap film using single-particle diffusivity measurements in thin films, and using the two-particle correlation measurements in all films.

Decoupling of translational and rotational diffusion in quasi-2D colloidal fluids

We observe the translational and rotational diffusion of dimer tracer particles in quasi-2D colloidal samples. The dimers are in dense samples of two different sizes of spherical colloidal particles, with the area fraction ϕ of the particles varying from dilute to nearly glassy. At low ϕ, rotational and translational diffusion have a ratio set by the dimer size, as expected. At higher ϕ, dimers become caged by their neighboring particles, and both rotational and translational diffusion become slow. For short dimers, we observe rapid reorientations so that the rotational diffusion is faster than the translational diffusion: the two modes of diffusion are decoupled and have different ϕ dependence. Longer dimers do not exhibit fast rotations, and we find that their translational and rotational diffusion stay coupled for all ϕ. Our results bridge prior results that used spheres (very fast rotation) and long ellipsoids (very slow rotation).

Mesoscopic model of temporal and spatial heterogeneity in aging colloids

A model of dense hard sphere colloids building on simple notions of particle mobility and spatial coherence is presented and shown to reproduce results of experiments and simulations for key quantities such as the intermediate scattering function, the particle mean-square displacement and the χ4 mobility correlation function. All results are explained by two emerging and interrelated dynamical properties: i) a rate of intermittent events, quakes, which decreases as the inverse of the system age t, leading to μq(tw, t) ∝ log(t/tw) as the average number of quakes occurring between the ‘waiting time’ tw and the current time t; ii) a length scale characterizing correlated domains, which increases linearly in log t. This leads to simple and accurate scaling forms expressed in terms of the single variable, t/tw, preferable to the established use of tw and of the lag time τ = t − tw as variables in two-point correlation functions. Finally, we propose to use χ4 (tw, t) experimentally to extract the growing length scale of an aging colloid and suggest that a suitable scaling of the probability density function of particle displacement can experimentally reveal the rate of quakes.We develop a simple and effective description of the dynamics of dense hard sphere colloids in the aging regime deep in the glassy phase. Our description complements the many efforts to understand the onset of jamming in low density colloids, whose dynamics is still time-homogeneous. Based on a small set of principles, our model provides emergent dynamic heterogeneity, reproduces the known results for dense hard sphere colloids and makes detailed, experimentally-testable predictions for canonical observables in glassy dynamics. In particular, we reproduce the shape of the intermediate scattering function and particle mean-square displacements for jammed colloidal systems, and we predict a growth for the peak of the χ(4) mobility correlation function that is logarithmic in waiting-time. At the same time, our model suggests a novel unified description for the irreversible aging dynamics of structural and quenched glasses based on the dynamical properties of growing clusters of highly correlated degrees of freedom.