Gehrels, E. W. Responsive and Dynamic Systems from DNA-Mediated Colloidal Interactions, 2018. Publisher's VersionAbstract
Grafting DNA oligonucleotides to colloidal particles leads to specific, reversible interactions between those particles. However, these interactions have been used almost exclusively to create non-responsive systems through equilibrium pathways. In this thesis, I explore different ways to precisely control the response of these particles to changes in their environment and demonstrate how this new control can be used to make systems with complex, dynamic behaviors.
DNA-mediated colloidal interactions are limited by the steep and monotonic dependence of the interaction strength on temperature, which hinders their use in self-assembly applications and limits the complexity of the systems that can be realized. I show how to modify the dependence on temperature in a controlled way by incorporating DNA strand-displacement reactions. This method allows us to make multicomponent systems that self-assemble over a wide range of temperatures, melt upon cooling, transition between structures with different compositions, or have multiple melting transitions. I create this wide range of behaviors simply by adding a small number of DNA strands to the solution, demonstrating that the approach is modular and straightforward to implement. 
These strand-displacement reactions enable systems to dynamically rearrange in time. We demonstrate a system where, by thermal ratcheting, a single particle (the dancer) can be driven to move through a programmed sequence of steps along a one-dimensional track composed of other particles. We lay out the requirements for a system to exhibit controlled motion on the mesoscale, and we demonstrate how these conditions can be realized experimentally. Specifically, we show how the non-monotonic phase behavior enabled by strand-displacement reactions allows us to turn on and off interactions between different pairs of particles, and thereby drive the motion of the dancer. We discuss the capabilities and limitations of using these interactions for applications in dynamic systems. 
One such limitation is that a single variable---the temperature of the system---simultaneously controls interactions between several species of particles. We therefore aim to independently modulate interactions between many species. To this end, we present a new approach to dynamically control interactions between DNA-coated colloids using light. We infiltrate particles with dyes so that when we illuminate them with the appropriate wavelength, they heat. As a result, by uniformly illuminating samples with unfocused light, we can reversibly turn on and off the attractive interactions between particles. Although the light is incident on the entire sample, the heating is local to the particles. Therefore, by using multiple dyes, we can independently address the interactions between different sets of particles by using different wavelengths of light. This method of heating produces a short-range temperature gradient that builds up and dissipates on a time scale of milliseconds. Thus, the particles can be heated much more efficiently than by external heating, and the propensity of the entire system to aggregate can be modulated in less than 50 milliseconds. This rapid modulation opens the door to many applications, including non-equilibrium self-assembly.
Gehrels, E. W. ; Rogers, W. B. ; Manoharan, V. N. Using DNA strand displacement to control interactions in DNA-grafted colloids. Soft Matter 2018, 14, 969-984. Publisher's VersionAbstract
Grafting DNA oligonucleotides to colloidal particles leads to specific, reversible interactions between those particles. However, the interaction strength varies steeply and monotonically with temperature, hindering the use of DNA-mediated interactions in self-assembly. We show how the dependence on temperature can be modified in a controlled way by incorporating DNA strand-displacement reactions. The method allows us to make multicomponent systems that can self-assemble over a wide range of temperatures, invert the dependence on temperature to design colloidal systems that melt upon cooling, controllably transition between structures with different compositions, or design systems with multiple melting transitions. This wide range of behaviors can be realized simply by adding a small number of DNA strands to the solution, making the approach modular and straightforward to implement. We conclude with practical considerations for designing systems of DNA-mediated colloidal interactions.
Gehrels et al. - 2018 - Using DNA strand displacement.pdf
Zeravcic, Z. ; Manoharan, V. N. ; Brenner, M. P. Colloquium: Toward living matter with colloidal particles. Reviews of Modern Physics 2017, 89, 031001. Publisher's VersionAbstract
A fundamental unsolved problem is to understand the differences between inanimate matter and living matter. Although this question might be framed as philosophical, there are many fundamental and practical reasons to pursue the development of synthetic materials with the properties of living ones. There are three fundamental properties of living materials that we seek to reproduce: The ability to spontaneously assemble complex structures, the ability to self-replicate, and the ability to perform complex and coordinated reactions that enable transformations impossible to realize if a single structure acted alone. The conditions that are required for a synthetic material to have these properties are currently unknown. This Colloquium examines whether these phenomena could emerge by programming interactions between colloidal particles, an approach that bootstraps off of recent advances in DNA nanotechnology and in the mathematics of sphere packings. The argument is made that the essential properties of living matter could emerge from colloidal interactions that are specific—so that each particle can be programmed to bind or not bind to any other particle—and also time dependent—so that the binding strength between two particles could increase or decrease in time at a controlled rate. There is a small regime of interaction parameters that gives rise to colloidal particles with lifelike properties, including self-assembly, self-replication, and metabolism. The parameter range for these phenomena can be identified using a combinatorial search over the set of known sphere packings.
Zeravcic et al. - 2017 - Colloquium Toward living matter with colloidal particles.pdf
Wang, A. ; Rogers, W. B. ; Manoharan, V. N. Effects of Contact-Line Pinning on the Adsorption of Nonspherical Colloids at Liquid Interfaces. Physical Review Letters 2017, 119, 108004. Publisher's VersionAbstract
The effects of contact-line pinning are well known in macroscopic systems but are only just beginning to be explored at the microscale in colloidal suspensions. We use digital holography to capture the fast three-dimensional dynamics of micrometer-sized ellipsoids breaching an oil-water interface. We find that the particle angle varies approximately linearly with the height, in contrast to results from simulations based on the minimization of the interfacial energy. Using a simple model of the motion of the contact line, we show that the observed coupling between translational and rotational degrees of freedom is likely due to contact-line pinning. We conclude that the dynamics of colloidal particles adsorbing to a liquid interface are not determined by the minimization of interfacial energy and viscous dissipation alone; contact-line pinning dictates both the time scale and pathway to equilibrium.
Wang et al. - 2017 - Effects of Contact-Line Pinning on the Adsorption.pdf
Kim, S. - H. ; Magkiriadou, S. ; Rhee, D. K. ; Lee, D. S. ; Yoo, P. J. ; Manoharan, V. N. ; Yi, G. - R. Inverse Photonic Glasses by Packing Bidisperse Hollow Microspheres with Uniform Cores. ACS Applied Materials & Interfaces 2017, 9 24155-24160. Publisher's VersionAbstract
A major fabrication challenge is producing disordered photonic materials with an angle-independent structural red color. Theoretical work has shown that such a color can be produced by fabricating inverse photonic glasses with monodisperse, nontouching voids in a silica matrix. Here, we demonstrate a route toward such materials and show that they have an angle-independent red color. We first synthesize monodisperse hollow silica particles with precisely controlled shell thickness and then make glassy colloidal structures by mixing two types of hollow particles with the same core size and different shell thicknesses. We then infiltrate the interstices with index-matched polymers, producing disordered porous materials with uniform, nontouching air voids. This procedure allows us to control the light-scattering form factor and structure factor of these porous materials independently, which is not possible to do in photonic glasses consisting of packed solid particles. The structure factor can be controlled by the shell thickness, which sets the distance between pores, whereas the pore size determines the peak wave vector of the form factor, which can be set below the visible range to keep the main structural color pure. By using a binary mixture of 246 and 268 nm hollow silica particles with 180 nm cores in an index-matched polymer matrix, we achieve angle-independent red color that can be tuned by controlling the shell thickness. Importantly, the width of the reflection peak can be kept constant, even for larger interparticle distances.
Kim et al. - 2017 - Inverse Photonic Glasses by Packing Bidisperse Hollow Spheres.pdf
Chomette, C. ; Tréguer-Delapierre, M. ; Schade, N. B. ; Manoharan, V. N. ; Lambert, O. ; Taveau, J. - C. ; Ravaine, S. ; Duguet, E. Colloidal Alchemy: Conversion of Polystyrene Nanoclusters into Gold. ChemNanoMat 2017, 3 160-163. Publisher's VersionAbstract
Isotropic plasmonic clusters consisting of a controlled number of gold satellites around a silica core are fabricated from silica/polystyrene tetrapod, hexapod, and dodecapod templates. The synthetic pathway includes stages of site-specific seed adsorption, seed-mediated growth, and iterative etching/regrowth to reshape the satellites into spheroids. Transmission electron microscopy and electron tomography provide evidence of the symmetry of the clusters. This work paves the way for a comprehensive study of their optical properties.
Chomette et al. - 2017 - Colloidal Alchemy.pdf
Manoharan, V. ; Magkiriadou, S. ; Park, J. - G. United States Patent 9541674: Photonic balls containing a microstructure of core-shell particles exhibiting angularly-independent structural color, 2017. Publisher's Version
Park, J. - G. ; Rogers, W. B. ; Magiriadou, S. ; Kodger, T. ; Kim, S. - H. ; Kim, Y. - S. ; Manoharan, V. N. Photonic-crystal hydrogels with a rapidly tunable stop band and high reflectivity across the visible. Optical Materials Express 2017, 7 253-263. Publisher's VersionAbstract
We present a new type of hydrogel photonic crystal with a stop band that can be rapidly modulated across the entire visible spectrum. We make these materials by using a high-molecular-weight polymer to induce a depletion attraction between polystyrene-poly(N-isopropylacrylamide-co-bisacrylamide-co-acrylic acid) core-shell particles. The resulting crystals display a stop band at visible wavelengths that can be tuned with temperature at a rate of 60 nm/s, nearly three orders of magnitude faster than previous photonic-crystal hydrogels. Above a critical concentration of depleting agent, the crystals do not melt even at 40 degrees Celsius. As a result, the stop band can be modulated continuously from red (650 nm) to blue (450 nm), with nearly constant reflectivity throughout the visible spectrum. The unusual thermal stability is due to the polymer used as the depleting agent, which is too large to enter the hydrogel mesh and therefore induces a large osmotic pressure that holds the particles together. The fast response rate is due to the collective diffusion coefficient of our hydrogel shells, which is more than three orders of magnitude larger than that of conventional bulk hydrogels. Finally, the constant reflectivity from red (650 nm) to blue (450 nm) is due to the core-shell design of the particles, whose scattering is dominated by the polystyrene cores and not the hydrogel. These findings provide new insights into the design of responsive photonic crystals for display applications and tunable lasers.
Park et al. - 2017 - Photonic-crystal hydrogels with a rapidly tunable stop band
Meng, G. ; Manoharan, V. N. ; Perro, A. Core–shell colloidal particles with dynamically tunable scattering properties. Soft Matter 2017, 13, 6293-6296. Publisher's VersionAbstract
We design polystyrene–poly(N′-isopropylacrylamide-co-acrylic acid) core–shell particles that exhibit dynamically tunable scattering. We show that under normal solvent conditions the shell is nearly index-matched to pure water, and the particle scattering is dominated by Rayleigh scattering from the core. As the temperature or salt concentration increases, both the scattering cross-section and the forward scattering increase, characteristic of Mie scatterers. The magnitude of the change in the scattering cross-section and scattering anisotropy can be controlled through the solvent conditions and the size of the core. Such particles may find use as optical switches or optical filters with tunable opacity.
Meng et al. - 2017 - Core–shell colloidal particles with dynamically tunable scattering properties.pdf
Kumar, S. K. ; Kumaraswamy, G. ; Prasad, B. L. V. ; Bandyopadhyaya, R. ; Granick, S. ; Gang, O. ; Manoharan, V. N. ; Frenkel, D. ; Kotov, N. A. Nanoparticle assembly: a perspective and some unanswered questions. Current Science 2017, 112, 1635-1641. Publisher's VersionAbstract
In early 2016, the Royal Society of Chemistry arranged a meeting on the topic ‘Nanoparticle Assemblies: from Fundamentals to Applications’ which was hosted at IIT-Bombay, Mumbai. The meeting brought several leading nanoscience and nanotechnology researchers to India and is only the second Faraday Discussions meeting to have been held in the country. The papers presented at the meeting and the resulting active discussions have been summarized in a Faraday Discussion issue. The broad range of topics discussed at the meeting led to an understanding on where we stand in the field of nanoparticle assembly, and also enunciated some of the outstanding fundamental and practical issues that remain to be resolved before these ideas can be applied to practical situations. Driven by these ideas, here we focus on four topics/questions: (i) Can we achieve function-driven design of nanoparticle assemblies? (ii) What is the minimal information needed to build a desired assembly? (iii) How complex a structure can one build? How can one make it responsive? What are the relative roles of equilibrium versus dynamics in the assembly process, and are we at a point where we can now pursue active assembly as a viable mode for creating complex assemblies? (iv) What are the applications that are being targeted and what are the barriers to implementation? In this perspective, we do not present an exhaustive survey of the vast literature in this area, but indicate overarching themes/questions that require immediate attention, largely based on the discussions at the Mumbai meeting.
Wang, A. ; McGorty, R. ; Kaz, D. M. ; Manoharan, V. N. Contact-line pinning controls how quickly colloidal particles equilibrate with liquid interfaces. Soft Matter 2016, 12, 8958-8967. Publisher's VersionAbstract
Previous experiments have shown that spherical colloidal particles relax to equilibrium slowly after they adsorb to a liquid-liquid interface, despite the large interfacial energy gradient driving the adsorption. The slow relaxation has been explained in terms of transient pinning and depinning of the contact line on the surface of the particles. However, the nature of the pinning sites has not been investigated in detail. We use digital holographic microscopy to track a variety of colloidal spheres---inorganic and organic, charge-stabilized and sterically stabilized, aqueous and non-aqueous---as they breach liquid interfaces. We find that nearly all of these particles relax logarithmically in time over timescales much larger than those expected from viscous dissipation alone. By comparing our results to theoretical models of the pinning dynamics, we infer the area per defect to be on the order of a few square nanometers for each of the colloids we examine, whereas the energy per defect can vary from a few $kT$ for non-aqueous and inorganic spheres to tens of $kT$ for aqueous polymer particles. The results suggest that the likely pinning sites are topographical features inherent to colloidal particles---surface roughness in the case of silica particles and grafted polymer ``hairs'' in the case of polymer particles. We conclude that the slow relaxation must be taken into account in experiments and applications, such as Pickering emulsions, that involve colloids attaching to interfaces. The effect is particularly important for aqueous polymer particles, which pin the contact line strongly.
Wang et al. - 2016 - Contact-line pinning controls how quickly.pdf
Rahmani, A. M. ; Wang, A. ; Manoharan, V. N. ; Colosqui, C. E. Colloidal particle adsorption at liquid interfaces: capillary driven dynamics and thermally activated kinetics. Soft Matter 2016, 12, 6365-6372. Publisher's VersionAbstract
The adsorption of single colloidal microparticles (0.5–1 μm radius) at a water–oil interface has been recently studied experimentally using digital holographic microscopy [Kaz et al., Nat. Mater., 2012, 11, 138–142]. An initially fast adsorption dynamics driven by capillary forces is followed by an unexpectedly slow relaxation to equilibrium that is logarithmic in time and can span hours or days. The slow relaxation kinetics has been attributed to the presence of surface “defects” with nanoscale dimensions (1–5 nm) that induce multiple metastable configurations of the contact line perimeter. A kinetic model considering thermally activated transitions between such metastable configurations has been proposed [Colosqui et al., Phys. Rev. Lett., 2013, 111, 028302] to predict both the relaxation rate and the crossover point to the slow logarithmic regime. However, the adsorption dynamics observed experimentally before the crossover point has remained unstudied. In this work, we propose a Langevin model that is able to describe the entire adsorption process of single colloidal particles by considering metastable states produced by surface defects and thermal motion of the particle and liquid interface. Invoking the fluctuation dissipation theorem, we introduce a drag term that considers significant dissipative forces induced by thermal fluctuations of the liquid interface. Langevin dynamics simulations based on the proposed adsorption model yield close agreement with experimental observations for different microparticles, capturing the crossover from (fast) capillary driven dynamics to (slow) thermally activated kinetics.
Rahmani et al. - 2016 - Colloidal particle adsorption at liquid interfaces.pdf
Perry, R. W. ; Manoharan, V. N. Segregation of “isotope” particles within colloidal molecules. Soft Matter 2016, 12, 2868-2876. Publisher's VersionAbstract

Clusters of spherical particles are called “colloidal molecules” because they adopt structures that resemble those of true molecules. In this analogy, the particles are the atoms, the attractive interactions between them are bonds, and the different structures that appear in equilibrium are isomers. We take this analogy a step further by doping colloidal molecules with colloidal “isotopes,” particles that have the same size but different bonding energies from the other particles in the system. Our molecules are two-dimensional clusters consisting of polystyrene and silica microspheres held together by depletion interactions. Using a combination of optical microscopy and particle tracking, we examine an ensemble of 4- and 5-particle molecules at different isotope ratios. We find that the isotopes tend to segregate to particular positions in the various isomers. We explain these findings using a statistical mechanical model that accounts for the rotational entropy of the isomers and the different interaction potentials between the different types of particles. The model shows how to optimize the yield of any particular isomer, so as to put the isotopes in desired locations. Our experiments and models show that even in systems of particles with isotropic interactions, the structures of self-assembled molecules can in principle be controlled to a surprisingly high extent.

Perry and Manoharan - 2016 - Segregation of isotope particles within colloidal molecules.pdf
Chomette, C. ; Duguet, E. ; Mornet, S. ; Yammine, E. ; Manoharan, V. N. ; Schade, N. B. ; Hubert, C. ; Ravaine, S. ; Perro, A. ; Treguer-Delapierre, M. Templated growth of gold satellites on dimpled silica cores. Faraday Discussions 2016, 191, 105-116. Publisher's VersionAbstract
We synthesize robust clusters of gold satellites positioned with tetrahedral symmetry on the surface of a patchy silica core by adsorption and growth of gold on the patches. First we conduct emulsion polymerization of styrene in the presence of 52 nm silica seeds whose surface has been modified with methacryloxymethyltriethoxysilane (MMS). We derive four-dimple particles from the resulting silica/polystyrene tetrapods. Polystyrene chains are covalently bound to the silica surface within the dimples due to the MMS grafts and they may be thiolated to induce adsorption of 12 nm gold particles. Using chloroauric acid, ascorbic acid and sodium citrate at room temperature, we grow gold from these 12 nm seeds without detachment from or deformation of the dimpled silica surface. We obtain gold satellites of tunable diameter up to 140 nm.
Chomette et al. - 2016 - Templated growth of gold satellites.pdf
Dimiduk, T. G. ; Manoharan, V. N. Bayesian approach to analyzing holograms of colloidal particles. Optics Express 2016, 24, 24045–24060. Publisher's VersionAbstract

We demonstrate a Bayesian approach to tracking and characterizing colloidal particles from in-line digital holograms. We model the formation of the hologram using Lorenz-Mie theory. We then use a tempered Markov-chain Monte Carlo method to sample the posterior probability distributions of the model parameters: particle position, size, and refractive index. Compared to least-squares fitting, our approach allows us to more easily incorporate prior information about the parameters and to obtain more accurate uncertainties, which are critical for both particle tracking and characterization experiments. Our approach also eliminates the need to supply accurate initial guesses for the parameters, so it requires little tuning.

Dimiduk and Manoharan - 2016 - Bayesian approach to analyzing holograms.pdf
Wang, A. ; Garmann, R. F. ; Manoharan, V. N. Tracking E. coli runs and tumbles with scattering solutions and digital holographic microscopy. Optics Express 2016, 24, 23719–23725. Publisher's VersionAbstract

We use in-line digital holographic microscopy to image freely swimming E. coli. We show that fitting a light scattering model to E. coli holograms can yield quantitative information about the bacterium&\#x02019;s body rotation and tumbles, offering a precise way to track fine details of bacterial motility. We are able to extract the cell&\#x02019;s three-dimensional (3D) position and orientation and recover behavior such as body angle rotation during runs, tumbles, and pole reversal. Our technique is label-free and capable of frame rates limited only by the camera.

Wang et al. - 2016 - Tracking E. coli runs and tumbles with scattering.pdf
Rogers, W. B. ; Shih, W. M. ; Manoharan, V. N. Using DNA to Program the Self-Assembly of Colloidal Nanoparticles and Microparticles. Nature Reviews Materials 2016. Publisher's VersionAbstract

DNA is not just the stuff of our genetic code; it is also a means to design self-assembling materials. Grafting DNA onto nano- and microparticles can, in principle, ‘program’ them with information that tells them exactly how to self-assemble. Although fully programmable assembly has not yet been realized, the groundwork has been laid: with an understanding of how specific interparticle attractions arise from DNA hybridization, we can now make systems that reliably assemble in and out of equilibrium. We discuss these advances, and the design rules that will allow us to control — and ultimately program — the assembly of new materials.

Rogers et al. - 2016 - Using DNA to program the self-assembly of colloidal nanoparticles and microparticles.pdf
Goldfain, A. M. ; Garmann, R. F. ; Jin, Y. ; Lahini, Y. ; Manoharan, V. N. Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages. The Journal of Physical Chemistry B 2016, 120, 6130–6138. Publisher's VersionAbstract

A complete understanding of the cellular pathways involved in viral infections will ultimately require a diverse arsenal of experimental techniques, including methods for tracking individual viruses and their interactions with the host. Here we demonstrate the use of holographic microscopy to track the position, orientation, and DNA content of unlabeled bacteriophages (phages) in solution near a planar, functionalized glass surface. We simultaneously track over 100 individual λ phages at a rate of 100 Hz across a 33 μm × 33 μm portion of the surface. The technique determines the in-plane motion of the phage to nanometer precision, and the height of the phage above the surface to 100 nm precision. Additionally, we track the DNA content of individual phages as they eject their genome following the addition of detergent-solubilized LamB receptor. The technique determines the fraction of DNA remaining in the phage to within 10% of the total 48.5 kilobase pairs. Analysis of the data reveals that under certain conditions, λ phages move along the surface with their heads down and intermittently stick to the surface by their tails, causing them to stand up. Furthermore, we find that in buffer containing high concentrations of both monovalent and divalent salts, λ phages eject their entire DNA in about 7 s. Taken together, these measurements highlight the potential of holographic microscopy to resolve the fast kinetics of the early stages of phage infection.

Goldfain et al. - 2016 - Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages.pdf
Manoharan, V. N. Colloidal matter: Packing, geometry, and entropy. Science 2015, 349, 1253751. Publisher's VersionAbstract

Colloidal particles with well-controlled shapes and interactions are an ideal experimental system for exploring how matter organizes itself. Like atoms and molecules, these particles form bulk phases such as liquids and crystals. But they are more than just crude analogs of atoms; they are a form of matter in their own right, with complex and interesting collective behavior not seen at the atomic scale. Their behavior is affected by geometrical or topological constraints, such as curved surfaces or the shapes of the particles. Because the interactions between the particles are often short-ranged, we can understand the effects of these constraints using geometrical concepts such as packing. The geometrical viewpoint gives us a window into how entropy affects not only the structure of matter, but also the dynamics of how it forms.

Manoharan, V. N. Colloids at interfaces: Pinned down. Nature Materials 2015, 14, 869-870. Publisher's VersionAbstract

(News and Views) A colloidal particle straddling an air/water interface experiences an unexpectedly large viscous drag.