About us

We are a research group in the School of Engineering and Applied Sciences and the Department of Physics at Harvard University. We do experiments to understand how complex systems such as interacting nanoparticles or proteins spontaneously order themselves — a process called self-assembly or self-organization. We use optical techniques that we develop in our lab to observe both natural systems (such as viruses) and synthetic ones (such as colloidal particles, perhaps dressed up with some interesting biomolecules) in three dimensions and on short time scales. We use the results of these studies to make useful materials and to gain a deeper understanding of the physics of assembly, organization, and life.

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Latest news

Annie's defense

Congratulations, Dr. Stephenson!

April 28, 2022
Hearty congratulations to Annie, who has defended her thesis, "Measuring and modeling light scattering in disordered systems for applications in structural color"!
Solomon virtually defending his thesis

Congratulations, Dr. Barkley!

May 5, 2021
Solomon has defended his thesis, "Applying Bayesian inference to measurements of colloidal dynamics"! Congratulations and best wishes for the future.

Recent Publications

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.
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.
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.
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.
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.


Manoharan Lab
McKay 530
9 Oxford St.
Cambridge, MA 02138
+1 (617) 495-9894