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

Congratulations Dr. Wang!

Congratulations Dr. Wang!

May 11, 2016

After concluding her thesis defense with an exciting grand finale, "The Self-Assembly of Man," Anna's committee emerged from their discussions quickly. They greeted her with smiles and handshakes, letting her know that her defense of her thesis, "Out-of-Equilibrium Dynamics of Colloidal Particles at Interfaces" had been successful. Congratulations Dr. Wang!

Welcome Miles and Rachel

January 1, 2016

Miles Faaborg is a first-year graduate student in applied physics. He will be working with Aaron and Rees on virus physics. Rachel Feynman is a research intern in the lab. She will be working with Irep on the artificial cells project. Welcome Miles and Rachel!

Welcome Samaneh

September 1, 2015

Dr. Samaneh Mashaghi is a postdoc in the lab working on the braided nanowires project. Welcome Samaneh!

Recent Publications

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 In Press, 2016.Abstract

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.

Faez, S. ; Latin, Y. ; Weidlich, S. ; Garmann, R. F. ; Wondraczek, K. ; Zeisberger, M. ; Schmidt, M. A. ; Orrit, M. ; Manoharan, V. N. Fast, label-free tracking of single viruses and weakly scattering nanoparticles in a nanofluidic optical fiber. ACS Nano 2015, 9 12349-12357. Publisher's VersionAbstract

High-speed tracking of single particles is a gateway to understanding physical, chemical, and biological processes at the nanoscale. It is also a major experimental challenge, particularly for small, nanometer-scale particles. Although methods such as confocal or fluorescence microscopy offer both high spatial resolution and high signal-to-background ratios, the fluorescence emission lifetime limits the measurement speed, while photobleaching and thermal diffusion limit the duration of measurements. Here we present a tracking method based on elastic light scattering that enables long-duration measurements of nanoparticle dynamics at rates of thousands of frames per second. We contain the particles within a single-mode silica fiber having a subwavelength, nanofluidic channel and illuminate them using the fiber’s strongly confined optical mode. The diffusing particles in this cylindrical geometry are continuously illuminated inside the collection focal plane. We show that the method can track unlabeled dielectric particles as small as 20 nm as well as individual cowpea chlorotic mottle virus (CCMV) virions—26 nm in size and 4.6 megadaltons in mass—at rates of over 3 kHz for durations of tens of seconds. Our setup is easily incorporated into common optical microscopes and extends their detection range to nanometer-scale particles and macromolecules. The ease-of-use and performance of this technique support its potential for widespread applications in medical diagnostics and micro total analysis systems.

Perry, R. W. ; Holmes-Cerfon, M. C. ; Brenner, M. P. ; Manoharan, V. N. Two-Dimensional Clusters of Colloidal Spheres: Ground States, Excited States, and Structural Rearrangements. Phys. Rev. Lett. 2015, 114, 228301. Publisher's VersionAbstract

We study experimentally what is arguably the simplest yet nontrivial colloidal system: two-dimensional clusters of six spherical particles bound by depletion interactions. These clusters have multiple, degenerate ground states whose equilibrium distribution is determined by entropic factors, principally the symmetry. We observe the equilibrium rearrangements between ground states as well as all of the low-lying excited states. In contrast to the ground states, the excited states have soft modes and low symmetry, and their occupation probabilities depend on the size of the configuration space reached through internal degrees of freedom, as well as a single “sticky parameter” encapsulating the depth and curvature of the potential. Using a geometrical model that accounts for the entropy of the soft modes and the diffusion rates along them, we accurately reproduce the measured rearrangement rates. The success of this model, which requires no fitting parameters or measurements of the potential, shows that the free-energy landscape of colloidal systems and the dynamics it governs can be understood geometrically.

Magkiriadou, S. Structural Color From Colloidal Glasses, 2015. Publisher's VersionAbstract

When a material has inhomogeneities at a lengthscale comparable to the wavelength of light, interference can give rise to structural colors: colors that originate from the interaction of the material's microstructure with light and do not require absorbing dyes. In this thesis we study a class of these materials, called photonic glasses, where the inhomogeneities form a dense and random arrangement. Photonic glasses have angle-independent structural colors that look like those of conventional dyes. However, when this work started, there was only a handful of colors accessible with photonic glasses, mostly hues of blue.

We use various types of colloidal particles to make photonic glasses, and we study, both theoretically and experimentally, how the optical properties of these glasses relate to their structure and constituent particles. Based on our observations from glasses of conventional particles, we construct a theoretical model that explains the scarcity of yellow, orange, and red photonic glasses. Guided by this model, we develop novel colloidal systems that allow a higher degree of control over structural color. We assemble glasses of soft, core-shell particles with scattering cores and transparent shells, where the resonant wavelength can be tuned independently of the reflectivity. We then encapsulate glasses of these core-shell particles into emulsion droplets of tunable size; in this system, we observe, for the first time, angle-independent structural colors that cover the entire visible spectrum. To enhance color saturation, we begin experimenting with inverse glasses, where the refractive index of the particles is lower than the refractive index of the medium, with promising results. Finally, based on our theoretical model for scattering from colloidal glasses, we begin an exploration of the color gamut that could be achieved with this technique, and we find that photonic glasses are a promising approach to a new type of long-lasting, non-toxic, and tunable pigment.

Perry, R. W. Internal Dynamics of Equilibrium Colloidal Clusters, 2015. Publisher's VersionAbstract

Colloidal clusters, aggregates of a few micrometer-sized spherical particles, are a model experimental system for understanding the physics of self-assembly and processes such as nucleation. Colloidal clusters are well suited for studies on these topics because they are the simplest colloidal system with internal degrees of freedom. Clusters made from particles that weakly attract one another continually rearrange between different structures. By characterizing these internal dynamics and the structures connected by the rearrangement pathways, we seek to understand the statistical physics underlying self-assembly and equilibration.

In this thesis, we examine the rearrangement dynamics of colloidal clusters and analyze the equilibrium distributions of ground and excited states. We prepare clusters of up to ten microspheres bound by short-range depletion interactions that are tuned to allow equilibration between multiple isostatic arrangements. To study these clusters, we use bright-field and digital holographic microscopy paired with computational post-processing to amass ensemble-averaged and time-averaged probabilities.

We study both two-dimensional (2D) and three-dimensional (3D) clusters composed of either one or two species of particles. To learn about geometrical nucleation barriers, we track rearrangements of particles within freely rotating and translating 3D clusters. We show that rearrangements occur on a timescale of seconds, consistent with diffusion-dominated internal dynamics. To better understand excited states and transition pathways, we track hundreds of rearrangements between degenerate ground states in 2D clusters. We show that the rearrangement rates can be understood using a model with two parameters, which account for the diffusion coefficient along the excited-state rearrangement pathways and the interaction potential. To explore new methods to control self-assembly, we analyze clusters of two species with different masses and different interactions. We find that the interactions allow for control over the intracluster placement of each species, while the masses have no influence. To provide a theoretical framework for understanding these observations, we derive the classical partition function of colloidal clusters in terms of translational, rotational, and vibrational degrees of freedom. We show that the masses of the particles enter the partition function through the kinetic energy but have no effect on the probabilities of states that differ only in where the masses are placed. This result is consistent with our experiments.

Overall, this work shows that the equilibrium distribution of self-assembled colloidal clusters is well-modeled by classical statistical physics, and that the rearrangement dynamics of colloidal clusters can be understood by incorporating diffusion and the effect of the interaction potential. Because both the structures and dynamics can be accurately predicted, these clusters are a promising system for self-assembling novel materials and for studying the emergence of phase transitions.

Schade, N. B. Self-Assembly of Plasmonic Nanoclusters for Optical Metafluids, 2015. Publisher's VersionAbstract

I discuss experimental progress towards developing a material with an isotropic, negative index of refraction at optical frequencies. The simplest way to make such a material is to create a metafluid, or a disordered collection of subwavelength, isotropic electromagnetic resonators. Small clusters of metal particles, such as tetrahedra, serve as these constituents. What is needed are methods for manufacturing these structures with high precision and in sufficient yield that their resonances are identical.

Jonathan Fan et al. [Science, 328 (5982), 1135-1138, 2010] demonstrated that colloidal self-assembly is a means of preparing electromagnetic resonators from metal nanoparticles. However, the resonances are sensitive to the separation gaps between particles. Standard synthesis routes for metal nanoparticles yield crystals or nanoshells that are inadequate for metafluids due to polydispersity, faceting, and thermal instabilities. To ensure that the separation gaps and resonances are uniform, more monodisperse spherical particles are needed. An additional challenge is the self-assembly of tetrahedral clusters in high yield from these particles. In self-assembly approaches that others have examined previously, the yield of any particular type of cluster is low.

In this dissertation I present solutions to several of these problems, developed in collaboration with my research group and others. We demonstrate that slow chemical etching can transform octahedral gold crystals into ultrasmooth, monodisperse nanospheres. The particles can serve as seeds for the growth of larger octahedra which can in turn be etched. The size of the gold nanospheres can therefore be adjusted as desired. We further show that in colloidal mixtures of two sphere species that strongly bind to one another, the sphere size ratio determines the size distribution of self-assembled clusters. At a critical size ratio, tetrahedral clusters assemble in high yield. We explain the experimentally observed 90% yield with a nonequilibrium “random parking” model based on irreversible binding. Simulations based on this model reveal that 100% yield of tetrahedra is possible in principle. Finally, we combine these results and present methods for the self-assembly and purification of tetrahedral plasmonic nanoclusters, the simplest building blocks for isotropic metafluids.

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Contact

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

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