@article {718126,
	title = {Effect of coat-protein concentration on the self-assembly of bacteriophage MS2 capsids around RNA},
	journal = {Nanoscale},
	year = {2024},
	url = {https://pubs.rsc.org/en/content/articlelanding/2024/nr/d3nr03292b/unauth},
	author = {Williams, L. A. and Neophytou, A. and Garmann, R. F. and Chakrabarti, R. and Manoharan, V. N.}
}
@article {718121,
	title = {Geometric frustration of hard-disk packings on cones},
	journal = {Physical Review E},
	volume = {108},
	number = {5},
	year = {2023},
	pages = {054608},
	url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.108.054608},
	author = {Sun, J. H. and Plummer, A. and Zhang, G. H. and D.R. Nelson and Manoharan, V. N.}
}
@article {718116,
	title = {Precise characterization of nanometer-scale systems using interferometric scattering microscopy and Bayesian analysis},
	journal = {Applied Optics},
	volume = {62},
	number = {27},
	year = {2023},
	pages = {7205-7215},
	url = {https://opg.optica.org/ao/abstract.cfm?uri=ao-62-27-7205},
	author = {de Wit, X. M. and Paine, A. W. and Martin, C. and Goldfain, A. M. and Garmann, R. F. and Manoharan, V. N.}
}
@article {718111,
	title = {3D-printed machines that manipulate microscopic objects using capillary forces},
	journal = {Nature},
	volume = {611},
	year = {2022},
	pages = {68-73},
	url = {https://www.nature.com/articles/s41586-022-05234-7},
	author = {Zeng, C. and Faaborg, M. W. and Sherif, A. and Falk, M. J. and Hajian, R. and Xiao, M. and Hartig, K. and Bar-Sinai, Y. and M.P. Brenner}
}
@article {718106,
	title = {In-line holographic microscopy with model-based analysis},
	journal = {Nature Reviews Methods Primers},
	volume = {2},
	number = {1},
	year = {2022},
	pages = {83},
	url = {https://www.nature.com/articles/s43586-022-00165-z},
	author = {Martin, C. and Altman, L. E. and Rawat, S. and Wang, A. and Grier, D. G. and Manoharan, V. N.}
}
@article {718101,
	title = {Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {119},
	number = {39},
	year = {2022},
	pages = {e2206292119},
	url = {https://www.pnas.org/doi/abs/10.1073/pnas.2206292119},
	author = {Garmann, R. F. and Goldfain, A. M. and Tanimoto, C. R. and Beren, C. E. and Vasquez, F. F. and Villareal, D. A. and Knobler, C. M. and Gelbart, W. M. and Manoharan, V. N.}
}
@article {718096,
	title = {Predicting the structural colors of films of disordered photonic balls},
	journal = {ACS Photonics},
	volume = {10},
	number = {1},
	year = {2022},
	pages = {58-70},
	url = {https://pubs.acs.org/doi/abs/10.1021/acsphotonics.2c00892},
	author = {Stephenson, A. B. and Xiao, M. and Hwang, V. and Qu, L. and Odorisio, P. A. and M. Burke and Task, K. and Deisenroth, T. and Barkley, S. and Darji, R. H. and Manoharan, V. N.}
}
@article {718091,
	title = {Programming Directed Motion with DNA-Grafted Particles},
	journal = {ACS Nano},
	volume = {16},
	number = {6},
	year = {2022},
	pages = {9195-9202},
	url = {https://pubs.acs.org/doi/abs/10.1021/acsnano.2c01454},
	author = {Gehrels, E. W. and Rogers, W. B. and Zeravcic, Z. and Manoharan, V. N.}
}
@article {718086,
	title = {Voltage-tunable elastomer composites that use shape instabilities for rapid structural color changes},
	journal = {Materials Horizons},
	volume = {9},
	number = {7},
	year = {2022},
	pages = {1954-1961},
	url = {https://pubs.rsc.org/en/content/articlelanding/2022/mh/d2mh00374k/unauth},
	author = {Xiao, M. and Mao, J. and Kollosche, M. and Hwang, V. and D.R. Clarke and Manoharan, V. N.}
}
@article {718081,
	title = {Geometrical frustration and defect formation in growth of colloidal nanoparticle crystals on a cylinder: Implications for assembly of chiral nanomaterials},
	journal = {ACS Applied Nano Materials},
	volume = {4},
	number = {10},
	year = {2021},
	pages = {10682-10691},
	url = {https://pubs.acs.org/doi/abs/10.1021/acsanm.1c02126},
	author = {Tanjeem, N. and Wilkin, W. H. and D.A. Beller and Rycroft, C. H. and Manoharan, V. N.}
}
@article {718076,
	title = {Investigating the trade-off between color saturation and angle-independence in photonic glasses},
	journal = {Optics Express},
	volume = {29},
	number = {14},
	year = {2021},
	pages = {21212-21224},
	url = {https://opg.optica.org/oe/fulltext.cfm?uri=oe-29-14-21212\&id=452661},
	author = {Xiao, M. and Stephenson, A. B. and Neophytou, A. and Hwang, V. and Chakrabarti, D. and Manoharan, V. N.}
}
@article {718071,
	title = {Improving holographic particle characterization by modeling spherical aberration},
	journal = {Optics Express},
	volume = {29},
	number = {12},
	year = {2021},
	pages = {18212-18223},
	url = {https://opg.optica.org/oe/fulltext.cfm?uri=oe-29-12-18212\&id=451440},
	author = {Martin, C. and Leahy, B. and Manoharan, V. N.}
}
@article {718066,
	title = {Designing angle-independent structural colors using Monte Carlo simulations of multiple scattering},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	number = {4},
	year = {2021},
	pages = {e2015551118},
	author = {Hwang, V. and Stephenson, A. B. and Barkley, S. and Brandt, S. and Xiao, M. and Aizenberg, J. and Manoharan, V. N.}
}
@article {718061,
	title = {Self-assembly of patchy colloidal rods into photonic crystals robust to stacking faults},
	journal = {ACS nano},
	volume = {15},
	number = {2},
	year = {2021},
	pages = {2668-2678},
	url = {https://pubs.acs.org/doi/abs/10.1021/acsnano.0c07824},
	author = {Neophytou, A. and Manoharan, V. N. and Chakrabarti, D.}
}
@magazinearticle {718056,
	title = {A field guide to angle-independent structural color},
	journal = {Physics Today},
	volume = {74},
	number = {1},
	year = {2021},
	pages = {62-63},
	url = {https://pubs.aip.org/physicstoday/article-abstract/74/1/62/396298/A-field-guide-to-angle-independent-structural},
	author = {Manoharan, V. N. and Stephenson, A. B.}
}
@article {718051,
	title = {Polyhedral plasmonic nanoclusters through multi-step colloidal chemistry},
	journal = {Materials Horizons},
	volume = {8},
	number = {2},
	year = {2021},
	pages = {565-570},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/mh/d0mh01311k/unauth},
	author = {Tanjeem, N. and Chomette, C. and Schade, N. B. and Ravaine, S. and Duguet, E. and Treguer-Delapierre, M. and Manoharan, V. N.}
}
@article {718046,
	title = {Controlled assembly of icosahedral colloidal clusters for structural coloration},
	journal = {Chemistry of Materials},
	volume = {32},
	number = {22},
	year = {2020},
	pages = {9704-9712},
	url = {https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.0c03391},
	author = {C. Kim and Jung, K. and Yu, J. W. and S. Park and Kim, S.-H. and Lee, W. B. and Hwang, H. and Manoharan, V. N. and Moon, J. H.}
}
@article {718041,
	title = {Precise measurements in digital holographic microscopy by modeling the optical train},
	journal = {Journal of Applied Physics},
	volume = {128},
	number = {6},
	year = {2020},
	url = {https://pubs.aip.org/aip/jap/article/128/6/060902/1063708},
	author = {Alexander, R. and Leahy, B. and Manoharan, V. N.}
}
@article {718036,
	title = {Tracking and analyzing the Brownian motion of nano-objects inside hollow core fibers},
	journal = {ACS Sensors},
	volume = {5},
	number = {3},
	year = {2020},
	pages = {879-886},
	url = {https://pubs.acs.org/doi/abs/10.1021/acssensors.0c00339},
	author = {Forster, R. and Weidlich, S. and Nissen, M. and Wieduwilt, T. and Kolbelke, J. and Goldfain, A. M. and Chiang, T. K. and Garmann, R. F. and Manoharan, V. N. and Lahini, Y. and Schmidt, M. A.}
}
@article {718031,
	title = {Effects of multiple scattering on angle-independent structural color in disordered colloidal materials},
	journal = {Physical Review E},
	volume = {101},
	number = {1},
	year = {2020},
	pages = {012614},
	url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.101.012614},
	author = {Hwang, V. and Stephenson, A. B. and Magkiriadou, S. and Park, J.-G. and Manoharan, V. N.}
}
@article {718026,
	title = {Large depth-of-field tracking of colloidal spheres in holographic microscopy by modeling the objective lens},
	journal = {Optics Express},
	volume = {28},
	number = {2},
	year = {2020},
	pages = {1061-1075},
	url = {https://opg.optica.org/oe/fulltext.cfm?uri=oe-28-2-1061\&id=425675},
	author = {Leahy, B. and Alexander, R. and Martin, C. and Barkley, S. and Manoharan, V. N.}
}
@article {718021,
	title = {Modulating and addressing interactions in polymer colloids using light},
	journal = {Materials Horizons},
	volume = {7},
	number = {2},
	year = {2020},
	pages = {586-591},
	url = {https://pubs.rsc.org/en/content/articlelanding/2019/mh/c9mh01115c/unauth},
	author = {Gehrels, E. W. and Klein, E. D. and Manoharan, V. N.}
}
@article {718016,
	title = {Measurements of the self-assembly kinetics of individual viral capsids around their RNA genome},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {116},
	number = {45},
	year = {2019},
	pages = {22485-22490},
	url = {https://www.pnas.org/doi/abs/10.1073/pnas.1909223116},
	author = {Garmann, R. F. and Goldfain, A. M. and Manoharan, V. N.}
}
@article {718011,
	title = {Before the breach: Interactions between colloidal particles and liquid interfaces at nanoscale separations},
	journal = {Physical Review E},
	volume = {100},
	number = {4},
	year = {2019},
	pages = {042605},
	url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.100.042605},
	author = {Wang, A. and Zwanikken, J. W. and Kaz, D. M. and McGorty, R. and Goldfain, A. M. and Rogers, W. B. and Manoharan, V. N.}
}
@article {717981,
	title = {Random sequential adsorption of spheres on a cylinder},
	journal = {Europhysics Letters},
	volume = {127},
	number = {3},
	year = {2019},
	pages = {38004},
	url = {https://iopscience.iop.org/article/10.1209/0295-5075/127/38004/meta},
	author = {Memet, E. and Tanjeem, N. and Greboval, C. and Manoharan, V. N. and L. Mahadevan}
}
@article {717976,
	title = {Holographic microscopy with Python and HoloPy},
	journal = {Computing in Science \& Engineering},
	volume = {22},
	number = {5},
	year = {2019},
	pages = {72-82},
	url = {https://ieeexplore.ieee.org/abstract/document/8742661},
	author = {Barkley, S. and Dimiduk, T. G. and Fung, J. and Kaz, D. M. and Manoharan, V. N. and McGorty, R. and Perry, R. W. and Wang, A.}
}
@article {717971,
	title = {Solution-Processable Photonic Inks of Mie-Resonant Hollow Carbon{\textendash}Silica Nanospheres},
	journal = {Small},
	volume = {15},
	number = {23},
	year = {2019},
	pages = {1900931},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201900931},
	author = {Kim, S.-H. and Hwang, V. and Lee, S. G. and Ha, J.-W. and Manoharan, V. N. and Yi, G.-R.}
}
@article {717966,
	title = {Active colloidal particles in emulsion droplets: a model system for the cytoplasm},
	journal = {The European Physical Journal Special Topics},
	volume = {227},
	year = {2019},
	pages = {2413-2424},
	url = {https://link.springer.com/article/10.1140/epjst/e2019-800026-y},
	author = {Horowitz, V. R. and Chambers, Z. C. and Gozen, I. and Dimiduk, T. G. and Manoharan, V. N.}
}
@article {717961,
	title = {Physical interpretation of the partition function for colloidal clusters},
	journal = {Physical Review E},
	volume = {98},
	number = {3},
	year = {2018},
	pages = {032608},
	url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.98.032608},
	author = {Klein, E. D. and Perry, R. W. and Manoharan, V. N.}
}
@mastersthesis {635878,
	title = {Responsive and Dynamic Systems from DNA-Mediated Colloidal Interactions},
	year = {2018},
	type = {PhD Thesis},
	abstract = {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.\&nbsp;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.\&nbsp;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.},
	url = {https://dash.harvard.edu/handle/1/39947212},
	author = {Emily W. Gehrels}
}
@article {603986,
	title = {Using DNA strand displacement to control interactions in DNA-grafted colloids},
	journal = {Soft Matter},
	volume = {14},
	number = {6},
	year = {2018},
	month = {04 Jan 2018},
	pages = {969-984},
	abstract = {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.},
	url = {http://dx.doi.org/10.1039/C7SM01722G},
	author = {Emily W. Gehrels and W. Benjamin Rogers and Vinothan N. Manoharan}
}
@article {603985,
	title = {Colloquium: Toward living matter with colloidal particles},
	journal = {Reviews of Modern Physics},
	volume = {89},
	number = {3},
	year = {2017},
	pages = {031001},
	abstract = {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{\textemdash}so that each particle can be programmed to bind or not bind to any other particle{\textemdash}and also time dependent{\textemdash}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.},
	url = {http://dx.doi.org/10.1103/RevModPhys.89.031001},
	author = {Zorana Zeravcic and Vinothan N. Manoharan and Michael P. Brenner}
}
@article {603983,
	title = {Effects of Contact-Line Pinning on the Adsorption of Nonspherical Colloids at Liquid Interfaces},
	journal = {Physical Review Letters},
	volume = {119},
	number = {10},
	year = {2017},
	note = {Supplementary movie available from article page on PRL website},
	pages = {108004},
	abstract = {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.},
	url = {http://dx.doi.org/10.1103/PhysRevLett.119.108004},
	author = {Wang, Anna and W. Benjamin Rogers and Vinothan N. Manoharan}
}
@article {603981,
	title = {Inverse Photonic Glasses by Packing Bidisperse Hollow Microspheres with Uniform Cores},
	journal = {ACS Applied Materials \& Interfaces},
	volume = {9},
	number = {28},
	year = {2017},
	pages = {24155-24160},
	abstract = {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.},
	url = {http://dx.doi.org/10.1021/acsami.7b02098},
	author = {Kim, Seung-Hyun and Sofia Magkiriadou and Rhee, Do Kyung and Lee, Doo Sung and Yoo, Pil J. and Vinothan N. Manoharan and Gi-Ra Yi}
}
@article {603980,
	title = {Colloidal Alchemy: Conversion of Polystyrene Nanoclusters into Gold},
	journal = {ChemNanoMat},
	volume = {3},
	number = {3},
	year = {2017},
	pages = {160-163},
	abstract = {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.},
	url = {http://dx.doi.org/10.1002/cnma.201600315},
	author = {Cyril Chomette and Mona Tr{\'e}guer-Delapierre and Schade, Nicholas B. and Vinothan N. Manoharan and Olivier Lambert and Jean-Christophe Taveau and Serge Ravaine and Etienne Duguet}
}
@patent {603977,
	title = {United States Patent 9541674: Photonic balls containing a microstructure of core-shell particles exhibiting angularly-independent structural color},
	volume = {9541674},
	number = {U.S Patent and Trademark Office},
	year = {2017},
	edition = {United States of America},
	chapter = {US},
	url = {http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2\&Sect2=HITOFF\&p=1\&u=\%2Fnetahtml\%2FPTO\%2Fsearch-bool.html\&r=1\&f=G\&l=50\&co1=AND\&d=PTXT\&s1=9,541,674.PN.\&OS=PN/9,541,674\&RS=PN/9,541,674},
	author = {Vinothan Manoharan and Sofia Magkiriadou and Jin-Gyu Park}
}
@article {603975,
	title = {Photonic-crystal hydrogels with a rapidly tunable stop band and high reflectivity across the visible},
	journal = {Optical Materials Express},
	volume = {7},
	number = {1},
	year = {2017},
	note = {Open access: PDF of published article},
	pages = {253-263},
	abstract = {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.},
	url = {http://dx.doi.org/10.1364/OME.7.000253},
	author = {Jin-Gyu Park and W. Benjamin Rogers and Sofia Magiriadou and Tom Kodger and Shin-Hyun Kim and Young-Seok Kim and Vinothan N. Manoharan}
}
@article {603924,
	title = {Core{\textendash}shell colloidal particles with dynamically tunable scattering properties},
	journal = {Soft Matter},
	volume = {13},
	number = {37},
	year = {2017},
	pages = {6293-6296},
	abstract = {We design polystyrene{\textendash}poly(N'-isopropylacrylamide-co-acrylic acid) core{\textendash}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.},
	url = {http://dx.doi.org/10.1039/C7SM01740E},
	author = {Guangnan Meng and Vinothan N. Manoharan and Adeline Perro}
}
@article {603923,
	title = {Nanoparticle assembly: a perspective and some unanswered questions},
	journal = {Current Science},
	volume = {112},
	number = {8},
	year = {2017},
	note = {Open access: full-text PDF},
	pages = {1635-1641},
	abstract = {In early 2016, the Royal Society of Chemistry arranged a meeting on the topic {\textquoteleft}Nanoparticle Assemblies: from Fundamentals to Applications{\textquoteright} 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.},
	url = {http://dx.doi.org/10.18520/cs/v112/i08/1635-1641},
	author = {Sanat K. Kumar and Guruswamy Kumaraswamy and Bhagavatula L. V. Prasad and Rajdip Bandyopadhyaya and Steve Granick and Oleg Gang and Vinothan N. Manoharan and Daan Frenkel and Nicholas A. Kotov}
}
@article {603970,
	title = {Contact-line pinning controls how quickly colloidal particles equilibrate with liquid interfaces},
	journal = {Soft Matter},
	volume = {12},
	number = {43},
	year = {2016},
	pages = {8958-8967},
	abstract = {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 {\textquoteleft}{\textquoteleft}hairs{\textquoteright}{\textquoteright} 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.},
	url = {http://dx.doi.org/10.1039/C6SM01690A},
	author = {Wang, Anna and McGorty, Ryan and David M. Kaz and Vinothan N. Manoharan}
}
@article {603918,
	title = {Colloidal particle adsorption at liquid interfaces: capillary driven dynamics and thermally activated kinetics},
	journal = {Soft Matter},
	volume = {12},
	number = {30},
	year = {2016},
	pages = {6365-6372},
	abstract = {The adsorption of single colloidal microparticles (0.5{\textendash}1 μm radius) at a water{\textendash}oil interface has been recently studied experimentally using digital holographic microscopy [Kaz et al., Nat. Mater., 2012, 11, 138{\textendash}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 {\textquotedblleft}defects{\textquotedblright} with nanoscale dimensions (1{\textendash}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.},
	url = {http://dx.doi.org/10.1039/C6SM00966B},
	author = {Amir M. Rahmani and Wang, Anna and Vinothan N. Manoharan and Carlos E. Colosqui}
}
@article {480876,
	title = {Segregation of {\textquotedblleft}isotope{\textquotedblright} particles within colloidal molecules},
	journal = {Soft Matter},
	volume = {12},
	number = {11},
	year = {2016},
	month = {08 March 2016},
	pages = {2868-2876},
	abstract = {Clusters of spherical particles are called {\textquotedblleft}colloidal molecules{\textquotedblright} 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 {\textquotedblleft}isotopes,{\textquotedblright} 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.},
	url = {http://dx.doi.org/10.1039/C5SM02851E},
	author = {Rebecca W. Perry and Vinothan N. Manoharan}
}
@article {C6FD00022C,
	title = {Templated growth of gold satellites on dimpled silica cores},
	journal = {Faraday Discussions},
	volume = {191},
	year = {2016},
	pages = {105-116},
	publisher = {The Royal Society of Chemistry},
	abstract = {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.},
	doi = {10.1039/C6FD00022C},
	url = {http://dx.doi.org/10.1039/C6FD00022C},
	author = {Chomette, C. and Duguet, E. and Mornet, S. and Yammine, E. and Manoharan, V. N. and Schade, N. B. and Hubert, C. and Ravaine, S. and Perro, A. and Treguer-Delapierre, M.}
}
@article {Dimiduk:16,
	title = {Bayesian approach to analyzing holograms of colloidal particles},
	journal = {Optics Express},
	volume = {24},
	number = {21},
	year = {2016},
	month = {17 Oct 2016},
	pages = {24045{\textendash}24060},
	publisher = {OSA},
	abstract = {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.},
	keywords = {Digital holography, Holography, inverse problems, Inverse scattering, Three-dimensional sensing},
	doi = {10.1364/OE.24.024045},
	url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-24-21-24045},
	author = {Thomas G. Dimiduk and Vinothan N. Manoharan}
}
@article {Wang:16,
	title = {Tracking E. coli runs and tumbles with scattering solutions and digital holographic microscopy},
	journal = {Optics Express},
	volume = {24},
	number = {21},
	year = {2016},
	note = {Open access: PDF of published article},
	month = {17 Oct 2016},
	pages = {23719{\textendash}23725},
	publisher = {OSA},
	abstract = {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\&amp;\#x02019;s body rotation and tumbles, offering a precise way to track fine details of bacterial motility. We are able to extract the cell\&amp;\#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.},
	keywords = {Digital holography, Holography, inverse problems, Inverse scattering, Medical and biological imaging, Three-dimensional microscopy},
	doi = {10.1364/OE.24.023719},
	url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-24-21-23719},
	author = {Wang, Anna and Garmann, Rees F. and Vinothan N. Manoharan}
}
@article {456421,
	title = {Using DNA to Program the Self-Assembly of Colloidal Nanoparticles and Microparticles},
	journal = {Nature Reviews Materials},
	year = {2016},
	month = {01 March, 2016},
	abstract = {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, {\textquoteleft}program{\textquoteright} 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 {\textemdash} and ultimately program {\textemdash} the assembly of new materials.},
	url = {http://dx.doi.org/10.1038/natrevmats.2016.8},
	author = {W. Benjamin Rogers and William M. Shih and Vinothan N. Manoharan}
}
@article {goldfain2016dynamic,
	title = {Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages},
	journal = {The Journal of Physical Chemistry B},
	volume = {120},
	number = {26},
	year = {2016},
	note = {Supplementary movies available at the ACS Publications web site.},
	month = {07 July 2016},
	pages = {6130{\textendash}6138},
	publisher = {ACS Publications},
	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 {\texttimes} 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.},
	url = {http://dx.doi.org/10.1021/acs.jpcb.6b02153},
	author = {Goldfain, Aaron M and Garmann, Rees F and Jin, Yan and Lahini, Yoav and Vinothan N. Manoharan}
}
@article {480966,
	title = {Colloidal matter: Packing, geometry, and entropy},
	journal = {Science},
	volume = {349},
	number = {6251},
	year = {2015},
	month = {28 August 2015},
	pages = {1253751},
	abstract = {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.},
	url = {http://dx.doi.org/10.1126/science.1253751},
	author = {Vinothan N. Manoharan}
}
@article {481036,
	title = {Colloids at interfaces: Pinned down},
	journal = {Nature Materials},
	volume = {14},
	number = {9},
	year = {2015},
	month = {September 2015},
	pages = {869-870},
	abstract = {(News and Views) A colloidal particle straddling an air/water interface experiences an unexpectedly large viscous drag.},
	url = {http://dx.doi.org/10.1038/nmat4400},
	author = {Vinothan N. Manoharan}
}
@article {480896,
	title = {Celebrating Soft Matter{\textquoteright}s 10th anniversary: Testing the foundations of classical entropy: colloid experiments},
	journal = {Soft Matter},
	volume = {11},
	number = {33},
	year = {2015},
	month = {12 August 2015},
	pages = {6538-6546},
	abstract = {Defining the entropy of classical particles raises a number of paradoxes and ambiguities, some of which have been known for over a century. Several, such as Gibbs{\textquoteright} paradox, involve the fact that classical particles are distinguishable, and in textbooks these are often {\textquoteleft}resolved{\textquoteright} by appeal to the quantum-mechanical indistinguishability of atoms or molecules of the same type. However, questions then remain of how to correctly define the entropy of large poly-atomic particles such as colloids in suspension, of which no two are exactly alike. By performing experiments on such colloids, one can establish that certain definitions of the classical entropy fit the data, while others in the literature do not. Specifically, the experimental facts point firmly to an {\textquoteleft}informatic{\textquoteright} interpretation that dates back to Gibbs: entropy is determined by the number of microstates that we as observers choose to treat as equivalent when we identify a macrostate. This approach, unlike some others, can account for the existence of colloidal crystals, and for the observed abundances of colloidal clusters of different shapes. We also address some lesser-known paradoxes whereby the physics of colloidal assemblies, which ought to be purely classical, seems to involve quantum mechanics directly. The experimental symptoms of such involvement are predicted to be {\textquoteleft}isotope effects{\textquoteright} in which colloids with different inertial masses, but otherwise identical sizes and properties, show different aggregation statistics. These paradoxes are caused by focussing one{\textquoteright}s attention on some classical degrees while neglecting others; when all are treated equally, all isotope effects are found to vanish.},
	url = {http://dx.doi.org/10.1039/C5SM01014D},
	author = {Michael E. Cates and Vinothan N. Manoharan}
}
@article {410036,
	title = {Fast, label-free tracking of single viruses and weakly scattering nanoparticles in a nanofluidic optical fiber},
	journal = {ACS Nano},
	volume = {9},
	number = {12},
	year = {2015},
	month = {3 Nov, 2015},
	pages = {12349-12357},
	abstract = {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{\textquoteright}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{\textemdash}26 nm in size and 4.6 megadaltons in mass{\textemdash}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.},
	url = {http://pubs.acs.org/doi/abs/10.1021/acsnano.5b05646},
	author = {Faez, Sanli and Latin, Yoav and Weidlich, Stefan and Garmann, Rees F. and Wondraczek, Katrin and Zeisberger, Matthias and Schmidt, Markus A. and Orrit, Michel and Vinothan N. Manoharan}
}
@mastersthesis {283571,
	title = {Internal Dynamics of Equilibrium Colloidal Clusters},
	year = {2015},
	type = {PhD thesis},
	abstract = {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.},
	url = {http://dash.harvard.edu/handle/1/17465314},
	author = {Rebecca W. Perry}
}
@mastersthesis {283576,
	title = {Self-Assembly of Plasmonic Nanoclusters for Optical Metafluids},
	year = {2015},
	type = {PhD thesis},
	abstract = {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 {\textquotedblleft}random parking{\textquotedblright} 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.},
	url = {http://dash.harvard.edu/handle/1/17467519},
	author = {Schade, Nicholas B.}
}
@article {283496,
	title = {A Simple RNA-DNA Scaffold Templates the Assembly of Monofunctional Virus-Like Particles},
	journal = {JACS},
	volume = {137},
	number = {24},
	year = {2015},
	month = {24 June 2015},
	pages = {7584{\textendash}7587},
	abstract = {Using the components of a particularly well-studied plant virus, cowpea chlorotic mottle virus (CCMV), we demonstrate the synthesis of virus-like particles (VLPs) with one end of the packaged RNA extending out of the capsid and into the surrounding solution. This construct breaks the otherwise perfect symmetry of the capsid and provides a straightforward route for monofunctionalizing VLPs using the principles of DNA nanotechnology. It also allows physical manipulation of the packaged RNA, a previously inaccessible part of the viral architecture. Our synthesis does not involve covalent chemistry of any kind; rather, we trigger capsid assembly on a scaffold of viral RNA that is hybridized at one end to a complementary DNA strand. Interaction of CCMV capsid protein with this RNA-DNA template leads to selective packaging of the RNA portion into a well-formed capsid but leaves the hybridized portion poking out of the capsid through a small hole. We show that the nucleic acid protruding from the capsid is capable of binding free DNA strands and DNA-functionalized colloidal particles. Separately, we show that the RNA-DNA scaffold can be used to nucleate virus formation on a DNA-functionalized surface. We believe this self-assembly strategy can be adapted to viruses other than CCMV.},
	url = {http://dx.doi.org/10.1021/jacs.5b03770},
	author = {Garmann, Rees F. and Sportsman, Richard and Beren, Christian and Vinothan N. Manoharan and Knobler, Charles M. and Gelbart, William M.}
}
@mastersthesis {283566,
	title = {Structural Color From Colloidal Glasses},
	year = {2015},
	type = {PhD thesis},
	abstract = {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{\textquoteright}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.},
	url = {http://dash.harvard.edu/handle/1/14226099},
	author = {Sofia Magkiriadou}
}
@article {283506,
	title = {Two-Dimensional Clusters of Colloidal Spheres: Ground States, Excited States, and Structural Rearrangements},
	journal = {Phys. Rev. Lett.},
	volume = {114},
	number = {22},
	year = {2015},
	month = {3 Jun 2015},
	pages = {228301},
	abstract = {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 {\textquotedblleft}sticky parameter{\textquotedblright} 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.},
	url = {http://dx.doi.org/10.1103/PhysRevLett.114.228301},
	author = {Rebecca W. Perry and Holmes-Cerfon, Miranda C. and Brenner, Michael P and Vinothan N. Manoharan}
}
@article {252801,
	title = {Osmotic-Pressure-Mediated Control of Structural Colors of Photonic Capsules},
	journal = {Chemistry of Materials},
	volume = {27},
	number = {3},
	year = {2015},
	month = {10 Feb 2015},
	pages = {1014{\textendash}1020},
	abstract = {Crystalline or glassy materials made of colloidal nanoparticles show distinctive photonic effects; the crystals exhibit sparkling colors with strong iridescence, while the glasses show noniridescent colors. Both colors are the results of constructive interference of the reflected light by the nonadsorbing nanostructures. Such colored materials have potential applications as nonfading colorants in reflective color displays, optical sensors, coatings, and cosmetics. All of these applications require granular format of the nanostructures; however, precise control of the nanostructures from amorphous to crystalline over the submillimeter length scale remains challenging. Here, we present micrometer-level control of photonic nanostructures confined in microcapsules through osmotic-pressure-mediated concentration. We encapsulate aqueous suspensions of colloidal particles using double-emulsion drops with ultrathin layers of photocurable resin. The microcapsules are then isotropically compressed by imposing a positive osmotic pressure difference that forces the water out through the thin resin membrane. We find that the internal nanostructure of our photonic microcapsules can be kinetically controlled from crystalline to amorphous; slow concentration in small pressure gradients yields colloidal crystals with sparkling color patterns, whereas fast concentration in large pressure gradients yields glassy packing with only short-range order, which show uniform color with little iridescence. By polymerizing the thin monomeric shell, we permanently fix these nanostructures. Our findings provide new insights into the design and synthesis of optical materials with controlled structural colors.},
	url = {http://dx.doi.org/10.1021/cm5043292},
	author = {Tae Min Choi and Jin-Gyu Park and Young-Seok Kim and Vinothan N. Manoharan and Shin-Hyun Kim}
}
@article {242441,
	title = {Programming colloidal phase transitions with DNA strand displacement},
	journal = {Science},
	volume = {347},
	number = {6222},
	year = {2015},
	note = {Highlighted in Nature Materials},
	pages = {639-642},
	abstract = {DNA-grafted nanoparticles have been called {\textquotedblleft}programmable atom-equivalents{\textquotedblright}: Like atoms, they form three-dimensional crystals, but unlike atoms, the particles themselves carry information (the sequences of the grafted strands) that can be used to {\textquotedblleft}program{\textquotedblright} the equilibrium crystal structures. We show that the programmability of these colloids can be generalized to the full temperature-dependent phase diagram, not just the crystal structures themselves. We add information to the buffer in the form of soluble DNA strands designed to compete with the grafted strands through strand displacement. Using only two displacement reactions, we program phase behavior not found in atomic systems or other DNA-grafted colloids, including arbitrarily wide gas-solid coexistence, reentrant melting, and even reversible transitions between distinct crystal phases.},
	url = {http://www.sciencemag.org/content/347/6222/639.abstract},
	author = {William Benjamin Rogers and Vinothan N. Manoharan}
}
@mastersthesis {283556,
	title = {Self-Assembly of Colloidal Spheres with Specific Interactions},
	year = {2014},
	type = {PhD thesis},
	abstract = {In this thesis, I discuss engineering colloidal particles to have specific, isotropic interactions and studying their cluster geometries in equilibrium. I discuss light scattering experiments showing that a highly specific protein, Dscam, is unstable against thermal aggregation. This result lead me to use DNA instead to control interparticle specificity. I coated 1-micron diameter polystyrene particles uniformly with DNA. I used fluorescence microscopy with oxygen-scavenging enzymes to observe these particles self-assembling in clusters. These experiments show that a packing of 6 spheres that is rarely seen in a single-component system is observed very often in an optimized 3-species system. Then I show experiments using the same 3 species but 9 total particles, finding that the equilibrium yields of the most likely cluster relative to other stable clusters are lower than at 6 particles. I conclude from these experiments that optimizing the assembly of an otherwise unlikely configuration may require nearly as many species as particles. Finally, I investigate the scalability of self-assembly of particles with isotropic and specific interactions theoretically. I use both exact and approximate partition functions to show that spheres with specific interactions can have energy landscapes with thermodynamically large numbers of strictly local minima relative to the number of their ground states. Compared to single-component systems, these systems of many different species may spend much more time in kinetic traps and never reach their ground states. Finally, I discuss briefly some directions for further study, including questions of how the results in this thesis may be related to protein folding and complex formation.},
	url = {http://dash.harvard.edu/handle/1/12274201?show=full},
	author = {Jesse W. Collins}
}
@article {252806,
	title = {Absence of red structural color in photonic glasses, bird feathers, and certain beetles},
	journal = {Physical Review E},
	volume = {90},
	year = {2014},
	pages = {062302},
	abstract = {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.},
	url = {http://dx.doi.org/10.1103/PhysRevE.90.062302},
	author = {Sofia Magkiriadou and Jin-Gyu Park and Young-Seok Kim and Vinothan N. Manoharan}
}
@patent {252826,
	title = {Photonic balls containing a microstructure of core-shell particles exhibiting angularly-independent structural color},
	volume = {US20140254017 A1},
	number = {U.S. Patent and Trademark Office},
	year = {2014},
	edition = {United States of America},
	chapter = {US},
	abstract = {A photonic assembly for observing a preselected color includes an assembly of colloidal particles in a continuous liquid phase, the colloidal particles comprising a core scattering center and a shell layer surrounding the core, wherein the core scattering center is selected to scatter light having a predetermined wavelength, and wherein the shell has a thickness selected to provide an overall colloidal particle size that is about the same dimension as the wavelength of preselected color to be observed.},
	author = {Vinothan Manoharan and Sofia Magkiriadou and Jin-Gyu Park}
}
@article {252821,
	title = {Random-subset fitting of digital holograms for fast three-dimensional particle tracking [Invited]},
	journal = {Applied Optics},
	volume = {53},
	number = {27},
	year = {2014},
	pages = {G177-G183},
	abstract = {Fitting scattering solutions to time series of digital holograms is a precise way to measure three-dimensional dynamics of microscale objects such as colloidal particles. However, this inverse-problem approach is computationally expensive. We show that the computational time can be reduced by an order of magnitude or more by fitting to a random subset of the pixels in a hologram. We demonstrate our algorithm on experimentally measured holograms of micrometer-scale colloidal particles, and we show that 20-fold increases in speed, relative to fitting full frames, can be attained while introducing errors in the particle positions of 10\&nbsp;nm or less. The method is straightforward to implement and works for any scattering model. It also enables a parallelization strategy wherein random-subset fitting is used to quickly determine initial guesses that are subsequently used to fit full frames in parallel. This approach may prove particularly useful for studying rare events, such as nucleation, that can only be captured with high frame rates over long times.},
	url = {http://dx.doi.org/10.1364/AO.53.00G177},
	author = {Dimiduk, Thomas G and Rebecca W. Perry and Fung, Jerome and Vinothan N. Manoharan}
}
@article {252811,
	title = {Size limits of self-assembled colloidal structures made using specific interactions},
	journal = {PNAS},
	volume = {111},
	number = {45},
	year = {2014},
	month = {11 Nov 2014},
	pages = {15918 {\textendash} 15923},
	abstract = {We establish size limitations for assembling structures of controlled size and shape out of colloidal particles with short-ranged interactions. Through simulations we show that structures with highly variable shapes made out of dozens of particles can form with high yield, as long as each particle in the structure binds only to the particles in their local environment. To understand this, we identify the excited states that compete with the ground-state structure and demonstrate that these excited states have a completely topological characterization, valid when the interparticle interactions are short-ranged. This allows complete enumeration of the energy landscape and gives bounds on how large a colloidal structure can assemble with high yield. For large structures the yield can be significant, even with hundreds of particles.},
	url = {http://dx.doi.org/10.1073/pnas.1411765111},
	author = {Zorana Zeravcic and Vinothan N. Manoharan and Brenner, Michael P}
}
@article {252816,
	title = {Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles},
	journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
	volume = {146},
	year = {2014},
	pages = {499{\textendash}509},
	abstract = {We present a new, high-speed technique to track the three-dimensional translation and rotation of non-spherical colloidal particles. We capture digital holograms of micrometer-scale silica rods and sub-micrometer-scale Janus particles freely diffusing in water, and then fit numerical scattering models based on the discrete dipole approximation to the measured holograms. This inverse-scattering approach allows us to extract the position and orientation of the particles as a function of time, along with static parameters including the size, shape, and refractive index. The best-fit sizes and refractive indices of both particles agree well with expected values. The technique is able to track the center of mass of the rod to a precision of 35\&nbsp;nm and its orientation to a precision of 1.5{\textdegree}, comparable to or better than the precision of other 3D diffusion measurements on non-spherical particles. Furthermore, the measured translational and rotational diffusion coefficients for the silica rods agree with hydrodynamic predictions for a spherocylinder to within 0.3\%. We also show that although the Janus particles have only weak optical asymmetry, the technique can track their 2D translation and azimuthal rotation over a depth of field of several micrometers, yielding independent measurements of the effective hydrodynamic radius that agree to within 0.2\%. The internal and external consistency of these measurements validate the technique. Because the discrete dipole approximation can model scattering from arbitrarily shaped particles, our technique could be used in a range of applications, including particle tracking, microrheology, and fundamental studies of colloidal self-assembly or microbial motion.},
	url = {http://dx.doi.org/10.1016/j.jqsrt.2013.12.019},
	author = {Wang, Anna and Dimiduk, Thomas G and Fung, Jerome and Razavi, Sepideh and Kretzschmar, Ilona and Kundan Chaudhary and Vinothan N. Manoharan}
}
@article {252461,
	title = { Elastic Instability of a Crystal Growing on a Curved Surface },
	journal = {Science},
	volume = {343},
	number = {6171},
	year = {2014},
	note = {See also:

News story from the Harvard Gazette
Blog post on chemistry.com

Supporting information:

Supplementary Methods
Supplementary Movie 1
Supplementary Movie 2
Supplementary Movie 3
Supplementary Movie 4

Download PDF},
	pages = {634-637},
	abstract = {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.},
	url = {http://dx.doi.org/10.1126/science.1244827},
	author = {Guangnan Meng and Jayson Paulose and Nelson, David R and Vinothan N. Manoharan}
}
@article {252456,
	title = { Osmotic-pressure-controlled concentration of colloidal particles in thin-shelled capsules },
	journal = {Nature Communications},
	volume = {5},
	year = {2014},
	note = {Download PDF},
	pages = {3068},
	abstract = {Colloidal crystals are promising structures for photonic applications requiring dynamic control over optical properties. However, for ease of processing and reconfigurability, the crystals should be encapsulated to form {\textquoteleft}ink{\textquoteright} capsules rather than confined in a thin film. Here we demonstrate a class of encapsulated colloidal photonic structures whose optical properties can be controlled through osmotic pressure. The ordering and separation of the particles within the microfluidically created capsules can be tuned by changing the colloidal concentration through osmotic pressure-induced control of the size of the individual capsules, modulating photonic stop band. The rubber capsules exhibit a reversible change in the diffracted colour, depending on osmotic pressure, a property we call osmochromaticity. The high encapsulation efficiency and capsule uniformity of this microfluidic approach, combined with the highly reconfigurable shapes and the broad control over photonic properties, make this class of structures particularly suitable for photonic applications such as electronic inks and reflective displays.},
	url = {http://dx.doi.org/10.1038/ncomms4068},
	author = {Shin-Hyun Kim and Jin-Gyu Park and Tae Min Choi and Vinothan N. Manoharan and Weitz, David A.}
}
@article {242471,
	title = {Breaking trade-offs between translucency and diffusion in particle-doped films},
	journal = {Optical Materials Express},
	volume = {4},
	number = {12},
	year = {2014},
	pages = {2621-2631},
	abstract = {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.},
	url = {http://www.opticsinfobase.org/ome/abstract.cfm?uri=ome-4-12-2621},
	author = {William Benjamin Rogers and Madelein Corbett and Sofia Magkiriadou and Philippe Guarillof and Vinothan N. Manoharan}
}
@article {242436,
	title = {Full-Spectrum Photonic Pigments with Non-iridescent Structural Colors through Colloidal Assembly},
	journal = {Angewandte Chemie International Edition},
	volume = {53},
	number = {11},
	year = {2014},
	pages = {2899-2903},
	abstract = {Structurally colored materials could potentially replace dyes and pigments in many applications, but it is challenging to fabricate structural colors that mimic the appearance of absorbing pigments. We demonstrate the microfluidic fabrication of {\textquotedblleft}photonic pigments{\textquotedblright} consisting of microcapsules containing dense amorphous packings of core{\textendash}shell colloidal particles. These microcapsules show non-iridescent structural colors that are independent of viewing angle, a critical requirement for applications such as displays or coatings. We show that the design of the microcapsules facilitates the suppression of incoherent and multiple scattering, enabling the fabrication of photonic pigments with colors spanning the visible spectrum. Our findings should provide new insights into the design and synthesis of materials with structural colors.},
	url = {http://dx.doi.org/10.1002/anie.201309306},
	author = {Jin-Gyu Park and Shin-Hyun Kim and Sofia Magkiriadou and Tae Min Choi and Young-Seok Kim and Vinothan N. Manoharan}
}
@article {242456,
	title = {Synchronized reinjection and coalescence of droplets in microfluidics},
	journal = {Lab on a Chip},
	volume = {14},
	number = {3},
	year = {2014},
	note = {Supplementary Information
Supplementary Movie 1
Supplementary Movie 2
Supplementary Movie 3
Supplementary Movie 4},
	pages = {509-513},
	abstract = {Coalescence of two kinds of pre-processed droplets is necessary to perform chemical and biological assays in droplet-based microfluidics. However, a robust technique to accomplish this does not exist. Here we present a microfluidic device to synchronize the reinjection of two different kinds of droplets and coalesce them, using hydrostatic pressure in conjunction with a conventional syringe pump. We use a device consisting of two opposing T-junctions for reinjecting two kinds of droplets and control the flows of the droplets by applying gravity-driven hydrostatic pressure. The hydrostatic-pressure operation facilitates balancing the droplet reinjection rates and allows us to synchronize the reinjection. Furthermore, we present a simple but robust module to coalesce two droplets that sequentially come into the module, regardless of their arrival times. These re-injection and coalescence techniques might be used in lab-on-chip applications requiring droplets with controlled numbers of solid materials, which can be made by coalescing two pre-processed droplets that are formed and sorted in devices.},
	url = {http://dx.doi.org/10.1039/C3LC51214B},
	author = {Manhee Lee and Jesse W. Collins and Donald M. Aubrecht and Ralph Sperling and Laura Solomon and Jong-Wook Ha and Gi-Ra Yi and Weitz, David A. and Vinothan N. Manoharan}
}
@article {252446,
	title = { Generalization of the optical theorem for light scattering from a particle at a planar interface },
	journal = {Journal of the Optical Society of America A},
	volume = {30},
	number = {12},
	year = {2013},
	pages = {2519-2525},
	abstract = {The optical theorem provides a powerful tool for calculating the extinction cross section of a particle from a solution to Maxwell{\textquoteright}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.},
	url = {http://dx.doi.org/10.1364/JOSAA.30.002519},
	author = {Alex Small and Fung, Jerome and Vinothan N. Manoharan}
}
@article {252416,
	title = {Glycans pattern the phase behaviour of lipid membranes},
	journal = {Nature Materials},
	volume = {12},
	year = {2013},
	note = {See the Perspective by Jay T. Groves in Nature Materials},
	month = {Feb 2013},
	pages = {128-133},
	abstract = {Hydrated networks of glycans (polysaccharides){\textemdash}in the form of cell walls, periplasms or gel-like matrices{\textemdash}are ubiquitously present adjacent to cellular plasma membranes. Yet, despite their abundance, the function of glycans in the extracellular milieu is largely unknown. Here we show that the spatial configuration of glycans controls the phase behaviour of multiphase model lipid membranes: inhomogeneous glycan networks stabilize large lipid domains at the characteristic length scale of the network, whereas homogeneous networks suppress macroscopic lipid phase separation. We also find that glycan-patterned phase separation is thermally reversible{\textemdash}thus indicating that the effect is thermodynamic rather than kinetic{\textemdash}and that phase patterning probably results from a preferential interaction of glycans with ordered lipid phases. These findings have implications for membrane-mediated transport processes, potentially rationalize long-standing observations that differentiate the behaviour of native and model membranes and may indicate an intimate coupling between cellular lipidomes and glycomes.},
	url = {http://dx.doi.org/10.1038/nmat3492},
	author = {Anand Bala~Subramaniam and Guido Guidotti and Vinothan N. Manoharan and Howard A. Stone}
}
@article {252431,
	title = { Holographic Measurements of Anisotropic Three-Dimensional Diffusion of Colloidal Clusters },
	journal = {Physical Review E},
	volume = {88},
	number = {2},
	year = {2013},
	note = {Supplementary Information
Download PDF},
	pages = {020302},
	abstract = {We measure all nonzero elements of the three-dimensional diffusion tensor D for clusters of colloidal spheres to a precision of 1\% or better using digital holographic microscopy. We study both dimers and triangular trimers of spheres, for which no analytical calculations of the diffusion tensor exist. We observe anisotropic rotational and translational diffusion arising from the asymmetries of the clusters. In the case of the three-particle triangular cluster, we also detect a small but statistically significant difference in the rotational diffusion about the two in-plane axes. We attribute this difference to weak breaking of threefold rotational symmetry due to a small amount of particle polydispersity. Our experimental measurements agree well with numerical calculations and show how diffusion constants can be measured under conditions relevant to colloidal self-assembly, where theoretical and even numerical prediction is difficult.},
	url = {http://dx.doi.org/10.1103/PhysRevE.88.020302},
	author = {Fung, Jerome and Vinothan N. Manoharan}
}
@mastersthesis {252436,
	title = {Measuring the 3D Dynamics of Multiple Colloidal Particles with Digital Holographic Microscopy},
	year = {2013},
	type = {PhD Thesis},
	abstract = {We discuss digital holographic microscopy (DHM), a 3D imaging technique capable of measuring the positions of micron-sized colloidal particles with nanometer precision and sub-millisecond temporal resolution. We use exact electromagnetic scattering solutions to model holograms of multiple colloidal spheres. While the Lorenz-Mie solution for scattering by isolated spheres has previously been used to model digital holograms, we apply for the first time an exact multisphere superposition scattering model that is capable of modeling holograms from spheres that are sufficiently close together to exhibit optical coupling.},
	url = {http://dash.harvard.edu/bitstream/handle/1/11181215/Fung_gsas.harvard_0084L_11200.pdf},
	author = {Fung, Jerome}
}
@proceedings {252421,
	title = {Relaxation dynamics of colloidal particles at liquid interfaces},
	journal = {AIP Conference Proceedings},
	volume = {1518},
	year = {2013},
	note = { Presented at 4th International Symposium on Slow Dynamics in Complex Systems in Sendai, Japan
Download PDF},
	pages = {336-343},
	publisher = {American Institute of Physics},
	address = {Sendai, Japan},
	abstract = {We study the dynamics of colloidal particles as they approach and breach a water-oil interface. We use a fast 3D imaging technique, digital holographic microscopy, to track particles with 2 nm precision and sub-millisecond time resolution. We find that polystyrene particles dispersed in water or water-glycerol mixtures relax logarithmically with time after breaching the interface and do not reach equilibrium on experimental timescales. By contrast, decane-dispersed PMMA particles show fast dynamics and reach a steady-state height within milliseconds. We attribute the difference to the surface properties of the particles. We also probe the dependence of the relaxation rate on surface charge by studying carboxyl-functionalized particles under varying acid concentrations. We conclude that the slow relaxation may be due to contact-line pinning on topographical defects rather than surface charges.},
	url = {http://dx.doi.org/10.1063/1.4794594},
	author = {Wang, Anna and Kaz, David M and McGorty, Ryan and Vinothan N. Manoharan}
}
@article {252426,
	title = { Tetrahedral colloidal clusters from random parking of bidisperse spheres },
	journal = {Physical Review Letters},
	volume = {110},
	number = {14},
	year = {2013},
	note = {See also the commentary by Mike Cates in the Journal Club for Condensed Matter Physics
Supporting information
Download PDF},
	pages = {148303},
	abstract = {Using experiments and simulations, we investigate the clusters that form when colloidal spheres stick irreversibly to{\textemdash}or {\textquotedblleft}park{\textquotedblright} on{\textemdash}smaller spheres. We use either oppositely charged particles or particles labeled with complementary DNA sequences, and we vary the ratio α of large to small sphere radii. Once bound, the large spheres cannot rearrange, and thus the clusters do not form dense or symmetric packings. Nevertheless, this stochastic aggregation process yields a remarkably narrow distribution of clusters with nearly 90\% tetrahedra at α=2.45. The high yield of tetrahedra, which reaches 100\% in simulations at α=2.41, arises not simply because of packing constraints, but also because of the existence of a long-time lower bound that we call the {\textquotedblleft}minimum parking{\textquotedblright} number. We derive this lower bound from solutions to the classic mathematical problem of spherical covering, and we show that there is a critical size ratio αc=(1+√2)≈2.41, close to the observed point of maximum yield, where the lower bound equals the upper bound set by packing constraints. The emergence of a critical value in a random aggregation process offers a robust method to assemble uniform clusters for a variety of applications, including metamaterials.},
	url = {http://dx.doi.org/10.1103/PhysRevLett.110.148303},
	author = {Schade, Nicholas B. and Holmes-Cerfon, Miranda C. and Elizabeth R. Chen and Aronzon, Dina and Jesse W. Collins and Fan, Jonathan A. and Capasso, Federico and Vinothan N. Manoharan}
}
@article {252441,
	title = { Ultrasmooth, Highly Spherical Monocrystalline Gold Particles for Precision Plasmonics },
	journal = {ACS Nano},
	volume = {7},
	number = {12},
	year = {2013},
	note = {Supporting informationSupporting Information (movie)},
	pages = {11064-11070},
	abstract = {Ultrasmooth, highly spherical monocrystalline gold particles were prepared by a cyclic process of slow growth followed by slow chemical etching, which selectively removes edges and vertices. The etching process effectively makes the surface tension isotropic, so that spheres are favored under quasi-static conditions. It is scalable up to particle sizes of 200 nm or more. The resulting spherical crystals display uniform scattering spectra and consistent optical coupling at small separations, even showing Fano-like resonances in small clusters. The high monodispersity of the particles we demonstrate should facilitate the self-assembly of nanoparticle clusters with uniform optical resonances, which could in turn be used to fabricate optical metafluids. Narrow size distributions are required to control not only the spectral features but also the morphology and yield of clusters in certain assembly schemes.},
	url = {http://dx.doi.org/10.1021/nn404765w},
	author = {Lee, You-Jin and Schade, Nicholas B. and Sun, Li and Fan, Jonathan A. and Bae, Doo Ri and Mariscal, Marcelo M. and Lee, Gaehang and Capasso, Federico and Sacanna, Stefano and Vinothan N. Manoharan and Gi-Ra Yi}
}
@article {252451,
	title = { Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles },
	journal = {Journal of Quantitative Spectroscopy and Radiative Transfer },
	volume = {146},
	year = {2013},
	note = {Download PDF},
	pages = {499{\textendash}509},
	abstract = {We present a new, high-speed technique to track the three-dimensional translation and rotation of non-spherical colloidal particles. We capture digital holograms of micrometer-scale silica rods and sub-micrometer-scale Janus particles freely diffusing in water, and then fit numerical scattering models based on the discrete dipole approximation to the measured holograms. This inverse-scattering approach allows us to extract the position and orientation of the particles as a function of time, along with static parameters including the size, shape, and refractive index. The best-fit sizes and refractive indices of both particles agree well with expected values. The technique is able to track the center of mass of the rod to a precision of 35 nm and its orientation to a precision of 1.5{\textdegree}, comparable to or better than the precision of other 3D diffusion measurements on non-spherical particles. Furthermore, the measured translational and rotational diffusion coefficients for the silica rods agree with hydrodynamic predictions for a spherocylinder to within 0.3\%. We also show that although the Janus particles have only weak optical asymmetry, the technique can track their 2D translation and azimuthal rotation over a depth of field of several micrometers, yielding independent measurements of the effective hydrodynamic radius that agree to within 0.2\%. The internal and external consistency of these measurements validate the technique. Because the discrete dipole approximation can model scattering from arbitrarily shaped particles, our technique could be used in a range of applications, including particle tracking, microrheology, and fundamental studies of colloidal self-assembly or microbial motion.},
	url = {http://dx.doi.org/10.1016/j.jqsrt.2013.12.019},
	author = {Wang, Anna and Dimiduk, Thomas G and Fung, Jerome and Razavi, Sepideh and Kretzschmar, Ilona and Kundan Chaudhary and Vinothan N. Manoharan}
}
@article {252406,
	title = { Colloids with valence and specific directional bonding },
	journal = {Nature},
	volume = {491},
	number = {7422},
	year = {2012},
	pages = {51-55},
	abstract = {The ability to design and assemble three-dimensional structures from colloidal particles is limited by the absence of specific directional bonds. As a result, complex or low-coordination structures, common in atomic and molecular systems, are rare in the colloidal domain. Here we demonstrate a general method for creating the colloidal analogues of atoms with valence: colloidal particles with chemically distinct surface patches that imitate hybridized atomic orbitals, including sp, sp2, sp3, sp3d, sp3d2 and sp3d3. Functionalized with DNA with single-stranded sticky ends, patches on different particles can form highly directional bonds through programmable, specific and reversible DNA hybridization. These features allow the particles to self-assemble into |[lsquo]|colloidal molecules|[rsquo]| with triangular, tetrahedral and other bonding symmetries, and should also give access to a rich variety of new microstructured colloidal materials.},
	url = {http://dx.doi.org/10.1038/nature11564},
	author = {Yufeng Wang and Yu Wang and Dana R. Breed and Vinothan N. Manoharan and Lang Feng and Andrew D. Hollingsworth and Marcus Weck and David J. Pine}
}
@article {252396,
	title = { Disordered packings of core-shell particles with angle-independent structural colors },
	journal = {Optical Materials Express},
	volume = {2},
	number = {10},
	year = {2012},
	note = {Open access
Perspective from Spotlight on Optics.
Download PDF},
	pages = {1343-1352},
	abstract = {Making materials that display angle-independent structural color requires control over both scattering and short-range correlations in the refractive index. We demonstrate a simple way to make such materials by packing core-shell colloidal particles consisting of high-refractive-index cores and soft, transparent shells. The core-shell structure allows us to control the scattering cross-section of the particles independently of the interparticle distance, which sets the resonance condition. At the same time, the softness of the shells makes it easy to assemble disordered structures through centrifugation. We show that packings of these particles display angle-independent structural colors that can be tuned by changing the shell diameter, either by using different particles or simply by varying the concentration of the suspension. The transparency of the suspensions can be tuned independently of the color by changing the core diameter. These materials might be useful for electronic displays, cosmetics, or long-lasting dyes.},
	url = {http://dx.doi.org/10.1364/OME.2.001343},
	author = {Sofia Magkiriadou and Jin-Gyu Park and Young-Seok Kim and Vinothan N. Manoharan}
}
@article {252411,
	title = { Imaging Multiple Colloidal Particles by Fitting Electromagnetic Scattering Solutions to Digital Holograms },
	journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
	volume = {113},
	number = {18},
	year = {2012},
	note = {Download PDF},
	pages = {2482-2489},
	abstract = {Digital holographic microscopy is a fast three-dimensional (3D) imaging tool with many applications in soft matter physics. Recent studies have shown that electromagnetic scattering solutions can be fit to digital holograms to obtain the 3D positions of isolated colloidal spheres with nanometer precision and millisecond temporal resolution. Here we describe the results of new techniques that extend the range of systems that can be studied with fitting. We show that an exact multisphere superposition scattering solution can fit holograms of colloidal clusters containing up to six spheres. We also introduce an approximate and computationally simpler solution, Mie superposition, that is valid for multiple spheres spaced several wavelengths or more from one another. We show that this method can be used to analyze holograms of several spheres on an emulsion droplet, and we give a quantitative criterion for assessing its validity.},
	url = {http://dx.doi.org/10.1016/j.jqsrt.2012.06.007},
	author = {Fung, Jerome and Rebecca W. Perry and Dimiduk, Thomas G and Vinothan N. Manoharan}
}
@article {252386,
	title = { Physical ageing of the contact line on colloidal particles at liquid interfaces },
	journal = {Nature Materials},
	volume = {11},
	number = {2},
	year = {2012},
	note = {Perspective by Ignacio Pagonabarraga
Download PDF},
	pages = {138-142},
	abstract = {Young{\textquoteright}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 has been used to explain why colloids often bind to liquid interfaces, and has been exploited in emulsification, water purification, mineral recovery, encapsulation and the making of nanostructured materials. However, 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. The relaxation appears logarithmic in time, indicating that complete equilibration may take months. Surprisingly, viscous dissipation appears to play little role. Instead, the observed dynamics, which bear strong resemblance to ageing 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.},
	url = {http://dx.doi.org/10.1038/nmat3190},
	author = {Kaz, David M and McGorty, Ryan and Madhav Mani and Brenner, Michael P and Vinothan N. Manoharan}
}
@article {252401,
	title = { Plasmonic Mode Engineering with Templated Self-Assembled Nanoclusters },
	journal = {Nano Letters},
	volume = {12},
	number = {10},
	year = {2012},
	note = {Download PDF},
	pages = {5318-5324},
	abstract = {Plasmonic nanoparticle assemblies are a materials platform in which optical modes, resonant frequencies, and near-field intensities can be specified by the number and position of nanoparticles in a cluster. A current challenge is to achieve clusters with higher yields and new types of shapes. In this Letter, we show that a broad range of plasmonic nanoshell nanoclusters can be assembled onto a lithographically defined elastomeric substrate with relatively high yields using templated assembly. We assemble and measure the optical properties of three cluster types: Fano-resonant heptamers, linear chains, and rings of nanoparticles. The yield of heptamer clusters is measured to be over 30\%. The assembly of plasmonic nanoclusters on an elastomer paves the way for new classes of plasmonic nanocircuits and colloidal metamaterials that can be transfer-printed onto various substrate media.},
	url = {http://dx.doi.org/10.1021/nl302650t},
	author = {Fan, Jonathan A. and Bao, Kui and Sun, Li and Bao, Jiming and Vinothan N. Manoharan and Nordlander, Peter and Capasso, Federico}
}
@article {252391,
	title = {Real-space studies of the structure and dynamics of self-assembled colloidal clusters},
	journal = {Faraday Discussions},
	volume = {159},
	number = {1},
	year = {2012},
	pages = {211-234},
	abstract = {The energetics and assembly pathways of small clusters may yield insights into processes occurring at the earliest stages of nucleation. We use a model system consisting of micrometer-sized, spherical colloidal particles to study the structure and dynamics of small clusters, where the number of particles is small (N \&lt;= 10). The particles interact through a short-range depletion attraction with a depth of a few k_B T. We describe two methods to form colloidal clusters, one based on isolating the particles in microwells and another based on directly assembling clusters in the gas phase using optical tweezers. We use the first technique to obtain ensemble-averaged probabilities of cluster structures as a function of N. These experiments show that clusters with symmetries compatible with crystalline order are rarely formed under equilibrium conditions. We use the second technique to study the dynamics of the clusters, and in particular how they transition between free-energy minima. To monitor the clusters we use a fast three-dimensional imaging technique, digital holographic microscopy, that can resolve the positions of each particle in the cluster with 30-45 nm precision on millisecond timescales. The real-space measurements allow us to obtain estimates for the lifetimes of the energy minima and the transition states. It is not yet clear whether the observed dynamics are relevant for small nuclei, which may not have sufficient time to transition between states before other particles or clusters attach to them. However, the measurements do provide some glimpses into how systems containing a small number of particles traverse their free-energy landscape.},
	url = {http://dx.doi.org/10.1039/C2FD20061A},
	author = {Rebecca W. Perry and Guangnan Meng and Dimiduk, Thomas G and Fung, Jerome and Vinothan N. Manoharan}
}
@mastersthesis {252366,
	title = { Colloidal Particles and Liquid Interfaces: A Spectrum of Interactions },
	year = {2011},
	type = {PhD Thesis},
	abstract = {Young{\textquoteright}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 emulsi⬚cation, water puri⬚cation, mineral recovery, encapsulation, and the making of nanostructured materials. But little is known about the dynamics of binding, or any aspect of the interaction between a particle and an interface outside of equilibrium. This thesis explores the spectrum of particle-interface interactions, from non-binding to non-adsorptive binding and ⬚finally adsorptive binding and the relaxation toward equilibrium that ensues. Chapter 2 reviews the importance of interfacial particles in materials science, and serves as a partial motivation for the work presented here. Chapter 3 describes the apparatus and experimental procedures employed in the acquisition of our data, with a short review of experiments that led to the current set. Special attention is paid to the optical apparatus and the custom sample cells we designed. Chapter 4 deals with non-adsorptive interactions between colloidal particles and liquid interfaces. A theoretical discussion founded on (but not wedded to) classical DLVO theory is presented before the results of our experiments are analyzed. It is shown that particle interface interactions may be purely repulsive or contain an attractive component that results in binding to the interface that is not associated with breach. In chapter 5 the adsorption of polystyrene microspheres to a water-oil interface is shown to be 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. Finally, in chapter 6, I propose a number of intriguing experiments that build on the knowledge presented in this thesis, and probe areas that were inaccessible because of the ⬚finiteness of my tenure in graduate school.},
	author = {Kaz, David M}
}
@mastersthesis {252371,
	title = { Colloidal Particles at Fluid Interfaces and the Interface of Colloidal Fluids },
	year = {2011},
	type = {PhD Thesis},
	abstract = {Holographic microscopy is a unifying theme in the different projects discussed in this thesis. The technique allows one to observe microscopic objects, like colloids and droplets, in a three-dimensional (3D) volume. Unlike scanning 3D optical techniques, holography captures a sample{\textquoteright}s 3D information in a single image: the hologram. Therefore, one can capture 3D information at video frame rates. The price for such speed is paid in computation time. The 3D information must be extracted from the image by methods such as reconstruction or fitting the hologram to scattering calculations. Using holography, we observe a single colloidal particle approach, penetrate and then slowly equilibrate at an oil{\textendash}water interface. Because the particle moves along the optical axis (z-axis) and perpendicular to the interface holography is used to determine its position. We are able to locate the particle{\textquoteright}s z-position to within a few nanometers with a time resolution below a millisecond. We find that the capillary force pulling the particle into the interface is not balanced by a hydrodynamic force. Rather, a larger-than-viscous dissipation associated with the three-phase contact-line slipping over the particle{\textquoteright}s surface results in equilibration on time scales orders of magnitude longer than the minute time scales over which our setup allows us to examine. A separate project discussed here also examines colloidal particles and fluid-fluid interfaces. But the fluids involved are composed of colloids. With a colloid and polymer water-based mixture we study the phase separation of the colloid-rich (or liquid) and colloid-poor (or gas) region. In comparison to the oil{\textendash}water interface in the previously mentioned project, the interface between the colloidal liquid and gas phases has a surface tension nearly six orders of magnitude smaller. So interfacial fluctuations are observable under microscopy. We also use holographic microscopy to study this system but not to track particles with great time and spatial resolution. Rather, holography allows us to observe nucleation of the liquid phase occurring throughout our sample volume.},
	author = {McGorty, Ryan}
}
@article {252381,
	title = { Deriving Finite Sphere Packings },
	journal = {SIAM Journal on Discrete Mathematics},
	volume = {25},
	number = {4},
	year = {2011},
	note = {See also "The Science of Sticky Spheres" by Brian Hayes (American Scientist 2012).
Download PDF},
	pages = {1860},
	abstract = {Sphere packing problems have a rich history in both mathematics and physics; yet, relatively few analytical analyses of sphere packings exist, and answers to seemingly simple questions are unknown. Here, we present an analytical method for deriving all packings of $n$ spheres in $\mathbb{R}^3$ satisfying minimal rigidity constraints ($\geq 3$ contacts per sphere and $\geq 3n-6$ total contacts). We derive such packings for $n \leq 10$ and provide a preliminary set of maximum contact packings for $10 \&lt; n \leq 20$. The resultant set of packings has some striking features; among them are the following: (i) all minimally rigid packings for $n \leq 9$ have exactly $3n-6$ contacts; (ii) nonrigid packings satisfying minimal rigidity constraints arise for $n \geq 9$; (iii) the number of ground states (i.e., packings with the maximum number of contacts) oscillates with respect to $n$; (iv) for $10 \leq n \leq 20$ there are only a small number of packings with the maximum number of contacts, and for $10 \leq n \&lt; 13$ these are all commensurate with the hexagonal close-packed lattice. The general method presented here may have applications to other related problems in mathematics, such as the Erd{\"o}s repeated distance problem and Euclidean distance matrix completion problems.},
	url = {http://dx.doi.org/10.1137/100784424},
	author = {Natalie Arkus and Vinothan N. Manoharan and Brenner, Michael P}
}
@article {252376,
	title = {DNA-Enabled Self-Assembly of Plasmonic Nanoclusters},
	journal = {Nano Letters},
	volume = {11},
	number = {11},
	year = {2011},
	note = {Reprint\&nbsp;(requires free registration with ACS)},
	pages = {4859-4864},
	abstract = {DNA nanotechnology provides a versatile foundation for the chemical assembly of nanostructures. Plasmonic nanoparticle assemblies are of particular interest because they can be tailored to exhibit a broad range of electromagnetic phenomena. In this Letter, we report the assembly of DNA-functionalized nanoparticles into heteropentamer clusters, which consist of a smaller gold sphere surrounded by a ring of four larger spheres. Magnetic and Fano-like resonances are observed in individual clusters. The DNA plays a dual role: it selectively assembles the clusters in solution and functions as an insulating spacer between the conductive nanoparticles. These particle assemblies can be generalized to a new class of DNA-enabled plasmonic heterostructures that comprise various active and passive materials and other forms of DNA scaffolding.},
	url = {http://dx.doi.org/10.1021/nl203194m},
	author = {Fan, Jonathan A. and He, Yu and Bao, Kui and Wu, Chihhui and Bao, Jiming and Schade, Nicholas B. and Vinothan N. Manoharan and Shvets, Gennady and Nordlander, Peter and Liu, David R. and Capasso, Federico}
}
@article {252361,
	title = { Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy },
	journal = {Optics Express},
	volume = {19},
	number = {9},
	year = {2011},
	note = {Open access
Download PDF},
	pages = {8051-8065},
	abstract = {We discuss a new method for simultaneously probing translational, rotational, and vibrational dynamics in dilute colloidal suspensions using digital holographic microscopy (DHM). We record digital holograms of clusters of 1-μm-diameter colloidal spheres interacting through short-range attractions, and we fit the holograms to an exact model of the scattering from multiple spheres. The model, based on the T-matrix formulation, accounts for multiple scattering and near-field coupling. We also explicitly account for the non-asymptotic radial decay of the scattered fields, allowing us to accurately fit holograms recorded with the focal plane located as little as 15 μm from the particle. Applying the fitting technique to a time-series of holograms of Brownian dimers allows simultaneous measurement of six dynamical modes {\textemdash} three translational, two rotational, and one vibrational {\textemdash} on timescales ranging from 10-3 to 1 s. We measure the translational and rotational diffusion constants to a precision of 0.6\%, and we use the vibrational data to measure the interaction potential between the spheres to a precision of \~{}50 nm in separation distance. Finally, we show that the fitting technique can be used to measure dynamics of clusters containing three or more spheres.},
	url = {http://dx.doi.org/10.1364/OE.19.008051},
	author = {Fung, Jerome and K. Eric Martin and Rebecca W. Perry and Kaz, David M and McGorty, Ryan and Vinothan N. Manoharan}
}
@article {252356,
	title = { Molecular Forces and Self Assembly: In Colloid, Nano Sciences and Biology (Book Review) },
	journal = {Physics Today},
	volume = {64},
	number = {2},
	year = {2011},
	note = {Download PDF},
	pages = {48},
	url = {http://dx.doi.org/10.1063/1.3554316},
	author = {Vinothan N. Manoharan}
}
@article {252351,
	title = { Bulk Synthesis of Polymer-Inorganic Colloidal Clusters },
	journal = {Langmuir},
	volume = {26},
	number = {24},
	year = {2010},
	note = {Reprint\&nbsp;(requires free registration with ACS)},
	pages = {18669-18675},
	abstract = {We describe a procedure to synthesize colloidal clusters with polyhedral morphologies in high yield (liter quantities at up to 70\% purity) using a combination of emulsion polymerization and inorganic surface chemistry. We show that the synthesis initially used for silica-polystyrene hybrid clusters can be generalized to create clusters from other inorganic and polymer particles. We also show that high yields of particular morphologies can be obtained by precise control of the inorganic seed particle size, a finding that can be explained using a hard-sphere packing model. These clusters can be further chemically modified for a variety of applications. Introducing a cross-linker leads to colloidal clusters that can be index matched in an appropriate solvent, allowing them to be used for particle tracking or optical studies of colloidal self-assembly. Also, depositing a thin silica layer on these colloids allows the surface properties to be controlled using silane chemistry.},
	url = {http://dx.doi.org/10.1021/la103308w},
	author = {Adeline Perro and Vinothan N. Manoharan}
}
@article {252341,
	title = {Colloidal self-assembly at an interface},
	journal = {Materials Today},
	volume = {13},
	number = {6},
	year = {2010},
	note = {Download PDF
},
	pages = {34-42},
	abstract = {Mix a drop of water into a vial of oil. With some surfactant and a vigorous shake, that one droplet has become thousands, and the total interfacial area has increased by an order of magnitude or more. Like the folded membranes in our mitochondria, the alveoli in our lungs, and the catalytic converters in our cars, oil-water emulsions contain a vast reservoir of interfacial area that can be used to control and transform the things that encounter it. The oil-water interface is especially well-suited to directing the assembly of colloidal particles, which bind to it rapidly and often irreversibly.},
	url = {http://dx.doi.org/10.1016/S1369-7021(10)70107-3},
	author = {McGorty, Ryan and Fung, Jerome and David Kaz and Vinothan N. Manoharan}
}
@article {252346,
	title = { Fano-like Interference in Self-Assembled Plasmonic Quadrumer Clusters },
	journal = {Nano Letters},
	volume = {10},
	number = {11},
	year = {2010},
	note = {Reprint\&nbsp;(requires free registration with ACS)},
	pages = {4680-4685},
	abstract = {Assemblies of strongly interacting metallic nanoparticles are the basis for plasmonic nanostructure engineering. We demonstrate that clusters of four identical spherical particles self-assembled into a close-packed asymmetric quadrumer support strong Fano-like interference. This feature is highly sensitive to the polarization of the incident electric field due to orientation-dependent coupling between particles in the cluster. This structure demonstrates how careful design of self-assembled colloidal systems can lead to the creation of new plasmonic modes and the enabling of interference effects in plasmonic systems.},
	url = {http://dx.doi.org/10.1021/nl1029732},
	author = {Fan, Jonathan A. and Bao, Kui and Wu, Chihhui and Bao, Jiming and Rizia Bardhan and Naomi J. Halas and Vinothan N. Manoharan and Shvets, Gennady and Nordlander, Peter and Capasso, Federico}
}
@article {252336,
	title = {Self-Assembled Plasmonic Nanoparticle Clusters},
	journal = {Science},
	volume = {328},
	number = {5982},
	year = {2010},
	note = {Download PDF},
	pages = {1135-1138},
	abstract = {The self-assembly of colloids is an alternative to top-down processing that enables the fabrication of nanostructures. We show that self-assembled clusters of metal-dielectric spheres are the basis for nanophotonic structures. By tailoring the number and position of spheres in close-packed clusters, plasmon modes exhibiting strong magnetic and Fano-like resonances emerge. The use of identical spheres simplifies cluster assembly and facilitates the fabrication of highly symmetric structures. Dielectric spacers are used to tailor the interparticle spacing in these clusters to be approximately 2 nanometers. These types of chemically synthesized nanoparticle clusters can be generalized to other two- and three-dimensional structures and can serve as building blocks for new metamaterials.},
	url = {http://dx.doi.org/10.1126/science.1187949},
	author = {Fan, Jonathan A. and Wu, Chihhui and Bao, Kui and Bao, Jiming and Rizia Bardhan and Naomi J. Halas and Vinothan N. Manoharan and Nordlander, Peter and Shvets, Gennady and Capasso, Federico}
}
@conference {252331,
	title = {A Simple, Inexpensive Holographic Microscope},
	booktitle = {Digital Holography and Three-Dimensional Imaging 2010 (OSA Topical Meeting)},
	year = {2010},
	note = {Download PDF
See also\&nbsp;BioTechniques News Article by Lisa Grauer},
	month = {11-14 April},
	pages = {Paper JMA38},
	publisher = {Optical Society of America},
	organization = {Optical Society of America},
	address = {Miami, FL},
	abstract = {We have built a simple holographic microscope completely out of consumer components. We obtain at least 2.8 μm resolution and depth of field greater than 200 μm from an instrument costing less than $1000.},
	url = {Digital Holography and Three-Dimensional Imaging 2010 (OSA Topical Meeting)},
	author = {Dimiduk, Thomas G and Ekaterina A. Kosheleva and David Kaz and McGorty, Ryan and Emily J. Gardel and Vinothan N. Manoharan}
}
@proceedings {249121,
	title = {Digital Holographic Microscopy for 3D Imaging of Complex Fluids and Biological Systems},
	journal = {Frontiers of Engineering: Reports on Leading-edge Engineering from the 2009 Symposium},
	year = {2010},
	note = {Full Text
Download PDF},
	pages = {5-12},
	address = {Irvine, CA},
	url = {http://books.nap.edu/openbook.php?record_id=12821\&page=5},
	author = {Vinothan N. Manoharan}
}
@article {249116,
	title = {The Free-Energy Landscape of Clusters of Attractive Hard Spheres},
	journal = {Science},
	volume = {327},
	number = {5965},
	year = {2010},
	note = {
Perspective by John C. Crocker (Crocker, J. C. (2010). Turning Away from High Symmetry. Science, 327 (5965), 535-536.
Commentary by Mike Cates in the Journal Club for Condensed Matter Physics

Download PDF
},
	pages = {560-563},
	abstract = {The study of clusters has provided a tangible link between local geometry and bulk condensed matter, but experiments have not yet systematically explored the thermodynamics of the smallest clusters. Here we present experimental measurements of the structures and free energies of colloidal clusters in which the particles act as hard spheres with short-range attractions. We found that highly symmetric clusters are strongly suppressed by rotational entropy, whereas the most stable clusters have anharmonic vibrational modes or extra bonds. Many of these clusters are subsets of close-packed lattices. As the number of particles increases from 6 to 10, we observe the emergence of a complex free-energy landscape with a small number of ground states and many local minima.},
	url = {http://dx.doi.org/10.1126/science.1181263},
	author = {Guangnan Meng and Natalie Arkus and Brenner, Michael P and Vinothan N. Manoharan}
}
@article {249086,
	title = {Design and Synthesis of Model Transparent Aqueous Colloids with Optimal Scattering Properties},
	journal = {Langmuir},
	volume = {25},
	number = {19},
	year = {2009},
	note = {Reprint (requires free registration with ACS)},
	pages = {11295-11298},
	abstract = {We demonstrate the synthesis and self-assembly of colloidal particles with independently controlled diameter and scattering cross section. We show that it is possible to prepare bulk colloidal suspensions that are nearly transparent in water, while the particles themselves can be individually resolved using optical microscopy. These particles may be ideal model colloids for real-space studies of self-assembly in aqueous media. Moreover, they illustrate the degree to which the optical properties of colloids can be engineered through straightforward chemistry.},
	url = {http://dx.doi.org/10.1021/la902861x},
	author = {Adeline Perro and Guangnan Meng and Fung, Jerome and Vinothan N. Manoharan}
}
@article {249066,
	title = {Minimal Energy Clusters of Hard Spheres with Short Range Attractions},
	journal = {Physical Review Letters},
	volume = {103},
	number = {11},
	year = {2009},
	pages = {118303-4},
	abstract = {We calculate the ground states of hard-sphere clusters, in which n identical hard spherical particles bind by isotropic short-ranged attraction. Combining graph theoretic enumeration with basic geometry, we analytically solve for clusters of n\&lt;=10 particles satisfying minimal rigidity constraints. For n\&lt;=9 the ground state degeneracy increases exponentially with n, but for n\&gt;9 the degeneracy decreases due to the formation of structures with \&gt;3n-6 contacts. Interestingly, for n=10 and possibly at n=11 and n=12, the ground states of this system are subsets of hexagonal close-packed crystals. The ground states are not icosahedra at n=12 and n=13. We relate our results to the structure and thermodynamics of suspensions of colloidal particles with short-ranged attractions.},
	url = {http://dx.doi.org/10.1103/PhysRevLett.103.118303},
	author = {Natalie Arkus and Vinothan N. Manoharan and Brenner, Michael P}
}
@article {249096,
	title = {RNA folding and hydrolysis terms explain ATP-independence of RNA interference in human systems},
	journal = {Oligonucleotides},
	volume = {19},
	number = {4},
	year = {2009},
	pages = {341-346},
	abstract = {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.},
	url = {http://dx.doi.org/10.1089/oli.2009.0186},
	author = {Nicole Ali and Vinothan N. Manoharan}
}
@proceedings {249051,
	title = {Self-Assembly of Polyhedral Hybrid Colloidal Particles},
	journal = {MRS Proceedings},
	volume = {1135},
	year = {2009},
	pages = {1135-CC06-08},
	address = {Boston, MA},
	abstract = {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.},
	url = {http://dx.doi.org/10.1557/PROC-1135-CC06-08},
	author = {Adeline Perro and Etienne Duguet and Serge Ravaine and Vinothan N. Manoharan}
}
@conference {249016,
	title = {Measuring Dynamics and Interactions of Colloidal Particles with Digital Holographic Microscopy},
	booktitle = {Digital Holography and Three-Dimensional Imaging Proceedings},
	volume = {paper DTuB1},
	year = {2008},
	note = {Download PDF},
	month = {17-19 March},
	publisher = {Optical Society of America Technical Digest (CD)},
	organization = {Optical Society of America Technical Digest (CD)},
	address = {St. Petersburg, Florida},
	abstract = {Micrometer-sized colloidal particles are a model system for understanding self-assembly in condensed matter. Here I present the results of digital holographic microscopy experiments that probe the 3D structure and dynamics of these systems.},
	url = {http://dx.doi.org/10.1364/DH.2008.DTuB1},
	author = {McGorty, Ryan and Fung, Jerome and David Kaz and Steven Ahn and Vinothan N. Manoharan}
}
@article {249031,
	title = {Surfactant-Assisted Synthesis of Uniform Titania Microspheres and Their Clusters},
	journal = {Chemistry of Materials},
	volume = {20},
	number = {8},
	year = {2008},
	note = {Download PDF},
	pages = {2704-2710},
	abstract = {In this study, we demonstrate the surfactant-assisted synthesis of uniform-sized titania microspheres and their clusters for highly responsive optical materials. Monodisperse titanium glycolate microspheres were produced by controlled hydrolysis of glycolated titanium butoxide in acetone using surfactant as a stabilizer. The diameter of as-prepared particles ranged from 230 to 650 nm and was finely controlled by changing the concentrations of titanium butoxide and surfactant. In particular, the tunable range of the particle size was at a few tens of nanometers scale by the surfactant concentration, which was much finer than that by the concentration of titanium butoxide. Then, as-prepared titanium glycolate microspheres were transformed into monodisperse titania microspheres of anatase phase by heat treatment. Pure clusters of titania microspheres with an identical configuration were obtained by encapsulating a certain number of microspheres in emulsion droplets and subsequently evaporating the emulsion phase to induce self-assembly. Dynamic and static light scattering experiments show that the pure clusters with an identical configuration were well dispersed, and the refractive index of anatase phase titania microspheres was about 2.2. In addition, monodisperse Eu-doped titanium glycolate microspheres were prepared for phosphorescence sources by adding both a soluble precursor Eu(NO3)3-5H2O and glycolated titanium butoxide in acetone. Finally, photoluminescence properties of Eu-doped titania microspheres were examined after annealing.},
	url = {http://dx.doi.org/10.1021/cm7035772},
	author = {Hyung Kyun Yu and Gi-Ra Yi and Ji-Hwan Kang and Young-Sang Cho and Vinothan N. Manoharan and David J. Pine and Seung-Man Yang}
}
@article {249006,
	title = {Colloidal spheres confined by liquid droplets: Geometry, physics, and physical chemistry},
	journal = {Solid State Communications},
	volume = {139},
	number = {11-12},
	year = {2006},
	pages = {557-561},
	abstract = {I discuss how colloidal particles organize when they are confined by emulsion droplets. In these systems, the interplay between surface tension and interparticle repulsion drives the formation of complex, non-crystalline 3D arrangements. These can be classified into three groups: colloidosomes, or Pickering emulsions, structures that form when particles are bound to the interface of a spherical droplet; colloidal clusters, small polyhedral configurations of colloids formed by capillary forces generated in an evaporating emulsion droplet; and supraparticles, hall-shaped crystallites formed in the interior of emulsion droplets. I discuss the preparation, properties, and structure of each of these systems, using relevant results from geometry to describe how the particles organize.},
	url = {http://dx.doi.org/10.1016/j.ssc.2006.04.038},
	author = {Vinothan N. Manoharan}
}
@article {248996,
	title = {Self-organization of bidisperse colloids in water droplets},
	journal = {Journal of the American Chemical Society},
	volume = {127},
	number = {4},
	year = {2005},
	note = {Download PDF},
	pages = {15968-15975},
	abstract = {Most of the colloidal clusters have been produced from oil-in-water emulsions with identical microspheres dispersed in oil droplets. Here, we present new types of binary colloidal clusters from phase-inverted water-in-oil emulsions using various combinations of two different colloids with several size ratios: monodisperse silica or polystyrene microspheres for larger particles and silica or titania nanoparticles for smaller particles. Obviously, a better understanding of how finite groups of different colloids self-organize in a confined geometry may help us control the structure of matter at multiple length scales. In addition, since aqueous dispersions have much better phase stability, we could produce much more diverse colloidal materials from water-in-oil emulsions rather than from oil-in-water emulsions. Interestingly, the configurations of the large microspheres were not changed by the presence of the small particles. However, the arrangement of the smaller particles was strongly dependent on the nature of the interparticle interactions. The experimentally observed structural evolutions were consistent with the numerical simulations calculated using Surface Evolver. These clusters with nonisotropic structures can be used as building blocks for novel colloidal structures with unusual properties or by themselves as light scatterers, diffusers, and complex adaptive matter exhibiting emergent behavior.},
	url = {http://dx.doi.org/10.1021/ja0550632},
	author = {Young-Sang Cho and Gi-Ra Yi and Jong-Min Lim and Shin-Hyun Kim and Vinothan N. Manoharan and David J. Pine and Seung-Man Yang}
}
