132 results on '"Vinothan N. Manoharan"'
Search Results
2. Predicting the Structural Colors of Films of Disordered Photonic Balls
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Anna B. Stephenson, Ming Xiao, Victoria Hwang, Liangliang Qu, Paul A. Odorisio, Michael Burke, Keith Task, Ted Deisenroth, Solomon Barkley, Rupa H. Darji, and Vinothan N. Manoharan
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Physics::Optics ,Soft Condensed Matter (cond-mat.soft) ,FOS: Physical sciences ,Condensed Matter - Soft Condensed Matter ,Electrical and Electronic Engineering ,Atomic and Molecular Physics, and Optics ,Optics (physics.optics) ,Physics - Optics ,Biotechnology ,Electronic, Optical and Magnetic Materials - Abstract
Photonic balls are spheres tens of micrometers in diameter containing assemblies of nanoparticles or nanopores with a spacing comparable to the wavelength of light. When these nanoscale features are disordered, but still correlated, the photonic balls can show structural color with low angle-dependence. Their colors, combined with the ability to add them to a liquid formulation, make photonic balls a promising new type of pigment particle for paints, coatings, and other applications. However, it is challenging to predict the color of materials made from photonic balls, because the sphere geometry and multiple scattering must be accounted for. To address these challenges, we develop a multiscale modeling approach involving Monte Carlo simulations of multiple scattering at two different scales: we simulate multiple scattering and absorption within a photonic ball and then use the results to simulate multiple scattering and absorption in a film of photonic balls. After validating against experimental spectra, we use the model to show that films of photonic balls scatter light in fundamentally different ways than do homogeneous films of nanopores or nanoparticles, because of their increased surface area and refraction at the interfaces of the balls. Both effects tend to sharply reduce color saturation relative to a homogeneous nanostructured film. We show that saturated colors can be achieved by placing an absorber directly in the photonic balls and mitigating surface roughness. With these design rules, we show that photonic-ball films have an advantage over homogeneous nanostructured films: their colors are even less dependent on the angle.
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- 2022
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3. 3D-printed machines that manipulate microscopic objects using capillary forces
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Cheng Zeng, Maya Winters Faaborg, Ahmed Sherif, Martin J. Falk, Rozhin Hajian, Ming Xiao, Kara Hartig, Yohai Bar-Sinai, Michael P. Brenner, and Vinothan N. Manoharan
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Multidisciplinary - Abstract
Objects that deform a liquid interface are subject to capillary forces, which can be harnessed to assemble the objects
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- 2022
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4. Voltage-tunable elastomer composites that use shape instabilities for rapid structural color changes
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Ming Xiao, Jie Mao, Matthias Kollosche, Victoria Hwang, David R. Clarke, and Vinothan N. Manoharan
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Excipients ,Optics and Photonics ,Photons ,Elastomers ,Mechanics of Materials ,Process Chemistry and Technology ,Color ,Colorimetry ,General Materials Science ,Electrical and Electronic Engineering - Abstract
Structurally colored materials can switch colors in response to external stimuli, which makes them potentially useful as colorimetric sensors, dynamic displays, and camouflage. However, their applications are limited by the angular dependence, slow response, and absence of synchronous control in time and space. In addition, out-of-plane deformation from shape instability easily occurs in photonic films, leading to inhomogeneous colors in photonic-crystal materials. To address these challenges, we combine structurally colored photonic glasses and dielectric elastomer actuators. We use an external voltage signal to tune color changes quickly (much less than 0.1 s). The photonic glassses produce colors with low angular dependence, so that their colors are homogeneous even when they become curved due to voltage-triggered instabilities (buckling or wrinkling). As proof of concept, we present a pixelated display in which segments can be independently and rapidly turned on and off. This wide-angle, instability-tolerant, color-changing platform could be used in next-generation soft and curved color displays, camouflage with both shape and color changes, and multifunctional sensors.
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- 2022
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5. Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays
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Timothy K. Chiang, Ofer Kimchi, Herman K. Dhaliwal, Daniel A. Villarreal, Fernando F. Vasquez, Vinothan N. Manoharan, Michael P. Brenner, and Rees F. Garmann
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Article - Abstract
We describe a simple method to infer intramolecular connections in a population of long RNA molecules in vitro. First we add DNA oligonucleotide “patches” that perturb the RNA connections, then we use a microarray containing a complete set of DNA oligonucleotide “probes” to record where perturbations occur. The pattern of perturbations reveals couplings between different regions of the RNA sequence, from which we infer connections as well as their prevalences in the population. We validate this patch-probe method using the 1,058-nucleotide RNA genome of satellite tobacco mosaic virus (STMV), which has previously been shown to have multiple long-range connections. Our results not only indicate long duplexes that agree with previous structures but also reveal the prevalence of competing connections. Together, these results suggest that globally-folded and locally-folded structures coexist in solution. We show that the prevalence of connections changes when pseudouridine, an important component of natural and synthetic RNA molecules, is substituted for uridine in STMV RNA.
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- 2023
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6. Geometrical Frustration and Defect Formation in Growth of Colloidal Nanoparticle Crystals on a Cylinder: Implications for Assembly of Chiral Nanomaterials
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William Wilkin, Daniel A. Beller, Nabila Tanjeem, Chris H. Rycroft, and Vinothan N. Manoharan
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Colloid ,Materials science ,Geometrical frustration ,Cylinder ,Nanoparticle ,General Materials Science ,Nanotechnology ,Nanomaterials - Published
- 2021
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7. In-line holographic microscopy with model-based analysis
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Caroline Martin, Lauren E. Altman, Siddharth Rawat, Anna Wang, David G. Grier, and Vinothan N. Manoharan
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General Medicine ,General Chemistry - Published
- 2022
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8. Single-particle studies of the effects of RNA–protein interactions on the self-assembly of RNA virus particles
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Rees F. Garmann, Aaron M. Goldfain, Cheylene R. Tanimoto, Christian E. Beren, Fernando F. Vasquez, Daniel A. Villarreal, Charles M. Knobler, William M. Gelbart, and Vinothan N. Manoharan
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Capsid ,Multidisciplinary ,Virion ,RNA Viruses ,RNA, Viral ,Bromovirus - Abstract
Understanding the pathways by which simple RNA viruses self-assemble from their coat proteins and RNA is of practical and fundamental interest. Although RNA–protein interactions are thought to play a critical role in the assembly, our understanding of their effects is limited because the assembly process is difficult to observe directly. We address this problem by using interferometric scattering microscopy, a sensitive optical technique with high dynamic range, to follow the in vitro assembly kinetics of more than 500 individual particles of brome mosaic virus (BMV)—for which RNA–protein interactions can be controlled by varying the ionic strength of the buffer. We find that when RNA–protein interactions are weak, BMV assembles by a nucleation-and-growth pathway in which a small cluster of RNA-bound proteins must exceed a critical size before additional proteins can bind. As the strength of RNA–protein interactions increases, the nucleation time becomes shorter and more narrowly distributed, but the time to grow a capsid after nucleation is largely unaffected. These results suggest that the nucleation rate is controlled by RNA–protein interactions, while the growth process is driven less by RNA–protein interactions and more by protein–protein interactions and intraprotein forces. The nucleated pathway observed with the plant virus BMV is strikingly similar to that previously observed with bacteriophage MS2, a phylogenetically distinct virus with a different host kingdom. These results raise the possibility that nucleated assembly pathways might be common to other RNA viruses.
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- 2022
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9. Deriving Finite Sphere Packings.
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Natalie Arkus, Vinothan N. Manoharan, and Michael P. Brenner
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- 2011
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10. Controlled Assembly of Icosahedral Colloidal Clusters for Structural Coloration
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Hyerim Hwang, Shin-Hyun Kim, Cheolho Kim, Jun Hyuk Moon, Sanghyuk Park, Vinothan N. Manoharan, Won Bo Lee, Kinam Jung, and Ji Woong Yu
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endocrine system ,Materials science ,Icosahedral symmetry ,General Chemical Engineering ,digestive, oral, and skin physiology ,food and beverages ,02 engineering and technology ,General Chemistry ,Colloidal crystal ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Colloidal clusters ,complex mixtures ,01 natural sciences ,0104 chemical sciences ,body regions ,Colloid ,Chemical physics ,Materials Chemistry ,Cluster (physics) ,0210 nano-technology ,Structural coloration - Abstract
Icosahedral colloidal clusters are a new class of spherical colloidal crystals. This cluster allows for potentially superior optical properties in comparison to conventional onion-like colloidal su...
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- 2020
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11. Tracking and Analyzing the Brownian Motion of Nano-objects Inside Hollow Core Fibers
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Jens Kobelke, Vinothan N. Manoharan, Mona Nissen, Torsten Wieduwilt, Ronny Förster, Aaron M. Goldfain, Timothy Chiang, Rees F. Garmann, Yoav Lahini, Markus A. Schmidt, and Stefan Weidlich
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Metal Nanoparticles ,Bioengineering ,02 engineering and technology ,Tracking (particle physics) ,01 natural sciences ,Diffusion ,Motion ,Optics ,Fluidics ,Instrumentation ,Brownian motion ,Fluid Flow and Transfer Processes ,Physics ,business.industry ,Process Chemistry and Technology ,010401 analytical chemistry ,021001 nanoscience & nanotechnology ,Frame rate ,Bacteriophage lambda ,0104 chemical sciences ,Mean squared displacement ,Core (optical fiber) ,Line (geometry) ,Particle ,Gold ,0210 nano-technology ,business ,Nanospheres - Abstract
Tracking and analyzing the individual diffusion of nanoscale objects such as proteins and viruses is an important methodology in life science. Here, we show a sensor that combines the efficiency of light line illumination with the advantages of fluidic confinement. Tracking of freely diffusing nano-objects inside water-filled hollow core fibers with core diameters of tens of micrometers using elastically scattered light from the core mode allows retrieving information about the Brownian motion and the size of each particle of the investigated ensemble individually using standard tracking algorithms and the mean squared displacement analysis. Specifically, we successfully measure the diameter of every gold nanosphere in an ensemble that consists of several hundreds of 40 nm particles, with an individual precision below 17% (±8 nm). In addition, we confirm the relevance of our approach with respect to bioanalytics by analyzing 70 nm λ-phages. Overall these features, together with the strongly reduced demand for memory space, principally allows us to record thousands of frames and to achieve high frame rates for high precision tracking of nanoscale objects.
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- 2020
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12. Modulating and addressing interactions in polymer colloids using light
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Emily W. Gehrels, Vinothan N. Manoharan, and Ellen Klein
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chemistry.chemical_classification ,Millisecond ,Materials science ,Process Chemistry and Technology ,02 engineering and technology ,Polymer ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Light intensity ,Wavelength ,Colloid ,chemistry ,Mechanics of Materials ,Chemical physics ,Absorption band ,Thermal ,Particle ,General Materials Science ,Electrical and Electronic Engineering ,0210 nano-technology - Abstract
DNA-mediated linkages between colloidal particles enable controlled assembly and, by virtue of the sharp thermal binding–unbinding transition, provide a mechanism to create switchable structures. However, bulk thermal heating limits switching times to tens of seconds or more. We show that the timescale can be reduced to milliseconds by using light to dynamically control interactions among DNA-coated colloidal particles. We dye particles, such that when they are uniformly illuminated with unfocused light with a wavelength in the absorption band of the dye, they locally heat. We show that the interactions can be reversibly switched by modulating the light intensity. By using multiple dyes and different wavelengths of light, we independently address interactions between different sets of particles. Calculations show that light-driven heating produces local temperature gradients around the constituent particles that build up and dissipate on timescales of milliseconds, and experiments show that particle interactions can be modulated on timescales of 50 ms or less. This light-driven control is straightforward to implement in existing DNA-coated colloidal systems and opens the door to sequential and non-equilibrium assembly schemes.
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- 2020
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13. Charged hydrophobic colloids at an oil–aqueous phase interface
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Colm P. Kelleher, Anna Wang, Guillermo Iván Guerrero-García, Andrew D. Hollingsworth, Rodrigo E. Guerra, Bhaskar Jyoti Krishnatreya, David G. Grier, Vinothan N. Manoharan, and Paul M. Chaikin
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- 2015
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14. Designing angle-independent structural colors using Monte Carlo simulations of multiple scattering
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Solomon Barkley, Joanna Aizenberg, Soeren Brandt, Victoria Hwang, Ming Xiao, Vinothan N. Manoharan, and Anna B. Stephenson
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Multidisciplinary ,Scale (ratio) ,Computer science ,Scattering ,Monte Carlo method ,FOS: Physical sciences ,Parameterized complexity ,Physics - Applied Physics ,Applied Physics (physics.app-ph) ,02 engineering and technology ,Surface finish ,Condensed Matter - Soft Condensed Matter ,021001 nanoscience & nanotechnology ,01 natural sciences ,Light scattering ,010309 optics ,Experimental system ,Physical Sciences ,0103 physical sciences ,Soft Condensed Matter (cond-mat.soft) ,Statistical physics ,0210 nano-technology ,Visible spectrum - Abstract
Disordered nanostructures with correlations on the scale of visible wavelengths can show angle-independent structural colors. These materials could replace dyes in some applications because the color is tunable and resists photobleaching. However, designing nanostructures with a prescribed color is difficult, especially when the application -- cosmetics or displays, for example -- requires specific component materials. A general approach to solving this constrained design problem is modeling and optimization: using a model that predicts the color of a given system, one optimizes the model parameters under constraints to achieve a target color. For this approach to work, the model must make accurate predictions, which is challenging because disordered nanostructures have multiple scattering. To address this challenge, we develop a Monte Carlo model that simulates multiple scattering of light in disordered arrangements of spherical particles or voids. The model produces quantitative agreement with measurements when we account for roughness on the surface of the film, particle polydispersity, and wavelength-dependent absorption in the components. Unlike discrete numerical simulations, our model is parameterized in terms of experimental variables, simplifying the connection between simulation and fabrication. To demonstrate this approach, we reproduce the color of the male mountain bluebird (Sialia currucoides) in an experimental system, using prescribed components and a microstructure that is easy to fabricate. Finally, we use the model to find the limits of angle-independent structural colors for a given system. These results enable an engineering design approach to structural color for many different applications.
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- 2021
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15. Self-Assembly of Patchy Colloidal Rods into Photonic Crystals Robust to Stacking Faults
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Vinothan N. Manoharan, Dwaipayan Chakrabarti, and Andreas Neophytou
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Materials science ,business.industry ,General Engineering ,Stacking ,General Physics and Astronomy ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Rod ,Colloidal photonic crystals ,0104 chemical sciences ,Colloid ,Optoelectronics ,General Materials Science ,Self-assembly ,0210 nano-technology ,business ,Photonic crystal ,Visible spectrum - Abstract
Diamond-structured colloidal photonic crystals are much sought-after for their applications in visible light management because of their ability to support a complete photonic band gap (PBG). However, their realization
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- 2021
16. Polyhedral plasmonic nanoclusters through multi-step colloidal chemistry
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Etienne Duguet, Cyril Chomette, Nicholas Schade, Serge Ravaine, Vinothan N. Manoharan, Mona Tréguer-Delapierre, Nabila Tanjeem, Harvard University [Cambridge], Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Centre de Recherche Paul Pascal (CRPP), Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the LabEx AMADEus (ANR-10-LABX-42) and IdEx Bordeaux (ANR-10-IDEX-03-02), that is, the Investissements d’Avenir programme of the French government managed by the Agence Nationale de la Recherche. The research was partially supported by the National Science Foundation through the Harvard University Materials Research Science and Engineering Center under grant number DMR-2011754. This work was performed in part at the Center for Nanoscale Systems (CNS), a member of the National Nanotechnology Coordinated Infrastructure Network (NNCI), which is supported by the National Science Foundation under NSF award no. 1541959. CNS is part of Harvard University., ANR-10-LABX-0042,AMADEus,Advanced Materials by Design(2010), and ANR-10-IDEX-0003,IDEX BORDEAUX,Initiative d'excellence de l'Université de Bordeaux(2010)
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Materials science ,Process Chemistry and Technology ,Interface and colloid science ,Dispersity ,Emulsion polymerization ,Nanotechnology ,[CHIM.MATE]Chemical Sciences/Material chemistry ,02 engineering and technology ,Dielectric ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Nanoclusters ,chemistry.chemical_compound ,chemistry ,Mechanics of Materials ,Cluster (physics) ,General Materials Science ,Polystyrene ,Electrical and Electronic Engineering ,0210 nano-technology ,Plasmon - Abstract
International audience; We describe a new approach to making plasmonic metamolecules with well-controlled resonances at optical wavelengths. Metamolecules are highly symmetric, subwavelength-scale clusters of metal and dielectric. They are of interest for metafluids, isotropic optical materials with applications in imaging and optical communications. For such applications, the morphology must be precisely controlled: the optical response is sensitive to nanometer-scale variations in the thickness of metal coatings and the distances between metal surfaces. To achieve this precision, we use a multi-step colloidal synthesis approach. Starting from highly monodisperse silica seeds, we grow octahedral clusters of polystyrene spheres using seeded-growth emulsion polymerization. We then overgrow the silica and remove the polystyrene to create a dimpled template. Finally, we attach six silica satellites to the template and coat them with gold. Using single-cluster spectroscopy, we show that the plasmonic resonances are reproducible from cluster to cluster. By comparing the spectra to theory, we show that the multi-step synthesis approach can control the distances between metallic surfaces to nanometer-scale precision. More broadly, our approach shows how metamolecules can be produced in bulk by combining different, high-yield colloidal synthesis steps, analogous to how small molecules are produced by multi-step chemical reactions.
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- 2021
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17. A field guide to angle-independent structural color
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Anna B. Stephenson and Vinothan N. Manoharan
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Physics ,Field (physics) ,business.industry ,Scattering ,Physics::Medical Physics ,Physics::Optics ,General Physics and Astronomy ,Angle independent ,Astrophysics::Cosmology and Extragalactic Astrophysics ,Quantitative Biology::Other ,01 natural sciences ,Refraction ,Computer Science::Graphics ,Optics ,0103 physical sciences ,010306 general physics ,business ,010303 astronomy & astrophysics ,Structural coloration ,Hue - Abstract
The hues of blue birds come from constructive interference, but scattering and refraction also matter.
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- 2021
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18. Effects of multiple scattering on angle-independent structural color in disordered colloidal materials
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Anna B. Stephenson, Victoria Hwang, Jin-Gyu Park, Sofia Magkiriadou, and Vinothan N. Manoharan
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Work (thermodynamics) ,Materials science ,genetic structures ,pigments ,heterogenous substances ,FOS: Physical sciences ,Condensed Matter - Soft Condensed Matter ,01 natural sciences ,Spectral line ,quasi-amorphous arrays ,010305 fluids & plasmas ,nanostructures ,0103 physical sciences ,010306 general physics ,Scattering ,feather barbs ,Computational physics ,Wavelength ,photonic-crystal ,Soft Condensed Matter (cond-mat.soft) ,SPHERES ,conductivity ,dielectricity constants ,light ,Saturation (chemistry) ,band ,Structural coloration ,Physics - Optics ,Optics (physics.optics) ,Visible spectrum - Abstract
Disordered packings of colloidal spheres show angle-independent structural color when the particles are on the scale of the wavelength of visible light. Previous work has shown that the positions of the peaks in the reflectance spectra can be predicted accurately from a single-scattering model that accounts for the effective refractive index of the material. This agreement shows that the main color peak arises from short-range correlations between particles. However, the single-scattering model does not quantitatively reproduce the observed color: the main peak in the reflectance spectrum is much broader and the reflectance at low wavelengths is much larger than predicted by the model. We use a combination of experiment and theory to understand these features. We find that one significant contribution to the breadth of the main peak is light that is scattered, totally internally reflected from the boundary of the sample, and then scattered again. The high reflectance at low wavelengths also results from multiple scattering but can be traced to the increase in the scattering cross section of individual particles with decreasing wavelength. Both of these effects tend to reduce the saturation of the structural color, which limits the use of these materials in applications. We show that while the single-scattering model cannot reproduce the observed saturations, it can be used as a design tool to reduce the amount of multiple scattering and increase the color saturation of materials, even in the absence of absorbing components.
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- 2020
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19. Before the breach: Interactions between colloidal particles and liquid interfaces at nanoscale separations
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David M. Kaz, Anna Wang, Ryan McGorty, Aaron M. Goldfain, Vinothan N. Manoharan, W. Benjamin Rogers, and Jos Zwanikken
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Materials science ,Aqueous two-phase system ,01 natural sciences ,Pickering emulsion ,010305 fluids & plasmas ,Ion ,Nonlinear system ,Chemical physics ,Colloidal particle ,0103 physical sciences ,Particle ,Digital holographic microscopy ,010306 general physics ,Nanoscopic scale - Abstract
Particles bound to fluid-fluid interfaces are widely used to study self-assembly and to make materials such as Pickering emulsions. In both contexts, the lateral interactions between such particles have been studied extensively. However, much less is known about the normal interactions between a particle and the interface prior to contact. We use digital holographic microscopy to measure the dynamics of individual micrometer-size colloidal particles as they approach an interface between an aqueous phase and oil. Our measurements show that the interaction between the particle and interface changes nonmonotonically as a function of salt concentration, from repulsive at 1 mM to attractive at tens of mM to negligible at 100 mM and attractive again above 200 mM. In the attractive regimes, the particles can bind to the interface at nanometer-scale separation without breaching it. Classical Derjaguin-Landau-Verwey-Overbeek theory does not explain these observations. However, a theory that accounts for nonlinear screening and correlations between the ions does predict the nonmonotonic dependence on salt concentration and produces trajectories that agree with experimental data. We further show that the normal interactions determine the lateral interactions between particles that are bound to the interface. Because the interactions we observe occur at salt concentrations used to make Pickering emulsions and other particle-laden interfaces, our results suggest that particle arrangements at the interface are likely out of equilibrium on experimental timescales.
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- 2019
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20. Investigating the trade-off between color saturation and angle-independence in photonic glasses
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Anna B. Stephenson, Ming Xiao, Vinothan N. Manoharan, Victoria Hwang, Andreas Neophytou, and Dwaipayan Chakrabarti
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Materials science ,Color difference ,Condensed matter physics ,business.industry ,Scattering ,Monte Carlo method ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,010309 optics ,Optics ,0103 physical sciences ,Photonics ,0210 nano-technology ,business ,Saturation (chemistry) ,Structure factor ,Structural coloration ,Photonic crystal - Abstract
Photonic glasses—isotropic structures with short-range correlations—can produce structural colors with little angle-dependence, making them an alternative to dyes in applications such as cosmetics, coatings, and displays. However, the low angle-dependence is often accompanied by low color saturation. To investigate how the short-range correlations affect the trade-off between saturation and angle-independence, we vary the structure factor and use a Monte Carlo model of multiple scattering to investigate the resulting optical properties. We use structure factors derived from analytical models and calculated from simulations of disordered sphere packings. We show that the trade-off is controlled by the first peak of the structure factor. It is possible to break the trade-off by tuning the width of this peak and controlling the sample thickness. Practically, this result shows that the protocol used to pack particles into a photonic glass is important to the optical properties.
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- 2021
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21. Improving holographic particle characterization by modeling spherical aberration
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Brian Leahy, Caroline Martin, and Vinothan N. Manoharan
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Holography ,FOS: Physical sciences ,Physics::Optics ,02 engineering and technology ,01 natural sciences ,law.invention ,010309 optics ,Optics ,law ,0103 physical sciences ,Microscopy ,Physics ,business.industry ,Astrophysics::Instrumentation and Methods for Astrophysics ,Radius ,021001 nanoscience & nanotechnology ,Atomic and Molecular Physics, and Optics ,Characterization (materials science) ,Spherical aberration ,Particle ,Scattering theory ,0210 nano-technology ,business ,Refractive index ,Physics - Optics ,Optics (physics.optics) - Abstract
Holographic microscopy combined with forward modeling and inference allows colloidal particles to be characterized and tracked in three dimensions with high precision. However, current models ignore the effects of optical aberrations on hologram formation. We investigate the effects of spherical aberration on the structure of single-particle holograms and on the accuracy of particle characterization. We find that in a typical experimental setup, spherical aberration can result in systematic shifts of about 2% in the inferred refractive index and radius. We show that fitting with a model that accounts for spherical aberration decreases this aberration-dependent error by a factor of two or more, even when the level of spherical aberration in the optical train is unknown. With the new generative model, the inferred parameters are consistent across different levels of aberration, making particle characterization more robust.
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- 2021
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22. Core–shell colloidal particles with dynamically tunable scattering properties
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Adeline Perro, Guangnan Meng, and Vinothan N. Manoharan
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Materials science ,Scattering ,business.industry ,Small-angle X-ray scattering ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Molecular physics ,Light scattering ,0104 chemical sciences ,Condensed Matter::Soft Condensed Matter ,symbols.namesake ,X-ray Raman scattering ,Optics ,Light scattering by particles ,symbols ,Grazing-incidence small-angle scattering ,Biological small-angle scattering ,Rayleigh scattering ,0210 nano-technology ,business - Abstract
We design polystyrene-poly(N'-isopropylacrylamide-co-acrylic acid) core-shell particles that exhibit dynamically tunable scattering. We show that under normal solvent conditions the shell is nearly index-matched to pure water, and the particle scattering is dominated by Rayleigh scattering from the core. As the temperature or salt concentration increases, both the scattering cross-section and the forward scattering increase, characteristic of Mie scatterers. The magnitude of the change in the scattering cross-section and scattering anisotropy can be controlled through the solvent conditions and the size of the core. Such particles may find use as optical switches or optical filters with tunable opacity.
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- 2017
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23. Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages
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Aaron M. Goldfain, Yan Jin, Rees F. Garmann, Yoav Lahini, and Vinothan N. Manoharan
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0301 basic medicine ,viruses ,Detergents ,Holography ,Nanotechnology ,Buffers ,medicine.disease_cause ,Tracking (particle physics) ,Genome ,Diffusion ,Motion ,03 medical and health sciences ,chemistry.chemical_compound ,Planar ,Bacterial Proteins ,Position (vector) ,Microscopy ,Escherichia coli ,Image Processing, Computer-Assisted ,Materials Chemistry ,medicine ,Physical and Theoretical Chemistry ,Orientation (computer vision) ,Bacteriophage lambda ,3. Good health ,Surfaces, Coatings and Films ,Solutions ,030104 developmental biology ,chemistry ,DNA, Viral ,Biophysics ,Salts ,Glass ,DNA - Abstract
A complete understanding of the cellular pathways involved in viral infections will ultimately require a diverse arsenal of experimental techniques, including methods for tracking individual viruses and their interactions with the host. Here we demonstrate the use of holographic microscopy to track the position, orientation, and DNA content of unlabeled bacteriophages (phages) in solution near a planar, functionalized glass surface. We simultaneously track over 100 individual λ phages at a rate of 100 Hz across a 33 μm × 33 μm portion of the surface. The technique determines the in-plane motion of the phage to nanometer precision, and the height of the phage above the surface to 100 nm precision. Additionally, we track the DNA content of individual phages as they eject their genome following the addition of detergent-solubilized LamB receptor. The technique determines the fraction of DNA remaining in the phage to within 10% of the total 48.5 kilobase pairs. Analysis of the data reveals that under certain conditions, λ phages move along the surface with their heads down and intermittently stick to the surface by their tails, causing them to stand up. Furthermore, we find that in buffer containing high concentrations of both monovalent and divalent salts, λ phages eject their entire DNA in about 7 s. Taken together, these measurements highlight the potential of holographic microscopy to resolve the fast kinetics of the early stages of phage infection.
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- 2016
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24. Self-Assembly of Polyhedral Hybrid Colloidal Particles
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Perro, Adeline, Duguet, Etienne, Ravaine, Serge, and Vinothan, N. Manoharan
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- 2008
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25. Secondary Structures of Very Large RNAs via High-Throughput Oligonucleotide-Binding Microarrays
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Megan Engel, Rees F. Garmann, Ofer Kimchi, Timothy Chiang, Michael Brenner, and Vinothan N. Manoharan
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Oligonucleotide ,Chemistry ,Biophysics ,Computational biology ,DNA microarray ,Throughput (business) - Published
- 2021
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26. Precise measurements in digital holographic microscopy by modeling the optical train
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Brian Leahy, Ronald Alexander, and Vinothan N. Manoharan
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010302 applied physics ,Microscope ,Computer science ,Perspective (graphical) ,Holography ,General Physics and Astronomy ,Context (language use) ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Field (computer science) ,law.invention ,law ,0103 physical sciences ,Microscopy ,Electronic engineering ,Particle ,Digital holographic microscopy ,0210 nano-technology - Abstract
In the past few years, the venerable field of holographic microscopy has been revitalized by computational data analysis. It is now possible to fit a generative (forward) model of scattering directly to experimentally obtained holograms of complex microscopic objects. This approach enables precision measurements: it allows the motion of colloidal particles and biological organisms to be tracked with nanometer-scale precision and their optical properties to be inferred particle by particle. In this Perspective, we discuss how the model-based inference approach to holographic microscopy has opened up new applications. We also discuss how it must evolve to meet the needs of emerging applications that demand lower systematic uncertainties and higher precision. In this context, we present some new results on how modeling the optical train of the microscope can enable better measurements of the positions of spherical and nonspherical colloidal particles. Finally, we discuss how machine learning might play a role in future advances. Though we do not exhaustively catalog all the developments in this field, we show a few examples and some new results that spotlight open questions and opportunities.
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- 2020
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27. Solution-Processable Photonic Inks of Mie-Resonant Hollow Carbon-Silica Nanospheres
- Author
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Gi-Ra Yi, Vinothan N. Manoharan, Sang Goo Lee, Jong-Wook Ha, Seung-Hyun Kim, and Victoria Hwang
- Subjects
Materials science ,business.industry ,Scattering ,Mie scattering ,Physics::Optics ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Biomaterials ,Condensed Matter::Materials Science ,Optoelectronics ,General Materials Science ,Self-assembly ,Photonics ,0210 nano-technology ,business ,Science, technology and society ,Absorption (electromagnetic radiation) ,Saturation (magnetic) ,Structural coloration ,Biotechnology - Abstract
Hollow carbon-silica nanospheres that exhibit angle-independent structural color with high saturation and minimal absorption are made. Through scattering calculations, it is shown that the structural color arises from Mie resonances that are tuned precisely by varying the thickness of the shells. Since the color does not depend on the spatial arrangement of the particles, the coloration is angle independent and vibrant in powders and liquid suspensions. These properties make hollow carbon-silica nanospheres ideal for applications, and their potential in making flexible, angle-independent films and 3D printed films is explored.
- Published
- 2019
28. Large depth-of-field tracking of colloidal spheres in holographic microscopy by modeling the objective lens
- Author
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Solomon Barkley, Caroline Martin, Vinothan N. Manoharan, Brian Leahy, and Ronald Alexander
- Subjects
Materials science ,Microscope ,business.industry ,Holography ,FOS: Physical sciences ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Tracking (particle physics) ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,law.invention ,010309 optics ,Lens (optics) ,Optics ,Cardinal point ,law ,0103 physical sciences ,Microscopy ,Particle ,Depth of field ,0210 nano-technology ,business ,Physics - Optics ,Optics (physics.optics) - Abstract
Holographic microscopy has developed into a powerful tool for 3D particle tracking, yielding nanometer-scale precision at high frame rates. However, current particle tracking algorithms ignore the effect of the microscope objective on the formation of the recorded hologram. As a result, particle tracking in holographic microscopy is currently limited to particles well above the microscope focus. Here, we show that modeling the effect of an aberration-free lens allows tracking of particles above, near, and below the focal plane in holographic microscopy, doubling the depth of field. Finally, we use our model to determine the conditions under which ignoring the effect of the lens is justified and in what conditions it leads to systematic errors.
- Published
- 2019
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29. Random sequential adsorption of spheres on a cylinder
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Charlie Greboval, Vinothan N. Manoharan, Edvin Memet, Nabila Tanjeem, and Lakshminarayanan Mahadevan
- Subjects
Materials science ,05 social sciences ,General Physics and Astronomy ,FOS: Physical sciences ,Biomolecules (q-bio.BM) ,02 engineering and technology ,Radius ,Function (mathematics) ,Mechanics ,Condensed Matter - Soft Condensed Matter ,Microsphere ,Condensed Matter::Soft Condensed Matter ,Colloid ,Random sequential adsorption ,Quantitative Biology - Biomolecules ,FOS: Biological sciences ,0202 electrical engineering, electronic engineering, information engineering ,C++ string handling ,Cylinder ,Soft Condensed Matter (cond-mat.soft) ,020201 artificial intelligence & image processing ,SPHERES ,0509 other social sciences ,050904 information & library sciences - Abstract
Inspired by observations of beads packed on a thin string in such systems as sea-grapes and dental plaque, we study the random sequential adsorption of spheres on a cylinder. We determine the asymptotic fractional coverage of the cylinder as a function of the sole parameter in the problem, the ratio of the sphere radius to the cylinder radius (for a very long cylinder) using a combination of analysis and numerical simulations. Examining the asymptotic structures, we find weak chiral ordering on sufficiently small spatial scales. Experiments involving colloidal microspheres that can attach irreversibly to a silica wire via electrostatic forces or DNA hybridization allow us to verify our predictions for the asymptotic coverage.
- Published
- 2019
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30. Physical interpretation of the partition function for colloidal clusters
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Vinothan N. Manoharan, Rebecca W. Perry, and Ellen Klein
- Subjects
Physics ,Work (thermodynamics) ,Partition function (quantum field theory) ,Structure (category theory) ,FOS: Physical sciences ,02 engineering and technology ,Condensed Matter - Soft Condensed Matter ,Moment of inertia ,021001 nanoscience & nanotechnology ,Colloidal clusters ,01 natural sciences ,Interpretation (model theory) ,0103 physical sciences ,Cluster (physics) ,Soft Condensed Matter (cond-mat.soft) ,Statistical physics ,010306 general physics ,0210 nano-technology ,Symmetry number - Abstract
Colloidal clusters consist of small numbers of colloidal particles bound by weak, short-range attractions. The equilibrium probability of observing a cluster in a particular geometry is well-described by a statistical mechanical model originally developed for molecules. To explain why this model fits experimental data so well, we derive the partition function classically, with no quantum mechanical considerations. Then, by comparing and contrasting the derivation in particle coordinates with that in center-of-mass coordinates, we physically interpret the terms in the center-of-mass formulation, which is equivalent to the high-temperature partition function for molecules. We discuss, from a purely classical perspective, how and why cluster characteristics such as the symmetry number, moments of inertia, and vibrational frequencies affect the equilibrium probabilities.
- Published
- 2018
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31. Holographic Microscopy with Python and HoloPy
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Jerome Fung, Thomas G. Dimiduk, Vinothan N. Manoharan, Solomon Barkley, Anna Wang, Rebecca W. Perry, David M. Kaz, and Ryan McGorty
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Microscope ,General Computer Science ,Computer science ,Computation ,Holography ,Inference ,FOS: Physical sciences ,02 engineering and technology ,ENCODE ,Interference (wave propagation) ,01 natural sciences ,law.invention ,Data modeling ,010309 optics ,law ,Computer graphics (images) ,0103 physical sciences ,FOS: Electrical engineering, electronic engineering, information engineering ,computer.programming_language ,Image and Video Processing (eess.IV) ,General Engineering ,Python (programming language) ,Electrical Engineering and Systems Science - Image and Video Processing ,021001 nanoscience & nanotechnology ,0210 nano-technology ,computer ,Optics (physics.optics) ,Physics - Optics - Abstract
A holographic microscope captures interference patterns, or holograms, that encode three-dimensional (3D) information about the object being viewed. Computation is essential to extracting that 3D information. By wrapping low-level scattering codes and taking advantage of Python's data analysis ecosystem, HoloPy makes it easy for experimentalists to use modern, sophisticated inference methods to analyze holograms. The resulting data can be used to understand how small particles or microorganisms move and interact. The project illustrates how computational tools can enable experimental methods and new experiments.
- Published
- 2018
32. Colloidal particle adsorption at liquid interfaces: capillary driven dynamics and thermally activated kinetics
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Amir M. Rahmani, Anna Wang, Carlos E. Colosqui, and Vinothan N. Manoharan
- Subjects
Fluctuation-dissipation theorem ,Materials science ,Capillary action ,Kinetics ,FOS: Physical sciences ,Thermal fluctuations ,02 engineering and technology ,General Chemistry ,Condensed Matter - Soft Condensed Matter ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,3. Good health ,0104 chemical sciences ,Adsorption ,Chemical physics ,Soft Condensed Matter (cond-mat.soft) ,Relaxation (physics) ,Particle ,0210 nano-technology ,Langevin dynamics - Abstract
The adsorption of single colloidal microparticles (0.5--1 $\mu$m radius) at a water-oil interface has been recently studied experimentally using digital holographic microscopy [Kaz \textit{et al., Nat. Mater.}, 2012, \textbf{11}, 138--142]. An initially fast adsorption dynamics driven by capillary forces is followed by an unexpectedly slow relaxation to equilibrium that is logarithmic in time and can span hours or days. The slow relaxation kinetics has been attributed to the presence of surface "defects" with nanoscale dimensions (1--5\,nm) that induce multiple metastable configurations of the contact line perimeter. A kinetic model considering thermally activated transitions between such metastable configurations has been proposed [Colosqui \textit{et al., Phys. Rev. Lett.}, 2013, \textbf{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., Comment: 8 pages, 4 figures
- Published
- 2016
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33. Modeling and Theory: general discussion
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Hima Bindu Kolli, Madivala G. Basavaraj, Ajeet K. Srivastav, G. V. Pavan Kumar, Alison J. Edwards, Priyadarshi Roy Chowdhury, Guruswamy Kumaraswamy, Bijai Prasad, Nirmalya Bachhar, Debdas Dhabal, Mohamed Laradji, Rajdip Bandyopadhyaya, Ranjini Bandyopadhyay, Jacques Jestin, Charusita Chakravarty, Mukta Tripathy, Sanat K. Kumar, Yogesh M. Joshi, Sudeep N. Punnathanam, Vimala Sridurai, Sunil Kumar, Jayant K. Singh, Oleg Gang, Vinothan N. Manoharan, Robert Botet, Daan Frenkel, Lynn M. Walker, Pedro A. Sánchez, Siddharth Kulkarni, Hari O. S. Yadav, Sofia S. Kantorovich, Nicholas A. Kotov, Vandana Shinde, and Erika Eiser
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Text mining ,010304 chemical physics ,Computer science ,business.industry ,0103 physical sciences ,Physical and Theoretical Chemistry ,010402 general chemistry ,business ,01 natural sciences ,Data science ,0104 chemical sciences - Published
- 2016
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34. Segregation of 'isotope' particles within colloidal molecules
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Rebecca W. Perry and Vinothan N. Manoharan
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Isotope ,Isotropy ,Doping ,Nanotechnology ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,law.invention ,chemistry.chemical_compound ,Colloid ,chemistry ,Optical microscope ,Chemical physics ,law ,Molecule ,Polystyrene ,Physics::Chemical Physics ,0210 nano-technology ,Entropy (order and disorder) - Abstract
Clusters of spherical particles are called "colloidal molecules" because they adopt structures that resemble those of true molecules. In this analogy, the particles are the atoms, the attractive interactions between them are bonds, and the different structures that appear in equilibrium are isomers. We take this analogy a step further by doping colloidal molecules with colloidal "isotopes," particles that have the same size but different bonding energies from the other particles in the system. Our molecules are two-dimensional clusters consisting of polystyrene and silica microspheres held together by depletion interactions. Using a combination of optical microscopy and particle tracking, we examine an ensemble of 4- and 5-particle molecules at different isotope ratios. We find that the isotopes tend to segregate to particular positions in the various isomers. We explain these findings using a statistical mechanical model that accounts for the rotational entropy of the isomers and the different interaction potentials between the different types of particles. The model shows how to optimize the yield of any particular isomer, so as to put the isotopes in desired locations. Our experiments and models show that even in systems of particles with isotropic interactions, the structures of self-assembled molecules can in principle be controlled to a surprisingly high extent.
- Published
- 2016
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35. Using DNA strand displacement to control interactions in DNA-grafted colloids
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W. Benjamin Rogers, Vinothan N. Manoharan, and Emily W. Gehrels
- Subjects
Models, Molecular ,Materials science ,Interaction strength ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Phase Transition ,chemistry.chemical_compound ,Colloid ,Colloids ,Range (particle radiation) ,Base Sequence ,Oligonucleotide ,business.industry ,Design systems ,General Chemistry ,DNA ,Modular design ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,0104 chemical sciences ,chemistry ,Chemical physics ,Nucleic Acid Conformation ,Thermodynamics ,0210 nano-technology ,business ,Dna strand displacement - 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.
- Published
- 2018
36. Active colloidal particles in emulsion droplets: A model system for the cytoplasm
- Author
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Thomas G. Dimiduk, Vinothan N. Manoharan, Zachary Chambers, Viva R. Horowitz, and Irep Gözen
- Subjects
0303 health sciences ,Materials science ,Artificial cell ,Diffusion ,Rotation around a fixed axis ,General Physics and Astronomy ,FOS: Physical sciences ,Janus particles ,Condensed Matter - Soft Condensed Matter ,01 natural sciences ,Coupling (electronics) ,03 medical and health sciences ,Chemical physics ,0103 physical sciences ,Molecular motor ,Particle ,Soft Condensed Matter (cond-mat.soft) ,General Materials Science ,Liquid bubble ,Physical and Theoretical Chemistry ,010306 general physics ,030304 developmental biology - Abstract
In living cells, molecular motors create activity that enhances the diffusion of particles throughout the cytoplasm, and not just ones attached to the motors. We demonstrate initial steps toward creating artificial cells that mimic this phenomenon. Our system consists of active, Pt-coated Janus particles and passive tracers confined to emulsion droplets. We track the motion of both the active particles and passive tracers in a hydrogen peroxide solution, which serves as the fuel to drive the motion. We first show that correcting for bulk translational and rotational motion of the droplets induced by bubble formation is necessary to accurately track the particles. After drift correction, we find that the active particles show enhanced diffusion in the interior of the droplets and are not captured by the droplet interface. At the particle and hydrogen peroxide concentrations we use, we observe little coupling between the active and passive particles. We discuss the possible reasons for lack of coupling and describe ways to improve the system to more effectively mimic cytoplasmic activity.
- Published
- 2018
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- View/download PDF
37. Osmotic-Pressure-Mediated Control of Structural Colors of Photonic Capsules
- Author
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Youngseok Kim, Tae Min Choi, Jin-Gyu Park, Shin-Hyun Kim, and Vinothan N. Manoharan
- Subjects
Length scale ,Nanostructure ,Materials science ,Aqueous solution ,business.industry ,General Chemical Engineering ,Nanotechnology ,General Chemistry ,Amorphous solid ,Iridescence ,Materials Chemistry ,Osmotic pressure ,Photonics ,business ,Structural coloration - 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 pos...
- Published
- 2015
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38. Colloquium : Toward living matter with colloidal particles
- Author
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Michael Brenner, Zorana Zeravcic, and Vinothan N. Manoharan
- Subjects
Physics ,Colloidal particle ,0103 physical sciences ,General Physics and Astronomy ,Nanotechnology ,02 engineering and technology ,021001 nanoscience & nanotechnology ,010306 general physics ,0210 nano-technology ,01 natural sciences ,Living matter ,Living systems - Abstract
Living systems are undoubtedly complicated. The complicated behaviors result from interactions between many different components. In this Colloquium colloidal systems are shown to exhibit lifelike behavior such as spontaneous assembly of complex structures, the ability to self-replicate, and the ability to perform complex and coordinated metaboliclike behavior. This behavior arises from programming of the interactions between components of the colloidal system.
- Published
- 2017
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39. Inverse Photonic Glasses by Packing Bidisperse Hollow Microspheres with Uniform Cores
- Author
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Pil J. Yoo, Doo Sung Lee, Do Kyung Rhee, Gi-Ra Yi, Vinothan N. Manoharan, Seung-Hyun Kim, and Sofia Magkiriadou
- Subjects
chemistry.chemical_classification ,Fabrication ,Materials science ,Dispersity ,Shell (structure) ,Physics::Optics ,Nanotechnology ,02 engineering and technology ,Polymer ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter::Disordered Systems and Neural Networks ,01 natural sciences ,0104 chemical sciences ,Photonic metamaterial ,Condensed Matter::Soft Condensed Matter ,Colloid ,chemistry ,General Materials Science ,Self-assembly ,Composite material ,0210 nano-technology ,Porous medium - 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.
- Published
- 2017
40. RNA Structure and Kinetics Including Pseudoknots through Complete Landscape Enumeration
- Author
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Rees F. Garmann, Ofer Kimchi, Michael Brenner, Tristan Cragnolini, Vinothan N. Manoharan, and Lucy J. Colwell
- Subjects
Chemistry ,Kinetics ,Biophysics ,Enumeration ,Computational biology ,Nucleic acid structure - Published
- 2019
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- View/download PDF
41. Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles
- Author
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Kundan Chaudhary, Jerome Fung, Ilona Kretzschmar, Vinothan N. Manoharan, Thomas G. Dimiduk, Sepideh Razavi, and Anna Wang
- Subjects
Microrheology ,FOS: Physical sciences ,02 engineering and technology ,Condensed Matter - Soft Condensed Matter ,Discrete dipole approximation ,Tracking (particle physics) ,01 natural sciences ,Light scattering ,010309 optics ,Optics ,0103 physical sciences ,Spectroscopy ,Physics ,Range (particle radiation) ,Radiation ,Scattering ,business.industry ,Rotational diffusion ,021001 nanoscience & nanotechnology ,Atomic and Molecular Physics, and Optics ,Computational physics ,Soft Condensed Matter (cond-mat.soft) ,Particle ,0210 nano-technology ,business ,Optics (physics.optics) ,Physics - Optics - 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 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$^\circ$, 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., 11 pages, 9 figures, 2 tables
- Published
- 2014
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42. Full-Spectrum Photonic Pigments with Non-iridescent Structural Colors through Colloidal Assembly
- Author
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Jin-Gyu Park, Youngseok Kim, Tae Min Choi, Shin-Hyun Kim, Vinothan N. Manoharan, and Sofia Magkiriadou
- Subjects
Materials science ,Fabrication ,Nanostructure ,business.industry ,Nanotechnology ,General Medicine ,General Chemistry ,Viewing angle ,Catalysis ,Amorphous solid ,Iridescence ,Photonics ,business ,Structural coloration ,Visible spectrum - 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 "photonic pigments" consisting of microcapsules containing dense amorphous packings of core-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.
- Published
- 2014
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43. Ultrasmooth, Highly Spherical Monocrystalline Gold Particles for Precision Plasmonics
- Author
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Stefano Sacanna, Nicholas Schade, Federico Capasso, Marcelo M. Mariscal, Jonathan A. Fan, Li Sun, You-Jin Lee, Doo Ri Bae, Gaehang Lee, Gi-Ra Yi, and Vinothan N. Manoharan
- Subjects
Nanotecnología ,Materials science ,Scattering ,Dispersity ,PLASMONIC ,General Engineering ,General Physics and Astronomy ,Nanoparticle ,Nanotechnology ,COMPUTER SIMULATIONS ,INGENIERÍAS Y TECNOLOGÍAS ,ETCHING ,Nano-materiales ,Molecular physics ,Isotropic etching ,Monocrystalline silicon ,Etching (microfabrication) ,NANOPARTICLES ,Particle ,General Materials Science ,Plasmon - 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. Fil: Lee, You Jin. Sungkyunkwan University; Corea del Sur. Korea Basic Science Institute; Corea del Sur Fil: Schade, Nicholas B.. Harvard University; Estados Unidos Fil: Sun, Li. Harvard University; Estados Unidos Fil: Fan, Jonathan A.. University of Illinois; Estados Unidos Fil: Bae, Doo Ri. Korea Basic Science Institute; Corea del Sur Fil: Mariscal, Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina Fil: Lee, Gaehang. Korea Basic Science Institute; Corea del Sur Fil: Capasso, Federico. Harvard University; Estados Unidos Fil: Sacanna, Stefano. University of New York; Estados Unidos Fil: Manoharan, Vinothan N.. Harvard University; Estados Unidos Fil: Yi, Gi Ra. Sungkyunkwan University; Corea del Sur
- Published
- 2013
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44. Colloidal Alchemy: Conversion of Polystyrene Nanoclusters into Gold
- Author
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Vinothan N. Manoharan, Jean-Christophe Taveau, Etienne Duguet, Cyril Chomette, Olivier Lambert, Serge Ravaine, Mona Tréguer-Delapierre, Nicholas Schade, Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Université de Bordeaux (UB), Department of Physics and the Division of Engineering and Applied Sciences (Harvard University), Harvard University [Cambridge], Chimie et Biologie des Membranes et des Nanoobjets (CBMN), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches Paul Pascal (CRPP), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0042,AMADEus,Advanced Materials by Design(2010), ANR-10-IDEX-0003,IDEX BORDEAUX,Initiative d'excellence de l'Université de Bordeaux(2010), and Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Materials science ,seedmediated growth ,Energy Engineering and Power Technology ,Nanotechnology ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Nanoclusters ,Biomaterials ,Colloid ,chemistry.chemical_compound ,Adsorption ,Etching (microfabrication) ,Materials Chemistry ,Plasmon ,plasmonic clusters ,platonic solids ,Renewable Energy, Sustainability and the Environment ,technology, industry, and agriculture ,[CHIM.MATE]Chemical Sciences/Material chemistry ,gold ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Electron tomography ,chemistry ,Transmission electron microscopy ,silica ,Polystyrene ,0210 nano-technology - Abstract
International audience; 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 comprehensive study of their optical properties.
- Published
- 2017
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45. Tracking E. coli runs and tumbles with scattering solutions and digital holographic microscopy
- Author
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Rees F. Garmann, Anna Wang, and Vinothan N. Manoharan
- Subjects
Rotation ,Holography ,02 engineering and technology ,Tracking (particle physics) ,01 natural sciences ,Light scattering ,law.invention ,010309 optics ,Optics ,law ,Orientation (geometry) ,0103 physical sciences ,Escherichia coli ,Physics ,Microscopy ,business.industry ,Equipment Design ,021001 nanoscience & nanotechnology ,Frame rate ,Atomic and Molecular Physics, and Optics ,Digital holographic microscopy ,0210 nano-technology ,business ,Digital holography - 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’s body rotation and tumbles, offering a precise way to track fine details of bacterial motility. We are able to extract the cell’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.
- Published
- 2016
46. Effects of contact-line pinning on the adsorption of nonspherical colloids at liquid interfaces
- Author
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W. Benjamin Rogers, Vinothan N. Manoharan, and Anna Wang
- Subjects
Coupling ,Materials science ,Condensed matter physics ,Dynamics (mechanics) ,FOS: Physical sciences ,General Physics and Astronomy ,Nanotechnology ,02 engineering and technology ,Condensed Matter - Soft Condensed Matter ,021001 nanoscience & nanotechnology ,01 natural sciences ,Surface energy ,Condensed Matter::Soft Condensed Matter ,Colloid ,0103 physical sciences ,Soft Condensed Matter (cond-mat.soft) ,Particle ,010306 general physics ,0210 nano-technology ,Pinning force ,Microscale chemistry ,Digital holography - 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 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 minimization of interfacial energy and viscous dissipation alone; contact-line pinning dictates both the timescale and pathway to equilibrium., 17 pages, 5 figures, 1 movie
- Published
- 2016
47. Contact-line pinning controls how quickly colloidal particles equilibrate with liquid interfaces
- Author
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Vinothan N. Manoharan, David M. Kaz, Anna Wang, and Ryan McGorty
- Subjects
chemistry.chemical_classification ,Aqueous solution ,Materials science ,Relaxation (NMR) ,FOS: Physical sciences ,02 engineering and technology ,General Chemistry ,Polymer ,Surface finish ,Condensed Matter - Soft Condensed Matter ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Surface energy ,Pickering emulsion ,0104 chemical sciences ,Condensed Matter::Soft Condensed Matter ,Colloid ,chemistry ,Chemical physics ,Soft Condensed Matter (cond-mat.soft) ,SPHERES ,0210 nano-technology - 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 "hairs" in the case of polymer particles. We conclude that the slow relaxation must be taken into account in experiments and applications, such as Pickering emulsions, that involve colloids attaching to interfaces. The effect is particularly important for aqueous polymer particles, which pin the contact line strongly., 26 pages, 7 figures
- Published
- 2016
48. Applications to Soft Matter: general discussion
- Author
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Ajeet K. Srivastav, G. V. Pavan Kumar, Guruswamy Kumaraswamy, Vimala Sridurai, Ranjini Bandyopadhyay, Erika Eiser, Nirmalya Bachhar, Radhika Poojari, Lynn M. Walker, Lola González-García, Madivala G. Basavaraj, Nicholas A. Kotov, Sanat K. Kumar, Sudeep N. Punnathanam, Madhura Som, Bijai Prasad, Rajdip Bandyopadhyaya, Yogesh M. Joshi, Mukta Tripathy, Siddharth Kulkarni, Mario Tagliazucchi, Vinothan N. Manoharan, Oleg Gang, Alamgir Karim, Alison J. Edwards, Priyadarshi Roy Chowdhury, Charusita Chakravarty, Andrea R. Tao, Gourav Shrivastav, Neena S. John, Zakiya Shireen, Yon Ju-Nam, and Daan Frenkel
- Subjects
Computer science ,Soft matter ,Physical and Theoretical Chemistry ,Data science - Published
- 2016
49. Glycans pattern the phase behaviour of lipid membranes
- Author
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Howard A. Stone, Vinothan N. Manoharan, Guido Guidotti, and Anand Bala Subramaniam
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Glycan ,Spatial configuration ,Polysaccharide ,Models, Biological ,Phase Transition ,Membrane Lipids ,Polysaccharides ,Phase (matter) ,Materials Testing ,Molecule ,Organic chemistry ,General Materials Science ,chemistry.chemical_classification ,biology ,Chemistry ,Mechanical Engineering ,Cell Membrane ,Temperature ,Proteins ,Membranes, Artificial ,General Chemistry ,Condensed Matter Physics ,carbohydrates (lipids) ,Membrane ,Mechanics of Materials ,Biophysics ,biology.protein ,Thermodynamics ,lipids (amino acids, peptides, and proteins) - Abstract
Hydrated networks of glycans (polysaccharides)--in the form of cell walls, periplasms or gel-like matrices--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--thus indicating that the effect is thermodynamic rather than kinetic--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.
- Published
- 2012
- Full Text
- View/download PDF
50. Colloids with valence and specific directional bonding
- Author
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Yufeng Wang, Andrew D. Hollingsworth, Dana R. Breed, David J. Pine, Marcus Weck, Vinothan N. Manoharan, Lang Feng, and Yubao Wang
- Subjects
Microscopy, Confocal ,Multidisciplinary ,Valence (chemistry) ,Surface Properties ,Chemistry ,digestive, oral, and skin physiology ,Amidines ,Biotin ,Nanotechnology ,DNA ,complex mixtures ,Microspheres ,Kinetics ,Colloid ,Sticky and blunt ends ,Atomic orbital ,Colloidal particle ,Tetrahedron ,Polystyrenes ,Molecule ,Colloids ,Self-assembly - 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 ‘colloidal molecules’ with triangular, tetrahedral and other bonding symmetries, and should also give access to a rich variety of new microstructured colloidal materials. A general method of creating colloidal particles that can self-assemble into ‘colloidal molecules’ is described: surface patches with well-defined symmetries are functionalized using DNA with single-stranded sticky ends and imitate hybridized atomic orbitals to form highly directional bonds. Chemists routinely use atoms that can form directional bonds to assemble complex and useful molecular structures. But larger colloidal particles have proved less conducive to rational assembly because they lack specific directional bonds. David Pine and colleagues now report a way around this problem that could lead to the creation of a rich variety of new micro-structured colloidal materials with technologically useful properties. Using microsphere clusters as intermediates, they create colloidal particles with chemically distinct and precisely located 'sticky patches' on the surface — up to 7 per particle — that enable specific and highly directional bonding. Using this system, they assemble 'colloidal molecules' exhibiting a wide range of bonding symmetries.
- Published
- 2012
- Full Text
- View/download PDF
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