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Probing the Conformational Distributions of Sub-Persistence Length DNA

Description: We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle X-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble FRET) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs (bp) are consistent with a simple worm-like chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 bp) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.
Date: June 8, 2009
Creator: Mastroianni, Alexander; Sivak, David; Geissler, Phillip & Alivisatos, Paul
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A nanocrystal strain gauge for luminescence detection of mechanical forces

Description: Local microscale stresses play a crucial role in inhomogeneous mechanical processes from cell motility to material failure. However, it remains difficult to spatially resolve stress at these small length scales. While contact-probe and non-contact based techniques have been used to quantify local mechanical behavior in specific systems with high stiffness or stress and spatial resolution, these methods cannot be used to study a majority of micromechanical systems due to spectroscopic and geometrical constraints. We present here the design and implementation of a luminescent nanocrystal strain gauge, the CdSe/CdS core/shell tetrapod. The tetrapod can be incorporated into many materials, yielding a local stress measurement through optical fluorescence spectroscopy of the electronically confined CdSe core states. The stress response of the tetrapod is calibrated and utilized to study mechanical behavior in single polymer fibers. We expect that tetrapods can be used to investigate local stresses in many other mechanical systems.
Date: July 26, 2010
Creator: Choi, Charina; Koski, Kristie; Olson, Andrew & Alivisatos, Paul
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A luminescent nanocrystal stress gauge

Description: Microscale mechanical forces can determine important outcomes ranging from the site of material fracture to stem cell fate. However, local stresses in a vast majority of systems cannot be measured due to the limitations of current techniques. In this work, we present the design and implementation of the CdSe/CdS core/shell tetrapod nanocrystal, a local stress sensor with bright luminescence readout. We calibrate the tetrapod luminescence response to stress, and use the luminescence signal to report the spatial distribution of local stresses in single polyester fibers under uniaxial strain. The bright stress-dependent emission of the tetrapod, its nanoscale size, and its colloidal nature provide a unique tool that may be incorporated into a variety of micromechanical systems including materials and biological samples to quantify local stresses with high spatial resolution.
Date: October 25, 2010
Creator: Choi, Charina; Koski, Kristie; Olson, Andrew & Alivisatos, Paul
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A Nanocrystal Sensor for Luminescence Detection of Cellular Forces

Description: Quantum dots have been used as bright fluorescent tags with high photostability to probe numerous biological systems. In this work we present the tetrapod quantum dot as a dynamic, next-generation nanocrystal probe that fluorescently reports cellular forces with spatial and temporal resolution. Its small size and colloidal state suggest that the tetrapod may be further developed as a tool to measure cellular forces in vivo and with macromolecular spatial resolution.
Date: September 29, 2011
Creator: Choi, Charina; Chou, Jonathan; Lutker, Katie; Werb, Zena & Alivisatos, Paul
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Surfactant-Assisted Hydrothermal Synthesis of Single Phase Pyrite FeS2 Nanocrystals

Description: Iron pyrite nanocrystals with high purity have been synthesized through a surfactant-assisted hydrothermal reaction under optimum pH value. These pyrite nanocrystals represent a new group of well-defined nanoscale structures for high-performance photovoltaic solar cells based on non-toxic and earth abundant materials.
Date: March 27, 2009
Creator: Wadia, Cyrus; Wu, Yue; Gul, Sheraz; Volkman, Steven; Guo, Jinghua & Alivisatos, Paul
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Electric Field Assisted Assembly of Perpendicular Oriented NanorodSuperlattices

Description: We observe the assembly of CdS nanorod superlattices by thecombination of a DC electric field and solvent evaporation. In eachelectric field (1 V/um) assisted assembly, CdS nanorods (5 x 30 nm)suspended initially in toluene were observed to align perpendicularly tothe substrate. Azimuthal alignment along the nanorod crystal faces andthe presence of stacking faults indicate that both 2D and 3D assemblieswere formed by a process of controlled super crystal growth.
Date: April 10, 2006
Creator: Ryan, Kevin M.; Mastroianni, Alex; Stancil, Kimani A.; Liu,Haitao & Alivisatos, Paul A.
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Mechanical and Electrical Properties of CdTe Tetrapods Studied byAtomic Force Microscopy

Description: The mechanical and electrical properties of CdTe tetrapod-shaped nanocrystals have been studied with atomic force microscopy. Tapping mode images of tetrapods deposited on silicon wafers revealed that they contact the surface with the ends of three arms. The length of these arms was found to be 130 {+-} 10 nm. A large fraction of the tetrapods had a shortened vertical arm as a result of fracture during sample preparation. Fracture also occurs when the applied load is a few nanonewtons. Compression experiments with the AFM tip indicate that tetrapods with the shortened vertical arm deform elastically when the applied force was less than 50 nN. Above 90 nN additional fracture events occurred that further shorted the vertical arm. Loads above 130 nN produced irreversible damage to the other arms as well. Current-voltage characteristics of tetrapods deposited on gold indicated semiconducting behavior with a current gap of {approx}2 eV at low loads (<50 nN) and a narrowing to about 1 eV at loads between 60 and 110 nN. Atomic calculation of the deformation suggests that the ends of the tetrapod arms are stuck during compression so that the deformations are due to bending modes. The reduction of the current gap is due to electrostatic effects, rather than strain deformation effects inside the tetrapod.
Date: August 30, 2007
Creator: Fang, Liang; Park, Jeong Young; Cui, Yi; Alivisatos, Paul; Shcrier, Joshua; Lee, Byounghak et al.
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Lithographically-directed self-assembly of nanostructures

Description: The combination of lithography and self-assembly provides apowerful means of organizing solution-synthesized nanostructures for awide variety of applications. We have developed a fluidic assembly methodthat relies on the local pinning of a moving liquid contact line bylithographically produced topographic features to concentratenanoparticles at those features. The final stages of the assembly processare controlled first by long-range immersion capillary forces and then bythe short-range electrostatic and Van der Waal's interactions. We havesuccessfully assembled nanoparticles from 50 nm to 2 nm in size usingthis technique and have also demonstrated the controlled positioning ofmore complex nanotetrapod structures. We have used this process toassemble Au nanoparticles into pre-patterned electrode structures andhave performed preliminary electrical characterization of the devices soformed. The fluidic assembly method is capable of very high yield, interms of positioning nanostructures at each lithographically-definedlocation, and of excellent specificity, with essentially no particledeposition between features.
Date: September 21, 2004
Creator: Liddle, J. Alexander; Cui, Yi & Alivisatos, Paul
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Isolation of Discrete Nanoparticle-DNA Conjugates for Plasmonic Applications

Description: Discrete DNA-gold nanoparticle conjugates with DNA lengths as short as 15 bases for both 5 nm and 20 nm gold particles have been purified by anion-exchange HPLC. Conjugates comprising short DNA (<40 bases) and large gold particles (>_ 20 nm) are difficult to purify by other means, and are potential substrates for plasmon coupling experiments. Conjugate purity is demonstrated by hybridizing complementary conjugates to form discrete structures, which are visualized by TEM.
Date: April 11, 2008
Creator: Alivisatos, Paul; Claridge, Shelley A.; Liang, Huiyang W.; Basu, Sourav Roger; Frechet, Jean M.J. & Alivisatos, A. Paul
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Nanoplasmonic molecular ruler for nuclease activity and DNAfootprinting

Description: We have constructed a nanoplasmonic molecular ruler, which can perform label-free and real-time monitoring of DNA length changes and perform DNA footprinting. The ruler was created by tethering double-stranded DNA to single Au nanoparticles. The scattering spectra of Au-DNA nanoconjugates showed red-shifted peak plasmon resonance wavelength dependent on DNA length, which can be measured with sub-nanometer axial resolution, averaging {approx}1.24 nm peak wavelength shift per DNA base pair. The spectra of individual Au-DNA nanoconjugates in the presence of nuclease showed a time-resolved dependence on the reaction dynamics, allowing quantitative, kinetic and real-time measurement of nuclease activity. The ruler was further developed into a new DNA footprinting platform. We showed the specific binding of a protein to DNA and the accurate mapping of its footprint. This work promises a very fast and convenient platform for mapping DNA-protein interactions, for nuclease activity monitoring, and for other DNA size-based methods.
Date: August 15, 2006
Creator: Chen, Fanqing Frank; Liu, Gang L.; Yin, Yadong; Gerion, Daniele; Kunchakarra, Siri; Mukherjee, Bipasha et al.
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Electronic structure of cobalt nanocrystals suspended inliquid

Description: The electronic structure of cobalt nanocrystals suspended in liquid as a function of size has been investigated using in-situ x-ray absorption and emission spectroscopy. A sharp absorption peak associated with the ligand molecules is found that increases in intensity upon reducing the nanocrystal size. X-ray Raman features due to d-d and to charge-transfer excitations of ligand molecules are identified. The study reveals the local symmetry of the surface of {var_epsilon}-Co phase nanocrystals, which originates from a dynamic interaction between Co nanocrystals and surfactant + solvent molecules.
Date: July 16, 2007
Creator: Liu, Hongjian; Guo, Jinghua; Yin, Yadong; Augustsson, Andreas; Dong, Chungli; Nordgren, Joseph et al.
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Reactivity of Au nanoparticles supported over SiO2 and TiO2 studiedby ambient pressure photoelectron spectroscopy

Description: The influence of the metal cluster size and the identity of the support on the reactivity of gold based catalysts have been studied in the CO oxidation reaction. To overcome the structural complexity of the supported catalysts, gold nanoparticles synthesized from colloidal chemistry with precisely controlled size have been used. Those particles were supported over SiO{sub 2} and TiO{sub 2} and their catalytic activity was measured in a flow reactor. The reaction rate was dependent on the particle size and the support, suggesting two reaction pathways in the CO oxidation reaction. In parallel, ambient pressure photoelectron spectroscopy (APPS) has been performed under reaction conditions using bidimensional model catalysts prepared upon supporting the Au nanoparticles over planar polycrystalline SiO{sub 2} and TiO{sub 2} thin films by means of the Langmuir-Blodgett (LB) technique to mimic the characteristic of the powder samples. In this way, the catalytically active surface was characterized under true reaction conditions, revealing that during CO oxidation gold remains in the metallic state.
Date: April 15, 2009
Creator: Herranz, Tirma; Deng, Xingyi; Cabot, Andreu; Alivisatos, Paul; Liu, Zhi; Soler-Illia, Galo et al.
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Conjugation of DNA to Silanized Colloidal Semiconductor Nanocrystalline Quantum Dots

Description: Water-soluble, highly fluorescent, silanized semiconductor nanocrystals with different surface charges were synthesized. To covalently attach the nanocrystals to biological macromolecules with a variety of mild coupling chemistries, the outermost siloxane shells were derivatized with thiol, amino, or carboxyl functional groups. Single- or double-stranded DNA was coupled to the nanocrystal surfaces by using commercially available bifunctional cross-linker. Conjugation had little effect on the optical properties of the nanocrystals, and the resulting conjugates were more stable than previously reported systems. By using the strategies developed in this study, most biomolecules can be covalently coupled to semiconductor nanocrystals. These nanocrystal-DNA conjugates promise to be a versatile tool for fluorescence imaging and probing of biological systems.
Date: September 10, 2001
Creator: Parak, Wolfgang J.; Gerion, Daniele; Zanchet, Daniela; Waerz, Anke S.; Micheel, Christine; Williams, Shara C. et al.
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The concept of delayed nucleation in nanocrystal growthdemonstrated for the case of iron oxide nanodisks

Description: A comprehensive study of iron oxide nanocrystal growth through non-hydrolitic, surfactant-mediated thermal reaction of iron pentacarbonyl and an oxidizer has been conducted, which includes size control, anisotropic shape evolution, and crystallographic phase transition of monodisperse iron oxide colloidal nanocrystals. The reaction was monitored by in situ UV-Vis spectroscopy taking advantage of the color change accompanying the iron oxide colloid formation allowing measurement of the induction time for nucleation. Features of the synthesis such as the size control and reproducibility are related to the occurrence of the observed delayed nucleation process. As a separate source of iron and oxygen is adopted, phase control could also be achieved by sequential injections of oxidizer.
Date: September 9, 2005
Creator: Casula, Maria F.; Jun, Young-wook; Zaziski, David J.; Chan, EmoryM.; Corrias, Anna & Alivisatos, Paul A.
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