Publications

2012
Halvorsen K, Wong WP. Binary DNA nanostructures for data encryption. PLoS One 2012;7(9):e44212.Abstract

We present a simple and secure system for encrypting and decrypting information using DNA self-assembly. Binary data is encoded in the geometry of DNA nanostructures with two distinct conformations. Removing or leaving out a single component reduces these structures to an encrypted solution of ssDNA, whereas adding back this missing "decryption key" causes the spontaneous formation of the message through self-assembly, enabling rapid read out via gel electrophoresis. Applications include authentication, secure messaging, and barcoding.

2012_halvorsen_plos.pdf
Zhao W, Cui CH, Bose S, Guo D, Shen C, Wong WP, Halvorsen K, Farokhzad OC, Teo GSL, Phillips JA, Dorfman DM, Karnik R, Karp JM. Bioinspired multivalent DNA network for capture and release of cells. Proc Natl Acad Sci U S A 2012;109(48):19626-31.Abstract

Capture and isolation of flowing cells and particulates from body fluids has enormous implications in diagnosis, monitoring, and drug testing, yet monovalent adhesion molecules used for this purpose result in inefficient cell capture and difficulty in retrieving the captured cells. Inspired by marine creatures that present long tentacles containing multiple adhesive domains to effectively capture flowing food particulates, we developed a platform approach to capture and isolate cells using a 3D DNA network comprising repeating adhesive aptamer domains that extend over tens of micrometers into the solution. The DNA network was synthesized from a microfluidic surface by rolling circle amplification where critical parameters, including DNA graft density, length, and sequence, could readily be tailored. Using an aptamer that binds to protein tyrosine kinase-7 (PTK7) that is overexpressed on many human cancer cells, we demonstrate that the 3D DNA network significantly enhances the capture efficiency of lymphoblast CCRF-CEM cells over monovalent aptamers and antibodies, yet maintains a high purity of the captured cells. When incorporated in a herringbone microfluidic device, the 3D DNA network not only possessed significantly higher capture efficiency than monovalent aptamers and antibodies, but also outperformed previously reported cell-capture microfluidic devices at high flow rates. This work suggests that 3D DNA networks may have broad implications for detection and isolation of cells and other bioparticles.

2012_zhao_pnas.pdf
Pelletier J, Halvorsen K, Ha B-Y, Paparcone R, Sandler SJ, Woldringh CL, Wong WP, Jun S. Physical manipulation of the Escherichia coli chromosome reveals its soft nature. Proc Natl Acad Sci U S A 2012;109(40):E2649-56.Abstract

Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called the nucleoid. Although many proteins involved in this process have been identified, the nature of the global forces that shape and segregate the chromosomes has remained unclear because of limited knowledge of the micromechanical properties of the chromosome. In this work, we demonstrate experimentally the fundamentally soft nature of the bacterial chromosome and the entropic forces that can compact it in a crowded intracellular environment. We developed a unique "micropiston" and measured the force-compression behavior of single Escherichia coli chromosomes in confinement. Our data show that forces on the order of 100 pN and free energies on the order of 10(5) k(B)T are sufficient to compress the chromosome to its in vivo size. For comparison, the pressure required to hold the chromosome at this size is a thousand-fold smaller than the surrounding turgor pressure inside the cell. Furthermore, by manipulation of molecular crowding conditions (entropic forces), we were able to observe in real time fast (approximately 10 s), abrupt, reversible, and repeatable compaction-decompaction cycles of individual chromosomes in confinement. In contrast, we observed much slower dissociation kinetics of a histone-like protein HU from the whole chromosome during its in vivo to in vitro transition. These results for the first time provide quantitative, experimental support for a physical model in which the bacterial chromosome behaves as a loaded entropic spring in vivo.

2012_pelletier_pnas.pdf
2011
Giribet G, Sharma PP, Benavides LR, Boyer SL, Clouse RM, de Bivort BL, Dimitrov D, Kawaguchi GY, Murienne J, Schwendinger PJ. Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biological Journal of the Linnean Society 2011;105:92-130. 2011_giribet_jrnl_.pdf
Richards CT. Building a robotic link between muscle dynamics and hydrodynamics. J Exp Biol 2011;214(Pt 14):2381-9.Abstract

This study used a novel feedback approach to control a robotic foot using force and length signals transmitted from an isolated Xenopus laevis frog muscle. The foot's environment (inertial versus hydrodynamic), gearing (outlever/inlever) and size were changed to alter the muscle's load. Upon nerve stimulation (250 Hz, 80 ms train duration), variation in loading generated a range of muscle stress (19.8±5.3 to 66.0±22.5 kPa), work (1.89±0.67 to 6.87±2.96 J kg(-1) muscle) and power (12.4±7.5 to 64.8±28.3 W kg(-1) muscle; mean ± s.d., N=6 frogs). Inertial versus hydrodynamic loading dramatically shifted contractile dynamics. With the foot in water, the muscle generated ∼30% higher force, yet shortened slower, producing lower power than inertial loading. Power increased in air from 22.6±5.8 to 63.6±27.2 W kg(-1) muscle in response to doubling the gear ratio, but did not increase in water. Surprisingly, altering foot size diminished muscle performance in water, causing power to drop significantly from 41.6±11.1 to 25.1±8.0 W kg(-1) muscle as foot area was doubled. Thus, morphological modifications influenced muscle dynamics independently of neural control; however, changes in loading environment and gearing affected contractile output more strongly than changes in foot size. Confirming recent theory, these findings demonstrate how muscle contractile output can be modulated solely by altering the mechanical environment.

2011_richards_jrnl_of_experimental_biology.pdf
Schonbrun E, Seo K, Crozier KB. Reconfigurable imaging systems using elliptical nanowires. Nano Lett 2011;11(10):4299-303.Abstract

Materials that have subwavelength structure can add degrees of freedom to optical system design that are not possible with bulk materials. We demonstrate two lenses that are composed out of lithographically patterned arrays of elliptical cross-section silicon nanowires, which can dynamically reconfigure their imaging properties in response to the polarization of the illumination. In each element, two different focusing functions are polarization encoded into a single lens. The first nanowire lens has a different focal length for each linear polarization state, thereby realizing the front end of a nonmechanical zoom imaging system. The second nanowire lens has a different optical axis for each linear polarization state, demonstrating stereoscopic image capture from a single physical aperture.

2011_schonbrun_ltr.pdf
Wrubel J, Gabrielse G, Klothammer WS, Larochelle P, McConnell R, Richerme P, Grzonka D, Oelert W, Sefzick T, Zielinski M, Borbely JS, George MC, Hessels EA, Storry CH, Weel M, Mullers A, Walz J, Speck A. Pumped helium system for cooling positron and electron traps to 1.2 K. In: Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 2011 p. 232–240.
Yang KJ, Noh H, Rooks MJ, Solomon GS, Vollmer F, Cao H. Lasing in localized modes of a slow light photonic crystal waveguide. Applied Physics Letters 2011;98:241107. 2011_vollmer_apl.pdf
Wilson LG, Harrison AW, Poon WCK, Puertas AM. Microrheology and the fluctuation theorem in dense colloids. EPL 2011;93(5):58007. 2011_wilson_epl.pdf
Dong M, Sahin O. A nanomechanical interface to rapid single-molecule interactions. Nat Commun 2011;2:247.Abstract

Single-molecule techniques provide opportunities for molecularly precise imaging, manipulation, assembly and biophysical studies. Owing to the kinetics of bond rupture processes, rapid single-molecule measurements can reveal novel bond rupture mechanisms, probe single-molecule events with short lifetimes and enhance the interaction forces supplied by single molecules. Rapid measurements will also increase throughput necessary for technological use of single-molecule techniques. Here we report a nanomechanical sensor that allows single-molecule force spectroscopy on the previously unexplored microsecond timescale. We probed bond lifetimes around 5 μs and observed significant enhancements in molecular interaction forces. Our loading-rate-dependent measurements provide experimental evidence for an additional energy barrier in the biotin-streptavidin complex. We also demonstrate quantitative mapping of rapid single-molecule interactions with high spatial resolution. This nanomechanical interface may allow studies of molecular processes with short lifetimes and development of novel biological imaging, single-molecule manipulation and assembly technologies.

2011_dong_nature_communications.pdf
Narayana S, Sato Y. Quantum coherence in a superfluid Josephson junction. Phys Rev Lett 2011;106(5):055302.Abstract

We report a new kind of experiment in which we take an array of nanoscale apertures that form a superfluid (4)He Josephson junction and apply quantum phase gradients directly along the array. We observe collective coherent behaviors from aperture elements, leading to quantum interference. Connections to superconducting and Bose-Einstein condensate Josephson junctions as well as phase coherence among the superfluid aperture array are discussed.

2011_narayana_prl_2.pdf
Wilson LG, Poon WCK. Small-world rheology: an introduction to probe-based active microrheology. Phys Chem Chem Phys 2011;13(22):10617-30.Abstract

We introduce active, probe-based microrheological techniques for measuring the flow and deformation of complex fluids. These techniques are ideal for mechanical characterization either when little sample is available, or when samples show significant spatial heterogeneity. We review recent results, paying particular attention to comparing and contrasting rheological parameters obtained from micro- and macro-rheological techniques.

2011_wilson_pccp.pdf
Narayana S, Sato Y. Superfluid quantum interference in multiple-turn reciprocal geometry. Phys Rev Lett 2011;106(25):255301.Abstract

We report the observation of superfluid quantum interference in a compact, large-area matter-wave interferometer consisting of a multiple-turn interfering path in reciprocal geometry. Utilizing the Sagnac effect from Earth's rotation in conjunction with a phase shifter made of superfluid heat current, we demonstrate that such a scheme can be extended for sensitive rotation sensing as well as for general interferometry.

2011_narayana_prl.pdf
Mandal P, Speck A, Ko C, Ramanathan S. Terahertz spectroscopy studies on epitaxial vanadium dioxide thin films across the metal-insulator transition. Opt Lett 2011;36(10):1927-9.Abstract

We present results on terahertz (THz) spectroscopy on epitaxial vanadium dioxide (VO(2)) films grown on sapphire across the metal-insulator transition. X-ray diffraction indicates the VO(2) film is highly oriented with the crystallographic relationship: (002)(film)//(0006)(sub) and [010](film)//[2 ̅1 ̅10](sub). THz studies measuring the change in transmission as a function of temperature demonstrate an 85% reduction in transmission as the thin film completes its phase transition to the conducting phase, which is much greater than the previous observation on polycrystalline films. This indicates the crucial role of microstructure and phase homogeneity in influencing THz properties.

2011_mandal_optics_ltr.pdf
Pinto N, Cox DD. GPU Metaprogramming: A Case Study in Biologically-Inspired Computer Vision. In: GPU Computing Gems, Jade Edition. Morgan Kaufmann Publishers; 2011
Pinto N, Cox DD. Beyond Simple Features: A Large-Scale Feature Search Approach to Unconstrained Face Recognition. IEEE Automatic Face and Gesture Recognition 2011; 2011_cox_.pdf
Halvorsen K, Schaak D, Wong WP. Nanoengineering a single-molecule mechanical switch using DNA self-assembly. Nanotechnology 2011;22(49):494005.Abstract

The ability to manipulate and observe single biological molecules has led to both fundamental scientific discoveries and new methods in nanoscale engineering. A common challenge in many single-molecule experiments is reliably linking molecules to surfaces, and identifying their interactions. We have met this challenge by nanoengineering a novel DNA-based linker that behaves as a force-activated switch, providing a molecular signature that can eliminate errant data arising from non-specific and multiple interactions. By integrating a receptor and ligand into a single piece of DNA using DNA self-assembly, a single tether can be positively identified by force-extension behavior, and receptor-ligand unbinding easily identified by a sudden increase in tether length. Additionally, under proper conditions the exact same pair of molecules can be repeatedly bound and unbound. Our approach is simple, versatile and modular, and can be easily implemented using standard commercial reagents and laboratory equipment. In addition to improving the reliability and accuracy of force measurements, this single-molecule mechanical switch paves the way for high-throughput serial measurements, single-molecule on-rate studies, and investigations of population heterogeneity.

2011_halvorsen_nanotechnology.pdf
Pinto N, Stone Z, Zickler T, Cox DD. Scaling-up Biologically-Inspired Computer Vision: A Case-Study on Facebook. IEEE Computer Vision and Pattern Recognition, Workshop on Biologically Consistent Vision 2011; 2011_pinto_.pdf
2010
Clouse R, de Bivort BL, Giribet G. Phylogenetic signals in morphometric data. Cladistics 2010;27:1-4.
de Bivort BL, Clouse RM, Giribet G. A morphometrics-based phylogeny of the temperate Gondwanan mite harvestmen (Opiliones, Cyphophthalmi, Pettalidae). Journal of Zoological Systematics and Evolutionary Research 2010;In press 2010_de_bivort_.pdf

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