Publications

2011
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
de Bivort BL, Giribet G. A systematic revision of South African Pettalidae (Arachnida : Opiliones : Cyphophthalmi) based on a combined analysis of discrete and continuous characters with the description of seven new species. Invertebrate Systematics 2010;24:371-406. 2010_giribet_csiro.pdf
Richards CT. Kinematics and hydrodynamics analysis of swimming anurans reveals striking inter-specific differences in the mechanism for producing thrust. J Exp Biol 2010;213(4):621-34.Abstract

This study aimed to compare the swimming kinematics and hydrodynamics within and among aquatic and semi-aquatic/terrestrial frogs. High-speed video was used to obtain kinematics of the leg joints and feet as animals swam freely across their natural range of speeds. Blade element analysis was then used to model the hydrodynamic thrust as a function of foot kinematics. Two purely aquatic frogs, Xenopus laevis and Hymenochirus boettgeri, were compared with two semi-aquatic/terrestrial frogs, Rana pipiens and Bufo americanus. The four species performed similarly. Among swimming strokes, peak stroke velocity ranged from 3.3+/-1.1 to 20.9+/-2.5, from 6.8+/-2.1 to 28.6+/-3.7 and from 4.9+/-0.5 to 20.9+/-4.1 body lengths per second (BL s(-1)) in X. laevis, H. boettgeri and R. pipiens, respectively (means +/- s.d.; N=4 frogs for each). B. americanus swam much more slowly at 3.1+/-0.3 to 7.0+/-2.0 BL s(-1) (N=3 frogs). Time-varying joint kinematics patterns were superficially similar among species. Because foot kinematics result from the cumulative motion of joints proximal to the feet, small differences in time-varying joint kinematics among species resulted in species-specific foot kinematics (therefore hydrodynamics) patterns. To obtain a simple measure of the hydrodynamically useful motion of the foot, this study uses 'effective foot velocity' (EFV): a measure of the component of foot velocity along the axis of swimming. Resolving EFV into translational and rotational components allows predictions of species-specific propulsion strategies. Additionally, a novel kinematic analysis is presented here that enables the partitioning of translational and rotational foot velocity into velocity components contributed by extension at each individual limb joint. Data from the kinematics analysis show that R. pipiens and B. americanus translated their feet faster than their body moved forward, resulting in positive net translational EFV. Conversely, translational EFV was slower than the body velocity in H. boettgeri and X. laevis, resulting in negative net translational EFV. Consequently, the translational component of thrust (caused mostly by hip, knee and ankle extension) was twofold higher than rotational thrust in Rana pipiens. Likewise, rotational components of thrust were nearly twofold higher than translational components in H. boettgeri. X. laevis, however, was the most skewed species observed, generating nearly 100% of total thrust by foot rotation generated by hip, ankle and tmt extension. Thus, this study presents a simple kinematics analysis that is predictive of hydrodynamic differences among species. Such differences in kinematics reveal a continuum of different propulsive strategies ranging from mostly rotation-powered (X. laevis) to mostly translation-powered (R. pipiens) swimming.

2010_richards_jrnl.pdf
Roy S, Prasad M, Topolancik J, Vollmer F. All-optical switching with bacteriorhodopsin protein coated microcavities and its application to low power computing circuits. Journal of Applied Physics 2010;107:053115. 2010_roy_aip.pdf
Gabrielse G, Klothammer WS, McConnell R, Richerme P, Wrubel J, Kalra R, Novitski D, Grzonka D, Oelert W, Sefzick T, Zielinski M, Borbely JS, George MC, Hessels EA, Storry CH, Weel M, Mullers A, Walz J, Speck A. Centrifugal Separation of Antiprotons and Electrons. Phys. Rev. Lett. 2010;105:213002. 2010_gabrielse_prl.pdf
Spicer R, Groover A. Evolution of development of vascular cambia and secondary growth. New Phytol 2010;186(3):577-92.Abstract

Secondary growth from vascular cambia results in radial, woody growth of stems. The innovation of secondary vascular development during plant evolution allowed the production of novel plant forms ranging from massive forest trees to flexible, woody lianas. We present examples of the extensive phylogenetic variation in secondary vascular growth and discuss current knowledge of genes that regulate the development of vascular cambia and woody tissues. From these foundations, we propose strategies for genomics-based research in the evolution of development, which is a next logical step in the study of secondary growth.

2010_spicer_rev._new_phytologist.pdf
Speck A, Mandal P. Half-cycle-pulse-train induced state redistribution of Rydberg atoms. Physical Review A 2010;81:013401. 2010_mandal_pr.pdf
Okada K, Bartolini F, Deaconescu AM, Moseley JB, Dogic Z, Grigorieff N, Gundersen GG, Goode BL. Adenomatous polyposis coli protein nucleates actin assembly and synergizes with the formin mDia1. J Cell Biol 2010;189(7):1087-96.Abstract

The tumor suppressor protein adenomatous polyposis coli (APC) regulates cell protrusion and cell migration, processes that require the coordinated regulation of actin and microtubule dynamics. APC localizes in vivo to microtubule plus ends and actin-rich cortical protrusions, and has well-documented direct effects on microtubule dynamics. However, its potential effects on actin dynamics have remained elusive. Here, we show that the C-terminal "basic" domain of APC (APC-B) potently nucleates the formation of actin filaments in vitro and stimulates actin assembly in cells. Nucleation is achieved by a mechanism involving APC-B dimerization and recruitment of multiple actin monomers. Further, APC-B nucleation activity is synergistic with its in vivo binding partner, the formin mDia1. Together, APC-B and mDia1 overcome a dual cellular barrier to actin assembly imposed by profilin and capping protein. These observations define a new function for APC and support an emerging view of collaboration between distinct actin assembly-promoting factors with complementary activities.

2010_okada_jrnl.pdf
Narayana S, Sato Y. Compact miniature high-resolution thermometer. IEEE Transactions on Applied Superconductivity 2010;20:2402. 2010_sato_ieee.pdf
Narayana S, Sato Y. Direct observation of dynamical bifurcation in a superfluid Josephson junction. Phys Rev Lett 2010;105(20):205302.Abstract

We report a direct observation of dynamical bifurcation between two plasma oscillation states of a superfluid Josephson junction. We excite the superfluid plasma resonance into a nonlinear regime by driving below the natural plasma frequency and observe a clear transition between two dynamical states. We also demonstrate bifurcation by changing the potential well with temperature variations.

2010_narayana_prl.pdf
Barry E, Dogic Z. Entropy driven self-assembly of nonamphiphilic colloidal membranes. Proc Natl Acad Sci U S A 2010;107(23):10348-53.Abstract

We demonstrate that homogeneous monodisperse rods in the presence of attractive interactions assemble into equilibrium 2D fluid-like membranes composed of a one-rod length thick monolayer of aligned rods. Unique features of our system allow us to simultaneously investigate properties of these membranes at both continuum and molecular lengthscales. Analysis of thermal fluctuations at continuum lengthscales yields the membranes' lateral compressibility and bending rigidity and demonstrates that the properties of colloidal membranes are comparable to those of traditional lipid bilayers. Fluctuations at molecular lengthscales, in which single rods protrude from the membrane surface, are directly measured by comparing the positions of individual fluorescently labeled rods within a membrane to that of the membrane's continuum conformation. As two membranes approach each other in suspension, protrusion fluctuations are suppressed leading to effective repulsive interactions. Motivated by these observations, we propose an entropic mechanism that explains the stability of colloidal membranes and offers a general design principle for the self-assembly of 2D nanostructured materials from rod-like molecules.

2010_dogic_pnas.pdf
Sato Y. Fiske-amplified superfluid interferometry. Physical Review B 2010;81:172502. 2010_sato_pr.pdf
Fischer P, Ghosh A, Premasiri WR, Ziegler LD. Nanostructured Plasmonic Surfaces for Surface Enhanced Raman Scattering   of Bacteria. XXII International Conference on Raman Spectroscopy 2010;1267:994-995.
Pinto N, Cox DD. An Evaluation of the Invariance Properties of a Biologically-Inspired System for Unconstrained Face Recognition. ICST Conference on Biologically Inspired Network, Information, and Computing Systems 2010;

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