Publications

2008
Ghosh A, Sheridon NK, Fischer P. Voltage-Controllable Magnetic Composite Based on Multifunctional Polyethylene Microparticles. Small 2008;4(11):1956-1958.
Cox DD, Papanastassiou AM, Oreper D, Andken BB, DiCarlo JJ. High-resolution three-dimensional microelectrode brain mapping using stereo microfocal X-ray imaging. J Neurophysiol 2008;100(5):2966-76.Abstract
Much of our knowledge of brain function has been gleaned from studies using microelectrodes to characterize the response properties of individual neurons in vivo. However, because it is difficult to accurately determine the location of a microelectrode tip within the brain, it is impossible to systematically map the fine three-dimensional spatial organization of many brain areas, especially in deep structures. Here, we present a practical method based on digital stereo microfocal X-ray imaging that makes it possible to estimate the three-dimensional position of each and every microelectrode recording site in "real time" during experimental sessions. We determined the system's ex vivo localization accuracy to be better than 50 microm, and we show how we have used this method to coregister hundreds of deep-brain microelectrode recordings in monkeys to a common frame of reference with median error of <150 microm. We further show how we can coregister those sites with magnetic resonance images (MRIs), allowing for comparison with anatomy, and laying the groundwork for more detailed electrophysiology/functional MRI comparison. Minimally, this method allows one to marry the single-cell specificity of microelectrode recording with the spatial mapping abilities of imaging techniques; furthermore, it has the potential of yielding fundamentally new kinds of high-resolution maps of brain function.
Cox DD, DiCarlo JJ. Does learned shape selectivity in inferior temporal cortex automatically generalize across retinal position?. J Neurosci 2008;28(40):10045-55.Abstract

Biological visual systems have the remarkable ability to recognize objects despite confounding factors such as object position, size, pose, and lighting. In primates, this ability likely results from neuronal responses at the highest stage of the ventral visual stream [inferior temporal cortex (IT)] that signal object identity while tolerating these factors. However, for even the apparently simplest IT tolerance ("invariance"), tolerance to object position on the retina, little is known about how this feat is achieved. One possibility is that IT position tolerance is innate in that discriminatory power for newly learned objects automatically generalizes across position. Alternatively, visual experience plays a role in developing position tolerance. To test these ideas, we trained adult monkeys in a difficult object discrimination task in which their visual experience with novel objects was restricted to a single retinal position. After training, we recorded the spiking activity of an unbiased population of IT neurons and found that it contained significantly greater selectivity among the newly learned objects at the experienced position compared with a carefully matched, non-experienced position. Interleaved testing with other objects shows that this difference cannot be attributed to a bias in spatial attention or neuronal sampling. We conclude from these results that, at least under some conditions, full transfer of IT neuronal selectivity across retinal position is not automatic. This finding raises the possibility that visual experience plays a role in building neuronal tolerance in the ventral visual stream and the recognition abilities it supports.

2008_cox_jrnl.pdf
Pinto N, DiCarlo JJ, Cox DD. Establishing Good Benchmarks and Baselines for Face Recognition. European Conference on Computer Vision, Workshop on Faces in Real Life Images 2008; 2008_pinto_researchgate.pdf
Heinrich V, Wong WP, Halvorsen K, Evans E. Imaging biomolecular interactions by fast three-dimensional tracking of laser-confined carrier particles. Langmuir 2008;24(4):1194-203.Abstract

The quantitative study of the near-equilibrium structural behavior of individual biomolecules requires high-resolution experimental approaches with longtime stability. We present a new technique to explore the dynamics of weak intramolecular interactions. It is based on the analysis of the 3D Brownian fluctuations of a laser-confined glass bead that is tethered to a flat surface by the biomolecule of interest. A continuous autofocusing mechanism allows us to maintain or adjust the height of the optical trap with nanometer accuracy over long periods of time. The resulting remarkably stable trapping potential adds a well-defined femto-to-piconewton force bias to the energy landscape of molecular configurations. A combination of optical interferometry and advanced pattern-tracking algorithms provides the 3D bead positions with nanometer spatial and >120 Hz temporal resolution. The analysis of accumulated 3D positions has allowed us not only to identify small single biomolecules but also to characterize their nanomechanical behavior, for example, the force-extension relations of short oligonucleotides and the unfolding/refolding transitions of small protein tethers.

2008_heinrich_.pdf
Pinto N, Cox DD, DiCarlo JJ. Why is real-world visual object recognition hard?. PLoS Comput Biol 2008;4(1):e27.Abstract

Progress in understanding the brain mechanisms underlying vision requires the construction of computational models that not only emulate the brain's anatomy and physiology, but ultimately match its performance on visual tasks. In recent years, "natural" images have become popular in the study of vision and have been used to show apparently impressive progress in building such models. Here, we challenge the use of uncontrolled "natural" images in guiding that progress. In particular, we show that a simple V1-like model--a neuroscientist's "null" model, which should perform poorly at real-world visual object recognition tasks--outperforms state-of-the-art object recognition systems (biologically inspired and otherwise) on a standard, ostensibly natural image recognition test. As a counterpoint, we designed a "simpler" recognition test to better span the real-world variation in object pose, position, and scale, and we show that this test correctly exposes the inadequacy of the V1-like model. Taken together, these results demonstrate that tests based on uncontrolled natural images can be seriously misleading, potentially guiding progress in the wrong direction. Instead, we reexamine what it means for images to be natural and argue for a renewed focus on the core problem of object recognition--real-world image variation.

2008_pinto_open_access.pdf
2007
Ahn Y, Tsen W, Kim B, Park Y-W, Park J. Photocurrent Imaging of p−n Junctionsin Ambipolar Carbon NanotubeTransistors. Nano letters 2007;7(11):3320-3323.Abstract

We use scanning photocurrent microscopy (SPCM) to investigate the properties of internal p- n junctions in ambipolar carbon nanotube (CNT) transistors. Our SPCM images show strong signals near metal contacts whose polarity and positions change depending on the gate bias. SPCM images analyzed in conjunction with the overall conductance also indicate the existence and gate-dependent evolution of internal p-n junctions near contacts in the n-type operation regime. To determine the -n junction position and the depletion width with a nanometer scale-resolution, a Gaussian fit was used. We also measure the electric potential profile of partially suspended CNT devices at different gate biases which shows that induced local fields can be imaged using the SPCM technique. Our experiment clearly demonstrates that SPCM is a valuable tool for imaging and optimizing electrical and optoelectronic properties of CNT based devices.

2007_ahn_nano_ltr.pdf
Richards CT, Biewener AA. Modulation of in vivo muscle power output during swimming in the African clawed frog (Xenopus laevis). J Exp Biol 2007;210(Pt 18):3147-59.Abstract

The goal of this study is to explore how swimming animals produce the wide range of performance that is seen across their natural behaviors. In vivo recordings of plantaris longus muscle length change were obtained by sonomicrometry. Simultaneous with muscle length data, force measurements were obtained using a novel tendon buckle force transducer placed on the Achilles tendon of Xenopus laevis frogs during brief accelerating bursts of swimming. In vivo work loops revealed that the plantaris generates a variable amount of positive muscle work over a range of swimming cycle durations (from 0.23 to 0.76 s), resulting in a large range of cycle power output (from 2.32 to 74.17 W kg(-1) muscle). Cycle duration correlated negatively with cycle power, and cycle work correlated positively (varying as a function of peak cycle stress and, to a much lesser extent, fascicle strain amplitude). However, variation in cycle duration only contributed to 12% of variation in power, with cycle work accounting for the remaining 88%. Peak cycle stress and strain amplitude were also highly variable, yet peak stress was a much stronger predictor of cycle work than strain amplitude. Additionally, EMG intensity correlated positively with peak muscle stress (r(2)=0.53). Although the timing of muscle recruitment (EMG phase and EMG duty cycle) varied considerably within and among frogs, neither parameter correlated strongly with cycle power, cycle work, peak cycle stress or strain amplitude. These results suggest that relatively few parameters (cycle duration, peak cycle stress and strain amplitude) vary to permit a wide range of muscle power output, which allows anurans to swim over a large range of velocities and accelerations.

2007_richards_j_exp_biology.pdf
Topolancik J, Ilic B, Vollmer F. Experimental observation of strong photon localization in disordered photonic crystal waveguides. Physical Review Latters 2007;99 2007_vollmer_apl_99.pdf
Topolancik J, Ilic B, Vollmer F. Experimental observation of strong photon localization in disordered photonic crystal waveguides. Physical Review Latters 2007;99 2007_vollmer_apl_99.pdf
Topolancik J, Vollmer F, Ilic B. Random high-Q cavities in disordered photonic crystal waveguides. Applied Physics Letters 2007;91 2007_vollmer_apl_91.pdf
Spicer R, Holbrook MN. Effects of carbon dioxide and oxygen on sapwood respiration in five temperate tree species. J Exp Bot 2007;58(6):1313-20.Abstract

The gaseous environment surrounding parenchyma in woody tissue is low in O2 and high in CO2, but it is not known to what extent this affects respiration or might play a role in cell death during heartwood formation. Sapwood respiration was measured in two conifers and three angiosperms following equilibration to levels of O2 and CO2 common within stems, using both inner and outer sapwood to test for an effect of age. Across all species and tissue ages, lowering the O2 level from 10% to 5% (v/v) resulted in about a 25% decrease in respiration in the absence of CO2, but a non-significant decrease at 10% CO2. The inhibitory effect of 10% CO2 was smaller and only significant at 10% O2, where it reduced respiration by about 14%. Equilibration to a wider range of gas combinations in Pinus strobus L. showed the same effect: 10% CO2 inhibited respiration by about 15% at both 20% and 10% O2, but had no net effect at 5% O2. In an extreme treatment, 1% O2+20% CO2 increased respiration by over 30% relative to 1% O2 alone, suggesting a shift in metabolic response to high CO2 as O2 decreases. Although an increase in respiration would be detrimental under limiting O2, this extreme gas combination is unlikely to exist within most stems. Instead, moderate reductions in respiration under realistic O2 and CO2 levels suggest that within-stem gas composition does not severely limit respiration and is unlikely to cause the death of xylem parenchyma during heartwood formation.

2007_spicer_j_exp_botany.pdf
Sahin O, Magonov S, Su C, Quate CF, Solgaard O. An atomic force microscope tip designed to measure time-varying nanomechanical forces. Nat Nanotechnol 2007;2(8):507-14.Abstract
Tapping-mode atomic force microscopy (AFM), in which the vibrating tip periodically approaches, interacts and retracts from the sample surface, is the most common AFM imaging method. The tip experiences attractive and repulsive forces that depend on the chemical and mechanical properties of the sample, yet conventional AFM tips are limited in their ability to resolve these time-varying forces. We have created a specially designed cantilever tip that allows these interaction forces to be measured with good (sub-microsecond) temporal resolution and material properties to be determined and mapped in detail with nanoscale spatial resolution. Mechanical measurements based on these force waveforms are provided at a rate of 4 kHz. The forces and contact areas encountered in these measurements are orders of magnitude smaller than conventional indentation and AFM-based indentation techniques that typically provide data rates around 1 Hz. We use this tool to quantify and map nanomechanical changes in a binary polymer blend in the vicinity of its glass transition.
Sahin O. Harnessing bifurcations in tapping-mode atomic force microscopy to calibrate time-varying tip-sample force measurements. Rev Sci Instrum 2007;78(10):103707.Abstract
Torsional harmonic cantilevers allow measurement of time-varying tip-sample forces in tapping-mode atomic force microscopy. Accuracy of these force measurements is important for quantitative nanomechanical measurements. Here we demonstrate a method to convert the torsional deflection signals into a calibrated force wave form with the use of nonlinear dynamical response of the tapping cantilever. Specifically the transitions between steady oscillation regimes are used to calibrate the torsional deflection signals.
Brangwynne CP, Koenderink GH, Barry E, Dogic Z, MacKintosh FC, Weitz DA. Bending dynamics of fluctuating biopolymers probed by automated high-resolution filament tracking. Biophys J 2007;93(1):346-59.Abstract

Microscope images of fluctuating biopolymers contain a wealth of information about their underlying mechanics and dynamics. However, successful extraction of this information requires precise localization of filament position and shape from thousands of noisy images. Here, we present careful measurements of the bending dynamics of filamentous (F-)actin and microtubules at thermal equilibrium with high spatial and temporal resolution using a new, simple but robust, automated image analysis algorithm with subpixel accuracy. We find that slender actin filaments have a persistence length of approximately 17 microm, and display a q(-4)-dependent relaxation spectrum, as expected from viscous drag. Microtubules have a persistence length of several millimeters; interestingly, there is a small correlation between total microtubule length and rigidity, with shorter filaments appearing softer. However, we show that this correlation can arise, in principle, from intrinsic measurement noise that must be carefully considered. The dynamic behavior of the bending of microtubules also appears more complex than that of F-actin, reflecting their higher-order structure. These results emphasize both the power and limitations of light microscopy techniques for studying the mechanics and dynamics of biopolymers.

2007_dogic_biophys_jrnl.pdf
Speck A, Gabrielse G, Larochelle P, Le Sage D, Levitt B, Kolthammer WS, McConnell R, Wrubel J, Grzonka D, Oelert W, Sefzick T, Zhang Z, Comeau D, George MC, Hessels EA, Storry CH, Weel M, Walz J. Density and Geometry of Single Component Plasmas. Physics Letters B 2007;650:119-123. 2007_speck_phys_let_b.pdf
Ren H-C, Vollmer F, Arnold S, Libchaber A. High-Q microsphere biosensor - analysis for adsorption of rodlike bacteria. Opt Express 2007;15(25):17410-23.Abstract

Theory is developed for frequency shift and linewidth-broadening induced by rodlike bacteria bound to micro-optical resonators. Optical shift of whispering gallery modes (WGMs) is modeled by introducing a form factor that accounts for random horizontal orientation of cylindrical bacteria bound by their high refractive index cell walls. Linewidth-broadening is estimated from scattering losses. Analytic results are confirmed by measurement using E.Coli as model system (~10(2) bacteria/mm(2) sensitivity), establishing the WGM biosensor as sensitive technique for detection and analysis of micro-organisms.

2007_ren_.pdf
Lien V, Vollmer F. Microfluidic flow rate detection based on integrated optical fiber cantilever. Lab Chip 2007;7(10):1352-6.Abstract

We demonstrate an integrated microfluidic flow sensor with ultra-wide dynamic range, suitable for high throughput applications such as flow cytometry and particle sorting/counting. A fiber-tip cantilever transduces flow rates to optical signal readout, and we demonstrate a dynamic range from 0 to 1500 microL min(-1) for operation in water. Fiber-optic sensor alignment is guided by preformed microfluidic channels, and the dynamic range can be adjusted in a one-step chemical etch. An overall non-linear response is attributed to the far-field angular distribution of single-mode fiber output.

2007_vollmer_lab_chip.pdf
Topolancik J, Vollmer F. Photoinduced transformations in bacteriorhodopsin membrane monitored with optical microcavities. Biophys J 2007;92(6):2223-9.Abstract

Photoinduced molecular transformations in a self-assembled bacteriorhodopsin (bR) monolayer are monitored by observing shifts in the near-infrared resonant wavelengths of linearly polarized modes circulating in a microsphere cavity. We quantify the molecular polarizability change upon all-trans to 13-cis isomerization and deprotonation of the chromophore retinal ( approximately -57 A(3)) and determine its orientation relative to the bR membrane ( approximately 61 degrees ). Our observations establish optical microcavities as a sensitive off-resonant spectroscopic tool for probing conformations and orientations of molecular self-assemblies and for measuring changes of molecular polarizability at optical frequencies. We provide a general estimate of the sensitivity of the technique and discuss possible applications.

2007_topolancik_jrnl.pdf
Ghosh A, Fazal FM, Fischer P. Circular differential double diffraction in chiral media. Opt Lett 2007;32(13):1836-8.Abstract
In an optically active liquid the diffraction angle depends on the circular polarization state of the incident light beam. We report the observation of circular differential diffraction in an isotropic chiral medium, and we demonstrate that double diffraction is an alternate means to determine the handedness (enantiomeric excess) of a solution.

Pages