Publications

2007
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.
Ahn Y, Park J. Efficient Visible Light Detection Using Individual Germanium Nanowire Field Effect Transistors. Appl. Phys. Letts. 2007;91:162102.Abstract

We report photoconductivity (PC) in individual germanium nanowire field effect transistors (GeFETs). PC measurements with a global illumination reveal that GeFETs can be used as a polarization-sensitive nanoscale light detector in the visible range. It is also found that the PC shows sensitive optical response especially in the low intensity regime. We observe a high internal gain in PC in conjunction with strong saturation behavior, which is attributed to the filling of surface trapping states. This mechanism for high internal gain is consistent with spatially resolved scanning photocurrent measurements, whose results confirm that optical absorption is in the linear regime.

2007_park_apl.pdf
Vollmer F, Fischer P. Frequency-domain displacement sensing with a fiber ring-resonator containing a variable gap. Sensors and Actuators A-Physical 2007;134(2):410-413. 2007_vollmer_sensors_actuators.pdf
Ghosh A, Hill W,  Fischer P. Observation of the Faraday effect via beam deflection in a longitudinal magnetic field. Physical Review A 2007;76(5) 2007_ghosh_prl_.pdf
2006
Topolancik J, Vollmer F. All-optical switching in the near infrared with bacteriorhodopsin-coated microcavities. Applied Physics Letters 2006;89:184103. 2006_vollmer_apl.pdf
Cebers A, Dogic Z, Janmey PA. Counterion-mediated attraction and kinks on loops of semiflexible polyelectrolyte bundles. Phys. Rev. Lett. 2006;96:247801. 2006_dogic_prl_96_june.pdf
Barry E, Hensel Z, Dogic Z, Shribak M, Oldenbourg R. Entropy-driven formation of a chiral liquid-crystalline phase of helical filaments. Phys Rev Lett 2006;96(1):018305.Abstract

We study the liquid-crystalline phase behavior of a concentrated suspension of helical flagella isolated from Salmonella typhimurium. Flagella are prepared with different polymorphic states, some of which have a pronounced helical character while others assume a rodlike shape. We show that the static phase behavior and dynamics of chiral helices are very different when compared to simpler achiral hard rods. With increasing concentration, helical flagella undergo an entropy-driven first order phase transition to a liquid-crystalline state having a novel chiral symmetry.

2006_dogic_prl_96_jan.pdf
Lewis KC, Bazzaz FA, Liao Q, Orians CM. Geographic patterns of herbivory and resource allocation to defense, growth, and reproduction in an invasive biennial, Alliaria petiolata. Oecologia 2006;148(3):384-95.Abstract

We investigated geographic patterns of herbivory and resource allocation to defense, growth, and reproduction in an invasive biennial, Alliaria petiolata, to test the hypothesis that escape from herbivory in invasive species permits enhanced growth and lower production of defensive chemicals. We quantified herbivore damage, concentrations of sinigrin, and growth and reproduction inside and outside herbivore exclusion treatments, in field populations in the native and invasive ranges. As predicted, unmanipulated plants in the native range (Hungary, Europe) experienced greater herbivore damage than plants in the introduced range (Massachusetts and Connecticut, USA), providing evidence for enemy release, particularly in the first year of growth. Nevertheless, European populations had consistently larger individuals than US populations (rosettes were, for example, eightfold larger) and also had greater reproductive output, but US plants produced larger seeds at a given plant height. Moreover, flowering plants showed significant differences in concentrations of sinigrin in the invasive versus native range, although the direction of the difference was variable, suggesting the influence of environmental effects. Overall, we observed less herbivory, but not increased growth or decreased defense in the invasive range. Geographical differences in performance and leaf chemistry appear to be due to variation in the environment, which could have masked evolved differences in allocation.

2006_lewis_oecologia.pdf
Dogic Z, Fraden S. Ordered phases of filamentous viruses. Curr. Opinion in Coll. & Inter. Sci. 2006;11:47-55. 2006_dogic_current_opinion.pdf
Kang KG, Lettinga MP, Dogic Z, Dhont JKG. Vorticity banding in rodlike virus suspensions. Phys. Rev. E  2006;74:026307. 2006_dogic_phys_rev_e.pdf
Fischer P, Champagne B. Nonlinear Optical Properties of Chiral Liquids: Electric-dipolar pseudoscalars in nonlinear optics. In: Challenges and Advances in Computational Chemistry and Physics. 2006 p. 359-381.
Ghosh A, Fischer P. Chiral molecules split light: Reflection and refraction in a chiral liquid. Phys Rev Lett 2006;97(17):173002.Abstract

A light beam changes direction as it enters a liquid at an angle from another medium, such as air. Should the liquid contain molecules that lack mirror symmetry, then it has been predicted by Fresnel that the light beam will not only change direction, but will actually split into two separate beams with a small difference in the respective angles of refraction. Here we report the observation of this phenomenon. We also demonstrate that the angle of reflection does not equal the angle of incidence in a chiral medium. Unlike conventional optical rotation, which depends on the path-length through the sample, the reported reflection and refraction phenomena arise within a few wavelengths at the interface and thereby suggest a new approach to polarimetry that can be used in microfluidic volumes.

2006_fischer_arxiv.pdf
Buckingham AD, Fischer P. Direct chiral discrimination in NMR spectroscopy. Chemical Physics 2006;324(1):111-116. 2006_fischer_chemphys.pdf
Wong WP, Halvorsen K. The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur. Opt Express 2006;14(25):12517-31.Abstract

Dynamical instrument limitations, such as finite detection bandwidth, do not simply add statistical errors to fluctuation measurements, but can create significant systematic biases that affect the measurement of steady-state properties. Such effects must be considered when calibrating ultra-sensitive force probes by analyzing the observed Brownian fluctuations. In this article, we present a novel method for extracting the true spring constant and diffusion coefficient of a harmonically confined Brownian particle that extends the standard equipartition and power spectrum techniques to account for video-image motion blur. These results are confirmed both numerically with a Brownian dynamics simulation, and experimentally with laser optical tweezers.

2006_wong_optics_express.pdf
Vollmer F, Fischer P. Ring-resonator-based frequency-domain optical activity measurements of a chiral liquid. Opt Lett 2006;31(4):453-5.Abstract

Chiral liquids rotate the plane of polarization of linearly polarized light and are therefore optically active. Here we show that optical rotation can be observed in the frequency domain. A chiral liquid introduced in a fiber-loop ring resonator that supports left and right circularly polarized modes gives rise to relative frequency shifts that are a direct measure of the liquid's circular birefringence and hence of its optical activity. The effect is in principle not diminished if the circumference of the ring is reduced. The technique is similarly applicable to refractive index and linear birefringence measurements.

2006_vollmer_optics_let.pdf

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