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.

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.

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.

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.

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.

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.

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
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.

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.

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