Steady-state MreB helices inside bacteria: dynamics without motors

Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasi-static evolution of the helical pitch with cell growth, as well as timescales of helix turnover and denovo establishment. We find that while the body of a polarized MreB helix treadmills towards its slow-growing end, the fast-growing tips of laterally associated protofilaments move towards the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.Comment: 7 figures, 1 tabl

How to measure the Bogoliubov quasiparticle amplitudes in a trapped condensate

We propose an experiment, based on two consecutive Bragg pulses, to measure the momentum distribution of quasiparticle excitations in a trapped Bose gas at low temperature. With the first pulse one generates a bunch of excitations carrying momentum $q$, whose Doppler line is measured by the second pulse. We show that this experiment can provide direct access to the amplitudes $u_{q}$ and $v_{q}$ characterizing the Bogoliubov transformations from particles to quasiparticles. We simulate the behavior of the nonuniform gas by numerically solving the time dependent Gross-Pitaevskii equation.Comment: 12 pages, 4 figures include

Combining Business Intelligence with Semantic Technologies: The CUBIST Project

This paper describes the European Framework Seven CUBIST project, which ran from October 2010 to September 2013. The project aimed to combine the best elements of traditional BI with the newer, semantic, technologies of the Sematic Web, in the form of RDF and FCA. CUBIST’s purpose was to provide end-users with "conceptually relevant and user friendly visual analytics" to allow them to explore their data in new ways, discovering hidden meaning and solving hitherto difficult problems. To this end, three of the partners in CUBIST were use-cases: recruitment consultancy, computational biology and the space industry. Each use-case provided their own requirements and evaluated how well the CUBIST outcomes addressed them

Interparticle interactions:Energy potentials, energy transfer, and nanoscale mechanical motion in response to optical radiation

In the interactions between particles of material with slightly different electronic levels, unusually large shifts in the pair potential can result from photoexcitation, and on subsequent electronic excitation transfer. To elicit these phenomena, it is necessary to understand the fundamental differences between a variety of optical properties deriving from dispersion interactions, and processes such as resonance energy transfer that occur under laser irradiance. This helps dispel some confusion in the recent literature. By developing and interpreting the theory at a deeper level, one can anticipate that in suitable systems, light absorption and energy transfer will be accompanied by significant displacements in interparticle separation, leading to nanoscale mechanical motion

Effect of atmospheric turbulence on propagation properties of optical vortices formed by using coherent laser beam arrays

In this paper, we consider the effect of the atmospheric turbulence on the propagation of optical vertex formed from the radial coherent laser beam array, with the initially well-defined phase distribution. The propagation formula of the radial coherent laser array passing through the turbulent atmosphere is analytically derived by using the extended Huygens-Fresnel diffraction integral. Based on the derived formula, the effect of the atmospheric turbulence on the propagation properties of such laser arrays has been studied in great detail. Our main results show that the atmospheric turbulence may result in the prohibition of the formation of the optical vortex or the disappearance of the formed optical vortex, which are very different from that in the free space. The formed optical vortex with the higher topological charge may propagate over a much longer distance in the moderate or weak turbulent atmosphere. After the sufficient long-distance atmospheric propagation, all the output beams (even with initially different phase distributions) finally lose the vortex property and gradually become the Gaussian-shaped beams, and in this case the output beams actually become incoherent light fields due to the decoherence effect of the turbulent atmosphere.Comment: 10 pages, 5 figure

Laser-controlled fluorescence in two-level systems

The ability to modify the character of fluorescent emission by a laser-controlled, optically nonlinear process has recently been shown theoretically feasible, and several possible applications have already been identified. In operation, a pulse of off-resonant probe laser beam, of sufficient intensity, is applied to a system exhibiting fluorescence, during the interval of excited- state decay following the initial excitation. The result is a rate of decay that can be controllably modified, the associated changes in fluorescence behavior affording new, chemically specific information. In this paper, a two-level emission model is employed in the further analysis of this all-optical process; the results should prove especially relevant to the analysis and imaging of physical systems employing fluorescent markers, these ranging from quantum dots to green fluorescence protein. Expressions are presented for the laser-controlled fluorescence anisotropy exhibited by samples in which the fluorophores are randomly oriented. It is also shown that, in systems with suitably configured electronic levels and symmetry properties, fluorescence emission can be produced from energy levels that would normally decay nonradiatively. © 2010 American Chemical Society

A photonic basis for deriving nonlinear optical response

Nonlinear optics is generally first presented as an extension of conventional optics. Typically the subject is introduced with reference to a classical oscillatory electric polarization, accommodating correction terms that become significant at high intensities. The material parameters that quantify the extent of the nonlinear response are cast as coefficients in a power series - nonlinear optical susceptibilities signifying a propensity to generate optical harmonics, for example. Taking the subject to a deeper level requires a more detailed knowledge of the structure and properties of each nonlinear susceptibility tensor, the latter differing in form according to the process under investigation. Typically, the derivations involve intricate development based on time-dependent perturbation theory, assisted by recourse to a set of Feynman diagrams. This paper presents a more direct route to the required results, based on photonic rather than semiclassical principles, and offers a significantly clearer perspective on the photophysics underlying nonlinear optical response. The method, here illustrated by specific application to harmonic generation and down-conversion processes, is simple, intuitive and readily amenable for processes of arbitrary photonic order. © 2009 IOP Publishing Ltd

Herschel evidence for disk flattening or gas depletion in transitional disks

Transitional disks are protoplanetary disks characterized by reduced near- and mid-infrared emission with respect to full disks. This characteristic spectral energy distribution indicates the presence of an optically thin inner cavity within the dust disk believed to mark the disappearance of the primordial massive disk. We present new Herschel Space Observatory PACS spectra of [OI] 63 micron for 21 transitional disks. Our survey complements the larger Herschel GASPS program "Gas in Protoplanetary Systems" (Dent et al. 2013) by quadrupling the number of transitional disks observed with PACS at this wavelength. [OI] 63 micron traces material in the outer regions of the disk, beyond the inner cavity of most transitional disks. We find that transitional disks have [OI] 63 micron line luminosities two times fainter than their full disk counterparts. We self consistently determine various stellar properties (e.g. bolometric luminosity, FUV excess, etc.) and disk properties (e.g. disk dust mass, etc.) that could influence the [OI] 63 micron line luminosity and we find no correlations that can explain the lower [OI] 63 micron line luminosities in transitional disks. Using a grid of thermo-chemical protoplanetary disk models, we conclude that either transitional disks are less flared than full disks or they possess lower gas-to-dust ratios due to a depletion of gas mass. This result suggests that transitional disks are more evolved than their full disk counterparts, possibly even at large radii.Comment: Accepted for publication in ApJ; 52 pages, 16 figures, 8 table