In-line Geometries Research Articles

A Simple Expression for the Screening of Excitonic Couplings between Chlorophylls as Inferred for Photosystem I Trimers.

The Coulomb coupling between transition densities of the pigments in photosynthetic pigment-protein complexes, termed excitonic coupling, is a key factor for the description of optical spectra and energy transfer. A challenging question is the quantification of the screening of the excitonic coupling by the optical polarizability of the environment. We use the equivalence between the sophisticated quantum chemical polarizable continuum (PCM) model and the simple electrostatic Poisson-TrEsp approach to analyze the distance and orientation dependence of the dielectric screening between chlorophylls in photosystem I trimers. On the basis of these calculations we find that the vacuum couplings Vmn(0) and the couplings in the dielectric medium Vmn=fmnVmn(0) are related by the empirical screening factor fmn=0.60+39.6θ(|κmn|-1.17)exp(-0.56Rmn/Å), where κmn is the usual orientational factor of the dipole-dipole coupling between the pigments, Rmn is the center-to-center distance, and the Heaviside-function θ(|κmn|-1.17) ensures that the exponential distance dependence only contributes for in-line type dipole geometries. We are confident that the present expression can be applied also to other pigment-protein complexes with chlorophyll or related pigments of similar shape. The variance between the Poisson-TrEsp and the approximate coupling values is found to decrease by a factor of 8 and 3-4 using the present expression, instead of an exponential distance dependent or constant screening factor, respectively, assumed previously in the literature.

CGAN-assisted imaging through stationary scattering media.

Analyzing images taken through scattering media is challenging, owing to speckle decorrelations from perturbations in the media. For in-line imaging modalities, which are appealing because they are compact, require no moving parts, and are robust, negating the effects of such scattering becomes particularly challenging. Here we explore the use of conditional generative adversarial networks (cGANs) to mitigate the effects of the additional scatterers in in-line geometries, including digital holographic microscopy. Using light scattering simulations and experiments on objects of interest with and without additional scatterers, we find that cGANs can be quickly trained with minuscule datasets and can also efficiently learn the one-to-one statistical mapping between the cross-domain input-output image pairs. Importantly, the output images are faithful enough to enable quantitative feature extraction. We also show that with rapid training using only 20 image pairs, it is possible to negate this undesired scattering to accurately localize diffraction-limited impulses with high spatial accuracy, therefore transforming a shift variant system to a linear shift invariant (LSI) system.

Performance analysis of phase retrieval using transport of intensity with digital holography [Invited

The performance of direct and unwrapped phase retrieval, which combines digital holography with the transport of intensity, is examined in detail in this paper. In this technique, digital holography is used to numerically reconstruct the intensities at different planes around the image plane, and phase retrieval is achieved by the transport of intensity. Digital holography with transport of intensity is examined for inline and off-axis geometries. The effect of twin images in the inline case is evaluated. Phase-shifting digital holography with transport of intensity is introduced. The performance of digital holography with transport of intensity is compared with traditional off-axis single- and dual-wavelength techniques, which employ standard phase unwrapping algorithms. Simulations and experiments are performed to determine and compare the accuracy of phase retrieval through a mean-squared-error figure of merit as well as the computational speeds of the various methods.

Marlim R3D: A realistic model for controlled-source electromagnetic simulations — Phase 2: The controlled-source electromagnetic data set

Synthetic data provided by geoelectric earth models are a powerful tool to evaluate a priori a controlled-source electromagnetic (CSEM) workflow effectiveness. Marlim R3D (MR3D) is an open-source complex and realistic geoelectric model for CSEM simulations of the postsalt turbiditic reservoirs at the Brazilian offshore margin. We have developed a 3D CSEM finite-difference time-domain forward study to generate the full-azimuth CSEM data set for the MR3D earth model. To that end, we fabricated a full-azimuth survey with 45 towlines striking the north–south and east–west directions over a total of 500 receivers evenly spaced at 1 km intervals along the rugged seafloor of the MR3D model. To correctly represent the thin, disconnected, and complex geometries of the studied reservoirs, we have built a finely discretized mesh of [Formula: see text] cells leading to a large mesh with a total of approximately 90 million cells. We computed the six electromagnetic field components (Ex, Ey, Ez, Hx, Hy, and Hz) at six frequencies in the range of 0.125–1.25 Hz. In our efforts to mimic noise in real CSEM data, we summed to the data a multiplicative noise with a 1% standard deviation. Both CSEM data sets (noise free and noise added), with inline and broadside geometries, are distributed for research or commercial use, under the Creative Common License, at the Zenodo platform.

Estimation of effective thermal conductivity of packed beds incorporating effects of primary and secondary parameters

This paper presents a detailed description and experimental validation of a modified collocated unit cell model for the estimation of effective thermal conductivity of packed beds. The effect of primary and secondary parameters influencing the effective thermal conductivity viz. conductivity ratio (α) and concentration (ν) of the spherical particles (fraction of total volume occupied by the particles) of the packed bed, inter-particle gap, thermal contact conductance between the surfaces in contact, temperature, pressure and Knudsen number respectively are investigated in detail. Analytical expressions for effective thermal conductivity are derived for spatially periodic 2D square cylinder and in-line touching geometries based on the unit cell based thermal resistance approach. Using the developed model, the effective thermal conductivity of various packed materials in the conductivity ratio (ks/kf) range between 1–1000 and concentration (ν) 0 to 1 are predicted for varied temperature and pressure regimes. Predictions obtained from the developed model are compared against existing models available in literature in the pressure range 10−2 to 103 kPa at constant temperature. Furthermore, effective thermal conductivities of packed beds comprising of glass and ceramic beads are predicted using the developed model and compared with measured values obtained using the standard square guarded hot plate (SGHP) apparatus in the temperature range of 323–673 K. Both values are found to agree within ±12.24% and ±14.54% for glass and ceramic beads respectively.

Nonlinear polarization evolution of ultrashort pulses in polarization maintaining fibers.

We examine properties of an ultrashort laser pulse propagating through an artificial Saturable Absorber based on Nonlinear Polarization Evolution device which has been realized with Polarization Maintaining fibers only (PM NPE). We study and compare in-line and Faraday Mirror geometries showing that the latter is immune to errors in the PM NPE construction. Experimental results for the transmission measurements of the PM NPE setup for different input linear polarization angles and various input pulse powers are presented. We show that PM NPE topology is of crucial importance for controlling the properties of the output pulse as it rules the contribution of cross-phase modulation to an overall nonlinear phase change. We also demonstrate an excellent agreement between the numerical model and experimental results.

Vortex Structures in Exponentially Shaped Josephson Junctions

We report the numerical calculations of the static vortex structure and critical curves in exponentially shaped long Josephson junctions for in-line and overlap geometries. Stability of the static solutions is investigated by checking the sign of the smallest eigenvalue of the associated Sturm-Liouville problem. The change in the junction width leads to the renormalization of the magnetic flux in comparison with the case of a linear one-dimensional model. We study the influence of the model's parameters, and particularly, the shape parameter on the stability of the states of the magnetic flux. We compare the vortex structure and critical curves for the in-line and overlap geometries. Our numerically constructed critical curve of the Josephson junction matches well with the experimental one.

Vortex structures in exponentially shaped Josephson junctions

We report the numerical calculations of the static vortex structure and critical curves in exponentially shaped long Josephson junctions for in-line and overlap geometries. Each solution of the corresponding boundary value problem is associated with the Sturm-Liouville problem whose minimal eigenvalue allows to make a conclusion about the stability of the vortex. The change in width of the junction leads to the renormalization of the magnetic flux in comparison to the case of a linear one-dimensional model. We study the influence of the model's parameters and, particularly, the shape parameter on the stability of the states of the magnetic flux. We compare the vortex structure and critical curves for the in-line and overlap geometries. Our numerically constructed critical curve of the Josephson junction matches well with the experimental one.

Heat Transfer and Friction Factors for Flows Inside Circular Tubes With Concavity Surfaces

Heat transfer and friction coefficients measurements have been obtained for fully developed, turbulent internal flows in circular tubes with six different concavity (dimple) surface array geometries. Two different concavity depths and three different concavity array densities were tested using tube bulk flow Reynolds numbers from 20,000 to 90,000. Liquid-crystal thermography was used to measure the temperature distributions on the outside of the concavity tubes. Using the average heat transfer coefficient for the fully developed region, the overall heat transfer enhancements are compared to baseline smooth tube results. Friction coefficients are also compared to values for a smooth tube. Dimple depths of 0.2–0.4 relative to the dimple surface diameter were used, with surface area densities ranging from 0.3 to 0.7. Dimple arrays were all in-line geometries. The results showed that heat transfer enhancements for dimpled internal surfaces of circular passages can reach factors of 2 or more when the relative dimple depth is greater than 0.3 and the dimple array density is about 0.5 or higher. The associated friction factor multipliers for such configurations are in the range of 4–6. The present study provides a first insight into the heat transfer and friction effects of various concavity arrays for turbulent flows.

Flame hydrolysis deposition of glass on silicon for the integration of optical and microfluidic devices

Flame hydrolysis deposition (FHD) of glasses has previously found applications in the telecommunications industry. This paper shows how the technology can be used to deposit silica with different refractive indices and thereby produce low-loss planar waveguides for use in analytical applications. We also show that the glasses can be patterned using a new reactive ion etch and sealed using a modification of anodic bonding, such that the resulting microstructures can be readily incorporated within a lithographically defined "chip", integrating both optical and fluidic circuitry on the same device. In the example described in this paper, waveguides, analytical microtiter chambers and fluidic capillary channels, with the necessary high aspect ratio features (and with depths up to 40 microm) were all produced in glass, using the appropriate deposition and etching technologies. The performance of the chip was assessed in the framework of a low-volume fluorescence assay, using waveguides to address miniaturized microtiter chambers with volumes of 230 and 570 pL. Devices featuring different optical detection configurations, including both in-line and orthogonal waveguide geometries, were fabricated. In the optimal configuration, the experimental detection limit was determined as ca. 20 pM (equivalent to 10 zmol) of a cyanine fluorophore, Cy5. The applicability of the device as a biochip platform was further illustrated by analytical measurements on fluorescently labeled oligodeoxynucleotides.

Solution spectra and stability of current biased Josephson junctions in a magnetic field

We examine the solutions of the non-linear equations governing the behavior of a current biased Josephson junction. Both inline and overlap current bias geometries are considered. The solution space is investigated analytically and using numerical techniques. We characterize the types of solutions expected analytically and find good approximations for large magnetic fields. For small magnetic fields the solution space is large and its stability is entangled. We study this space and its stability as a function of magnetic field and applied bias current. Selective results are presented that characterize the general behavior of the solution space.

Phase locking of long Josephson junctions.

We present numerical simulations on the phase locking of solitons in long Josephson junctions by the application of external microwave signals. The full partial differential equation with boundary conditions has been used. Overlap and inline geometries are considered; the effects of dc magnetic fields and different configurations of the rf field have also been investigated.

Numerical study of entrained soliton motion in long Josephson junctions

We present the results of numerical simulations of entrainment by microwaves of a soliton in Josephson junctions of both the overlap and in-line geometries. The computation was based on the full partial differential equations with boundary conditions, making no use of perturbation theory or Fourier expansion. We confirm the perturbation prediction for the range of phase lock for overlap junctions, but we observe a major departure for the in-line geometry, due to soliton creation and annihilation. Outside the range of entrainment, the perturbation predictions are not reliable in either case: we observe quasiperiodicity, intermittency, or chaotic creation and annihilation, depending on junction geometry and parameter values.

Depolarized fluorescence photobleaching recovery

The effects of the fact that the laser sources typically used in fluorescence photobleaching recovery (FPR) experiments in the most commonly employed in-line microscope imaging geometries, are highly linearly polarized, are examined in some detail. The implications of the results, in particular for the interpretation of FPR data in complex cell membrane systems in terms of laterally mobile and immobile sub-populations of the labelled molecular species of concern, are discussed. Methods of experimentally eliminating the potentially major rotational diffusion-based “artifacts”, different from those appropriate to three-dimensional (solution or suspension) systems which require other than in-line geometries, are delineated.

Sources of Excitation in Tube Banks Due to Vortex Shedding

This paper describes experimental investigations of vortex shedding patterns in staggered and in-line tube banks consisting of four rows with transverse pitch to diameter ratios PT/d of 2.67 and longitudinal pitch to diameter ratios PL/d of 2.31. Single hot wire probes were used to obtain velocity power spectra in order to identify discrete frequencies of velocity fluctuation. Double hot wire probes provided phase correlations which could indicate conclusively the presence of vortex streets. Quite different results were obtained for the staggered and in-line geometries. While vortex street fluctuations were observed in both, an additional higher frequency fluctuation was observed in the staggered tube bank, the causal mechanism for which remains obscure.

Long and narrow Josephson tunnel junctions of mixed overlap and inline character

A model describing long Josephson junctions of mixed overlap and inline geometry is presented. The shape of the first zero field step is calculated for this model using a perturbation approach. The question of influence of external magnetic field on the maximum supercurrent is investigated for overlap, inline, and mixed overlap-inline geometries. A linear dependence is found for the inline model and for mixed overlap-inline junctions in agreement with experiments.

Perturbation calculation of magnetic field dependence of fluxon dynamics in long inline and overlap Josephson junctions

The motion of a single fluxon in long Josephson-junctions of overlap and inline geometries is investigated in the presence of an applied external magnetic field. The form of the first zero-field step for various parameters is given in closed analytic forms in both cases, and the differences and similarities between the two geometries are emphasized.

Fluxon motion in long overlap and in-line Josephson junctions

The motion of a single fluxon in long Josephson junctions of the overlap and inline geometries is investigated. It is concluded that if the junction is long and the damping is not too large then zero-field steps exist also in the inline junction. Thee zero-field steps are found to be mathematically identical to those of the overlap junctions in spite of the fact that the fluxon dynamics are quite different in the two cases.