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  • Article
    Wang S, Wang Z, Wu T.
    Phys Rev Lett. 2024 Feb 09;132(6):065106.
    Understanding the self-organization of the most promising internal transport barrier in fusion plasmas needs a long-time nonlinear gyrokinetic global simulation. The neighboring equilibrium update method is proposed, which solves the secularity problem in a perturbative simulation and speeds up the numerical computation by more than 10 times. It is found that the internal transport barrier emerges at the magnetic axis due to inward propagated turbulence avalanche, and its outward expansion is the catastrophe of self-organized structure induced by outward propagated avalanche.
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  • Article
    Bowers CA, Miller CT.
    Phys Rev E. 2023 Dec;108(6-2):065106.
    Carreau fluids occur routinely in porous medium systems for a range of applications, and the dependence of the viscosity for such fluids on the rate of strain tensor poses challenges to modeling at an averaged macroscale. Traditional approaches for macroscale modeling such flows have relied upon experimental observations of flows for generalized Newtonian fluids (GNFs) and a phenomenological approach referred to herein as the shift factor. A recently developed approach based upon averaging conservation and thermodynamic equations from the microscale for Cross model GNFs is extended to the case of Carreau fluids and shown to predict the flow through both isotropic and anisotropic media accurately without the need for GNF-flow experiments. The model is formulated in terms of rheological properties, a standard Newtonian resistance tensor, and a length-scale tensor, which does require estimation. An approach based upon measures of the morphology and topology of the pore space is developed to approximate this length-scale tensor. Thus, this work provides the missing components needed to predict Carreau GNF macroscale flow with only rheological information for the fluid and analysis of the pore morphology and topology independent of any fluid flow experiments. Accuracy of predictions based upon this approach is quantified, and extension to other GNFs is straightforward.
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  • Article
    Tergolina VB, Calzavarini E, Mompean G, Berti S.
    Phys Rev E. 2021 Dec;104(6-2):065106.
    Turbulence has been recognized as a factor of paramount importance for the survival or extinction of sinking phytoplankton species. However, dealing with its multiscale nature in models of coupled fluid and biological dynamics is a formidable challenge. Advection by coherent structures, such as those related to winter convection and Langmuir circulation, is also recognized to play a role in the survival and localization of phytoplankton. In this work we revisit a theoretically appealing model for phytoplankton vertical dynamics, and numerically investigate how large-scale fluid motions affect the survival conditions and the spatial distribution of the biological population. For this purpose, and to work with realistic parameter values, we adopt a kinematic flow field to account for the different spatial and temporal scales of turbulent motions. The dynamics of the population density are described by an advection-reaction-diffusion model with a spatially heterogeneous growth term proportional to sunlight availability. We explore the role of fluid transport by progressively increasing the complexity of the flow in terms of spatial and temporal scales. We find that, due to the large-scale circulation, phytoplankton accumulates in downwelling regions and its growth is reduced, confirming previous indications in slightly different conditions. We then explain the observed phenomenology in terms of a plankton filament model. Moreover, by contrasting the results in our different flow cases, we show that the large-scale coherent structures have an overwhelming importance. Indeed, we find that smaller-scale motions only quite weakly affect the dynamics, without altering the general mechanism identified. Such results are relevant for parametrizations in numerical models of phytoplankton life cycles in realistic oceanic flow conditions.
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  • Article
    Costa G, Barral A, Dubrulle B.
    Phys Rev E. 2023 Jun;107(6-2):065106.
    The three-dimensional reversible Navier-Stokes (RNS) equations are a modification of the dissipative Navier-Stokes (NS) equations, first introduced by Gallavotti [Phys. Lett. A 223, 91 (1996)0375-960110.1016/S0375-9601(96)00729-3], in which the energy or the enstrophy is kept constant by adjusting the viscosity over time. Spectral direct numerical simulations of this model were performed by Shukla et al. [Phys. Rev. E 100, 043104 (2019)2470-004510.1103/PhysRevE.100.043104] and Margazoglou et al. [Phys. Rev. E 105, 065110 (2022)10.1103/PhysRevE.105.065110]. Here we consider a linear, forced reversible system obtained by projecting RNS equations on a log lattice rather than on a linearly spaced grid in Fourier space, as is done in regular spectral numerical simulations. We perform numerical simulations of the system at extremely large resolutions, allowing us to explore regimes of parameters that were out of reach of the direct numerical simulations of Shukla et al. Using the nondimensionalized forcing as a control parameter, and the square root of enstrophy as the order parameter, we confirm the existence of a second-order phase transition well described by a mean-field Landau theory. The log-lattice projection allows us to probe the impact of the resolution, highlighting an imperfect transition at small resolutions with exponents differing from the mean-field predictions. Our findings are in qualitative agreement with predictions of a 1D nonlinear diffusive model, the reversible Leith model of turbulence. We then compare the statistics of the solutions of RNS and NS, in order to shed light on an adaptation of the Gallavotti conjecture, in which there is equivalence of statistics between the reversible and irreversible models, to the case where our reversible model conserves either the enstrophy or the energy. We deduce the conditions in which the two are equivalent. Our results support the validity of the conjecture and represent an instance of nonequilibrium system where ensemble equivalence holds for mean quantities.
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  • Article
    Zhang P, Song Y, Liu Y, Xia Z.
    Phys Rev E. 2022 Jun;105(6-2):065106.
    In this paper, direct numerical simulations have been performed to explore the equivalence of different thermal boundary conditions in compressible turbulent channel flows at fixed Re=6000,Ma=1.5. Three canonical types of thermal boundary conditions will be investigated at almost equivalent setups, including the first boundary condition with fixed wall temperature T_{w} (constant Dirichlet boundary condition), the second boundary condition with fixed wall heat-flux q_{w} (constant Neumann boundary condition), and the third boundary condition (Robin boundary condition). The turbulent statistics of the temperature and velocity fields, including mean profiles, root-mean-square values, second-order statistics, and normalized probability density functions, temperature stripes near the wall and the budget of internal energy have been analyzed in detail to clarify the differences caused by the different thermal boundary conditions. The results show that the three thermal boundary conditions have almost negligible effect on the velocity field, whereas some discernible deviations can be observed for the temperature field in the near-wall region with y^{+}≲30. Furthermore, the statistics from the second and third thermal boundary conditions are very close, enabling the usage of the second boundary condition to mimic the more complex third boundary conditions.
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  • Article
    Cunningham CJ, Pitschi V, Anderson P, Barry DA, Patterson C, Peshkur TA.
    PLoS One. 2013;8(6):e65106.
    Remediation of hydrocarbon contaminated soils can be performed both in situ and ex situ using chemical oxidants such as sodium persulfate. Standard methods for quantifying persulfate require either centrifugation or prolonged settling times. An optimized soil extraction procedure was developed for persulfate involving simple water extraction using a modified disposable syringe. This allows considerable saving of time and removes the need for centrifugation. The extraction time was reduced to only 5 min compared to 15 min for the standard approach. A comparison of the two approaches demonstrated that each provides comparable results. Comparisons were made using high (93 g kg(-1) soil) and low (9.3 g kg(-1) soil) additions of sodium persulfate to a petroleum hydrocarbon-contaminated soil, as well as sand spiked with diesel. Recoveries of 95±1% and 96±10% were observed with the higher application rate in the contaminated soil and spiked sand, respectively. Corresponding recoveries of 86±5% and 117±19% were measured for the lower application rate. Results were obtained in only 25 min and the method is well suited to batch analyses. In addition, it is suitable for application in a small field laboratory or even a mobile, vehicle-based system, as it requires minimal equipment and reagents.
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  • Article
    Santosh M, Panigrahi S, Bhattacharyya D, Sood AK, Maiti PK.
    J Chem Phys. 2012 Feb 14;136(6):065106.
    In an effort to design efficient platform for siRNA delivery, we combine all atom classical and quantum simulations to study the binding of small interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our results show that siRNA strongly binds to SWCNT surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the SWCNTs. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the SWCNT surface. However, molecular dynamics (MD) simulations of double strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This interesting difference is due to smaller interaction energy of thymidine of dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by dispersion corrected density functional theory (DFT) methods. After the optimal binding of siRNA to SWCNT, the complex is very stable which serves as one of the major mechanisms of siRNA delivery for biomedical applications. Since siRNA has to undergo unwinding process with the effect of RNA-induced silencing complex, our proposed delivery mechanism by SWCNT possesses potential advantages in achieving RNA interference.
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  • Article
    Cohen SI, Vendruscolo M, Dobson CM, Knowles TP.
    J Chem Phys. 2011 Aug 14;135(6):065106.
    Nucleated polymerisation processes are involved in many growth phenomena in nature, including the formation of cytoskeletal filaments and the assembly of sickle hemoglobin and amyloid fibrils. Closed form rate equations have, however, been challenging to derive for these growth phenomena in cases where secondary nucleation processes are active, a difficulty exemplified by the highly non-linear nature of the equation systems that describe monomer dependent secondary nucleation pathways. We explore here the use of fixed point analysis to provide self-consistent solutions to such growth problems. We present iterative solutions and discuss their convergence behaviour. We establish a range of closed form results for linear growth processes, including the scaling behaviours of the maximum growth rate and of the reaction end-point. We further show that a self-consistent approach applied to the master equation of filamentous growth allows the determination of the evolution of the shape of the length distribution including the mean, the standard deviation, and the mode. Our results highlight the power of fixed-point approaches in finding closed form self-consistent solutions to growth problems characterised by the highly non-linear master equations.
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  • Article
    Dias CL, Hynninen T, Ala-Nissila T, Foster AS, Karttunen M.
    J Chem Phys. 2011 Feb 14;134(6):065106.
    We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.
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  • Article
    Horejs C, Pum D, Sleytr UB, Tscheliessnig R.
    J Chem Phys. 2008 Feb 14;128(6):065106.
    S-layer proteins have a wide range of application potential due to their characteristic features concerning self-assembling, assembling on various surfaces, and forming of isoporous structures with functional groups located on the surface in an identical position and orientation. Although considerable knowledge has been experimentally accumulated on the structure, biochemistry, assemble characteristics, and genetics of S-layer proteins, no structural model at atomic resolution has been available so far. Therefore, neither the overall folding of the S-layer proteins-their tertiary structure-nor the exact amino acid or domain allocations in the lattices are known. In this paper, we describe the tertiary structure prediction for the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2. This calculation was based on its amino acid sequence using the mean force method (MF method) achieved by performing molecular dynamic simulations. This method includes mainly the thermodynamic aspects of protein folding as well as steric constraints of the amino acids and is therefore independent of experimental structure analysis problems resulting from biochemical properties of the S-layer proteins. Molecular dynamic simulations were performed in vacuum using the simulation software NAMD. The obtained tertiary structure of SbsB was systematically analyzed by using the mean force method, whereas the verification of the structure is based on calculating the global free energy minimum of the whole system. This corresponds to the potential of mean force, which is the thermodynamically most favorable conformation of the protein. Finally, an S-layer lattice was modeled graphically using CINEMA4D and compared with scanning force microscopy data down to a resolution of 1 nm. The results show that this approach leads to a thermodynamically favorable atomic model of the tertiary structure of the protein, which could be verified by both the MF Method and the lattice model.
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  • Article
    Bennewitz JW, Bigler BR, Schumaker SA, Hargus WA.
    Rev Sci Instrum. 2019 Jun;90(6):065106.
    An image processing technique is developed to automatically determine both average and instantaneous detonation wave properties within a rotating detonation rocket engine (RDRE) using high-speed imaging. This method entails segmenting the imaged RDRE annulus into 200 azimuthal bins and tracking integrated pixel intensity in each bin. By combining individual pixel intensity temporal histories across the azimuthal bins, this provides what is termed a detonation surface that visualizes the propagation of the individual detonation fronts azimuthally around the annulus. Average detonation modal properties including wave speed Ūwv, operational frequency fdet, and the number of waves m are determined automatically through a two-dimensional Fourier analysis of the detonation surface data. Also, instantaneous wave speeds Uwv for each individual detonation are determined by taking the numerical derivative of each waves' angular position temporal history from the detonation surface. This provides useful insight into wave-to-wave variability for an operating condition, as well as denoting modal transitions and mode stability. For the flow conditions investigated, the number of waves ranges from 2 to 14, with Ūwv varying between 900 and 1700 m/s, corresponding to 33%-71% of the ideal Chapman-Jouguet detonation speed; these modes exhibit an operational frequency of 20-45 kHz, with an average of 40 kHz. Overall, these measurements advance the understanding of RDRE's and may lead to performance gains above those achievable from constant pressure engines.
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  • Article
    Restrepo F, Zhao J, Chatterjee U.
    Rev Sci Instrum. 2022 Jun 01;93(6):065106.
    In recent years, distinct machine learning (ML) models have been separately used for feature extraction and noise reduction from energy-momentum dispersion intensity maps obtained from raw angle-resolved photoemission spectroscopy (ARPES) data. In this work, we employ a shallow variational auto-encoder neural network to demonstrate the prospect of using ML for both denoising of as well as feature extraction from ARPES dispersion maps.
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  • Article
    Lee T, Nonomura T, Asai K, Liu T.
    Rev Sci Instrum. 2018 Jun;89(6):065106.
    A data analysis method based on the linear least-squares (LLS) method was developed for the extraction of high-resolution skin friction fields from global luminescent oil film (GLOF) visualization images of a surface in an aerodynamic flow. In this method, the oil film thickness distribution and its spatiotemporal development are measured by detecting the luminescence intensity of the thin oil film. From the resulting set of GLOF images, the thin oil film equation is solved to obtain an ensemble-averaged (steady) skin friction field as an inverse problem. In this paper, the formulation of a discrete linear system of equations for the LLS method is described, and an error analysis is given to identify the main error sources and the relevant parameters. Simulations were conducted to evaluate the accuracy of the LLS method and the effects of the image patterns, image noise, and sample numbers on the results in comparison with the previous snapshot-solution-averaging (SSA) method. An experimental case is shown to enable the comparison of the results obtained using conventional oil flow visualization and those obtained using both the LLS and SSA methods. The overall results show that the LLS method is more reliable than the SSA method and the LLS method can yield a more detailed skin friction topology in an objective way.
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  • Article
    Wu J, Huang T, Zhu Z, Song K.
    Rev Sci Instrum. 2021 Jun 01;92(6):065106.
    With the miniaturization of inertial instruments, sensors mounted inside are vulnerable to interference. In a complex thermal transmission environment, temperature drift is the main factor restricting the precision of high-performance inertial sensors. To solve this problem, a new method for compensating the time-related cold starting temperature drift of the inertial sensors is introduced in this paper. Based on the perspective that temperature drift can be regarded as the response curve of the sensor system to temperature and temperature gradient, temperature compensation models of first-order, second-order, and higher-order are proposed. Meanwhile, the particle swarm optimization algorithm is used to solve the model parameters. Under various practical circumstances, the method can be used to flexibly compensate the temperature drift and reduce the standard deviation of the output signal by about four times. Compared to other models or algorithms, the simulation and experimental results indicate that the proposed model is superior in adaptability, stability, and reliability.
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  • Article
    Jiang H, Zhao Y, Gao J, Gao Z.
    Rev Sci Instrum. 2017 Jun;88(6):065106.
    The radiographic testing (RT) image of a steam turbine manufacturing enterprise has the characteristics of low gray level, low contrast, and blurriness, which lead to a substandard image quality. Moreover, it is not conducive for human eyes to detect and evaluate defects. This study proposes an adaptive pseudo-color enhancement method for weld radiographic images based on the hue, saturation, and intensity (HSI) color space and the self-transformation of pixels to solve these problems. First, the pixel's self-transformation is performed to the pixel value of the original RT image. The function value after the pixel's self-transformation is assigned to the HSI components in the HSI color space. Thereafter, the average intensity of the enhanced image is adaptively adjusted to 0.5 according to the intensity of the original image. Moreover, the hue range and interval can be adjusted according to personal habits. Finally, the HSI components after the adaptive adjustment can be transformed to display in the red, green, and blue color space. Numerous weld radiographic images from a steam turbine manufacturing enterprise are used to validate the proposed method. The experimental results show that the proposed pseudo-color enhancement method can improve image definition and make the target and background areas distinct in weld radiographic images. The enhanced images will be more conducive for defect recognition. Moreover, the image enhanced using the proposed method conforms to the human eye visual properties, and the effectiveness of defect recognition and evaluation can be ensured.
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  • Article
    Lapshin RV.
    Rev Sci Instrum. 2020 Jun 01;91(6):065106.
    A number of improvements have been added to the existing analytical model of hysteresis loops defined in parametric form. In particular, three phase shifts are included in the model, which permits us to tilt the hysteresis loop smoothly by the required angle at the split point as well as to smoothly change the curvature of the loop. As a result, the error of approximation of a hysteresis loop by the improved model does not exceed 1%, which is several times less than the error of the existing model. The improved model is capable of approximating most of the known types of rate-independent symmetrical hysteresis loops encountered in the practice of physical measurements. The model allows building smooth, piecewise-linear, hybrid, minor, mirror-reflected, inverse, reverse, double, and triple loops. One of the possible applications of the model developed is linearization of a probe microscope piezoscanner. The improved model can be found useful for the tasks of simulation of scientific instruments that contain hysteresis elements.
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  • Article
    Nouri NM, Mostafapour K, Bahadori R.
    Rev Sci Instrum. 2016 Jun;87(6):065106.
    Hydrodynamic coefficients or hydrodynamic derivatives of autonomous underwater vehicles (AUVs) play an important role in their development and maneuverability. The most popular way of estimating their coefficients is to implement captive model tests such as straight line tests and planar motion mechanism (PMM) tests in the towing tanks. This paper aims to develop an apparatus based on planar experiments of water tunnel in order to estimate hydrodynamic derivatives due to AUVs' acceleration and velocity. The capability of implementing straight line tests and PMM ones using mechanical oscillators located in the downstream flow of the model is considered in the design procedure of the system. The hydrodynamic derivatives that resulted from the acceleration and velocity of the AUV model were estimated using the apparatus that we developed. Static and dynamics test results were compared for the similar derivatives. The findings showed that the system provided the basis for conducting static tests, i.e., straight-line and dynamic tests that included pure pitch and pure heave. By conducting such tests in a water tunnel, we were able to eliminate errors related to the time limitation of the tests and the effects of surface waves in the towing tank on AUVs with applications in the deep sea.
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  • Article
    Cui Y, Hanley L.
    Rev Sci Instrum. 2015 Jun;86(6):065106.
    ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.
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  • Article
    Wen W, Zong G, Bi S.
    Rev Sci Instrum. 2014 Jun;85(6):065106.
    This paper proposes a bubble detection system based on the ultrasound transmission method, mainly for probing high-speed bubbles in the satellite propellant filling pipeline. First, three common ultrasonic detection methods are compared and the ultrasound transmission method is used in this paper. Then, the ultrasound beam in a vertical pipe is investigated, suggesting that the width of the beam used for detection is usually smaller than the internal diameter of the pipe, which means that when bubbles move close to the pipe wall, they may escape from being detected. A special device is designed to solve this problem. It can generate the spiral flow to force all the bubbles to ascend along the central line of the pipe. In the end, experiments are implemented to evaluate the performance of this system. Bubbles of five different sizes are generated and detected. Experiment results show that the sizes and quantity of bubbles can be estimated by this system. Also, the bubbles of different radii can be distinguished from each other. The numerical relationship between the ultrasound attenuation and the bubble radius is acquired and it can be utilized for estimating the unknown bubble size and measuring the total bubble volume.
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  • Article
    Avila K, Hof B.
    Rev Sci Instrum. 2013 Jun;84(6):065106.
    A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 10(1)-10(6)). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η < 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities.
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