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  • 2020-2023  (161)
  • 1995-1999  (123,269)
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  • 101
    Publication Date: 2021-08-03
    Language: English
    Type: article , doc-type:article
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  • 102
    Publication Date: 2021-03-05
    Description: Understanding the pathophysiological processes of cartilage degradation requires adequate model systems to develop therapeutic strategies towards osteoarthritis (OA). Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific disease aspects. This study aimed to combine in vitro and in silico modeling based on a tissue-engineering approach using mesenchymal condensation to mimic cytokine-induced cellular and matrix-related changes during cartilage degradation. Thus, scaffold-free cartilage-like constructs (SFCCs) were produced based on self-organization of mesenchymal stromal cells (mesenchymal condensation) and i) characterized regarding their cellular and matrix composition or secondly ii) treated with interleukin-1β (IL-1β) and tumor necrosis factor α (TNFα) for 3 weeks to simulate OA-related matrix degradation. In addition, an existing mathematical model based on partial differential equations was optimized and transferred to the underlying settings to simulate distribution of IL-1β, type II collagen degradation and cell number reduction. By combining in vitro and in silico methods, we aim to develop a valid, efficient alternative approach to examine and predict disease progression and effects of new therapeutics.
    Language: English
    Type: article , doc-type:article
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  • 103
    Publication Date: 2021-10-28
    Description: Motivated by the desire to numerically calculate rigorous upper and lower bounds on deviation probabilities over large classes of probability distributions, we present an adaptive algorithm for the reconstruction of increasing real-valued functions. While this problem is similar to the classical statistical problem of isotonic regression, the optimisation setting alters several characteristics of the problem and opens natural algorithmic possibilities. We present our algorithm, establish sufficient conditions for convergence of the reconstruction to the ground truth, and apply the method to synthetic test cases and a real-world example of uncertainty quantification for aerodynamic design.
    Language: English
    Type: article , doc-type:article
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  • 104
    Publication Date: 2020-09-14
    Language: English
    Type: article , doc-type:article
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  • 105
    Publication Date: 2021-04-16
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 106
    Publication Date: 2021-02-23
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 107
    Publication Date: 2021-03-26
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 108
    Publication Date: 2021-02-23
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 109
    Publication Date: 2022-03-14
    Description: It is a challenging task to fairly compare local solvers and heuristics against each other and against global solvers. How does one weigh a faster termination time against a better quality of the found solution? In this paper, we introduce the confined primal integral, a new performance measure that rewards a balance of speed and solution quality. It emphasizes the early part of the solution process by using an exponential decay. Thereby, it avoids that the order of solvers can be inverted by choosing an arbitrarily large time limit. We provide a closed analytic formula to compute the confined primal integral a posteriori and an incremental update formula to compute it during the run of an algorithm. For the latter, we show that we can drop one of the main assumptions of the primal integral, namely the knowledge of a fixed reference solution to compare against. Furthermore, we prove that the confined primal integral is a transitive measure when comparing local solves with different final solution values. Finally, we present a computational experiment where we compare a local MINLP solver that uses certain classes of cutting planes against a solver that does not. Both versions show very different tendencies w.r.t. average running time and solution quality, and we use the confined primal integral to argue which of the two is the preferred setting.
    Language: English
    Type: article , doc-type:article
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  • 110
    Publication Date: 2021-02-22
    Language: English
    Type: bookpart , doc-type:bookPart
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  • 111
    Publication Date: 2022-03-14
    Description: The Periodic Event Scheduling Problem is a well-studied NP-hard problem with applications in public transportation to find good periodic timetables. Among the most powerful heuristics to solve the periodic timetabling problem is the modulo network simplex method. In this paper, we consider the more difficult version with integrated passenger routing and propose a refined integrated variant to solve this problem on real-world-based instances.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 112
    Publication Date: 2021-02-05
    Language: English
    Type: article , doc-type:article
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  • 113
    Publication Date: 2022-03-14
    Description: Dual degeneracy, i.e., the presence of multiple optimal bases to a linear programming (LP) problem, heavily affects the solution process of mixed integer programming (MIP) solvers. Different optimal bases lead to different cuts being generated, different branching decisions being taken and different solutions being found by primal heuristics. Nevertheless, only a few methods have been published that either avoid or exploit dual degeneracy. The aim of the present paper is to conduct a thorough computational study on the presence of dual degeneracy for the instances of well-known public MIP instance collections. How many instances are affected by dual degeneracy? How degenerate are the affected models? How does branching affect degeneracy: Does it increase or decrease by fixing variables? Can we identify different types of degenerate MIPs? As a tool to answer these questions, we introduce a new measure for dual degeneracy: the variable–constraint ratio of the optimal face. It provides an estimate for the likelihood that a basic variable can be pivoted out of the basis. Furthermore, we study how the so-called cloud intervals—the projections of the optimal face of the LP relaxations onto the individual variables—evolve during tree search and the implications for reducing the set of branching candidates.
    Language: English
    Type: article , doc-type:article
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  • 114
    Publication Date: 2021-04-20
    Description: This article is mainly motivated by the urge to answer two kinds of questions regarding the Bundesliga, which is Germany’s primary football (soccer) division having the highest average stadium attendance worldwide: “At any point in the season, what is the lowest final rank a certain team can achieve?” and “At any point in the season, what is the highest final rank a certain team can achieve?”. Although we focus on the Bundesliga in particular, the integer programming formulations we introduce to answer these questions can easily be adapted to a variety of other league systems and tournaments.
    Language: English
    Type: article , doc-type:article
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  • 115
    Publication Date: 2021-07-06
    Description: Markov chain (MC) algorithms are ubiquitous in machine learning and statistics and many other disciplines. Typically, these algorithms can be formulated as acceptance rejection methods. In this work we present a novel estimator applicable to these methods, dubbed Markov chain importance sampling (MCIS), which efficiently makes use of rejected proposals. For the unadjusted Langevin algorithm, it provides a novel way of correcting the discretization error. Our estimator satisfies a central limit theorem and improves on error per CPU cycle, often to a large extent. As a by-product it enables estimating the normalizing constant, an important quantity in Bayesian machine learning and statistics.
    Language: English
    Type: article , doc-type:article
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  • 116
    Publication Date: 2021-02-23
    Description: The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures.
    Language: English
    Type: article , doc-type:article
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  • 117
    Publication Date: 2021-10-26
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 118
  • 119
    Publication Date: 2022-06-13
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 120
    Publication Date: 2022-06-13
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 121
    Publication Date: 2022-06-13
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 122
    Publication Date: 2022-06-13
    Language: English
    Type: article , doc-type:article
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  • 123
    Publication Date: 2022-06-13
    Language: English
    Type: article , doc-type:article
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  • 124
  • 125
    Publication Date: 2022-06-13
    Language: English
    Type: researchdata , doc-type:ResearchData
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  • 126
    Publication Date: 2022-06-13
    Description: Large capacity Storage Class Memory (SCM) opens new possibilities for workloads requiring a large memory footprint. We examine optimization strategies for a legacy Fortran application on systems with an heterogeneous memory configuration comprising SCM and DRAM. We present a performance study for the multigrid solver component of the large-eddy simulation framework PALM for different memory configurations with large capacity SCM. An important optimization approach is the explicit assignment of storage locations depending on the data access characteristic to take advantage of the heterogeneous memory configuration. We are able to demonstrate that an explicit control over memory locations provides better performance compared to transparent hardware settings. As on aforementioned systems the page management by the OS appears as critical performance factor, we study the impact of different huge page settings.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 127
    Publication Date: 2022-06-13
    Language: English
    Type: article , doc-type:article
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  • 128
    Publication Date: 2022-06-13
    Language: English
    Type: other , doc-type:Other
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  • 129
    Publication Date: 2022-06-27
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 130
    Publication Date: 2022-06-27
    Language: English
    Type: article , doc-type:article
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  • 131
    Publication Date: 2022-06-27
    Description: In this article we introduce a Minimum Cycle Partition Problem with Length Requirements (CPLR). This generalization of the Travelling Salesman Problem (TSP) originates from routing Unmanned Aerial Vehicles (UAVs). Apart from nonnegative edge weights, CPLR has an individual critical weight value associated with each vertex. A cycle partition, i.e., a vertex disjoint cycle cover, is regarded as a feasible solution if the length of each cycle, which is the sum of the weights of its edges, is not greater than the critical weight of each of its vertices. The goal is to find a feasible partition, which minimizes the number of cycles. In this article, a heuristic algorithm is presented together with a Mixed Integer Programming (MIP) formulation of CPLR. We furthermore introduce a conflict graph, whose cliques yield valid constraints for the MIP model. Finally, we report on computational experiments conducted on TSPLIB-based test instances.
    Language: English
    Type: bookpart , doc-type:bookPart
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  • 132
    Publication Date: 2022-07-07
    Language: English
    Type: bookpart , doc-type:bookPart
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  • 133
    Publication Date: 2022-07-19
    Description: Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and real (unlabeled) endoscopic data to bridge this performance generalization issue. Empirical results on two data sets (15 videos of the Cholec80 and EndoVis'15 dataset) highlight the effectiveness of the proposed Endo-Sim2Real method for instrument segmentation. We compare the segmentation of the proposed approach with state-of-the-art solutions and show that our method improves segmentation both in terms of quality and quantity.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 134
    Publication Date: 2022-07-19
    Description: An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time.
    Language: English
    Type: article , doc-type:article
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  • 135
    Publication Date: 2022-07-19
    Description: Automatic recognition of surgical phases is an important component for developing an intra-operative context-aware system. Prior work in this area focuses on recognizing short-term tool usage patterns within surgical phases. However, the difference between intra- and inter-phase tool usage patterns has not been investigated for automatic phase recognition. We developed a Recurrent Neural Network (RNN), in particular a state-preserving Long Short Term Memory (LSTM) architecture to utilize the long-term evolution of tool usage within complete surgical procedures. For fully automatic tool presence detection from surgical video frames, a Convolutional Neural Network (CNN) based architecture namely ZIBNet is employed. Our proposed approach outperformed EndoNet by 8.1% on overall precision for phase detection tasks and 12.5% on meanAP for tool recognition tasks.
    Language: English
    Type: article , doc-type:article
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  • 136
    Publication Date: 2022-07-19
    Description: We propose generalizations of the T²-statistics of Hotelling and the Bhattacharayya distance for data taking values in Lie groups. A key feature of the derived measures is that they are compatible with the group structure even for manifolds that do not admit any bi-invariant metric. This property, e.g., assures analysis that does not depend on the reference shape, thus, preventing bias due to arbitrary choices thereof. Furthermore, the generalizations agree with the common definitions for the special case of flat vector spaces guaranteeing consistency. Employing a permutation test setup, we further obtain nonparametric, two-sample testing procedures that themselves are bi-invariant and consistent. We validate our method in group tests revealing significant differences in hippocampal shape between individuals with mild cognitive impairment and normal controls.
    Language: English
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  • 137
    Publication Date: 2022-07-19
    Description: Motivation: The ever-rising volume of patients, high maintenance cost of operating rooms and time consuming analysis of surgical skills are fundamental problems that hamper the practical training of the next generation of surgeons. The hospitals prefer to keep the surgeons busy in real operations over training young surgeons for obvious economic reasons. One fundamental need in surgical training is the reduction of the time needed by the senior surgeon to review the endoscopic procedures performed by the young surgeon while minimizing the subjective bias in evaluation. The unprecedented performance of deep learning ushers the new age of data-driven automatic analysis of surgical skills. Method: Deep learning is capable of efficiently analyzing thousands of hours of laparoscopic video footage to provide an objective assessment of surgical skills. However, the traditional end-to-end setting of deep learning (video in, skill assessment out) is not explainable. Our strategy is to utilize the surgical process modeling framework to divide the surgical process into understandable components. This provides the opportunity to employ deep learning for superior yet automatic detection and evaluation of several aspects of laparoscopic cholecystectomy such as surgical tool and phase detection. We employ ZIBNet for the detection of surgical tool presence. ZIBNet employs pre-processing based on tool usage imbalance, a transfer learned 50-layer residual network (ResNet-50) and temporal smoothing. To encode the temporal evolution of tool usage (over the entire video sequence) that relates to the surgical phases, Long Short Term Memory (LSTM) units are employed with long-term dependency. Dataset: We used CHOLEC 80 dataset that consists of 80 videos of laparoscopic cholecystectomy performed by 13 surgeons, divided equally for training and testing. In these videos, up to three different tools (among 7 types of tools) can be present in a frame. Results: The mean average precision of the detection of all tools is 93.5 ranging between 86.8 and 99.3, a significant improvement (p 〈0.01) over the previous state-of-the-art. We observed that less frequent tools like Scissors, Irrigator, Specimen Bag etc. are more related to phase transitions. The overall precision (recall) of the detection of all surgical phases is 79.6 (81.3). Conclusion: While this is not the end goal for surgical skill analysis, the development of such a technological platform is essential toward a data-driven objective understanding of surgical skills. In future, we plan to investigate surgeon-in-the-loop analysis and feedback for surgical skill analysis.
    Language: English
    Type: other , doc-type:Other
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  • 138
    Publication Date: 2022-07-19
    Description: The images of D’Arcy Wentworth Thompson’s book “On Growth and Form” got an iconic status and became influential for biometrics and other mathematical approaches to organismic form. In particular, this is true for those of the chapter on the theory of transformation, which even has an impact on art and humanities. Based on his approach, Thompson formulated far-reaching conclusions with a partly anti-Darwinian stance. Here, we use the example of Thompson’s transformation of crab carapaces to test to what degree the transformation of grids, landmarks, and shapes result in congruent images. For comparison, we applied the same series of tests to digitized carapaces of real crabs. Both approaches show similar results. Only the simple transformations show a reasonable form of congruence. In particular, the transformations to majoid spider crabs reveal a complicated transformation of grids with partly crossing lines. By contrast, the carapace of the lithodid species is relatively easily created despite the fact that it is no brachyuran, but evolved a spider crab-like shape convergently from a hermit crab ancestor.
    Language: English
    Type: article , doc-type:article
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  • 139
    Publication Date: 2022-07-19
    Description: Intrinsic and parametric regression models are of high interest for the statistical analysis of manifold-valued data such as images and shapes. The standard linear ansatz has been generalized to geodesic regression on manifolds making it possible to analyze dependencies of random variables that spread along generalized straight lines. Nevertheless, in some scenarios, the evolution of the data cannot be modeled adequately by a geodesic. We present a framework for nonlinear regression on manifolds by considering Riemannian splines, whose segments are Bézier curves, as trajectories. Unlike variational formulations that require time-discretization, we take a constructive approach that provides efficient and exact evaluation by virtue of the generalized de Casteljau algorithm. We validate our method in experiments on the reconstruction of periodic motion of the mitral valve as well as the analysis of femoral shape changes during the course of osteoarthritis, endorsing Bézier spline regression as an effective and flexible tool for manifold-valued regression.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 140
    Publication Date: 2022-07-19
    Description: A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 141
    Publication Date: 2022-07-19
    Description: In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone.
    Language: English
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  • 142
    Publication Date: 2022-07-19
    Description: This study’s objective was the generation of a standardized geometry of the healthy nasal cavity. An average geometry of the healthy nasal cavity was generated using a statistical shape model based on 25 symptom-free subjects. Airflow within the average geometry and these geometries was calculated using fluid simulations. Integral measures of the nasal resistance, wall shear stresses (WSS) and velocities were calculated as well as cross-sectional areas (CSA). Furthermore, individual WSS and static pressure distributions were mapped onto the average geometry. The average geometry featured an overall more regular shape that resulted in less resistance, reduced wall shear stresses and velocities compared to the median of the 25 geometries. Spatial distributions of WSS and pressure of average geometry agreed well compared to the average distributions of all individual geometries. The minimal CSA of the average geometry was larger than the median of all individual geometries (83.4 vs. 74.7 mm²). The airflow observed within the average geometry of the healthy nasal cavity did not equal the average airflow of the individual geometries. While differences observed for integral measures were notable, the calculated values for the average geometry lay within the distributions of the individual parameters. Spatially resolved parameters differed less prominently.
    Language: English
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  • 143
    Publication Date: 2022-07-19
    Description: We present time-space trade-offs for computing the Euclidean minimum spanning tree of a set S of n point-sites in the plane. More precisely, we assume that S resides in a random-access memory that can only be read. The edges of the Euclidean minimum spanning tree EMST(S) have to be reported sequentially, and they cannot be accessed or modified afterwards. There is a parameter s in {1, ..., n} so that the algorithm may use O(s) cells of read-write memory (called the workspace) for its computations. Our goal is to find an algorithm that has the best possible running time for any given s between 1 and n. We show how to compute EMST(S) in O(((n^3)/(s^2)) log s) time with O(s) cells of workspace, giving a smooth trade-off between the two best-known bounds O(n^3) for s = 1 and O(n log n) for s = n. For this, we run Kruskal's algorithm on the "relative neighborhood graph" (RNG) of S. It is a classic fact that the minimum spanning tree of RNG(S) is exactly EMST(S). To implement Kruskal's algorithm with O(s) cells of workspace, we define s-nets, a compact representation of planar graphs. This allows us to efficiently maintain and update the components of the current minimum spanning forest as the edges are being inserted.
    Language: English
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  • 144
    Publication Date: 2022-07-19
    Description: In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 145
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 146
    Publication Date: 2022-07-19
    Description: An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 147
    Publication Date: 2022-07-19
    Description: We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets.
    Language: English
    Type: article , doc-type:article
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  • 148
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 149
    Publication Date: 2022-07-19
    Description: Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.
    Language: English
    Type: article , doc-type:article
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  • 150
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 151
    Publication Date: 2022-07-19
    Description: We analytically determine Jacobi fields and parallel transports and compute geodesic regression in Kendall’s shape space. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and thereby reduce the computational expense by several orders of magnitude over common, nonlinear constrained approaches. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As an example application we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative (OAI). Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data alone.
    Language: English
    Type: article , doc-type:article
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  • 152
    Publication Date: 2022-07-19
    Description: A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach.
    Language: English
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  • 153
    Publication Date: 2022-07-19
    Description: Conflicting hypotheses about the relationships among the major lineages of aculeate Hymenoptera clearly show the necessity of detailed comparative morphological studies. Using micro-computed tomography and 3D reconstructions, the skeletal musculature of the meso- and metathorax and the first and second abdominal segment in Apoidea are described. Females of Sceliphron destillatorium, Sphex (Fernaldina) lucae (both Sphecidae), and Ampulex compressa (Ampulicidae) were examined. The morphological terminology provided by the Hymenoptera Anatomy Ontology is used. Up to 42 muscles were found. The three species differ in certain numerical and structural aspects. Ampulicidae differs significantly from Sphecidae in the metathorax and the anterior abdomen. The metapleural apodeme and paracoxal ridge are weakly developed in Ampulicidae, which affect some muscular structures. Furthermore, the muscles that insert on the coxae and trochanters are broader and longer in Ampulicidae. A conspicuous characteristic of Sphecidae is the absence of the metaphragma. Overall, we identified four hitherto unrecognized muscles. Our work suggests additional investigations on structures discussed in this paper.
    Language: English
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  • 154
    Publication Date: 2022-07-19
    Description: We present an automated method for extrapolating missing regions in label data of the skull in an anatomically plausible manner. The ultimate goal is to design patient-speci� c cranial implants for correcting large, arbitrarily shaped defects of the skull that can, for example, result from trauma of the head. Our approach utilizes a 3D statistical shape model (SSM) of the skull and a 2D generative adversarial network (GAN) that is trained in an unsupervised fashion from samples of healthy patients alone. By � tting the SSM to given input labels containing the skull defect, a First approximation of the healthy state of the patient is obtained. The GAN is then applied to further correct and smooth the output of the SSM in an anatomically plausible manner. Finally, the defect region is extracted using morphological operations and subtraction between the extrapolated healthy state of the patient and the defective input labels. The method is trained and evaluated based on data from the MICCAI 2020 AutoImplant challenge. It produces state-of-the art results on regularly shaped cut-outs that were present in the training and testing data of the challenge. Furthermore, due to unsupervised nature of the approach, the method generalizes well to previously unseen defects of varying shapes that were only present in the hidden test dataset.
    Language: English
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  • 155
    Publication Date: 2022-09-22
    Description: A new virtual unfolding technique was applied to a silver scroll excavated in Jerash, Jordan, in 2014. As result of the unfolding, 17 lines of writing are clearly visible in the unfolded volumetric data that is published here.
    Language: English
    Type: researchdata , doc-type:ResearchData
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  • 156
    Publication Date: 2022-11-28
    Language: English
    Type: book , doc-type:book
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  • 157
  • 158
    Publication Date: 2022-11-28
    Language: English
    Type: incollection , doc-type:Other
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  • 159
    Publication Date: 2022-11-28
    Description: We present a novel kernel-based machine learning algorithm for identifying the low-dimensional geometry of the effective dynamics of high-dimensional multiscale stochastic systems. Recently, the authors developed a mathematical framework for the computation of optimal reaction coordinates of such systems that is based on learning a parameterization of a low-dimensional transition manifold in a certain function space. In this article, we enhance this approach by embedding and learning this transition manifold in a reproducing kernel Hilbert space, exploiting the favorable properties of kernel embeddings. Under mild assumptions on the kernel, the manifold structure is shown to be preserved under the embedding, and distortion bounds can be derived. This leads to a more robust and more efficient algorithm compared to the previous parameterization approaches.
    Language: English
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  • 160
    Publication Date: 2022-11-28
    Description: Markov State Models (MSM) sind der Goldstandard zur Modellierung biomolekularer Dynamik, da sie die Identifizierung und Analyse metastabiler Zustände ermöglichen. Die robuste Perron-Cluster-Cluster-Analyse (PCCA+) ist ein verbreiteter Spectral-Clustering-Algorithmus, der für das Clustering hochdimensionaler MSM verwendet wird. Da die PCCA+ auf reversible Prozesse beschränkt ist, wird sie zur Generalisierten PCCA+ (G-PCCA) verallgemeinert, die geeignet ist, nichtreversible Prozesse aufzuklären. Bernhard Reuter untersucht hier mittels G-PCCA die nichtthermischen Auswirkungen von Mikrowellen auf die Proteindynamik. Dazu führt er molekulardynamische Nichtgleichgewichtssimulationen des Amyloid-β-(1–40)-Peptids durch und modelliert diese.
    Language: German
    Type: book , doc-type:book
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  • 161
    Publication Date: 2022-11-28
    Language: English
    Type: incollection , doc-type:Other
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  • 162
    Publication Date: 2022-11-28
    Description: Model reduction of large Markov chains is an essential step in a wide array of techniques for understanding complex systems and for efficiently learning structures from high-dimensional data. We present a novel aggregation algorithm for compressing such chains that exploits a specific low-rank structure in the transition matrix which, e.g., is present in metastable systems, among others. It enables the recovery of the aggregates from a vastly undersampled transition matrix which in practical applications may gain a speedup of several orders of mag- nitude over methods that require the full transition matrix. Moreover, we show that the new technique is robust under perturbation of the transition matrix. The practical applicability of the new method is demonstrated by identifying a reduced model for the large-scale traffic flow patterns from real-world taxi trip data.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 163
    Publication Date: 2022-12-05
    Language: English
    Type: article , doc-type:article
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  • 164
    Book
    Book
    Wien [u.a.] :Springer, ; 1.1977 - 16.2003; damit Ersch. eingest.
    Title: Computing : archives for informatics and numerical computation; Supplementum
    Publisher: Wien [u.a.] :Springer,
    Year of publication: 1977-2003
    Dates of Publication: 1.1977 - 16.2003; damit Ersch. eingest.
    Type of Medium: Book
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  • 165
    Online Resource
    Online Resource
    Berlin ; Heidelberg :Springer, ; 1.1995(1996) - 8.2002
    Title: Journal of molecular modeling
    Publisher: Berlin ; Heidelberg :Springer,
    Year of publication: 1996-2002
    Dates of Publication: 1.1995(1996) - 8.2002
    ISSN: 0949-183X
    Type of Medium: Online Resource
    Language: Undetermined
    Subsequent Title: Forts. ---〉:Journal of molecular modeling
    Note: Kumuliert jeweils den abgeschlossenen Jg. der Internetausg.
    Parallel Title: Druckausg. ---〉:Molecular modeling annual
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  • 166
    Journal/Serial
    Journal/Serial
    New York, NY :ACM, ; 1.1969 - 7.1975/76; N.S. 1.1976 - 21.2001,1; damit Ersch. eingest.
    Title: SIGBIO newsletter /
    Author: Association for Computing Machinery / Special Interest Group on Biomedical Computing
    Publisher: New York, NY :ACM,
    Year of publication: 1969-2001
    Dates of Publication: 1.1969 - 7.1975/76; N.S. 1.1976 - 21.2001,1; damit Ersch. eingest.
    ISSN: 0163-5697
    Type of Medium: Journal/Serial
    Language: Undetermined
    Parallel Title: Internetausg. ---〉:Biomedical computing
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  • 167
    Journal/Serial
    Journal/Serial
    Los Alamitos, Calif. :Soc., ; 5.1997 - 8.2000; damit Ersch. eingest.
    Title: IEEE concurrency /
    Author: Institute of Electrical and Electronics Engineers / Computer Group
    Publisher: Los Alamitos, Calif. :Soc.,
    Year of publication: 1997-2000
    Dates of Publication: 5.1997 - 8.2000; damit Ersch. eingest.
    ISSN: 1092-3063
    Type of Medium: Journal/Serial
    Language: Undetermined
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  • 168
    Journal/Serial
    Journal/Serial
    New York, NY :North-Holland, ; 1.1984 - 46.2000
    Title: ¬The¬ journal of logic programming
    Publisher: New York, NY :North-Holland,
    Year of publication: 1984-2000
    Dates of Publication: 1.1984 - 46.2000
    ISSN: 0743-1066
    Type of Medium: Journal/Serial
    Language: Undetermined
    Subsequent Title: Forts. ---〉:¬The¬ journal of logic and algebraic programming
    Parallel Title: Internetausg. ---〉:¬The¬ journal of logic and algebraic programming
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  • 169
    Journal/Serial
    Journal/Serial
    Amsterdam :CWI, ; 1.1988 - 12.1999; damit Ersch. eingest.
    Title: CWI quarterly
    Author: Centrum voor Wiskunde en Informatica 〈Amsterdam〉
    Publisher: Amsterdam :CWI,
    Year of publication: 1988-1999
    Dates of Publication: 1.1988 - 12.1999; damit Ersch. eingest.
    ISSN: 0168-826X , 0922-5366
    Type of Medium: Journal/Serial
    Language: Undetermined
    Former Title: Vorg. ---〉:Centrum voor Wiskunde en Informatica 〈Amsterdam〉: CWI newsletter
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  • 170
    E-Resource
    E-Resource
    Oxford :Univ. Press, ; 1.1996/97 - 3.1999; damit Ersch. eingest.
    Title: Medical image analysis CD : an international journal of computer vision, visualization and image- guided intervention in medicine
    Publisher: Oxford :Univ. Press,
    Year of publication: 1996-1999
    Dates of Publication: 1.1996/97 - 3.1999; damit Ersch. eingest.
    ISSN: 1361-8431
    Type of Medium: Electronic Resource
    Language: Undetermined
    Parallel Title: Druckausg. ---〉:Medical image analysis
    Parallel Title: Internetausg. ---〉:Medical image analysis
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  • 171
    Book
    Book
    New York, NY :ACM, ; Nachgewiesen 2.1971 - 20.1999,4; damit Ersch. eingest.
    Title: Computer personnel : a quarterly publ. of the Special Interest Group on Computer Personnel Research, SIGCPR
    Publisher: New York, NY :ACM,
    Year of publication: 1971-1999
    Dates of Publication: Nachgewiesen 2.1971 - 20.1999,4; damit Ersch. eingest.
    ISSN: 0160-2497
    Type of Medium: Book
    Parallel Title: Internetausg. ---〉:Computer personnel
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  • 172
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 1987-1996 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A Reynolds stress closure is developed for homogeneous shear-free turbulence subjected to a strong magnetic field at low magnetic Reynolds numbers. A scalar dimensionality anisotropy parameter is introduced to carry information about the distribution of energy in spectral space. This information is vital in modeling MHD turbulence, as it determines both magnitude and anisotropy of the Joule dissipation tensor. The Joule dissipation tensor is modeled by a tensor function, which is bilinear in the Reynolds stress anisotropy and the unit direction vector of the magnetic field. The tensor function coefficients are second-order in the scalar dimensionality parameter. A phenomenological transport equation for the dimensionality parameter is proposed. The model is closed using the pressure–strain model of Sarkar, Speziale and Gatski and a magnetic destruction term in the standard dissipation equation. The purely magnetic linear problem contains no undetermined constants, while the complete model contains two constants. Model predictions for the case of decaying turbulence show very good agreement with direct numerical simulations. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 173
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 2006-2011 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The expansion into eigenfunctions of a general disturbance in a viscous flow is possible only when both the discrete and continuous modes of the Orr–Sommerfeld equation are employed. Proper implementation of the boundary conditions and a method for computation of the continuous modes are developed. The unique phenomenon known as shear sheltering is discussed and illustrated. It is shown that the penetration depth of disturbances into the boundary layer has a dependence on frequency and Reynolds number similar to that of a Stokes layer. A simple model that captures this dependence is developed. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 174
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 2055-2060 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The principle of minimum Fisher information (MFI) and the theory of random Gaussian fields are used to work out the joint distribution function of the density and velocity in homogeneous, isotropic, stationary, nearly incompressible turbulence, in the case where the velocity and pressure are correlated. The appropriate Fisher variables seem to be the mass flux, the density, and the generalized heat function (enthalpy) or pressure head. It is shown that simple constraints on the minimization may be chosen to give a good fit to the pressure distribution function found in recent direct numerical simulations and experiments, where the PDF is exponential for negative p and roughly exp[−(p/p0)3/2]p−1/2 for positive p. In this case, the fit is an improvement on a past MFI calculation, in which the correlations between p and u were not accounted for. In addition, the form of the conditional average 〈p|u〉 as found from direct numerical simulations is taken into consideration. The theory of random Gaussian velocity fields predicts 〈p|u〉=〈p|0〉−βu2, where u2≡u⋅u and β≤1/8 is a constant. In conjunction with this theory, MFI predicts a specific dependence of the conditional average 〈ux2|p〉 on p, where ux is a typical velocity component. The conditional PDF P(ux|p) is slightly non-Gaussian, but P(ux) is Gaussian. The relation 2〈u2δp〉2=〈u2〉[〈u2(δp)2〉−〈u2〉〈(δp)2〉] is predicted. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 175
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 2099-2101 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Transient disturbance growth in parallel two-phase flow is studied. When the disturbance growth is measured in terms of the kinetic energy norm, which is commonly used for single-phase flow, the disturbance growth function does not converge as the number of eigenmodes used in the computation increases. A solution to this problem is presented in the form of a norm that also includes the potential energy of the disturbed interface. This solution is used to examine the two-phase flow experiment by Kao and Park. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 176
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 2108-2110 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Consistency conditions for the prediction of turbulent flows in a rotating frame are examined. It is shown that the dissipation rate should vanish along with the eddy viscosity in the limit of rapid rotations. The latter result is also true when the eddy viscosity is anisotropic and formally follows from the explicit algebraic stress approximation as well as from a phenomenological treatment. The former result has been built into the modeled dissipation rate equation of recent turbulence models where the second result has been violated. In fact, some of these models have the eddy viscosity going to infinity while the dissipation rate vanishes, leading to an inconsistency. For consistency, both of these conditions must be satisfied. The implications of these results for turbulence modeling are thoroughly discussed. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 177
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 1564-1587 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The dynamics of an interface between two incompressible, inviscid, irrotational, and immiscible liquids with densities ρ1 and ρ2 under the influence of a time-dependent gravitational field g(t) is investigated. A Hamiltonian formulation of the system is adopted leading to a perturbative expansion of the equations of motion for the canonical variables. Equations, accurate up to third order in the perturbation amplitude are derived. They are able to describe the initial stage of instability "saturation." The latter equations are integrated iteratively for two standard limiting cases: constant gravity (classical Rayleigh–Taylor instability), g(t)≡g0, and impulsive Richtmyer–Meshkov loading, g(t)=v0δ(t−t0). The comparative growth of various two-dimensional structures and rectangular and hexagonal cells is evaluated. Surface tension effects are considered. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 178
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 1597-1610 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The feasibility of controlling flow patterns of Rayleigh–Bénard convection in a fluid layer confined in a circular cylinder heated from below and cooled from above (the Rayleigh–Bénard problem) is investigated numerically. It is demonstrated that, through the use of feedback control, it is possible to stabilize the no-motion (conductive) state, thereby postponing the transition from a no-motion state to cellular convection. The control system utilizes multiple sensors and actuators. The actuators consist of individually controlled heaters positioned on the bottom surface of the cylinder. The sensors are installed at the fluid's midheight. The sensors monitor the deviation of the fluid's temperatures from preset desired values and direct the actuators to act in such a way so as to eliminate these deviations. The numerical predictions are critically compared with experimental observations. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 179
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 1635-1657 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: In this paper the generation and evolution of an edge-wave packet are studied experimentally and numerically. In the laboratory an edge-wave packet is first generated on a sloping beach by a hinge-type wave-maker. Both the free surface displacement and velocity field are measured along several on-offshore cross sections. Numerical results are also obtained by solving the linear shallow-water wave equations and are compared with experimental data. Numerically predicted wave evolution characteristics are in good agreement with those shown by laboratory data. Analyses of the wave amplitude density spectra of both numerical solutions and experimental data show that wave packets are indeed trapped in the nearshore region and consist of a mixture of Stokes and higher-mode edge waves. Furthermore, the Stokes mode dominates in the low frequency range. Two additional wave-maker designs, i.e., the piston-type and the reverse hinge-type, are investigated numerically. Away from the wave-maker the wave forms (time histories) of the wave packets are insensitive to the details of wave-maker movements. The effects of beach slope on the evolution of wave packets are investigated. The behavior of the velocity field and the attenuation rates of runup amplitudes are also discussed. © 1998 American Institute of Physics.
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  • 180
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    Physics of Fluids 10 (1998), S. 1672-1684 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The interaction of a near-critical axisymmetric incompressible swirling flow in a straight pipe with small inlet azimuthal vorticity perturbations is studied. Certain flow conditions that may reflect the physical situation are prescribed along the pipe inlet and outlet. It is first demonstrated that under these conditions a regular-expansion solution in terms of the small azimuthal vorticity perturbations has a singular behavior around the critical swirl. This singularity infers that large-amplitude disturbances may be induced by the small perturbations when the incoming flow to the pipe has a swirl level around the critical swirl. In order to understand the nature of flows in this swirl range, a small-disturbance analysis is developed. It shows that under the prescribed inlet/outlet conditions, a small but finite inlet azimuthal vorticity perturbation breaks the transcritical bifurcation of solutions of the Euler equations at the critical swirl into two branches of perturbed solutions. When the azimuthal vorticity perturbations are positive these branches show a regular behavior. However, when they are negative, the perturbed branches fold at limit points near the critical swirl, with a finite gap between the two branches, and no near-columnar equilibrium state can exist for an incoming flow with swirl close to the critical level. The flow must develop large disturbances in this swirl range. Beyond this range, two equilibrium states may exist under the same inlet/outlet conditions. When the negative inlet vorticity perturbations become larger in their size, this special behavior uniformly changes into a branch of single equilibrium state for each incoming swirl. The relevance of the results to the appearance of the axisymmetric vortex breakdown in a pipe and the control of this phenomenon using inlet vorticity perturbations is also discussed. The results suggest that, in general, positive inlet azimuthal vorticity perturbations may be used to delay vortex breakdown to higher swirl levels whereas negative perturbations induce the appearance of vortex breakdown at levels below the critical swirl. © 1998 American Institute of Physics.
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  • 181
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    Physics of Fluids 10 (1998), S. 1725-1732 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Static pressure fluctuations measured in the atmospheric surface layer over a grass covered forest clearing are studied in the context of Townsend's 1961 hypothesis regarding the effect of the outer region on the inner region. It is shown that large-scale pressure features are actively straining the inertial-scale pressure fluctuations, thus invalidating the direct extension of Kolmogorov's 1941 hypothesis to the spectral scaling of pressure within the inertial subrange. A parameter describing the large scale pressure fluctuations is added to the set of variables responsible for inertial-range pressure differences and dimensional analysis is employed to derive an improved scaling law for pressure spectra which more closely matches these and previous experimental results. An examination of the Poisson equation for pressure is conducted and found to support the dimensional and experimental results. © 1998 American Institute of Physics.
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  • 182
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    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 1757-1766 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We consider the resistive steady states of a uniformly conducting magnetofluid inside a toroidal boundary. The problem becomes tractable in the limit of slow flow: i.e., low Reynolds number, which may be in turn justified when the viscous Lundquist number is small. Previous calculations are extended to apprehend the toroidal component of the necessary flow. The emerging pattern is one of helical vortices which seem likely to be ubiquitous in toroidal geometry, and which disappear in the "straight-cylinder approximation." © 1998 American Institute of Physics.
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  • 183
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    Physics of Fluids 10 (1998), S. 1742-1756 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The interactions of flows generated by ionic discharges with wall turbulence are not only of interest for turbulence control, but also for devices of industrial importance, such as wire-plate electrostatic precipitators (ESPs). Under conditions of uniform discharge, in wire-plate ESPs, arrays of regular, spanwise vortices are found in the absence of a through-flow. These arise from ionic discharges from the spanwise wires placed between the grounded plates on each side. The interactions of such electrohydrodynamic (EHD) flows with a turbulent through-flow are still poorly understood. Direct numerical simulation (DNS) is an attractive method for investigating such problems since the details of the interactions can be unraveled, and the results are directly applicable to industrial-scale systems because their Reynolds numbers are typically quite low. In this study, pseudospectral channel flow simulations were performed with the electrohydrodynamic effects being modeled by a spatially varying body-force term in the equations of fluid motion. The interactions between EHD flows and wall structures were elucidated by examining the instantaneous structure of the flow field. Results indicate that the mean flow, the EHD flows, and the turbulence field undergo significant modifications caused by mutual interaction. First, it is found that EHD flows reduce drag, allowing larger flow rates for a given pressure drop. Second, the EHD flows themselves appear weakened by the presence of the through-flow, particularly in the central region of the channel. The EHD flows affect the turbulence field by both increasing dissipation and turbulence production, the overall turbulence level being determined by the balance between the increased dissipation and production. Even though high EHD flow intensities may increase streamwise and wall-normal turbulence intensities, the Reynolds stress is reduced, consistent with the observed reduction in drag. From a mechanistic viewpoint, there are indications that EHD flows of the type investigated here reduce drag by decreasing the relative importance of the positive Reynolds stress contributions, i.e., second (ejections) and fourth (sweeps) quadrant events, compared to the negative Reynolds stress contributions, i.e., first and third quadrant events. © 1998 American Institute of Physics.
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  • 184
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    Physics of Fluids 10 (1998), S. 1246-1248 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The conditional moment closure with second-order approximation for the reaction rate and an equation for the conditional fluctuations of the temperature increments before autoignition of a turbulent nonpremixed flow has been developed for one-step chemistry. The explicit incorporation of conditional variances is necessitated due to the temperature fluctuations induced by heat losses from the reaction zone before ignition, as indicated by recent direct numerical simulations (DNS). Predicted ignition times and reaction zone structure are in very good agreement with DNS data and the differences between the first- and second-order closure are discussed. © 1998 American Institute of Physics.
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  • 185
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    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 1273-1290 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A temperature gradient is applied along a fluid filled slot with a flat upper interface, establishing flow via thermocapillarity and/or buoyancy. There is a known parallel flow along the slot, in which the fluid velocity varies vertically, and there is a known convected temperature profile. This parallel flow is then subjected to gravitational modulation or "jitter" which is applied at low frequency and in various directions. For gravity modulations in the plane of the basic flow, analytic solutions for velocity and temperature profiles are obtained for jitter of arbitrary amplitude. These solutions involve modifications to the earlier parallel flow solutions. Jitter in the vertical direction generates vorticity due to coupling with the applied horizontal temperature gradient. This alternately cooperates or competes with the steady basic flow over a cycle of the modulation, but does not qualitatively change the flow or temperature profiles. Jitter applied along the slot produces vorticity only when coupled to vertical convected temperature gradients and so is important when the basic flow is sufficiently strong (large Marangoni and/or Rayleigh number). Various cases are considered for the basic flow, which may be driven by thermocapillarity alone, by vertical gravity alone or by a mixture of thermocapillarity and vertical gravity. When strong streamwise jitter is added to any of these cases, the flow profile alternates during the modulation cycle between boundary layer structures and vertically stacked cells. The type of structure selected depends on the sense of the horizontal thermal stratification with respect to the jitter, and in that part of the cycle where this stratification is unstable, there are particular amplitudes of jitter which can give strong cellular motions or runaways. These runaways represent a resonant interaction with stationary Rayleigh-Bénard cells. © 1998 American Institute of Physics.
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  • 186
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    Physics of Fluids 10 (1998), S. 1329-1343 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Stability and bifurcation analyses of a partially melted or solidified material heated from below and cooled from above in a cavity, the so-called two-phase Rayleigh–Benard problem, are conducted by a finite-volume/Newton's method. Bifurcation analysis techniques using a numerical Jacobian and an iterative matrix solver suitable to this large complicated system are adopted. The onset and evolution of melt flows coupling with the heat conduction in the solid and a deformable melt/solid interface are illustrated through detailed bifurcation diagrams, and the linear stability of each flow family is carefully examined. Some comparison with the one-phase system is performed. Results are presented for a variety of parameters of interest, including the Rayleigh number, aspect ratio, and tilt angle. Although most calculations are presented for the melt with a Prandtl number of one, the effects of Prandtl number on the onset of cellular convection and the sensitivity of symmetry breaking by tilting are examined. Furthermore, the dynamic responses of an unstable static state to stable solutions after small disturbances are illustrated, and the effect of heat of fusion is discussed. © 1998 American Institute of Physics.
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  • 187
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    Physics of Fluids 10 (1998), S. 1375-1383 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The problem of the motion of a porous sphere in a viscous fluid has three pertinent characteristic times: two for the external flow field of the viscous fluid and a third one for the internal flow field, inside the porous material. Because of this, a singular perturbation method must be used to obtain an analytical solution to the governing differential equations and for the determination of the flow field outside the porous sphere. Such a method is used here, and a solution is obtained, by using the so-called Saffman boundary condition at the interface between the porous sphere and the outside fluid. This solution is valid at finite but small Reynolds numbers. Thus, general expressions for the hydrodynamic force acting on the porous sphere and, hence, for the drag coefficient of the sphere are obtained. This general expression yields, as special cases, other known expressions for the drag coefficients, which were derived under more restrictive conditions, such as creeping flow, no-slip boundary conditions or zero permeability (solid) spheres. © 1998 American Institute of Physics.
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  • 188
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    Physics of Fluids 10 (1998), S. 1419-1427 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Results of discrete element method (DEM) simulation and magnetic resonance imaging (MRI) experiments are compared for monodisperse granular materials flowing in a half-filled horizontal rotating cylinder. Because opacity is not a problem for MRI, a long cylinder with an aspect ratio ∼7 was used and the flow in a thin transverse slice near the center was studied. The particles were mustard seeds and the ratio of cylinder diameter to particle diameter was approximately 50. The parameters compared were dynamic angle of repose, velocity field in a plane perpendicular to the cylinder axis, and velocity fluctuations at rotation rates up to 30 rpm. The agreement between DEM and MRI was good when the friction coefficient and nonsphericity were adjusted in the simulation for the best fit. © 1998 American Institute of Physics.
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  • 189
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    Physics of Fluids 10 (1998), S. 1438-1448 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The collapse of an axisymmetric mixed region in a continuously stratified pycnocline is analyzed using direct simulation of the Navier–Stokes equations in the Boussinesq limit. Attention is focused on cylindrical mixed regions of size comparable to the thickness of the pycnocline, which lies between two deep layers of different densities. Computed results show that the collapse leads to the formation of a cylindrical internal gravity wave that encloses a concentrated toroidal vortex. The vortex roll-up is related to the strain-induced intensification of vorticity and is found to be most pronounced for "tall" and horizontally compact mixed regions. The wave and vortex gradually decay as they spread radially in the pycnocline. After significant decay has occurred, the vortex disintegrates but the wave continues to propagate away from the mixed region. A sharp-nosed intrusion is left in the wake of the wave, which is no longer able to transport fluid. A Lagrangian particle scheme is used to visualize and quantify the wave structure. Analysis of particle distributions shows that the toroidal vortices entrain ambient stratified fluid into their cores. It is found that the speed of the cylindrical solitary wave is lower than the two-dimensional (2D) weakly-nonlinear prediction. In addition, unlike the 2D case, the wave speed does not appear to be a simple function of the wave amplitude. The vortex decay is finally analyzed in terms of a simplified model on the viscous cancellation of the two strained vortices of opposite sign. An approximate qualitative agreement between model predictions and computations is found. The comparison highlights the role of viscous diffusion of vorticity as well as the contributions of entrainment and baroclinic vorticity generation to the vortex decay. © 1998 American Institute of Physics.
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  • 190
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    Physics of Fluids 10 (1998), S. 1512-1518 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The oblique stagnation-point flow of an electrically conducting fluid in the presence of a magnetic field is a highly nonlinear problem whose solution is of interest even in the simplest of geometries. The problem models the flow of a viscous conducting fluid near a point where a separation vortex reattaches itself to a rigid boundary. A similarity solution exists which reduces the problem to a coupled system of four ordinary differential equations which can be integrated numerically. The problem has two independent parameters, the conductivity of the fluid and the strength of the magnetic field. Solutions are tabulated for a variety of cases involving the two parameters. The geometry of the flow as well as that of the induced magnetic field is determined near the point of reattachment. © 1998 American Institute of Physics.
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  • 191
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    Physics of Fluids 10 (1998), S. 1537-1539 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The turbulence source terms in the equation for the mean vorticity near the walls of a smooth corner are examined through correlations involving the fluctuating vorticity field. A manifestation of the corner effect is the specific asymmetries of the estimated probability density functions for the production terms. These can be used to extract the type of three-dimensional structures that contribute in the production of mean vorticity. © 1998 American Institute of Physics.
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  • 192
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    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 1543-1543 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
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  • 193
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    Physics of Fluids 10 (1998), S. 1550-1563 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The axisymmetric creeping motion of multiple composite spheres is analyzed to investigate the hydrodynamic interactions among these particles. A composite particle referred to in this paper is a spherical solid core covered with a permeable shell, whose thickness can be arbitrary. The Stokes equation and the Brinkman equation are used to describe the flow fields outside and inside the particle, respectively. For two identical composite spheres with thin porous layers in near contact, a lubrication analysis is employed to examine their relative motion. Analytic expressions for the pressure and the drag force are obtained for the layers having high permeability. For general cases, a boundary collocation method is applied to numerically solve for the unknown coefficients in the series solutions for the flow behavior of the multiple particles. The resulting drag forces are in good agreement with the predictions from the lubrication analysis and the reflection method. In general, the strength of hydrodynamic interaction among composite particles lies between the values among permeable particles with the same permeabilities and among solid particles. The hydrodynamic behavior for composite spheres may be approximated by that for permeable spheres when the porous layer is sufficiently thick, depending on the permeability. When the particles undergo relative motion, the drag increases with decreasing distance between them. However, the drag on the particle with larger size or lower permeability may reach a minimum at a certain distance for a chain of dissimilar particles, rather than in contact, when they translate at the same velocity. © 1998 American Institute of Physics.
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  • 194
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    Physics of Fluids 10 (1998), S. 1621-1634 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The transition from two-dimensional thermoconvective steady flow to a time-dependent flow is considered for a liquid with a high Prandtl number (Pr=105) in a liquid bridge with a curved free surface. Both thermocapillary and buoyancy mechanisms of convection are taken into account. The computer program developed for this simulation transforms the original nonrectangular physical domain into a rectangular computational domain. To solve the problem in body-fitted curvilinear coordinates, the time-dependent Navier–Stokes equations were approximated by central differences on a stretched mesh. For liquid bridges with a flat interface, the instability corresponding to an azimuthal wave number of m=0 is not found for the investigated range of Marangoni numbers. The instability corresponding to an m=0 is found for relatively low Marangoni numbers only in liquid bridges with a nonflat, free surface, and nonzero Rayleigh number. The steady state becomes unstable to axially running waves. It is shown that the onset of instability depends strongly upon the volume of the liquid. The stability boundary is reported for the aspect ratio Γ=height/radius=4/3 and for a wide range of liquid bridge volumes. The physical mechanism of the oscillations is based on the temporal interaction of the temperature sensitive free surface with the small local disturbances, created by temperature distribution inside the liquid bridge. © 1998 American Institute of Physics.
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  • 195
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    Physics of Fluids 10 (1998), S. 1658-1665 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Experiments on the onset of buoyant instabilities leading to periodic formation of vortical structures in planar buoyant plumes of helium and helium/air mixtures injected into quiescent air are reported for a range of nozzle widths (w=20–70 mm), plume fluid densities (pure helium to that approaching air), and velocities at the nozzle exit. First, the plume parameters corresponding to the onset of the oscillatory instability were experimentally determined by varying the nozzle exit velocity for different nozzle widths and plume fluid densities in two different nozzle configurations. These configurations corresponded to a freestanding rectangular nozzle and a rectangular nozzle surrounded by a flat plate in the plane of the nozzle exit. The observed plume behavior in the near field was characterized as nonoscillatory, transitional, or pulsatile. The onset of pulsations in the near field of these buoyant plumes (within a height of two nozzle widths) was best correlated in terms of the plume source Reynolds number and the plume fluid to ambient density ratio. It was also found that the boundary conditions surrounding the nozzle exit had an influence on the onset of plume instability in the near field. Specifically, at a given plume to the ambient density ratio, the plumes with flat plate surround were found to transition to the oscillatory state at a lower value of the threshold velocity and therefore are less stable than the plumes originating from freestanding nozzles. Subsequently, the plume oscillation frequencies were measured as a function of plume width, plume source velocity, and the density ratio for a range of these parameters. The plume oscillation frequency was found to correlate well in terms of the nondimensional parameters, Strouhal number, S=(fw)/Vp, and Richardson number, Ri=[(ρ∞−ρp)gw]/ρ∞Vp2, yielding a correlation S=0.55Ri0.45 determined for 1〈Ri〈102. This correlation is somewhat different from that of the axisymmetric buoyant plumes, which can be attributed to the differences in mixing rates and the strength of the local buoyancy flux in planar and axisymmetric plumes. The vortical structures formed in the unstable plumes also exhibit several distinct vortex pair modes. The centers of the formed vortex pairs, in general, do not remain colinear and distort with respect to each other when compared with the axisymmetric plume vortex rings, which are toroidal. The convection speeds of the vortex pair centers were also measured and reported in this study. © 1998 American Institute of Physics.
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  • 196
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    Physics of Fluids 10 (1998), S. 1191-1205 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The similarity form of the scalar-variance spectrum at high Schmidt numbers is investigated for nonstationary turbulence. Theoretical arguments show that Batchelor scaling may apply only at high Reynolds numbers. At low Reynolds numbers, Batchlor scaling is not possible unless the turbulence is stationary or the enstrophy decays asymptotically as t−2. When this latter condition is satisfied, it is shown from an analysis using both the Batchelor and Kraichnan models for the scalar-variance transfer spectrum that the k−1 power law in the viscous-convective subrange is modified. Results of direct numerical simulations of high Schmidt number passive scalar transport in stationary and decaying two-dimensional turbulence are compared to the theoretical analysis. For stationary turbulence, Batchelor scaling is shown to collapse the spectra at different Schmidt numbers and a k−1 viscous-convective subrange is observed. The Kraichnan model is shown to accurately predict the simulation spectrum. For nonstationary turbulence decaying at constant Reynolds number for which the enstrophy decays as t−2, scalar fields for different Schmidt numbers are simulated in situations with and without a uniform mean scalar gradient. The Kraichnan model is again shown to predict the spectra in these cases with different anomalous exponents in the viscous-convective subrange. © 1998 American Institute of Physics.
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  • 197
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    Physics of Fluids 10 (1998), S. 1234-1236 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The spreading of surfactant coated thin liquid films is often accompanied by an instability producing significant film corrugation, fingering and branching. Marangoni stresses, responsible for the rapid and spontaneous spreading, are suspected as the main cause of unstable flow. Traditional eigenvalue analysis of a self-similar solution describing Marangoni driven spreading has predicted only stable modes. We present results of a transient growth study which reveals enormous amplification of initially infinitesimal disturbances in the film thickness. This analysis provides, for the first time, evidence of an instability resembling experimental patterns. © 1998 American Institute of Physics.
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  • 198
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    Physics of Fluids 10 (1998), S. 1238-1238 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
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  • 199
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    Physics of Fluids 10 (1998), S. 1028-1030 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The classical result of Smoluchowski [Z. Phys. Chem. 92, 129 (1917)] for the collision rate of monodisperse particles in a laminar shear flow is shown to be inaccurate due to the inclusion of the self-collision. In the present work we extend Smoluchowski's result by excluding the self-collision in the counting of collision pairs. A numerical simulation for particle collisions in a laminar shear flow at very low concentration is carried out to validate the extended result of Smoluchowski. Good agreement for the collision rate between the numerical simulation and the prediction based on the extended expression is obtained. © 1998 American Institute of Physics.
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  • 200
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    Physics of Fluids 10 (1998), S. 1034-1036 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A power series mathematical solution is advanced for the problem of instability of an inviscid liquid sheet of parabolic velocity profile emanated from a nozzle into an inviscid gas. A comparison of the instability of a sheet of parabolic velocity profile with one of a uniform velocity profile is performed in order to deduce the effects of velocity profile relaxation on instability. The results show that for both antisymmetrical and symmetrical disturbances departure from uniformity of the velocity profile causes the instability to be reduced. The physical interpretation and practical implications of the present findings are discussed. © 1998 American Institute of Physics.
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