The performance of the k-epsilon and k-omega two-equation turbulence models was investigated in computational simulations of the neutrally stratified atmospheric boundary layer developing above various terrain types. ...
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The performance of the k-epsilon and k-omega two-equation turbulence models was investigated in computational simulations of the neutrally stratified atmospheric boundary layer developing above various terrain types. This was achieved by using a proposed methodology that mimics the experimental setup in the boundary layer wind tunnel and accounts for a decrease in turbulence parameters with height, as observed in the atmosphere. An important feature of this approach is pressure regulation along the computational domain that is additionally supported by the nearly constant turbulent kinetic energy to Reynolds shear stress ratio at all heights. In addition to the mean velocity and turbulent kinetic energy commonly simulated in previous relevant studies, this approach focuses on the appropriate prediction of Reynolds shear stress as well. The computational results agree very well with experimental results. In particular, the difference between the calculated and measured mean velocity, turbulent kinetic energy and Reynolds shear stress profiles is less than +/- 10% in most parts of the computational domain.
computational simulations of glass extrusion are performed to quantify the effects of material behavior and slip at the die/glass interface on the die swell. Experimental data for three glass types are used to guide t...
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computational simulations of glass extrusion are performed to quantify the effects of material behavior and slip at the die/glass interface on the die swell. Experimental data for three glass types are used to guide the computational study, which considers glass material to be viscous with and without shear thinning and viscoelastic using the Maxwell upper-convected model. The study starts with assuming no-slip at the glass/die interface to see if material behavior alone can explain the die swell results, and then considers slip using the Navier model where interface shear is directly proportional to the relative slip speed at the interface. Consistent with the possibility of slip and intended high viscosity applications, viscosity ranging from 10(7.4)-10(8.8)Pas was used. Based on optimization of the various input parameters required to achieve the measured die swell and ram force values, the study concludes that interface slip occurred as only extreme values of the shear thinning parameters provided an alternative.
Predicting phonation conditions that are benign to voice health remains a biomechanically relevant problem. Our objective is to provide insight into vocal fold (VF) hydration based on continuum-based VF models that ar...
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Predicting phonation conditions that are benign to voice health remains a biomechanically relevant problem. Our objective is to provide insight into vocal fold (VF) hydration based on continuum-based VF models that are able to compute VF stresses during phonation and a scheme for the extraction and generalization of such computational data based on the principle of linear superposition. Because VF tissue is poroelastic, spatial gradients of VF hydrostatic stresses computed for a given phonation condition determine VF interstitial fluid flow. The present approach transforms, based on linear superposition principles, the computed interstitial fluid velocities at the particular phonation to those at an arbitrary phonation condition. Intersititial fluid flow characteristics for a range of phonation conditions are compared. For phonation conditions with no or moderate collision, no dehydration per vibration cycle is predicted throughout the VF. For more severe collision conditions, tissue dehydration is restricted to a region close to the glottal surface. Interstitial fluid displacement in the VF is found to be heterogeneous and strongly dependent on the phonation condition. A phonation condition is found to exist for which dehydration peaks. The proposed method significantly expands the scope and relevance of conducting isolated numerical simulations of VF vibration. Copyright (c) 2014 John Wiley & Sons, Ltd.
Simulations of delivery of IgG1 Fab, an anti vascular epithelial growth factor (VEGF) macromolecular drug for the treatment of age related macular degeneration (AMD), from an episcleral thermally responsive-poly(N-iso...
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Simulations of delivery of IgG1 Fab, an anti vascular epithelial growth factor (VEGF) macromolecular drug for the treatment of age related macular degeneration (AMD), from an episcleral thermally responsive-poly(N-isopolyacrylamide) (NIPAM)-gel implant, arc made to evaluate the effectiveness of sustained delivery. The model of the human eye used in the above simulations is validated as far as its anatomical and physiological features by the agreement observed in comparing results of simulations of intravitreal fluorescein delivery with relevant experimental data. Simulations of IgG1 Fab delivery from an episcleral NIPAM-gel implant to the posterior eye, with the previously validated anatomically and physiologically correct model of the human eye, show that drug therapeutic levels in the posterior eye are sustained for 8 weeks similarly to those associated with intravitreal injection of IgG1 Fab. Thus, delivery of the macromolecular anti-VEGF drug IgG1 Fab from an episcleral NIPAM-gel implant seems to be a viable alternative to more invasive, risk-related delivery by intravitreal injection, as effective and sustainable as the latter. (C) 2014 Elsevier Ltd. All rights reserved
Kinesin is a walking motor protein that shuttles cellular cargoes along microtubules (MTs). This protein is considered as an information processor capable of sensing cellular inputs and transforming them into mechanic...
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Kinesin is a walking motor protein that shuttles cellular cargoes along microtubules (MTs). This protein is considered as an information processor capable of sensing cellular inputs and transforming them into mechanical steps. Here, we propose a computational model to describe the mechanochemical kinetics underlying forward and backward stepping behavior of kinesin motor as a digital circuit designed based on an adenosine triphosphate (ATP)-driven finite state machine. Kinetic analysis suggests that the backward stepping of kinesin is mainly driven by ATP hydrolysis, whereas ATP synthesis rises the duration of this stepping. It is shown that kinesin pausing due to waiting for ATP binding at limiting ATP concentration ([ATP]) and low backward loads could be longer than that caused by low rate of ATP synthesis under high backward loads. These findings indicate that the pausing duration of kinesin in MT-bound (M center dot K) kinetic state is affected by [ATP], which in turn affects its velocity at fixed loads. We show that the proposed computational model accurately simulates the forward and backward stepping behavior of kinesin motor under different [ATP] and loads.
Burdukov et al. [6] showed experimentally that enhancement of coal reactivity when micronized in a high-impact disintegrator mill makes it possible to attain self-igniting and self-sustaining (autothermal) compact-fla...
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Burdukov et al. [6] showed experimentally that enhancement of coal reactivity when micronized in a high-impact disintegrator mill makes it possible to attain self-igniting and self-sustaining (autothermal) compact-flame combustion in a cold environment, akin to that of heavy oil. We present computational modeling of autothermal combustion of mechanically-activated microground coal in a 5 MW pilot-scale combustor that complements the experiments of Burdukov et al. [7]. The aim was to verify the applicability of the comprehensive model of pulverized coal combustion to microground coal and to validate the submodel of the coal reactivity enhancement. The modeling follows the standard RANS approach to computing two-phase (reactive dispersed particles in gaseous medium) multi-component system, but with several new modifications related to particle heat transfer and their reactions. For reference, the study includes also the case with non-activated coal of the same granulation micronized in a vibrocentrifugal mill. The computations showed good agreement with the measurements and observations confirming that the model can reproduce the autothermal combustion of activated micronized coal and, thus, be employed with credible certainty to the computational design and optimization of new combustion (and gasification) devices fired with mechanically activated coal dust. (C) 2014 Elsevier Ltd. All rights reserved.
Temporal masking curves (TMCs) are often used to estimate cochlear compression in individuals with normal and impaired hearing. These estimates may yield a wide range of individual differences, even among subjects wit...
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Temporal masking curves (TMCs) are often used to estimate cochlear compression in individuals with normal and impaired hearing. These estimates may yield a wide range of individual differences, even among subjects with similar quiet thresholds. This study used an auditory model to assess potential sources of variance in TMCs from 51 listeners in Poling et al. [J Assoc Res Otolaryngol, 13:91-108 (2012)]. These sources included threshold elevation, the contribution of outer and inner hair cell dysfunction to threshold elevation, compression of the off-frequency linear reference, and detection efficiency. Simulations suggest that detection efficiency is a primary factor contributing to individual differences in TMCs measured in normal-hearing subjects, while threshold elevation and the contribution of outer and inner hair cell dysfunction are primary factors in hearing-impaired subjects. Approximating the most compressive growth rate of the cochlear response from TMCs was achieved only in subjects with the highest detection efficiency. Simulations included off-frequency nonlinearity in basilar membrane and inner hair cell processing;however, this nonlinearity did not improve predictions, suggesting that other sources, such as the decay of masking and the strength of the medial olivocochlear reflex, may mimic off-frequency nonlinearity. Findings from this study suggest that sources of individual differences can play a strong role in behavioral estimates of compression, and these sources should be considered when using forward masking to study cochlear function in individual listeners or across groups of listeners.
Stem cell migration is crucial in many biological processes such as embryogenesis, histogenesis, and stem cell biology. It is also an important process in physiology, and in medicine, it can contribute to develop effe...
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Stem cell migration is crucial in many biological processes such as embryogenesis, histogenesis, and stem cell biology. It is also an important process in physiology, and in medicine, it can contribute to develop effective stem cell therapies. While there is a large body of experimental evidence that attempts to understand the biological and physiological mechanisms governing stem cell activity in the organism, computational modeling studies are scarce. Because stem cell migration is affected by biological diversity and the complexity of the cells' microenvironment, experiments are hard to conduct and corresponding measurements are sophisticated. computational modeling is a good complementary method to help us understand this process. Here, a mini-review is presented discussing the existing efforts and the unsolved key issues in stem cell migration. In addition, existing computational models studying the migration of differentiated cells are briefly discussed in the context of how they can be applied to increase our understanding of the dynamics involved in stem cell migration: Particular emphasis is placed on how biomechanical aspects of migration are explored in these models.
We have performed computational modeling of the free-convective flow in the gap between two coaxial cylinders on the basis of complete Navier-Stokes equations from the viewpoint of the compressible gas model. To stabi...
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We have performed computational modeling of the free-convective flow in the gap between two coaxial cylinders on the basis of complete Navier-Stokes equations from the viewpoint of the compressible gas model. To stabilize numerical calculations of the viscous compressible gas at small Mach numbers, we used the preconditioning method based on the application of physical variables and the dual time stepping method. We have investigated the flow structure in the gap between the cylinders and the heat-transfer characteristics on the surface of the outer and inner cylinders at various Rayleigh numbers.
Gene regulatory interactions underlying the early stages of non-genotoxic carcinogenesis are poorly understood. Here, we have identified key candidate regulators of phenobarbital (PB)-mediated mouse liver tumorigenesi...
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Gene regulatory interactions underlying the early stages of non-genotoxic carcinogenesis are poorly understood. Here, we have identified key candidate regulators of phenobarbital (PB)-mediated mouse liver tumorigenesis, a well-characterized model of non-genotoxic carcinogenesis, by applying a new computational modeling approach to a comprehensive collection of in vivo gene expression studies. We have combined our previously developed motif activity response analysis (MARA), which models gene expression patterns in terms of computationally predicted transcription factor binding sites with singular value decomposition (SVD) of the inferred motif activities, to disentangle the roles that different transcriptional regulators play in specific biological pathways of tumor promotion. Furthermore, transgenic mouse models enabled us to identify which of these regulatory activities was downstream of constitutive androstane receptor and beta-catenin signaling, both crucial components of PB-mediated liver tumorigenesis. We propose novel roles for E2F and ZFP161 in PB-mediated hepatocyte proliferation and suggest that PB-mediated suppression of ESR1 activity contributes to the development of a tumor-prone environment. Our study shows that combining MARA with SVD allows for automated identification of independent transcription regulatory programs within a complex in vivo tissue environment and provides novel mechanistic insights into PB-mediated hepatocarcinogenesis.
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