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We investigated hydrodynamic phenomena inside several passive microfluidic mixers using a Lattice Boltzmann method (LBM) based on particle mesoscopic kinetic equations. Mixing processes were simulated in a Slanted grooved micro-mixer (SGM), a Staggered herringbone grooved micro-mixer (SHM), and a Bi-layered staggered herringbone grooved micro-mixer (BSHM). Then, the effects of six geometric mixer parameters (i.e., groove height to channel height ratio, groove width to groove pitch length ratio, groove pitch to groove height ratio, groove intersection angle, herringbone groove asymmetric ratio and bi-layered groove asymmetric ratio) on mixing were investigated using computed cross-flow velocity and helicity density distributions in the flow cross-section. We demonstrated that helicity density provides sufficient information to analyze micro helical motion within a micro-mixer, allowing for micro-mixer design optimization.

The surface of first part of study is textured with microscopic pillars of prototypical top geometries as a rectangle. The second one is textured with a hierarchical structure, composed of secondary pillar structures added on the primary texture. The length ratio between two scales of texture is 1:16. We evaluated the non-wetting characteristics of two types of surfaces by measuring CAs as well as the transition from the Wenzel’s to Cassie’s regimes. We measure the Contact angles (CAs), using the Lattice Boltzmann model (LBM), for two different surface configurations. We evaluated the effect of the hierarchical structure; the robustness of the Cassie regime is enhanced and the apparent contact angle is increased by the secondary structures. This is achieved by increasing the energy barrier against the transition between wetting and non-wetting regimes.

Conventional patterned wettability with a periodic checkerboard pattern shows intermediate critical heat flux (CHF) between uniform hydrophilic and hydrophobic surfaces. To solve this high superheat problem and maintain the high CHF, we propose adaptive fraction control of the pitch of hydrophobic dots. With actual heat source, the temperature distribution is the highest at the center and decreases as the radius from the center increases. Patterned wettability in the high temperature region is created with a low area fraction of hydrophobic dots, while the area fraction gradually increases with distance from the center. Using this adaptive fraction control, CHF can be avoided in the center region and superheat can be dropped for nucleation in the outer region at low temperature. However, if the concentration gradient of hydrophobic dots is too large, nucleation at the center of surface will be suppressed and boiling crisis will occur in the outer region. Therefore we also optimized the concentration of hydrophobic dots with respect to CHF and start of nucleation. In this research, a multiphase single component lattice Boltzmann model was used for the simulation. The simulation model is modified to establish heterogeneous wettability. The effects of size and concentration of hydrophobic dots are analyzed by observing the tendency of CHF, superheat, and local Nusselt number.

High-resolution large-eddy simulation of the flow over a large wind farm (64 wind turbines) is performed using the HIGRAD/FIRETEC-WindBlade model, which is a high-performance computing wind turbine–atmosphere interaction model that uses the Lagrangian actuator line method to represent rotating turbine blades. These high-resolution large-eddy simulation results are used to parameterize the thrust and power coefficients that contain information about turbine interference effects within the wind farm. Those coefficients are then incorporated into the WRF (Weather Research and Forecasting) model in order to evaluate interference effects in larger-scale models. In the high-resolution WindBlade wind farm simulation, insufficient distance between turbines creates the interference between turbines, including significant vertical variations in momentum and turbulent intensity. The characteristics of the wake are further investigated by analyzing the distribution of the vorticity and turbulent intensity. Quadrant analysis in the turbine and post-turbine areas reveals that the ejection motion induced by the presence of the wind turbines is dominant compared to that in the other quadrants, indicating that the sweep motion is increased at the location where strong wake recovery occurs. Regional-scale WRF simulations reveal that although the turbulent mixing induced by the wind farm is partly diffused to the upper region, there is no significant change in the boundary layer depth. The velocity deficit does not appear to be very sensitive to the local distribution of turbine coefficients. However, differences of about 5% on parameterized turbulent kinetic energy were found depending on the turbine coefficient distribution. Therefore, turbine coefficients that consider interference in the wind farm should be used in wind farm parameterization for larger-scale models to better describe sub-grid scale turbulent processes.

Stacked graphene-oxide (GO) membranes have been reported to have promising potential for desalination. One key issue in the development of such membranes is understanding the atomistic water-permeation mechanism determined by the highly variable nature of GO (including membrane morphology, surface chemistry, osmotic pressure, and surface area). To clearly understand this variability, not only individual but also synergistic effects, i.e., the nonlinear cumulative effects of membrane properties, should be investigated. Hence, this paper explores how lateral and vertical permeation mechanisms differ with changes in the morphology and surface chemistry, either discretely or simultaneously, using both experiments and simulations. Experiments reveal that the GO water-permeation performance is dominated by the heterogeneous structural and chemical nature of GO. To investigate individual and synergistic effects on water dynamics, we performed molecular-dynamics simulations. The synergistic effects were more marked on the lateral permeation mechanisms than on the vertical mechanism in GO membranes. When the membrane nanochannels had a narrow intersheet distance or no gap overlap, the lateral permeation mechanism was found to be completely different owing to the interplay between these properties.

Single cell characterization of protein epitopes is usually associated with fluorescent Flow Cytometry, which can be both costly and time consuming to optimize for multiple epitopes. To overcome the limitations of this method, we introduce Genomic Cytometry that utilizes cellular indexing of transcriptomes and protein epitopes by next-generation sequencing (CITE-seq) technology instead of flow. Genomic Cytometry is based on staining cells with antibodies conjugated to unique 15-bp DNA barcodes instead of fluorophores. After sequencing and data analysis the barcode read number can be linked to protein abundance. We utilized Genomic Cytometry to simultaneously analyze over 50 different protein biomarkers in a single scalable workflow. The application is ideal for characterization of heterogeneous cell populations such as tumors including their immune content. In addition to profiling a number cell surface protein markers that exceeds capabilities of traditional flow cytometry the technology allows for assessment of single cell gene expression data to link protein and genomic data sets. Corresponding pre-analytical and 10X Genomics-based analytical workflows were established for human PBMC samples, as well as for solid tissue including tumor specimens derived from mouse syngeneic tumor models. Data analysis pipelines were developed and validated that includes custom scripts. We ran a number of cross-platform validation studies (mouse and human cells) and found that the Genomic Cytometry is highly correlative to fluorescent flow. Multiplex methods were implemented to allow pooling of samples to reduce biases related to sample manipulation. The method enables large-scale single-cell sequencing experiments. In proof of concept experiments, a number of preclinical models, such as MC38 and H22, were deeply analyzed using CITE-seq approach. Genomic Cytometry enables rapid and cost effective characterization of both immune-oncology (I-O) models and modes of action of new I-O molecules in order to develop more differentiated therapeutics. Citation Format: Joon Sang Lee, Shannon McGrath, Emma Wang, Maximilian Rogers-Grazado, Yu-an Zhang, Natalia Malkova, Jack Pollard, Alexei Protopopov. Genomic cytometry characterization of preclinical models for development of immune-oncology therapeutics [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 174.

During flow boiling in microchannels, the physics of a bubble is closely related to the heat transfer performance of different hydrophobic patterns. However, the heat transfer properties of various patterns are yet to be investigated. In this study, we conducted a numerical investigation into bubble coalescence characteristics and heat transfer performance of three patterns, namely crosswise, parallel, and dotted patterns, for flow boiling in a microchannel, and evaluated the influence of the hydrophobic area fraction for each pattern. In the transport equation, we employed a mass transfer model based on a two-phase mixture flow for the vaporization and condensation processes. In addition, we used the volume-of-fluid method to track the dispersed phase's interface using the local volume fraction. Although the parallel pattern at low mass flux facilitating bubble movement exhibited a good heat transfer performance, the dotted pattern displayed a better performance at high mass fluxes due to its higher nucleation site density. Additionally, very wide or narrow hydrophobic areas are unsuitable for heat transfer. Narrow areas limit bubble nucleation. A hydrophobic area fraction of 0.165 for the crossed pattern and of 0.32 for the parallel and dotted pattern produced the best heat transfer performances.

Active control technology of particles in a microchannel using optical force, is an area of interest to scientists in various field today. The optical force is generated by momentum change caused by refraction and reflection of light. The generated optical force changes the surface of the particle to change the angle of incidence of light, so that the force generated by the change in the momentum of light changes. Interpreting this technique through simulation is a complex task. The deformation of a particle, interaction between the surrounding fluid and particle, and reflection and refection of light need to be analyzed simultaneously to be simulated. In this study, a deformable particle in a microchannel with optical sources was simulated with a three-dimensional lattice Boltzmann immersed boundary method. The beam originating from the optical source is analyzed by dividing it into individual ray. To calculate the optical forces acting on the particle, the intensity, momentum and direction of ray were calculated. First, the optical separator problem with one optical source was analyzed by measuring the distance traveled by the optical force. Second, the optical stretcher problem with two optical sources was studied by analyzing the relationship between the intensity of the optical source and the deformation of the particles.

Microchannel flow boiling is a cooling method studied in microscale heat-cooling, which has become an important field of research with the development of high-density integrated circuits. The change in microchannel surface characteristics affects thermal fluid behavior, and existing studies have optimized heat transfer by changing surf ace wettability characteristics. However, a surface with heterogeneous wettability also has the potential to improve heat transfer. In this case, heat transfer would be optimized by applying the optimal heterogeneous wettability surface to channel flow boiling. In this study, a change in cooling efficiency was observed, by setting a hydrophobic and hydrophilic wettability pattern on the channel surface under the microchannel flow boiling condition, using a lattice Boltzmann method simulation. In the rectangular microchannel structure, the hydrophobic-hydrophilic patterned wettability was oriented perpendicular to the flow direction. The bubble nucleation and the heat transfer coefficient were observed in each case by varying the length of the pattern and the ratio of the hydrophobic-hydrophilic area. It was found that the minimum pattern length in which individual bubbles can occur, and the wettability pattern in which the bubble nucleation-departure cycle is maintained, are advantageous for increasing the efficiency of heat transfer in channel flow boiling.

The compressible filtered Navier-Stokes equations were solved using a second order accurate finite volume method with low Mach number preconditioning. A dynamic subgrid-scale stress model accounted for the subgrid-scale turbulence. The study focused on the effects of buoyancy and rotation on the structure of turbulence and transport processes including heat transfer. Several different physical arrangements were studied as outlined below. The effects of buoyancy were first studied in a vertical channel using large eddy simulation (LES). The walls were maintained at constant temperatures, one heated and the other cooled, at temperature ratios of 1.01, 1.99 and 3.00. Results showed that aiding and opposing buoyancy forces emerge near the heated and cooled walls, respectively, while the pressure gradient drives the mean flow upwards. Buoyancy effects on the mean velocity, temperature, and turbulent intensities were observed near the walls. In the aiding flow, the turbulent intensities and heat transfer were suppressed and the flow was relaminarized at large values of Grashof number. In the opposing flow, however, turbulence was enhanced with increased velocity fluctuations. Another buoyancy study considered turbulent flow in a vertically oriented annulus. Isofiux wall boundary conditions with low and high heating were imposed on the inner wall while the outer wall was adiabatic. Comparisons were made with available experimental data. The re­ sults showed that the strong heating and buoyancy force caused distortions of the flow structure resulting in reduction of turbulent intensities, shear stress, and turbulent heat flux, particularly near the heated wall. Flow in an annular pipe with and without an outer wall rotation about its axis was first investigated at moderate Reynolds numbers. A non-uniform grid in the radial direction yielded very accurate solutions using a reasonable number of grid points. The mean and turbulent quantities of the non-rotating annular pipe flow have been compared with the available exper­ imental and numerical data. When the outer pipe wall was rotated, a significant reduction of turbulent kinetic energy was realized near the rotating wall and the intensity of bursting effects appeared to decrease. This modification of the turbulent structures was related to vor­ tical structure changes near the rotating outer wall. It has been observed that the wall vortices were pushed in the direction of rotation and their intensity increased near the non-rotating wall. The consequent effect was to enhance the turbulent kinetic energy and increase the heat transfer coefficient there. Secondly, a large eddy simulation has been performed to investigate the effect of swirl on the heat and momentum transfer in an annular pipe flow with a rotating inner wall. The numerical results are summarized and compared with the experimental results of previous studies. The simulations indicated that the Nusselt number and the wall friction coefficient increased with increasing rotation speed of the wall. It was also observed that the axial velocity profile became flattened and turbulent intensities were enhanced due to swirl. This modification of the turbulent structures was closely related to the increase of the Nusselt number and the friction coefficient. As a part of the study of rotation effects, large eddy simulation of a rotating ribbed channel flow with heat transfer was investigated. The rotation axis was parallel to the spanwise direc­ tion of the parallel plate channel. Uniform heat flux was applied to the channel for two rates of rotation. The results showed that the rotation consistently altered the turbulent structures near the walls. Near the stable (leading) side, the turbulent intensities and heat transfer were suppressed, but turbulence was enhanced with increasing shear stress and turbulent kinetic energy near the unstable (trailing) side.

In this study, we analyzed the rheological characteristics of double emulsions by using a three-dimensional lattice Boltzmann model. Numerical simulations indicate that interactions between multiple interfaces play a vital role in determining the shear stress on interfaces and affect deformations, which influence the relative viscosity of double emulsions. The large shear stress induced by droplets in contact increases the relative viscosity for high volume fractions. The double emulsions also show shear-thinning behavior, which corresponds with the Carreau model. The interfacial interference between the core and the deforming shell cause the relative viscosity to increase with increasing core-droplet radius. Finally, we investigated the dependence of the double-emulsion viscosity on the core-droplet viscosity. At high shear rates, the relative viscosity increases with increasing core-droplet viscosity. However, the trend is opposite at low shear rates, which results from the high inward flow (Marangoni flow) at low core-droplet viscosity.

Background: The impact of various coronary lesion geometries on fractional flow reserve (FFR) is poorly understood. Methods and Results: A total of 1552 coronary lesions in 1236 patients from a prospective Interventional Cardiology Research In-cooperation Society Fractional Flow Reserve and Intravascular Ultrasound registry were assessed using quantitative coronary angiography, intravascular ultrasound, and FFR. Computational fluid dynamics simulation was performed for theoretical validation. Patients with complex geometries, such as longitudinal eccentricity, cross-sectional eccentricity, and surface roughness, showed significantly lower FFR values. In multivariable analysis, distal longitudinal eccentricity (adjusted odds ratio, 1.55; 95% confidence interval, 1.04–2.87; P =0.031), cross-sectional eccentricity (adjusted odds ratio, 1.65; 95% confidence interval, 1.27–2.14; P P =0.033), as well as male sex, left anterior descending artery territory, proximal location, high degree of diameter stenosis, long lesion, and high plaque burden, were identified as independent predictors for significantly low FFR values (≤0.80). Computational simulation supported the impact of lesion geometry on FFR. Conclusions: The complex coronary lesion geometries were independently associated with reduced FFR values. The visual–functional mismatch between coronary angiography and FFR could be partly attributable to local geometric factors. Clinical Trial Registration: URL: https://www.clinicaltrials.gov . Unique identifier: NCT01366404.

Recently, the development of durable hydrophobic surfaces has received much attention, with anti-icing applications in harsh environments such as aircrafts, wind turbines, power lines, and marine vessels. In this paper we describe a design methodology employing a lattice Boltzmann method to determine the optimal geometry of microstructures to achieve superhydrophobicity. We describe a top-down fabrication method to form superhydrophobic micro-hierarchical metal surface using photolithography, nanoimprinting, and continuous metal-to-metal replication using pulse-reverse-current electrochemical deposition. The surfaces were formed of nickel, which has a large hardness and is resistant to corrosion, making it suitable for use in harsh external conditions. We compared the measured wettability of fabricated micro-hierarchical metal surface with that from numerical simulations. The contact angle and contact angle hysteresis of four metal surfaces were measured (i.e., a bare surface, a random nanostructured surface, an engineered nanostructured surface, and an engineered hierarchical structured surface), and the anti-icing properties of these four metal surfaces were investigated.

We present the results of measuring the viscometric flow of concentrated rigid-sphere suspensions with constant-viscosity matrices, both Newtonian (silicone oil) and non-Newtonian (Boger fluid: corn syrup (79.4%)–glycerin (19.8%)–4%PAA water (0.78%)). Various problems with the measurements are discussed, including settling due to density differences. The effect of sphere roughness on shear rheology is a main concern of the work. The viscosities of silicone oil and Boger fluid suspensions were increased by increasing sphere roughness, and the normal stress difference N1 − N2 in the Boger fluid suspension also increased with roughness.

We simulate an emulsion system under simple shear rates to analyze its rheological characteristics using the lattice Boltzmann method (LBM). We calculate the relative viscosity of an emulsion under a simple shear flow along with changes in temperature, shear rate, and surfactant concentration. The relative viscosity of emulsions decreased with an increase in temperature. We observed the shear-thinning phenomena, which is responsible for the inverse proportion between the shear rate and viscosity. An increase in the interfacial tension caused a decrease in the relative viscosity of the decane-in-water emulsion because the increased deformation caused by the decreased interfacial tension significantly influenced the wall shear stress. § 이 논문은 대한기계학회 2014년도 추계학술대회(2014. 11. 11.-14., 김대중컨벤션센터) 발표논문임. † Corresponding Author, joonlee@yonsei.ac.kr C 2015 The Korean Society of Mechanical Engineers

Sensitivity studies of blade angle and twisted angle are numerically investigated to optimize the Savonius blade. As blade angle increases, the contact area between blade and wind decreases, showing the suppression of the vortex generation near blade. Compared to the blade angle of 0 degree, the blade angle of 20 degree shows about 2.6% increment of power efficiency. Based on the blade angle of 20 degree, sensitivity studies of the twisted angle are performed. The result indicates that the adjustment of the twisted angle causes the torque of blade to increase. Optimized blade can suppress the formation of the vortex structure in rear region. Also, wind flows without disturbance of vortex when passing through the optimized blade. The 1kw vertical wind turbine system with optimized blade can generate 4442.2kWh per year and have 53% capacity factor.

To explore the effect of hydrophobicity on cloud cavitation, the behaviors of cloud cavitation over the Clark-Y hydrofoil under various slip condition were investigated. Large eddy simulation (LES) was used for the turbulence model. The mass transfer model, which was considered to be a two-phase mixture flow, was used for the vaporization and condensation processes in the transport equation. The volume of fluid (VOF) scheme was used to track the interface of the dispersed phase by using the local volume fraction. Slip strength was controlled using the friction coefficient. The cavitation model in this study agreed with experimental and previous numerical studies. The results show that as the slip strength grew stronger, the friction drag was reduced; the cavity became longer and the shedding frequency decreased. For this reason, cloud cavitation is stabilized in condition of strong slip strength. Thus, a relatively weak re-entrant jet occurs in conditions of strong slip strength which gives rise to small amount of vapor shedding at the closure. This means that cloud cavitation instability was alleviated as the hydrophobicity increased.

This is a one-step POC biosensor that guarantees rapid assay times, low-cost analysis, simple handling, stability, and is easy to mass product. However, it has several drawbacks such as limited sample volume and relatively low sensitivity. To overcome these disadvantages, we have designed and fabricated the µ-PAD to confine fluid flow by creating a hydrophobic channel in the paper to improve the sensitivity. The channel pattern was drawn by a computer-aided design program and directly printed by a commercially available wax printer which generates the hydrophobic channel pattern. While maintaining a constant sample, absorption, and conjugation pad, the width of the detection pad was reduced from 5 mm to 2 mm at intervals of 1 mm. The intensity of bands from the single- and double-orifice patterns increased identically compared with the device with no orifice. The relative intensity of the signal bands increased from 141 to 158. Also, numerical simulation was performed to validate the experimental result by using lattice Boltzmann method. We observed that the sensitivity was enhanced at a specific detection pad width (3 mm). Therefore, our simple structural change of the channel led to improve the colorimetric intensity. Cortisol, which is a known stress biomarker, was used to validation the device, an enhanced signal was obtained indicating that our device can be used for the detection psychological stress in humans.

An emulsion system was simulated under simple shear rates to analyse its rheological characteristics using the lattice Boltzmann method. The relative viscosity of an emulsion under a simple shear flow along with changes in temperature, shear rate, surfactant concentration and droplet size was calculated. The relative viscosity of emulsions decreased with increase in temperature. The shear thinning phenomena explaining the inverse proportion between shear rate and viscosity were observed. An increase in the surfactant concentration caused an increase in the relative viscosity for a decane-in-water emulsion, because the increased deformation caused by the decreased interfacial tension significantly influenced the wall shear stress. An increase in droplet size caused a decrease in the relative viscosity and smaller shear thinning behaviour because of decreased aggregational and repulsive forces within the emulsion system.

Droplet movement on heterogeneous surfaces was simulated with a computational fluid dynamics (CFD) modeling method known as the lattice Boltzmann method (LBM). Motions of droplets were also analyzed in terms of kinetic, gravitational, and surface free energy. The first part of this study focused on the transportation of droplets by chemical actuation on a surface divided by five chemical bends, each having a different hydrophobicity, establishing a gradual progression from hydrophobic to hydrophilic phases. The second part of this study focused on the transportation of droplets by a surface with a structural gradient having its two halves textured with microscopic pillars, corresponding to a difference in hydrophobicity. In the first part of the study, the numerical results showed that a droplet tended to move to a less hydrophobic region with surface free energy reduction by spreading and decaying. This indicates that the surface free energy was converted into kinetic energy and gave mobility to the droplet. In the second part, three steps of the droplet motion were observed: spreading, recoiling, and translation.

The rheology studies of complex fluid with deformable particles such as red blood cells (RBCs) are highly interested for a broad range of research works in biological systems, the cosmetic industries, mining and petroleum industries and home products. However, predicting the rheological behavior of soft particles in matrix is one of the most challenging and complicated problems in material and fluid sciences. The complication is arisen by the particles collision and interactions with the surrounding fluid. A full description of the rheology of soft particles requires a complete understanding of the deformation of particles itself [1], interactions among particles, interaction between the particles and the surrounding fluid [2], and interactions between channel and particles. Thus consideration of above factors can lead to a better understanding of the rheological behavior of suspensions with soft particles. A suspension system of soft particles which is composed of a fluid-filled interior covered by an elastic membrane is simulated to study its rheological characteristics under various condition as shown in Fig. 1. In this study, the rheological behaviors of the soft particle suspension are observed with respect to several variations, for instance, shear rate, volume fraction, deformability of the particles, and various channel. A combination model of the three dimensional lattice Boltzmann method (LBM) and the immersed boundary method (IBM) are used to simulate these suspension systems. With the aid of a numerical simulation, which can help in visualizing the particle behavior, and correlate it to rheological behavior of each particles, the physics behind the relative viscosity change was analyzed. To validate the soft particle model, the ratio of length to width for the stretching of soft particle was measured. For the single particle deformation in the flow, the boundary thickness was analyzed, which was related to the repulsive force critical for the interaction between the particle and wall, the effect of stiffness of RBCs on transit time in a microchannel was analyzed, which was proven to not be crucial for modeling of the soft particle. To see the interaction between wall property and suspension flow, soft particles in hydrophobic and hydrophilic surface microfluidic channels was simulated. To see the interaction among cells, red blood cells in shear flow with various aggregation condition was simulated The time for cells to pass through the channel is measured at different values of shear modulus, along with analysis of the degree of deformation and transit time in Fig.2. Moreover, the velocity and deformation of cells as a function of boundary thickness and the effect of volume conservation stiffness were studied in Fig.3. The surface properties of the channel are changed using the tangential momentum accommodation coefficient on the channel boundary to set the hydrophobic surface in the simulation. The relative apparent viscosity is used to calculate systematic flow resistance in Fig.4. The results indicate that the flow rate and flow profile varied with respect to the surface property under a constant pressure gradient in Fig.5.

We conducted a large eddy simulation of the stable boundary layer in order to investigate the coherent structure of the Kelvin–Helmholtz instability (KHI). The simulations were performed using the initial conditions based on the Beaufort Sea Arctic Stratus Experiment. We used the Richardson criteria and the linear stability analysis methods to detect the KHI and to adopt the eigenvalue and the two-point correlation methods to identify the vortex cores near the KHI region. In the two-point correlation analysis, the rotating configuration of the KHI varied in angles and lengths, according to the difference in the distance to the inversion layer. These vortex cores were divided into four components in different directions, defined by the signs of the x and y vorticities (Wx and Wy, respectively), and the vortex cores of the two components related to the negative Wy were elongated along the streamwise direction. The ratio between the sweeps and the ejections exhibited a linear trend as the boundary layer became more stable. Also, the sweep motion was dominant to the ejection motion for a high-stability index of 1.63. Furthermore, the plot of the vortex angles versus the stability index illustrated a linear relationship, indicating that the varying trends of the vortex angles were independent from the distance to the inversion layer in a sensitivity study of the vortex angle.

Small-scale dynamic experiments were performed using explosive charges shallow buried in water or in various soil types at differing initial states. Using the results from these experiments, it was discovered that the amount of momentum transferred to a rigid target is relatively independent of soil type but that mostly depends on the initial air-filled void content of the soil and the effect of water content on the yield strength of the soil. Data from quasi-static tests of soils at a number of initial states along with known results for the higher pressure behavior of water-quartz mixtures were combined to construct soil models at various initial soil states. Computations were performed in order to evaluate the sensitivity of rigid plate loading to various facets of constitutive behavior described in the soil models in order to better understand the causes for the newly revealed parametric relationship. The computations closely matched the experimental results, thereby supporting theories regarding the parametric relations. The results from the computations offered insight into the mechanics behind the parametric relations.

The effect of CO2 on the opening of stomata in the intact leaf of Commelina communis has been investigated. Full opening of stomatal apertures(around 18 μm) was achieved in the intact leaf by addition of CO2(900 μmol mol -1 ). At 90 minutes, the stomatal apertures of leaves treated with CO2 free air were reduced. In contrast, stomata opened most widely with the treatment of CO2 air at 90 minutes. The effects of light, CO2 air and CO2 free air on the change of membrane potential difference(PD) were measured. Fast hyperpolarization of guard cell membrane PD was recorded reaching up to -12 mV in response to light. If CO2 free air was given firstly, there was no response. When light was given after CO2 free air, the light effect was very clear. At the onset of CO2 air, the PD showed a dramatic hyperpolarization to about -25 mV. Changes in the pH of apoplast in intact leaves in response to CO2 air were observed. CO2 air caused a change of 0.4 pH unit. Therefore, it can be hypothesized that CO2 flowing could stimulate proton efflux which is a necessary precursor of stomatal opening.

We investigate the path selection (navigation) of a single moving vesicle in a microfluidic channel network using a lattice Boltzmann-immersed boundary method (IBM). The lattice Boltzmann method is used to determine incompressible fluid flow with a regular Eulerian grid. The IBM is used to study a vesicle with a Lagrangian grid. Previous studies of microchannels suggest that the path selection of a bubble at a T-shaped junction depends on the flow rates in downstream channels. We perform simulations to observe the path selection of a vesicle with three different capillary numbers at a tertiary junction. The hypothesis that higher flow rate determines path selection is not validated by our data on low capillary number (Ca ≤ 0.025) of a vesicle in tertiary downstream channels. We use the resultant velocity hypothesis to explain the path selection of a vesicle in microfluidic systems. Our results suggest that, for a low capillary number, instead of being affected by the viscous force from a high flow rate, a vesicle in a tertiary junction tends to follow the resultant velocity hypothesis. We analyze the change in hydrodynamic resistance caused by the movement of a vesicle to support the resultant velocity hypothesis. We also study the residence time of a vesicle at a junction for different cases and analyze the relationship between the residence time and the resultant velocity. The resultant velocity (rather than the flow rate in individual channels) can be used to predict the path selection of a vesicle in low capillary number. In addition, the residence time of vesicle is decided by average velocity of each channel.

The interaction between two deformable droplets consists of unique dynamic characteristics that are not present during the interaction of solid bodies. A thin film of surrounding fluid is entrapped between the droplets and then drains out under the influence of an external force before the droplets can adhere or coalesce. The drainage process during the coalescence of two similar droplets has received significant research interest due to the presence of dynamical interactions between the droplets. Surprisingly, the film drainage process between two partial engulfing immiscible droplets has not been studied yet. Using a numerical study, we investigate the film drainage between two partial engulfing immiscible droplets. We vary the interfacial tensions between the droplets and surrounding fluid in wide ranges to observe the film drainage time between the droplets. Based on our simulations, we identified three regimes of fast, intermediate and delayed drainage. We found that the film drainage of two immiscible droplets exhibits additional flow into or out of the film, which does not exist in the film drainage of identical droplets. This additional flow can either increase or decrease the rate of film drainage between the droplets, depending on the interfacial tension of droplets with the surrounding fluid and the interfacial tension of the two immiscible droplets.

A combination of soil characterizations, computations and small-scale experiments were performed in order to better understand the behavior of shallow-buried explosives. The constitutive behavior of the soil was determined using a combination of high pressure quasi-static tests and effective stress theory; the motion of rigid objects impacted by the material flow resulting from blast experiments was measured by use of high-speed digital video photography. Computations that simulated the blast experiments were performed by use of an arbitrary Lagrangian Eulerian (ALE) treatment in a nonlinear finite element code. We used a factorial design approach to deduce the underlying mechanics of such systems. Using this approach, we found that, for water and for dry and partially saturated granular materials lower deviatoric yield strength was a key factor which caused sand or water to flow more readily thereby producing higher levels of momentum loading to bodies in close proximity to the buried explosive. We found that higher bulk stiffness and mass density were moderately important factors although they were less significant than was the shear strength of the medium containing the explosive.

Atomic scale friction of graphene strongly depends on the commensurability which is related to the rotational motion. Despite the crucial role of the rotational motion of bi-layer graphene, there is no direct study of it. In this paper, the mechanism of the rotational motion of the graphene flake on graphene substrate using molecular dynamics simulations was studied. Simulation model with rotational force was developed to observe the friction behavior of graphene. Various parametric studies were performed by controlling variables such as flake size, load, orientation of rotational force and spring constant. Graphene flakes with commensurate orientations showed a clear stick-and-slip motion during the rotation. Variation of flake size and load affected adhesion force which caused the nonlinear friction behavior. Two specific stacking orientations, namely AA and AB stacking, showed relatively stable rotational motion compared to others. Translational motion was also observed simultaneously during slip event of AA and AB stacking orientation. Finally, based on these overall observations, the pathway of flake by rotation was explained along with the effect of spring constant.

A 2-year-old girl, previously healthy, was brought to the emergency department because of significant cramping abdominal pain with recurrent hematochezia after an accidental hydrogen peroxide enema (35%, 5 mL) by her caregiver. She was hospitalized to the pediatric department and treated with nothing per mouth, intravenous fluid and parenteral antibiotic therapy. Laboratory, radiologic and endoscopic evaluation was performed during the admission period. She was discharged in a fully recovered state on the tenth hospital day, and this is the first case report of acute chemical colitis by accidental hydrogen peroxide enema in children.

Introduction: Treatment of head and neck squamous cell cancer (HNSCC) frequently includes surgery, radiation, chemotherapy, targeted agents, and increasingly combination of the former with immune checkpoint inhibition. An understanding of the mechanisms mediating response to these therapies as well as biomarkers that can better tailor therapy on an individualized basis and reduce treatment-related toxicity would benefit patients. Methods: To uncover these mechanisms and biomarkers, we analyzed whole transcriptome RNA-Seq data of two different cohorts of head and neck squamous cell cancer patients: pre and post-treatment samples from radiation therapy and pre-treatment samples from anti-PD1 therapy. We evaluated the abundance of eight immune and two stromal cell populations and pathway activity changes by using Gene Set Variation Analysis (GSVA). Results and Conclusions: Following radiation genes involved in epithelial to mesenchymal transition, extracellular matrix remodeling, and wound healing are upregulated. Additionally, there is evidence of tumor microenvironment remodeling post-radiation consistent with increased fibroblast abundance and decreased immune cell infiltration. Furthermore, innately resistant tumors to anti-PD1 also display similar signatures of gene regulation, suggesting a common mechanism mediating response to both types of treatment. Notably, these signatures are strongly correlated to activation of the transforming growth factor (TGF-β) signaling pathway and suggest that attenuating its signaling may improve anti-PD-1 response and also response to radiation treatment in head and neck squamous cell cancer. Citation Format: Joon Sang Lee, Michele Sanicola-Nadel, Alexei Protopopov, Emma Wang, Joachim Theilhaber, Tun Tun Lin, Michael Korrer, Sohini Roy, Young Jun Kim, Jack Pollard. Discovery of biomarkers predicting response to radiation and anti PD1 therapy in head and neck squamous cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5140.

Modeling circulatory system can help the diagnosis of vessels and predict future risk of diseases. However, the complicated geometry, elasticity of blood vessel, and pulsatile flow of blood put the accurate circulatory system modeling in a challenging task. Various modeling methods are developed to improve its accuracy. LBM solver can easily convert medical image data into lattice grid coordinates. Non-Newtonian model considers viscoelasticity of blood. Also, wall boundary treatment using ghost nodes improves the accuracy of fluid modeling. Finally, impedance boundary condition can successfully develop the effect of wave reflection at the outlet of computational domain. These efficient modeling techniques are not yet well combined each other. The purpose of this paper is to apply these methods in the circulatory system modeling to observe the relationship between vessel elasticity and blood flow wave reflection. Flow rate differences and shear stresses are analyzed by reflecting various vessel ages.

Next Generation Sequencing (NGS) has revolutionized biomedical research in recent years. It is now commonly used to identify rare variants through re-sequencing individual genomes. Due to the cost of NGS, researchers have considered pooling samples as a cost-effective alternative to individual sequencing. In this article, we consider the estimation of allele frequencies of rare variants through the NGS technologies with pooled DNA samples with or without barcodes. We consider three methods for estimating allele frequencies from such data, including raw sequencing counts, inferred genotypes, and expected minor allele counts and compare their performance. Our simulation results suggest that the estimator based on inferred genotypes overall performs better than or as well as the other two estimators. When the sequencing coverage is low, biases and MSEs can be sensitive to the choice of the prior probabilities of genotypes for the estimators based on inferred genotypes and expected minor allele counts so that more accurate specification of prior probabilities is critical to lower biases and MSEs. Our study shows that the optimal number of barcodes in a pool is relatively robust to the frequencies of rare variants at a specific coverage depth. We provide general guidelines on using DNA pooling with barcoding for the estimation of allele frequencies of rare variants.

A red blood cell (RBC) in a microfluidic channel is highly interesting for scientists in various fields of research on biological systems. This system has been studied extensively by empirical, analytical, and numerical methods. Nonetheless, research of predicting the behavior of an RBC in a microchannel is still an interesting area. The complications arise from deformation of an RBC and interactions among the surrounding fluid, wall, and RBCs. In this study, a pressure-driven RBC in a microchannel was simulated with a three-dimensional lattice Boltzmann method of an immersed boundary. First, the effect of boundary thickness on the interaction between the wall and cell was analyzed by measuring the time of passage through the narrow channel. Second, the effect of volume conservation stiffness was studied. Finally, the effect of global area stiffness was analyzed.

Background— Intravascular optical coherence tomography (OCT) imaging provides limited information on the functional assessment of coronary stenosis. We evaluated a new approach to OCT image–based computation modeling, which can be used to estimate the fractional flow reserve (FFR) in patients with intermediate coronary stenosis. Methods and Results— Ninety-two patients with intermediate diameter stenosis in the left anterior descending artery underwent both FFR measurement with pressure wires and OCT examination. Using the OCT data, a computational fluid dynamics algorithm was used to calculate the computational FFR (FFR OCT ). The diagnostic performance of the FFR OCT was assessed based on the pressure wire–based FFR. The median FFR and FFR OCT values were 0.86 (0.79–0.89) and 0.89 (0.82–0.94), respectively. The average diameter stenosis in quantitative coronary angiography and area stenosis in OCT were 58.1±13.4% and 67.5±13.5%, respectively. The FFR OCT was better correlated to the FFR than were the anatomic variables ( r =0.72; P r =0.46; P r =0.57; P OCT resulted in 88.0% accuracy, 68.7% sensitivity, and 95.6% specificity. The positive and negative predictive values were 84.2% and 89.0%, respectively. Conclusions— The computation of FFR OCT enables assessment not only of anatomic information, but also of the functional significance of intermediate stenosis. This measurement may be a useful approach for the simultaneous evaluation of the functional and anatomic severity of coronary stenosis.

Stick-slip motion is the most well-known phenomenon in nano-tribology. Maier et al. previously studied the dependency of slip time on contact geometry. In their work, they were able to identify the intermediate state during slip motion. However, detailed study of this intermediate state is difficult due to the fast dynamics. In a friction force microscopy experiment, various parameters, such as surface roughness, temperature, defects, and oxidation condition, affect the tribological behaviors. Hence, current experimental techniques only measure the average or maximum friction and describe the simple shape of stick-slip motion. Molecular dynamics simulation represents an effective solution for this issue. Dong et al. reviewed the molecular dynamics simulation approach with regard to the nano-tribology. The advantage of molecular dynamics simulation is that it can provide detailed information and direct visualization of the tribological phenomena on a time scale of a few nanoseconds. In this study, we investigate the detailed mechanism of stick-slip motion in nanoscale. Molecular dynamics simulation precisely mimics friction force microscopy experiments. In molecular dynamics simulations, a crystalline Si tip slides on a graphene surface, and the tip size is varied. The simulation results provide evidence of the intermediate state during slip motion and reveal the hierarchical structure of the stick-slip motion in nanoscale. Detailed relations among stick-slip motion, contact geometry, and energy state are also analyzed.

In tumours that harbour wild-type p53, p53 protein function is frequently disabled by the mouse double minute 2 protein (MDM2, or HDM2 in humans). Multiple HDM2 antagonists are currently in clinical development. Preclinical data indicate that TP53 mutations are a possible mechanism of acquired resistance to HDM2 inhibition; however, this resistance mechanism has not been reported in patients. Utilizing liquid biopsies, here we demonstrate that TP53 mutations appear in circulating cell-free DNA obtained from patients with de-differentiated liposarcoma being treated with an inhibitor of the HDM2–p53 interaction (SAR405838). TP53 mutation burden increases over time and correlates with change in tumour size, likely representing selection of TP53 mutant clones resistant to HDM2 inhibition. These results provide the first clinical demonstration of the emergence of TP53 mutations in response to an HDM2 antagonist and have significant implications for the clinical development of this class of molecules., Pre-clinical studies have shown that TP53 mutations can account for acquired resistance to HDM2 antagonists. This study provides clinical evidence for the emergence of TP53 mutations in circulating cell-free DNA, seen in 5 out of 20 de-differentiated liposarcoma patients treated with an HDM2 antagonist.

Molecular Dynamics(분자동역학), Cation Aggregation(양이온응집), Ionic Liquid(이온성액체),Water-ILs System(물-이온성액체혼합시스템)초록: Ionic Liquids (ILs) 는표준상태에서액체이온으로존재하는물질로여러가지방법으로다양한특성을띄게할수있다. 이런성질을적절하게이용하여계면활성제등다양한분야로의응용이가능하다. ILs의한종류인1-10-alkyl-3-methylimidazolium bromide([C10mim][Br]) 은특정한환경에서양친매성을가진다. 이번논문에서우리는분자동역학을이용하여수용액에서의[C10mim][Br]의응집거동에대한연구를진행하였다. 정준모듬(canonical ensemble)을이용하여모사간시스템의부피와온도를일정하게 유지시키고 5ns 동안의 전산모사를 통하여 얻은 radial distribution function(RDF)을 이용하여[C10mim][Br]과물분자간의상호작용및그분포의특성에대하여논의하였다. 분자동역학적계산을위하여LAMMPS 코드를사용하였고, VMD 코드를이용하여후처리(post processing)을진행하였다.Abstract: Ionic liquids (ILs) existing in the liquid ion form under standard conditions show a unique properties.1-10-Alkyl-3-methyl-imidazolium bromide ([C10mim][Br]) is one of the ILs that shows amphiphilic characteristics underspecific conditions. This property enables it to function as a surfactant, and therefore, it finds applications in a wide rangeof areas. In this study, we tried to predict the behavior, especially the aggregation aspect, of [C10mim][Br] in an aqueoussolution using molecular dynamics (MD) simulations. The canonical (NVT) ensemble was used to relax the system andtrace the trajectory of atoms. Several case studies were simulated and the interaction among [C10mim]+, [Br]-, and waterwas analyzed using the radial distribution function of each atom. The density distribution function was also used for thestructural analysis of the entire system. We used the Large-scale Atomic/Molecular Massively Parallel Simulator(LAMMPS) code for the present MD simulations.

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is performed by obtaining sequential MRI images, before, during and after the injection of a contrast agent. It is usually used to observe the exchange of contrast agent between the vascular space and extravascular extracellular space (EES), and provide information about blood volume and microvascular permeability. To estimate the kinetic parameters derived from the pharmacokinetic model, accurate knowledge of the arterial input function (AIF) is very important. However, the AIF is usually unknown, and it remains very difficult to obtain such information noninvasively. In this article, without knowledge of the AIF, we applied a reference region (RR) model to analyze the kinetic parameters. The RR model usually depends on kinetic parameters found in previous studies of a reference region. However, both the assignment of reference region parameters (intersubject variation) and the selection of the reference region itself (intrasubject variation) may confound the results obtained by RR methods. Instead of using literature values for those pharmacokinetic parameters of the reference region, we proposed to use two pharmacokinetic parameter ratios between the tissue of interest (TOI) and the reference region. Specifically, one parameter K R is calculated as the ratio between the volume transfer constant K trans of the TOI and RR. Similarly, another parameter V R is calculated as the ratio between the extravascular extracellular volume fraction v e of the TOI and RR. To investigate the consistency of the two ratios, the K trans of the RR was varied ranging from 0.1 to 1.0 min −1 , covering the cited literature values. A simulated dataset with different levels of Gaussian noises and an in vivo dataset acquired from five canine brains with spontaneous occurring brain tumors were used to study the proposed ratios. It is shown from both datasets that these ratios are independent of K trans of the RR, implying that there is potentially no need to obtain information about literature values from the reference region for future pharmacokinetic modeling and analysis.

Predicting the rheological properties of emulsions is one of the most challenging and complicated problems in material and fluid sciences. Substantial complications in prediction of rheology arise due to the deformability and aggregation of emulsions. Thus a better understanding of deformation and aggregation of emulsions can lead to a better understanding of the shear thinning region of emulsions. Though numerous experimental and theoretical studies were performed to obtain rheological correlations of emulsions, their inability to visualize and understand the droplet deformation in the presence of large volume fractions has stagnated our understanding of the shear thinning behavior of emulsions. With the aid of a numerical tool, which can help in visualizing the droplet deformation and correlate it to rheological behavior of emulsions, we have made an attempt to understand the physics behind the shear thinning behavior and also predict its rheological characteristics for emulsions at different volume fractions. In this article, we try to obtain a theoretical understanding of the influence of deformation and de-aggregation of droplets on the emulsion rheology. Simulations performed in this article using a multi-component lattice Boltzmann model are used to quantify (a) relative viscosity of emulsions with change in shear rate, (b) relative viscosity of emulsions with change in time, (c) effect of deformation of droplets on the shear thinning region in emulsions, and (d) relative viscosity of emulsions with change in volume fraction.

Experimental and computational investigations were performed in order to better understand the mechanical response of rigid targets with various geometries to the detonation of shallow buried explosives. The motion of the targets was measured by use of high-speed digital video photography. This work involved flat targets, targets that were downwardly convex, and targets that were downwardly concave with explosive charges located at various positions beneath the targets. It was observed that, in general, angled hulls – whether downwardly concave or convex – tended to reduce the amount of momentum imparted to the center of mass of the targets. Computations were performed by use of an arbitrary Langrangian–Eulerian treatment in a nonlinear finite element code. A model based on quasi-static test evaluations of wet concrete sand was used for prediction of the soil behavior. The computational technique provided very good agreement between computation and experiment.

SUMMARY A direct numerical simulation technique based on two-way coupling is presented to study a particle-laden, decaying isotropic turbulent flow. Physical characteristics of turbulence modulation because of the mono-dispersed (i.e., particles with single Stokes number) and poly-dispersed particles (i.e., particles with more than one Stokes number) were investigated. A scale dependent effective viscosity that summarizes the aspects of the interaction between the velocity field and particles is defined in the study. Particles of Stokes number (St) 3.2,6.4 and 12.8 were used in performing the simulations. Poly-dispersed particles were acquired by mixing particles of two different Stokes numbers at a time. As a whole, decay of turbulence because of the poly-dispersed particles is observed to be larger than that of the decay of turbulence because of the mono-dispersed particles. Simulations of poly-dispersed particle indicate nonlinear characteristics in the modification of the temporal evolution of turbulence energy and dissipation. The scale dependent effective viscosity, which correlates with the energy spectrum plot, indicates that the decay of turbulence is mostly observed at the intermediate scales of turbulence. The effective viscosity for the simulations of the poly-dispersed particles was calculated to be higher than that of the simulations of the mono-dispersed particles. Copyright © 2011 John Wiley & Sons, Ltd.

This article discusses a novel phenomenological approach for suppressing the coalescence in the Gunstensen multi-component lattice Boltzmann method (LBM). The suppression of coalescence is achieved by perturbing the terminal nodes of the ambient fluid’s thin layer trapped between the approaching droplets. This additional perturbation creates a local high pressure fluid layer which eventually leads to suppressing the coalescence of the neighboring droplets while maintaining a suitable qualitative force balance representative of the physical intermolecular forces which act between them.

The advent of next-generation sequencing technologies has facilitated the detection of rare variants. Despite the significant cost reduction, sequencing cost is still high for large-scale studies. In this article, we examine DNA pooling as a cost-effective strategy for rare variant detection. We consider the optimal number of individuals in a DNA pool to detect an allele with a specific minor allele frequency (MAF) under a given coverage depth and detection threshold. We found that the optimal number of individuals in a pool is indifferent to the MAF at the same coverage depth and detection threshold. In addition, when the individual contributions to each pool are equal, the total number of individuals across different pools required in an optimal design to detect a variant with a desired power is similar at different coverage depths. When the contributions are more variable, more individuals tend to be needed for higher coverage depths. Our study provides general guidelines on using DNA pooling for more cost-effective identifications of rare variants. Genet. Epidemiol. 35:139-147, 2011. © 2011 Wiley-Liss, Inc.

Behavioral compatibility between subtypes and supertypes in object-oriented systems is a very important issue to enable the substitution between object types since it supports the extension and evolution of an object oriented system. In other words, the subtype must be guaranteed that it can provide all behaviors (operations) of the supertype for replacing the supertype with the subtype. Invocation consistency checking is one of techniques to verify behavioral compatibility between two object types. The technique confirms weather an object type can accept all sequence of operations of the other object type or not. The classical methods rule checks behavioral compatibility by verifying invocation consistency of two object types. The rule argues that subtypes meet behavioral compatibility with supertypes if the subtypes' preconditions of inherited operations are weakened and postconditions are strengthened. Noting that the classical methods rule is not sufficient for checking behavioral compatibility between objects, we propose an extended methods rule on the basis of the classical methods rule. Based on the proposed extended methods rule, we have implemented a tool, BCCT, to automatically check behavioral compatibility between two objects.

This paper proposes an extension scheme for the application of the single phase multi-block lattice Boltzmann method (LBM) to the multiphase Gunstensen model, in which the grid is refined in a specific part of the domain where a fluid–fluid interface evolves, and the refined grid is free to migrate with the suspended phase in the flow direction. The method is applicable to single and multiphase flows, and it was demonstrated by simulating a benchmark single phase flow around a 2D asymmetrically placed cylinder in a channel and for investigating the shear lift of 2D neutrally buoyant drop in a parabolic flow.

The lattice Boltzmann method (LBM) has emerged as a powerful numerical fluid solver especially in the areas of multi-component and multi-phase mixtures. However the LBM uses the particle velocity for the determination of the model time step required by the Courant–Friedrichs–Lewy (CFL) stability condition. This degrades the LBM efficiency, when compared with standard CFD solvers which use instead the macroscopic velocity for the CFL requirements. This paper discusses the development and validation of a 3D migrating multi-block model aiming at the acceleration of the LBM solution. The proposed algorithm is especially applicable to the Gunstensen multi-component model, in which a fine grid block engulfs the fluid–fluid interface and migrates with it. This increases the efficiency of the LBM since less iteration steps are required in areas of marginal interest, and it enables a better interface resolution because the fluid interface is always covered with finer grid. The method was demonstrated by simulating the case of a 3D rising bubble in infinite medium, in which the model results for the bubble terminal velocity were in good agreement with a semi-analytical solution, and the produced shapes fitted very well an experimental shape regime map.