Modeling cell contractility responses to acoustic tweezing cytometry

Acoustic tweezing cytometry(ATC)is a recently developed method for cell mechanics regulation.Tar-geted microbubbles,which are attached to integrins and subsequently the actin cytoskeleton,anchor,amplify and transmit the mechanical energy in an acoustic field inside the cells,eliciting prominent cy-toskeleton contractile force increases in various cell types.We propose that a mechanochemical con-version mechanism is critical for the high efficiency of ATC to activate cell contractility responses.Our models predict key experimental observations.Moreover,we study the influences of ATC parameters(ul-trasound center frequency,pulse repetition frequency,duty cycle,and acoustic pressure),cell areas,the number of ATC stimuli,and extracellular matrix rigidity on cell contractility responses to ATC.The simu-lation results suggest that it is large molecules,rather than small ions,that facilitate global responses to the local ATC stimulation,and the incorporation of visible stress fiber bundles improves the accuracy of modeling.

Multi-dimensional Simulation of Phase Change by a 0D-2D Model Coupling via Stefan Condition

Considering phase changes associated with a high-temperature molten material cooled down from the outside,this work presents an improvement of the modelling and the numerical simulation of such processes for an application pertaining to the safety of light water nuclear reactors.Postulating a core meltdown accident,the behaviour of the core melt(aka corium)into a steel vessel is of tremendous importance when evaluating the vessel integrity.Evaluating correctly the heat fluxes requires the numerical simulation of the interaction between the liquid material and its solid counterpart which forms during the solidification process,but also may melt back.To simulate this configuration,encoun-tered in various industrial applications,one considers a bi-phase model constituted by a liquid phase in contact and interaction with its solid phase.The liquid phase may solidify in presence of low energetic source,while the solid phase may melt due to an intense heat flux from the high-temperature liquid.In the frame of the in-house legacy code,several simplifying assumptions(0D multi-layer discretization,instantaneous heat transfer via a quadratic temperature profile in solids)are made for the modelling of such phase changes.In the present work,these shortcomings are illustrated and further overcome by solving a 2D heat conduction model in the solid by a mixed Raviart-Thomas finite element method coupled to the liquid phase due to heat and mass exchanges through Stefan condition.The liquid phase is modeled with a 0D multi-layer approach.The 0D-liquid and 2D-solid mod-els are coupled by a Stefan like phase change interface model.Several sanity checks are performed to assess the validity of the approach on 1D and 2D academical configurations for which exact or reference solutions are available.Then more advanced situations(genu-ine multi-dimensional phase changes and an"industrial-like scenario")are simulated to verify the appropriate behavior of the obtained coupled simulation scheme.

A Study of Prospective Barriers,Benefits and Measures for Building Information Modeling(BIM)Adoption in Nepalese AEC Industry

The construction industry needs modern construction methodology and technology to improve sustainability and production performance.Building Information Modelling(BIM)technology supports improving the quality of products by reducing design and construction defects,risks to the health and safety of workers,and reduce overall project cost and delivery time.The BIM has capabilities,but it is still undiscovered and unable to exploit the full scale of its benefits in the Architectural Engineering and Construction(AEC)industry.There is a trend to adopt the BIM level 1,which is limited to 2D and only in a few cases 3D models uses in the design and construction of residential and commercial buildings,particularly in Nepal.Hence,this paper focuses on providing insight into the BIM benefits and identifies the potential barriers while adopting BIM Level 3 in Nepal.This was accomplished by developing a 4DBIM model of a multi-story residential building in Nepal and conducting the industry survey via focus group with the AEC professionals based on the developed 4DBIM model.A comprehensive literature review was conducted and presented the findings of the BIM benefits and barriers while adopting BIM.The study found that commercial and governmental projects can immediately be adopted BIM technology.It is concluded that the unavailability of skilled BIM users and the lack of proper policies for BIM adoption are key barriers in Nepal.Hence,the new policy is required to achieve and exploit the full scale of the BIM benefits and improve the project delivery in terms of quality,cost and time including the health and safety of workers and the sustainability of the AEC industry.

Simulation of the Hydrodynamic Functioning of the Cavally River Using a Coupled 1D-2D Model in the Ity Area (Zouan-Hounien in Côte d’Ivoire)

In recent years, the Cavally River has been subject to multiple activities, including the construction of diversion channels and a bridge that makes it vulnerable to flooding. In order to assess the impact of these hydraulic structures on the river hydrodynamic functioning, a 1D-2D model was realized. The implementation of the 1D-2D model consisted of first running the 1D model, then the 2D model, and finally in coupling them. The 1D-2D model was designed with the 1988 flood hydrograph, a Manning’s coefficient of 0.052 m1/3/s for the minor bed and 0.06 m1/3/s for the major bed. The results of the hydraulic model show that the velocities are almost identical to those of the Cavally in natural operation. The values of the velocities are included between 0.4 m/s and 1.3 m/s at the level of the minor bed of the river and between 0.06 m/s and 0.71 m/s at the level of the floodplains. The average water level for flood propagation is 262.37 ± 0.44 m before construction of the structures and 262.23 ± 0.85 m after construction of the structures. The 0.41 m reduction in water level due to the diversion canal and bridge is negligible compared to the total fluctuations of the Cavally River, which vary from 6 to 7 m over the year.

Influence of formation heterogeneity on foam flooding performance using 2D and 3D models:an experimental study

The formation heterogeneity is considered as one of the major factors limiting the application of foam flooding.In this paper,influences of formation properties,such as permeability,permeability distribution,interlayer,sedimentary rhythm and 3D heterogeneity,on the mobility control capability and oil displacement efficiency of foam flooding,were systematically investigated using 2D homogeneous and 2D/3D heterogeneous models under 120°C and salinity of 20×10~4 mg/L.The flow resistance of foam was promoted as the permeability increased,which thus resulted in a considerable oil recovery behavior.In the scenario of the vertical heterogeneous formations,it was observed that the permeability of the high-permeable layer was crucial to foam mobility control,and the positive rhythm appeared favorable to improve the foam flooding performance.The additional oil recovery increased to about 40%.The interlayer was favorable for the increases in mobility reduction factor and oil recovery of foam flooding when the low permeability ratio was involved.For the 3D heterogeneous formations,foam could efficiently adjust the areal and vertical heterogeneity through mobility control and gravity segregation,and thus enhancing the oil recovery to 11%–14%.The results derived from this work may provide some insight for the field test designs of foam flooding.

Measuring and modeling two-dimensional irrigation infiltration under film-mulched furrows

Furrow irrigation with film-mulched agricultural beds is being promoted in the arid region of northwest China because it improves water utilization. Two-dimensional infiltration patterns under film-mulched furrows can provide guidelines and criteria for irrigation design and operation. Our objective was to investigate soil water dynamics during ponding irrigation infiltration of mulched furrows in a cross-sectional ridge-furrow configuration, using laboratory experiments and mathematical simulations. Six experimental treatments, with two soil types （silt loam and sandy loam）, were investigated to monitor the wetting patterns and soil water distribution in a cuboid soil chamber. Irrigation of mulched furrows clearly increased water lateral infiltration on ridge shoulders and ridges, due to enhancement of capillary driving force. Increases to both initial soil water content （SWC） and irrigation water level resulted in increased wetted soil volume. Empirical regression equations accurately estimated the wetted lateral distance （Rl） and downward distance （Rd） with elapsed time in a variably wetted soil medium. Optimization of model parameters followed by the Inverse approach resulted in satisfactory agreement between observed and predicted cumulative infiltration and SWC. On the basis of model calibration, HYDRUS-2D model can accurately simulate two-dimensional soil water dynamics under irrigation of mulched furrows. There were significant differences in wetting patterns between unmulched and mulched furrow irrigation using HYDRUS-2D simulation. The Rd under the mulched furrows was 32.14% less than the unmulched furrows. Therefore, film-mulched furrows are recommended in a furrow irrigation system.

Velocity and Structural Modeling of Mesozoic Chiltan Limestone and Goru Formation for Hydrocarbon Evaluation in the Bitrisim Area, Lower Indus Basin, Pakistan

The present study focuses on building a workflow for structural interpretation and velocity modeling and implementing to Jurassic-Cretaceous succession （Chiltan Limestone and Massive sand of the Lower Goru Formation）. 2D-Migrated seismic sections of the area are used as data set and in order to confirm the presence of hydrocarbons in the study area, P and S-wave seismic velocities are estimated from single-component seismic data. Some specific issues in the use of seismic data for modeling and hydrocarbon evaluation need to deal with including distinguishing the reservoir and cap rocks, and the effects of faults, folds and presence of hydrocarbons on these rocks. This study has carried out the structural interpretation and modeling of the seismic data for the identification of traps. The results demonstrate existence of appropriate structural traps in the form of horst and grabens in the area. 2D and 3D velocity modeling of the horizons indicates the presence of high velocity zones in the eastern half of the study while relatively low velocity zones are encountered in the western half of the area. Two wells were drilled in the study area （i.e. Fateh-01 and Ichhri-01） and both are dry. Immature hydrocarbons migration is considered as a failure reason for Fateh-01 and Ichhri-01 well.

An Implicit Coupled 1D/2D Model for Unsteady Subcritical Flow in Channel Networks and Embayment

In this study, 1D and 2D shallow-water models were coupled to simulate unsteady flow in channel networks and embayment. The 1D model solved the 1D shallow-water equations (St. Venant) using the Preissmann box method and targeted long narrow reaches of the river networks, while the 2D model targeted broad channels and embayment and solved the 2D shallow-water equations using a semi-implicit scheme applied to an unstructured grid of triangular cells. The 1D and 2D models were solved simultaneously by building a matrix for the free surface elevation at every 1D junction and 2D cell center. Velocities were then computed explicitly based on the results at the previous time step and the updated water level. The originality of the scheme arose from a novel coupling method. The results showed that the coupled 1D/2D model produced identical results as the full 2D model in classical to benchmark problems with considerable savings in computational effort. Application of the model to the Pearl River Estuary in southern China showed that complex patterns of tidal wave propagation could be efficiently modeled.

Validation of the Ability of Full Configuration Interaction Quantum Monte Carlo for Studying the 2D Hubbard Model

To validate the ability of full configuration interaction quantum Monte Carlo （FCIQMC） for studying the 2D Hubbard model near half-filling regime, the ground state energies of a 4×44×4 square lattice system with various interaction strengths are calculated. It is found that the calculated results are in good agreement with those obtained by exact diagonalization （i.e., the exact values for a given basis set） when the population of psi particles （psips） is higher than the critical population required to correctly sample the ground state wave function. In addition, the variations of the average computational time per 20 Monte Carlo cycles with the coupling strength and the number of processors are also analyzed. The calculated results show that the computational efficiency of an FCIQMC calculation is mainly affected by the total population of psips and the communication between processors. These results can provide useful references for understanding the FCIQMC algorithm, studying the ground state properties of the 2D Hubbard model for the larger system size by the FCIQMC method and using a computational budget as effectively as possible.

Numerical Modeling of Sediment Transport and Its Effect on Algal Biomass Distribution in Lake Pontchartrain Due to Flood Release from Bonnet CarréSpillway

In order to protect the city of New Orleans from the Mississippi River flooding, the Bonnet Carré Spillway (BCS) was constructed from 1929 to 1936 to divert flood water from the river into Lake Pontchartrain and then into the Gulf of Mexico. During the BCS opening for flood release, large amounts of freshwater, nutrients, sediment, etc. were discharged into Lake Pontchartrain, and caused a lot of environmental problems. To evaluate the environmental impacts of the flood water on lake ecosystems, a two-dimensional numerical model was developed based on CCHE2D and applied to simulate the flow circulation, sediment transport and algal biomass distribution in Lake Pontchartrain. The effect of sediment concentration on the growth of algae was considered in the model. The numerical model was calibrated using field measured data provided by USGS, and then it was validated by the BCS Opening Event in 1997. The simulated results were generally in good agreement with filed data and satellite imagery. The field observation and numerical model show that during the spillway opening for flood release, the sediment concentration is very high, which greatly restricts the growth of algae, so there is no algal bloom observed in the lake. After the closure of BCS, the sediment concentration in the lake reduces gradually, and the nutrient concentration of the lake is still high. Under these conditions, numerical results and satellite imagery showed that the chlorophyll concentration was high and algal bloom might occur.

2D Coupled 3D:A New Numerical Model for Dual - Structured - Aquifer System

This paper points out that a successful numerical simulation is to construct a correct conceptional model which is very dose to the natural condition. A new model, two dimensional coupled three dimensional model (2D -3D ) is presented in the Present paper,which is the most suitable one for the dual - structured - aquifer system. An example of Wenyinghu area is shown.By using the 2D-3D model, a satisfied result of the simulated area is achieved.

A fast hybrid simulation approach of ion energy and angular distributions in biased inductively coupled Ar plasmas

In this work,a two-dimensional hybrid model,which consists of a bulk fluid module,a sheath module and an ion Monte-Carlo module,is developed to investigate the modulation of ion energy and angular distributions at different radial positions in a biased argon inductively coupled plasma.The results indicate that when the bias voltage amplitude increases or the bias frequency decreases,the ion energy peak separation width becomes wider.Besides,the widths of the ion energy peaks at the edge of the substrate are smaller than those at the center due to the lower plasma density there,indicating the nonuniformity of the ion energy distribution function(IEDF)along the radial direction.As the pressure increases from 1 to 10 Pa,the discrepancy of the IEDFs at different radial positions becomes more obvious,i.e.the IEDF at the radial edge is characterized by multiple low energy peaks.When a dual frequency bias source is applied,the IEDF exhibits three or four peaks,and it could be modulated efficiently by the relative phase between the two bias frequencies.The results obtained in this work could help to improve the radial uniformity of the IEDF and thus the etching process.

Assessment of hydrocarbon generation potential and thermal maturity of the deep offshore Lamu Basin, Kenya

In this study, the secondary well data for Cretaceous to Miocene cutting samples in four deep offshore exploration wells, i.e., Pomboo-1 in the north, Kubwa-1 in the central, Simba-1 and Kiboko-1 in the south of the deep offshore Lamu Basin were assessed for identifying source rock presence and examining thermal maturity of the source rocks. The 2D basin modelling was used to analyse the bulk gas transformation in the basin. Total organic carbon (TOC) content values for the wells range from 0.09 wt % to 2.23 wt % with an average of 0.78 wt %. The average organic richness is higher in the Upper Cretaceous (0.83 wt %) than in the Palaeogene (0.65 wt %), Lower Cretaceous (0.28 wt %) and Upper Jurassic (0.30 wt %). The S_(1) averages for the Upper Cretaceous are 3.76 mg HC/g rock in Pomboo-1 and 0.31mg HC/g rock in Kubwa-1. The S_(2) averages for the Upper Cretaceous are 5.00 mg HC/g rock in Pomboo-1 and 0.72 mg HC/g rock in Kubwa-1. Hydrogen index (HI) values vary between 4 and 512 mg HC/g TOC with an average of 157.09 mg HC/g TOC. Organic matters were identified as mixed types of Ⅱ-Ⅲ (oil and gas prone) and Ⅲ-Ⅳ (gas prone) kerogen in the potential source rocks. The HI and S_(2) yield values are exceptionally high for the observed TOC values in Pomboo-1. The vitrinite reflectance and Tmax values of deep offshore Lamu Basin are in the ranges of 0.38%–0.72% and 360–441 ℃, respectively. It suggests the existence of both immature and mature source rocks. Vitrinite reflectance maturity favours near coastal region in the Upper Cretaceous. These results explain why Pomboo-1, Kubwa-1, Simba-1 and Kiboko-1 wells were dry. The temperatures are still cool for hydrocarbon generation in deep offshore. The critical risk for deep offshore Lamu Basin is charge, primarily source presence, and a lack of definitive evidence of a deep-water marine source rock being present. The four wells penetrate good quality reservoir and seal rocks, but source rock presence and maturity remain the critical play risk in the deep offshore Lamu Basin.

Imaging Rock Density Distribution beneath Liwa Fracture Zone in the Southern Part of the Great Sumatran Fault System, Indonesia

We have imaged rock density distribution beneath Liwa fracture zone in the southern part of the the Sumatran Fault Zone by modelling and inverting Bouguer gravity data in two-and three-dimensional environments, respectively. The purpose of this study is aimed to figure out the subsurface distribution of rock densities associated with subsurface basement structure representing the evidence of trans-tensional tectonic product in the SF. In the gravity modeling, to eliminate distortions to the measured gravity values before modelling and inverting the data, Bouguer anomalies obtained in field measurements are reduced to the horizontal plane of z = +800 m as a representation of the average elevation in Liwa. For the inversion, we used algorithm implementing depth-and minimum volume weighting parameters in order to obtain a smooth model with better vertical resolution. The two-dimensional models show clearly surface topography of the basement rocks and the presence of normal faults. The reduced Bouguer anomaly of +800 m elevation shows the presence of structural lineaments extending primarily in a northwest-southeast direction, parallel to Sumatran Fault Zone and older graben faults showing a negative flower structure. From the three-dimensional inversion, the model illustrates an increase of density contrast, lower values being found near the surface and higher values in the deeper parts. The lower density contrast of 0.15 to 0.3 g/cm3 found in the rock groups at depths of 2 km and less is characteristic of relatively homogeneous and poorly compacted rocks. Rocks with moderate to high density contrast (>1.0 g/cm3) are recognized at depths of over 2 km. This model suggests a change of basement morphology as a function of depth, and delineates structural lineaments extending in northwest-southeast direction. This study supports the previous thought that Liwa area is underlain by graben structures, formed by trans-tensional tectonic events. Higher-density Tertiary volcanic breccia and lower-density Quaternary volcanic products of the Ranau Formation form the basement rocks and the overlying younger sediments, respectively.

Numerical Simulation of Residual Circulation due to Bottom Roughness Variability Under Tidal Flows in A Semi-Enclosed Bay

Nowadays there are some chronic serious environmental problems, such as eutrophication, blue tide and so on, in a complicated coastal zone or a semi-enclosed bay, because the water exchanges between an inner bay and an outer sea is weak compared with the supply of contaminant. Under this situation, a method to improve the water quality by 3-dimensional small unsymmetrical structures has been proposed by Komatsu et al. In this paper, several numerical simulations of the tidal current and concentration for various arrangements of bottom roughness in a semi-enclosed model bay are carfled out with a depth-averaged 2-D numerical model. The model is solved by the hybrid finite analytic method with nonstaggered grid. And the SIMPLES algorithm with Rhie and Chow＇ s momentum interpolation technique is used for the simulation. The effect of Komatsu＇ s method for water purification is examined by numerical simulation. The result of numerical experiment indicates that it is possible to generate a new tidal residual current and to activate a tidal exchange by bottom roughness arrangement only.

Identification of Convective and Stratiform Clouds Based on the Improved DBSCAN Clustering Algorithm

A convective and stratiform cloud classification method for weather radar is proposed based on the density-based spatial clustering of applications with noise(DBSCAN)algorithm.To identify convective and stratiform clouds in different developmental phases,two-dimensional(2D)and three-dimensional(3D)models are proposed by applying reflectivity factors at 0.5°and at 0.5°,1.5°,and 2.4°elevation angles,respectively.According to the thresholds of the algorithm,which include echo intensity,the echo top height of 35 dBZ(ET),density threshold,andεneighborhood,cloud clusters can be marked into four types:deep-convective cloud(DCC),shallow-convective cloud(SCC),hybrid convective-stratiform cloud(HCS),and stratiform cloud(SFC)types.Each cloud cluster type is further identified as a core area and boundary area,which can provide more abundant cloud structure information.The algorithm is verified using the volume scan data observed with new-generation S-band weather radars in Nanjing,Xuzhou,and Qingdao.The results show that cloud clusters can be intuitively identified as core and boundary points,which change in area continuously during the process of convective evolution,by the improved DBSCAN algorithm.Therefore,the occurrence and disappearance of convective weather can be estimated in advance by observing the changes of the classification.Because density thresholds are different and multiple elevations are utilized in the 3D model,the identified echo types and areas are dissimilar between the 2D and 3D models.The 3D model identifies larger convective and stratiform clouds than the 2D model.However,the developing convective clouds of small areas at lower heights cannot be identified with the 3D model because they are covered by thick stratiform clouds.In addition,the 3D model can avoid the influence of the melting layer and better suggest convective clouds in the developmental stage.

Numerical simulation of tumor-induced angiogenesis influenced by the extra-cellular matrix mechanical environment

To investigate tumor-induced angiogenesis under the influence of the mechanical environments inside and outside the tumor, mathematical model of tumor angiogenesis was developed. In the model, extra-cellular matrix （ECM） was treated as a thin plane. The displacement of ECM is obtained from the force balance equation consisted of the ECs traction, the ECM visco-elastic forces and the exter- nal forces. Simulation results show that a layered capillary network is obtained with a well vascularized region at the periphery of the tumor. The present model can be used as a valid theoretical method in the basic researches in tumorinduced angiogenesis.

Quasi-3D Numerical Simulation of Tidal Hydrodynamic Field

Based on the 2D horizontal plane numerical model, a quasi-3D numerical model is established for coastal regions of shallow water. The characteristics of this model are that the velocity profiles;can be obtained at the same time when the equations of the value of difference between the horizontal current velocity and its depth-averaged velocity in the vertical direction are solved and the results obtained are consistent with the results of the 2D, model. The circulating flow in the rectangular area induced by wind is simulated and applied to the tidal flow field of the radial sandbanks in the South Yellow Sea. The computational results from this quasi-3D model are in good agreement with analytical results and observed data. The solution of the finite difference equations has been found to be stable, and the model is simple, effective and practical.

Beam steering characteristics in high-power quantum-cascade lasers emitting at∼4.6µm

A beam steering effect of high-power quantum cascade(QC) lasers emitting at 4.6 μm was investigated. The continuous wave(CW) output power of an uncoated, 6-mm-long, 7.5-μm-wide buried-heterostructure QC laser at 25℃ was as high as 854.2 m W. The maximum beam steering angle was offset by ±14.2° from the facet normal(0°) in pulsed mode. The phenomenon was judged explicitly by combining the diffraction limit theory and Fourier transform of the spectra. It was also verified by finite element method software simulation and the calculation of two-dimensional(2 D)effective-index model. The observed steering is consistent with a theory for coherence between the two lowest order lateral modes. Therefore, we have established an intrinsic linkage between the spectral instabilities and the beam steering by using the Fourier transform of the spectra, and further presented an extremely valid method to judge the beam steering. The content of this method includes both three equidistant peak positions in the Fourier transform of the spectra and the beam quality located between once the diffraction limit(DL) and twice the DL.

Root length density distribution and associated soil water dynamics for tomato plants under furrow irrigation in a solar greenhouse

Furrow irrigation is a traditional widely-used irrigation method in the world. Understanding the dynamics of soil water distribution is essential to developing effective furrow irrigation strategies, especially in water-limited regions. The objectives of this study are to analyze root length density distribution and to explore soil water dynamics by simulating soil water content using a HYDRUS-2D model with consideration of root water uptake for furrow irrigated tomato plants in a solar greenhouse in Northwest China. Soil water contents were also in-situ observed by the ECH_2O sensors from 4 June to 19 June and from 21 June to 4 July, 2012. Results showed that the root length density of tomato plants was concentrated in the 0–50 cm soil layers, and radiated 0–18 cm toward the furrow and 0–30 cm along the bed axis. Soil water content values simulated by the HYDRUS-2D model agreed well with those observed by the ECH_2O sensors, with regression coefficient of 0.988, coefficient of determination of 0.89, and index of agreement of 0.97. The HYDRUS-2D model with the calibrated parameters was then applied to explore the optimal irrigation scheduling. Infrequent irrigation with a large amount of water for each irrigation event could result in 10%–18% of the irrigation water losses. Thus we recommend high irrigation frequency with a low amount of water for each irrigation event in greenhouses for arid region. The maximum high irrigation amount and the suitable irrigation interval required to avoid plant water stress and drainage water were 34 mm and 6 days, respectively, for given daily average transpiration rate of 4.0 mm/d. To sum up, the HYDRUS-2D model with consideration of root water uptake can be used to improve irrigation scheduling for furrow irrigated tomato plants in greenhouses in arid regions.