Physically Based, Hydrologic Model Results Based on Three Precipitation Products

The main objective of the study is to examine the accuracy of and differences among simulated streamflows driven by rainfall estimates from a network of 22 rain gauges spread over a 2,170 km2 watershed, NEXRAD Stage III radar data, and Tropical Rainfall Measuring Mission (TRMM) 3B42 satellite data. The Gridded Surface Subsurface Hydrologic Analysis (GSSHA), a physically based, distributed parameter, grid-structured, hydrologic model, was used to simulate the June-2002 flooding event in the Upper Guadalupe River watershed in south central Texas. There were significant differences between the rainfall fields estimated by the three types of measurement technologies. These differences resulted in even larger differences in the simulated hydrologic response of the watershed. In general, simulations driven by radar rainfall yielded better results than those driven by satellite or rain-gauge estimates. This study also presents an overview of effects of land cover changes on runoff and stream discharge. The results demonstrate that, for major rainfall events similar to the 2002 event, the effect of urbanization on the watershed in the past two decades would not have made any significant effect on the hydrologic response. The effect of urbanization on the hydrologic response increases as the size of the rainfall event decreases.

Nonlinear dynamic analysis of dragonfly inspired piezoelectrically driven flapping and pitching wing

The nonlinear equations for coupled elastic flapping-twisting motion of a dragonfly in- spired smart flapping wing are used for a flapping wing actuated from the root by a PZT unimorph in the piezofan configuration. Excitation by the piezoelectric harmonic force generates only the flap bending motion, which in turn, induces the elastic twist motion due to interaction between flexural and torsional vibrations modes. An unsteady aerodynamic model is used to obtain the aerodynamic forces. Numerical simulations are performed using a wing whose size is the same as the dragonfly Sympetrum Frequens wing. It is found that the value of average lift reaches to its maximum when the smart flapping wing is excited at a frequency closer to the natural frequency in torsion. Moreover, consideration of the elastic twisting of flapping wing leads to an increase in the lift force. It is also found that the flapping wing generates sufficient lift to support its own weight and carry a small pay- load. Therefore, the piezoelectrically actuated smart flapping wing based on the geometry of Sympetrum Frequens wing and undergoing flapping-twisting motions may be considered as a potential candidate for use in MAV applications.

Interface capturing simulations of acoustically driven bubble dynamics in and near tissue

Tissue injury during therapeutic ultrasound or lithotripsy is thought, in cases, to be due to the action of cavitation bubbles. Assessing this and mitigating it is challenging since bubble dynamics in the complex confinement of tissues or in small blood vessels are challenging to predict. Simulations tools require specialized algorithms to simultaneously represent strong acoustic waves and shocks, topologically complex liquid‐vapor phase boundaries, and the complex viscoelastic material dynamics of tissue. We discuss advances in a simulation tool for such situations. A single‐mesh Eulerian solver is used to solve the governing equations. Special sharpening terms maintain the liquid‐vapor interface in face of the finite numerical dissipation included in the scheme to accurately capture shocks. A recent enhancement to this formulation has significantly improved this interface capturing procedure, which is demonstrated for simulation of the Rayleigh collapse of a bubble. The solver also transports elastic stresses and can thus be used to assess the effects of elastic properties on bubble dynamics. A shock‐induced bubble collapse adjacent to a model elastic tissue is used to demonstrate this and draw some conclusions regarding the injury suppressing role that tissue elasticity might play.

A Study of Early Afterdepolarizations in a Model for Human Ventricular Tissue

Sudden cardiac death is often caused by cardiac arrhythmias. Recently, special attention has been given to a certain arrhythmogenic condition, the long-QT syndrome, which occurs as a result of genetic mutations or drug toxicity. The underlying mechanisms of arrhythmias, caused by the long-QT syndrome, are not fully understood. However, arrhythmias are often connected to special excitations of cardiac cells, called early afterdepolarizations (EADs), which are depolarizations during the repolarizing phase of the action potential. So far, EADs have been studied mainly in isolated cardiac cells. However, the question on how EADs at the single-cell level can result in fibrillation at the tissue level, especially in human cell models, has not been widely studied yet. In this paper, we study wave patterns that result from single-cell EAD dynamics in a mathematical model for human ventricular cardiac tissue. We induce EADs by modeling experimental conditions which have been shown to evoke EADs at a single-cell level: by an increase of L-type Ca currents and a decrease of the delayed rectifier potassium currents. We show that, at the tissue level and depending on these parameters, three types of abnormal wave patterns emerge. We classify them into two types of spiral fibrillation and one type of oscillatory dynamics. Moreover, we find that the emergent wave patterns can be driven by calcium or sodium currents and we find phase waves in the oscillatory excitation regime. From our simulations we predict that arrhythmias caused by EADs can occur during normal wave propagation and do not require tissue heterogeneities. Experimental verification of our results is possible for experiments at the cell-culture level, where EADs can be induced by an increase of the L-type calcium conductance and by the application of I-Kr blockers, and the properties of the emergent patterns can be studied by optical mapping of the voltage and calcium.

Dynamics of a driven magneto-martensitic ribbon

We investigate the dynamics of a sinusoidally driven ferromagnetic martensitic ribbon by adopting a recently introduced model that involves strain and magnetization as order parameters. Retaining only the dominant mode of excitation we reduce the coupled set of partial differential equations for strain and magnetization to a set of coupled ordinary nonlinear equations for the strain and magnetization amplitudes. The equation for the strain amplitude takes the form of parametrically driven oscillator. Finite strain amplitude can only be induced beyond a critical value of the strength of the magnetic field. Chaotic response is seen for a range of values of all the physically interesting parameters. The nature of the bifurcations depends on the choice of temperature relative to the ordering of the Curie and the martensite transformation temperatures. We have studied the nature of response as a function of the strength and frequency of the magnetic field, and magneto-elastic coupling. In general, the bifurcation diagrams with respect to these parameters do not follow any standard route. The rich dynamics exhibited by the model is further illustrated by the presence of mixed mode oscillations seen for low frequencies. The geometric structure of the mixed mode oscillations in the phase space has an unusual deep crater structure with an outer and inner cone on which the orbits circulate. We suggest that these features should be seen in experiments on driven magneto-martensitic ribbons. (C) 2014 Elsevier B. V. All rights reserved.

Solar driven Adsorption Desalination system

Desalination is one of the most traditional processes to generate potable water. With the rise in demand for potable water and paucity of fresh water resources, this process has gained special importance. Conventional thermal desalination processes involves evaporative methods such as multi-stage flash and solar distils, which are found to be energy intensive, whereas reverse osmosis based systems have high operating and maintenance costs. The present work describes the Adsorption Desalination (AD) system, which is an emerging process of thermal desalination cum refrigeration capable of utilizing low grade heat easily obtainable from even non-concentrating type solar collectors. The system employs a combination of flash evaporation and thermal compression to generate cooling and desalinated water. The current study analyses the system dynamics of a 4-bed single stage silica-gel plus water based AD system. A lumped model is developed using conservation of energy and mass coupled with the kinetics of adsorption/desorption process. The constitutive equations for the system components viz. evaporator, adsorber and condenser, are solved and the performance of the system is evaluated for a single stage AD system at various condenser temperatures and cycle times to determine optimum operating conditions required for desalination and cooling. (C) 2013 P. Dutta. Published by Elsevier Ltd.

Sensitivity of meteorological input and soil properties in simulating aerosols (dust, PM10, and BC) using CHIMERE chemistry transport model

The objective of this study is to evaluate the ability of a European chemistry transport model, `CHIMERE' driven by the US meteorological model MM5, in simulating aerosol concentrations dust, PM10 and black carbon (BC)] over the Indian region. An evaluation of a meteorological event (dust storm); impact of change in soil-related parameters and meteorological input grid resolution on these aerosol concentrations has been performed. Dust storm simulation over Indo-Gangetic basin indicates ability of the model to capture dust storm events. Measured (AERONET data) and simulated parameters such as aerosol optical depth (AOD) and Angstrom exponent are used to evaluate the performance of the model to capture the dust storm event. A sensitivity study is performed to investigate the impact of change in soil characteristics (thickness of the soil layer in contact with air, volumetric water, and air content of the soil) and meteorological input grid resolution on the aerosol (dust, PM10, BC) distribution. Results show that soil parameters and meteorological input grid resolution have an important impact on spatial distribution of aerosol (dust, PM10, BC) concentrations.

Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes-S. cerevisiae, D. melanogaster, C. elegans, M. musculus, T. rubripes and H. sapiens-and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P. falciparum sheds light on possible strategies in host-pathogen interactions.

Colored polydimethylsiloxane micropillar arrays for high throughput measurements of forces applied by genetic model organisms

Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color enhances contrast making it easier to detect and track pillar displacement driven by the organism. Second, we developed a semiautomated graphical user interface to analyze the images for pillar displacement, thus reducing the analysis time for each animal to minutes. The addition of color reduced the Young's modulus of PDMS. Therefore, the dye-PDMS composite was characterized using Yeoh's hyperelastic model and the pillars were calibrated using a silicon based force sensor. We used our device to measure forces exerted by wild type and mutant Caenorhabditis elegans moving on an agarose surface. Wild type C. elegans exert an average force of similar to 1 mu N on an individual pillar and a total average force of similar to 7.68 mu N. We show that the middle of C. elegans exerts more force than its extremities. We find that C. elegans mutants with defective body wall muscles apply significantly lower force on individual pillars, while mutants defective in sensing externally applied mechanical forces still apply the same average force per pillar compared to wild type animals. Average forces applied per pillar are independent of the length, diameter, or cuticle stiffness of the animal. We also used the device to measure, for the first time, forces applied by Drosophila melanogaster larvae. Peristaltic waves occurred at 0.4Hz applying an average force of similar to 1.58 mu N on a single pillar. Our colored microfluidic device along with its displacement tracking software allows us to measure forces applied by multiple model organisms that crawl or slither to travel through their environment. (C) 2015 AIP Publishing LLC.

Surface motions and intraplate continental deformation in Alaska driven by mantle flow

The degree to which the lithosphere and mantle are coupled and contribute to surface deformation beneath continental regions remains a fundamental question in the field of geodynamics. Here we use a new approach with a surface deformation field constrained by GPS, geologic, and seismicity data, together with a lithospheric geodynamic model, to solve for tractions inferred to be generated by mantle convection that (1) drive extension within interior Alaska generating southward directed surface motions toward the southern convergent plate boundary, (2) result in accommodation of the relative motions between the Pacific and North America in a comparatively small zone near the plate boundary, and (3) generate the observed convergence within the North American plate interior in the Mackenzie mountains in northwestern Canada. The evidence for deeper mantle influence on surface deformation beneath a continental region suggests that this mechanism may be an important contributing driver to continental plate assemblage and breakup.

An Optimizing Code Generator for a Class of Lattice-Boltzmann Computations

The Lattice-Boltzmann method (LBM), a promising new particle-based simulation technique for complex and multiscale fluid flows, has seen tremendous adoption in recent years in computational fluid dynamics. Even with a state-of-the-art LBM solver such as Palabos, a user has to still manually write the program using library-supplied primitives. We propose an automated code generator for a class of LBM computations with the objective to achieve high performance on modern architectures. Few studies have looked at time tiling for LBM codes. We exploit a key similarity between stencils and LBM to enable polyhedral optimizations and in turn time tiling for LBM. We also characterize the performance of LBM with the Roofline performance model. Experimental results for standard LBM simulations like Lid Driven Cavity, Flow Past Cylinder, and Poiseuille Flow show that our scheme consistently outperforms Palabos-on average by up to 3x while running on 16 cores of an Intel Xeon (Sandybridge). We also obtain an improvement of 2.47x on the SPEC LBM benchmark.

Electrically driven intracellular and extracellular nanomanipulators evoke neurogenic/cardiomyogenic differentiation in human mesenchymal stem cells

Nanomechanical intervention through electroactuation is an effective strategy to guide stem cell differentiation for tissue engineering and regenerative medicine. In the present study, we elucidate that physical forces exerted by electroactuated gold nanoparticles (GNPs) have a strong influence in regulating the lineage commitment of human mesenchymal stem cells (hMSCs). A novel platform that combines intracellular and extracellular GNPs as nano-manipulators was designed to trigger neurogenic/cardiomyogenic differentiation in hMSCs, in electric field stimulated culture condition. In order to mimic the native microenvironment of nerve and cardiac tissues, hMSCs were treated with physiologically relevant direct current electric field (DC EF) or pulsed electric field (PEF) stimuli, respectively. When exposed to regular intermittent cycles of DC EF stimuli, majority of the GNP actuated hMSCs acquired longer filopodial extensions with multiple branch-points possessing neural-like architecture. Such morphological changes were consistent with higher mRNA expression level for neural-specific markers. On the other hand, PEF elicited cardiomyogenic differentiation, which is commensurate with the tubelike morphological alterations along with the upregulation of cardiac specific markers. The observed effect was significantly promoted even by intracellular actuation and was found to be substrate independent. Further, we have substantiated the participation of oxidative signaling, G0/G1 cell cycle arrest and intracellular calcium Ca2+] elevation as the key upstream regulators dictating GNP assisted hMSC differentiation. Thus, by adopting dual stimulation protocols, we could successfully divert the DC EF exposed cells to differentiate predominantly into neural-like cells and PEF treated cells into cardiomyogenic-like cells, via nanoactuation of GNPs. Such a novel multifaceted approach can be exploited to combat tissue loss following brain injury or heart failure. (C) 2015 Elsevier Ltd. All rights reserved.

Enhanced Metastatic Potential in a 3D Tissue Scaffold toward a Comprehensive in Vitro Model for Breast Cancer Metastasis

Metastasis is clinically the most challenging and lethal aspect of breast cancer. While animal-based xenograft models are expensive and time-consuming, conventional two-dimensional (2D) cell culture systems fail to mimic in vivo signaling. In this study we have developed a three-dimensional (3D) scaffold system that better mimics the topography and mechanical properties of the breast tumor, thus recreating the tumor microenvironment in vitro to study breast cancer metastasis. Porous poly(e-caprolactone) (PCL) scaffolds of modulus 7.0 +/- 0.5 kPa, comparable to that of breast tumor tissue were fabricated, on which MDA-MB-231 cells proliferated forming tumoroids. A comparative gene expression analysis revealed that cells growing in the scaffolds expressed increased levels of genes implicated in the three major events of metastasis, viz., initiation, progression, and the site-specific colonization compared to cells grown in conventional 2D tissue culture polystyrene (TCPS) dishes. The cells cultured in scaffolds showed increased invasiveness and sphere efficiency in vitro and increased lung metastasis in vivo. A global gene expression analysis revealed a significant increase in the expression of genes involved in cell cell and cell matrix interactions and tissue remodeling, cancer inflammation, and the PI3K/Akt, Wnt, NF-kappaB, and HIFI signaling pathways all of which are implicated in metastasis. Thus, culturing breast cancer cells in 3D scaffolds that mimic the in vivo tumor-like microenvironment enhances their metastatic potential. This system could serve as a comprehensive in vitro model to investigate the manifold mechanisms of breast cancer metastasis.

Numerical study of driven flows of shear thinning viscoelastic fluids in rectangular cavities

In this work, we present a numerical study of flow of shear thinning viscoelastic fluids in rectangular lid driven cavities for a wide range of aspect ratios (depth to width ratio) varying from 1/16 to 4. In particular, the effect of elasticity, inertia, model parameters and polymer concentration on flow features in rectangular driven cavity has been studied for two shear thinning viscoelastic fluids, namely, Giesekus and linear PTT. We perform numerical simulations using the symmetric square root representation of the conformation tensor to stabilize the numerical scheme against the high Weissenberg number problem. The variation in flow structures associated with merging and splitting of elongated vortices in shallow cavities and coalescence of corner eddies to yield a second primary vortex in deep cavities with respect to the variation in flow parameters is discussed. We discuss the effect of the dominant eigenvalues and the corresponding eigenvectors on the location of the primary eddy in the cavity. We also demonstrate, by performing numerical simulations for shallow and deep cavities, that where the Deborah number (based on convective time scale) characterizes the elastic behaviour of the fluid in deep cavities, Weissenberg number (based on shear rate) should be used for shallow cavities. (C) 2016 Elsevier B.V. All rights reserved.