Non-Newtonian particulate flow simulation: A direct-forcing immersed boundary-lattice Boltzmann approach

NASA Astrophysics Data System (ADS)

Amiri Delouei, A.; Nazari, M.; Kayhani, M. H.; Kang, S. K.; Succi, S.

2016-04-01

In the current study, a direct-forcing immersed boundary-non-Newtonian lattice Boltzmann method (IB-NLBM) is developed to investigate the sedimentation and interaction of particles in shear-thinning and shear-thickening fluids. In the proposed IB-NLBM, the non-linear mechanics of non-Newtonian particulate flows is detected by combination of the most desirable features of immersed boundary and lattice Boltzmann methods. The noticeable roles of non-Newtonian behavior on particle motion, settling velocity and generalized Reynolds number are investigated by simulating benchmark problem of one-particle sedimentation under the same generalized Archimedes number. The effects of extra force due to added accelerated mass are analyzed on the particle motion which have a significant impact on shear-thinning fluids. For the first time, the phenomena of interaction among the particles, such as Drafting, Kissing, and Tumbling in non-Newtonian fluids are investigated by simulation of two-particle sedimentation and twelve-particle sedimentation. The results show that increasing the shear-thickening behavior of fluid leads to a significant increase in the kissing time. Moreover, the transverse position of particles for shear-thinning fluids during the tumbling interval is different from Newtonian and the shear-thickening fluids. The present non-Newtonian particulate study can be applied in several industrial and scientific applications, like the non-Newtonian sedimentation behavior of particles in food industrial and biological fluids.

Capturing microscopic features of bone remodeling into a macroscopic model based on biological rationales of bone adaptation.

PubMed

Kim, Young Kwan; Kameo, Yoshitaka; Tanaka, Sakae; Adachi, Taiji

2017-10-01

To understand Wolff's law, bone adaptation by remodeling at the cellular and tissue levels has been discussed extensively through experimental and simulation studies. For the clinical application of a bone remodeling simulation, it is significant to establish a macroscopic model that incorporates clarified microscopic mechanisms. In this study, we proposed novel macroscopic models based on the microscopic mechanism of osteocytic mechanosensing, in which the flow of fluid in the lacuno-canalicular porosity generated by fluid pressure gradients plays an important role, and theoretically evaluated the proposed models, taking biological rationales of bone adaptation into account. The proposed models were categorized into two groups according to whether the remodeling equilibrium state was defined globally or locally, i.e., the global or local uniformity models. Each remodeling stimulus in the proposed models was quantitatively evaluated through image-based finite element analyses of a swine cancellous bone, according to two introduced criteria associated with the trabecular volume and orientation at remodeling equilibrium based on biological rationales. The evaluation suggested that nonuniformity of the mean stress gradient in the local uniformity model, one of the proposed stimuli, has high validity. Furthermore, the adaptive potential of each stimulus was discussed based on spatial distribution of a remodeling stimulus on the trabecular surface. The theoretical consideration of a remodeling stimulus based on biological rationales of bone adaptation would contribute to the establishment of a clinically applicable and reliable simulation model of bone remodeling.

Mechanics of undulatory swimming in a frictional fluid.

PubMed

Ding, Yang; Sharpe, Sarah S; Masse, Andrew; Goldman, Daniel I

2012-01-01

The sandfish lizard (Scincus scincus) swims within granular media (sand) using axial body undulations to propel itself without the use of limbs. In previous work we predicted average swimming speed by developing a numerical simulation that incorporated experimentally measured biological kinematics into a multibody sandfish model. The model was coupled to an experimentally validated soft sphere discrete element method simulation of the granular medium. In this paper, we use the simulation to study the detailed mechanics of undulatory swimming in a "granular frictional fluid" and compare the predictions to our previously developed resistive force theory (RFT) which models sand-swimming using empirically determined granular drag laws. The simulation reveals that the forward speed of the center of mass (CoM) oscillates about its average speed in antiphase with head drag. The coupling between overall body motion and body deformation results in a non-trivial pattern in the magnitude of lateral displacement of the segments along the body. The actuator torque and segment power are maximal near the center of the body and decrease to zero toward the head and the tail. Approximately 30% of the net swimming power is dissipated in head drag. The power consumption is proportional to the frequency in the biologically relevant range, which confirms that frictional forces dominate during sand-swimming by the sandfish. Comparison of the segmental forces measured in simulation with the force on a laterally oscillating rod reveals that a granular hysteresis effect causes the overestimation of the body thrust forces in the RFT. Our models provide detailed testable predictions for biological locomotion in a granular environment.

Coupling LAMMPS with Lattice Boltzmann fluid solver: theory, implementation, and applications

NASA Astrophysics Data System (ADS)

Tan, Jifu; Sinno, Talid; Diamond, Scott

2016-11-01

Studying of fluid flow coupled with solid has many applications in biological and engineering problems, e.g., blood cell transport, particulate flow, drug delivery. We present a partitioned approach to solve the coupled Multiphysics problem. The fluid motion is solved by the Lattice Boltzmann method, while the solid displacement and deformation is simulated by Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The coupling is achieved through the immersed boundary method so that the expensive remeshing step is eliminated. The code can model both rigid and deformable solids. The code also shows very good scaling results. It was validated with classic problems such as migration of rigid particles, ellipsoid particle's orbit in shear flow. Examples of the applications in blood flow, drug delivery, platelet adhesion and rupture are also given in the paper. NIH.

Lattice Boltzmann simulations of flapping wings: The flock effect and the lateral wind effect

NASA Astrophysics Data System (ADS)

de Rosis, Alessandro

2014-02-01

In this paper, numerical analysis aiming at simulating biological organisms immersed in a fluid are carried out. The fluid domain is modeled through the lattice Boltzmann (LB) method, while the immersed boundary method is used to account for the position of the organisms idealized as rigid bodies. The time discontinuous Galerkin method is employed to compute body motion. An explicit coupling strategy to combine the adopted numerical methods is proposed. The vertical take-off of a couple of butterflies is numerically simulated in different scenarios, showing the mutual interaction that a butterfly exerts on the other one. Moreover, the effect of lateral wind is investigated. A critical threshold value of the lateral wind is defined, thus corresponding to an increasing arduous take-off.

Fluid-Structure Interaction Simulation of Prosthetic Aortic Valves: Comparison between Immersed Boundary and Arbitrary Lagrangian-Eulerian Techniques for the Mesh Representation

PubMed Central

Iannaccone, Francesco; Degroote, Joris; Vierendeels, Jan; Segers, Patrick

2016-01-01

In recent years the role of FSI (fluid-structure interaction) simulations in the analysis of the fluid-mechanics of heart valves is becoming more and more important, being able to capture the interaction between the blood and both the surrounding biological tissues and the valve itself. When setting up an FSI simulation, several choices have to be made to select the most suitable approach for the case of interest: in particular, to simulate flexible leaflet cardiac valves, the type of discretization of the fluid domain is crucial, which can be described with an ALE (Arbitrary Lagrangian-Eulerian) or an Eulerian formulation. The majority of the reported 3D heart valve FSI simulations are performed with the Eulerian formulation, allowing for large deformations of the domains without compromising the quality of the fluid grid. Nevertheless, it is known that the ALE-FSI approach guarantees more accurate results at the interface between the solid and the fluid. The goal of this paper is to describe the same aortic valve model in the two cases, comparing the performances of an ALE-based FSI solution and an Eulerian-based FSI approach. After a first simplified 2D case, the aortic geometry was considered in a full 3D set-up. The model was kept as similar as possible in the two settings, to better compare the simulations’ outcomes. Although for the 2D case the differences were unsubstantial, in our experience the performance of a full 3D ALE-FSI simulation was significantly limited by the technical problems and requirements inherent to the ALE formulation, mainly related to the mesh motion and deformation of the fluid domain. As a secondary outcome of this work, it is important to point out that the choice of the solver also influenced the reliability of the final results. PMID:27128798

Advances in modelling of biomimetic fluid flow at different scales

PubMed Central

2011-01-01

The biomimetic flow at different scales has been discussed at length. The need of looking into the biological surfaces and morphologies and both geometrical and physical similarities to imitate the technological products and processes has been emphasized. The complex fluid flow and heat transfer problems, the fluid-interface and the physics involved at multiscale and macro-, meso-, micro- and nano-scales have been discussed. The flow and heat transfer simulation is done by various CFD solvers including Navier-Stokes and energy equations, lattice Boltzmann method and molecular dynamics method. Combined continuum-molecular dynamics method is also reviewed. PMID:21711847

Petroleum dynamics in the sea and influence of subsea dispersant injection during Deepwater Horizon.

PubMed

Gros, Jonas; Socolofsky, Scott A; Dissanayake, Anusha L; Jun, Inok; Zhao, Lin; Boufadel, Michel C; Reddy, Christopher M; Arey, J Samuel

2017-09-19

During the Deepwater Horizon disaster, a substantial fraction of the 600,000-900,000 tons of released petroleum liquid and natural gas became entrapped below the sea surface, but the quantity entrapped and the sequestration mechanisms have remained unclear. We modeled the buoyant jet of petroleum liquid droplets, gas bubbles, and entrained seawater, using 279 simulated chemical components, for a representative day (June 8, 2010) of the period after the sunken platform's riser pipe was pared at the wellhead (June 4-July 15). The model predicts that 27% of the released mass of petroleum fluids dissolved into the sea during ascent from the pared wellhead (1,505 m depth) to the sea surface, thereby matching observed volatile organic compound (VOC) emissions to the atmosphere. Based on combined results from model simulation and water column measurements, 24% of released petroleum fluid mass became channeled into a stable deep-water intrusion at 900- to 1,300-m depth, as aqueously dissolved compounds (∼23%) and suspended petroleum liquid microdroplets (∼0.8%). Dispersant injection at the wellhead decreased the median initial diameters of simulated petroleum liquid droplets and gas bubbles by 3.2-fold and 3.4-fold, respectively, which increased dissolution of ascending petroleum fluids by 25%. Faster dissolution increased the simulated flows of water-soluble compounds into biologically sparse deep water by 55%, while decreasing the flows of several harmful compounds into biologically rich surface water. Dispersant injection also decreased the simulated emissions of VOCs to the atmosphere by 28%, including a 2,000-fold decrease in emissions of benzene, which lowered health risks for response workers.

Petroleum dynamics in the sea and influence of subsea dispersant injection during Deepwater Horizon

PubMed Central

Gros, Jonas; Socolofsky, Scott A.; Dissanayake, Anusha L.; Jun, Inok; Zhao, Lin; Boufadel, Michel C.; Reddy, Christopher M.; Arey, J. Samuel

2017-01-01

During the Deepwater Horizon disaster, a substantial fraction of the 600,000–900,000 tons of released petroleum liquid and natural gas became entrapped below the sea surface, but the quantity entrapped and the sequestration mechanisms have remained unclear. We modeled the buoyant jet of petroleum liquid droplets, gas bubbles, and entrained seawater, using 279 simulated chemical components, for a representative day (June 8, 2010) of the period after the sunken platform’s riser pipe was pared at the wellhead (June 4–July 15). The model predicts that 27% of the released mass of petroleum fluids dissolved into the sea during ascent from the pared wellhead (1,505 m depth) to the sea surface, thereby matching observed volatile organic compound (VOC) emissions to the atmosphere. Based on combined results from model simulation and water column measurements, 24% of released petroleum fluid mass became channeled into a stable deep-water intrusion at 900- to 1,300-m depth, as aqueously dissolved compounds (∼23%) and suspended petroleum liquid microdroplets (∼0.8%). Dispersant injection at the wellhead decreased the median initial diameters of simulated petroleum liquid droplets and gas bubbles by 3.2-fold and 3.4-fold, respectively, which increased dissolution of ascending petroleum fluids by 25%. Faster dissolution increased the simulated flows of water-soluble compounds into biologically sparse deep water by 55%, while decreasing the flows of several harmful compounds into biologically rich surface water. Dispersant injection also decreased the simulated emissions of VOCs to the atmosphere by 28%, including a 2,000-fold decrease in emissions of benzene, which lowered health risks for response workers. PMID:28847967

Fluid pumping using magnetic cilia

NASA Astrophysics Data System (ADS)

Hanasoge, Srinivas; Ballard, Matt; Alexeev, Alexander; Hesketh, Peter; Woodruff School of Mechanical Engineering Team

2016-11-01

Using experiments and computer simulations, we examine fluid pumping by artificial magnetic cilia fabricated using surface micromachining techniques. An asymmetry in forward and recovery strokes of the elastic cilia causes the net pumping in a creeping flow regime. We show this asymmetry in the ciliary strokes is due to the change in magnetization of the elastic cilia combined with viscous force due to the fluid. Specifically, the time scale for forward stroke is mostly governed by the magnetic forces, whereas the time scale for the recovery stroke is determined by the elastic and viscous forces. These different time scales result in different cilia deformation during forward and backward strokes which in turn lead to the asymmetry in the ciliary motion. To disclose the physics of magnetic cilia pumping we use a hybrid lattice Boltzmann and lattice spring method. We validate our model by comparing the simulation results with the experimental data. The results of our study will be useful to design microfluidic systems for fluid mixing and particle manipulation including different biological particles. USDA and NSF.

From video to computation of biological fluid-structure interaction problems

NASA Astrophysics Data System (ADS)

Dillard, Seth I.; Buchholz, James H. J.; Udaykumar, H. S.

2016-04-01

This work deals with the techniques necessary to obtain a purely Eulerian procedure to conduct CFD simulations of biological systems with moving boundary flow phenomena. Eulerian approaches obviate difficulties associated with mesh generation to describe or fit flow meshes to body surfaces. The challenges associated with constructing embedded boundary information, body motions and applying boundary conditions on the moving bodies for flow computation are addressed in the work. The overall approach is applied to the study of a fluid-structure interaction problem, i.e., the hydrodynamics of swimming of an American eel, where the motion of the eel is derived from video imaging. It is shown that some first-blush approaches do not work, and therefore, careful consideration of appropriate techniques to connect moving images to flow simulations is necessary and forms the main contribution of the paper. A combination of level set-based active contour segmentation with optical flow and image morphing is shown to enable the image-to-computation process.

Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

PubMed Central

Sonne, Jacob; Jensen, Morten Ø.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

2007-01-01

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ∼48 Å2. To obtain fluid (Lα) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field. PMID:17400696

Evaporative concentration on a paper-based device to concentrate analytes in a biological fluid.

PubMed

Wong, Sharon Y; Cabodi, Mario; Rolland, Jason; Klapperich, Catherine M

2014-12-16

We report the first demonstration of using heat on a paper device to rapidly concentrate a clinically relevant analyte of interest from a biological fluid. Our technology relies on the application of localized heat to a paper strip to evaporate off hundreds of microliters of liquid to concentrate the target analyte. This method can be used to enrich for a target analyte that is present at low concentrations within a biological fluid to enhance the sensitivity of downstream detection methods. We demonstrate our method by concentrating the tuberculosis-specific glycolipid, lipoarabinomannan (LAM), a promising urinary biomarker for the detection and diagnosis of tuberculosis. We show that the heat does not compromise the subsequent immunodetectability of LAM, and in 20 min, the tuberculosis biomarker was concentrated by nearly 20-fold in simulated urine. Our method requires only 500 mW of power, and sample flow is self-driven via capillary action. As such, our technology can be readily integrated into portable, battery-powered, instrument-free diagnostic devices intended for use in low-resource settings.

Numerical simulations of flying and swimming of biological systems with the viscous vortex particle method

NASA Astrophysics Data System (ADS)

Eldredge, Jeff

2005-11-01

Many biological mechanisms of locomotion involve the interaction of a fluid with a deformable surface undergoing large unsteady motion. Analysis of such problems poses a significant challenge to conventional grid-based computational approaches. Particularly in the moderate Reynolds number regime where many insects and fish function, viscous and inertial processes are both important, and vorticity serves a crucial role. In this work, the viscous vortex particle method is shown to provide an efficient, intuitive simulation approach for investigation of these biological systems. In contrast with a grid-based approach, the method solves the Navier--Stokes equations by tracking computational particles that carry smooth blobs of vorticity and exchange strength with one another to account for viscous diffusion. Thus, computational resources are focused on the physically relevant features of the flow, and there is no need for artificial boundary conditions. Building from previously-developed techniques for the creation of vorticity to enforce no-throughflow and no-slip conditions, the present method is extended to problems of coupled fluid--body dynamics by enforcement of global conservation of momenta. The application to several two-dimensional model problems is demonstrated, including single and multiple flapping wings and free swimming of a three-linkage fish.

Corrosion resistance and biological activity of TiO2 implant coatings produced in oxygen-rich environments.

PubMed

Zhang, Rui; Wan, Yi; Ai, Xing; Liu, Zhanqiang; Zhang, Dong

2017-01-01

The physical and chemical properties of bio-titanium alloy implant surfaces play an important role in their corrosion resistance and biological activity. New turning and turning-rolling processes are presented, employing an oxygen-rich environment in order to obtain titanium dioxide layers that can both protect implants from corrosion and also promote cell adhesion. The surface topographies, surface roughnesses and chemical compositions of the sample surfaces were obtained using scanning electron microscopy, a white light interferometer, and the Auger electron spectroscopy, respectively. The corrosion resistance of the samples in a simulated body fluid was determined using electrochemical testing. Biological activity on the samples was also analyzed, using a vitro cell culture system. The results show that compared with titanium oxide layers formed using a turning process in air, the thickness of the titanium oxide layers formed using turning and turning-rolling processes in an oxygen-rich environment increased by 4.6 and 7.3 times, respectively. Using an oxygen-rich atmosphere in the rolling process greatly improves the corrosion resistance of the resulting samples in a simulated body fluid. On samples produced using the turning-rolling process, cells spread quickly and exhibited the best adhesion characteristics.

Multi-Constituent Simulation of Thrombus Deposition

NASA Astrophysics Data System (ADS)

Wu, Wei-Tao; Jamiolkowski, Megan A.; Wagner, William R.; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F.

2017-02-01

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices.

Multi-Constituent Simulation of Thrombus Deposition

PubMed Central

Wu, Wei-Tao; Jamiolkowski, Megan A.; Wagner, William R.; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F.

2017-01-01

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices. PMID:28218279

Multi-Constituent Simulation of Thrombus Deposition.

PubMed

Wu, Wei-Tao; Jamiolkowski, Megan A; Wagner, William R; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F

2017-02-20

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices.

Design, modeling and simulation of MEMS-based silicon Microneedles

NASA Astrophysics Data System (ADS)

Amin, F.; Ahmed, S.

2013-06-01

The advancement in semiconductor process engineering and nano-scale fabrication technology has made it convenient to transport specific biological fluid into or out of human skin with minimum discomfort. Fluid transdermal delivery systems such as Microneedle arrays are one such emerging and exciting Micro-Electro Mechanical System (MEMS) application which could lead to a total painless fluid delivery into skin with controllability and desirable yield. In this study, we aimed to revisit the problem with modeling, design and simulations carried out for MEMS based silicon hollow out of plane microneedle arrays for biomedical applications particularly for transdermal drug delivery. An approximate 200 μm length of microneedle with 40 μm diameter of lumen has been successfully shown formed by isotropic and anisotropic etching techniques using MEMS Pro design tool. These microneedles are arranged in size of 2 × 4 matrix array with center to center spacing of 750 μm. Furthermore, comparisons for fluid flow characteristics through these microneedle channels have been modeled with and without the contribution of the gravitational forces using mathematical models derived from Bernoulli Equation. Physical Process simulations have also been performed on TCAD SILVACO to optimize the design of these microneedles aligned with the standard Si-Fabrication lines.

Modern Chemistry Techniques Applied to Metal Behavior and Chelation in Medical and Environmental Systems ? Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutton, M; Andresen, B; Burastero, S R

2005-02-03

This report details the research and findings generated over the course of a 3-year research project funded by Lawrence Livermore National Laboratory (LLNL) Laboratory Directed Research and Development (LDRD). Originally tasked with studying beryllium chemistry and chelation for the treatment of Chronic Beryllium Disease and environmental remediation of beryllium-contaminated environments, this work has yielded results in beryllium and uranium solubility and speciation associated with toxicology; specific and effective chelation agents for beryllium, capable of lowering beryllium tissue burden and increasing urinary excretion in mice, and dissolution of beryllium contamination at LLNL Site 300; {sup 9}Be NMR studies previously unstudied atmore » LLNL; secondary ionization mass spec (SIMS) imaging of beryllium in spleen and lung tissue; beryllium interactions with aerogel/GAC material for environmental cleanup. The results show that chelator development using modern chemical techniques such as chemical thermodynamic modeling, was successful in identifying and utilizing tried and tested beryllium chelators for use in medical and environmental scenarios. Additionally, a study of uranium speciation in simulated biological fluids identified uranium species present in urine, gastric juice, pancreatic fluid, airway surface fluid, simulated lung fluid, bile, saliva, plasma, interstitial fluid and intracellular fluid.« less

Bioelectrical Impedance and The Frequency Dependent Current Conduction Through Biological Tissues: A Short Review

NASA Astrophysics Data System (ADS)

Kanti Bera, Tushar

2018-03-01

Biological tissues are developed with biological cells which exhibit complex electrical impedance called electrical bioimpedance. Under an alternating electrical excitation the bioimpedance varies with the tissue anatomy, composition and the signal frequency. The current penetration and conduction paths vary with frequency of the applied signal. Bioimpedance spectroscopy is used to study the frequency response of the electrical impedance of biological materials noninvasively. In bioimpedance spectroscopy, a low amplitude electrical signal is injected to the tissue sample or body parts to characterization the sample in terms of its bioimpedance. The electrical current conduction phenomena, which is highly influenced by the tissue impedance and the signal frequency, is an important phenomena which should be studied to understand the bioimpedance techniques like bioelectrical impedance analysis (BIA), EIS, or else. In this paper the origin of bioelectrical impedance and current conduction phenomena has been reviewed to present a brief summary of bioelectrical impedance and the frequency dependent current conduction through biological tissues. Simulation studies are conducted with alternation current injection through a two dimensional model of biological tissues containing finite number of biological cells suspended in extracellular fluid. The paper demonstrates the simulation of alternating current conduction through biological tissues conducted by COMSOL Multiphysics. Simulation studies also show the frequency response of the tissue impedance for different tissue compositions.

Rahman Prize Lecture: Lattice Boltzmann simulation of complex states of flowing matter

NASA Astrophysics Data System (ADS)

Succi, Sauro

Over the last three decades, the Lattice Boltzmann (LB) method has gained a prominent role in the numerical simulation of complex flows across an impressively broad range of scales, from fully-developed turbulence in real-life geometries, to multiphase flows in micro-fluidic devices, all the way down to biopolymer translocation in nanopores and lately, even quark-gluon plasmas. After a brief introduction to the main ideas behind the LB method and its historical developments, we shall present a few selected applications to complex flow problems at various scales of motion. Finally, we shall discuss prospects for extreme-scale LB simulations of outstanding problems in the physics of fluids and its interfaces with material sciences and biology, such as the modelling of fluid turbulence, the optimal design of nanoporous gold catalysts and protein folding/aggregation in crowded environments.

The fate of calcium carbonate nanoparticles administered by oral route: absorption and their interaction with biological matrices

PubMed Central

Lee, Jeong-A; Kim, Mi-Kyung; Kim, Hyoung-Mi; Lee, Jong Kwon; Jeong, Jayoung; Kim, Young-Rok; Oh, Jae-Min; Choi, Soo-Jin

2015-01-01

Background Orally administered particles rapidly interact with biological fluids containing proteins, enzymes, electrolytes, and other biomolecules to eventually form particles covered by a corona, and this corona potentially affects particle uptake, fate, absorption, distribution, and elimination in vivo. This study explored relationships between the biological interactions of calcium carbonate particles and their biokinetics. Methods We examined the effects of food grade calcium carbonates of different particle size (nano [N-Cal] and bulk [B-Cal]: specific surface areas of 15.8 and 0.83 m2/g, respectively) on biological interactions in in vitro simulated physiological fluids, ex vivo biofluids, and in vivo in gastrointestinal fluid. Moreover, absorption and tissue distribution of calcium carbonates were evaluated following a single dose oral administration to rats. Results N-Cal interacted more with biomatrices than bulk materials in vitro and ex vivo, as evidenced by high fluorescence quenching ratios, but it did not interact more actively with biomatrices in vivo. Analysis of coronas revealed that immunoglobulin, apolipoprotein, thrombin, and fibrinogen, were the major corona proteins, regardless of particle size. A biokinetic study revealed that orally delivered N-Cal was more rapidly absorbed into the blood stream than B-Cal, but no significant differences were observed between the two in terms of absorption efficiencies or tissue distributions. Both calcium carbonates were primarily present as particulate forms in gastrointestinal fluids but enter the circulatory system in dissolved Ca2+, although both types showed partial phase transformation to dicalcium phosphate dihydrate. Relatively low dissolution (about 4%), no remarkable protein–particle interaction, and the major particulate fate of calcium carbonate in vivo gastrointestinal fluids can explain its low oral absorption (about 4%) regardless of particle size. Conclusion We conclude that calcium carbonate nanoparticles can act more actively with biological matrices in vitro and ex vivo, but that in vivo, their biological interactions and biokinetics are not affected by particle size. PMID:25848250

The fate of calcium carbonate nanoparticles administered by oral route: absorption and their interaction with biological matrices.

PubMed

Lee, Jeong-A; Kim, Mi-Kyung; Kim, Hyoung-Mi; Lee, Jong Kwon; Jeong, Jayoung; Kim, Young-Rok; Oh, Jae-Min; Choi, Soo-Jin

2015-01-01

Orally administered particles rapidly interact with biological fluids containing proteins, enzymes, electrolytes, and other biomolecules to eventually form particles covered by a corona, and this corona potentially affects particle uptake, fate, absorption, distribution, and elimination in vivo. This study explored relationships between the biological interactions of calcium carbonate particles and their biokinetics. We examined the effects of food grade calcium carbonates of different particle size (nano [N-Cal] and bulk [B-Cal]: specific surface areas of 15.8 and 0.83 m(2)/g, respectively) on biological interactions in in vitro simulated physiological fluids, ex vivo biofluids, and in vivo in gastrointestinal fluid. Moreover, absorption and tissue distribution of calcium carbonates were evaluated following a single dose oral administration to rats. N-Cal interacted more with biomatrices than bulk materials in vitro and ex vivo, as evidenced by high fluorescence quenching ratios, but it did not interact more actively with biomatrices in vivo. Analysis of coronas revealed that immunoglobulin, apolipoprotein, thrombin, and fibrinogen, were the major corona proteins, regardless of particle size. A biokinetic study revealed that orally delivered N-Cal was more rapidly absorbed into the blood stream than B-Cal, but no significant differences were observed between the two in terms of absorption efficiencies or tissue distributions. Both calcium carbonates were primarily present as particulate forms in gastrointestinal fluids but enter the circulatory system in dissolved Ca(2+), although both types showed partial phase transformation to dicalcium phosphate dihydrate. Relatively low dissolution (about 4%), no remarkable protein-particle interaction, and the major particulate fate of calcium carbonate in vivo gastrointestinal fluids can explain its low oral absorption (about 4%) regardless of particle size. We conclude that calcium carbonate nanoparticles can act more actively with biological matrices in vitro and ex vivo, but that in vivo, their biological interactions and biokinetics are not affected by particle size.

Microgravity Fluids for Biology, Workshop

NASA Technical Reports Server (NTRS)

Griffin, DeVon; Kohl, Fred; Massa, Gioia D.; Motil, Brian; Parsons-Wingerter, Patricia; Quincy, Charles; Sato, Kevin; Singh, Bhim; Smith, Jeffrey D.; Wheeler, Raymond M.

2013-01-01

Microgravity Fluids for Biology represents an intersection of biology and fluid physics that present exciting research challenges to the Space Life and Physical Sciences Division. Solving and managing the transport processes and fluid mechanics in physiological and biological systems and processes are essential for future space exploration and colonization of space by humans. Adequate understanding of the underlying fluid physics and transport mechanisms will provide new, necessary insights and technologies for analyzing and designing biological systems critical to NASAs mission. To enable this mission, the fluid physics discipline needs to work to enhance the understanding of the influence of gravity on the scales and types of fluids (i.e., non-Newtonian) important to biology and life sciences. In turn, biomimetic, bio-inspired and synthetic biology applications based on physiology and biology can enrich the fluid mechanics and transport phenomena capabilities of the microgravity fluid physics community.

In Vitro Dissolution Tests of Plutonium and Americium Containing Contamination Originating From ZPPR Fuel Plates

DOE Office of Scientific and Technical Information (OSTI.GOV)

William F. Bauer; Brian K. Schuetz; Gary M. Huestis

2012-09-01

Assessing the extent of internal dose is of concern whenever workers are exposed to airborne radionuclides or other contaminants. Internal dose determinations depend upon a reasonable estimate of the expected biological half-life of the contaminants in the respiratory tract. One issue with refractory elements is determining the dissolution rate of the element. Actinides such as plutonium (Pu) and Americium (Am) tend to be very refractory and can have biological half-lives of tens of years. In the event of an exposure, the dissolution rates of the radionuclides of interest needs to be assessed in order to assign the proper internal dosemore » estimates. During the November 2011 incident at the Idaho National Laboratory (INL) involving a ZPPR fuel plate, air filters in a constant air monitor (CAM) and a giraffe filter apparatus captured airborne particulate matter. These filters were used in dissolution rate experiments to determine the apparent dissolution half-life of Pu and Am in simulated biological fluids. This report describes these experiments and the results. The dissolution rates were found to follow a three term exponential decay equation. Differences were noted depending upon the nature of the biological fluid simulant. Overall, greater than 95% of the Pu and 93% of the Am were in a very slow dissolving component with dissolution half-lives of over 10 years.« less

Simulation by bondgraphs

NASA Astrophysics Data System (ADS)

Thoma, Jean Ulrich

The fundamental principles and applications of the bond graph method, in which a system is represented on paper by letter elements and their interconnections (bonds), are presented in an introduction for engineering students. Chapters are devoted to simulation and graphical system models; bond graphs as networks for power and signal exchange; the simulation and design of mechanical engineering systems; the simulation of fluid power systems and hydrostatic devices; electrical circuits, drives, and components; practical procedures and problems of bond-graph-based numerical simulation; and applications to thermodynamics, chemistry, and biology. Also included are worked examples of applications to robotics, shocks and collisions, ac circuits, hydraulics, and a hydropneumatic fatigue-testing machine.

Stability of plant virus-based nanocarriers in gastrointestinal fluids† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7nr07182e

PubMed Central

Evans, David J.; Baldelli Bombelli, Francesca; Lomonossoff, George P.

2018-01-01

Cowpea mosaic virus (CPMV) is a plant virus which is being extensively investigated as a drug delivery and vaccine nanocarrier for parenteral administration. However, to date little is known about the suitability of plant-based nanocarriers for oral delivery. In this study, the colloidal (i.e. aggregation), physical (i.e. denaturation) and chemical (i.e. digestion of the polypeptides) stability of CPMV and its empty virus-like particles (eVLPs) in conditions resembling the gastrointestinal fluids were evaluated. The nanoparticles were incubated in various simulated gastric and intestinal fluids and in pig gastric and intestinal fluids. CPMV and eVLPs had similar stabilities. In simulated gastric media, they were stable at pH ≥ 2.5. At lower pH destabilisation of the particle structure occurred, which, in turn, rendered the polypeptides extremely sensitive to pepsin digestion. However, both CPMV and eVLPs were stable in simulated intestinal fluids, in pig gastric fluids and in pig intestinal fluids. Thus CPMV, despite being a protein-based nanoparticle, was much more resistant to the harsh GI conditions than soluble proteins. Remarkably, both CPMV and eVLPs incubated in pig gastric and intestinal fluids were not subject to protein adsorption, with no formation of a detectable protein corona. The lack of a protein corona on CPMV and eVLP surfaces in GI fluids would imply that, if orally administered, these nanoparticles could maintain their native surface characteristics; thus, their biological interactions would remain predictable and unchanged. In summary, CPMV and eVLPs can be considered promising nanocarriers for applications requiring oral delivery, given their chemical, physical and colloidal stability and lack of protein adsorption from the environment in most of the tested conditions. PMID:29231944

Mesoscale modeling: solving complex flows in biology and biotechnology.

PubMed

Mills, Zachary Grant; Mao, Wenbin; Alexeev, Alexander

2013-07-01

Fluids are involved in practically all physiological activities of living organisms. However, biological and biorelated flows are hard to analyze due to the inherent combination of interdependent effects and processes that occur on a multitude of spatial and temporal scales. Recent advances in mesoscale simulations enable researchers to tackle problems that are central for the understanding of such flows. Furthermore, computational modeling effectively facilitates the development of novel therapeutic approaches. Among other methods, dissipative particle dynamics and the lattice Boltzmann method have become increasingly popular during recent years due to their ability to solve a large variety of problems. In this review, we discuss recent applications of these mesoscale methods to several fluid-related problems in medicine, bioengineering, and biotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modeling the Impact of Fracture Growth on Fluid Displacements in Deformable Porous Media

NASA Astrophysics Data System (ADS)

Santillán, D.; Cueto-Felgueroso, L.; Juanes, R.

2015-12-01

Coupled flow and geomechanics is a critical research challenge in engineering and the geosciences. The flow of a fluid through a deformable porous media is present in manyenvironmental, industrial, and biological processes,such as the removal of pollutants from underground water bodies, enhanced geothermal systems, unconventional hydrocarbon resources or enhanced oil recovery techniques. However, the injection of a fluid can generate or propagate fractures, which are preferential flow paths. Using numerical simulation, we study the interplay between injection and rock mechanics, and elucidate fracture propagation as a function of injection rate, initial crack topology and mechanical rock properties. Finally, we discuss the role of fracture growth on fluid displacements in porous media. Figure: An example of fracture (in red) propagated in a porous media (in blue)

Implementation and clinical application of a deformation method for fast simulation of biological tissue formed by fibers and fluid.

PubMed

Sardinha, Ana Gabriella de Oliveira; Oyama, Ceres Nunes de Resende; de Mendonça Maroja, Armando; Costa, Ivan F

2016-01-01

The aim of this paper is to provide a general discussion, algorithm, and actual working programs of the deformation method for fast simulation of biological tissue formed by fibers and fluid. In order to demonstrate the benefit of the clinical applications software, we successfully used our computational program to deform a 3D breast image acquired from patients, using a 3D scanner, in a real hospital environment. The method implements a quasi-static solution for elastic global deformations of objects. Each pair of vertices of the surface is connected and defines an elastic fiber. The set of all the elastic fibers defines a mesh of smaller size than the volumetric meshes, allowing for simulation of complex objects with less computational effort. The behavior similar to the stress tensor is obtained by the volume conservation equation that mixes the 3D coordinates. Step by step, we show the computational implementation of this approach. As an example, a 2D rectangle formed by only 4 vertices is solved and, for this simple geometry, all intermediate results are shown. On the other hand, actual implementations of these ideas in the form of working computer routines are provided for general 3D objects, including a clinical application.

Experimentally Testing Hydrothermal Vent Origin of Life on Enceladus and Other Icy/Ocean Worlds.

PubMed

Barge, Laura M; White, Lauren M

2017-09-01

We review various laboratory strategies and methods that can be utilized to simulate prebiotic processes and origin of life in hydrothermal vent systems on icy/ocean worlds. Crucial steps that could be simulated in the laboratory include simulations of water-rock chemistry (e.g., serpentinization) to produce hydrothermal fluids, the types of mineral catalysts and energy gradients produced in vent interfaces where hydrothermal fluids interface with the surrounding seawater, and simulations of biologically relevant chemistry in flow-through gradient systems (i.e., far-from-equilibrium experiments). We describe some examples of experimental designs in detail, which are adaptable and could be used to test particular hypotheses about ocean world energetics or mineral/organic chemistry. Enceladus among the ocean worlds provides an ideal test case, since the pressure at the ocean floor is more easily simulated in the lab. Results for Enceladus could be extrapolated with further experiments and modeling to understand other ocean worlds. Key Words: Enceladus-Ocean worlds-Icy worlds-Hydrothermal vent-Iron sulfide-Gradient. Astrobiology 17, 820-833.

Gravity-Driven Thin Film Flow of an Ellis Fluid.

PubMed

Kheyfets, Vitaly O; Kieweg, Sarah L

2013-12-01

The thin film lubrication approximation has been studied extensively for moving contact lines of Newtonian fluids. However, many industrial and biological applications of the thin film equation involve shear-thinning fluids, which often also exhibit a Newtonian plateau at low shear. This study presents new numerical simulations of the three-dimensional (i.e. two-dimensional spreading), constant-volume, gravity-driven, free surface flow of an Ellis fluid. The numerical solution was validated with a new similarity solution, compared to previous experiments, and then used in a parametric study. The parametric study centered around rheological data for an example biological application of thin film flow: topical drug delivery of anti-HIV microbicide formulations, e.g. hydroxyethylcellulose (HEC) polymer solutions. The parametric study evaluated how spreading length and front velocity saturation depend on Ellis parameters. A lower concentration polymer solution with smaller zero shear viscosity ( η 0 ), τ 1/2 , and λ values spread further. However, when comparing any two fluids with any possible combinations of Ellis parameters, the impact of changing one parameter on spreading length depends on the direction and magnitude of changes in the other two parameters. In addition, the isolated effect of the shear-thinning parameter, λ , on the front velocity saturation depended on τ 1/2 . This study highlighted the relative effects of the individual Ellis parameters, and showed that the shear rates in this flow were in both the shear-thinning and plateau regions of rheological behavior, emphasizing the importance of characterizing the full range of shear-rates in rheological measurements. The validated numerical model and parametric study provides a useful tool for future steps to optimize flow of a fluid with rheological behavior well-described by the Ellis constitutive model, in a range of industrial and biological applications.

Computational Fluid Dynamics Investigation of Human Aspiration in Low Velocity Air: Orientation Effects on Nose-Breathing Simulations

PubMed Central

Anderson, Kimberly R.; Anthony, T. Renée

2014-01-01

An understanding of how particles are inhaled into the human nose is important for developing samplers that measure biologically relevant estimates of exposure in the workplace. While previous computational mouth-breathing investigations of particle aspiration have been conducted in slow moving air, nose breathing still required exploration. Computational fluid dynamics was used to estimate nasal aspiration efficiency for an inhaling humanoid form in low velocity wind speeds (0.1–0.4 m s−1). Breathing was simplified as continuous inhalation through the nose. Fluid flow and particle trajectories were simulated over seven discrete orientations relative to the oncoming wind (0, 15, 30, 60, 90, 135, 180°). Sensitivities of the model simplification and methods were assessed, particularly the placement of the recessed nostril surface and the size of the nose. Simulations identified higher aspiration (13% on average) when compared to published experimental wind tunnel data. Significant differences in aspiration were identified between nose geometry, with the smaller nose aspirating an average of 8.6% more than the larger nose. Differences in fluid flow solution methods accounted for 2% average differences, on the order of methodological uncertainty. Similar trends to mouth-breathing simulations were observed including increasing aspiration efficiency with decreasing freestream velocity and decreasing aspiration with increasing rotation away from the oncoming wind. These models indicate nasal aspiration in slow moving air occurs only for particles <100 µm. PMID:24665111

Coupling molecular dynamics with lattice Boltzmann method based on the immersed boundary method

NASA Astrophysics Data System (ADS)

Tan, Jifu; Sinno, Talid; Diamond, Scott

2017-11-01

The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable solids exposed to flow. The code was validated with the classic problem of rigid ellipsoid particle orbit in shear flow, blood cell stretching test and effective blood viscosity, and demonstrated essentially linear scaling over 16 cores. An example of the fluid-solid coupling was given for flexible filaments (drug carriers) transport in a flowing blood cell suspensions, highlighting the advantages and capabilities of the developed code. NIH 1U01HL131053-01A1.

Geophysical fluid dynamics: whence, whither and why?

PubMed Central

2016-01-01

This article discusses the role of geophysical fluid dynamics (GFD) in understanding the natural environment, and in particular the dynamics of atmospheres and oceans on Earth and elsewhere. GFD, as usually understood, is a branch of the geosciences that deals with fluid dynamics and that, by tradition, seeks to extract the bare essence of a phenomenon, omitting detail where possible. The geosciences in general deal with complex interacting systems and in some ways resemble condensed matter physics or aspects of biology, where we seek explanations of phenomena at a higher level than simply directly calculating the interactions of all the constituent parts. That is, we try to develop theories or make simple models of the behaviour of the system as a whole. However, these days in many geophysical systems of interest, we can also obtain information for how the system behaves by almost direct numerical simulation from the governing equations. The numerical model itself then explicitly predicts the emergent phenomena—the Gulf Stream, for example—something that is still usually impossible in biology or condensed matter physics. Such simulations, as manifested, for example, in complicated general circulation models, have in some ways been extremely successful and one may reasonably now ask whether understanding a complex geophysical system is necessary for predicting it. In what follows we discuss such issues and the roles that GFD has played in the past and will play in the future. PMID:27616918

Generating Inviscid and Viscous Fluid Flow Simulations over a Surface Using a Quasi-simultaneous Technique

NASA Technical Reports Server (NTRS)

Sturdza, Peter (Inventor); Martins-Rivas, Herve (Inventor); Suzuki, Yoshifumi (Inventor)

2014-01-01

A fluid-flow simulation over a computer-generated surface is generated using a quasi-simultaneous technique. The simulation includes a fluid-flow mesh of inviscid and boundary-layer fluid cells. An initial fluid property for an inviscid fluid cell is determined using an inviscid fluid simulation that does not simulate fluid viscous effects. An initial boundary-layer fluid property a boundary-layer fluid cell is determined using the initial fluid property and a viscous fluid simulation that simulates fluid viscous effects. An updated boundary-layer fluid property is determined for the boundary-layer fluid cell using the initial fluid property, initial boundary-layer fluid property, and an interaction law. The interaction law approximates the inviscid fluid simulation using a matrix of aerodynamic influence coefficients computed using a two-dimensional surface panel technique and a fluid-property vector. An updated fluid property is determined for the inviscid fluid cell using the updated boundary-layer fluid property.

Engineering fluid flow using sequenced microstructures

NASA Astrophysics Data System (ADS)

Amini, Hamed; Sollier, Elodie; Masaeli, Mahdokht; Xie, Yu; Ganapathysubramanian, Baskar; Stone, Howard A.; di Carlo, Dino

2013-05-01

Controlling the shape of fluid streams is important across scales: from industrial processing to control of biomolecular interactions. Previous approaches to control fluid streams have focused mainly on creating chaotic flows to enhance mixing. Here we develop an approach to apply order using sequences of fluid transformations rather than enhancing chaos. We investigate the inertial flow deformations around a library of single cylindrical pillars within a microfluidic channel and assemble these net fluid transformations to engineer fluid streams. As these transformations provide a deterministic mapping of fluid elements from upstream to downstream of a pillar, we can sequentially arrange pillars to apply the associated nested maps and, therefore, create complex fluid structures without additional numerical simulation. To show the range of capabilities, we present sequences that sculpt the cross-sectional shape of a stream into complex geometries, move and split a fluid stream, perform solution exchange and achieve particle separation. A general strategy to engineer fluid streams into a broad class of defined configurations in which the complexity of the nonlinear equations of fluid motion are abstracted from the user is a first step to programming streams of any desired shape, which would be useful for biological, chemical and materials automation.

Generating Inviscid and Viscous Fluid-Flow Simulations over an Aircraft Surface Using a Fluid-Flow Mesh

NASA Technical Reports Server (NTRS)

Rodriguez, David L. (Inventor); Sturdza, Peter (Inventor)

2013-01-01

Fluid-flow simulation over a computer-generated aircraft surface is generated using inviscid and viscous simulations. A fluid-flow mesh of fluid cells is obtained. At least one inviscid fluid property for the fluid cells is determined using an inviscid fluid simulation that does not simulate fluid viscous effects. A set of intersecting fluid cells that intersects the aircraft surface are identified. One surface mesh polygon of the surface mesh is identified for each intersecting fluid cell. A boundary-layer prediction point for each identified surface mesh polygon is determined. At least one boundary-layer fluid property for each boundary-layer prediction point is determined using the at least one inviscid fluid property of the corresponding intersecting fluid cell and a boundary-layer simulation that simulates fluid viscous effects. At least one updated fluid property for at least one fluid cell is determined using the at least one boundary-layer fluid property and the inviscid fluid simulation.

Computational Modeling of Aerosol Hazard Arising from the Opening of an Anthrax Letter in an Open-Office Complex

NASA Astrophysics Data System (ADS)

Lien, F. S.; Ji, H.; Yee, E.

Early experimental work, conducted at Defence R&D Canada — Suffield, measured and characterized the personal and environmental contamination associated with the simulated opening of anthrax-tainted letters under a number of different scenarios. A better understanding of the physical and biological processes is considerably significant for detecting, assessing, and formulating potential mitigation strategies for managing these risks. These preliminary experimental investigations have been extended to simulate the contamination from the opening of anthrax-tainted letters in an Open-Office environment using Computational Fluid Dynamics (CFD). Bacillus globigii (BG) was used as a biological simulant for anthrax, with 0.1 gram of the simulant released from opened letters in the experiments conducted. The accuracy of the model for prediction of the spatial distribution of BG spores in the office is first assessed quantitatively by comparison with measured SF6 concentrations (the baseline experiment), and then qualitatively by comparison with measured BG concentrations obtained under a number of scenarios, some involving people moving within various offices.

Modeling the interactions between compliant microcapsules and pillars in microchannels

NASA Astrophysics Data System (ADS)

Zhu, Guangdong; Alexeev, Alexander; Kumacheva, Eugenia; Balazs, Anna C.

2007-07-01

Using a computational model, we investigate the motion of microcapsules inside a microchannel that encompasses a narrow constriction. The microcapsules are composed of a compliant, elastic shell and an encapsulated fluid; these fluid-filled shells model synthetic polymeric microcapsules or biological cells (e.g., leukocytes). Driven by an imposed flow, the capsules are propelled along the microchannel and through the constricted region, which is formed by two pillars that lie in registry, extending from the top and bottom walls of the channels. The tops of these pillars (facing into the microchannel) are modified to exhibit either a neutral or an attractive interaction with the microcapsules. The pillars (and constriction) model topological features that can be introduced into microfluidic devices or the physical and chemical heterogeneities that are inherently present in biological vessels. To simulate the behavior of this complex system, we employ a hybrid method that integrates the lattice Boltzmann model (LBM) for fluid dynamics and the lattice spring model (LSM) for the micromechanics of elastic solids. Through this LBM/LSM technique, we probe how the capsule's stiffness and interaction with the pillars affect its passage through the chambers. The results yield guidelines for regulating the movement of microcarriers in microfluidic systems and provide insight into the flow properties of biological cells in capillaries.

Non-integer viscoelastic constitutive law to model soft biological tissues to in-vivo indentation.

PubMed

Demirci, Nagehan; Tönük, Ergin

2014-01-01

During the last decades, derivatives and integrals of non-integer orders are being more commonly used for the description of constitutive behavior of various viscoelastic materials including soft biological tissues. Compared to integer order constitutive relations, non-integer order viscoelastic material models of soft biological tissues are capable of capturing a wider range of viscoelastic behavior obtained from experiments. Although integer order models may yield comparably accurate results, non-integer order material models have less number of parameters to be identified in addition to description of an intermediate material that can monotonically and continuously be adjusted in between an ideal elastic solid and an ideal viscous fluid. In this work, starting with some preliminaries on non-integer (fractional) calculus, the "spring-pot", (intermediate mechanical element between a solid and a fluid), non-integer order three element (Zener) solid model, finally a user-defined large strain non-integer order viscoelastic constitutive model was constructed to be used in finite element simulations. Using the constitutive equation developed, by utilizing inverse finite element method and in vivo indentation experiments, soft tissue material identification was performed. The results indicate that material coefficients obtained from relaxation experiments, when optimized with creep experimental data could simulate relaxation, creep and cyclic loading and unloading experiments accurately. Non-integer calculus viscoelastic constitutive models, having physical interpretation and modeling experimental data accurately is a good alternative to classical phenomenological viscoelastic constitutive equations.

Active elastohydrodynamics of vesicles in narrow blind constrictions

NASA Astrophysics Data System (ADS)

Fai, T. G.; Kusters, R.; Harting, J.; Rycroft, C. H.; Mahadevan, L.

2017-11-01

Fluid-resistance limited transport of vesicles through narrow constrictions is a recurring theme in many biological and engineering applications. Inspired by the motor-driven movement of soft membrane-bound vesicles into closed neuronal dendritic spines, here we study this problem using a combination of passive three-dimensional simulations and a simplified semianalytical theory for the active transport of vesicles forced through constrictions by molecular motors. We show that the motion of these objects is characterized by two dimensionless quantities related to the geometry and to the strength of forcing relative to the vesicle elasticity. We use numerical simulations to characterize the transit time for a vesicle forced by fluid pressure through a constriction in a channel and find that relative to an open channel, transport into a blind end leads to the formation of a smaller forward-flowing lubrication layer that strongly impedes motion. When the fluid pressure forcing is complemented by forces due to molecular motors that are responsible for vesicle trafficking into dendritic spines, we find that the competition between motor forcing and fluid drag results in multistable dynamics reminiscent of the real system. Our study highlights the role of nonlocal hydrodynamic effects in determining the kinetics of vesicular transport in constricted geometries.

Artificial heart for humanoid robot

NASA Astrophysics Data System (ADS)

Potnuru, Akshay; Wu, Lianjun; Tadesse, Yonas

2014-03-01

A soft robotic device inspired by the pumping action of a biological heart is presented in this study. Developing artificial heart to a humanoid robot enables us to make a better biomedical device for ultimate use in humans. As technology continues to become more advanced, the methods in which we implement high performance and biomimetic artificial organs is getting nearer each day. In this paper, we present the design and development of a soft artificial heart that can be used in a humanoid robot and simulate the functions of a human heart using shape memory alloy technology. The robotic heart is designed to pump a blood-like fluid to parts of the robot such as the face to simulate someone blushing or when someone is angry by the use of elastomeric substrates and certain features for the transport of fluids.

Fluid-structure interaction involving large deformations: 3D simulations and applications to biological systems

NASA Astrophysics Data System (ADS)

Tian, Fang-Bao; Dai, Hu; Luo, Haoxiang; Doyle, James F.; Rousseau, Bernard

2014-02-01

Three-dimensional fluid-structure interaction (FSI) involving large deformations of flexible bodies is common in biological systems, but accurate and efficient numerical approaches for modeling such systems are still scarce. In this work, we report a successful case of combining an existing immersed-boundary flow solver with a nonlinear finite-element solid-mechanics solver specifically for three-dimensional FSI simulations. This method represents a significant enhancement from the similar methods that are previously available. Based on the Cartesian grid, the viscous incompressible flow solver can handle boundaries of large displacements with simple mesh generation. The solid-mechanics solver has separate subroutines for analyzing general three-dimensional bodies and thin-walled structures composed of frames, membranes, and plates. Both geometric nonlinearity associated with large displacements and material nonlinearity associated with large strains are incorporated in the solver. The FSI is achieved through a strong coupling and partitioned approach. We perform several validation cases, and the results may be used to expand the currently limited database of FSI benchmark study. Finally, we demonstrate the versatility of the present method by applying it to the aerodynamics of elastic wings of insects and the flow-induced vocal fold vibration.

Translational and rotational diffusion of Janus nanoparticles at liquid interfaces

NASA Astrophysics Data System (ADS)

Rezvantalab, Hossein; Shojaei-Zadeh, Shahab

2014-11-01

We use molecular dynamics simulations to understand the thermal motion of nanometer-sized Janus particles at the interface between two immiscible fluids. We consider spherical nanoparticles composed of two sides with different affinity to fluid phases, and evaluate their dynamics and changes in fluid structure as a function of particle size and surface chemistry. We show that as the amphiphilicity increases upon enhancing the wetting of each side with its favored fluid, the in-plane diffusivity at the interface becomes slower. Detail analysis of the fluid structure reveals that this is mainly due to formation of a denser adsorption layer around more amphiphilic particles, which leads to increased drag acting against nanoparticle motion. Similarly, the rotational thermal motion of Janus particles is reduced compared to their homogeneous counterparts as a result of the higher resistance of neighboring fluid species against rotation. We also incorporate the influence of fluid density and surface tension on the interfacial dynamics of such Janus nanoparticles. Our findings may have implications in understanding the adsorption mechanism of drugs and protein molecules with anisotropic surface properties to biological interfaces including cell membranes.

Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trebotich, D

We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscousmore » flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.« less

Modeling complex biological flows in multi-scale systems using the APDEC framework

NASA Astrophysics Data System (ADS)

Trebotich, David

2006-09-01

We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

Cytoskeletal Dynamics and Fluid Flow in Drosophila Oocytes

NASA Astrophysics Data System (ADS)

de Canio, Gabriele; Goldstein, Raymond; Lauga, Eric

2015-11-01

The biological world includes a broad range of phenomena in which transport in a fluid plays a central role. Among these is the fundamental issue of cell polarity arising during development, studied historically using the model organism Drosophila melanogaster. The polarity of the oocyte is known to be induced by the translocation of mRNAs by kinesin motor proteins along a dense microtubule cytoskeleton, a process which also induces cytoplasmic streaming. Recent experimental observations have revealed the remarkable fluid-structure interactions that occur as the streaming flows back-react on the microtubules. In this work we use a combination of theory and simulations to address the interplay between the fluid flow and the configuration of cytoskeletal filaments leading to the directed motion inside the oocyte. We show in particular that the mechanical coupling between the fluid motion and the orientation of the microtubules can lead to a transition to coherent motion within the oocyte, as observed. Supported by EPSRC and ERC Advanced Investigator Grant 247333.

An analytical poroelastic model for ultrasound elastography imaging of tumors

NASA Astrophysics Data System (ADS)

Tauhidul Islam, Md; Chaudhry, Anuj; Unnikrishnan, Ginu; Reddy, J. N.; Righetti, Raffaella

2018-01-01

The mechanical behavior of biological tissues has been studied using a number of mechanical models. Due to the relatively high fluid content and mobility, many biological tissues have been modeled as poroelastic materials. Diseases such as cancers are known to alter the poroelastic response of a tissue. Tissue poroelastic properties such as compressibility, interstitial permeability and fluid pressure also play a key role for the assessment of cancer treatments and for improved therapies. At the present time, however, a limited number of poroelastic models for soft tissues are retrievable in the literature, and the ones available are not directly applicable to tumors as they typically refer to uniform tissues. In this paper, we report the analytical poroelastic model for a non-uniform tissue under stress relaxation. Displacement, strain and fluid pressure fields in a cylindrical poroelastic sample containing a cylindrical inclusion during stress relaxation are computed. Finite element simulations are then used to validate the proposed theoretical model. Statistical analysis demonstrates that the proposed analytical model matches the finite element results with less than 0.5% error. The availability of the analytical model and solutions presented in this paper may be useful to estimate diagnostically relevant poroelastic parameters such as interstitial permeability and fluid pressure, and, in general, for a better interpretation of clinically-relevant ultrasound elastography results.

An agent-based method for simulating porous fluid-saturated structures with indistinguishable components

NASA Astrophysics Data System (ADS)

Kashani, Jamal; Pettet, Graeme John; Gu, YuanTong; Zhang, Lihai; Oloyede, Adekunle

2017-10-01

Single-phase porous materials contain multiple components that intermingle up to the ultramicroscopic level. Although the structures of the porous materials have been simulated with agent-based methods, the results of the available methods continue to provide patterns of distinguishable solid and fluid agents which do not represent materials with indistinguishable phases. This paper introduces a new agent (hybrid agent) and category of rules (intra-agent rule) that can be used to create emergent structures that would more accurately represent single-phase structures and materials. The novel hybrid agent carries the characteristics of system's elements and it is capable of changing within itself, while also responding to its neighbours as they also change. As an example, the hybrid agent under one-dimensional cellular automata formalism in a two-dimensional domain is used to generate patterns that demonstrate the striking morphological and characteristic similarities with the porous saturated single-phase structures where each agent of the ;structure; carries semi-permeability property and consists of both fluid and solid in space and at all times. We conclude that the ability of the hybrid agent to change locally provides an enhanced protocol to simulate complex porous structures such as biological tissues which could facilitate models for agent-based techniques and numerical methods.

Dispersal and fallout simulations for urban consequences management (u)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grinstein, Fernando F; Wachtor, Adam J; Nelson, Matt

2010-01-01

Hazardous chemical, biological, or radioactive releases from leaks, spills, fires, or blasts, may occur (intentionally or accidentally) in urban environments during warfare or as part of terrorist attacks on military bases or other facilities. The associated contaminant dispersion is complex and semi-chaotic. Urban predictive simulation capabilities can have direct impact in many threat-reduction areas of interest, including, urban sensor placement and threat analysis, contaminant transport (CT) effects on surrounding civilian population (dosages, evacuation, shelter-in-place), education and training of rescue teams and services. Detailed simulations for the various processes involved are in principle possible, but generally not fast. Predicting urban airflowmore » accompanied by CT presents extremely challenging requirements. Crucial technical issues include, simulating turbulent fluid and particulate transport, initial and boundary condition modeling incorporating a consistent stratified urban boundary layer with realistic wind fluctuations, and post-processing of the simulation results for practical consequences management. Relevant fluid dynamic processes to be simulated include, detailed energetic and contaminant sources, complex building vortex shedding and flows in recirculation zones, and modeling of particle distributions, including particulate fallout, as well as deposition, re-suspension and evaporation. Other issues include, modeling building damage effects due to eventual blasts, addressing appropriate regional and atmospheric data reduction.« less

Laser irradiation of Mg-Al-Zn alloy: Reduced electrochemical kinetics and enhanced performance in simulated body fluid.

PubMed

Florian, David C; Melia, Michael A; Steuer, Fritz W; Briglia, Bruce F; Purzycki, Michael K; Scully, John R; Fitz-Gerald, James M

2017-05-11

As a lightweight metal with mechanical properties similar to natural bone, Mg and its alloys are great prospects for biodegradable, load bearing implants. However, rapid degradation and H 2 gas production in physiological media has prevented widespread use of Mg alloys. Surface heterogeneities in the form of intermetallic particles dominate the corrosion response. This research shows that surface homogenization significantly improved the biological corrosion response observed during immersion in simulated body fluid (SBF). The laser processed Mg alloy exhibited a 50% reduction in mass loss and H 2 evolution after 24 h of immersion in SBF when compared to the wrought, cast alloy. The laser processed samples exhibited increased wettability as evident from wetting angle studies, further suggesting improved biocompatibility. Electrochemical analysis by potentiodynamic polarization measurements showed that the anodic and cathodic kinetics were reduced following laser processing and are attributed to the surface chemical homogeneity.

Pressure-driven laminar flow switching for rapid exchange of solution environment around surface adhered biological particles

PubMed Central

Allen, Peter B.; Milne, Graham; Doepker, Byron R.; Chiu, Daniel T.

2010-01-01

This paper describes a technique for rapidly exchanging the solution environment near a surface by displacing laminar flow fluid streams using sudden changes in applied pressure. The method employs off-chip solenoid valves to induce pressure changes, which is important in keeping the microfluidic design simple and the operation of the system robust. The performance of this technique is characterized using simulation and validated with experiments. This technique adds to the microfluidic tool box that is currently available for manipulating the solution environment around biological particles and molecules. PMID:20221560

A review of bioactive silicate ceramics.

PubMed

Wu, Chengtie; Chang, Jiang

2013-06-01

Silicate bioceramics, as a new family of biomaterials, have received significant attention in their application to hard tissue regeneration. Some silicate bioceramics have shown excellent apatite mineralization in simulated body fluids and their ionic products have been shown to enhance the proliferation, osteogenic differentiation and gene expression of stem cells. In this paper, we review the advances in the research of silicate system bioceramics, including preparation methods, mechanical strength, apatite mineralization, dissolution and in vitro and in vivo biological properties. The biological properties and the corresponding mechanism have been highlighted. A look forward to the application of silicate bioceramics to bone regeneration is further suggested.

Spontaneous mirror-symmetry breaking induces inverse energy cascade in 3D active fluids

PubMed Central

Słomka, Jonasz; Dunkel, Jörn

2017-01-01

Classical turbulence theory assumes that energy transport in a 3D turbulent flow proceeds through a Richardson cascade whereby larger vortices successively decay into smaller ones. By contrast, an additional inverse cascade characterized by vortex growth exists in 2D fluids and gases, with profound implications for meteorological flows and fluid mixing. The possibility of a helicity-driven inverse cascade in 3D fluids had been rejected in the 1970s based on equilibrium-thermodynamic arguments. Recently, however, it was proposed that certain symmetry-breaking processes could potentially trigger a 3D inverse cascade, but no physical system exhibiting this phenomenon has been identified to date. Here, we present analytical and numerical evidence for the existence of an inverse energy cascade in an experimentally validated 3D active fluid model, describing microbial suspension flows that spontaneously break mirror symmetry. We show analytically that self-organized scale selection, a generic feature of many biological and engineered nonequilibrium fluids, can generate parity-violating Beltrami flows. Our simulations further demonstrate how active scale selection controls mirror-symmetry breaking and the emergence of a 3D inverse cascade. PMID:28193853

Characterization of Fluid Flow through a Simplified Heart Valve Model

NASA Astrophysics Data System (ADS)

Katija, Kakani

2005-11-01

Research has shown that the leading vortex of a starting jet makes a larger contribution to mass transport than a straight jet. Physical processes terminate growth of the leading vortex ring at a stroke ratio (L/D) between 3.5 and 4.5. This has enhanced the idea that biological systems optimize vortex formation for fluid transport. Of present interest is how fluid transport through a heart valve induces flutter of the valve leaflets. An attempt to characterize the fluid flow through a heart valve was made using a simplified cylinder-string system. Experiments were conducted in a water tank where a piston pushed fluid out of a cylinder (of diameter D) into surrounding fluid. A latex string was attached to the end of the cylinder to simulate a heart valve leaflet. The FFT of the string motion was computed to quantify the flutter behavior observed in the cylinder-string system. By increasing the stroke ratio, the amplitude of transverse oscillations for all string lengths increases. For the string length D/2, the occurrence of flutter coincides with the formation of the vortex ring trailing jet.

Biocorrosion properties of antibacterial Ti-10Cu sintered alloy in several simulated biological solutions.

PubMed

Liu, Cong; Zhang, Erlin

2015-03-01

Ti-10Cu sintered alloy has shown strong antibacterial properties against S. aureus and E. coli and good cell biocompatibility, which displays potential application in dental application. The corrosion behaviors of the alloy in five different simulated biological solutions have been investigated by electrochemical technology, surface observation, roughness measurement and immersion test. Five different simulated solutions were chosen to simulate oral condition, oral condition with F(-) ion, human body fluids with different pH values and blood system. It has been shown that Ti-10Cu alloy exhibits high corrosion rate in Saliva pH 3.5 solution and Saliva pH 6.8 + 0.2F solution but low corrosion rate in Hank's, Tyrode's and Saliva pH 6.8 solutions. The corrosion rate of Ti-10Cu alloy was in a order of Hank's, Tyrode's, Saliva pH 6.8, Saliva-pH 3.5 and Saliva pH 6.8 + 0.2F from slow to fast. All results indicated acid and F(-) containing conditions prompt the corrosion reaction of Ti-Cu alloy. It was suggested that the Cu ion release in the biological environments, especially in the acid and F(-) containing condition would lead to high antibacterial properties without any cell toxicity, displaying wide potential application of this alloy.

RI: Rheology as a Tool for Understanding the Mechanics of Live Ant Aggregations, Part 2

DTIC Science & Technology

2016-11-04

measure rheological properties of biological fluids. Using this machine, we were able to characterize non-Newtonian fluids such as frog saliva...order to measure rheological properties of biological fluids. Using this machine, we were able to characterize non-Newtonian fluids such as frog...GA, 30332 Objective An Anton Parr MCR 501 rheometer was purchased in order to measure rheological properties of biological fluids. Using this

Fluid, solid and fluid-structure interaction simulations on patient-based abdominal aortic aneurysm models.

PubMed

Kelly, Sinead; O'Rourke, Malachy

2012-04-01

This article describes the use of fluid, solid and fluid-structure interaction simulations on three patient-based abdominal aortic aneurysm geometries. All simulations were carried out using OpenFOAM, which uses the finite volume method to solve both fluid and solid equations. Initially a fluid-only simulation was carried out on a single patient-based geometry and results from this simulation were compared with experimental results. There was good qualitative and quantitative agreement between the experimental and numerical results, suggesting that OpenFOAM is capable of predicting the main features of unsteady flow through a complex patient-based abdominal aortic aneurysm geometry. The intraluminal thrombus and arterial wall were then included, and solid stress and fluid-structure interaction simulations were performed on this, and two other patient-based abdominal aortic aneurysm geometries. It was found that the solid stress simulations resulted in an under-estimation of the maximum stress by up to 5.9% when compared with the fluid-structure interaction simulations. In the fluid-structure interaction simulations, flow induced pressure within the aneurysm was found to be up to 4.8% higher than the value of peak systolic pressure imposed in the solid stress simulations, which is likely to be the cause of the variation in the stress results. In comparing the results from the initial fluid-only simulation with results from the fluid-structure interaction simulation on the same patient, it was found that wall shear stress values varied by up to 35% between the two simulation methods. It was concluded that solid stress simulations are adequate to predict the maximum stress in an aneurysm wall, while fluid-structure interaction simulations should be performed if accurate prediction of the fluid wall shear stress is necessary. Therefore, the decision to perform fluid-structure interaction simulations should be based on the particular variables of interest in a given study.

Particle sedimentation in a sheared viscoelastic fluid

NASA Astrophysics Data System (ADS)

Murch, William L.; Krishnan, Sreenath; Shaqfeh, Eric S. G.; Iaccarino, Gianluca

2017-11-01

Particle suspensions are ubiquitous in engineered processes, biological systems, and natural settings. For an engineering application - whether the intent is to suspend and transport particles (e.g., in hydraulic fracturing fluids) or allow particles to sediment (e.g., in industrial separations processes) - understanding and prediction of the particle mobility is critical. This task is often made challenging by the complex nature of the fluid phase, for example, due to fluid viscoelasticity. In this talk, we focus on a fully 3D flow problem in a viscoelastic fluid: a settling particle with a shear flow applied in the plane perpendicular to gravity (referred to as orthogonal shear). Previously, it has been shown that an orthogonal shear flow can reduce the settling rate of particles in viscoelastic fluids. Using experiments and numerical simulations across a wide range of sedimentation and shear Weissenberg number, this talk will address the underlying physical mechanism responsible for the additional drag experienced by a rigid sphere settling in a confined viscoelastic fluid with orthogonal shear. We will then explore multiple particle effects, and discuss the implications and extensions of this work for particle suspensions. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-114747 (WLM).

Inertial migration of elastic particles in a pressure-driven power-law fluid

NASA Astrophysics Data System (ADS)

Bowie, Samuel; Alexeev, Alexander

2016-11-01

Using three-dimensional computer simulations, we study the cross-stream migration of deformable particles in a channel filled with a non-Newtonian fluid driven by a pressure gradient. Our numerical approach integrates lattice Boltzmann method and lattice spring method in order to model fluid structural interactions of the elastic particle and the surrounding power fluid in the channel. The particles are modeled as elastic shells filled with a viscous fluid that are initially spherical. We focus on the regimes where the inertial effects cannot be neglected and cause cross-stream drift of particles. We probe the flow with different power law indexes including both the shear thickening and thinning fluids. We also examine migration of particles of with different elasticity and relative size. To isolate the non-Newtonian effects on particle migration, we compare the results with the inertial migration results found in the case where the channel is filled with a simple Newtonian fluid. The results can be useful for applications requiring high throughput separation, sorting, and focusing of both synthetic particles and biological cells in microfluidic devices. Financial support provided by National Science Foundation (NSF) Grant No. CMMI1538161.

From the track to the ocean: Using flow control to improve marine bio-logging tags for cetaceans

PubMed Central

Fiore, Giovani; Anderson, Erik; Garborg, C. Spencer; Murray, Mark; Johnson, Mark; Moore, Michael J.; Howle, Laurens

2017-01-01

Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force component at high speeds. In order to reduce lift and minimize total hydrodynamic loading this work presents a new tag design (Model A) that incorporates a hydrodynamic body, a channel to reduce fluid speed differences above and below the housing and wing to redirect flow to counter lift. Additionally, three derivatives of the Model A design were used to examine the contribution of individual flow control features to overall performance. Hydrodynamic loadings of four models were compared using computational fluid dynamics (CFD). The Model A design eliminated all lift force and generated up to ~30 N of downward force in simulated 6 m/s aligned flow. The simulations were validated using particle image velocimetry (PIV) to experimentally characterize the flow around the tag design. The results of these experiments confirm the trends predicted by the simulations and demonstrate the potential benefit of flow control elements for the reduction of tag induced forces on the animal. PMID:28196148

THE FLUIDS AND COMBUSTION FACILITY: ENABLING THE EXPLORATION OF SPACE

NASA Technical Reports Server (NTRS)

Weiland, Karen J.; Gati, Frank G.; Hill, Myron E.; OMalley, Terence; Zurawski, Robert L.

2005-01-01

The Fluids and Combustion Facility (FCF) is an International Space Station facility designed to support physical and biological research as well as technology experiments in space. The FCF consists of two racks called the Combustion Integrated Rack (CIR) and the Fluids Integrated Rack (FIR). The capabilities of the CIR and the FIR and plans for their utilization will support the President s vision for space exploration. The CIR will accommodate physical research and technology experiments that address needs in the areas of spacecraft fire prevention, detection and suppression, incineration of solid wastes, and power generation. Initial experiments will provide data to support design decisions for exploration spacecraft. The CIR provides a large sealed chamber in a near-weightless environment. The chamber supports many simulated atmospheres including lunar or Martian environments. The FIR will accommodate experiments that address needs for advanced life support, power, propulsion, and spacecraft thermal control systems. The FIR can also serve as a platform for experiments that address human health and performance, medical technologies, and biological sciences. The FIR provides a large volume for payload hardware, reconfigurable diagnostics, customizable software, active rack-level vibration isolation, and data acquisition and management in a nearly uniform temperature environment.

The Fluids and Combustion Facility: Enabling the Exploration of Space

NASA Technical Reports Server (NTRS)

Weiland, Karen J.; Gati, Frank G.; Hill, Myron E.; O'Malley Terence F.; Zurawski, Robert L.

2005-01-01

The Fluids and Combustion Facility (FCF) is an International Space Station facility designed to support physical and biological research as well as technology experiments in space. The FCF consists of two racks called the Combustion Integrated Rack (CIR) and the Fluids Integrated Rack (FIR). The capabilities of the CIR and the FIR and plans for their utilization will support the President's vision for space exploration. The CIR will accommodate physical research and technology experiments that address needs in the areas of spacecraft fire prevention, detection and suppression, incineration of solid wastes, and power generation. Initial experiments will provide data to support design decisions for exploration spacecraft. The CIR provides a large sealed chamber in a near-weightless environment. The chamber supports many simulated atmospheres including lunar or Martian environments. The FIR will accommodate experiments that address needs for advanced life support, power, propulsion, and spacecraft thermal control systems. The FIR can also serve as a platform for experiments that address human health and performance, medical technologies, and biological sciences. The FIR provides a large volume for payload hardware, reconfigurable diagnostics, customizable software, active rack-level vibration isolation, and data acquisition and management in a nearly uniform temperature environment.

Applications of computational fluid dynamics (CFD) in the modelling and design of ventilation systems in the agricultural industry: a review.

PubMed

Norton, Tomás; Sun, Da-Wen; Grant, Jim; Fallon, Richard; Dodd, Vincent

2007-09-01

The application of computational fluid dynamics (CFD) in the agricultural industry is becoming ever more important. Over the years, the versatility, accuracy and user-friendliness offered by CFD has led to its increased take-up by the agricultural engineering community. Now CFD is regularly employed to solve environmental problems of greenhouses and animal production facilities. However, due to a combination of increased computer efficacy and advanced numerical techniques, the realism of these simulations has only been enhanced in recent years. This study provides a state-of-the-art review of CFD, its current applications in the design of ventilation systems for agricultural production systems, and the outstanding challenging issues that confront CFD modellers. The current status of greenhouse CFD modelling was found to be at a higher standard than that of animal housing, owing to the incorporation of user-defined routines that simulate crop biological responses as a function of local environmental conditions. Nevertheless, the most recent animal housing simulations have addressed this issue and in turn have become more physically realistic.

Immersed boundary methods for simulating fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sotiropoulos, Fotis; Yang, Xiaolei

2014-02-01

Fluid-structure interaction (FSI) problems commonly encountered in engineering and biological applications involve geometrically complex flexible or rigid bodies undergoing large deformations. Immersed boundary (IB) methods have emerged as a powerful simulation tool for tackling such flows due to their inherent ability to handle arbitrarily complex bodies without the need for expensive and cumbersome dynamic re-meshing strategies. Depending on the approach such methods adopt to satisfy boundary conditions on solid surfaces they can be broadly classified as diffused and sharp interface methods. In this review, we present an overview of the fundamentals of both classes of methods with emphasis on solution algorithms for simulating FSI problems. We summarize and juxtapose different IB approaches for imposing boundary conditions, efficient iterative algorithms for solving the incompressible Navier-Stokes equations in the presence of dynamic immersed boundaries, and strong and loose coupling FSI strategies. We also present recent results from the application of such methods to study a wide range of problems, including vortex-induced vibrations, aquatic swimming, insect flying, human walking and renewable energy. Limitations of such methods and the need for future research to mitigate them are also discussed.

Physically-Based Modelling and Real-Time Simulation of Fluids.

NASA Astrophysics Data System (ADS)

Chen, Jim Xiong

1995-01-01

Simulating physically realistic complex fluid behaviors presents an extremely challenging problem for computer graphics researchers. Such behaviors include the effects of driving boats through water, blending differently colored fluids, rain falling and flowing on a terrain, fluids interacting in a Distributed Interactive Simulation (DIS), etc. Such capabilities are useful in computer art, advertising, education, entertainment, and training. We present a new method for physically-based modeling and real-time simulation of fluids in computer graphics and dynamic virtual environments. By solving the 2D Navier -Stokes equations using a CFD method, we map the surface into 3D using the corresponding pressures in the fluid flow field. This achieves realistic real-time fluid surface behaviors by employing the physical governing laws of fluids but avoiding extensive 3D fluid dynamics computations. To complement the surface behaviors, we calculate fluid volume and external boundary changes separately to achieve full 3D general fluid flow. To simulate physical activities in a DIS, we introduce a mechanism which uses a uniform time scale proportional to the clock-time and variable time-slicing to synchronize physical models such as fluids in the networked environment. Our approach can simulate many different fluid behaviors by changing the internal or external boundary conditions. It can model different kinds of fluids by varying the Reynolds number. It can simulate objects moving or floating in fluids. It can also produce synchronized general fluid flows in a DIS. Our model can serve as a testbed to simulate many other fluid phenomena which have never been successfully modeled previously.

Biology's built-in Faraday cages

NASA Astrophysics Data System (ADS)

Klee, Maurice M.

2014-05-01

Biological fluids are water-based, ionic conductors. As such, they have both high relative dielectric constants and substantial conductivities, meaning they are lossy dielectrics. These fluids contain charged molecules (free charges), whose movements play roles in essentially all cellular processes from metabolism to communication with other cells. Using the problem of a point source in air above a biological fluid of semi-infinite extent, the bound charges in the fluid are shown to perform the function of a fast-acting Faraday cage, which protects the interior of the fluid from external electric fields. Free charges replace bound charges in accordance with the fluid's relaxation time, thereby providing a smooth transition between the initial protection provided by the bound charges and the steady state protection provided by the free charges. The electric fields within the biological fluid are thus small for all times just as they would be inside a classical Faraday cage.

Application of computational fluid dynamics to closed-loop bioreactors: I. Characterization and simulation of fluid-flow pattern and oxygen transfer.

PubMed

Littleton, Helen X; Daigger, Glen T; Strom, Peter F

2007-06-01

A full-scale, closed-loop bioreactor (Orbal oxidation ditch, Envirex brand technologies, Siemens, Waukesha, Wisconsin), previously examined for simultaneous biological nutrient removal (SBNR), was further evaluated using computational fluid dynamics (CFD). A CFD model was developed first by imparting the known momentum (calculated by tank fluid velocity and mass flowrate) to the fluid at the aeration disc region. Oxygen source (aeration) and sink (consumption) terms were introduced, and statistical analysis was applied to the CFD simulation results. The CFD model was validated with field data obtained from a test tank and a full-scale tank. The results indicated that CFD could predict the mixing pattern in closed-loop bioreactors. This enables visualization of the flow pattern, both with regard to flow velocity and dissolved-oxygen-distribution profiles. The velocity and oxygen-distribution gradients suggested that the flow patterns produced by directional aeration in closed-loop bioreactors created a heterogeneous environment that can result in dissolved oxygen variations throughout the bioreactor. Distinct anaerobic zones on a macroenvironment scale were not observed, but it is clear that, when flow passed around curves, a secondary spiral flow was generated. This second current, along with the main recirculation flow, could create alternating anaerobic and aerobic conditions vertically and horizontally, which would allow SBNR to occur. Reliable SBNR performance in Orbal oxidation ditches may be a result, at least in part, of such a spatially varying environment.

The effect of fault-bend folding on seismic velocity in the marginal ridge of accretionary prisms

USGS Publications Warehouse

Cai, Y.; Wang, Chun-Yong; Hwang, W.-t.; Cochrane, G.R.

1995-01-01

Fluid venting in accretionary prisms, which feeds chemosynthetic biological communities, occurs mostly on the marginal thrust ridge. New seismic data for the marginal ridge of the Cascadia prism show significantly lower velocity than that in the adjacent oceanic basin and place important constraints on the interpretations of why fluid venting occurs mostly on the marginal ridge. We employed a finite-element method to analyze a typical fault-bend folding model to explain the phenomenon. The fault in the model is simulated by contact elements. The elements are characterized not only by finite sliding along a slide line, but also by elastoplastic deformation. We present the results of a stress analysis which show that the marginal ridge is under subhorizontal extension and the frontal thrust is under compression. This state of stress favors the growth of tensile cracks in the marginal ridge, facilitates fluid flow and reduces seismic velocities therein; on the other hand, it may close fluid pathways along the frontal thrust and divert fluid flow to the marginal ridge. ?? 1995 Birkha??user Verlag.

The potential for biologically catalyzed anaerobic methane oxidation on ancient Mars.

PubMed

Marlow, Jeffrey J; Larowe, Douglas E; Ehlmann, Bethany L; Amend, Jan P; Orphan, Victoria J

2014-04-01

This study examines the potential for the biologically mediated anaerobic oxidation of methane (AOM) coupled to sulfate reduction on ancient Mars. Seven distinct fluids representative of putative martian groundwater were used to calculate Gibbs energy values in the presence of dissolved methane under a range of atmospheric CO2 partial pressures. In all scenarios, AOM is exergonic, ranging from -31 to -135 kJ/mol CH4. A reaction transport model was constructed to examine how environmentally relevant parameters such as advection velocity, reactant concentrations, and biomass production rate affect the spatial and temporal dependences of AOM reaction rates. Two geologically supported models for ancient martian AOM are presented: a sulfate-rich groundwater with methane produced from serpentinization by-products, and acid-sulfate fluids with methane from basalt alteration. The simulations presented in this study indicate that AOM could have been a feasible metabolism on ancient Mars, and fossil or isotopic evidence of this metabolic pathway may persist beneath the surface and in surface exposures of eroded ancient terrains.

The wettability and swelling of selected mucoadhesive polymers in simulated saliva and vaginal fluids.

PubMed

Rojewska, M; Olejniczak-Rabinek, M; Bartkowiak, A; Snela, A; Prochaska, K; Lulek, J

2017-08-01

The surface properties play a particularly important role in the mucoadhesive drug delivery systems. In these formulations, the adsorption of polymer matrix to mucous membrane is limited by the wetting and swelling process of the polymer structure. Hence, the performance of mucoadhesive drug delivery systems made of polymeric materials depends on multiple factors, such as contact angle, surface free energy and water absorption rate. The aim of our study was to analyze the effect of model saliva and vaginal fluids on the wetting properties of selected mucoadhesive (Carbopol 974P NF, Noveon AA-1, HEC) and film-forming (Kollidon VA 64) polymers as well as their blends at the weight ratio 1:1 and 1:1:1, prepared in the form of discs. Surface properties of the discs were determined by measurements of advancing contact angle on the surface of polymers and their blends using the sessile drop method. The surface energy was determined by the OWRK method. Additionally, the mass swelling factor and hydration percentage of examined polymers and their blends in simulated biological fluids were evaluated. Copyright © 2017 Elsevier B.V. All rights reserved.

Uranium(VI) Binding Forms in Selected Human Body Fluids: Thermodynamic Calculations versus Spectroscopic Measurements.

PubMed

Osman, Alfatih A A; Geipel, Gerhard; Barkleit, Astrid; Bernhard, Gert

2015-02-16

Human exposure to uranium increasingly becomes a subject of interest in many scientific disciplines such as environmental medicine, toxicology, and radiation protection. Knowledge about uranium chemical binding forms(speciation) in human body fluids can be of great importance to understand not only its biokinetics but also its relevance in risk assessment and in designing decorporation therapy in the case of accidental overexposure. In this study, thermodynamic calculations of uranium speciation in relevant simulated and original body fluids were compared with spectroscopic data after ex-situ uranium addition. For the first time, experimental data on U(VI) speciation in body fluids (saliva, sweat, urine) was obtained by means of cryogenic time-resolved laser-induced fluorescence spectroscopy (cryo-TRLFS) at 153 K. By using the time dependency of fluorescence decay and the band positions of the emission spectra, various uranyl complexes were demonstrated in the studied samples. The variations of the body fluids in terms of chemical composition, pH, and ionic strength resulted in different binding forms of U(VI). The speciation of U(VI) in saliva and in urine was affected by the presence of bioorganic ligands, whereas in sweat, the distribution depends mainly on inorganic ligands. We also elucidated the role of biological buffers, i.e., phosphate (H(2)PO(4−)/HPO(4)(2−)) on U(VI) distribution, and the system Ca(2+)/UO(2)(2+)/PO(4)(3−) was discussed in detail in both saliva and urine. The theoretical speciation calculations of the main U(VI) species in the investigated body fluids were significantly consistent with the spectroscopic data. Laser fluorescence spectroscopy showed success and reliability for direct determination of U(VI) in such biological matrices with the possibility for further improvement.

Hazard assessment of W and Mo sulphide nanomaterials for automotive use

NASA Astrophysics Data System (ADS)

Corazzari, Ingrid; Deorsola, Fabio A.; Gulino, Giulia; Aldieri, Elisabetta; Bensaid, Samir; Turci, Francesco; Fino, Debora

2014-05-01

Engineered nanomaterials (ENMs) are growing in interest and use due to the enhancements envisaged in many applications. ENM hazard identification and exposure scenarios are growing in interest too. Inhalation, ingestion and assimilation through skin during ENM production or use have to be considered as possible events, and potential ENM toxicity has to be investigated before new ENM-based products are placed on the market. To design new ENM-based additive in lubricants for automotive application, the European FP7 Project AddNano is investigating the use of fullerene-like inorganic nanomaterials, including transition metal disulphides. In this work, the potential toxicities of well-characterized pristine MoS2 and WS2 ENMs were evaluated by in vitro cellular and a cell-free chemical tests. Cytotoxicity and oxidative stress on human pulmonary epithelial cells (A549), ENM surface reactivity (free radical production and lipid peroxidation), and ENM durability in simulated biological fluids were evaluated. In all tests, WS2 did not elicit a response significantly different from the negative control. MoS2 showed a moderate cellular toxicity at the highest dose and was inert in all other circumstances. Both WS2 and MoS2 were soluble in simulated biological fluids, suggesting a short durability in vivo. The low overall biological and chemical reactivity of WS2 and MoS2 suggests that tested nanomaterials are unlikely to be an hazard, as far as human respiratory system is concerned. Data could be usefully implemented in the context of environmental risk assessment and life cycle assessment.

Breaking symmetry in non-planar bifurcations: distribution of flow and wall shear stress.

PubMed

Lu, Yiling; Lu, Xiyun; Zhuang, Lixian; Wang, Wen

2002-01-01

Non-planarity in blood vessels is known to influence arterial flows and wall shear stress. To gain insight, computational fluid dynamics (CFD) has been used to investigate effects of curvature and out-of-plane geometry on the distribution of fluid flows and wall shear stresses in a hypothetical non-planar bifurcation. Three-dimensional Navier-Stokes equations for a steady state Newtonian fluid were solved numerically using a finite element method. Non-planarity in one of the two daughter vessels is found to deflect flow from the inner wall of the vessel to the outer wall and to cause changes in the distribution of wall shear stresses. Results from this study agree to experimental observations and CFD simulations in the literature, and support the view that non-planarity in blood vessels is a factor with important haemodynamic significance and may play a key role in vascular biology and pathophysiology.

Electrophoresis demonstration on Apollo 16

NASA Technical Reports Server (NTRS)

Snyder, R. S.

1972-01-01

Free fluid electrophoresis, a process used to separate particulate species according to surface charge, size, or shape was suggested as a promising technique to utilize the near zero gravity condition of space. Fluid electrophoresis on earth is disturbed by gravity-induced thermal convection and sedimentation. An apparatus was developed to demonstrate the principle and possible problems of electrophoresis on Apollo 14 and the separation boundary between red and blue dye was photographed in space. The basic operating elements of the Apollo 14 unit were used for a second flight demonstration on Apollo 16. Polystyrene latex particles of two different sizes were used to simulate the electrophoresis of large biological particles. The particle bands in space were extremely stable compared to ground operation because convection in the fluid was negligible. Electrophoresis of the polystyrene latex particle groups according to size was accomplished although electro-osmosis in the flight apparatus prevented the clear separation of two particle bands.

Three-link Swimming in Sand

NASA Astrophysics Data System (ADS)

Hatton, R. L.; Ding, Yang; Masse, Andrew; Choset, Howie; Goldman, Daniel

2011-11-01

Many animals move within in granular media such as desert sand. Recent biological experiments have revealed that the sandfish lizard uses an undulatory gait to swim within sand. Models reveal that swimming occurs in a frictional fluid in which inertial effects are small and kinematics dominate. To understand the fundamental mechanics of swimming in granular media (GM), we examine a model system that has been well-studied in Newtonian fluids: the three-link swimmer. We create a physical model driven by two servo-motors, and a discrete element simulation of the swimmer. To predict optimal gaits we use a recent geometric mechanics theory combined with empirically determined resistive force laws for GM. We develop a kinematic relationship between the swimmer's shape and position velocities and construct connection vector field and constraint curvature function visualizations of the system dynamics. From these we predict optimal gaits for forward, lateral and rotational motion. Experiment and simulation are in accord with the theoretical predictions; thus geometric tools can be used to study locomotion in GM.

Fluid Dynamics Appearing during Simulated Microgravity Using Random Positioning Machines

PubMed Central

Stern, Philip; Casartelli, Ernesto; Egli, Marcel

2017-01-01

Random Positioning Machines (RPMs) are widely used as tools to simulate microgravity on ground. They consist of two gimbal mounted frames, which constantly rotate biological samples around two perpendicular axes and thus distribute the Earth’s gravity vector in all directions over time. In recent years, the RPM is increasingly becoming appreciated as a laboratory instrument also in non-space-related research. For instance, it can be applied for the formation of scaffold-free spheroid cell clusters. The kinematic rotation of the RPM, however, does not only distribute the gravity vector in such a way that it averages to zero, but it also introduces local forces to the cell culture. These forces can be described by rigid body analysis. Although RPMs are commonly used in laboratories, the fluid motion in the cell culture flasks on the RPM and the possible effects of such on cells have not been examined until today; thus, such aspects have been widely neglected. In this study, we used a numerical approach to describe the fluid dynamic characteristic occurring inside a cell culture flask turning on an operating RPM. The simulations showed that the fluid motion within the cell culture flask never reached a steady state or neared a steady state condition. The fluid velocity depends on the rotational velocity of the RPM and is in the order of a few centimeters per second. The highest shear stresses are found along the flask walls; depending of the rotational velocity, they can reach up to a few 100 mPa. The shear stresses in the “bulk volume,” however, are always smaller, and their magnitude is in the order of 10 mPa. In conclusion, RPMs are highly appreciated as reliable tools in microgravity research. They have even started to become useful instruments in new research fields of mechanobiology. Depending on the experiment, the fluid dynamic on the RPM cannot be neglected and needs to be taken into consideration. The results presented in this study elucidate the fluid motion and provide insight into the convection and shear stresses that occur inside a cell culture flask during RPM experiments. PMID:28135286

Directed Fluid Transport and Mixing with Biomimetic Cilia Arrays

NASA Astrophysics Data System (ADS)

Shields, A. R.; Evans, B. A.; Carstens, B. L.; Falvo, M. R.; Washburn, S.; Superfine, R.

2009-03-01

We present results on the long-range, directed fluid transport and fluidic mixing produced by the collective beating of arrays of biomimetic cilia. These artificial cilia are arrays of free-standing nanorods roughly the size of biological cilia, which we fabricate from a polymer-magnetic nanoparticle composite material and actuate with permanent magnets to mimic biological cilia. Biological cilia have evolved to produce microscale fluid transport and are increasingly being recognized as critical components in a wide range of biological systems. However, despite much effort cilia generated fluid flows remain an area of active study. In the last decade, cilia-driven fluid flow in the embryonic node of vertebrates has been implicated as the initial left-right symmetry breaking event in these embryos. With silia we generate directional fluid transport by mimicking the tilted conical beating of these nodal cilia. By seeding fluorescent microparticles into the fluid we have noted the existence of two distinct flow regimes. The fluid flow is directional and coherent above the cilia tips, while between the cilia tips and the floor particle motion is complicated and suggestive of chaotic advection.

Simulation of magnetic active polymers for versatile microfluidic devices

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Özelt, Harald; Fischbacher, Johann; Reichel, Franz; Exl, Lukas; Bance, Simon; Kataeva, Nadezhda; Binder, Claudia; Brückl, Hubert; Schrefl, Thomas

2013-01-01

We propose to use a compound of magnetic nanoparticles (20-100 nm) embedded in a flexible polymer (Polydimethylsiloxane PDMS) to filter circulating tumor cells (CTCs). The analysis of CTCs is an emerging tool for cancer biology research and clinical cancer management including the detection, diagnosis and monitoring of cancer. The combination of experiments and simulations lead to a versatile microfluidic lab-on-chip device. Simulations are essential to understand the influence of the embedded nanoparticles in the elastic PDMS when applying a magnetic gradient field. It combines finite element calculations of the polymer, magnetic simulations of the embedded nanoparticles and the fluid dynamic calculations of blood plasma and blood cells. With the use of magnetic active polymers a wide range of tunable microfluidic structures can be created. The method can help to increase the yield of needed isolated CTCs.

Bioprocess scale-up/down as integrative enabling technology: from fluid mechanics to systems biology and beyond.

PubMed

Delvigne, Frank; Takors, Ralf; Mudde, Rob; van Gulik, Walter; Noorman, Henk

2017-09-01

Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology. For that purpose, a full scale-up/down computational framework is already available. This framework links computational fluid dynamics (CFD), metabolic flux analysis and agent-based modelling (ABM) for a better understanding of the cell lifelines in a heterogeneous environment. Ultimately, this framework can be used for the design of scale-down simulators and/or metabolically engineered cells able to cope with environmental fluctuations typically found in large-scale bioreactors. However, this framework still needs some refinements, such as a better integration of gas-liquid flows in CFD, and taking into account intrinsic biological noise in ABM. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Spontaneous ordering and vortex states of active fluids in circular confinement

NASA Astrophysics Data System (ADS)

Theillard, Maxime; Ezhilan, Barath; Saintillan, David

2015-11-01

Recent experimental, theoretical and simulation studies have shown that confinement can profoundly affect self-organization in active suspensions leading to striking features such as directed fluid pumping in planar confinement, formation of steady and spontaneous vortices in radial confinement. Motivated by this, we study the dynamics in a suspension of biologically active particles confined in spherical geometries using a mean-field kinetic theory for which we developed a novel numerical solver. In the case of circular confinement, we conduct a systematic exploration of the entire parameter space and distinguish 3 broad states: no-flow, stable vortex and chaotic and several interesting sub-states. Our efficient numerical framework is also employed to study 3D effects and dynamics in more complex geometries.

Surface tension in human pathophysiology and its application as a medical diagnostic tool

PubMed Central

Fathi-Azarbayjani, Anahita; Jouyban, Abolghasem

2015-01-01

Introduction: Pathological features of disease appear to be quite different. Despite this diversity, the common feature of various disorders underlies physicochemical and biochemical factors such as surface tension. Human biological fluids comprise various proteins and phospholipids which are capable of adsorption at fluid interfaces and play a vital role in the physiological function of human organs. Surface tension of body fluids correlates directly to the development of pathological states. Methods: In this review, the variety of human diseases mediated by the surface tension changes of biological phenomena and the failure of biological fluids to remain in their native state are discussed. Results: Dynamic surface tension measurements of human biological fluids depend on various parameters such as sex, age and changes during pregnancy or certain disease. It is expected that studies of surface tension behavior of human biological fluids will provide additional information and might become useful in medical practice. Theoretical background on surface tension measurement and surface tension values of reference fluids obtained from healthy and sick patients are depicted. Conclusion: It is well accepted that no single biomarker will be effective in clinical diagnosis. The surface tension measurement combined with routine lab tests may be a novel non-invasive method which can not only facilitate the discovery of diagnostic models for various diseases and its severity, but also be a useful tool for monitoring treatment efficacy. We therefore expect that studies of surface tension behavior of human biological fluids will provide additional useful information in medical practice. PMID:25901295

Nano-swimmers in biological membranes and propulsion hydrodynamics in two dimensions.

PubMed

Huang, Mu-Jie; Chen, Hsuan-Yi; Mikhailov, Alexander S

2012-11-01

Active protein inclusions in biological membranes can represent nano-swimmers and propel themselves in lipid bilayers. A simple model of an active inclusion with three particles (domains) connected by variable elastic links is considered. First, the membrane is modeled as a two-dimensional viscous fluid and propulsion behavior in two dimensions is examined. After that, an example of a microscopic dynamical simulation is presented, where the lipid bilayer structure of the membrane is resolved and the solvent effects are included by multiparticle collision dynamics. Statistical analysis of data reveals ballistic motion of the swimmer, in contrast to the classical diffusion behavior found in the absence of active transitions between the states.

A numerical study of the effects of bell pulsation dynamics and oral arms on the exchange currents generated by the upside-down jellyfish Cassiopea xamachana.

PubMed

Hamlet, Christina; Santhanakrishnan, Arvind; Miller, Laura A

2011-06-01

Mathematical and experimental studies of the flows generated by jellyfish have focused primarily on mechanisms of swimming. More recent work has also considered the fluid dynamics of feeding from currents generated during swimming. Here we capitalize on the benthic lifestyle of the upside-down jellyfish (Cassiopea xamachana) to explore the fluid dynamics of feeding uncoupled from swimming. A two-dimensional mathematical model is developed to capture the fundamental characteristics of the motion of the unique concave bell shape. Given the prominence of the oral arms, this structure is included and modeled as a porous layer that perturbs the flow generated by bell contractions. The immersed boundary method is used to solve the fluid-structure interaction problem. Velocity fields obtained from live organisms using digital particle image velocimetry were used to validate the numerical simulations. Parameter sweeps were used to numerically explore the effects of changes in pulse dynamics and the properties of the oral arms independently. Numerical experiments allow the opportunity to examine physical effects and limits within and beyond the biologically relevant range to develop a better understanding of the system. The presence of the prominent oral arm structures in the field of flow increased the flux of new fluid from along the substrate to the bell. The numerical simulations also showed that the presence of pauses between bell expansion and the next contraction alters the flow of the fluid over the bell and through the oral arms.

Full cell simulation and the evaluation of the buffer system on air-cathode microbial fuel cell

NASA Astrophysics Data System (ADS)

Ou, Shiqi; Kashima, Hiroyuki; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

2017-04-01

This paper presents a computational model of a single chamber, air-cathode MFC. The model considers losses due to mass transport, as well as biological and electrochemical reactions, in both the anode and cathode half-cells. Computational fluid dynamics and Monod-Nernst analysis are incorporated into the reactions for the anode biofilm and cathode Pt catalyst and biofilm. The integrated model provides a macro-perspective of the interrelation between the anode and cathode during power production, while incorporating microscale contributions of mass transport within the anode and cathode layers. Model considerations include the effects of pH (H+/OH- transport) and electric field-driven migration on concentration overpotential, effects of various buffers and various amounts of buffer on the pH in the whole reactor, and overall impacts on the power output of the MFC. The simulation results fit the experimental polarization and power density curves well. Further, this model provides insight regarding mass transport at varying current density regimes and quantitative delineation of overpotentials at the anode and cathode. Overall, this comprehensive simulation is designed to accurately predict MFC performance based on fundamental fluid and kinetic relations and guide optimization of the MFC system.

Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling.

PubMed

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-17

Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide a link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which governs the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modeling and highlight the opportunities for future developments in this area.

OpenFLUID: an open-source software environment for modelling fluxes in landscapes

NASA Astrophysics Data System (ADS)

Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

2013-04-01

Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network transfer, diagnosis and prediction of water quality taking into account human activities, study of the effect of spatial organization on hydrological fluxes, modelling of surface-subsurface water exchanges, … At LISAH research unit, OpenFLUID is the supporting development platform of the MHYDAS model, which is a distributed model for agrosystems (Moussa et al., 2002, Hydrological Processes, 16, 393-412). OpenFLUID web site : http://www.openfluid-project.org

Mechanics of Undulatory Swimming in a Frictional Fluid

PubMed Central

Ding, Yang; Sharpe, Sarah S.; Masse, Andrew; Goldman, Daniel I.

2012-01-01

The sandfish lizard (Scincus scincus) swims within granular media (sand) using axial body undulations to propel itself without the use of limbs. In previous work we predicted average swimming speed by developing a numerical simulation that incorporated experimentally measured biological kinematics into a multibody sandfish model. The model was coupled to an experimentally validated soft sphere discrete element method simulation of the granular medium. In this paper, we use the simulation to study the detailed mechanics of undulatory swimming in a “granular frictional fluid” and compare the predictions to our previously developed resistive force theory (RFT) which models sand-swimming using empirically determined granular drag laws. The simulation reveals that the forward speed of the center of mass (CoM) oscillates about its average speed in antiphase with head drag. The coupling between overall body motion and body deformation results in a non-trivial pattern in the magnitude of lateral displacement of the segments along the body. The actuator torque and segment power are maximal near the center of the body and decrease to zero toward the head and the tail. Approximately 30% of the net swimming power is dissipated in head drag. The power consumption is proportional to the frequency in the biologically relevant range, which confirms that frictional forces dominate during sand-swimming by the sandfish. Comparison of the segmental forces measured in simulation with the force on a laterally oscillating rod reveals that a granular hysteresis effect causes the overestimation of the body thrust forces in the RFT. Our models provide detailed testable predictions for biological locomotion in a granular environment. PMID:23300407

Directed Fluid Transport with Biomimetic ``Silia'' Arrays

NASA Astrophysics Data System (ADS)

Shields, A. R.; Evans, B. A.; Carstens, B. L.; Falvo, M. R.; Washburn, S.; Superfine, R.

2008-10-01

We present results on the long-range, directed fluid transport produced by the collective beating of arrays of biomimetic ``silia.'' Silia are arrays of free-standing nanorods roughly the size of biological cilia, which we fabricate from a polymer-magnetic nanoparticle composite material. With external permanent magnets we actuate our silia such that their motion mimics the beating of biological cilia. Biological cilia have evolved to produce microscale fluid transport and are increasingly being recognized as critical components in a wide range of biological systems. However, despite much effort cilia generated fluid flows remain an area of active study. In the last decade, cilia-driven fluid flow in the embryonic node of vertebrates has been implicated as the initial left-right symmetry breaking event in these embryos. With silia we generate directional fluid transport by mimicking the tilted conical beating of these nodal cilia and seek to answer open questions about the nature of particle advection in such a system. By seeding fluorescent microparticles into the fluid we have noted the existence of two distinct flow regimes. The fluid flow is directional and coherent above the tips of the silia, while between the silia tips and floor particle motion is complicated and suggestive of chaotic advection.

Microscopic and continuum descriptions of Janus motor fluid flow fields

PubMed Central

Reigh, Shang Yik; Schofield, Jeremy; Kapral, Raymond

2016-01-01

Active media, whose constituents are able to move autonomously, display novel features that differ from those of equilibrium systems. In addition to naturally occurring active systems such as populations of swimming bacteria, active systems of synthetic self-propelled nanomotors have been developed. These synthetic systems are interesting because of their potential applications in a variety of fields. Janus particles, synthetic motors of spherical geometry with one hemisphere that catalyses the conversion of fuel to product and one non-catalytic hemisphere, can propel themselves in solution by self-diffusiophoresis. In this mechanism, the concentration gradient generated by the asymmetric catalytic activity leads to a force on the motor that induces fluid flows in the surrounding medium. These fluid flows are studied in detail through microscopic simulations of Janus motor motion and continuum theory. It is shown that continuum theory is able to capture many, but not all, features of the dynamics of the Janus motor and the velocity fields of the fluid. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’. PMID:27698037

Exact and approximate solutions for transient squeezing flow

NASA Astrophysics Data System (ADS)

Lang, Ji; Santhanam, Sridhar; Wu, Qianhong

2017-10-01

In this paper, we report two novel theoretical approaches to examine a fast-developing flow in a thin fluid gap, which is widely observed in industrial applications and biological systems. The problem is featured by a very small Reynolds number and Strouhal number, making the fluid convective acceleration negligible, while its local acceleration is not. We have developed an exact solution for this problem which shows that the flow starts with an inviscid limit when the viscous effect has no time to appear and is followed by a subsequent developing flow, in which the viscous effect continues to penetrate into the entire fluid gap. An approximate solution is also developed using a boundary layer integral method. This solution precisely captures the general behavior of the transient fluid flow process and agrees very well with the exact solution. We also performed numerical simulation using Ansys-CFX. Excellent agreement between the analytical and the numerical solutions is obtained, indicating the validity of the analytical approaches. The study presented herein fills the gap in the literature and will have a broad impact on industrial and biomedical applications.

Crystallography of biological fluid as a method for evaluating its physicochemical characteristics.

PubMed

Martusevich, A K; Kamakin, N F

2007-03-01

Using an integral qualitative and quantitative approach to the studies of initiation of the biological material crystallogenesis, we showed in experiments with normal human saliva that the external characteristics of biological fluid (pH, osmolality, and environmental temperature) determine the results of crystallization (tesigraphic facies). The main external (macroenvironment) and inner (microenvironment) factors of biological fluid crystal formation, determining specific features of the tesigraphic facies, were distinguished and classified. The informative value of differential analysis of biomaterial properties by means of modulating the environmental conditions is established.

Two-Fluid Models and Interfacial Area Transport in Microgravity Condition

NASA Technical Reports Server (NTRS)

Ishii, Mamoru; Sun, Xiao-Dong; Vasavada, Shilp

2004-01-01

The objective of the present study is to develop a two-fluid model formulation with interfacial area transport equation applicable for microgravity conditions. The new model is expected to make a leapfrog improvement by furnishing the constitutive relations for the interfacial interaction terms with the interfacial area transport equation, which can dynamically model the changes of the interfacial structures. In the first year of this three-year project supported by the U.S. NASA, Office of Biological and Physics Research, the primary focus is to design and construct a ground-based, microgravity two-phase flow simulation facility, in which two immiscible fluids with close density will be used. In predicting the two-phase flow behaviors in any two-phase flow system, the interfacial transfer terms are among the most essential factors in the modeling. These interfacial transfer terms in a two-fluid model specify the rate of phase change, momentum exchange, and energy transfer at the interface between the two phases. For the two-phase flow under the microgravity condition, the stability of the fluid particle interface and the interfacial structures are quite different from those under normal gravity condition. The flow structure may not reach an equilibrium condition and the two fluids may be loosely coupled such that the inertia terms of each fluid should be considered separately by use of the two-fluid model. Previous studies indicated that, unless phase-interaction terms are accurately modeled in the two-fluid model, the complex modeling does not necessarily warrant an accurate solution.

Fluid models and simulations of biological cell phenomena

NASA Technical Reports Server (NTRS)

Greenspan, H. P.

1982-01-01

The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

Biological and Mechanical Effects of Micro-Nanostructured Titanium Surface on an Osteoblastic Cell Line In vitro and Osteointegration In vivo.

PubMed

Hao, Jingzu; Li, Ying; Li, Baoe; Wang, Xiaolin; Li, Haipeng; Liu, Shimin; Liang, Chunyong; Wang, Hongshui

2017-09-01

Hybrid micro-nanostructure implant surface was produced on titanium (Ti) surface by acid etching and anodic oxidation to improve the biological and mechanical properties. The biological properties of the micro-nanostructure were investigated by simulated body fluid (SBF) soaking test and MC3T3-E1 cell co-culture experiment. The cell proliferation, spreading, and bone sialoprotein (BSP) gene expression were examined by MTT, SEM, and reverse transcription-polymerase chain reaction (RT-PCR), respectively. In addition, the mechanical properties were evaluated by instrumented nanoindentation test and friction-wear test. Furthermore, the effect of the micro-nanostructure surface on implant osteointegration was examined by in vivo experiment. The results showed that the formation of bone-like apatite was accelerated on the micro-nanostructured Ti surface after immersion in simulated body fluid, and the proliferation, spreading, and BSP gene expression of the MC3T3-E1 cells were also upregulated on the modified surface. The micro-nanostructured Ti surface displayed decreased friction coefficient, stiffness value, and Young's modulus which were much closer to those of the cortical bone, compared to the polished Ti surface. This suggested much better mechanical match to the surrounding bone tissue of the micro-nanostructured Ti surface. Furthermore, the in vivo animal experiment showed that after implantation in the rat femora, the micro-nanostructure surface displayed higher bonding strength between bone tissues and implant; hematoxylin and eosin (H&E) staining suggested that much compact osteoid tissue was observed at the interface of Micro-nano-Ti-bone than polished Ti-bone interface after implantation. Based on these results mentioned above, it was concluded that the improved biological and mechanical properties of the micro-nanostructure endowed Ti surface with good biocompatibility and better osteointegration, implying the enlarged application of the micro-nanostructure surface Ti implants in future.

Advances in cardiovascular fluid mechanics: bench to bedside.

PubMed

Dasi, Lakshmi P; Sucosky, Philippe; de Zelicourt, Diane; Sundareswaran, Kartik; Jimenez, Jorge; Yoganathan, Ajit P

2009-04-01

This paper presents recent advances in cardiovascular fluid mechanics that define the current state of the art. These studies include complex multimodal investigations with advanced measurement and simulation techniques. We first discuss the complex flows within the total cavopulmonary connection in Fontan patients. We emphasize the quantification of energy losses by studying the importance of caval offsets as well as the differences among various Fontan surgical protocols. In our studies of the fluid mechanics of prosthetic heart valves, we reveal for the first time the full three-dimensional complexity of flow fields in the vicinity of bileaflet and trileaflet valves and the microscopic hinge flow dynamics. We also present results of these valves functioning in a patient-specific native aorta geometry. Our in vitro mitral valve studies show the complex mechanism of the native mitral valve apparatus. We demonstrate that the different components of the mitral valve have independent and synergistically complex functions that allow the valve to operate efficiently. We also show how valve mechanics change under pathological and repair conditions associated with enlarged ventricles. Finally, our ex vivo studies on the interactions between the aortic valve and its surrounding hemodynamic environment are aimed at providing insights into normal valve function and valve pathology. We describe the development of organ- and tissue-culture systems and the biological response of the tissue subjected to their respective simulated mechanical environment. The studies noted above have enhanced our understanding of the complex fluid mechanics associated with the cardiovascular system and have led to new translational technologies.

Swarming Patterns in a Two-Dimensional Kinematic Model for Biological Groups

NASA Astrophysics Data System (ADS)

Topaz, Chad

2004-03-01

We construct a continuum model for the motion of biological organisms experiencing social interactions and study its pattern-forming behavior. The model takes the form of a conservation law in two spatial dimensions. Social interactions are modeled in the velocity term, which is nonlocal in the population density. The dynamics of the model may be uniquely decomposed into incompressible motion and potential motion. For the purely incompressible case, the model resembles that for fluid dynamical vortex patches. There exist solutions that have constant population density and compact support for all time. Numerical simulations produce rotating structures with circular cores and spiral arms, reminiscent of naturally observed swarms such as ant mills. For the purely potential case, the model resembles a nonlocal (forwards or backwards) porous media equation, describing aggregation or dispersion of the population. For the aggregative case, the population clumps into regions of high and low density with a predictable characteristic length scale that is confirmed by numerical simulations.

Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach.

PubMed

Arrieta, Jorge; Cartwright, Julyan H E; Gouillart, Emmanuelle; Piro, Nicolas; Piro, Oreste; Tuval, Idan

2015-01-01

Mixing fluid in a container at low Reynolds number--in an inertialess environment--is not a trivial task. Reciprocating motions merely lead to cycles of mixing and unmixing, so continuous rotation, as used in many technological applications, would appear to be necessary. However, there is another solution: movement of the walls in a cyclical fashion to introduce a geometric phase. We show using journal-bearing flow as a model that such geometric mixing is a general tool for using deformable boundaries that return to the same position to mix fluid at low Reynolds number. We then simulate a biological example: we show that mixing in the stomach functions because of the "belly phase," peristaltic movement of the walls in a cyclical fashion introduces a geometric phase that avoids unmixing.

Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach

PubMed Central

Arrieta, Jorge; Cartwright, Julyan H. E.; Gouillart, Emmanuelle; Piro, Nicolas; Piro, Oreste; Tuval, Idan

2015-01-01

Mixing fluid in a container at low Reynolds number— in an inertialess environment—is not a trivial task. Reciprocating motions merely lead to cycles of mixing and unmixing, so continuous rotation, as used in many technological applications, would appear to be necessary. However, there is another solution: movement of the walls in a cyclical fashion to introduce a geometric phase. We show using journal-bearing flow as a model that such geometric mixing is a general tool for using deformable boundaries that return to the same position to mix fluid at low Reynolds number. We then simulate a biological example: we show that mixing in the stomach functions because of the “belly phase,” peristaltic movement of the walls in a cyclical fashion introduces a geometric phase that avoids unmixing. PMID:26154384

Seeking simplicity for the understanding of multiphase flows

NASA Astrophysics Data System (ADS)

Stone, Howard A.

2017-10-01

Fluid mechanics is a discipline with rich phenomena, with motions occurring over an enormous range of length scales, and spanning a wide range of laminar and turbulent flows, instabilities, and applications in industry, nature, biology, and medicine. The subfield of complex fluids typically refers to those flows where the complexity is introduced, for example, by the presence of suspended particles, multiple phases, soft boundaries, and electrokinetic effects; several distinct multiphase flows of Newtonian fluids make up the examples in this article. Interfaces play a significant role and modify the flow with feedback that further changes the shapes of the interfaces. I will provide examples of our work highlighting (i) new features of classical instabilities triggered by changes in geometry, (ii) multiphase flows relevant to the design of liquid-infused substrates exhibiting effective slip while retaining the trapped liquid, and (iii) unexpected dynamics in flow at a T-junction. The interplay of experiments and mathematical models and/or simulations is critical to the new understanding developed.

Adjustable Autonomy Testbed

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Schrenkenghost, Debra K.

2001-01-01

The Adjustable Autonomy Testbed (AAT) is a simulation-based testbed located in the Intelligent Systems Laboratory in the Automation, Robotics and Simulation Division at NASA Johnson Space Center. The purpose of the testbed is to support evaluation and validation of prototypes of adjustable autonomous agent software for control and fault management for complex systems. The AA T project has developed prototype adjustable autonomous agent software and human interfaces for cooperative fault management. This software builds on current autonomous agent technology by altering the architecture, components and interfaces for effective teamwork between autonomous systems and human experts. Autonomous agents include a planner, flexible executive, low level control and deductive model-based fault isolation. Adjustable autonomy is intended to increase the flexibility and effectiveness of fault management with an autonomous system. The test domain for this work is control of advanced life support systems for habitats for planetary exploration. The CONFIG hybrid discrete event simulation environment provides flexible and dynamically reconfigurable models of the behavior of components and fluids in the life support systems. Both discrete event and continuous (discrete time) simulation are supported, and flows and pressures are computed globally. This provides fast dynamic simulations of interacting hardware systems in closed loops that can be reconfigured during operations scenarios, producing complex cascading effects of operations and failures. Current object-oriented model libraries support modeling of fluid systems, and models have been developed of physico-chemical and biological subsystems for processing advanced life support gases. In FY01, water recovery system models will be developed.

Scalability Test of Multiscale Fluid-Platelet Model for Three Top Supercomputers

PubMed Central

Zhang, Peng; Zhang, Na; Gao, Chao; Zhang, Li; Gao, Yuxiang; Deng, Yuefan; Bluestein, Danny

2016-01-01

We have tested the scalability of three supercomputers: the Tianhe-2, Stampede and CS-Storm with multiscale fluid-platelet simulations, in which a highly-resolved and efficient numerical model for nanoscale biophysics of platelets in microscale viscous biofluids is considered. Three experiments involving varying problem sizes were performed: Exp-S: 680,718-particle single-platelet; Exp-M: 2,722,872-particle 4-platelet; and Exp-L: 10,891,488-particle 16-platelet. Our implementations of multiple time-stepping (MTS) algorithm improved the performance of single time-stepping (STS) in all experiments. Using MTS, our model achieved the following simulation rates: 12.5, 25.0, 35.5 μs/day for Exp-S and 9.09, 6.25, 14.29 μs/day for Exp-M on Tianhe-2, CS-Storm 16-K80 and Stampede K20. The best rate for Exp-L was 6.25 μs/day for Stampede. Utilizing current advanced HPC resources, the simulation rates achieved by our algorithms bring within reach performing complex multiscale simulations for solving vexing problems at the interface of biology and engineering, such as thrombosis in blood flow which combines millisecond-scale hematology with microscale blood flow at resolutions of micro-to-nanoscale cellular components of platelets. This study of testing the performance characteristics of supercomputers with advanced computational algorithms that offer optimal trade-off to achieve enhanced computational performance serves to demonstrate that such simulations are feasible with currently available HPC resources. PMID:27570250

Coarsening dynamics of binary liquids with active rotation.

PubMed

Sabrina, Syeda; Spellings, Matthew; Glotzer, Sharon C; Bishop, Kyle J M

2015-11-21

Active matter comprised of many self-driven units can exhibit emergent collective behaviors such as pattern formation and phase separation in both biological (e.g., mussel beds) and synthetic (e.g., colloidal swimmers) systems. While these behaviors are increasingly well understood for ensembles of linearly self-propelled "particles", less is known about the collective behaviors of active rotating particles where energy input at the particle level gives rise to rotational particle motion. A recent simulation study revealed that active rotation can induce phase separation in mixtures of counter-rotating particles in 2D. In contrast to that of linearly self-propelled particles, the phase separation of counter-rotating fluids is accompanied by steady convective flows that originate at the fluid-fluid interface. Here, we investigate the influence of these flows on the coarsening dynamics of actively rotating binary liquids using a phenomenological, hydrodynamic model that combines a Cahn-Hilliard equation for the fluid composition with a Navier-Stokes equation for the fluid velocity. The effect of active rotation is introduced though an additional force within the Navier-Stokes equations that arises due to gradients in the concentrations of clockwise and counter-clockwise rotating particles. Depending on the strength of active rotation and that of frictional interactions with the stationary surroundings, we observe and explain new dynamical behaviors such as "active coarsening" via self-generated flows as well as the emergence of self-propelled "vortex doublets". We confirm that many of the qualitative behaviors identified by the continuum model can also be found in discrete, particle-based simulations of actively rotating liquids. Our results highlight further opportunities for achieving complex dissipative structures in active materials subject to distributed actuation.

Chemical Speciation and Bioaccessibility of Arsenic and Chromiumin Chromated Copper Arsenate-Treated Wood and Soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nico, Peter S.; Ruby, Michael V.; Lowney, Yvette W.

This research compares the As and Cr chemistry ofdislodgeable residues from Chromated Copper Arsenate (CCA)-treated woodcollected by two different techniques (directly from the board surfaceeither by rubbing with a soft bristle brush or from human hands aftercontact with CCA-treated wood), and demonstrates that these materials areequivalent in terms of the chemical form and bonding of As and Cr and interms of the As leaching behavior. This finding links the extensivechemical characterization and bioavailability testing that has been donepreviously on the brush-removed residue to a material that is derivedfrom human skin contact with CCA-treated wood. Additionally, thisresearch characterizes the arsenic presentmore » in biological fluids (sweatand simulated gastric fluid) following contact with these residues. Thedata demonstrate that in biological fluids, the arsenic is presentprimarily as free arsenate ions.Arsenic-containing soils were alsoextracted into human sweat to evaluate the potential for arsenicdissolution from soils at the skin surface. For soils from field sites,only a small fraction of the total arsenic is soluble in sweat. Based oncomparisons to reference materials that have been used in in vivo dermalabsorption studies, these findings suggest that the actual relativebioavailability via dermal absorption of As from CCA-residues and soilmay be well below the current default value of 3 percent used by U.S.EPA.« less

ToF-SIMS images and spectra of biomimetic calcium silicate-based cements after storage in solutions simulating the effects of human biological fluids

NASA Astrophysics Data System (ADS)

Torrisi, A.; Torrisi, V.; Tuccitto, N.; Gandolfi, M. G.; Prati, C.; Licciardello, A.

2010-01-01

ToF-SIMS images were obtained from a section of a tooth, obturated by means of a new calcium-silicate based cement (wTCF) after storage for 1 month in a saline solutions (DPBS), in order to simulate the body fluid effects on the obturation. Afterwards, ToF-SIMS spectra were obtained from model samples, prepared by using the same cement paste, after storage for 1 month and 8 months in two different saline solutions (DPBS and HBSS). ToF-SIMS spectra were also obtained from fluorine-free cement (wTC) samples after storage in HBSS for 1 month and 8 months and used for comparison. It was found that the composition of both the saline solution and the cement influenced the composition of the surface of disks and that longer is the storage greater are the differences. Segregation phenomena occur both on the cement obturation of the tooth and on the surface of the disks prepared by using the same cement. Indirect evidences of formation of new crystalline phases are supplied.

Multi-resolution Delta-plus-SPH with tensile instability control: Towards high Reynolds number flows

NASA Astrophysics Data System (ADS)

Sun, P. N.; Colagrossi, A.; Marrone, S.; Antuono, M.; Zhang, A. M.

2018-03-01

It is well known that the use of SPH models in simulating flow at high Reynolds numbers is limited because of the tensile instability inception in the fluid region characterized by high vorticity and negative pressure. In order to overcome this issue, the δ+-SPH scheme is modified by implementing a Tensile Instability Control (TIC). The latter consists of switching the momentum equation to a non-conservative formulation in the unstable flow regions. The loss of conservation properties is shown to induce small errors, provided that the particle distribution is regular. The latter condition can be ensured thanks to the implementation of a Particle Shifting Technique (PST). The novel variant of the δ+-SPH is proved to be effective in preventing the onset of tensile instability. Several challenging benchmark tests involving flows past bodies at large Reynolds numbers have been used. Within this a simulation characterized by a deforming foil that resembles a fish-like swimming body is used as a practical application of the δ+-SPH model in biological fluid mechanics.

Flow Dynamics of Contrast Dispersion in the Aorta

NASA Astrophysics Data System (ADS)

Eslami, Parastou; Seo, Jung-Hee; Chen, Marcus; Mittal, Rajat

2016-11-01

The time profile of the contrast concentration or arterial input function (AIF) has many fundamental clinical implications and is of importance for many imaging modalities and diagnosis such as MR perfusion, CT perfusion and CT angiography (CTA). Contrast dispersion in CTA has been utilized to develop a novel method- Transluminal Attenuation Flow Encoding (TAFE)- to estimate coronary blood flow (CBF). However, in clinical practice, AIF is only available in the descending aorta and is used as a surrogate of the AIF at the coronary ostium. In this work we use patient specific computational models of the complete aorta to investigate the fluid dynamics of contrast dispersion in the aorta. The simulation employs a realistic kinematic model of the aortic valve and the dispersion patterns are correlated with the complex dynamics of the pulsatile flow in the curved aorta. The simulations allow us to determine the implications of using the descending aorta AIF as a surrogate for the AIF at the coronary ostium. PE is supported by the NIH Individual Partnership Program. -/abstract- Category: 4.7.1: Biological fluid dynamics: Physiological - Cardiovasc This work was done at Johns Hopkins University.

Point-particle method to compute diffusion-limited cellular uptake.

PubMed

Sozza, A; Piazza, F; Cencini, M; De Lillo, F; Boffetta, G

2018-02-01

We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used to calibrate the method, linking the numerical parameters to the physical particle radius and uptake rate. We study the configurations of multiple absorbers of increasing complexity to examine the performance of the method by comparing our simulations with available exact analytical or numerical results. We demonstrate the potential of the method to resolve the complex diffusive interactions, here quantified by the Sherwood number, measuring the uptake rate in terms of that of isolated absorbers. We implement the method in a pseudospectral solver that can be generalized to include fluid motion and fluid-particle interactions. As a test case of the presence of a flow, we consider the uptake rate by a particle in a linear shear flow. Overall, our method represents a powerful and flexible computational tool that can be employed to investigate many complex situations in biology, chemistry, and related sciences.

RI: Rheology as a Tool for Understanding the Mechanics of Live Ant Aggregations, Part 1

DTIC Science & Technology

2016-11-04

measure rheological properties of biological fluids. Using this machine, we were able to characterize non -Newtonian fluids such as frog saliva...GA 30332 -0420 ABSTRACT Number of Papers published in peer-reviewed journals: Number of Papers published in non peer-reviewed journals: Final Report...order to measure rheological properties of biological fluids. Using this machine, we were able to characterize non -Newtonian fluids such as frog

Is the whole the sum of its parts? Agent-based modelling of wastewater treatment systems.

PubMed

Schuler, A J; Majed, N; Bucci, V; Hellweger, F L; Tu, Y; Gu, A Z

2011-01-01

Agent-based models (ABMS) simulate individual units within a system, such as the bacteria in a biological wastewater treatment system. This paper outlines past, current and potential future applications of ABMs to wastewater treatment. ABMs track heterogeneities within microbial populations, and this has been demonstrated to yield different predictions of bulk behaviors than the conventional, "lumped" approaches for enhanced biological phosphorus removal (EBPR) completely mixed reactors systems. Current work included the application of the ABM approach to bacterial adaptation/evolution, using the model system of individual EBPR bacteria that are allowed to evolve a kinetic parameter (maximum glycogen storage) in a competitive environment. The ABM approach was successfully implemented to a simple anaerobic-aerobic system and it was found the differing initial states converged to the same optimal solution under uncertain hydraulic residence times associated with completely mixed hydraulics. In another study, an ABM was developed and applied to simulate the heterogeneity in intracellular polymer storage compounds, including polyphosphate (PP), in functional microbial populations in enhanced biological phosphorus removal (EBPR) process. The simulation results were compared to the experimental measurements of single-cell abundance of PP in polyphosphate accumulating organisms (PAOs), performed using Raman microscopy. The model-predicted heterogeneity was generally consistent with observations, and it was used to investigate the relative contribution of external (different life histories) and internal (biological) mechanisms leading to heterogeneity. In the future, ABMs could be combined with computational fluid dynamics (CFD) models to understand incomplete mixing, more intracellular states and mechanisms can be incorporated, and additional experimental verification is needed.

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

NASA Astrophysics Data System (ADS)

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

2017-11-01

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

Nasal airflow simulations suggest convergent adaptation in Neanderthals and modern humans.

PubMed

de Azevedo, S; González, M F; Cintas, C; Ramallo, V; Quinto-Sánchez, M; Márquez, F; Hünemeier, T; Paschetta, C; Ruderman, A; Navarro, P; Pazos, B A; Silva de Cerqueira, C C; Velan, O; Ramírez-Rozzi, F; Calvo, N; Castro, H G; Paz, R R; González-José, R

2017-11-21

Both modern humans (MHs) and Neanderthals successfully settled across western Eurasian cold-climate landscapes. Among the many adaptations considered as essential to survival in such landscapes, changes in the nasal morphology and/or function aimed to humidify and warm the air before it reaches the lungs are of key importance. Unfortunately, the lack of soft-tissue evidence in the fossil record turns difficult any comparative study of respiratory performance. Here, we reconstruct the internal nasal cavity of a Neanderthal plus two representatives of climatically divergent MH populations (southwestern Europeans and northeastern Asians). The reconstruction includes mucosa distribution enabling a realistic simulation of the breathing cycle in different climatic conditions via computational fluid dynamics. Striking across-specimens differences in fluid residence times affecting humidification and warming performance at the anterior tract were found under cold/dry climate simulations. Specifically, the Asian model achieves a rapid air conditioning, followed by the Neanderthals, whereas the European model attains a proper conditioning only around the medium-posterior tract. In addition, quantitative-genetic evolutionary analyses of nasal morphology provided signals of stabilizing selection for MH populations, with the removal of Arctic populations turning covariation patterns compatible with evolution by genetic drift. Both results indicate that, departing from important craniofacial differences existing among Neanderthals and MHs, an advantageous species-specific respiratory performance in cold climates may have occurred in both species. Fluid dynamics and evolutionary biology independently provided evidence of nasal evolution, suggesting that adaptive explanations regarding complex functional phenotypes require interdisciplinary approaches aimed to quantify both performance and evolutionary signals on covariation patterns.

Disregarded Effect of Biological Fluids in siRNA Delivery: Human Ascites Fluid Severely Restricts Cellular Uptake of Nanoparticles.

PubMed

Dakwar, George R; Braeckmans, Kevin; Demeester, Joseph; Ceelen, Wim; De Smedt, Stefaan C; Remaut, Katrien

2015-11-04

Small interfering RNA (siRNA) offers a great potential for the treatment of various diseases and disorders. Nevertheless, inefficient in vivo siRNA delivery hampers its translation into the clinic. While numerous successful in vitro siRNA delivery stories exist in reduced-protein conditions, most studies so far overlook the influence of the biological fluids present in the in vivo environment. In this study, we compared the transfection efficiency of liposomal formulations in Opti-MEM (low protein content, routinely used for in vitro screening) and human undiluted ascites fluid obtained from a peritoneal carcinomatosis patient (high protein content, representing the in vivo situation). In Opti-MEM, all formulations are biologically active. In ascites fluid, however, the biological activity of all lipoplexes is lost except for lipofectamine RNAiMAX. The drop in transfection efficiency was not correlated to the physicochemical properties of the nanoparticles, such as premature siRNA release and aggregation of the nanoparticles in the human ascites fluid. Remarkably, however, all of the formulations except for lipofectamine RNAiMAX lost their ability to be taken up by cells following incubation in ascites fluid. To take into account the possible effects of a protein corona formed around the nanoparticles, we recommend always using undiluted biological fluids for the in vitro optimization of nanosized siRNA formulations next to conventional screening in low-protein content media. This should tighten the gap between in vitro and in vivo performance of nanoparticles and ensure the optimal selection of nanoparticles for further in vivo studies.

Fluid-structure interaction simulations of deformable structures with non-linear thin shell elements

NASA Astrophysics Data System (ADS)

Asgharzadeh, Hafez; Hedayat, Mohammadali; Borazjani, Iman; Scientific Computing; Biofluids Laboratory Team

2017-11-01

Large deformation of structures in a fluid is simulated using a strongly coupled partitioned fluid-structure interaction (FSI) approach which is stabilized with under-relaxation and the Aitken acceleration technique. The fluid is simulated using a recently developed implicit Newton-Krylov method with a novel analytical Jacobian. Structures are simulated using a triangular thin-shell finite element formulation, which considers only translational degrees of freedom. The thin-shell method is developed on the top of a previously implemented membrane finite element formulation. A sharp interface immersed boundary method is used to handle structures in the fluid domain. The developed FSI framework is validated against two three-dimensional experiments: (1) a flexible aquatic vegetation in the fluid and (2) a heaving flexible panel in fluid. Furthermore, the developed FSI framework is used to simulate tissue heart valves, which involve large deformations and non-linear material properties. This work was supported by American Heart Association (AHA) Grant 13SDG17220022 and the Center of Computational Research (CCR) of University at Buffalo.

Full cell simulation and the evaluation of the buffer system on air-cathode microbial fuel cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ou, Shiqi; Kashima, Hiroyuki; Aaron, Douglas S.

This paper presents a computational model of a single chamber, air-cathode MFC. The model considers losses due to mass transport, as well as biological and electrochemical reactions, in both the anode and cathode half-cells. Computational fluid dynamics and Monod-Nernst analysis are incorporated into the reactions for the anode biofilm and cathode Pt catalyst and biofilm. The integrated model provides a macro-perspective of the interrelation between the anode and cathode during power production, while incorporating microscale contributions of mass transport within the anode and cathode layers. Model considerations include the effects of pH (H +/OH – transport) and electric field-driven migrationmore » on concentration overpotential, effects of various buffers and various amounts of buffer on the pH in the whole reactor, and overall impacts on the power output of the MFC. The simulation results fit the experimental polarization and power density curves well. Further, this model provides insight regarding mass transport at varying current density regimes and quantitative delineation of overpotentials at the anode and cathode. Altogether, this comprehensive simulation is designed to accurately predict MFC performance based on fundamental fluid and kinetic relations and guide optimization of the MFC system.« less

Full cell simulation and the evaluation of the buffer system on air-cathode microbial fuel cell

DOE PAGES

Ou, Shiqi; Kashima, Hiroyuki; Aaron, Douglas S.; ...

2017-02-23

This paper presents a computational model of a single chamber, air-cathode MFC. The model considers losses due to mass transport, as well as biological and electrochemical reactions, in both the anode and cathode half-cells. Computational fluid dynamics and Monod-Nernst analysis are incorporated into the reactions for the anode biofilm and cathode Pt catalyst and biofilm. The integrated model provides a macro-perspective of the interrelation between the anode and cathode during power production, while incorporating microscale contributions of mass transport within the anode and cathode layers. Model considerations include the effects of pH (H +/OH – transport) and electric field-driven migrationmore » on concentration overpotential, effects of various buffers and various amounts of buffer on the pH in the whole reactor, and overall impacts on the power output of the MFC. The simulation results fit the experimental polarization and power density curves well. Further, this model provides insight regarding mass transport at varying current density regimes and quantitative delineation of overpotentials at the anode and cathode. Altogether, this comprehensive simulation is designed to accurately predict MFC performance based on fundamental fluid and kinetic relations and guide optimization of the MFC system.« less

The characterization of exosomes from biological fluids of patients with different types of cancer

NASA Astrophysics Data System (ADS)

Yunusova, N. V.; Tamkovich, S. N.; Stakheeva, M. N.; Grigor'eva, A. A.; Somov, A. K.; Tugutova, E. A.; Kolomiets, L. A.; Molchanov, S. V.; Afanas'ev, S. G.; Kakurina, G. V.; Choinzonov, E. L.; Kondakova, I. V.

2017-09-01

Exosomes are extracellular membrane structures involved in many physiological and pathological processes including cancerogenesis and metastasis. The purpose of the study was to isolate, identify and analyze the total content of exosomes in biological fluids. The exosomes from the plasma and ascites samples of the patients with ovarian cancer, from the blood plasma of the patients with colorectal and head and neck squamous cell cancer as well as from the blood plasma of healthy donors were characterized using transmission electron microscopy and flow cytometry. The subpopulations of the exosomes in the biological fluids of the patients with different types of cancer were similar, but the protein concentrations of exosomes were different. In this paper we present the methodological approaches allowing us to obtain high quality exosome preparations from biological fluids.

Exact and Approximate Solutions for Transient Squeezing Flow

NASA Astrophysics Data System (ADS)

Lang, Ji; Santhanam, Sridhar; Wu, Qianhong

2017-11-01

In this paper, we report two novel theoretical approaches to examine a fast-developing flow in a thin fluid gap, which is widely observed in industrial applications and biological systems. The problem is featured by a very small Reynolds number and Strouhal number, making the fluid convective acceleration is negligible, while its local acceleration is not. We have developed an exact solution for this problem which shows that the flow starts with an inviscid limit when the viscous effect has no time to appear, and is followed by a subsequent developing flow, in which the viscous effect continues to penetrate into the entire fluid gap. An approximate solution is also developed using a boundary layer integral method. This solution precisely captures the general behavior of the transient fluid flow process, and agrees very well with the exact solution. We also performed numerical simulation using Ansys-CFX. Excellent agreement between the analytical and the numerical solutions is obtained, indicating the validity of the analytical approaches. The study presented herein fills the gap in the literature, and will have a broad impact in industrial and biomedical applications. This work is supported by National Science Foundation CBET Fluid Dynamics Program under Award #1511096, and supported by the Seed Grant from The Villanova Center for the Advancement of Sustainability in Engineering (VCASE).

Determination of nitrate in biological fluids by HPLC.

PubMed

Ashraf, Muhammad; Ghalloo, Bilal Ahmed; Hayat, Muhammad Munawar; Rahman, Jameel; Ejaz, Samina; Iqbal, Muhammad; -Nasim, Faizul Hassan

2017-01-01

Nitrate is the stable product of nitric oxide, which is physiologically active radical, an immunomodulator and a neuromodulator; its quantification in biological fluids is important to study the physiological and biochemical nature. Therefore, the purpose of this study was to quantify nitrate in different biological fluids like serum, cerebrospinal fluid (CSF) and ascetic fluid (ASF) using HPLC technique. A new HPLC method for the estimation of nitrate in serum, CSF and ASF was developed using the mobile phase of 1.0mM each of Na 2 CO 3 and NaHCO 3 (1:1, v/v, pH 5 with H 3 PO 4 ) at a flow rate of 1.0mLmin -1 . Eluate was detected at 220nm with the retention time of nitrate 2.55 min. The LOD and LOQ values of nitrate were 0.03μgmL -1 and 0.098μgmL -1 , respectively. Nitrate was eluted through SAX Hypersil column of 150 × 4.6mm, id, 5μm particle size. Run time was 10min. The method was validated according to the FDA guidelines and was found linear in the range of 0.39 to 50μgmL -1 and CV was <3%, within limits of FDA guidelines. The method was used successfully for the estimation of nitrate in biological fluids like serum, CSF and ASF of 20 patients each. This is an alternate and reproducible method for the detection of nitrates in biological fluids.

Modelling and simulation of passive Lab-on-a-Chip (LoC) based micromixer for clinical application

NASA Astrophysics Data System (ADS)

Saikat, Chakraborty; Sharath, M.; Srujana, M.; Narayan, K.; Pattnaik, Prasant Kumar

2016-03-01

In biomedical application, micromixer is an important component because of many processes requires rapid and efficient mixing. At micro scale, the flow is Laminar due to small channel size which enables controlled rapid mixing. The reduction in analysis time along with high throughput can be achieved with the help of rapid mixing. In LoC application, micromixer is used for mixing of fluids especially for the devices which requires efficient mixing. Micromixer of this type of microfluidic devices with a rapid mixing is useful in application such as DNA/RNA synthesis, drug delivery system & biological agent detection. In this work, we design and simulate a microfluidic based passive rapid micromixer for lab-on-a-chip application.

Numerical analysis of wavefront aberration correction using multielectrode electrowetting-based devices.

PubMed

Zohrabi, Mo; Cormack, Robert H; Mccullough, Connor; Supekar, Omkar D; Gibson, Emily A; Bright, Victor M; Gopinath, Juliet T

2017-12-11

We present numerical simulations of multielectrode electrowetting devices used in a novel optical design to correct wavefront aberration. Our optical system consists of two multielectrode devices, preceded by a single fixed lens. The multielectrode elements function as adaptive optical devices that can be used to correct aberrations inherent in many imaging setups, biological samples, and the atmosphere. We are able to accurately simulate the liquid-liquid interface shape using computational fluid dynamics. Ray tracing analysis of these surfaces shows clear evidence of aberration correction. To demonstrate the strength of our design, we studied three different input aberrations mixtures that include astigmatism, coma, trefoil, and additional higher order aberration terms, with amplitudes as large as one wave at 633 nm.

The impact of ARM on climate modeling

DOE PAGES

Randall, David A.; Del Genio, Anthony D.; Donner, Lee J.; ...

2016-07-15

Climate models are among humanity’s most ambitious and elaborate creations. They are designed to simulate the interactions of the atmosphere, ocean, land surface, and cryosphere on time scales far beyond the limits of deterministic predictability and including the effects of time-dependent external forcings. The processes involved include radiative transfer, fluid dynamics, microphysics, and some aspects of geochemistry, biology, and ecology. The models explicitly simulate processes on spatial scales ranging from the circumference of Earth down to 100 km or smaller and implicitly include the effects of processes on even smaller scales down to a micron or so. In addition, themore » atmospheric component of a climate model can be called an atmospheric global circulation model (AGCM).« less

Turbulent Flow Effects on the Biological Performance of Hydro-Turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richmond, Marshall C.; Romero Gomez, Pedro DJ

2014-08-25

The hydro-turbine industry uses Computational Fluid Dynamics (CFD) tools to predict the flow conditions as part of the design process for new and rehabilitated turbine units. Typically the hydraulic design process uses steady-state simulations based on Reynolds-Averaged Navier-Stokes (RANS) formulations for turbulence modeling because these methods are computationally efficient and work well to predict averaged hydraulic performance, e.g. power output, efficiency, etc. However, in view of the increasing emphasis on environmental concerns, such as fish passage, the consideration of the biological performance of hydro-turbines is also required in addition to hydraulic performance. This leads to the need to assess whethermore » more realistic simulations of the turbine hydraulic environment -those that resolve unsteady turbulent eddies not captured in steady-state RANS computations- are needed to better predict the occurrence and extent of extreme flow conditions that could be important in the evaluation of fish injury and mortality risks. In the present work, we conduct unsteady, eddy-resolving CFD simulations on a Kaplan hydro-turbine at a normal operational discharge. The goal is to quantify the impact of turbulence conditions on both the hydraulic and biological performance of the unit. In order to achieve a high resolution of the incoming turbulent flow, Detached Eddy Simulation (DES) turbulence model is used. These transient simulations are compared to RANS simulations to evaluate whether extreme hydraulic conditions are better captured with advanced eddy-resolving turbulence modeling techniques. The transient simulations of key quantities such as pressure and hydraulic shear flow that arise near the various components (e.g. wicket gates, stay vanes, runner blades) are then further analyzed to evaluate their impact on the statistics for the lowest absolute pressure (nadir pressures) and for the frequency of collisions that are known to cause mortal injury in fish passing through hydro-turbines.« less

Stochastic Simulation of Complex Fluid Flows

DTIC Science & Technology

The PI has developed novel numerical algorithms and computational codes to simulate the Brownian motion of rigidparticles immersed in a viscous fluid...processes and to the design of novel nanofluid materials. Therandom Brownian motion of particles in fluid can be accounted for in fluid-structure

Dynamic dielectrophoresis model of multi-phase ionic fluids.

PubMed

Yan, Ying; Luo, Jing; Guo, Dan; Wen, Shizhu

2015-01-01

Ionic-based dielectrophoretic microchips have attracted significant attention due to their wide-ranging applications in electro kinetic and biological experiments. In this work, a numerical method is used to simulate the dynamic behaviors of ionic droplets in a microchannel under the effect of dielectrophoresis. When a discrete liquid dielectric is encompassed within a continuous fluid dielectric placed in an electric field, an electric force is produced due to the dielectrophoresis effect. If either or both of the fluids are ionic liquids, the magnitude and even the direction of the force will be changed because the net ionic charge induced by an electric field can affect the polarization degree of the dielectrics. However, using a dielectrophoresis model, assuming ideal dielectrics, results in significant errors. To avoid the inaccuracy caused by the model, this work incorporates the electrode kinetic equation and defines a relationship between the polarization charge and the net ionic charge. According to the simulation conditions presented herein, the electric force obtained in this work has an error exceeding 70% of the actual value if the false effect of net ionic charge is not accounted for, which would result in significant issues in the design and optimization of experimental parameters. Therefore, there is a clear motivation for developing a model adapted to ionic liquids to provide precise control for the dielectrophoresis of multi-phase ionic liquids.

A collision scheme for hybrid fluid-particle simulation of plasmas

NASA Astrophysics Data System (ADS)

Nguyen, Christine; Lim, Chul-Hyun; Verboncoeur, John

2006-10-01

Desorption phenomena at the wall of a tokamak can lead to the introduction of impurities at the edge of a thermonuclear plasma. In particular, the use of carbon as a constituent of the tokamak wall, as planned for ITER, requires the study of carbon and hydrocarbon transport in the plasma, including understanding of collisional interaction with the plasma. These collisions can result in new hydrocarbons, hydrogen, secondary electrons and so on. Computational modeling is a primary tool for studying these phenomena. XOOPIC [1] and OOPD1 are widely used computer modeling tools for the simulation of plasmas. Both are particle type codes. Particle simulation gives more kinetic information than fluid simulation, but more computation time is required. In order to reduce this disadvantage, hybrid simulation has been developed, and applied to the modeling of collisions. Present particle simulation tools such as XOOPIC and OODP1 employ a Monte Carlo model for the collisions between particle species and a neutral background gas defined by its temperature and pressure. In fluid-particle hybrid plasma models, collisions include combinations of particle and fluid interactions categorized by projectile-target pairing: particle-particle, particle-fluid, and fluid-fluid. For verification of this hybrid collision scheme, we compare simulation results to analytic solutions for classical plasma models. [1] Verboncoeur et al. Comput. Phys. Comm. 87, 199 (1995).

A mechanistic Individual-based Model of microbial communities.

PubMed

Jayathilake, Pahala Gedara; Gupta, Prashant; Li, Bowen; Madsen, Curtis; Oyebamiji, Oluwole; González-Cabaleiro, Rebeca; Rushton, Steve; Bridgens, Ben; Swailes, David; Allen, Ben; McGough, A Stephen; Zuliani, Paolo; Ofiteru, Irina Dana; Wilkinson, Darren; Chen, Jinju; Curtis, Tom

2017-01-01

Accurate predictive modelling of the growth of microbial communities requires the credible representation of the interactions of biological, chemical and mechanical processes. However, although biological and chemical processes are represented in a number of Individual-based Models (IbMs) the interaction of growth and mechanics is limited. Conversely, there are mechanically sophisticated IbMs with only elementary biology and chemistry. This study focuses on addressing these limitations by developing a flexible IbM that can robustly combine the biological, chemical and physical processes that dictate the emergent properties of a wide range of bacterial communities. This IbM is developed by creating a microbiological adaptation of the open source Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). This innovation should provide the basis for "bottom up" prediction of the emergent behaviour of entire microbial systems. In the model presented here, bacterial growth, division, decay, mechanical contact among bacterial cells, and adhesion between the bacteria and extracellular polymeric substances are incorporated. In addition, fluid-bacteria interaction is implemented to simulate biofilm deformation and erosion. The model predicts that the surface morphology of biofilms becomes smoother with increased nutrient concentration, which agrees well with previous literature. In addition, the results show that increased shear rate results in smoother and more compact biofilms. The model can also predict shear rate dependent biofilm deformation, erosion, streamer formation and breakup.

A mechanistic Individual-based Model of microbial communities

PubMed Central

Gupta, Prashant; Li, Bowen; Madsen, Curtis; Oyebamiji, Oluwole; González-Cabaleiro, Rebeca; Rushton, Steve; Bridgens, Ben; Swailes, David; Allen, Ben; McGough, A. Stephen; Zuliani, Paolo; Ofiteru, Irina Dana; Wilkinson, Darren; Chen, Jinju; Curtis, Tom

2017-01-01

Accurate predictive modelling of the growth of microbial communities requires the credible representation of the interactions of biological, chemical and mechanical processes. However, although biological and chemical processes are represented in a number of Individual-based Models (IbMs) the interaction of growth and mechanics is limited. Conversely, there are mechanically sophisticated IbMs with only elementary biology and chemistry. This study focuses on addressing these limitations by developing a flexible IbM that can robustly combine the biological, chemical and physical processes that dictate the emergent properties of a wide range of bacterial communities. This IbM is developed by creating a microbiological adaptation of the open source Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). This innovation should provide the basis for “bottom up” prediction of the emergent behaviour of entire microbial systems. In the model presented here, bacterial growth, division, decay, mechanical contact among bacterial cells, and adhesion between the bacteria and extracellular polymeric substances are incorporated. In addition, fluid-bacteria interaction is implemented to simulate biofilm deformation and erosion. The model predicts that the surface morphology of biofilms becomes smoother with increased nutrient concentration, which agrees well with previous literature. In addition, the results show that increased shear rate results in smoother and more compact biofilms. The model can also predict shear rate dependent biofilm deformation, erosion, streamer formation and breakup. PMID:28771505

Development of a solenoid actuated planar valveless micropump with single and multiple inlet-outlet arrangements

NASA Astrophysics Data System (ADS)

Kumar, N.; George, D.; Sajeesh, P.; Manivannan, P. V.; Sen, A. K.

2016-07-01

We report a planar solenoid actuated valveless micropump with multiple inlet-outlet configurations. The self-priming characteristics of the multiple inlet-multiple outlet micropump are studied. The filling dynamics of the micropump chamber during start-up and the effects of fluid viscosity, voltage and frequency on the dynamics are investigated. Numerical simulations for multiple inlet-multiple outlet micropumps are carried out using fluid structure algorithm. With DI water and at 5.0 Vp-p, 20 Hz frequency, the two inlet-two outlet micropump provides a maximum flow rate of 336 μl min-1 and maximum back pressure of 441 Pa. Performance characteristics of the two inlet-two outlet micropump are studied for aqueous fluids of different viscosity. Transport of biological cell lines and diluted blood samples are demonstrated; the flow rate-frequency characteristics are studied. Viability of cells during pumping with multiple inlet multiple outlet configuration is also studied in this work, which shows 100% of cells are viable. Application of the proposed micropump for simultaneous pumping, mixing and distribution of fluids is demonstrated. The proposed integrated, standalone and portable micropump is suitable for drug delivery, lab-on-chip and micro-total-analysis applications.

Modeling of Soft Poroelastic Tissue in Time-Harmonic MR Elastography

PubMed Central

Perriñez, Phillip R.; Kennedy, Francis E.; Van Houten, Elijah E. W.; Weaver, John B.; Paulsen, Keith D.

2010-01-01

Elastography is an emerging imaging technique that focuses on assessing the resistance to deformation of soft biological tissues in vivo. Magnetic resonance elastography (MRE) uses measured displacement fields resulting from low-amplitude, low-frequency (10 Hz–1 kHz) time-harmonic vibration to recover images of the elastic property distribution of tissues including breast, liver, muscle, prostate, and brain. While many soft tissues display complex time-dependent behavior not described by linear elasticity, the models most commonly employed in MRE parameter reconstructions are based on elastic assumptions. Further, elasticity models fail to include the interstitial fluid phase present in vivo. Alternative continuum models, such as consolidation theory, are able to represent tissue and other materials comprising two distinct phases, generally consisting of a porous elastic solid and penetrating fluid. MRE reconstructions of simulated elastic and poroelastic phantoms were performed to investigate the limitations of current-elasticity-based methods in producing accurate elastic parameter estimates in poroelastic media. The results indicate that linearly elastic reconstructions of fluid-saturated porous media at amplitudes and frequencies relevant to steady-state MRE can yield misleading effective property distributions resulting from the complex interaction between their solid and fluid phases. PMID:19272864

Cellular fluid mechanics.

PubMed

Kamm, Roger D

2002-01-01

The coupling of fluid dynamics and biology at the level of the cell is an intensive area of investigation because of its critical role in normal physiology and disease. Microcirculatory flow has been a focus for years, owing to the complexity of cell-cell or cell-glycocalyx interactions. Noncirculating cells, particularly those that comprise the walls of the circulatory system, experience and respond biologically to fluid dynamic stresses. In this article, we review the more recent studies of circulating cells, with an emphasis on the role of the glycocalyx on red-cell motion in small capillaries and on the deformation of leukocytes passing through the microcirculation. We also discuss flows in the vicinity of noncirculating cells, the influence of fluid dynamic shear stress on cell biology, and diffusion in the lipid bi-layer, all in the context of the important fluid-dynamic phenomena.

Method of and apparatus for determining the similarity of a biological analyte from a model constructed from known biological fluids

DOEpatents

Robinson, Mark R.; Ward, Kenneth J.; Eaton, Robert P.; Haaland, David M.

1990-01-01

The characteristics of a biological fluid sample having an analyte are determined from a model constructed from plural known biological fluid samples. The model is a function of the concentration of materials in the known fluid samples as a function of absorption of wideband infrared energy. The wideband infrared energy is coupled to the analyte containing sample so there is differential absorption of the infrared energy as a function of the wavelength of the wideband infrared energy incident on the analyte containing sample. The differential absorption causes intensity variations of the infrared energy incident on the analyte containing sample as a function of sample wavelength of the energy, and concentration of the unknown analyte is determined from the thus-derived intensity variations of the infrared energy as a function of wavelength from the model absorption versus wavelength function.

Polyelectrolyte Structure and Interactions in Model Cystic Fibrosis Sputum

NASA Astrophysics Data System (ADS)

Slimmer, Scott; Angelini, Thomas; Liang, Hongjun; Butler, John; Wong, Gerard C. L.

2002-03-01

Cystic fibrosis sputum is a complex fluid consisting of a number of components, including mucin (a glycoprotein), lysozyme (a cationic polypeptide), water, salt, as well as a high concentration of a number of anionic biological polyelectrolytes such as DNA and F-actin. The interactions governing these components are poorly understood, but may have important clinical consequences. For example, the formation of these biological polyelectrolytes into ordered gel phases may contribute significantly to the observed high viscosity of CF sputum. In this work, a number of model systems were created to simulate CF sputum in vitro, in order to elucidate the contributions of the different components. Preliminary results will be presented. This work was supported by NSF DMR-0071761, DOE DEFG02-91ER45439, the Beckman Young Investigator Program, and the Cystic Fibrosis Foundation.

Actin - Lysozyme Interactions in Model Cystic Fibrosis Sputum

NASA Astrophysics Data System (ADS)

Sanders, Lori; Slimmer, Scott; Angelini, Thomas; Wong, Gerard C. L.

2003-03-01

Cystic fibrosis sputum is a complex fluid consisting of mucin (a glycoprotein), lysozyme (a cationic polypeptide), water, salt, as well as a high concentration of a number of anionic biological polyelectrolytes such as DNA and F-actin. The interactions governing these components are poorly understood, but may have important clinical consequences. For example, the formation of these biological polyelectrolytes into ordered gel phases may contribute significantly to the observed high viscosity of CF sputum. In this work, a number of model systems containing actin, lysozyme, and KCl were created to simulate CF sputum in vitro. These model systems were studied using small angle x-ray scattering and confocal fluorescence microscopy. Preliminary results will be presented. This work was supported by NSF DMR-0071761, the Beckman Young Investigator Program, and the Cystic Fibrosis Foundation.

Harnessing Thermoresponsive Aptamers and Gels To Trap and Release Nanoparticles

NASA Astrophysics Data System (ADS)

Liu, Ya; Kuksenok, Olga; He, Ximin; Aizenberg, Michael; Aizenberg, Joanna; Balazs, Anna

We use computational modeling to design a device that can controllably trap and release particles in solution in response to variations in temperature. The system exploits the thermoresponsive properties of end-grafted fibers and the underlying gel substrate. The fibers mimic the temperature-dependent behavior of biological aptamers, which form a hairpin structure at low temperatures (T) and unfold at higher T, consequently losing their binding affinity. The gel substrate exhibits a lower critical solution temperature and thus, expands at low tempertures and contracts at higher T. By developing a new dissipative particle dynamics simulation, we examine the behavior of this hybrid system in a flowing fluid that contains buoyant nanoparticles. Our findings provide guidelines for creating fluidic devices that are effective at purifying contaminated solutions or trapping cells for biological assays.

Water Hammer Simulations of MMH Propellant - New Capability Demonstration of the Generalized Fluid Flow Simulation Program

NASA Technical Reports Server (NTRS)

Burkhardt, Z.; Ramachandran, N.; Majumdar, A.

2017-01-01

Fluid Transient analysis is important for the design of spacecraft propulsion system to ensure structural stability of the system in the event of sudden closing or opening of the valve. Generalized Fluid System Simulation Program (GFSSP), a general purpose flow network code developed at NASA/MSFC is capable of simulating pressure surge due to sudden opening or closing of valve when thermodynamic properties of real fluid are available for the entire range of simulation. Specifically GFSSP needs an accurate representation of pressure-density relationship in order to predict pressure surge during a fluid transient. Unfortunately, the available thermodynamic property programs such as REFPROP, GASP or GASPAK does not provide the thermodynamic properties of Monomethylhydrazine (MMH). This paper will illustrate the process used for building a customized table of properties of state variables from available properties and speed of sound that is required by GFSSP for simulation. Good agreement was found between the simulations and measured data. This method can be adopted for modeling flow networks and systems with other fluids whose properties are not known in detail in order to obtain general technical insight. Rigorous code validation of this approach will be done and reported at a future date.

Monte Carlo simulations of dipolar and quadrupolar linear Kihara fluids. A test of thermodynamic perturbation theory

NASA Astrophysics Data System (ADS)

Garzon, B.

Several simulations of dipolar and quadrupolar linear Kihara fluids using the Monte Carlo method in the canonical ensemble have been performed. Pressure and internal energy have been directly determined from simulations and Helmholtz free energy using thermodynamic integration. Simulations were carried out for fluids of fixed elongation at two different densities and several values of temperature and dipolar or quadrupolar moment for each density. Results are compared with the perturbation theory developed by Boublik for this same type of fluid and good agreement between simulated and theoretical values was obtained especially for quadrupole fluids. Simulations are also used to obtain the liquid structure giving the first few coefficients of the expansion of pair correlation functions in terms of spherical harmonics. Estimations of the triple point temperature to critical temperature ratio are given for some dipole and quadrupole linear fluids. The stability range of the liquid phase of these substances is shortly discussed and an analysis about the opposite roles of the dipole moment and the molecular elongation on this stability is also given.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

2013-02-26

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

2014-04-15

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

2015-11-24

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Ion specific correlations in bulk and at biointerfaces.

PubMed

Kalcher, I; Horinek, D; Netz, R R; Dzubiella, J

2009-10-21

Ion specific effects are ubiquitous in any complex colloidal or biological fluid in bulk or at interfaces. The molecular origins of these 'Hofmeister effects' are not well understood and their theoretical description poses a formidable challenge to the modeling and simulation community. On the basis of the combination of atomistically resolved molecular dynamics (MD) computer simulations and statistical mechanics approaches, we present a few selected examples of specific electrolyte effects in bulk, at simple neutral and charged interfaces, and on a short α-helical peptide. The structural complexity in these strongly Coulomb-correlated systems is highlighted and analyzed in the light of available experimental data. While in general the comparison of MD simulations to experiments often lacks quantitative agreement, mostly because molecular force fields and coarse-graining procedures remain to be optimized, the consensus as regards trends provides important insights into microscopic hydration and binding mechanisms.

Chiral separation of amino acids in biological fluids by micellar electrokinetic chromatography with laser-induced fluorescence detection.

PubMed

Thorsén, G; Bergquist, J

2000-08-18

A method is presented for the chiral analysis of amino acids in biological fluids using micellar electrokinetic chromatography (MEKC) and laser-induced fluorescence (LIF). The amino acids are derivatized with the chiral reagent (+/-)-1-(9-anthryl)-2-propyl chloroformate (APOC) and separated using a mixed micellar separation system. No tedious pre-purification of samples is required. The excellent separation efficiency and good detection capabilities of the MEKC-LIF system are exemplified in the analysis of urine and cerebrospinal fluid. This is the first time MEKC has been reported for chiral analysis of amino acids in biological fluids. The amino acids D-alanine, D-glutamine, and D-aspartic acid have been observed in cerebrospinal fluid, and D-alanine and D-glutamic acid in urine. To the best of our knowledge no measurements of either D-alanine in cerebrospinal fluid or D-glutamic acid in urine have been presented in the literature before.

Immersed Boundary Simulations of Active Fluid Droplets

PubMed Central

Hawkins, Rhoda J.

2016-01-01

We present numerical simulations of active fluid droplets immersed in an external fluid in 2-dimensions using an Immersed Boundary method to simulate the fluid droplet interface as a Lagrangian mesh. We present results from two example systems, firstly an active isotropic fluid boundary consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility. Secondly, a droplet filled with an active polar fluid with homeotropic anchoring at the droplet interface. These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom. The simulations outlined here will be useful for quantifying the wide range of dynamics observable in these active systems and modelling the effects of confinement in a consistent and adaptable way. PMID:27606609

Enabling fluorescent biosensors for the forensic identification of body fluids.

PubMed

Frascione, Nunzianda; Gooch, James; Daniel, Barbara

2013-11-12

The search for body fluids often forms a crucial element of many forensic investigations. Confirming fluid presence at a scene can not only support or refute the circumstantial claims of a victim, suspect or witness, but may additionally provide a valuable source of DNA for further identification purposes. However, current biological fluid testing techniques are impaired by a number of well-characterised limitations; they often give false positives, cannot be used simultaneously, are sample destructive and lack the ability to visually locate fluid depositions. These disadvantages can negatively affect the outcome of a case through missed or misinterpreted evidence. Biosensors are devices able to transduce a biological recognition event into a measurable signal, resulting in real-time analyte detection. The use of innovative optical sensing technology may enable the highly specific and non-destructive detection of biological fluid depositions through interaction with several fluid-endogenous biomarkers. Despite considerable impact in a variety of analytical disciplines, biosensor application within forensic analyses may be considered extremely limited. This article aims to explore a number of prospective biosensing mechanisms and to outline the challenges associated with their adaptation towards detection of fluid-specific analytes.

Impact of a large density gradient on linear and nonlinear edge-localized mode simulations

DOE PAGES

Xi, P. W.; Xu, X. Q.; Xia, T. Y.; ...

2013-09-27

Here, the impact of a large density gradient on edge-localized modes (ELMs) is studied linearly and nonlinearly by employing both two-fluid and gyro-fluid simulations. In two-fluid simulations, the ion diamagnetic stabilization on high-n modes disappears when the large density gradient is taken into account. But gyro-fluid simulations show that the finite Larmor radius (FLR) effect can effectively stabilize high-n modes, so the ion diamagnetic effect alone is not sufficient to represent the FLR stabilizing effect. We further demonstrate that additional gyroviscous terms must be kept in the two-fluid model to recover the linear results from the gyro-fluid model. Nonlinear simulations show that the density variation significantly weakens the E × B shearing at the top of the pedestal and thus leads to more energy loss during ELMs. The turbulence spectrum after an ELM crash is measured and has the relation ofmore » $$P(k_{z})\\propto k_{z}^{-3.3}$$ .« less

Thermal Analysis System

NASA Technical Reports Server (NTRS)

DiStefano, III, Frank James (Inventor); Wobick, Craig A. (Inventor); Chapman, Kirt Auldwin (Inventor); McCloud, Peter L. (Inventor)

2014-01-01

A thermal fluid system modeler including a plurality of individual components. A solution vector is configured and ordered as a function of one or more inlet dependencies of the plurality of individual components. A fluid flow simulator simulates thermal energy being communicated with the flowing fluid and between first and second components of the plurality of individual components. The simulation extends from an initial time to a later time step and bounds heat transfer to be substantially between the flowing fluid, walls of tubes formed in each of the individual components of the plurality, and between adjacent tubes. Component parameters of the solution vector are updated with simulation results for each of the plurality of individual components of the simulation.

Numerical Temperature And Fluid-Flow Modelling For The Topographic Effects On Hydrothermal Circulation; A case study in Lucy Strike Vent Field

NASA Astrophysics Data System (ADS)

Erçetin, Engin; Düşünür Doǧan, Doǧa

2017-04-01

The aim of the study is to present a numerical temperature and fluid-flow modelling for the topographic effects on hydrothermal circulation. Bathymetry can create a major disturbance on fluid flow pattern. ANSYS Fluent Computational fluid dynamics software is used for simulations. Coupled fluid flow and temperature quations are solved using a 2-Dimensional control volume finite difference approach. Darcy's law is assumed to hold, the fluid is considered to be anormal Boussinesq incompressible fluid neglecting inertial effects. Several topographic models were simulated and both temperature and fluid flow calculations obtained for this study. The preliminary simulations examine the effect of a ingle bathymetric high on a single plume and the secondary study of simulations investigates the effect of multiple bathymetric highs on multiple plume. The simulations were also performed for the slow spreading Lucky Strike segment along the Mid-Atlantic Ridge (MAR), one of the best studied regions along the MAR, where a 3.4 km deep magma chamber extending 6 km along-axis is found at its center. The Lucky Strike segment displays a transitional morphology between that of the FAMOUS - North FAMOUS segments, which are characterized by well-developed axial valleys typical of slow-spreading segments, and that of the Menez Gwen segment, characterized by an axial high at the segment center. Lucky Strike Segment hosts a central volcano and active vent field located at the segment center and thus constitutes an excellent case study to simulate the effects of bathymetry on fluid flow. Results demonstrate that bathymetric relief has an important influence on hydrothermal flow. Subsurface pressure alterations can be formed by bathymetric highs, for this reason, bathymetric relief ought to be considered while simulating hydrothermal circulation systems. Results of this study suggest the dominant effect of bathymetric highs on fluid flow pattern and Darcy velocities will be presented. Keywords: Hydrothermal Circulation, Lucky Strike, Bathymetry - Topography, Vent Location, Fluid Flow, Numerical Modelling

Fluid Structural Analysis of Human Cerebral Aneurysm Using Their Own Wall Mechanical Properties

PubMed Central

Valencia, Alvaro; Burdiles, Patricio; Ignat, Miguel; Mura, Jorge; Rivera, Rodrigo; Sordo, Juan

2013-01-01

Computational Structural Dynamics (CSD) simulations, Computational Fluid Dynamics (CFD) simulation, and Fluid Structure Interaction (FSI) simulations were carried out in an anatomically realistic model of a saccular cerebral aneurysm with the objective of quantifying the effects of type of simulation on principal fluid and solid mechanics results. Eight CSD simulations, one CFD simulation, and four FSI simulations were made. The results allowed the study of the influence of the type of material elements in the solid, the aneurism's wall thickness, and the type of simulation on the modeling of a human cerebral aneurysm. The simulations use their own wall mechanical properties of the aneurysm. The more complex simulation was the FSI simulation completely coupled with hyperelastic Mooney-Rivlin material, normal internal pressure, and normal variable thickness. The FSI simulation coupled in one direction using hyperelastic Mooney-Rivlin material, normal internal pressure, and normal variable thickness is the one that presents the most similar results with respect to the more complex FSI simulation, requiring one-fourth of the calculation time. PMID:24151523

Laser bioengineering of glass-titanium implants surface

NASA Astrophysics Data System (ADS)

Lusquiños, F.; Arias-González, F.; Penide, J.; del Val, J.; Comesaña, R.; Quintero, F.; Riveiro, A.; Boutinguiza, M.; Pascual, M. J.; Durán, A.; Pou, J.

2013-11-01

Osseointegration is the mean challenge when surgical treatments fight against load-bearing bone diseases. Absolute bone replacement by a synthetic implant has to be completed not only from the mechanics point of view, but also from a biological approach. Suitable strength, resilience and stress distribution of titanium alloy implants are spoiled by the lack of optimal biological characteristics. The inert quality of extra low interstitial titanium alloy, which make it the most attractive metallic alloy for biomedical applications, oppose to an ideal surface with bone cell affinity, and capable to stimulate bone attachment bone growth. Diverse laser treatments have been proven as effective tools to modify surface properties, such as wettability in contact to physiological fluids, or osteoblast guided and slightly enhanced attachment. The laser surface cladding can go beyond by providing titanium alloy surfaces with osteoconduction and osteoinduction properties. In this research work, the laser radiation is used to produce bioactive glass coatings on Ti6Al4V alloy substrates. Specific silicate bioactive glass compositions has been investigated to achieve suitable surface tension and viscosity temperature behavior during processing, and to provide with the required release of bone growth gene up regulation agents in the course of resorption mediated by physiological fluids. The produced coatings and interfaces, the surface osteoconduction properties, and the chemical species release in simulated physiological fluid were characterized by scanning electron microscopy (SEM), hot stage microscopy (HSM), X-ray diffraction (XRD), X ray fluorescence (XRF), and Fourier transform infrared spectroscopy (FTIR).

The influence of buffer system and biological fluids on the degradation of magnesium.

PubMed

Törne, Karin; Örnberg, Andreas; Weissenrieder, Jonas

2017-08-01

The influence of frequently used buffer system 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) compared to CO 2 /HCO3- on the corrosion of magnesium is investigated. Samples were immersed in simulated body fluid (m-SBF) while monitored by electrochemical impedance spectroscopy (EIS) for up to 30 days. In CO 2 /HCO3- the initial corrosion rate was 0.11 mm yr -1 . An inner protective layer of magnesium oxide was formed within the first 30 min exposure and subsequently covered by an outer layer of apatite within 24 h . The corrosion mechanism thereafter is best described as passive pitting with a porosity of ∼10%. Using HEPES as buffer agent increased the corrosion rate to 3.37 mm yr -1 . Cross sectional microscopy show a porous outer corrosion layer allowing rapid diffusion of aggressive ions through the film. Here the EIS results are best described by an active pitting model with an inner layer 5 to 10 times less protective compared to the inner layer formed without HEPES. Further the suitability of human whole blood and plasma as in vitro models for Mg degradation was evaluated. Mg corrosion caused coagulation after 24 h in both biological fluids. The corrosion during the first 24 h is similar to the corrosion in m-SBF with HEPES. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1490-1502, 2017. © 2016 Wiley Periodicals, Inc.

Blast and the Consequences on Traumatic Brain Injury-Multiscale Mechanical Modeling of Brain

DTIC Science & Technology

2011-02-17

blast simulation. LS-DYNA as an explicit FE code has been employed to simulate this multi- material fluid –structure interaction problem. The 3-D head...formulation is implemented to model the air-blast simulation. LS-DYNA as an explicit FE code has been employed to simulate this multi-material fluid ...Biomechanics Study of Influencing Parameters for brain under Impact ............................... 12 5.1 The Impact of Cerebrospinal Fluid

Membrane materials for storing biological samples intended for comparative nanotoxicological testing

NASA Astrophysics Data System (ADS)

Metelkin, A.; Kuznetsov, D.; Kolesnikov, E.; Chuprunov, K.; Kondakov, S.; Osipov, A.; Samsonova, J.

2015-11-01

The study is aimed at identifying the samples of most promising membrane materials for storing dry specimens of biological fluids (Dried Blood Spots, DBS technology). Existing sampling systems using cellulose fiber filter paper have a number of drawbacks such as uneven distribution of the sample spot, dependence of the spot spreading area on the individual biosample properties, incomplete washing-off of the sample due to partially inconvertible sorption of blood components on cellulose fibers, etc. Samples of membrane materials based on cellulose, polymers and glass fiber with applied biosamples were studied using methods of scanning electron microscopy, FT-IR spectroscopy and surface-wetting measurement. It was discovered that cellulose-based membrane materials sorb components of biological fluids inside their structure, while membranes based on glass fiber display almost no interaction with the samples and biological fluid components dry to films in the membrane pores between the structural fibers. This characteristic, together with the fact that membrane materials based on glass fiber possess sufficient strength, high wetting properties and good storage capacity, attests them as promising material for dry samples of biological fluids storage systems.

Statistical analysis of polarization interference images of biological fluids polycrystalline films in the tasks of optical anisotropy weak changes differentiation

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Dubolazov, O. V.; Ushenko, V. O.; Zhytaryuk, V. G.; Prydiy, O. G.; Pavlyukovich, N.; Pavlyukovich, O.

2018-01-01

In this paper, we present the results of a statistical analysis of polarization-interference images of optically thin histological sections of biological tissues and polycrystalline films of biological fluids of human organs. A new analytical parameter is introduced-the local contrast of the interference pattern in the plane of a polarizationinhomogeneous microscopic image of a biological preparation. The coordinate distributions of the given parameter and the sets of statistical moments of the first-fourth order that characterize these distributions are determined. On this basis, the differentiation of degenerative-dystrophic changes in the myocardium and the polycrystalline structure of the synovial fluid of the human knee with different pathologies is realized.

Rationalization of reduced penetration of drugs through ceramide gel phase membrane.

PubMed

Paloncýová, Markéta; DeVane, Russell H; Murch, Bruce P; Berka, Karel; Otyepka, Michal

2014-11-25

Since computing resources have advanced enough to allow routine molecular simulation studies of drug molecules interacting with biologically relevant membranes, a considerable amount of work has been carried out with fluid phospholipid systems. However, there is very little work in the literature on drug interactions with gel phase lipids. This poses a significant limitation for understanding permeation through the stratum corneum where the primary pathway is expected to be through a highly ordered lipid matrix. To address this point, we analyzed the interactions of p-aminobenzoic acid (PABA) and its ethyl (benzocaine) and butyl (butamben) esters with two membrane bilayers, which differ in their fluidity at ambient conditions. We considered a dioleoylphosphatidylcholine (DOPC) bilayer in a fluid state and a ceramide 2 (CER2, ceramide NS) bilayer in a gel phase. We carried out unbiased (100 ns long) and biased z-constraint molecular dynamics simulations and calculated the free energy profiles of all molecules along the bilayer normal. The free energy profiles converged significantly slower for the gel phase. While the compounds have comparable affinities for both membranes, they exhibit penetration barriers almost 3 times higher in the gel phase CER2 bilayer. This elevated barrier and slower diffusion in the CER2 bilayer, which are caused by the high ordering of CER2 lipid chains, explain the low permeability of the gel phase membranes. We also compared the free energy profiles from MD simulations with those obtained from COSMOmic. This method provided the same trends in behavior for the guest molecules in both bilayers; however, the penetration barriers calculated by COSMOmic did not differ between membranes. In conclusion, we show how membrane fluid properties affect the interaction of drug-like molecules with membranes.

Preparation and characterization of glycidyl methacrylate organo bridges grafted mesoporous silica SBA-15 as ibuprofen and mesalamine carrier for controlled release.

PubMed

Rehman, Fozia; Rahim, Abdur; Airoldi, Claudio; Volpe, Pedro L O

2016-02-01

Mesoporous silica SBA-15 was synthesized and functionalized with bridged polysilsesquioxane monomers obtained by the reaction of 3-aminopropyltriethoxy silane with glycidyl methacrylate in 2:1 ratio. The synthesized mesoporous silica materials were characterized by elemental analysis, infrared spectroscopy, nuclear magnetic resonance spectroscopy, nitrogen adsorption, X-ray diffraction, thermogravimetry and scanning electron microscopy. The nuclear magnetic resonance in the solid state is in agreement with the sequence of carbon distributed in the attached organic chains, as expected for organically functionalized mesoporous silica. After functionalization with organic bridges the BET surface area was reduced from 1311.80 to 494.2m(2)g(-1) and pore volume was reduced from 1.98 to 0.89cm(3)g(-1), when compared to original precursor silica. Modification of the silica surface with organic bridges resulted in high loading capacity and controlled release of ibuprofen and mesalamine in biological fluids. The Korsmeyer-Peppas model better fits the release data indicating Fickian diffusion and zero order kinetics for synthesized mesoporous silica. The drug release rate from the modified silica was slow in simulated gastric fluid, (pH1.2) where less than 10% of mesalamine and ibuprofen were released in initial 8h, while comparatively high release rates were observed in simulated intestinal (pH6.8) and simulated body fluids (pH7.2). The preferential release of mesalamine at intestinal pH suggests that the modified silica could be a simple, efficient, inexpensive and convenient carrier for colon targeted drugs, such a mesalamine and also as a controlled drug release system. Copyright © 2015 Elsevier B.V. All rights reserved.

Contractile and chiral activities codetermine the helicity of swimming droplet trajectories

NASA Astrophysics Data System (ADS)

Tjhung, Elsen; Cates, Michael E.; Marenduzzo, Davide

2017-05-01

Active fluids are a class of nonequilibrium systems where energy is injected into the system continuously by the constituent particles themselves. Many examples, such as bacterial suspensions and actomyosin networks, are intrinsically chiral at a local scale, so that their activity involves torque dipoles alongside the force dipoles usually considered. Although many aspects of active fluids have been studied, the effects of chirality on them are much less known. Here, we study by computer simulation the dynamics of an unstructured droplet of chiral active fluid in three dimensions. Our model considers only the simplest possible combination of chiral and achiral active stresses, yet this leads to an unprecedented range of complex motilities, including oscillatory swimming, helical swimming, and run-and-tumble motion. Strikingly, whereas the chirality of helical swimming is the same as the microscopic chirality of torque dipoles in one regime, the two are opposite in another. Some of the features of these motility modes resemble those of some single-celled protozoa, suggesting that underlying mechanisms may be shared by some biological systems and synthetic active droplets.

Computational Analysis of Human Blood Flow

NASA Astrophysics Data System (ADS)

Panta, Yogendra; Marie, Hazel; Harvey, Mark

2009-11-01

Fluid flow modeling with commercially available computational fluid dynamics (CFD) software is widely used to visualize and predict physical phenomena related to various biological systems. In this presentation, a typical human aorta model was analyzed assuming the blood flow as laminar with complaint cardiac muscle wall boundaries. FLUENT, a commercially available finite volume software, coupled with Solidworks, a modeling software, was employed for the preprocessing, simulation and postprocessing of all the models.The analysis mainly consists of a fluid-dynamics analysis including a calculation of the velocity field and pressure distribution in the blood and a mechanical analysis of the deformation of the tissue and artery in terms of wall shear stress. A number of other models e.g. T branches, angle shaped were previously analyzed and compared their results for consistency for similar boundary conditions. The velocities, pressures and wall shear stress distributions achieved in all models were as expected given the similar boundary conditions. The three dimensional time dependent analysis of blood flow accounting the effect of body forces with a complaint boundary was also performed.

Demonstration of Anisotropic Fluid Closure Capturing the Kinetic Structure of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Ohia, Obioma

2012-10-01

Magnetic reconnection in collisionless plasmas plays an important role in space and laboratory plasmas. Allowing magnetic stress to be reduced by a rearrangement of magnetic line topology, this process is often accompanied by a large release of magnetic field energy, which can heat the plasma, drive large scale flows, or accelerate particles. Reconnection has been widely studied through fluid models and kinetic simulations. While two-fluid models often reproduce the fast reconnection that is observed in nature and seen in kinetic simulations, it is found that the structure surrounding the electron diffusion region and the electron current layer differ vastly between fluid models and kinetic simulations [1]. Recently, using an adiabatic solution of the Vlasov equation, a new fluid closure has been obtained for electrons that relate parallel and perpendicular pressures to the density and magnetic field [2]. Here we present the results of fluid simulation, developed using the HiFi framework [3], that implements new equations of state for guide-field reconnection. The new fluid closure accurately accounts for the anisotropic electron pressure that builds in the reconnection region due to electric and magnetic trapping of electrons. In contrast to previous fluid models, our fluid simulation reproduces the detailed reconnection region as observed in fully kinetic simulations [4]. We hereby demonstrate that the new fluid closure self-consistently captures all the physics relevant to the structure of the reconnection region, providing a gateway to a renewed and deeper theoretical understanding for reconnection in weakly collisional regimes.[4pt] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0pt] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0pt] [3] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011). [0pt] [4] Ohia O, et al., Phys. Rev. Lett. In Press (2012).

Computer simulation to predict energy use, greenhouse gas emissions and costs for production of fluid milk using alternative processing methods

USDA-ARS?s Scientific Manuscript database

Computer simulation is a useful tool for benchmarking the electrical and fuel energy consumption and water use in a fluid milk plant. In this study, a computer simulation model of the fluid milk process based on high temperature short time (HTST) pasteurization was extended to include models for pr...

Effect of surface roughness and size of beam on squeeze-film damping—Molecular dynamics simulation study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Hojin; Strachan, Alejandro

2015-11-28

We use large-scale molecular dynamics (MD) to characterize fluid damping between a substrate and an approaching beam. We focus on the near contact regime where squeeze film (where fluid gap is comparable to the mean free path of the gas molecules) and many-body effects in the fluid become dominant. The MD simulations provide explicit description of many-body and non-equilibrium processes in the fluid as well as the surface topography. We study how surface roughness and beam width increases the damping coefficient due to their effect on fluid mobility. We find that the explicit simulations are in good agreement with priormore » direct simulation Monte Carlo results except at near-contact conditions where many-body effects in the compressed fluid lead the increased damping and weaker dependence on beam width. We also show that velocity distributions near the beam edges and for short gaps deviate from the Boltzmann distribution indicating a degree of local non-equilibrium. These results will be useful to parameterize compact models used for microsystem device-level simulations and provide insight into mesoscale simulations of near-contact damping.« less

Generation of monoclonal antibodies and development of an immunofluorometric assay for the detection of CUZD1 in tissues and biological fluids.

PubMed

Farkona, Sofia; Soosaipillai, Antoninus; Filippou, Panagiota; Korbakis, Dimitrios; Serra, Stefano; Rückert, Felix; Diamandis, Eleftherios P; Blasutig, Ivan M

2017-12-01

CUB and zona pellucida-like domain-containing protein 1 (CUZD1) was identified as a pancreas-specific protein and was proposed as a candidate biomarker for pancreatic related disorders. CUZD1 protein levels in tissues and biological fluids have not been extensively examined. The purpose of the present study was to generate specific antibodies targeting CUZD1 to assess CUZD1 expression within tissues and biological fluids. Mouse monoclonal antibodies against CUZD1 were generated and used to perform immunohistochemical analyses and to develop a sensitive and specific enzyme-linked immunosorbent assay (ELISA). CUZD1 protein expression was assessed in various human tissue extracts and biological fluids and in gel filtration chromatography-derived fractions of pancreatic tissue extract, pancreatic juice and recombinant protein. Immunohistochemical staining of CUZD1 in pancreatic tissue showed that the protein is localized to the acinar cells and the lumen of the acini. Western blot analysis detected the protein in pancreatic tissue extract and pancreatic juice. The newly developed ELISA measured CUZD1 in high levels in pancreas and in much lower but detectable levels in several other tissues. In the biological fluids tested, CUZD1 expression was detected exclusively in pancreatic juice. The analysis of gel filtration chromatography-derived fractions of pancreatic tissue extract, pancreatic juice and recombinant CUZD1 suggested that the protein exists in high molecular weight protein complexes. This study describes the development of tools targeting CUZD1 protein, its tissue expression pattern and levels in several biological fluids. These new tools will facilitate future investigations aiming to delineate the role of CUZD1 in physiology and pathobiology. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Biological properties of nanostructured Ti incorporated with Ca, P and Ag by electrochemical method.

PubMed

Li, Baoe; Hao, Jingzu; Min, Yang; Xin, Shigang; Guo, Litong; He, Fei; Liang, Chunyong; Wang, Hongshui; Li, Haipeng

2015-06-01

TiO2 nanotube arrays were synthesized on Ti surface by anodic oxidation. The elements of Ca and P were simultaneously incorporated during nanotubes growth in SBF electrolyte, and then Ag was introduced to nanotube arrays by cathodic deposition, which endowed the good osseointegration and antibacterial property of Ti. The bioactivity of the Ti surface was evaluated by simulated body fluid soaking test. The biocompatibility was investigated by in vitro cell culture test. And the antibacterial effect against Staphylococcus aureus was examined by the bacterial counting method. The results showed that the incorporation of Ca, P and Ag elements had no significant influence on the formation of nanotube arrays on Ti surface during electrochemical treatment. Compared to the polished or nanotubular Ti surface, TiO2 nanotube arrays incorporated with Ca, P and Ag increased the formation of bone-like apatite in simulated body fluid, enhanced cell adhesion and proliferation, and inhibited the bacterial growth. Based on these results, it can be concluded that the nanostructured Ti incorporated with Ca, P and Ag by electrochemical method has promising applications as implant material. Copyright © 2015 Elsevier B.V. All rights reserved.

Fish gotta swim, Birds gotta fly, I gotta do Feynmann Graphs 'til I die: A continuum Theory of Flocking

NASA Astrophysics Data System (ADS)

Toner, John; Tu, Yu-Hai

2002-05-01

We have developed a new continuum dynamical model for the collective motion of large "flocks" of biological organisms (e.g., flocks of birds, schools of fish, herds of wildebeest, hordes of bacteria, slime molds, etc.) . This model does for flocks what the Navier-Stokes equation does for fluids. The model predicts that, unlike simple fluids, flocks show huge fluctuation effects in spatial dimensions d < 4 that radically change their behavior. In d=2, it is only these effects that make it possible for the flock to move coherently at all. This explains why a million wildebeest can march together across the Serengeti plain, despite the fact that a million physicists gathered on the same plane could NOT all POINT in the same direction. Detailed quantitative predictions of this theory agree beautifully with computer simulations of flock motion.

Passive Microfluidic device for Sub Millisecond Mixing

PubMed Central

McMahon, Jay; Mohamed, Hisham; Barnard, David; Shaikh, Tanvir R.; Mannella, Carmen A.; Wagenknecht, Terence; Lu, Toh-Ming

2009-01-01

We report the investigation of a novel microfluidic mixing device to achieve submillisecond mixing. The micromixer combines two fluid streams of several microliters per second into a mixing compartment integrated with two T- type premixers and 4 butterfly-shaped in-channel mixing elements. We have employed three dimensional fluidic simulations to evaluate the mixing efficiency, and have constructed physical devices utilizing conventional microfabrication techniques. The simulation indicated thorough mixing at flow rate as low as 6 µL/s. The corresponding mean residence time is 0.44 ms for 90% of the particles simulated, or 0.49 ms for 95% of the particles simulated, respectively. The mixing efficiency of the physical device was also evaluated using fluorescein dye solutions and FluoSphere-red nanoparticles suspensions. The constructed micromixers achieved thorough mixing at the same flow rate of 6 µL/s, with the mixing indices of 96% ± 1%, and 98% ± 1% for the dye and the nanoparticle, respectively. The experimental results are consistent with the simulation data. The device demonstrated promising capabilities for time resolved studies for macromolecular dynamics of biological macromolecules. PMID:20161619

A fast platform for simulating semi-flexible fiber suspensions applied to cell mechanics

NASA Astrophysics Data System (ADS)

Nazockdast, Ehssan; Rahimian, Abtin; Zorin, Denis; Shelley, Michael

2017-01-01

We present a novel platform for the large-scale simulation of three-dimensional fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space in three dimensions. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular assemblies of flexible fibers. We use non-local slender body theory to compute the fluid-structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multipole method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by nonlinear Euler-Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit time-stepping to resolve large fiber deformations, and to allow time-steps not excessively constrained by temporal stiffness or fiber-fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries. Finally to demonstrate the general applicability of the method, we simulate the sedimentation of a cloud of semi-flexible fibers.

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scalingmore » laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.« less

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

DOE PAGES

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; ...

2017-11-27

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scalingmore » laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.« less

Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.

PubMed

Ando, Tadashi; Yu, Isseki; Feig, Michael; Sugita, Yuji

2016-11-23

The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data. In most of the previous studies on the crowding effects, a uniform crowder size is assumed, which is in contrast to the inhomogeneous size distribution of macromolecules in a living cell. Here, we evaluate the free energy changes upon macromolecular association in a cell-like inhomogeneous crowding system via a theory of hard-sphere fluids and free energy calculations using Brownian dynamics trajectories. The inhomogeneous crowding model based on 41 different types of macromolecules represented by spheres with different radii mimics the physiological concentrations of macromolecules in the cytoplasm of Mycoplasma genitalium. The free energy changes of macromolecular association evaluated by the theory and simulations were in good agreement with each other. The crowder size distribution affects both specific and nonspecific molecular associations, suggesting that not only the volume fraction but also the size distribution of macromolecules are important factors for evaluating in vivo crowding effects. This study relates in vitro experiments on macromolecular crowding to in vivo crowding effects by using the theory of hard-sphere fluids with crowder-size heterogeneity.

A poroelastic finite element model of the bone-cartilage unit to determine the effects of changes in permeability with osteoarthritis.

PubMed

Stender, Michael E; Regueiro, Richard A; Ferguson, Virginia L

2017-02-01

The changes experienced in synovial joints with osteoarthritis involve coupled chemical, biological, and mechanical processes. The aim of this study was to investigate the consequences of increasing permeability in articular cartilage (AC), calcified cartilage (CC), subchondral cortical bone (SCB), and subchondral trabecular bone (STB) as observed with osteoarthritis. Two poroelastic finite element models were developed using a depth-dependent anisotropic model of AC with strain-dependent permeability and poroelastic models of calcified tissues (CC, SCB, and STB). The first model simulated a bone-cartilage unit (BCU) in uniaxial unconfined compression, while the second model simulated spherical indentation of the AC surface. Results indicate that the permeability of AC is the primary determinant of the BCU's poromechanical response while the permeability of calcified tissues exerts no appreciable effect on the force-indentation response of the BCU. In spherical indentation simulations with osteoarthritic permeability properties, fluid velocities were larger in magnitude and distributed over a smaller area compared to normal tissues. In vivo, this phenomenon would likely lead to chondrocyte death, tissue remodeling, alterations in joint lubrication, and the progression of osteoarthritis. For osteoarthritic and normal tissue permeability values, fluid flow was predicted to occur across the osteochondral interface. These results help elucidate the consequences of increases in the permeability of the BCU that occur with osteoarthritis. Furthermore, this study may guide future treatments to counteract osteoarthritis.

Thin-film-transistor array: an exploratory attempt for high throughput cell manipulation using electrowetting principle

NASA Astrophysics Data System (ADS)

Shaik, F. Azam; Cathcart, G.; Ihida, S.; Lereau-Bernier, M.; Leclerc, E.; Sakai, Y.; Toshiyoshi, H.; Tixier-Mita, A.

2017-05-01

In lab-on-a-chip (LoC) devices, microfluidic displacement of liquids is a key component. electrowetting on dielectric (EWOD) is a technique to move fluids, with the advantage of not requiring channels, pumps or valves. Fluids are discretized into droplets on microelectrodes and moved by applying an electric field via the electrodes to manipulate the contact angle. Micro-objects, such as biological cells, can be transported inside of these droplets. However, the design of conventional microelectrodes, made by standard micro-fabrication techniques, fixes the path of the droplets, and limits the reconfigurability of paths and thus limits the parallel processing of droplets. In that respect, thin film transistor (TFT) technology presents a great opportunity as it allows infinitely reconfigurable paths, with high parallelizability. We propose here to investigate the possibility of using TFT array devices for high throughput cell manipulation using EWOD. A COMSOL based 2D simulation coupled with a MATLAB algorithm was used to simulate the contact angle modulation, displacement and mixing of droplets. These simulations were confirmed by experimental results. The EWOD technique was applied to a droplet of culture medium containing HepG2 carcinoma cells and demonstrated no negative effects on the viability of the cells. This confirms the possibility of applying EWOD techniques to cellular applications, such as parallel cell analysis.

An Experimental and numerical Study for squeezing flow

NASA Astrophysics Data System (ADS)

Nathan, Rungun; Lang, Ji; Wu, Qianhong; Vucbmss Team

2017-11-01

We report an experimental and numerical study to examine the transient squeezing flow driven by sudden external impacts. The phenomenon is widely observed in industrial applications, e.g. squeeze dampers, or in biological systems, i.e. joints lubrication. However, there is a lack of investigation that captures the transient flow feature during the process. An experimental setup was developed that contains a piston instrumented with a laser displacement sensor and a pressure transducer. The heavy piston was released from rest, creating a fast compaction on the thin fluid gap underneath. The motion of the piston and the fluid pressure build-up was recorded. For this dynamic process, a CFD simulation was performed which shows excellent agreement with the experimental data. Both the numerical and experimental results show that, the squeezing flow starts with the inviscid limit when the viscous fluid effect has no time to appear, and thereafter becomes a developing flow, in which the inviscid core flow region decreases and the viscous wall region increases until the entire fluid gap is filled with viscous fluid flow. The study presented herein, filling the gap in the literature, will have broad impacts in industrial and biomedical applications. This research was supported by the National Science Foundation under Award 1511096, and supported by the Seed Grant from The Villanova Center for the Advancement of Sustainability in Engineering (VCASE).

Oxygen isotope ratio measurements on carbon dioxide generated by reaction of microliter quantities of biological fluids with guanidine hydrochloride

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, W.W.; Lee, L.S.; Klein, P.D.

1987-03-01

Guanidine hydrochloride was used to convert water in biological fluids to carbon dioxide for oxygen isotope ratio measurements. Five 10-..mu..L aliquots each of five different saliva, urine, plasma, and human milk samples were allowed to react with 100 mg of guanidine hydrochloride at 260/sup 0/C to produce ammonia and carbon dioxide. Ammonia was removed with 100% phosphoric acid and carbon dioxide was cryogenically purified before isotope ratio measurement. At natural abundances, the delta/sup 18/O values of the biological fluids were reproducible to within 0.16% (standard deviation) and accurate to within 0.11 +/- 0.73% (x vector +/- SD) of the H/submore » 2/O-CO/sub 2/ equilibration values. At a 250% enrichment level of /sup 18/O, the delta/sup 18/O values of the biological fluids were reproducible to within 0.95% and accurate to -1.27 +/- 2.25%.« less

Interactions of microbicide nanoparticles with a simulated vaginal fluid.

PubMed

das Neves, José; Rocha, Cristina M R; Gonçalves, Maria Pilar; Carrier, Rebecca L; Amiji, Mansoor; Bahia, Maria Fernanda; Sarmento, Bruno

2012-11-05

The interaction with cervicovaginal mucus presents the potential to impact the performance of drug nanocarriers. These systems must migrate through this biological fluid in order to deliver their drug payload to the underlying mucosal surface. We studied the ability of dapivirine-loaded polycaprolactone (PCL)-based nanoparticles (NPs) to interact with a simulated vaginal fluid (SVF) incorporating mucin. Different surface modifiers were used to produce NPs with either negative (poloxamer 338 NF and sodium lauryl sulfate) or positive (cetyltrimethylammonium bromide) surface charge. Studies were performed using the mucin particle method, rheological measurements, and real-time multiple particle tracking. Results showed that SVF presented rheological properties similar to those of human cervicovaginal mucus. Analysis of NP transport indicated mild interactions with mucin and low adhesive potential. In general, negatively charged NPs underwent subdiffusive transport in SVF, i.e., hindered as compared to their diffusion in water, but faster than for positively charged NPs. These differences were increased when the pH of SVF was changed from 4.2 to 7.0. Diffusivity was 50- and 172-fold lower in SVF at pH 4.2 than in water for negatively charged and positively charged NPs, respectively. At pH 7.0, this decrease was around 20- and 385-fold, respectively. The estimated times required to cross a layer of SVF were equal to or lower than 1.7 h for negatively charged NPs, while for positively charged NPs these values were equal to or higher than 7 h. Overall, our results suggest that negatively charged PCL NPs may be suitable to be used as carriers in order to deliver dapivirine and potentially other antiretroviral drugs to the cervicovaginal mucosal lining. Also, they further reinforce the importance in characterizing the interactions of nanosystems with mucus fluids or surrogates when considering mucosal drug delivery.

Opuntia ficus indica peel derived pectin mediated hydroxyapatite nanoparticles: synthesis, spectral characterization, biological and antimicrobial activities.

PubMed

Gopi, D; Kanimozhi, K; Kavitha, L

2015-04-15

In the present study, we have adapted a facile and efficient green route for the synthesis of HAP nanoparticles using pectin as a template which was extracted from the peel of prickly pear (Opuntia ficus indica) fruits. The concentration of pectin plays a major role in the behavior of crystallinity, purity, morphology as well as biological property of the as-synthesized HAP nanoparticles. The extracted pectin and the as-synthesized nanoparticles were characterized by various analytical techniques. The in vitro apatite formation on the surface of the as-synthesized nanoparticles in simulated body fluid (SBF) for various days showed an enhanced bioactivity. Also, the antimicrobial activity was investigated using various microorganisms. All the results revealed the formation of pure, low crystalline and discrete granular like HAP nanoparticles of size around 25 nm with enhanced biological and antimicrobial activities. Hence the as-synthesized nanoparticles can act as a better bone regenerating material in the field of biomedicine. Copyright © 2015 Elsevier B.V. All rights reserved.

Opuntia ficus indica peel derived pectin mediated hydroxyapatite nanoparticles: Synthesis, spectral characterization, biological and antimicrobial activities

NASA Astrophysics Data System (ADS)

Gopi, D.; Kanimozhi, K.; Kavitha, L.

2015-04-01

In the present study, we have adapted a facile and efficient green route for the synthesis of HAP nanoparticles using pectin as a template which was extracted from the peel of prickly pear (Opuntia ficus indica) fruits. The concentration of pectin plays a major role in the behavior of crystallinity, purity, morphology as well as biological property of the as-synthesized HAP nanoparticles. The extracted pectin and the as-synthesized nanoparticles were characterized by various analytical techniques. The in vitro apatite formation on the surface of the as-synthesized nanoparticles in simulated body fluid (SBF) for various days showed an enhanced bioactivity. Also, the antimicrobial activity was investigated using various microorganisms. All the results revealed the formation of pure, low crystalline and discrete granular like HAP nanoparticles of size around 25 nm with enhanced biological and antimicrobial activities. Hence the as-synthesized nanoparticles can act as a better bone regenerating material in the field of biomedicine.

[Biological activity evaluation of porous HA ceramics using NH4 HCO3/PVA as pore-creating agents].

PubMed

Wang, Songquan; Zhang, Dekun

2010-12-01

Porous HA ceramics were prepared by using NH4 HCO3/PVA as pore-formed material along with biological glass as intensifier, and these ceramics were immersed in Locke's Physiological Saline and Simulate Body Fluid (SBF). The changes of phase composition, grain size and crystallinity of porous HA ceramics before and after immersion were investigated by X-Ray Diffraction (XRD) and Scanning Electron Microscopy (SEM). The biological activity was evaluated. The porous HA ceramics showed various degrees of decomposition after immersion in the two solution systems, but there was no evident change in respect to crystallinity. Besides, the impact of different degrees of solution systems on the change of grain size and planar preferred orientation was observed. The TCP phase of the ceramics immersed in Locke's Physiological Saline decomposed and there was no crystal growth on the surface of ceramics; however, the grain size of ceramics immersed in SBF became refined in certain degree and the surface of ceramics took on the new crystal growth.

PREFACE: Complex dynamics of fluids in disordered and crowded environments Complex dynamics of fluids in disordered and crowded environments

NASA Astrophysics Data System (ADS)

Coslovich, Daniele; Kahl, Gerhard; Krakoviack, Vincent

2011-06-01

Over the past two decades, the dynamics of fluids under nanoscale confinement has attracted much attention. Motivation for this rapidly increasing interest is based on both practical and fundamental reasons. On the practical and rather applied side, problems in a wide range of scientific topics, such as polymer and colloidal sciences, rheology, geology, or biophysics, benefit from a profound understanding of the dynamical behaviour of confined fluids. Further, effects similar to those observed in confinement are expected in fluids whose constituents have strong size or mass asymmetry, and in biological systems where crowding and obstruction phenomena in the cytosol are responsible for clear separations of time scales for macromolecular transport in the cell. In fundamental research, on the other hand, the interest focuses on the complex interplay between confinement and structural relaxation, which is responsible for the emergence of new phenomena in the dynamics of the system: in confinement, geometric constraints associated with the pore shape are imposed to the adsorbed fluids and an additional characteristic length scale, i.e. the pore size, comes into play. For many years, the topic has been mostly experimentally driven. Indeed, a broad spectrum of systems has been investigated by sophisticated experimental techniques, while theoretical and simulation studies were rather scarce due to conceptual and computational issues. In the past few years, however, theory and simulations could largely catch up with experiments. On one side, new theories have been put forward that duly take into account the porosity, the connectivity, and the randomness of the confinement. On the other side, the ever increasing available computational power now allows investigations that were far out of reach a few years ago. Nowadays, instead of isolated state points, systematic investigations on the dynamics of confined fluids, covering a wide range of system parameters, can be realized. In fact, theory and simulations were recently able to predict new and surprising dynamical features, such as the occurrence of sub-diffusive laws, which result from the trapping due to the geometric and topological constraints and/or quenched disorder, the presence of both continuous and discontinuous glass transitions, and diffusion-localization transitions. Together, theory and simulations are thus able to contribute to a deeper insight into the complex dynamical behaviour of fluids in disordered confinement. Still, many yet unsolved problems remain. The fact that theoretical and simulation approaches have caught up with experimental investigations, has motivated us to organize a workshop on the dynamics of fluids confined in disordered environments, so as to bring together the different communities working in this field: theory and simulations, with their recent developments based on the mode-coupling theory of the glass transition, and experiments, with particular emphasis on colloidal systems and novel techniques. In an effort to give credit to recent developments in related problems of biophysical relevance, an entire session of the programme was dedicated to anomalous diffusion in crowded environments. The workshop was thus aimed at providing a deeper understanding of the complex dynamics of fluids in confinement as well as up-to-date perspectives on the interdisciplinary applications of this field of research. We are proud to say that all 32 contacted speakers accepted our invitation. Additional participants were attracted by our scientific programme, contributing poster presentations to the workshop. In total, close to 50 participants were registered, arriving from 11 different countries (including the US, Japan, and Mexico). Thus we conclude that the workshop indeed addressed a highly topical scientific field. From the scientific point of view a broad range of problems was covered, ranging from biophysics over soft matter to fermion systems. From the vivid discussions it became evident that the close scientific contact between theory, simulation and experiment brought along a fruitful and mutually inspiring atmosphere. On the theoretical side, these discussions have allowed clarification of several connections between the dynamics of models of fluids in porous media (quenched-annealed, pinned particles models), those of well-known limiting cases (Lorentz gas), of realistic models of liquids with strong dynamic asymmetry (asymmetric size and mass mixtures, sodium silicates, polymers blends) and even of bulk glass-formers. On the experimental side, it appeared that soft matter systems may provide an excellent test-bed to verify the theoretical predictions. From the concluding discussion it was also clear that addressing related issues relevant to biology still remains an open challenge for the future. In view of all this, it was concluded that within a short time period a workshop with analogous scope should be organized to address the progress made on both fundamental and interdisciplinary aspects. The realization of this workshop was made possible by generous financial support from CECAM, Centre Blaise Pascal-ENS de Lyon, and the ESF network 'Molecular Simulations in Biosystems and Material Science' (SimBioMa). Complex dynamics of fluids in disordered and crowded environments contents Phonon dispersions of cluster crystals Tim Neuhaus and Christos N Likos Challenges in determining anomalous diffusion in crowded fluids Marcel Hellmann, Joseph Klafter, Dieter W Heermann and Matthias Weiss Diffusion of active tracers in fluctuating fields David S Dean and Vincent Démery Self-diffusion of non-interacting hard spheres in particle gels Jean-Christophe Gimel and Taco Nicolai Probing glassy states in binary mixtures of soft interpenetrable colloids E Stiakakis, B M Erwin, D Vlassopoulos, M Cloitre, A Munam, M Gauthier, H Iatrou and N Hadjichristidis Fluids with quenched disorder: scaling of the free energy barrier near critical points T Fischer and R L C Vink Lennard-Jones binary mixture in disordered matrices: exploring the mode coupling scenario at increasing confinement P Gallo and M Rovere Static and dynamic contributions to anomalous chain dynamics in polymer blends Marco Bernabei, Angel J Moreno and J Colmenero Anomalous transport of a tracer on percolating clusters Markus Spanner, Felix Höfling, Gerd E Schröder-Turk, Klaus Mecke and Thomas Franosch Long-wavelength anomalies in the asymptotic behavior of mode-coupling theory S K Schnyder, F Höfling, T Franosch and Th Voigtmann Dynamic arrest of colloids in porous environments: disentangling crowding and confinement Jan Kurzidim, Daniele Coslovich and Gerhard Kahl Slow dynamics, dynamic heterogeneities, and fragility of supercooled liquids confined in random media Kang Kim, Kunimasa Miyazaki and Shinji Saito

The Stokesian hydrodynamics of flexing, stretching filaments

NASA Astrophysics Data System (ADS)

Shelley, Michael J.; Ueda, Tetsuji

2000-11-01

A central element of many fundamental problems in physics and biology lies in the interaction of a viscous fluid with slender, elastic filaments. Examples arise in the dynamics of biological fibers, the motility of microscopic organisms, and in phase transitions of liquid crystals. When considering the dynamics on the scale of a single filament, the surrounding fluid can often be assumed to be inertialess and hence governed by the Stokes’ equations. A typical simplification then is to assume a local relation, along the filament, between the force per unit length exerted by the filament upon the fluid and the velocity of the filament. While this assumption can be justified through slender-body theory as the leading-order effect, this approximation is only logarithmically separated (in aspect ratio) from the next-order contribution capturing the first effects of non-local interactions mediated by the surrounding fluid; non-local interactions become increasingly important as a filament comes within proximity to itself, or another filament. Motivated by a pattern forming system in isotropic to smectic-A phase transitions, we consider the non-local Stokesian dynamics of a growing elastica immersed in a fluid. The non-local interactions of the filament with itself are included using a modification of the slender-body theory of Keller and Rubinow. This modification is asymptotically equivalent, and removes an instability of their formulation at small, unphysical length-scales. Within this system, the filament lives on a marginal stability boundary, driven by a continual process of growth and buckling. Repeated bucklings result in filament flex, which, coupled to the non-local interactions and mediated by elastic response, leads to the development of space-filling patterns. We develop numerical methods to solve this system accurately and efficiently, even in the presence of temporal stiffness and the close self-approach of the filament. While we have ignored many of the thermodynamic aspects of this system, our simulations show good qualitative agreement with experimental observations. Our results also suggest that non-locality, induced by the surrounding fluid, will be important to understanding the dynamics of related filament systems.

Tuning the surface microstructure of titanate coatings on titanium implants for enhancing bioactivity of implants

PubMed Central

Wang, Hui; Lai, Yue-Kun; Zheng, Ru-Yue; Bian, Ye; Zhang, Ke-Qin; Lin, Chang-Jian

2015-01-01

Biological performance of artificial implant materials is closely related to their surface characteristics, such as microtopography, and composition. Therefore, convenient fabrication of artificial implant materials with a cell-friendly surface structure and suitable composition was of great significance for current tissue engineering. In this work, titanate materials with a nanotubular structure were successfully fabricated through a simple chemical treatment. Immersion test in a simulated body fluid and in vitro cell culture were used to evaluate the biological performance of the treated samples. The results demonstrate that the titanate layer with a nanotubular structure on Ti substrates can promote the apatite-inducing ability remarkably and greatly enhance cellular responses. This highlights the potential of such titanate biomaterials with the special nanoscale structure and effective surface composition for biomedical applications such as bone implants. PMID:26089665

Unconditionally energy stable numerical schemes for phase-field vesicle membrane model

NASA Astrophysics Data System (ADS)

Guillén-González, F.; Tierra, G.

2018-02-01

Numerical schemes to simulate the deformation of vesicles membranes via minimizing the bending energy have been widely studied in recent times due to its connection with many biological motivated problems. In this work we propose a new unconditionally energy stable numerical scheme for a vesicle membrane model that satisfies exactly the conservation of volume constraint and penalizes the surface area constraint. Moreover, we extend these ideas to present an unconditionally energy stable splitting scheme decoupling the interaction of the vesicle with a surrounding fluid. Finally, the well behavior of the proposed schemes are illustrated through several computational experiments.

Shape control and compartmentalization in active colloidal cells

PubMed Central

Spellings, Matthew; Engel, Michael; Klotsa, Daphne; Sabrina, Syeda; Drews, Aaron M.; Nguyen, Nguyen H. P.; Bishop, Kyle J. M.; Glotzer, Sharon C.

2015-01-01

Small autonomous machines like biological cells or soft robots can convert energy input into control of function and form. It is desired that this behavior emerges spontaneously and can be easily switched over time. For this purpose we introduce an active matter system that is loosely inspired by biology and which we term an active colloidal cell. The active colloidal cell consists of a boundary and a fluid interior, both of which are built from identical rotating spinners whose activity creates convective flows. Similarly to biological cell motility, which is driven by cytoskeletal components spread throughout the entire volume of the cell, active colloidal cells are characterized by highly distributed energy conversion. We demonstrate that we can control the shape of the active colloidal cell and drive compartmentalization by varying the details of the boundary (hard vs. flexible) and the character of the spinners (passive vs. active). We report buckling of the boundary controlled by the pattern of boundary activity, as well as formation of core–shell and inverted Janus phase-separated configurations within the active cell interior. As the cell size is increased, the inverted Janus configuration spontaneously breaks its mirror symmetry. The result is a bubble–crescent configuration, which alternates between two degenerate states over time and exhibits collective migration of the fluid along the boundary. Our results are obtained using microscopic, non–momentum-conserving Langevin dynamics simulations and verified via a phase-field continuum model coupled to a Navier–Stokes equation. PMID:26253763

Shape control and compartmentalization in active colloidal cells.

PubMed

Spellings, Matthew; Engel, Michael; Klotsa, Daphne; Sabrina, Syeda; Drews, Aaron M; Nguyen, Nguyen H P; Bishop, Kyle J M; Glotzer, Sharon C

2015-08-25

Small autonomous machines like biological cells or soft robots can convert energy input into control of function and form. It is desired that this behavior emerges spontaneously and can be easily switched over time. For this purpose we introduce an active matter system that is loosely inspired by biology and which we term an active colloidal cell. The active colloidal cell consists of a boundary and a fluid interior, both of which are built from identical rotating spinners whose activity creates convective flows. Similarly to biological cell motility, which is driven by cytoskeletal components spread throughout the entire volume of the cell, active colloidal cells are characterized by highly distributed energy conversion. We demonstrate that we can control the shape of the active colloidal cell and drive compartmentalization by varying the details of the boundary (hard vs. flexible) and the character of the spinners (passive vs. active). We report buckling of the boundary controlled by the pattern of boundary activity, as well as formation of core-shell and inverted Janus phase-separated configurations within the active cell interior. As the cell size is increased, the inverted Janus configuration spontaneously breaks its mirror symmetry. The result is a bubble-crescent configuration, which alternates between two degenerate states over time and exhibits collective migration of the fluid along the boundary. Our results are obtained using microscopic, non-momentum-conserving Langevin dynamics simulations and verified via a phase-field continuum model coupled to a Navier-Stokes equation.

Effect of protein corona magnetite nanoparticles derived from bread in vitro digestion on Caco-2 cells morphology and uptake.

PubMed

Di Silvio, Desirè; Rigby, Neil; Bajka, Balazs; Mackie, Alan; Baldelli Bombelli, Francesca

2016-06-01

Nanoparticles (NPs) in biological fluids immediately interact with proteins forming a biomolecular corona (PC) that imparts their biological identity. While several studies on the formation of the PC in human plasma have been reported, the PC of orally administrated NPs has been less investigated, mostly in the presence of a food matrix. In fact, food matrixes when digested are subject of several dynamic changes that will certainly affect the PC formed on the NPs. The lack of studies on this topic is clearly related to the difficulty in isolating representative PC NPs from such a complex environment. In this work magnetite NPs were added to in vitro simulated digestion simultaneously with bread and PC NPs were isolated after gastric and duodenal phases by sucrose gradient ultracentrifugation (UC). The PC NPs were characterized in terms of size and protein composition. Translocation studies were then performed on Caco-2 monolayers in a serum free environment and cell morphology was characterized by confocal microscopy. PC NPs isolated from gastric and duodenal phases were different in size, surface charge and protein corona composition. NP cellular uptake was enhanced by the digestive PC inducing morphology changes in the cell monolayer. Overall, in this work we were able to isolate PC NPs from digested fluids in the presence of a food matrix and study their biological response on Caco-2 cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

Shape control and compartmentalization in active colloidal cells

DOE PAGES

Spellings, Matthew; Engel, Michael; Klotsa, Daphne; ...

2015-08-07

Small autonomous machines like biological cells or soft robots can convert energy input into control of function and form. It is desired that this behavior emerges spontaneously and can be easily switched over time. For this purpose, in this paper we introduce an active matter system that is loosely inspired by biology and which we term an active colloidal cell. The active colloidal cell consists of a boundary and a fluid interior, both of which are built from identical rotating spinners whose activity creates convective flows. Similarly to biological cell motility, which is driven by cytoskeletal components spread throughout themore » entire volume of the cell, active colloidal cells are characterized by highly distributed energy conversion. We demonstrate that we can control the shape of the active colloidal cell and drive compartmentalization by varying the details of the boundary (hard vs. flexible) and the character of the spinners (passive vs. active). We report buckling of the boundary controlled by the pattern of boundary activity, as well as formation of core–shell and inverted Janus phase-separated configurations within the active cell interior. As the cell size is increased, the inverted Janus configuration spontaneously breaks its mirror symmetry. The result is a bubble–crescent configuration, which alternates between two degenerate states over time and exhibits collective migration of the fluid along the boundary. Finally, our results are obtained using microscopic, non–momentum-conserving Langevin dynamics simulations and verified via a phase-field continuum model coupled to a Navier–Stokes equation.« less

Viscoelasticity promotes collective swimming of sperm

NASA Astrophysics Data System (ADS)

Tung, Chih-Kuan; Harvey, Benedict B.; Fiore, Alyssa G.; Ardon, Florencia; Suarez, Susan S.; Wu, Mingming

From flocking birds to swarming insects, interactions of organisms large and small lead to the emergence of collective dynamics. Here, we report striking collective swimming of bovine sperm, with sperm orienting in the same direction within each cluster, enabled by the viscoelasticity of the fluid. A long-chain polyacrylamide solution was used as a model viscoelastic fluid such that its rheology can be fine-tuned to mimic that of bovine cervical mucus. In viscoelastic fluid, sperm formed dynamic clusters, and the cluster size increased with elasticity of the polyacrylamide solution. In contrast, sperm swam randomly and individually in Newtonian fluids of similar viscosity. Analysis of the fluid motion surrounding individual swimming sperm indicated that sperm-fluid interaction is facilitated by the elastic component of the fluid. We note that almost all biological fluids (e.g. mucus and blood) are viscoelastic in nature, this finding highlights the importance of fluid elasticity in biological function. We will discuss what the orientation fluctuation within a cluster reveals about the interaction strength. Supported by NIH Grant 1R01HD070038.

Computer simulation of preflight blood volume reduction as a countermeasure to fluid shifts in space flight

NASA Technical Reports Server (NTRS)

Simanonok, K. E.; Srinivasan, R.; Charles, J. B.

1992-01-01

Fluid shifts in weightlessness may cause a central volume expansion, activating reflexes to reduce the blood volume. Computer simulation was used to test the hypothesis that preadaptation of the blood volume prior to exposure to weightlessness could counteract the central volume expansion due to fluid shifts and thereby attenuate the circulatory and renal responses resulting in large losses of fluid from body water compartments. The Guyton Model of Fluid, Electrolyte, and Circulatory Regulation was modified to simulate the six degree head down tilt that is frequently use as an experimental analog of weightlessness in bedrest studies. Simulation results show that preadaptation of the blood volume by a procedure resembling a blood donation immediately before head down bedrest is beneficial in damping the physiologic responses to fluid shifts and reducing body fluid losses. After ten hours of head down tilt, blood volume after preadaptation is higher than control for 20 to 30 days of bedrest. Preadaptation also produces potentially beneficial higher extracellular volume and total body water for 20 to 30 days of bedrest.

Simulation study on the trembling shear behavior of eletrorheological fluid.

PubMed

Yang, F; Gong, X L; Xuan, S H; Jiang, W Q; Jiang, C X; Zhang, Z

2011-07-01

The trembling shear behavior of electrorheological (ER) fluids has been investigated by using a computer simulation method, and a shear-slide boundary model is proposed to understand this phenomenon. A thiourea-doped Ba-Ti-O ER fluid which shows a trembling shear behavior was first prepared and then systematically studied by both theoretical and experimental methods. The shear curves of ER fluids in the dynamic state were simulated with shear rates from 0.1 to 1000 s(-1) under different electric fields. The simulation results of the flow curves match the experimental results very well. The trembling shear curves are divided into four regions and each region can be explained by the proposed model.

Amniotic fluid: the use of high-dimensional biology to understand fetal well-being.

PubMed

Kamath-Rayne, Beena D; Smith, Heather C; Muglia, Louis J; Morrow, Ardythe L

2014-01-01

Our aim was to review the use of high-dimensional biology techniques, specifically transcriptomics, proteomics, and metabolomics, in amniotic fluid to elucidate the mechanisms behind preterm birth or assessment of fetal development. We performed a comprehensive MEDLINE literature search on the use of transcriptomic, proteomic, and metabolomic technologies for amniotic fluid analysis. All abstracts were reviewed for pertinence to preterm birth or fetal maturation in human subjects. Nineteen articles qualified for inclusion. Most articles described the discovery of biomarker candidates, but few larger, multicenter replication or validation studies have been done. We conclude that the use of high-dimensional systems biology techniques to analyze amniotic fluid has significant potential to elucidate the mechanisms of preterm birth and fetal maturation. However, further multicenter collaborative efforts are needed to replicate and validate candidate biomarkers before they can become useful tools for clinical practice. Ideally, amniotic fluid biomarkers should be translated to a noninvasive test performed in maternal serum or urine.

Water Hammer Simulations of Monomethylhydrazine Propellant

NASA Technical Reports Server (NTRS)

Burkhardt, Zachary; Ramachandran, N.; Majumdar, A.

2017-01-01

Fluid Transient analysis is important for the design of spacecraft propulsion system to ensure structural stability of the system in the event of sudden closing or opening of the valve. Generalized Fluid System Simulation Program (GFSSP), a general purpose flow network code developed at NASA/MSFC is capable of simulating pressure surge due to sudden opening or closing of valve when thermodynamic properties of real fluid are available for the entire range of simulation. Specifically GFSSP needs an accurate representation of pressure density relationship in order to predict pressure surge during a fluid transient. Unfortunately, the available thermodynamic property programs such as REFPROP, GASP or GASPAK do not provide the thermodynamic properties of Monomethylhydrazine(MMH). This work illustrates the process used for building a customized table of properties of state variables from available properties and speed of sound that is required by GFSSP for simulation. Good agreement was found between the simulations and measured data. This method can be adopted for modeling flow networks and systems with other fluids whose properties are not known in detail in order to obtain general technical insight.

Modeling of Fluid-Membrane Interaction in Cellular Microinjection Process

NASA Astrophysics Data System (ADS)

Karzar-Jeddi, Mehdi; Diaz, Jhon; Olgac, Nejat; Fan, Tai-Hsi

2009-11-01

Cellular microinjection is a well-accepted method to deliver matters such as sperm, nucleus, or macromolecules into biological cells. To improve the success rate of in vitro fertilization and to establish the ideal operating conditions for a novel computer controlled rotationally oscillating intracytoplasmic sperm injection (ICSI) technology, we investigate the fluid-membrane interactions in the ICSI procedure. The procedure consists of anchoring the oocyte (a developing egg) using a holding pipette, penetrating oocyte's zona pellucida (the outer membrane) and the oolemma (the plasma or inner membrane) using an injection micropipette, and finally to deliver sperm into the oocyte for fertilization. To predict the large deformation of the oocyte membranes up to the piercing of the oolemma and the motion of fluids across both membranes, the dynamic fluid-pipette-membrane interactions are formulated by the coupled Stokes' equations and the continuum membrane model based on Helfrich's energy theory. A boundary integral model is developed to simulate the transient membrane deformation and the local membrane stress induced by the longitudinal motion of the injection pipette. The model captures the essential features of the membranes shown on optical images of ICSI experiments, and is capable of suggesting the optimal deformation level of the oolemma to start the rotational oscillations for piercing into the oolemma.

Scaling of Guide-Field Magnetic Reconnection using Anisotropic Fluid Closure

NASA Astrophysics Data System (ADS)

Ohia, O.; Egedal, J.; Lukin, V. S.; Daughton, W.; Le, A.

2012-10-01

Collisionless magnetic reconnection, a process linked to solar flares, coronal mass ejections, and magnetic substorms, has been widely studied through fluid models and fully kinetic simulations. While fluid models often reproduce the fast reconnection rate of fully kinetic simulations, significant differences are observed in the structure of the reconnection regions [1]. However, guide-field fluid simulations implementing new equations of state that accurately account for the anisotropic electron pressure [2] reproduce the detailed reconnection region observed in kinetic simulations [3]. Implementing this two-fluid simulation using the HiFi framework [4], we study the force balance of the electron layers in guide-field reconnection and derive scaling laws for their characteristics.[1ex] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0ex] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0ex] [3] Ohia O, et al., Phys. Rev. Lett. In Press (2012).[0ex] [4] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011)

Determination of the bioaccessible fraction of metals in urban aerosol using simulated lung fluids

NASA Astrophysics Data System (ADS)

Coufalík, Pavel; Mikuška, Pavel; Matoušek, Tomáš; Večeřa, Zbyněk

2016-09-01

Determination of the bioaccessible fraction of metals in atmospheric aerosol is a significant issue with respect to air pollution in the urban environment. The aim of this work was to compare of metal bioaccessibility determined according to the extraction yields of six simulated lung fluids. Aerosol samples of the PM1 fraction were collected in Brno, Czech Republic. The total contents of Cd, Ce, Cr, Cu, Fe, Mn, Ni, Pb, V, and Zn in the samples were determined and their enrichment factors were calculated. The bioaccessible proportions of elements were determined by means of extraction in Gamble's solution, Gamble's solution with dipalmitoyl phosphatidyl choline (DPPC), artificial lysosomal fluid, saline, water, and in a newly proposed solution based on DPPC, referred to as "Simulated Alveoli Fluid" (SAF). The chemical composition and surface tension of the simulated lung fluids were the main parameters influencing extraction yields. Gamble's solutions and the newly designed solution of SAF exhibited the lowest extraction efficiency, and also had the lowest surface tensions. The bioaccessibility of particulate metals should be assessed by synthetic lung fluids with a low surface tension, which simulate better the behavior and composition of native lung surfactant. The bioaccessibility of metals in aerosol assessed by means of the extraction in water or artificial lysosomal fluid can be overestimated.

Optimization and development of a core-in-cup tablet for modulated release of theophylline in simulated gastrointestinal fluids.

PubMed

Danckwerts, M P

2000-07-01

A triple-layer core-in-cup tablet that can release theophylline in simulated gastrointestinal (GI) fluids at three distinct rates has been developed. The first layer is an immediate-release layer; the second layer is a sustained-release layer; and the last layer is a boost layer, which was designed to coincide with a higher nocturnal dose of theophylline. The study consisted of two stages. The first stage optimized the sustained-release layer of the tablet to release theophylline over a period of 12 hr. Results from this stage indicated that 30% w/w acacia gum was the best polymer and concentration to use when compressed to a hardness of 50 N/m2. The second stage of the study involved the investigation of the final triple-layer core-in-cup tablet to release theophylline at three different rates in simulated GI fluids. The triple-layer modulated core-in-cup tablet successfully released drug in simulated fluids at an initial rate of 40 mg/min, followed by a rate of 0.4085 mg/min, in simulated gastric fluid TS, 0.1860 mg/min in simulated intestinal fluid TS, and finally by a boosted rate of 0.6952 mg/min.

Countermeasures to microgravity

NASA Technical Reports Server (NTRS)

Luttges, Marvin W.

1989-01-01

Biological systems ranging from the most simple to the most complex generally survive exposure to microgravity. Changes in many characteristics of biological systems are well documented as a consequence of space flight. Attempts to devise countermeasures to microgravity may have direct pragmatic consequences for crew protection and may provide additional insights into the nature of microgravity influences on biological systems. Some of the most well documented changes occur in humans who have experienced space flight. Changes appear to be transient. Space adaption syndrome occurs relatively briefly whereas bone deterioration may require months of postflight time for restoration. It seems critical to recognize that these changes and others may derive from rather passive, active or even reactive changes in the biological systems that are hosts to them. For example, hydrostatic fluid redistributions may be quite passive occurrences that are realized through extensive fluid channels. Changes occur in cell metabolism because of fluid, nutrient and gas redistributions. Equally important are the misconstrued messages likely to be carried by fluid redistributions. These reactive events can trigger, for example, loss of fluids and electrolytes through altered kidney function. Each of these considerations must be evaluated in regard to the biological site affected. Countermeasures to the vast range of biological changes and sites are difficult to envision. The most obvious countermeasure is the restoration of gravity-like influences. Some options are discussed. Recent work has focussed on the use of magnetic fields. Pulsed electromagnetic fields (PEMF) are shown to alleviate bone deterioration produced in rodents exposed to tail suspension. Methods of PEMF exposure are consistent with human use in space. Related methods may provide muscular and neural benefits.

The Toxicological Geochemistry of Dusts, Soils, and Other Earth Materials: Insights From In Vitro Physiologically-based Geochemical Leach Tests

NASA Astrophysics Data System (ADS)

Plumlee, G. S.; Ziegler, T. L.; Lamothe, P.; Meeker, G. P.; Sutley, S.

2003-12-01

Exposure to mineral dusts, soils, and other earth materials results in chemical reactions between the materials and different body fluids that include, depending upon the exposure route, lung fluids, gastrointestinal fluids, and perspiration. In vitro physiologically-based geochemical leach tests provide useful insights into these chemical reactions and their potential toxicological implications. We have conducted such leach tests on a variety of earth materials, including asbestos, volcanic ash, dusts from dry lake beds, mine wastes, wastes left from the roasting of mercury ores, mineral processing wastes, coal dusts and coal fly ash, various soils, and complex dusts generated by the World Trade Center collapse. Size-fractionated samples of earth materials that have been well-characterized mineralogically and chemically are reacted at body temperature (37 C) for periods from 2 hours up to multiple days with various proportions of simulated lung, gastric, intestinal, and/or plasma-based fluids. Results indicate that different earth materials may have quite different solubility and dissolution behavior in vivo, depending upon a) the mineralogic makeup of the material, and b) the exposure route. For example, biodurable minerals such as asbestos and volcanic ash particles, whose health effects result because they dissolve very slowly in vivo, bleed off low levels of trace metals into the simulated lung fluids; these include metals such as Fe and Cr that are suspected by health scientists of contributing to the generation of reactive oxygen species and resulting DNA damage in vivo. In contrast, dry lake bed dusts and concrete-rich dusts are highly alkaline and bioreactive, and cause substantial pH increases and other chemical changes in the simulated body fluids. Many of the earth materials tested contain a variety of metals that can be quite soluble (bioaccessible), depending upon the material and the simulated body fluid composition. For example, due to their acidic pH and high chloride concentrations, simulated gastric fluids are most efficient at solubilizing metals such as Hg, Pb, Zn, and others that form strong chloride complexes; although these metals tend to partially reprecipitate in the near-neutral simulated intestinal fluids, complexes with organic ligands (i.e., amino and carboxylic acids) enhance their solubility. These metals are also quite soluble in near-neutral, protein-rich plasma-based fluids because they form strong complexes with the proteins. In contrast, metalloids that form oxyanion species (such as As, Cr, Mo, W) are commonly more soluble in near-neutral pH simulated lung fluids than in simulated gastric fluids.

Effect of fluid-colloid interactions on the mobility of a thermophoretic microswimmer in non-ideal fluids.

PubMed

Fedosov, Dmitry A; Sengupta, Ankush; Gompper, Gerhard

2015-09-07

Janus colloids propelled by light, e.g., thermophoretic particles, offer promising prospects as artificial microswimmers. However, their swimming behavior and its dependence on fluid properties and fluid-colloid interactions remain poorly understood. Here, we investigate the behavior of a thermophoretic Janus colloid in its own temperature gradient using numerical simulations. The dissipative particle dynamics method with energy conservation is used to investigate the behavior in non-ideal and ideal-gas like fluids for different fluid-colloid interactions, boundary conditions, and temperature-controlling strategies. The fluid-colloid interactions appear to have a strong effect on the colloid behavior, since they directly affect heat exchange between the colloid surface and the fluid. The simulation results show that a reduction of the heat exchange at the fluid-colloid interface leads to an enhancement of colloid's thermophoretic mobility. The colloid behavior is found to be different in non-ideal and ideal fluids, suggesting that fluid compressibility plays a significant role. The flow field around the colloid surface is found to be dominated by a source-dipole, in agreement with the recent theoretical and simulation predictions. Finally, different temperature-control strategies do not appear to have a strong effect on the colloid's swimming velocity.

Using artificial intelligence to control fluid flow computations

NASA Technical Reports Server (NTRS)

Gelsey, Andrew

1992-01-01

Computational simulation is an essential tool for the prediction of fluid flow. Many powerful simulation programs exist today. However, using these programs to reliably analyze fluid flow and other physical situations requires considerable human effort and expertise to set up a simulation, determine whether the output makes sense, and repeatedly run the simulation with different inputs until a satisfactory result is achieved. Automating this process is not only of considerable practical importance but will also significantly advance basic artificial intelligence (AI) research in reasoning about the physical world.

Hybrid Method for Power Control Simulation of a Single Fluid Plasma Thruster

NASA Astrophysics Data System (ADS)

Jaisankar, S.; Sheshadri, T. S.

2018-05-01

Propulsive plasma flow through a cylindrical-conical diverging thruster is simulated by a power controlled hybrid method to obtain the basic flow, thermodynamic and electromagnetic variables. Simulation is based on a single fluid model with electromagnetics being described by the equations of potential Poisson, Maxwell and the Ohm's law while the compressible fluid dynamics by the Navier Stokes in cylindrical form. The proposed method solved the electromagnetics and fluid dynamics separately, both to segregate the two prominent scales for an efficient computation and for the delivery of voltage controlled rated power. The magnetic transport is solved for steady state while fluid dynamics is allowed to evolve in time along with an electromagnetic source using schemes based on generalized finite difference discretization. The multistep methodology with power control is employed for simulating fully ionized propulsive flow of argon plasma through the thruster. Numerical solution shows convergence of every part of the solver including grid stability causing the multistep hybrid method to converge for a rated power delivery. Simulation results are reasonably in agreement with the reported physics of plasma flow in the thruster thus indicating the potential utility of this hybrid computational framework, especially when single fluid approximation of plasma is relevant.

Numerical simulations of hydrothermal circulation resulting from basalt intrusions in a buried spreading center

USGS Publications Warehouse

Fisher, A.T.; Narasimhan, T.N.

1991-01-01

A two-dimensional, one by two-kilometer section through the seafloor was simulated with a numerical model to investigate coupled fluid and heat flow resulting from basalt intrusions in a buried spreading center. Boundary and initial conditions and physical properties of both sediments and basalt were constrained by field surveys and drilling in the Guaymas Basin, central Gulf of California. Parametric variations in these studies included sediment and basalt permeability, anisotropy in sediment permeability, and the size of heat sources. Faults were introduced through new intrusions both before and after cooling.Background heat input caused fluid convection at velocities ≤ 3 cm a−1 through shallow sediments. Eighty to ninety percent of the heat introduced at the base of the simulations exited through the upper, horizontal surface, even when the vertical boundaries were made permeable to fluid flow. The simulated injection of a 25–50 m thick basalt intrusion at a depth of 250 m resulted in about 10 yr of pore-fluid expulsion through the sea-floor in all cases, leaving the sediments above the intrusions strongly underpressured. A longer period of fluid recharge followed, sometimes accompanied by reductions in total seafloor heat output of 10% in comparison to pre-intrusion values. Additional discharge-recharge events were dispersed chaotically through the duration of the cooling period. These cycles in heat and fluid flow resulted from the response of the simulated system to a thermodynamic shock, the sudden emplacement of a large heat source, and not from mechanical displacement of sediments and pore fluids, which was not simulated.Water/rock mass ratios calculated from numerical simulations are in good agreement with geochemical estimates from materials recovered from the Guaymas Basin, assuming a bulk basalt permeability value of at least 10−17 m2/(10−2 mD). The addition of faults through intrusions and sediments in these simulations did not facilitate continuous, rapid venting. Increased heat input at the base of the faults resulted in temporarily greater fluid discharge, but the flow could not be sustained because the modeled system could not recharge cold fluid quickly enough to remove sufficient heat through the vents.

Mapping of polycrystalline films of biological fluids utilizing the Jones-matrix formalism

NASA Astrophysics Data System (ADS)

Ushenko, Vladimir A.; Dubolazov, Alexander V.; Pidkamin, Leonid Y.; Sakchnovsky, Michael Yu; Bodnar, Anna B.; Ushenko, Yuriy A.; Ushenko, Alexander G.; Bykov, Alexander; Meglinski, Igor

2018-02-01

Utilizing a polarized light approach, we reconstruct the spatial distribution of birefringence and optical activity in polycrystalline films of biological fluids. The Jones-matrix formalism is used for an accessible quantitative description of these types of optical anisotropy. We demonstrate that differentiation of polycrystalline films of biological fluids can be performed based on a statistical analysis of the distribution of rotation angles and phase shifts associated with the optical activity and birefringence, respectively. Finally, practical operational characteristics, such as sensitivity, specificity and accuracy of the Jones-matrix reconstruction of optical anisotropy, were identified with special emphasis on biomedical application, specifically for differentiation of bile films taken from healthy donors and from patients with cholelithiasis.

Dissociation of Hexavalent Chromium from Sanded Paint Particles into a Simulated Lung Fluid

DTIC Science & Technology

2006-06-01

was simulated with a porcine based mucin . Sanded particles were collected based on particle size into the impactor’s six petri dishes, which...was used to imitate particle deposition onto a layer of lung fluid. The lung fluid was simulated with a porcine based mucin . Sanded particles were...documented as those directly related to corrosion control such as maintenance, repair, treatment , washing, painting, depainting, and sealing. These

Forensic interlaboratory evaluation of the ForFLUID kit for vaginal fluids identification.

PubMed

Giampaoli, Saverio; Alessandrini, Federica; Berti, Andrea; Ripani, Luigi; Choi, Ajin; Crab, Roselien; De Vittori, Elisabetta; Egyed, Balazs; Haas, Cordula; Lee, Hwan Young; Korabecná, Marie; Noel, Fabrice; Podini, Daniele; Tagliabracci, Adriano; Valentini, Alessio; Romano Spica, Vincenzo

2014-01-01

Identification of vaginal fluids is an important step in the process of sexual assaults confirmation. Advances in both microbiology and molecular biology defined technical approaches allowing the discrimination of body fluids. These protocols are based on the identification of specific bacterial communities by microfloraDNA (mfDNA) amplification. A multiplex real time-PCR assay (ForFLUID kit) has been developed for identifying biological fluids and for discrimination among vaginal, oral and fecal samples. In order to test its efficacy and reliability of the assay in the identification of vaginal fluids, an interlaboratory evaluation has been performed on homogeneous vaginal swabs. All the involved laboratories were able to correctly recognize all the vaginal swabs, and no false positives were identified when the assay was applied on non-vaginal samples. The assay represents an useful molecular tool that can be easily adopted by forensic geneticists involved in vaginal fluid identification. Copyright © 2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Ion distributions in electrolyte confined by multiple dielectric interfaces

NASA Astrophysics Data System (ADS)

Jing, Yufei; Zwanikken, Jos W.; Jadhao, Vikram; de La Cruz, Monica

2014-03-01

The distribution of ions at dielectric interfaces between liquids characterized by different dielectric permittivities is crucial to nanoscale assembly processes in many biological and synthetic materials such as cell membranes, colloids and oil-water emulsions. The knowledge of ionic structure of these systems is also exploited in energy storage devices such as double-layer super-capacitors. The presence of multiple dielectric interfaces often complicates computing the desired ionic distributions via simulations or theory. Here, we use coarse-grained models to compute the ionic distributions in a system of electrolyte confined by two planar dielectric interfaces using Car-Parrinello molecular dynamics simulations and liquid state theory. We compute the density profiles for various electrolyte concentrations, stoichiometric ratios and dielectric contrasts. The explanations for the trends in these profiles and discuss their effects on the behavior of the confined charged fluid are also presented.

Energy for biologic sulfate reduction in a hydrothermally formed ocean on Europa

NASA Astrophysics Data System (ADS)

Zolotov, Mikhail Y.; Shock, Everett L.

2003-04-01

Formation of a sulfate-bearing ocean on Jupiter's satellite Europa by quenched hydrothermal fluids provides a source of metabolic energy for low-temperature sulfate-reducing organisms that use dissolved H2 as an electron donor. Inhibition of thermodynamically favorable sulfate reduction in cooled hydrothermal fluids creates the potential for biologic reduction. Both high temperature and reduced conditions of ocean-forming hydrothermal solutions favor sulfate reduction in quenched fluids. The maximum amount of energy available to support autotrophic sulfate reduction is on the order of a few kilojoules per kilogram of water and is limited by the low abundances of either H2 or sulfate in ocean-forming fluids. Although this irreplaceable energy source might have supported early life on Europa, maintenance of biologic sulfate reduction throughout the ocean's history would require a supply of organic compounds from endogenic sources or from the satellite's surface.

Fast 2D Fluid-Analytical Simulation of IEDs and Plasma Uniformity in Multi-frequency CCPs

NASA Astrophysics Data System (ADS)

Kawamura, E.; Lieberman, M. A.; Graves, D. B.

2014-10-01

A fast 2D axisymmetric fluid-analytical model using the finite elements tool COMSOL is interfaced with a 1D particle-in-cell (PIC) code to study ion energy distributions (IEDs) in multi-frequency argon capacitively coupled plasmas (CCPs). A bulk fluid plasma model which solves the time-dependent plasma fluid equations is coupled with an analytical sheath model which solves for the sheath parameters. The fluid-analytical results are used as input to a PIC simulation of the sheath region of the discharge to obtain the IEDs at the wafer electrode. Each fluid-analytical-PIC simulation on a moderate 2.2 GHz CPU workstation with 8 GB of memory took about 15-20 minutes. The 2D multi-frequency fluid-analytical model was compared to 1D PIC simulations of a symmetric parallel plate discharge, showing good agreement. Fluid-analytical simulations of a 2/60/162 MHz argon CCP with a typical asymmetric reactor geometry were also conducted. The low 2 MHz frequency controlled the sheath width and voltage while the higher frequencies controlled the plasma production. A standing wave was observable at the highest frequency of 162 MHz. Adding 2 MHz power to a 60 MHz discharge or 162 MHz to a dual frequency 2 MHz/60 MHz discharge enhanced the plasma uniformity. This work was supported by the Department of Energy Office of Fusion Energy Science Contract DE-SC000193, and in part by gifts from Lam Research Corporation and Micron Corporation.

Treatment of waste metalworking fluid by a hybrid ozone-biological process.

PubMed

Jagadevan, Sheeja; Graham, Nigel J; Thompson, Ian P

2013-01-15

In metal machining processes, the regulation of heat generation and lubrication at the contact point are achieved by application of a fluid referred to as metalworking fluid (MWF). MWFs inevitably become operationally exhausted with age and intensive use, which leads to compromised properties, thereby necessitating their safe disposal. Disposal of this waste through a biological route is an increasingly attractive option, since it is effective with relatively low energy demands. However, successful biological treatment is challenging since MWFs are chemically complex, and include biocides specifically to retard microbial deterioration whilst the fluids are operational. In this study remediation of the recalcitrant component of a semi-synthetic MWF by a novel hybrid ozone-bacteriological treatment, was investigated. The hybrid treatment proved to be effective and reduced the chemical oxygen demand by 72% (26.9% and 44.9% reduction after ozonation and biological oxidation respectively). Furthermore, a near-complete degradation of three non-biodegradable compounds (viz. benzotriazole, monoethanolamine, triethanolamine), commonly added as biocides and corrosion inhibitors in MWF formulations, under ozonation was observed. Copyright © 2012 Elsevier B.V. All rights reserved.

Digital Rock Simulation of Flow in Carbonate Samples

NASA Astrophysics Data System (ADS)

Klemin, D.; Andersen, M.

2014-12-01

Reservoir engineering has becomes more complex to deal with current challenges, so core analysts must understand and model pore geometries and fluid behaviors at pores scales more rapidly and realistically. We introduce an industry-unique direct hydrodynamic pore flow simulator that operates on pore geometries from digital rock models obtained using microCT or 3D scanning electron microscope (SEM) images. The PVT and rheological models used in the simulator represent real reservoir fluids. Fluid-solid interactions are introduced using distributed micro-scale wetting properties. The simulator uses density functional approach applied for hydrodynamics of complex systems. This talk covers selected applications of the simulator. We performed microCT scanning of six different carbonate rock samples from homogeneous limestones to vuggy carbonates. From these, we constructed digital rock models representing pore geometries for the simulator. We simulated nonreactive tracer flow in all six digital models using a digital fluid description that included a passive tracer solution. During the simulation, we evaluated the composition of the effluent. Results of tracer flow simulations corresponded well with experimental data of nonreactive tracer floods for the same carbonate rock types. This simulation data of the non-reactive tracer flow can be used to calculate the volume of the rock accessible by the fluid, which can be further used to predict response of a porous medium to a reactive fluid. The described digital core analysis workflow provides a basis for a wide variety of activities, including input to design acidizing jobs and evaluating treatment efficiency and EOR economics. Digital rock multiphase flow simulations of a scanned carbonate rock evaluated the effect of wettability on flow properties. Various wetting properties were tested: slightly oil wet, slightly water wet, and water wet. Steady-state relative permeability simulations yielded curves for all three ranges of wetting properties. The wetting variation affected phase mobility and residual phase saturations for primary oil flood and floods with varying ratios of oil and water.

Fast 2D fluid-analytical simulation of ion energy distributions and electromagnetic effects in multi-frequency capacitive discharges

NASA Astrophysics Data System (ADS)

Kawamura, E.; Lieberman, M. A.; Graves, D. B.

2014-12-01

A fast 2D axisymmetric fluid-analytical plasma reactor model using the finite elements simulation tool COMSOL is interfaced with a 1D particle-in-cell (PIC) code to study ion energy distributions (IEDs) in multi-frequency capacitive argon discharges. A bulk fluid plasma model, which solves the time-dependent plasma fluid equations for the ion continuity and electron energy balance, is coupled with an analytical sheath model, which solves for the sheath parameters. The time-independent Helmholtz equation is used to solve for the fields and a gas flow model solves for the steady-state pressure, temperature and velocity of the neutrals. The results of the fluid-analytical model are used as inputs to a PIC simulation of the sheath region of the discharge to obtain the IEDs at the target electrode. Each 2D fluid-analytical-PIC simulation on a moderate 2.2 GHz CPU workstation with 8 GB of memory took about 15-20 min. The multi-frequency 2D fluid-analytical model was compared to 1D PIC simulations of a symmetric parallel-plate discharge, showing good agreement. We also conducted fluid-analytical simulations of a multi-frequency argon capacitively coupled plasma (CCP) with a typical asymmetric reactor geometry at 2/60/162 MHz. The low frequency 2 MHz power controlled the sheath width and sheath voltage while the high frequencies controlled the plasma production. A standing wave was observable at the highest frequency of 162 MHz. We noticed that adding 2 MHz power to a 60 MHz discharge or 162 MHz to a dual frequency 2 MHz/60 MHz discharge can enhance the plasma uniformity. We found that multiple frequencies were not only useful for controlling IEDs but also plasma uniformity in CCP reactors.

Effect of pore geometry on the compressibility of a confined simple fluid

NASA Astrophysics Data System (ADS)

Dobrzanski, Christopher D.; Maximov, Max A.; Gor, Gennady Y.

2018-02-01

Fluids confined in nanopores exhibit properties different from the properties of the same fluids in bulk; among these properties is the isothermal compressibility or elastic modulus. The modulus of a fluid in nanopores can be extracted from ultrasonic experiments or calculated from molecular simulations. Using Monte Carlo simulations in the grand canonical ensemble, we calculated the modulus for liquid argon at its normal boiling point (87.3 K) adsorbed in model silica pores of two different morphologies and various sizes. For spherical pores, for all the pore sizes (diameters) exceeding 2 nm, we obtained a logarithmic dependence of fluid modulus on the vapor pressure. Calculation of the modulus at saturation showed that the modulus of the fluid in spherical pores is a linear function of the reciprocal pore size. The calculation of the modulus of the fluid in cylindrical pores appeared too scattered to make quantitative conclusions. We performed additional simulations at higher temperature (119.6 K), at which Monte Carlo insertions and removals become more efficient. The results of the simulations at higher temperature confirmed both regularities for cylindrical pores and showed quantitative difference between the fluid moduli in pores of different geometries. Both of the observed regularities for the modulus stem from the Tait-Murnaghan equation applied to the confined fluid. Our results, along with the development of the effective medium theories for nanoporous media, set the groundwork for analysis of the experimentally measured elastic properties of fluid-saturated nanoporous materials.

Hydrothermal fluid flow and deformation in large calderas: Inferences from numerical simulations

USGS Publications Warehouse

Hurwitz, S.; Christiansen, L.B.; Hsieh, P.A.

2007-01-01

Inflation and deflation of large calderas is traditionally interpreted as being induced by volume change of a discrete source embedded in an elastic or viscoelastic half-space, though it has also been suggested that hydrothermal fluids may play a role. To test the latter hypothesis, we carry out numerical simulations of hydrothermal fluid flow and poroelastic deformation in calderas by coupling two numerical codes: (1) TOUGH2 [Pruess et al., 1999], which simulates flow in porous or fractured media, and (2) BIOT2 [Hsieh, 1996], which simulates fluid flow and deformation in a linearly elastic porous medium. In the simulations, high-temperature water (350??C) is injected at variable rates into a cylinder (radius 50 km, height 3-5 km). A sensitivity analysis indicates that small differences in the values of permeability and its anisotropy, the depth and rate of hydrothermal injection, and the values of the shear modulus may lead to significant variations in the magnitude, rate, and geometry of ground surface displacement, or uplift. Some of the simulated uplift rates are similar to observed uplift rates in large calderas, suggesting that the injection of aqueous fluids into the shallow crust may explain some of the deformation observed in calderas.

Fluid extraction across pumping and permeable walls in the viscous limit

NASA Astrophysics Data System (ADS)

Herschlag, G.; Liu, J.-G.; Layton, A. T.

2016-04-01

In biological transport mechanisms such as insect respiration and renal filtration, fluid travels along a leaky channel allowing material exchange with systems exterior to the channel. The channels in these systems may undergo peristaltic pumping which is thought to enhance the material exchange. To date, little analytic work has been done to study the effect of pumping on material extraction across the channel walls. In this paper, we examine a fluid extraction model in which fluid flowing through a leaky channel is exchanged with fluid in a reservoir. The channel walls are allowed to contract and expand uniformly, simulating a pumping mechanism. In order to efficiently determine solutions of the model, we derive a formal power series solution for the Stokes equations in a finite channel with uniformly contracting/expanding permeable walls. This flow has been well studied in the case in which the normal velocity at the channel walls is proportional to the wall velocity. In contrast we do not assume flow that is proportional to the wall velocity, but flow that is driven by hydrostatic pressure, and we use Darcy's law to close our system for normal wall velocity. We incorporate our flow solution into a model that tracks the material pressure exterior to the channel. We use this model to examine flux across the channel-reservoir barrier and demonstrate that pumping can either enhance or impede fluid extraction across channel walls. We find that associated with each set of physical flow and pumping parameters, there are optimal reservoir conditions that maximize the amount of material flowing from the channel into the reservoir.

Silicon photonic resonator for label-free bio-sensing application

NASA Astrophysics Data System (ADS)

Udomsom, Suruk; Mankong, Ukrit; Theera-Umpon, Nipon; Ittipratheep, Nattapol; Umezawa, Toshimasa; Matsumoto, Atsushi; Yamamoto, Naokatsu

2018-03-01

In medical diagnostics there is an increasing demand for biosensors that can specifically detect biological analytes in a fluid. Especially label-free sensing, consistings of a transducer with biorecognition molecules immobilized on its surface without relying on fluorescent dye. In this paper we study the design and fabrication of a silicon nanowire photonic ring resonator and its feasibility as a biosensor. We have simulated and fabricated racetrack ring resonators which have a few tenths of micrometer gap, up to 0.5 μm between the input / output waveguides and the resonators. It is found that the devices can be designed with large Q factors. Sensitivity to biomaterial detection has been simulated for antibody (goat anti-mouse IgG) - antigen (mouse IgG) using 3-dimensional Finite Difference Time Domain technique. The simulated results show that the ring resonator has a response 15 nm resonance shift per refractive index unit. Antibody coating method is also discussed in this paper which can be applied to other antibody-antigen types.

Pore-scale observation and 3D simulation of wettability effects on supercritical CO2 - brine immiscible displacement in drainage

NASA Astrophysics Data System (ADS)

Hu, R.; Wan, J.; Chen, Y.

2016-12-01

Wettability is a factor controlling the fluid-fluid displacement pattern in porous media and significantly affects the flow and transport of supercritical (sc) CO2 in geologic carbon sequestration. Using a high-pressure micromodel-microscopy system, we performed drainage experiments of scCO2 invasion into brine-saturated water-wet and intermediate-wet micromodels; we visualized the scCO2 invasion morphology at pore-scale under reservoir conditions. We also performed pore-scale numerical simulations of the Navier-Stokes equations to obtain 3D details of fluid-fluid displacement processes. Simulation results are qualitatively consistent with the experiments, showing wider scCO2 fingering, higher percentage of scCO2 and more compact displacement pattern in intermediate-wet micromodel. Through quantitative analysis based on pore-scale simulation, we found that the reduced wettability reduces the displacement front velocity, promotes the pore-filling events in the longitudinal direction, delays the breakthrough time of invading fluid, and then increases the displacement efficiency. Simulated results also show that the fluid-fluid interface area follows a unified power-law relation with scCO2 saturation, and show smaller interface area in intermediate-wet case which suppresses the mass transfer between the phases. These pore-scale results provide insights for the wettability effects on CO2 - brine immiscible displacement in geologic carbon sequestration.

Acoustic microstreaming due to an ultrasound contrast microbubble near a wall

NASA Astrophysics Data System (ADS)

Mobadersany, Nima; Sarkar, Kausik

2017-11-01

In an ultrasound field, in addition to the sinusoidal motion of fluid particles, particles experience a steady streaming velocity due to nonlinear second order effects. Here, we have simulated the microstreaming flow near a plane rigid wall caused by the pulsations of contrast microbubbles. Although these microbubbles were initially developed as a contrast enhancing agents for ultrasound imaging, they generate additional therapeutic effects that can be harnessed for targeted drug delivery or blood brain barrier (BBB) opening. The microbubbles have a gas core coated with a stabilizing layer of lipids or proteins. We use analytical models as well as boundary element (BEM) simulation to simulate the flow around these bubbles implementing interfacial rheology models for the coating. The microstreaming flow is characterized by two wall bounded vortices. The size of the vortices decreases with the decrease of the separation from the wall. The vortex-induced shear stress is simulated and analyzed as a function of excitation parameters and geometry. These microstreaming shear stress plays a critical role in increasing the membrane permeability facilitating drug delivery or rupturing biological tissues.

Comparing human peritoneal fluid and phosphate-buffered saline for drug delivery: do we need bio-relevant media?

PubMed

Bhusal, Prabhat; Rahiri, Jamie Lee; Sua, Bruce; McDonald, Jessica E; Bansal, Mahima; Hanning, Sara; Sharma, Manisha; Chandramouli, Kaushik; Harrison, Jeff; Procter, Georgina; Andrews, Gavin; Jones, David S; Hill, Andrew G; Svirskis, Darren

2018-06-01

An understanding of biological fluids at the site of administration is important to predict the fate of drug delivery systems in vivo. Little is known about peritoneal fluid; therefore, we have investigated this biological fluid and compared it to phosphate-buffered saline, a synthetic media commonly used for in vitro evaluation of intraperitoneal drug delivery systems. Human peritoneal fluid samples were analysed for electrolyte, protein and lipid levels. In addition, physicochemical properties were measured alongside rheological parameters. Significant inter-patient variations were observed with regard to pH (p < 0.001), buffer capacity (p < 0.05), osmolality (p < 0.001) and surface tension (p < 0.05). All the investigated physicochemical properties of peritoneal fluid differed from phosphate-buffered saline (p < 0.001). Rheological examination of peritoneal fluid demonstrated non-Newtonian shear thinning behaviour and predominantly exhibited the characteristics of an entangled network. Inter-patient and inter-day variability in the viscosity of peritoneal fluid was observed. The solubility of the local anaesthetic lidocaine in peritoneal fluid was significantly higher (p < 0.05) when compared to phosphate-buffered saline. Interestingly, the dissolution rate of lidocaine was not significantly different between the synthetic and biological media. Importantly, and with relevance to intraperitoneal drug delivery systems, the sustained release of lidocaine from a thermosensitive gel formulation occurred at a significantly faster rate into peritoneal fluid. Collectively, these data demonstrate the variation between commonly used synthetic media and human peritoneal fluid. The differences in drug release rates observed illustrate the need for bio-relevant media, which ultimately would improve in vitro-in vivo correlation.

Lattice-Boltzmann simulation of coalescence-driven island coarsening

USGS Publications Warehouse

Basagaoglu, H.; Green, C.T.; Meakin, P.; McCoy, B.J.

2004-01-01

The first-order phase separation in a thin fluid film was simulated using a two-dimensional lattice-Boltzman model (LBM) with fluid-fluid interactions. The effects of the domain size on the intermediate asymptotic island size distribution were also discussed. It was observed that the overall process is dominated by coalescence which is independent of island mass. The results show that the combined effects of growth, coalescence, and Ostwald ripening control the phase transition process in the LBM simulations.

Detection of contamination of municipal water distribution systems

DOEpatents

Cooper, John F [Oakland, CA

2012-01-17

A system for the detection of contaminates of a fluid in a conduit. The conduit is part of a fluid distribution system. A chemical or biological sensor array is connected to the conduit. The sensor array produces an acoustic signal burst in the fluid upon detection of contaminates in the fluid. A supervisory control system connected to the fluid and operatively connected to the fluid distribution system signals the fluid distribution system upon detection of contaminates in the fluid.

Swimming & Propulsion in Viscoelastic Media

NASA Astrophysics Data System (ADS)

Arratia, Paulo

2012-02-01

Many microorganisms have evolved within complex fluids, which include soil, intestinal fluid, and mucus. The material properties or rheology of such fluids can strongly affect an organism's swimming behavior. A major challenge is to understand the mechanism of propulsion in media that exhibit both solid- and fluid-like behavior, such as viscoelastic fluids. In this talk, we present experiments that explore the swimming behavior of biological organisms and artificial particles in viscoelastic media. The organism is the nematode Caenorhabditis elegans, a roundworm widely used for biological research that swims by generating traveling waves along its body. Overall, we find that fluid elasticity hinders self-propulsion compared to Newtonian fluids due to the enhanced resistance to flow near hyperbolic points for viscoelastic fluids. As fluid elasticity increases, the nematode's propulsion speed decreases. These results are consistent with recent theoretical models for undulating sheets and cylinders. In order to gain further understanding on propulsion in viscoelastic media, we perform experiments with simple reciprocal artificial `swimmers' (magnetic dumbbell particles) in polymeric and micellar solutions. We find that self-propulsion is possible in viscoelastic media even if the motion is reciprocal.

Computer animation challenges for computational fluid dynamics

NASA Astrophysics Data System (ADS)

Vines, Mauricio; Lee, Won-Sook; Mavriplis, Catherine

2012-07-01

Computer animation requirements differ from those of traditional computational fluid dynamics (CFD) investigations in that visual plausibility and rapid frame update rates trump physical accuracy. We present an overview of the main techniques for fluid simulation in computer animation, starting with Eulerian grid approaches, the Lattice Boltzmann method, Fourier transform techniques and Lagrangian particle introduction. Adaptive grid methods, precomputation of results for model reduction, parallelisation and computation on graphical processing units (GPUs) are reviewed in the context of accelerating simulation computations for animation. A survey of current specific approaches for the application of these techniques to the simulation of smoke, fire, water, bubbles, mixing, phase change and solid-fluid coupling is also included. Adding plausibility to results through particle introduction, turbulence detail and concentration on regions of interest by level set techniques has elevated the degree of accuracy and realism of recent animations. Basic approaches are described here. Techniques to control the simulation to produce a desired visual effect are also discussed. Finally, some references to rendering techniques and haptic applications are mentioned to provide the reader with a complete picture of the challenges of simulating fluids in computer animation.

Effect of electron Monte Carlo collisions on a hybrid simulation of a low-pressure capacitively coupled plasma

NASA Astrophysics Data System (ADS)

Hwang, Seok Won; Lee, Ho-Jun; Lee, Hae June

2014-12-01

Fluid models have been widely used and conducted successfully in high pressure plasma simulations where the drift-diffusion and the local-field approximation are valid. However, fluid models are not able to demonstrate non-local effects related to large electron energy relaxation mean free path in low pressure plasmas. To overcome this weakness, a hybrid model coupling electron Monte Carlo collision (EMCC) method with the fluid model is introduced to obtain precise electron energy distribution functions using pseudo-particles. Steady state simulation results by a one-dimensional hybrid model which includes EMCC method for the collisional reactions but uses drift-diffusion approximation for electron transport in a fluid model are compared with those of a conventional particle-in-cell (PIC) and a fluid model for low pressure capacitively coupled plasmas. At a wide range of pressure, the hybrid model agrees well with the PIC simulation with a reduced calculation time while the fluid model shows discrepancy in the results of the plasma density and the electron temperature.

Three-dimensional three-phase model for simulation of hydrodynamics, oxygen mass transfer, carbon oxidation, nitrification and denitrification in an oxidation ditch.

PubMed

Lei, Li; Ni, Jinren

2014-04-15

A three-dimensional three-phase fluid model, supplemented by laboratory data, was developed to simulate the hydrodynamics, oxygen mass transfer, carbon oxidation, nitrification and denitrification processes in an oxidation ditch. The model provided detailed phase information on the liquid flow field, gas hold-up distribution and sludge sedimentation. The three-phase model described water-gas, water-sludge and gas-sludge interactions. Activated sludge was taken to be in a pseudo-solid phase, comprising an initially separated solid phase that was transported and later underwent biological reactions with the surrounding liquidmedia. Floc parameters were modified to improve the sludge viscosity, sludge density, oxygen mass transfer rate, and carbon substrate uptake due to adsorption onto the activated sludge. The validation test results were in very satisfactory agreement with laboratory data on the behavior of activated sludge in an oxidation ditch. By coupling species transport and biological process models, reasonable predictions are made of: (1) the biochemical kinetics of dissolved oxygen, chemical oxygen demand (COD) and nitrogen variation, and (2) the physical kinematics of sludge sedimentation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of lactoferrin derived peptides on simulants of biological warfare agents.

PubMed

Sijbrandij, Tjitske; Ligtenberg, Antoon J; Nazmi, Kamran; Veerman, Enno C I; Bolscher, Jan G M; Bikker, Floris J

2017-01-01

Lactoferrin (LF) is an important immune protein in neutrophils and secretory fluids of mammals. Bovine LF (bLF) harbours two antimicrobial stretches, lactoferricin and lactoferampin, situated in close proximity in the N1 domain. To mimic these antimicrobial domain parts a chimeric peptide (LFchimera) has been constructed comprising parts of both stretches (LFcin17-30 and LFampin265-284). To investigate the potency of this construct to combat a set of Gram positive and Gram negative bacteria which are regarded as simulants for biological warfare agents, the effect on bacterial killing, membrane permeability and membrane polarity were determined in comparison to the constituent peptides and the native bLF. Furthermore we aimed to increase the antimicrobial potency of the bLF derived peptides by cationic amino acid substitutions. Overall, the bactericidal activity of the peptides could be related to membrane disturbing effects, i.e. membrane permeabilization and depolarization. Those effects were most prominent for the LFchimera. Arginine residues were found to be crucial for displaying antimicrobial activity, as lysine to arginine substitutions resulted in an increased antimicrobial activity, affecting mostly LFampin265-284 whereas arginine to lysine substitutions resulted in a decreased bactericidal activity, predominantly in case of LFcin17-30.

The effect of nanobioceramic reinforcement on mechanical and biological properties of Co-base alloy/hydroxyapatite nanocomposite.

PubMed

Bahrami, M; Fathi, M H; Ahmadian, M

2015-03-01

The goal of the present research was to fabricate, characterize, and evaluate mechanical and biological properties of Co-base alloy composites with different amounts of hydroxyapatite (HA) nanopowder reinforcement. The powder of Co-Cr-Mo alloy was mixed with different amounts of HA by ball milling and it was then cold pressed and sintered. X-ray diffraction (XRD) and scanning electron microscopy (SEM) techniques were used. Microhardness measurement and compressive tests were also carried out. Bioactivity behavior was evaluated in simulated body fluid (SBF). A significant decrease in modulus elasticity and an increase in microhardness of the sintered composites were observed. Apatite formation on the surface of the composites showed that it could successfully convert bioinert Co-Cr-Mo alloy to bioactive type by adding 10, 15, and 20wt.% HA which have lower modulus elasticity and higher microhardness. Copyright © 2014 Elsevier B.V. All rights reserved.

Accelerated lattice Boltzmann model for colloidal suspensions rheology and interface morphology

NASA Astrophysics Data System (ADS)

Farhat, Hassan

Colloids are ubiquitous in the food, medical, cosmetic, polymer, water purification and pharmaceutical industries. Colloids thermal, mechanical and storage properties are highly dependent on their interface morphology and their rheological behavior. Numerical methods provide a cheap and reliable virtual laboratory for the study of colloids. However efficiency is a major concern to address when using numerical methods for practical applications. This work introduces the main building-blocks for an improved lattice Boltzmann-based numerical tool designed for the study of colloidal rheology and interface morphology. The efficiency of the proposed model is enhanced by using the recently developed and validated migrating multi-block algorithms for the lattice Boltzmann method (LBM). The migrating multi-block was used to simulate single component, multi-component, multiphase and single component multiphase flows. Results were validated by experimental, numerical and analytical solutions. The contamination of the fluid-fluid interface influences the colloids morphology. This issue was addressed by the introduction of the hybrid LBM for surfactant-covered droplets. The module was used for the simulation of surfactant-covered droplet deformation under shear and uniaxial extensional flows respectively and under buoyancy. Validation with experimental and theoretical results was provided. Colloids are non-Newtonian fluids which exhibit rich rheological behavior. The suppression of coalescence module is the part of the proposed model which facilitates the study of colloids rheology. The model results for the relative viscosity were in agreement with some theoretical results. Biological suspensions such as blood are macro-colloids by nature. The study of the blood flow in the microvasculature was heuristically approached by assuming the red blood cells as surfactant covered droplets. The effects of interfacial tension on the flow velocity and the droplet exclusion from the walls in parabolic flows were in qualitative agreement with some experimental and numerical results. The Fahraeus and the Fahraeus-Lindqvist effects were reproduced. The proposed LBM model provides a flexible numerical platform consisting of various modules which could be used separately or in combination for the study of a variety of colloids and biological suspensions flow deformation problems.

Green Algae as Model Organisms for Biological Fluid Dynamics

NASA Astrophysics Data System (ADS)

Goldstein, Raymond E.

2015-01-01

In the past decade, the volvocine green algae, spanning from the unicellular Chlamydomonas to multicellular Volvox, have emerged as model organisms for a number of problems in biological fluid dynamics. These include flagellar propulsion, nutrient uptake by swimming organisms, hydrodynamic interactions mediated by walls, collective dynamics and transport within suspensions of microswimmers, the mechanism of phototaxis, and the stochastic dynamics of flagellar synchronization. Green algae are well suited to the study of such problems because of their range of sizes (from 10 μm to several millimeters), their geometric regularity, the ease with which they can be cultured, and the availability of many mutants that allow for connections between molecular details and organism-level behavior. This review summarizes these recent developments and highlights promising future directions in the study of biological fluid dynamics, especially in the context of evolutionary biology, that can take advantage of these remarkable organisms.

Application of foam-extend on turbulent fluid-structure interaction

NASA Astrophysics Data System (ADS)

Rege, K.; Hjertager, B. H.

2017-12-01

Turbulent flow around flexible structures is likely to induce structural vibrations which may eventually lead to fatigue failure. In order to assess the fatigue life of these structures, it is necessary to take the action of the flow on the structure into account, but also the influence of the vibrating structure on the fluid flow. This is achieved by performing fluid-structure interaction (FSI) simulations. In this work, we have investigated the capability of a FSI toolkit for the finite volume computational fluid dynamics software foam-extend to simulate turbulence-induced vibrations of a flexible structure. A large-eddy simulation (LES) turbulence model has been implemented to a basic FSI problem of a flexible wall which is placed in a confined, turbulent flow. This problem was simulated for 2.32 seconds. This short simulation required over 200 computation hours, using 20 processor cores. Thereby, it has been shown that the simulation of FSI with LES is possible, but also computationally demanding. In order to make turbulent FSI simulations with foam-extend more applicable, more sophisticated turbulence models and/or faster FSI iteration schemes should be applied.

Fluid flows and forces in development: functions, features and biophysical principles

PubMed Central

Freund, Jonathan B.; Goetz, Jacky G.; Hill, Kent L.; Vermot, Julien

2012-01-01

Throughout morphogenesis, cells experience intracellular tensile and contractile forces on microscopic scales. Cells also experience extracellular forces, such as static forces mediated by the extracellular matrix and forces resulting from microscopic fluid flow. Although the biological ramifications of static forces have received much attention, little is known about the roles of fluid flows and forces during embryogenesis. Here, we focus on the microfluidic forces generated by cilia-driven fluid flow and heart-driven hemodynamics, as well as on the signaling pathways involved in flow sensing. We discuss recent studies that describe the functions and the biomechanical features of these fluid flows. These insights suggest that biological flow determines many aspects of cell behavior and identity through a specific set of physical stimuli and signaling pathways. PMID:22395739

Swimming by reciprocal motion at low Reynolds number.

PubMed

Qiu, Tian; Lee, Tung-Chun; Mark, Andrew G; Morozov, Konstantin I; Münster, Raphael; Mierka, Otto; Turek, Stefan; Leshansky, Alexander M; Fischer, Peer

2014-11-04

Biological microorganisms swim with flagella and cilia that execute nonreciprocal motions for low Reynolds number (Re) propulsion in viscous fluids. This symmetry requirement is a consequence of Purcell's scallop theorem, which complicates the actuation scheme needed by microswimmers. However, most biomedically important fluids are non-Newtonian where the scallop theorem no longer holds. It should therefore be possible to realize a microswimmer that moves with reciprocal periodic body-shape changes in non-Newtonian fluids. Here we report a symmetric 'micro-scallop', a single-hinge microswimmer that can propel in shear thickening and shear thinning (non-Newtonian) fluids by reciprocal motion at low Re. Excellent agreement between our measurements and both numerical and analytical theoretical predictions indicates that the net propulsion is caused by modulation of the fluid viscosity upon varying the shear rate. This reciprocal swimming mechanism opens new possibilities in designing biomedical microdevices that can propel by a simple actuation scheme in non-Newtonian biological fluids.

Predictive models for pressure-driven fluid infusions into brain parenchyma

NASA Astrophysics Data System (ADS)

Raghavan, Raghu; Brady, Martin

2011-10-01

Direct infusions into brain parenchyma of biological therapeutics for serious brain diseases have been, and are being, considered. However, individual brains, as well as distinct cytoarchitectural regions within brains, vary in their response to fluid flow and pressure. Further, the tissue responds dynamically to these stimuli, requiring a nonlinear treatment of equations that would describe fluid flow and drug transport in brain. We here report in detail on an individual-specific model and a comparison of its prediction with simulations for living porcine brains. Two critical features we introduced into our model—absent from previous ones, but requirements for any useful simulation—are the infusion-induced interstitial expansion and the backflow. These are significant determinants of the flow. Another feature of our treatment is the use of cross-property relations to obtain individual-specific parameters that are coefficients in the equations. The quantitative results are at least encouraging, showing a high fraction of overlap between the computed and measured volumes of distribution of a tracer molecule and are potentially clinically useful. Several improvements are called for; principally a treatment of the interstitial expansion more fundamentally based on poroelasticity and a better delineation of the diffusion tensor of a particle confined to the interstitial spaces.

Flow-driven Assembly of Microcapsule Towers

NASA Astrophysics Data System (ADS)

Shum, Henry; Balazs, Anna

2016-11-01

Large populations of the slime mold, Dictyostelium discoideum, are able to aggregate over a surface and collectively form a long, vertical stalk. Inspired by this biological behavior, we develop a synthetic mechanism for assembling tower-like structures using microcapsules as the building blocks. We accomplish this in simulations by generating a fluid flow field that draws microcapsules together along a surface and lifts them up at a central point. We considered a fluid flow generated by the local release of a chemical species from a patch on the surface. The concentration gradient of the diffusing chemical species causes radial diffusioosmotic flow along the solid surface toward the patch. Adhesive interactions keep the microcapsules attached to the surface as they are drawn together above the patch. To build a tower-like structure, some of the microcapsules must detach from the surface but remain attached to the rest of the cluster. The upward directed fluid flow above the patch then draws out the cluster into a tower shape. The final morphology of the aggregate structure depends on the flow field, the adhesive capsule-capsule and capsule-surface interaction strengths, and the sedimentation force on the capsules. Tuning these factors changes the structures that are produced.

Self-Propulsion of a Flapping Airfoil Using Cyber-Physical Fluid Dynamics

NASA Astrophysics Data System (ADS)

Young, Jay; Asselin, Daniel; Williamson, C. H. K.

2017-11-01

The fluid dynamics of biologically-inspired flapping propulsion provides a fertile testing ground for the field of unsteady aerodynamics, serving as important groundwork for the design and development of underwater vehicles and micro air vehicles (MAVs). These technologies can provide low cost, compact, and maneuverable means for terrain mapping, search and rescue operations, and reconnaissance. However, most laboratory experiments and simulations have been conducted using tethered airfoils with an imposed freestream velocity, which does not necessarily reflect the conditions under which an airfoil employed as a propulsor would operate. Using a closed-loop force-feedback control system, defined as Cyber-Physical Fluid Dynamics, or CPFD (Mackowski & Williamson 2011, 2015, & 2016), we allow a flapping airfoil to fly forward freely, achieving an equilibrium velocity at which thrust and drag are balanced. We study a combination of actively and passively controlled pitching and heaving dynamics in order to find motions that minimize the energy expended per distance traveled by the propulsion system. This work was supported by the National Science Foundation and the Air Force Office of Scientific Research Grant No. FA9550-15-1-0243, monitored by Dr. Douglas Smith.

Direct simulation of electroosmosis around a spherical particle with inhomogeneously acquired surface charge.

PubMed

Alizadeh, Amer; Wang, Moran

2017-03-01

Uncovering electroosmosis around an inhomogeneously acquired charge spherical particle in a confined space could provide detailed insights into its broad applications from biology to geology. In the present study, we developed a direct simulation method with the effects of inhomogeneously acquired charges on the particle surface considered, which has been validated by the available analytical and experimental data. Modeling results reveal that the surface charge and zeta potential, which are acquired through chemical interactions, strongly depend on the local solution properties and the particle size. The surface charge and zeta potential of the particle would significantly vary with the tangential positions on the particle surface by increasing the particle radius. Moreover, regarding the streaming potential for a particle-fluid tube system, our results uncover that the streaming potential has a reverse relation with the particle size in a micro or nanotube. To explain this phenomenon, we present a simple relation that bridges the streaming potential with the particle size and tube radius, zeta potential, bulk and surface conductivity. This relation could predict good results specifically for higher ion concentrations and provide deeper understanding of the particle size effects on the streaming potential measurements of the particle fluid tube system. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Powder metallurgical low-modulus Ti-Mg alloys for biomedical applications.

PubMed

Liu, Yong; Li, Kaiyang; Luo, Tao; Song, Min; Wu, Hong; Xiao, Jian; Tan, Yanni; Cheng, Ming; Chen, Bing; Niu, Xinrui; Hu, Rong; Li, Xiaohui; Tang, Huiping

2015-11-01

In this work, powder metallurgical (PM) Ti-Mg alloys were prepared using combined techniques of mechanical alloying and spark plasma sintering. The alloys mainly consist of super saturations of Mg in Ti matrix, and some laminar structured Ti- and Mg-rich phases. The PM Ti-Mg alloys contain a homogeneous mixtures of nanocrystalline Mg and Ti phases. The novel microstructures result in unconventional mechanical and biological properties. It has been shown that the PM Ti-Mg alloys have a much lower compression modulus (36-50GPa) compared to other Ti alloys, but still remain a very high compressive strength (1500-1800MPa). In addition, the PM Ti-Mg alloys show good biocompatibility and bioactivity. Mg can dissolve in the simulated body fluids, and induce the formation of the calcium phosphate layer. The compression modulus of PM Ti-Mg alloys decreases with the amount of Mg, while the bioactivity increases. Although the corrosion resistance of Ti-Mg alloys decreases with the content of Mg, the alloys still show good stability in simulated body fluid under electrochemical conditions. The indirect and direct cytotoxicity results show that PM Ti-Mg alloys have a good biocompatibility to NIH-3T3 cells. Therefore, the PM Ti-Mg alloys are promising candidates in biomedical applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Physical mechanism and modeling of heat generation and transfer in magnetic fluid hyperthermia through Néelian and Brownian relaxation: a review.

PubMed

Suriyanto; Ng, E Y K; Kumar, S D

2017-03-23

Current clinically accepted technologies for cancer treatment still have limitations which lead to the exploration of new therapeutic methods. Since the past few decades, the hyperthermia treatment has attracted the attention of investigators owing to its strong biological rationales in applying hyperthermia as a cancer treatment modality. Advancement of nanotechnology offers a potential new heating method for hyperthermia by using nanoparticles which is termed as magnetic fluid hyperthermia (MFH). In MFH, superparamagnetic nanoparticles dissipate heat through Néelian and Brownian relaxation in the presence of an alternating magnetic field. The heating power of these particles is dependent on particle properties and treatment settings. A number of pre-clinical and clinical trials were performed to test the feasibility of this novel treatment modality. There are still issues yet to be solved for the successful transition of this technology from bench to bedside. These issues include the planning, execution, monitoring and optimization of treatment. The modeling and simulation play crucial roles in solving some of these issues. Thus, this review paper provides a basic understanding of the fundamental and rationales of hyperthermia and recent development in the modeling and simulation applied to depict the heat generation and transfer phenomena in the MFH.

Phytate (IP6) is a powerful agent for preventing calcifications in biological fluids: usefulness in renal lithiasis treatment.

PubMed

Grases, F; Costa-Bauzá, A

1999-01-01

The extraordinary capacity of phytate (myo-inositol hexaphosphate), a substance present in blood, urine, interstitial and intracellular fluids, to inhibit crystallization of calcium salts (oxalate and phosphate) is discussed. Its role in preventing calcium renal stone formation is specifically presented and discussed. "In vitro" and "in vivo" experiments, as well as clinical studies clearly demonstrated that phytate plays an important role as a crystallization inhibitor of calcium salts in biological fluids and becomes a clear alternative in the treatment of calcium oxalate renal lithiasis.

The effect of dentinal fluid flow during loading in various directions--simulation of fluid-structure interaction.

PubMed

Su, Kuo-Chih; Chang, Chih-Han; Chuang, Shu-Fen; Ng, Eddie Yin-Kwee

2013-06-01

This study uses a fluid-structure interaction (FSI) simulation to evaluate the fluid flow in a dental intrapulpal chamber induced by the deformation of the tooth structure during loading in various directions. The FSI is used for the biomechanics simulation of dental intrapulpal responses with the force loading gradually increasing from 0 to 100N at 0°, 30°, 45°, 60°, and 90° on the tooth surface in 1s, respectively. The effect of stress or deformation on tooth and fluid flow changes in the pulp chamber are evaluated. A horizontal loading force on a tooth may induce tooth structure deformation, which increases fluid flow velocity in the coronal pulp. Thus, horizontal loading on a tooth may easily induce tooth pain. This study suggests that experiments to investigate the relationship between loading in various directions and dental pain should avoid measuring the bulk pulpal fluid flow from radicular pulp, but rather should measure the dentinal fluid flow in the dentinal tubules or coronal pulp. The FSI analysis used here could provide a powerful tool for investigating problems with coupled solid and fluid structures in dental biomechanics. Copyright © 2012 Elsevier Ltd. All rights reserved.

Broadband attenuation and nonlinear propagation in biological fluids: an experimental facility and measurements.

PubMed

Verma, Prashant K; Humphrey, Victor F; Duck, Francis A

2005-12-01

The design and construction of a versatile experimental facility for making measurements of the frequency-dependence of attenuation coefficient (over the range 1 MHz to 25 MHz) and nonlinear propagation in samples of biological fluids is described. The main feature of the facility is the ability to perform all of the measurements on the same sample of fluid within a short period of time and under temperature control. In particular, the facility allows the axial development of nonlinear waveform distortion to be measured with a wideband bilaminar polyvinylidene difluoride membrane hydrophone to study nonlinear propagation in biological fluids. The system uses a variable length bellows to contain the fluid, with transparent Mylar end-windows to couple the acoustic field into the fluid. Example results for the frequency-dependence of attenuation of Dow Corning 200/350 silicone fluid, used as a standard fluid, are presented and shown to be in good agreement with alternative measurements. Measurements of finite amplitude propagation in amniotic fluid, urine and 4.5% human albumin solutions at physiological temperature (37 degrees C) are presented and compared with theoretical predictions using existing models. The measurements were made using a 2.25-MHz single-element transducer coupled to a polymethyl methacrylate lens with a focal amplitude gain of 12 in water. The transducer was driven with an eight-cycle tone burst at source pressures up to 0.137 MPa. In general, given an accurate knowledge of the medium parameters and source conditions, the agreement with theoretical prediction is good for the first five harmonics.

Biomineralization of superhydrophilic vertically aligned carbon nanotubes.

PubMed

Marsi, Teresa Cristina O; Santos, Tiago G; Pacheco-Soares, Cristina; Corat, Evaldo J; Marciano, Fernanda R; Lobo, Anderson O

2012-03-06

Vertically aligned carbon nanotubes (VACNT) promise a great role for the study of tissue regeneration. In this paper, we introduce a new biomimetic mineralization routine employing superhydrophilic VACNT films as highly stable template materials. The biomineralization was obtained after VACNT soaking in simulated body fluid solution. Detailed structural analysis reveals that the polycrystalline biological apatites formed due to the -COOH terminations attached to VACNT tips after oxygen plasma etching. Our approach not only provides a novel route for nanostructured materials, but also suggests that COOH termination sites can play a significant role in biomimetic mineralization. These new nanocomposites are very promising as nanobiomaterials due to the excellent human osteoblast adhesion.

Chemical-Reaction-Controlled Phase Separated Drops: Formation, Size Selection, and Coarsening

NASA Astrophysics Data System (ADS)

Wurtz, Jean David; Lee, Chiu Fan

2018-02-01

Phase separation under nonequilibrium conditions is exploited by biological cells to organize their cytoplasm but remains poorly understood as a physical phenomenon. Here, we study a ternary fluid model in which phase-separating molecules can be converted into soluble molecules, and vice versa, via chemical reactions. We elucidate using analytical and simulation methods how drop size, formation, and coarsening can be controlled by the chemical reaction rates, and categorize the qualitative behavior of the system into distinct regimes. Ostwald ripening arrest occurs above critical reaction rates, demonstrating that this transition belongs entirely to the nonequilibrium regime. Our model is a minimal representation of the cell cytoplasm.

Simulation of two-phase flow in horizontal fracture networks with numerical manifold method

NASA Astrophysics Data System (ADS)

Ma, G. W.; Wang, H. D.; Fan, L. F.; Wang, B.

2017-10-01

The paper presents simulation of two-phase flow in discrete fracture networks with numerical manifold method (NMM). Each phase of fluids is considered to be confined within the assumed discrete interfaces in the present method. The homogeneous model is modified to approach the mixed fluids. A new mathematical cover formation for fracture intersection is proposed to satisfy the mass conservation. NMM simulations of two-phase flow in a single fracture, intersection, and fracture network are illustrated graphically and validated by the analytical method or the finite element method. Results show that the motion status of discrete interface significantly depends on the ratio of mobility of two fluids rather than the value of the mobility. The variation of fluid velocity in each fracture segment and the driven fluid content are also influenced by the ratio of mobility. The advantages of NMM in the simulation of two-phase flow in a fracture network are demonstrated in the present study, which can be further developed for practical engineering applications.

Fluid-structure interaction dynamic simulation of spring-loaded pressure relief valves under seismic wave

NASA Astrophysics Data System (ADS)

Lv, Dongwei; Zhang, Jian; Yu, Xinhai

2018-05-01

In this paper, a fluid-structure interaction dynamic simulation method of spring-loaded pressure relief valve was established. The dynamic performances of the fluid regions and the stress and strain of the structure regions were calculated at the same time by accurately setting up the contact pairs between the solid parts and the coupling surfaces between the fluid regions and the structure regions. A two way fluid-structure interaction dynamic simulation of a simplified pressure relief valve model was carried out. The influence of vertical sinusoidal seismic waves on the performance of the pressure relief valve was preliminarily investigated by loading sine waves. Under vertical seismic waves, the pressure relief valve will flutter, and the reseating pressure was affected by the amplitude and frequency of the seismic waves. This simulation method of the pressure relief valve under vertical seismic waves can provide effective means for investigating the seismic performances of the valves, and make up for the shortcomings of the experiment.

Plasma-Sheath-Surface Dynamics

DTIC Science & Technology

1990-09-01

Particle Simulations of Cross-Field Plasma Sheaths," Phys. Fluids B, pp 1069- 1082 , May 1990. IJ. Morey and C.K. Birdsall, "Traveling Wave-Tube Simulation...Theilhaber, "Analytic Solutions and Particle Simulations of Cross-Field Plasma Sheaths," Phys. Fluids B, pp 1069- 1082 , May 1990. S.E. Parker, and C.K

Differential Geometry Based Multiscale Models

PubMed Central

Wei, Guo-Wei

2010-01-01

Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atom-istic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier–Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson–Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson–Nernst–Planck equations that are coupled to generalized Navier–Stokes equations for fluid dynamics, Newton's equation for molecular dynamics, and potential and surface driving geometric flows for the micro-macro interface. For excessively large aqueous macromolecular complexes in chemistry and biology, we further develop differential geometry based multiscale fluid-electro-elastic models to replace the expensive molecular dynamics description with an alternative elasticity formulation. PMID:20169418

Consider a non-spherical elephant: computational fluid dynamics simulations of heat transfer coefficients and drag verified using wind tunnel experiments.

PubMed

Dudley, Peter N; Bonazza, Riccardo; Porter, Warren P

2013-07-01

Animal momentum and heat transfer analysis has historically used direct animal measurements or approximations to calculate drag and heat transfer coefficients. Research can now use modern 3D rendering and computational fluid dynamics software to simulate animal-fluid interactions. Key questions are the level of agreement between simulations and experiments and how superior they are to classical approximations. In this paper we compared experimental and simulated heat transfer and drag calculations on a scale model solid aluminum African elephant casting. We found good agreement between experimental and simulated data and large differences from classical approximations. We used the simulation results to calculate coefficients for heat transfer and drag of the elephant geometry. Copyright © 2013 Wiley Periodicals, Inc.

Simulation of a Magneto-Rheological Fluid Based, Jamming, Soft Gripper Using the Soft Sphere DEM in LIGGGHTS

NASA Astrophysics Data System (ADS)

Leps, Thomas; Hartzell, Christine; Wereley, Norman; Choi, Young

2017-11-01

Jamming soft grippers are excellent universal grippers due to their low dependence on the shape of objects to be grabbed, and low stiffness, mitigating the need for object shape data and expensive force control of a stiff system. These grippers now rely on jamming transitions of dry grains under atmospheric pressure to hold objects. In order to expand their use to space environments, a gripper using magnetic actuation of a magneto-rheological fluid (MR Gripper) is being developed. The MR fluid is a suspension of μm scale iron grains in a silicone oil. When un-magnetized the fluid behaves as a dense suspension with low Bagnold number. When magnetized, it behaves like a jammed granular material, with magnetic forces between the grains dominating. We are simulating the gripper using LIGGGHTS, an open-source soft sphere DEM code. We have modeled both the deformable gripper membrane and the MR fluid itself using the LIGGGHTS framework. To our knowledge, this is the first time that the induced magnetic dipoles required to accurately simulate the jamming behavior of MR fluids have been modeled in LIGGGHTS. This simulation allows the rapid optimization of the hardware and magnetic field geometries, as well as the fluid behavior, without time consuming, and costly prototype revisions.

Reciprocal Effects between Fluid and Crystallized Intelligence and Their Dependence on Parents' Socioeconomic Status and Education

ERIC Educational Resources Information Center

Rindermann, Heiner; Flores-Mendoza, Carmen; Mansur-Alves, Marcela

2010-01-01

The investment theory of Cattell supposes an influence of fluid on crystallized intelligence. The development of fluid intelligence largely depends on biological factors, of crystallized intelligence on fluid intelligence and environmental stimulation. To test this theory two contrasting samples representing a broad ability range were chosen, a…

A New Proof of Concept in Bacterial Reduction: Antimicrobial Action of Violet-Blue Light (405 nm) in Ex Vivo Stored Plasma

PubMed Central

Maclean, Michelle; Anderson, John G.; MacGregor, Scott J.; White, Tracy

2016-01-01

Bacterial contamination of injectable stored biological fluids such as blood plasma and platelet concentrates preserved in plasma at room temperature is a major health risk. Current pathogen reduction technologies (PRT) rely on the use of chemicals and/or ultraviolet light, which affects product quality and can be associated with adverse events in recipients. 405 nm violet-blue light is antibacterial without the use of photosensitizers and can be applied at levels safe for human exposure, making it of potential interest for decontamination of biological fluids such as plasma. As a pilot study to test whether 405 nm light is capable of inactivating bacteria in biological fluids, rabbit plasma and human plasma were seeded with bacteria and treated with a 405 nm light emitting diode (LED) exposure system (patent pending). Inactivation was achieved in all tested samples, ranging from low volumes to prebagged plasma. 99.9% reduction of low density bacterial populations (≤103 CFU mL−1), selected to represent typical “natural” contamination levels, was achieved using doses of 144 Jcm−2. The penetrability of 405 nm light, permitting decontamination of prebagged plasma, and the nonrequirement for photosensitizing agents provide a new proof of concept in bacterial reduction in biological fluids, especially injectable fluids relevant to transfusion medicine. PMID:27774337

Application research of computational mass-transfer differential equation in MBR concentration field simulation.

PubMed

Li, Chunqing; Tie, Xiaobo; Liang, Kai; Ji, Chanjuan

2016-01-01

After conducting the intensive research on the distribution of fluid's velocity and biochemical reactions in the membrane bioreactor (MBR), this paper introduces the use of the mass-transfer differential equation to simulate the distribution of the chemical oxygen demand (COD) concentration in MBR membrane pool. The solutions are as follows: first, use computational fluid dynamics to establish a flow control equation model of the fluid in MBR membrane pool; second, calculate this model by adopting direct numerical simulation to get the velocity field of the fluid in membrane pool; third, combine the data of velocity field to establish mass-transfer differential equation model for the concentration field in MBR membrane pool, and use Seidel iteration method to solve the equation model; last but not least, substitute the real factory data into the velocity and concentration field model to calculate simulation results, and use visualization software Tecplot to display the results. Finally by analyzing the nephogram of COD concentration distribution, it can be found that the simulation result conforms the distribution rule of the COD's concentration in real membrane pool, and the mass-transfer phenomenon can be affected by the velocity field of the fluid in membrane pool. The simulation results of this paper have certain reference value for the design optimization of the real MBR system.

Fluid-Structure Interaction Modeling of Intracranial Aneurysm Hemodynamics: Effects of Different Assumptions

NASA Astrophysics Data System (ADS)

Rajabzadeh Oghaz, Hamidreza; Damiano, Robert; Meng, Hui

2015-11-01

Intracranial aneurysms (IAs) are pathological outpouchings of cerebral vessels, the progression of which are mediated by complex interactions between the blood flow and vasculature. Image-based computational fluid dynamics (CFD) has been used for decades to investigate IA hemodynamics. However, the commonly adopted simplifying assumptions in CFD (e.g. rigid wall) compromise the simulation accuracy and mask the complex physics involved in IA progression and eventual rupture. Several groups have considered the wall compliance by using fluid-structure interaction (FSI) modeling. However, FSI simulation is highly sensitive to numerical assumptions (e.g. linear-elastic wall material, Newtonian fluid, initial vessel configuration, and constant pressure outlet), the effects of which are poorly understood. In this study, a comprehensive investigation of the sensitivity of FSI simulations in patient-specific IAs is investigated using a multi-stage approach with a varying level of complexity. We start with simulations incorporating several common simplifications: rigid wall, Newtonian fluid, and constant pressure at the outlets, and then we stepwise remove these simplifications until the most comprehensive FSI simulations. Hemodynamic parameters such as wall shear stress and oscillatory shear index are assessed and compared at each stage to better understand the sensitivity of in FSI simulations for IA to model assumptions. Supported by the National Institutes of Health (1R01 NS 091075-01).

Simulating single-phase and two-phase non-Newtonian fluid flow of a digital rock scanned at high resolution

NASA Astrophysics Data System (ADS)

Tembely, Moussa; Alsumaiti, Ali M.; Jouini, Mohamed S.; Rahimov, Khurshed; Dolatabadi, Ali

2017-11-01

Most of the digital rock physics (DRP) simulations focus on Newtonian fluids and overlook the detailed description of rock-fluid interaction. A better understanding of multiphase non-Newtonian fluid flow at pore-scale is crucial for optimizing enhanced oil recovery (EOR). The Darcy scale properties of reservoir rocks such as the capillary pressure curves and the relative permeability are controlled by the pore-scale behavior of the multiphase flow. In the present work, a volume of fluid (VOF) method coupled with an adaptive meshing technique is used to perform the pore-scale simulation on a 3D X-ray micro-tomography (CT) images of rock samples. The numerical model is based on the resolution of the Navier-Stokes equations along with a phase fraction equation incorporating the dynamics contact model. The simulations of a single phase flow for the absolute permeability showed a good agreement with the literature benchmark. Subsequently, the code is used to simulate a two-phase flow consisting of a polymer solution, displaying a shear-thinning power law viscosity. The simulations enable to access the impact of the consistency factor (K), the behavior index (n), along with the two contact angles (advancing and receding) on the relative permeability.

Faster Aerodynamic Simulation With Cart3D

NASA Technical Reports Server (NTRS)

2003-01-01

A NASA-developed aerodynamic simulation tool is ensuring the safety of future space operations while providing designers and engineers with an automated, highly accurate computer simulation suite. Cart3D, co-winner of NASA's 2002 Software of the Year award, is the result of over 10 years of research and software development conducted by Michael Aftosmis and Dr. John Melton of Ames Research Center and Professor Marsha Berger of the Courant Institute at New York University. Cart3D offers a revolutionary approach to computational fluid dynamics (CFD), the computer simulation of how fluids and gases flow around an object of a particular design. By fusing technological advancements in diverse fields such as mineralogy, computer graphics, computational geometry, and fluid dynamics, the software provides a new industrial geometry processing and fluid analysis capability with unsurpassed automation and efficiency.

Characterization of 17-4 PH stainless steel foam for biomedical applications in simulated body fluid and artificial saliva environments.

PubMed

Mutlu, Ilven; Oktay, Enver

2013-04-01

Highly porous 17-4 PH stainless steel foam for biomedical applications was produced by space holder technique. Metal release and weight loss from 17-4 PH stainless steel foams was investigated in simulated body fluid and artificial saliva environments by static immersion tests. Inductively coupled plasma-mass spectrometer was employed to measure the concentrations of various metal ions released from the 17-4 PH stainless steel foams into simulated body fluids and artificial saliva. Effect of immersion time and pH value on metal release and weight loss in simulated body fluid and artificial saliva were determined. Pore morphology, pore size and mechanical properties of the 17-4 PH stainless steel foams were close to human cancellous bone. Copyright © 2012 Elsevier B.V. All rights reserved.

Hybrid atomistic simulation of fluid uptake in a deformable solid

NASA Astrophysics Data System (ADS)

Moghadam, Mahyar M.; Rickman, J. M.

2014-01-01

Fluid imbibition via diffusion in a deformable solid results in solid stresses that may, in turn, alter subsequent fluid uptake. To examine this interplay between diffusional and elastic fields, we employed a hybrid Monte Carlo-molecular dynamics scheme to model the coupling of a fluid reservoir to a deformable solid, and then simulated the resulting fluid permeation into the solid. By monitoring the instantaneous structure factor and solid dimensions, we were able to determine the compositional strain associated with imbibition, and the diffusion coefficient in the Fickian regime was obtained from the time dependence of the fluid uptake. Finally, for large, mobile fluid atoms, a non-Fickian regime was highlighted and possible mechanisms for this behavior were identified.

Error and Uncertainty Quantification in the Numerical Simulation of Complex Fluid Flows

NASA Technical Reports Server (NTRS)

Barth, Timothy J.

2010-01-01

The failure of numerical simulation to predict physical reality is often a direct consequence of the compounding effects of numerical error arising from finite-dimensional approximation and physical model uncertainty resulting from inexact knowledge and/or statistical representation. In this topical lecture, we briefly review systematic theories for quantifying numerical errors and restricted forms of model uncertainty occurring in simulations of fluid flow. A goal of this lecture is to elucidate both positive and negative aspects of applying these theories to practical fluid flow problems. Finite-element and finite-volume calculations of subsonic and hypersonic fluid flow are presented to contrast the differing roles of numerical error and model uncertainty. for these problems.

Deep Learning for Flow Sculpting: Insights into Efficient Learning using Scientific Simulation Data

NASA Astrophysics Data System (ADS)

Stoecklein, Daniel; Lore, Kin Gwn; Davies, Michael; Sarkar, Soumik; Ganapathysubramanian, Baskar

2017-04-01

A new technique for shaping microfluid flow, known as flow sculpting, offers an unprecedented level of passive fluid flow control, with potential breakthrough applications in advancing manufacturing, biology, and chemistry research at the microscale. However, efficiently solving the inverse problem of designing a flow sculpting device for a desired fluid flow shape remains a challenge. Current approaches struggle with the many-to-one design space, requiring substantial user interaction and the necessity of building intuition, all of which are time and resource intensive. Deep learning has emerged as an efficient function approximation technique for high-dimensional spaces, and presents a fast solution to the inverse problem, yet the science of its implementation in similarly defined problems remains largely unexplored. We propose that deep learning methods can completely outpace current approaches for scientific inverse problems while delivering comparable designs. To this end, we show how intelligent sampling of the design space inputs can make deep learning methods more competitive in accuracy, while illustrating their generalization capability to out-of-sample predictions.

Modeling Physiological Systems in the Human Body as Networks of Quasi-1D Fluid Flows

NASA Astrophysics Data System (ADS)

Staples, Anne

2008-11-01

Extensive research has been done on modeling human physiology. Most of this work has been aimed at developing detailed, three-dimensional models of specific components of physiological systems, such as a cell, a vein, a molecule, or a heart valve. While efforts such as these are invaluable to our understanding of human biology, if we were to construct a global model of human physiology with this level of detail, computing even a nanosecond in this computational being's life would certainly be prohibitively expensive. With this in mind, we derive the Pulsed Flow Equations, a set of coupled one-dimensional partial differential equations, specifically designed to capture two-dimensional viscous, transport, and other effects, and aimed at providing accurate and fast-to-compute global models for physiological systems represented as networks of quasi one-dimensional fluid flows. Our goal is to be able to perform faster-than-real time simulations of global processes in the human body on desktop computers.

Evaluation of a bio-based hydrophobic cellulose laurate film as biomaterial--study on biodegradation and cytocompatibility.

PubMed

Crépy, Lucie; Monchau, Francine; Chai, Feng; Raoul, Gwénaël; Hivart, Philippe; Hildebrand, Hartmut F; Martin, Patrick; Joly, Nicolas

2012-05-01

The study aims to validate an original bio-based material, obtained by grafting fatty chains, and more especially lauric chains (C12) onto cellulose, for medical applications. The mechanical properties of the synthesized cellulose laurate (C12) are close to those of petrochemical ones such as low density polyethylene. This cellulose-based polymer is transparent, flexible, and hydrophobic. To evaluate the stability of the cellulosic films in biological fluids the samples are soaked in simulated body fluid or blood plasma for a few hours to 6 months, and then submitted to mechanical and chemical analyses. The simultaneously performed cytocompatibility tests were the colony-forming viability, the vitality and cell proliferation tests using NIH 3T3 fibroblasts and MC 3T3 osteoblast-like cells. The results show the stability, the biocompatibility, and the noncytotoxicity of the synthesized cellulose laurate films. This biomaterial may so be considered for surgical applications. Copyright © 2012 Wiley Periodicals, Inc.

Physics-based animation of large-scale splashing liquids, elastoplastic solids, and model-reduced flow

NASA Astrophysics Data System (ADS)

Gerszewski, Daniel James

Physical simulation has become an essential tool in computer animation. As the use of visual effects increases, the need for simulating real-world materials increases. In this dissertation, we consider three problems in physics-based animation: large-scale splashing liquids, elastoplastic material simulation, and dimensionality reduction techniques for fluid simulation. Fluid simulation has been one of the greatest successes of physics-based animation, generating hundreds of research papers and a great many special effects over the last fifteen years. However, the animation of large-scale, splashing liquids remains challenging. We show that a novel combination of unilateral incompressibility, mass-full FLIP, and blurred boundaries is extremely well-suited to the animation of large-scale, violent, splashing liquids. Materials that incorporate both plastic and elastic deformations, also referred to as elastioplastic materials, are frequently encountered in everyday life. Methods for animating such common real-world materials are useful for effects practitioners and have been successfully employed in films. We describe a point-based method for animating elastoplastic materials. Our primary contribution is a simple method for computing the deformation gradient for each particle in the simulation. Given the deformation gradient, we can apply arbitrary constitutive models and compute the resulting elastic forces. Our method has two primary advantages: we do not store or compare to an initial rest configuration and we work directly with the deformation gradient. The first advantage avoids poor numerical conditioning and the second naturally leads to a multiplicative model of deformation appropriate for finite deformations. One of the most significant drawbacks of physics-based animation is that ever-higher fidelity leads to an explosion in the number of degrees of freedom. This problem leads us to the consideration of dimensionality reduction techniques. We present several enhancements to model-reduced fluid simulation that allow improved simulation bases and two-way solid-fluid coupling. Specifically, we present a basis enrichment scheme that allows us to combine data-driven or artistically derived bases with more general analytic bases derived from Laplacian Eigenfunctions. Additionally, we handle two-way solid-fluid coupling in a time-splitting fashion---we alternately timestep the fluid and rigid body simulators, while taking into account the effects of the fluid on the rigid bodies and vice versa. We employ the vortex panel method to handle solid-fluid coupling and use dynamic pressure to compute the effect of the fluid on rigid bodies. Taken together, these contributions have advanced the state-of-the art in physics-based animation and are practical enough to be used in production pipelines.

Thermodynamic modeling of non-ideal mineral-fluid equilibria in the system Si-Al-Fe-Mg-Ca-Na-K-H-O-Cl at elevated temperatures and pressures: Implications for hydrothermal mass transfer in granitic rocks

NASA Astrophysics Data System (ADS)

Dolejš, David; Wagner, Thomas

2008-01-01

We present the results of thermodynamic modeling of fluid-rock interaction in the system Si-Al-Fe-Mg-Ca-Na-H-O-Cl using the GEM-Selektor Gibbs free energy minimization code. Combination of non-ideal mixing properties in solids with multicomponent aqueous fluids represents a substantial improvement and it provides increased accuracy over existing modeling strategies. Application to the 10-component system allows us to link fluid composition and speciation with whole-rock mineralogy, mass and volume changes. We have simulated granite-fluid interaction over a wide range of conditions (200-600 °C, 100 MPa, 0-5 m Cl and fluid/rock ratios of 10-2-104) in order to explore composition of magmatic fluids of variable salinity, temperature effects on fluid composition and speciation and to simulate several paths of alteration zoning. At low fluid/rock ratios (f/r) the fluid composition is buffered by the silicate-oxide assemblage and remains close to invariant. This behavior extends to a f/r of 0.1 which exceeds the amount of exsolved magmatic fluids controlled by water solubility in silicate melts. With increasing peraluminosity of the parental granite, the Na-, K- and Fe-bearing fluids become more acidic and the oxidation state increases as a consequence of hydrogen and ferrous iron transfer to the fluid. With decreasing temperature, saline fluids become more Ca- and Na-rich, change from weakly acidic to alkaline, and become significantly more oxidizing. Large variations in Ca/Fe and Ca/Mg ratios in the fluid are a potential geothermometer. The mineral assemblage changes from cordierite-biotite granites through two-mica granites to chlorite-, epidote- and zeolite-bearing rocks. We have carried out three rock-titration simulations: (1) reaction with the 2 m NaCl fluid leads to albitization, chloritization and desilication, reproducing essential features observed in episyenites, (2) infiltration of a high-temperature fluid into the granite at 400 °C leads to hydrolytic alteration commencing with alkali-feldspar breakdown and leading to potassic, phyllic and argillic assemblages; this is associated with reduction and iron metasomatism as observed in nature and (3) interaction with a multicomponent fluid at 600 °C produces sodic-calcic metasomatism. Na, Ca and Fe are the most mobile elements whereas immobility of Al is limited by f/r ∼ 400. All simulations predict a volume decrease by 3.4-5.4%, i.e., porosity formation at f/r < 30. At higher fluid/rock ratios simulation (2) produces a substantial volume increase (59%) due to mineral precipitation, whereas simulation (3) predicts a volume decrease by 49% at the advanced albitization-desilication stage. Volume changes closely correlate with mass changes of SiO2 and are related to silica solubility in fluids. The combined effects of oxygen fugacity, fluid acidity and pH for breakdown of aqueous metal complexes and precipitation of ore minerals were evaluated by means of reduced activity products. Sharp increases in saturation indexes for oxidative breakdown occur at each alteration zone whereas reductive breakdown or involvement of other chloride complexes favor precipitation at high fluid/rock ratios only. Calculations of multicomponent aqueous-solid equilibria at high temperatures and pressures are able to accurately predict rock mineralogy and fluid chemistry and are applicable to diverse reactive flow processes in the Earth's crust.

Controlled release of anticancer drug methotrexate from biodegradable gelatin microspheres.

PubMed

Narayani, R; Rao, K P

1994-01-01

Biodegradable hydrophilic gelatin microspheres containing the anticancer drug methotrexate (MTX) of different mean particle sizes (1-5, 5-10, and 15-20 microns) were prepared by polymer dispersion technique and crosslinked with glutaraldehyde. The microspheres were uniform, smooth, solid and in the form of free-flowing powder. About 80 per cent of MTX was incorporated in gelatin microspheres of different sizes. The in vitro release of MTX was investigated in two different media, namely simulated gastric and intestinal fluids. The release profiles indicated that gelatin microspheres released MTX in a zero-order fashion for 4-6 days in simulated gastric fluid and for 5-8 days in simulated intestinal fluid. The rate of release of MTX decreased with increase in the particle size of the microspheres. MTX release was faster in gastric fluid when compared to intestinal fluid.

Evaluation and correction for optical scattering variations in laser speckle rheology of biological fluids.

PubMed

Hajjarian, Zeinab; Nadkarni, Seemantini K

2013-01-01

Biological fluids fulfill key functionalities such as hydrating, protecting, and nourishing cells and tissues in various organ systems. They are capable of these versatile tasks owing to their distinct structural and viscoelastic properties. Characterizing the viscoelastic properties of bio-fluids is of pivotal importance for monitoring the development of certain pathologies as well as engineering synthetic replacements. Laser Speckle Rheology (LSR) is a novel optical technology that enables mechanical evaluation of tissue. In LSR, a coherent laser beam illuminates the tissue and temporal speckle intensity fluctuations are analyzed to evaluate mechanical properties. The rate of temporal speckle fluctuations is, however, influenced by both optical and mechanical properties of tissue. Therefore, in this paper, we develop and validate an approach to estimate and compensate for the contributions of light scattering to speckle dynamics and demonstrate the capability of LSR for the accurate extraction of viscoelastic moduli in phantom samples and biological fluids of varying optical and mechanical properties.

Evaluation and Correction for Optical Scattering Variations in Laser Speckle Rheology of Biological Fluids

PubMed Central

Hajjarian, Zeinab; Nadkarni, Seemantini K.

2013-01-01

Biological fluids fulfill key functionalities such as hydrating, protecting, and nourishing cells and tissues in various organ systems. They are capable of these versatile tasks owing to their distinct structural and viscoelastic properties. Characterizing the viscoelastic properties of bio-fluids is of pivotal importance for monitoring the development of certain pathologies as well as engineering synthetic replacements. Laser Speckle Rheology (LSR) is a novel optical technology that enables mechanical evaluation of tissue. In LSR, a coherent laser beam illuminates the tissue and temporal speckle intensity fluctuations are analyzed to evaluate mechanical properties. The rate of temporal speckle fluctuations is, however, influenced by both optical and mechanical properties of tissue. Therefore, in this paper, we develop and validate an approach to estimate and compensate for the contributions of light scattering to speckle dynamics and demonstrate the capability of LSR for the accurate extraction of viscoelastic moduli in phantom samples and biological fluids of varying optical and mechanical properties. PMID:23705028

Sizing nanomaterials in bio-fluids by cFRAP enables protein aggregation measurements and diagnosis of bio-barrier permeability

NASA Astrophysics Data System (ADS)

Xiong, Ranhua; Vandenbroucke, Roosmarijn E.; Broos, Katleen; Brans, Toon; van Wonterghem, Elien; Libert, Claude; Demeester, Jo; de Smedt, Stefaan C.; Braeckmans, Kevin

2016-09-01

Sizing nanomaterials in complex biological fluids, such as blood, remains a great challenge in spite of its importance for a wide range of biomedical applications. In drug delivery, for instance, it is essential that aggregation of protein-based drugs is avoided as it may alter their efficacy or elicit immune responses. Similarly it is of interest to determine which size of molecules can pass through biological barriers in vivo to diagnose pathologies, such as sepsis. Here, we report on continuous fluorescence recovery after photobleaching (cFRAP) as a analytical method enabling size distribution measurements of nanomaterials (1-100 nm) in undiluted biological fluids. We demonstrate that cFRAP allows to measure protein aggregation in human serum and to determine the permeability of intestinal and vascular barriers in vivo. cFRAP is a new analytical technique that paves the way towards exciting new applications that benefit from nanomaterial sizing in bio-fluids.

A sealed capsule system for biological and liquid shock-recovery experiments.

PubMed

Leighs, James A; Appleby-Thomas, Gareth J; Stennett, Chris; Hameed, Amer; Wilgeroth, James M; Hazell, Paul J

2012-11-01

This paper presents an experimental method designed to one-dimensionally shock load and subsequently recover liquid samples. Resultant loading profiles have been interrogated via hydrocode simulation as the nature of the target did not allow for direct application of the diagnostics typically employed in shock physics (e.g., manganin stress gauges or Heterodyne velocimeter (Het-V)). The target setup has been experimentally tested using aluminium flyer plates accelerated by a 50-mm bore single-stage gas-gun reaching projectile impact velocities of up to ~500 ms(-1) (corresponding to peak pressures of up to ca. 4 GPa being experienced by fluid samples). Recovered capsules survived well showing only minor signs of damage. Modelled gauge traces have been validated through the use of a (slightly modified) experiment in which a Het-V facing the rear of the inner capsule was employed. In these tests, good correlation between simulated and experimental traces was observed.

A sealed capsule system for biological and liquid shock-recovery experiments

NASA Astrophysics Data System (ADS)

Leighs, James A.; Appleby-Thomas, Gareth J.; Stennett, Chris; Hameed, Amer; Wilgeroth, James M.; Hazell, Paul J.

2012-11-01

This paper presents an experimental method designed to one-dimensionally shock load and subsequently recover liquid samples. Resultant loading profiles have been interrogated via hydrocode simulation as the nature of the target did not allow for direct application of the diagnostics typically employed in shock physics (e.g., manganin stress gauges or Heterodyne velocimeter (Het-V)). The target setup has been experimentally tested using aluminium flyer plates accelerated by a 50-mm bore single-stage gas-gun reaching projectile impact velocities of up to ˜500 ms-1 (corresponding to peak pressures of up to ca. 4 GPa being experienced by fluid samples). Recovered capsules survived well showing only minor signs of damage. Modelled gauge traces have been validated through the use of a (slightly modified) experiment in which a Het-V facing the rear of the inner capsule was employed. In these tests, good correlation between simulated and experimental traces was observed.

Guided self-assembly of magnetic beads for biomedical applications

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Nguyen, Ha; Reichel, Franz; Exl, Lukas; Bance, Simon; Fischbacher, Johann; Özelt, Harald; Kovacs, Alexander; Brandl, Martin; Schrefl, Thomas

2014-02-01

Micromagnetic beads are widely used in biomedical applications for cell separation, drug delivery, and hyperthermia cancer treatment. Here we propose to use self-organized magnetic bead structures which accumulate on fixed magnetic seeding points to isolate circulating tumor cells. The analysis of circulating tumor cells is an emerging tool for cancer biology research and clinical cancer management including the detection, diagnosis and monitoring of cancer. Microfluidic chips for isolating circulating tumor cells use either affinity, size or density capturing methods. We combine multiphysics simulation techniques to understand the microscopic behavior of magnetic beads interacting with soft magnetic accumulation points used in lab-on-chip technologies. Our proposed chip technology offers the possibility to combine affinity and size capturing with special antibody-coated bead arrangements using a magnetic gradient field created by Neodymium Iron Boron permanent magnets. The multiscale simulation environment combines magnetic field computation, fluid dynamics and discrete particle dynamics.

Fluid pressure responses for a Devil's Slide-like system: problem formulation and simulation

USGS Publications Warehouse

Thomas, Matthew A.; Loague, Keith; Voss, Clifford I.

2015-01-01

This study employs a hydrogeologic simulation approach to investigate subsurface fluid pressures for a landslide-prone section of the central California, USA, coast known as Devil's Slide. Understanding the relative changes in subsurface fluid pressures is important for systems, such as Devil's Slide, where slope creep can be interrupted by episodic slip events. Surface mapping, exploratory core, tunnel excavation records, and dip meter data were leveraged to conceptualize the parameter space for three-dimensional (3D) Devil's Slide-like simulations. Field observations (i.e. seepage meter, water retention, and infiltration experiments; well records; and piezometric data) and groundwater flow simulation (i.e. one-dimensional vertical, transient, and variably saturated) were used to design the boundary conditions for 3D Devil's Slide-like problems. Twenty-four simulations of steady-state saturated subsurface flow were conducted in a concept-development mode. Recharge, heterogeneity, and anisotropy are shown to increase fluid pressures for failure-prone locations by up to 18.1, 4.5, and 1.8% respectively. Previous estimates of slope stability, driven by simple water balances, are significantly improved upon with the fluid pressures reported here. The results, for a Devil's Slide-like system, provide a foundation for future investigations

Smoothed Particle Hydrodynamics: A consistent model for interfacial multiphase fluid flow simulations

NASA Astrophysics Data System (ADS)

Krimi, Abdelkader; Rezoug, Mehdi; Khelladi, Sofiane; Nogueira, Xesús; Deligant, Michael; Ramírez, Luis

2018-04-01

In this work, a consistent Smoothed Particle Hydrodynamics (SPH) model to deal with interfacial multiphase fluid flows simulation is proposed. A modification to the Continuum Stress Surface formulation (CSS) [1] to enhance the stability near the fluid interface is developed in the framework of the SPH method. A non-conservative first-order consistency operator is used to compute the divergence of stress surface tensor. This formulation benefits of all the advantages of the one proposed by Adami et al. [2] and, in addition, it can be applied to more than two phases fluid flow simulations. Moreover, the generalized wall boundary conditions [3] are modified in order to be well adapted to multiphase fluid flows with different density and viscosity. In order to allow the application of this technique to wall-bounded multiphase flows, a modification of generalized wall boundary conditions is presented here for using the SPH method. In this work we also present a particle redistribution strategy as an extension of the damping technique presented in [3] to smooth the initial transient phase of gravitational multiphase fluid flow simulations. Several computational tests are investigated to show the accuracy, convergence and applicability of the proposed SPH interfacial multiphase model.

Flexible Inhibitor Fluid-Structure Interaction Simulation in RSRM.

NASA Astrophysics Data System (ADS)

Wasistho, Bono

2005-11-01

We employ our tightly coupled fluid/structure/combustion simulation code 'Rocstar-3' for solid propellant rocket motors to study 3D flows past rigid and flexible inhibitors in the Reusable Solid Rocket Motor (RSRM). We perform high resolution simulations of a section of the rocket near the center joint slot at 100 seconds after ignition, using inflow conditions based on less detailed 3D simulations of the full RSRM. Our simulations include both inviscid and turbulent flows (using LES dynamic subgrid-scale model), and explore the interaction between the inhibitor and the resulting fluid flow. The response of the solid components is computed by an implicit finite element solver. The internal mesh motion scheme in our block-structured fluid solver enables our code to handle significant changes in geometry. We compute turbulent statistics and determine the compound instabilities originated from the natural hydrodynamic instabilities and the inhibitor motion. The ultimate goal is to studdy the effect of inhibitor flexing on the turbulent field.

Responses, applications, and analysis of microgravity effects on bacteria

NASA Astrophysics Data System (ADS)

Benoit, Michael Robert

Spaceflight causes many changes to the growth and behavior of bacteria, most likely because of microgravity. However, we do not fully understand the gravity-dependent mechanisms that alter bacterial cell physiology. Furthermore, the literature consists of many contradictory results, creating controversy over the mechanisms by which spaceflight affects bacterial cultures. The research described in this dissertation combines empirical, analytical, and numerical modeling techniques aimed at characterizing the various gravity-dependent phenomena that act on bacteria. While reviewing the literature, I identified an interesting trend in prior experimental results regarding bacterial motility. With this information, we can begin to explain some of the seemingly contradictory findings. This discovery should help to resolve several controversial theories in the field of space microbiology. Chapter 3 describes a microbial antibiotic production experiment conducted onboard the International Space Station. The results corroborated earlier findings of increased antibiotic production for samples taken during the first two weeks of spaceflight. For later samples, however, a reversal occurred, showing decreased production in the spaceflight samples. This insight highlights the benefit of conducting long duration experiments in space to fully evaluate biological responses. Chapter 4 describes a novel technique for preventing bacterial cell sedimentation to partially simulate microgravity in ground-based experiments. The results of this study showed a correlation between cell sedimentation and bacterial growth. As documented in Chapter 5, I investigated the use of digital holographic interferometry to measure extracellular fluid density changes caused by bacterial metabolism. The results showed that fluid density changes surrounding individual bacteria were too small to measure directly. Therefore, I used mathematical analyses and numerical model simulations (described in Chapter 6) to evaluate changes in extracellular fluid density on convective mass transport. From the theoretical analysis results, I predicted convective and diffusive transport regimes for bacteria grown under microgravity, 1 g, and hyper-gravity conditions. Finally, using a numerical model, I successfully simulated an experimentally observed phenomenon of buoyancy-driven convection created by cellular metabolism.

A critical review of approaches and limitations of inhalation bioavailability and bioaccessibility of metal(loid)s from ambient particulate matter or dust.

PubMed

Kastury, Farzana; Smith, Euan; Juhasz, Albert L

2017-01-01

Inhalation of metal(loid)s in ambient particulate matter (APM) represents a significant exposure pathway to humans. Although exposure assessment associated with this pathway is currently based on total metal(loid) content, a bioavailability (i.e. absorption in the systemic circulation) and/or bioaccessibility (i.e. solubility in simulated lung fluid) based approach may more accurately quantify exposure. Metal(loid) bioavailability-bioaccessibility assessment from APM is inherently complex and lacks consensus. This paper reviews the discrepancies that impede the adoption of a universal protocol for the assessment of inhalation bioaccessibility. Exposure assessment approaches for in-vivo bioavailability, in-vitro cell culture and in-vitro bioaccessibility (composition of simulated lungs fluid, physico-chemical and methodological considerations) are critiqued in the context of inhalation exposure refinement. An important limitation of bioavailability and bioaccessibility studies is the use of considerably higher than environmental metal(loid) concentration, which diminishing their relevance to human exposure scenarios. Similarly, individual metal(loid) studies have been criticised due to complexities of APM metal(loid) mixtures which may impart synergistic or antagonistic effects compared to single metal(loid) exposure. Although a number of different simulated lung fluid (SLF) compositions have been used in metal(loid) bioaccessibility studies, information regarding the comparative leaching efficiency among these different SLF and comparisons to in-vivo bioavailability data is lacking. In addition, the particle size utilised is often not representative of what is deposited in the lungs while assay parameters (extraction time, solid to liquid ratio, temperature and agitation) are often not biologically relevant. Research needs are identified in order to develop robust in-vitro bioaccessibility protocols for the assessment or prediction of metal(loid) bioavailability in APM for the refinement of inhalation exposure. Copyright © 2016 Elsevier B.V. All rights reserved.

A heterogeneous system based on GPU and multi-core CPU for real-time fluid and rigid body simulation

NASA Astrophysics Data System (ADS)

da Silva Junior, José Ricardo; Gonzalez Clua, Esteban W.; Montenegro, Anselmo; Lage, Marcos; Dreux, Marcelo de Andrade; Joselli, Mark; Pagliosa, Paulo A.; Kuryla, Christine Lucille

2012-03-01

Computational fluid dynamics in simulation has become an important field not only for physics and engineering areas but also for simulation, computer graphics, virtual reality and even video game development. Many efficient models have been developed over the years, but when many contact interactions must be processed, most models present difficulties or cannot achieve real-time results when executed. The advent of parallel computing has enabled the development of many strategies for accelerating the simulations. Our work proposes a new system which uses some successful algorithms already proposed, as well as a data structure organisation based on a heterogeneous architecture using CPUs and GPUs, in order to process the simulation of the interaction of fluids and rigid bodies. This successfully results in a two-way interaction between them and their surrounding objects. As far as we know, this is the first work that presents a computational collaborative environment which makes use of two different paradigms of hardware architecture for this specific kind of problem. Since our method achieves real-time results, it is suitable for virtual reality, simulation and video game fluid simulation problems.

Labyrinth and cerebral-spinal fluid pressure changes in guinea pigs and monkeys during simulated zero G

NASA Technical Reports Server (NTRS)

Parker, D. E.

1977-01-01

This study was undertaken to explore the hypothesis that shifts of body fluids from the legs and torso toward the head contribute to the motion sickness experienced by astronauts and cosmonauts. The shifts in body fluids observed during zero-G exposure were simulated by elevating guinea pigs' and monkeys' torsos and hindquarters. Cerebral-spinal fluid pressure was recorded from a transducer located in a brain ventricle; labyrinth fluid pressure was recorded from a pipette cemented in a hole in a semicircular canal. An anticipated divergence in cerebral-spinal fluid pressure and labyrinth fluid pressure during torso elevation was not observed. The results of this study do not support a fluid shift mechanism of zero-G-induced motion sickness. However, a more complete test of the fluid shift mechanism would be obtained if endolymph and perilymph pressure changes were determined separately; we have been unable to perform this test to date.

Diffusion-controlled reactions modeling in Geant4-DNA

NASA Astrophysics Data System (ADS)

Karamitros, M.; Luan, S.; Bernal, M. A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H. N.; Stepan, V.; Incerti, S.

2014-10-01

Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k-d tree data structure for quickly locating, for a given molecule, its closest reactants. The performance advantage is presented in terms of complexity, and the accuracy of the new algorithm is demonstrated by simulating radiation chemistry in the context of the Geant4-DNA project. Application The time-dependent radiolytic yields of the main chemical species formed after irradiation are computed for incident protons at different energies (from 50 MeV to 500 keV). Both the time-evolution and energy dependency of the yields are discussed. The evolution, at one microsecond, of the yields of hydroxyls and solvated electrons with respect to the linear energy transfer is compared to theoretical and experimental data. According to our results, at high linear energy transfer, modeling radiation chemistry in the trading compartment representation might be adopted.

Comparison of competing segmentation standards for X-ray computed topographic imaging using Lattice Boltzmann techniques

NASA Astrophysics Data System (ADS)

Larsen, J. D.; Schaap, M. G.

2013-12-01

Recent advances in computing technology and experimental techniques have made it possible to observe and characterize fluid dynamics at the micro-scale. Many computational methods exist that can adequately simulate fluid flow in porous media. Lattice Boltzmann methods provide the distinct advantage of tracking particles at the microscopic level and returning macroscopic observations. While experimental methods can accurately measure macroscopic fluid dynamics, computational efforts can be used to predict and gain insight into fluid dynamics by utilizing thin sections or computed micro-tomography (CMT) images of core sections. Although substantial effort have been made to advance non-invasive imaging methods such as CMT, fluid dynamics simulations, and microscale analysis, a true three dimensional image segmentation technique has not been developed until recently. Many competing segmentation techniques are utilized in industry and research settings with varying results. In this study lattice Boltzmann method is used to simulate stokes flow in a macroporous soil column. Two dimensional CMT images were used to reconstruct a three dimensional representation of the original sample. Six competing segmentation standards were used to binarize the CMT volumes which provide distinction between solid phase and pore space. The permeability of the reconstructed samples was calculated, with Darcy's Law, from lattice Boltzmann simulations of fluid flow in the samples. We compare simulated permeability from differing segmentation algorithms to experimental findings.

Measurement with microscopic MRI and simulation of flow in different aneurysm models.

PubMed

Edelhoff, Daniel; Walczak, Lars; Frank, Frauke; Heil, Marvin; Schmitz, Inge; Weichert, Frank; Suter, Dieter

2015-10-01

The impact and the development of aneurysms depend to a significant degree on the exchange of liquid between the regular vessel and the pathological extension. A better understanding of this process will lead to improved prediction capabilities. The aim of the current study was to investigate fluid-exchange in aneurysm models of different complexities by combining microscopic magnetic resonance measurements with numerical simulations. In order to evaluate the accuracy and applicability of these methods, the fluid-exchange process between the unaltered vessel lumen and the aneurysm phantoms was analyzed quantitatively using high spatial resolution. Magnetic resonance flow imaging was used to visualize fluid-exchange in two different models produced with a 3D printer. One model of an aneurysm was based on histological findings. The flow distribution in the different models was measured on a microscopic scale using time of flight magnetic resonance imaging. The whole experiment was simulated using fast graphics processing unit-based numerical simulations. The obtained simulation results were compared qualitatively and quantitatively with the magnetic resonance imaging measurements, taking into account flow and spin-lattice relaxation. The results of both presented methods compared well for the used aneurysm models and the chosen flow distributions. The results from the fluid-exchange analysis showed comparable characteristics concerning measurement and simulation. Similar symmetry behavior was observed. Based on these results, the amount of fluid-exchange was calculated. Depending on the geometry of the models, 7% to 45% of the liquid was exchanged per second. The result of the numerical simulations coincides well with the experimentally determined velocity field. The rate of fluid-exchange between vessel and aneurysm was well-predicted. Hence, the results obtained by simulation could be validated by the experiment. The observed deviations can be caused by the noise in the measurement and by the limited resolution of the simulation. The resulting differences are small enough to allow reliable predictions of the flow distribution in vessels with stents and for pulsed blood flow.

Invasion-Flowback Processes During Hydraulic Fracturing Well Interference

NASA Astrophysics Data System (ADS)

Kenzhekhanov, Shaken; He, Kai; Xu, Liang; Lord, Paul; Lozano, Martin; Neeves, Keith; Yin, Xiaolong

2017-11-01

Drainage-imbibition cycles that simulate hydraulic fracturing fluid's invasion and flowback during well interference were investigated using NOA81 microfluidic micromodels. Well interference is quite common in unconventional oil and gas fields. It is not unusual for the fracturing fluid injected into a well to be discovered in a nearby well. Normally, the effect of such interference is considered to be negative, as fracturing fluid will be imbibed into the porous rock and block the flow path of hydrocarbons. However, field data show that some interferences are beneficial, and microfluidic experiments presented in this study show that surfactant in the fracturing fluid may be a reason for the observed positive interference. Two fluid drainage-imbibition cycles were conducted in micromodels. The first cycle simulates fracturing of the old well and the second cycle simulates fluid invasion from the new well into the old well's fracture network. The experimental data show that while most such interferences indeed can cause production loss, when the old well's fracturing fluid does not contain surfactant yet the new well's fracturing fluid does, interference can be positive, as the residual water saturation in the porous medium is effectively reduced by surfactants.

The Use of Computational Fluid Dynamics in the Development of Ventricular Assist Devices

PubMed Central

Fraser, Katharine H.; Taskin, M. Ertan; Griffith, Bartley P.; Wu, Zhongjun J.

2010-01-01

Progress in the field of prosthetic cardiovascular devices has significantly contributed to the rapid advancements in cardiac therapy during the last four decades. The concept of mechanical circulatory assistance was established with the first successful clinical use of heart-lung machines for cardiopulmonary bypass. Since then a variety of devices have been developed to replace or assist diseased components of the cardiovascular system. Ventricular assist devices (VADs) are basically mechanical pumps designed to augment or replace the function of one or more chambers of the failing heart. Computational Fluid Dynamics (CFD) is an attractive tool in the development process of VADs, allowing numerous different designs to be characterized for their functional performance virtually, for a wide range of operating conditions, without the physical device being fabricated. However, VADs operate in a flow regime which is traditionally difficult to simulate; the transitional region at the boundary of laminar and turbulent flow. Hence different methods have been used and the best approach is debatable. In addition to these fundamental fluid dynamic issues, blood consists of biological cells. Device-induced biological complications are a serious consequence of VAD use. The complications include blood damage (haemolysis, blood cell activation), thrombosis and emboli. Patients are required to take anticoagulation medication constantly which may cause bleeding. Despite many efforts blood damage models have still not been implemented satisfactorily into numerical analysis of VADs, which severely undermines the full potential of CFD. This paper reviews the current state of the art CFD for analysis of blood pumps, including a practical critical review of the studies to date, which should help device designers choose the most appropriate methods; a summary of blood damage models and the difficulties in implementing them into CFD; and current gaps in knowledge and areas for future work. PMID:21075669

Vapor-liquid equilibrium and critical asymmetry of square well and short square well chain fluids.

PubMed

Li, Liyan; Sun, Fangfang; Chen, Zhitong; Wang, Long; Cai, Jun

2014-08-07

The critical behavior of square well fluids with variable interaction ranges and of short square well chain fluids have been investigated by grand canonical ensemble Monte Carlo simulations. The critical temperatures and densities were estimated by a finite-size scaling analysis with the help of histogram reweighting technique. The vapor-liquid coexistence curve in the near-critical region was determined using hyper-parallel tempering Monte Carlo simulations. The simulation results for coexistence diameters show that the contribution of |t|(1-α) to the coexistence diameter dominates the singular behavior in all systems investigated. The contribution of |t|(2β) to the coexistence diameter is larger for the system with a smaller interaction range λ. While for short square well chain fluids, longer the chain length, larger the contribution of |t|(2β). The molecular configuration greatly influences the critical asymmetry: a short soft chain fluid shows weaker critical asymmetry than a stiff chain fluid with same chain length.

An experimental and finite element poroelastic creep response analysis of an intervertebral hydrogel disc model in axial compression.

PubMed

Silva, P; Crozier, S; Veidt, M; Pearcy, M J

2005-07-01

A hydrogel intervertebral disc (IVD) model consisting of an inner nucleus core and an outer anulus ring was manufactured from 30 and 35% by weight Poly(vinyl alcohol) hydrogel (PVA-H) concentrations and subjected to axial compression in between saturated porous endplates at 200 N for 11 h, 30 min. Repeat experiments (n=4) on different samples (N=2) show good reproducibility of fluid loss and axial deformation. An axisymmetric nonlinear poroelastic finite element model with variable permeability was developed using commercial finite element software to compare axial deformation and predicted fluid loss with experimental data. The FE predictions indicate differential fluid loss similar to that of biological IVDs, with the nucleus losing more water than the anulus, and there is overall good agreement between experimental and finite element predicted fluid loss. The stress distribution pattern indicates important similarities with the biological IVD that includes stress transference from the nucleus to the anulus upon sustained loading and renders it suitable as a model that can be used in future studies to better understand the role of fluid and stress in biological IVDs.

Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Voulgarakis, Nikolaos K.; Satish, Siddarth; Chu, Jhih-Wei

2009-12-01

A multiscale computational method is developed to model the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulations. To capture the elastic responses that emerge at small length scales, we attach an additional rheological model parallel to the macroscopic constitutive equation of a fluid. The widely used linear Maxwell model is employed as a working choice; other models can be used as well. For a fluid that is Newtonian in the macroscopic limit, this approach results in a parallel Newtonian-Maxwell model. For water, argon, and an ionic liquid, the power spectrum of momentum field autocorrelation functions of the parallel Newtonian-Maxwell model agrees very well with those calculated from all-atom MD simulations. To incorporate thermal fluctuations, we generalize the equations of FHD to work with non-Markovian rheological models and colored noise. The fluctuating stress tensor (white noise) is integrated in time in the same manner as its dissipative counterpart and numerical simulations indicate that this approach accurately preserves the set temperature in a FHD simulation. By mapping position and velocity vectors in the molecular representation onto field variables, we bridge the non-Markovian FHD with atomistic MD simulations. Through this mapping, we quantitatively determine the transport coefficients of the parallel Newtonian-Maxwell model for water and argon from all-atom MD simulations. For both fluids, a significant enhancement in elastic responses is observed as the wave number of hydrodynamic modes is reduced to a few nanometers. The mapping from particle to field representations and the perturbative strategy of developing constitutive equations provide a useful framework for modeling the nanoscale viscoelasticity of fluids.

Proteomic analysis of Bombyx mori molting fluid: Insights into the molting process.

PubMed

Liu, Hua-Wei; Wang, Luo-Ling; Tang, Xin; Dong, Zhao-Ming; Guo, Peng-Chao; Zhao, Dong-Chao; Xia, Qing-You; Zhao, Ping

2018-02-20

Molting is an essential biological process occurring multiple times throughout the life cycle of most Ecdysozoa. Molting fluids accumulate and function in the exuvial space during the molting process. In this study, we used liquid chromatography-tandem mass spectrometry to investigate the molting fluids to analyze the molecular mechanisms of molting in the silkworm, Bombyx mori. In total, 375 proteins were identified in molting fluids from the silkworm at 14-16h before pupation and eclosion, including 12 chitin metabolism-related enzymes, 35 serine proteases, 15 peptidases, and 38 protease inhibitors. Gene ontology analysis indicated that "catalytic" constitutes the most enriched function in the molting fluid. Gene expression patterns and bioinformatic analyses suggested that numerous enzymes are involved in the degradation of cuticle proteins and chitin. Protein-protein interaction network and activity analyses showed that protease inhibitors are involved in the regulation of multiple pathways in molting fluid. Additionally, many immune-related proteins may be involved in the immune defense during molting. These results provide a comprehensive proteomic insight into proteolytic enzymes and protease inhibitors in molting fluid, and will likely improve the current understanding of physiological processes in insect molting. Insect molting constitutes a dynamic physiological process. To better understand this process, we used LC-MS/MS to investigate the proteome of silkworm molting fluids and identified key proteins involved in silkworm molting. The biological processes of the old cuticle degradation pathway and immune defense response were analyzed in the proteome of silkworm molting fluid. We report that protease inhibitors serve as key factors in the regulation of the molting process. The proteomic results provide new insight into biological molting processes in insects. Copyright © 2017 Elsevier B.V. All rights reserved.

A closed-form analytical model for predicting 3D boundary layer displacement thickness for the validation of viscous flow solvers

NASA Astrophysics Data System (ADS)

Kumar, V. R. Sanal; Sankar, Vigneshwaran; Chandrasekaran, Nichith; Saravanan, Vignesh; Natarajan, Vishnu; Padmanabhan, Sathyan; Sukumaran, Ajith; Mani, Sivabalan; Rameshkumar, Tharikaa; Nagaraju Doddi, Hema Sai; Vysaprasad, Krithika; Sharan, Sharad; Murugesh, Pavithra; Shankar, S. Ganesh; Nejaamtheen, Mohammed Niyasdeen; Baskaran, Roshan Vignesh; Rahman Mohamed Rafic, Sulthan Ariff; Harisrinivasan, Ukeshkumar; Srinivasan, Vivek

2018-02-01

A closed-form analytical model is developed for estimating the 3D boundary-layer-displacement thickness of an internal flow system at the Sanal flow choking condition for adiabatic flows obeying the physics of compressible viscous fluids. At this unique condition the boundary-layer blockage induced fluid-throat choking and the adiabatic wall-friction persuaded flow choking occur at a single sonic-fluid-throat location. The beauty and novelty of this model is that without missing the flow physics we could predict the exact boundary-layer blockage of both 2D and 3D cases at the sonic-fluid-throat from the known values of the inlet Mach number, the adiabatic index of the gas and the inlet port diameter of the internal flow system. We found that the 3D blockage factor is 47.33 % lower than the 2D blockage factor with air as the working fluid. We concluded that the exact prediction of the boundary-layer-displacement thickness at the sonic-fluid-throat provides a means to correctly pinpoint the causes of errors of the viscous flow solvers. The methodology presented herein with state-of-the-art will play pivotal roles in future physical and biological sciences for a credible verification, calibration and validation of various viscous flow solvers for high-fidelity 2D/3D numerical simulations of real-world flows. Furthermore, our closed-form analytical model will be useful for the solid and hybrid rocket designers for the grain-port-geometry optimization of new generation single-stage-to-orbit dual-thrust-motors with the highest promising propellant loading density within the given envelope without manifestation of the Sanal flow choking leading to possible shock waves causing catastrophic failures.

Evaluation of Working Fluids for Organic Rankine Cycle Based on Exergy Analysis

NASA Astrophysics Data System (ADS)

Setiawan, D.; Subrata, I. D. M.; Purwanto, Y. A.; Tambunan, A. H.

2018-05-01

One of the crucial aspects to determine the performance of Organic Rankine Cycle (ORC) is the selection of appropriate working fluids. This paper describes the simulative performance of several organic fluid and water as working fluid of an ORC based on exergy analysis with a heat source from waste heat recovery. The simulation was conducted by using Engineering Equation Solver (EES). The effect of several parameters and thermodynamic properties of working fluid was analyzed, and part of them was used as variables for the simulation in order to determine their sensitivity to the exergy efficiency changes. The results of this study showed that water is not appropriate to be used as working fluid at temperature lower than 130 °C, because the expansion process falls in saturated area. It was also found that Benzene had the highest exergy efficiency, i.e. about 10.49%, among the dry type working fluid. The increasing turbine inlet temperature did not lead to the increase of exergy efficiency when using organic working fluids with critical temperature near heat source temperature. Meanwhile, exergy efficiency decreasing linearly with the increasing condenser inlet temperature. In addition, it was found that working fluid with high latent heat of vaporization and specific heat exert in high exergy efficiency.

Particles at fluid-fluid interfaces: A new Navier-Stokes-Cahn-Hilliard surface- phase-field-crystal model.

PubMed

Aland, Sebastian; Lowengrub, John; Voigt, Axel

2012-10-01

Colloid particles that are partially wetted by two immiscible fluids can become confined to fluid-fluid interfaces. At sufficiently high volume fractions, the colloids may jam and the interface may crystallize. The fluids together with the interfacial colloids form an emulsion with interesting material properties and offer an important route to new soft materials. A promising approach to simulate these emulsions was presented in Aland et al. [Phys. Fluids 23, 062103 (2011)], where a Navier-Stokes-Cahn-Hilliard model for the macroscopic two-phase fluid system was combined with a surface phase-field-crystal model for the microscopic colloidal particles along the interface. Unfortunately this model leads to spurious velocities which require very fine spatial and temporal resolutions to accurately and stably simulate. In this paper we develop an improved Navier-Stokes-Cahn-Hilliard-surface phase-field-crystal model based on the principles of mass conservation and thermodynamic consistency. To validate our approach, we derive a sharp interface model and show agreement with the improved diffuse interface model. Using simple flow configurations, we show that the new model has much better properties and does not lead to spurious velocities. Finally, we demonstrate the solid-like behavior of the crystallized interface by simulating the fall of a solid ball through a colloid-laden multiphase fluid.

Study report on modification of the long term circulatory model for the simulation of bed rest

NASA Technical Reports Server (NTRS)

Leonard, J. I.; Grounds, D. J.

1977-01-01

Modifications were made of the circulatory, fluid, and electrolyte control model which was based on the model of Guyton. The modifications included separate leg compartments and the addition of gravity dependency. It was found that these modifications allowed for more accurate bed rest simulation by simulating changes in the orthostatic gradient and simulating the response to the fluid shifts associated with bed rest.

Local fluid shifts and edema in humans during simulated microgravity

NASA Technical Reports Server (NTRS)

Hargens, Alan R.

1991-01-01

Local fluid shifts and edema in humans during simulated microgravity is studied. Recent results and significance and future plans on the following research topics are discussed: mechanisms of headward edema formation during head-down tilt; postural responses of head and foot microcirculations and their sensitivity to bed rest; and transcapillary fluid transport associated with lower body negative pressure (LBNP) with and without saline ingestion.

Hydroxyl Radical Formation from HULIS and Fe(II) Interactions: Fulvic Acid-Fe(II) Complexes in Simulated and Human Lung Fluids

NASA Astrophysics Data System (ADS)

Gonzalez, D.

2017-12-01

Inhalation of fine particulate matter (PM2.5) has long been associated with adverse health outcomes. However, the causative agents and underlying mechanisms for these health effects have yet to be identified. One hypothesis is that PM2.5 deposited in the alveoli produce an excess of highly reactive radicals, leading to oxidative stress. The OH radical may be the most physiologically damaging, capable of oxidizing of lipids, proteins and DNA. Due to the variability and uncertainty in PM2.5 composition, the components that contribute to OH formation are not well understood. Soluble Fe is a component of PM2.5that produces OH under physiological conditions. Humic-like substances are water soluble organics found in biomass burning and tobacco smoke. Humic-like substances are capable of binding to Fe and enhancing OH formation, but this chemistry is not well understood. In this work, we use soil derived fulvic acid as a surrogate for Humic-like substances and investigate its effect on OH formation from Fe(II) under conditions relevant to the lungs. We use a fluorescent OH trapping probe, chemical kinetics and thermodynamic modeling to investigate OH formation from fulvic acid and Fe(II) dissolved in simulated and human lung fluids. In simulated lung fluid, we find that fulvic acid binds to Fe(II) and enhances the rate of key reactions that form OH. When fulvic acid is added to human lung fluids containing Fe(II), an enhancement of OH formation is observed. In human lung fluid, fulvic acid and metal binding proteins compete for Fe binding. These metal binding proteins are typically not found in simulated lung fluids. Results show that fulvic acid strongly binds Fe(II) and catalyzes key reactions that form OH in both simulated and human lung fluids. These results may help explain the role of Humic-like substances and Fe in oxidative stress and adverse health outcomes. Furthermore, we suggest that future studies employ simulated lung fluids containing metal binding proteins to better reflect human lung fluids.

Melting/freezing behavior of a fluid confined in porous glasses and MCM-41: Dielectric spectroscopy and molecular simulation

NASA Astrophysics Data System (ADS)

Sliwinska-Bartkowiak, Malgorzata; Dudziak, Grazyna; Sikorski, Roman; Gras, Roman; Radhakrishnan, Ravi; Gubbins, Keith E.

2001-01-01

We report both experimental measurements and molecular simulations of the melting and freezing behavior of fluids in nanoporous media. The experimental studies are for nitrobenzene in the silica-based pores of controlled pore glass, Vycor, and MCM-41. Dielectric relaxation spectroscopy is used to determine melting points and the orientational relaxation times of the nitrobenzene molecules in the bulk and the confined phase. Monte Carlo simulations, together with a bond orientational order parameter method, are used to determine the melting point and fluid structure inside cylindrical pores modeled on silica. Qualitative comparison between experiment and simulation are made for the shift in the freezing temperatures and the structure of confined phases. From both the experiments and the simulations, it is found that the confined fluid freezes into a single crystalline structure for average pore diameters greater than 20σ, where σ is the diameter of the fluid molecule. For average pore sizes between 20σ and 15σ, part of the confined fluid freezes into a frustrated crystal structure with the rest forming an amorphous region. For pore sizes smaller than 15σ, even the partial crystallization did not occur. Our measurements and calculations show clear evidence of a novel intermediate "contact layer" phase lying between liquid and crystal; the contact layer is the confined molecular layer adjacent to the pore wall and experiences a deeper fluid-wall potential energy compared to the inner layers. We also find evidence of a liquid to "hexatic" transition in the quasi-two-dimensional contact layer at high temperatures.

Process and kinetics of bonelike apatite formation on sintered hydroxyapatite in a simulated body fluid.

PubMed

Kim, Hyun-Min; Himeno, Teruyuki; Kokubo, Tadashi; Nakamura, Takashi

2005-07-01

The surfaces of two hydroxyapatites (HA), which have been sintered at different temperatures of 800 and 1200 degrees C, was investigated as a function of soaking time in simulated body fluid (SBF) using transmission electron microscopy (TEM) attached with energy-dispersive spectrometry (EDX) and laser electrophoresis spectroscopy. The TEM-EDX indicated that after soaking in SBF, both the HAs form bonelike apatite by undergoing the same surface structural change, i.e., formations of a Ca-rich amorphous or nano-crystalline calcium phosphate (ACP) and a Ca-poor ACP, which eventually crystallized into bonelike apatite. Zeta potential characterized by the electrophoresis indicated that during exposure to SBF, the HA surfaces reveal negative surface charge, thereby interacting with the positive calcium ions in the fluid to form the Ca-rich ACP, which gains positive surface charge. The Ca-rich ACP on the HAs then interacts with the negative phosphate ions in the fluid to form the Ca-poor ACP, which stabilizes by being crystallized into bonelike apatite with a low solubility in the SBF. The exposure times for formations of these phases of the Ca-rich ACP, the Ca-poor ACP as well as the apatite were, however, all late on HA sintered at 1200 degrees C, compared with the HA sintered at 800 degrees C. This phenomenon was attributed to a lower initial negative surface charge of the HA sintered at 800 degrees C than of that one sintered at 1200 degrees C, owing to poverty in surface hydroxyl and phosphate groups which are responsible for the surface negativity of the HA. These indicate that sintered temperature of HA might influence not in terms of the process but in terms of the rate of formation of biologically active bonelike apatite on its surface, through which the HA integrates with living bone.

Numerical Simulations of Single Flow Element in a Nuclear Thermal Thrust Chamber

NASA Technical Reports Server (NTRS)

Cheng, Gary; Ito, Yasushi; Ross, Doug; Chen, Yen-Sen; Wang, Ten-See

2007-01-01

The objective of this effort is to develop an efficient and accurate computational methodology to predict both detailed and global thermo-fluid environments of a single now element in a hypothetical solid-core nuclear thermal thrust chamber assembly, Several numerical and multi-physics thermo-fluid models, such as chemical reactions, turbulence, conjugate heat transfer, porosity, and power generation, were incorporated into an unstructured-grid, pressure-based computational fluid dynamics solver. The numerical simulations of a single now element provide a detailed thermo-fluid environment for thermal stress estimation and insight for possible occurrence of mid-section corrosion. In addition, detailed conjugate heat transfer simulations were employed to develop the porosity models for efficient pressure drop and thermal load calculations.

Use of computational fluid dynamics in respiratory medicine.

PubMed

Fernández Tena, Ana; Casan Clarà, Pere

2015-06-01

Computational Fluid Dynamics (CFD) is a computer-based tool for simulating fluid movement. The main advantages of CFD over other fluid mechanics studies include: substantial savings in time and cost, the analysis of systems or conditions that are very difficult to simulate experimentally (as is the case of the airways), and a practically unlimited level of detail. We used the Ansys-Fluent CFD program to develop a conducting airway model to simulate different inspiratory flow rates and the deposition of inhaled particles of varying diameters, obtaining results consistent with those reported in the literature using other procedures. We hope this approach will enable clinicians to further individualize the treatment of different respiratory diseases. Copyright © 2014 SEPAR. Published by Elsevier Espana. All rights reserved.

Swimming by reciprocal motion at low Reynolds number

PubMed Central

Qiu, Tian; Lee, Tung-Chun; Mark, Andrew G.; Morozov, Konstantin I.; Münster, Raphael; Mierka, Otto; Turek, Stefan; Leshansky, Alexander M.; Fischer, Peer

2014-01-01

Biological microorganisms swim with flagella and cilia that execute nonreciprocal motions for low Reynolds number (Re) propulsion in viscous fluids. This symmetry requirement is a consequence of Purcell’s scallop theorem, which complicates the actuation scheme needed by microswimmers. However, most biomedically important fluids are non-Newtonian where the scallop theorem no longer holds. It should therefore be possible to realize a microswimmer that moves with reciprocal periodic body-shape changes in non-Newtonian fluids. Here we report a symmetric ‘micro-scallop’, a single-hinge microswimmer that can propel in shear thickening and shear thinning (non-Newtonian) fluids by reciprocal motion at low Re. Excellent agreement between our measurements and both numerical and analytical theoretical predictions indicates that the net propulsion is caused by modulation of the fluid viscosity upon varying the shear rate. This reciprocal swimming mechanism opens new possibilities in designing biomedical microdevices that can propel by a simple actuation scheme in non-Newtonian biological fluids. PMID:25369018

Modeling flow for modified concentric cylinder rheometer geometry

NASA Astrophysics Data System (ADS)

Ekeruche, Karen; Connelly, Kelly; Kavehpour, H. Pirouz

2016-11-01

Rheology experiments on biological fluids can be difficult when samples are limited in volume, sensitive to degradation, and delicate to extract from tissues. A probe-like geometry has been developed to perform shear creep experiments on biological fluids and to use the creep response to characterize fluid material properties. This probe geometry is a modified concentric cylinder setup, where the gap is large and we assume the inner cylinder rotates in an infinite fluid. To validate this assumption we perform shear creep tests with the designed probe on Newtonian and non-Newtonian fluids and vary the outer cylinder container diameter. We have also created a numerical model based on the probe geometry setup to compare with experimental results at different outer cylinder diameters. A creep test is modeled by applying rotation to the inner cylinder and solving for the deformation of the fluid throughout the gap. Steady state viscosity values are calculated from creep compliance curves and compared between experimental and numerical results.

Parallel Simulation of Subsonic Fluid Dynamics on a Cluster of Workstations.

DTIC Science & Technology

1994-11-01

inside wind musical instruments. Typical simulations achieve $80\\%$ parallel efficiency (speedup/processors) using 20 HP-Apollo workstations. Detailed...TERMS AI, MIT, Artificial Intelligence, Distributed Computing, Workstation Cluster, Network, Fluid Dynamics, Musical Instruments 17. SECURITY...for example, the flow of air inside wind musical instruments. Typical simulations achieve 80% parallel efficiency (speedup/processors) using 20 HP

Numerical simulation of miscible viscous fingering with viscosity change in a displacing fluid by chemical reaction

NASA Astrophysics Data System (ADS)

Omori, Keiichiro; Nagatsu, Yuichiro

2017-11-01

Viscous fingering (VF) with viscosity changes by chemical reactions in case of miscible systems have been investigated both experimentally and theoretically in the recent years. Nagatsu et al. investigated experimentally miscible VF in which viscosity of the displaced fluid or the displacing one is changed by fast chemical reaction They showed that VF was more dense by the viscosity increase whereas less dense by the viscosity increase regardless of whether the viscosity change occurs in the displaced fluid or displacing one. From a theoretical viewpoint, numerical simulation performed on the reactive VF where viscosity of the displaced fluid is changed by instantaneously fast chemical reaction. The results had a good agreement with those in the corresponding experiment. In this work, we have conducted numerical simulation on such reactive VF where viscosity of the displacing fluid is changed. We have found the results have a good agreement with the corresponding experimental ones.

Four-fluid MHD Simulations of the Plasma and Neutral Gas Environment of Comet Churyumov-Gerasimenko Near Perihelio

NASA Astrophysics Data System (ADS)

Huang, Z.; Toth, G.; Gombosi, T. I.; Jia, X.; Rubin, M.; Hansen, K. C.; Fougere, N.; Bieler, A. M.; Shou, Y.; Altwegg, K.; Combi, M. R.; Tenishev, V.

2015-12-01

The neutral and plasma environment is critical in understanding the interaction of comet Churyumov-Gerasimenko (CG), the target of the Rosetta mission, and the solar wind. To serve this need and support the Rosetta mission, we develop a 3-D four fluid model, which is based on BATS-R-US within the SWMF (Space Weather Modeling Framework) that solves the governing multi-fluid MHD equations and the Euler equations for the neutral gas fluid. These equations describe the behavior and interactions of the cometary heavy ions, the solar wind protons, the electrons, and the neutrals. This model incorporates different mass loading processes, including photo and electron impact ionization, charge exchange, dissociative ion-electron recombination, and collisional interactions between different fluids. We simulate the near nucleus plasma and neutral gas environment near perihelion with a realistic shape model of CG and compare our simulation results with Rosetta observations.

Virtual reality aided visualization of fluid flow simulations with application in medical education and diagnostics.

PubMed

Djukic, Tijana; Mandic, Vesna; Filipovic, Nenad

2013-12-01

Medical education, training and preoperative diagnostics can be drastically improved with advanced technologies, such as virtual reality. The method proposed in this paper enables medical doctors and students to visualize and manipulate three-dimensional models created from CT or MRI scans, and also to analyze the results of fluid flow simulations. Simulation of fluid flow using the finite element method is performed, in order to compute the shear stress on the artery walls. The simulation of motion through the artery is also enabled. The virtual reality system proposed here could shorten the length of training programs and make the education process more effective. © 2013 Published by Elsevier Ltd.

A two-fluid study of oblique tearing modes in a force-free current sheet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akçay, Cihan, E-mail: akcay@lanl.gov; Daughton, William; Lukin, Vyacheslav S.

2016-01-15

Kinetic simulations have demonstrated that three-dimensional reconnection in collisionless regimes proceeds through the formation and interaction of magnetic flux ropes, which are generated due to the growth of tearing instabilities at multiple resonance surfaces. Since kinetic simulations are intrinsically expensive, it is desirable to explore the feasibility of reduced two-fluid models to capture this complex evolution, particularly, in the strong guide field regime, where two-fluid models are better justified. With this goal in mind, this paper compares the evolution of the collisionless tearing instability in a force-free current sheet with a two-fluid model and fully kinetic simulations. Our results indicatemore » that the most unstable modes are oblique for guide fields larger than the reconnecting field, in agreement with the kinetic results. The standard two-fluid tearing theory is extended to address the tearing instability at oblique angles. The resulting theory yields a flat oblique spectrum and underestimates the growth of oblique modes in a similar manner to kinetic theory relative to kinetic simulations.« less

A two-fluid study of oblique tearing modes in a force-free current sheet

DOE PAGES

Akçay, Cihan; Daughton, William; Lukin, Vyacheslav S.; ...

2016-01-01

Kinetic simulations have demonstrated that three-dimensional reconnection in collisionless regimes proceeds through the formation and interaction of magnetic flux ropes, which are generated due to the growth of tearing instabilities at multiple resonance surfaces. Because kinetic simulations are intrinsically expensive, it is desirable to explore the feasibility of reduced two-fluid models to capture this complex evolution, particularly, in the strong guide field regime, where two-fluid models are better justified. With this goal in mind, this paper compares the evolution of the collisionless tearing instability in a force-free current sheet with a two-fluid model and fully kinetic simulations. Our results indicatemore » that the most unstable modes are oblique for guide fields larger than the reconnecting field, in agreement with the kinetic results. The standard two-fluid tearing theory is extended to address the tearing instability at oblique angles. As a results this theory yields a flat oblique spectrum and underestimates the growth of oblique modes in a similar manner to kinetic theory relative to kinetic simulations.« less

Simulations of the kinematic dynamo onset of spherical Couette flows with smooth and rough boundaries.

PubMed

Finke, K; Tilgner, A

2012-07-01

We study numerically the dynamo transition of an incompressible electrically conducting fluid filling the gap between two concentric spheres. In a first series of simulations, the fluid is driven by the rotation of a smooth inner sphere through no-slip boundary conditions, whereas the outer sphere is stationary. In a second series a volume force intended to simulate a rough surface drives the fluid next to the inner sphere within a layer of thickness one-tenth of the gap width. We investigate the effect of the boundary layer thickness on the dynamo threshold in the turbulent regime. The simulations show that the boundary forcing simulating the rough surface lowers the necessary rotation rate, which may help to improve spherical dynamo experiments.

Enhanced Remedial Amendment Delivery through Fluid Viscosity Modifications: Experiments and numerical simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong, Lirong; Oostrom, Martinus; Wietsma, Thomas W.

2008-07-29

Abstract Heterogeneity is often encountered in subsurface contamination characterization and remediation. Low-permeability zones are typically bypassed when remedial fluids are injected into subsurface heterogeneous aquifer systems. Therefore, contaminants in the bypassed areas may not be contacted by the amendments in the remedial fluid, which may significantly prolong the remediation operations. Laboratory experiments and numerical studies have been conducted to develop the Mobility-Controlled Flood (MCF) technology for subsurface remediation and to demonstrate the capability of this technology in enhancing the remedial amendments delivery to the lower permeability zones in heterogeneous systems. Xanthan gum, a bio-polymer, was used to modify the viscositymore » of the amendment-containing remedial solutions. Sodium mono-phosphate and surfactant were the remedial amendment used in this work. The enhanced delivery of the amendments was demonstrated in two-dimensional (2-D) flow cell experiments, packed with heterogeneous systems. The impact of polymer concentration, fluid injection rate, and permeability contract in the heterogeneous systems has been studied. The Subsurface Transport over Multiple Phases (STOMP) simulator was modified to include polymer-induced shear thinning effects. Shear rates of polymer solutions were computed from pore-water velocities using a relationship proposed in the literature. Viscosity data were subsequently obtained from empirical viscosity-shear rate relationships derived from laboratory data. The experimental and simulation results clearly show that the MCF technology is capable of enhancing the delivery of remedial amendments to subsurface lower permeability zones. The enhanced delivery significantly improved the NAPL removal from these zones and the sweeping efficiency on a heterogeneous system was remarkably increased when a polymer fluid was applied. MCF technology is also able to stabilize the fluid displacing front when there is a density difference between the fluids. The modified STOMP simulator was able to predict the experimental observed fluid displacing behavior. The simulator may be used to predict the subsurface remediation performance when a shear thinning fluid is used to remediate a heterogeneous system.« less

Locomotion at Low Reynolds Number: Dynamics in Newtonian and Non-Newtonian Systems with Biomedical Applications

NASA Astrophysics Data System (ADS)

Gagnon, David A.

Swimming microorganisms such as bacteria, spermatozoa, algae, and nematodes are critical to ubiquitous biological phenomena such as disease and infection, ecosystem dynamics, and mammalian fertilization. While there has been much scientific and practical interest in studying these swimmers in Newtonian (water-like) fluids, there are fewer systematic experimental studies on swimming through non-Newtonian (non-water-like) fluids with biologically-relevant mechanical properties. These organisms commonly swim through viscoelastic, structured, or shear-rate-dependent fluids, such as blood, mucus, and living tissues. Furthermore, the small length scales of these organisms dictate that their motion is dominated by viscous forces and inertia is negligible. Using rheology, microscopy, particle tracking, and image processing techniques, we examine the interaction of low Reynolds number swimmers and non-Newtonian fluids including viscoelastic, locally-anisotropic, and shear-thinning fluids. We then apply our understanding of locomotion to the study of the genetic disease Spinal Muscular Atrophy.

Methods for separating particles and/or nucleic acids using isotachophoresis

DOEpatents

Jung, Byoungsok; Ness, Kevin; Rose, Klint A.

2016-03-15

According to one embodiment, a method includes co-feeding fluids comprising a leading electrolyte, a trailing electrolyte, and at least one of DNA and RNA to a channel, and applying an electric field to the fluids in a direction perpendicular to an axis of the channel for inducing transverse isotachophoresis. In another embodiment, a method includes co-feeding fluids to a channel. The fluids include a leading electrolyte, a trailing electrolyte, biological objects, at least one of DNA and RNA, and a spacer electrolyte having an electrophoretic mobility that is between an electrophoretic mobility of at least some of the biological objects and an electrophoretic mobility of the at least one of the DNA and the RNA. The method also includes applying an electric field to the fluids in a direction perpendicular to an axis of the channel for inducing transverse isotachophoresis. Other methods of isotachophoresis are disclosed in addition to these.

Single-step preparation of selected biological fluids for the high performance liquid chromatographic analysis of fat-soluble vitamins and antioxidants.

PubMed

Lazzarino, Giacomo; Longo, Salvatore; Amorini, Angela Maria; Di Pietro, Valentina; D'Urso, Serafina; Lazzarino, Giuseppe; Belli, Antonio; Tavazzi, Barbara

2017-12-08

Fat-soluble vitamins and antioxidants are of relevance in health and disease. Current methods to extract these compounds from biological fluids mainly need use of multi-steps and multi organic solvents. They are time-consuming and difficult to apply to treat simultaneously large sample number. We here describe a single-step, one solvent extraction of fat-soluble vitamins and antioxidants from biological fluids, and the chromatographic separation of all-trans-retinoic acid, 25-hydroxycholecalciferol, all-trans-retinol, astaxanthin, lutein, zeaxanthin, trans-β-apo-8'-carotenal, γ-tocopherol, β-cryptoxanthin, α-tocopherol, phylloquinone, lycopene, α-carotene, β-carotene and coenzyme Q 10 . Extraction is obtained by adding one volume of biological fluid to two acetonitrile volumes, vortexing for 60s and incubating for 60min at 37°C under agitation. HPLC separation occurs in 30min using Hypersil C18, 100×4.6mm, 5μm particle size column, gradient from 70% methanol+30% H 2 O to 100% acetonitrile, flow rate of 1.0ml/min and 37°C column temperature. Compounds are revealed using highly sensitive UV-VIS diode array detector. The HPLC method suitability was assessed in terms of sensitivity, reproducibility and recovery. Using the present extraction and chromatographic conditions we obtained values of the fat-soluble vitamins and antioxidants in serum from 50 healthy controls similar to those found in literature. Additionally, the profile of these compounds was also measured in seminal plasma from 20 healthy fertile donors. Results indicate that this simple, rapid and low cost sample processing is suitable to extract fat-soluble vitamins and antioxidants from biological fluids and can be applied in clinical and nutritional studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Effective Elastic and Neutron Capture Cross Section Calculations Corresponding to Simulated Fluid Properties from CO2 Push-Pull Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chugunov, Nikita; Altundas, Bilgin

The submission contains a .xls files consisting of 10 excel sheets, which contain combined list of pressure, saturation, salinity, temperature profiles from the simulation of CO2 push-pull using Brady reservoir model and the corresponding effective compressional and shear velocity, bulk density, and fluid and time-lapse neutron capture cross section profiles of rock at times 0 day (baseline) through 14 days. First 9 sheets (each named after the corresponding CO2 push-pull simulation time) contains simulated pressure, saturation, temperature, salinity profiles and the corresponding effective elastic and neutron capture cross section profiles of rock matrix at the time of CO2 injection. Eachmore » sheet contains two sets of effective compressional velocity profiles of the rock, one based on Gassmann and the other based on Patchy saturation model. Effective neutron capture cross section calculations are done using a proprietary neutron cross-section simulator (SNUPAR) whereas for the thermodynamic properties of CO2 and bulk density of rock matrix filled with fluid, a standalone fluid substitution tool by Schlumberger is used. Last sheet in the file contains the bulk modulus of solid rock, which is inverted from the rock properties (porosity, sound speed etc) based on Gassmann model. Bulk modulus of solid rock in turn is used in the fluid substitution.« less

A CONTINUUM HARD-SPHERE MODEL OF PROTEIN ADSORPTION

PubMed Central

Finch, Craig; Clarke, Thomas; Hickman, James J.

2012-01-01

Protein adsorption plays a significant role in biological phenomena such as cell-surface interactions and the coagulation of blood. Two-dimensional random sequential adsorption (RSA) models are widely used to model the adsorption of proteins on solid surfaces. Continuum equations have been developed so that the results of RSA simulations can be used to predict the kinetics of adsorption. Recently, Brownian dynamics simulations have become popular for modeling protein adsorption. In this work a continuum model was developed to allow the results from a Brownian dynamics simulation to be used as the boundary condition in a computational fluid dynamics (CFD) simulation. Brownian dynamics simulations were used to model the diffusive transport of hard-sphere particles in a liquid and the adsorption of the particles onto a solid surface. The configuration of the adsorbed particles was analyzed to quantify the chemical potential near the surface, which was found to be a function of the distance from the surface and the fractional surface coverage. The near-surface chemical potential was used to derive a continuum model of adsorption that incorporates the results from the Brownian dynamics simulations. The equations of the continuum model were discretized and coupled to a CFD simulation of diffusive transport to the surface. The kinetics of adsorption predicted by the continuum model closely matched the results from the Brownian dynamics simulation. This new model allows the results from mesoscale simulations to be incorporated into micro- or macro-scale CFD transport simulations of protein adsorption in practical devices. PMID:23729843

Shaded computer graphic techniques for visualizing and interpreting analytic fluid flow models

NASA Technical Reports Server (NTRS)

Parke, F. I.

1981-01-01

Mathematical models which predict the behavior of fluid flow in different experiments are simulated using digital computers. The simulations predict values of parameters of the fluid flow (pressure, temperature and velocity vector) at many points in the fluid. Visualization of the spatial variation in the value of these parameters is important to comprehend and check the data generated, to identify the regions of interest in the flow, and for effectively communicating information about the flow to others. The state of the art imaging techniques developed in the field of three dimensional shaded computer graphics is applied to visualization of fluid flow. Use of an imaging technique known as 'SCAN' for visualizing fluid flow, is studied and the results are presented.

Generalized Fluid System Simulation Program (GFSSP) Version 6 - General Purpose Thermo-Fluid Network Analysis Software

NASA Technical Reports Server (NTRS)

Majumdar, Alok; Leclair, Andre; Moore, Ric; Schallhorn, Paul

2011-01-01

GFSSP stands for Generalized Fluid System Simulation Program. It is a general-purpose computer program to compute pressure, temperature and flow distribution in a flow network. GFSSP calculates pressure, temperature, and concentrations at nodes and calculates flow rates through branches. It was primarily developed to analyze Internal Flow Analysis of a Turbopump Transient Flow Analysis of a Propulsion System. GFSSP development started in 1994 with an objective to provide a generalized and easy to use flow analysis tool for thermo-fluid systems.

The laser radiation action on the crystal formation processes in the biological fluids

NASA Astrophysics Data System (ADS)

Malov, Alexander N.; Vaichas, Andrey A.; Novikova, Evgeniya A.

2016-11-01

The results of an experimental study of the laser radiation effect on the crystal`s formation in the volume of biological fluids that are complex multi-component solutions have been discussing. Are investigated white and natural bile in vitro. The qualitative changes were observed. Thus, at the bottom of the cell in which bile is not exposed to the laser radiation, the crystals are formed. In the irradiated bile gallstone has a thin layer of a homogeneous viscous colloidal liquid with very small, visible in polarized light crystalline formations was got. Irradiated laser bile's gallstone was covered evenly white deposit without surface defect unlike gallstone in bile without radiation exposure. A possible mechanism to explain the laser radiation action on the mineral formation in biological fluids and also practical application of this effect have been suggesting too.

The Impact of Solid Surface Features on Fluid-Fluid Interface Configuration

NASA Astrophysics Data System (ADS)

Araujo, J. B.; Brusseau, M. L. L.

2017-12-01

Pore-scale fluid processes in geological media are critical for a broad range of applications such as radioactive waste disposal, carbon sequestration, soil moisture distribution, subsurface pollution, land stability, and oil and gas recovery. The continued improvement of high-resolution image acquisition and processing have provided a means to test the usefulness of theoretical models developed to simulate pore-scale fluid processes, through the direct quantification of interfaces. High-resolution synchrotron X-ray microtomography is used in combination with advanced visualization tools to characterize fluid distributions in natural geologic media. The studies revealed the presence of fluid-fluid interface associated with macroscopic features on the surfaces of the solids such as pits and crevices. These features and respective fluid interfaces, which are not included in current theoretical or computational models, may have a significant impact on accurate simulation and understanding of multi-phase flow, energy, heat and mass transfer processes.

A portable extensional rheometer for measuring the viscoelasticity of pitcher plant and other sticky liquids in the field.

PubMed

Collett, Catherine; Ardron, Alia; Bauer, Ulrike; Chapman, Gary; Chaudan, Elodie; Hallmark, Bart; Pratt, Lee; Torres-Perez, Maria Dolores; Wilson, D Ian

2015-01-01

Biological fluids often have interesting and unusual physical properties to adapt them for their specific purpose. Laboratory-based rheometers can be used to characterise the viscoelastic properties of such fluids. This, however, can be challenging as samples often do not retain their natural properties in storage while conventional rheometers are fragile and expensive devices ill-suited for field measurements. We present a portable, low-cost extensional rheometer designed specifically to enable in situ studies of biological fluids in the field. The design of the device (named Seymour) is based on a conventional capillary break-up extensional rheometer (the Cambridge Trimaster). It works by rapidly stretching a small fluid sample between two metal pistons. A battery-operated solenoid switch triggers the pistons to move apart rapidly and a compact, robust and inexpensive, USB 3 high speed camera is used to record the thinning and break-up of the fluid filament that forms between the pistons. The complete setup runs independently of mains electricity supply and weighs approximately 1 kg. Post-processing and analysis of the recorded images to extract rheological parameters is performed using open source software. The device was tested both in the laboratory and in the field, in Brunei Darussalam, using calibration fluids (silicone oil and carboxymethyl cellulose solutions) as well as Nepenthes pitcher plant trapping fluids as an example of a viscoelastic biological fluid. The fluid relaxation times ranged from 1 ms to over 1 s. The device gave comparable performance to the Cambridge Trimaster. Differences in fluid viscoelasticity between three species were quantified, as well as the change in viscoelasticity with storage time. This, together with marked differences between N. rafflesiana fluids taken from greenhouse and wild plants, confirms the need for a portable device. Proof of concept of the portable rheometer was demonstrated. Quantitative measurements of pitcher plant fluid viscoelasticity were made in the natural habitat for the first time. The device opens up opportunities for studying a wide range of plant fluids and secretions, under varying experimental conditions, or with changing temperatures and weather conditions.

Molecular mechanics and structure of the fluid-solid interface in simple fluids

NASA Astrophysics Data System (ADS)

Wang, Gerald J.; Hadjiconstantinou, Nicolas G.

2017-09-01

Near a fluid-solid interface, the fluid spatial density profile is highly nonuniform at the molecular scale. This nonuniformity can have profound effects on the dynamical behavior of the fluid and has been shown to play an especially important role when modeling a wide variety of nanoscale heat and momentum transfer phenomena. We use molecular-mechanics arguments and molecular-dynamics (MD) simulations to develop a better understanding of the structure of the first fluid layer directly adjacent to the solid in the layering regime, as delineated by a nondimensional number that compares the effects of wall-fluid interaction to thermal energy. Using asymptotic analysis of the Nernst-Planck equation, we show that features of the fluid density profile close to the wall, such as the areal density of the first layer ΣFL (defined as the number of atoms in this layer per unit of fluid-solid interfacial area), can be expressed as polynomial functions of the fluid average density ρave. This is found to be in agreement with MD simulations, which also show that the width of the first layer hFL is a linear function of the average density and only a weak function of the temperature T . These results can be combined to show that, for system average densities corresponding to a dense fluid (ρave≥0.7 ), the ratio C ≡ΣFLρavehFL, representing a density enhancement with respect to the bulk fluid, depends only weakly on temperature and is essentially independent of density. Further MD simulations suggest that the above results, nominally valid for large systems (solid in contact with semi-infinite fluid), also describe fluid-solid interfaces under considerable nanoconfinement, provided ρave is appropriately defined.

Modeling Tools Predict Flow in Fluid Dynamics

NASA Technical Reports Server (NTRS)

2010-01-01

"Because rocket engines operate under extreme temperature and pressure, they present a unique challenge to designers who must test and simulate the technology. To this end, CRAFT Tech Inc., of Pipersville, Pennsylvania, won Small Business Innovation Research (SBIR) contracts from Marshall Space Flight Center to develop software to simulate cryogenic fluid flows and related phenomena. CRAFT Tech enhanced its CRUNCH CFD (computational fluid dynamics) software to simulate phenomena in various liquid propulsion components and systems. Today, both government and industry clients in the aerospace, utilities, and petrochemical industries use the software for analyzing existing systems as well as designing new ones."

Microgravity

NASA Image and Video Library

1998-11-04

Computer simulation of atmospheric flow corresponds well to imges taken during the second Geophysical Fluid Flow Cell (BFFC) mission. The top shows a view from the pole, while the bottom shows a view from the equator. Red corresponds to hot fluid rising while blue shows cold fluid falling. This simulation was developed by Anil Deane of the University of Maryland, College Park and Paul Fischer of Argorne National Laboratory. Credit: NASA/Goddard Space Flight Center

Simulation of Tsunami Resistance of a Pinus Thunbergii tree in Coastal Forest in Japan

NASA Astrophysics Data System (ADS)

Nanko, K.; Suzuki, S.; Noguchi, H.; Hagino, H.

2015-12-01

Forests reduce fluid force of tsunami, whereas extreme tsunami sometimes breaks down the forest trees. It is difficult to estimate the interactive relationship between the fluid and the trees because fluid deform tree architecture and deformed tree changes flow field. Dynamic tree deformation and fluid behavior should be clarified by fluid-structure interaction analysis. For the initial step, we have developed dynamic simulation of tree sway and breakage caused by tsunami based on a vibrating system with multiple degrees of freedom. The target specie of the simulation was Japanese black pine (pinus thunbergii), which is major specie in the coastal forest to secure livelihood area from the damage by blown sand and salt in Japanese coastal area. For the simulation, a tree was segmented into 0.2 m long circular truncated cones. Turning moment induced by tsunami and self-weight was calculated at each segment bottom. Tree deformation was computed on multi-degree-of-freedom vibration equation. Tree sway was simulated by iterative calculation of the tree deformation with time step 0.05 second with temporally varied flow velocity of tsunami. From the calculation of bending stress and turning moment at tree base, we estimated resistance of a Pinus thunbergii tree from tsunami against tree breakage.

Food matrix effects on in vitro digestion of microencapsulated tuna oil powder.

PubMed

Shen, Zhiping; Apriani, Christina; Weerakkody, Rangika; Sanguansri, Luz; Augustin, Mary Ann

2011-08-10

Tuna oil, containing 53 mg of eicosapentaenoic acid (EPA) and 241 mg of docosahexaenoic acid (DHA) per gram of oil, delivered as a neat microencapsulated tuna oil powder (25% oil loading) or in food matrices (orange juice, yogurt, or cereal bar) fortified with microencapsulated tuna oil powder was digested in simulated gastric fluid or sequentially in simulated gastric fluid and simulated intestinal fluid. The level of fortification was equivalent to 1 g of tuna oil per recommended serving size (i.e., per 200 g of orange juice or yogurt or 60 g of cereal bar). The changes in particle size of oil droplets during digestion were influenced by the method of delivery of the microencapsulated tuna oil powder. Lipolysis in simulated gastric fluid was low, with only 4.4-6.1% EPA and ≤1.5% DHA released after digestion (as a % of total fatty acids present). After sequential exposure to simulated gastric and intestinal fluids, much higher extents of lipolysis of both glycerol-bound EPA and DHA were obtained (73.2-78.6% for the neat powder, fortified orange juice, and yogurt; 60.3-64.0% for the fortified cereal bar). This research demonstrates that the choice of food matrix may influence the lipolysis of microencapsulated tuna oil.

Preliminary results from a four-working space, double-acting piston, Stirling engine controls model

NASA Technical Reports Server (NTRS)

Daniele, C. J.; Lorenzo, C. F.

1980-01-01

A four working space, double acting piston, Stirling engine simulation is being developed for controls studies. The development method is to construct two simulations, one for detailed fluid behavior, and a second model with simple fluid behaviour but containing the four working space aspects and engine inertias, validate these models separately, then upgrade the four working space model by incorporating the detailed fluid behaviour model for all four working spaces. The single working space (SWS) model contains the detailed fluid dynamics. It has seven control volumes in which continuity, energy, and pressure loss effects are simulated. Comparison of the SWS model with experimental data shows reasonable agreement in net power versus speed characteristics for various mean pressure levels in the working space. The four working space (FWS) model was built to observe the behaviour of the whole engine. The drive dynamics and vehicle inertia effects are simulated. To reduce calculation time, only three volumes are used in each working space and the gas temperature are fixed (no energy equation). Comparison of the FWS model predicted power with experimental data shows reasonable agreement. Since all four working spaces are simulated, the unique capabilities of the model are exercised to look at working fluid supply transients, short circuit transients, and piston ring leakage effects.

Fluid simulations of plasma turbulence at ion scales: Comparison with Vlasov-Maxwell simulations

NASA Astrophysics Data System (ADS)

Perrone, D.; Passot, T.; Laveder, D.; Valentini, F.; Sulem, P. L.; Zouganelis, I.; Veltri, P.; Servidio, S.

2018-05-01

Comparisons are presented between a hybrid Vlasov-Maxwell (HVM) simulation of turbulence in a collisionless plasma and fluid reductions. These include Hall-magnetohydrodynamics (HMHD) and Landau fluid (LF) or finite Larmor radius-Landau fluid (FLR-LF) models that retain pressure anisotropy and low-frequency kinetic effects such as Landau damping and, for the last model, finite Larmor radius (FLR) corrections. The problem is considered in two space dimensions, when initial conditions involve moderate-amplitude perturbations of a homogeneous equilibrium plasma subject to an out-of-plane magnetic field. LF turns out to provide an accurate description of the velocity field up to the ion Larmor radius scale, and even to smaller scales for the magnetic field. Compressibility nevertheless appears significantly larger at the sub-ion scales in the fluid models than in the HVM simulation. High frequency kinetic effects, such as cyclotron resonances, not retained by fluid descriptions, could be at the origin of this discrepancy. A significant temperature anisotropy is generated, with a bias towards the perpendicular component, the more intense fluctuations being rather spread out and located in a broad vicinity of current sheets. Non-gyrotropic pressure tensor components are measured and are shown to reach a significant fraction of the total pressure fluctuations, with intense regions closely correlated with current sheets.

On the kinetics of the capillary imbibition of a simple fluid through a designed nanochannel using the molecular dynamics simulation approach.

PubMed

Ahadian, Samad; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2010-12-15

A molecular dynamics (MD) approach was employed to simulate the imbibition of a designed nanopore by a simple fluid (i.e., a Lennard-Jones (LJ) fluid). The length of imbibition as a function of time for various interactions between the LJ fluid and the pore wall was recorded for this system (i.e., the LJ fluid and the nanopore). By and large, the kinetics of imbibition was successfully described by the Lucas-Washburn (LW) equation, although deviation from it was observed in some cases. This lack of agreement is due to the neglect of the dynamic contact angle (DCA) in the LW equation. Two commonly used models (i.e., hydrodynamic and molecular-kinetic (MK) models) were thus employed to calculate the DCA. It is demonstrated that the MK model is able to justify the simulation results in which are not in good agreement with the simple LW equation. However, the hydrodynamic model is not capable of doing that. Further investigation of the MD simulation data revealed an interesting fact that there is a direct relationship between the wall-fluid interaction and the speed of the capillary imbibition. More evidence to support this claim is presented. Copyright © 2010 Elsevier Inc. All rights reserved.

Atomistic Monte Carlo Simulation of Lipid Membranes

PubMed Central

Wüstner, Daniel; Sklenar, Heinz

2014-01-01

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. PMID:24469314

Backward Raman Amplification in the Long-wavelength Infrared

DTIC Science & Technology

2016-12-29

mechanism for generating intense, broad bandwidth, long-wavelength infrared radiation. An electromagnetic finite-difference time-domain simulation...couples a finite-difference time-domain electromagnetic solver with a collisional, relativistic cold fluid plasma model [30]. The simulation domain... electromagnetic simulations coupled to a relativistic cold fluid plasma model with electron- ion collisions. Using a pump pulse that could be generated by a CO

Neutral Buoyancy Simulator - Fluid line repair kit development

NASA Technical Reports Server (NTRS)

1997-01-01

Marshall's Neutral Buoyancy Simulator (NBS) is used to simulate the gravitational fields and buoyancy effects outer space has on astronauts and their ability to perform tasks in this environment. In this example, a diver performs a temporary fluid line repair task using a repair kit developed by Marshall engineers. The analysis will determine the value of this repair kit and its feasibility.

A simulation for teaching the basic and clinical science of fluid therapy.

PubMed

Rawson, Richard E; Dispensa, Marilyn E; Goldstein, Richard E; Nicholson, Kimberley W; Vidal, Noni Korf

2009-09-01

The course "Management of Fluid and Electrolyte Disorders" is an applied physiology course taught using lectures and paper-based cases. The course approaches fluid therapy from both basic science and clinical perspectives. While paper cases provide a basis for application of basic science concepts, they lack key components of genuine clinical cases that, by nature, are diverse, change over time, and respond in unique ways to therapeutic interventions. We developed a dynamic model using STELLA software that simulates normal and abnormal fluid and electrolyte balance in the dog. Students interact, not with the underlying model, but with a user interface that provides sufficient data (skin turgor, chemistry panel, etc.) for the clinical assessment of patients and an opportunity for treatment. Students administer fluids and supplements, and the model responds in "real time," requiring regular reassessment and, potentially, adaptation of the treatment strategy. The level of success is determined by clinical outcome, including improvement, deterioration, or death. We expected that the simulated cases could be used to teach both the clinical and basic science of fluid therapy. The simulation provides exposure to a realistic clinical environment, and students tend to focus on this aspect of the simulation while, for the most part, ignoring an exploration of the underlying physiological basis for patient responses. We discuss how the instructor's expertise can provide sufficient support, feedback, and scaffolding so that students can extract maximum understanding of the basic science in the context of assessing and treating at the clinical level.

SAGE 2D and 3D Simulations of the Explosive Venting of Supercritical Fluids Through Porous Media

NASA Astrophysics Data System (ADS)

Weaver, R.; Gisler, G.; Svensen, H.; Mazzini, A.

2008-12-01

Magmatic intrusive events in large igneous provinces heat sedimentary country rock leading to the eventual release of volatiles. This has been proposed as a contributor to climate change and other environmental impacts. By means of numerical simulations, we examine ways in which these volatiles can be released explosively from depth. Gases and fluids cooked out of country rock by metamorphic heating may be confined for a time by impermeable clays or other barriers, developing high pressures and supercritical fluids. If confinement is suddenly breached (by an earthquake for example) in such a way that the fluid has access to porous sediments, a violent eruption of a non-magmatic mixture of fluid and sediment may result. Surface manifestations of these events could be hydrothermal vent complexes, kimberlite pipes, pockmarks, or mud volcanoes. These are widespread on Earth, especially in large igneous provinces, as in the Karoo Basin of South Africa, the North Sea off the Norwegian margin, and the Siberian Traps. We have performed 2D and 3D simulations with the Sage hydrocode (from Los Alamos and Science Applications International) of supercritical venting in a variety of geometries and configurations. The simulations show several different patterns of propagation and fracturing in porous or otherwise weakened overburden, dependent on depth, source conditions (fluid availability, temperature, and pressure), and manner of confinement breach. Results will be given for a variety of 2D and 3D simulations of these events exploring the release of volatiles into the atmosphere.

Engineering Fracking Fluids with Computer Simulation

NASA Astrophysics Data System (ADS)

Shaqfeh, Eric

2015-11-01

There are no comprehensive simulation-based tools for engineering the flows of viscoelastic fluid-particle suspensions in fully three-dimensional geometries. On the other hand, the need for such a tool in engineering applications is immense. Suspensions of rigid particles in viscoelastic fluids play key roles in many energy applications. For example, in oil drilling the ``drilling mud'' is a very viscous, viscoelastic fluid designed to shear-thin during drilling, but thicken at stoppage so that the ``cuttings'' can remain suspended. In a related application known as hydraulic fracturing suspensions of solids called ``proppant'' are used to prop open the fracture by pumping them into the well. It is well-known that particle flow and settling in a viscoelastic fluid can be quite different from that which is observed in Newtonian fluids. First, it is now well known that the ``fluid particle split'' at bifurcation cracks is controlled by fluid rheology in a manner that is not understood. Second, in Newtonian fluids, the presence of an imposed shear flow in the direction perpendicular to gravity (which we term a cross or orthogonal shear flow) has no effect on the settling of a spherical particle in Stokes flow (i.e. at vanishingly small Reynolds number). By contrast, in a non-Newtonian liquid, the complex rheological properties induce a nonlinear coupling between the sedimentation and shear flow. Recent experimental data have shown both the shear thinning and the elasticity of the suspending polymeric solutions significantly affects the fluid-particle split at bifurcations, as well as the settling rate of the solids. In the present work, we use the Immersed Boundary Method to develop computer simulations of viscoelastic flow in suspensions of spheres to study these problems. These simulations allow us to understand the detailed physical mechanisms for the remarkable physical behavior seen in practice, and actually suggest design rules for creating new fluid recipes.

The impact of splay faults on fluid flow, solute transport, and pore pressure distribution in subduction zones: A case study offshore the Nicoya Peninsula, Costa Rica

NASA Astrophysics Data System (ADS)

Lauer, Rachel M.; Saffer, Demian M.

2015-04-01

Observations of seafloor seeps on the continental slope of many subduction zones illustrate that splay faults represent a primary hydraulic connection to the plate boundary at depth, carry deeply sourced fluids to the seafloor, and are in some cases associated with mud volcanoes. However, the role of these structures in forearc hydrogeology remains poorly quantified. We use a 2-D numerical model that simulates coupled fluid flow and solute transport driven by fluid sources from tectonically driven compaction and smectite transformation to investigate the effects of permeable splay faults on solute transport and pore pressure distribution. We focus on the Nicoya margin of Costa Rica as a case study, where previous modeling and field studies constrain flow rates, thermal structure, and margin geology. In our simulations, splay faults accommodate up to 33% of the total dewatering flux, primarily along faults that outcrop within 25 km of the trench. The distribution and fate of dehydration-derived fluids is strongly dependent on thermal structure, which determines the locus of smectite transformation. In simulations of a cold end-member margin, smectite transformation initiates 30 km from the trench, and 64% of the dehydration-derived fluids are intercepted by splay faults and carried to the middle and upper slope, rather than exiting at the trench. For a warm end-member, smectite transformation initiates 7 km from the trench, and the associated fluids are primarily transmitted to the trench via the décollement (50%), and faults intercept only 21% of these fluids. For a wide range of splay fault permeabilities, simulated fluid pressures are near lithostatic where the faults intersect overlying slope sediments, providing a viable mechanism for the formation of mud volcanoes.

A Unified Model of Geostrophic Adjustment and Frontogenesis

NASA Astrophysics Data System (ADS)

Taylor, John; Shakespeare, Callum

2013-11-01

Fronts, or regions with strong horizontal density gradients, are ubiquitous and dynamically important features of the ocean and atmosphere. In the ocean, fronts are associated with enhanced air-sea fluxes, turbulence, and biological productivity, while atmospheric fronts are associated with some of the most extreme weather events. Here, we describe a new mathematical framework for describing the formation of fronts, or frontogenesis. This framework unifies two classical problems in geophysical fluid dynamics, geostrophic adjustment and strain-driven frontogenesis, and provides a number of important extensions beyond previous efforts. The model solutions closely match numerical simulations during the early stages of frontogenesis, and provide a means to describe the development of turbulence at mature fronts.

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis

PubMed Central

Hanson, Erin K.; Ballantyne, Jack

2014-01-01

Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive, screening of biological evidence. PMID:24715968

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis.

PubMed

Hanson, Erin K; Ballantyne, Jack

2013-01-01

Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive, screening of biological evidence.

Nonlinear Two Fluid and Kinetic ELM Simulations

NASA Astrophysics Data System (ADS)

Strauss, H. R.; Sugiyama, L.; Chang, C. S.; Ku, S.; Hientzsch, B.; Breslau, J.; Park, W.; Samtaney, R.; Adams, M.; Jardin, S.

2006-04-01

Simulations of ELMs using dissipative MHD, two fluid MHD, and neoclassical kinetic physics models are being carried out using the M3D code [1]. Resistive MHD simulations of nonlinear edge pressure and current driven instabilities have been performed, initialized with realistic DIIID equilibria. Simulations show the saturation of the modes and relaxation of equilbrium profiles. Linear simulations including two fluid effects show the stabilization of toroidal mode number n = 10 modes, when the Hall parameter H, the ratio of ion skin depth to major radius, exceeds a threshhold. Nonlinear simulations are being done including gyroviscous stabilization. Kinetic effects are incorporated by coupling with the XGC code [2], which is able to simulate the edge plasma density and pressure pedestal buildup. These profiles are being used to initialize M3D simulations of an ELM crash and pedestal relaxation. The goal is to simulate an ELM cycle. [1] Park, W., Belova, E.V., Fu, G.Y., Tang, X.Z., Strauss, H.R., Sugiyama, L.E., Phys. Plas. 6, 1796 (1999).[2] Chang, C.S., Ku, S., and Weitzner, H., Phys. Plas. 11, 2649 (2004)

"Active" drops as phantom models for living cells: a mesoscopic particle-based approach.

PubMed

Dallavalle, Marco; Lugli, Francesca; Rapino, Stefania; Zerbetto, Francesco

2016-04-21

Drops and biological cells share some morphological features and visco-elastic properties. The modelling of drops by mesoscopic non-atomistic models has been carried out to a high degree of success in recent years. We extend such treatment and discuss a simple, drop-like model to describe the interactions of the outer layer of cells with the surfaces of materials. Cells are treated as active mechanical objects that are able to generate adhesion forces. They appear with their true size and are made of "parcels of fluids" or beads. The beads are described by (very) few quantities/parameters related to fundamental chemical forces such as hydrophilicity and lipophilicity that represent an average of the properties of a patch of material or an area of the cell(s) surface. The investigation of adhesion dynamics, motion of individual cells, and the collective behavior of clusters of cells on materials is possible. In the simulations, the drops become active soft matter objects and different from regular droplets they do not fuse when in contact, their trajectories are not Brownian, and they can be forced "to secrete" molecules, to name some of the properties targeted by the modeling. The behavior that emerges from the simulations allows ascribing some cell properties to their mechanics, which are related to their biological features.

Propulsion of helical flagella near boundaries

NASA Astrophysics Data System (ADS)

Rodenborn, Bruce; Giesbrecht, Grant; Ni, Katha; Vock, Isaac

The presence of nearby boundaries is known to have dramatic effects on the swimming behavior of microorganisms because of the no-slip condition at the boundary. Microorganisms that use a helical flagellum experience forces both along the axis of the helix and in the direction perpendicular to the axis. These low Reynolds number boundary effects have primarily been studied using live bacteria and using numerical simulations. However, small scale measurements give limited information about the forces and torques on the microorganisms. Furthermore, numerical studies are approximate because they have generally used Stokeslet-based simulations with image Stokeslets to represent the effects of the boundaries. Instead, we directly measure the propulsion of macroscopic helical flagella with diameter 12 mm using a fluid with viscosity 105 times that of water to ensure the Reynolds number in the experiments is much less than unity, just as for bacteria. We measure the parallel and perpendicular forces as a function of boundary distance to determine the nonzero elements of the propulsive matrix for axial rotation near a boundary. We then compare our results to the theory and simulations of Lauga et al. and to biological measurements.

Particles at fluid-fluid interfaces: A new Navier-Stokes-Cahn-Hilliard surface-phase-field-crystal model

PubMed Central

Aland, Sebastian; Lowengrub, John; Voigt, Axel

2013-01-01

Colloid particles that are partially wetted by two immiscible fluids can become confined to fluid-fluid interfaces. At sufficiently high volume fractions, the colloids may jam and the interface may crystallize. The fluids together with the interfacial colloids form an emulsion with interesting material properties and offer an important route to new soft materials. A promising approach to simulate these emulsions was presented in Aland et al. [Phys. Fluids 23, 062103 (2011)], where a Navier-Stokes-Cahn-Hilliard model for the macroscopic two-phase fluid system was combined with a surface phase-field-crystal model for the microscopic colloidal particles along the interface. Unfortunately this model leads to spurious velocities which require very fine spatial and temporal resolutions to accurately and stably simulate. In this paper we develop an improved Navier-Stokes-Cahn-Hilliard-surface phase-field-crystal model based on the principles of mass conservation and thermodynamic consistency. To validate our approach, we derive a sharp interface model and show agreement with the improved diffuse interface model. Using simple flow configurations, we show that the new model has much better properties and does not lead to spurious velocities. Finally, we demonstrate the solid-like behavior of the crystallized interface by simulating the fall of a solid ball through a colloid-laden multiphase fluid. PMID:23214691

A heterogeneous computing environment for simulating astrophysical fluid flows

NASA Technical Reports Server (NTRS)

Cazes, J.

1994-01-01

In the Concurrent Computing Laboratory in the Department of Physics and Astronomy at Louisiana State University we have constructed a heterogeneous computing environment that permits us to routinely simulate complicated three-dimensional fluid flows and to readily visualize the results of each simulation via three-dimensional animation sequences. An 8192-node MasPar MP-1 computer with 0.5 GBytes of RAM provides 250 MFlops of execution speed for our fluid flow simulations. Utilizing the parallel virtual machine (PVM) language, at periodic intervals data is automatically transferred from the MP-1 to a cluster of workstations where individual three-dimensional images are rendered for inclusion in a single animation sequence. Work is underway to replace executions on the MP-1 with simulations performed on the 512-node CM-5 at NCSA and to simultaneously gain access to more potent volume rendering workstations.

Hybrid biological, electron beam and zero-valent nano iron treatment of recalcitrant metalworking fluids.

PubMed

Thill, Patrick G; Ager, Duane K; Vojnovic, Borivoj; Tesh, Sarah J; Scott, Thomas B; Thompson, Ian P

2016-04-15

Hybrid approaches for the remediation and detoxification of toxic recalcitrant industrial wastewater were investigated. The focus was waste metalworking fluid, which was selected as a representative model of other waste streams that are toxic, recalcitrant and that require more sustainable routes of safe disposal. The hybrid approaches included biodegradation, electron beam irradiation and zero-valent nano iron advanced oxidation processes that were employed individually and in sequence employing a factorial design. To compare process performance operationally exhausted and pristine metalworking fluid were compared. Sequential hybrid electron beam irradiation, biological, nanoscale zero-valent iron and biological treatment lead to synergistic detoxification and degradation of both recalcitrant streams, as determined by complementary surrogates and lead to overall improved COD removal of 92.8 ± 1.4% up from 85.9 ± 3.4% for the pristine metalworking fluid. Electron beam pre-treatment enabled more effective biotreatment, achieving 69.5 ± 8% (p = 0.005) and 24.6 ± 4.8% (p = 0.044) COD reductions. Copyright © 2016. Published by Elsevier Ltd.

A FRAMEWORK FOR FINE-SCALE COMPUTATIONAL FLUID DYNAMICS AIR QUALITY MODELING AND ANALYSIS

EPA Science Inventory

Fine-scale Computational Fluid Dynamics (CFD) simulation of pollutant concentrations within roadway and building microenvironments is feasible using high performance computing. Unlike currently used regulatory air quality models, fine-scale CFD simulations are able to account rig...

Physical-chemical characterization and biological assessment of simple and lithium-doped biological-derived hydroxyapatite thin films for a new generation of metallic implants

NASA Astrophysics Data System (ADS)

Popescu, A. C.; Florian, P. E.; Stan, G. E.; Popescu-Pelin, G.; Zgura, I.; Enculescu, M.; Oktar, F. N.; Trusca, R.; Sima, L. E.; Roseanu, A.; Duta, L.

2018-05-01

We report on the synthesis by PLD of simple and lithium-doped biological-origin hydroxyapatite (HA) films. The role of doping reagents (Li2CO3, Li3PO4) on the morphology, structure, chemical composition, bonding strength and cytocompatibility of the films was investigated. SEM investigations of the films evidenced a surface morphology consisting of particles with mean diameters of (5-7) μm. GIXRD analyses demonstrated that the synthesized structures consisted of HA phase only, with different degrees of crystallinity, mainly influenced by the doping reagent type. After only three days of immersion in simulated body fluid, FTIR spectra showed a remarkable growth of a biomimetic apatitic film, indicative of a high biomineralization capacity of the coatings. EDS analyses revealed a quasi-stoichiometric target-to-substrate transfer, the values inferred for the Ca/P ratio corresponding to a biological apatite. All synthesized structures displayed a hydrophilic behavior, suitable for attachment of osteoblast cells. In vitro cell viability tests showed that the presence of Li2CO3 and Li3PO4 as doping reagents promoted the hMSC growth on film surfaces. Taking into consideration these enhanced characteristics, corroborated with a low fabrication cost generated by sustainable resources, one should consider the lithium-doped biological-derived materials as promising prospective solutions for a next generation of coated implants with rapid osteointegration.

Determination of the thermodynamic correction factor of fluids confined in nano-metric slit pores from molecular simulation

NASA Astrophysics Data System (ADS)

Collell, Julien; Galliero, Guillaume

2014-05-01

The multi-component diffusive mass transport is generally quantified by means of the Maxwell-Stefan diffusion coefficients when using molecular simulations. These coefficients can be related to the Fick diffusion coefficients using the thermodynamic correction factor matrix, which requires to run several simulations to estimate all the elements of the matrix. In a recent work, Schnell et al. ["Thermodynamics of small systems embedded in a reservoir: A detailed analysis of finite size effects," Mol. Phys. 110, 1069-1079 (2012)] developed an approach to determine the full matrix of thermodynamic factors from a single simulation in bulk. This approach relies on finite size effects of small systems on the density fluctuations. We present here an extension of their work for inhomogeneous Lennard Jones fluids confined in slit pores. We first verified this extension by cross validating the results obtained from this approach with the results obtained from the simulated adsorption isotherms, which allows to determine the thermodynamic factor in porous medium. We then studied the effects of the pore width (from 1 to 15 molecular sizes), of the solid-fluid interaction potential (Lennard Jones 9-3, hard wall potential) and of the reduced fluid density (from 0.1 to 0.7 at a reduced temperature T* = 2) on the thermodynamic factor. The deviation of the thermodynamic factor compared to its equivalent bulk value decreases when increasing the pore width and becomes insignificant for reduced pore width above 15. We also found that the thermodynamic factor is sensitive to the magnitude of the fluid-fluid and solid-fluid interactions, which softens or exacerbates the density fluctuations.

Simulations of Bingham plastic flows with the multiple-relaxation-time lattice Boltzmann model

NASA Astrophysics Data System (ADS)

Chen, SongGui; Sun, QiCheng; Jin, Feng; Liu, JianGuo

2014-03-01

Fresh cement mortar is a type of workable paste, which can be well approximated as a Bingham plastic and whose flow behavior is of major concern in engineering. In this paper, Papanastasiou's model for Bingham fluids is solved by using the multiplerelaxation-time lattice Boltzmann model (MRT-LB). Analysis of the stress growth exponent m in Bingham fluid flow simulations shows that Papanastasiou's model provides a good approximation of realistic Bingham plastics for values of m > 108. For lower values of m, Papanastasiou's model is valid for fluids between Bingham and Newtonian fluids. The MRT-LB model is validated by two benchmark problems: 2D steady Poiseuille flows and lid-driven cavity flows. Comparing the numerical results of the velocity distributions with corresponding analytical solutions shows that the MRT-LB model is appropriate for studying Bingham fluids while also providing better numerical stability. We further apply the MRT-LB model to simulate flow through a sudden expansion channel and the flow surrounding a round particle. Besides the rich flow structures obtained in this work, the dynamics fluid force on the round particle is calculated. Results show that both the Reynolds number Re and the Bingham number Bn affect the drag coefficients C D , and a drag coefficient with Re and Bn being taken into account is proposed. The relationship of Bn and the ratio of unyielded zone thickness to particle diameter is also analyzed. Finally, the Bingham fluid flowing around a set of randomly dispersed particles is simulated to obtain the apparent viscosity and velocity fields. These results help simulation of fresh concrete flowing in porous media.

Determination of the thermodynamic correction factor of fluids confined in nano-metric slit pores from molecular simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collell, Julien; Galliero, Guillaume, E-mail: guillaume.galliero@univ-pau.fr

2014-05-21

The multi-component diffusive mass transport is generally quantified by means of the Maxwell-Stefan diffusion coefficients when using molecular simulations. These coefficients can be related to the Fick diffusion coefficients using the thermodynamic correction factor matrix, which requires to run several simulations to estimate all the elements of the matrix. In a recent work, Schnell et al. [“Thermodynamics of small systems embedded in a reservoir: A detailed analysis of finite size effects,” Mol. Phys. 110, 1069–1079 (2012)] developed an approach to determine the full matrix of thermodynamic factors from a single simulation in bulk. This approach relies on finite size effectsmore » of small systems on the density fluctuations. We present here an extension of their work for inhomogeneous Lennard Jones fluids confined in slit pores. We first verified this extension by cross validating the results obtained from this approach with the results obtained from the simulated adsorption isotherms, which allows to determine the thermodynamic factor in porous medium. We then studied the effects of the pore width (from 1 to 15 molecular sizes), of the solid-fluid interaction potential (Lennard Jones 9-3, hard wall potential) and of the reduced fluid density (from 0.1 to 0.7 at a reduced temperature T* = 2) on the thermodynamic factor. The deviation of the thermodynamic factor compared to its equivalent bulk value decreases when increasing the pore width and becomes insignificant for reduced pore width above 15. We also found that the thermodynamic factor is sensitive to the magnitude of the fluid-fluid and solid-fluid interactions, which softens or exacerbates the density fluctuations.« less

Microfluidic chambers using fluid walls for cell biology.

PubMed

Soitu, Cristian; Feuerborn, Alexander; Tan, Ann Na; Walker, Henry; Walsh, Pat A; Castrejón-Pita, Alfonso A; Cook, Peter R; Walsh, Edmond J

2018-06-12

Many proofs of concept have demonstrated the potential of microfluidics in cell biology. However, the technology remains inaccessible to many biologists, as it often requires complex manufacturing facilities (such as soft lithography) and uses materials foreign to cell biology (such as polydimethylsiloxane). Here, we present a method for creating microfluidic environments by simply reshaping fluids on a substrate. For applications in cell biology, we use cell media on a virgin Petri dish overlaid with an immiscible fluorocarbon. A hydrophobic/fluorophilic stylus then reshapes the media into any pattern by creating liquid walls of fluorocarbon. Microfluidic arrangements suitable for cell culture are made in minutes using materials familiar to biologists. The versatility of the method is demonstrated by creating analogs of a common platform in cell biology, the microtiter plate. Using this vehicle, we demonstrate many manipulations required for cell culture and downstream analysis, including feeding, replating, cloning, cryopreservation, lysis plus RT-PCR, transfection plus genome editing, and fixation plus immunolabeling (when fluid walls are reconfigured during use). We also show that mammalian cells grow and respond to stimuli normally, and worm eggs develop into adults. This simple approach provides biologists with an entrée into microfluidics. Copyright © 2018 the Author(s). Published by PNAS.

Bulk properties and near-critical behaviour of SiO2 fluid

NASA Astrophysics Data System (ADS)

Green, Eleanor C. R.; Artacho, Emilio; Connolly, James A. D.

2018-06-01

Rocky planets and satellites form through impact and accretion processes that often involve silicate fluids at extreme temperatures. First-principles molecular dynamics (FPMD) simulations have been used to investigate the bulk thermodynamic properties of SiO2 fluid at high temperatures (4000-6000 K) and low densities (500-2240 kg m-3), conditions which are relevant to protoplanetary disc condensation. Liquid SiO2 is highly networked at the upper end of this density range, but depolymerises with increasing temperature and volume, in a process characterised by the formation of oxygen-oxygen (Odbnd O) pairs. The onset of vaporisation is closely associated with the depolymerisation process, and is likely to be non-stoichiometric at high temperature, initiated via the exsolution of O2 molecules to leave a Si-enriched fluid. By 6000 K the simulated fluid is supercritical. A large anomaly in the constant-volume heat capacity occurs near the critical temperature. We present tabulated thermodynamic properties for silica fluid that reconcile observations from FPMD simulations with current knowledge of the SiO2 melting curve and experimental Hugoniot curves.

Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wood, Irene; Martini, M. Florencia; Pickholz, Mónica

2013-08-01

In this work, we report a molecular dynamics (MD) simulations study of relevant biological molecules as serotonin (neutral and protonated) and its precursors, tryptophan and 5-hydroxy-tryptophan, in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC). The simulations were carried out at the fluid lamellar phase of POPC at constant pressure and temperature conditions. Two guest molecules of each type were initially placed at the water phase. We have analyzed, the main localization, preferential orientation and specific interactions of the guest molecules within the bilayer. During the simulation run, the four molecules were preferentially found at the water-lipid interphase. We found that the interactions that stabilized the systems are essentially hydrogen bonds, salt bridges and cation-π. None of the guest molecules have access to the hydrophobic region of the bilayer. Besides, zwitterionic molecules have access to the water phase, while protonated serotonin is anchored in the interphase. Even taking into account that these simulations were done using a model membrane, our results suggest that the studied molecules could not cross the blood brain barrier by diffusion. These results are in good agreement with works that show that serotonin and Trp do not cross the BBB by simple diffusion.

In vitro assessment of arsenic mobility in historical mine waste dust using simulated lung fluid.

PubMed

Martin, Rachael; Dowling, Kim; Nankervis, Scott; Pearce, Dora; Florentine, Singarayer; McKnight, Stafford

2018-06-01

Exposure studies have linked arsenic (As) ingestion with disease in mining-affected populations; however, inhalation of mine waste dust as a pathway for pulmonary toxicity and systemic absorption has received limited attention. A biologically relevant extractant was used to assess the 24-h lung bioaccessibility of As in dust isolated from four distinct types of historical gold mine wastes common to regional Victoria, Australia. Mine waste particles less than 20 µm in size (PM 20 ) were incubated in a simulated lung fluid containing a major surface-active component found in mammalian lungs, dipalmitoylphosphatidylcholine. The supernatants were extracted, and their As contents measured after 1, 2, 4, 8 and 24 h. The resultant As solubility profiles show rapid dissolution followed by a more modest increasing trend, with between 75 and 82% of the total 24-h bioaccessible As released within the first 8 h. These profiles are consistent with the solubility profile of scorodite, a secondary As-bearing phase detected by X-ray diffraction in one of the investigated waste materials. Compared with similar studies, the cumulative As concentrations released at the 24-h time point were extremely low (range 297 ± 6-3983 ± 396 µg L -1 ), representing between 0.020 ± 0.002 and 0.036 ± 0.003% of the total As in the PM 20 .

Differential Rotation in Solar-like Convective Envelopes: Influence of Overshoot and Magnetism

NASA Astrophysics Data System (ADS)

Beaudoin, Patrice; Strugarek, Antoine; Charbonneau, Paul

2018-05-01

We present a set of four global Eulerian/semi-Lagrangian fluid solver (EULAG) hydrodynamical (HD) and magnetohydrodynamical (MHD) simulations of solar convection, two of which are restricted to the nominal convection zone, and the other two include an underlying stably stratified fluid layer. While all four simulations generate reasonably solar-like latitudinal differential rotation profiles where the equatorial region rotates faster than the polar regions, the rotational isocontours vary significantly among them. In particular, the purely HD simulation with a stable layer alone can break the Taylor–Proudman theorem and produce approximately radially oriented rotational isocontours at medium to high latitudes. We trace this effect to the buildup of a significant latitudinal temperature gradient in the stable fluid immediately beneath the convection zone, which imprints itself on the lower convection zone. It develops naturally in our simulations as a consequence of convective overshoot and rotational influence of rotation on convective energy fluxes. This favors the establishment of a thermal wind balance that allows evading the Taylor–Proudman constraint. A much smaller latitudinal temperature gradient develops in the companion MHD simulation that includes a stable fluid layer, reflecting the tapering of deep convective overshoot that occurs at medium to high latitudes, which is caused by the strong magnetic fields that accumulate across the base of the convection zone. The stable fluid layer also has a profound impact on the large-scale magnetic cycles developing in the two MHD simulations. Even though both simulations operate in the same convective parameter regime, the simulation that includes a stable layer eventually loses cyclicity and transits to a non-solar, steady quadrupolar state.

User's guide of TOUGH2-EGS-MP: A Massively Parallel Simulator with Coupled Geomechanics for Fluid and Heat Flow in Enhanced Geothermal Systems VERSION 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong, Yi; Fakcharoenphol, Perapon; Wang, Shihao

2013-12-01

TOUGH2-EGS-MP is a parallel numerical simulation program coupling geomechanics with fluid and heat flow in fractured and porous media, and is applicable for simulation of enhanced geothermal systems (EGS). TOUGH2-EGS-MP is based on the TOUGH2-MP code, the massively parallel version of TOUGH2. In TOUGH2-EGS-MP, the fully-coupled flow-geomechanics model is developed from linear elastic theory for thermo-poro-elastic systems and is formulated in terms of mean normal stress as well as pore pressure and temperature. Reservoir rock properties such as porosity and permeability depend on rock deformation, and the relationships between these two, obtained from poro-elasticity theories and empirical correlations, are incorporatedmore » into the simulation. This report provides the user with detailed information on the TOUGH2-EGS-MP mathematical model and instructions for using it for Thermal-Hydrological-Mechanical (THM) simulations. The mathematical model includes the fluid and heat flow equations, geomechanical equation, and discretization of those equations. In addition, the parallel aspects of the code, such as domain partitioning and communication between processors, are also included. Although TOUGH2-EGS-MP has the capability for simulating fluid and heat flows coupled with geomechanical effects, it is up to the user to select the specific coupling process, such as THM or only TH, in a simulation. There are several example problems illustrating applications of this program. These example problems are described in detail and their input data are presented. Their results demonstrate that this program can be used for field-scale geothermal reservoir simulation in porous and fractured media with fluid and heat flow coupled with geomechanical effects.« less

Intraoperative stroke volume optimization using stroke volume, arterial pressure, and heart rate: closed-loop (learning intravenous resuscitator) versus anesthesiologists.

PubMed

Rinehart, Joseph; Chung, Elena; Canales, Cecilia; Cannesson, Maxime

2012-10-01

The authors compared the performance of a group of anesthesia providers to closed-loop (Learning Intravenous Resuscitator [LIR]) management in a simulated hemorrhage scenario using cardiac output monitoring. A prospective cohort study. In silico simulation. University hospital anesthesiologists and the LIR closed-loop fluid administration system. Using a patient simulator, a 90-minute simulated hemorrhage protocol was run, which included a 1,200-mL blood loss over 30 minutes. Twenty practicing anesthesiology providers were asked to manage this scenario by providing fluids and vasopressor medication at their discretion. The simulation program was also run 20 times with the LIR closed-loop algorithm managing fluids and an additional 20 times with no intervention. Simulated patient weight, height, heart rate, mean arterial pressure, and cardiac output (CO) were similar at baseline. The mean stroke volume, the mean arterial pressure, CO, and the final CO were higher in the closed-loop group than in the practitioners group, and the coefficient of variance was lower. The closed-loop group received slightly more fluid (2.1 v 1.9 L, p < 0.05) than the anesthesiologist group. Despite the roughly similar volumes of fluid given, the closed-loop maintained more stable hemodynamics than the practitioners primarily because the fluid was given earlier in the protocol and CO optimized before the hemorrhage began, whereas practitioners tended to resuscitate well but only after significant hemodynamic change indicated the need. Overall, these data support the potential usefulness of this closed-loop algorithm in clinical settings in which dynamic predictors are not available or applicable. Published by Elsevier Inc.

Active learning of constitutive relation from mesoscopic dynamics for macroscopic modeling of non-Newtonian flows

NASA Astrophysics Data System (ADS)

Zhao, Lifei; Li, Zhen; Caswell, Bruce; Ouyang, Jie; Karniadakis, George Em

2018-06-01

We simulate complex fluids by means of an on-the-fly coupling of the bulk rheology to the underlying microstructure dynamics. In particular, a continuum model of polymeric fluids is constructed without a pre-specified constitutive relation, but instead it is actively learned from mesoscopic simulations where the dynamics of polymer chains is explicitly computed. To couple the bulk rheology of polymeric fluids and the microscale dynamics of polymer chains, the continuum approach (based on the finite volume method) provides the transient flow field as inputs for the (mesoscopic) dissipative particle dynamics (DPD), and in turn DPD returns an effective constitutive relation to close the continuum equations. In this multiscale modeling procedure, we employ an active learning strategy based on Gaussian process regression (GPR) to minimize the number of expensive DPD simulations, where adaptively selected DPD simulations are performed only as necessary. Numerical experiments are carried out for flow past a circular cylinder of a non-Newtonian fluid, modeled at the mesoscopic level by bead-spring chains. The results show that only five DPD simulations are required to achieve an effective closure of the continuum equations at Reynolds number Re = 10. Furthermore, when Re is increased to 100, only one additional DPD simulation is required for constructing an extended GPR-informed model closure. Compared to traditional message-passing multiscale approaches, applying an active learning scheme to multiscale modeling of non-Newtonian fluids can significantly increase the computational efficiency. Although the method demonstrated here obtains only a local viscosity from the polymer dynamics, it can be extended to other multiscale models of complex fluids whose macro-rheology is unknown.

System for Dispensing a Precise Amount of Fluid

DOEpatents

Benett, William J.; Krulevitch, Peter A.; Visuri, Steven R.; Dzenitis, John M.; Ness, Kevin D.

2008-08-12

A dispensing system delivers a precise amount of fluid for biological or chemical processing and/or analysis. Dispensing means moves the fluid. The dispensing means is operated by a pneumatic force. Connection means delivers the fluid to the desired location. An actuator means provides the pneumatic force to the dispensing means. Valving means transmits the pneumatic force from the actuator means to the dispensing means.

Fluid Simulation in the Movies: Navier and Stokes Must Be Circulating in Their Graves

NASA Astrophysics Data System (ADS)

Tessendorf, Jerry

2010-11-01

Fluid simulations based on the Incompressible Navier-Stokes equations are commonplace computer graphics tools in the visual effects industry. These simulations mostly come from custom C++ code written by the visual effects companies. Their significant impact in films was recognized in 2008 with Academy Awards to four visual effects companies for their technical achievement. However artists are not fluid dynamicists, and fluid dynamics simulations are expensive to use in a deadline-driven production environment. As a result, the simulation algorithms are modified to limit the computational resources, adapt them to production workflow, and to respect the client's vision of the film plot. Eulerian solvers on fixed rectangular grids use a mix of momentum solvers, including Semi-Lagrangian, FLIP, and QUICK. Incompressibility is enforced with FFT, Conjugate Gradient, and Multigrid methods. For liquids, a levelset field tracks the free surface. Smooth Particle Hydrodynamics is also used, and is part of a hybrid Eulerian-SPH liquid simulator. Artists use all of them in a mix and match fashion to control the appearance of the simulation. Specially designed forces and boundary conditions control the flow. The simulation can be an input to artistically driven procedural particle simulations that enhance the flow with more detail and drama. Post-simulation processing increases the visual detail beyond the grid resolution. Ultimately, iterative simulation methods that fit naturally in the production workflow are extremely desirable but not yet successful. Results from some efforts for iterative methods are shown, and other approaches motivated by the history of production are proposed.

Skylab fluid mechanics simulations: Oscillation, rotation, collision and coalescence of water droplets under low-gravity environment

NASA Technical Reports Server (NTRS)

Vaughan, O. H., Jr.; Hung, R. J.

1975-01-01

Skylab 4 crew members performed a series of demonstrations showing the oscillations, rotations, as well as collision coalescence of water droplets which simulate various physical models of fluids under low gravity environment. The results from Skylab demonstrations provide information and illustrate the potential of an orbiting space-oriented research laboratory for the study of more sophisticated fluid mechanic experiments. Experiments and results are discussed.

Implementation of Interaction Algorithm to Non-Matching Discrete Interfaces Between Structure and Fluid Mesh

NASA Technical Reports Server (NTRS)

Chen, Shu-Po

1999-01-01

This paper presents software for solving the non-conforming fluid structure interfaces in aeroelastic simulation. It reviews the algorithm of interpolation and integration, highlights the flexibility and the user-friendly feature that allows the user to select the existing structure and fluid package, like NASTRAN and CLF3D, to perform the simulation. The presented software is validated by computing the High Speed Civil Transport model.

Preliminary Numerical Simulations of Nozzle Formation in the Host Rock of Supersonic Volcanic Jets

NASA Astrophysics Data System (ADS)

Wohletz, K. H.; Ogden, D. E.; Glatzmaier, G. A.

2006-12-01

Recognizing the difficulty in quantitatively predicting how a vent changes during an explosive eruption, Kieffer (Kieffer, S.W., Rev. Geophys. 27, 1989) developed the theory of fluid dynamic nozzles for volcanism, utilizing a highly developed predictive scheme used extensively in aerodynamics for design of jet and rocket nozzles. Kieffer's work shows that explosive eruptions involve flow from sub to supersonic conditions through the vent and that these conditions control the erosion of the vent to nozzle shapes and sizes that maximize mass flux. The question remains how to predict the failure and erosion of vent host rocks by a high-speed, multiphase, compressible fluid that represents an eruption column. Clearly, in order to have a quantitative model of vent dynamics one needs a robust computational method for a turbulent, compressible, multiphase fluid. Here we present preliminary simulations of fluid flowing from a high-pressure reservoir through an eroding conduit and into the atmosphere. The eruptive fluid is modeled as an ideal gas, the host rock as a simple incompressible fluid with sandstone properties. Although these simulations do not yet include the multiphase dynamics of the eruptive fluid or the solid mechanics of the host rock, the evolution of the host rock into a supersonic nozzle is clearly seen. Our simulations show shock fronts both above the conduit, where the gas has expanded into the atmosphere, and within the conduit itself, thereby influencing the dynamics of the jet decompression.

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

A simple and sensitive determination of histamine and N tau-methylhistamine in biological fluids by high-performance liquid chromatography with electrochemical detection.

PubMed

Houdi, A A; Crooks, P A; Van Loon, G R; Schubert, C A

1987-05-01

The determination of picomolar levels of histamine and its major metabolite, N tau-methylhistamine, in biological fluids was achieved using reversed-phase liquid chromatography coupled with electrochemical detection. A simple sample purification procedure for blood and urine samples was carried out prior to analysis using an Amberlite CG-50 cation-exchange resin, which afforded an excellent recovery of both compounds.

A Hybrid Model for Multiscale Laser Plasma Simulations with Detailed Collisional Physics

DTIC Science & Technology

2017-06-23

the effects of inelastic collisions on the Multi-Fluid description of plasmas. 15. SUBJECT TERMS Electric propulsion; plasma; collisional...modeling as well as the effects of inelastic collisions on the Multi-Fluid description of plasmas. This work has been recognized in two workshop...encountered during simulation was to define when breakdown occurred during the simulation and correlating the results to the experimentally determined

Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations

DTIC Science & Technology

2017-05-23

Dynamics Simulations Ghanshyam L. Vaghjiani Air Force Research Laboratory (AFMC) AFRL/RQRS 1 Ara Drive Edwards AFB, CA 93524-7013 Air Force...Aerospace Systems Directorate Air Force Research Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil IMPROVED...PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release

A universal fluid cell for the imaging of biological specimens in the atomic force microscope.

PubMed

Kasas, Sandor; Radotic, Ksenja; Longo, Giovanni; Saha, Bashkar; Alonso-Sarduy, Livan; Dietler, Giovanni; Roduit, Charles

2013-04-01

Recently, atomic force microscope (AFM) manufacturers have begun producing instruments specifically designed to image biological specimens. In most instances, they are integrated with an inverted optical microscope, which permits concurrent optical and AFM imaging. An important component of the set-up is the imaging chamber, whose design determines the nature of the experiments that can be conducted. Many different imaging chamber designs are available, usually designed to optimize a single parameter, such as the dimensions of the substrate or the volume of fluid that can be used throughout the experiment. In this report, we present a universal fluid cell, which simultaneously optimizes all of the parameters that are important for the imaging of biological specimens in the AFM. This novel imaging chamber has been successfully tested using mammalian, plant, and microbial cells. Copyright © 2013 Wiley Periodicals, Inc.

PVDF Sensor Stimulated by Infrared Radiation for Temperature Monitoring in Microfluidic Devices.

PubMed

Pullano, Salvatore A; Mahbub, Ifana; Islam, Syed K; Fiorillo, Antonino S

2017-04-13

This paper presents a ferroelectric polymer-based temperature sensor designed for microfluidic devices. The integration of the sensor into a system-on-a-chip platform facilitates quick monitoring of localized temperature of a biological fluid, avoiding errors in the evaluation of thermal evolution of the fluid during analysis. The contact temperature sensor is fabricated by combining a thin pyroelectric film together with an infrared source, which stimulates the active element located on the top of the microfluidic channel. An experimental setup was assembled to validate the analytical model and to characterize the response rate of the device. The evaluation procedure and the operating range of the temperature also make this device suitable for applications where the localized temperature monitoring of biological samples is necessary. Additionally, ease of integration with standard microfluidic devices makes the proposed sensor an attractive option for in situ analysis of biological fluids.

Kirigami artificial muscles with complex biologically inspired morphologies

NASA Astrophysics Data System (ADS)

Sareh, Sina; Rossiter, Jonathan

2013-01-01

In this paper we present bio-inspired smart structures which exploit the actuation of flexible ionic polymer composites and the kirigami design principle. Kirigami design is used to convert planar actuators into active 3D structures capable of large out-of-plane displacement and that replicate biological mechanisms. Here we present the burstbot, a fluid control and propulsion mechanism based on the atrioventricular cuspid valve, and the vortibot, a spiral actuator based on Vorticella campanula, a ciliate protozoa. Models derived from biological counterparts are used as a platform for design optimization and actuator performance measurement. The symmetric and asymmetric fluid interactions of the burstbot are investigated and the effectiveness in fluid transport applications is demonstrated. The vortibot actuator is geometrically optimized as a camera positioner capable of 360° scanning. Experimental results for a one-turn spiral actuator show complex actuation derived from a single degree of freedom control signal.

Measurement with microscopic MRI and simulation of flow in different aneurysm models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edelhoff, Daniel, E-mail: daniel.edelhoff@tu-dortmund.de; Frank, Frauke; Heil, Marvin

2015-10-15

Purpose: The impact and the development of aneurysms depend to a significant degree on the exchange of liquid between the regular vessel and the pathological extension. A better understanding of this process will lead to improved prediction capabilities. The aim of the current study was to investigate fluid-exchange in aneurysm models of different complexities by combining microscopic magnetic resonance measurements with numerical simulations. In order to evaluate the accuracy and applicability of these methods, the fluid-exchange process between the unaltered vessel lumen and the aneurysm phantoms was analyzed quantitatively using high spatial resolution. Methods: Magnetic resonance flow imaging was usedmore » to visualize fluid-exchange in two different models produced with a 3D printer. One model of an aneurysm was based on histological findings. The flow distribution in the different models was measured on a microscopic scale using time of flight magnetic resonance imaging. The whole experiment was simulated using fast graphics processing unit-based numerical simulations. The obtained simulation results were compared qualitatively and quantitatively with the magnetic resonance imaging measurements, taking into account flow and spin–lattice relaxation. Results: The results of both presented methods compared well for the used aneurysm models and the chosen flow distributions. The results from the fluid-exchange analysis showed comparable characteristics concerning measurement and simulation. Similar symmetry behavior was observed. Based on these results, the amount of fluid-exchange was calculated. Depending on the geometry of the models, 7% to 45% of the liquid was exchanged per second. Conclusions: The result of the numerical simulations coincides well with the experimentally determined velocity field. The rate of fluid-exchange between vessel and aneurysm was well-predicted. Hence, the results obtained by simulation could be validated by the experiment. The observed deviations can be caused by the noise in the measurement and by the limited resolution of the simulation. The resulting differences are small enough to allow reliable predictions of the flow distribution in vessels with stents and for pulsed blood flow.« less

An analytical study of reduced-gravity flow dynamics

NASA Technical Reports Server (NTRS)

Bradshaw, R. D.; Kramer, J. L.; Zich, J. L.

1976-01-01

Addition of surface tension forces to a marker-and-cell code and the performance of four incompressible fluid simulations in reduced gravity, were studied. This marker-and-cell code has a variable grid capability with arbitrary curved boundaries and time dependent acceleration fields. The surface tension logic includes a spline fit of surface marker particles as well as contact angle logic for straight and curved wall boundaries. Three types of flow motion were simulated with the improved code: impulsive settling in a model Centaur LH2 tank, continuous settling in a model and full scale Centaur LO2 tank and mixing in a Centaur LH2 tank. The impulsive settling case confirmed a drop tower analysis which indicated more orderly fluid collection flow patterns with this method providing a potential savings in settling propellants. In the LO2 tank, fluid collection and flow simulation into the thrust barrel were achieved. The mixing simulation produced good results indicating both the development of the flow field and fluid interface behavior.

Eulerian-Lagrangian Simulations of Transonic Flutter Instabilities

NASA Technical Reports Server (NTRS)

Bendiksen, Oddvar O.

1994-01-01

This paper presents an overview of recent applications of Eulerian-Lagrangian computational schemes in simulating transonic flutter instabilities. This approach, the fluid-structure system is treated as a single continuum dynamics problem, by switching from an Eulerian to a Lagrangian formulation at the fluid-structure boundary. This computational approach effectively eliminates the phase integration errors associated with previous methods, where the fluid and structure are integrated sequentially using different schemes. The formulation is based on Hamilton's Principle in mixed coordinates, and both finite volume and finite element discretization schemes are considered. Results from numerical simulations of transonic flutter instabilities are presented for isolated wings, thin panels, and turbomachinery blades. The results suggest that the method is capable of reproducing the energy exchange between the fluid and the structure with significantly less error than existing methods. Localized flutter modes and panel flutter modes involving traveling waves can also be simulated effectively with no a priori knowledge of the type of instability involved.

Methods for compressible fluid simulation on GPUs using high-order finite differences

NASA Astrophysics Data System (ADS)

Pekkilä, Johannes; Väisälä, Miikka S.; Käpylä, Maarit J.; Käpylä, Petri J.; Anjum, Omer

2017-08-01

We focus on implementing and optimizing a sixth-order finite-difference solver for simulating compressible fluids on a GPU using third-order Runge-Kutta integration. Since graphics processing units perform well in data-parallel tasks, this makes them an attractive platform for fluid simulation. However, high-order stencil computation is memory-intensive with respect to both main memory and the caches of the GPU. We present two approaches for simulating compressible fluids using 55-point and 19-point stencils. We seek to reduce the requirements for memory bandwidth and cache size in our methods by using cache blocking and decomposing a latency-bound kernel into several bandwidth-bound kernels. Our fastest implementation is bandwidth-bound and integrates 343 million grid points per second on a Tesla K40t GPU, achieving a 3 . 6 × speedup over a comparable hydrodynamics solver benchmarked on two Intel Xeon E5-2690v3 processors. Our alternative GPU implementation is latency-bound and achieves the rate of 168 million updates per second.

Hydrodynamic cavitation in Stokes flow of anisotropic fluids.

PubMed

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G; Sengupta, Anupam

2017-05-30

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids.

Hydrodynamic cavitation in Stokes flow of anisotropic fluids

PubMed Central

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G.; Sengupta, Anupam

2017-01-01

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids. PMID:28555615

Hydrodynamic cavitation in Stokes flow of anisotropic fluids

NASA Astrophysics Data System (ADS)

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G.; Sengupta, Anupam

2017-05-01

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids.

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments.

PubMed

Dona, Anthony C; Kyriakides, Michael; Scott, Flora; Shephard, Elizabeth A; Varshavi, Dorsa; Veselkov, Kirill; Everett, Jeremy R

2016-01-01

Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), the latter typically with hyphenation to a chromatography system such as liquid chromatography (LC), in a configuration known as LC-MS. With both NMR and MS-based detection technologies, the identification of the metabolites in the biological sample remains a significant obstacle and bottleneck. This article provides guidance on methods for metabolite identification in biological fluids using NMR spectroscopy, and is illustrated with examples from recent studies on mice.

Specificity of Intramembrane Protein–Lipid Interactions

PubMed Central

Contreras, Francesc-Xabier; Ernst, Andreas Max; Wieland, Felix; Brügger, Britta

2011-01-01

Our concept of biological membranes has markedly changed, from the fluid mosaic model to the current model that lipids and proteins have the ability to separate into microdomains, differing in their protein and lipid compositions. Since the breakthrough in crystallizing membrane proteins, the most powerful method to define lipid-binding sites on proteins has been X-ray and electron crystallography. More recently, chemical biology approaches have been developed to analyze protein–lipid interactions. Such methods have the advantage of providing highly specific cellular probes. With the advent of novel tools to study functions of individual lipid species in membranes together with structural analysis and simulations at the atomistic resolution, a growing number of specific protein–lipid complexes are defined and their functions explored. In the present article, we discuss the various modes of intramembrane protein–lipid interactions in cellular membranes, including examples for both annular and nonannular bound lipids. Furthermore, we will discuss possible functional roles of such specific protein–lipid interactions as well as roles of lipids as chaperones in protein folding and transport. PMID:21536707

Fully kinetic simulations of dense plasma focus Z-pinch devices.

PubMed

Schmidt, A; Tang, V; Welch, D

2012-11-16

Dense plasma focus Z-pinch devices are sources of copious high energy electrons and ions, x rays, and neutrons. The mechanisms through which these physically simple devices generate such high-energy beams in a relatively short distance are not fully understood. We now have, for the first time, demonstrated a capability to model these plasmas fully kinetically, allowing us to simulate the pinch process at the particle scale. We present here the results of the initial kinetic simulations, which reproduce experimental neutron yields (~10(7)) and high-energy (MeV) beams for the first time. We compare our fluid, hybrid (kinetic ions and fluid electrons), and fully kinetic simulations. Fluid simulations predict no neutrons and do not allow for nonthermal ions, while hybrid simulations underpredict neutron yield by ~100x and exhibit an ion tail that does not exceed 200 keV. Only fully kinetic simulations predict MeV-energy ions and experimental neutron yields. A frequency analysis in a fully kinetic simulation shows plasma fluctuations near the lower hybrid frequency, possibly implicating lower hybrid drift instability as a contributor to anomalous resistivity in the plasma.

Numerical investigation of fluid mud motion using a three-dimensional hydrodynamic and two-dimensional fluid mud coupling model

NASA Astrophysics Data System (ADS)

Yang, Xiaochen; Zhang, Qinghe; Hao, Linnan

2015-03-01

A water-fluid mud coupling model is developed based on the unstructured grid finite volume coastal ocean model (FVCOM) to investigate the fluid mud motion. The hydrodynamics and sediment transport of the overlying water column are solved using the original three-dimensional ocean model. A horizontal two-dimensional fluid mud model is integrated into the FVCOM model to simulate the underlying fluid mud flow. The fluid mud interacts with the water column through the sediment flux, current, and shear stress. The friction factor between the fluid mud and the bed, which is traditionally determined empirically, is derived with the assumption that the vertical distribution of shear stress below the yield surface of fluid mud is identical to that of uniform laminar flow of Newtonian fluid in the open channel. The model is validated by experimental data and reasonable agreement is found. Compared with numerical cases with fixed friction factors, the results simulated with the derived friction factor exhibit the best agreement with the experiment, which demonstrates the necessity of the derivation of the friction factor.

Development of an Efficient CFD Model for Nuclear Thermal Thrust Chamber Assembly Design

NASA Technical Reports Server (NTRS)

Cheng, Gary; Ito, Yasushi; Ross, Doug; Chen, Yen-Sen; Wang, Ten-See

2007-01-01

The objective of this effort is to develop an efficient and accurate computational methodology to predict both detailed thermo-fluid environments and global characteristics of the internal ballistics for a hypothetical solid-core nuclear thermal thrust chamber assembly (NTTCA). Several numerical and multi-physics thermo-fluid models, such as real fluid, chemically reacting, turbulence, conjugate heat transfer, porosity, and power generation, were incorporated into an unstructured-grid, pressure-based computational fluid dynamics solver as the underlying computational methodology. The numerical simulations of detailed thermo-fluid environment of a single flow element provide a mechanism to estimate the thermal stress and possible occurrence of the mid-section corrosion of the solid core. In addition, the numerical results of the detailed simulation were employed to fine tune the porosity model mimic the pressure drop and thermal load of the coolant flow through a single flow element. The use of the tuned porosity model enables an efficient simulation of the entire NTTCA system, and evaluating its performance during the design cycle.

A symbiotic approach to fluid equations and non-linear flux-driven simulations of plasma dynamics

NASA Astrophysics Data System (ADS)

Halpern, Federico

2017-10-01

The fluid framework is ubiquitous in studies of plasma transport and stability. Typical forms of the fluid equations are motivated by analytical work dating several decades ago, before computer simulations were indispensable, and can be, therefore, not optimal for numerical computation. We demonstrate a new first-principles approach to obtaining manifestly consistent, skew-symmetric fluid models, ensuring internal consistency and conservation properties even in discrete form. Mass, kinetic, and internal energy become quadratic (and always positive) invariants of the system. The model lends itself to a robust, straightforward discretization scheme with inherent non-linear stability. A simpler, drift-ordered form of the equations is obtained, and first results of their numerical implementation as a binary framework for bulk-fluid global plasma simulations are demonstrated. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences, Theory Program, under Award No. DE-FG02-95ER54309.

Oral fluid vs. Urine Analysis to Monitor Synthetic Cannabinoids and Classic Drugs Recent Exposure

PubMed Central

Blandino, Vincent; Wetzel, Jillian; Kim, Jiyoung; Haxhi, Petrit; Curtis, Richard; Concheiro, Marta

2018-01-01

Background Urine is a common biological sample to monitor recent drug exposure, and oral fluid is an alternative matrix of increasing interest in clinical and forensic toxicology. Limited data are available about oral fluid vs. urine drug disposition, especially for synthetic cannabinoids. Objective To compare urine and oral fluid as biological matrices to monitor recent drug exposure among HIV-infected homeless individuals. Methods Seventy matched urine and oral fluid samples were collected from 13 participants. Cannabis, amphetamines, benzodiazepines, cocaine and opiates were analyzed in urine by the enzyme-multiplied-immunoassay-technique and in oral fluid by liquid chromatography tandem mass spectrometry (LC-MSMS). Eleven synthetic cannabinoids were analyzed in urine and in oral fluid by LC-MSMS. Results Five oral fluid samples were positive for AB-FUBINACA. In urine, 4 samples tested positive for synthetic cannabinoids PB-22, 5-Fluoro-PB-22, AB-FUBINACA, and metabolites UR-144 5-pentanoic acid and UR-144 4-hydroxypentyl. In only one case, oral fluid and urine results matched, both specimens being AB-FUBINACA positive. For cannabis, 40 samples tested positive in urine and 30 in oral fluid (85.7% match). For cocaine, 37 urine and 52 oral fluid samples were positive (75.7% match). Twenty-four urine samples were positive for opiates, and 25 in oral fluid (81.4% match). For benzodiazepines, 23 samples were positive in urine and 25 in oral fluid (85.7% match). Conclusion/Discussion These results offer new information about drugs disposition between urine and oral fluid. Oral fluid is a good alternative matrix to urine for monitoring cannabis, cocaine, opiates and benzodiazepines recent use; however, synthetic cannabinoids showed mixed results. PMID:29173162

Oral Fluid vs. Urine Analysis to Monitor Synthetic Cannabinoids and Classic Drugs Recent Exposure.

PubMed

Blandino, Vincent; Wetzel, Jillian; Kim, Jiyoung; Haxhi, Petrit; Curtis, Richard; Concheiro, Marta

2017-01-01

Urine is a common biological sample to monitor recent drug exposure, and oral fluid is an alternative matrix of increasing interest in clinical and forensic toxicology. Limited data are available about oral fluid vs. urine drug disposition, especially for synthetic cannabinoids. To compare urine and oral fluid as biological matrices to monitor recent drug exposure among HIV-infected homeless individuals. Seventy matched urine and oral fluid samples were collected from 13 participants. Cannabis, amphetamines, benzodiazepines, cocaine and opiates were analyzed in urine by the enzyme-multipliedimmunoassay- technique and in oral fluid by liquid chromatography tandem mass spectrometry (LCMSMS). Eleven synthetic cannabinoids were analyzed in urine and in oral fluid by LC-MSMS. Five oral fluid samples were positive for AB-FUBINACA. In urine, 4 samples tested positive for synthetic cannabinoids PB-22, 5-Fluoro-PB-22, AB-FUBINACA, and metabolites UR-144 5-pentanoic acid and UR-144 4-hydroxypentyl. In only one case, oral fluid and urine results matched, both specimens being AB-FUBINACA positive. For cannabis, 40 samples tested positive in urine and 30 in oral fluid (85.7% match). For cocaine, 37 urine and 52 oral fluid samples were positive (75.7% match). Twenty-four urine samples were positive for opiates, and 25 in oral fluid (81.4% match). For benzodiazepines, 23 samples were positive in urine and 25 in oral fluid (85.7% match). These results offer new information about drugs disposition between urine and oral fluid. Oral fluid is a good alternative matrix to urine for monitoring cannabis, cocaine, opiates and benzodiazepines recent use; however, synthetic cannabinoids showed mixed results. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

3D Parallel Multigrid Methods for Real-Time Fluid Simulation

NASA Astrophysics Data System (ADS)

Wan, Feifei; Yin, Yong; Zhang, Suiyu

2018-03-01

The multigrid method is widely used in fluid simulation because of its strong convergence. In addition to operating accuracy, operational efficiency is also an important factor to consider in order to enable real-time fluid simulation in computer graphics. For this problem, we compared the performance of the Algebraic Multigrid and the Geometric Multigrid in the V-Cycle and Full-Cycle schemes respectively, and analyze the convergence and speed of different methods. All the calculations are done on the parallel computing of GPU in this paper. Finally, we experiment with the 3D-grid for each scale, and give the exact experimental results.

Changes in the metabolome and microRNA levels in biological fluids might represent biomarkers of neurotoxicity: A trimethyltin study

EPA Science Inventory

Neurotoxicity has been linked with exposure to a number of common drugs and chemicals, yet efficient, accurate, and minimally-invasive methods to detect it are lacking. Fluid-based biomarkers such as those found in serum, plasma, urine, and cerebrospinal fluid (CSF) have great po...

Automated GC-MS analysis of free amino acids in biological fluids.

PubMed

Kaspar, Hannelore; Dettmer, Katja; Gronwald, Wolfram; Oefner, Peter J

2008-07-15

A gas chromatography-mass spectrometry (GC-MS) method was developed for the quantitative analysis of free amino acids as their propyl chloroformate derivatives in biological fluids. Derivatization with propyl chloroformate is carried out directly in the biological samples without prior protein precipitation or solid-phase extraction of the amino acids, thereby allowing automation of the entire procedure, including addition of reagents, extraction and injection into the GC-MS. The total analysis time was 30 min and 30 amino acids could be reliably quantified using 19 stable isotope-labeled amino acids as internal standards. Limits of detection (LOD) and lower limits of quantification (LLOQ) were in the range of 0.03-12 microM and 0.3-30 microM, respectively. The method was validated using a certified amino acid standard and reference plasma, and its applicability to different biological fluids was shown. Intra-day precision for the analysis of human urine, blood plasma, and cell culture medium was 2.0-8.8%, 0.9-8.3%, and 2.0-14.3%, respectively, while the inter-day precision for human urine was 1.5-14.1%.

[Sample preparation and bioanalysis in mass spectrometry].

PubMed

Bourgogne, Emmanuel; Wagner, Michel

2015-01-01

The quantitative analysis of compounds of clinical interest of low molecular weight (<1000 Da) in biological fluids is currently in most cases performed by liquid chromatography-mass spectrometry (LC-MS). Analysis of these compounds in biological fluids (plasma, urine, saliva, hair...) is a difficult task requiring a sample preparation. Sample preparation is a crucial part of chemical/biological analysis and in a sense is considered the bottleneck of the whole analytical process. The main objectives of sample preparation are the removal of potential interferences, analyte preconcentration, and converting (if needed) the analyte into a more suitable form for detection or separation. Without chromatographic separation, endogenous compounds, co-eluted products may affect a quantitative method in mass spectrometry performance. This work focuses on three distinct parts. First, quantitative bioanalysis will be defined, different matrices and sample preparation techniques currently used in bioanalysis by mass spectrometry of/for small molecules of clinical interest in biological fluids. In a second step the goals of sample preparation will be described. Finally, in a third step, sample preparation strategies will be made either directly ("dilute and shoot") or after precipitation.

Transient Nonequilibrium Molecular Dynamic Simulations of Thermal Conductivity: 1. Simple Fluids

NASA Astrophysics Data System (ADS)

Hulse, R. J.; Rowley, R. L.; Wilding, W. V.

2005-01-01

Thermal conductivity has been previously obtained from molecular dynamics (MD) simulations using either equilibrium (EMD) simulations (from Green--Kubo equations) or from steady-state nonequilibrium (NEMD) simulations. In the case of NEMD, either boundary-driven steady states are simulated or constrained equations of motion are used to obtain steady-state heat transfer rates. Like their experimental counterparts, these nonequilibrium steady-state methods are time consuming and may have convection problems. Here we report a new transient method developed to provide accurate thermal conductivity predictions from MD simulations. In the proposed MD method, molecules that lie within a specified volume are instantaneously heated. The temperature decay of the system of molecules inside the heated volume is compared to the solution of the transient energy equation, and the thermal diffusivity is regressed. Since the density of the fluid is set in the simulation, only the isochoric heat capacity is needed in order to obtain the thermal conductivity. In this study the isochoric heat capacity is determined from energy fluctuations within the simulated fluid. The method is valid in the liquid, vapor, and critical regions. Simulated values for the thermal conductivity of a Lennard-Jones (LJ) fluid were obtained using this new method over a temperature range of 90 to 900 K and a density range of 1-35 kmol · m-3. These values compare favorably with experimental values for argon. The new method has a precision of ±10%. Compared to other methods, the algorithm is quick, easy to code, and applicable to small systems, making the simulations very efficient.

Methods for simulation-based analysis of fluid-structure interaction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barone, Matthew Franklin; Payne, Jeffrey L.

2005-10-01

Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonalmore » decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.« less

Simulation of plume dynamics by the Lattice Boltzmann Method

NASA Astrophysics Data System (ADS)

Mora, Peter; Yuen, David A.

2017-09-01

The Lattice Boltzmann Method (LBM) is a semi-microscopic method to simulate fluid mechanics by modelling distributions of particles moving and colliding on a lattice. We present 2-D simulations using the LBM of a fluid in a rectangular box being heated from below, and cooled from above, with a Rayleigh of Ra = 108, similar to current estimates of the Earth's mantle, and a Prandtl number of 5000. At this Prandtl number, the flow is found to be in the non-inertial regime where the inertial terms denoted I ≪ 1. Hence, the simulations presented lie within the regime of relevance for geodynamical problems. We obtain narrow upwelling plumes with mushroom heads and chutes of downwelling fluid as expected of a flow in the non-inertial regime. The method developed demonstrates that the LBM has great potential for simulating thermal convection and plume dynamics relevant to geodynamics, albeit with some limitations.

Real-Time Wing-Vortex and Pressure Distribution Estimation on Wings Via Displacements and Strains in Unsteady and Transitional Flight Conditions

DTIC Science & Technology

2016-09-07

approach in co simulation with fluid-dynamics solvers is used. An original variational formulation is developed for the inverse problem of...by the inverse solution meshing. The same approach is used to map the structural and fluid interface kinematics and loads during the fluid structure...co-simulation. The inverse analysis is verified by reconstructing the deformed solution obtained with a corresponding direct formulation, based on

Intracellular Fluid Mechanics: Coupling Cytoplasmic Flow with Active Cytoskeletal Gel

NASA Astrophysics Data System (ADS)

Mogilner, Alex; Manhart, Angelika

2018-01-01

The cell is a mechanical machine, and continuum mechanics of the fluid cytoplasm and the viscoelastic deforming cytoskeleton play key roles in cell physiology. We review mathematical models of intracellular fluid mechanics, from cytoplasmic fluid flows, to the flow of a viscous active cytoskeletal gel, to models of two-phase poroviscous flows, to poroelastic models. We discuss application of these models to cell biological phenomena, such as organelle positioning, blebbing, and cell motility. We also discuss challenges of understanding fluid mechanics on the cellular scale.

Two-fluid (plasma-neutral) Extended-MHD simulations of spheromak configurations in the HIT-SI experiment with PSI-Tet

NASA Astrophysics Data System (ADS)

Sutherland, D. A.; Hansen, C. J.; Jarboe, T. R.

2017-10-01

A self-consistent, two-fluid (plasma-neutral) dynamic neutral model has been implemented into the 3-D, Extended-MHD code PSI-Tet. A monatomic, hydrogenic neutral fluid reacts with a plasma fluid through elastic scattering collisions and three inelastic collision reactions: electron-impact ionization, radiative recombination, and resonant charge-exchange. Density, momentum, and energy are evolved for both the plasma and neutral species. The implemented plasma-neutral model in PSI-Tet is being used to simulate decaying spheromak configurations in the HIT-SI experimental geometry, which is being compare to two-photon absorption laser induced fluorescence measurements (TALIF) made on the HIT-SI3 experiment. TALIF is used to measure the absolute density and temperature of monatomic deuterium atoms. Neutral densities on the order of 1015 m-3 and neutral temperatures between 0.6-1.7 eV were measured towards the end of decay of spheromak configurations with initial toroidal currents between 10-12 kA. Validation results between TALIF measurements and PSI-Tet simulations with the implemented dynamic neutral model will be presented. Additionally, preliminary dynamic neutral simulations of the HIT-SI/HIT-SI3 spheromak plasmas sustained with inductive helicity injection will be presented. Lastly, potential benefits of an expansion of the two-fluid model into a multi-fluid model that includes multiple neutral species and tracking of charge states will be discussed.

Fully-coupled aeroelastic simulation with fluid compressibility — For application to vocal fold vibration

PubMed Central

Yang, Jubiao; Wang, Xingshi; Krane, Michael; Zhang, Lucy T.

2017-01-01

In this study, a fully-coupled fluid–structure interaction model is developed for studying dynamic interactions between compressible fluid and aeroelastic structures. The technique is built based on the modified Immersed Finite Element Method (mIFEM), a robust numerical technique to simulate fluid–structure interactions that has capabilities to simulate high Reynolds number flows and handles large density disparities between the fluid and the solid. For accurate assessment of this intricate dynamic process between compressible fluid, such as air and aeroelastic structures, we included in the model the fluid compressibility in an isentropic process and a solid contact model. The accuracy of the compressible fluid solver is verified by examining acoustic wave propagations in a closed and an open duct, respectively. The fully-coupled fluid–structure interaction model is then used to simulate and analyze vocal folds vibrations using compressible air interacting with vocal folds that are represented as layered viscoelastic structures. Using physiological geometric and parametric setup, we are able to obtain a self-sustained vocal fold vibration with a constant inflow pressure. Parametric studies are also performed to study the effects of lung pressure and vocal fold tissue stiffness in vocal folds vibrations. All the case studies produce expected airflow behavior and a sustained vibration, which provide verification and confidence in our future studies of realistic acoustical studies of the phonation process. PMID:29527067

Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

PubMed

Müller, Erich A; Jackson, George

2014-01-01

A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

The detection and discrimination of human body fluids using ATR FT-IR spectroscopy.

PubMed

Orphanou, Charlotte-Maria; Walton-Williams, Laura; Mountain, Harry; Cassella, John

2015-07-01

Blood, saliva, semen and vaginal secretions are the main human body fluids encountered at crime scenes. Currently presumptive tests are routinely utilised to indicate the presence of body fluids, although these are often subject to false positives and limited to particular body fluids. Over the last decade more sensitive and specific body fluid identification methods have been explored, such as mRNA analysis and proteomics, although these are not yet appropriate for routine application. This research investigated the application of ATR FT-IR spectroscopy for the detection and discrimination of human blood, saliva, semen and vaginal secretions. The results demonstrated that ATR FT-IR spectroscopy can detect and distinguish between these body fluids based on the unique spectral pattern, combination of peaks and peak frequencies corresponding to the macromolecule groups common within biological material. Comparisons with known abundant proteins relevant to each body fluid were also analysed to enable specific peaks to be attributed to the relevant protein components, which further reinforced the discrimination and identification of each body fluid. Overall, this preliminary research has demonstrated the potential for ATR FT-IR spectroscopy to be utilised in the routine confirmatory screening of biological evidence due to its quick and robust application within forensic science. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

From Geochemistry to Biochemistry: Simulating Prebiotic Chemistry Driven by Geochemical Gradients in Alkaline Hydrothermal Vents

NASA Astrophysics Data System (ADS)

Barge, Laurie

2016-07-01

Planetary water-rock interfaces generate energy in the form of redox, pH, and thermal gradients, and these disequilibria are particularly focused in hydrothermal vent systems where the reducing, heated hydrothermal fluid feeds back into the more oxidizing ocean. Alkaline hydrothermal vents have been proposed as a likely location for the origin of life on the early Earth due to various factors: including the hydrothermal pH / Eh gradients that resemble the ubiquitous electrical / proton gradients in biology, the catalytic hydrothermal precipitates that resemble inorganic catalysts in enzymes, and the presence of electron donors and acceptors in hydrothermal systems (e.g. H2 + CH4 and CO2) that are thought to have been utilized in the earliest metabolisms. Of particular importance for the emergence of metabolism are the mineral "chimneys" that precipitate at the vent fluid / seawater interface. Hydrothermal chimneys are flow-through chemical reactors that form porous and permeable inorganic membranes transecting geochemical gradients; in some ways similar to biological membranes that transect proton / ion gradients and harness these disequilibria to drive metabolism. These emergent chimney structures in the far-from-equilibrium system of the alkaline vent have many properties of interest to the origin of life that can be simulated in the laboratory: for example, they can generate electrical energy and drive redox reactions, and produce catalytic minerals (in particular the metal sulfides and iron oxyhydroxides - "green rust") that can facilitate chemical reactions towards proto-metabolic cycles and biosynthesis. Many of the factors prompting interest in alkaline hydrothermal vents on Earth may also have been present on early Mars, or even presently within icy worlds such as Europa or Enceladus - thus, understanding the disequilibria and resulting prebiotic chemistry in these systems can be of great use in assessing the potential for other environments in the Solar System where life could have emerged.

Physical and mathematical cochlear models

NASA Astrophysics Data System (ADS)

Lim, Kian-Meng

2000-10-01

The cochlea is an intricate organ in the inner ear responsible for our hearing. Besides acting as a transducer to convert mechanical sound vibrations to electrical neural signals, the cochlea also amplifies and separates the sound signal into its spectral components for further processing in the brain. It operates over a broad-band of frequency and a huge dynamic range of input while maintaining a low power consumption. The present research takes the approach of building cochlear models to study and understand the underlying mechanics involved in the functioning of the cochlea. Both physical and mathematical models of the cochlea are constructed. The physical model is a first attempt to build a life- sized replica of the human cochlea using advanced micro- machining techniques. The model takes a modular design, with a removable silicon-wafer based partition membrane encapsulated in a plastic fluid chamber. Preliminary measurements in the model are obtained and they compare roughly with simulation results. Parametric studies on the design parameters of the model leads to an improved design of the model. The studies also revealed that the width and orthotropy of the basilar membrane in the cochlea have significant effects on the sharply tuned responses observed in the biological cochlea. The mathematical model is a physiologically based model that includes three-dimensional viscous fluid flow and a tapered partition with variable properties along its length. A hybrid asymptotic and numerical method provides a uniformly valid and efficient solution to the short and long wave regions in the model. Both linear and non- linear activity are included in the model to simulate the active cochlea. The mathematical model has successfully reproduced many features of the response in the biological cochlea, as observed in experiment measurements performed on animals. These features include sharply tuned frequency responses, significant amplification with inclusion of activity, and non-linear effects such as compression of response with stimulus level, two-tone suppression and the generation of harmonic and distortion products.

The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca

2014-01-01

Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of themore » simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.« less

COMPARING SIMULATED AND EXPERIMENTAL HYSTERETIC TWO- PHASE TRANSIENT FLUID FLOW PHENOMENA

EPA Science Inventory

A hysteretic model for two-phase permeability (k)-saturation (S)-pressure (P) relations is outlined that accounts for effects of nonwetting fluid entrapment. The model can be employed in unsaturated fluid flow computer codes to predict temporal and spatial fluid distributions. Co...

Pore scale simulations for the extension of the Darcy-Forchheimer law to shear thinning fluids

NASA Astrophysics Data System (ADS)

Tosco, Tiziana; Marchisio, Daniele; Lince, Federica; Boccardo, Gianluca; Sethi, Rajandrea

2014-05-01

Flow of non-Newtonian fluids through porous media at high Reynolds numbers is often encountered in chemical, pharmaceutical and food as well as petroleum and groundwater engineering and in many other industrial applications (1 - 2). In particular, the use of shear thinning polymeric solutions has been recently proposed to improve colloidal stability of micro- and nanoscale zerovalent iron particles (MZVI and NZVI) for groundwater remediation. In all abovementioned applications, it is of paramount importance to correctly predict the pressure drop resulting from non-Newtonian fluid flow through the porous medium. For small Reynolds numbers, usually up to 1, typical of laboratory column tests, the extended Darcy law is known to be applicable also to non Newtonian fluids, provided that all non-Newtonian effects are lumped together into a proper viscosity parameter (1,3). For higher Reynolds numbers (eg. close to the injection wells) non linearities between pressure drop and flow rate arise, and the Darcy-Forchheimer law holds for Newtonian fluids, while for non-Newtonian fluids, it has been demonstrated that, at least for simple rheological models (eg. power law fluids) a generalized Forchheimer law can be applied, even if the determination of the flow parameters (permeability K, inertial coefficient β, and equivalent viscosity) is not straightforward. This work (co-funded by European Union project AQUAREHAB FP7 - Grant Agreement Nr. 226565) aims at proposing an extended formulation of the Darcy-Forchheimer law also for shear-thinning fluids, and validating it against results of pore-scale simulations via computational fluid dynamics (4). Flow simulations were performed using Fluent 12.0 on four different 2D porous domains for Newtonian and non-Newtonian fluids (Cross, Ellis and Carreau models). The micro-scale flow simulation results are analyzed in terms of 'macroscale' pressure drop between inlet and outlet of the model domain as a function of flow rate. The results of flow simulations show the superposition of two contributions to pressure drops: one, strictly related to the non-Newtonian properties of the fluid, dominates at low Reynolds numbers, while a quadratic one, arising at higher Reynolds numbers, is dependent only on the porous medium properties. The results suggest that, for Newtonian flow, the porous medium can be fully described by two macroscopic parameters, namely permeability K and inertial coefficient β. Conversely, for non-Newtonian flow, an additional parameter is required, represented by the shift factor α, which depends on the properties of both porous medium and fluid, which is not easy to be determined in laboratory tests, but can be in turn calculated from 2D or 3D pore-scale flow simulations, following the approach which was adopted in this work. References 1. Sorbie, K.S. Polymer-improved oil recovery; Blackie ; CRC Press: Glasgow, Boca Raton, Fla., 1991. 2. Xue, D.; Sethi, R. Viscoelastic gels of guar and xanthan gum mixtures provide long-term stabilization of iron micro- and nanoparticles. J Nanopart Res 2012, 14(11). 3. Bird, R.B.; Armstrong, R.C.; Hassager, O. Dynamics of polymeric liquids. Volume 1. Fluid mechanics; John Wiley and Sons Inc.: New York - NY, 1977. 4. Tosco, T.; Marchisio, D.L.; Lince, F.; Sethi, R. Extension of the Darcy-Forchheimer Law for Shear-Thinning Fluids and Validation via Pore-Scale Flow Simulations. Transport in Porous Media 2013, 96(1), 1-20.

Lattice Boltzmann simulations of liquid CO2 displacing water in a 2D heterogeneous micromodel at reservoir pressure conditions.

PubMed

Chen, Yu; Li, Yaofa; Valocchi, Albert J; Christensen, Kenneth T

2018-05-01

We employed the color-fluid lattice Boltzmann multiphase model to simulate liquid CO 2 displacing water documented in experiments in a 2D heterogeneous micromodel at reservoir pressure conditions. The main purpose is to investigate whether lattice Boltzmann simulation can reproduce the CO 2 invasion patterns observed in these experiments for a range of capillary numbers. Although the viscosity ratio used in the simulation matches the experimental conditions, the viscosity of the fluids in the simulation is higher than that of the actual fluids used in the experiments. Doing so is required to enhance numerical stability, and is a common strategy employed in the literature when using the lattice Boltzmann method to simulate CO 2 displacing water. The simulations reproduce qualitatively similar trends of changes in invasion patterns as the capillary number is increased. However, the development of secondary CO 2 pathways, a key feature of the invasion patterns in the simulations and experiments, is found to occur at a much higher capillary number in the simulations compared with the experiments. Additional numerical simulations were conducted to investigate the effect of the absolute value of viscosity on the invasion patterns while maintaining the viscosity ratio and capillary number fixed. These results indicate that the use of a high viscosity (which significantly reduces the inertial effect in the simulations) suppresses the development of secondary CO 2 pathways, leading to a different fluid distribution compared with corresponding experiments at the same capillary number. Therefore, inertial effects are not negligible in drainage process with liquid CO 2 and water despite the low Reynolds number based on the average velocity, as the local velocity can be much higher due to Haines jump events. These higher velocities, coupled with the low viscosity of CO 2 , further amplifies the inertial effect. Therefore, we conclude that caution should be taken when using proxy fluids that only rely on the capillary number and viscosity ratio in both experiment and simulation. Copyright © 2017 Elsevier B.V. All rights reserved.

Messenger RNA biomarker signatures for forensic body fluid identification revealed by targeted RNA sequencing.

PubMed

Hanson, E; Ingold, S; Haas, C; Ballantyne, J

2018-05-01

The recovery of a DNA profile from the perpetrator or victim in criminal investigations can provide valuable 'source level' information for investigators. However, a DNA profile does not reveal the circumstances by which biological material was transferred. Some contextual information can be obtained by a determination of the tissue or fluid source of origin of the biological material as it is potentially indicative of some behavioral activity on behalf of the individual that resulted in its transfer from the body. Here, we sought to improve upon established RNA based methods for body fluid identification by developing a targeted multiplexed next generation mRNA sequencing assay comprising a panel of approximately equal sized gene amplicons. The multiplexed biomarker panel includes several highly specific gene targets with the necessary specificity to definitively identify most forensically relevant biological fluids and tissues (blood, semen, saliva, vaginal secretions, menstrual blood and skin). In developing the biomarker panel we evaluated 66 gene targets, with a progressive iteration of testing target combinations that exhibited optimal sensitivity and specificity using a training set of forensically relevant body fluid samples. The current assay comprises 33 targets: 6 blood, 6 semen, 6 saliva, 4 vaginal secretions, 5 menstrual blood and 6 skin markers. We demonstrate the sensitivity and specificity of the assay and the ability to identify body fluids in single source and admixed stains. A 16 sample blind test was carried out by one lab with samples provided by the other participating lab. The blinded lab correctly identified the body fluids present in 15 of the samples with the major component identified in the 16th. Various classification methods are being investigated to permit inference of the body fluid/tissue in dried physiological stains. These include the percentage of reads in a sample that are due to each of the 6 tissues/body fluids tested and inter-sample differential gene expression revealed by agglomerative hierarchical clustering. Copyright © 2018 Elsevier B.V. All rights reserved.

A comprehensive Guyton model analysis of physiologic responses to preadapting the blood volume as a countermeasure to fluid shifts

NASA Technical Reports Server (NTRS)

Simanonok, K. E.; Srinivasan, R. S.; Myrick, E. E.; Blomkalns, A. L.; Charles, J. B.

1994-01-01

The Guyton model of fluid, electrolyte, and circulatory regulation is an extensive mathematical model capable of simulating a variety of experimental conditions. It has been modified for use at NASA to simulate head-down tilt, a frequently used analog of weightlessness. Weightlessness causes a headward shift of body fluids that is believed to expand central blood volume, triggering a series of physiologic responses resulting in large losses of body fluids. We used the modified Guyton model to test the hypothesis that preadaptation of the blood volume before weightless exposure could counteract the central volume expansion caused by fluid shifts, and thereby attenuate the circulatory and renal responses that result in body fluid losses. Simulation results show that circulatory preadaptation, by a procedure resembling blood donation immediately before head-down bedrest, is effective in damping the physiologic responses to fluid shifts and reducing body fluid losses. After 10 hours of head-down tilt, preadaptation also produces higher blood volume, extracellular volume, and total body water for 20 to 30 days of bedrest, compared with non-preadapted control. These results indicate that circulatory preadaptation before current Space Shuttle missions may be beneficial for the maintenance of reentry and postflight orthostatic tolerance in astronauts. This paper presents a comprehensive examination of the simulation results pertaining to changes in relevant physiologic variables produced by blood volume reduction before a prolonged head-down tilt. The objectives were to study and develop the countermeasure theoretically, to aid in planning experimental studies of the countermeasure, and to identify potentially disadvantageous physiologic responses that may be caused by the countermeasure.

A competitive enzyme-linked immunosorbent assay for quantification of tetrastatin in body fluids and tumor extracts.

PubMed

Dupont-Deshorgue, A; Oudart, J B; Brassart, B; Deslee, G; Perotin, J M; Diebold, M D; Monboisse, J C; Ramont, L; Brassart-Pasco, S

2015-08-01

Basement membrane collagens or derived fragments are measured in biological fluids such as blood and urine of patients and appear to be useful for diagnosis, prognostication, or treatment monitoring as proposed for endostatin, a fragment of collagen XVIII, or tumstatin, a fragment of collagen IV. Tetrastatin, the NC1 alpha 4 collagen IV domain, was previously reported to inhibit tumor growth and angiogenesis. The aim of this study was to develop and validate a method to measure tetrastatin concentrations in human fluids. We developed a competitive enzyme-linked immunosorbent assay (ELISA). It allowed measuring tetrastatin levels in human serum, bronchial aspiration and bronchoalveolar lavage fluids, and lung tissue extracts. The tetrastatin level was significantly higher in tumor tissues than in healthy lung tissues. Tetrastatin competitive ELISA could be useful to quantify tetrastatin in tissues and biological fluids for the diagnosis or prognostication of diseases in which basement membrane metabolism may be altered, especially tumor progression. Copyright © 2015 Elsevier Inc. All rights reserved.

Numerical and experimental hydrodynamic analysis of suction cup bio-logging tag designs for marine mammals

NASA Astrophysics Data System (ADS)

Murray, Mark; Shorter, Alex; Howle, Laurens; Johnson, Mark; Moore, Michael

2012-11-01

The improvement and miniaturization of sensing technologies has made bio-logging tags, utilized for the study of marine mammal behavior, more practical. These sophisticated sensing packages require a housing which protects the electronics from the environment and provides a means of attachment to the animal. The hydrodynamic forces on these housings can inadvertently remove the tag or adversely affect the behavior or energetics of the animal. A modification to the original design of a suction cup bio-logging tag housing was desired to minimize the adverse forces. In this work, hydrodynamic loading of two suction cup tag designs, original and modified designs, were analyzed using computational fluid dynamics (CFD) models and validated experimentally. Overall, the simulation and experimental results demonstrated that a tag housing that minimized geometric disruptions to the flow reduced drag forces, and that a tag housing with a small frontal cross-sectional area close to the attachment surface reduced lift forces. Preliminary results from experimental work with a common dolphin cadaver indicates that the suction cups used to attach the tags to the animal provide sufficient attachment force to resist failure at predicted drag and lift forces in 10 m/s flow.

Simulation of a Canard in Fluid Flow Driven by a Piezoelectric Beam with a Software Control Loop

DTIC Science & Technology

2014-04-01

The canard is actuated by a piezoelectric beam that bends as voltage is applied. The voltage is controlled by a software subroutine that measures...Dynamic system Modeling Co-simulation Simulation Abaqus Finite element analysis (FEA) Finite element method (FEM) Computational...is unlimited. i CONTENTS Page Introduction 1 Model Description 1 Fluid Model 2 Structural Model 3 Control Subroutine 4 Results 4

Thermal-Hydrology Simulations of Disposal of High-Level Radioactive Waste in a Single Deep Borehole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadgu, Teklu; Stein, Emily; Hardin, Ernest

2015-11-01

Simulations of thermal-hydrology were carried out for the emplacement of spent nuclear fuel canisters and cesium and strontium capsules using the PFLOTRAN simulator. For the cesium and strontium capsules the analysis looked at disposal options such as different disposal configurations and surface aging of waste to reduce thermal effects. The simulations studied temperature and fluid flux in the vicinity of the borehole. Simulation results include temperature and vertical flux profiles around the borehole at selected depths. Of particular importance are peak temperature increases, and fluxes at the top of the disposal zone. Simulations of cesium and strontium capsule disposal predictmore » that surface aging and/or emplacement of the waste at the top of the disposal zone reduces thermal effects and vertical fluid fluxes. Smaller waste canisters emplaced over a longer disposal zone create the smallest thermal effect and vertical fluid fluxes no matter the age of the waste or depth of emplacement.« less

Integrity and stability of oral liposomes containing bile salts studied in simulated and ex vivo gastrointestinal media.

PubMed

Hu, Shunwen; Niu, Mengmeng; Hu, Fuqiang; Lu, Yi; Qi, Jianping; Yin, Zongning; Wu, Wei

2013-01-30

The objective of this study was to investigate the integrtity and stability of oral liposomes containing glycocholate (SGC-Lip) in simulated gastrointestinal (GI) media and ex vivo GI media from rats in comparison with conventional liposomes (CH-Lip) composed of soybean phosphatidylcholine and cholesterol. Membrane integrity of liposomes was evaluated by monitoring calcein release, particle size and distribution in different simulated GI media. The stability of liposomes encapsulating insulin was investigated in simulated GI fluids containing pepsin or pancreatin and ex vivo GI enzyme fluids. Simulated GI media with low pH or physiological bile salts resulted in significant increase in calcein release, but dynamic laser scattering data showed that the size and distribution were generally stable. SGC-Lip retained the major amount of the initially encapsulated insulin as compared with CH-Lip in simulated GI fluids (SGF, FaSSGF, SIF and FeSSIF-V2). SGC-Lip retained respectively 17.1% and 20.5% of the initially encapsulated insulin in ex vivo GI fluid, which were also significantly more than CH-Lip. These results suggested that SGC-Lip could protect insulin from degradation to some degree during their transit through the gastrointestinal tract and contributed to enhanced oral absorption. Copyright © 2012 Elsevier B.V. All rights reserved.

Simulation of swimming strings immersed in a viscous fluid flow

NASA Astrophysics Data System (ADS)

Huang, Wei-Xi; Sung, Hyung Jin

2006-11-01

In nature, many phenomena involve interactions between flexible bodies and their surrounding viscous fluid, such as a swimming fish or a flapping flag. The intrinsic dynamics is complicate and not well understood. A flexible string can be regarded as a one-dimensional flag model. Many similarities can be found between the flapping string and swimming fish, although different wake speed results in a drag force for the flapping string and a propulsion force for the swimming fish. In the present study, we propose a mathematical formulation for swimming strings immersed in a viscous fluid flow. Fluid motion is governed by the Navier-Stokes equations and a momentum forcing is added in order to bring the fluid to move at the same velocity with the immersed surface. A flexible inextensible string model is described by another set of equations with an additional momentum forcing which is a result of the fluid viscosity and the pressure difference across the string. The momentum forcing is calculated by a feedback loop. Simulations of several numerical examples are carried out, including a hanging string which starts moving under gravity without ambient fluid, a swinging string immersed in a quiescent viscous fluid, a string swimming within a uniform surrounding flow, and flow over two side-by-side strings. The numerical results agree well with the theoretical analysis and previous experimental observations. Further simulation of a swimming fish is under consideration.

Sodium imaging of the human knee using soft inversion recovery fluid attenuation.

PubMed

Feldman, Rebecca E; Stobbe, Robert; Watts, Alexander; Beaulieu, Christian

2013-09-01

Sodium signal strength in MRI is low when compared with (1)H. Thus, image voxel volumes must be relatively large in order to produce a sufficient signal-to-noise ratio (SNR). The measurement of sodium in cartilage is hindered by conflation with signal from the adjacent fluid spaces. Inversion recovery can be used to null signal from fluid, but reduces SNR. The purpose of this work was to optimize inversion recovery sodium MRI to enhance cartilage SNR while nulling fluid. Sodium relaxation was first measured for knee cartilage (T1=21±1 ms, T(2 fast)(∗)=0.8±0.2 ms, T(2 slow)(∗)=19.7±0.5 ms) and fluid (T1=48±3 ms, T2(∗)=47±4 ms) in nine healthy subjects at 4.7 T. The rapid relaxation of cartilage in relation to fluid permits the use of a lengthened inversion pulse to preferentially invert the fluid components. Simulations of inversion pulse length were performed to yield a cartilage SNR enhancing combination of parameters that nulled fluid. The simulations were validated in a phantom and then in vivo. B0 inhomogeneity was measured and the effect of off-resonance during the soft inversion pulse was assessed with simulation. Soft inversion recovery yielded twice the SNR and much improved sodium images of cartilage in human knee with little confounding signal from fluid. Copyright © 2013 Elsevier Inc. All rights reserved.

Parallel Three-Dimensional Computation of Fluid Dynamics and Fluid-Structure Interactions of Ram-Air Parachutes

NASA Technical Reports Server (NTRS)

Tezduyar, Tayfun E.

1998-01-01

This is a final report as far as our work at University of Minnesota is concerned. The report describes our research progress and accomplishments in development of high performance computing methods and tools for 3D finite element computation of aerodynamic characteristics and fluid-structure interactions (FSI) arising in airdrop systems, namely ram-air parachutes and round parachutes. This class of simulations involves complex geometries, flexible structural components, deforming fluid domains, and unsteady flow patterns. The key components of our simulation toolkit are a stabilized finite element flow solver, a nonlinear structural dynamics solver, an automatic mesh moving scheme, and an interface between the fluid and structural solvers; all of these have been developed within a parallel message-passing paradigm.

Nano- and microparticles at fluid and biological interfaces.

PubMed

Dasgupta, S; Auth, T; Gompper, G

2017-09-20

Systems with interfaces are abundant in both technological applications and biology. While a fluid interface separates two fluids, membranes separate the inside of vesicles from the outside, the interior of biological cells from the environment, and compartmentalize cells into organelles. The physical properties of interfaces are characterized by interface tension, those of membranes are characterized by bending and stretching elasticity. Amphiphilic molecules like surfactants that are added to a system with two immiscible fluids decrease the interface tension and induce a bending rigidity. Lipid bilayer membranes of vesicles can be stretched or compressed by osmotic pressure; in biological cells, also the presence of a cytoskeleton can induce membrane tension. If the thickness of the interface or the membrane is small compared with its lateral extension, both can be described using two-dimensional mathematical surfaces embedded in three-dimensional space. We review recent work on the interaction of particles with interfaces and membranes. This can be micrometer-sized particles at interfaces that stabilise emulsions or form colloidosomes, as well as typically nanometer-sized particles at membranes, such as viruses, parasites, and engineered drug delivery systems. In both cases, we first discuss the interaction of single particles with interfaces and membranes, e.g. particles in external fields, non-spherical particles, and particles at curved interfaces, followed by interface-mediated interaction between two particles, many-particle interactions, interface and membrane curvature-induced phenomena, and applications.

Nano- and microparticles at fluid and biological interfaces

NASA Astrophysics Data System (ADS)

Dasgupta, S.; Auth, T.; Gompper, G.

2017-09-01

Systems with interfaces are abundant in both technological applications and biology. While a fluid interface separates two fluids, membranes separate the inside of vesicles from the outside, the interior of biological cells from the environment, and compartmentalize cells into organelles. The physical properties of interfaces are characterized by interface tension, those of membranes are characterized by bending and stretching elasticity. Amphiphilic molecules like surfactants that are added to a system with two immiscible fluids decrease the interface tension and induce a bending rigidity. Lipid bilayer membranes of vesicles can be stretched or compressed by osmotic pressure; in biological cells, also the presence of a cytoskeleton can induce membrane tension. If the thickness of the interface or the membrane is small compared with its lateral extension, both can be described using two-dimensional mathematical surfaces embedded in three-dimensional space. We review recent work on the interaction of particles with interfaces and membranes. This can be micrometer-sized particles at interfaces that stabilise emulsions or form colloidosomes, as well as typically nanometer-sized particles at membranes, such as viruses, parasites, and engineered drug delivery systems. In both cases, we first discuss the interaction of single particles with interfaces and membranes, e.g. particles in external fields, non-spherical particles, and particles at curved interfaces, followed by interface-mediated interaction between two particles, many-particle interactions, interface and membrane curvature-induced phenomena, and applications.

Advanced Supercritical Carbon Dioxide Brayton Cycle Development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Mark; Sienicki, James; Moisseytsev, Anton

2015-10-21

Fluids operating in the supercritical state have promising characteristics for future high efficiency power cycles. In order to develop power cycles using supercritical fluids, it is necessary to understand the flow characteristics of fluids under both supercritical and two-phase conditions. In this study, a Computational Fluid Dynamic (CFD) methodology was developed for supercritical fluids flowing through complex geometries. A real fluid property module was implemented to provide properties for different supercritical fluids. However, in each simulation case, there is only one species of fluid. As a result, the fluid property module provides properties for either supercritical CO 2 (S-CO 2)more » or supercritical water (SCW). The Homogeneous Equilibrium Model (HEM) was employed to model the two-phase flow. HEM assumes two phases have same velocity, pressure, and temperature, making it only applicable for the dilute dispersed two-phase flow situation. Three example geometries, including orifices, labyrinth seals, and valves, were used to validate this methodology with experimental data. For the first geometry, S-CO 2 and SCW flowing through orifices were simulated and compared with experimental data. The maximum difference between the mass flow rate predictions and experimental measurements is less than 5%. This is a significant improvement as previous works can only guarantee 10% error. In this research, several efforts were made to help this improvement. First, an accurate real fluid module was used to provide properties. Second, the upstream condition was determined by pressure and density, which determines supercritical states more precise than using pressure and temperature. For the second geometry, the flow through labyrinth seals was studied. After a successful validation, parametric studies were performed to study geometric effects on the leakage rate. Based on these parametric studies, an optimum design strategy for the see-through labyrinth seals was proposed. A stepped labyrinth seal, which mimics the behavior of the labyrinth seal used in the Sandia National Laboratory (SNL) S-CO 2 Brayton cycle, was also tested in the experiment along with simulations performed. The rest of this study demonstrates the difference of valves' behavior under supercritical fluid and normal fluid conditions. A small-scale valve was tested in the experiment facility using S-CO 2. Different percentages of opening valves were tested, and the measured mass flow rate agreed with simulation predictions. Two transients from a real S-CO 2 Brayton cycle design provided the data for valve selection. The selected valve was studied using numerical simulation, as experimental data is not available.« less

High Performance Parallel Processing (HPPP) Finite Element Simulation of Fluid Structure Interactions Final Report CRADA No. TC-0824-94-A

DOE Office of Scientific and Technical Information (OSTI.GOV)

Couch, R.; Ziegler, D. P.

This project was a muki-partner CRADA. This was a partnership between Alcoa and LLNL. AIcoa developed a system of numerical simulation modules that provided accurate and efficient threedimensional modeling of combined fluid dynamics and structural response.

[Individualized fluid-solid coupled model of intracranial aneurysms based on computed tomography angiography data].

PubMed

Wang, Fuyu; Xu, Bainan; Sun, Zhenghui; Liu, Lei; Wu, Chen; Zhang, Xiaojun

2012-10-01

To establish an individualized fluid-solid coupled model of intracranial aneurysms based on computed tomography angiography (CTA) image data. The original Dicom format image data from a patient with an intracranial aneurysm were imported into Mimics software to construct the 3D model. The fluid-solid coupled model was simulated with ANSYS and CFX software, and the sensitivity of the model was analyzed. The difference between the rigid model and fluid-solid coupled model was also compared. The fluid-solid coupled model of intracranial aneurysm was established successfully, which allowed direct simulation of the blood flow of the intracranial aneurysm and the deformation of the solid wall. The pressure field, stress field, and distribution of Von Mises stress and deformation of the aneurysm could be exported from the model. A small Young's modulus led to an obvious deformation of the vascular wall, and the walls with greater thicknesses had smaller deformations. The rigid model and the fluid-solid coupled model showed more differences in the wall shear stress and blood flow velocity than in pressure. The fluid-solid coupled model more accurately represents the actual condition of the intracranial aneurysm than the rigid model. The results of numerical simulation with the model are reliable to study the origin, growth and rupture of the aneurysms.

The Sedimentation of Particles under Orthogonal Shear in Viscoelastic Fluids

NASA Astrophysics Data System (ADS)

Murch, William L.; Krishnan, Sreenath; Shaqfeh, Eric S. G.

2016-11-01

Many engineering applications, including oil and gas recovery, require the suspension of particles in viscoelastic fluids during fluid transport and processing. A topic of specific importance involves such particle suspensions experiencing an applied shear flow in a direction perpendicular to gravity (referred to as orthogonal shear). Previously, it has been shown that particle sedimentation coupled with an orthogonal shear flow can reduce the particle settling rate in elastic fluids. The underlying mechanism of this enhanced coupling drag is not fully understood, particularly at finite Weissenberg numbers. This talk examines the role of fluid elasticity on a single, non-Brownian, rigid sphere settling in orthogonal shear using experiments and numerical simulations. New experiments were performed in a Taylor-Couette flow cell using Boger fluids to study the coupling drag as a function of the shear and sedimentation Weissenberg numbers as well as particle confinement. The elastic effect was also studied with fully 3D simulations of flow past a rigid sphere, using the FENE-P constitutive model to describe the polymeric fluid rheology. These simulations show good agreement with the experiments and allow for further insight into the mechanism of elasticity-enhanced drag. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship.

3D Reconstruction of Chick Embryo Vascular Geometries Using Non-invasive High-Frequency Ultrasound for Computational Fluid Dynamics Studies.

PubMed

Tan, Germaine Xin Yi; Jamil, Muhammad; Tee, Nicole Gui Zhen; Zhong, Liang; Yap, Choon Hwai

2015-11-01

Recent animal studies have provided evidence that prenatal blood flow fluid mechanics may play a role in the pathogenesis of congenital cardiovascular malformations. To further these researches, it is important to have an imaging technique for small animal embryos with sufficient resolution to support computational fluid dynamics studies, and that is also non-invasive and non-destructive to allow for subject-specific, longitudinal studies. In the current study, we developed such a technique, based on ultrasound biomicroscopy scans on chick embryos. Our technique included a motion cancelation algorithm to negate embryonic body motion, a temporal averaging algorithm to differentiate blood spaces from tissue spaces, and 3D reconstruction of blood volumes in the embryo. The accuracy of the reconstructed models was validated with direct stereoscopic measurements. A computational fluid dynamics simulation was performed to model fluid flow in the generated construct of a Hamburger-Hamilton (HH) stage 27 embryo. Simulation results showed that there were divergent streamlines and a low shear region at the carotid duct, which may be linked to the carotid duct's eventual regression and disappearance by HH stage 34. We show that our technique has sufficient resolution to produce accurate geometries for computational fluid dynamics simulations to quantify embryonic cardiovascular fluid mechanics.

Static and dynamic properties of smoothed dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Alizadehrad, Davod; Fedosov, Dmitry A.

2018-03-01

In this paper, static and dynamic properties of the smoothed dissipative particle dynamics (SDPD) method are investigated. We study the effect of method parameters on SDPD fluid properties, such as structure, speed of sound, and transport coefficients, and show that a proper choice of parameters leads to a well-behaved and accurate fluid model. In particular, the speed of sound, the radial distribution function (RDF), shear-thinning of viscosity, the mean-squared displacement (〈R2 〉 ∝ t), and the Schmidt number (Sc ∼ O (103) - O (104)) can be controlled, such that the model exhibits a fluid-like behavior for a wide range of temperatures in simulations. Furthermore, in addition to the consideration of fluid density variations for fluid compressibility, a more challenging test of incompressibility is performed by considering the Poisson ratio and divergence of velocity field in an elongational flow. Finally, as an example of complex-fluid flow, we present the applicability and validity of the SDPD method with an appropriate choice of parameters for the simulation of cellular blood flow in irregular geometries. In conclusion, the results demonstrate that the SDPD method is able to approximate well a nearly incompressible fluid behavior, which includes hydrodynamic interactions and consistent thermal fluctuations, thereby providing, a powerful approach for simulations of complex mesoscopic systems.

Active chiral fluids.

PubMed

Fürthauer, S; Strempel, M; Grill, S W; Jülicher, F

2012-09-01

Active processes in biological systems often exhibit chiral asymmetries. Examples are the chirality of cytoskeletal filaments which interact with motor proteins, the chirality of the beat of cilia and flagella as well as the helical trajectories of many biological microswimmers. Here, we derive constitutive material equations for active fluids which account for the effects of active chiral processes. We identify active contributions to the antisymmetric part of the stress as well as active angular momentum fluxes. We discuss four types of elementary chiral motors and their effects on a surrounding fluid. We show that large-scale chiral flows can result from the collective behavior of such motors even in cases where isolated motors do not create a hydrodynamic far field.

Bioactive ceramic-based materials with designed reactivity for bone tissue regeneration

PubMed Central

Ohtsuki, Chikara; Kamitakahara, Masanobu; Miyazaki, Toshiki

2009-01-01

Bioactive ceramics have been used clinically to repair bone defects owing to their biological affinity to living bone; i.e. the capability of direct bonding to living bone, their so-called bioactivity. However, currently available bioactive ceramics do not satisfy every clinical application. Therefore, the development of novel design of bioactive materials is necessary. Bioactive ceramics show osteoconduction by formation of biologically active bone-like apatite through chemical reaction of the ceramic surface with surrounding body fluid. Hence, the control of their chemical reactivity in body fluid is essential to developing novel bioactive materials as well as biodegradable materials. This paper reviews novel bioactive materials designed based on chemical reactivity in body fluid. PMID:19158015

[The incidence and distribution of accidents with biological fluids among health personnel and the general population].

PubMed

Imaz Iglesia, I; Gómez López, L I; Fernández Martínez, J A; Mareca Doñate, R; Sangrador Arenas, L A

1996-01-01

To assess the informative usefulness of the Registry, to calculate the incidence rates of accident with biological fluids among health care workers and in the community, to know about the postaccident rate of seroconversion to HIV and to identify risk groups. A descriptive study of the HIV records file of the Registry of Accidental Contacts to Biological Fluids in the Clinic Hospital of Zaragoza was conducted, between January 1987 and September 1993. The registry includes the reports of health care workers and the general population of Health Area III in Aragón (Spain), except for the Calatayud's Hospital. Incidence rates, rate ratios and their 95% confidence intervals were calculated. A total number of 595 accidents were reported, in none of them and HIV infection occurred subsequently. The incidence rate in health care workers was of 1.7 reports per 100 workers per year, while in the community it was of 8.1 per 100,000 people. The housekeeping staff was the group with a higher incidence (rate = 6.7; 95% IC: 3-14.8) and the type of accident more frequently described was needlestick injury. The incidence of reported accidents has increased in the community and in health care workers, which may be due to the increase in the reporting. In health care workers, the incidence in 1993 was within the range reported from other countries. The perception of risk is universal after accidents with unknown biological fluids. The correct disposal of material with biological contamination should be the more important preventive action.

Computational fluid dynamics applications to improve crop production systems

USDA-ARS?s Scientific Manuscript database

Computational fluid dynamics (CFD), numerical analysis and simulation tools of fluid flow processes have emerged from the development stage and become nowadays a robust design tool. It is widely used to study various transport phenomena which involve fluid flow, heat and mass transfer, providing det...

A new dipolar potential for numerical simulations of polar fluids on the 4D hypersphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caillol, Jean-Michel, E-mail: Jean-Michel.Caillol@th.u-psud.fr; Trulsson, Martin, E-mail: martin.trulsson@lptms.u-psud.fr

2014-09-28

We present a new method for Monte Carlo or Molecular Dynamics numerical simulations of three-dimensional polar fluids. The simulation cell is defined to be the surface of the northern hemisphere of a four-dimensional (hyper)sphere. The point dipoles are constrained to remain tangent to the sphere and their interactions are derived from the basic laws of electrostatics in this geometry. The dipole-dipole potential has two singularities which correspond to the following boundary conditions: when a dipole leaves the northern hemisphere at some point of the equator, it reappears at the antipodal point bearing the same dipole moment. We derive all themore » formal expressions needed to obtain the thermodynamic and structural properties of a polar liquid at thermal equilibrium in actual numerical simulation. We notably establish the expression of the static dielectric constant of the fluid as well as the behavior of the pair correlation at large distances. We report and discuss the results of extensive numerical Monte Carlo simulations for two reference states of a fluid of dipolar hard spheres and compare these results with previous methods with a special emphasis on finite size effects.« less

A new dipolar potential for numerical simulations of polar fluids on the 4D hypersphere

NASA Astrophysics Data System (ADS)

Caillol, Jean-Michel; Trulsson, Martin

2014-09-01

We present a new method for Monte Carlo or Molecular Dynamics numerical simulations of three-dimensional polar fluids. The simulation cell is defined to be the surface of the northern hemisphere of a four-dimensional (hyper)sphere. The point dipoles are constrained to remain tangent to the sphere and their interactions are derived from the basic laws of electrostatics in this geometry. The dipole-dipole potential has two singularities which correspond to the following boundary conditions: when a dipole leaves the northern hemisphere at some point of the equator, it reappears at the antipodal point bearing the same dipole moment. We derive all the formal expressions needed to obtain the thermodynamic and structural properties of a polar liquid at thermal equilibrium in actual numerical simulation. We notably establish the expression of the static dielectric constant of the fluid as well as the behavior of the pair correlation at large distances. We report and discuss the results of extensive numerical Monte Carlo simulations for two reference states of a fluid of dipolar hard spheres and compare these results with previous methods with a special emphasis on finite size effects.

Finite Element Modeling of Non-linear Coupled Interacting Fault System

NASA Astrophysics Data System (ADS)

Xing, H. L.; Zhang, J.; Wyborn, D.

2009-04-01

PANDAS - Parallel Adaptive static/dynamic Nonlinear Deformation Analysis System - a novel supercomputer simulation tool is developed for simulating the highly non-linear coupled geomechanical-fluid flow-thermal systems involving heterogeneously fractured geomaterials. PANDAS includes the following key components: Pandas/Pre, ESyS_Crustal, Pandas/Thermo, Pandas/Fluid and Pandas/Post as detailed in the following: • Pandas/Pre is developed to visualise the microseismicity events recorded during the hydraulic stimulation process to further evaluate the fracture location and evolution and geological setting of a certain reservoir, and then generate the mesh by it and/or other commercial graphics software (such as Patran) for the further finite element analysis of various cases; The Delaunay algorithm is applied as a suitable method for mesh generation using such a point set; • ESyS_Crustal is a finite element code developed for the interacting fault system simulation, which employs the adaptive static/dynamic algorithm to simulate the dynamics and evolution of interacting fault systems and processes that are relevant on short to mediate time scales in which several dynamic phenomena related with stick-slip instability along the faults need to be taken into account, i.e. (a). slow quasi-static stress accumulation, (b) rapid dynamic rupture, (c) wave propagation and (d) corresponding stress redistribution due to the energy release along the multiple fault boundaries; those are needed to better describe ruputure/microseimicity/earthquake related phenomena with applications in earthquake forecasting, hazard quantification, exploration, and environmental problems. It has been verified with various available experimental results[1-3]; • Pandas/Thermo is a finite element method based module for the thermal analysis of the fractured porous media; the temperature distribution is calculated from the heat transfer induced by the thermal boundary conditions without/with the coupled fluid effects and the geomechanical energy conversion for the pure/coupled thermal analysis. • Pandas/Fluid is a finite element method based module for simulating the fluid flow in the fractured porous media; the fluid flow velocity and pressure are calculated from energy equilibrium equations without/together with the coupling effects of the thermal and solid rock deformation for an independent/coupled fluid flow analysis; • Pandas/Post is to visualise the simulation results through the integration of VTK and/or Patran. All the above modules can be used independently/together to simulate individual/coupled phenomena (such as interacting fault system dynamics, heat flow and fluid flow) without/with coupling effects. PANDAS has been applied to the following issues: • visualisation of the microseismic events to monitor and determine where/how the underground rupture proceeds during a hydraulic stimulation, to generate the mesh using the recorded data for determining the domain of the ruptured zone and to evaluate the material parameters (i.e. the permeability) for the further numerical analysis; • interacting fault system simulation to determine the relevant complicated dynamic rupture process. • geomechanical-fluid flow coupling analysis to investigate the interactions between fluid flow and deformation in the fractured porous media under different loading conditions. • thermo-fluid flow coupling analysis of a fractured geothermal reservoir system. PANDAS will be further developed for a multiscale simulation of multiphase dynamic behaviour for a certain fractured geothermal reservoir. More details and additional application examples will be given during the presentation. References [1] Xing, H. L., Makinouchi, A. and Mora, P. (2007). Finite element modeling of interacting fault system, Physics of the Earth and Planetary Interiors, 163, 106-121.doi:10.1016/j.pepi.2007.05.006 [2] Xing, H. L., Mora, P., Makinouchi, A. (2006). An unified friction description and its application to simulation of frictional instability using finite element method. Philosophy Magazine, 86, 3453-3475 [3] Xing, H. L., Mora, P.(2006). Construction of an intraplate fault system model of South Australia, and simulation tool for the iSERVO institute seed project.. Pure and Applied Geophysics. 163, 2297-2316. DOI 10.1007/s00024-006-0127-x

Optimization in Cardiovascular Modeling

NASA Astrophysics Data System (ADS)

Marsden, Alison L.

2014-01-01

Fluid mechanics plays a key role in the development, progression, and treatment of cardiovascular disease. Advances in imaging methods and patient-specific modeling now reveal increasingly detailed information about blood flow patterns in health and disease. Building on these tools, there is now an opportunity to couple blood flow simulation with optimization algorithms to improve the design of surgeries and devices, incorporating more information about the flow physics in the design process to augment current medical knowledge. In doing so, a major challenge is the need for efficient optimization tools that are appropriate for unsteady fluid mechanics problems, particularly for the optimization of complex patient-specific models in the presence of uncertainty. This article reviews the state of the art in optimization tools for virtual surgery, device design, and model parameter identification in cardiovascular flow and mechanobiology applications. In particular, it reviews trade-offs between traditional gradient-based methods and derivative-free approaches, as well as the need to incorporate uncertainties. Key future challenges are outlined, which extend to the incorporation of biological response and the customization of surgeries and devices for individual patients.

Preparation and characterization of HA microflowers coating on AZ31 magnesium alloy by micro-arc oxidation and a solution treatment

NASA Astrophysics Data System (ADS)

Tang, Hui; Yu, Dezhen; Luo, Yan; Wang, Fuping

2013-01-01

Magnesium and its alloys are potential biodegradable implant materials due to their attractive biological properties. But the use of magnesium is still hampered by its poor corrosion resistance in physiological fluids. In this work, hydroxyapatite microflowers coating is fabricated by micro-arc oxidation and a solution treatment on AZ31 magnesium alloy. The microstructure and composition are analyzed by scanning electron microscopy (SEM), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FT-IR). The potentiodynamic polarization and electrochemical impedance spectroscopy are studied in simulated body fluid (SBF) solution, and the apatite-forming ability is studied also. The results show that the corrosion resistance of the magnesium alloy has been enhanced by MAO coating. And the solution treatment can improve the corrosion resistance of the MAO sample, by forming a barrier layer on the surface of the MAO coating, and by penetrating into the outer layer of the MAO film, sealing the micropores and micro-cracks existed in the MAO coating. In addition, the MAO-ST coating also exhibits a high ability to form apatite.

Numerical Simulation of Two Phase Flows

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing

2001-01-01

Two phase flows can be found in broad situations in nature, biology, and industry devices and can involve diverse and complex mechanisms. While the physical models may be specific for certain situations, the mathematical formulation and numerical treatment for solving the governing equations can be general. Hence, we will require information concerning each individual phase as needed in a single phase. but also the interactions between them. These interaction terms, however, pose additional numerical challenges because they are beyond the basis that we use to construct modern numerical schemes, namely the hyperbolicity of equations. Moreover, due to disparate differences in time scales, fluid compressibility and nonlinearity become acute, further complicating the numerical procedures. In this paper, we will show the ideas and procedure how the AUSM-family schemes are extended for solving two phase flows problems. Specifically, both phases are assumed in thermodynamic equilibrium, namely, the time scales involved in phase interactions are extremely short in comparison with those in fluid speeds and pressure fluctuations. Details of the numerical formulation and issues involved are discussed and the effectiveness of the method are demonstrated for several industrial examples.

Deep Learning for Flow Sculpting: Insights into Efficient Learning using Scientific Simulation Data

PubMed Central

Stoecklein, Daniel; Lore, Kin Gwn; Davies, Michael; Sarkar, Soumik; Ganapathysubramanian, Baskar

2017-01-01

A new technique for shaping microfluid flow, known as flow sculpting, offers an unprecedented level of passive fluid flow control, with potential breakthrough applications in advancing manufacturing, biology, and chemistry research at the microscale. However, efficiently solving the inverse problem of designing a flow sculpting device for a desired fluid flow shape remains a challenge. Current approaches struggle with the many-to-one design space, requiring substantial user interaction and the necessity of building intuition, all of which are time and resource intensive. Deep learning has emerged as an efficient function approximation technique for high-dimensional spaces, and presents a fast solution to the inverse problem, yet the science of its implementation in similarly defined problems remains largely unexplored. We propose that deep learning methods can completely outpace current approaches for scientific inverse problems while delivering comparable designs. To this end, we show how intelligent sampling of the design space inputs can make deep learning methods more competitive in accuracy, while illustrating their generalization capability to out-of-sample predictions. PMID:28402332

Diffusion-controlled reactions modeling in Geant4-DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karamitros, M., E-mail: matkara@gmail.com; CNRS, INCIA, UMR 5287, F-33400 Talence; Luan, S.

2014-10-01

Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing allmore » the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest reactants. The performance advantage is presented in terms of complexity, and the accuracy of the new algorithm is demonstrated by simulating radiation chemistry in the context of the Geant4-DNA project. Application The time-dependent radiolytic yields of the main chemical species formed after irradiation are computed for incident protons at different energies (from 50 MeV to 500 keV). Both the time-evolution and energy dependency of the yields are discussed. The evolution, at one microsecond, of the yields of hydroxyls and solvated electrons with respect to the linear energy transfer is compared to theoretical and experimental data. According to our results, at high linear energy transfer, modeling radiation chemistry in the trading compartment representation might be adopted.« less

Drag penalty due to the asperities in the substrate of super-hydrophobic and liquid infused surfaces

NASA Astrophysics Data System (ADS)

Garcia Cartagena, Edgardo J.; Arenas, Isnardo; Leonardi, Stefano

2017-11-01

Direct numerical simulations of two superposed fluids in a turbulent channel with a textured surface made of pinnacles of random height have been performed. The viscosity ratio between the two fluids are N =μo /μi = 50 (μo and μi are the viscosities of outer and inner fluid respectively) mimicking a super-hydrophobic surface (water over air) and N=2.5 (water over heptane) resembling a liquid infused surface. Two set of simulations have been performed varying the Reynolds number, Reτ = 180 and Reτ = 390 . The interface between the two fluids is flat simulating infinite surface tension. The position of the interface between the two fluids has been varied in the vertical direction from the base of the substrate (what would be a rough wall) to the highest point of the roughness. Drag reduction is very sensitive to the position of the interface between the two fluids. Asperities above the interface induce a large form drag and diminish considerably the drag reduction. When the mean height of the surface measured from the interface in the outer fluid is greater than one wall unit, k+ > 1 , the drag increases with respect to a smooth wall. Present results provide a guideline to the accuracy required in manufacturing super-hydrophobic and liquid infused surfaces. This work was supported under ONR MURI Grants N00014-12-0875 and N00014-12- 1-0962, Program Manager Dr. Ki-Han Kim. Numerical simulations were performed on the Texas Advanced Computer Center.

Numerical simulations of stick-slip in fluid saturated granular fault gouge

NASA Astrophysics Data System (ADS)

Dorostkar, O.; Johnson, P. A.; Guyer, R. A.; Marone, C.; Carmeliet, J.

2016-12-01

Fluids play a key role in determining the frictional strength and stability of faults. For example, fluid flow and fluid-solid interaction in fault gouge can trigger seismicity, alter earthquake nucleation properties and cause fault zone weakening. We present results of 3D numerical simulations of stick-slip behavior in dry and saturated granular fault gouge. In the saturated case, the gouge is fully saturated and drainage is possible through the boundaries. We model the solid phase (particles) with the discrete element method (DEM) while the fluid is described by the Navier-Stokes equations and solved by computational fluid dynamics (CFD). In our model, granular gouge is sheared between two rough plates under boundary conditions of constant normal stress and constant shearing velocity at the layer boundaries. A phase-space study including shearing velocity and normal stress is taken to identify the conditions for stick-slip regime. We analyzed slip events for dry and saturated cases to determine shear stress drop, released kinetic energy and compaction. The presence of fluid tends to cause larger slip events. We observe a close correlation between the kinetic energy of the particles and of the fluid. In short, during slip, fluid flow induced by the failure and compaction of the granular system, mobilizes the particles, which increases their kinetic energy, leading to greater slip. We further observe that the solid-fluid interaction forces are equal or larger than the solid-solid interaction forces during the slip event, indicating the important influence of the fluid on the granular system. Our simulations can explain the behaviors observed in experimental studies and we are working to apply our results to tectonic faults.

Passive scalar entrainment and mixing in a forced, spatially-developing mixing layer

NASA Technical Reports Server (NTRS)

Lowery, P. S.; Reynolds, W. C.; Mansour, N. N.

1987-01-01

Numerical simulations are performed for the forced, spatially-developing plane mixing layer in two and three dimensions. Transport of a passive scalar field is included in the computation. This, together with the allowance for spatial development in the simulations, affords the opportunity for study of the asymmetric entrainment of irrotational fluid into the layer. The inclusion of a passive scalar field provides a means for simulating the effect of this entrainment asymmetry on the generation of 'products' from a 'fast' chemical reaction. Further, the three-dimensional simulations provide useful insight into the effect of streamwise structures on these entrainment and 'fast' reaction processes. Results from a two-dimensional simulation indicate 1.22 parts high-speed fluid are entrained for every one part low-speed fluid. Inclusion of streamwise vortices at the inlet plane of a three-dimensional simulation indicate a further increase in asymmetric entrainment - 1.44:1. Results from a final three-dimensional simulation are presented. In this case, a random velocity perturbation is imposed at the inlet plane. The results indicate the 'natural' development of the large spanwise structures characteristic of the mixing layer.

Entropic lattice Boltzmann model for charged leaky dielectric multiphase fluids in electrified jets.

PubMed

Lauricella, Marco; Melchionna, Simone; Montessori, Andrea; Pisignano, Dario; Pontrelli, Giuseppe; Succi, Sauro

2018-03-01

We present a lattice Boltzmann model for charged leaky dielectric multiphase fluids in the context of electrified jet simulations, which are of interest for a number of production technologies including electrospinning. The role of nonlinear rheology on the dynamics of electrified jets is considered by exploiting the Carreau model for pseudoplastic fluids. We report exploratory simulations of charged droplets at rest and under a constant electric field, and we provide results for charged jet formation under electrospinning conditions.

Vortex locking in direct numerical simulations of quantum turbulence.

PubMed

Morris, Karla; Koplik, Joel; Rouson, Damian W I

2008-07-04

Direct numerical simulations are used to examine the locking of quantized superfluid vortices and normal fluid vorticity in evolving turbulent flows. The superfluid is driven by the normal fluid, which undergoes either a decaying Taylor-Green flow or a linearly forced homogeneous isotropic turbulent flow, although the back reaction of the superfluid on the normal fluid flow is omitted. Using correlation functions and wavelet transforms, we present numerical and visual evidence for vortex locking on length scales above the intervortex spacing.

A High Performance Computing Approach to the Simulation of Fluid Solid Interaction Problems with Rigid and Flexible Components (Open Access Publisher’s Version)

DTIC Science & Technology

2014-08-01

performance computing, smoothed particle hydrodynamics, rigid body dynamics, flexible body dynamics ARMAN PAZOUKI ∗, RADU SERBAN ∗, DAN NEGRUT ∗ A...HIGH PERFORMANCE COMPUTING APPROACH TO THE SIMULATION OF FLUID-SOLID INTERACTION PROBLEMS WITH RIGID AND FLEXIBLE COMPONENTS This work outlines a unified...are implemented to model rigid and flexible multibody dynamics. The two- way coupling of the fluid and solid phases is supported through use of

In vitro dynamic swelling behaviors of radiation synthesized polyacrylamide with crosslinkers in the simulated physiological body fluids

NASA Astrophysics Data System (ADS)

Saraydın, Dursun; Işıkver, Yasemin; Karadağ, Erdener; Sahiner, Nurettin; Güven, Olgun

2002-03-01

Acrylamide hydrogels, containing different amounts and types of crosslinkers, were synthesized via γ-irradiation technique. Their swellings in simulated body fluids, such as physiological saline (0.89% NaCl) isoosmotic phosphate buffer at pH 7.4, gastric fluid at pH 1.1 (glycine-HCl), protein (aqueous solution of bovine serum albumin), urine (aqueous solution of urea), glucose and distilled water, were studied. Equilibrium swellings of the hydrogels were changed in the range 27-85 depending upon the fluids, type and amount of crosslinkers. The diffusion exponents were found over half for all hydrogels.

Transport suction apparatus and absorption materials evaluation

NASA Technical Reports Server (NTRS)

Krupa, Debra T.; Gosbee, John

1991-01-01

The specific objectives were as follows. The effectiveness and function was evaluated of the hand held, manually powered v-vac for suction during microgravity. The function was evaluated of the battery powered laerdal suction unit in microgravity. The two units in control of various types of simulated bodily fluids were compared. Various types of tubing and attachments were evaluated which are required to control the collection of bodily fluids during transport. Various materials were evaluated for absorption of simulated bodily fluids. And potential problems were identified for waste management and containment of secretions and fluids during transport. Test procedures, results, and conclusions are briefly discussed.

Fluid Dynamics Lagrangian Simulation Model

NASA Astrophysics Data System (ADS)

Hyman, Ellis

1994-02-01

The work performed by Science Applications International Corporation (SAIC) on this contract, Fluid Dynamics Lagrangian Simulation Model, Contract Number N00014-89-C-2106, SAIC Project Number 01-0157-03-0768, focused on a number of research topics in fluid dynamics. The work was in support of the programs of NRL's Laboratory for Computational Physics and Fluid Dynamics and covered the period from 10 September 1989 to 9 December 1993. In the following sections, we describe each of the efforts and the results obtained. Much of the research work has resulted in journal publications. These are included in Appendices of this report for which the reader is referred for complete details.

External gear pumps operating with non-Newtonian fluids: Modelling and experimental validation

NASA Astrophysics Data System (ADS)

Rituraj, Fnu; Vacca, Andrea

2018-06-01

External Gear Pumps are used in various industries to pump non-Newtonian viscoelastic fluids like plastics, paints, inks, etc. For both design and analysis purposes, it is often a matter of interest to understand the features of the displacing action realized by meshing of the gears and the description of the behavior of the leakages for this kind of pumps. However, very limited work can be found in literature about methodologies suitable to model such phenomena. This article describes the technique of modelling external gear pumps that operate with non-Newtonian fluids. In particular, it explains how the displacing action of the unit can be modelled using a lumped parameter approach which involves dividing fluid domain into several control volumes and internal flow connections. This work is built upon the HYGESim simulation tool, conceived by the authors' research team in the last decade, which is for the first time extended for the simulation of non-Newtonian fluids. The article also describes several comparisons between simulation results and experimental data obtained from numerous experiments performed for validation of the presented methodology. Finally, operation of external gear pump with fluids having different viscosity characteristics is discussed.

Direct numerical simulation of particle alignment in viscoelastic fluids

NASA Astrophysics Data System (ADS)

Hulsen, Martien; Jaensson, Nick; Anderson, Patrick

2016-11-01

Rigid particles suspended in viscoelastic fluids under shear can align in string-like structures in flow direction. To unravel this phenomenon, we present 3D direct numerical simulations of the alignment of two and three rigid, non-Brownian particles in a shear flow of a viscoelastic fluid. The equations are solved on moving, boundary-fitted meshes, which are locally refined to accurately describe the polymer stresses around and in between the particles. A small minimal gap size between the particles is introduced. The Giesekus model is used and the effect of the Weissenberg number, shear thinning and solvent viscosity is investigated. Alignment of two and three particles is observed. Morphology plots have been created for various combinations of fluid parameters. Alignment is mainly governed by the value of the elasticity parameter S, defined as half of the ratio between the first normal stress difference and shear stress of the suspending fluid. Alignment appears to occur above a critical value of S, which decreases with increasing shear thinning. This result, together with simulations of a shear-thinning Carreau fluid, leads us to the conclusion that normal stress differences are essential for particle alignment to occur, but it is also strongly promoted by shear thinning.

Two-fluid 2.5D code for simulations of small scale magnetic fields in the lower solar atmosphere

NASA Astrophysics Data System (ADS)

Piantschitsch, Isabell; Amerstorfer, Ute; Thalmann, Julia Katharina; Hanslmeier, Arnold; Lemmerer, Birgit

2015-08-01

Our aim is to investigate magnetic reconnection as a result of the time evolution of magnetic flux tubes in the solar chromosphere. A new numerical two-fluid code was developed, which will perform a 2.5D simulation of the dynamics from the upper convection zone up to the transition region. The code is based on the Total Variation Diminishing Lax-Friedrichs method and includes the effects of ion-neutral collisions, ionisation/recombination, thermal/resistive diffusivity as well as collisional/resistive heating. What is innovative about our newly developed code is the inclusion of a two-fluid model in combination with the use of analytically constructed vertically open magnetic flux tubes, which are used as initial conditions for our simulation. First magnetohydrodynamic (MHD) tests have already shown good agreement with known results of numerical MHD test problems like e.g. the Orszag-Tang vortex test, the Current Sheet test or the Spherical Blast Wave test. Furthermore, the single-fluid approach will also be applied to the initial conditions, in order to compare the different rates of magnetic reconnection in both codes, the two-fluid code and the single-fluid one.

Distribution of \\0x03949-Tetrahydrocannabinol and 11-Nor-9-Carboxy-\\0x03949-Tetrahydrocannabinol acid in postmortem biological fluids and tissues from pilots fatally injured in aviation accidents.

DOT National Transportation Integrated Search

2013-12-01

Despite a long history of research on the pharmacology of 9-tetrahydrocannabinol (THC), the primary active cannabinoid in marijuana, little is known of its distribution in postmortem fluids and tissues. This study presents postmortem fluid and tiss...

The Maze of the Cerebrospinal Fluid Discovery

PubMed Central

2013-01-01

The author analyzes a historical, long, and tortuous way to discover the cerebrospinal fluid. At least 35 physicians and anatomists described in the text have laid the fundamentals of recognition of this biological fluid's presence. On the basis of crucial anatomical, experimental, and clinical works there are four greatest physicians who should be considered as equal cerebrospinal fluid's discoverers: Egyptian Imhotep, Venetian Nicolo Massa, Italian Domenico Felice Cotugno, and French François Magendie. PMID:24396600

Color mapping of one specific velocity of a biological fluid flows with complex geometry using optical coherence tomography

NASA Astrophysics Data System (ADS)

Potlov, A. Yu.; Frolov, S. V.; Proskurin, S. G.

2018-04-01

The method of Doppler color mapping of one specific (previously chosen) velocity in a turbulent flow inside biological tissues using optical coherence tomography is described. The key features of the presented method are: the raw data are separated into three parts, corresponding to the unmoving biological tissue, the positively and negatively directed biological fluid flows; the further independent signal processing procedure yields the structure image and two images of the chosen velocity, which are then normalised, encoded and joined. The described method can be used to obtain in real time the anatomical maps of the chosen velocities in normal and pathological states. The described method can be applied not only in optical coherence tomography, but also in endoscopic and Doppler ultrasonic medical imaging systems.

Four-fluid MHD Simulations of the Plasma and Neutral Gas Environment of Comet Churyumov-Gerasimenko Near Perihelion

NASA Astrophysics Data System (ADS)

Huang, Z.; Toth, G.; Gombosi, T.; Jia, X.; Rubin, M.; Fougere, N.; Tenishev, V.; Combi, M.; Bieler, A.; Hansen, K.; Shou, Y.; Altwegg, K.

2015-10-01

We develop a 3-D four fluid model to study the plasma environment of comet Churyumov- Gerasimenko (CG), which is the target of the Rosetta mission. Our model is based on BATS-R-US within the SWMF (Space Weather Modeling Framework) that solves the governing multifluid MHD equations and and the Euler equations for the neutral gas fluid. These equations describe the behavior and interactions of the cometary heavy ions, the solar wind protons, the electrons, and the neutrals. This model incorporates mass loading processes, including photo and electron impact ionization, furthermore taken into account are charge exchange, dissociative ion-electron recombination, as well as collisional interactions between different fluids. We simulate the near nucleus plasma and neutral gas environment with a realistic shape model of CG near perihelion and compare our simulation results with Rosetta observations.

Comparative study of the biodegradability of porous silicon films in simulated body fluid.

PubMed

Peckham, J; Andrews, G T

2015-01-01

The biodegradability of oxidized microporous, mesoporous and macroporous silicon films in a simulated body fluid with ion concentrations similar to those found in human blood plasma were studied using gravimetry. Film dissolution rates were determined by periodically weighing the samples after removal from the fluid. The dissolution rates for microporous silicon were found to be higher than those for mesoporous silicon of comparable porosity. The dissolution rate of macroporous silicon was much lower than that for either microporous or mesoporous silicon. This is attributed to the fact that its specific surface area is much lower than that of microporous and mesoporous silicon. Using an equation adapted from [Surf. Sci. Lett. 306 (1994), L550-L554], the dissolution rate of porous silicon in simulated body fluid can be estimated if the film thickness and specific surface area are known.

Coulomb interactions in charged fluids.

PubMed

Vernizzi, Graziano; Guerrero-García, Guillermo Iván; de la Cruz, Monica Olvera

2011-07-01

The use of Ewald summation schemes for calculating long-range Coulomb interactions, originally applied to ionic crystalline solids, is a very common practice in molecular simulations of charged fluids at present. Such a choice imposes an artificial periodicity which is generally absent in the liquid state. In this paper we propose a simple analytical O(N(2)) method which is based on Gauss's law for computing exactly the Coulomb interaction between charged particles in a simulation box, when it is averaged over all possible orientations of a surrounding infinite lattice. This method mitigates the periodicity typical of crystalline systems and it is suitable for numerical studies of ionic liquids, charged molecular fluids, and colloidal systems with Monte Carlo and molecular dynamics simulations.

Development of Functional or Medical Foods for Oral Administration of Insulin for Diabetes Treatment: Gastroprotective Edible Microgels.

PubMed

Sun, Quancai; Zhang, Zipei; Zhang, Ruojie; Gao, Ruichang; McClements, David Julian

2018-05-16

Insulin and an antacid [Mg(OH) 2 ] were co-encapsulated inside calcium alginate microgels (diameter = 280 μm) using a vibrating nozzle injector. Confocal microscopy indicated that insulin was successfully encapsulated inside the microgels and remained inside them after they were exposed to simulated gastric conditions. Localized fluorescence intensity measurements indicated that the internal pH of the antacid-loaded microgels was around pH 7.4 after incubation in acidic gastric fluids but below the limit of detection (pH < 4) in the antacid-free microgels. After incubation in small intestine conditions, around 30% of the insulin was released from the antacid-loaded microgels over a 2 h period. Encapsulation of insulin within the antacid-loaded microgels increased its biological activity after exposure to simulated gastric conditions. In particular, the encapsulated insulin significantly increased Akt phosphorylation at both Thr308 and Ser473 in L6 myotubes when compared to free insulin.

Design and control of rotating soil-like substrate plant-growing facility based on plant water requirement and computational fluid dynamics simulation

NASA Astrophysics Data System (ADS)

Hu, Dawei; Li, Leyuan; Liu, Hui; Zhang, Houkai; Fu, Yuming; Sun, Yi; Li, Liang

It is necessary to process inedible plant biomass into soil-like substrate (SLS) by bio-compost to realize biological resource sustainable utilization. Although similar to natural soil in structure and function, SLS often has uneven water distribution adversely affecting the plant growth due to unsatisfactory porosity, permeability and gravity distribution. In this article, SLS plant-growing facility (SLS-PGF) were therefore rotated properly for cultivating lettuce, and the Brinkman equations coupled with laminar flow equations were taken as governing equations, and boundary conditions were specified by actual operating characteristics of rotating SLS-PGF. Optimal open-control law of the angular and inflow velocity was determined by lettuce water requirement and CFD simulations. The experimental result clearly showed that water content was more uniformly distributed in SLS under the action of centrifugal and Coriolis force, rotating SLS-PGF with the optimal open-control law could meet lettuce water requirement at every growth stage and achieve precise irrigation.

Role of Salt, Pressure, and Water Activity on Homogeneous Ice Nucleation.

PubMed

Espinosa, Jorge R; Soria, Guiomar D; Ramirez, Jorge; Valeriani, Chantal; Vega, Carlos; Sanz, Eduardo

2017-09-21

Pure water can be substantially supercooled below the melting temperature without transforming into ice. The achievable supercooling can be enhanced by adding solutes or by applying hydrostatic pressure. Avoiding ice formation is of great importance in the cryopreservation of food or biological samples. In this Letter, we investigate the similarity between the effects of pressure and salt on ice formation using a combination of state-of-the-art simulation techniques. We find that both hinder ice formation by increasing the energetic cost of creating the ice-fluid interface. Moreover, we examine the widely accepted proposal that the ice nucleation rate for different pressures and solute concentrations can be mapped through the activity of water [ Koop , L. ; Tsias , P. Nature , 2000 , 406 , 611 ]. We show that such a proposal is not consistent with the nucleation rates predicted in our simulations because it does not include all parameters affecting ice nucleation. Therefore, even though salt and pressure have a qualitatively similar effect on ice formation, they cannot be quantitatively mapped onto one another.

Correlation between length and tilt of lipid tails

NASA Astrophysics Data System (ADS)

Kopelevich, Dmitry I.; Nagle, John F.

2015-10-01

It is becoming recognized from simulations, and to a lesser extent from experiment, that the classical Helfrich-Canham membrane continuum mechanics model can be fruitfully enriched by the inclusion of molecular tilt, even in the fluid, chain disordered, biologically relevant phase of lipid bilayers. Enriched continuum theories then add a tilt modulus κθ to accompany the well recognized bending modulus κ. Different enrichment theories largely agree for many properties, but it has been noticed that there is considerable disagreement in one prediction; one theory postulates that the average length of the hydrocarbon chain tails increases strongly with increasing tilt and another predicts no increase. Our analysis of an all-atom simulation favors the latter theory, but it also shows that the overall tail length decreases slightly with increasing tilt. We show that this deviation from continuum theory can be reconciled by consideration of the average shape of the tails, which is a descriptor not obviously includable in continuum theory.

The Variety of Fluid Dynamics.

ERIC Educational Resources Information Center

Barnes, Francis; And Others

1980-01-01

Discusses three research topics which are concerned with eminently practical problems and deal at the same time with fundamental fluid dynamical problems. These research topics come from the general areas of chemical and biological engineering, geophysics, and pure mathematics. (HM)

Differentiation of five body fluids from forensic samples by expression analysis of four microRNAs using quantitative PCR.

PubMed

Sauer, Eva; Reinke, Ann-Kathrin; Courts, Cornelius

2016-05-01

Applying molecular genetic approaches for the identification of forensically relevant body fluids, which often yield crucial information for the reconstruction of a potential crime, is a current topic of forensic research. Due to their body fluid specific expression patterns and stability against degradation, microRNAs (miRNA) emerged as a promising molecular species, with a range of candidate markers published. The analysis of miRNA via quantitative Real-Time PCR, however, should be based on a relevant strategy of normalization of non-biological variances to deliver reliable and biologically meaningful results. The herein presented work is the as yet most comprehensive study of forensic body fluid identification via miRNA expression analysis based on a thoroughly validated qPCR procedure and unbiased statistical decision making to identify single source samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

In Vitro Studies Evaluating Leaching of Mercury from Mine Waste Calcine Using Simulated Human Body Fluids

PubMed Central

2010-01-01

In vitro bioaccessibility (IVBA) studies were carried out on samples of mercury (Hg) mine-waste calcine (roasted Hg ore) by leaching with simulated human body fluids. The objective was to estimate potential human exposure to Hg due to inhalation of airborne calcine particulates and hand-to-mouth ingestion of Hg-bearing calcines. Mine waste calcines collected from Hg mines at Almadén, Spain, and Terlingua, Texas, contain Hg sulfide, elemental Hg, and soluble Hg compounds, which constitute primary ore or compounds formed during Hg retorting. Elevated leachate Hg concentrations were found during calcine leaching using a simulated gastric fluid (as much as 6200 μg of Hg leached/g sample). Elevated Hg concentrations were also found in calcine leachates using a simulated lung fluid (as much as 9200 μg of Hg leached/g), serum-based fluid (as much as 1600 μg of Hg leached/g), and water of pH 5 (as much as 880 μg of Hg leached/g). The leaching capacity of Hg is controlled by calcine mineralogy; thus, calcines containing soluble Hg compounds contain higher leachate Hg concentrations. Results indicate that ingestion or inhalation of Hg mine-waste calcine may lead to increased Hg concentrations in the human body, especially through the ingestion pathway. PMID:20491469

In vitro studies evaluating leaching of mercury from mine waste calcine using simulated human body fluids.

PubMed

Gray, John E; Plumlee, Geoffrey S; Morman, Suzette A; Higueras, Pablo L; Crock, James G; Lowers, Heather A; Witten, Mark L

2010-06-15

In vitro bioaccessibility (IVBA) studies were carried out on samples of mercury (Hg) mine-waste calcine (roasted Hg ore) by leaching with simulated human body fluids. The objective was to estimate potential human exposure to Hg due to inhalation of airborne calcine particulates and hand-to-mouth ingestion of Hg-bearing calcines. Mine waste calcines collected from Hg mines at Almaden, Spain, and Terlingua, Texas, contain Hg sulfide, elemental Hg, and soluble Hg compounds, which constitute primary ore or compounds formed during Hg retorting. Elevated leachate Hg concentrations were found during calcine leaching using a simulated gastric fluid (as much as 6200 microg of Hg leached/g sample). Elevated Hg concentrations were also found in calcine leachates using a simulated lung fluid (as much as 9200 microg of Hg leached/g), serum-based fluid (as much as 1600 microg of Hg leached/g), and water of pH 5 (as much as 880 microg of Hg leached/g). The leaching capacity of Hg is controlled by calcine mineralogy; thus, calcines containing soluble Hg compounds contain higher leachate Hg concentrations. Results indicate that ingestion or inhalation of Hg mine-waste calcine may lead to increased Hg concentrations in the human body, especially through the ingestion pathway.

Three-Dimensional Multi-fluid Moment Simulation of Ganymede

NASA Astrophysics Data System (ADS)

Wang, L.; Germaschewski, K.; Hakim, A.; Bhattacharjee, A.; Dong, C.

2016-12-01

Plasmas in space environments, such as solar wind and Earth's magnetosphere, are often constituted of multiple species. Conventional MHD-based, single-fluid systems, have additional complications when multiple fluid species are introduced. We suggest space application of an alternative multi-fluid moment approach, treating each species on equal footing using exact evolution equations for moments of their distribution function, and electromagnetic fields through full Maxwell equations. Non-ideal effects like Hall effect, inertia, and even tensorial pressures, are self-consistently embedded without the need to explicitly solve a complicated Ohm's law. Previously, we have benchmarked this approach in classical test problems like the Orszag-Tang vortex and GEM reconnection challenge problem. Recently, we performed three-dimensional two-fluid simulation of the magnetosphere of Ganymede, using both five-moment (scalar pressures) and ten-moment (tensorial pressures) models. In both models, the formation of Alfven wing structure due to subsonic inflow is correctly captured, and the magnetic field data agree well with in-situ measurements from the Galileo flyby G8. The ten-moment simulation also showed the contribution of pressure tensor divergence to the reconnecting electric field. Initial results of coupling to state-of-art global simulation codes like OpenGGCM will also be shown, which will in the future provide a rigorous way for integration of ionospheric physics.

In vitro studies evaluating leaching of mercury from mine waste calcine using simulated human body fluids

USGS Publications Warehouse

Gray, John E.; Plumlee, Geoffrey S.; Morman, Suzette A.; Higueras, Pablo L.; Crock, James G.; Lowers, Heather A.; Witten, Mark L.

2010-01-01

In vitro bioaccessibility (IVBA) studies were carried out on samples of mercury (Hg) mine-waste calcine (roasted Hg ore) by leaching with simulated human body fluids. The objective was to estimate potential human exposure to Hg due to inhalation of airborne calcine particulates and hand-to-mouth ingestion of Hg-bearing calcines. Mine waste calcines collected from Hg mines at Almadén, Spain, and Terlingua, Texas, contain Hg sulfide, elemental Hg, and soluble Hg compounds, which constitute primary ore or compounds formed during Hg retorting. Elevated leachate Hg concentrations were found during calcine leaching using a simulated gastric fluid (as much as 6200 μg of Hg leached/g sample). Elevated Hg concentrations were also found in calcine leachates using a simulated lung fluid (as much as 9200 μg of Hg leached/g), serum-based fluid (as much as 1600 μg of Hg leached/g), and water of pH 5 (as much as 880 μg of Hg leached/g). The leaching capacity of Hg is controlled by calcine mineralogy; thus, calcines containing soluble Hg compounds contain higher leachate Hg concentrations. Results indicate that ingestion or inhalation of Hg mine-waste calcine may lead to increased Hg concentrations in the human body, especially through the ingestion pathway.

The cell biology of polycystic kidney disease

PubMed Central

Chapin, Hannah C.

2010-01-01

Polycystic kidney disease is a common genetic disorder in which fluid-filled cysts displace normal renal tubules. Here we focus on autosomal dominant polycystic kidney disease, which is attributable to mutations in the PKD1 and PKD2 genes and which is characterized by perturbations of renal epithelial cell growth control, fluid transport, and morphogenesis. The mechanisms that connect the underlying genetic defects to disease pathogenesis are poorly understood, but their exploration is shedding new light on interesting cell biological processes and suggesting novel therapeutic targets. PMID:21079243

Multi-d CFD Modeling of a Free-piston Stirling Convertor at NASA Glenn

NASA Technical Reports Server (NTRS)

Wilson, Scott D.; Dyson, Rodger W.; Tew, Roy C.; Ibrahim, Mounir B.

2004-01-01

A high efficiency Stirling Radioisotope Generator (SRG) is being developed for possible use in long duration space science missions. NASA s advanced technology goals for next generation Stirling convertors include increasing the Carnot efficiency and percent of Carnot efficiency. To help achieve these goals, a multidimensional Computational Fluid Dynamics (CFD) code is being developed to numerically model unsteady fluid flow and heat transfer phenomena of the oscillating working gas inside Stirling convertors. Simulations of the Stirling convertors for the SRG will help characterize the thermodynamic losses resulting from fluid flow and heat transfer between the working gas and solid walls. The current CFD simulation represents approximated 2-dimensional convertor geometry. The simulation solves the Navier Stokes equations for an ideal helium gas oscillating at low speeds. The current simulation results are discussed.

Microfluidic mixing using orbiting magnetic microbeads

NASA Astrophysics Data System (ADS)

Ballard, Matthew; Owen, Drew; Mao, Wenbin; Hesketh, Peter; Alexeev, Alexander

2013-11-01

Using three-dimensional simulations and experiments, we examine mixing in a microfluidic channel that incorporates a hybrid passive-active micromixer. The passive part of the mixer consists of a series of angled parallel ridges lining the top microchannel wall. The active component of the mixer is made up of microbeads rotating around small pillars on the bottom of the microchannel. In our simulations, we use a binary fluid lattice Boltzmann model to simulate the system and characterize the microfluidic mixing in the system. We consider the passive and active micromixers separately and evaluate their combined effect on the mixing of binary fluids. We compare our simulations with the experimental results obtained in a microchannel with magnetically actuated microbeads. Our findings guide the design of an efficient micromixer to be used in sampling in complex fluids. Financial support from NSF (CBET-1159726) is gratefully acknowledged.

Resolving the Impact of Biological Processes on Water Transport in Unsaturated Porous Media Through Nuclear Magnetic Resonance Micro-Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seymour, Joseph D.

2005-06-01

The magnetic resonance microscopy (MRM) work at Montana State University has extended the imaging of a single biofilm in a 1 mm capillary reactor to correlate T2 magnetic relaxation maps displaying biofilm structure with the corresponding velocity patterns in three dimensions in a Staphylococcus epidermidis biofilm fouled square capillary. A square duct geometry is chosen to provide correlation with existing experiments and simulations, as research bioreactors tend to be of square or rectangular cross section for optical or microelectrode access. The spatially resolved velocity data provide details on the impact of biofilm induced advection on mass transport from the bulkmore » fluid to the biofilm and through the capillary bioreactor.« less

Calcium phosphate composite cements based on simple mixture of brushite and apatite phases

NASA Astrophysics Data System (ADS)

Egorov, A. A.; Fedotov, A. Yu; Pereloma, I. S.; Teterina, A. Yu; Sergeeva, N. S.; Sviridova, I. K.; Kirsanova, V. A.; Akhmedova, S. A.; Nesterova, A. V.; Reshetov, I. V.; Barinov, S. M.; Komlev, V. S.

2018-04-01

The composite cements based on simple mixtures brishite and apatite with ratio 70/30, 50/50, 30/70 were developed. The processes of phase formation, microstructure and mechanical properties were studied. The kinetics of degradation in simulated body fluid depending on the microstructure and the materials phase composition was carried out. The biological test in vitro were performed using the MTT-test on the human fibroblast immortalized (hFB) cell line and the human osteosarcoma cell line MG-63. The materials didn’t have acute cytoxicity and possessed surface matrix properties. It was determined that the both line of cells actively proliferated, with viable cells values higher 20-60 % then control at all observation periods.

Convection-driven aggregation of micron sized capsules

NASA Astrophysics Data System (ADS)

Shklyaev, Oleg; Shum, Henry; Balazs, Anna

Collective dynamics of microcapsules often serve as a model for understanding behavior observed in colonies of biological cells. Using computer simulations, we explore the capability of chemically generated convection to assemble microcapsules into a colony with neighbors close enough to facilitate chemical communication. The microcapsules are assumed to carry a supply of chemical fuel. When this fuel, leaking out of the capsules, reacts at enzyme-covered sites of the chamber, the reaction generates fluid density variations driving flows. These flows carry the microcapsules, which tend to aggregate into colonies on and near the enzyme-covered sites. This aggregation continues until the reagent has been depleted and convection stops. We show that capsule colonies of predesigned shapes can be assembled by patterning the enzyme-covered surface.

Ebola Virus Stability on Surfaces and in Fluids in Simulated Outbreak Environments.

PubMed

Fischer, Robert; Judson, Seth; Miazgowicz, Kerri; Bushmaker, Trenton; Prescott, Joseph; Munster, Vincent J

2015-07-01

We evaluated the stability of Ebola virus on surfaces and in fluids under simulated environmental conditions for the climate of West Africa and for climate-controlled hospitals. This virus remains viable for a longer duration on surfaces in hospital conditions than in African conditions and in liquid than in dried blood.

Laser-launched flyers with organic working fluids

NASA Astrophysics Data System (ADS)

Mulford, Roberta; Swift, Damian

2003-10-01

The TRIDENT laser has been used to launch flyers by depositing IR energy in a thin layer of material - the working fluid - sandwiched between the flyer and a transparent substrate. We have investigated the use of working fluids based on organics, chosen as they are quite efficient absorbers of IR energy and should also convert heat to mechanical work more efficiently than materials such as carbon. A thermodynamically complete equation of state was developed for one of the fluids investigated experimentally - a carbohydrate solution - by chemical equilibrium calculations using the CHEETAH program. Continuum mechanics simulations were made of the flyer launch process, modeling the effect of the laser as energy deposition in the working fluid, and taking into account the compression and recoil of the substrate. We compare the simulations with a range of experiments and demonstrate the optimization of substrate and fluid thickness for a given flyer thickness and speed.

On a criterion of incipient motion and entrainment into suspension of a particle from cuttings bed in shear flow of non-Newtonian fluid

NASA Astrophysics Data System (ADS)

Ignatenko, Yaroslav; Bocharov, Oleg; May, Roland

2017-10-01

Solids transport is a major issue in high angle wells. Bed-load forms by sediment while transport and accompanied by intermittent contact with stream-bed by rolling, sliding and bouncing. The study presents the results of a numerical simulation of a laminar steady-state flow around a particle at rest and in free motion in a shear flow of Herschel-Bulkley fluid. The simulation was performed using the OpenFOAM open-source CFD package. A criterion for particle incipient motion and entrainment into suspension from cuttings bed (Shields criteria) based on forces and torques balance is discussed. Deflection of the fluid parameters from the ones of Newtonian fluid leads to decreasing of the drag and lift forces and the hydrodynamic moment. Thus, the critical shear stress (Shields parameter) for the considered non-Newtonian fluid must be greater than the one for a Newtonian fluid.

Numerical simulations of thermoacoustic waves in transcritical fluids employing the spectral difference approach

NASA Astrophysics Data System (ADS)

Scalo, Carlo; Migliorino, Mario Tindaro; Chapelier, Jean-Baptiste

2017-11-01

We investigate the stability properties of thermoacoustically unstable planar waves in transcritical fluids via high-fidelity Navier-Stokes simulations based on a Spectral Difference (SD) discretization coupled with the Peng-Robinson equation of state and Chung's method for the fluid transport properties. A canonical thermoacoustically unstable standing-wave resonator filled with supercritical CO2 kept in pseudoboiling conditions in the stack is considered. Real fluid effects near the critical point are shown to boost thermoacoustic energy production, as also confirmed by companion eigenvalue analysis supporting the closure of the acoustic energy budgets. A kink in the eigenmode shape is observed at the location of pseudo phase change, consistent with the abrupt change in base impedance. The current study demonstrates a transformative approach to thermoacoustic energy generation, exploiting otherwise unwanted fluid dynamics instabilities commonly observed in aeronautical applications employing transcritical fluids.

Bioactivity and electrochemical behavior of hydroxyapatite-silicon-multi walled carbon nano-tubes composite coatings synthesized by EPD on NiTi alloys in simulated body fluid.

PubMed

Khalili, V; Khalil-Allafi, J; Frenzel, J; Eggeler, G

2017-02-01

In order to improve the surface bioactivity of NiTi bone implant and corrosion resistance, hydroxyapatite coating with addition of 20wt% silicon, 1wt% multi walled carbon nano-tubes and both of them were deposited on a NiTi substrate using a cathodic electrophoretic method. The apatite formation ability was estimated using immersion test in the simulated body fluid for 10days. The SEM images of the surface of coatings after immersion in simulated body fluid show that the presence of silicon in the hydroxyapatite coatings accelerates in vitro growth of apatite layer on the coatings. The Open-circuit potential and electrochemical impedance spectroscopy were measured to evaluate the electrochemical behavior of the coatings in the simulated body fluid at 37°C. The results indicate that the compact structure of hydroxyapatite-20wt% silicon and hydroxyapatite-20wt% silicon-1wt% multi walled carbon nano-tubes coatings could efficiently increase the corrosion resistance of NiTi substrate. Copyright © 2016 Elsevier B.V. All rights reserved.

Mathematical inference in one point microrheology

NASA Astrophysics Data System (ADS)

Hohenegger, Christel; McKinley, Scott

2016-11-01

Pioneered by the work of Mason and Weitz, one point passive microrheology has been successfully applied to obtaining estimates of the loss and storage modulus of viscoelastic fluids when the mean-square displacement obeys a local power law. Using numerical simulations of a fluctuating viscoelastic fluid model, we study the problem of recovering the mechanical parameters of the fluid's memory kernel using statistical inference like mean-square displacements and increment auto-correlation functions. Seeking a better understanding of the influence of the assumptions made in the inversion process, we mathematically quantify the uncertainty in traditional one point microrheology for simulated data and demonstrate that a large family of memory kernels yields the same statistical signature. We consider both simulated data obtained from a full viscoelastic fluid simulation of the unsteady Stokes equations with fluctuations and from a Generalized Langevin Equation of the particle's motion described by the same memory kernel. From the theory of inverse problems, we propose an alternative method that can be used to recover information about the loss and storage modulus and discuss its limitations and uncertainties. NSF-DMS 1412998.

TopoDrive and ParticleFlow--Two Computer Models for Simulation and Visualization of Ground-Water Flow and Transport of Fluid Particles in Two Dimensions

USGS Publications Warehouse

Hsieh, Paul A.

2001-01-01

This report serves as a user?s guide for two computer models: TopoDrive and ParticleFlow. These two-dimensional models are designed to simulate two ground-water processes: topography-driven flow and advective transport of fluid particles. To simulate topography-driven flow, the user may specify the shape of the water table, which bounds the top of the vertical flow section. To simulate transport of fluid particles, the model domain is a rectangle with overall flow from left to right. In both cases, the flow is under steady state, and the distribution of hydraulic conductivity may be specified by the user. The models compute hydraulic head, ground-water flow paths, and the movement of fluid particles. An interactive visual interface enables the user to easily and quickly explore model behavior, and thereby better understand ground-water flow processes. In this regard, TopoDrive and ParticleFlow are not intended to be comprehensive modeling tools, but are designed for modeling at the exploratory or conceptual level, for visual demonstration, and for educational purposes.

Optofluidic bioimaging platform for quantitative phase imaging of lab on a chip devices using digital holographic microscopy.

PubMed

Pandiyan, Vimal Prabhu; John, Renu

2016-01-20

We propose a versatile 3D phase-imaging microscope platform for real-time imaging of optomicrofluidic devices based on the principle of digital holographic microscopy (DHM). Lab-on-chip microfluidic devices fabricated on transparent polydimethylsiloxane (PDMS) and glass substrates have attained wide popularity in biological sensing applications. However, monitoring, visualization, and characterization of microfluidic devices, microfluidic flows, and the biochemical kinetics happening in these devices is difficult due to the lack of proper techniques for real-time imaging and analysis. The traditional bright-field microscopic techniques fail in imaging applications, as the microfluidic channels and the fluids carrying biological samples are transparent and not visible in bright light. Phase-based microscopy techniques that can image the phase of the microfluidic channel and changes in refractive indices due to the fluids and biological samples present in the channel are ideal for imaging the fluid flow dynamics in a microfluidic channel at high resolutions. This paper demonstrates three-dimensional imaging of a microfluidic device with nanometric depth precisions and high SNR. We demonstrate imaging of microelectrodes of nanometric thickness patterned on glass substrate and the microfluidic channel. Three-dimensional imaging of a transparent PDMS optomicrofluidic channel, fluid flow, and live yeast cell flow in this channel has been demonstrated using DHM. We also quantify the average velocity of fluid flow through the channel. In comparison to any conventional bright-field microscope, the 3D depth information in the images illustrated in this work carry much information about the biological system under observation. The results demonstrated in this paper prove the high potential of DHM in imaging optofluidic devices; detection of pathogens, cells, and bioanalytes on lab-on-chip devices; and in studying microfluidic dynamics in real time based on phase changes.

Bions: A Family of Biomimetic Mineralo-Organic Complexes Derived from Biological Fluids

PubMed Central

Martel, Jan; Young, John D.

2013-01-01

Mineralo-organic nanoparticles form spontaneously in human body fluids when the concentrations of calcium and phosphate ions exceed saturation. We have shown previously that these mineralo-organic nanoparticles possess biomimetic properties and can reproduce the whole phenomenology of the so-called nanobacteria—mineralized entities initially described as the smallest microorganisms on earth. Here, we examine the possibility that various charged elements and ions may form mineral nanoparticles with similar properties in biological fluids. Remarkably, all the elements tested, including sodium, magnesium, aluminum, calcium, manganese, iron, cobalt, nickel, copper, zinc, strontium, and barium form mineralo-organic particles with bacteria-like morphologies and other complex shapes following precipitation with phosphate in body fluids. Upon formation, these mineralo-organic particles, which we term bions, invariably accumulate carbonate apatite during incubation in biological fluids; yet, the particles also incorporate additional elements and thus reflect the ionic milieu in which they form. Bions initially harbor an amorphous mineral phase that gradually converts to crystals in culture. Our results show that serum produces a dual inhibition-seeding effect on bion formation. Using a comprehensive proteomic analysis, we identify a wide range of proteins that bind to these mineral particles during incubation in medium containing serum. The two main binding proteins identified, albumin and fetuin-A, act as both inhibitors and seeders of bions in culture. Notably, bions possess several biomimetic properties, including the possibility to increase in size and number and to be sub-cultured in fresh culture medium. Based on these results, we propose that bions represent biological, mineralo-organic particles that may form in the body under both physiological and pathological homeostasis conditions. These mineralo-organic particles may be part of a physiological cycle that regulates the function, transport and disposal of elements and minerals in the human body. PMID:24086546

THERMO-HYDRO-MECHANICAL MODELING OF WORKING FLUID INJECTION AND THERMAL ENERGY EXTRACTION IN EGS FRACTURES AND ROCK MATRIX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robert Podgorney; Chuan Lu; Hai Huang

2012-01-01

Development of enhanced geothermal systems (EGS) will require creation of a reservoir of sufficient volume to enable commercial-scale heat transfer from the reservoir rocks to the working fluid. A key assumption associated with reservoir creation/stimulation is that sufficient rock volumes can be hydraulically fractured via both tensile and shear failure, and more importantly by reactivation of naturally existing fractures (by shearing), to create the reservoir. The advancement of EGS greatly depends on our understanding of the dynamics of the intimately coupled rock-fracture-fluid-heat system and our ability to reliably predict how reservoirs behave under stimulation and production. Reliable performance predictions ofmore » EGS reservoirs require accurate and robust modeling for strongly coupled thermal-hydrological-mechanical (THM) processes. Conventionally, these types of problems have been solved using operator-splitting methods, usually by coupling a subsurface flow and heat transport simulators with a solid mechanics simulator via input files. An alternative approach is to solve the system of nonlinear partial differential equations that govern multiphase fluid flow, heat transport, and rock mechanics simultaneously, using a fully coupled, fully implicit solution procedure, in which all solution variables (pressure, enthalpy, and rock displacement fields) are solved simultaneously. This paper describes numerical simulations used to investigate the poro- and thermal- elastic effects of working fluid injection and thermal energy extraction on the properties of the fractures and rock matrix of a hypothetical EGS reservoir, using a novel simulation software FALCON (Podgorney et al., 2011), a finite element based simulator solving fully coupled multiphase fluid flow, heat transport, rock deformation, and fracturing using a global implicit approach. Investigations are also conducted on how these poro- and thermal-elastic effects are related to fracture permeability evolution.« less

Analysis of the intraocular jet flows and pressure gradients induced by air and fluid infusion: mechanism of focal chorioretinal damage.

PubMed

Kim, Yong Joon; Jo, Sungkil; Moon, Daruchi; Joo, Youngcheol; Choi, Kyung Seek

2014-05-01

To comprehend the mechanism of focal chorioretinal damage by analysis of the pressure distribution and dynamic pressure induced by infused air during fluid-air exchange. A precise simulation featuring a model eye and a fluid circuit was designed to analyze fluid-air exchange. The pressure distribution, flow velocity, and dynamic pressure induced by infusion of air into an air-filled eye were analyzed using an approach based on fluid dynamics. The size of the port and the infusion pressure were varied during simulated iterations. We simulated infusion of an air-filled eye with balanced salt solution (BSS) to better understand the mechanism of chorioretinal damage induced by infused air. Infused air was projected straight toward a point on the retina contralateral to the infusion port (the "vulnerable point"). The highest pressure was evident at the vulnerable point, and the lowest pressure was recorded on most retinal areas. Simulations using greater infusion pressure and a port of larger size were associated with elevations in dynamic pressure and the pressure gradient. The pressure gradients were 2.8 and 5.1 mm Hg, respectively, when infusion pressures of 30 and 50 mm Hg were delivered through a 20-gauge port. The pressure gradient associated with BSS infusion was greater than that created by air, but lasted for only a moment. Our simulation explains the mechanism of focal chorioretinal damage in numerical terms. Infused air induces a prolonged increase in focal pressure on the vulnerable point, and this may be responsible for visual field defects arising after fluid-air exchange. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

Vapor-liquid equilibrium and equation of state of two-dimensional fluids from a discrete perturbation theory

NASA Astrophysics Data System (ADS)

Trejos, Víctor M.; Santos, Andrés; Gámez, Francisco

2018-05-01

The interest in the description of the properties of fluids of restricted dimensionality is growing for theoretical and practical reasons. In this work, we have firstly developed an analytical expression for the Helmholtz free energy of the two-dimensional square-well fluid in the Barker-Henderson framework. This equation of state is based on an approximate analytical radial distribution function for d-dimensional hard-sphere fluids (1 ≤ d ≤ 3) and is validated against existing and new simulation results. The so-obtained equation of state is implemented in a discrete perturbation theory able to account for general potential shapes. The prototypical Lennard-Jones and Yukawa fluids are tested in its two-dimensional version against available and new simulation data with semiquantitative agreement.

Simulation Of The Synovial Fluid In A Deformable Cavity

NASA Astrophysics Data System (ADS)

Martinez-Gutierrez, Nancy; Ibarra-Bracamontes, Laura A.

2016-11-01

The main components of a synovial joint are a cartilage and a biofluid known as the synovial fluid. The results were obtained using the FLUENT software to simulate the behavior of the synovial fluid within a deformable cavity with a simple geometry. The cartilage is represented as a porous region. By reducing the available region for the fluid, a fluid displacement into the cartilage is induced. The total pressure reached in the interface of the deformable cavity and the porous region is presented. The geometry and properties of the system are scaled to values found in a knee joint. The effect of deformation rate, fluid viscosity and properties of the porous medium on the total pressure reached are analyzed. The higher pressures are reached either for high deformation rate or when the fluid viscosity increases. This study was supported by the Mexican Council of Science and Technology (CONACyT) and by the Scientific Research Coordination of the University of Michoacan in Mexico.

Micro-Macro Simulation of Viscoelastic Fluids in Three Dimensions

NASA Astrophysics Data System (ADS)

Rüttgers, Alexander; Griebel, Michael

2012-11-01

The development of the chemical industry resulted in various complex fluids that cannot be correctly described by classical fluid mechanics. For instance, this includes paint, engine oils with polymeric additives and toothpaste. We currently perform multiscale viscoelastic flow simulations for which we have coupled our three-dimensional Navier-Stokes solver NaSt3dGPF with the stochastic Brownian configuration field method on the micro-scale. In this method, we represent a viscoelastic fluid as a dumbbell system immersed in a three-dimensional Newtonian liquid which leads to a six-dimensional problem in space. The approach requires large computational resources and therefore depends on an efficient parallelisation strategy. Our flow solver is parallelised with a domain decomposition approach using MPI. It shows excellent scale-up results for up to 128 processors. In this talk, we present simulation results for viscoelastic fluids in square-square contractions due to their relevance for many engineering applications such as extrusion. Another aspect of the talk is the parallel implementation in NaSt3dGPF and the parallel scale-up and speed-up behaviour.

Observation of 1-D time dependent non-propagating laser plasma structures using fluid and PIC codes

NASA Astrophysics Data System (ADS)

Verma, Deepa; Bera, Ratan Kumar; Kumar, Atul; Patel, Bhavesh; Das, Amita

2017-12-01

The manuscript reports the observation of time dependent localized and non-propagating structures in the coupled laser plasma system through 1-D fluid and Particle-In-Cell (PIC) simulations. It is reported that such structures form spontaneously as a result of collision amongst certain exact solitonic solutions. They are seen to survive as coherent entities for a long time up to several hundreds of plasma periods. Furthermore, it is shown that such time dependence can also be artificially recreated by significantly disturbing the delicate balance between the radiation and the density fields required for the exact non-propagating solution obtained by Esirkepov et al., JETP 68(1), 36-41 (1998). The ensuing time evolution is an interesting interplay between kinetic and field energies of the system. The electrostatic plasma oscillations are coupled with oscillations in the electromagnetic field. The inhomogeneity of the background and the relativistic nature, however, invariably produces large amplitude density perturbations leading to its wave breaking. In the fluid simulations, the signature of wave breaking can be discerned by a drop in the total energy which evidently gets lost to the grid. The PIC simulations are observed to closely follow the fluid simulations till the point of wave breaking. However, the total energy in the case of PIC simulations is seen to remain conserved throughout the simulations. At the wave breaking, the particles are observed to acquire thermal kinetic energy in the case of PIC. Interestingly, even after wave breaking, compact coherent structures with trapped radiation inside high-density peaks continue to exist both in PIC and fluid simulations. Although the time evolution does not exactly match in the two simulations as it does prior to the process of wave breaking, the time-dependent features exhibited by the remnant structures are characteristically similar.

Coupling Hydraulic Fracturing Propagation and Gas Well Performance for Simulation of Production in Unconventional Shale Gas Reservoirs

NASA Astrophysics Data System (ADS)

Wang, C.; Winterfeld, P. H.; Wu, Y. S.; Wang, Y.; Chen, D.; Yin, C.; Pan, Z.

2014-12-01

Hydraulic fracturing combined with horizontal drilling has made it possible to economically produce natural gas from unconventional shale gas reservoirs. An efficient methodology for evaluating hydraulic fracturing operation parameters, such as fluid and proppant properties, injection rates, and wellhead pressure, is essential for the evaluation and efficient design of these processes. Traditional numerical evaluation and optimization approaches are usually based on simulated fracture properties such as the fracture area. In our opinion, a methodology based on simulated production data is better, because production is the goal of hydraulic fracturing and we can calibrate this approach with production data that is already known. This numerical methodology requires a fully-coupled hydraulic fracture propagation and multi-phase flow model. In this paper, we present a general fully-coupled numerical framework to simulate hydraulic fracturing and post-fracture gas well performance. This three-dimensional, multi-phase simulator focuses on: (1) fracture width increase and fracture propagation that occurs as slurry is injected into the fracture, (2) erosion caused by fracture fluids and leakoff, (3) proppant subsidence and flowback, and (4) multi-phase fluid flow through various-scaled anisotropic natural and man-made fractures. Mathematical and numerical details on how to fully couple the fracture propagation and fluid flow parts are discussed. Hydraulic fracturing and production operation parameters, and properties of the reservoir, fluids, and proppants, are taken into account. The well may be horizontal, vertical, or deviated, as well as open-hole or cemented. The simulator is verified based on benchmarks from the literature and we show its application by simulating fracture network (hydraulic and natural fractures) propagation and production data history matching of a field in China. We also conduct a series of real-data modeling studies with different combinations of hydraulic fracturing parameters and present the methodology to design these operations with feedback of simulated production data. The unified model aids in the optimization of hydraulic fracturing design, operations, and production.

User's Guide of TOUGH2-EGS. A Coupled Geomechanical and Reactive Geochemical Simulator for Fluid and Heat Flow in Enhanced Geothermal Systems Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fakcharoenphol, Perapon; Xiong, Yi; Hu, Litang

TOUGH2-EGS is a numerical simulation program coupling geomechanics and chemical reactions for fluid and heat flows in porous media and fractured reservoirs of enhanced geothermal systems. The simulator includes the fully-coupled geomechanical (THM) module, the fully-coupled geochemical (THC) module, and the sequentially coupled reactive geochemistry (THMC) module. The fully-coupled flow-geomechanics model is developed from the linear elastic theory for the thermo-poro-elastic system and is formulated with the mean normal stress as well as pore pressure and temperature. The chemical reaction is sequentially coupled after solution of flow equations, which provides the flow velocity and phase saturation for the solute transportmore » calculation at each time step. In addition, reservoir rock properties, such as porosity and permeability, are subjected to change due to rock deformation and chemical reactions. The relationships between rock properties and geomechanical and chemical effects from poro-elasticity theories and empirical correlations are incorporated into the simulator. This report provides the user with detailed information on both mathematical models and instructions for using TOUGH2-EGS for THM, THC or THMC simulations. The mathematical models include the fluid and heat flow equations, geomechanical equation, reactive geochemistry equations, and discretization methods. Although TOUGH2-EGS has the capability for simulating fluid and heat flows coupled with both geomechanical and chemical effects, it is up to the users to select the specific coupling process, such as THM, THC, or THMC in a simulation. There are several example problems illustrating the applications of this program. These example problems are described in details and their input data are presented. The results demonstrate that this program can be used for field-scale geothermal reservoir simulation with fluid and heat flow, geomechanical effect, and chemical reaction in porous and fractured media.« less

Evaluation of a novel closed-loop fluid-administration system based on dynamic predictors of fluid responsiveness: an in silico simulation study.

PubMed

Rinehart, Joseph; Alexander, Brenton; Le Manach, Yannick; Hofer, Christoph; Tavernier, Benoit; Kain, Zeev N; Cannesson, Maxime

2011-01-01

Dynamic predictors of fluid responsiveness have made automated management of fluid resuscitation more practical. We present initial simulation data for a novel closed-loop fluid-management algorithm (LIR, Learning Intravenous Resuscitator). The performance of the closed-loop algorithm was tested in three phases by using a patient simulator including a pulse-pressure variation output. In the first phase, LIR was tested in three different hemorrhage scenarios and compared with no management. In the second phase, we compared LIR with 20 practicing anesthesiologists for the management of a simulated hemorrhage scenario. In the third phase, LIR was tested under conditions of noise and artifact in the dynamic predictor. In the first phase, we observed a significant difference between the unmanaged and the LIR groups in moderate to large hemorrhages in heart rate (76 ± 8 versus 141 ± 29 beats/min), mean arterial pressure (91 ± 6 versus 59 ± 26 mm Hg), and cardiac output (CO; (6.4 ± 0.9 versus 3.2 ± 1.8 L/min) (P < 0.005 for all comparisons). In the second phase, LIR intervened significantly earlier than the practitioners (16.0 ± 1.3 minutes versus 21.5 ± 5.6 minutes; P < 0.05) and gave more total fluid (2,675 ± 244 ml versus 1,968 ± 644 ml; P < 0.05). The mean CO was higher in the LIR group than in the practitioner group (5.9 ± 0.2 versus 5.2 ± 0.6 L/min; P < 0.05). Finally, in the third phase, despite the addition of noise to the pulse-pressure variation value, no significant difference was found across conditions in mean, final, or minimum CO. These data demonstrate that LIR is an effective volumetric resuscitator in simulated hemorrhage scenarios and improved physician management of the simulated hemorrhages.